From 354e20f43157f07f4600be4486648e49c61aa5c3 Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Fri, 30 Oct 2015 20:04:06 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14220
f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
src/ASPHERE/compute_erotate_asphere.cpp | 2 +-
src/ASPHERE/compute_temp_asphere.cpp | 12 +-
src/ASPHERE/fix_nh_asphere.cpp | 6 +-
src/ASPHERE/fix_nph_asphere.cpp | 2 +-
src/ASPHERE/fix_npt_asphere.cpp | 2 +-
src/ASPHERE/fix_nve_asphere.cpp | 6 +-
src/ASPHERE/fix_nve_asphere_noforce.cpp | 6 +-
src/ASPHERE/fix_nve_line.cpp | 6 +-
src/ASPHERE/fix_nve_tri.cpp | 6 +-
src/ASPHERE/fix_nvt_asphere.cpp | 2 +-
src/ASPHERE/pair_gayberne.cpp | 8 +-
src/ASPHERE/pair_line_lj.cpp | 8 +-
src/ASPHERE/pair_resquared.cpp | 8 +-
src/ASPHERE/pair_tri_lj.cpp | 10 +-
src/BODY/body_nparticle.cpp | 22 +-
src/BODY/compute_body_local.cpp | 8 +-
src/BODY/fix_nve_body.cpp | 6 +-
src/BODY/pair_body.cpp | 12 +-
src/CLASS2/angle_class2.cpp | 6 +-
src/CLASS2/angle_class2.h | 2 +-
src/CLASS2/bond_class2.cpp | 4 +-
src/CLASS2/bond_class2.h | 2 +-
src/CLASS2/dihedral_class2.cpp | 10 +-
src/CLASS2/dihedral_class2.h | 2 +-
src/CLASS2/improper_class2.cpp | 12 +-
src/CLASS2/improper_class2.h | 2 +-
src/CLASS2/pair_lj_class2.cpp | 6 +-
src/CLASS2/pair_lj_class2_coul_cut.cpp | 6 +-
src/CLASS2/pair_lj_class2_coul_long.cpp | 46 +-
src/COLLOID/fix_wall_colloid.cpp | 4 +-
src/COLLOID/pair_colloid.cpp | 12 +-
src/COLLOID/pair_yukawa_colloid.cpp | 4 +-
src/CORESHELL/compute_temp_cs.cpp | 24 +-
src/CORESHELL/pair_born_coul_long_cs.cpp | 12 +-
src/CORESHELL/pair_buck_coul_long_cs.cpp | 12 +-
src/CORESHELL/pair_coul_long_cs.cpp | 12 +-
src/CORESHELL/pair_lj_cut_coul_long_cs.cpp | 12 +-
src/DIPOLE/atom_vec_dipole.cpp | 4 +-
src/DIPOLE/pair_lj_cut_dipole_cut.cpp | 6 +-
src/DIPOLE/pair_lj_cut_dipole_long.cpp | 42 +-
src/DIPOLE/pair_lj_cut_dipole_long.h | 2 +-
src/DIPOLE/pair_lj_long_dipole_long.cpp | 36 +-
src/FLD/pair_brownian.cpp | 10 +-
src/FLD/pair_brownian_poly.cpp | 10 +-
src/FLD/pair_lubricate.cpp | 10 +-
src/FLD/pair_lubricateU.cpp | 12 +-
src/FLD/pair_lubricateU_poly.cpp | 12 +-
src/FLD/pair_lubricate_poly.cpp | 10 +-
src/GPU/fix_gpu.cpp | 18 +-
src/GPU/pair_beck_gpu.cpp | 28 +-
src/GPU/pair_beck_gpu.h | 2 +-
src/GPU/pair_born_coul_long_gpu.cpp | 40 +-
src/GPU/pair_born_coul_long_gpu.h | 2 +-
src/GPU/pair_born_coul_wolf_gpu.cpp | 68 +-
src/GPU/pair_born_coul_wolf_gpu.h | 2 +-
src/GPU/pair_born_gpu.cpp | 46 +-
src/GPU/pair_born_gpu.h | 2 +-
src/GPU/pair_buck_coul_cut_gpu.cpp | 8 +-
src/GPU/pair_buck_coul_long_gpu.cpp | 8 +-
src/GPU/pair_buck_gpu.cpp | 10 +-
src/GPU/pair_colloid_gpu.cpp | 68 +-
src/GPU/pair_colloid_gpu.h | 2 +-
src/GPU/pair_coul_cut_gpu.cpp | 10 +-
src/GPU/pair_coul_debye_gpu.cpp | 38 +-
src/GPU/pair_coul_debye_gpu.h | 2 +-
src/GPU/pair_coul_dsf_gpu.cpp | 24 +-
src/GPU/pair_coul_long_gpu.cpp | 10 +-
src/GPU/pair_dpd_gpu.cpp | 40 +-
src/GPU/pair_dpd_tstat_gpu.cpp | 42 +-
src/GPU/pair_eam_alloy_gpu.cpp | 16 +-
src/GPU/pair_eam_fs_gpu.cpp | 16 +-
src/GPU/pair_eam_gpu.cpp | 18 +-
src/GPU/pair_eam_gpu.h | 2 +-
src/GPU/pair_gauss_gpu.cpp | 38 +-
src/GPU/pair_gauss_gpu.h | 2 +-
src/GPU/pair_gayberne_gpu.cpp | 8 +-
src/GPU/pair_lj96_cut_gpu.cpp | 8 +-
src/GPU/pair_lj_charmm_coul_long_gpu.cpp | 8 +-
src/GPU/pair_lj_class2_coul_long_gpu.cpp | 8 +-
src/GPU/pair_lj_class2_gpu.cpp | 8 +-
src/GPU/pair_lj_cubic_gpu.cpp | 20 +-
src/GPU/pair_lj_cut_coul_cut_gpu.cpp | 8 +-
src/GPU/pair_lj_cut_coul_debye_gpu.cpp | 44 +-
src/GPU/pair_lj_cut_coul_debye_gpu.h | 2 +-
src/GPU/pair_lj_cut_coul_dsf_gpu.cpp | 22 +-
src/GPU/pair_lj_cut_coul_long_gpu.cpp | 10 +-
src/GPU/pair_lj_cut_coul_msm_gpu.cpp | 34 +-
src/GPU/pair_lj_cut_coul_msm_gpu.h | 2 +-
src/GPU/pair_lj_cut_dipole_cut_gpu.cpp | 66 +-
src/GPU/pair_lj_cut_dipole_cut_gpu.h | 2 +-
src/GPU/pair_lj_cut_gpu.cpp | 12 +-
src/GPU/pair_lj_expand_gpu.cpp | 10 +-
src/GPU/pair_lj_gromacs_gpu.cpp | 32 +-
src/GPU/pair_lj_gromacs_gpu.h | 2 +-
src/GPU/pair_lj_sdk_coul_long_gpu.cpp | 8 +-
src/GPU/pair_lj_sdk_gpu.cpp | 8 +-
src/GPU/pair_lj_sf_dipole_sf_gpu.cpp | 74 +-
src/GPU/pair_lj_sf_dipole_sf_gpu.h | 2 +-
src/GPU/pair_mie_cut_gpu.cpp | 30 +-
src/GPU/pair_mie_cut_gpu.h | 2 +-
src/GPU/pair_morse_gpu.cpp | 8 +-
src/GPU/pair_resquared_gpu.cpp | 8 +-
src/GPU/pair_soft_gpu.cpp | 32 +-
src/GPU/pair_soft_gpu.h | 2 +-
src/GPU/pair_sw_gpu.cpp | 24 +-
src/GPU/pair_table_gpu.cpp | 8 +-
src/GPU/pair_tersoff_gpu.cpp | 56 +-
src/GPU/pair_yukawa_colloid_gpu.cpp | 64 +-
src/GPU/pair_yukawa_colloid_gpu.h | 2 +-
src/GPU/pair_yukawa_gpu.cpp | 8 +-
src/GPU/pair_zbl_gpu.cpp | 52 +-
src/GPU/pair_zbl_gpu.h | 2 +-
src/GPU/pppm_gpu.cpp | 18 +-
src/GRANULAR/fix_freeze.cpp | 2 +-
src/GRANULAR/fix_pour.cpp | 26 +-
src/GRANULAR/fix_wall_gran.cpp | 6 +-
src/GRANULAR/pair_gran_hertz_history.cpp | 8 +-
src/GRANULAR/pair_gran_hooke.cpp | 6 +-
src/GRANULAR/pair_gran_hooke_history.cpp | 14 +-
src/KOKKOS/angle_charmm_kokkos.cpp | 4 +-
src/KOKKOS/angle_charmm_kokkos.h | 4 +-
src/KOKKOS/angle_harmonic_kokkos.cpp | 4 +-
src/KOKKOS/angle_harmonic_kokkos.h | 4 +-
src/KOKKOS/atom_kokkos.cpp | 4 +-
src/KOKKOS/atom_vec_angle_kokkos.cpp | 2 +-
src/KOKKOS/atom_vec_atomic_kokkos.cpp | 38 +-
src/KOKKOS/atom_vec_atomic_kokkos.h | 18 +-
src/KOKKOS/atom_vec_bond_kokkos.cpp | 2 +-
src/KOKKOS/atom_vec_charge_kokkos.cpp | 2 +-
src/KOKKOS/atom_vec_full_kokkos.cpp | 2 +-
src/KOKKOS/atom_vec_kokkos.h | 32 +-
src/KOKKOS/atom_vec_molecular_kokkos.cpp | 2 +-
src/KOKKOS/bond_fene_kokkos.cpp | 4 +-
src/KOKKOS/bond_fene_kokkos.h | 4 +-
src/KOKKOS/bond_harmonic_kokkos.cpp | 4 +-
src/KOKKOS/bond_harmonic_kokkos.h | 4 +-
src/KOKKOS/comm_kokkos.cpp | 14 +-
src/KOKKOS/comm_kokkos.h | 2 +-
src/KOKKOS/compute_temp_kokkos.cpp | 6 +-
src/KOKKOS/dihedral_charmm_kokkos.cpp | 10 +-
src/KOKKOS/dihedral_charmm_kokkos.h | 4 +-
src/KOKKOS/dihedral_opls_kokkos.cpp | 4 +-
src/KOKKOS/dihedral_opls_kokkos.h | 4 +-
src/KOKKOS/domain_kokkos.cpp | 24 +-
src/KOKKOS/fix_deform_kokkos.cpp | 6 +-
src/KOKKOS/fix_langevin_kokkos.cpp | 6 +-
src/KOKKOS/fix_langevin_kokkos.h | 4 +-
src/KOKKOS/fix_nh_kokkos.cpp | 8 +-
src/KOKKOS/fix_nph_kokkos.cpp | 2 +-
src/KOKKOS/fix_npt_kokkos.cpp | 2 +-
src/KOKKOS/fix_nve_kokkos.cpp | 4 +-
src/KOKKOS/fix_nve_kokkos.h | 2 +-
src/KOKKOS/fix_nvt_kokkos.cpp | 2 +-
src/KOKKOS/fix_wall_reflect_kokkos.cpp | 4 +-
src/KOKKOS/improper_harmonic_kokkos.cpp | 8 +-
src/KOKKOS/improper_harmonic_kokkos.h | 4 +-
src/KOKKOS/kokkos.cpp | 14 +-
src/KOKKOS/kokkos_type.h | 6 +-
src/KOKKOS/memory_kokkos.h | 44 +-
src/KOKKOS/modify_kokkos.cpp | 2 +-
src/KOKKOS/modify_kokkos.h | 2 +-
src/KOKKOS/neigh_bond_kokkos.cpp | 2 +-
src/KOKKOS/neigh_bond_kokkos.h | 4 +-
src/KOKKOS/neigh_list_kokkos.cpp | 10 +-
src/KOKKOS/neigh_list_kokkos.h | 2 +-
src/KOKKOS/neighbor_kokkos.cpp | 28 +-
src/KOKKOS/neighbor_kokkos.h | 16 +-
src/KOKKOS/pair_buck_coul_cut_kokkos.cpp | 10 +-
src/KOKKOS/pair_buck_coul_cut_kokkos.h | 2 +-
src/KOKKOS/pair_buck_coul_long_kokkos.cpp | 8 +-
src/KOKKOS/pair_buck_coul_long_kokkos.h | 2 +-
src/KOKKOS/pair_buck_kokkos.cpp | 10 +-
src/KOKKOS/pair_buck_kokkos.h | 2 +-
src/KOKKOS/pair_coul_cut_kokkos.cpp | 8 +-
src/KOKKOS/pair_coul_cut_kokkos.h | 2 +-
src/KOKKOS/pair_coul_debye_kokkos.cpp | 12 +-
src/KOKKOS/pair_coul_debye_kokkos.h | 2 +-
src/KOKKOS/pair_coul_dsf_kokkos.cpp | 12 +-
src/KOKKOS/pair_coul_dsf_kokkos.h | 2 +-
src/KOKKOS/pair_coul_long_kokkos.cpp | 8 +-
src/KOKKOS/pair_coul_long_kokkos.h | 2 +-
src/KOKKOS/pair_coul_wolf_kokkos.cpp | 10 +-
src/KOKKOS/pair_coul_wolf_kokkos.h | 2 +-
src/KOKKOS/pair_eam_alloy_kokkos.cpp | 8 +-
src/KOKKOS/pair_eam_alloy_kokkos.h | 6 +-
src/KOKKOS/pair_eam_fs_kokkos.cpp | 8 +-
src/KOKKOS/pair_eam_fs_kokkos.h | 6 +-
src/KOKKOS/pair_eam_kokkos.cpp | 22 +-
src/KOKKOS/pair_eam_kokkos.h | 8 +-
..._lj_charmm_coul_charmm_implicit_kokkos.cpp | 18 +-
...ir_lj_charmm_coul_charmm_implicit_kokkos.h | 2 +-
.../pair_lj_charmm_coul_charmm_kokkos.cpp | 18 +-
.../pair_lj_charmm_coul_charmm_kokkos.h | 2 +-
.../pair_lj_charmm_coul_long_kokkos.cpp | 16 +-
src/KOKKOS/pair_lj_charmm_coul_long_kokkos.h | 2 +-
src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp | 8 +-
.../pair_lj_class2_coul_long_kokkos.cpp | 8 +-
src/KOKKOS/pair_lj_class2_coul_long_kokkos.h | 2 +-
src/KOKKOS/pair_lj_class2_kokkos.cpp | 12 +-
src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp | 8 +-
src/KOKKOS/pair_lj_cut_coul_cut_kokkos.h | 2 +-
src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp | 8 +-
src/KOKKOS/pair_lj_cut_coul_debye_kokkos.h | 2 +-
src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp | 10 +-
src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.h | 2 +-
src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp | 8 +-
src/KOKKOS/pair_lj_cut_coul_long_kokkos.h | 2 +-
src/KOKKOS/pair_lj_cut_kokkos.cpp | 12 +-
src/KOKKOS/pair_lj_cut_kokkos.h | 2 +-
src/KOKKOS/pair_lj_expand_kokkos.cpp | 12 +-
src/KOKKOS/pair_lj_expand_kokkos.h | 2 +-
.../pair_lj_gromacs_coul_gromacs_kokkos.cpp | 14 +-
.../pair_lj_gromacs_coul_gromacs_kokkos.h | 2 +-
src/KOKKOS/pair_lj_gromacs_kokkos.cpp | 14 +-
src/KOKKOS/pair_lj_gromacs_kokkos.h | 2 +-
src/KOKKOS/pair_lj_sdk_kokkos.cpp | 12 +-
src/KOKKOS/pair_lj_sdk_kokkos.h | 2 +-
src/KOKKOS/pair_sw_kokkos.cpp | 10 +-
src/KOKKOS/pair_sw_kokkos.h | 4 +-
src/KOKKOS/pair_table_kokkos.cpp | 16 +-
src/KOKKOS/pair_table_kokkos.h | 8 +-
src/KOKKOS/pair_tersoff_kokkos.cpp | 62 +-
src/KOKKOS/pair_tersoff_kokkos.h | 10 +-
src/KOKKOS/pair_tersoff_mod_kokkos.cpp | 84 +-
src/KOKKOS/pair_tersoff_mod_kokkos.h | 10 +-
src/KOKKOS/pair_tersoff_zbl_kokkos.cpp | 86 +-
src/KOKKOS/pair_tersoff_zbl_kokkos.h | 10 +-
src/KOKKOS/verlet_kokkos.cpp | 4 +-
src/KOKKOS/verlet_kokkos.h | 2 +-
src/KSPACE/ewald.cpp | 36 +-
src/KSPACE/ewald_disp.cpp | 28 +-
src/KSPACE/fft3d.cpp | 8 +-
src/KSPACE/fft3d.h | 4 +-
src/KSPACE/fft3d_wrap.cpp | 2 +-
src/KSPACE/fix_tune_kspace.cpp | 12 +-
src/KSPACE/fix_tune_kspace.h | 2 +-
src/KSPACE/gridcomm.cpp | 56 +-
src/KSPACE/msm.cpp | 30 +-
src/KSPACE/msm.h | 10 +-
src/KSPACE/msm_cg.cpp | 10 +-
src/KSPACE/msm_cg.h | 2 +-
src/KSPACE/pair_born_coul_long.cpp | 10 +-
src/KSPACE/pair_born_coul_msm.cpp | 12 +-
src/KSPACE/pair_buck_coul_long.cpp | 14 +-
src/KSPACE/pair_buck_coul_msm.cpp | 12 +-
src/KSPACE/pair_buck_long_coul_long.cpp | 22 +-
src/KSPACE/pair_coul_long.cpp | 8 +-
src/KSPACE/pair_coul_msm.cpp | 8 +-
src/KSPACE/pair_lj_charmm_coul_long.cpp | 8 +-
src/KSPACE/pair_lj_charmm_coul_msm.cpp | 28 +-
src/KSPACE/pair_lj_cut_coul_long.cpp | 8 +-
src/KSPACE/pair_lj_cut_coul_msm.cpp | 12 +-
src/KSPACE/pair_lj_cut_tip4p_long.cpp | 8 +-
src/KSPACE/pair_lj_long_coul_long.cpp | 58 +-
src/KSPACE/pair_lj_long_coul_long.h | 2 +-
src/KSPACE/pair_lj_long_tip4p_long.cpp | 100 +-
src/KSPACE/pair_lj_long_tip4p_long.h | 2 +-
src/KSPACE/pair_tip4p_long.cpp | 8 +-
src/KSPACE/pppm.cpp | 38 +-
src/KSPACE/pppm.h | 12 +-
src/KSPACE/pppm_cg.cpp | 10 +-
src/KSPACE/pppm_disp.cpp | 670 ++++----
src/KSPACE/pppm_disp.h | 26 +-
src/KSPACE/pppm_disp_tip4p.cpp | 38 +-
src/KSPACE/pppm_disp_tip4p.h | 4 +-
src/KSPACE/pppm_stagger.cpp | 20 +-
src/KSPACE/pppm_stagger.h | 2 +-
src/KSPACE/pppm_tip4p.cpp | 14 +-
src/KSPACE/remap.cpp | 18 +-
src/KSPACE/remap_wrap.cpp | 2 +-
src/MANYBODY/fix_qeq_comb.cpp | 10 +-
src/MANYBODY/fix_qeq_comb.h | 2 +-
src/MANYBODY/pair_adp.cpp | 10 +-
src/MANYBODY/pair_airebo.cpp | 12 +-
src/MANYBODY/pair_airebo.h | 2 +-
src/MANYBODY/pair_bop.cpp | 104 +-
src/MANYBODY/pair_bop.h | 4 +-
src/MANYBODY/pair_comb.cpp | 12 +-
src/MANYBODY/pair_comb3.cpp | 640 +++----
src/MANYBODY/pair_comb3.h | 56 +-
src/MANYBODY/pair_eam.cpp | 10 +-
src/MANYBODY/pair_eam.h | 2 +-
src/MANYBODY/pair_eam_alloy.cpp | 6 +-
src/MANYBODY/pair_eam_fs.cpp | 6 +-
src/MANYBODY/pair_eim.cpp | 10 +-
src/MANYBODY/pair_eim.h | 2 +-
src/MANYBODY/pair_lcbop.cpp | 10 +-
src/MANYBODY/pair_lcbop.h | 2 +-
src/MANYBODY/pair_nb3b_harmonic.cpp | 44 +-
src/MANYBODY/pair_nb3b_harmonic.h | 4 +-
src/MANYBODY/pair_polymorphic.cpp | 58 +-
src/MANYBODY/pair_polymorphic.h | 22 +-
src/MANYBODY/pair_sw.cpp | 8 +-
src/MANYBODY/pair_tersoff.cpp | 8 +-
src/MANYBODY/pair_tersoff_mod.cpp | 40 +-
src/MANYBODY/pair_tersoff_mod.h | 12 +-
src/MANYBODY/pair_tersoff_zbl.cpp | 8 +-
src/MANYBODY/pair_vashishta.cpp | 24 +-
src/MC/fix_atom_swap.cpp | 106 +-
src/MC/fix_atom_swap.h | 8 +-
src/MC/fix_bond_break.cpp | 14 +-
src/MC/fix_bond_break.h | 2 +-
src/MC/fix_bond_create.cpp | 40 +-
src/MC/fix_bond_create.h | 2 +-
src/MC/fix_bond_swap.cpp | 8 +-
src/MC/fix_gcmc.cpp | 336 ++--
src/MC/fix_gcmc.h | 14 +-
src/MC/fix_tfmc.cpp | 30 +-
src/MC/pair_dsmc.cpp | 10 +-
src/MEAM/pair_meam.cpp | 10 +-
src/MISC/compute_msd_nongauss.cpp | 2 +-
src/MISC/compute_ti.cpp | 42 +-
src/MISC/compute_ti.h | 2 +-
src/MISC/fix_deposit.cpp | 28 +-
src/MISC/fix_deposit.h | 2 +-
src/MISC/fix_efield.cpp | 22 +-
src/MISC/fix_efield.h | 2 +-
src/MISC/fix_evaporate.cpp | 6 +-
src/MISC/fix_gld.cpp | 52 +-
src/MISC/fix_gld.h | 2 +-
src/MISC/fix_oneway.cpp | 2 +-
src/MISC/fix_orient_fcc.cpp | 8 +-
src/MISC/fix_thermal_conductivity.cpp | 8 +-
src/MISC/fix_ttm.cpp | 8 +-
src/MISC/fix_viscosity.cpp | 10 +-
src/MISC/pair_nm_cut.cpp | 36 +-
src/MISC/pair_nm_cut_coul_cut.cpp | 36 +-
src/MISC/pair_nm_cut_coul_long.cpp | 32 +-
src/MOLECULE/angle_charmm.cpp | 4 +-
src/MOLECULE/angle_charmm.h | 2 +-
src/MOLECULE/angle_cosine.cpp | 4 +-
src/MOLECULE/angle_cosine.h | 2 +-
src/MOLECULE/angle_cosine_delta.cpp | 4 +-
src/MOLECULE/angle_cosine_delta.h | 2 +-
src/MOLECULE/angle_cosine_periodic.cpp | 4 +-
src/MOLECULE/angle_cosine_periodic.h | 2 +-
src/MOLECULE/angle_cosine_squared.cpp | 4 +-
src/MOLECULE/angle_cosine_squared.h | 2 +-
src/MOLECULE/angle_harmonic.cpp | 4 +-
src/MOLECULE/angle_harmonic.h | 2 +-
src/MOLECULE/angle_table.cpp | 6 +-
src/MOLECULE/angle_table.h | 2 +-
src/MOLECULE/atom_vec_angle.cpp | 4 +-
src/MOLECULE/atom_vec_bond.cpp | 2 +-
src/MOLECULE/atom_vec_full.cpp | 2 +-
src/MOLECULE/atom_vec_molecular.cpp | 6 +-
src/MOLECULE/atom_vec_template.cpp | 8 +-
src/MOLECULE/bond_fene.cpp | 8 +-
src/MOLECULE/bond_fene.h | 2 +-
src/MOLECULE/bond_fene_expand.cpp | 6 +-
src/MOLECULE/bond_fene_expand.h | 2 +-
src/MOLECULE/bond_harmonic.cpp | 4 +-
src/MOLECULE/bond_harmonic.h | 2 +-
src/MOLECULE/bond_morse.cpp | 4 +-
src/MOLECULE/bond_morse.h | 2 +-
src/MOLECULE/bond_nonlinear.cpp | 4 +-
src/MOLECULE/bond_nonlinear.h | 2 +-
src/MOLECULE/bond_quartic.cpp | 6 +-
src/MOLECULE/bond_quartic.h | 2 +-
src/MOLECULE/bond_table.cpp | 6 +-
src/MOLECULE/bond_table.h | 2 +-
src/MOLECULE/dihedral_charmm.cpp | 10 +-
src/MOLECULE/dihedral_charmm.h | 2 +-
src/MOLECULE/dihedral_harmonic.cpp | 10 +-
src/MOLECULE/dihedral_harmonic.h | 2 +-
src/MOLECULE/dihedral_helix.cpp | 10 +-
src/MOLECULE/dihedral_helix.h | 2 +-
src/MOLECULE/dihedral_multi_harmonic.cpp | 8 +-
src/MOLECULE/dihedral_multi_harmonic.h | 2 +-
src/MOLECULE/dihedral_opls.cpp | 8 +-
src/MOLECULE/dihedral_opls.h | 2 +-
src/MOLECULE/improper_cvff.cpp | 10 +-
src/MOLECULE/improper_cvff.h | 2 +-
src/MOLECULE/improper_harmonic.cpp | 10 +-
src/MOLECULE/improper_harmonic.h | 2 +-
src/MOLECULE/improper_umbrella.cpp | 10 +-
src/MOLECULE/improper_umbrella.h | 2 +-
src/MOLECULE/pair_hbond_dreiding_lj.cpp | 8 +-
src/MOLECULE/pair_hbond_dreiding_morse.cpp | 8 +-
src/MOLECULE/pair_lj_charmm_coul_charmm.cpp | 8 +-
.../pair_lj_charmm_coul_charmm_implicit.cpp | 4 +-
src/MOLECULE/pair_lj_cut_tip4p_cut.cpp | 20 +-
src/MOLECULE/pair_tip4p_cut.cpp | 8 +-
src/MPIIO/dump_atom_mpiio.cpp | 2 +-
src/MPIIO/dump_cfg_mpiio.cpp | 52 +-
src/MPIIO/dump_custom_mpiio.cpp | 6 +-
src/MPIIO/dump_xyz_mpiio.cpp | 6 +-
src/MPIIO/restart_mpiio.cpp | 4 +-
src/OPT/pair_eam_opt.cpp | 4 +-
src/OPT/pair_lj_charmm_coul_long_opt.cpp | 4 +-
src/OPT/pair_lj_cut_coul_long_opt.cpp | 2 +-
src/OPT/pair_lj_cut_opt.cpp | 2 +-
src/OPT/pair_lj_cut_tip4p_long_opt.cpp | 2 +-
src/OPT/pair_lj_long_coul_long_opt.cpp | 66 +-
src/OPT/pair_morse_opt.cpp | 4 +-
src/PERI/atom_vec_peri.cpp | 10 +-
src/PERI/compute_damage_atom.cpp | 8 +-
src/PERI/compute_dilatation_atom.cpp | 6 +-
src/PERI/compute_dilatation_atom.h | 4 +-
src/PERI/compute_plasticity_atom.cpp | 4 +-
src/PERI/fix_peri_neigh.cpp | 56 +-
src/PERI/fix_peri_neigh.h | 8 +-
src/PERI/pair_peri_eps.cpp | 102 +-
src/PERI/pair_peri_lps.cpp | 14 +-
src/PERI/pair_peri_pmb.cpp | 10 +-
src/PERI/pair_peri_ves.cpp | 44 +-
src/PERI/pair_peri_ves.h | 6 +-
src/POEMS/fix_poems.cpp | 16 +-
src/PYTHON/python.cpp | 24 +-
src/PYTHON/python.h | 2 +-
src/QEQ/fix_qeq.cpp | 14 +-
src/QEQ/fix_qeq_dynamic.cpp | 14 +-
src/QEQ/fix_qeq_point.cpp | 10 +-
src/QEQ/fix_qeq_shielded.cpp | 14 +-
src/QEQ/fix_qeq_slater.cpp | 26 +-
src/REAX/fix_reax_bonds.cpp | 4 +-
src/REAX/fix_reax_bonds.h | 2 +-
src/REAX/pair_reax.cpp | 12 +-
src/REPLICA/compute_event_displace.cpp | 8 +-
src/REPLICA/fix_event.cpp | 4 +-
src/REPLICA/fix_event_prd.cpp | 4 +-
src/REPLICA/fix_event_tad.cpp | 4 +-
src/REPLICA/fix_neb.cpp | 8 +-
src/REPLICA/neb.cpp | 14 +-
src/REPLICA/neb.h | 2 +-
src/REPLICA/prd.cpp | 16 +-
src/REPLICA/tad.cpp | 20 +-
src/REPLICA/temper.cpp | 6 +-
src/REPLICA/verlet_split.cpp | 6 +-
src/RIGID/compute_erotate_rigid.cpp | 6 +-
src/RIGID/compute_ke_rigid.cpp | 4 +-
src/RIGID/fix_rattle.cpp | 138 +-
src/RIGID/fix_rigid.cpp | 78 +-
src/RIGID/fix_rigid.h | 10 +-
src/RIGID/fix_rigid_nh.cpp | 364 ++--
src/RIGID/fix_rigid_nh.h | 16 +-
src/RIGID/fix_rigid_nh_small.cpp | 368 ++--
src/RIGID/fix_rigid_nh_small.h | 16 +-
src/RIGID/fix_rigid_nph.cpp | 14 +-
src/RIGID/fix_rigid_nph.h | 2 +-
src/RIGID/fix_rigid_nph_small.cpp | 18 +-
src/RIGID/fix_rigid_nph_small.h | 2 +-
src/RIGID/fix_rigid_npt.cpp | 16 +-
src/RIGID/fix_rigid_npt.h | 2 +-
src/RIGID/fix_rigid_npt_small.cpp | 18 +-
src/RIGID/fix_rigid_npt_small.h | 2 +-
src/RIGID/fix_rigid_nve.cpp | 2 +-
src/RIGID/fix_rigid_nve.h | 2 +-
src/RIGID/fix_rigid_nve_small.cpp | 2 +-
src/RIGID/fix_rigid_nve_small.h | 2 +-
src/RIGID/fix_rigid_nvt.cpp | 10 +-
src/RIGID/fix_rigid_nvt.h | 2 +-
src/RIGID/fix_rigid_nvt_small.cpp | 10 +-
src/RIGID/fix_rigid_nvt_small.h | 2 +-
src/RIGID/fix_rigid_small.cpp | 82 +-
src/RIGID/fix_rigid_small.h | 4 +-
src/RIGID/fix_shake.cpp | 42 +-
src/RIGID/fix_shake.h | 2 +-
src/SHOCK/fix_append_atoms.cpp | 6 +-
src/SHOCK/fix_msst.cpp | 6 +-
src/SHOCK/fix_nphug.cpp | 8 +-
src/SHOCK/fix_wall_piston.cpp | 6 +-
src/SNAP/compute_sna_atom.cpp | 28 +-
src/SNAP/compute_sna_atom.h | 4 +-
src/SNAP/compute_snad_atom.cpp | 24 +-
src/SNAP/compute_snad_atom.h | 4 +-
src/SNAP/compute_snav_atom.cpp | 24 +-
src/SNAP/compute_snav_atom.h | 4 +-
src/SNAP/pair_snap.cpp | 64 +-
src/SNAP/sna.cpp | 70 +-
src/SNAP/sna.h | 4 +-
src/SRD/fix_srd.cpp | 32 +-
src/SRD/fix_wall_srd.cpp | 4 +-
src/STUBS/mpi.c | 24 +-
src/STUBS/mpi.h | 10 +-
src/USER-ATC/fix_atc.cpp | 118 +-
src/USER-ATC/fix_atc.h | 20 +-
src/USER-AWPMD/atom_vec_wavepacket.cpp | 12 +-
src/USER-AWPMD/fix_nve_awpmd.cpp | 8 +-
src/USER-AWPMD/pair_awpmd_cut.cpp | 8 +-
src/USER-CG-CMM/angle_sdk.cpp | 4 +-
src/USER-CG-CMM/angle_sdk.h | 2 +-
src/USER-CG-CMM/lj_sdk_common.h | 2 +-
src/USER-CG-CMM/pair_lj_sdk.cpp | 8 +-
src/USER-CG-CMM/pair_lj_sdk_coul_long.cpp | 18 +-
src/USER-CG-CMM/pair_lj_sdk_coul_msm.cpp | 10 +-
src/USER-CG-CMM/pair_lj_sdk_coul_msm.h | 2 +-
src/USER-COLVARS/colvarproxy_lammps.cpp | 2 +-
src/USER-CUDA/comm_cuda.cpp | 2 +-
src/USER-CUDA/compute_pe_cuda.cpp | 2 +-
src/USER-CUDA/compute_pressure_cuda.cpp | 2 +-
src/USER-CUDA/compute_temp_cuda.cpp | 2 +-
src/USER-CUDA/compute_temp_partial_cuda.cpp | 2 +-
src/USER-CUDA/cuda.cpp | 12 +-
src/USER-CUDA/domain_cuda.cpp | 10 +-
src/USER-CUDA/fft3d_cuda.cpp | 2 +-
src/USER-CUDA/fft3d_wrap_cuda.cpp | 2 +-
src/USER-CUDA/fix_aveforce_cuda.cpp | 2 +-
src/USER-CUDA/fix_shake_cuda.cpp | 4 +-
src/USER-CUDA/neighbor_cuda.cpp | 2 +-
src/USER-CUDA/pair_eam_cuda.cpp | 2 +-
src/USER-CUDA/pair_eam_cuda.h | 2 +-
src/USER-CUDA/pair_gran_hooke_cuda.cpp | 4 +-
src/USER-CUDA/pair_tersoff_zbl_cuda.cpp | 8 +-
src/USER-CUDA/pppm_cuda.cpp | 8 +-
src/USER-CUDA/pppm_old.cpp | 10 +-
src/USER-CUDA/pppm_old.h | 2 +-
src/USER-CUDA/verlet_cuda.cpp | 2 +-
src/USER-DIFFRACTION/compute_saed.cpp | 136 +-
src/USER-DIFFRACTION/compute_saed.h | 4 +-
src/USER-DIFFRACTION/compute_saed_consts.h | 12 +-
src/USER-DIFFRACTION/compute_xrd.cpp | 114 +-
src/USER-DIFFRACTION/compute_xrd.h | 8 +-
src/USER-DIFFRACTION/compute_xrd_consts.h | 486 +++---
src/USER-DIFFRACTION/fix_saed_vtk.cpp | 70 +-
src/USER-DIFFRACTION/fix_saed_vtk.h | 6 +-
src/USER-DRUDE/compute_temp_drude.cpp | 18 +-
src/USER-DRUDE/fix_drude.cpp | 48 +-
src/USER-DRUDE/fix_drude_transform.cpp | 16 +-
src/USER-DRUDE/fix_langevin_drude.cpp | 52 +-
src/USER-DRUDE/pair_lj_cut_thole_long.cpp | 20 +-
src/USER-DRUDE/pair_thole.cpp | 16 +-
src/USER-EFF/atom_vec_electron.cpp | 12 +-
src/USER-EFF/compute_ke_atom_eff.cpp | 6 +-
src/USER-EFF/compute_ke_eff.cpp | 6 +-
src/USER-EFF/compute_temp_deform_eff.cpp | 10 +-
src/USER-EFF/compute_temp_eff.cpp | 10 +-
src/USER-EFF/compute_temp_region_eff.cpp | 10 +-
src/USER-EFF/fix_langevin_eff.cpp | 8 +-
src/USER-EFF/fix_nh_eff.cpp | 4 +-
src/USER-EFF/fix_nph_eff.cpp | 2 +-
src/USER-EFF/fix_npt_eff.cpp | 2 +-
src/USER-EFF/fix_nve_eff.cpp | 10 +-
src/USER-EFF/fix_nvt_eff.cpp | 4 +-
src/USER-EFF/fix_nvt_sllod_eff.cpp | 4 +-
src/USER-EFF/fix_temp_rescale_eff.cpp | 6 +-
src/USER-EFF/pair_eff_cut.cpp | 20 +-
src/USER-FEP/compute_fep.cpp | 42 +-
src/USER-FEP/fix_adapt_fep.cpp | 18 +-
src/USER-FEP/fix_adapt_fep.h | 2 +-
src/USER-FEP/pair_coul_cut_soft.cpp | 12 +-
src/USER-FEP/pair_coul_long_soft.cpp | 14 +-
.../pair_lj_charmm_coul_long_soft.cpp | 40 +-
src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp | 20 +-
src/USER-FEP/pair_lj_cut_coul_long_soft.cpp | 40 +-
src/USER-FEP/pair_lj_cut_soft.cpp | 26 +-
src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp | 12 +-
src/USER-FEP/pair_tip4p_long_soft.cpp | 8 +-
src/USER-H5MD/dump_h5md.cpp | 10 +-
src/USER-INTEL/fix_intel.cpp | 18 +-
src/USER-INTEL/fix_intel.h | 24 +-
src/USER-INTEL/intel_buffers.cpp | 10 +-
src/USER-INTEL/intel_buffers.h | 38 +-
src/USER-INTEL/intel_preprocess.h | 4 +-
src/USER-INTEL/neigh_half_bin_intel.cpp | 88 +-
src/USER-INTEL/pair_gayberne_intel.cpp | 100 +-
src/USER-INTEL/pair_gayberne_intel.h | 6 +-
.../pair_lj_charmm_coul_long_intel.cpp | 20 +-
.../pair_lj_cut_coul_long_intel.cpp | 16 +-
src/USER-INTEL/pair_lj_cut_intel.cpp | 8 +-
src/USER-INTEL/pair_sw_intel.cpp | 30 +-
src/USER-INTEL/pair_sw_intel.h | 2 +-
src/USER-INTEL/verlet_intel.cpp | 6 +-
src/USER-INTEL/verlet_split_intel.cpp | 6 +-
src/USER-LB/fix_lb_fluid.cpp | 626 +++----
src/USER-LB/fix_lb_fluid.h | 38 +-
src/USER-LB/fix_lb_momentum.cpp | 38 +-
src/USER-LB/fix_lb_momentum.h | 2 +-
src/USER-LB/fix_lb_pc.cpp | 80 +-
src/USER-LB/fix_lb_pc.h | 4 +-
src/USER-LB/fix_lb_rigid_pc_sphere.cpp | 222 +--
src/USER-LB/fix_lb_rigid_pc_sphere.h | 6 +-
src/USER-LB/fix_lb_viscous.cpp | 14 +-
src/USER-LB/fix_lb_viscous.h | 4 +-
src/USER-MGPT/mgpt_linalg.cpp | 4 +-
src/USER-MGPT/mgpt_readpot.cpp | 20 +-
src/USER-MGPT/mgpt_readpot.h | 4 +-
src/USER-MGPT/mgpt_splinetab.cpp | 12 +-
src/USER-MGPT/mgpt_splinetab.h | 6 +-
src/USER-MGPT/pair_mgpt.cpp | 376 ++--
src/USER-MGPT/pair_mgpt.h | 120 +-
src/USER-MISC/angle_cosine_shift.cpp | 4 +-
src/USER-MISC/angle_cosine_shift.h | 2 +-
src/USER-MISC/angle_cosine_shift_exp.cpp | 4 +-
src/USER-MISC/angle_cosine_shift_exp.h | 2 +-
src/USER-MISC/angle_dipole.cpp | 4 +-
src/USER-MISC/angle_dipole.h | 2 +-
src/USER-MISC/angle_fourier.cpp | 10 +-
src/USER-MISC/angle_fourier.h | 4 +-
src/USER-MISC/angle_fourier_simple.cpp | 8 +-
src/USER-MISC/angle_fourier_simple.h | 4 +-
src/USER-MISC/angle_quartic.cpp | 10 +-
src/USER-MISC/angle_quartic.h | 4 +-
src/USER-MISC/bond_harmonic_shift.cpp | 4 +-
src/USER-MISC/bond_harmonic_shift.h | 2 +-
src/USER-MISC/bond_harmonic_shift_cut.cpp | 4 +-
src/USER-MISC/bond_harmonic_shift_cut.h | 2 +-
src/USER-MISC/compute_ackland_atom.cpp | 6 +-
src/USER-MISC/compute_basal_atom.cpp | 10 +-
src/USER-MISC/compute_temp_rotate.cpp | 8 +-
src/USER-MISC/dihedral_cosine_shift_exp.cpp | 10 +-
src/USER-MISC/dihedral_cosine_shift_exp.h | 2 +-
src/USER-MISC/dihedral_fourier.cpp | 32 +-
src/USER-MISC/dihedral_fourier.h | 4 +-
src/USER-MISC/dihedral_nharmonic.cpp | 20 +-
src/USER-MISC/dihedral_nharmonic.h | 4 +-
src/USER-MISC/dihedral_quadratic.cpp | 20 +-
src/USER-MISC/dihedral_quadratic.h | 4 +-
src/USER-MISC/dihedral_table.cpp | 2 +-
src/USER-MISC/fix_addtorque.cpp | 10 +-
src/USER-MISC/fix_ave_correlate_long.cpp | 66 +-
src/USER-MISC/fix_ave_correlate_long.h | 14 +-
src/USER-MISC/fix_ave_spatial_sphere.cpp | 112 +-
src/USER-MISC/fix_ave_spatial_sphere.h | 18 +-
src/USER-MISC/fix_gle.cpp | 16 +-
src/USER-MISC/fix_ipi.cpp | 10 +-
src/USER-MISC/fix_pimd.cpp | 328 ++--
src/USER-MISC/fix_pimd.h | 42 +-
src/USER-MISC/fix_smd.cpp | 6 +-
src/USER-MISC/fix_srp.cpp | 74 +-
src/USER-MISC/fix_srp.h | 4 +-
src/USER-MISC/fix_ti_rs.cpp | 30 +-
src/USER-MISC/fix_ti_rs.h | 2 +-
src/USER-MISC/fix_ti_spring.cpp | 34 +-
src/USER-MISC/fix_ti_spring.h | 4 +-
src/USER-MISC/fix_ttm_mod.cpp | 18 +-
src/USER-MISC/improper_cossq.cpp | 10 +-
src/USER-MISC/improper_cossq.h | 2 +-
src/USER-MISC/improper_fourier.cpp | 30 +-
src/USER-MISC/improper_fourier.h | 4 +-
src/USER-MISC/improper_ring.cpp | 6 +-
src/USER-MISC/improper_ring.h | 2 +-
src/USER-MISC/pair_cdeam.cpp | 10 +-
src/USER-MISC/pair_coul_diel.cpp | 8 +-
src/USER-MISC/pair_edip.cpp | 10 +-
src/USER-MISC/pair_gauss_cut.cpp | 8 +-
src/USER-MISC/pair_list.cpp | 12 +-
src/USER-MISC/pair_list.h | 6 +-
src/USER-MISC/pair_lj_sf.cpp | 6 +-
src/USER-MISC/pair_lj_sf_dipole_sf.cpp | 6 +-
src/USER-MISC/pair_meam_spline.cpp | 10 +-
src/USER-MISC/pair_meam_sw_spline.cpp | 28 +-
src/USER-MISC/pair_meam_sw_spline.h | 16 +-
src/USER-MISC/pair_srp.cpp | 190 +-
src/USER-MISC/pair_srp.h | 4 +-
src/USER-MISC/pair_tersoff_table.cpp | 8 +-
src/USER-MOLFILE/reader_molfile.cpp | 6 +-
src/USER-OMP/dihedral_charmm_omp.cpp | 4 +-
src/USER-OMP/dihedral_class2_omp.cpp | 2 +-
.../dihedral_cosine_shift_exp_omp.cpp | 2 +-
src/USER-OMP/dihedral_fourier_omp.cpp | 2 +-
src/USER-OMP/dihedral_harmonic_omp.cpp | 2 +-
src/USER-OMP/dihedral_helix_omp.cpp | 2 +-
src/USER-OMP/dihedral_multi_harmonic_omp.cpp | 2 +-
src/USER-OMP/dihedral_nharmonic_omp.cpp | 2 +-
src/USER-OMP/dihedral_opls_omp.cpp | 2 +-
src/USER-OMP/dihedral_quadratic_omp.cpp | 2 +-
src/USER-OMP/ewald_omp.cpp | 2 +-
src/USER-OMP/fix_gravity_omp.cpp | 8 +-
src/USER-OMP/fix_nh_asphere_omp.cpp | 10 +-
src/USER-OMP/fix_nh_sphere_omp.cpp | 4 +-
src/USER-OMP/fix_nph_asphere_omp.cpp | 2 +-
src/USER-OMP/fix_nph_omp.cpp | 2 +-
src/USER-OMP/fix_nph_sphere_omp.cpp | 2 +-
src/USER-OMP/fix_nphug_omp.cpp | 8 +-
src/USER-OMP/fix_npt_asphere_omp.cpp | 2 +-
src/USER-OMP/fix_npt_omp.cpp | 2 +-
src/USER-OMP/fix_npt_sphere_omp.cpp | 2 +-
src/USER-OMP/fix_nve_sphere_omp.cpp | 6 +-
src/USER-OMP/fix_nvt_asphere_omp.cpp | 2 +-
src/USER-OMP/fix_nvt_omp.cpp | 2 +-
src/USER-OMP/fix_nvt_sllod_omp.cpp | 4 +-
src/USER-OMP/fix_nvt_sphere_omp.cpp | 2 +-
src/USER-OMP/fix_qeq_comb_omp.cpp | 6 +-
src/USER-OMP/fix_rigid_nh_omp.cpp | 112 +-
src/USER-OMP/fix_rigid_nh_omp.h | 4 +-
src/USER-OMP/fix_rigid_nph_omp.cpp | 18 +-
src/USER-OMP/fix_rigid_nph_omp.h | 2 +-
src/USER-OMP/fix_rigid_npt_omp.cpp | 18 +-
src/USER-OMP/fix_rigid_npt_omp.h | 2 +-
src/USER-OMP/fix_rigid_nve_omp.cpp | 2 +-
src/USER-OMP/fix_rigid_nve_omp.h | 2 +-
src/USER-OMP/fix_rigid_nvt_omp.cpp | 10 +-
src/USER-OMP/fix_rigid_nvt_omp.h | 2 +-
src/USER-OMP/fix_rigid_omp.cpp | 6 +-
src/USER-OMP/fix_rigid_small_omp.cpp | 10 +-
src/USER-OMP/fix_shear_history_omp.cpp | 4 +-
src/USER-OMP/fix_wall_gran_omp.cpp | 2 +-
src/USER-OMP/improper_class2_omp.cpp | 2 +-
src/USER-OMP/improper_cossq_omp.cpp | 2 +-
src/USER-OMP/improper_cvff_omp.cpp | 2 +-
src/USER-OMP/improper_fourier_omp.cpp | 2 +-
src/USER-OMP/improper_harmonic_omp.cpp | 2 +-
src/USER-OMP/improper_ring_omp.cpp | 2 +-
src/USER-OMP/improper_umbrella_omp.cpp | 2 +-
src/USER-OMP/msm_cg_omp.cpp | 10 +-
src/USER-OMP/pair_adp_omp.cpp | 4 +-
src/USER-OMP/pair_airebo_omp.cpp | 2 +-
src/USER-OMP/pair_beck_omp.cpp | 2 +-
src/USER-OMP/pair_born_coul_long_omp.cpp | 2 +-
src/USER-OMP/pair_born_coul_msm_omp.cpp | 2 +-
src/USER-OMP/pair_born_coul_wolf_omp.cpp | 2 +-
src/USER-OMP/pair_born_omp.cpp | 2 +-
src/USER-OMP/pair_brownian_omp.cpp | 2 +-
src/USER-OMP/pair_brownian_poly_omp.cpp | 2 +-
src/USER-OMP/pair_buck_coul_cut_omp.cpp | 2 +-
src/USER-OMP/pair_buck_coul_long_omp.cpp | 2 +-
src/USER-OMP/pair_buck_coul_msm_omp.cpp | 2 +-
src/USER-OMP/pair_buck_long_coul_long_omp.cpp | 2 +-
src/USER-OMP/pair_buck_omp.cpp | 2 +-
src/USER-OMP/pair_cdeam_omp.cpp | 4 +-
src/USER-OMP/pair_colloid_omp.cpp | 2 +-
src/USER-OMP/pair_comb_omp.cpp | 2 +-
src/USER-OMP/pair_coul_cut_omp.cpp | 2 +-
src/USER-OMP/pair_coul_cut_soft_omp.cpp | 2 +-
src/USER-OMP/pair_coul_debye_omp.cpp | 2 +-
src/USER-OMP/pair_coul_diel_omp.cpp | 2 +-
src/USER-OMP/pair_coul_dsf_omp.cpp | 2 +-
src/USER-OMP/pair_coul_long_omp.cpp | 2 +-
src/USER-OMP/pair_coul_long_soft_omp.cpp | 2 +-
src/USER-OMP/pair_coul_msm_omp.cpp | 2 +-
src/USER-OMP/pair_coul_wolf_omp.cpp | 2 +-
src/USER-OMP/pair_dpd_omp.cpp | 2 +-
src/USER-OMP/pair_dpd_tstat_omp.cpp | 2 +-
src/USER-OMP/pair_eam_alloy_omp.cpp | 6 +-
src/USER-OMP/pair_eam_fs_omp.cpp | 6 +-
src/USER-OMP/pair_eam_omp.cpp | 4 +-
src/USER-OMP/pair_edip_omp.cpp | 2 +-
src/USER-OMP/pair_eim_omp.cpp | 4 +-
src/USER-OMP/pair_gauss_cut_omp.cpp | 2 +-
src/USER-OMP/pair_gauss_omp.cpp | 2 +-
src/USER-OMP/pair_gayberne_omp.cpp | 2 +-
src/USER-OMP/pair_gran_hertz_history_omp.cpp | 2 +-
src/USER-OMP/pair_gran_hooke_history_omp.cpp | 4 +-
src/USER-OMP/pair_gran_hooke_omp.cpp | 2 +-
src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp | 2 +-
.../pair_hbond_dreiding_morse_omp.cpp | 2 +-
src/USER-OMP/pair_line_lj_omp.cpp | 2 +-
src/USER-OMP/pair_lj96_cut_omp.cpp | 2 +-
...air_lj_charmm_coul_charmm_implicit_omp.cpp | 2 +-
.../pair_lj_charmm_coul_charmm_omp.cpp | 2 +-
src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp | 2 +-
.../pair_lj_charmm_coul_long_soft_omp.cpp | 2 +-
src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp | 2 +-
src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp | 2 +-
src/USER-OMP/pair_lj_class2_coul_long_omp.cpp | 2 +-
src/USER-OMP/pair_lj_class2_omp.cpp | 2 +-
src/USER-OMP/pair_lj_cubic_omp.cpp | 2 +-
src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp | 2 +-
.../pair_lj_cut_coul_cut_soft_omp.cpp | 6 +-
src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp | 2 +-
src/USER-OMP/pair_lj_cut_coul_dsf_omp.cpp | 4 +-
src/USER-OMP/pair_lj_cut_coul_long_omp.cpp | 2 +-
.../pair_lj_cut_coul_long_soft_omp.cpp | 10 +-
src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp | 2 +-
src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp | 2 +-
src/USER-OMP/pair_lj_cut_omp.cpp | 2 +-
src/USER-OMP/pair_lj_cut_soft_omp.cpp | 6 +-
src/USER-OMP/pair_lj_cut_tip4p_cut_omp.cpp | 2 +-
src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp | 2 +-
.../pair_lj_cut_tip4p_long_soft_omp.cpp | 6 +-
src/USER-OMP/pair_lj_expand_omp.cpp | 2 +-
.../pair_lj_gromacs_coul_gromacs_omp.cpp | 2 +-
src/USER-OMP/pair_lj_gromacs_omp.cpp | 2 +-
src/USER-OMP/pair_lj_long_coul_long_omp.cpp | 2 +-
src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp | 6 +-
src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp | 2 +-
src/USER-OMP/pair_lj_sdk_coul_msm_omp.cpp | 2 +-
src/USER-OMP/pair_lj_sdk_omp.cpp | 2 +-
src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp | 2 +-
src/USER-OMP/pair_lj_sf_omp.cpp | 2 +-
src/USER-OMP/pair_lj_smooth_linear_omp.cpp | 2 +-
src/USER-OMP/pair_lj_smooth_omp.cpp | 2 +-
src/USER-OMP/pair_lubricate_omp.cpp | 2 +-
src/USER-OMP/pair_lubricate_poly_omp.cpp | 2 +-
src/USER-OMP/pair_meam_spline_omp.cpp | 4 +-
src/USER-OMP/pair_morse_omp.cpp | 2 +-
src/USER-OMP/pair_nb3b_harmonic_omp.cpp | 2 +-
src/USER-OMP/pair_nm_cut_coul_cut_omp.cpp | 2 +-
src/USER-OMP/pair_nm_cut_coul_long_omp.cpp | 2 +-
src/USER-OMP/pair_nm_cut_omp.cpp | 2 +-
src/USER-OMP/pair_peri_lps_omp.cpp | 4 +-
src/USER-OMP/pair_peri_pmb_omp.cpp | 4 +-
src/USER-OMP/pair_resquared_omp.cpp | 2 +-
src/USER-OMP/pair_soft_omp.cpp | 2 +-
src/USER-OMP/pair_sw_omp.cpp | 2 +-
src/USER-OMP/pair_table_omp.cpp | 2 +-
src/USER-OMP/pair_tersoff_mod_omp.cpp | 2 +-
src/USER-OMP/pair_tersoff_omp.cpp | 2 +-
src/USER-OMP/pair_tersoff_table_omp.cpp | 2 +-
src/USER-OMP/pair_tersoff_zbl_omp.cpp | 8 +-
src/USER-OMP/pair_tip4p_cut_omp.cpp | 2 +-
src/USER-OMP/pair_tip4p_long_omp.cpp | 2 +-
src/USER-OMP/pair_tip4p_long_soft_omp.cpp | 4 +-
src/USER-OMP/pair_tri_lj_omp.cpp | 2 +-
src/USER-OMP/pair_vashishta_omp.cpp | 2 +-
src/USER-OMP/pair_yukawa_colloid_omp.cpp | 2 +-
src/USER-OMP/pair_yukawa_omp.cpp | 2 +-
src/USER-OMP/pair_zbl_omp.cpp | 2 +-
src/USER-OMP/respa_omp.cpp | 4 +-
src/USER-PHONON/fix_phonon.cpp | 48 +-
src/USER-PHONON/fix_phonon.h | 12 +-
src/USER-QMMM/fix_qmmm.cpp | 14 +-
src/USER-QTB/fix_qbmsst.cpp | 162 +-
src/USER-QTB/fix_qbmsst.h | 8 +-
src/USER-QTB/fix_qtb.cpp | 54 +-
src/USER-QTB/fix_qtb.h | 2 +-
src/USER-QUIP/pair_quip.cpp | 26 +-
src/USER-QUIP/pair_quip.h | 8 +-
src/USER-REAXC/compute_spec_atom.cpp | 20 +-
src/USER-REAXC/compute_spec_atom.h | 6 +-
src/USER-REAXC/fix_qeq_reax.cpp | 16 +-
src/USER-REAXC/fix_reaxc_bonds.cpp | 6 +-
src/USER-REAXC/fix_reaxc_bonds.h | 2 +-
src/USER-REAXC/fix_reaxc_species.cpp | 82 +-
src/USER-REAXC/fix_reaxc_species.h | 2 +-
src/USER-REAXC/pair_reax_c.cpp | 14 +-
src/USER-REAXC/pair_reax_c.h | 4 +-
src/USER-REAXC/reaxc_bonds.cpp | 24 +-
src/USER-REAXC/reaxc_ffield.cpp | 2 +-
src/USER-REAXC/reaxc_torsion_angles.cpp | 6 +-
src/USER-REAXC/reaxc_types.h | 14 +-
src/USER-SMD/atom_vec_smd.cpp | 6 +-
src/USER-SMD/compute_smd_contact_radius.cpp | 2 +-
src/USER-SMD/compute_smd_damage.cpp | 2 +-
src/USER-SMD/compute_smd_hourglass_error.cpp | 2 +-
src/USER-SMD/compute_smd_internal_energy.cpp | 2 +-
src/USER-SMD/compute_smd_plastic_strain.cpp | 2 +-
.../compute_smd_plastic_strain_rate.cpp | 2 +-
src/USER-SMD/compute_smd_rho.cpp | 2 +-
src/USER-SMD/compute_smd_tlsph_defgrad.cpp | 6 +-
src/USER-SMD/compute_smd_tlsph_defgrad.h | 2 +-
src/USER-SMD/compute_smd_tlsph_dt.cpp | 2 +-
src/USER-SMD/compute_smd_tlsph_num_neighs.cpp | 2 +-
src/USER-SMD/compute_smd_tlsph_shape.cpp | 6 +-
src/USER-SMD/compute_smd_tlsph_shape.h | 2 +-
src/USER-SMD/compute_smd_tlsph_strain.cpp | 6 +-
src/USER-SMD/compute_smd_tlsph_strain.h | 2 +-
.../compute_smd_tlsph_strain_rate.cpp | 2 +-
src/USER-SMD/compute_smd_tlsph_strain_rate.h | 2 +-
src/USER-SMD/compute_smd_tlsph_stress.cpp | 2 +-
src/USER-SMD/compute_smd_tlsph_stress.h | 2 +-
.../compute_smd_triangle_mesh_vertices.cpp | 6 +-
.../compute_smd_triangle_mesh_vertices.h | 2 +-
src/USER-SMD/compute_smd_ulsph_effm.cpp | 2 +-
src/USER-SMD/compute_smd_ulsph_num_neighs.cpp | 2 +-
src/USER-SMD/compute_smd_ulsph_strain.cpp | 6 +-
src/USER-SMD/compute_smd_ulsph_strain.h | 2 +-
.../compute_smd_ulsph_strain_rate.cpp | 2 +-
src/USER-SMD/compute_smd_ulsph_strain_rate.h | 2 +-
src/USER-SMD/compute_smd_ulsph_stress.cpp | 2 +-
src/USER-SMD/compute_smd_ulsph_stress.h | 2 +-
src/USER-SMD/compute_smd_vol.cpp | 2 +-
src/USER-SMD/fix_smd_adjust_dt.cpp | 6 +-
src/USER-SMD/fix_smd_integrate_tlsph.cpp | 8 +-
src/USER-SMD/fix_smd_integrate_ulsph.cpp | 10 +-
.../fix_smd_move_triangulated_surface.cpp | 10 +-
src/USER-SMD/fix_smd_setvel.cpp | 4 +-
.../fix_smd_tlsph_reference_configuration.cpp | 6 +-
src/USER-SMD/fix_smd_wall_surface.cpp | 2 +-
src/USER-SMD/pair_smd_hertz.cpp | 8 +-
src/USER-SMD/pair_smd_hertz.h | 2 +-
src/USER-SMD/pair_smd_tlsph.cpp | 8 +-
.../pair_smd_triangulated_surface.cpp | 8 +-
src/USER-SMD/pair_smd_triangulated_surface.h | 2 +-
src/USER-SMD/pair_smd_ulsph.cpp | 8 +-
src/USER-SMD/smd_material_models.cpp | 2 +-
src/USER-SMTBQ/pair_smtbq.cpp | 1524 ++++++++---------
src/USER-SPH/atom_vec_meso.cpp | 8 +-
src/USER-SPH/compute_meso_e_atom.cpp | 2 +-
src/USER-SPH/compute_meso_rho_atom.cpp | 2 +-
src/USER-SPH/compute_meso_t_atom.cpp | 2 +-
src/USER-SPH/fix_meso.cpp | 12 +-
src/USER-SPH/fix_meso_stationary.cpp | 10 +-
src/USER-SPH/pair_sph_heatconduction.cpp | 4 +-
src/USER-SPH/pair_sph_idealgas.cpp | 4 +-
src/USER-SPH/pair_sph_lj.cpp | 4 +-
src/USER-SPH/pair_sph_rhosum.cpp | 6 +-
src/USER-SPH/pair_sph_taitwater.cpp | 4 +-
src/USER-SPH/pair_sph_taitwater_morris.cpp | 4 +-
src/USER-TALLY/compute_force_tally.cpp | 4 +-
src/USER-TALLY/compute_force_tally.h | 4 +-
src/USER-TALLY/compute_heat_flux_tally.cpp | 6 +-
src/USER-TALLY/compute_heat_flux_tally.h | 2 +-
src/USER-TALLY/compute_pe_tally.cpp | 6 +-
src/USER-TALLY/compute_pe_tally.h | 2 +-
src/USER-TALLY/compute_stress_tally.cpp | 8 +-
src/USER-TALLY/compute_stress_tally.h | 2 +-
src/VORONOI/compute_voronoi_atom.cpp | 10 +-
src/XTC/dump_xtc.cpp | 12 +-
src/XTC/dump_xtc.h | 2 +-
src/angle.cpp | 4 +-
src/angle.h | 2 +-
src/angle_hybrid.cpp | 6 +-
src/angle_hybrid.h | 2 +-
src/atom.cpp | 46 +-
src/atom.h | 2 +-
src/atom_map.cpp | 10 +-
src/atom_vec.cpp | 10 +-
src/atom_vec.h | 4 +-
src/atom_vec_atomic.cpp | 2 +-
src/atom_vec_body.cpp | 16 +-
src/atom_vec_charge.cpp | 2 +-
src/atom_vec_ellipsoid.cpp | 10 +-
src/atom_vec_hybrid.cpp | 8 +-
src/atom_vec_hybrid.h | 2 +-
src/atom_vec_line.cpp | 10 +-
src/atom_vec_sphere.cpp | 14 +-
src/atom_vec_tri.cpp | 10 +-
src/balance.cpp | 32 +-
src/balance.h | 2 +-
src/body.cpp | 6 +-
src/body.h | 2 +-
src/bond.cpp | 4 +-
src/bond.h | 2 +-
src/bond_hybrid.cpp | 6 +-
src/bond_hybrid.h | 2 +-
src/change_box.cpp | 8 +-
src/citeme.cpp | 4 +-
src/citeme.h | 2 +-
src/comm.cpp | 14 +-
src/comm.h | 8 +-
src/comm_brick.cpp | 18 +-
src/comm_brick.h | 2 +-
src/comm_tiled.cpp | 62 +-
src/comm_tiled.h | 2 +-
src/compute.cpp | 10 +-
src/compute_angle_local.cpp | 4 +-
src/compute_angmom_chunk.cpp | 4 +-
src/compute_bond_local.cpp | 4 +-
src/compute_centro_atom.cpp | 4 +-
src/compute_chunk_atom.cpp | 70 +-
src/compute_cluster_atom.cpp | 6 +-
src/compute_cna_atom.cpp | 6 +-
src/compute_com_chunk.cpp | 2 +-
src/compute_contact_atom.cpp | 6 +-
src/compute_coord_atom.cpp | 12 +-
src/compute_dihedral_local.cpp | 4 +-
src/compute_displace_atom.cpp | 4 +-
src/compute_erotate_sphere.cpp | 2 +-
src/compute_erotate_sphere_atom.cpp | 4 +-
src/compute_group_group.cpp | 8 +-
src/compute_gyration.cpp | 2 +-
src/compute_gyration_chunk.cpp | 4 +-
src/compute_heat_flux.cpp | 4 +-
src/compute_improper_local.cpp | 4 +-
src/compute_inertia_chunk.cpp | 6 +-
src/compute_ke.cpp | 2 +-
src/compute_ke_atom.cpp | 2 +-
src/compute_msd.cpp | 4 +-
src/compute_msd_chunk.cpp | 4 +-
src/compute_omega_chunk.cpp | 8 +-
src/compute_pair.cpp | 4 +-
src/compute_pair_local.cpp | 6 +-
src/compute_pe.cpp | 4 +-
src/compute_pe_atom.cpp | 2 +-
src/compute_pressure.cpp | 8 +-
src/compute_property_atom.cpp | 12 +-
src/compute_property_chunk.cpp | 4 +-
src/compute_property_local.cpp | 2 +-
src/compute_rdf.cpp | 6 +-
src/compute_rdf.h | 2 +-
src/compute_reduce.cpp | 4 +-
src/compute_reduce_region.cpp | 4 +-
src/compute_slice.cpp | 4 +-
src/compute_stress_atom.cpp | 6 +-
src/compute_temp.cpp | 6 +-
src/compute_temp_chunk.cpp | 6 +-
src/compute_temp_com.cpp | 8 +-
src/compute_temp_deform.cpp | 6 +-
src/compute_temp_partial.cpp | 6 +-
src/compute_temp_profile.cpp | 10 +-
src/compute_temp_ramp.cpp | 8 +-
src/compute_temp_region.cpp | 6 +-
src/compute_temp_sphere.cpp | 6 +-
src/compute_torque_chunk.cpp | 4 +-
src/compute_vacf.cpp | 2 +-
src/compute_vcm_chunk.cpp | 6 +-
src/create_atoms.cpp | 14 +-
src/create_bonds.cpp | 12 +-
src/create_box.cpp | 20 +-
src/delete_atoms.cpp | 26 +-
src/delete_bonds.cpp | 10 +-
src/dihedral.cpp | 4 +-
src/dihedral.h | 2 +-
src/dihedral_hybrid.cpp | 6 +-
src/dihedral_hybrid.h | 2 +-
src/displace_atoms.cpp | 12 +-
src/domain.cpp | 34 +-
src/domain.h | 6 +-
src/dump.cpp | 26 +-
src/dump.h | 4 +-
src/dump_atom.cpp | 6 +-
src/dump_cfg.cpp | 50 +-
src/dump_custom.cpp | 36 +-
src/dump_dcd.cpp | 10 +-
src/dump_image.cpp | 10 +-
src/dump_local.cpp | 10 +-
src/dump_movie.cpp | 6 +-
src/dump_xyz.cpp | 2 +-
src/error.cpp | 4 +-
src/finish.cpp | 26 +-
src/fix.cpp | 4 +-
src/fix_adapt.cpp | 22 +-
src/fix_adapt.h | 2 +-
src/fix_addforce.cpp | 4 +-
src/fix_ave_atom.cpp | 6 +-
src/fix_ave_atom.h | 2 +-
src/fix_ave_chunk.cpp | 26 +-
src/fix_ave_chunk.h | 2 +-
src/fix_ave_correlate.cpp | 8 +-
src/fix_ave_correlate.h | 2 +-
src/fix_ave_histo.cpp | 8 +-
src/fix_ave_histo.h | 2 +-
src/fix_ave_histo_weight.cpp | 98 +-
src/fix_ave_histo_weight.h | 4 +-
src/fix_ave_spatial.cpp | 26 +-
src/fix_ave_spatial.h | 2 +-
src/fix_ave_time.cpp | 34 +-
src/fix_ave_time.h | 2 +-
src/fix_aveforce.cpp | 6 +-
src/fix_balance.cpp | 6 +-
src/fix_balance.h | 2 +-
src/fix_box_relax.cpp | 6 +-
src/fix_deform.cpp | 6 +-
src/fix_drag.cpp | 6 +-
src/fix_dt_reset.cpp | 6 +-
src/fix_enforce2d.cpp | 2 +-
src/fix_external.cpp | 8 +-
src/fix_gravity.cpp | 8 +-
src/fix_group.cpp | 8 +-
src/fix_heat.cpp | 20 +-
src/fix_indent.cpp | 6 +-
src/fix_langevin.cpp | 20 +-
src/fix_langevin.h | 6 +-
src/fix_lineforce.cpp | 6 +-
src/fix_minimize.cpp | 2 +-
src/fix_momentum.cpp | 6 +-
src/fix_move.cpp | 6 +-
src/fix_move.h | 2 +-
src/fix_nh.cpp | 18 +-
src/fix_nh_sphere.cpp | 2 +-
src/fix_nph.cpp | 2 +-
src/fix_nph_sphere.cpp | 2 +-
src/fix_npt.cpp | 2 +-
src/fix_npt_sphere.cpp | 2 +-
src/fix_nve.cpp | 4 +-
src/fix_nve_limit.cpp | 8 +-
src/fix_nve_noforce.cpp | 4 +-
src/fix_nve_sphere.cpp | 6 +-
src/fix_nvt.cpp | 2 +-
src/fix_nvt_sllod.cpp | 4 +-
src/fix_nvt_sphere.cpp | 2 +-
src/fix_planeforce.cpp | 6 +-
src/fix_press_berendsen.cpp | 6 +-
src/fix_print.cpp | 4 +-
src/fix_print.h | 2 +-
src/fix_property_atom.cpp | 28 +-
src/fix_read_restart.cpp | 2 +-
src/fix_recenter.cpp | 4 +-
src/fix_respa.cpp | 4 +-
src/fix_restrain.cpp | 10 +-
src/fix_setforce.cpp | 4 +-
src/fix_shear_history.cpp | 8 +-
src/fix_spring.cpp | 6 +-
src/fix_spring_rg.cpp | 6 +-
src/fix_spring_self.cpp | 4 +-
src/fix_store.cpp | 10 +-
src/fix_store_force.cpp | 2 +-
src/fix_store_state.cpp | 4 +-
src/fix_temp_berendsen.cpp | 6 +-
src/fix_temp_csld.cpp | 10 +-
src/fix_temp_csvr.cpp | 6 +-
src/fix_temp_rescale.cpp | 6 +-
src/fix_tmd.cpp | 8 +-
src/fix_tmd.h | 2 +-
src/fix_vector.cpp | 10 +-
src/fix_viscous.cpp | 6 +-
src/fix_wall.cpp | 8 +-
src/fix_wall_harmonic.cpp | 2 +-
src/fix_wall_lj1043.cpp | 12 +-
src/fix_wall_lj1043.h | 2 +-
src/fix_wall_lj126.cpp | 2 +-
src/fix_wall_lj93.cpp | 2 +-
src/fix_wall_reflect.cpp | 4 +-
src/fix_wall_region.cpp | 6 +-
src/force.cpp | 34 +-
src/force.h | 2 +-
src/group.cpp | 68 +-
src/group.h | 2 +-
src/image.cpp | 14 +-
src/image.h | 4 +-
src/improper.cpp | 6 +-
src/improper.h | 2 +-
src/improper_hybrid.cpp | 6 +-
src/improper_hybrid.h | 2 +-
src/info.cpp | 4 +-
src/input.cpp | 158 +-
src/input.h | 4 +-
src/integrate.cpp | 2 +-
src/irregular.cpp | 10 +-
src/irregular.h | 2 +-
src/kspace.cpp | 10 +-
src/kspace.h | 14 +-
src/lammps.cpp | 22 +-
src/lammps.h | 2 +-
src/lattice.cpp | 6 +-
src/library.cpp | 8 +-
src/library.h | 2 +-
src/lmptype.h | 6 +-
src/lmpwindows.h | 4 +-
src/main.cpp | 4 +-
src/math_extra.cpp | 6 +-
src/math_extra.h | 6 +-
src/math_vector.h | 4 +-
src/memory.cpp | 6 +-
src/memory.h | 68 +-
src/min.cpp | 6 +-
src/min_cg.cpp | 6 +-
src/min_fire.cpp | 2 +-
src/min_hftn.cpp | 4 +-
src/min_linesearch.cpp | 2 +-
src/min_quickmin.cpp | 4 +-
src/min_sd.cpp | 4 +-
src/minimize.cpp | 2 +-
src/modify.cpp | 14 +-
src/modify.h | 2 +-
src/molecule.cpp | 112 +-
src/molecule.h | 8 +-
src/my_page.h | 8 +-
src/my_pool_chunk.h | 2 +-
src/neigh_bond.cpp | 44 +-
src/neigh_list.cpp | 2 +-
src/neigh_request.cpp | 2 +-
src/neigh_request.h | 4 +-
src/neighbor.cpp | 36 +-
src/output.cpp | 12 +-
src/pair.cpp | 68 +-
src/pair.h | 2 +-
src/pair_beck.cpp | 6 +-
src/pair_born.cpp | 10 +-
src/pair_born_coul_wolf.cpp | 8 +-
src/pair_buck.cpp | 8 +-
src/pair_buck_coul_cut.cpp | 8 +-
src/pair_coul_cut.cpp | 10 +-
src/pair_coul_debye.cpp | 8 +-
src/pair_coul_dsf.cpp | 38 +-
src/pair_coul_dsf.h | 4 +-
src/pair_coul_streitz.cpp | 52 +-
src/pair_coul_streitz.h | 8 +-
src/pair_coul_wolf.cpp | 8 +-
src/pair_dpd.cpp | 8 +-
src/pair_dpd_tstat.cpp | 4 +-
src/pair_gauss.cpp | 14 +-
src/pair_hybrid.cpp | 12 +-
src/pair_hybrid.h | 2 +-
src/pair_hybrid_overlay.cpp | 6 +-
src/pair_lj96_cut.cpp | 8 +-
src/pair_lj_cubic.cpp | 8 +-
src/pair_lj_cut.cpp | 8 +-
src/pair_lj_cut_coul_cut.cpp | 10 +-
src/pair_lj_cut_coul_debye.cpp | 4 +-
src/pair_lj_cut_coul_dsf.cpp | 68 +-
src/pair_lj_cut_coul_dsf.h | 6 +-
src/pair_lj_expand.cpp | 16 +-
src/pair_lj_gromacs.cpp | 8 +-
src/pair_lj_gromacs_coul_gromacs.cpp | 8 +-
src/pair_lj_smooth.cpp | 6 +-
src/pair_lj_smooth_linear.cpp | 6 +-
src/pair_mie_cut.cpp | 20 +-
src/pair_morse.cpp | 8 +-
src/pair_soft.cpp | 10 +-
src/pair_table.cpp | 8 +-
src/pair_yukawa.cpp | 4 +-
src/pair_zbl.cpp | 68 +-
src/pointers.h | 2 +-
src/random_mars.cpp | 2 +-
src/random_park.cpp | 2 +-
src/rcb.cpp | 82 +-
src/rcb.h | 10 +-
src/read_data.cpp | 80 +-
src/read_data.h | 4 +-
src/read_dump.cpp | 16 +-
src/read_dump.h | 2 +-
src/read_restart.cpp | 58 +-
src/read_restart.h | 2 +-
src/reader.cpp | 4 +-
src/reader_native.cpp | 4 +-
src/reader_xyz.cpp | 4 +-
src/region.cpp | 6 +-
src/region_block.cpp | 4 +-
src/region_cone.cpp | 6 +-
src/region_cylinder.cpp | 6 +-
src/region_intersect.cpp | 8 +-
src/region_plane.cpp | 6 +-
src/region_prism.cpp | 6 +-
src/region_sphere.cpp | 6 +-
src/region_union.cpp | 8 +-
src/replicate.cpp | 4 +-
src/rerun.cpp | 4 +-
src/respa.cpp | 8 +-
src/run.cpp | 4 +-
src/set.cpp | 18 +-
src/special.cpp | 4 +-
src/thermo.cpp | 24 +-
src/timer.cpp | 8 +-
src/timer.h | 2 +-
src/universe.cpp | 10 +-
src/universe.h | 2 +-
src/update.cpp | 16 +-
src/variable.cpp | 118 +-
src/variable.h | 4 +-
src/velocity.cpp | 12 +-
src/verlet.cpp | 2 +-
src/write_data.cpp | 34 +-
src/write_data.h | 2 +-
src/write_dump.cpp | 4 +-
src/write_restart.cpp | 16 +-
src/write_restart.h | 2 +-
1219 files changed, 10111 insertions(+), 10111 deletions(-)
diff --git a/src/ASPHERE/compute_erotate_asphere.cpp b/src/ASPHERE/compute_erotate_asphere.cpp
index 5b9612ee1e..afec2a9b28 100644
--- a/src/ASPHERE/compute_erotate_asphere.cpp
+++ b/src/ASPHERE/compute_erotate_asphere.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
+#include <mpi.h>
#include "compute_erotate_asphere.h"
#include "math_extra.h"
#include "atom.h"
diff --git a/src/ASPHERE/compute_temp_asphere.cpp b/src/ASPHERE/compute_temp_asphere.cpp
index 0f2fea0356..f3db5dea92 100755
--- a/src/ASPHERE/compute_temp_asphere.cpp
+++ b/src/ASPHERE/compute_temp_asphere.cpp
@@ -15,8 +15,8 @@
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "string.h"
+#include <mpi.h>
+#include <string.h>
#include "compute_temp_asphere.h"
#include "math_extra.h"
#include "atom.h"
@@ -55,7 +55,7 @@ ComputeTempAsphere::ComputeTempAsphere(LAMMPS *lmp, int narg, char **arg) :
int iarg = 3;
while (iarg < narg) {
if (strcmp(arg[iarg],"bias") == 0) {
- if (iarg+2 > narg)
+ if (iarg+2 > narg)
error->all(FLERR,"Illegal compute temp/asphere command");
tempbias = 1;
int n = strlen(arg[iarg+1]) + 1;
@@ -63,7 +63,7 @@ ComputeTempAsphere::ComputeTempAsphere(LAMMPS *lmp, int narg, char **arg) :
strcpy(id_bias,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"dof") == 0) {
- if (iarg+2 > narg)
+ if (iarg+2 > narg)
error->all(FLERR,"Illegal compute temp/asphere command");
if (strcmp(arg[iarg+1],"rotate") == 0) mode = ROTATE;
else if (strcmp(arg[iarg+1],"all") == 0) mode = ALL;
@@ -107,7 +107,7 @@ void ComputeTempAsphere::init()
if (tempbias) {
int i = modify->find_compute(id_bias);
- if (i < 0)
+ if (i < 0)
error->all(FLERR,"Could not find compute ID for temperature bias");
tbias = modify->compute[i];
if (tbias->tempflag == 0)
@@ -267,7 +267,7 @@ double ComputeTempAsphere::compute_scalar()
MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
if (dynamic || tempbias == 2) dof_compute();
- if (dof < 0.0 && natoms_temp > 0.0)
+ if (dof < 0.0 && natoms_temp > 0.0)
error->all(FLERR,"Temperature compute degrees of freedom < 0");
scalar *= tfactor;
return scalar;
diff --git a/src/ASPHERE/fix_nh_asphere.cpp b/src/ASPHERE/fix_nh_asphere.cpp
index ced5470ada..2eee28dc1c 100644
--- a/src/ASPHERE/fix_nh_asphere.cpp
+++ b/src/ASPHERE/fix_nh_asphere.cpp
@@ -15,9 +15,9 @@
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
-#include "string.h"
-#include "stdlib.h"
-#include "math.h"
+#include <string.h>
+#include <stdlib.h>
+#include <math.h>
#include "math_extra.h"
#include "fix_nh_asphere.h"
#include "atom.h"
diff --git a/src/ASPHERE/fix_nph_asphere.cpp b/src/ASPHERE/fix_nph_asphere.cpp
index a1a113a337..10549ca1b8 100644
--- a/src/ASPHERE/fix_nph_asphere.cpp
+++ b/src/ASPHERE/fix_nph_asphere.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "fix_nph_asphere.h"
#include "modify.h"
#include "error.h"
diff --git a/src/ASPHERE/fix_npt_asphere.cpp b/src/ASPHERE/fix_npt_asphere.cpp
index dab72dc29f..2625bc6391 100755
--- a/src/ASPHERE/fix_npt_asphere.cpp
+++ b/src/ASPHERE/fix_npt_asphere.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "fix_npt_asphere.h"
#include "modify.h"
#include "error.h"
diff --git a/src/ASPHERE/fix_nve_asphere.cpp b/src/ASPHERE/fix_nve_asphere.cpp
index 78eebc8820..2ac3f95c53 100755
--- a/src/ASPHERE/fix_nve_asphere.cpp
+++ b/src/ASPHERE/fix_nve_asphere.cpp
@@ -15,9 +15,9 @@
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <string.h>
#include "fix_nve_asphere.h"
#include "math_extra.h"
#include "atom.h"
diff --git a/src/ASPHERE/fix_nve_asphere_noforce.cpp b/src/ASPHERE/fix_nve_asphere_noforce.cpp
index 1cbc8fb16c..34fb57159c 100644
--- a/src/ASPHERE/fix_nve_asphere_noforce.cpp
+++ b/src/ASPHERE/fix_nve_asphere_noforce.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "string.h"
-#include "stdlib.h"
+#include <math.h>
+#include <string.h>
+#include <stdlib.h>
#include "fix_nve_asphere_noforce.h"
#include "math_extra.h"
#include "atom.h"
diff --git a/src/ASPHERE/fix_nve_line.cpp b/src/ASPHERE/fix_nve_line.cpp
index be9b42a7a1..554242fb5b 100644
--- a/src/ASPHERE/fix_nve_line.cpp
+++ b/src/ASPHERE/fix_nve_line.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <string.h>
#include "fix_nve_line.h"
#include "atom.h"
#include "atom_vec_line.h"
diff --git a/src/ASPHERE/fix_nve_tri.cpp b/src/ASPHERE/fix_nve_tri.cpp
index 71fe4d72dc..f859ce08c8 100644
--- a/src/ASPHERE/fix_nve_tri.cpp
+++ b/src/ASPHERE/fix_nve_tri.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <string.h>
#include "fix_nve_tri.h"
#include "math_extra.h"
#include "atom.h"
diff --git a/src/ASPHERE/fix_nvt_asphere.cpp b/src/ASPHERE/fix_nvt_asphere.cpp
index 796bbdf40c..5b8b943ab4 100755
--- a/src/ASPHERE/fix_nvt_asphere.cpp
+++ b/src/ASPHERE/fix_nvt_asphere.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "fix_nvt_asphere.h"
#include "group.h"
#include "modify.h"
diff --git a/src/ASPHERE/pair_gayberne.cpp b/src/ASPHERE/pair_gayberne.cpp
index b22a4fc70f..4aae7177da 100755
--- a/src/ASPHERE/pair_gayberne.cpp
+++ b/src/ASPHERE/pair_gayberne.cpp
@@ -15,10 +15,10 @@
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_gayberne.h"
#include "math_extra.h"
#include "atom.h"
diff --git a/src/ASPHERE/pair_line_lj.cpp b/src/ASPHERE/pair_line_lj.cpp
index 7f97902c57..2124b455f6 100644
--- a/src/ASPHERE/pair_line_lj.cpp
+++ b/src/ASPHERE/pair_line_lj.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_line_lj.h"
#include "atom.h"
#include "atom_vec_line.h"
diff --git a/src/ASPHERE/pair_resquared.cpp b/src/ASPHERE/pair_resquared.cpp
index adf8c54660..870ec95740 100755
--- a/src/ASPHERE/pair_resquared.cpp
+++ b/src/ASPHERE/pair_resquared.cpp
@@ -15,10 +15,10 @@
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_resquared.h"
#include "math_extra.h"
#include "atom.h"
diff --git a/src/ASPHERE/pair_tri_lj.cpp b/src/ASPHERE/pair_tri_lj.cpp
index 257341e602..4823664de8 100644
--- a/src/ASPHERE/pair_tri_lj.cpp
+++ b/src/ASPHERE/pair_tri_lj.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_tri_lj.h"
#include "math_extra.h"
#include "atom.h"
@@ -476,7 +476,7 @@ void PairTriLJ::init_style()
neighbor->request(this,instance_me);
}
-
+
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
diff --git a/src/BODY/body_nparticle.cpp b/src/BODY/body_nparticle.cpp
index b8e981e172..ccb3a63182 100644
--- a/src/BODY/body_nparticle.cpp
+++ b/src/BODY/body_nparticle.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdlib.h"
+#include <stdlib.h>
#include "body_nparticle.h"
#include "math_extra.h"
#include "atom_vec_body.h"
@@ -25,14 +25,14 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-BodyNparticle::BodyNparticle(LAMMPS *lmp, int narg, char **arg) :
+BodyNparticle::BodyNparticle(LAMMPS *lmp, int narg, char **arg) :
Body(lmp, narg, arg)
{
if (narg != 3) error->all(FLERR,"Invalid body nparticle command");
int nmin = force->inumeric(FLERR,arg[1]);
int nmax = force->inumeric(FLERR,arg[2]);
- if (nmin <= 0 || nmin > nmax)
+ if (nmin <= 0 || nmin > nmax)
error->all(FLERR,"Invalid body nparticle command");
size_forward = 0;
@@ -90,7 +90,7 @@ int BodyNparticle::unpack_border_body(AtomVecBody::Bonus *bonus, double *buf)
populate bonus data structure with data file values
------------------------------------------------------------------------- */
-void BodyNparticle::data_body(int ibonus, int ninteger, int ndouble,
+void BodyNparticle::data_body(int ibonus, int ninteger, int ndouble,
char **ifile, char **dfile)
{
AtomVecBody::Bonus *bonus = &avec->bonus[ibonus];
@@ -98,22 +98,22 @@ void BodyNparticle::data_body(int ibonus, int ninteger, int ndouble,
// error in data file if any values are NULL
for (int i = 0; i < ninteger; i++)
- if (ifile[i] == NULL)
+ if (ifile[i] == NULL)
error->one(FLERR,"Invalid format in Bodies section of data file");
for (int i = 0; i < ndouble; i++)
if (dfile[i] == NULL)
error->one(FLERR,"Invalid format in Bodies section of data file");
- // set ninteger, ndouble in bonus and allocate 2 vectors of ints, doubles
+ // set ninteger, ndouble in bonus and allocate 2 vectors of ints, doubles
- if (ninteger != 1)
+ if (ninteger != 1)
error->one(FLERR,"Incorrect # of integer values in "
"Bodies section of data file");
int nsub = atoi(ifile[0]);
if (nsub < 1)
error->one(FLERR,"Incorrect integer value in "
"Bodies section of data file");
- if (ndouble != 6 + 3*nsub)
+ if (ndouble != 6 + 3*nsub)
error->one(FLERR,"Incorrect # of floating-point values in "
"Bodies section of data file");
@@ -144,7 +144,7 @@ void BodyNparticle::data_body(int ibonus, int ninteger, int ndouble,
double max;
max = MAX(inertia[0],inertia[1]);
max = MAX(max,inertia[2]);
-
+
if (inertia[0] < EPSILON*max) inertia[0] = 0.0;
if (inertia[1] < EPSILON*max) inertia[1] = 0.0;
if (inertia[2] < EPSILON*max) inertia[2] = 0.0;
@@ -169,9 +169,9 @@ void BodyNparticle::data_body(int ibonus, int ninteger, int ndouble,
double cross[3];
MathExtra::cross3(ex_space,ey_space,cross);
if (MathExtra::dot3(cross,ez_space) < 0.0) MathExtra::negate3(ez_space);
-
+
// create initial quaternion
-
+
MathExtra::exyz_to_q(ex_space,ey_space,ez_space,bonus->quat);
// bonus->dvalue = sub-particle displacements in body frame
diff --git a/src/BODY/compute_body_local.cpp b/src/BODY/compute_body_local.cpp
index 3ba146642e..474d132ab4 100644
--- a/src/BODY/compute_body_local.cpp
+++ b/src/BODY/compute_body_local.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "string.h"
+#include <math.h>
+#include <string.h>
#include "compute_body_local.h"
#include "atom.h"
#include "atom_vec_body.h"
@@ -61,7 +61,7 @@ ComputeBodyLocal::ComputeBodyLocal(LAMMPS *lmp, int narg, char **arg) :
int indexmax = bptr->noutcol();
for (int i = 0; i < nvalues; i++) {
- if (which[i] == INDEX && (index[i] < 0 || index[i] >= indexmax))
+ if (which[i] == INDEX && (index[i] < 0 || index[i] >= indexmax))
error->all(FLERR,"Invalid index in compute body/local command");
}
@@ -92,7 +92,7 @@ void ComputeBodyLocal::init()
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
- if (mask[i] & groupbit)
+ if (mask[i] & groupbit)
if (body[i] < 0) nonbody = 1;
int flag;
diff --git a/src/BODY/fix_nve_body.cpp b/src/BODY/fix_nve_body.cpp
index 27212ce0af..edc88ed3b4 100644
--- a/src/BODY/fix_nve_body.cpp
+++ b/src/BODY/fix_nve_body.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <string.h>
#include "fix_nve_body.h"
#include "math_extra.h"
#include "atom.h"
diff --git a/src/BODY/pair_body.cpp b/src/BODY/pair_body.cpp
index 4d565e0ed1..86fea7e859 100644
--- a/src/BODY/pair_body.cpp
+++ b/src/BODY/pair_body.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_body.h"
#include "math_extra.h"
#include "atom.h"
@@ -178,7 +178,7 @@ void PairBody::compute(int eflag, int vflag)
torque[i][0] += ti[0];
torque[i][1] += ti[1];
torque[i][2] += ti[2];
-
+
if (newton_pair || j < nlocal) {
fj[0] = -delx*fpair;
fj[1] = -dely*fpair;
@@ -465,7 +465,7 @@ void PairBody::body2space(int i)
AtomVecBody::Bonus *bonus = &avec->bonus[ibonus];
int nsub = bptr->nsub(bonus);
double *coords = bptr->coords(bonus);
-
+
dnum[i] = nsub;
dfirst[i] = ndiscrete;
diff --git a/src/CLASS2/angle_class2.cpp b/src/CLASS2/angle_class2.cpp
index 09ff5860e9..ceeba55678 100644
--- a/src/CLASS2/angle_class2.cpp
+++ b/src/CLASS2/angle_class2.cpp
@@ -15,9 +15,9 @@
Contributing author: Eric Simon (Cray)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "string.h"
-#include "stdlib.h"
+#include <math.h>
+#include <string.h>
+#include <stdlib.h>
#include "angle_class2.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/CLASS2/angle_class2.h b/src/CLASS2/angle_class2.h
index 202dda6fab..1d595d5f6a 100644
--- a/src/CLASS2/angle_class2.h
+++ b/src/CLASS2/angle_class2.h
@@ -20,7 +20,7 @@ AngleStyle(class2,AngleClass2)
#ifndef LMP_ANGLE_CLASS2_H
#define LMP_ANGLE_CLASS2_H
-#include "stdio.h"
+#include <stdio.h>
#include "angle.h"
namespace LAMMPS_NS {
diff --git a/src/CLASS2/bond_class2.cpp b/src/CLASS2/bond_class2.cpp
index 19b4916210..b87deed5a6 100644
--- a/src/CLASS2/bond_class2.cpp
+++ b/src/CLASS2/bond_class2.cpp
@@ -15,8 +15,8 @@
Contributing author: Eric Simon (Cray)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdlib.h>
#include "bond_class2.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/CLASS2/bond_class2.h b/src/CLASS2/bond_class2.h
index 6c54a71360..51e2c939a7 100644
--- a/src/CLASS2/bond_class2.h
+++ b/src/CLASS2/bond_class2.h
@@ -20,7 +20,7 @@ BondStyle(class2,BondClass2)
#ifndef LMP_BOND_CLASS2_H
#define LMP_BOND_CLASS2_H
-#include "stdio.h"
+#include <stdio.h>
#include "bond.h"
namespace LAMMPS_NS {
diff --git a/src/CLASS2/dihedral_class2.cpp b/src/CLASS2/dihedral_class2.cpp
index 579e195c2a..9e907f87b7 100644
--- a/src/CLASS2/dihedral_class2.cpp
+++ b/src/CLASS2/dihedral_class2.cpp
@@ -15,9 +15,9 @@
Contributing author: Eric Simon (Cray)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "string.h"
-#include "stdlib.h"
+#include <math.h>
+#include <string.h>
+#include <stdlib.h>
#include "dihedral_class2.h"
#include "atom.h"
#include "neighbor.h"
@@ -205,8 +205,8 @@ void DihedralClass2::compute(int eflag, int vflag)
MPI_Comm_rank(world,&me);
if (screen) {
char str[128];
- sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " "
- TAGINT_FORMAT " " TAGINT_FORMAT " "
+ sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT,
me,update->ntimestep,
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
diff --git a/src/CLASS2/dihedral_class2.h b/src/CLASS2/dihedral_class2.h
index c55a740300..e8309dad7a 100644
--- a/src/CLASS2/dihedral_class2.h
+++ b/src/CLASS2/dihedral_class2.h
@@ -20,7 +20,7 @@ DihedralStyle(class2,DihedralClass2)
#ifndef LMP_DIHEDRAL_CLASS2_H
#define LMP_DIHEDRAL_CLASS2_H
-#include "stdio.h"
+#include <stdio.h>
#include "dihedral.h"
namespace LAMMPS_NS {
diff --git a/src/CLASS2/improper_class2.cpp b/src/CLASS2/improper_class2.cpp
index b4ccd77e77..c813954805 100644
--- a/src/CLASS2/improper_class2.cpp
+++ b/src/CLASS2/improper_class2.cpp
@@ -15,9 +15,9 @@
Contributing author: Eric Simon (Cray)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "string.h"
-#include "stdlib.h"
+#include <math.h>
+#include <string.h>
+#include <stdlib.h>
#include "improper_class2.h"
#include "atom.h"
#include "neighbor.h"
@@ -156,8 +156,8 @@ void ImproperClass2::compute(int eflag, int vflag)
MPI_Comm_rank(world,&me);
if (screen) {
char str[128];
- sprintf(str,"Improper problem: %d " BIGINT_FORMAT " "
- TAGINT_FORMAT " " TAGINT_FORMAT " "
+ sprintf(str,"Improper problem: %d " BIGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT,
me,update->ntimestep,
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
@@ -853,5 +853,5 @@ void ImproperClass2::write_data(FILE *fp)
for (int i = 1; i <= atom->nimpropertypes; i++)
fprintf(fp,"%d %g %g %g %g %g %g\n",i,aa_k1[i],aa_k2[i],aa_k3[i],
aa_theta0_1[i]*180.0/MY_PI,aa_theta0_2[i]*180.0/MY_PI,
- aa_theta0_3[i]*180.0/MY_PI);
+ aa_theta0_3[i]*180.0/MY_PI);
}
diff --git a/src/CLASS2/improper_class2.h b/src/CLASS2/improper_class2.h
index 33ddd8cde0..f814da96c5 100644
--- a/src/CLASS2/improper_class2.h
+++ b/src/CLASS2/improper_class2.h
@@ -20,7 +20,7 @@ ImproperStyle(class2,ImproperClass2)
#ifndef LMP_IMPROPER_CLASS2_H
#define LMP_IMPROPER_CLASS2_H
-#include "stdio.h"
+#include <stdio.h>
#include "improper.h"
namespace LAMMPS_NS {
diff --git a/src/CLASS2/pair_lj_class2.cpp b/src/CLASS2/pair_lj_class2.cpp
index 9ae9613a74..0974769b9c 100644
--- a/src/CLASS2/pair_lj_class2.cpp
+++ b/src/CLASS2/pair_lj_class2.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
#include "pair_lj_class2.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/CLASS2/pair_lj_class2_coul_cut.cpp b/src/CLASS2/pair_lj_class2_coul_cut.cpp
index 23f4d36141..c7c4738689 100644
--- a/src/CLASS2/pair_lj_class2_coul_cut.cpp
+++ b/src/CLASS2/pair_lj_class2_coul_cut.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
#include "pair_lj_class2_coul_cut.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/CLASS2/pair_lj_class2_coul_long.cpp b/src/CLASS2/pair_lj_class2_coul_long.cpp
index 7801e1687f..62ffdab6e1 100644
--- a/src/CLASS2/pair_lj_class2_coul_long.cpp
+++ b/src/CLASS2/pair_lj_class2_coul_long.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_lj_class2_coul_long.h"
#include "atom.h"
#include "comm.h"
@@ -136,18 +136,18 @@ void PairLJClass2CoulLong::compute(int eflag, int vflag)
prefactor = qqrd2e * qtmp*q[j]/r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
- } else {
- union_int_float_t rsq_lookup;
- rsq_lookup.f = rsq;
- itable = rsq_lookup.i & ncoulmask;
- itable >>= ncoulshiftbits;
- fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
- table = ftable[itable] + fraction*dftable[itable];
- forcecoul = qtmp*q[j] * table;
- if (factor_coul < 1.0) {
- table = ctable[itable] + fraction*dctable[itable];
- prefactor = qtmp*q[j] * table;
- forcecoul -= (1.0-factor_coul)*prefactor;
+ } else {
+ union_int_float_t rsq_lookup;
+ rsq_lookup.f = rsq;
+ itable = rsq_lookup.i & ncoulmask;
+ itable >>= ncoulshiftbits;
+ fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
+ table = ftable[itable] + fraction*dftable[itable];
+ forcecoul = qtmp*q[j] * table;
+ if (factor_coul < 1.0) {
+ table = ctable[itable] + fraction*dctable[itable];
+ prefactor = qtmp*q[j] * table;
+ forcecoul -= (1.0-factor_coul)*prefactor;
}
}
} else forcecoul = 0.0;
@@ -172,11 +172,11 @@ void PairLJClass2CoulLong::compute(int eflag, int vflag)
if (eflag) {
if (rsq < cut_coulsq) {
- if (!ncoultablebits || rsq <= tabinnersq)
- ecoul = prefactor*erfc;
- else {
- table = etable[itable] + fraction*detable[itable];
- ecoul = qtmp*q[j] * table;
+ if (!ncoultablebits || rsq <= tabinnersq)
+ ecoul = prefactor*erfc;
+ else {
+ table = etable[itable] + fraction*detable[itable];
+ ecoul = qtmp*q[j] * table;
}
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
} else ecoul = 0.0;
@@ -251,7 +251,7 @@ void PairLJClass2CoulLong::settings(int narg, char **arg)
void PairLJClass2CoulLong::coeff(int narg, char **arg)
{
- if (narg < 4 || narg > 6)
+ if (narg < 4 || narg > 6)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
@@ -299,7 +299,7 @@ void PairLJClass2CoulLong::init_style()
error->all(FLERR,"Pair style requires a KSpace style");
g_ewald = force->kspace->g_ewald;
- // setup force tables
+ // setup force tables
if (ncoultablebits) init_tables(cut_coul,NULL);
}
diff --git a/src/COLLOID/fix_wall_colloid.cpp b/src/COLLOID/fix_wall_colloid.cpp
index 41e8e9740a..7c0203ac5f 100644
--- a/src/COLLOID/fix_wall_colloid.cpp
+++ b/src/COLLOID/fix_wall_colloid.cpp
@@ -15,8 +15,8 @@
Contributing authors: Jeremy Lechman (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "string.h"
+#include <math.h>
+#include <string.h>
#include "fix_wall_colloid.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/COLLOID/pair_colloid.cpp b/src/COLLOID/pair_colloid.cpp
index ef0978ab01..b5d83233ab 100644
--- a/src/COLLOID/pair_colloid.cpp
+++ b/src/COLLOID/pair_colloid.cpp
@@ -15,10 +15,10 @@
Contributing author: Pieter in 't Veld (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_colloid.h"
#include "atom.h"
#include "comm.h"
@@ -144,7 +144,7 @@ void PairColloid::compute(int eflag, int vflag)
evdwl = 2.0/9.0*fR *
(1.0-(K[1]*(K[1]*(K[1]/3.0+3.0*K[2])+4.2*K[4])+K[2]*K[4]) *
sigma6[itype][jtype]/K[6]) - offset[itype][jtype];
- if (rsq <= K[1])
+ if (rsq <= K[1])
error->one(FLERR,"Overlapping small/large in pair colloid");
break;
@@ -183,7 +183,7 @@ void PairColloid::compute(int eflag, int vflag)
if (eflag)
evdwl += a12[itype][jtype]/6.0 *
(2.0*K[0]*(K[7]+K[8])-log(K[8]/K[7])) - offset[itype][jtype];
- if (r <= K[1])
+ if (r <= K[1])
error->one(FLERR,"Overlapping large/large in pair colloid");
break;
}
diff --git a/src/COLLOID/pair_yukawa_colloid.cpp b/src/COLLOID/pair_yukawa_colloid.cpp
index 13d632526f..9b8d0ecaad 100644
--- a/src/COLLOID/pair_yukawa_colloid.cpp
+++ b/src/COLLOID/pair_yukawa_colloid.cpp
@@ -15,8 +15,8 @@
Contributing authors: Randy Schunk (Sandia)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdlib.h>
#include "pair_yukawa_colloid.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/CORESHELL/compute_temp_cs.cpp b/src/CORESHELL/compute_temp_cs.cpp
index 8714b5201d..43bf7b8e5e 100644
--- a/src/CORESHELL/compute_temp_cs.cpp
+++ b/src/CORESHELL/compute_temp_cs.cpp
@@ -16,10 +16,10 @@
(hendrik.heenen at mytum.com)
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "stdlib.h"
-#include "string.h"
-#include "math.h"
+#include <mpi.h>
+#include <stdlib.h>
+#include <string.h>
+#include <math.h>
#include "compute_temp_cs.h"
#include "atom.h"
#include "atom_vec.h"
@@ -57,12 +57,12 @@ ComputeTempCS::ComputeTempCS(LAMMPS *lmp, int narg, char **arg) :
// find and define groupbits for core and shell groups
cgroup = group->find(arg[3]);
- if (cgroup == -1)
+ if (cgroup == -1)
error->all(FLERR,"Cannot find specified group ID for core particles");
groupbit_c = group->bitmask[cgroup];
sgroup = group->find(arg[4]);
- if (sgroup == -1)
+ if (sgroup == -1)
error->all(FLERR,"Cannot find specified group ID for shell particles");
groupbit_s = group->bitmask[sgroup];
@@ -228,9 +228,9 @@ double ComputeTempCS::compute_scalar()
vcm_pairs();
- // calculate thermal scalar in respect to atom velocities as center-of-mass
+ // calculate thermal scalar in respect to atom velocities as center-of-mass
// velocities of its according core/shell pairs
-
+
double **v = atom->v;
int *mask = atom->mask;
int *type = atom->type;
@@ -256,12 +256,12 @@ double ComputeTempCS::compute_scalar()
MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
if (dynamic) dof_compute();
- if (dof < 0.0 && natoms_temp > 0.0)
+ if (dof < 0.0 && natoms_temp > 0.0)
error->all(FLERR,"Temperature compute degrees of freedom < 0");
scalar *= tfactor;
return scalar;
}
-
+
/* ---------------------------------------------------------------------- */
void ComputeTempCS::compute_vector()
@@ -313,7 +313,7 @@ void ComputeTempCS::vcm_pairs()
maxatom = atom->nmax;
memory->create(vint,maxatom,3,"temp/cs:vint");
}
-
+
// vcm = COM velocity of each CS pair
// vint = internal velocity of each C/S atom, used as bias
@@ -327,7 +327,7 @@ void ComputeTempCS::vcm_pairs()
tagint partnerID;
for (i = 0; i < nlocal; i++) {
- if ((mask[i] & groupbit) &&
+ if ((mask[i] & groupbit) &&
(mask[i] & groupbit_c || mask[i] & groupbit_s)) {
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
diff --git a/src/CORESHELL/pair_born_coul_long_cs.cpp b/src/CORESHELL/pair_born_coul_long_cs.cpp
index 87c8680860..7d0d9c9416 100644
--- a/src/CORESHELL/pair_born_coul_long_cs.cpp
+++ b/src/CORESHELL/pair_born_coul_long_cs.cpp
@@ -15,10 +15,10 @@
Contributing author: Hendrik Heenen (hendrik.heenen@mytum.de)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_born_coul_long_cs.h"
#include "atom.h"
#include "comm.h"
@@ -118,8 +118,8 @@ void PairBornCoulLongCS::compute(int eflag, int vflag)
r = sqrt(rsq);
prefactor = qqrd2e * qtmp*q[j];
if (factor_coul < 1.0) {
- // When bonded parts are being calculated a minimal distance (EPS_EWALD)
- // has to be added to the prefactor and erfc in order to make the
+ // When bonded parts are being calculated a minimal distance (EPS_EWALD)
+ // has to be added to the prefactor and erfc in order to make the
// used approximation functions valid
grij = g_ewald * (r+EPS_EWALD);
expm2 = exp(-grij*grij);
diff --git a/src/CORESHELL/pair_buck_coul_long_cs.cpp b/src/CORESHELL/pair_buck_coul_long_cs.cpp
index 1d269da58f..822ec10497 100644
--- a/src/CORESHELL/pair_buck_coul_long_cs.cpp
+++ b/src/CORESHELL/pair_buck_coul_long_cs.cpp
@@ -15,10 +15,10 @@
Contributing author: Hendrik Heenen (hendrik.heenen@mytum.de)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_buck_coul_long_cs.h"
#include "atom.h"
#include "comm.h"
@@ -118,8 +118,8 @@ void PairBuckCoulLongCS::compute(int eflag, int vflag)
r = sqrt(rsq);
prefactor = qqrd2e * qtmp*q[j];
if (factor_coul < 1.0) {
- // When bonded parts are being calculated a minimal distance (EPS_EWALD)
- // has to be added to the prefactor and erfc in order to make the
+ // When bonded parts are being calculated a minimal distance (EPS_EWALD)
+ // has to be added to the prefactor and erfc in order to make the
// used approximation functions for the Ewald correction valid
grij = g_ewald * (r+EPS_EWALD);
expm2 = exp(-grij*grij);
diff --git a/src/CORESHELL/pair_coul_long_cs.cpp b/src/CORESHELL/pair_coul_long_cs.cpp
index 05cf53c9b0..9177e9a061 100644
--- a/src/CORESHELL/pair_coul_long_cs.cpp
+++ b/src/CORESHELL/pair_coul_long_cs.cpp
@@ -15,10 +15,10 @@
Contributing author: Hendrik Heenen (hendrik.heenen@mytum.de)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_coul_long_cs.h"
#include "atom.h"
#include "comm.h"
@@ -116,8 +116,8 @@ void PairCoulLongCS::compute(int eflag, int vflag)
r = sqrt(rsq);
prefactor = qqrd2e * scale[itype][jtype] * qtmp*q[j];
if (factor_coul < 1.0) {
- // When bonded parts are being calculated a minimal distance (EPS_EWALD)
- // has to be added to the prefactor and erfc in order to make the
+ // When bonded parts are being calculated a minimal distance (EPS_EWALD)
+ // has to be added to the prefactor and erfc in order to make the
// used approximation functions for the Ewald correction valid
grij = g_ewald * (r+EPS_EWALD);
expm2 = exp(-grij*grij);
diff --git a/src/CORESHELL/pair_lj_cut_coul_long_cs.cpp b/src/CORESHELL/pair_lj_cut_coul_long_cs.cpp
index fe9ba28696..e2ffda148f 100644
--- a/src/CORESHELL/pair_lj_cut_coul_long_cs.cpp
+++ b/src/CORESHELL/pair_lj_cut_coul_long_cs.cpp
@@ -15,10 +15,10 @@
Contributing author: Hendrik Heenen (hendrik.heenen@mytum.de)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_lj_cut_coul_long_cs.h"
#include "atom.h"
#include "comm.h"
@@ -124,8 +124,8 @@ void PairLJCutCoulLongCS::compute(int eflag, int vflag)
r = sqrt(rsq);
prefactor = qqrd2e * qtmp*q[j];
if (factor_coul < 1.0) {
- // When bonded parts are being calculated a minimal distance (EPS_EWALD)
- // has to be added to the prefactor and erfc in order to make the
+ // When bonded parts are being calculated a minimal distance (EPS_EWALD)
+ // has to be added to the prefactor and erfc in order to make the
// used approximation functions for the Ewald correction valid
grij = g_ewald * (r+EPS_EWALD);
expm2 = exp(-grij*grij);
diff --git a/src/DIPOLE/atom_vec_dipole.cpp b/src/DIPOLE/atom_vec_dipole.cpp
index 07c8d203d8..5d69f03376 100644
--- a/src/DIPOLE/atom_vec_dipole.cpp
+++ b/src/DIPOLE/atom_vec_dipole.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdlib.h>
#include "atom_vec_dipole.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/DIPOLE/pair_lj_cut_dipole_cut.cpp b/src/DIPOLE/pair_lj_cut_dipole_cut.cpp
index d874348718..53c977f876 100755
--- a/src/DIPOLE/pair_lj_cut_dipole_cut.cpp
+++ b/src/DIPOLE/pair_lj_cut_dipole_cut.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdlib.h>
#include "pair_lj_cut_dipole_cut.h"
#include "atom.h"
#include "neighbor.h"
@@ -22,7 +22,7 @@
#include "memory.h"
#include "error.h"
#include "update.h"
-#include "string.h"
+#include <string.h>
using namespace LAMMPS_NS;
diff --git a/src/DIPOLE/pair_lj_cut_dipole_long.cpp b/src/DIPOLE/pair_lj_cut_dipole_long.cpp
index 824bbf734a..3f44579b8f 100755
--- a/src/DIPOLE/pair_lj_cut_dipole_long.cpp
+++ b/src/DIPOLE/pair_lj_cut_dipole_long.cpp
@@ -5,16 +5,16 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_lj_cut_dipole_long.h"
#include "atom.h"
#include "comm.h"
@@ -26,7 +26,7 @@
#include "memory.h"
#include "error.h"
#include "update.h"
-#include "string.h"
+#include <string.h>
using namespace LAMMPS_NS;
@@ -50,7 +50,7 @@ PairLJCutDipoleLong::PairLJCutDipoleLong(LAMMPS *lmp) : Pair(lmp)
}
/* ----------------------------------------------------------------------
- free all arrays
+ free all arrays
------------------------------------------------------------------------- */
PairLJCutDipoleLong::~PairLJCutDipoleLong()
@@ -153,7 +153,7 @@ void PairLJCutDipoleLong::compute(int eflag, int vflag)
pdotp = mu[i][0]*mu[j][0] + mu[i][1]*mu[j][1] + mu[i][2]*mu[j][2];
pidotr = mu[i][0]*delx + mu[i][1]*dely + mu[i][2]*delz;
pjdotr = mu[j][0]*delx + mu[j][1]*dely + mu[j][2]*delz;
-
+
g0 = qtmp*q[j];
g1 = qtmp*pjdotr - q[j]*pidotr + pdotp;
g2 = -pidotr*pjdotr;
@@ -166,10 +166,10 @@ void PairLJCutDipoleLong::compute(int eflag, int vflag)
g0b1_g1b2_g2b3 = g0*b1 + g1*b2 + g2*b3;
fdx = delx * g0b1_g1b2_g2b3 -
- b1 * (qtmp*mu[j][0] - q[j]*mu[i][0]) +
+ b1 * (qtmp*mu[j][0] - q[j]*mu[i][0]) +
b2 * (pjdotr*mu[i][0] + pidotr*mu[j][0]);
fdy = dely * g0b1_g1b2_g2b3 -
- b1 * (qtmp*mu[j][1] - q[j]*mu[i][1]) +
+ b1 * (qtmp*mu[j][1] - q[j]*mu[i][1]) +
b2 * (pjdotr*mu[i][1] + pidotr*mu[j][1]);
fdz = delz * g0b1_g1b2_g2b3 -
b1 * (qtmp*mu[j][2] - q[j]*mu[i][2]) +
@@ -204,13 +204,13 @@ void PairLJCutDipoleLong::compute(int eflag, int vflag)
d1 = (d0 + pre1*expm2) * r2inv;
d2 = (3.0*d1 + pre2*expm2) * r2inv;
d3 = (5.0*d2 + pre3*expm2) * r2inv;
-
+
g0d1_g1d2_g2d3 = g0*d1 + g1*d2 + g2*d3;
fax = delx * g0d1_g1d2_g2d3 -
- d1 * (qtmp*mu[j][0] - q[j]*mu[i][0]) +
+ d1 * (qtmp*mu[j][0] - q[j]*mu[i][0]) +
d2 * (pjdotr*mu[i][0] + pidotr*mu[j][0]);
fay = dely * g0d1_g1d2_g2d3 -
- d1 * (qtmp*mu[j][1] - q[j]*mu[i][1]) +
+ d1 * (qtmp*mu[j][1] - q[j]*mu[i][1]) +
d2 * (pjdotr*mu[i][1] + pidotr*mu[j][1]);
faz = delz * g0d1_g1d2_g2d3 -
d1 * (qtmp*mu[j][2] - q[j]*mu[i][2]) +
@@ -271,7 +271,7 @@ void PairLJCutDipoleLong::compute(int eflag, int vflag)
fx = qqrd2e*forcecoulx + delx*fforce;
fy = qqrd2e*forcecouly + dely*fforce;
fz = qqrd2e*forcecoulz + delz*fforce;
-
+
// force & torque accumulation
f[i][0] += fx;
@@ -316,7 +316,7 @@ void PairLJCutDipoleLong::compute(int eflag, int vflag)
}
/* ----------------------------------------------------------------------
- allocate all arrays
+ allocate all arrays
------------------------------------------------------------------------- */
void PairLJCutDipoleLong::allocate()
@@ -343,12 +343,12 @@ void PairLJCutDipoleLong::allocate()
}
/* ----------------------------------------------------------------------
- global settings
+ global settings
------------------------------------------------------------------------- */
void PairLJCutDipoleLong::settings(int narg, char **arg)
{
- if (narg < 1 || narg > 2)
+ if (narg < 1 || narg > 2)
error->all(FLERR,"Incorrect args in pair_style command");
cut_lj_global = force->numeric(FLERR,arg[0]);
@@ -371,7 +371,7 @@ void PairLJCutDipoleLong::settings(int narg, char **arg)
void PairLJCutDipoleLong::coeff(int narg, char **arg)
{
- if (narg < 4 || narg > 5)
+ if (narg < 4 || narg > 5)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
@@ -419,12 +419,12 @@ double PairLJCutDipoleLong::init_one(int i, int j)
lj2[i][j] = 24.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
lj3[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
lj4[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
-
+
if (offset_flag) {
double ratio = sigma[i][j] / cut_lj[i][j];
offset[i][j] = 4.0 * epsilon[i][j] * (pow(ratio,12.0) - pow(ratio,6.0));
} else offset[i][j] = 0.0;
-
+
cut_ljsq[j][i] = cut_ljsq[i][j];
lj1[j][i] = lj1[i][j];
lj2[j][i] = lj2[i][j];
@@ -449,7 +449,7 @@ void PairLJCutDipoleLong::init_style()
// insure use of KSpace long-range solver, set g_ewald
- if (force->kspace == NULL)
+ if (force->kspace == NULL)
error->all(FLERR,"Pair style requires a KSpace style");
g_ewald = force->kspace->g_ewald;
diff --git a/src/DIPOLE/pair_lj_cut_dipole_long.h b/src/DIPOLE/pair_lj_cut_dipole_long.h
index 9c04a31d24..d2d441e0e9 100755
--- a/src/DIPOLE/pair_lj_cut_dipole_long.h
+++ b/src/DIPOLE/pair_lj_cut_dipole_long.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/DIPOLE/pair_lj_long_dipole_long.cpp b/src/DIPOLE/pair_lj_long_dipole_long.cpp
index 0e5a0222c7..248865ef72 100755
--- a/src/DIPOLE/pair_lj_long_dipole_long.cpp
+++ b/src/DIPOLE/pair_lj_long_dipole_long.cpp
@@ -15,10 +15,10 @@
Contributing author: Pieter J. in 't Veld and Stan Moore (Sandia)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "math_const.h"
#include "math_vector.h"
#include "pair_lj_long_dipole_long.h"
@@ -173,7 +173,7 @@ void *PairLJLongDipoleLong::extract(const char *id, int &dim)
"B", "sigma", "epsilon", "ewald_order", "ewald_cut", "ewald_mix",
"cut_coul", "cut_vdwl", NULL};
void *ptrs[] = {
- lj4, sigma, epsilon, &ewald_order, &cut_coul, &mix_flag, &cut_coul,
+ lj4, sigma, epsilon, &ewald_order, &cut_coul, &mix_flag, &cut_coul,
&cut_lj_global, NULL};
int i;
@@ -189,7 +189,7 @@ void *PairLJLongDipoleLong::extract(const char *id, int &dim)
void PairLJLongDipoleLong::coeff(int narg, char **arg)
{
- if (narg < 4 || narg > 5)
+ if (narg < 4 || narg > 5)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
@@ -247,14 +247,14 @@ void PairLJLongDipoleLong::init_style()
// ensure use of KSpace long-range solver, set g_ewald
if (ewald_order&(1<<3)) { // r^-1 kspace
- if (force->kspace == NULL)
+ if (force->kspace == NULL)
error->all(FLERR,"Pair style requires a KSpace style");
for (i=0; style3[i]&&strcmp(force->kspace_style, style3[i]); ++i);
if (!style3[i])
error->all(FLERR,"Pair style requires use of kspace_style ewald/disp");
}
if (ewald_order&(1<<6)) { // r^-6 kspace
- if (force->kspace == NULL)
+ if (force->kspace == NULL)
error->all(FLERR,"Pair style requires a KSpace style");
for (i=0; style6[i]&&strcmp(force->kspace_style, style6[i]); ++i);
if (!style6[i])
@@ -313,7 +313,7 @@ double PairLJLongDipoleLong::init_one(int i, int j)
//if (cut_respa && MIN(cut_lj[i][j],cut_coul) < cut_respa[3])
//error->all(FLERR,"Pair cutoff < Respa interior cutoff");
-
+
if (offset_flag) {
double ratio = sigma[i][j] / cut_lj[i][j];
offset[i][j] = 4.0 * epsilon[i][j] * (pow(ratio,12.0) - pow(ratio,6.0));
@@ -423,7 +423,7 @@ void PairLJLongDipoleLong::compute(int eflag, int vflag)
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
-
+
double **x = atom->x, *x0 = x[0];
double **mu = atom->mu, *mu0 = mu[0], *imu, *jmu;
double **tq = atom->torque, *tq0 = tq[0], *tqi;
@@ -445,7 +445,7 @@ void PairLJLongDipoleLong::compute(int eflag, int vflag)
double B0, B1, B2, B3, G0, G1, G2, mudi, mudj, muij;
vector force_d = VECTOR_NULL, ti = VECTOR_NULL, tj = VECTOR_NULL;
vector mui, muj, xi, d;
-
+
double C1 = 2.0 * g_ewald / MY_PIS;
double C2 = 2.0 * g2 * C1;
double C3 = 2.0 * g2 * C2;
@@ -460,14 +460,14 @@ void PairLJLongDipoleLong::compute(int eflag, int vflag)
cutsqi = cutsq[typei]; cut_ljsqi = cut_ljsq[typei];
memcpy(xi, x0+(i+(i<<1)), sizeof(vector));
memcpy(mui, imu = mu0+(i<<2), sizeof(vector));
-
+
jneighn = (jneigh = list->firstneigh[i])+list->numneigh[i];
for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
j = *jneigh;
ni = sbmask(j); // special index
j &= NEIGHMASK;
-
+
{ register double *xj = x0+(j+(j<<1));
d[0] = xi[0] - xj[0]; // pair vector
d[1] = xi[1] - xj[1];
@@ -496,7 +496,7 @@ void PairLJLongDipoleLong::compute(int eflag, int vflag)
G1 = qi*mudj-qj*mudi+muij;
G2 = -mudi*mudj;
force_coul = G0*B1+G1*B2+G2*B3;
-
+
mudi *= B2; mudj *= B2; // torque contribs
ti[0] = mudj*d[0]+(qj*d[0]-muj[0])*B1;
ti[1] = mudj*d[1]+(qj*d[1]-muj[1])*B1;
@@ -552,7 +552,7 @@ void PairLJLongDipoleLong::compute(int eflag, int vflag)
register double f = special_lj[ni], t = rn*(1.0-f);
force_lj = f*(rn *= rn)*lj1i[typej]-
g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq+t*lj2i[typej];
- if (eflag) evdwl =
+ if (eflag) evdwl =
f*rn*lj3i[typej]-g6*((a2+1.0)*a2+0.5)*x2+t*lj4i[typej];
}
}
@@ -641,8 +641,8 @@ double PairLJLongDipoleLong::single(int i, int j, int itype, int jtype,
G1 = qi*mudj-qj*mudi+muij;
G2 = -mudi*mudj;
force_coul = G0*B1+G1*B2+G2*B3;
-
- eng += G0*B0+G1*B1+G2*B2;
+
+ eng += G0*B0+G1*B1+G2*B2;
if (factor_coul < 1.0) { // adj part, eqn 2.13
force_coul -= (f = force->qqrd2e*(1.0-factor_coul)/r)*(
(3.0*G1+6.0*muij+15.0*G2*r2inv)*r2inv+G0);
@@ -672,7 +672,7 @@ double PairLJLongDipoleLong::single(int i, int j, int itype, int jtype,
eng += factor_lj*(r6inv*(r6inv*lj3[itype][jtype]-
lj4[itype][jtype])-offset[itype][jtype]);
}
- }
+ }
else force_lj = 0.0;
fforce = (force_coul+force_lj)*r2inv;
diff --git a/src/FLD/pair_brownian.cpp b/src/FLD/pair_brownian.cpp
index 3aa96288ba..c1cc523d32 100755
--- a/src/FLD/pair_brownian.cpp
+++ b/src/FLD/pair_brownian.cpp
@@ -15,10 +15,10 @@
Contributing authors: Amit Kumar and Michael Bybee (UIUC)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_brownian.h"
#include "atom.h"
#include "atom_vec.h"
@@ -502,7 +502,7 @@ void PairBrownian::init_style()
if (strcmp(modify->fix[i]->style,"deform") == 0)
flagdeform = 1;
else if (strstr(modify->fix[i]->style,"wall") != NULL) {
- if (flagwall)
+ if (flagwall)
error->all(FLERR,
"Cannot use multiple fix wall commands with pair brownian");
flagwall = 1; // Walls exist
diff --git a/src/FLD/pair_brownian_poly.cpp b/src/FLD/pair_brownian_poly.cpp
index c0a958ea7d..84c56109d1 100644
--- a/src/FLD/pair_brownian_poly.cpp
+++ b/src/FLD/pair_brownian_poly.cpp
@@ -16,10 +16,10 @@
Dave Heine (Corning), polydispersity
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_brownian_poly.h"
#include "atom.h"
#include "atom_vec.h"
@@ -365,7 +365,7 @@ void PairBrownianPoly::init_style()
if (strcmp(modify->fix[i]->style,"deform") == 0)
flagdeform = 1;
else if (strstr(modify->fix[i]->style,"wall") != NULL) {
- if (flagwall)
+ if (flagwall)
error->all(FLERR,
"Cannot use multiple fix wall commands with pair brownian");
flagwall = 1; // Walls exist
diff --git a/src/FLD/pair_lubricate.cpp b/src/FLD/pair_lubricate.cpp
index 79046e445d..ea398c340a 100755
--- a/src/FLD/pair_lubricate.cpp
+++ b/src/FLD/pair_lubricate.cpp
@@ -16,10 +16,10 @@
Amit Kumar and Michael Bybee (UIUC)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_lubricate.h"
#include "atom.h"
#include "atom_vec.h"
@@ -575,7 +575,7 @@ void PairLubricate::init_style()
"fix deform remap option");
}
if (strstr(modify->fix[i]->style,"wall") != NULL) {
- if (flagwall)
+ if (flagwall)
error->all(FLERR,
"Cannot use multiple fix wall commands with pair lubricate");
flagwall = 1; // Walls exist
diff --git a/src/FLD/pair_lubricateU.cpp b/src/FLD/pair_lubricateU.cpp
index 66e9ab1400..214bc3c2f3 100644
--- a/src/FLD/pair_lubricateU.cpp
+++ b/src/FLD/pair_lubricateU.cpp
@@ -15,11 +15,11 @@
Contributing authors: Amit Kumar and Michael Bybee (UIUC)
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <mpi.h>
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_lubricateU.h"
#include "atom.h"
#include "atom_vec.h"
@@ -1800,7 +1800,7 @@ void PairLubricateU::init_style()
if (strcmp(modify->fix[i]->style,"deform") == 0)
flagdeform = 1;
else if (strstr(modify->fix[i]->style,"wall") != NULL) {
- if (flagwall)
+ if (flagwall)
error->all(FLERR,
"Cannot use multiple fix wall commands with "
"pair lubricateU");
diff --git a/src/FLD/pair_lubricateU_poly.cpp b/src/FLD/pair_lubricateU_poly.cpp
index 02734c058b..6a032987d9 100644
--- a/src/FLD/pair_lubricateU_poly.cpp
+++ b/src/FLD/pair_lubricateU_poly.cpp
@@ -17,11 +17,11 @@
Dave Heine (Corning), polydispersity
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <mpi.h>
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_lubricateU_poly.h"
#include "atom.h"
#include "atom_vec.h"
@@ -1153,7 +1153,7 @@ void PairLubricateUPoly::init_style()
if (strcmp(modify->fix[i]->style,"deform") == 0)
flagdeform = 1;
else if (strstr(modify->fix[i]->style,"wall") != NULL){
- if (flagwall)
+ if (flagwall)
error->all(FLERR,
"Cannot use multiple fix wall commands with "
"pair lubricateU");
diff --git a/src/FLD/pair_lubricate_poly.cpp b/src/FLD/pair_lubricate_poly.cpp
index 937c5a315a..3701e2d789 100644
--- a/src/FLD/pair_lubricate_poly.cpp
+++ b/src/FLD/pair_lubricate_poly.cpp
@@ -17,10 +17,10 @@
Dave Heine (Corning), polydispersity
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_lubricate_poly.h"
#include "atom.h"
#include "atom_vec.h"
@@ -471,7 +471,7 @@ void PairLubricatePoly::init_style()
"fix deform remap option");
}
if (strstr(modify->fix[i]->style,"wall") != NULL) {
- if (flagwall)
+ if (flagwall)
error->all(FLERR,
"Cannot use multiple fix wall commands with "
"pair lubricate/poly");
diff --git a/src/GPU/fix_gpu.cpp b/src/GPU/fix_gpu.cpp
index 1dea4dc467..ddd82b30b5 100644
--- a/src/GPU/fix_gpu.cpp
+++ b/src/GPU/fix_gpu.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
-#include "stdlib.h"
+#include <string.h>
+#include <stdlib.h>
#include "fix_gpu.h"
#include "atom.h"
#include "force.h"
@@ -40,7 +40,7 @@ extern int lmp_init_device(MPI_Comm world, MPI_Comm replica,
const int first_gpu, const int last_gpu,
const int gpu_mode, const double particle_split,
const int nthreads, const int t_per_atom,
- const double cell_size, char *opencl_flags,
+ const double cell_size, char *opencl_flags,
const int block_pair);
extern void lmp_clear_device();
extern double lmp_gpu_forces(double **f, double **tor, double *eatom,
@@ -89,7 +89,7 @@ FixGPU::FixGPU(LAMMPS *lmp, int narg, char **arg) :
if (ngpu <= 0) error->all(FLERR,"Illegal package gpu command");
int first_gpu = 0;
int last_gpu = ngpu-1;
-
+
// options
_gpu_mode = GPU_NEIGH;
@@ -172,7 +172,7 @@ FixGPU::FixGPU(LAMMPS *lmp, int narg, char **arg) :
if (binsize == 0.0) binsize = -1.0;
int gpu_flag = lmp_init_device(universe->uworld, world, first_gpu, last_gpu,
_gpu_mode, _particle_split, nthreads,
- threads_per_atom, binsize, opencl_flags,
+ threads_per_atom, binsize, opencl_flags,
block_pair);
GPU_EXTRA::check_flag(gpu_flag,error,world);
}
@@ -200,8 +200,8 @@ int FixGPU::setmask()
void FixGPU::init()
{
// GPU package cannot be used with atom_style template
-
- if (atom->molecular == 2)
+
+ if (atom->molecular == 2)
error->all(FLERR,"GPU package does not (yet) work with "
"atom_style template");
@@ -219,7 +219,7 @@ void FixGPU::init()
// neighbor list builds on the GPU with triclinic box is not yet supported
- if ((_gpu_mode == GPU_NEIGH || _gpu_mode == GPU_HYB_NEIGH) &&
+ if ((_gpu_mode == GPU_NEIGH || _gpu_mode == GPU_HYB_NEIGH) &&
domain->triclinic)
error->all(FLERR,"Cannot use package gpu neigh yes with triclinic box");
@@ -229,7 +229,7 @@ void FixGPU::init()
error->warning(FLERR,"Using package gpu without any pair style defined");
// make sure fdotr virial is not accumulated multiple times
-
+
if (force->pair_match("hybrid",1) != NULL) {
PairHybrid *hybrid = (PairHybrid *) force->pair;
for (int i = 0; i < hybrid->nstyles; i++)
diff --git a/src/GPU/pair_beck_gpu.cpp b/src/GPU/pair_beck_gpu.cpp
index 614c088b03..c813186640 100644
--- a/src/GPU/pair_beck_gpu.cpp
+++ b/src/GPU/pair_beck_gpu.cpp
@@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
-
+
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
-
+
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@@ -15,9 +15,9 @@
Contributing author: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
#include "pair_beck_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +32,7 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include "string.h"
+#include <string.h>
#include "gpu_extra.h"
#include "math_special.h"
@@ -54,7 +54,7 @@ int ** beck_gpu_compute_n(const int ago, const int inum,
const bool eatom, const bool vatom, int &host_start,
int **ilist, int **jnum,
const double cpu_time, bool &success);
-void beck_gpu_compute(const int ago, const int inum, const int nall,
+void beck_gpu_compute(const int ago, const int inum, const int nall,
double **host_x, int *host_type, int *ilist, int *numj,
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
@@ -68,7 +68,7 @@ PairBeckGPU::PairBeckGPU(LAMMPS *lmp) : PairBeck(lmp), gpu_mode(GPU_FORCE)
respa_enable = 0;
reinitflag = 0;
cpu_time = 0.0;
- GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
+ GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
@@ -86,10 +86,10 @@ void PairBeckGPU::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
-
+
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
-
+
bool success = true;
int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
@@ -98,7 +98,7 @@ void PairBeckGPU::compute(int eflag, int vflag)
atom->x, atom->type, domain->sublo,
domain->subhi, atom->tag, atom->nspecial,
atom->special, eflag, vflag, eflag_atom,
- vflag_atom, host_start,
+ vflag_atom, host_start,
&ilist, &numneigh, cpu_time, success);
} else {
inum = list->inum;
@@ -125,7 +125,7 @@ void PairBeckGPU::compute(int eflag, int vflag)
void PairBeckGPU::init_style()
{
- if (force->newton_pair)
+ if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with beck/gpu pair style");
// Repeat cutsq calculation because done after call to init_style
@@ -171,7 +171,7 @@ double PairBeckGPU::memory_usage()
/* ---------------------------------------------------------------------- */
-void PairBeckGPU::cpu_compute(int start, int inum, int eflag, int vflag,
+void PairBeckGPU::cpu_compute(int start, int inum, int eflag, int vflag,
int *ilist, int *numneigh, int **firstneigh) {
int i,j,ii,jj,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
diff --git a/src/GPU/pair_beck_gpu.h b/src/GPU/pair_beck_gpu.h
index 4ae04a82a6..8fd2cfad45 100644
--- a/src/GPU/pair_beck_gpu.h
+++ b/src/GPU/pair_beck_gpu.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/GPU/pair_born_coul_long_gpu.cpp b/src/GPU/pair_born_coul_long_gpu.cpp
index 7873912020..4e457de4a5 100644
--- a/src/GPU/pair_born_coul_long_gpu.cpp
+++ b/src/GPU/pair_born_coul_long_gpu.cpp
@@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
-
+
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
-
+
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@@ -15,9 +15,9 @@
Contributing author: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
#include "pair_born_coul_long_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -33,7 +33,7 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include "string.h"
+#include <string.h>
#include "kspace.h"
#include "gpu_extra.h"
@@ -51,9 +51,9 @@ using namespace MathConst;
// External functions from cuda library for atom decomposition
int borncl_gpu_init(const int ntypes, double **cutsq, double **host_rhoinv,
- double **host_born1, double **host_born2,
- double **host_born3, double **host_a,
- double **host_c, double **host_d,
+ double **host_born1, double **host_born2,
+ double **host_born3, double **host_a,
+ double **host_c, double **host_d,
double **sigma, double **offset, double *special_lj,
const int inum, const int nall, const int max_nbors,
const int maxspecial, const double cell_size,
@@ -63,7 +63,7 @@ int borncl_gpu_init(const int ntypes, double **cutsq, double **host_rhoinv,
void borncl_gpu_clear();
int** borncl_gpu_compute_n(const int ago, const int inum_full, const int nall,
double **host_x, int *host_type, double *sublo,
- double *subhi, tagint *tag, int **nspecial,
+ double *subhi, tagint *tag, int **nspecial,
tagint **special, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
int **ilist, int **jnum, const double cpu_time,
@@ -79,13 +79,13 @@ double borncl_gpu_bytes();
/* ---------------------------------------------------------------------- */
-PairBornCoulLongGPU::PairBornCoulLongGPU(LAMMPS *lmp) :
+PairBornCoulLongGPU::PairBornCoulLongGPU(LAMMPS *lmp) :
PairBornCoulLong(lmp), gpu_mode(GPU_FORCE)
{
respa_enable = 0;
reinitflag = 0;
cpu_time = 0.0;
- GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
+ GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
@@ -103,12 +103,12 @@ void PairBornCoulLongGPU::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
-
+
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
-
+
bool success = true;
- int *ilist, *numneigh, **firstneigh;
+ int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
inum = atom->nlocal;
firstneigh = borncl_gpu_compute_n(neighbor->ago, inum, nall, atom->x,
@@ -147,7 +147,7 @@ void PairBornCoulLongGPU::init_style()
if (!atom->q_flag)
error->all(FLERR,
"Pair style born/coul/long/gpu requires atom attribute q");
- if (force->newton_pair)
+ if (force->newton_pair)
error->all(FLERR,
"Cannot use newton pair with born/coul/long/gpu pair style");
@@ -179,12 +179,12 @@ void PairBornCoulLongGPU::init_style()
int maxspecial=0;
if (atom->molecular)
maxspecial=atom->maxspecial;
- int success = borncl_gpu_init(atom->ntypes+1, cutsq, rhoinv,
+ int success = borncl_gpu_init(atom->ntypes+1, cutsq, rhoinv,
born1, born2, born3, a, c, d, sigma,
offset, force->special_lj, atom->nlocal,
atom->nlocal+atom->nghost, 300, maxspecial,
cell_size, gpu_mode, screen, cut_ljsq,
- cut_coulsq, force->special_coul,
+ cut_coulsq, force->special_coul,
force->qqrd2e, g_ewald);
GPU_EXTRA::check_flag(success,error,world);
@@ -284,7 +284,7 @@ void PairBornCoulLongGPU::cpu_compute(int start, int inum, int eflag,
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
} else ecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
- evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv
+ evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv
+ d[itype][jtype]*r6inv*r2inv - offset[itype][jtype];
evdwl *= factor_lj;
} else evdwl = 0.0;
diff --git a/src/GPU/pair_born_coul_long_gpu.h b/src/GPU/pair_born_coul_long_gpu.h
index f188f93d1f..e929826a24 100644
--- a/src/GPU/pair_born_coul_long_gpu.h
+++ b/src/GPU/pair_born_coul_long_gpu.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/GPU/pair_born_coul_wolf_gpu.cpp b/src/GPU/pair_born_coul_wolf_gpu.cpp
index 5d09b0325f..4a7e0f223c 100644
--- a/src/GPU/pair_born_coul_wolf_gpu.cpp
+++ b/src/GPU/pair_born_coul_wolf_gpu.cpp
@@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
-
+
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
-
+
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@@ -15,9 +15,9 @@
Contributing authors: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
#include "pair_born_coul_wolf_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -33,7 +33,7 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include "string.h"
+#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
@@ -42,9 +42,9 @@ using namespace MathConst;
// External functions from cuda library for atom decomposition
int borncw_gpu_init(const int ntypes, double **cutsq, double **host_rhoinv,
- double **host_born1, double **host_born2,
- double **host_born3, double **host_a, double **host_c,
- double **host_d, double **sigma, double **offset,
+ double **host_born1, double **host_born2,
+ double **host_born3, double **host_a, double **host_c,
+ double **host_d, double **sigma, double **offset,
double *special_lj, const int inum,
const int nall, const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen,
@@ -54,7 +54,7 @@ int borncw_gpu_init(const int ntypes, double **cutsq, double **host_rhoinv,
void borncw_gpu_clear();
int ** borncw_gpu_compute_n(const int ago, const int inum_full, const int nall,
double **host_x, int *host_type, double *sublo,
- double *subhi, tagint *tag, int **nspecial,
+ double *subhi, tagint *tag, int **nspecial,
tagint **special, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
int **ilist, int **jnum, const double cpu_time,
@@ -70,13 +70,13 @@ double borncw_gpu_bytes();
/* ---------------------------------------------------------------------- */
-PairBornCoulWolfGPU::PairBornCoulWolfGPU(LAMMPS *lmp) : PairBornCoulWolf(lmp),
+PairBornCoulWolfGPU::PairBornCoulWolfGPU(LAMMPS *lmp) : PairBornCoulWolf(lmp),
gpu_mode(GPU_FORCE)
{
respa_enable = 0;
reinitflag = 0;
cpu_time = 0.0;
- GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
+ GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
@@ -94,10 +94,10 @@ void PairBornCoulWolfGPU::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
-
+
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
-
+
bool success = true;
int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
@@ -106,8 +106,8 @@ void PairBornCoulWolfGPU::compute(int eflag, int vflag)
atom->x, atom->type, domain->sublo,
domain->subhi, atom->tag, atom->nspecial,
atom->special, eflag, vflag, eflag_atom,
- vflag_atom, host_start,
- &ilist, &numneigh, cpu_time, success,
+ vflag_atom, host_start,
+ &ilist, &numneigh, cpu_time, success,
atom->q, domain->boxlo, domain->prd);
} else {
inum = list->inum;
@@ -135,7 +135,7 @@ void PairBornCoulWolfGPU::compute(int eflag, int vflag)
void PairBornCoulWolfGPU::init_style()
{
- if (force->newton_pair)
+ if (force->newton_pair)
error->all(FLERR,
"Cannot use newton pair with born/coul/wolf/gpu pair style");
@@ -159,18 +159,18 @@ void PairBornCoulWolfGPU::init_style()
cut_coulsq = cut_coul * cut_coul;
double e_shift = erfc(alf*cut_coul)/cut_coul;
- double f_shift = -(e_shift+ 2.0*alf/MY_PIS * exp(-alf*alf*cut_coul*cut_coul)) /
- cut_coul;
+ double f_shift = -(e_shift+ 2.0*alf/MY_PIS * exp(-alf*alf*cut_coul*cut_coul)) /
+ cut_coul;
int maxspecial=0;
if (atom->molecular)
maxspecial=atom->maxspecial;
- int success = borncw_gpu_init(atom->ntypes+1, cutsq, rhoinv,
- born1, born2, born3, a, c, d, sigma, offset,
+ int success = borncw_gpu_init(atom->ntypes+1, cutsq, rhoinv,
+ born1, born2, born3, a, c, d, sigma, offset,
force->special_lj, atom->nlocal,
atom->nlocal+atom->nghost, 300, maxspecial,
cell_size, gpu_mode, screen, cut_ljsq,
- cut_coulsq, force->special_coul, force->qqrd2e,
+ cut_coulsq, force->special_coul, force->qqrd2e,
alf, e_shift, f_shift);
GPU_EXTRA::check_flag(success,error,world);
@@ -178,7 +178,7 @@ void PairBornCoulWolfGPU::init_style()
int irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
- }
+ }
}
/* ---------------------------------------------------------------------- */
@@ -203,7 +203,7 @@ void PairBornCoulWolfGPU::cpu_compute(int start, int inum, int eflag, int vflag,
int *jlist;
evdwl = ecoul = 0.0;
-
+
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
@@ -212,10 +212,10 @@ void PairBornCoulWolfGPU::cpu_compute(int start, int inum, int eflag, int vflag,
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
double qqrd2e = force->qqrd2e;
-
+
double e_shift = erfc(alf*cut_coul)/cut_coul;
- double f_shift = -(e_shift+ 2.0*alf/MY_PIS * exp(-alf*alf*cut_coul*cut_coul)) /
- cut_coul;
+ double f_shift = -(e_shift+ 2.0*alf/MY_PIS * exp(-alf*alf*cut_coul*cut_coul)) /
+ cut_coul;
// loop over neighbors of my atoms
@@ -247,13 +247,13 @@ void PairBornCoulWolfGPU::cpu_compute(int start, int inum, int eflag, int vflag,
if (rsq < cutsq[itype][jtype]) {
r2inv = 1.0/rsq;
-
+
if (rsq < cut_coulsq) {
r = sqrt(rsq);
prefactor = qqrd2e*qtmp*q[j]/r;
- erfcc = erfc(alf*r);
+ erfcc = erfc(alf*r);
erfcd = exp(-alf*alf*r*r);
- v_sh = (erfcc - e_shift*r) * prefactor;
+ v_sh = (erfcc - e_shift*r) * prefactor;
dvdrr = (erfcc/rsq + 2.0*alf/MY_PIS * erfcd/r) + f_shift;
forcecoul = dvdrr*rsq*prefactor;
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
@@ -263,12 +263,12 @@ void PairBornCoulWolfGPU::cpu_compute(int start, int inum, int eflag, int vflag,
r6inv = r2inv*r2inv*r2inv;
r = sqrt(rsq);
rexp = exp((sigma[itype][jtype]-r)*rhoinv[itype][jtype]);
- forceborn = born1[itype][jtype]*r*rexp - born2[itype][jtype]*r6inv +
+ forceborn = born1[itype][jtype]*r*rexp - born2[itype][jtype]*r6inv +
born3[itype][jtype]*r2inv*r6inv;
} else forceborn = 0.0;
-
+
fpair = (factor_coul*forcecoul + factor_lj*forceborn) * r2inv;
-
+
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
diff --git a/src/GPU/pair_born_coul_wolf_gpu.h b/src/GPU/pair_born_coul_wolf_gpu.h
index 0aec3a4b35..6eb03f3e1a 100644
--- a/src/GPU/pair_born_coul_wolf_gpu.h
+++ b/src/GPU/pair_born_coul_wolf_gpu.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/GPU/pair_born_gpu.cpp b/src/GPU/pair_born_gpu.cpp
index 4df91fde15..e80a6509ad 100644
--- a/src/GPU/pair_born_gpu.cpp
+++ b/src/GPU/pair_born_gpu.cpp
@@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
-
+
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
-
+
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@@ -15,9 +15,9 @@
Contributing author: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
#include "pair_born_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +32,7 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include "string.h"
+#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
@@ -40,19 +40,19 @@ using namespace LAMMPS_NS;
// External functions from cuda library for atom decomposition
int born_gpu_init(const int ntypes, double **cutsq, double **host_rhoinv,
- double **host_born1, double **host_born2, double **host_born3,
- double **host_a, double **host_c, double **host_d,
- double **host_sigma, double **offset, double *special_lj,
+ double **host_born1, double **host_born2, double **host_born3,
+ double **host_a, double **host_c, double **host_d,
+ double **host_sigma, double **offset, double *special_lj,
const int inum, const int nall, const int max_nbors,
- const int maxspecial, const double cell_size,
+ const int maxspecial, const double cell_size,
int &gpu_mode, FILE *screen);
void born_gpu_reinit(const int ntypes, double **host_rhoinv,
double **host_born1, double **host_born2, double **host_born3,
double **host_a, double **host_c, double **host_d,
double **offset);
void born_gpu_clear();
-int ** born_gpu_compute_n(const int ago, const int inum_full,
- const int nall, double **host_x, int *host_type,
+int ** born_gpu_compute_n(const int ago, const int inum_full,
+ const int nall, double **host_x, int *host_type,
double *sublo, double *subhi, tagint *tag, int **nspecial,
tagint **special, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
@@ -71,7 +71,7 @@ PairBornGPU::PairBornGPU(LAMMPS *lmp) : PairBorn(lmp), gpu_mode(GPU_FORCE)
{
respa_enable = 0;
cpu_time = 0.0;
- GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
+ GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
@@ -89,10 +89,10 @@ void PairBornGPU::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
-
+
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
-
+
bool success = true;
int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
@@ -101,7 +101,7 @@ void PairBornGPU::compute(int eflag, int vflag)
atom->x, atom->type, domain->sublo,
domain->subhi, atom->tag, atom->nspecial,
atom->special, eflag, vflag, eflag_atom,
- vflag_atom, host_start,
+ vflag_atom, host_start,
&ilist, &numneigh, cpu_time, success);
} else {
inum = list->inum;
@@ -128,7 +128,7 @@ void PairBornGPU::compute(int eflag, int vflag)
void PairBornGPU::init_style()
{
- if (force->newton_pair)
+ if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with born/gpu pair style");
// Repeat cutsq calculation because done after call to init_style
@@ -151,7 +151,7 @@ void PairBornGPU::init_style()
int maxspecial=0;
if (atom->molecular)
maxspecial=atom->maxspecial;
- int success = born_gpu_init(atom->ntypes+1, cutsq, rhoinv,
+ int success = born_gpu_init(atom->ntypes+1, cutsq, rhoinv,
born1, born2, born3, a, c, d, sigma,
offset, force->special_lj, atom->nlocal,
atom->nlocal+atom->nghost, 300, maxspecial,
@@ -170,7 +170,7 @@ void PairBornGPU::init_style()
void PairBornGPU::reinit()
{
Pair::reinit();
-
+
born_gpu_reinit(atom->ntypes+1, rhoinv, born1, born2, born3,
a, c, d, offset);
}
@@ -185,7 +185,7 @@ double PairBornGPU::memory_usage()
/* ---------------------------------------------------------------------- */
-void PairBornGPU::cpu_compute(int start, int inum, int eflag, int vflag,
+void PairBornGPU::cpu_compute(int start, int inum, int eflag, int vflag,
int *ilist, int *numneigh, int **firstneigh) {
int i,j,ii,jj,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
@@ -225,7 +225,7 @@ void PairBornGPU::cpu_compute(int start, int inum, int eflag, int vflag,
r6inv = r2inv*r2inv*r2inv;
r = sqrt(rsq);
rexp = exp((sigma[itype][jtype]-r)*rhoinv[itype][jtype]);
- forceborn = born1[itype][jtype]*r*rexp - born2[itype][jtype]*r6inv +
+ forceborn = born1[itype][jtype]*r*rexp - born2[itype][jtype]*r6inv +
born3[itype][jtype]*r2inv*r6inv;
fpair = factor_lj*forceborn*r2inv;
@@ -234,7 +234,7 @@ void PairBornGPU::cpu_compute(int start, int inum, int eflag, int vflag,
f[i][2] += delz*fpair;
if (eflag) {
- evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv +
+ evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv +
d[itype][jtype]*r6inv*r2inv - offset[itype][jtype];
evdwl *= factor_lj;
}
diff --git a/src/GPU/pair_born_gpu.h b/src/GPU/pair_born_gpu.h
index e5961de998..49c76fadf6 100644
--- a/src/GPU/pair_born_gpu.h
+++ b/src/GPU/pair_born_gpu.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/GPU/pair_buck_coul_cut_gpu.cpp b/src/GPU/pair_buck_coul_cut_gpu.cpp
index e00fb88c02..e74020dd3a 100644
--- a/src/GPU/pair_buck_coul_cut_gpu.cpp
+++ b/src/GPU/pair_buck_coul_cut_gpu.cpp
@@ -15,9 +15,9 @@
Contributing authors: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
#include "pair_buck_coul_cut_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +32,7 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include "string.h"
+#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
diff --git a/src/GPU/pair_buck_coul_long_gpu.cpp b/src/GPU/pair_buck_coul_long_gpu.cpp
index bb93b1d08c..c2a37fc3dc 100644
--- a/src/GPU/pair_buck_coul_long_gpu.cpp
+++ b/src/GPU/pair_buck_coul_long_gpu.cpp
@@ -15,9 +15,9 @@
Contributing author: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
#include "pair_buck_coul_long_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +32,7 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include "string.h"
+#include <string.h>
#include "kspace.h"
#include "gpu_extra.h"
diff --git a/src/GPU/pair_buck_gpu.cpp b/src/GPU/pair_buck_gpu.cpp
index de64bfd90c..1e9b838ec8 100644
--- a/src/GPU/pair_buck_gpu.cpp
+++ b/src/GPU/pair_buck_gpu.cpp
@@ -15,9 +15,9 @@
Contributing author: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
#include "pair_buck_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +32,7 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include "string.h"
+#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
@@ -167,7 +167,7 @@ void PairBuckGPU::init_style()
void PairBuckGPU::reinit()
{
Pair::reinit();
-
+
buck_gpu_reinit(atom->ntypes+1, cutsq, rhoinv, buck1, buck2,
a, c, offset);
}
diff --git a/src/GPU/pair_colloid_gpu.cpp b/src/GPU/pair_colloid_gpu.cpp
index 1b164df8f6..d4e8224238 100644
--- a/src/GPU/pair_colloid_gpu.cpp
+++ b/src/GPU/pair_colloid_gpu.cpp
@@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
-
+
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
-
+
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@@ -15,9 +15,9 @@
Contributing author: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
#include "pair_colloid_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +32,7 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include "string.h"
+#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
@@ -40,22 +40,22 @@ using namespace LAMMPS_NS;
// External functions from cuda library for atom decomposition
int colloid_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
- double **host_lj2, double **host_lj3, double **host_lj4,
- double **offset, double *special_lj, double **host_a12,
- double **host_a1, double **host_a2, double **host_d1,
- double **host_d2, double **host_sigma3, double **host_sigma6,
- int **host_form, const int nlocal,
+ double **host_lj2, double **host_lj3, double **host_lj4,
+ double **offset, double *special_lj, double **host_a12,
+ double **host_a1, double **host_a2, double **host_d1,
+ double **host_d2, double **host_sigma3, double **host_sigma6,
+ int **host_form, const int nlocal,
const int nall, const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen);
void colloid_gpu_clear();
int ** colloid_gpu_compute_n(const int ago, const int inum,
- const int nall, double **host_x, int *host_type,
+ const int nall, double **host_x, int *host_type,
double *sublo, double *subhi, tagint *tag, int **nspecial,
tagint **special, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
int **ilist, int **jnum,
const double cpu_time, bool &success);
-void colloid_gpu_compute(const int ago, const int inum, const int nall,
+void colloid_gpu_compute(const int ago, const int inum, const int nall,
double **host_x, int *host_type, int *ilist, int *numj,
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
@@ -69,7 +69,7 @@ PairColloidGPU::PairColloidGPU(LAMMPS *lmp) : PairColloid(lmp), gpu_mode(GPU_FOR
respa_enable = 0;
reinitflag = 0;
cpu_time = 0.0;
- GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
+ GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
@@ -87,10 +87,10 @@ void PairColloidGPU::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
-
+
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
-
+
bool success = true;
int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
@@ -99,7 +99,7 @@ void PairColloidGPU::compute(int eflag, int vflag)
atom->x, atom->type, domain->sublo,
domain->subhi, atom->tag, atom->nspecial,
atom->special, eflag, vflag, eflag_atom,
- vflag_atom, host_start,
+ vflag_atom, host_start,
&ilist, &numneigh, cpu_time, success);
} else {
inum = list->inum;
@@ -126,7 +126,7 @@ void PairColloidGPU::compute(int eflag, int vflag)
void PairColloidGPU::init_style()
{
- if (force->newton_pair)
+ if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with colloid/gpu pair style");
// Repeat cutsq calculation because done after call to init_style
@@ -160,7 +160,7 @@ void PairColloidGPU::init_style()
if (atom->molecular)
maxspecial=atom->maxspecial;
int success = colloid_gpu_init(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4,
- offset, force->special_lj, a12, a1, a2,
+ offset, force->special_lj, a12, a1, a2,
d1, d2, sigma3, sigma6, _form, atom->nlocal,
atom->nlocal+atom->nghost, 300, maxspecial,
cell_size, gpu_mode, screen);
@@ -184,8 +184,8 @@ double PairColloidGPU::memory_usage()
/* ---------------------------------------------------------------------- */
-void PairColloidGPU::cpu_compute(int start, int inum, int eflag, int vflag,
- int *ilist, int *numneigh, int **firstneigh)
+void PairColloidGPU::cpu_compute(int start, int inum, int eflag, int vflag,
+ int *ilist, int *numneigh, int **firstneigh)
{
int i,j,ii,jj,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
@@ -224,16 +224,16 @@ void PairColloidGPU::cpu_compute(int start, int inum, int eflag, int vflag,
if (rsq >= cutsq[itype][jtype]) continue;
switch (form[itype][jtype]) {
- case SMALL_SMALL:
+ case SMALL_SMALL:
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
fpair = factor_lj*forcelj*r2inv;
- if (eflag)
+ if (eflag)
evdwl = r6inv*(r6inv*lj3[itype][jtype]-lj4[itype][jtype]) -
offset[itype][jtype];
break;
-
+
case SMALL_LARGE:
c2 = a2[itype][jtype];
K[1] = c2*c2;
@@ -244,14 +244,14 @@ void PairColloidGPU::cpu_compute(int start, int inum, int eflag, int vflag,
K[3] *= K[3]*K[3];
K[6] = K[3]*K[3];
fR = sigma3[itype][jtype]*a12[itype][jtype]*c2*K[1]/K[3];
- fpair = 4.0/15.0*fR*factor_lj *
- (2.0*(K[1]+K[2]) * (K[1]*(5.0*K[1]+22.0*K[2])+5.0*K[4]) *
+ fpair = 4.0/15.0*fR*factor_lj *
+ (2.0*(K[1]+K[2]) * (K[1]*(5.0*K[1]+22.0*K[2])+5.0*K[4]) *
sigma6[itype][jtype]/K[6]-5.0) / K[0];
- if (eflag)
- evdwl = 2.0/9.0*fR *
+ if (eflag)
+ evdwl = 2.0/9.0*fR *
(1.0-(K[1]*(K[1]*(K[1]/3.0+3.0*K[2])+4.2*K[4])+K[2]*K[4]) *
sigma6[itype][jtype]/K[6]) - offset[itype][jtype];
- if (rsq <= K[1])
+ if (rsq <= K[1])
error->one(FLERR,"Overlapping small/large in pair colloid");
break;
@@ -284,17 +284,17 @@ void PairColloidGPU::cpu_compute(int start, int inum, int eflag, int vflag,
fR = a12[itype][jtype]*sigma6[itype][jtype]/r/37800.0;
evdwl = fR * (h[0]-h[1]-h[2]+h[3]);
dUR = evdwl/r + 5.0*fR*(g[0]+g[1]-g[2]-g[3]);
- dUA = -a12[itype][jtype]/3.0*r*((2.0*K[0]*K[7]+1.0)*K[7] +
+ dUA = -a12[itype][jtype]/3.0*r*((2.0*K[0]*K[7]+1.0)*K[7] +
(2.0*K[0]*K[8]-1.0)*K[8]);
fpair = factor_lj * (dUR+dUA)/r;
if (eflag)
- evdwl += a12[itype][jtype]/6.0 *
+ evdwl += a12[itype][jtype]/6.0 *
(2.0*K[0]*(K[7]+K[8])-log(K[8]/K[7])) - offset[itype][jtype];
- if (r <= K[1])
+ if (r <= K[1])
error->one(FLERR,"Overlapping large/large in pair colloid");
break;
}
-
+
if (eflag) evdwl *= factor_lj;
f[i][0] += delx*fpair;
diff --git a/src/GPU/pair_colloid_gpu.h b/src/GPU/pair_colloid_gpu.h
index 5bb524e890..78ecfbc59a 100644
--- a/src/GPU/pair_colloid_gpu.h
+++ b/src/GPU/pair_colloid_gpu.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/GPU/pair_coul_cut_gpu.cpp b/src/GPU/pair_coul_cut_gpu.cpp
index 04345b9209..c66a0a8ef4 100644
--- a/src/GPU/pair_coul_cut_gpu.cpp
+++ b/src/GPU/pair_coul_cut_gpu.cpp
@@ -15,9 +15,9 @@
Contributing author: Trung Dac Nguyen
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
#include "pair_coul_cut_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +32,7 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include "string.h"
+#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
@@ -172,7 +172,7 @@ void PairCoulCutGPU::init_style()
void PairCoulCutGPU::reinit()
{
Pair::reinit();
-
+
coul_gpu_reinit(atom->ntypes+1, scale);
}
diff --git a/src/GPU/pair_coul_debye_gpu.cpp b/src/GPU/pair_coul_debye_gpu.cpp
index 19ae6b3162..2b5d608fc7 100644
--- a/src/GPU/pair_coul_debye_gpu.cpp
+++ b/src/GPU/pair_coul_debye_gpu.cpp
@@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
-
+
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
-
+
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@@ -15,9 +15,9 @@
Contributing author: Trung Dac Nguyen (ndtrung@umich.edu)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
#include "pair_coul_debye_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +32,7 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include "string.h"
+#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
@@ -46,15 +46,15 @@ int cdebye_gpu_init(const int ntypes, double **host_scale, double **cutsq,
const double qqrd2e, const double kappa);
void cdebye_gpu_reinit(const int ntypes, double **host_scale);
void cdebye_gpu_clear();
-int ** cdebye_gpu_compute_n(const int ago, const int inum, const int nall,
- double **host_x, int *host_type,
+int ** cdebye_gpu_compute_n(const int ago, const int inum, const int nall,
+ double **host_x, int *host_type,
double *sublo, double *subhi, tagint *tag, int **nspecial,
tagint **special, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
int **ilist, int **jnum, const double cpu_time,
bool &success, double *host_q, double *boxlo,
double *prd);
-void cdebye_gpu_compute(const int ago, const int inum, const int nall,
+void cdebye_gpu_compute(const int ago, const int inum, const int nall,
double **host_x, int *host_type,
int *ilist, int *numj, int **firstneigh,
const bool eflag, const bool vflag, const bool eatom,
@@ -65,12 +65,12 @@ double cdebye_gpu_bytes();
/* ---------------------------------------------------------------------- */
-PairCoulDebyeGPU::PairCoulDebyeGPU(LAMMPS *lmp) :
+PairCoulDebyeGPU::PairCoulDebyeGPU(LAMMPS *lmp) :
PairCoulDebye(lmp), gpu_mode(GPU_FORCE)
{
respa_enable = 0;
cpu_time = 0.0;
- GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
+ GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
@@ -88,12 +88,12 @@ void PairCoulDebyeGPU::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
-
+
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
-
+
bool success = true;
- int *ilist, *numneigh, **firstneigh;
+ int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
inum = atom->nlocal;
firstneigh = cdebye_gpu_compute_n(neighbor->ago, inum, nall, atom->x,
@@ -101,7 +101,7 @@ void PairCoulDebyeGPU::compute(int eflag, int vflag)
atom->tag, atom->nspecial, atom->special,
eflag, vflag, eflag_atom, vflag_atom,
host_start, &ilist, &numneigh, cpu_time,
- success, atom->q, domain->boxlo,
+ success, atom->q, domain->boxlo,
domain->prd);
} else {
inum = list->inum;
@@ -132,7 +132,7 @@ void PairCoulDebyeGPU::init_style()
if (!atom->q_flag)
error->all(FLERR,"Pair style coul/debye/gpu requires atom attribute q");
- if (force->newton_pair)
+ if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with coul/debye/gpu pair style");
// Repeat cutsq calculation because done after call to init_style
@@ -174,7 +174,7 @@ void PairCoulDebyeGPU::init_style()
void PairCoulDebyeGPU::reinit()
{
Pair::reinit();
-
+
cdebye_gpu_reinit(atom->ntypes+1, scale);
}
@@ -188,7 +188,7 @@ double PairCoulDebyeGPU::memory_usage()
/* ---------------------------------------------------------------------- */
-void PairCoulDebyeGPU::cpu_compute(int start, int inum, int eflag,
+void PairCoulDebyeGPU::cpu_compute(int start, int inum, int eflag,
int vflag, int *ilist,
int *numneigh, int **firstneigh)
{
diff --git a/src/GPU/pair_coul_debye_gpu.h b/src/GPU/pair_coul_debye_gpu.h
index eebb44c357..9cc379d1ed 100644
--- a/src/GPU/pair_coul_debye_gpu.h
+++ b/src/GPU/pair_coul_debye_gpu.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/GPU/pair_coul_dsf_gpu.cpp b/src/GPU/pair_coul_dsf_gpu.cpp
index 55e398738b..d2d060281c 100644
--- a/src/GPU/pair_coul_dsf_gpu.cpp
+++ b/src/GPU/pair_coul_dsf_gpu.cpp
@@ -15,9 +15,9 @@
Contributing author: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
#include "pair_coul_dsf_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +32,7 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include "string.h"
+#include <string.h>
#include "gpu_extra.h"
#define MY_PIS 1.77245385090551602729
@@ -52,8 +52,8 @@ int cdsf_gpu_init(const int ntypes, const int nlocal, const int nall,
const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen,
const double host_cut_coulsq,
- double *host_special_coul, const double qqrd2e,
- const double e_shift, const double f_shift,
+ double *host_special_coul, const double qqrd2e,
+ const double e_shift, const double f_shift,
const double alpha);
void cdsf_gpu_clear();
int ** cdsf_gpu_compute_n(const int ago, const int inum,
@@ -75,7 +75,7 @@ double cdsf_gpu_bytes();
/* ---------------------------------------------------------------------- */
-PairCoulDSFGPU::PairCoulDSFGPU(LAMMPS *lmp) : PairCoulDSF(lmp),
+PairCoulDSFGPU::PairCoulDSFGPU(LAMMPS *lmp) : PairCoulDSF(lmp),
gpu_mode(GPU_FORCE)
{
respa_enable = 0;
@@ -164,10 +164,10 @@ void PairCoulDSFGPU::init_style()
double cell_size = sqrt(maxcut) + neighbor->skin;
cut_coulsq = cut_coul * cut_coul;
- double erfcc = erfc(alpha*cut_coul);
+ double erfcc = erfc(alpha*cut_coul);
double erfcd = exp(-alpha*alpha*cut_coul*cut_coul);
- f_shift = -(erfcc/cut_coulsq + 2.0/MY_PIS*alpha*erfcd/cut_coul);
- e_shift = erfcc/cut_coul - f_shift*cut_coul;
+ f_shift = -(erfcc/cut_coulsq + 2.0/MY_PIS*alpha*erfcd/cut_coul);
+ e_shift = erfcc/cut_coul - f_shift*cut_coul;
int maxspecial=0;
if (atom->molecular)
@@ -248,10 +248,10 @@ void PairCoulDSFGPU::cpu_compute(int start, int inum, int eflag, int vflag,
erfcd = exp(-alpha*alpha*r*r);
t = 1.0 / (1.0 + EWALD_P*alpha*r);
erfcc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * erfcd;
- forcecoul = prefactor * (erfcc/r + 2.0*alpha/MY_PIS * erfcd +
+ forcecoul = prefactor * (erfcc/r + 2.0*alpha/MY_PIS * erfcd +
r*f_shift) * r;
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
-
+
fpair = forcecoul * r2inv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
diff --git a/src/GPU/pair_coul_long_gpu.cpp b/src/GPU/pair_coul_long_gpu.cpp
index 68742efbcd..a1864a4002 100644
--- a/src/GPU/pair_coul_long_gpu.cpp
+++ b/src/GPU/pair_coul_long_gpu.cpp
@@ -15,9 +15,9 @@
Contributing author: Axel Kohlmeyer (Temple)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
#include "pair_coul_long_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +32,7 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include "string.h"
+#include <string.h>
#include "kspace.h"
#include "gpu_extra.h"
@@ -181,7 +181,7 @@ void PairCoulLongGPU::init_style()
void PairCoulLongGPU::reinit()
{
Pair::reinit();
-
+
cl_gpu_reinit(atom->ntypes+1, scale);
}
diff --git a/src/GPU/pair_dpd_gpu.cpp b/src/GPU/pair_dpd_gpu.cpp
index dacdaa5e56..c82ed97485 100644
--- a/src/GPU/pair_dpd_gpu.cpp
+++ b/src/GPU/pair_dpd_gpu.cpp
@@ -15,9 +15,9 @@
Contributing author: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
#include "pair_dpd_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -33,7 +33,7 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include "string.h"
+#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
@@ -49,10 +49,10 @@ void dpd_gpu_clear();
int ** dpd_gpu_compute_n(const int ago, const int inum_full, const int nall,
double **host_x, int *host_type, double *sublo,
double *subhi, tagint *tag, int **nspecial,
- tagint **special, const bool eflag, const bool vflag,
- const bool eatom, const bool vatom, int &host_start,
+ tagint **special, const bool eflag, const bool vflag,
+ const bool eatom, const bool vatom, int &host_start,
int **ilist, int **jnum, const double cpu_time, bool &success,
- double **host_v, const double dtinvsqrt,
+ double **host_v, const double dtinvsqrt,
const int seed, const int timestep,
double *boxlo, double *prd);
void dpd_gpu_compute(const int ago, const int inum_full, const int nall,
@@ -60,7 +60,7 @@ void dpd_gpu_compute(const int ago, const int inum_full, const int nall,
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success, tagint *tag,
- double **host_v, const double dtinvsqrt,
+ double **host_v, const double dtinvsqrt,
const int seed, const int timestep,
const int nlocal, double *boxlo, double *prd);
double dpd_gpu_bytes();
@@ -75,7 +75,7 @@ double dpd_gpu_bytes();
#define _USE_UNIFORM_SARU_LCG
#endif
-// References:
+// References:
// 1. Y. Afshar, F. Schmid, A. Pishevar, S. Worley, Comput. Phys. Comm. 184 (2013), 1119–1128.
// 2. C. L. Phillips, J. A. Anderson, S. C. Glotzer, Comput. Phys. Comm. 230 (2011), 7191-7201.
// PRNG period = 3666320093*2^32 ~ 2^64 ~ 10^19
@@ -87,9 +87,9 @@ double dpd_gpu_bytes();
#define TWO_N32 0.232830643653869628906250e-9f /* 2^-32 */
// specifically implemented for steps = 1; high = 1.0; low = -1.0
-// returns uniformly distributed random numbers u in [-1.0;1.0]
-// using the inherent LCG, then multiply u with sqrt(3) to "match"
-// with a normal random distribution.
+// returns uniformly distributed random numbers u in [-1.0;1.0]
+// using the inherent LCG, then multiply u with sqrt(3) to "match"
+// with a normal random distribution.
// Afshar et al. mutlplies u in [-0.5;0.5] with sqrt(12)
// Curly brackets to make variables local to the scope.
#ifdef _USE_UNIFORM_SARU_LCG
@@ -119,8 +119,8 @@ double dpd_gpu_bytes();
#endif
// specifically implemented for steps = 1; high = 1.0; low = -1.0
-// returns uniformly distributed random numbers u in [-1.0;1.0] using TEA8
-// then multiply u with sqrt(3) to "match" with a normal random distribution
+// returns uniformly distributed random numbers u in [-1.0;1.0] using TEA8
+// then multiply u with sqrt(3) to "match" with a normal random distribution
// Afshar et al. mutlplies u in [-0.5;0.5] with sqrt(12)
#ifdef _USE_UNIFORM_SARU_TEA8
#define numtyp double
@@ -159,7 +159,7 @@ double dpd_gpu_bytes();
#endif
// specifically implemented for steps = 1; high = 1.0; low = -1.0
-// returns two uniformly distributed random numbers r1 and r2 in [-1.0;1.0],
+// returns two uniformly distributed random numbers r1 and r2 in [-1.0;1.0],
// and uses the polar method (Marsaglia's) to transform to a normal random value
// This is used to compared with CPU DPD using RandMars::gaussian()
#ifdef _USE_GAUSSIAN_SARU_LCG
@@ -232,7 +232,7 @@ void PairDPDGPU::compute(int eflag, int vflag)
int inum, host_start;
double dtinvsqrt = 1.0/sqrt(update->dt);
-
+
bool success = true;
int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
@@ -242,7 +242,7 @@ void PairDPDGPU::compute(int eflag, int vflag)
atom->tag, atom->nspecial, atom->special,
eflag, vflag, eflag_atom, vflag_atom,
host_start, &ilist, &numneigh, cpu_time,
- success, atom->v, dtinvsqrt, seed,
+ success, atom->v, dtinvsqrt, seed,
update->ntimestep,
domain->boxlo, domain->prd);
} else {
@@ -252,8 +252,8 @@ void PairDPDGPU::compute(int eflag, int vflag)
firstneigh = list->firstneigh;
dpd_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
- vflag_atom, host_start, cpu_time, success,
- atom->tag, atom->v, dtinvsqrt, seed,
+ vflag_atom, host_start, cpu_time, success,
+ atom->tag, atom->v, dtinvsqrt, seed,
update->ntimestep,
atom->nlocal, domain->boxlo, domain->prd);
}
@@ -296,7 +296,7 @@ void PairDPDGPU::init_style()
int maxspecial=0;
if (atom->molecular)
maxspecial=atom->maxspecial;
- int success = dpd_gpu_init(atom->ntypes+1, cutsq, a0, gamma, sigma,
+ int success = dpd_gpu_init(atom->ntypes+1, cutsq, a0, gamma, sigma,
cut, force->special_lj, false, atom->nlocal,
atom->nlocal+atom->nghost, 300, maxspecial,
cell_size, gpu_mode, screen);
diff --git a/src/GPU/pair_dpd_tstat_gpu.cpp b/src/GPU/pair_dpd_tstat_gpu.cpp
index b5233027f9..e051a13a0b 100644
--- a/src/GPU/pair_dpd_tstat_gpu.cpp
+++ b/src/GPU/pair_dpd_tstat_gpu.cpp
@@ -15,9 +15,9 @@
Contributing author: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
#include "pair_dpd_tstat_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -33,7 +33,7 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include "string.h"
+#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
@@ -49,8 +49,8 @@ void dpd_gpu_clear();
int ** dpd_gpu_compute_n(const int ago, const int inum_full, const int nall,
double **host_x, int *host_type, double *sublo,
double *subhi, tagint *tag, int **nspecial,
- tagint **special, const bool eflag, const bool vflag,
- const bool eatom, const bool vatom, int &host_start,
+ tagint **special, const bool eflag, const bool vflag,
+ const bool eatom, const bool vatom, int &host_start,
int **ilist, int **jnum, const double cpu_time, bool &success,
double **host_v, const double dtinvsqrt,
const int seed, const int timestep,
@@ -60,7 +60,7 @@ void dpd_gpu_compute(const int ago, const int inum_full, const int nall,
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success, tagint *tag,
- double **host_v, const double dtinvsqrt,
+ double **host_v, const double dtinvsqrt,
const int seed, const int timestep,
const int nlocal, double *boxlo, double *prd);
void dpd_gpu_update_coeff(int ntypes, double **host_a0, double **host_gamma,
@@ -77,7 +77,7 @@ double dpd_gpu_bytes();
#define _USE_UNIFORM_SARU_LCG
#endif
-// References:
+// References:
// 1. Y. Afshar, F. Schmid, A. Pishevar, S. Worley, Comput. Phys. Comm. 184 (2013), 1119–1128.
// 2. C. L. Phillips, J. A. Anderson, S. C. Glotzer, Comput. Phys. Comm. 230 (2011), 7191-7201.
// PRNG period = 3666320093*2^32 ~ 2^64 ~ 10^19
@@ -89,9 +89,9 @@ double dpd_gpu_bytes();
#define TWO_N32 0.232830643653869628906250e-9f /* 2^-32 */
// specifically implemented for steps = 1; high = 1.0; low = -1.0
-// returns uniformly distributed random numbers u in [-1.0;1.0]
-// using the inherent LCG, then multiply u with sqrt(3) to "match"
-// with a normal random distribution.
+// returns uniformly distributed random numbers u in [-1.0;1.0]
+// using the inherent LCG, then multiply u with sqrt(3) to "match"
+// with a normal random distribution.
// Afshar et al. mutlplies u in [-0.5;0.5] with sqrt(12)
// Curly brackets to make variables local to the scope.
#ifdef _USE_UNIFORM_SARU_LCG
@@ -121,8 +121,8 @@ double dpd_gpu_bytes();
#endif
// specifically implemented for steps = 1; high = 1.0; low = -1.0
-// returns uniformly distributed random numbers u in [-1.0;1.0] using TEA8
-// then multiply u with sqrt(3) to "match" with a normal random distribution
+// returns uniformly distributed random numbers u in [-1.0;1.0] using TEA8
+// then multiply u with sqrt(3) to "match" with a normal random distribution
// Afshar et al. mutlplies u in [-0.5;0.5] with sqrt(12)
#ifdef _USE_UNIFORM_SARU_TEA8
#define numtyp double
@@ -161,7 +161,7 @@ double dpd_gpu_bytes();
#endif
// specifically implemented for steps = 1; high = 1.0; low = -1.0
-// returns two uniformly distributed random numbers r1 and r2 in [-1.0;1.0],
+// returns two uniformly distributed random numbers r1 and r2 in [-1.0;1.0],
// and uses the polar method (Marsaglia's) to transform to a normal random value
// This is used to compared with CPU DPD using RandMars::gaussian()
#ifdef _USE_GAUSSIAN_SARU_LCG
@@ -241,7 +241,7 @@ void PairDPDTstatGPU::compute(int eflag, int vflag)
for (int i = 1; i <= atom->ntypes; i++)
for (int j = i; j <= atom->ntypes; j++)
sigma[i][j] = sigma[j][i] = sqrt(2.0*boltz*temperature*gamma[i][j]);
-
+
dpd_gpu_update_coeff(atom->ntypes+1, a0, gamma, sigma, cut);
}
@@ -249,7 +249,7 @@ void PairDPDTstatGPU::compute(int eflag, int vflag)
int inum, host_start;
double dtinvsqrt = 1.0/sqrt(update->dt);
-
+
bool success = true;
int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
@@ -259,7 +259,7 @@ void PairDPDTstatGPU::compute(int eflag, int vflag)
atom->tag, atom->nspecial, atom->special,
eflag, vflag, eflag_atom, vflag_atom,
host_start, &ilist, &numneigh, cpu_time,
- success, atom->v, dtinvsqrt, seed,
+ success, atom->v, dtinvsqrt, seed,
update->ntimestep,
domain->boxlo, domain->prd);
} else {
@@ -269,8 +269,8 @@ void PairDPDTstatGPU::compute(int eflag, int vflag)
firstneigh = list->firstneigh;
dpd_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
- vflag_atom, host_start, cpu_time, success,
- atom->tag, atom->v, dtinvsqrt, seed,
+ vflag_atom, host_start, cpu_time, success,
+ atom->tag, atom->v, dtinvsqrt, seed,
update->ntimestep,
atom->nlocal, domain->boxlo, domain->prd);
}
@@ -313,7 +313,7 @@ void PairDPDTstatGPU::init_style()
int maxspecial=0;
if (atom->molecular)
maxspecial=atom->maxspecial;
- int success = dpd_gpu_init(atom->ntypes+1, cutsq, a0, gamma, sigma,
+ int success = dpd_gpu_init(atom->ntypes+1, cutsq, a0, gamma, sigma,
cut, force->special_lj, true, atom->nlocal,
atom->nlocal+atom->nghost, 300, maxspecial,
cell_size, gpu_mode, screen);
@@ -410,7 +410,7 @@ void PairDPDTstatGPU::cpu_compute(int start, int inum, int eflag, int vflag,
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
-
+
if (evflag) ev_tally_full(i,0.0,0.0,fpair,delx,dely,delz);
}
}
diff --git a/src/GPU/pair_eam_alloy_gpu.cpp b/src/GPU/pair_eam_alloy_gpu.cpp
index 9fb914cb0b..4ba784da28 100644
--- a/src/GPU/pair_eam_alloy_gpu.cpp
+++ b/src/GPU/pair_eam_alloy_gpu.cpp
@@ -15,9 +15,9 @@
Contributing authors: Trung Dac Nguyen (ORNL), W. Michael Brown (ORNL)
------------------------------------------------------------------------- */
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_eam_alloy_gpu.h"
#include "atom.h"
#include "force.h"
@@ -39,10 +39,10 @@ int eam_alloy_gpu_init(const int ntypes, double host_cutforcesq,
int **host_type2rhor, int **host_type2z2r,
int *host_type2frho, double ***host_rhor_spline,
double ***host_z2r_spline, double ***host_frho_spline,
- double rdr, double rdrho, double rhomax,
- int nrhor, int nrho, int nz2r, int nfrho, int nr,
- const int nlocal, const int nall, const int max_nbors,
- const int maxspecial, const double cell_size, int &gpu_mode,
+ double rdr, double rdrho, double rhomax,
+ int nrhor, int nrho, int nz2r, int nfrho, int nr,
+ const int nlocal, const int nall, const int max_nbors,
+ const int maxspecial, const double cell_size, int &gpu_mode,
FILE *screen, int &fp_size);
void eam_alloy_gpu_clear();
int** eam_alloy_gpu_compute_n(const int ago, const int inum_full, const int nall,
@@ -233,7 +233,7 @@ double PairEAMAlloyGPU::single(int i, int j, int itype, int jtype,
/* ---------------------------------------------------------------------- */
-int PairEAMAlloyGPU::pack_forward_comm(int n, int *list, double *buf,
+int PairEAMAlloyGPU::pack_forward_comm(int n, int *list, double *buf,
int pbc_flag,int *pbc)
{
int i,j,m;
diff --git a/src/GPU/pair_eam_fs_gpu.cpp b/src/GPU/pair_eam_fs_gpu.cpp
index 3c5c486a69..c64a7d7e91 100644
--- a/src/GPU/pair_eam_fs_gpu.cpp
+++ b/src/GPU/pair_eam_fs_gpu.cpp
@@ -15,9 +15,9 @@
Contributing authors: Trung Dac Nguyen (ORNL), W. Michael Brown (ORNL)
------------------------------------------------------------------------- */
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_eam_fs_gpu.h"
#include "atom.h"
#include "force.h"
@@ -39,10 +39,10 @@ int eam_fs_gpu_init(const int ntypes, double host_cutforcesq,
int **host_type2rhor, int **host_type2z2r,
int *host_type2frho, double ***host_rhor_spline,
double ***host_z2r_spline, double ***host_frho_spline,
- double rdr, double rdrho, double rhomax,
- int nrhor, int nrho, int nz2r, int nfrho, int nr,
- const int nlocal, const int nall, const int max_nbors,
- const int maxspecial, const double cell_size, int &gpu_mode,
+ double rdr, double rdrho, double rhomax,
+ int nrhor, int nrho, int nz2r, int nfrho, int nr,
+ const int nlocal, const int nall, const int max_nbors,
+ const int maxspecial, const double cell_size, int &gpu_mode,
FILE *screen, int &fp_size);
void eam_fs_gpu_clear();
int** eam_fs_gpu_compute_n(const int ago, const int inum_full, const int nall,
@@ -233,7 +233,7 @@ double PairEAMFSGPU::single(int i, int j, int itype, int jtype,
/* ---------------------------------------------------------------------- */
-int PairEAMFSGPU::pack_forward_comm(int n, int *list, double *buf,
+int PairEAMFSGPU::pack_forward_comm(int n, int *list, double *buf,
int pbc_flag,int *pbc)
{
int i,j,m;
diff --git a/src/GPU/pair_eam_gpu.cpp b/src/GPU/pair_eam_gpu.cpp
index c9aba74c25..ea75ff8ca8 100644
--- a/src/GPU/pair_eam_gpu.cpp
+++ b/src/GPU/pair_eam_gpu.cpp
@@ -15,10 +15,10 @@
Contributing authors: Trung Dac Nguyen (ORNL), W. Michael Brown (ORNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_eam_gpu.h"
#include "atom.h"
#include "force.h"
@@ -41,10 +41,10 @@ int eam_gpu_init(const int ntypes, double host_cutforcesq,
int **host_type2rhor, int **host_type2z2r,
int *host_type2frho, double ***host_rhor_spline,
double ***host_z2r_spline, double ***host_frho_spline,
- double rdr, double rdrho, double rhomax,
- int nrhor, int nrho, int nz2r, int nfrho, int nr,
- const int nlocal, const int nall, const int max_nbors,
- const int maxspecial, const double cell_size, int &gpu_mode,
+ double rdr, double rdrho, double rhomax,
+ int nrhor, int nrho, int nz2r, int nfrho, int nr,
+ const int nlocal, const int nall, const int max_nbors,
+ const int maxspecial, const double cell_size, int &gpu_mode,
FILE *screen, int &fp_size);
void eam_gpu_clear();
int** eam_gpu_compute_n(const int ago, const int inum_full, const int nall,
@@ -237,7 +237,7 @@ double PairEAMGPU::single(int i, int j, int itype, int jtype,
/* ---------------------------------------------------------------------- */
-int PairEAMGPU::pack_forward_comm(int n, int *list, double *buf,
+int PairEAMGPU::pack_forward_comm(int n, int *list, double *buf,
int pbc_flag,int *pbc)
{
int i,j,m;
diff --git a/src/GPU/pair_eam_gpu.h b/src/GPU/pair_eam_gpu.h
index ffdb790382..ccc6b6f8c6 100644
--- a/src/GPU/pair_eam_gpu.h
+++ b/src/GPU/pair_eam_gpu.h
@@ -20,7 +20,7 @@ PairStyle(eam/gpu,PairEAMGPU)
#ifndef LMP_PAIR_EAM_GPU_H
#define LMP_PAIR_EAM_GPU_H
-#include "stdio.h"
+#include <stdio.h>
#include "pair_eam.h"
namespace LAMMPS_NS {
diff --git a/src/GPU/pair_gauss_gpu.cpp b/src/GPU/pair_gauss_gpu.cpp
index c7b47131a6..a8cb695b3a 100644
--- a/src/GPU/pair_gauss_gpu.cpp
+++ b/src/GPU/pair_gauss_gpu.cpp
@@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
-
+
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
-
+
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@@ -15,9 +15,9 @@
Contributing author: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
#include "pair_gauss_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +32,7 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include "string.h"
+#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
@@ -40,20 +40,20 @@ using namespace LAMMPS_NS;
// External functions from cuda library for atom decomposition
int gauss_gpu_init(const int ntypes, double **cutsq, double **host_a,
- double **b, double **offset, double *special_lj, const int nlocal,
+ double **b, double **offset, double *special_lj, const int nlocal,
const int nall, const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen);
int gauss_gpu_reinit(const int ntypes, double **cutsq, double **host_a,
double **b, double **offset);
void gauss_gpu_clear();
int ** gauss_gpu_compute_n(const int ago, const int inum,
- const int nall, double **host_x, int *host_type,
+ const int nall, double **host_x, int *host_type,
double *sublo, double *subhi, tagint *tag, int **nspecial,
tagint **special, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
int **ilist, int **jnum,
const double cpu_time, bool &success);
-void gauss_gpu_compute(const int ago, const int inum, const int nall,
+void gauss_gpu_compute(const int ago, const int inum, const int nall,
double **host_x, int *host_type, int *ilist, int *numj,
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
@@ -66,7 +66,7 @@ PairGaussGPU::PairGaussGPU(LAMMPS *lmp) : PairGauss(lmp), gpu_mode(GPU_FORCE)
{
respa_enable = 0;
cpu_time = 0.0;
- GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
+ GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
@@ -84,10 +84,10 @@ void PairGaussGPU::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
-
+
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
-
+
bool success = true;
int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
@@ -96,7 +96,7 @@ void PairGaussGPU::compute(int eflag, int vflag)
atom->x, atom->type, domain->sublo,
domain->subhi, atom->tag, atom->nspecial,
atom->special, eflag, vflag, eflag_atom,
- vflag_atom, host_start,
+ vflag_atom, host_start,
&ilist, &numneigh, cpu_time, success);
} else {
inum = list->inum;
@@ -123,7 +123,7 @@ void PairGaussGPU::compute(int eflag, int vflag)
void PairGaussGPU::init_style()
{
- if (force->newton_pair)
+ if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with gauss/gpu pair style");
// Repeat cutsq calculation because done after call to init_style
@@ -164,7 +164,7 @@ void PairGaussGPU::init_style()
void PairGaussGPU::reinit()
{
Pair::reinit();
-
+
gauss_gpu_reinit(atom->ntypes+1, cutsq, a, b, offset);
}
@@ -178,7 +178,7 @@ double PairGaussGPU::memory_usage()
/* ---------------------------------------------------------------------- */
-void PairGaussGPU::cpu_compute(int start, int inum, int eflag, int vflag,
+void PairGaussGPU::cpu_compute(int start, int inum, int eflag, int vflag,
int *ilist, int *numneigh, int **firstneigh) {
int i,j,ii,jj,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
@@ -214,8 +214,8 @@ void PairGaussGPU::cpu_compute(int start, int inum, int eflag, int vflag,
if (rsq < cutsq[itype][jtype]) {
r2inv = 1.0/rsq;
- forcelj = - 2.0*a[itype][jtype]*b[itype][jtype] * rsq *
- exp(-b[itype][jtype]*rsq);
+ forcelj = - 2.0*a[itype][jtype]*b[itype][jtype] * rsq *
+ exp(-b[itype][jtype]*rsq);
fpair = factor_lj*forcelj*r2inv;
f[i][0] += delx*fpair;
diff --git a/src/GPU/pair_gauss_gpu.h b/src/GPU/pair_gauss_gpu.h
index d4ffae23cb..bda2e2644a 100644
--- a/src/GPU/pair_gauss_gpu.h
+++ b/src/GPU/pair_gauss_gpu.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/GPU/pair_gayberne_gpu.cpp b/src/GPU/pair_gayberne_gpu.cpp
index 75191f9313..aae8fb2b71 100644
--- a/src/GPU/pair_gayberne_gpu.cpp
+++ b/src/GPU/pair_gayberne_gpu.cpp
@@ -15,9 +15,9 @@
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
#include "pair_gayberne_gpu.h"
#include "math_extra.h"
#include "atom.h"
@@ -34,7 +34,7 @@
#include "universe.h"
#include "domain.h"
#include "update.h"
-#include "string.h"
+#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
diff --git a/src/GPU/pair_lj96_cut_gpu.cpp b/src/GPU/pair_lj96_cut_gpu.cpp
index 7dacbf68bc..813daa4da2 100644
--- a/src/GPU/pair_lj96_cut_gpu.cpp
+++ b/src/GPU/pair_lj96_cut_gpu.cpp
@@ -15,9 +15,9 @@
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
#include "pair_lj96_cut_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +32,7 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include "string.h"
+#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
diff --git a/src/GPU/pair_lj_charmm_coul_long_gpu.cpp b/src/GPU/pair_lj_charmm_coul_long_gpu.cpp
index df88bd0777..b951567f45 100644
--- a/src/GPU/pair_lj_charmm_coul_long_gpu.cpp
+++ b/src/GPU/pair_lj_charmm_coul_long_gpu.cpp
@@ -15,9 +15,9 @@
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
#include "pair_lj_charmm_coul_long_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +32,7 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include "string.h"
+#include <string.h>
#include "kspace.h"
#include "gpu_extra.h"
diff --git a/src/GPU/pair_lj_class2_coul_long_gpu.cpp b/src/GPU/pair_lj_class2_coul_long_gpu.cpp
index b675f87d50..f7c874cb65 100644
--- a/src/GPU/pair_lj_class2_coul_long_gpu.cpp
+++ b/src/GPU/pair_lj_class2_coul_long_gpu.cpp
@@ -15,9 +15,9 @@
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
#include "pair_lj_class2_coul_long_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +32,7 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include "string.h"
+#include <string.h>
#include "kspace.h"
#include "gpu_extra.h"
diff --git a/src/GPU/pair_lj_class2_gpu.cpp b/src/GPU/pair_lj_class2_gpu.cpp
index b34fc60700..cc6866db1c 100644
--- a/src/GPU/pair_lj_class2_gpu.cpp
+++ b/src/GPU/pair_lj_class2_gpu.cpp
@@ -15,9 +15,9 @@
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
#include "pair_lj_class2_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +32,7 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include "string.h"
+#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
diff --git a/src/GPU/pair_lj_cubic_gpu.cpp b/src/GPU/pair_lj_cubic_gpu.cpp
index 904c7f4ca9..516ac7d154 100644
--- a/src/GPU/pair_lj_cubic_gpu.cpp
+++ b/src/GPU/pair_lj_cubic_gpu.cpp
@@ -15,9 +15,9 @@
Contributing author: Trung Dac Nguyen (ndactrung@gmail.com)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
#include "pair_lj_cubic_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +32,7 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include "string.h"
+#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
@@ -40,9 +40,9 @@ using namespace PairLJCubicConstants;
// External functions from cuda library for atom decomposition
-int ljcb_gpu_init(const int ntypes, double **cutsq, double **cut_inner_sq,
- double **cut_inner, double **sigma, double **epsilon,
- double **host_lj1, double **host_lj2, double **host_lj3,
+int ljcb_gpu_init(const int ntypes, double **cutsq, double **cut_inner_sq,
+ double **cut_inner, double **sigma, double **epsilon,
+ double **host_lj1, double **host_lj2, double **host_lj3,
double **host_lj4, double *special_lj, const int nlocal,
const int nall, const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen);
@@ -64,7 +64,7 @@ double ljcb_gpu_bytes();
/* ---------------------------------------------------------------------- */
-PairLJCubicGPU::PairLJCubicGPU(LAMMPS *lmp) : PairLJCubic(lmp),
+PairLJCubicGPU::PairLJCubicGPU(LAMMPS *lmp) : PairLJCubic(lmp),
gpu_mode(GPU_FORCE)
{
respa_enable = 0;
@@ -91,7 +91,7 @@ void PairLJCubicGPU::compute(int eflag, int vflag)
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
-
+
bool success = true;
int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
@@ -151,7 +151,7 @@ void PairLJCubicGPU::init_style()
if (atom->molecular)
maxspecial=atom->maxspecial;
int success = ljcb_gpu_init(atom->ntypes+1, cutsq, cut_inner_sq,
- cut_inner, sigma, epsilon, lj1, lj2,
+ cut_inner, sigma, epsilon, lj1, lj2,
lj3, lj4, force->special_lj, atom->nlocal,
atom->nlocal+atom->nghost, 300, maxspecial,
cell_size, gpu_mode, screen);
diff --git a/src/GPU/pair_lj_cut_coul_cut_gpu.cpp b/src/GPU/pair_lj_cut_coul_cut_gpu.cpp
index 9a964e3668..840c07680f 100644
--- a/src/GPU/pair_lj_cut_coul_cut_gpu.cpp
+++ b/src/GPU/pair_lj_cut_coul_cut_gpu.cpp
@@ -15,9 +15,9 @@
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
#include "pair_lj_cut_coul_cut_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +32,7 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include "string.h"
+#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
diff --git a/src/GPU/pair_lj_cut_coul_debye_gpu.cpp b/src/GPU/pair_lj_cut_coul_debye_gpu.cpp
index 724d0d9d03..39108d8558 100644
--- a/src/GPU/pair_lj_cut_coul_debye_gpu.cpp
+++ b/src/GPU/pair_lj_cut_coul_debye_gpu.cpp
@@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
-
+
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
-
+
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@@ -15,9 +15,9 @@
Contributing author: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
#include "pair_lj_cut_coul_debye_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +32,7 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include "string.h"
+#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
@@ -40,23 +40,23 @@ using namespace LAMMPS_NS;
// External functions from cuda library for atom decomposition
int ljcd_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
- double **host_lj2, double **host_lj3, double **host_lj4,
- double **offset, double *special_lj, const int nlocal,
+ double **host_lj2, double **host_lj3, double **host_lj4,
+ double **offset, double *special_lj, const int nlocal,
const int nall, const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen,
double **host_cut_ljsq, double **host_cut_coulsq,
double *host_special_coul, const double qqrd2e,
const double kappa);
void ljcd_gpu_clear();
-int ** ljcd_gpu_compute_n(const int ago, const int inum, const int nall,
- double **host_x, int *host_type,
+int ** ljcd_gpu_compute_n(const int ago, const int inum, const int nall,
+ double **host_x, int *host_type,
double *sublo, double *subhi, tagint *tag, int **nspecial,
tagint **special, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
int **ilist, int **jnum, const double cpu_time,
bool &success, double *host_q, double *boxlo,
double *prd);
-void ljcd_gpu_compute(const int ago, const int inum, const int nall,
+void ljcd_gpu_compute(const int ago, const int inum, const int nall,
double **host_x, int *host_type,
int *ilist, int *numj, int **firstneigh,
const bool eflag, const bool vflag, const bool eatom,
@@ -67,13 +67,13 @@ double ljcd_gpu_bytes();
/* ---------------------------------------------------------------------- */
-PairLJCutCoulDebyeGPU::PairLJCutCoulDebyeGPU(LAMMPS *lmp) :
+PairLJCutCoulDebyeGPU::PairLJCutCoulDebyeGPU(LAMMPS *lmp) :
PairLJCutCoulDebye(lmp), gpu_mode(GPU_FORCE)
{
respa_enable = 0;
reinitflag = 0;
cpu_time = 0.0;
- GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
+ GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
@@ -91,12 +91,12 @@ void PairLJCutCoulDebyeGPU::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
-
+
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
-
+
bool success = true;
- int *ilist, *numneigh, **firstneigh;
+ int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
inum = atom->nlocal;
firstneigh = ljcd_gpu_compute_n(neighbor->ago, inum, nall, atom->x,
@@ -104,7 +104,7 @@ void PairLJCutCoulDebyeGPU::compute(int eflag, int vflag)
atom->tag, atom->nspecial, atom->special,
eflag, vflag, eflag_atom, vflag_atom,
host_start, &ilist, &numneigh, cpu_time,
- success, atom->q, domain->boxlo,
+ success, atom->q, domain->boxlo,
domain->prd);
} else {
inum = list->inum;
@@ -135,7 +135,7 @@ void PairLJCutCoulDebyeGPU::init_style()
if (!atom->q_flag)
error->all(FLERR,"Pair style lj/cut/coul/debye/gpu requires atom attribute q");
- if (force->newton_pair)
+ if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with lj/cut/coul/debye/gpu pair style");
// Repeat cutsq calculation because done after call to init_style
@@ -161,8 +161,8 @@ void PairLJCutCoulDebyeGPU::init_style()
int success = ljcd_gpu_init(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4,
offset, force->special_lj, atom->nlocal,
atom->nlocal+atom->nghost, 300, maxspecial,
- cell_size, gpu_mode, screen, cut_ljsq,
- cut_coulsq, force->special_coul,
+ cell_size, gpu_mode, screen, cut_ljsq,
+ cut_coulsq, force->special_coul,
force->qqrd2e, kappa);
GPU_EXTRA::check_flag(success,error,world);
@@ -183,7 +183,7 @@ double PairLJCutCoulDebyeGPU::memory_usage()
/* ---------------------------------------------------------------------- */
-void PairLJCutCoulDebyeGPU::cpu_compute(int start, int inum, int eflag,
+void PairLJCutCoulDebyeGPU::cpu_compute(int start, int inum, int eflag,
int vflag, int *ilist,
int *numneigh, int **firstneigh)
{
diff --git a/src/GPU/pair_lj_cut_coul_debye_gpu.h b/src/GPU/pair_lj_cut_coul_debye_gpu.h
index 2c6f2bbbf3..6b0f2ed8d7 100644
--- a/src/GPU/pair_lj_cut_coul_debye_gpu.h
+++ b/src/GPU/pair_lj_cut_coul_debye_gpu.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp b/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp
index b1d48bd968..efca1a2c51 100644
--- a/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp
+++ b/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp
@@ -15,9 +15,9 @@
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
#include "pair_lj_cut_coul_dsf_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +32,7 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include "string.h"
+#include <string.h>
#include "gpu_extra.h"
#define MY_PIS 1.77245385090551602729
@@ -54,8 +54,8 @@ int ljd_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
const int nall, const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen,
double **host_cut_ljsq, const double host_cut_coulsq,
- double *host_special_coul, const double qqrd2e,
- const double e_shift, const double f_shift,
+ double *host_special_coul, const double qqrd2e,
+ const double e_shift, const double f_shift,
const double alpha);
void ljd_gpu_clear();
int ** ljd_gpu_compute_n(const int ago, const int inum,
@@ -165,10 +165,10 @@ void PairLJCutCoulDSFGPU::init_style()
double cell_size = sqrt(maxcut) + neighbor->skin;
cut_coulsq = cut_coul * cut_coul;
- double erfcc = erfc(alpha*cut_coul);
+ double erfcc = erfc(alpha*cut_coul);
double erfcd = exp(-alpha*alpha*cut_coul*cut_coul);
- f_shift = -(erfcc/cut_coulsq + 2.0/MY_PIS*alpha*erfcd/cut_coul);
- e_shift = erfcc/cut_coul - f_shift*cut_coul;
+ f_shift = -(erfcc/cut_coulsq + 2.0/MY_PIS*alpha*erfcd/cut_coul);
+ e_shift = erfcc/cut_coul - f_shift*cut_coul;
int maxspecial=0;
if (atom->molecular)
@@ -262,7 +262,7 @@ void PairLJCutCoulDSFGPU::cpu_compute(int start, int inum, int eflag, int vflag,
erfcd = exp(-alpha*alpha*r*r);
t = 1.0 / (1.0 + EWALD_P*alpha*r);
erfcc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * erfcd;
- forcecoul = prefactor * (erfcc/r + 2.0*alpha/MY_PIS * erfcd +
+ forcecoul = prefactor * (erfcc/r + 2.0*alpha/MY_PIS * erfcd +
r*f_shift) * r;
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
}
@@ -278,7 +278,7 @@ void PairLJCutCoulDSFGPU::cpu_compute(int start, int inum, int eflag, int vflag,
offset[itype][jtype];
evdwl *= factor_lj;
} else evdwl = 0.0;
-
+
if (rsq < cut_coulsq) {
ecoul = prefactor * (erfcc - r*e_shift - rsq*f_shift);
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
diff --git a/src/GPU/pair_lj_cut_coul_long_gpu.cpp b/src/GPU/pair_lj_cut_coul_long_gpu.cpp
index d5025ffda9..8ea7a7f07b 100644
--- a/src/GPU/pair_lj_cut_coul_long_gpu.cpp
+++ b/src/GPU/pair_lj_cut_coul_long_gpu.cpp
@@ -15,9 +15,9 @@
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
#include "pair_lj_cut_coul_long_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +32,7 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include "string.h"
+#include <string.h>
#include "kspace.h"
#include "gpu_extra.h"
@@ -200,7 +200,7 @@ void PairLJCutCoulLongGPU::init_style()
void PairLJCutCoulLongGPU::reinit()
{
Pair::reinit();
-
+
ljcl_gpu_reinit(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4, offset, cut_ljsq);
}
diff --git a/src/GPU/pair_lj_cut_coul_msm_gpu.cpp b/src/GPU/pair_lj_cut_coul_msm_gpu.cpp
index 4972ce57b1..7d8be01e81 100644
--- a/src/GPU/pair_lj_cut_coul_msm_gpu.cpp
+++ b/src/GPU/pair_lj_cut_coul_msm_gpu.cpp
@@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
-
+
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
-
+
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@@ -15,9 +15,9 @@
Contributing author: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
#include "pair_lj_cut_coul_msm_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -33,7 +33,7 @@
#include "update.h"
#include "domain.h"
#include "kspace.h"
-#include "string.h"
+#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
@@ -56,7 +56,7 @@ int ** ljcm_gpu_compute_n(const int ago, const int inum,
const bool eatom, const bool vatom, int &host_start,
int **ilist, int **jnum, const double cpu_time,
bool &success, double *host_q, double *boxlo, double *prd);
-void ljcm_gpu_compute(const int ago, const int inum, const int nall,
+void ljcm_gpu_compute(const int ago, const int inum, const int nall,
double **host_x, int *host_type, int *ilist, int *numj,
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
@@ -72,7 +72,7 @@ PairLJCutCoulMSMGPU::PairLJCutCoulMSMGPU(LAMMPS *lmp) :
respa_enable = 0;
reinitflag = 0;
cpu_time = 0.0;
- GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
+ GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
@@ -90,10 +90,10 @@ void PairLJCutCoulMSMGPU::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
-
+
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
-
+
bool success = true;
int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
@@ -132,8 +132,8 @@ void PairLJCutCoulMSMGPU::compute(int eflag, int vflag)
void PairLJCutCoulMSMGPU::init_style()
{
cut_respa = NULL;
-
- if (force->newton_pair)
+
+ if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with lj/cut/coul/msm/gpu pair style");
if (force->kspace->scalar_pressure_flag)
@@ -161,7 +161,7 @@ void PairLJCutCoulMSMGPU::init_style()
// setup force tables
if (ncoultablebits) init_tables(cut_coul,cut_respa);
-
+
int maxspecial=0;
if (atom->molecular)
maxspecial=atom->maxspecial;
@@ -192,7 +192,7 @@ double PairLJCutCoulMSMGPU::memory_usage()
/* ---------------------------------------------------------------------- */
-void PairLJCutCoulMSMGPU::cpu_compute(int start, int inum, int eflag, int vflag,
+void PairLJCutCoulMSMGPU::cpu_compute(int start, int inum, int eflag, int vflag,
int *ilist, int *numneigh, int **firstneigh) {
int i,j,ii,jj,jnum,itype,jtype,itable;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
@@ -209,7 +209,7 @@ void PairLJCutCoulMSMGPU::cpu_compute(int start, int inum, int eflag, int vflag,
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
double qqrd2e = force->qqrd2e;
-
+
// loop over neighbors of my atoms
for (ii = start; ii < inum; ii++) {
@@ -289,7 +289,7 @@ void PairLJCutCoulMSMGPU::cpu_compute(int start, int inum, int eflag, int vflag,
evdwl *= factor_lj;
} else evdwl = 0.0;
}
-
+
if (evflag) ev_tally_full(i,evdwl,ecoul,fpair,delx,dely,delz);
}
}
diff --git a/src/GPU/pair_lj_cut_coul_msm_gpu.h b/src/GPU/pair_lj_cut_coul_msm_gpu.h
index 88360e30d2..ca18ca89e4 100644
--- a/src/GPU/pair_lj_cut_coul_msm_gpu.h
+++ b/src/GPU/pair_lj_cut_coul_msm_gpu.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp b/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp
index 348fe44b24..3b5f0c1283 100755
--- a/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp
+++ b/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp
@@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
-
+
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
-
+
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@@ -15,9 +15,9 @@
Contributing author: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
#include "pair_lj_cut_dipole_cut_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +32,7 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include "string.h"
+#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
@@ -40,40 +40,40 @@ using namespace LAMMPS_NS;
// External functions from cuda library for atom decomposition
int dpl_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
- double **host_lj2, double **host_lj3, double **host_lj4,
- double **offset, double *special_lj, const int nlocal,
+ double **host_lj2, double **host_lj3, double **host_lj4,
+ double **offset, double *special_lj, const int nlocal,
const int nall, const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen,
double **host_cut_ljsq, double **host_cut_coulsq,
double *host_special_coul, const double qqrd2e);
void dpl_gpu_clear();
int ** dpl_gpu_compute_n(const int ago, const int inum,
- const int nall, double **host_x, int *host_type,
- double *sublo, double *subhi, tagint *tag,
- int **nspecial, tagint **special, const bool eflag,
- const bool vflag, const bool eatom, const bool vatom,
- int &host_start, int **ilist, int **jnum,
- const double cpu_time, bool &success,
- double *host_q, double **host_mu,
+ const int nall, double **host_x, int *host_type,
+ double *sublo, double *subhi, tagint *tag,
+ int **nspecial, tagint **special, const bool eflag,
+ const bool vflag, const bool eatom, const bool vatom,
+ int &host_start, int **ilist, int **jnum,
+ const double cpu_time, bool &success,
+ double *host_q, double **host_mu,
double *boxlo, double *prd);
void dpl_gpu_compute(const int ago, const int inum,
const int nall, double **host_x, int *host_type,
int *ilist, int *numj, int **firstneigh,
const bool eflag, const bool vflag, const bool eatom,
const bool vatom, int &host_start, const double cpu_time,
- bool &success, double *host_q, double **host_mu,
+ bool &success, double *host_q, double **host_mu,
const int nlocal, double *boxlo, double *prd);
double dpl_gpu_bytes();
/* ---------------------------------------------------------------------- */
-PairLJCutDipoleCutGPU::PairLJCutDipoleCutGPU(LAMMPS *lmp) : PairLJCutDipoleCut(lmp),
+PairLJCutDipoleCutGPU::PairLJCutDipoleCutGPU(LAMMPS *lmp) : PairLJCutDipoleCut(lmp),
gpu_mode(GPU_FORCE)
{
respa_enable = 0;
reinitflag = 0;
cpu_time = 0.0;
- GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
+ GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
@@ -91,12 +91,12 @@ void PairLJCutDipoleCutGPU::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
-
+
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
-
+
bool success = true;
- int *ilist, *numneigh, **firstneigh;
+ int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
inum = atom->nlocal;
firstneigh = dpl_gpu_compute_n(neighbor->ago, inum, nall, atom->x,
@@ -104,7 +104,7 @@ void PairLJCutDipoleCutGPU::compute(int eflag, int vflag)
atom->tag, atom->nspecial, atom->special,
eflag, vflag, eflag_atom, vflag_atom,
host_start, &ilist, &numneigh, cpu_time,
- success, atom->q, atom->mu, domain->boxlo,
+ success, atom->q, atom->mu, domain->boxlo,
domain->prd);
} else {
inum = list->inum;
@@ -134,8 +134,8 @@ void PairLJCutDipoleCutGPU::init_style()
{
if (!atom->q_flag || !atom->mu_flag || !atom->torque_flag)
error->all(FLERR,"Pair dipole/cut/gpu requires atom attributes q, mu, torque");
-
- if (force->newton_pair)
+
+ if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with dipole/cut/gpu pair style");
if (strcmp(update->unit_style,"electron") == 0)
@@ -186,7 +186,7 @@ double PairLJCutDipoleCutGPU::memory_usage()
/* ---------------------------------------------------------------------- */
void PairLJCutDipoleCutGPU::cpu_compute(int start, int inum, int eflag, int vflag,
- int *ilist, int *numneigh,
+ int *ilist, int *numneigh,
int **firstneigh)
{
int i,j,ii,jj,jnum,itype,jtype;
@@ -247,7 +247,7 @@ void PairLJCutDipoleCutGPU::cpu_compute(int start, int inum, int eflag, int vfla
forcecoulx = forcecouly = forcecoulz = 0.0;
tixcoul = tiycoul = tizcoul = 0.0;
tjxcoul = tjycoul = tjzcoul = 0.0;
-
+
if (rsq < cut_coulsq[itype][jtype]) {
if (qtmp != 0.0 && q[j] != 0.0) {
@@ -259,7 +259,7 @@ void PairLJCutDipoleCutGPU::cpu_compute(int start, int inum, int eflag, int vfla
forcecoulz += pre1*delz;
}
- if (mu[i][3] > 0.0 && mu[j][3] > 0.0) {
+ if (mu[i][3] > 0.0 && mu[j][3] > 0.0) {
r3inv = r2inv*rinv;
r5inv = r3inv*r2inv;
r7inv = r5inv*r2inv;
@@ -276,7 +276,7 @@ void PairLJCutDipoleCutGPU::cpu_compute(int start, int inum, int eflag, int vfla
forcecoulx += pre1*delx + pre2*mu[i][0] + pre3*mu[j][0];
forcecouly += pre1*dely + pre2*mu[i][1] + pre3*mu[j][1];
forcecoulz += pre1*delz + pre2*mu[i][2] + pre3*mu[j][2];
-
+
crossx = pre4 * (mu[i][1]*mu[j][2] - mu[i][2]*mu[j][1]);
crossy = pre4 * (mu[i][2]*mu[j][0] - mu[i][0]*mu[j][2]);
crossz = pre4 * (mu[i][0]*mu[j][1] - mu[i][1]*mu[j][0]);
@@ -289,7 +289,7 @@ void PairLJCutDipoleCutGPU::cpu_compute(int start, int inum, int eflag, int vfla
tjzcoul += -crossz + pre3 * (mu[j][0]*dely - mu[j][1]*delx);
}
- if (mu[i][3] > 0.0 && q[j] != 0.0) {
+ if (mu[i][3] > 0.0 && q[j] != 0.0) {
r3inv = r2inv*rinv;
r5inv = r3inv*r2inv;
pidotr = mu[i][0]*delx + mu[i][1]*dely + mu[i][2]*delz;
@@ -304,7 +304,7 @@ void PairLJCutDipoleCutGPU::cpu_compute(int start, int inum, int eflag, int vfla
tizcoul += pre2 * (mu[i][0]*dely - mu[i][1]*delx);
}
- if (mu[j][3] > 0.0 && qtmp != 0.0) {
+ if (mu[j][3] > 0.0 && qtmp != 0.0) {
r3inv = r2inv*rinv;
r5inv = r3inv*r2inv;
pjdotr = mu[j][0]*delx + mu[j][1]*dely + mu[j][2]*delz;
@@ -327,7 +327,7 @@ void PairLJCutDipoleCutGPU::cpu_compute(int start, int inum, int eflag, int vfla
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
forcelj *= factor_lj * r2inv;
} else forcelj = 0.0;
-
+
// total force
fq = factor_coul*qqrd2e;
@@ -349,7 +349,7 @@ void PairLJCutDipoleCutGPU::cpu_compute(int start, int inum, int eflag, int vfla
ecoul = qtmp*q[j]*rinv;
if (mu[i][3] > 0.0 && mu[j][3] > 0.0)
ecoul += r3inv*pdotp - 3.0*r5inv*pidotr*pjdotr;
- if (mu[i][3] > 0.0 && q[j] != 0.0)
+ if (mu[i][3] > 0.0 && q[j] != 0.0)
ecoul += -q[j]*r3inv*pidotr;
if (mu[j][3] > 0.0 && qtmp != 0.0)
ecoul += qtmp*r3inv*pjdotr;
diff --git a/src/GPU/pair_lj_cut_dipole_cut_gpu.h b/src/GPU/pair_lj_cut_dipole_cut_gpu.h
index 687c158217..b665137955 100755
--- a/src/GPU/pair_lj_cut_dipole_cut_gpu.h
+++ b/src/GPU/pair_lj_cut_dipole_cut_gpu.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/GPU/pair_lj_cut_gpu.cpp b/src/GPU/pair_lj_cut_gpu.cpp
index 39c95df5b6..ef97269772 100644
--- a/src/GPU/pair_lj_cut_gpu.cpp
+++ b/src/GPU/pair_lj_cut_gpu.cpp
@@ -15,9 +15,9 @@
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
#include "pair_lj_cut_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +32,7 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include "string.h"
+#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
@@ -91,7 +91,7 @@ void PairLJCutGPU::compute(int eflag, int vflag)
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
-
+
bool success = true;
int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
@@ -170,7 +170,7 @@ void PairLJCutGPU::init_style()
void PairLJCutGPU::reinit()
{
Pair::reinit();
-
+
ljl_gpu_reinit(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4, offset);
}
diff --git a/src/GPU/pair_lj_expand_gpu.cpp b/src/GPU/pair_lj_expand_gpu.cpp
index 1bafd362bd..33bbf60600 100644
--- a/src/GPU/pair_lj_expand_gpu.cpp
+++ b/src/GPU/pair_lj_expand_gpu.cpp
@@ -15,9 +15,9 @@
Contributing author: Inderaj Bains (NVIDIA), ibains@nvidia.com
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
#include "pair_lj_expand_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +32,7 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include "string.h"
+#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
@@ -167,7 +167,7 @@ void PairLJExpandGPU::init_style()
void PairLJExpandGPU::reinit()
{
Pair::reinit();
-
+
lje_gpu_reinit(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4, offset, shift);
}
diff --git a/src/GPU/pair_lj_gromacs_gpu.cpp b/src/GPU/pair_lj_gromacs_gpu.cpp
index ca71a49314..5833b8198f 100644
--- a/src/GPU/pair_lj_gromacs_gpu.cpp
+++ b/src/GPU/pair_lj_gromacs_gpu.cpp
@@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
-
+
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
-
+
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@@ -15,9 +15,9 @@
Contributing author: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
#include "pair_lj_gromacs_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +32,7 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include "string.h"
+#include <string.h>
#include "kspace.h"
#include "gpu_extra.h"
@@ -46,7 +46,7 @@ int ljgrm_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
const int nall, const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen,
double **host_ljsw1, double **host_ljsw2, double **host_ljsw3,
- double **host_ljsw4, double **host_ljsw5,
+ double **host_ljsw4, double **host_ljsw5,
double **cut_inner, double **cut_innersq);
void ljgrm_gpu_clear();
int ** ljgrm_gpu_compute_n(const int ago, const int inum_full,
@@ -65,13 +65,13 @@ double ljgrm_gpu_bytes();
/* ---------------------------------------------------------------------- */
-PairLJGromacsGPU::PairLJGromacsGPU(LAMMPS *lmp) :
+PairLJGromacsGPU::PairLJGromacsGPU(LAMMPS *lmp) :
PairLJGromacs(lmp), gpu_mode(GPU_FORCE)
{
respa_enable = 0;
reinitflag = 0;
cpu_time = 0.0;
- GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
+ GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
@@ -89,12 +89,12 @@ void PairLJGromacsGPU::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
-
+
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
-
+
bool success = true;
- int *ilist, *numneigh, **firstneigh;
+ int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
inum = atom->nlocal;
firstneigh = ljgrm_gpu_compute_n(neighbor->ago, inum, nall,
@@ -128,7 +128,7 @@ void PairLJGromacsGPU::compute(int eflag, int vflag)
void PairLJGromacsGPU::init_style()
{
- if (force->newton_pair)
+ if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with lj/gromacs/gpu pair style");
// Repeat cutsq calculation because done after call to init_style
@@ -155,7 +155,7 @@ void PairLJGromacsGPU::init_style()
int success = ljgrm_gpu_init(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4,
force->special_lj, atom->nlocal,
atom->nlocal+atom->nghost, 300, maxspecial,
- cell_size, gpu_mode, screen, ljsw1, ljsw2,
+ cell_size, gpu_mode, screen, ljsw1, ljsw2,
ljsw3, ljsw4, ljsw5, cut_inner, cut_inner_sq);
GPU_EXTRA::check_flag(success,error,world);
@@ -218,7 +218,7 @@ void PairLJGromacsGPU::cpu_compute(int start, int inum, int eflag,
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
if (rsq > cut_inner_sq[itype][jtype]) {
- r = sqrt(rsq);
+ r = sqrt(rsq);
t = r - cut_inner[itype][jtype];
fswitch = r*t*t*(ljsw1[itype][jtype] + ljsw2[itype][jtype]*t);
forcelj += fswitch;
diff --git a/src/GPU/pair_lj_gromacs_gpu.h b/src/GPU/pair_lj_gromacs_gpu.h
index f27d521b29..4f00662021 100644
--- a/src/GPU/pair_lj_gromacs_gpu.h
+++ b/src/GPU/pair_lj_gromacs_gpu.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/GPU/pair_lj_sdk_coul_long_gpu.cpp b/src/GPU/pair_lj_sdk_coul_long_gpu.cpp
index 426b5dfae9..0b8d0f3b31 100644
--- a/src/GPU/pair_lj_sdk_coul_long_gpu.cpp
+++ b/src/GPU/pair_lj_sdk_coul_long_gpu.cpp
@@ -15,9 +15,9 @@
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
#include "pair_lj_sdk_coul_long_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +32,7 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include "string.h"
+#include <string.h>
#include "kspace.h"
#include "gpu_extra.h"
diff --git a/src/GPU/pair_lj_sdk_gpu.cpp b/src/GPU/pair_lj_sdk_gpu.cpp
index e19860d607..e7e9b690f3 100644
--- a/src/GPU/pair_lj_sdk_gpu.cpp
+++ b/src/GPU/pair_lj_sdk_gpu.cpp
@@ -15,9 +15,9 @@
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
#include "pair_lj_sdk_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +32,7 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include "string.h"
+#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
diff --git a/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp b/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp
index 81ec6c1d02..5b22bebf7f 100755
--- a/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp
+++ b/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp
@@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
-
+
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
-
+
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@@ -15,9 +15,9 @@
Contributing author: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
#include "pair_lj_sf_dipole_sf_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +32,7 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include "string.h"
+#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
@@ -40,20 +40,20 @@ using namespace LAMMPS_NS;
// External functions from cuda library for atom decomposition
int dplsf_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
- double **host_lj2, double **host_lj3, double **host_lj4,
- double *special_lj, const int nlocal,
+ double **host_lj2, double **host_lj3, double **host_lj4,
+ double *special_lj, const int nlocal,
const int nall, const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen,
double **host_cut_ljsq, double **host_cut_coulsq,
double *host_special_coul, const double qqrd2e);
void dplsf_gpu_clear();
int ** dplsf_gpu_compute_n(const int ago, const int inum,
- const int nall, double **host_x, int *host_type,
+ const int nall, double **host_x, int *host_type,
double *sublo, double *subhi, tagint *tag, int **nspecial,
tagint **special, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
int **ilist, int **jnum, const double cpu_time,
- bool &success, double *host_q, double **host_mu,
+ bool &success, double *host_q, double **host_mu,
double *boxlo, double *prd);
void dplsf_gpu_compute(const int ago, const int inum,
const int nall, double **host_x, int *host_type,
@@ -66,13 +66,13 @@ double dplsf_gpu_bytes();
/* ---------------------------------------------------------------------- */
-PairLJSFDipoleSFGPU::PairLJSFDipoleSFGPU(LAMMPS *lmp) : PairLJSFDipoleSF(lmp),
+PairLJSFDipoleSFGPU::PairLJSFDipoleSFGPU(LAMMPS *lmp) : PairLJSFDipoleSF(lmp),
gpu_mode(GPU_FORCE)
{
respa_enable = 0;
reinitflag = 0;
cpu_time = 0.0;
- GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
+ GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
@@ -90,12 +90,12 @@ void PairLJSFDipoleSFGPU::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
-
+
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
-
+
bool success = true;
- int *ilist, *numneigh, **firstneigh;
+ int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
inum = atom->nlocal;
firstneigh = dplsf_gpu_compute_n(neighbor->ago, inum, nall, atom->x,
@@ -103,7 +103,7 @@ void PairLJSFDipoleSFGPU::compute(int eflag, int vflag)
atom->tag, atom->nspecial, atom->special,
eflag, vflag, eflag_atom, vflag_atom,
host_start, &ilist, &numneigh, cpu_time,
- success, atom->q, atom->mu, domain->boxlo,
+ success, atom->q, atom->mu, domain->boxlo,
domain->prd);
} else {
inum = list->inum;
@@ -133,8 +133,8 @@ void PairLJSFDipoleSFGPU::init_style()
{
if (!atom->q_flag || !atom->mu_flag || !atom->torque_flag)
error->all(FLERR,"Pair dipole/sf/gpu requires atom attributes q, mu, torque");
-
- if (force->newton_pair)
+
+ if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with dipole/sf/gpu pair style");
if (strcmp(update->unit_style,"electron") == 0)
@@ -261,7 +261,7 @@ void PairLJSFDipoleSFGPU::cpu_compute(int start, int inum, int eflag, int vflag,
forcecoulz += pre1*delz;
}
- if (mu[i][3] > 0.0 && mu[j][3] > 0.0) {
+ if (mu[i][3] > 0.0 && mu[j][3] > 0.0) {
r3inv = r2inv*rinv;
r5inv = r3inv*r2inv;
rcutcoul2inv=1.0/cut_coulsq[itype][jtype];
@@ -269,7 +269,7 @@ void PairLJSFDipoleSFGPU::cpu_compute(int start, int inum, int eflag, int vflag,
pdotp = mu[i][0]*mu[j][0] + mu[i][1]*mu[j][1] + mu[i][2]*mu[j][2];
pidotr = mu[i][0]*delx + mu[i][1]*dely + mu[i][2]*delz;
pjdotr = mu[j][0]*delx + mu[j][1]*dely + mu[j][2]*delz;
-
+
afac = 1.0 - rsq*rsq * rcutcoul2inv*rcutcoul2inv;
pre1 = afac * ( pdotp - 3.0 * r2inv * pidotr * pjdotr );
aforcecoulx = pre1*delx;
@@ -282,15 +282,15 @@ void PairLJSFDipoleSFGPU::cpu_compute(int start, int inum, int eflag, int vflag,
bforcecoulx = bfac * (pjdotr*mu[i][0]+pidotr*mu[j][0]-presf*delx);
bforcecouly = bfac * (pjdotr*mu[i][1]+pidotr*mu[j][1]-presf*dely);
bforcecoulz = bfac * (pjdotr*mu[i][2]+pidotr*mu[j][2]-presf*delz);
-
+
forcecoulx += 3.0 * r5inv * ( aforcecoulx + bforcecoulx );
forcecouly += 3.0 * r5inv * ( aforcecouly + bforcecouly );
forcecoulz += 3.0 * r5inv * ( aforcecoulz + bforcecoulz );
-
+
pre2 = 3.0 * bfac * r5inv * pjdotr;
pre3 = 3.0 * bfac * r5inv * pidotr;
pre4 = -bfac * r3inv;
-
+
crossx = pre4 * (mu[i][1]*mu[j][2] - mu[i][2]*mu[j][1]);
crossy = pre4 * (mu[i][2]*mu[j][0] - mu[i][0]*mu[j][2]);
crossz = pre4 * (mu[i][0]*mu[j][1] - mu[i][1]*mu[j][0]);
@@ -303,13 +303,13 @@ void PairLJSFDipoleSFGPU::cpu_compute(int start, int inum, int eflag, int vflag,
tjzcoul += -crossz + pre3 * (mu[j][0]*dely - mu[j][1]*delx);
}
- if (mu[i][3] > 0.0 && q[j] != 0.0) {
+ if (mu[i][3] > 0.0 && q[j] != 0.0) {
r3inv = r2inv*rinv;
r5inv = r3inv*r2inv;
- pidotr = mu[i][0]*delx + mu[i][1]*dely + mu[i][2]*delz;
+ pidotr = mu[i][0]*delx + mu[i][1]*dely + mu[i][2]*delz;
rcutcoul2inv=1.0/cut_coulsq[itype][jtype];
pre1 = 3.0 * q[j] * r5inv * pidotr * (1-rsq*rcutcoul2inv);
- pqfac = 1.0 - 3.0*rsq*rcutcoul2inv +
+ pqfac = 1.0 - 3.0*rsq*rcutcoul2inv +
2.0*rsq*sqrt(rsq)*rcutcoul2inv*sqrt(rcutcoul2inv);
pre2 = q[j] * r3inv * pqfac;
@@ -321,7 +321,7 @@ void PairLJSFDipoleSFGPU::cpu_compute(int start, int inum, int eflag, int vflag,
tizcoul += pre2 * (mu[i][0]*dely - mu[i][1]*delx);
}
- if (mu[j][3] > 0.0 && qtmp != 0.0) {
+ if (mu[j][3] > 0.0 && qtmp != 0.0) {
r3inv = r2inv*rinv;
r5inv = r3inv*r2inv;
pjdotr = mu[j][0]*delx + mu[j][1]*dely + mu[j][2]*delz;
@@ -337,7 +337,7 @@ void PairLJSFDipoleSFGPU::cpu_compute(int start, int inum, int eflag, int vflag,
tjxcoul += -pre2 * (mu[j][1]*delz - mu[j][2]*dely);
tjycoul += -pre2 * (mu[j][2]*delx - mu[j][0]*delz);
tjzcoul += -pre2 * (mu[j][0]*dely - mu[j][1]*delx);
- }
+ }
}
// LJ interaction
@@ -345,22 +345,22 @@ void PairLJSFDipoleSFGPU::cpu_compute(int start, int inum, int eflag, int vflag,
if (rsq < cut_ljsq[itype][jtype]) {
r6inv = r2inv*r2inv*r2inv;
forceljcut = r6inv*(lj1[itype][jtype]*r6inv-lj2[itype][jtype])*r2inv;
-
+
rcutlj2inv = 1.0 / cut_ljsq[itype][jtype];
rcutlj6inv = rcutlj2inv * rcutlj2inv * rcutlj2inv;
- forceljsf = (lj1[itype][jtype]*rcutlj6inv - lj2[itype][jtype]) *
+ forceljsf = (lj1[itype][jtype]*rcutlj6inv - lj2[itype][jtype]) *
rcutlj6inv * rcutlj2inv;
forcelj = factor_lj * (forceljcut - forceljsf);
} else forcelj = 0.0;
-
+
// total force
fq = factor_coul*qqrd2e;
fx = fq*forcecoulx + delx*forcelj;
fy = fq*forcecouly + dely*forcelj;
fz = fq*forcecoulz + delz*forcelj;
-
+
// force & torque accumulation
f[i][0] += fx;
@@ -376,7 +376,7 @@ void PairLJSFDipoleSFGPU::cpu_compute(int start, int inum, int eflag, int vflag,
pow((1.0-sqrt(rsq)/sqrt(cut_coulsq[itype][jtype])),2);
if (mu[i][3] > 0.0 && mu[j][3] > 0.0)
ecoul += bfac * (r3inv*pdotp - 3.0*r5inv*pidotr*pjdotr);
- if (mu[i][3] > 0.0 && q[j] != 0.0)
+ if (mu[i][3] > 0.0 && q[j] != 0.0)
ecoul += -q[j]*r3inv * pqfac * pidotr;
if (mu[j][3] > 0.0 && qtmp != 0.0)
ecoul += qtmp*r3inv * qpfac * pjdotr;
@@ -389,9 +389,9 @@ void PairLJSFDipoleSFGPU::cpu_compute(int start, int inum, int eflag, int vflag,
rsq*rcutlj2inv +
rcutlj6inv*(-7*lj3[itype][jtype]*rcutlj6inv+4*lj4[itype][jtype]);
evdwl *= factor_lj;
- } else evdwl = 0.0;
- }
-
+ } else evdwl = 0.0;
+ }
+
if (evflag) ev_tally_xyz_full(i,evdwl,ecoul,
fx,fy,fz,delx,dely,delz);
}
diff --git a/src/GPU/pair_lj_sf_dipole_sf_gpu.h b/src/GPU/pair_lj_sf_dipole_sf_gpu.h
index ba1b93292c..79df327293 100755
--- a/src/GPU/pair_lj_sf_dipole_sf_gpu.h
+++ b/src/GPU/pair_lj_sf_dipole_sf_gpu.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/GPU/pair_mie_cut_gpu.cpp b/src/GPU/pair_mie_cut_gpu.cpp
index 3a6334f85e..4857928a27 100644
--- a/src/GPU/pair_mie_cut_gpu.cpp
+++ b/src/GPU/pair_mie_cut_gpu.cpp
@@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
-
+
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
-
+
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@@ -15,9 +15,9 @@
Contributing author: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
#include "pair_mie_cut_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +32,7 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include "string.h"
+#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
@@ -47,13 +47,13 @@ int mie_gpu_init(const int ntypes, double **cutsq, double **host_mie1,
const double cell_size, int &gpu_mode, FILE *screen);
void mie_gpu_clear();
int ** mie_gpu_compute_n(const int ago, const int inum,
- const int nall, double **host_x, int *host_type,
+ const int nall, double **host_x, int *host_type,
double *sublo, double *subhi, tagint *tag, int **nspecial,
tagint **special, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
int **ilist, int **jnum,
const double cpu_time, bool &success);
-void mie_gpu_compute(const int ago, const int inum, const int nall,
+void mie_gpu_compute(const int ago, const int inum, const int nall,
double **host_x, int *host_type, int *ilist, int *numj,
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
@@ -67,7 +67,7 @@ PairMIECutGPU::PairMIECutGPU(LAMMPS *lmp) : PairMIECut(lmp), gpu_mode(GPU_FORCE)
respa_enable = 0;
reinitflag = 0;
cpu_time = 0.0;
- GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
+ GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
@@ -85,10 +85,10 @@ void PairMIECutGPU::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
-
+
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
-
+
bool success = true;
int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
@@ -125,8 +125,8 @@ void PairMIECutGPU::compute(int eflag, int vflag)
void PairMIECutGPU::init_style()
{
cut_respa = NULL;
-
- if (force->newton_pair)
+
+ if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with mie/cut/gpu pair style");
// Repeat cutsq calculation because done after call to init_style
@@ -172,7 +172,7 @@ double PairMIECutGPU::memory_usage()
/* ---------------------------------------------------------------------- */
-void PairMIECutGPU::cpu_compute(int start, int inum, int eflag, int vflag,
+void PairMIECutGPU::cpu_compute(int start, int inum, int eflag, int vflag,
int *ilist, int *numneigh, int **firstneigh) {
int i,j,ii,jj,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
diff --git a/src/GPU/pair_mie_cut_gpu.h b/src/GPU/pair_mie_cut_gpu.h
index ed5a1d43de..2e9096e172 100644
--- a/src/GPU/pair_mie_cut_gpu.h
+++ b/src/GPU/pair_mie_cut_gpu.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/GPU/pair_morse_gpu.cpp b/src/GPU/pair_morse_gpu.cpp
index ad2b3b0b37..b72a6afaf4 100644
--- a/src/GPU/pair_morse_gpu.cpp
+++ b/src/GPU/pair_morse_gpu.cpp
@@ -15,9 +15,9 @@
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
#include "pair_morse_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +32,7 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include "string.h"
+#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
diff --git a/src/GPU/pair_resquared_gpu.cpp b/src/GPU/pair_resquared_gpu.cpp
index f26883376c..d83a63c467 100644
--- a/src/GPU/pair_resquared_gpu.cpp
+++ b/src/GPU/pair_resquared_gpu.cpp
@@ -15,9 +15,9 @@
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
#include "pair_resquared_gpu.h"
#include "math_extra.h"
#include "atom.h"
@@ -34,7 +34,7 @@
#include "universe.h"
#include "domain.h"
#include "update.h"
-#include "string.h"
+#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
diff --git a/src/GPU/pair_soft_gpu.cpp b/src/GPU/pair_soft_gpu.cpp
index b36d5d27be..aa0268025c 100644
--- a/src/GPU/pair_soft_gpu.cpp
+++ b/src/GPU/pair_soft_gpu.cpp
@@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
-
+
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
-
+
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@@ -15,9 +15,9 @@
Contributing author: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
#include "pair_soft_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +32,7 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include "string.h"
+#include <string.h>
#include "gpu_extra.h"
#include "math_const.h"
@@ -48,13 +48,13 @@ void soft_gpu_reinit(const int ntypes, double **cutsq, double **host_prefactor,
double **host_cut);
void soft_gpu_clear();
int ** soft_gpu_compute_n(const int ago, const int inum,
- const int nall, double **host_x, int *host_type,
+ const int nall, double **host_x, int *host_type,
double *sublo, double *subhi, tagint *tag, int **nspecial,
tagint **special, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
int **ilist, int **jnum,
const double cpu_time, bool &success);
-void soft_gpu_compute(const int ago, const int inum, const int nall,
+void soft_gpu_compute(const int ago, const int inum, const int nall,
double **host_x, int *host_type, int *ilist, int *numj,
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
@@ -70,7 +70,7 @@ PairSoftGPU::PairSoftGPU(LAMMPS *lmp) : PairSoft(lmp), gpu_mode(GPU_FORCE)
{
respa_enable = 0;
cpu_time = 0.0;
- GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
+ GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
@@ -88,10 +88,10 @@ void PairSoftGPU::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
-
+
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
-
+
bool success = true;
int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
@@ -100,7 +100,7 @@ void PairSoftGPU::compute(int eflag, int vflag)
atom->x, atom->type, domain->sublo,
domain->subhi, atom->tag, atom->nspecial,
atom->special, eflag, vflag, eflag_atom,
- vflag_atom, host_start,
+ vflag_atom, host_start,
&ilist, &numneigh, cpu_time, success);
} else {
inum = list->inum;
@@ -127,7 +127,7 @@ void PairSoftGPU::compute(int eflag, int vflag)
void PairSoftGPU::init_style()
{
- if (force->newton_pair)
+ if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with soft/gpu pair style");
// Repeat cutsq calculation because done after call to init_style
@@ -168,7 +168,7 @@ void PairSoftGPU::init_style()
void PairSoftGPU::reinit()
{
Pair::reinit();
-
+
soft_gpu_reinit(atom->ntypes+1, cutsq, prefactor, cut);
}
@@ -182,7 +182,7 @@ double PairSoftGPU::memory_usage()
/* ---------------------------------------------------------------------- */
-void PairSoftGPU::cpu_compute(int start, int inum, int eflag, int vflag,
+void PairSoftGPU::cpu_compute(int start, int inum, int eflag, int vflag,
int *ilist, int *numneigh, int **firstneigh) {
int i,j,ii,jj,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
diff --git a/src/GPU/pair_soft_gpu.h b/src/GPU/pair_soft_gpu.h
index da14c292a5..61e8ee3db5 100644
--- a/src/GPU/pair_soft_gpu.h
+++ b/src/GPU/pair_soft_gpu.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/GPU/pair_sw_gpu.cpp b/src/GPU/pair_sw_gpu.cpp
index 70e271122d..67faf98da4 100644
--- a/src/GPU/pair_sw_gpu.cpp
+++ b/src/GPU/pair_sw_gpu.cpp
@@ -15,10 +15,10 @@
Contributing author: Mike Brown (ORNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_sw_gpu.h"
#include "atom.h"
#include "neighbor.h"
@@ -37,14 +37,14 @@ using namespace LAMMPS_NS;
// External functions from cuda library for atom decomposition
-int sw_gpu_init(const int ntypes, const int inum, const int nall, const int max_nbors,
+int sw_gpu_init(const int ntypes, const int inum, const int nall, const int max_nbors,
const double cell_size, int &gpu_mode, FILE *screen,
int* host_map, const int nelements, int*** host_elem2param, const int nparams,
const double* sw_epsilon, const double* sw_sigma,
const double* sw_lambda, const double* sw_gamma,
const double* sw_costheta, const double* sw_biga,
const double* sw_bigb, const double* sw_powerp,
- const double* sw_powerq, const double* sw_cut,
+ const double* sw_powerq, const double* sw_cut,
const double* sw_cutsq);
void sw_gpu_clear();
int ** sw_gpu_compute_n(const int ago, const int inum,
@@ -116,8 +116,8 @@ void PairSWGPU::compute(int eflag, int vflag)
firstneigh = list->firstneigh;
sw_gpu_compute(neighbor->ago, atom->nlocal, nall, inum+list->gnum,
- atom->x, atom->type, ilist, numneigh, firstneigh, eflag,
- vflag, eflag_atom, vflag_atom, host_start, cpu_time,
+ atom->x, atom->type, ilist, numneigh, firstneigh, eflag,
+ vflag, eflag_atom, vflag_atom, host_start, cpu_time,
success);
}
if (!success)
@@ -180,10 +180,10 @@ void PairSWGPU::init_style()
costheta[i] = params[i].costheta;
}
- int success = sw_gpu_init(atom->ntypes+1, atom->nlocal, atom->nlocal+atom->nghost, 300,
- cell_size, gpu_mode, screen, map, nelements,
- elem2param, nparams, epsilon,
- sigma, lambda, gamma, costheta, biga, bigb,
+ int success = sw_gpu_init(atom->ntypes+1, atom->nlocal, atom->nlocal+atom->nghost, 300,
+ cell_size, gpu_mode, screen, map, nelements,
+ elem2param, nparams, epsilon,
+ sigma, lambda, gamma, costheta, biga, bigb,
powerp, powerq, _cut, _cutsq);
memory->destroy(epsilon);
diff --git a/src/GPU/pair_table_gpu.cpp b/src/GPU/pair_table_gpu.cpp
index 6b1ca065c0..b0a38eb461 100644
--- a/src/GPU/pair_table_gpu.cpp
+++ b/src/GPU/pair_table_gpu.cpp
@@ -15,9 +15,9 @@
Contributing authors: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
#include "pair_table_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +32,7 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include "string.h"
+#include <string.h>
#include "gpu_extra.h"
#define LOOKUP 0
diff --git a/src/GPU/pair_tersoff_gpu.cpp b/src/GPU/pair_tersoff_gpu.cpp
index 36019e4b35..eea3fbc06d 100644
--- a/src/GPU/pair_tersoff_gpu.cpp
+++ b/src/GPU/pair_tersoff_gpu.cpp
@@ -15,10 +15,10 @@
Contributing author: Trung Dac Nguyen (ndactrung@gmail.com)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_tersoff_gpu.h"
#include "atom.h"
#include "neighbor.h"
@@ -37,19 +37,19 @@ using namespace LAMMPS_NS;
// External functions from cuda library for atom decomposition
-int tersoff_gpu_init(const int ntypes, const int inum, const int nall,
+int tersoff_gpu_init(const int ntypes, const int inum, const int nall,
const int max_nbors, const double cell_size, int &gpu_mode,
- FILE *screen, int* host_map, const int nelements,
- int*** host_elem2param, const int nparams,
- const double* ts_lam1, const double* ts_lam2,
- const double* ts_lam3, const double* ts_powermint,
+ FILE *screen, int* host_map, const int nelements,
+ int*** host_elem2param, const int nparams,
+ const double* ts_lam1, const double* ts_lam2,
+ const double* ts_lam3, const double* ts_powermint,
const double* ts_biga, const double* ts_bigb,
- const double* ts_bigr, const double* ts_bigd,
- const double* ts_c1, const double* ts_c2,
- const double* ts_c3, const double* ts_c4,
- const double* ts_c, const double* ts_d,
- const double* ts_h, const double* ts_gamma,
- const double* ts_beta, const double* ts_powern,
+ const double* ts_bigr, const double* ts_bigd,
+ const double* ts_c1, const double* ts_c2,
+ const double* ts_c3, const double* ts_c4,
+ const double* ts_c, const double* ts_d,
+ const double* ts_h, const double* ts_gamma,
+ const double* ts_beta, const double* ts_powern,
const double* ts_cutsq);
void tersoff_gpu_clear();
int ** tersoff_gpu_compute_n(const int ago, const int inum_full,
@@ -59,10 +59,10 @@ int ** tersoff_gpu_compute_n(const int ago, const int inum_full,
const bool eatom, const bool vatom, int &host_start,
int **ilist, int **jnum, const double cpu_time,
bool &success);
-void tersoff_gpu_compute(const int ago, const int nlocal, const int nall,
- const int nlist, double **host_x, int *host_type,
- int *ilist, int *numj, int **firstneigh, const bool eflag,
- const bool vflag, const bool eatom, const bool vatom,
+void tersoff_gpu_compute(const int ago, const int nlocal, const int nall,
+ const int nlist, double **host_x, int *host_type,
+ int *ilist, int *numj, int **firstneigh, const bool eflag,
+ const bool vflag, const bool eatom, const bool vatom,
int &host_start, const double cpu_time, bool &success);
double tersoff_gpu_bytes();
extern double lmp_gpu_forces(double **f, double **tor, double *eatom,
@@ -120,8 +120,8 @@ void PairTersoffGPU::compute(int eflag, int vflag)
firstneigh = list->firstneigh;
tersoff_gpu_compute(neighbor->ago, atom->nlocal, nall, inum+list->gnum,
- atom->x, atom->type, ilist, numneigh, firstneigh, eflag,
- vflag, eflag_atom, vflag_atom, host_start, cpu_time,
+ atom->x, atom->type, ilist, numneigh, firstneigh, eflag,
+ vflag, eflag_atom, vflag_atom, host_start, cpu_time,
success);
}
if (!success)
@@ -159,7 +159,7 @@ void PairTersoffGPU::init_style()
lam1 = lam2 = lam3 = powermint = NULL;
biga = bigb = bigr = bigd = NULL;
c1 = c2 = c3 = c4 = NULL;
- c = d = h = gamma = NULL;
+ c = d = h = gamma = NULL;
beta = powern = _cutsq = NULL;
memory->create(lam1,nparams,"pair:lam1");
@@ -204,12 +204,12 @@ void PairTersoffGPU::init_style()
_cutsq[i] = params[i].cutsq;
}
- int success = tersoff_gpu_init(atom->ntypes+1, atom->nlocal,
- atom->nlocal+atom->nghost, 300,
- cell_size, gpu_mode, screen, map, nelements,
+ int success = tersoff_gpu_init(atom->ntypes+1, atom->nlocal,
+ atom->nlocal+atom->nghost, 300,
+ cell_size, gpu_mode, screen, map, nelements,
elem2param, nparams, lam1, lam2, lam3,
- powermint, biga, bigb, bigr, bigd,
- c1, c2, c3, c4, c, d, h, gamma,
+ powermint, biga, bigb, bigr, bigd,
+ c1, c2, c3, c4, c, d, h, gamma,
beta, powern, _cutsq);
memory->destroy(lam1);
@@ -232,7 +232,7 @@ void PairTersoffGPU::init_style()
memory->destroy(powern);
memory->destroy(_cutsq);
- if (success == -10)
+ if (success == -10)
error->all(FLERR, "Pair tersoff/gpu only works with 1 thread per atom for now.");
GPU_EXTRA::check_flag(success,error,world);
diff --git a/src/GPU/pair_yukawa_colloid_gpu.cpp b/src/GPU/pair_yukawa_colloid_gpu.cpp
index febdc33040..4041bd2ebf 100644
--- a/src/GPU/pair_yukawa_colloid_gpu.cpp
+++ b/src/GPU/pair_yukawa_colloid_gpu.cpp
@@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
-
+
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
-
+
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@@ -15,9 +15,9 @@
Contributing author: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
#include "pair_yukawa_colloid_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,17 +32,17 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include "string.h"
+#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
// External functions from cuda library for atom decomposition
-int ykcolloid_gpu_init(const int ntypes, double **cutsq, double **host_a,
+int ykcolloid_gpu_init(const int ntypes, double **cutsq, double **host_a,
double **host_offset, double *special_lj, const int inum,
const int nall, const int max_nbors, const int maxspecial,
- const double cell_size, int &gpu_mode, FILE *screen,
+ const double cell_size, int &gpu_mode, FILE *screen,
const double kappa);
void ykcolloid_gpu_clear();
int ** ykcolloid_gpu_compute_n(const int ago, const int inum_full,
@@ -52,9 +52,9 @@ int ** ykcolloid_gpu_compute_n(const int ago, const int inum_full,
const bool eatom, const bool vatom, int &host_start,
int **ilist, int **jnum, const double cpu_time,
bool &success, double *host_rad);
-void ykcolloid_gpu_compute(const int ago, const int inum_full,
- const int nall, double **host_x, int *host_type,
- int *ilist, int *numj, int **firstneigh,
+void ykcolloid_gpu_compute(const int ago, const int inum_full,
+ const int nall, double **host_x, int *host_type,
+ int *ilist, int *numj, int **firstneigh,
const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success, double *host_rad);
@@ -62,13 +62,13 @@ double ykcolloid_gpu_bytes();
/* ---------------------------------------------------------------------- */
-PairYukawaColloidGPU::PairYukawaColloidGPU(LAMMPS *lmp) : PairYukawaColloid(lmp),
+PairYukawaColloidGPU::PairYukawaColloidGPU(LAMMPS *lmp) : PairYukawaColloid(lmp),
gpu_mode(GPU_FORCE)
{
respa_enable = 0;
reinitflag = 0;
cpu_time = 0.0;
- GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
+ GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
@@ -86,31 +86,31 @@ void PairYukawaColloidGPU::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
-
+
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
-
+
bool success = true;
int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
inum = atom->nlocal;
firstneigh = ykcolloid_gpu_compute_n(neighbor->ago, inum, nall,
- atom->x, atom->type,
+ atom->x, atom->type,
domain->sublo,
- domain->subhi, atom->tag,
- atom->nspecial, atom->special,
+ domain->subhi, atom->tag,
+ atom->nspecial, atom->special,
eflag, vflag, eflag_atom,
- vflag_atom, host_start, &ilist,
- &numneigh, cpu_time,
+ vflag_atom, host_start, &ilist,
+ &numneigh, cpu_time,
success, atom->radius);
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
- ykcolloid_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
- ilist, numneigh, firstneigh, eflag, vflag,
- eflag_atom, vflag_atom, host_start, cpu_time,
+ ykcolloid_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
+ ilist, numneigh, firstneigh, eflag, vflag,
+ eflag_atom, vflag_atom, host_start, cpu_time,
success, atom->radius);
}
if (!success)
@@ -131,8 +131,8 @@ void PairYukawaColloidGPU::init_style()
{
if (!atom->sphere_flag)
error->all(FLERR,"Pair yukawa/colloid/gpu requires atom style sphere");
-
- if (force->newton_pair)
+
+ if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with yukawa/colloid/gpu pair style");
// Repeat cutsq calculation because done after call to init_style
@@ -151,11 +151,11 @@ void PairYukawaColloidGPU::init_style()
}
}
double cell_size = sqrt(maxcut) + neighbor->skin;
-
+
int maxspecial=0;
if (atom->molecular)
maxspecial=atom->maxspecial;
- int success = ykcolloid_gpu_init(atom->ntypes+1, cutsq, a,
+ int success = ykcolloid_gpu_init(atom->ntypes+1, cutsq, a,
offset, force->special_lj, atom->nlocal,
atom->nlocal+atom->nghost, 300, maxspecial,
cell_size, gpu_mode, screen, kappa);
@@ -178,8 +178,8 @@ double PairYukawaColloidGPU::memory_usage()
/* ---------------------------------------------------------------------- */
-void PairYukawaColloidGPU::cpu_compute(int start, int inum, int eflag,
- int vflag, int *ilist, int *numneigh,
+void PairYukawaColloidGPU::cpu_compute(int start, int inum, int eflag,
+ int vflag, int *ilist, int *numneigh,
int **firstneigh) {
int i,j,ii,jj,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair,radi,radj;
@@ -215,7 +215,7 @@ void PairYukawaColloidGPU::cpu_compute(int start, int inum, int eflag,
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
radj = radius[j];
-
+
if (rsq < cutsq[itype][jtype]) {
r = sqrt(rsq);
rinv = 1.0/r;
@@ -223,7 +223,7 @@ void PairYukawaColloidGPU::cpu_compute(int start, int inum, int eflag,
forceyukawa = a[itype][jtype] * screening;
fpair = factor*forceyukawa * rinv;
-
+
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
diff --git a/src/GPU/pair_yukawa_colloid_gpu.h b/src/GPU/pair_yukawa_colloid_gpu.h
index 7366770e24..218cfa3320 100644
--- a/src/GPU/pair_yukawa_colloid_gpu.h
+++ b/src/GPU/pair_yukawa_colloid_gpu.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/GPU/pair_yukawa_gpu.cpp b/src/GPU/pair_yukawa_gpu.cpp
index 5e4a0dc778..fcb0ae56bc 100644
--- a/src/GPU/pair_yukawa_gpu.cpp
+++ b/src/GPU/pair_yukawa_gpu.cpp
@@ -15,9 +15,9 @@
Contributing author: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
#include "pair_yukawa_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +32,7 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include "string.h"
+#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
diff --git a/src/GPU/pair_zbl_gpu.cpp b/src/GPU/pair_zbl_gpu.cpp
index 4795e9e939..faf6e9b29d 100644
--- a/src/GPU/pair_zbl_gpu.cpp
+++ b/src/GPU/pair_zbl_gpu.cpp
@@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
-
+
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
-
+
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@@ -16,9 +16,9 @@
------------------------------------------------------------------------- */
#include "lmptype.h"
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
#include "pair_zbl_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -33,30 +33,30 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include "string.h"
+#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
// External functions from cuda library for atom decomposition
-int zbl_gpu_init(const int ntypes, double **cutsq, double **host_sw1,
- double **host_sw2, double **host_sw3, double **host_sw4,
- double **host_sw5, double **host_d1a, double **host_d2a,
- double **host_d3a, double **host_d4a, double **host_zze,
+int zbl_gpu_init(const int ntypes, double **cutsq, double **host_sw1,
+ double **host_sw2, double **host_sw3, double **host_sw4,
+ double **host_sw5, double **host_d1a, double **host_d2a,
+ double **host_d3a, double **host_d4a, double **host_zze,
double cut_globalsq, double cut_innersq, double cut_inner,
- const int inum, const int nall, const int max_nbors,
- const int maxspecial, const double cell_size,
+ const int inum, const int nall, const int max_nbors,
+ const int maxspecial, const double cell_size,
int &gpu_mode, FILE *screen);
void zbl_gpu_clear();
int ** zbl_gpu_compute_n(const int ago, const int inum,
- const int nall, double **host_x, int *host_type,
+ const int nall, double **host_x, int *host_type,
double *sublo, double *subhi, tagint *tag, int **nspecial,
tagint **special, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
int **ilist, int **jnum,
const double cpu_time, bool &success);
-void zbl_gpu_compute(const int ago, const int inum, const int nall,
+void zbl_gpu_compute(const int ago, const int inum, const int nall,
double **host_x, int *host_type, int *ilist, int *numj,
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
@@ -70,7 +70,7 @@ PairZBLGPU::PairZBLGPU(LAMMPS *lmp) : PairZBL(lmp), gpu_mode(GPU_FORCE)
respa_enable = 0;
reinitflag = 0;
cpu_time = 0.0;
- GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
+ GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
@@ -88,10 +88,10 @@ void PairZBLGPU::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
-
+
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
-
+
bool success = true;
int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
@@ -100,7 +100,7 @@ void PairZBLGPU::compute(int eflag, int vflag)
atom->x, atom->type, domain->sublo,
domain->subhi, atom->tag, atom->nspecial,
atom->special, eflag, vflag, eflag_atom,
- vflag_atom, host_start,
+ vflag_atom, host_start,
&ilist, &numneigh, cpu_time, success);
} else {
inum = list->inum;
@@ -127,7 +127,7 @@ void PairZBLGPU::compute(int eflag, int vflag)
void PairZBLGPU::init_style()
{
- if (force->newton_pair)
+ if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with zbl/gpu pair style");
// Repeat cutsq calculation because done after call to init_style
@@ -153,10 +153,10 @@ void PairZBLGPU::init_style()
int maxspecial=0;
if (atom->molecular)
maxspecial=atom->maxspecial;
- int success = zbl_gpu_init(atom->ntypes+1, cutsq, sw1, sw2, sw3, sw4,
- sw5, d1a, d2a, d3a, d4a, zze,
+ int success = zbl_gpu_init(atom->ntypes+1, cutsq, sw1, sw2, sw3, sw4,
+ sw5, d1a, d2a, d3a, d4a, zze,
cut_globalsq, cut_innersq, cut_inner,
- atom->nlocal, atom->nlocal+atom->nghost,
+ atom->nlocal, atom->nlocal+atom->nghost,
300, maxspecial, cell_size, gpu_mode, screen);
GPU_EXTRA::check_flag(success,error,world);
@@ -177,7 +177,7 @@ double PairZBLGPU::memory_usage()
/* ---------------------------------------------------------------------- */
-void PairZBLGPU::cpu_compute(int start, int inum, int eflag, int vflag,
+void PairZBLGPU::cpu_compute(int start, int inum, int eflag, int vflag,
int *ilist, int *numneigh, int **firstneigh) {
int i,j,ii,jj,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
@@ -215,7 +215,7 @@ void PairZBLGPU::cpu_compute(int start, int inum, int eflag, int vflag,
if (rsq > cut_innersq) {
t = r - cut_inner;
- fswitch = t*t *
+ fswitch = t*t *
(sw1[itype][jtype] + sw2[itype][jtype]*t);
fpair += fswitch;
}
@@ -229,7 +229,7 @@ void PairZBLGPU::cpu_compute(int start, int inum, int eflag, int vflag,
evdwl = e_zbl(r, itype, jtype);
evdwl += sw5[itype][jtype];
if (rsq > cut_innersq) {
- eswitch = t*t*t *
+ eswitch = t*t*t *
(sw3[itype][jtype] + sw4[itype][jtype]*t);
evdwl += eswitch;
}
diff --git a/src/GPU/pair_zbl_gpu.h b/src/GPU/pair_zbl_gpu.h
index f0035968fa..f7a28870bc 100644
--- a/src/GPU/pair_zbl_gpu.h
+++ b/src/GPU/pair_zbl_gpu.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/GPU/pppm_gpu.cpp b/src/GPU/pppm_gpu.cpp
index f38752c0ee..b34fd30a0d 100644
--- a/src/GPU/pppm_gpu.cpp
+++ b/src/GPU/pppm_gpu.cpp
@@ -15,11 +15,11 @@
Contributing authors: Mike Brown (ORNL), Axel Kohlmeyer (Temple)
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "string.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "math.h"
+#include <mpi.h>
+#include <string.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
#include "pppm_gpu.h"
#include "atom.h"
#include "comm.h"
@@ -153,7 +153,7 @@ void PPPMGPU::init()
bool respa_value=false;
if (strstr(update->integrate_style,"respa"))
- respa_value=true;
+ respa_value=true;
if (order>8)
error->all(FLERR,"Cannot use order greater than 8 with pppm/gpu.");
@@ -202,7 +202,7 @@ void PPPMGPU::compute(int eflag, int vflag)
// invoke allocate_peratom() if needed for first time
if (eflag || vflag) ev_setup(eflag,vflag);
- else evflag = evflag_atom = eflag_global = vflag_global =
+ else evflag = evflag_atom = eflag_global = vflag_global =
eflag_atom = vflag_atom = 0;
// If need per-atom energies/virials, allocate per-atom arrays here
@@ -272,7 +272,7 @@ void PPPMGPU::compute(int eflag, int vflag)
// extra per-atom energy/virial communication
if (evflag_atom) {
- if (differentiation_flag == 1 && vflag_atom)
+ if (differentiation_flag == 1 && vflag_atom)
cg_peratom->forward_comm(this,FORWARD_AD_PERATOM);
else if (differentiation_flag == 0)
cg_peratom->forward_comm(this,FORWARD_IK_PERATOM);
@@ -636,7 +636,7 @@ void PPPMGPU::unpack_reverse(int flag, FFT_SCALAR *buf, int nlist, int *list)
FFT_SCALAR *dest = &density_brick_gpu[nzlo_out][nylo_out][nxlo_out];
for (int i = 0; i < nlist; i++)
dest[list[i]] += buf[i];
- }
+ }
}
/* ----------------------------------------------------------------------
diff --git a/src/GRANULAR/fix_freeze.cpp b/src/GRANULAR/fix_freeze.cpp
index 655edd844b..3cfee675b2 100644
--- a/src/GRANULAR/fix_freeze.cpp
+++ b/src/GRANULAR/fix_freeze.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "fix_freeze.h"
#include "atom.h"
#include "update.h"
diff --git a/src/GRANULAR/fix_pour.cpp b/src/GRANULAR/fix_pour.cpp
index d20b359fb2..8086a68d40 100644
--- a/src/GRANULAR/fix_pour.cpp
+++ b/src/GRANULAR/fix_pour.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "fix_pour.h"
#include "atom.h"
#include "atom_vec.h"
@@ -123,10 +123,10 @@ FixPour::FixPour(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,"Fix pour molecule must have coordinates");
if (onemols[i]->typeflag == 0)
error->all(FLERR,"Fix pour molecule must have atom types");
- if (ntype+onemols[i]->ntypes <= 0 ||
+ if (ntype+onemols[i]->ntypes <= 0 ||
ntype+onemols[i]->ntypes > atom->ntypes)
error->all(FLERR,"Invalid atom type in fix pour mol command");
-
+
if (atom->molecular == 2 && onemols != atom->avec->onemols)
error->all(FLERR,"Fix pour molecule template ID must be same "
"as atom style template ID");
@@ -238,7 +238,7 @@ FixPour::FixPour(LAMMPS *lmp, int narg, char **arg) :
} else if (dstyle == POLY) {
volume_one = 0.0;
for (int i = 0; i < npoly; i++)
- volume_one += (4.0/3.0 * MY_PI *
+ volume_one += (4.0/3.0 * MY_PI *
radius_poly[i]*radius_poly[i]*radius_poly[i]) * frac_poly[i];
}
} else {
@@ -301,7 +301,7 @@ int FixPour::setmask()
void FixPour::init()
{
- if (domain->triclinic)
+ if (domain->triclinic)
error->all(FLERR,"Cannot use fix pour with triclinic box");
// insure gravity fix exists
@@ -516,7 +516,7 @@ void FixPour::pre_exchange()
// default to 0.5, if radii not defined in Molecule
// same as atom->avec->create_atom(), invoked below
- if (onemols[imol]->radiusflag)
+ if (onemols[imol]->radiusflag)
coords[i][3] = onemols[imol]->radius[i];
else coords[i][3] = 0.5;
@@ -781,7 +781,7 @@ int FixPour::outside(int dim, double value, double lo, double hi)
} else {
if (value < lo || value > hi) return 1;
}
- }
+ }
if (value < lo || value > hi) return 1;
return 0;
@@ -819,7 +819,7 @@ void FixPour::xyz_random(double h, double *coord)
double FixPour::radius_sample()
{
if (dstyle == ONE) return radius_one;
- if (dstyle == RANGE) return radius_lo +
+ if (dstyle == RANGE) return radius_lo +
random->uniform()*(radius_hi-radius_lo);
double value = random->uniform();
@@ -884,9 +884,9 @@ void FixPour::options(int narg, char **arg)
if (mode != MOLECULE) error->all(FLERR,"Illegal fix deposit command");
if (iarg+nmol+1 > narg) error->all(FLERR,"Illegal fix deposit command");
molfrac[0] = force->numeric(FLERR,arg[iarg+1]);
- for (int i = 1; i < nmol; i++)
+ for (int i = 1; i < nmol; i++)
molfrac[i] = molfrac[i-1] + force->numeric(FLERR,arg[iarg+i+1]);
- if (molfrac[nmol-1] < 1.0-EPSILON || molfrac[nmol-1] > 1.0+EPSILON)
+ if (molfrac[nmol-1] < 1.0-EPSILON || molfrac[nmol-1] > 1.0+EPSILON)
error->all(FLERR,"Illegal fix deposit command");
molfrac[nmol-1] = 1.0;
iarg += nmol+1;
@@ -934,7 +934,7 @@ void FixPour::options(int narg, char **arg)
dstyle = POLY;
npoly = force->inumeric(FLERR,arg[iarg+2]);
if (npoly <= 0) error->all(FLERR,"Illegal fix pour command");
- if (iarg+3 + 2*npoly > narg)
+ if (iarg+3 + 2*npoly > narg)
error->all(FLERR,"Illegal fix pour command");
radius_poly = new double[npoly];
frac_poly = new double[npoly];
diff --git a/src/GRANULAR/fix_wall_gran.cpp b/src/GRANULAR/fix_wall_gran.cpp
index d1cc90369c..b49b2043b2 100644
--- a/src/GRANULAR/fix_wall_gran.cpp
+++ b/src/GRANULAR/fix_wall_gran.cpp
@@ -15,9 +15,9 @@
Contributing authors: Leo Silbert (SNL), Gary Grest (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "fix_wall_gran.h"
#include "atom.h"
#include "domain.h"
diff --git a/src/GRANULAR/pair_gran_hertz_history.cpp b/src/GRANULAR/pair_gran_hertz_history.cpp
index d10dd809d5..f7937fd664 100644
--- a/src/GRANULAR/pair_gran_hertz_history.cpp
+++ b/src/GRANULAR/pair_gran_hertz_history.cpp
@@ -15,10 +15,10 @@
Contributing authors: Leo Silbert (SNL), Gary Grest (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
-#include "stdio.h"
-#include "string.h"
+#include <math.h>
+#include <stdlib.h>
+#include <stdio.h>
+#include <string.h>
#include "pair_gran_hertz_history.h"
#include "atom.h"
#include "update.h"
diff --git a/src/GRANULAR/pair_gran_hooke.cpp b/src/GRANULAR/pair_gran_hooke.cpp
index 7e3f52eedf..79503e07b9 100644
--- a/src/GRANULAR/pair_gran_hooke.cpp
+++ b/src/GRANULAR/pair_gran_hooke.cpp
@@ -15,9 +15,9 @@
Contributing authors: Leo Silbert (SNL), Gary Grest (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <string.h>
#include "pair_gran_hooke.h"
#include "atom.h"
#include "force.h"
diff --git a/src/GRANULAR/pair_gran_hooke_history.cpp b/src/GRANULAR/pair_gran_hooke_history.cpp
index a2dbd84efd..ec156b4acd 100644
--- a/src/GRANULAR/pair_gran_hooke_history.cpp
+++ b/src/GRANULAR/pair_gran_hooke_history.cpp
@@ -15,10 +15,10 @@
Contributing authors: Leo Silbert (SNL), Gary Grest (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_gran_hooke_history.h"
#include "atom.h"
#include "atom_vec.h"
@@ -472,12 +472,12 @@ void PairGranHookeHistory::init_style()
onerad_dynamic[i] = onerad_frozen[i] = 0.0;
if (ipour >= 0) {
itype = i;
- onerad_dynamic[i] =
+ onerad_dynamic[i] =
*((double *) modify->fix[ipour]->extract("radius",itype));
}
if (idep >= 0) {
itype = i;
- onerad_dynamic[i] =
+ onerad_dynamic[i] =
*((double *) modify->fix[idep]->extract("radius",itype));
}
}
@@ -759,7 +759,7 @@ double PairGranHookeHistory::single(int i, int j, int itype, int jtype,
/* ---------------------------------------------------------------------- */
-int PairGranHookeHistory::pack_forward_comm(int n, int *list, double *buf,
+int PairGranHookeHistory::pack_forward_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
diff --git a/src/KOKKOS/angle_charmm_kokkos.cpp b/src/KOKKOS/angle_charmm_kokkos.cpp
index 180cac613d..cb70462765 100755
--- a/src/KOKKOS/angle_charmm_kokkos.cpp
+++ b/src/KOKKOS/angle_charmm_kokkos.cpp
@@ -15,8 +15,8 @@
Contributing author: Stan Moore (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdlib.h>
#include "angle_charmm_kokkos.h"
#include "atom_kokkos.h"
#include "neighbor_kokkos.h"
diff --git a/src/KOKKOS/angle_charmm_kokkos.h b/src/KOKKOS/angle_charmm_kokkos.h
index 9c203f35f0..3ff623044b 100755
--- a/src/KOKKOS/angle_charmm_kokkos.h
+++ b/src/KOKKOS/angle_charmm_kokkos.h
@@ -57,9 +57,9 @@ class AngleCharmmKokkos : public AngleCharmm {
const F_FLOAT &delx2, const F_FLOAT &dely2, const F_FLOAT &delz2) const;
protected:
-
+
class NeighborKokkos *neighborKK;
-
+
typename ArrayTypes<DeviceType>::t_x_array_randomread x;
typename ArrayTypes<DeviceType>::t_f_array f;
typename ArrayTypes<DeviceType>::t_int_2d anglelist;
diff --git a/src/KOKKOS/angle_harmonic_kokkos.cpp b/src/KOKKOS/angle_harmonic_kokkos.cpp
index dee0e8246d..c5976f1bff 100755
--- a/src/KOKKOS/angle_harmonic_kokkos.cpp
+++ b/src/KOKKOS/angle_harmonic_kokkos.cpp
@@ -15,8 +15,8 @@
Contributing author: Stan Moore (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdlib.h>
#include "angle_harmonic_kokkos.h"
#include "atom_kokkos.h"
#include "neighbor_kokkos.h"
diff --git a/src/KOKKOS/angle_harmonic_kokkos.h b/src/KOKKOS/angle_harmonic_kokkos.h
index ddf045c74b..0fe906fbb7 100755
--- a/src/KOKKOS/angle_harmonic_kokkos.h
+++ b/src/KOKKOS/angle_harmonic_kokkos.h
@@ -58,9 +58,9 @@ class AngleHarmonicKokkos : public AngleHarmonic {
const F_FLOAT &delx2, const F_FLOAT &dely2, const F_FLOAT &delz2) const;
protected:
-
+
class NeighborKokkos *neighborKK;
-
+
typename ArrayTypes<DeviceType>::t_x_array_randomread x;
typename ArrayTypes<DeviceType>::t_f_array f;
typename ArrayTypes<DeviceType>::t_int_2d anglelist;
diff --git a/src/KOKKOS/atom_kokkos.cpp b/src/KOKKOS/atom_kokkos.cpp
index 6ae27aac0e..352121fa92 100644
--- a/src/KOKKOS/atom_kokkos.cpp
+++ b/src/KOKKOS/atom_kokkos.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
+#include <mpi.h>
#include "atom_kokkos.h"
#include "atom_vec.h"
#include "atom_vec_kokkos.h"
@@ -247,7 +247,7 @@ void AtomKokkos::deallocate_topology()
------------------------------------------------------------------------- */
void AtomKokkos::sync_modify(ExecutionSpace execution_space,
- unsigned int datamask_read,
+ unsigned int datamask_read,
unsigned int datamask_modify)
{
sync(execution_space,datamask_read);
diff --git a/src/KOKKOS/atom_vec_angle_kokkos.cpp b/src/KOKKOS/atom_vec_angle_kokkos.cpp
index 5217435b51..f07e4a9e66 100644
--- a/src/KOKKOS/atom_vec_angle_kokkos.cpp
+++ b/src/KOKKOS/atom_vec_angle_kokkos.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdlib.h"
+#include <stdlib.h>
#include "atom_vec_angle_kokkos.h"
#include "atom_kokkos.h"
#include "comm_kokkos.h"
diff --git a/src/KOKKOS/atom_vec_atomic_kokkos.cpp b/src/KOKKOS/atom_vec_atomic_kokkos.cpp
index ddef28df2d..e9b3115d16 100644
--- a/src/KOKKOS/atom_vec_atomic_kokkos.cpp
+++ b/src/KOKKOS/atom_vec_atomic_kokkos.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdlib.h"
+#include <stdlib.h>
#include "atom_vec_atomic_kokkos.h"
#include "atom_kokkos.h"
#include "comm_kokkos.h"
@@ -87,28 +87,28 @@ void AtomVecAtomicKokkos::grow(int n)
void AtomVecAtomicKokkos::grow_reset()
{
- tag = atomKK->tag;
- d_tag = atomKK->k_tag.d_view;
+ tag = atomKK->tag;
+ d_tag = atomKK->k_tag.d_view;
h_tag = atomKK->k_tag.h_view;
- type = atomKK->type;
- d_type = atomKK->k_type.d_view;
+ type = atomKK->type;
+ d_type = atomKK->k_type.d_view;
h_type = atomKK->k_type.h_view;
- mask = atomKK->mask;
- d_mask = atomKK->k_mask.d_view;
+ mask = atomKK->mask;
+ d_mask = atomKK->k_mask.d_view;
h_mask = atomKK->k_mask.h_view;
- image = atomKK->image;
- d_image = atomKK->k_image.d_view;
+ image = atomKK->image;
+ d_image = atomKK->k_image.d_view;
h_image = atomKK->k_image.h_view;
- x = atomKK->x;
- d_x = atomKK->k_x.d_view;
+ x = atomKK->x;
+ d_x = atomKK->k_x.d_view;
h_x = atomKK->k_x.h_view;
- v = atomKK->v;
- d_v = atomKK->k_v.d_view;
+ v = atomKK->v;
+ d_v = atomKK->k_v.d_view;
h_v = atomKK->k_v.h_view;
- f = atomKK->f;
- d_f = atomKK->k_f.d_view;
+ f = atomKK->f;
+ d_f = atomKK->k_f.d_view;
h_f = atomKK->k_f.h_view;
}
@@ -187,8 +187,8 @@ struct AtomVecAtomicKokkos_PackComm {
/* ---------------------------------------------------------------------- */
-int AtomVecAtomicKokkos::pack_comm_kokkos(const int &n,
- const DAT::tdual_int_2d &list,
+int AtomVecAtomicKokkos::pack_comm_kokkos(const int &n,
+ const DAT::tdual_int_2d &list,
const int & iswap,
const DAT::tdual_xfloat_2d &buf,
const int &pbc_flag,
@@ -1127,7 +1127,7 @@ int AtomVecAtomicKokkos::unpack_exchange(double *buf)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
- modified(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK |
+ modified(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK |
MASK_MASK | IMAGE_MASK);
int m = 1;
@@ -1275,7 +1275,7 @@ void AtomVecAtomicKokkos::create_atom(int itype, double *coord)
initialize other atom quantities
------------------------------------------------------------------------- */
-void AtomVecAtomicKokkos::data_atom(double *coord, tagint imagetmp,
+void AtomVecAtomicKokkos::data_atom(double *coord, tagint imagetmp,
char **values)
{
int nlocal = atom->nlocal;
diff --git a/src/KOKKOS/atom_vec_atomic_kokkos.h b/src/KOKKOS/atom_vec_atomic_kokkos.h
index 291f6b4b78..6e73f4ee3c 100644
--- a/src/KOKKOS/atom_vec_atomic_kokkos.h
+++ b/src/KOKKOS/atom_vec_atomic_kokkos.h
@@ -53,25 +53,25 @@ class AtomVecAtomicKokkos : public AtomVecKokkos {
bigint memory_usage();
void grow_reset();
- int pack_comm_kokkos(const int &n, const DAT::tdual_int_2d &k_sendlist,
+ int pack_comm_kokkos(const int &n, const DAT::tdual_int_2d &k_sendlist,
const int & iswap,
const DAT::tdual_xfloat_2d &buf,
const int &pbc_flag, const int pbc[]);
- void unpack_comm_kokkos(const int &n, const int &nfirst,
+ void unpack_comm_kokkos(const int &n, const int &nfirst,
const DAT::tdual_xfloat_2d &buf);
- int pack_comm_self(const int &n, const DAT::tdual_int_2d &list,
- const int & iswap, const int nfirst,
+ int pack_comm_self(const int &n, const DAT::tdual_int_2d &list,
+ const int & iswap, const int nfirst,
const int &pbc_flag, const int pbc[]);
- int pack_border_kokkos(int n, DAT::tdual_int_2d k_sendlist,
+ int pack_border_kokkos(int n, DAT::tdual_int_2d k_sendlist,
DAT::tdual_xfloat_2d buf,int iswap,
int pbc_flag, int *pbc, ExecutionSpace space);
- void unpack_border_kokkos(const int &n, const int &nfirst,
- const DAT::tdual_xfloat_2d &buf,
+ void unpack_border_kokkos(const int &n, const int &nfirst,
+ const DAT::tdual_xfloat_2d &buf,
ExecutionSpace space);
- int pack_exchange_kokkos(const int &nsend,DAT::tdual_xfloat_2d &buf,
+ int pack_exchange_kokkos(const int &nsend,DAT::tdual_xfloat_2d &buf,
DAT::tdual_int_1d k_sendlist,
DAT::tdual_int_1d k_copylist,
- ExecutionSpace space, int dim,
+ ExecutionSpace space, int dim,
X_FLOAT lo, X_FLOAT hi);
int unpack_exchange_kokkos(DAT::tdual_xfloat_2d &k_buf, int nrecv,
int nlocal, int dim, X_FLOAT lo, X_FLOAT hi,
diff --git a/src/KOKKOS/atom_vec_bond_kokkos.cpp b/src/KOKKOS/atom_vec_bond_kokkos.cpp
index c04cc893be..65ac756956 100644
--- a/src/KOKKOS/atom_vec_bond_kokkos.cpp
+++ b/src/KOKKOS/atom_vec_bond_kokkos.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdlib.h"
+#include <stdlib.h>
#include "atom_vec_bond_kokkos.h"
#include "atom_kokkos.h"
#include "comm_kokkos.h"
diff --git a/src/KOKKOS/atom_vec_charge_kokkos.cpp b/src/KOKKOS/atom_vec_charge_kokkos.cpp
index 40b87c91b2..34e7bbae93 100644
--- a/src/KOKKOS/atom_vec_charge_kokkos.cpp
+++ b/src/KOKKOS/atom_vec_charge_kokkos.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdlib.h"
+#include <stdlib.h>
#include "atom_vec_charge_kokkos.h"
#include "atom_kokkos.h"
#include "comm_kokkos.h"
diff --git a/src/KOKKOS/atom_vec_full_kokkos.cpp b/src/KOKKOS/atom_vec_full_kokkos.cpp
index a8472b4713..10043d5dd0 100644
--- a/src/KOKKOS/atom_vec_full_kokkos.cpp
+++ b/src/KOKKOS/atom_vec_full_kokkos.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdlib.h"
+#include <stdlib.h>
#include "atom_vec_full_kokkos.h"
#include "atom_kokkos.h"
#include "comm_kokkos.h"
diff --git a/src/KOKKOS/atom_vec_kokkos.h b/src/KOKKOS/atom_vec_kokkos.h
index 4ad62c8f9c..b10c4a2156 100644
--- a/src/KOKKOS/atom_vec_kokkos.h
+++ b/src/KOKKOS/atom_vec_kokkos.h
@@ -27,43 +27,43 @@ class AtomVecKokkos : public AtomVec {
virtual void sync(ExecutionSpace space, unsigned int mask) = 0;
virtual void modified(ExecutionSpace space, unsigned int mask) = 0;
- virtual int
- pack_comm_self(const int &n, const DAT::tdual_int_2d &list,
- const int & iswap, const int nfirst,
+ virtual int
+ pack_comm_self(const int &n, const DAT::tdual_int_2d &list,
+ const int & iswap, const int nfirst,
const int &pbc_flag, const int pbc[]) = 0;
//{return 0;}
- virtual int
- pack_comm_kokkos(const int &n, const DAT::tdual_int_2d &list,
+ virtual int
+ pack_comm_kokkos(const int &n, const DAT::tdual_int_2d &list,
const int & iswap, const DAT::tdual_xfloat_2d &buf,
const int &pbc_flag, const int pbc[]) = 0;
//{return 0;}
- virtual void
- unpack_comm_kokkos(const int &n, const int &nfirst,
+ virtual void
+ unpack_comm_kokkos(const int &n, const int &nfirst,
const DAT::tdual_xfloat_2d &buf) = 0;
- virtual int
- pack_border_kokkos(int n, DAT::tdual_int_2d k_sendlist,
+ virtual int
+ pack_border_kokkos(int n, DAT::tdual_int_2d k_sendlist,
DAT::tdual_xfloat_2d buf,int iswap,
int pbc_flag, int *pbc, ExecutionSpace space) = 0;
//{return 0;};
- virtual void
- unpack_border_kokkos(const int &n, const int &nfirst,
- const DAT::tdual_xfloat_2d &buf,
+ virtual void
+ unpack_border_kokkos(const int &n, const int &nfirst,
+ const DAT::tdual_xfloat_2d &buf,
ExecutionSpace space) = 0;
- virtual int
- pack_exchange_kokkos(const int &nsend, DAT::tdual_xfloat_2d &buf,
+ virtual int
+ pack_exchange_kokkos(const int &nsend, DAT::tdual_xfloat_2d &buf,
DAT::tdual_int_1d k_sendlist,
DAT::tdual_int_1d k_copylist,
ExecutionSpace space, int dim, X_FLOAT lo, X_FLOAT hi) = 0;
//{return 0;};
- virtual int
+ virtual int
unpack_exchange_kokkos(DAT::tdual_xfloat_2d &k_buf, int nrecv,
int nlocal, int dim, X_FLOAT lo, X_FLOAT hi,
ExecutionSpace space) = 0;
//{return 0;};
protected:
-
+
class CommKokkos *commKK;
};
diff --git a/src/KOKKOS/atom_vec_molecular_kokkos.cpp b/src/KOKKOS/atom_vec_molecular_kokkos.cpp
index a577dda355..848e146ac8 100644
--- a/src/KOKKOS/atom_vec_molecular_kokkos.cpp
+++ b/src/KOKKOS/atom_vec_molecular_kokkos.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdlib.h"
+#include <stdlib.h>
#include "atom_vec_molecular_kokkos.h"
#include "atom_kokkos.h"
#include "comm_kokkos.h"
diff --git a/src/KOKKOS/bond_fene_kokkos.cpp b/src/KOKKOS/bond_fene_kokkos.cpp
index a0543fd8a8..c8b643261a 100755
--- a/src/KOKKOS/bond_fene_kokkos.cpp
+++ b/src/KOKKOS/bond_fene_kokkos.cpp
@@ -15,8 +15,8 @@
Contributing author: Stan Moore (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdlib.h>
#include "bond_fene_kokkos.h"
#include "atom_kokkos.h"
#include "neighbor_kokkos.h"
diff --git a/src/KOKKOS/bond_fene_kokkos.h b/src/KOKKOS/bond_fene_kokkos.h
index c82e35c545..ef37992925 100755
--- a/src/KOKKOS/bond_fene_kokkos.h
+++ b/src/KOKKOS/bond_fene_kokkos.h
@@ -57,9 +57,9 @@ class BondFENEKokkos : public BondFENE {
const F_FLOAT &dely, const F_FLOAT &delz) const;
protected:
-
+
class NeighborKokkos *neighborKK;
-
+
typename ArrayTypes<DeviceType>::t_x_array_randomread x;
typename ArrayTypes<DeviceType>::t_f_array f;
typename ArrayTypes<DeviceType>::t_int_2d bondlist;
diff --git a/src/KOKKOS/bond_harmonic_kokkos.cpp b/src/KOKKOS/bond_harmonic_kokkos.cpp
index f90df92fb3..ba2ab19a04 100755
--- a/src/KOKKOS/bond_harmonic_kokkos.cpp
+++ b/src/KOKKOS/bond_harmonic_kokkos.cpp
@@ -15,8 +15,8 @@
Contributing author: Stan Moore (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdlib.h>
#include "bond_harmonic_kokkos.h"
#include "atom_kokkos.h"
#include "neighbor_kokkos.h"
diff --git a/src/KOKKOS/bond_harmonic_kokkos.h b/src/KOKKOS/bond_harmonic_kokkos.h
index 6988fc5a4b..f2d692c9cc 100755
--- a/src/KOKKOS/bond_harmonic_kokkos.h
+++ b/src/KOKKOS/bond_harmonic_kokkos.h
@@ -57,9 +57,9 @@ class BondHarmonicKokkos : public BondHarmonic {
const F_FLOAT &dely, const F_FLOAT &delz) const;
protected:
-
+
class NeighborKokkos *neighborKK;
-
+
typename ArrayTypes<DeviceType>::t_x_array_randomread x;
typename ArrayTypes<DeviceType>::t_f_array f;
typename ArrayTypes<DeviceType>::t_int_2d bondlist;
diff --git a/src/KOKKOS/comm_kokkos.cpp b/src/KOKKOS/comm_kokkos.cpp
index b2a1f9f7a6..94571594a1 100644
--- a/src/KOKKOS/comm_kokkos.cpp
+++ b/src/KOKKOS/comm_kokkos.cpp
@@ -187,7 +187,7 @@ void CommKokkos::forward_comm_device(int dummy)
else buf = NULL;
if (size_forward_recv[iswap]) {
- buf = atomKK->k_x.view<DeviceType>().ptr_on_device() +
+ buf = atomKK->k_x.view<DeviceType>().ptr_on_device() +
firstrecv[iswap]*atomKK->k_x.view<DeviceType>().dimension_1();
MPI_Irecv(buf,size_forward_recv[iswap],MPI_DOUBLE,
recvproc[iswap],0,world,&request);
@@ -480,7 +480,7 @@ void CommKokkos::exchange_device()
k_count.modify<LMPHostType>();
k_count.sync<DeviceType>();
- BuildExchangeListFunctor<DeviceType>
+ BuildExchangeListFunctor<DeviceType>
f(atomKK->k_x,k_exchange_sendlist,k_count,k_sendflag,
nlocal,dim,lo,hi);
Kokkos::parallel_for(nlocal,f);
@@ -512,7 +512,7 @@ void CommKokkos::exchange_device()
k_exchange_copylist.modify<LMPHostType>();
k_exchange_copylist.sync<DeviceType>();
- nsend =
+ nsend =
avec->pack_exchange_kokkos(k_count.h_view(0),k_buf_send,
k_exchange_sendlist,k_exchange_copylist,
ExecutionSpaceFromDevice<DeviceType>::
@@ -634,11 +634,11 @@ struct BuildBorderListFunctor {
typename AT::t_int_2d sendlist;
typename AT::t_int_1d nsend;
- BuildBorderListFunctor(typename AT::tdual_x_array _x,
+ BuildBorderListFunctor(typename AT::tdual_x_array _x,
typename AT::tdual_int_2d _sendlist,
- typename AT::tdual_int_1d _nsend,int _nfirst,
+ typename AT::tdual_int_1d _nsend,int _nfirst,
int _nlast, int _dim,
- X_FLOAT _lo, X_FLOAT _hi, int _iswap,
+ X_FLOAT _lo, X_FLOAT _hi, int _iswap,
int _maxsendlist):
x(_x.template view<DeviceType>()),
sendlist(_sendlist.template view<DeviceType>()),
@@ -649,7 +649,7 @@ struct BuildBorderListFunctor {
KOKKOS_INLINE_FUNCTION
void operator() (typename Kokkos::TeamPolicy<DeviceType>::member_type dev) const {
- const int chunk = ((nlast - nfirst + dev.league_size() - 1 ) /
+ const int chunk = ((nlast - nfirst + dev.league_size() - 1 ) /
dev.league_size());
const int teamstart = chunk*dev.league_rank() + nfirst;
const int teamend = (teamstart + chunk) < nlast?(teamstart + chunk):nlast;
diff --git a/src/KOKKOS/comm_kokkos.h b/src/KOKKOS/comm_kokkos.h
index a6aeca3a59..587b030595 100644
--- a/src/KOKKOS/comm_kokkos.h
+++ b/src/KOKKOS/comm_kokkos.h
@@ -21,7 +21,7 @@ namespace LAMMPS_NS {
class CommKokkos : public CommBrick {
public:
-
+
bool exchange_comm_classic;
bool forward_comm_classic;
diff --git a/src/KOKKOS/compute_temp_kokkos.cpp b/src/KOKKOS/compute_temp_kokkos.cpp
index bb5e2799c2..df5b0fa090 100755
--- a/src/KOKKOS/compute_temp_kokkos.cpp
+++ b/src/KOKKOS/compute_temp_kokkos.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "string.h"
+#include <mpi.h>
+#include <string.h>
#include "compute_temp_kokkos.h"
#include "atom_kokkos.h"
#include "update.h"
@@ -69,7 +69,7 @@ double ComputeTempKokkos<DeviceType>::compute_scalar()
MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
if (dynamic) dof_compute();
- if (dof < 0.0 && natoms_temp > 0.0)
+ if (dof < 0.0 && natoms_temp > 0.0)
error->all(FLERR,"Temperature compute degrees of freedom < 0");
scalar *= tfactor;
return scalar;
diff --git a/src/KOKKOS/dihedral_charmm_kokkos.cpp b/src/KOKKOS/dihedral_charmm_kokkos.cpp
index 6d7275fed2..6042a1a75b 100755
--- a/src/KOKKOS/dihedral_charmm_kokkos.cpp
+++ b/src/KOKKOS/dihedral_charmm_kokkos.cpp
@@ -15,8 +15,8 @@
Contributing author: Stan Moore (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdlib.h>
#include "dihedral_charmm_kokkos.h"
#include "atom_kokkos.h"
#include "comm.h"
@@ -180,7 +180,7 @@ void DihedralCharmmKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (eflag_atom) {
k_eatom.template modify<DeviceType>();
k_eatom.template sync<LMPHostType>();
-
+
k_eatom_pair.template modify<DeviceType>();
k_eatom_pair.template sync<LMPHostType>();
for (int i = 0; i < n; i++)
@@ -431,8 +431,8 @@ void DihedralCharmmKokkos<DeviceType>::allocate()
k_lj14_4 = DAT::tdual_ffloat_2d("DihedralCharmm:lj14_4",n+1,n+1);
d_lj14_1 = k_lj14_1.d_view;
- d_lj14_2 = k_lj14_2.d_view;
- d_lj14_3 = k_lj14_3.d_view;
+ d_lj14_2 = k_lj14_2.d_view;
+ d_lj14_3 = k_lj14_3.d_view;
d_lj14_4 = k_lj14_4.d_view;
int nd = atom->ndihedraltypes;
diff --git a/src/KOKKOS/dihedral_charmm_kokkos.h b/src/KOKKOS/dihedral_charmm_kokkos.h
index 7c34519616..2ebae7e985 100755
--- a/src/KOKKOS/dihedral_charmm_kokkos.h
+++ b/src/KOKKOS/dihedral_charmm_kokkos.h
@@ -122,9 +122,9 @@ class DihedralCharmmKokkos : public DihedralCharmm {
const F_FLOAT &dely, const F_FLOAT &delz) const;
protected:
-
+
class NeighborKokkos *neighborKK;
-
+
typename AT::t_x_array_randomread x;
typename AT::t_int_1d_randomread atomtype;
typename AT::t_ffloat_1d_randomread q;
diff --git a/src/KOKKOS/dihedral_opls_kokkos.cpp b/src/KOKKOS/dihedral_opls_kokkos.cpp
index 8aaa052676..608e8d9754 100755
--- a/src/KOKKOS/dihedral_opls_kokkos.cpp
+++ b/src/KOKKOS/dihedral_opls_kokkos.cpp
@@ -15,8 +15,8 @@
Contributing author: Stan Moore (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdlib.h>
#include "dihedral_opls_kokkos.h"
#include "atom_kokkos.h"
#include "comm.h"
diff --git a/src/KOKKOS/dihedral_opls_kokkos.h b/src/KOKKOS/dihedral_opls_kokkos.h
index 7e7d9100e2..183c39ea37 100755
--- a/src/KOKKOS/dihedral_opls_kokkos.h
+++ b/src/KOKKOS/dihedral_opls_kokkos.h
@@ -59,9 +59,9 @@ class DihedralOPLSKokkos : public DihedralOPLS {
const F_FLOAT &vb3x, const F_FLOAT &vb3y, const F_FLOAT &vb3z) const;
protected:
-
+
class NeighborKokkos *neighborKK;
-
+
typename AT::t_x_array_randomread x;
typename AT::t_f_array f;
typename AT::t_int_2d dihedrallist;
diff --git a/src/KOKKOS/domain_kokkos.cpp b/src/KOKKOS/domain_kokkos.cpp
index 5bb796b0fb..dff5bddc69 100644
--- a/src/KOKKOS/domain_kokkos.cpp
+++ b/src/KOKKOS/domain_kokkos.cpp
@@ -45,7 +45,7 @@ struct DomainPBCFunctor {
DomainPBCFunctor(double* _lo, double* _hi, double* _period,
DAT::tdual_x_array _x, DAT::tdual_v_array _v,
- DAT::tdual_int_1d _mask, DAT::tdual_imageint_1d _image,
+ DAT::tdual_int_1d _mask, DAT::tdual_imageint_1d _image,
int _deform_groupbit, double* _h_rate,
int _xperiodic, int _yperiodic, int _zperiodic):
x(_x.view<DeviceType>()), v(_v.view<DeviceType>()),
@@ -82,7 +82,7 @@ struct DomainPBCFunctor {
image[i] = otherdims | idim;
}
}
-
+
if (PERIODIC && yperiodic) {
if (x(i,1) < lo[1]) {
x(i,1) += period[1];
@@ -110,7 +110,7 @@ struct DomainPBCFunctor {
image[i] = otherdims | (idim << IMGBITS);
}
}
-
+
if (PERIODIC && zperiodic) {
if (x(i,2) < lo[2]) {
x(i,2) += period[2];
@@ -174,13 +174,13 @@ void DomainKokkos::pbc()
if (xperiodic || yperiodic || zperiodic) {
if (deform_vremap) {
- DomainPBCFunctor<LMPDeviceType,1,1>
+ DomainPBCFunctor<LMPDeviceType,1,1>
f(lo,hi,period,
atomKK->k_x,atomKK->k_v,atomKK->k_mask,atomKK->k_image,
deform_groupbit,h_rate,xperiodic,yperiodic,zperiodic);
Kokkos::parallel_for(nlocal,f);
} else {
- DomainPBCFunctor<LMPDeviceType,1,0>
+ DomainPBCFunctor<LMPDeviceType,1,0>
f(lo,hi,period,
atomKK->k_x,atomKK->k_v,atomKK->k_mask,atomKK->k_image,
deform_groupbit,h_rate,xperiodic,yperiodic,zperiodic);
@@ -188,13 +188,13 @@ void DomainKokkos::pbc()
}
} else {
if (deform_vremap) {
- DomainPBCFunctor<LMPDeviceType,0,1>
+ DomainPBCFunctor<LMPDeviceType,0,1>
f(lo,hi,period,
atomKK->k_x,atomKK->k_v,atomKK->k_mask,atomKK->k_image,
deform_groupbit,h_rate,xperiodic,yperiodic,zperiodic);
Kokkos::parallel_for(nlocal,f);
} else {
- DomainPBCFunctor<LMPDeviceType,0,0>
+ DomainPBCFunctor<LMPDeviceType,0,0>
f(lo,hi,period,
atomKK->k_x,atomKK->k_v,atomKK->k_mask,atomKK->k_image,
deform_groupbit,h_rate,xperiodic,yperiodic,zperiodic);
@@ -226,7 +226,7 @@ void DomainKokkos::remap_all()
if (triclinic == 0) {
for (int i=0; i<3; i++) {
- lo[i] = boxlo[i];
+ lo[i] = boxlo[i];
hi[i] = boxhi[i];
period[i] = prd[i];
}
@@ -269,7 +269,7 @@ void DomainKokkos::operator()(TagDomain_remap_all, const int &i) const {
}
x(i,0) = MAX(x(i,0),lo[0]);
}
-
+
if (yperiodic) {
while (x(i,1) < lo[1]) {
x(i,1) += period[1];
@@ -289,7 +289,7 @@ void DomainKokkos::operator()(TagDomain_remap_all, const int &i) const {
}
x(i,1) = MAX(x(i,1),lo[1]);
}
-
+
if (zperiodic) {
while (x(i,2) < lo[2]) {
x(i,2) += period[2];
@@ -357,8 +357,8 @@ void DomainKokkos::operator()(TagDomain_image_flip, const int &i) const {
ybox -= p_flip*zbox;
xbox -= m_flip*ybox + n_flip*zbox;
- image[i] = ((imageint) (xbox + IMGMAX) & IMGMASK) |
- (((imageint) (ybox + IMGMAX) & IMGMASK) << IMGBITS) |
+ image[i] = ((imageint) (xbox + IMGMAX) & IMGMASK) |
+ (((imageint) (ybox + IMGMAX) & IMGMASK) << IMGBITS) |
(((imageint) (zbox + IMGMAX) & IMGMASK) << IMG2BITS);
}
diff --git a/src/KOKKOS/fix_deform_kokkos.cpp b/src/KOKKOS/fix_deform_kokkos.cpp
index 7da7d301be..0050fdc5e4 100755
--- a/src/KOKKOS/fix_deform_kokkos.cpp
+++ b/src/KOKKOS/fix_deform_kokkos.cpp
@@ -15,9 +15,9 @@
Contributing author: Pieter in 't Veld (SNL)
------------------------------------------------------------------------- */
-#include "string.h"
-#include "stdlib.h"
-#include "math.h"
+#include <string.h>
+#include <stdlib.h>
+#include <math.h>
#include "fix_deform_kokkos.h"
#include "atom_kokkos.h"
#include "update.h"
diff --git a/src/KOKKOS/fix_langevin_kokkos.cpp b/src/KOKKOS/fix_langevin_kokkos.cpp
index cd34d3a964..e7dc6f9ba2 100644
--- a/src/KOKKOS/fix_langevin_kokkos.cpp
+++ b/src/KOKKOS/fix_langevin_kokkos.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <string.h>
#include "fix_langevin_kokkos.h"
#include "atom_masks.h"
#include "atom_kokkos.h"
diff --git a/src/KOKKOS/fix_langevin_kokkos.h b/src/KOKKOS/fix_langevin_kokkos.h
index 6f50230b62..a9d015f6a1 100644
--- a/src/KOKKOS/fix_langevin_kokkos.h
+++ b/src/KOKKOS/fix_langevin_kokkos.h
@@ -42,7 +42,7 @@ namespace LAMMPS_NS {
fz += rhs.fz;
return *this;
}
-
+
KOKKOS_INLINE_FUNCTION
volatile s_FSUM& operator+=(const volatile s_FSUM &rhs) volatile {
fx += rhs.fx;
@@ -92,7 +92,7 @@ namespace LAMMPS_NS {
private:
class CommKokkos *commKK;
-
+
double *rmass;
typename ArrayTypes<DeviceType>::tdual_double_2d k_franprev;
typename ArrayTypes<DeviceType>::t_double_2d d_franprev;
diff --git a/src/KOKKOS/fix_nh_kokkos.cpp b/src/KOKKOS/fix_nh_kokkos.cpp
index bdf1bd3917..d8225b90b5 100755
--- a/src/KOKKOS/fix_nh_kokkos.cpp
+++ b/src/KOKKOS/fix_nh_kokkos.cpp
@@ -15,9 +15,9 @@
Contributing author: Stan Moore (SNL)
------------------------------------------------------------------------- */
-#include "string.h"
-#include "stdlib.h"
-#include "math.h"
+#include <string.h>
+#include <stdlib.h>
+#include <math.h>
#include "fix_nh_kokkos.h"
#include "math_extra.h"
#include "atom.h"
@@ -245,7 +245,7 @@ void FixNHKokkos<DeviceType>::final_integrate()
// re-compute temp before nh_v_press()
// only needed for temperature computes with BIAS on reneighboring steps:
- // b/c some biases store per-atom values (e.g. temp/profile)
+ // b/c some biases store per-atom values (e.g. temp/profile)
// per-atom values are invalid if reneigh/comm occurred
// since temp->compute() in initial_integrate()
diff --git a/src/KOKKOS/fix_nph_kokkos.cpp b/src/KOKKOS/fix_nph_kokkos.cpp
index 1eddaad8ab..08a7ea166d 100755
--- a/src/KOKKOS/fix_nph_kokkos.cpp
+++ b/src/KOKKOS/fix_nph_kokkos.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "fix_nph_kokkos.h"
#include "modify.h"
#include "error.h"
diff --git a/src/KOKKOS/fix_npt_kokkos.cpp b/src/KOKKOS/fix_npt_kokkos.cpp
index 880bf0126f..6ae0add690 100755
--- a/src/KOKKOS/fix_npt_kokkos.cpp
+++ b/src/KOKKOS/fix_npt_kokkos.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "fix_npt_kokkos.h"
#include "modify.h"
#include "error.h"
diff --git a/src/KOKKOS/fix_nve_kokkos.cpp b/src/KOKKOS/fix_nve_kokkos.cpp
index 3bc1a5629b..aa7698badc 100644
--- a/src/KOKKOS/fix_nve_kokkos.cpp
+++ b/src/KOKKOS/fix_nve_kokkos.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdio.h"
-#include "string.h"
+#include <stdio.h>
+#include <string.h>
#include "fix_nve_kokkos.h"
#include "atom_masks.h"
#include "atom_kokkos.h"
diff --git a/src/KOKKOS/fix_nve_kokkos.h b/src/KOKKOS/fix_nve_kokkos.h
index 4ec6405ec5..578e0f46cc 100644
--- a/src/KOKKOS/fix_nve_kokkos.h
+++ b/src/KOKKOS/fix_nve_kokkos.h
@@ -55,7 +55,7 @@ class FixNVEKokkos : public FixNVE {
void final_integrate_rmass_item(int) const;
private:
-
+
typename ArrayTypes<DeviceType>::t_x_array x;
typename ArrayTypes<DeviceType>::t_v_array v;
diff --git a/src/KOKKOS/fix_nvt_kokkos.cpp b/src/KOKKOS/fix_nvt_kokkos.cpp
index 3045f1a4f4..43fa07ea5a 100755
--- a/src/KOKKOS/fix_nvt_kokkos.cpp
+++ b/src/KOKKOS/fix_nvt_kokkos.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "fix_nvt_kokkos.h"
#include "group.h"
#include "modify.h"
diff --git a/src/KOKKOS/fix_wall_reflect_kokkos.cpp b/src/KOKKOS/fix_wall_reflect_kokkos.cpp
index 2876b0836a..cd6501d50e 100755
--- a/src/KOKKOS/fix_wall_reflect_kokkos.cpp
+++ b/src/KOKKOS/fix_wall_reflect_kokkos.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdlib.h"
-#include "string.h"
+#include <stdlib.h>
+#include <string.h>
#include "fix_wall_reflect_kokkos.h"
#include "atom_kokkos.h"
#include "comm.h"
diff --git a/src/KOKKOS/improper_harmonic_kokkos.cpp b/src/KOKKOS/improper_harmonic_kokkos.cpp
index 4f96a65c1d..f614b3dbc2 100755
--- a/src/KOKKOS/improper_harmonic_kokkos.cpp
+++ b/src/KOKKOS/improper_harmonic_kokkos.cpp
@@ -15,9 +15,9 @@
Contributing author: Stan Moore (SNL)
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "math.h"
-#include "stdlib.h"
+#include <mpi.h>
+#include <math.h>
+#include <stdlib.h>
#include "improper_harmonic_kokkos.h"
#include "atom_kokkos.h"
#include "comm.h"
@@ -225,7 +225,7 @@ void ImproperHarmonicKokkos<DeviceType>::operator()(TagImproperHarmonicCompute<N
const F_FLOAT domega = acos(c) - d_chi[type];
F_FLOAT a = d_k[type] * domega;
- F_FLOAT eimproper = 0.0;
+ F_FLOAT eimproper = 0.0;
if (eflag) eimproper = a*domega;
a = -a * 2.0/s;
diff --git a/src/KOKKOS/improper_harmonic_kokkos.h b/src/KOKKOS/improper_harmonic_kokkos.h
index 921bbdcaf2..dc7a12af4d 100755
--- a/src/KOKKOS/improper_harmonic_kokkos.h
+++ b/src/KOKKOS/improper_harmonic_kokkos.h
@@ -59,9 +59,9 @@ class ImproperHarmonicKokkos : public ImproperHarmonic {
const F_FLOAT &vb3x, const F_FLOAT &vb3y, const F_FLOAT &vb3z) const;
protected:
-
+
class NeighborKokkos *neighborKK;
-
+
typename AT::t_x_array_randomread x;
typename AT::t_f_array f;
typename AT::t_int_2d improperlist;
diff --git a/src/KOKKOS/kokkos.cpp b/src/KOKKOS/kokkos.cpp
index de3fcc831f..03626a5c6c 100644
--- a/src/KOKKOS/kokkos.cpp
+++ b/src/KOKKOS/kokkos.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdio.h"
-#include "string.h"
-#include "stdlib.h"
-#include "ctype.h"
+#include <stdio.h>
+#include <string.h>
+#include <stdlib.h>
+#include <ctype.h>
#include "kokkos.h"
#include "lammps.h"
#include "force.h"
@@ -44,7 +44,7 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
device = atoi(arg[iarg+1]);
iarg += 2;
- } else if (strcmp(arg[iarg],"g") == 0 ||
+ } else if (strcmp(arg[iarg],"g") == 0 ||
strcmp(arg[iarg],"gpus") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Invalid Kokkos command-line args");
int ngpu = atoi(arg[iarg+1]);
@@ -208,9 +208,9 @@ void KokkosLMP::accelerator(int narg, char **arg)
int KokkosLMP::neigh_list_kokkos(int m)
{
NeighborKokkos *nk = (NeighborKokkos *) neighbor;
- if (nk->lists_host[m] && nk->lists_host[m]->d_numneigh.dimension_0())
+ if (nk->lists_host[m] && nk->lists_host[m]->d_numneigh.dimension_0())
return 1;
- if (nk->lists_device[m] && nk->lists_device[m]->d_numneigh.dimension_0())
+ if (nk->lists_device[m] && nk->lists_device[m]->d_numneigh.dimension_0())
return 1;
return 0;
}
diff --git a/src/KOKKOS/kokkos_type.h b/src/KOKKOS/kokkos_type.h
index 1f9087c3cc..15d2eb5525 100644
--- a/src/KOKKOS/kokkos_type.h
+++ b/src/KOKKOS/kokkos_type.h
@@ -262,7 +262,7 @@ typedef tdual_int_scalar::t_dev_um t_int_scalar_um;
typedef tdual_int_scalar::t_dev_const_um t_int_scalar_const_um;
typedef Kokkos::
- DualView<LMP_FLOAT, LMPDeviceType::array_layout, LMPDeviceType>
+ DualView<LMP_FLOAT, LMPDeviceType::array_layout, LMPDeviceType>
tdual_float_scalar;
typedef tdual_float_scalar::t_dev t_float_scalar;
typedef tdual_float_scalar::t_dev_const t_float_scalar_const;
@@ -372,7 +372,7 @@ typedef tdual_xfloat_2d::t_dev_um t_xfloat_2d_um;
typedef tdual_xfloat_2d::t_dev_const_um t_xfloat_2d_const_um;
typedef tdual_xfloat_2d::t_dev_const_randomread t_xfloat_2d_randomread;
-//2d X_FLOAT array n*4
+//2d X_FLOAT array n*4
#ifdef LMP_KOKKOS_NO_LEGACY
typedef Kokkos::DualView<X_FLOAT*[3], Kokkos::LayoutLeft, LMPDeviceType> tdual_x_array;
#else
@@ -467,7 +467,7 @@ typedef tdual_efloat_2d::t_dev_um t_efloat_2d_um;
typedef tdual_efloat_2d::t_dev_const_um t_efloat_2d_const_um;
typedef tdual_efloat_2d::t_dev_const_randomread t_efloat_2d_randomread;
-//2d E_FLOAT array n*3
+//2d E_FLOAT array n*3
typedef Kokkos::DualView<E_FLOAT*[3], Kokkos::LayoutRight, LMPDeviceType> tdual_e_array;
typedef tdual_e_array::t_dev t_e_array;
diff --git a/src/KOKKOS/memory_kokkos.h b/src/KOKKOS/memory_kokkos.h
index 034fbca239..8ade198c40 100644
--- a/src/KOKKOS/memory_kokkos.h
+++ b/src/KOKKOS/memory_kokkos.h
@@ -20,7 +20,7 @@
------------------------------------------------------------------------- */
template <typename TYPE>
-TYPE create_kokkos(TYPE &data, typename TYPE::value_type *&array,
+TYPE create_kokkos(TYPE &data, typename TYPE::value_type *&array,
int n1, const char *name)
{
data = TYPE(name,n1);
@@ -29,8 +29,8 @@ TYPE create_kokkos(TYPE &data, typename TYPE::value_type *&array,
}
template <typename TYPE, typename HTYPE>
- TYPE create_kokkos(TYPE &data, HTYPE &h_data,
- typename TYPE::value_type *&array, int n1,
+ TYPE create_kokkos(TYPE &data, HTYPE &h_data,
+ typename TYPE::value_type *&array, int n1,
const char *name)
{
data = TYPE(std::string(name),n1);
@@ -63,11 +63,11 @@ template <typename TYPE, typename HTYPE>
------------------------------------------------------------------------- */
template <typename TYPE>
-TYPE grow_kokkos(TYPE &data, typename TYPE::value_type *&array,
+TYPE grow_kokkos(TYPE &data, typename TYPE::value_type *&array,
int n1, const char *name)
{
if (array == NULL) return create_kokkos(data,array,n1,name);
-
+
data.resize(n1);
array = data.h_view.ptr_on_device();
return data;
@@ -151,7 +151,7 @@ TYPE create_kokkos(TYPE &data, int n1, int n2, int n3, int n4, int n5 , int n6 ,
template <typename TYPE, typename HTYPE>
- TYPE create_kokkos(TYPE &data, HTYPE &h_data, int n1, int n2,
+ TYPE create_kokkos(TYPE &data, HTYPE &h_data, int n1, int n2,
const char *name)
{
data = TYPE(std::string(name),n1,n2);
@@ -164,13 +164,13 @@ template <typename TYPE, typename HTYPE>
}
template <typename TYPE>
-TYPE create_kokkos(TYPE &data, typename TYPE::value_type **&array,
+TYPE create_kokkos(TYPE &data, typename TYPE::value_type **&array,
int n1, int n2, const char *name)
{
data = TYPE(std::string(name),n1,n2);
bigint nbytes = ((bigint) sizeof(typename TYPE::value_type *)) * n1;
array = (typename TYPE::value_type **) smalloc(nbytes,name);
-
+
bigint n = 0;
for (int i = 0; i < n1; i++) {
if(n2==0)
@@ -183,8 +183,8 @@ TYPE create_kokkos(TYPE &data, typename TYPE::value_type **&array,
}
template <typename TYPE, typename HTYPE>
- TYPE create_kokkos(TYPE &data, HTYPE &h_data,
- typename TYPE::value_type **&array, int n1, int n2,
+ TYPE create_kokkos(TYPE &data, HTYPE &h_data,
+ typename TYPE::value_type **&array, int n1, int n2,
const char *name)
{
data = TYPE(std::string(name),n1,n2);
@@ -195,7 +195,7 @@ template <typename TYPE, typename HTYPE>
#endif
bigint nbytes = ((bigint) sizeof(typename TYPE::value_type *)) * n1;
array = (typename TYPE::value_type **) smalloc(nbytes,name);
-
+
bigint n = 0;
for (int i = 0; i < n1; i++) {
if(n2==0)
@@ -213,57 +213,57 @@ template <typename TYPE, typename HTYPE>
------------------------------------------------------------------------- */
template <typename TYPE>
-TYPE grow_kokkos(TYPE &data, typename TYPE::value_type **&array,
+TYPE grow_kokkos(TYPE &data, typename TYPE::value_type **&array,
int n1, int n2, const char *name)
{
if (array == NULL) return create_kokkos(data,array,n1,n2,name);
data.resize(n1,n2);
bigint nbytes = ((bigint) sizeof(typename TYPE::value_type *)) * n1;
array = (typename TYPE::value_type**) srealloc(array,nbytes,name);
-
+
for (int i = 0; i < n1; i++)
if(n2==0)
array[i] = NULL;
else
array[i] = &data.h_view(i,0);
-
+
return data;
}
template <typename TYPE>
-TYPE create_kokkos(TYPE &data, typename TYPE::value_type **&array,
+TYPE create_kokkos(TYPE &data, typename TYPE::value_type **&array,
int n1, const char *name)
{
data = TYPE(std::string(name),n1);
bigint nbytes = ((bigint) sizeof(typename TYPE::value_type *)) * n1;
array = (typename TYPE::value_type **) smalloc(nbytes,name);
-
+
for (int i = 0; i < n1; i++)
if(data.h_view.dimension_1()==0)
array[i] = NULL;
else
array[i] = &data.h_view(i,0);
-
+
return data;
}
template <typename TYPE>
-TYPE grow_kokkos(TYPE &data, typename TYPE::value_type **&array,
+TYPE grow_kokkos(TYPE &data, typename TYPE::value_type **&array,
int n1, const char *name)
{
if (array == NULL) return create_kokkos(data,array,n1,name);
-
+
data.resize(n1);
-
+
bigint nbytes = ((bigint) sizeof(typename TYPE::value_type *)) * n1;
array = (typename TYPE::value_type **) smalloc(nbytes,name);
-
+
for (int i = 0; i < n1; i++)
if(data.h_view.dimension_1()==0)
array[i] = NULL;
else
array[i] = &data.h_view(i,0);
-
+
return data;
}
diff --git a/src/KOKKOS/modify_kokkos.cpp b/src/KOKKOS/modify_kokkos.cpp
index 4fcd136156..b6078960c4 100644
--- a/src/KOKKOS/modify_kokkos.cpp
+++ b/src/KOKKOS/modify_kokkos.cpp
@@ -23,7 +23,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-ModifyKokkos::ModifyKokkos(LAMMPS *lmp) : Modify(lmp)
+ModifyKokkos::ModifyKokkos(LAMMPS *lmp) : Modify(lmp)
{
atomKK = (AtomKokkos *) atom;
}
diff --git a/src/KOKKOS/modify_kokkos.h b/src/KOKKOS/modify_kokkos.h
index 7d1796dac5..b8e5f8de30 100644
--- a/src/KOKKOS/modify_kokkos.h
+++ b/src/KOKKOS/modify_kokkos.h
@@ -61,7 +61,7 @@ class ModifyKokkos : public Modify {
int min_reset_ref();
protected:
-
+
};
}
diff --git a/src/KOKKOS/neigh_bond_kokkos.cpp b/src/KOKKOS/neigh_bond_kokkos.cpp
index 5157df9970..e18fe6f372 100755
--- a/src/KOKKOS/neigh_bond_kokkos.cpp
+++ b/src/KOKKOS/neigh_bond_kokkos.cpp
@@ -28,7 +28,7 @@
#include "error.h"
#include "modify.h"
#include "fix.h"
-#include "string.h"
+#include <string.h>
#include "atom_masks.h"
#include "domain.h"
diff --git a/src/KOKKOS/neigh_bond_kokkos.h b/src/KOKKOS/neigh_bond_kokkos.h
index feb0874d50..6ce2b0734e 100755
--- a/src/KOKKOS/neigh_bond_kokkos.h
+++ b/src/KOKKOS/neigh_bond_kokkos.h
@@ -80,11 +80,11 @@ class NeighBondKokkos : protected Pointers {
int me;
private:
-
+
DAT::tdual_int_1d k_map_array;
typename AT::t_int_1d_randomread map_array;
-
+
DAT::tdual_int_1d k_sametag;
typename AT::t_int_1d_randomread sametag;
diff --git a/src/KOKKOS/neigh_list_kokkos.cpp b/src/KOKKOS/neigh_list_kokkos.cpp
index 4a1b77f3b6..302b6def62 100644
--- a/src/KOKKOS/neigh_list_kokkos.cpp
+++ b/src/KOKKOS/neigh_list_kokkos.cpp
@@ -31,7 +31,7 @@ void NeighListKokkos<Device>::clean_copy()
dnum = 0;
iskip = NULL;
ijskip = NULL;
-
+
ipage = NULL;
dpage = NULL;
maxstencil = 0;
@@ -49,11 +49,11 @@ void NeighListKokkos<Device>::grow(int nmax)
if (nmax <= maxatoms) return;
maxatoms = nmax;
- d_ilist =
+ d_ilist =
typename ArrayTypes<Device>::t_int_1d("neighlist:ilist",maxatoms);
- d_numneigh =
+ d_numneigh =
typename ArrayTypes<Device>::t_int_1d("neighlist:numneigh",maxatoms);
- d_neighbors =
+ d_neighbors =
typename ArrayTypes<Device>::t_neighbors_2d("neighlist:neighbors",
maxatoms,maxneighs);
@@ -77,7 +77,7 @@ void NeighListKokkos<Device>::stencil_allocate(int smax, int style)
if (style == BIN) {
if (smax > maxstencil) {
maxstencil = smax;
- d_stencil =
+ d_stencil =
memory->create_kokkos(d_stencil,h_stencil,stencil,maxstencil,
"neighlist:stencil");
if (ghostflag) {
diff --git a/src/KOKKOS/neigh_list_kokkos.h b/src/KOKKOS/neigh_list_kokkos.h
index 8dc80b83b7..5200b24595 100644
--- a/src/KOKKOS/neigh_list_kokkos.h
+++ b/src/KOKKOS/neigh_list_kokkos.h
@@ -28,7 +28,7 @@ class AtomNeighbors
const int num_neighs;
KOKKOS_INLINE_FUNCTION
- AtomNeighbors(int* const & firstneigh, const int & _num_neighs,
+ AtomNeighbors(int* const & firstneigh, const int & _num_neighs,
const int & stride):
num_neighs(_num_neighs), _firstneigh(firstneigh), _stride(stride) {};
KOKKOS_INLINE_FUNCTION
diff --git a/src/KOKKOS/neighbor_kokkos.cpp b/src/KOKKOS/neighbor_kokkos.cpp
index a09c47e104..a5206bbe88 100644
--- a/src/KOKKOS/neighbor_kokkos.cpp
+++ b/src/KOKKOS/neighbor_kokkos.cpp
@@ -27,7 +27,7 @@ enum{NSQ,BIN,MULTI}; // also in neigh_list.cpp
/* ---------------------------------------------------------------------- */
-NeighborKokkos::NeighborKokkos(LAMMPS *lmp) : Neighbor(lmp),
+NeighborKokkos::NeighborKokkos(LAMMPS *lmp) : Neighbor(lmp),
neighbond_host(lmp),neighbond_device(lmp)
{
atoms_per_bin = 16;
@@ -51,15 +51,15 @@ NeighborKokkos::~NeighborKokkos()
if (!copymode) {
memory->destroy_kokkos(k_cutneighsq,cutneighsq);
cutneighsq = NULL;
-
+
for (int i = 0; i < nlist_host; i++) delete lists_host[i];
delete [] lists_host;
for (int i = 0; i < nlist_device; i++) delete lists_device[i];
delete [] lists_device;
-
+
delete [] pair_build_device;
delete [] pair_build_host;
-
+
memory->destroy_kokkos(k_ex1_type,ex1_type);
memory->destroy_kokkos(k_ex2_type,ex2_type);
memory->destroy_kokkos(k_ex1_group,ex1_group);
@@ -68,7 +68,7 @@ NeighborKokkos::~NeighborKokkos()
memory->destroy_kokkos(k_ex1_bit,ex1_bit);
memory->destroy_kokkos(k_ex2_bit,ex2_bit);
memory->destroy_kokkos(k_ex_mol_bit,ex_mol_bit);
-
+
memory->destroy_kokkos(k_bondlist,bondlist);
memory->destroy_kokkos(k_anglelist,anglelist);
memory->destroy_kokkos(k_dihedrallist,dihedrallist);
@@ -170,36 +170,36 @@ int NeighborKokkos::init_lists_kokkos()
/* ---------------------------------------------------------------------- */
void NeighborKokkos::init_list_flags1_kokkos(int i)
-{
+{
if (lists_host[i]) {
lists_host[i]->buildflag = 1;
if (pair_build_host[i] == NULL) lists_host[i]->buildflag = 0;
if (requests[i]->occasional) lists_host[i]->buildflag = 0;
-
+
lists_host[i]->growflag = 1;
if (requests[i]->copy) lists_host[i]->growflag = 0;
-
+
lists_host[i]->stencilflag = 1;
if (style == NSQ) lists_host[i]->stencilflag = 0;
if (stencil_create[i] == NULL) lists_host[i]->stencilflag = 0;
-
+
lists_host[i]->ghostflag = 0;
if (requests[i]->ghost) lists_host[i]->ghostflag = 1;
if (requests[i]->ghost && !requests[i]->occasional) anyghostlist = 1;
}
-
+
if (lists_device[i]) {
lists_device[i]->buildflag = 1;
if (pair_build_device[i] == NULL) lists_device[i]->buildflag = 0;
if (requests[i]->occasional) lists_device[i]->buildflag = 0;
-
+
lists_device[i]->growflag = 1;
if (requests[i]->copy) lists_device[i]->growflag = 0;
-
+
lists_device[i]->stencilflag = 1;
if (style == NSQ) lists_device[i]->stencilflag = 0;
if (stencil_create[i] == NULL) lists_device[i]->stencilflag = 0;
-
+
lists_device[i]->ghostflag = 0;
if (requests[i]->ghost) lists_device[i]->ghostflag = 1;
if (requests[i]->ghost && !requests[i]->occasional) anyghostlist = 1;
@@ -209,7 +209,7 @@ void NeighborKokkos::init_list_flags1_kokkos(int i)
/* ---------------------------------------------------------------------- */
void NeighborKokkos::init_list_flags2_kokkos(int i)
-{
+{
if (lists_host[i]) {
if (lists_host[i]->buildflag) blist[nblist++] = i;
if (lists_host[i]->growflag && requests[i]->occasional == 0)
diff --git a/src/KOKKOS/neighbor_kokkos.h b/src/KOKKOS/neighbor_kokkos.h
index 9264a90524..17e9176bfb 100644
--- a/src/KOKKOS/neighbor_kokkos.h
+++ b/src/KOKKOS/neighbor_kokkos.h
@@ -280,10 +280,10 @@ struct NeighborKokkosBuildFunctor {
const NeighborKokkosExecute<Device> c;
const size_t sharedsize;
- NeighborKokkosBuildFunctor(const NeighborKokkosExecute<Device> &_c,
+ NeighborKokkosBuildFunctor(const NeighborKokkosExecute<Device> &_c,
const size_t _sharedsize):c(_c),
sharedsize(_sharedsize) {};
-
+
KOKKOS_INLINE_FUNCTION
void operator() (const int & i) const {
c.template build_Item<HALF_NEIGH,GHOST_NEWTON>(i);
@@ -304,7 +304,7 @@ struct NeighborKokkosBuildFunctorFullGhost {
const NeighborKokkosExecute<Device> c;
const size_t sharedsize;
- NeighborKokkosBuildFunctorFullGhost(const NeighborKokkosExecute<Device> &_c,
+ NeighborKokkosBuildFunctorFullGhost(const NeighborKokkosExecute<Device> &_c,
const size_t _sharedsize):c(_c),
sharedsize(_sharedsize) {};
@@ -331,17 +331,17 @@ struct NeighborClusterKokkosBuildFunctor {
}
};
-template<class DeviceType>
+template<class DeviceType>
struct TagNeighborCheckDistance{};
-template<class DeviceType>
+template<class DeviceType>
struct TagNeighborXhold{};
class NeighborKokkos : public Neighbor {
public:
typedef int value_type;
-
+
int nlist_host; // pairwise neighbor lists on Host
NeighListKokkos<LMPHostType> **lists_host;
@@ -360,11 +360,11 @@ class NeighborKokkos : public Neighbor {
~NeighborKokkos();
void init();
- template<class DeviceType>
+ template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void operator()(TagNeighborCheckDistance<DeviceType>, const int&, int&) const;
- template<class DeviceType>
+ template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void operator()(TagNeighborXhold<DeviceType>, const int&) const;
diff --git a/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp b/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp
index 7ffdf903f3..51547cea97 100644
--- a/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp
+++ b/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp
@@ -15,10 +15,10 @@
Contributing author: Ray Shan (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_buck_coul_cut_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
@@ -63,7 +63,7 @@ PairBuckCoulCutKokkos<DeviceType>::PairBuckCoulCutKokkos(LAMMPS *lmp):PairBuckCo
template<class DeviceType>
PairBuckCoulCutKokkos<DeviceType>::~PairBuckCoulCutKokkos()
{
-
+
if (!copymode) {
memory->destroy_kokkos(k_eatom,eatom);
memory->destroy_kokkos(k_vatom,vatom);
diff --git a/src/KOKKOS/pair_buck_coul_cut_kokkos.h b/src/KOKKOS/pair_buck_coul_cut_kokkos.h
index 90c9fdca53..41f34b3354 100644
--- a/src/KOKKOS/pair_buck_coul_cut_kokkos.h
+++ b/src/KOKKOS/pair_buck_coul_cut_kokkos.h
@@ -101,7 +101,7 @@ class PairBuckCoulCutKokkos : public PairBuckCoulCut {
typename ArrayTypes<DeviceType>::tdual_ffloat_2d k_cut_coulsq;
typename ArrayTypes<DeviceType>::t_ffloat_2d d_cut_coulsq;
-
+
int neighflag;
int nlocal,nall,eflag,vflag;
diff --git a/src/KOKKOS/pair_buck_coul_long_kokkos.cpp b/src/KOKKOS/pair_buck_coul_long_kokkos.cpp
index 3966b38043..57108ee6e0 100644
--- a/src/KOKKOS/pair_buck_coul_long_kokkos.cpp
+++ b/src/KOKKOS/pair_buck_coul_long_kokkos.cpp
@@ -15,10 +15,10 @@
Contributing author: Ray Shan (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_buck_coul_long_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
diff --git a/src/KOKKOS/pair_buck_coul_long_kokkos.h b/src/KOKKOS/pair_buck_coul_long_kokkos.h
index be506ce27f..55f746ec6d 100644
--- a/src/KOKKOS/pair_buck_coul_long_kokkos.h
+++ b/src/KOKKOS/pair_buck_coul_long_kokkos.h
@@ -105,7 +105,7 @@ class PairBuckCoulLongKokkos : public PairBuckCoulLong {
typename ArrayTypes<DeviceType>::t_ffloat_1d_randomread
d_rtable, d_drtable, d_ftable, d_dftable,
d_ctable, d_dctable, d_etable, d_detable;
-
+
int neighflag;
int nlocal,nall,eflag,vflag;
diff --git a/src/KOKKOS/pair_buck_kokkos.cpp b/src/KOKKOS/pair_buck_kokkos.cpp
index 7cabbeaf77..7d73160392 100755
--- a/src/KOKKOS/pair_buck_kokkos.cpp
+++ b/src/KOKKOS/pair_buck_kokkos.cpp
@@ -15,10 +15,10 @@
Contributing author: Stan Moore (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_buck_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
@@ -216,7 +216,7 @@ void PairBuckKokkos<DeviceType>::init_style()
int respa = 0;
if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;
- if (respa)
+ if (respa)
error->all(FLERR,"Cannot use Kokkos pair style with rRESPA inner/middle");
}
diff --git a/src/KOKKOS/pair_buck_kokkos.h b/src/KOKKOS/pair_buck_kokkos.h
index f0f461db0d..217bca7b34 100755
--- a/src/KOKKOS/pair_buck_kokkos.h
+++ b/src/KOKKOS/pair_buck_kokkos.h
@@ -87,7 +87,7 @@ class PairBuckKokkos : public PairBuck {
typename ArrayTypes<DeviceType>::tdual_ffloat_2d k_cutsq;
typename ArrayTypes<DeviceType>::t_ffloat_2d d_cutsq;
-
+
int neighflag;
int nlocal,nall,eflag,vflag;
diff --git a/src/KOKKOS/pair_coul_cut_kokkos.cpp b/src/KOKKOS/pair_coul_cut_kokkos.cpp
index 8ec7aa41ad..cfed188c5a 100644
--- a/src/KOKKOS/pair_coul_cut_kokkos.cpp
+++ b/src/KOKKOS/pair_coul_cut_kokkos.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_coul_cut_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
diff --git a/src/KOKKOS/pair_coul_cut_kokkos.h b/src/KOKKOS/pair_coul_cut_kokkos.h
index 4b2175eac9..754706ef4d 100644
--- a/src/KOKKOS/pair_coul_cut_kokkos.h
+++ b/src/KOKKOS/pair_coul_cut_kokkos.h
@@ -104,7 +104,7 @@ class PairCoulCutKokkos : public PairCoulCut {
typename ArrayTypes<DeviceType>::tdual_ffloat_2d k_cut_coulsq;
typename ArrayTypes<DeviceType>::t_ffloat_2d d_cut_coulsq;
-
+
int neighflag;
int nlocal,nall,eflag,vflag;
diff --git a/src/KOKKOS/pair_coul_debye_kokkos.cpp b/src/KOKKOS/pair_coul_debye_kokkos.cpp
index 50fb7f8162..ea28e325a5 100644
--- a/src/KOKKOS/pair_coul_debye_kokkos.cpp
+++ b/src/KOKKOS/pair_coul_debye_kokkos.cpp
@@ -15,10 +15,10 @@
Contributing author: Ray Shan (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_coul_debye_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
@@ -159,7 +159,7 @@ compute_fcoul(const F_FLOAT& rsq, const int& i, const int&j,
const F_FLOAT screening = exp(-kappa*r);
F_FLOAT forcecoul;
- forcecoul = qqrd2e * qtmp * q(j) * screening * (kappa + rinv) *
+ forcecoul = qqrd2e * qtmp * q(j) * screening * (kappa + rinv) *
(STACKPARAMS?m_params[itype][jtype].scale:params(itype,jtype).scale);
return factor_coul*forcecoul*r2inv;
@@ -181,7 +181,7 @@ compute_ecoul(const F_FLOAT& rsq, const int& i, const int&j,
const F_FLOAT r = 1.0/rinv;
const F_FLOAT screening = exp(-kappa*r);
- return factor_coul * qqrd2e * qtmp * q(j) * rinv * screening *
+ return factor_coul * qqrd2e * qtmp * q(j) * rinv * screening *
(STACKPARAMS?m_params[itype][jtype].scale:params(itype,jtype).scale);
}
diff --git a/src/KOKKOS/pair_coul_debye_kokkos.h b/src/KOKKOS/pair_coul_debye_kokkos.h
index 25bb15b162..8e6095401a 100644
--- a/src/KOKKOS/pair_coul_debye_kokkos.h
+++ b/src/KOKKOS/pair_coul_debye_kokkos.h
@@ -102,7 +102,7 @@ class PairCoulDebyeKokkos : public PairCoulDebye {
typename ArrayTypes<DeviceType>::tdual_ffloat_2d k_cut_coulsq;
typename ArrayTypes<DeviceType>::t_ffloat_2d d_cut_coulsq;
-
+
int neighflag;
int nlocal,nall,eflag,vflag;
diff --git a/src/KOKKOS/pair_coul_dsf_kokkos.cpp b/src/KOKKOS/pair_coul_dsf_kokkos.cpp
index f88efd0d8e..f80fe0d38e 100755
--- a/src/KOKKOS/pair_coul_dsf_kokkos.cpp
+++ b/src/KOKKOS/pair_coul_dsf_kokkos.cpp
@@ -15,10 +15,10 @@
Contributing author: Stan Moore (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_coul_dsf_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
@@ -287,7 +287,7 @@ void PairCoulDSFKokkos<DeviceType>::operator()(TagPairCoulDSFKernelA<NEIGHFLAG,N
const F_FLOAT erfcd = exp(-alpha*alpha*rsq);
const F_FLOAT t = 1.0 / (1.0 + EWALD_P*alpha*r);
const F_FLOAT erfcc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * erfcd;
- const F_FLOAT forcecoul = prefactor * (erfcc/r + 2.0*alpha/MY_PIS * erfcd +
+ const F_FLOAT forcecoul = prefactor * (erfcc/r + 2.0*alpha/MY_PIS * erfcd +
r*f_shift) * r;
const F_FLOAT fpair = forcecoul * r2inv;
@@ -424,7 +424,7 @@ void PairCoulDSFKokkos<DeviceType>::ev_tally(EV_FLOAT &ev, const int &i, const i
/* ---------------------------------------------------------------------- */
template<class DeviceType>
-KOKKOS_INLINE_FUNCTION
+KOKKOS_INLINE_FUNCTION
int PairCoulDSFKokkos<DeviceType>::sbmask(const int& j) const {
return j >> SBBITS & 3;
}
diff --git a/src/KOKKOS/pair_coul_dsf_kokkos.h b/src/KOKKOS/pair_coul_dsf_kokkos.h
index 31cb501bb7..f9bc250557 100755
--- a/src/KOKKOS/pair_coul_dsf_kokkos.h
+++ b/src/KOKKOS/pair_coul_dsf_kokkos.h
@@ -73,7 +73,7 @@ class PairCoulDSFKokkos : public PairCoulDSF {
DAT::t_efloat_1d d_eatom;
DAT::t_virial_array d_vatom;
-
+
int neighflag,newton_pair;
int nlocal,nall,eflag,vflag;
diff --git a/src/KOKKOS/pair_coul_long_kokkos.cpp b/src/KOKKOS/pair_coul_long_kokkos.cpp
index 7d92b634d5..150ed99296 100644
--- a/src/KOKKOS/pair_coul_long_kokkos.cpp
+++ b/src/KOKKOS/pair_coul_long_kokkos.cpp
@@ -15,10 +15,10 @@
Contributing author: Ray Shan (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_coul_long_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
diff --git a/src/KOKKOS/pair_coul_long_kokkos.h b/src/KOKKOS/pair_coul_long_kokkos.h
index db996f22b0..c546a10a28 100644
--- a/src/KOKKOS/pair_coul_long_kokkos.h
+++ b/src/KOKKOS/pair_coul_long_kokkos.h
@@ -109,7 +109,7 @@ class PairCoulLongKokkos : public PairCoulLong {
typename ArrayTypes<DeviceType>::t_ffloat_1d_randomread
d_rtable, d_drtable, d_ftable, d_dftable,
d_ctable, d_dctable, d_etable, d_detable;
-
+
int neighflag;
int nlocal,nall,eflag,vflag;
diff --git a/src/KOKKOS/pair_coul_wolf_kokkos.cpp b/src/KOKKOS/pair_coul_wolf_kokkos.cpp
index 6b951a1548..4d2804ce0f 100755
--- a/src/KOKKOS/pair_coul_wolf_kokkos.cpp
+++ b/src/KOKKOS/pair_coul_wolf_kokkos.cpp
@@ -15,10 +15,10 @@
Contributing author: Stan Moore (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_coul_wolf_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
@@ -426,7 +426,7 @@ void PairCoulWolfKokkos<DeviceType>::ev_tally(EV_FLOAT &ev, const int &i, const
/* ---------------------------------------------------------------------- */
template<class DeviceType>
-KOKKOS_INLINE_FUNCTION
+KOKKOS_INLINE_FUNCTION
int PairCoulWolfKokkos<DeviceType>::sbmask(const int& j) const {
return j >> SBBITS & 3;
}
diff --git a/src/KOKKOS/pair_coul_wolf_kokkos.h b/src/KOKKOS/pair_coul_wolf_kokkos.h
index 20a34f8eea..1efafca99c 100755
--- a/src/KOKKOS/pair_coul_wolf_kokkos.h
+++ b/src/KOKKOS/pair_coul_wolf_kokkos.h
@@ -73,7 +73,7 @@ class PairCoulWolfKokkos : public PairCoulWolf {
DAT::t_efloat_1d d_eatom;
DAT::t_virial_array d_vatom;
-
+
int neighflag,newton_pair;
int nlocal,nall,eflag,vflag;
diff --git a/src/KOKKOS/pair_eam_alloy_kokkos.cpp b/src/KOKKOS/pair_eam_alloy_kokkos.cpp
index 2e56307779..706cf0b523 100755
--- a/src/KOKKOS/pair_eam_alloy_kokkos.cpp
+++ b/src/KOKKOS/pair_eam_alloy_kokkos.cpp
@@ -15,10 +15,10 @@
Contributing authors: Stan Moore (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "kokkos.h"
#include "pair_kokkos.h"
#include "pair_eam_alloy_kokkos.h"
diff --git a/src/KOKKOS/pair_eam_alloy_kokkos.h b/src/KOKKOS/pair_eam_alloy_kokkos.h
index 2d48f0fde5..1187dc0a2d 100755
--- a/src/KOKKOS/pair_eam_alloy_kokkos.h
+++ b/src/KOKKOS/pair_eam_alloy_kokkos.h
@@ -23,7 +23,7 @@ PairStyle(eam/alloy/kk/host,PairEAMAlloyKokkos<LMPHostType>)
#ifndef LMP_PAIR_EAM_ALLOY_KOKKOS_H
#define LMP_PAIR_EAM_ALLOY_KOKKOS_H
-#include "stdio.h"
+#include <stdio.h>
#include "pair_kokkos.h"
#include "pair_eam.h"
#include "neigh_list_kokkos.h"
@@ -71,7 +71,7 @@ class PairEAMAlloyKokkos : public PairEAM {
KOKKOS_INLINE_FUNCTION
void operator()(TagPairEAMAlloyInitialize, const int&) const;
-
+
template<int NEIGHFLAG, int NEWTON_PAIR>
KOKKOS_INLINE_FUNCTION
void operator()(TagPairEAMAlloyKernelA<NEIGHFLAG,NEWTON_PAIR>, const int&) const;
@@ -106,7 +106,7 @@ class PairEAMAlloyKokkos : public PairEAM {
const F_FLOAT &epair, const F_FLOAT &fpair, const F_FLOAT &delx,
const F_FLOAT &dely, const F_FLOAT &delz) const;
- virtual int pack_forward_comm_kokkos(int, DAT::tdual_int_2d, int, DAT::tdual_xfloat_1d&,
+ virtual int pack_forward_comm_kokkos(int, DAT::tdual_int_2d, int, DAT::tdual_xfloat_1d&,
int, int *);
virtual void unpack_forward_comm_kokkos(int, int, DAT::tdual_xfloat_1d&);
virtual int pack_forward_comm(int, int *, double *, int, int *);
diff --git a/src/KOKKOS/pair_eam_fs_kokkos.cpp b/src/KOKKOS/pair_eam_fs_kokkos.cpp
index a95deb8542..6d96d3c33c 100755
--- a/src/KOKKOS/pair_eam_fs_kokkos.cpp
+++ b/src/KOKKOS/pair_eam_fs_kokkos.cpp
@@ -15,10 +15,10 @@
Contributing authors: Stan Moore (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "kokkos.h"
#include "pair_kokkos.h"
#include "pair_eam_fs_kokkos.h"
diff --git a/src/KOKKOS/pair_eam_fs_kokkos.h b/src/KOKKOS/pair_eam_fs_kokkos.h
index 9ffa121467..4ac0093988 100755
--- a/src/KOKKOS/pair_eam_fs_kokkos.h
+++ b/src/KOKKOS/pair_eam_fs_kokkos.h
@@ -23,7 +23,7 @@ PairStyle(eam/fs/kk/host,PairEAMFSKokkos<LMPHostType>)
#ifndef LMP_PAIR_EAM_FS_KOKKOS_H
#define LMP_PAIR_EAM_FS_KOKKOS_H
-#include "stdio.h"
+#include <stdio.h>
#include "pair_kokkos.h"
#include "pair_eam.h"
#include "neigh_list_kokkos.h"
@@ -71,7 +71,7 @@ class PairEAMFSKokkos : public PairEAM {
KOKKOS_INLINE_FUNCTION
void operator()(TagPairEAMFSInitialize, const int&) const;
-
+
template<int NEIGHFLAG, int NEWTON_PAIR>
KOKKOS_INLINE_FUNCTION
void operator()(TagPairEAMFSKernelA<NEIGHFLAG,NEWTON_PAIR>, const int&) const;
@@ -106,7 +106,7 @@ class PairEAMFSKokkos : public PairEAM {
const F_FLOAT &epair, const F_FLOAT &fpair, const F_FLOAT &delx,
const F_FLOAT &dely, const F_FLOAT &delz) const;
- virtual int pack_forward_comm_kokkos(int, DAT::tdual_int_2d, int, DAT::tdual_xfloat_1d&,
+ virtual int pack_forward_comm_kokkos(int, DAT::tdual_int_2d, int, DAT::tdual_xfloat_1d&,
int, int *);
virtual void unpack_forward_comm_kokkos(int, int, DAT::tdual_xfloat_1d&);
virtual int pack_forward_comm(int, int *, double *, int, int *);
diff --git a/src/KOKKOS/pair_eam_kokkos.cpp b/src/KOKKOS/pair_eam_kokkos.cpp
index 14cd2ab8c2..b643393f84 100755
--- a/src/KOKKOS/pair_eam_kokkos.cpp
+++ b/src/KOKKOS/pair_eam_kokkos.cpp
@@ -15,10 +15,10 @@
Contributing authors: Stan Moore (SNL), Christian Trott (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "kokkos.h"
#include "pair_kokkos.h"
#include "pair_eam_kokkos.h"
@@ -278,7 +278,7 @@ void PairEAMKokkos<DeviceType>::init_style()
int irequest = neighbor->nrequest - 1;
neighbor->requests[irequest]->
- kokkos_host = Kokkos::Impl::is_same<DeviceType,LMPHostType>::value &&
+ kokkos_host = Kokkos::Impl::is_same<DeviceType,LMPHostType>::value &&
!Kokkos::Impl::is_same<DeviceType,LMPDeviceType>::value;
neighbor->requests[irequest]->
kokkos_device = Kokkos::Impl::is_same<DeviceType,LMPDeviceType>::value;
@@ -294,7 +294,7 @@ void PairEAMKokkos<DeviceType>::init_style()
} else {
error->all(FLERR,"Cannot use chosen neighbor list style with pair eam/kk");
}
-
+
}
/* ----------------------------------------------------------------------
@@ -480,7 +480,7 @@ void PairEAMKokkos<DeviceType>::interpolate(int n, double delta, double *f, t_ho
/* ---------------------------------------------------------------------- */
template<class DeviceType>
-int PairEAMKokkos<DeviceType>::pack_forward_comm_kokkos(int n, DAT::tdual_int_2d k_sendlist, int iswap_in, DAT::tdual_xfloat_1d &buf,
+int PairEAMKokkos<DeviceType>::pack_forward_comm_kokkos(int n, DAT::tdual_int_2d k_sendlist, int iswap_in, DAT::tdual_xfloat_1d &buf,
int pbc_flag, int *pbc)
{
d_sendlist = k_sendlist.view<DeviceType>();
@@ -518,7 +518,7 @@ void PairEAMKokkos<DeviceType>::operator()(TagPairEAMUnpackForwardComm, const in
/* ---------------------------------------------------------------------- */
template<class DeviceType>
-int PairEAMKokkos<DeviceType>::pack_forward_comm(int n, int *list, double *buf,
+int PairEAMKokkos<DeviceType>::pack_forward_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j;
@@ -585,7 +585,7 @@ void PairEAMKokkos<DeviceType>::operator()(TagPairEAMKernelA<NEIGHFLAG,NEWTON_PA
// rho = density at each atom
// loop over neighbors of my atoms
-
+
// The rho array is atomic for Half/Thread neighbor style
Kokkos::View<F_FLOAT*, typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > rho = v_rho;
@@ -626,7 +626,7 @@ void PairEAMKokkos<DeviceType>::operator()(TagPairEAMKernelA<NEIGHFLAG,NEWTON_PA
rho[j] += ((rhor.x*p + rhor.y)*p + rhor.z)*p + rhor.w;
}
}
-
+
}
rho[i] += rhotmp;
}
@@ -714,7 +714,7 @@ void PairEAMKokkos<DeviceType>::operator()(TagPairEAMKernelAB<EFLAG>, const int
const F_FLOAT4 rhor = d_rhor_spline_b(d_type2rhor_ji,m);
rhotmp += ((rhor.x*p + rhor.y)*p + rhor.z)*p + rhor.w;
}
-
+
}
d_rho[i] += rhotmp;
diff --git a/src/KOKKOS/pair_eam_kokkos.h b/src/KOKKOS/pair_eam_kokkos.h
index 4bd43cd38a..b3d33bb37f 100755
--- a/src/KOKKOS/pair_eam_kokkos.h
+++ b/src/KOKKOS/pair_eam_kokkos.h
@@ -23,7 +23,7 @@ PairStyle(eam/kk/host,PairEAMKokkos<LMPHostType>)
#ifndef LMP_PAIR_EAM_KOKKOS_H
#define LMP_PAIR_EAM_KOKKOS_H
-#include "stdio.h"
+#include <stdio.h>
#include "pair_kokkos.h"
#include "pair_eam.h"
#include "neigh_list_kokkos.h"
@@ -68,7 +68,7 @@ class PairEAMKokkos : public PairEAM {
KOKKOS_INLINE_FUNCTION
void operator()(TagPairEAMInitialize, const int&) const;
-
+
template<int NEIGHFLAG, int NEWTON_PAIR>
KOKKOS_INLINE_FUNCTION
void operator()(TagPairEAMKernelA<NEIGHFLAG,NEWTON_PAIR>, const int&) const;
@@ -103,7 +103,7 @@ class PairEAMKokkos : public PairEAM {
const F_FLOAT &epair, const F_FLOAT &fpair, const F_FLOAT &delx,
const F_FLOAT &dely, const F_FLOAT &delz) const;
- virtual int pack_forward_comm_kokkos(int, DAT::tdual_int_2d, int, DAT::tdual_xfloat_1d&,
+ virtual int pack_forward_comm_kokkos(int, DAT::tdual_int_2d, int, DAT::tdual_xfloat_1d&,
int, int *);
virtual void unpack_forward_comm_kokkos(int, int, DAT::tdual_xfloat_1d&);
virtual int pack_forward_comm(int, int *, double *, int, int *);
@@ -158,7 +158,7 @@ class PairEAMKokkos : public PairEAM {
typename AT::t_int_2d d_sendlist;
typename AT::t_xfloat_1d_um v_buf;
-
+
int neighflag,newton_pair;
int nlocal,nall,eflag,vflag;
diff --git a/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp b/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp
index c2b05e8287..4e97e3ebd2 100644
--- a/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp
@@ -15,10 +15,10 @@
Contributing author: Ray Shan (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_lj_charmm_coul_charmm_implicit_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
@@ -195,8 +195,8 @@ compute_fpair(const F_FLOAT& rsq, const int& i, const int&j,
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
switch2 = 12.0*rsq * (cut_ljsq-rsq) * (rsq-cut_lj_innersq) / denom_lj;
- englj = r6inv *
- ((STACKPARAMS?m_params[itype][jtype].lj3:params(itype,jtype).lj3)*r6inv -
+ englj = r6inv *
+ ((STACKPARAMS?m_params[itype][jtype].lj3:params(itype,jtype).lj3)*r6inv -
(STACKPARAMS?m_params[itype][jtype].lj4:params(itype,jtype).lj4));
forcelj = forcelj*switch1 + englj*switch2;
}
@@ -215,9 +215,9 @@ compute_evdwl(const F_FLOAT& rsq, const int& i, const int&j,
const int& itype, const int& jtype) const {
const F_FLOAT r2inv = 1.0/rsq;
const F_FLOAT r6inv = r2inv*r2inv*r2inv;
- F_FLOAT englj, switch1;
+ F_FLOAT englj, switch1;
- englj = r6inv *
+ englj = r6inv *
((STACKPARAMS?m_params[itype][jtype].lj3:params(itype,jtype).lj3)*r6inv -
(STACKPARAMS?m_params[itype][jtype].lj4:params(itype,jtype).lj4));
@@ -268,7 +268,7 @@ compute_ecoul(const F_FLOAT& rsq, const int& i, const int&j,
const int& itype, const int& jtype, const F_FLOAT& factor_coul, const F_FLOAT& qtmp) const {
const F_FLOAT r2inv = 1.0/rsq;
- F_FLOAT ecoul, switch1;
+ F_FLOAT ecoul, switch1;
ecoul = qqrd2e * qtmp * q(j) * r2inv;
if (rsq > cut_coul_innersq) {
diff --git a/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.h b/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.h
index 06950756ea..0174d55768 100644
--- a/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.h
+++ b/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.h
@@ -105,7 +105,7 @@ class PairLJCharmmCoulCharmmImplicitKokkos : public PairLJCharmmCoulCharmmImplic
typename ArrayTypes<DeviceType>::t_ffloat_1d_randomread
d_rtable, d_drtable, d_ftable, d_dftable,
d_ctable, d_dctable, d_etable, d_detable;
-
+
int neighflag;
int nlocal,nall,eflag,vflag;
diff --git a/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp b/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp
index 2fa71aeebf..9b7b8d8d7a 100644
--- a/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp
@@ -15,10 +15,10 @@
Contributing author: Ray Shan (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_lj_charmm_coul_charmm_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
@@ -195,8 +195,8 @@ compute_fpair(const F_FLOAT& rsq, const int& i, const int&j,
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
switch2 = 12.0*rsq * (cut_ljsq-rsq) * (rsq-cut_lj_innersq) / denom_lj;
- englj = r6inv *
- ((STACKPARAMS?m_params[itype][jtype].lj3:params(itype,jtype).lj3)*r6inv -
+ englj = r6inv *
+ ((STACKPARAMS?m_params[itype][jtype].lj3:params(itype,jtype).lj3)*r6inv -
(STACKPARAMS?m_params[itype][jtype].lj4:params(itype,jtype).lj4));
forcelj = forcelj*switch1 + englj*switch2;
}
@@ -215,9 +215,9 @@ compute_evdwl(const F_FLOAT& rsq, const int& i, const int&j,
const int& itype, const int& jtype) const {
const F_FLOAT r2inv = 1.0/rsq;
const F_FLOAT r6inv = r2inv*r2inv*r2inv;
- F_FLOAT englj, switch1;
+ F_FLOAT englj, switch1;
- englj = r6inv *
+ englj = r6inv *
((STACKPARAMS?m_params[itype][jtype].lj3:params(itype,jtype).lj3)*r6inv -
(STACKPARAMS?m_params[itype][jtype].lj4:params(itype,jtype).lj4));
@@ -270,7 +270,7 @@ compute_ecoul(const F_FLOAT& rsq, const int& i, const int&j,
const F_FLOAT r2inv = 1.0/rsq;
const F_FLOAT rinv = sqrt(r2inv);
- F_FLOAT ecoul, switch1;
+ F_FLOAT ecoul, switch1;
ecoul = qqrd2e * qtmp * q(j) * rinv;
if (rsq > cut_coul_innersq) {
diff --git a/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.h b/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.h
index ee76bb193e..34134fd520 100644
--- a/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.h
+++ b/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.h
@@ -105,7 +105,7 @@ class PairLJCharmmCoulCharmmKokkos : public PairLJCharmmCoulCharmm {
typename ArrayTypes<DeviceType>::t_ffloat_1d_randomread
d_rtable, d_drtable, d_ftable, d_dftable,
d_ctable, d_dctable, d_etable, d_detable;
-
+
int neighflag;
int nlocal,nall,eflag,vflag;
diff --git a/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp b/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp
index 8809912cdd..ad41540b5e 100644
--- a/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp
@@ -15,10 +15,10 @@
Contributing author: Ray Shan (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_lj_charmm_coul_long_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
@@ -195,8 +195,8 @@ compute_fpair(const F_FLOAT& rsq, const int& i, const int&j,
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
switch2 = 12.0*rsq * (cut_ljsq-rsq) * (rsq-cut_lj_innersq) / denom_lj;
- englj = r6inv *
- ((STACKPARAMS?m_params[itype][jtype].lj3:params(itype,jtype).lj3)*r6inv -
+ englj = r6inv *
+ ((STACKPARAMS?m_params[itype][jtype].lj3:params(itype,jtype).lj3)*r6inv -
(STACKPARAMS?m_params[itype][jtype].lj4:params(itype,jtype).lj4));
forcelj = forcelj*switch1 + englj*switch2;
}
@@ -215,9 +215,9 @@ compute_evdwl(const F_FLOAT& rsq, const int& i, const int&j,
const int& itype, const int& jtype) const {
const F_FLOAT r2inv = 1.0/rsq;
const F_FLOAT r6inv = r2inv*r2inv*r2inv;
- F_FLOAT englj, switch1;
+ F_FLOAT englj, switch1;
- englj = r6inv *
+ englj = r6inv *
((STACKPARAMS?m_params[itype][jtype].lj3:params(itype,jtype).lj3)*r6inv -
(STACKPARAMS?m_params[itype][jtype].lj4:params(itype,jtype).lj4));
diff --git a/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.h b/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.h
index 039af94c55..f212540a14 100644
--- a/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.h
+++ b/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.h
@@ -105,7 +105,7 @@ class PairLJCharmmCoulLongKokkos : public PairLJCharmmCoulLong {
typename ArrayTypes<DeviceType>::t_ffloat_1d_randomread
d_rtable, d_drtable, d_ftable, d_dftable,
d_ctable, d_dctable, d_etable, d_detable;
-
+
int neighflag;
int nlocal,nall,eflag,vflag;
diff --git a/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp b/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp
index 283b88b579..9a451a744e 100644
--- a/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_lj_class2_coul_cut_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
diff --git a/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp b/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp
index 3e530afa3f..a9cb4fbbe1 100644
--- a/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_lj_class2_coul_long_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
diff --git a/src/KOKKOS/pair_lj_class2_coul_long_kokkos.h b/src/KOKKOS/pair_lj_class2_coul_long_kokkos.h
index 76728c36ff..b376906e49 100644
--- a/src/KOKKOS/pair_lj_class2_coul_long_kokkos.h
+++ b/src/KOKKOS/pair_lj_class2_coul_long_kokkos.h
@@ -102,7 +102,7 @@ class PairLJClass2CoulLongKokkos : public PairLJClass2CoulLong {
typename ArrayTypes<DeviceType>::t_ffloat_1d_randomread
d_rtable, d_drtable, d_ftable, d_dftable,
d_ctable, d_dctable, d_etable, d_detable;
-
+
int neighflag;
int nlocal,nall,eflag,vflag;
diff --git a/src/KOKKOS/pair_lj_class2_kokkos.cpp b/src/KOKKOS/pair_lj_class2_kokkos.cpp
index 62d228dfb1..9bc3989fff 100644
--- a/src/KOKKOS/pair_lj_class2_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_class2_kokkos.cpp
@@ -15,10 +15,10 @@
Contributing author: Ray Shan (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_lj_class2_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
@@ -210,7 +210,7 @@ void PairLJClass2Kokkos<DeviceType>::init_style()
int respa = 0;
if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;
- if (respa)
+ if (respa)
error->all(FLERR,"Cannot use Kokkos pair style with rRESPA inner/middle");
}
@@ -220,7 +220,7 @@ void PairLJClass2Kokkos<DeviceType>::init_style()
int irequest = neighbor->nrequest - 1;
neighbor->requests[irequest]->
- kokkos_host = Kokkos::Impl::is_same<DeviceType,LMPHostType>::value &&
+ kokkos_host = Kokkos::Impl::is_same<DeviceType,LMPHostType>::value &&
!Kokkos::Impl::is_same<DeviceType,LMPDeviceType>::value;
neighbor->requests[irequest]->
kokkos_device = Kokkos::Impl::is_same<DeviceType,LMPDeviceType>::value;
diff --git a/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp
index 12d6fe9178..c3b9439670 100644
--- a/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_lj_cut_coul_cut_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
diff --git a/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.h b/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.h
index 20ebfa3b03..a73af32b8d 100644
--- a/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.h
+++ b/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.h
@@ -100,7 +100,7 @@ class PairLJCutCoulCutKokkos : public PairLJCutCoulCut {
typename ArrayTypes<DeviceType>::tdual_ffloat_2d k_cut_coulsq;
typename ArrayTypes<DeviceType>::t_ffloat_2d d_cut_coulsq;
-
+
int neighflag;
int nlocal,nall,eflag,vflag;
diff --git a/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp
index 92908a62ab..4e3680bf30 100644
--- a/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp
@@ -15,10 +15,10 @@
Contributing author: Ray Shan (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_lj_cut_coul_debye_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
diff --git a/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.h b/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.h
index e5a5d76a16..6195fee90e 100644
--- a/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.h
+++ b/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.h
@@ -98,7 +98,7 @@ class PairLJCutCoulDebyeKokkos : public PairLJCutCoulDebye {
typename ArrayTypes<DeviceType>::tdual_ffloat_2d k_cut_coulsq;
typename ArrayTypes<DeviceType>::t_ffloat_2d d_cut_coulsq;
-
+
int neighflag;
int nlocal,nall,eflag,vflag;
diff --git a/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp
index 2c74fa91ca..480f2ad180 100644
--- a/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp
@@ -15,10 +15,10 @@
Contributing author: Ray Shan (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_lj_cut_coul_dsf_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
@@ -223,7 +223,7 @@ compute_fcoul(const F_FLOAT& rsq, const int& i, const int&j,
const F_FLOAT t = 1.0 / (1.0 + EWALD_P*alpha*r);
const F_FLOAT erfcc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * erfcd;
- return prefactor * (erfcc/r + 2.0*alpha/MY_PIS * erfcd + r*f_shift) *
+ return prefactor * (erfcc/r + 2.0*alpha/MY_PIS * erfcd + r*f_shift) *
r2inv;
}
diff --git a/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.h b/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.h
index 661125a1b7..4ce73f4a94 100644
--- a/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.h
+++ b/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.h
@@ -97,7 +97,7 @@ class PairLJCutCoulDSFKokkos : public PairLJCutCoulDSF {
typename ArrayTypes<DeviceType>::tdual_ffloat_2d k_cut_coulsq;
typename ArrayTypes<DeviceType>::t_ffloat_2d d_cut_coulsq;
-
+
int neighflag;
int nlocal,nall,eflag,vflag;
diff --git a/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp
index 590c890676..356fc4f2c5 100644
--- a/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_lj_cut_coul_long_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
diff --git a/src/KOKKOS/pair_lj_cut_coul_long_kokkos.h b/src/KOKKOS/pair_lj_cut_coul_long_kokkos.h
index 1700bd04c2..a18797e1aa 100644
--- a/src/KOKKOS/pair_lj_cut_coul_long_kokkos.h
+++ b/src/KOKKOS/pair_lj_cut_coul_long_kokkos.h
@@ -102,7 +102,7 @@ class PairLJCutCoulLongKokkos : public PairLJCutCoulLong {
typename ArrayTypes<DeviceType>::t_ffloat_1d_randomread
d_rtable, d_drtable, d_ftable, d_dftable,
d_ctable, d_dctable, d_etable, d_detable;
-
+
int neighflag;
int nlocal,nall,eflag,vflag;
diff --git a/src/KOKKOS/pair_lj_cut_kokkos.cpp b/src/KOKKOS/pair_lj_cut_kokkos.cpp
index 657848585c..1e400c6413 100644
--- a/src/KOKKOS/pair_lj_cut_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_cut_kokkos.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_lj_cut_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
@@ -201,7 +201,7 @@ void PairLJCutKokkos<DeviceType>::init_style()
int respa = 0;
if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;
- if (respa)
+ if (respa)
error->all(FLERR,"Cannot use Kokkos pair style with rRESPA inner/middle");
}
@@ -211,7 +211,7 @@ void PairLJCutKokkos<DeviceType>::init_style()
int irequest = neighbor->nrequest - 1;
neighbor->requests[irequest]->
- kokkos_host = Kokkos::Impl::is_same<DeviceType,LMPHostType>::value &&
+ kokkos_host = Kokkos::Impl::is_same<DeviceType,LMPHostType>::value &&
!Kokkos::Impl::is_same<DeviceType,LMPDeviceType>::value;
neighbor->requests[irequest]->
kokkos_device = Kokkos::Impl::is_same<DeviceType,LMPDeviceType>::value;
diff --git a/src/KOKKOS/pair_lj_cut_kokkos.h b/src/KOKKOS/pair_lj_cut_kokkos.h
index 4da4730650..37046e457a 100644
--- a/src/KOKKOS/pair_lj_cut_kokkos.h
+++ b/src/KOKKOS/pair_lj_cut_kokkos.h
@@ -87,7 +87,7 @@ class PairLJCutKokkos : public PairLJCut {
typename ArrayTypes<DeviceType>::tdual_ffloat_2d k_cutsq;
typename ArrayTypes<DeviceType>::t_ffloat_2d d_cutsq;
-
+
int neighflag;
int nlocal,nall,eflag,vflag;
diff --git a/src/KOKKOS/pair_lj_expand_kokkos.cpp b/src/KOKKOS/pair_lj_expand_kokkos.cpp
index 43efff0205..29473f14bc 100644
--- a/src/KOKKOS/pair_lj_expand_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_expand_kokkos.cpp
@@ -15,10 +15,10 @@
Contributing author: Ray Shan (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_lj_expand_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
@@ -213,7 +213,7 @@ void PairLJExpandKokkos<DeviceType>::init_style()
int respa = 0;
if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;
- if (respa)
+ if (respa)
error->all(FLERR,"Cannot use Kokkos pair style with rRESPA inner/middle");
}
@@ -223,7 +223,7 @@ void PairLJExpandKokkos<DeviceType>::init_style()
int irequest = neighbor->nrequest - 1;
neighbor->requests[irequest]->
- kokkos_host = Kokkos::Impl::is_same<DeviceType,LMPHostType>::value &&
+ kokkos_host = Kokkos::Impl::is_same<DeviceType,LMPHostType>::value &&
!Kokkos::Impl::is_same<DeviceType,LMPDeviceType>::value;
neighbor->requests[irequest]->
kokkos_device = Kokkos::Impl::is_same<DeviceType,LMPDeviceType>::value;
diff --git a/src/KOKKOS/pair_lj_expand_kokkos.h b/src/KOKKOS/pair_lj_expand_kokkos.h
index c8b8684cdc..1e7f57befd 100644
--- a/src/KOKKOS/pair_lj_expand_kokkos.h
+++ b/src/KOKKOS/pair_lj_expand_kokkos.h
@@ -91,7 +91,7 @@ class PairLJExpandKokkos : public PairLJExpand {
typename ArrayTypes<DeviceType>::tdual_ffloat_2d k_cutsq;
typename ArrayTypes<DeviceType>::t_ffloat_2d d_cutsq;
-
+
int neighflag;
int nlocal,nall,eflag,vflag;
diff --git a/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp b/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp
index 6fd07bd67c..7081dd5417 100644
--- a/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp
@@ -15,10 +15,10 @@
Contributing author: Ray Shan (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_lj_gromacs_coul_gromacs_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
@@ -185,7 +185,7 @@ compute_fpair(const F_FLOAT& rsq, const int& i, const int&j,
const F_FLOAT r = sqrt(rsq);
const F_FLOAT tlj = r - cut_lj_inner;
const F_FLOAT fswitch = r*tlj*tlj*
- ((STACKPARAMS?m_params[itype][jtype].ljsw1:params(itype,jtype).ljsw1) +
+ ((STACKPARAMS?m_params[itype][jtype].ljsw1:params(itype,jtype).ljsw1) +
(STACKPARAMS?m_params[itype][jtype].ljsw2:params(itype,jtype).ljsw2)*tlj);
forcelj += fswitch;
}
@@ -204,7 +204,7 @@ compute_evdwl(const F_FLOAT& rsq, const int& i, const int&j,
const F_FLOAT r2inv = 1.0/rsq;
const F_FLOAT r6inv = r2inv*r2inv*r2inv;
- F_FLOAT englj = r6inv *
+ F_FLOAT englj = r6inv *
((STACKPARAMS?m_params[itype][jtype].lj3:params(itype,jtype).lj3)*r6inv -
(STACKPARAMS?m_params[itype][jtype].lj4:params(itype,jtype).lj4));
englj += (STACKPARAMS?m_params[itype][jtype].ljsw5:params(itype,jtype).ljsw5);
@@ -213,7 +213,7 @@ compute_evdwl(const F_FLOAT& rsq, const int& i, const int&j,
const F_FLOAT r = sqrt(rsq);
const F_FLOAT tlj = r - cut_lj_inner;
const F_FLOAT eswitch = tlj*tlj*tlj *
- ((STACKPARAMS?m_params[itype][jtype].ljsw3:params(itype,jtype).ljsw3) +
+ ((STACKPARAMS?m_params[itype][jtype].ljsw3:params(itype,jtype).ljsw3) +
(STACKPARAMS?m_params[itype][jtype].ljsw4:params(itype,jtype).ljsw4)*tlj);
englj += eswitch;
}
diff --git a/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.h b/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.h
index 81db722433..3a69ba1172 100644
--- a/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.h
+++ b/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.h
@@ -105,7 +105,7 @@ class PairLJGromacsCoulGromacsKokkos : public PairLJGromacsCoulGromacs {
typename ArrayTypes<DeviceType>::t_ffloat_1d_randomread
d_rtable, d_drtable, d_ftable, d_dftable,
d_ctable, d_dctable, d_etable, d_detable;
-
+
int neighflag;
int nlocal,nall,eflag,vflag;
diff --git a/src/KOKKOS/pair_lj_gromacs_kokkos.cpp b/src/KOKKOS/pair_lj_gromacs_kokkos.cpp
index be9d5faaf1..d1699fe6b6 100644
--- a/src/KOKKOS/pair_lj_gromacs_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_gromacs_kokkos.cpp
@@ -15,10 +15,10 @@
Contributing author: Ray Shan (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_lj_gromacs_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
@@ -172,7 +172,7 @@ compute_fpair(const F_FLOAT& rsq, const int& i, const int&j,
const F_FLOAT r = sqrt(rsq);
const F_FLOAT tlj = r - (STACKPARAMS?m_params[itype][jtype].cut_inner:params(itype,jtype).cut_inner);
const F_FLOAT fswitch = r*tlj*tlj*
- ((STACKPARAMS?m_params[itype][jtype].ljsw1:params(itype,jtype).ljsw1) +
+ ((STACKPARAMS?m_params[itype][jtype].ljsw1:params(itype,jtype).ljsw1) +
(STACKPARAMS?m_params[itype][jtype].ljsw2:params(itype,jtype).ljsw2)*tlj);
forcelj += fswitch;
}
@@ -191,7 +191,7 @@ compute_evdwl(const F_FLOAT& rsq, const int& i, const int&j,
const F_FLOAT r2inv = 1.0/rsq;
const F_FLOAT r6inv = r2inv*r2inv*r2inv;
- F_FLOAT englj = r6inv *
+ F_FLOAT englj = r6inv *
((STACKPARAMS?m_params[itype][jtype].lj3:params(itype,jtype).lj3)*r6inv -
(STACKPARAMS?m_params[itype][jtype].lj4:params(itype,jtype).lj4));
englj += (STACKPARAMS?m_params[itype][jtype].ljsw5:params(itype,jtype).ljsw5);
@@ -200,7 +200,7 @@ compute_evdwl(const F_FLOAT& rsq, const int& i, const int&j,
const F_FLOAT r = sqrt(rsq);
const F_FLOAT tlj = r - (STACKPARAMS?m_params[itype][jtype].cut_inner:params(itype,jtype).cut_inner);
const F_FLOAT eswitch = tlj*tlj*tlj *
- ((STACKPARAMS?m_params[itype][jtype].ljsw3:params(itype,jtype).ljsw3) +
+ ((STACKPARAMS?m_params[itype][jtype].ljsw3:params(itype,jtype).ljsw3) +
(STACKPARAMS?m_params[itype][jtype].ljsw4:params(itype,jtype).ljsw4)*tlj);
englj += eswitch;
}
diff --git a/src/KOKKOS/pair_lj_gromacs_kokkos.h b/src/KOKKOS/pair_lj_gromacs_kokkos.h
index 717571e144..fd00a35d4e 100644
--- a/src/KOKKOS/pair_lj_gromacs_kokkos.h
+++ b/src/KOKKOS/pair_lj_gromacs_kokkos.h
@@ -108,7 +108,7 @@ class PairLJGromacsKokkos : public PairLJGromacs {
typename ArrayTypes<DeviceType>::t_ffloat_1d_randomread
d_rtable, d_drtable, d_ftable, d_dftable,
d_ctable, d_dctable, d_etable, d_detable;
-
+
int neighflag;
int nlocal,nall,eflag,vflag;
diff --git a/src/KOKKOS/pair_lj_sdk_kokkos.cpp b/src/KOKKOS/pair_lj_sdk_kokkos.cpp
index bc413d39f0..6ff9203535 100644
--- a/src/KOKKOS/pair_lj_sdk_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_sdk_kokkos.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_lj_sdk_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
@@ -242,7 +242,7 @@ void PairLJSDKKokkos<DeviceType>::init_style()
int respa = 0;
if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;
- if (respa)
+ if (respa)
error->all(FLERR,"Cannot use Kokkos pair style with rRESPA inner/middle");
}
@@ -252,7 +252,7 @@ void PairLJSDKKokkos<DeviceType>::init_style()
int irequest = neighbor->nrequest - 1;
neighbor->requests[irequest]->
- kokkos_host = Kokkos::Impl::is_same<DeviceType,LMPHostType>::value &&
+ kokkos_host = Kokkos::Impl::is_same<DeviceType,LMPHostType>::value &&
!Kokkos::Impl::is_same<DeviceType,LMPDeviceType>::value;
neighbor->requests[irequest]->
kokkos_device = Kokkos::Impl::is_same<DeviceType,LMPDeviceType>::value;
diff --git a/src/KOKKOS/pair_lj_sdk_kokkos.h b/src/KOKKOS/pair_lj_sdk_kokkos.h
index 517b6bc55f..f5ffdd8520 100644
--- a/src/KOKKOS/pair_lj_sdk_kokkos.h
+++ b/src/KOKKOS/pair_lj_sdk_kokkos.h
@@ -88,7 +88,7 @@ class PairLJSDKKokkos : public PairLJSDK {
typename ArrayTypes<DeviceType>::tdual_ffloat_2d k_cutsq;
typename ArrayTypes<DeviceType>::t_ffloat_2d d_cutsq;
-
+
int neighflag;
int nlocal,nall,eflag,vflag;
diff --git a/src/KOKKOS/pair_sw_kokkos.cpp b/src/KOKKOS/pair_sw_kokkos.cpp
index c773516e67..df15bfaf1a 100755
--- a/src/KOKKOS/pair_sw_kokkos.cpp
+++ b/src/KOKKOS/pair_sw_kokkos.cpp
@@ -15,10 +15,10 @@
Contributing author: Stan Moore (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_sw_kokkos.h"
#include "kokkos.h"
#include "pair_kokkos.h"
@@ -144,7 +144,7 @@ void PairSWKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairSWComputeFullA<FULL,0> >(0,inum),*this);
DeviceType::fence();
ev_all += ev;
-
+
if (evflag)
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairSWComputeFullB<FULL,1> >(0,ignum),*this,ev);
else
diff --git a/src/KOKKOS/pair_sw_kokkos.h b/src/KOKKOS/pair_sw_kokkos.h
index a73008ee1c..4be9c80fa3 100755
--- a/src/KOKKOS/pair_sw_kokkos.h
+++ b/src/KOKKOS/pair_sw_kokkos.h
@@ -83,12 +83,12 @@ class PairSWKokkos : public PairSW {
template<int NEIGHFLAG>
KOKKOS_INLINE_FUNCTION
- void ev_tally3(EV_FLOAT &ev, const int &i, const int &j, int &k,
+ void ev_tally3(EV_FLOAT &ev, const int &i, const int &j, int &k,
const F_FLOAT &evdwl, const F_FLOAT &ecoul,
F_FLOAT *fj, F_FLOAT *fk, F_FLOAT *drji, F_FLOAT *drki) const;
KOKKOS_INLINE_FUNCTION
- void ev_tally3_atom(EV_FLOAT &ev, const int &i,
+ void ev_tally3_atom(EV_FLOAT &ev, const int &i,
const F_FLOAT &evdwl, const F_FLOAT &ecoul,
F_FLOAT *fj, F_FLOAT *fk, F_FLOAT *drji, F_FLOAT *drki) const;
diff --git a/src/KOKKOS/pair_table_kokkos.cpp b/src/KOKKOS/pair_table_kokkos.cpp
index f0c6068bbe..a7e01649cc 100644
--- a/src/KOKKOS/pair_table_kokkos.cpp
+++ b/src/KOKKOS/pair_table_kokkos.cpp
@@ -15,10 +15,10 @@
Contributing author: Paul Crozier (SNL)
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <mpi.h>
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_table_kokkos.h"
#include "kokkos.h"
#include "atom.h"
@@ -368,7 +368,7 @@ void PairTableKokkos<DeviceType>::create_kokkos_tables()
h_table->f2(i,j) = tb->f2[j];
}
-
+
Kokkos::deep_copy(d_table->nshiftbits,h_table->nshiftbits);
Kokkos::deep_copy(d_table->nmask,h_table->nmask);
Kokkos::deep_copy(d_table->innersq,h_table->innersq);
@@ -465,12 +465,12 @@ void PairTableKokkos<DeviceType>::settings(int narg, char **arg)
if (allocated) {
memory->destroy(setflag);
-
+
d_table_const.tabindex = d_table->tabindex = typename ArrayTypes<DeviceType>::t_int_2d();
h_table->tabindex = typename ArrayTypes<LMPHostType>::t_int_2d();
- d_table_const.cutsq = d_table->cutsq = typename ArrayTypes<DeviceType>::t_ffloat_2d();
- h_table->cutsq = typename ArrayTypes<LMPHostType>::t_ffloat_2d();
+ d_table_const.cutsq = d_table->cutsq = typename ArrayTypes<DeviceType>::t_ffloat_2d();
+ h_table->cutsq = typename ArrayTypes<LMPHostType>::t_ffloat_2d();
}
allocated = 0;
diff --git a/src/KOKKOS/pair_table_kokkos.h b/src/KOKKOS/pair_table_kokkos.h
index 17068b3a87..09e64804b4 100644
--- a/src/KOKKOS/pair_table_kokkos.h
+++ b/src/KOKKOS/pair_table_kokkos.h
@@ -49,8 +49,8 @@ class PairTableKokkos : public Pair {
virtual ~PairTableKokkos();
virtual void compute(int, int);
-
- template<int TABSTYLE>
+
+ template<int TABSTYLE>
void compute_style(int, int);
/*template<int EVFLAG, int NEIGHFLAG, int NEWTON_PAIR, int TABSTYLE>
@@ -82,7 +82,7 @@ class PairTableKokkos : public Pair {
typename ArrayTypes<DeviceType>::t_ffloat_1d_randomread innersq,invdelta,deltasq6;
typename ArrayTypes<DeviceType>::t_ffloat_2d_randomread rsq,drsq,e,de,f,df,e2,f2;
};*/
- //Its faster not to use texture fetch if the number of tables is less than 32!
+ //Its faster not to use texture fetch if the number of tables is less than 32!
struct TableDeviceConst {
typename ArrayTypes<DeviceType>::t_ffloat_2d cutsq;
typename ArrayTypes<DeviceType>::t_int_2d tabindex;
@@ -147,7 +147,7 @@ class PairTableKokkos : public Pair {
protected:
int nlocal,nall,eflag,vflag,neighflag,newton_pair;
-
+
int update_table;
void create_kokkos_tables();
void cleanup_copy();
diff --git a/src/KOKKOS/pair_tersoff_kokkos.cpp b/src/KOKKOS/pair_tersoff_kokkos.cpp
index d32e18e66f..76743c8a7e 100755
--- a/src/KOKKOS/pair_tersoff_kokkos.cpp
+++ b/src/KOKKOS/pair_tersoff_kokkos.cpp
@@ -15,10 +15,10 @@
Contributing author: Ray Shan (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_tersoff_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
@@ -227,7 +227,7 @@ void PairTersoffKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairTersoffComputeFullA<FULL,0> >(0,inum),*this);
DeviceType::fence();
ev_all += ev;
-
+
if (evflag)
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairTersoffComputeFullB<FULL,1> >(0,ignum),*this,ev);
else
@@ -317,7 +317,7 @@ void PairTersoffKokkos<DeviceType>::operator()(TagPairTersoffComputeHalf<NEIGHFL
const F_FLOAT tmp_fce = ters_fc_k(itype,jtype,jtype,r);
const F_FLOAT tmp_fcd = ters_dfc(itype,jtype,jtype,r);
const F_FLOAT tmp_exp = exp(-paramskk(itype,jtype,jtype).lam1 * r);
- const F_FLOAT frep = -paramskk(itype,jtype,jtype).biga * tmp_exp *
+ const F_FLOAT frep = -paramskk(itype,jtype,jtype).biga * tmp_exp *
(tmp_fcd - tmp_fce*paramskk(itype,jtype,jtype).lam1) / r;
const F_FLOAT eng = tmp_fce * paramskk(itype,jtype,jtype).biga * tmp_exp;
@@ -335,7 +335,7 @@ void PairTersoffKokkos<DeviceType>::operator()(TagPairTersoffComputeHalf<NEIGHFL
}
// attractive: bond order
-
+
for (jj = 0; jj < jnum; jj++) {
j = d_neighbors(i,jj);
j &= NEIGHMASK;
@@ -350,7 +350,7 @@ void PairTersoffKokkos<DeviceType>::operator()(TagPairTersoffComputeHalf<NEIGHFL
bo_ij = 0.0;
if (rsq1 > cutsq1) continue;
rij = sqrt(rsq1);
-
+
for (kk = 0; kk < jnum; kk++) {
if (jj == kk) continue;
k = d_neighbors(i,kk);
@@ -386,12 +386,12 @@ void PairTersoffKokkos<DeviceType>::operator()(TagPairTersoffComputeHalf<NEIGHFL
if (EVFLAG) {
if (eflag) ev.evdwl += eng;
- if (vflag_either || eflag_atom)
+ if (vflag_either || eflag_atom)
this->template ev_tally<NEIGHFLAG>(ev,i,j,eng,fatt,delx1,dely1,delz1);
}
// attractive: three-body force
-
+
for (kk = 0; kk < jnum; kk++) {
if (jj == kk) continue;
k = d_neighbors(i,kk);
@@ -477,7 +477,7 @@ void PairTersoffKokkos<DeviceType>::operator()(TagPairTersoffComputeFullA<NEIGHF
const F_FLOAT tmp_fce = ters_fc_k(itype,jtype,jtype,r);
const F_FLOAT tmp_fcd = ters_dfc(itype,jtype,jtype,r);
const F_FLOAT tmp_exp = exp(-paramskk(itype,jtype,jtype).lam1 * r);
- const F_FLOAT frep = -paramskk(itype,jtype,jtype).biga * tmp_exp *
+ const F_FLOAT frep = -paramskk(itype,jtype,jtype).biga * tmp_exp *
(tmp_fcd - tmp_fce*paramskk(itype,jtype,jtype).lam1) / r;
const F_FLOAT eng = tmp_fce * paramskk(itype,jtype,jtype).biga * tmp_exp;
@@ -488,13 +488,13 @@ void PairTersoffKokkos<DeviceType>::operator()(TagPairTersoffComputeFullA<NEIGHF
if (EVFLAG) {
if (eflag)
ev.evdwl += 0.5*eng;
- if (vflag_either || eflag_atom)
+ if (vflag_either || eflag_atom)
this->template ev_tally<NEIGHFLAG>(ev,i,j,eng,frep,delx,dely,delz);
}
}
// attractive: bond order
-
+
for (jj = 0; jj < jnum; jj++) {
j = d_neighbors(i,jj);
j &= NEIGHMASK;
@@ -509,7 +509,7 @@ void PairTersoffKokkos<DeviceType>::operator()(TagPairTersoffComputeFullA<NEIGHF
bo_ij = 0.0;
if (rsq1 > cutsq1) continue;
rij = sqrt(rsq1);
-
+
for (kk = 0; kk < jnum; kk++) {
if (jj == kk) continue;
k = d_neighbors(i,kk);
@@ -542,12 +542,12 @@ void PairTersoffKokkos<DeviceType>::operator()(TagPairTersoffComputeFullA<NEIGHF
if (EVFLAG) {
if (eflag) ev.evdwl += 0.5*eng;
- if (vflag_either || eflag_atom)
+ if (vflag_either || eflag_atom)
this->template ev_tally<NEIGHFLAG>(ev,i,j,eng,fatt,delx1,dely1,delz1);
}
// attractive: three-body force
-
+
for (kk = 0; kk < jnum; kk++) {
if (jj == kk) continue;
k = d_neighbors(i,kk);
@@ -608,7 +608,7 @@ void PairTersoffKokkos<DeviceType>::operator()(TagPairTersoffComputeFullB<NEIGHF
const int jnum = d_numneigh[i];
// attractive: bond order
-
+
for (jj = 0; jj < jnum; jj++) {
j = d_neighbors(i,jj);
j &= NEIGHMASK;
@@ -626,7 +626,7 @@ void PairTersoffKokkos<DeviceType>::operator()(TagPairTersoffComputeFullB<NEIGHF
rij = sqrt(rsq1);
j_jnum = d_numneigh[j];
-
+
for (kk = 0; kk < j_jnum; kk++) {
k = d_neighbors(j,kk);
if (k == i) continue;
@@ -659,14 +659,14 @@ void PairTersoffKokkos<DeviceType>::operator()(TagPairTersoffComputeFullB<NEIGHF
f(i,2) -= delz1*fatt;
if (EVFLAG) {
- if (eflag)
+ if (eflag)
ev.evdwl += 0.5 * eng;
- if (vflag_either || eflag_atom)
+ if (vflag_either || eflag_atom)
this->template ev_tally<NEIGHFLAG>(ev,i,j,eng,fatt,delx1,dely1,delz1);
}
// attractive: three-body force
-
+
for (kk = 0; kk < j_jnum; kk++) {
k = d_neighbors(j,kk);
if (k == i) continue;
@@ -718,7 +718,7 @@ void PairTersoffKokkos<DeviceType>::operator()(TagPairTersoffComputeFullB<NEIGHF
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
double PairTersoffKokkos<DeviceType>::ters_fc_k(const int &i, const int &j,
- const int &k, const F_FLOAT &r) const
+ const int &k, const F_FLOAT &r) const
{
const F_FLOAT ters_R = paramskk(i,j,k).bigr;
const F_FLOAT ters_D = paramskk(i,j,k).bigd;
@@ -733,7 +733,7 @@ double PairTersoffKokkos<DeviceType>::ters_fc_k(const int &i, const int &j,
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
double PairTersoffKokkos<DeviceType>::ters_dfc(const int &i, const int &j,
- const int &k, const F_FLOAT &r) const
+ const int &k, const F_FLOAT &r) const
{
const F_FLOAT ters_R = paramskk(i,j,k).bigr;
const F_FLOAT ters_D = paramskk(i,j,k).bigd;
@@ -749,7 +749,7 @@ template<class DeviceType>
KOKKOS_INLINE_FUNCTION
double PairTersoffKokkos<DeviceType>::bondorder(const int &i, const int &j, const int &k,
const F_FLOAT &rij, const F_FLOAT &dx1, const F_FLOAT &dy1, const F_FLOAT &dz1,
- const F_FLOAT &rik, const F_FLOAT &dx2, const F_FLOAT &dy2, const F_FLOAT &dz2) const
+ const F_FLOAT &rik, const F_FLOAT &dx2, const F_FLOAT &dy2, const F_FLOAT &dz2) const
{
F_FLOAT arg, ex_delr;
@@ -800,10 +800,10 @@ double PairTersoffKokkos<DeviceType>::
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
double PairTersoffKokkos<DeviceType>::ters_fa_k(const int &i, const int &j,
- const int &k, const F_FLOAT &r) const
+ const int &k, const F_FLOAT &r) const
{
if (r > paramskk(i,j,k).bigr + paramskk(i,j,k).bigd) return 0.0;
- return -paramskk(i,j,k).bigb * exp(-paramskk(i,j,k).lam2 * r)
+ return -paramskk(i,j,k).bigb * exp(-paramskk(i,j,k).lam2 * r)
* ters_fc_k(i,j,k,r);
}
@@ -812,7 +812,7 @@ double PairTersoffKokkos<DeviceType>::ters_fa_k(const int &i, const int &j,
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
double PairTersoffKokkos<DeviceType>::ters_dfa(const int &i, const int &j,
- const int &k, const F_FLOAT &r) const
+ const int &k, const F_FLOAT &r) const
{
if (r > paramskk(i,j,k).bigr + paramskk(i,j,k).bigd) return 0.0;
return paramskk(i,j,k).bigb * exp(-paramskk(i,j,k).lam2 * r) *
@@ -824,7 +824,7 @@ double PairTersoffKokkos<DeviceType>::ters_dfa(const int &i, const int &j,
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
double PairTersoffKokkos<DeviceType>::ters_bij_k(const int &i, const int &j,
- const int &k, const F_FLOAT &bo) const
+ const int &k, const F_FLOAT &bo) const
{
const F_FLOAT tmp = paramskk(i,j,k).beta * bo;
if (tmp > paramskk(i,j,k).c1) return 1.0/sqrt(tmp);
@@ -841,7 +841,7 @@ double PairTersoffKokkos<DeviceType>::ters_bij_k(const int &i, const int &j,
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
double PairTersoffKokkos<DeviceType>::ters_dbij(const int &i, const int &j,
- const int &k, const F_FLOAT &bo) const
+ const int &k, const F_FLOAT &bo) const
{
const F_FLOAT tmp = paramskk(i,j,k).beta * bo;
if (tmp > paramskk(i,j,k).c1) return paramskk(i,j,k).beta * -0.5*pow(tmp,-1.5);
@@ -1119,7 +1119,7 @@ void PairTersoffKokkos<DeviceType>::ev_tally(EV_FLOAT &ev, const int &i, const i
template<class DeviceType>
template<int NEIGHFLAG>
KOKKOS_INLINE_FUNCTION
-void PairTersoffKokkos<DeviceType>::v_tally3(EV_FLOAT &ev, const int &i, const int &j, const int &k,
+void PairTersoffKokkos<DeviceType>::v_tally3(EV_FLOAT &ev, const int &i, const int &j, const int &k,
F_FLOAT *fj, F_FLOAT *fk, F_FLOAT *drij, F_FLOAT *drik) const
{
@@ -1191,7 +1191,7 @@ void PairTersoffKokkos<DeviceType>::v_tally3_atom(EV_FLOAT &ev, const int &i, co
/* ---------------------------------------------------------------------- */
template<class DeviceType>
-KOKKOS_INLINE_FUNCTION
+KOKKOS_INLINE_FUNCTION
int PairTersoffKokkos<DeviceType>::sbmask(const int& j) const {
return j >> SBBITS & 3;
}
diff --git a/src/KOKKOS/pair_tersoff_kokkos.h b/src/KOKKOS/pair_tersoff_kokkos.h
index ad5e04f9df..9612bc4d7f 100755
--- a/src/KOKKOS/pair_tersoff_kokkos.h
+++ b/src/KOKKOS/pair_tersoff_kokkos.h
@@ -23,7 +23,7 @@ PairStyle(tersoff/kk/host,PairTersoffKokkos<LMPHostType>)
#ifndef LMP_PAIR_TERSOFF_KOKKOS_H
#define LMP_PAIR_TERSOFF_KOKKOS_H
-#include "stdio.h"
+#include <stdio.h>
#include "pair_kokkos.h"
#include "pair_tersoff.h"
#include "neigh_list_kokkos.h"
@@ -143,7 +143,7 @@ class PairTersoffKokkos : public PairTersoff {
void vec3_scaleadd(const F_FLOAT k, const double x[3], const double y[3], double * const z) const {
z[0] = k*x[0]+y[0]; z[1] = k*x[1]+y[1]; z[2] = k*x[2]+y[2];
}
-
+
KOKKOS_INLINE_FUNCTION
int sbmask(const int& j) const;
@@ -152,7 +152,7 @@ class PairTersoffKokkos : public PairTersoff {
bigr=0;bigd=0;lam1=0;biga=0;cutsq=0;c1=0;c2=0;c3=0;c4=0;};
params_ters(int i){powerm=0;gamma=0;lam3=0;c=0;d=0;h=0;powern=0;beta=0;lam2=0;bigb=0;
bigr=0;bigd=0;lam1=0;biga=0;cutsq=0;c1=0;c2=0;c3=0;c4=0;};
- F_FLOAT powerm, gamma, lam3, c, d, h, powern, beta, lam2, bigb, bigr,
+ F_FLOAT powerm, gamma, lam3, c, d, h, powern, beta, lam2, bigb, bigr,
bigd, lam1, biga, cutsq, c1, c2, c3, c4;
};
@@ -164,11 +164,11 @@ class PairTersoffKokkos : public PairTersoff {
template<int NEIGHFLAG>
KOKKOS_INLINE_FUNCTION
- void v_tally3(EV_FLOAT &ev, const int &i, const int &j, const int &k,
+ void v_tally3(EV_FLOAT &ev, const int &i, const int &j, const int &k,
F_FLOAT *fj, F_FLOAT *fk, F_FLOAT *drij, F_FLOAT *drik) const;
KOKKOS_INLINE_FUNCTION
- void v_tally3_atom(EV_FLOAT &ev, const int &i, const int &j, const int &k,
+ void v_tally3_atom(EV_FLOAT &ev, const int &i, const int &j, const int &k,
F_FLOAT *fj, F_FLOAT *fk, F_FLOAT *drji, F_FLOAT *drjk) const;
void allocate();
diff --git a/src/KOKKOS/pair_tersoff_mod_kokkos.cpp b/src/KOKKOS/pair_tersoff_mod_kokkos.cpp
index ff84e2d392..57e4882f0f 100755
--- a/src/KOKKOS/pair_tersoff_mod_kokkos.cpp
+++ b/src/KOKKOS/pair_tersoff_mod_kokkos.cpp
@@ -15,10 +15,10 @@
Contributing author: Ray Shan (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_tersoff_mod_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
@@ -227,7 +227,7 @@ void PairTersoffMODKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairTersoffMODComputeFullA<FULL,0> >(0,inum),*this);
DeviceType::fence();
ev_all += ev;
-
+
if (evflag)
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairTersoffMODComputeFullB<FULL,1> >(0,ignum),*this,ev);
else
@@ -317,7 +317,7 @@ void PairTersoffMODKokkos<DeviceType>::operator()(TagPairTersoffMODComputeHalf<N
const F_FLOAT tmp_fce = ters_fc_k(itype,jtype,jtype,r);
const F_FLOAT tmp_fcd = ters_dfc(itype,jtype,jtype,r);
const F_FLOAT tmp_exp = exp(-paramskk(itype,jtype,jtype).lam1 * r);
- const F_FLOAT frep = -paramskk(itype,jtype,jtype).biga * tmp_exp *
+ const F_FLOAT frep = -paramskk(itype,jtype,jtype).biga * tmp_exp *
(tmp_fcd - tmp_fce*paramskk(itype,jtype,jtype).lam1) / r;
const F_FLOAT eng = tmp_fce * paramskk(itype,jtype,jtype).biga * tmp_exp;
@@ -335,7 +335,7 @@ void PairTersoffMODKokkos<DeviceType>::operator()(TagPairTersoffMODComputeHalf<N
}
// attractive: bond order
-
+
for (jj = 0; jj < jnum; jj++) {
j = d_neighbors(i,jj);
j &= NEIGHMASK;
@@ -350,7 +350,7 @@ void PairTersoffMODKokkos<DeviceType>::operator()(TagPairTersoffMODComputeHalf<N
bo_ij = 0.0;
if (rsq1 > cutsq1) continue;
rij = sqrt(rsq1);
-
+
for (kk = 0; kk < jnum; kk++) {
if (jj == kk) continue;
k = d_neighbors(i,kk);
@@ -386,12 +386,12 @@ void PairTersoffMODKokkos<DeviceType>::operator()(TagPairTersoffMODComputeHalf<N
if (EVFLAG) {
if (eflag) ev.evdwl += eng;
- if (vflag_either || eflag_atom)
+ if (vflag_either || eflag_atom)
this->template ev_tally<NEIGHFLAG>(ev,i,j,eng,fatt,delx1,dely1,delz1);
}
// attractive: three-body force
-
+
for (kk = 0; kk < jnum; kk++) {
if (jj == kk) continue;
k = d_neighbors(i,kk);
@@ -477,7 +477,7 @@ void PairTersoffMODKokkos<DeviceType>::operator()(TagPairTersoffMODComputeFullA<
const F_FLOAT tmp_fce = ters_fc_k(itype,jtype,jtype,r);
const F_FLOAT tmp_fcd = ters_dfc(itype,jtype,jtype,r);
const F_FLOAT tmp_exp = exp(-paramskk(itype,jtype,jtype).lam1 * r);
- const F_FLOAT frep = -paramskk(itype,jtype,jtype).biga * tmp_exp *
+ const F_FLOAT frep = -paramskk(itype,jtype,jtype).biga * tmp_exp *
(tmp_fcd - tmp_fce*paramskk(itype,jtype,jtype).lam1) / r;
const F_FLOAT eng = tmp_fce * paramskk(itype,jtype,jtype).biga * tmp_exp;
@@ -488,13 +488,13 @@ void PairTersoffMODKokkos<DeviceType>::operator()(TagPairTersoffMODComputeFullA<
if (EVFLAG) {
if (eflag)
ev.evdwl += 0.5*eng;
- if (vflag_either || eflag_atom)
+ if (vflag_either || eflag_atom)
this->template ev_tally<NEIGHFLAG>(ev,i,j,eng,frep,delx,dely,delz);
}
}
// attractive: bond order
-
+
for (jj = 0; jj < jnum; jj++) {
j = d_neighbors(i,jj);
j &= NEIGHMASK;
@@ -509,7 +509,7 @@ void PairTersoffMODKokkos<DeviceType>::operator()(TagPairTersoffMODComputeFullA<
bo_ij = 0.0;
if (rsq1 > cutsq1) continue;
rij = sqrt(rsq1);
-
+
for (kk = 0; kk < jnum; kk++) {
if (jj == kk) continue;
k = d_neighbors(i,kk);
@@ -542,12 +542,12 @@ void PairTersoffMODKokkos<DeviceType>::operator()(TagPairTersoffMODComputeFullA<
if (EVFLAG) {
if (eflag) ev.evdwl += 0.5*eng;
- if (vflag_either || eflag_atom)
+ if (vflag_either || eflag_atom)
this->template ev_tally<NEIGHFLAG>(ev,i,j,eng,fatt,delx1,dely1,delz1);
}
// attractive: three-body force
-
+
for (kk = 0; kk < jnum; kk++) {
if (jj == kk) continue;
k = d_neighbors(i,kk);
@@ -608,7 +608,7 @@ void PairTersoffMODKokkos<DeviceType>::operator()(TagPairTersoffMODComputeFullB<
const int jnum = d_numneigh[i];
// attractive: bond order
-
+
for (jj = 0; jj < jnum; jj++) {
j = d_neighbors(i,jj);
j &= NEIGHMASK;
@@ -626,7 +626,7 @@ void PairTersoffMODKokkos<DeviceType>::operator()(TagPairTersoffMODComputeFullB<
rij = sqrt(rsq1);
j_jnum = d_numneigh[j];
-
+
for (kk = 0; kk < j_jnum; kk++) {
k = d_neighbors(j,kk);
if (k == i) continue;
@@ -659,14 +659,14 @@ void PairTersoffMODKokkos<DeviceType>::operator()(TagPairTersoffMODComputeFullB<
f(i,2) -= delz1*fatt;
if (EVFLAG) {
- if (eflag)
+ if (eflag)
ev.evdwl += 0.5 * eng;
- if (vflag_either || eflag_atom)
+ if (vflag_either || eflag_atom)
this->template ev_tally<NEIGHFLAG>(ev,i,j,eng,fatt,delx1,dely1,delz1);
}
// attractive: three-body force
-
+
for (kk = 0; kk < j_jnum; kk++) {
k = d_neighbors(j,kk);
if (k == i) continue;
@@ -718,14 +718,14 @@ void PairTersoffMODKokkos<DeviceType>::operator()(TagPairTersoffMODComputeFullB<
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
double PairTersoffMODKokkos<DeviceType>::ters_fc_k(const int &i, const int &j,
- const int &k, const F_FLOAT &r) const
+ const int &k, const F_FLOAT &r) const
{
const F_FLOAT ters_R = paramskk(i,j,k).bigr;
const F_FLOAT ters_D = paramskk(i,j,k).bigd;
if (r < ters_R-ters_D) return 1.0;
if (r > ters_R+ters_D) return 0.0;
- return 0.5*(1.0 - 1.125*sin(MY_PI2*(r - ters_R)/ters_D) -
+ return 0.5*(1.0 - 1.125*sin(MY_PI2*(r - ters_R)/ters_D) -
0.125*sin(3.0*MY_PI2*(r - ters_R)/ters_D));
}
@@ -734,14 +734,14 @@ double PairTersoffMODKokkos<DeviceType>::ters_fc_k(const int &i, const int &j,
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
double PairTersoffMODKokkos<DeviceType>::ters_dfc(const int &i, const int &j,
- const int &k, const F_FLOAT &r) const
+ const int &k, const F_FLOAT &r) const
{
const F_FLOAT ters_R = paramskk(i,j,k).bigr;
const F_FLOAT ters_D = paramskk(i,j,k).bigd;
if (r < ters_R-ters_D) return 0.0;
if (r > ters_R+ters_D) return 0.0;
- return -(0.375*MY_PI4/ters_D) * (3.0*cos(MY_PI2*(r - ters_R)/ters_D) +
+ return -(0.375*MY_PI4/ters_D) * (3.0*cos(MY_PI2*(r - ters_R)/ters_D) +
cos(3.0*MY_PI2*(r - ters_R)/ters_D));
}
@@ -751,7 +751,7 @@ template<class DeviceType>
KOKKOS_INLINE_FUNCTION
double PairTersoffMODKokkos<DeviceType>::bondorder(const int &i, const int &j, const int &k,
const F_FLOAT &rij, const F_FLOAT &dx1, const F_FLOAT &dy1, const F_FLOAT &dz1,
- const F_FLOAT &rik, const F_FLOAT &dx2, const F_FLOAT &dy2, const F_FLOAT &dz2) const
+ const F_FLOAT &rik, const F_FLOAT &dx2, const F_FLOAT &dy2, const F_FLOAT &dz2) const
{
F_FLOAT arg, ex_delr;
@@ -781,9 +781,9 @@ double PairTersoffMODKokkos<DeviceType>::
const F_FLOAT ters_c5 = paramskk(i,j,k).c5;
const F_FLOAT tmp_h = (paramskk(i,j,k).h - cos)*(paramskk(i,j,k).h - cos);
- return ters_c1 + (ters_c2*tmp_h/(ters_c3 + tmp_h)) *
+ return ters_c1 + (ters_c2*tmp_h/(ters_c3 + tmp_h)) *
(1.0 + ters_c4*exp(-ters_c5*tmp_h));
-
+
}
/* ---------------------------------------------------------------------- */
@@ -801,7 +801,7 @@ double PairTersoffMODKokkos<DeviceType>::
const F_FLOAT g1 = (paramskk(i,j,k).h - cos)/(ters_c3 + tmp_h);
const F_FLOAT g2 = exp(-ters_c5*tmp_h);
- return -2.0*ters_c2*g1*((1 + ters_c4*g2)*(1 + g1*(cos - paramskk(i,j,k).h)) -
+ return -2.0*ters_c2*g1*((1 + ters_c4*g2)*(1 + g1*(cos - paramskk(i,j,k).h)) -
tmp_h*ters_c4*ters_c5*g2);
}
@@ -810,10 +810,10 @@ double PairTersoffMODKokkos<DeviceType>::
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
double PairTersoffMODKokkos<DeviceType>::ters_fa_k(const int &i, const int &j,
- const int &k, const F_FLOAT &r) const
+ const int &k, const F_FLOAT &r) const
{
if (r > paramskk(i,j,k).bigr + paramskk(i,j,k).bigd) return 0.0;
- return -paramskk(i,j,k).bigb * exp(-paramskk(i,j,k).lam2 * r)
+ return -paramskk(i,j,k).bigb * exp(-paramskk(i,j,k).lam2 * r)
* ters_fc_k(i,j,k,r);
}
@@ -822,7 +822,7 @@ double PairTersoffMODKokkos<DeviceType>::ters_fa_k(const int &i, const int &j,
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
double PairTersoffMODKokkos<DeviceType>::ters_dfa(const int &i, const int &j,
- const int &k, const F_FLOAT &r) const
+ const int &k, const F_FLOAT &r) const
{
if (r > paramskk(i,j,k).bigr + paramskk(i,j,k).bigd) return 0.0;
return paramskk(i,j,k).bigb * exp(-paramskk(i,j,k).lam2 * r) *
@@ -834,12 +834,12 @@ double PairTersoffMODKokkos<DeviceType>::ters_dfa(const int &i, const int &j,
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
double PairTersoffMODKokkos<DeviceType>::ters_bij_k(const int &i, const int &j,
- const int &k, const F_FLOAT &bo) const
+ const int &k, const F_FLOAT &bo) const
{
const F_FLOAT tmp = paramskk(i,j,k).beta * bo;
- if (tmp > paramskk(i,j,k).ca1)
+ if (tmp > paramskk(i,j,k).ca1)
return pow(tmp, -paramskk(i,j,k).powern/(2.0*paramskk(i,j,k).powern_del));
- if (tmp < paramskk(i,j,k).ca4)
+ if (tmp < paramskk(i,j,k).ca4)
return 1.0;
return pow(1.0 + pow(tmp,paramskk(i,j,k).powern), -1.0/(2.0*paramskk(i,j,k).powern_del));
}
@@ -849,17 +849,17 @@ double PairTersoffMODKokkos<DeviceType>::ters_bij_k(const int &i, const int &j,
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
double PairTersoffMODKokkos<DeviceType>::ters_dbij(const int &i, const int &j,
- const int &k, const F_FLOAT &bo) const
+ const int &k, const F_FLOAT &bo) const
{
const F_FLOAT tmp = paramskk(i,j,k).beta * bo;
- if (tmp > paramskk(i,j,k).ca1)
+ if (tmp > paramskk(i,j,k).ca1)
return -0.5*(paramskk(i,j,k).powern/paramskk(i,j,k).powern_del)*
pow(tmp,-0.5*(paramskk(i,j,k).powern/paramskk(i,j,k).powern_del)) / bo;
- if (tmp < paramskk(i,j,k).ca4)
+ if (tmp < paramskk(i,j,k).ca4)
return 0.0;
-
+
const F_FLOAT tmp_n = pow(tmp,paramskk(i,j,k).powern);
- return -0.5 *(paramskk(i,j,k).powern/paramskk(i,j,k).powern_del)*
+ return -0.5 *(paramskk(i,j,k).powern/paramskk(i,j,k).powern_del)*
pow(1.0+tmp_n, -1.0-(1.0/(2.0*paramskk(i,j,k).powern_del)))*tmp_n / bo;
}
@@ -1125,7 +1125,7 @@ void PairTersoffMODKokkos<DeviceType>::ev_tally(EV_FLOAT &ev, const int &i, cons
template<class DeviceType>
template<int NEIGHFLAG>
KOKKOS_INLINE_FUNCTION
-void PairTersoffMODKokkos<DeviceType>::v_tally3(EV_FLOAT &ev, const int &i, const int &j, const int &k,
+void PairTersoffMODKokkos<DeviceType>::v_tally3(EV_FLOAT &ev, const int &i, const int &j, const int &k,
F_FLOAT *fj, F_FLOAT *fk, F_FLOAT *drij, F_FLOAT *drik) const
{
@@ -1197,7 +1197,7 @@ void PairTersoffMODKokkos<DeviceType>::v_tally3_atom(EV_FLOAT &ev, const int &i,
/* ---------------------------------------------------------------------- */
template<class DeviceType>
-KOKKOS_INLINE_FUNCTION
+KOKKOS_INLINE_FUNCTION
int PairTersoffMODKokkos<DeviceType>::sbmask(const int& j) const {
return j >> SBBITS & 3;
}
diff --git a/src/KOKKOS/pair_tersoff_mod_kokkos.h b/src/KOKKOS/pair_tersoff_mod_kokkos.h
index 6b1d32d2b4..980b18475b 100755
--- a/src/KOKKOS/pair_tersoff_mod_kokkos.h
+++ b/src/KOKKOS/pair_tersoff_mod_kokkos.h
@@ -23,7 +23,7 @@ PairStyle(tersoff/mod/kk/host,PairTersoffMODKokkos<LMPHostType>)
#ifndef LMP_PAIR_TERSOFF_MOD_KOKKOS_H
#define LMP_PAIR_TERSOFF_MOD_KOKKOS_H
-#include "stdio.h"
+#include <stdio.h>
#include "pair_kokkos.h"
#include "pair_tersoff_mod.h"
#include "neigh_list_kokkos.h"
@@ -143,7 +143,7 @@ class PairTersoffMODKokkos : public PairTersoffMOD {
void vec3_scaleadd(const F_FLOAT k, const double x[3], const double y[3], double * const z) const {
z[0] = k*x[0]+y[0]; z[1] = k*x[1]+y[1]; z[2] = k*x[2]+y[2];
}
-
+
KOKKOS_INLINE_FUNCTION
int sbmask(const int& j) const;
@@ -152,7 +152,7 @@ class PairTersoffMODKokkos : public PairTersoffMOD {
lam1=0;biga=0;powern_del=0;cutsq=0;c1=0;c2=0;c3=0;c4=0;c5=0;ca1=0;ca4=0;};
params_ters(int i){powerm=0;lam3=0;h=0;powern=0;beta=0;lam2=0;bigb=0;bigr=0;bigd=0;
lam1=0;biga=0;powern_del=0;cutsq=0;c1=0;c2=0;c3=0;c4=0;c5=0;ca1=0;ca4=0;};
- F_FLOAT powerm, lam3, h, powern, beta, lam2, bigb, bigr, bigd,
+ F_FLOAT powerm, lam3, h, powern, beta, lam2, bigb, bigr, bigd,
lam1, biga, powern_del, cutsq, c1, c2, c3, c4, c5, ca1, ca4;
};
@@ -164,11 +164,11 @@ class PairTersoffMODKokkos : public PairTersoffMOD {
template<int NEIGHFLAG>
KOKKOS_INLINE_FUNCTION
- void v_tally3(EV_FLOAT &ev, const int &i, const int &j, const int &k,
+ void v_tally3(EV_FLOAT &ev, const int &i, const int &j, const int &k,
F_FLOAT *fj, F_FLOAT *fk, F_FLOAT *drij, F_FLOAT *drik) const;
KOKKOS_INLINE_FUNCTION
- void v_tally3_atom(EV_FLOAT &ev, const int &i, const int &j, const int &k,
+ void v_tally3_atom(EV_FLOAT &ev, const int &i, const int &j, const int &k,
F_FLOAT *fj, F_FLOAT *fk, F_FLOAT *drji, F_FLOAT *drjk) const;
void allocate();
diff --git a/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp b/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp
index 12e69e6802..9ab8288685 100755
--- a/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp
+++ b/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp
@@ -15,10 +15,10 @@
Contributing author: Ray Shan (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_tersoff_zbl_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
@@ -241,7 +241,7 @@ void PairTersoffZBLKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairTersoffZBLComputeFullA<FULL,0> >(0,inum),*this);
DeviceType::fence();
ev_all += ev;
-
+
if (evflag)
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairTersoffZBLComputeFullB<FULL,1> >(0,ignum),*this,ev);
else
@@ -333,19 +333,19 @@ void PairTersoffZBLKokkos<DeviceType>::operator()(TagPairTersoffZBLComputeHalf<N
const F_FLOAT tmp_fce = ters_fc_k(itype,jtype,jtype,r);
const F_FLOAT tmp_fcd = ters_dfc(itype,jtype,jtype,r);
const F_FLOAT tmp_exp = exp(-paramskk(itype,jtype,jtype).lam1 * r);
- const F_FLOAT frep_t = paramskk(itype,jtype,jtype).biga * tmp_exp *
+ const F_FLOAT frep_t = paramskk(itype,jtype,jtype).biga * tmp_exp *
(tmp_fcd - tmp_fce*paramskk(itype,jtype,jtype).lam1);
const F_FLOAT eng_t = tmp_fce * paramskk(itype,jtype,jtype).biga * tmp_exp;
// ZBL repulsive portion
const F_FLOAT esq = pow(global_e,2.0);
- const F_FLOAT a_ij = (0.8854*global_a_0) /
+ const F_FLOAT a_ij = (0.8854*global_a_0) /
(pow(paramskk(itype,jtype,jtype).Z_i,0.23) + pow(paramskk(itype,jtype,jtype).Z_j,0.23));
const F_FLOAT premult = (paramskk(itype,jtype,jtype).Z_i * paramskk(itype,jtype,jtype).Z_j * esq)/
(4.0*MY_PI*global_epsilon_0);
const F_FLOAT r_ov_a = r/a_ij;
- const F_FLOAT phi = 0.1818*exp(-3.2*r_ov_a) + 0.5099*exp(-0.9423*r_ov_a) +
+ const F_FLOAT phi = 0.1818*exp(-3.2*r_ov_a) + 0.5099*exp(-0.9423*r_ov_a) +
0.2802*exp(-0.4029*r_ov_a) + 0.02817*exp(-0.2016*r_ov_a);
const F_FLOAT dphi = (1.0/a_ij) * (-3.2*0.1818*exp(-3.2*r_ov_a) -
0.9423*0.5099*exp(-0.9423*r_ov_a) -
@@ -362,7 +362,7 @@ void PairTersoffZBLKokkos<DeviceType>::operator()(TagPairTersoffZBLComputeHalf<N
fermi_d_k(itype,jtype,jtype,r)*eng_t + fermi_k(itype,jtype,jtype,r)*frep_t) / r;
if (eflag)
- eng = (1.0 - fermi_k(itype,jtype,jtype,r)) * eng_z +
+ eng = (1.0 - fermi_k(itype,jtype,jtype,r)) * eng_z +
fermi_k(itype,jtype,jtype,r) * eng_t;
a_f(i,0) += delx*frep;
@@ -379,7 +379,7 @@ void PairTersoffZBLKokkos<DeviceType>::operator()(TagPairTersoffZBLComputeHalf<N
}
// attractive: bond order
-
+
for (jj = 0; jj < jnum; jj++) {
j = d_neighbors(i,jj);
j &= NEIGHMASK;
@@ -394,7 +394,7 @@ void PairTersoffZBLKokkos<DeviceType>::operator()(TagPairTersoffZBLComputeHalf<N
bo_ij = 0.0;
if (rsq1 > cutsq1) continue;
rij = sqrt(rsq1);
-
+
for (kk = 0; kk < jnum; kk++) {
if (jj == kk) continue;
k = d_neighbors(i,kk);
@@ -430,12 +430,12 @@ void PairTersoffZBLKokkos<DeviceType>::operator()(TagPairTersoffZBLComputeHalf<N
if (EVFLAG) {
if (eflag) ev.evdwl += eng;
- if (vflag_either || eflag_atom)
+ if (vflag_either || eflag_atom)
this->template ev_tally<NEIGHFLAG>(ev,i,j,eng,fatt,delx1,dely1,delz1);
}
// attractive: three-body force
-
+
for (kk = 0; kk < jnum; kk++) {
if (jj == kk) continue;
k = d_neighbors(i,kk);
@@ -523,19 +523,19 @@ void PairTersoffZBLKokkos<DeviceType>::operator()(TagPairTersoffZBLComputeFullA<
const F_FLOAT tmp_fce = ters_fc_k(itype,jtype,jtype,r);
const F_FLOAT tmp_fcd = ters_dfc(itype,jtype,jtype,r);
const F_FLOAT tmp_exp = exp(-paramskk(itype,jtype,jtype).lam1 * r);
- const F_FLOAT frep_t = paramskk(itype,jtype,jtype).biga * tmp_exp *
+ const F_FLOAT frep_t = paramskk(itype,jtype,jtype).biga * tmp_exp *
(tmp_fcd - tmp_fce*paramskk(itype,jtype,jtype).lam1);
const F_FLOAT eng_t = tmp_fce * paramskk(itype,jtype,jtype).biga * tmp_exp;
// ZBL repulsive portion
const F_FLOAT esq = pow(global_e,2.0);
- const F_FLOAT a_ij = (0.8854*global_a_0) /
+ const F_FLOAT a_ij = (0.8854*global_a_0) /
(pow(paramskk(itype,jtype,jtype).Z_i,0.23) + pow(paramskk(itype,jtype,jtype).Z_j,0.23));
const F_FLOAT premult = (paramskk(itype,jtype,jtype).Z_i * paramskk(itype,jtype,jtype).Z_j * esq)/
(4.0*MY_PI*global_epsilon_0);
const F_FLOAT r_ov_a = r/a_ij;
- const F_FLOAT phi = 0.1818*exp(-3.2*r_ov_a) + 0.5099*exp(-0.9423*r_ov_a) +
+ const F_FLOAT phi = 0.1818*exp(-3.2*r_ov_a) + 0.5099*exp(-0.9423*r_ov_a) +
0.2802*exp(-0.4029*r_ov_a) + 0.02817*exp(-0.2016*r_ov_a);
const F_FLOAT dphi = (1.0/a_ij) * (-3.2*0.1818*exp(-3.2*r_ov_a) -
0.9423*0.5099*exp(-0.9423*r_ov_a) -
@@ -552,7 +552,7 @@ void PairTersoffZBLKokkos<DeviceType>::operator()(TagPairTersoffZBLComputeFullA<
fermi_d_k(itype,jtype,jtype,r)*eng_t + fermi_k(itype,jtype,jtype,r)*frep_t) / r;
if (eflag)
- eng = (1.0 - fermi_k(itype,jtype,jtype,r)) * eng_z +
+ eng = (1.0 - fermi_k(itype,jtype,jtype,r)) * eng_z +
fermi_k(itype,jtype,jtype,r) * eng_t;
f(i,0) += delx*frep;
@@ -562,13 +562,13 @@ void PairTersoffZBLKokkos<DeviceType>::operator()(TagPairTersoffZBLComputeFullA<
if (EVFLAG) {
if (eflag)
ev.evdwl += 0.5*eng;
- if (vflag_either || eflag_atom)
+ if (vflag_either || eflag_atom)
this->template ev_tally<NEIGHFLAG>(ev,i,j,eng,frep,delx,dely,delz);
}
}
// attractive: bond order
-
+
for (jj = 0; jj < jnum; jj++) {
j = d_neighbors(i,jj);
j &= NEIGHMASK;
@@ -583,7 +583,7 @@ void PairTersoffZBLKokkos<DeviceType>::operator()(TagPairTersoffZBLComputeFullA<
bo_ij = 0.0;
if (rsq1 > cutsq1) continue;
rij = sqrt(rsq1);
-
+
for (kk = 0; kk < jnum; kk++) {
if (jj == kk) continue;
k = d_neighbors(i,kk);
@@ -616,12 +616,12 @@ void PairTersoffZBLKokkos<DeviceType>::operator()(TagPairTersoffZBLComputeFullA<
if (EVFLAG) {
if (eflag) ev.evdwl += 0.5*eng;
- if (vflag_either || eflag_atom)
+ if (vflag_either || eflag_atom)
this->template ev_tally<NEIGHFLAG>(ev,i,j,eng,fatt,delx1,dely1,delz1);
}
// attractive: three-body force
-
+
for (kk = 0; kk < jnum; kk++) {
if (jj == kk) continue;
k = d_neighbors(i,kk);
@@ -682,7 +682,7 @@ void PairTersoffZBLKokkos<DeviceType>::operator()(TagPairTersoffZBLComputeFullB<
const int jnum = d_numneigh[i];
// attractive: bond order
-
+
for (jj = 0; jj < jnum; jj++) {
j = d_neighbors(i,jj);
j &= NEIGHMASK;
@@ -700,7 +700,7 @@ void PairTersoffZBLKokkos<DeviceType>::operator()(TagPairTersoffZBLComputeFullB<
rij = sqrt(rsq1);
j_jnum = d_numneigh[j];
-
+
for (kk = 0; kk < j_jnum; kk++) {
k = d_neighbors(j,kk);
if (k == i) continue;
@@ -733,14 +733,14 @@ void PairTersoffZBLKokkos<DeviceType>::operator()(TagPairTersoffZBLComputeFullB<
f(i,2) -= delz1*fatt;
if (EVFLAG) {
- if (eflag)
+ if (eflag)
ev.evdwl += 0.5 * eng;
- if (vflag_either || eflag_atom)
+ if (vflag_either || eflag_atom)
this->template ev_tally<NEIGHFLAG>(ev,i,j,eng,fatt,delx1,dely1,delz1);
}
// attractive: three-body force
-
+
for (kk = 0; kk < j_jnum; kk++) {
k = d_neighbors(j,kk);
if (k == i) continue;
@@ -792,7 +792,7 @@ void PairTersoffZBLKokkos<DeviceType>::operator()(TagPairTersoffZBLComputeFullB<
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
double PairTersoffZBLKokkos<DeviceType>::ters_fc_k(const int &i, const int &j,
- const int &k, const F_FLOAT &r) const
+ const int &k, const F_FLOAT &r) const
{
const F_FLOAT ters_R = paramskk(i,j,k).bigr;
const F_FLOAT ters_D = paramskk(i,j,k).bigd;
@@ -807,7 +807,7 @@ double PairTersoffZBLKokkos<DeviceType>::ters_fc_k(const int &i, const int &j,
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
double PairTersoffZBLKokkos<DeviceType>::ters_dfc(const int &i, const int &j,
- const int &k, const F_FLOAT &r) const
+ const int &k, const F_FLOAT &r) const
{
const F_FLOAT ters_R = paramskk(i,j,k).bigr;
const F_FLOAT ters_D = paramskk(i,j,k).bigd;
@@ -823,7 +823,7 @@ template<class DeviceType>
KOKKOS_INLINE_FUNCTION
double PairTersoffZBLKokkos<DeviceType>::bondorder(const int &i, const int &j, const int &k,
const F_FLOAT &rij, const F_FLOAT &dx1, const F_FLOAT &dy1, const F_FLOAT &dz1,
- const F_FLOAT &rik, const F_FLOAT &dx2, const F_FLOAT &dy2, const F_FLOAT &dz2) const
+ const F_FLOAT &rik, const F_FLOAT &dx2, const F_FLOAT &dy2, const F_FLOAT &dz2) const
{
F_FLOAT arg, ex_delr;
@@ -874,10 +874,10 @@ double PairTersoffZBLKokkos<DeviceType>::
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
double PairTersoffZBLKokkos<DeviceType>::ters_fa_k(const int &i, const int &j,
- const int &k, const F_FLOAT &r) const
+ const int &k, const F_FLOAT &r) const
{
if (r > paramskk(i,j,k).bigr + paramskk(i,j,k).bigd) return 0.0;
- return -paramskk(i,j,k).bigb * exp(-paramskk(i,j,k).lam2 * r)
+ return -paramskk(i,j,k).bigb * exp(-paramskk(i,j,k).lam2 * r)
* ters_fc_k(i,j,k,r) * fermi_k(i,j,k,r);
}
@@ -886,12 +886,12 @@ double PairTersoffZBLKokkos<DeviceType>::ters_fa_k(const int &i, const int &j,
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
double PairTersoffZBLKokkos<DeviceType>::ters_dfa(const int &i, const int &j,
- const int &k, const F_FLOAT &r) const
+ const int &k, const F_FLOAT &r) const
{
if (r > paramskk(i,j,k).bigr + paramskk(i,j,k).bigd) return 0.0;
return paramskk(i,j,k).bigb * exp(-paramskk(i,j,k).lam2 * r) *
- (paramskk(i,j,k).lam2 * ters_fc_k(i,j,k,r) * fermi_k(i,j,k,r) -
- ters_dfc(i,j,k,r) * fermi_k(i,j,k,r) - ters_fc_k(i,j,k,r) *
+ (paramskk(i,j,k).lam2 * ters_fc_k(i,j,k,r) * fermi_k(i,j,k,r) -
+ ters_dfc(i,j,k,r) * fermi_k(i,j,k,r) - ters_fc_k(i,j,k,r) *
fermi_d_k(i,j,k,r));
}
@@ -900,7 +900,7 @@ double PairTersoffZBLKokkos<DeviceType>::ters_dfa(const int &i, const int &j,
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
double PairTersoffZBLKokkos<DeviceType>::ters_bij_k(const int &i, const int &j,
- const int &k, const F_FLOAT &bo) const
+ const int &k, const F_FLOAT &bo) const
{
const F_FLOAT tmp = paramskk(i,j,k).beta * bo;
if (tmp > paramskk(i,j,k).c1) return 1.0/sqrt(tmp);
@@ -917,7 +917,7 @@ double PairTersoffZBLKokkos<DeviceType>::ters_bij_k(const int &i, const int &j,
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
double PairTersoffZBLKokkos<DeviceType>::ters_dbij(const int &i, const int &j,
- const int &k, const F_FLOAT &bo) const
+ const int &k, const F_FLOAT &bo) const
{
const F_FLOAT tmp = paramskk(i,j,k).beta * bo;
if (tmp > paramskk(i,j,k).c1) return paramskk(i,j,k).beta * -0.5*pow(tmp,-1.5);
@@ -1128,7 +1128,7 @@ void PairTersoffZBLKokkos<DeviceType>::ters_dthbk(
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
double PairTersoffZBLKokkos<DeviceType>::fermi_k(const int &i, const int &j,
- const int &k, const F_FLOAT &r) const
+ const int &k, const F_FLOAT &r) const
{
return 1.0 / (1.0 + exp(-paramskk(i,j,k).ZBLexpscale *
(r - paramskk(i,j,k).ZBLcut)));
@@ -1139,11 +1139,11 @@ double PairTersoffZBLKokkos<DeviceType>::fermi_k(const int &i, const int &j,
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
double PairTersoffZBLKokkos<DeviceType>::fermi_d_k(const int &i, const int &j,
- const int &k, const F_FLOAT &r) const
+ const int &k, const F_FLOAT &r) const
{
- return paramskk(i,j,k).ZBLexpscale * exp(-paramskk(i,j,k).ZBLexpscale *
+ return paramskk(i,j,k).ZBLexpscale * exp(-paramskk(i,j,k).ZBLexpscale *
(r - paramskk(i,j,k).ZBLcut)) /
- pow(1.0 + exp(-paramskk(i,j,k).ZBLexpscale *
+ pow(1.0 + exp(-paramskk(i,j,k).ZBLexpscale *
(r - paramskk(i,j,k).ZBLcut)),2.0);
}
@@ -1219,7 +1219,7 @@ void PairTersoffZBLKokkos<DeviceType>::ev_tally(EV_FLOAT &ev, const int &i, cons
template<class DeviceType>
template<int NEIGHFLAG>
KOKKOS_INLINE_FUNCTION
-void PairTersoffZBLKokkos<DeviceType>::v_tally3(EV_FLOAT &ev, const int &i, const int &j, const int &k,
+void PairTersoffZBLKokkos<DeviceType>::v_tally3(EV_FLOAT &ev, const int &i, const int &j, const int &k,
F_FLOAT *fj, F_FLOAT *fk, F_FLOAT *drij, F_FLOAT *drik) const
{
@@ -1291,7 +1291,7 @@ void PairTersoffZBLKokkos<DeviceType>::v_tally3_atom(EV_FLOAT &ev, const int &i,
/* ---------------------------------------------------------------------- */
template<class DeviceType>
-KOKKOS_INLINE_FUNCTION
+KOKKOS_INLINE_FUNCTION
int PairTersoffZBLKokkos<DeviceType>::sbmask(const int& j) const {
return j >> SBBITS & 3;
}
diff --git a/src/KOKKOS/pair_tersoff_zbl_kokkos.h b/src/KOKKOS/pair_tersoff_zbl_kokkos.h
index a7f21e3eee..03e14b43e7 100755
--- a/src/KOKKOS/pair_tersoff_zbl_kokkos.h
+++ b/src/KOKKOS/pair_tersoff_zbl_kokkos.h
@@ -23,7 +23,7 @@ PairStyle(tersoff/zbl/kk/host,PairTersoffZBLKokkos<LMPHostType>)
#ifndef LMP_PAIR_TERSOFF_ZBL_KOKKOS_H
#define LMP_PAIR_TERSOFF_ZBL_KOKKOS_H
-#include "stdio.h"
+#include <stdio.h>
#include "pair_kokkos.h"
#include "pair_tersoff_zbl.h"
#include "neigh_list_kokkos.h"
@@ -143,7 +143,7 @@ class PairTersoffZBLKokkos : public PairTersoffZBL {
void vec3_scaleadd(const F_FLOAT k, const double x[3], const double y[3], double * const z) const {
z[0] = k*x[0]+y[0]; z[1] = k*x[1]+y[1]; z[2] = k*x[2]+y[2];
}
-
+
KOKKOS_INLINE_FUNCTION
int sbmask(const int& j) const;
@@ -152,7 +152,7 @@ class PairTersoffZBLKokkos : public PairTersoffZBL {
bigr=0;bigd=0;lam1=0;biga=0;cutsq=0;c1=0;c2=0;c3=0;c4=0;Z_i=0;Z_j=0;ZBLcut=0;ZBLexpscale=0;};
params_ters(int i){powerm=0;gamma=0;lam3=0;c=0;d=0;h=0;powern=0;beta=0;lam2=0;bigb=0;
bigr=0;bigd=0;lam1=0;biga=0;cutsq=0;c1=0;c2=0;c3=0;c4=0;Z_i=0;Z_j=0;ZBLcut=0;ZBLexpscale=0;};
- F_FLOAT powerm, gamma, lam3, c, d, h, powern, beta, lam2, bigb, bigr,
+ F_FLOAT powerm, gamma, lam3, c, d, h, powern, beta, lam2, bigb, bigr,
bigd, lam1, biga, cutsq, c1, c2, c3, c4, Z_i, Z_j, ZBLcut, ZBLexpscale;
};
@@ -164,11 +164,11 @@ class PairTersoffZBLKokkos : public PairTersoffZBL {
template<int NEIGHFLAG>
KOKKOS_INLINE_FUNCTION
- void v_tally3(EV_FLOAT &ev, const int &i, const int &j, const int &k,
+ void v_tally3(EV_FLOAT &ev, const int &i, const int &j, const int &k,
F_FLOAT *fj, F_FLOAT *fk, F_FLOAT *drij, F_FLOAT *drik) const;
KOKKOS_INLINE_FUNCTION
- void v_tally3_atom(EV_FLOAT &ev, const int &i, const int &j, const int &k,
+ void v_tally3_atom(EV_FLOAT &ev, const int &i, const int &j, const int &k,
F_FLOAT *fj, F_FLOAT *fk, F_FLOAT *drji, F_FLOAT *drjk) const;
void allocate();
diff --git a/src/KOKKOS/verlet_kokkos.cpp b/src/KOKKOS/verlet_kokkos.cpp
index 3d69547f34..67e852a7d9 100644
--- a/src/KOKKOS/verlet_kokkos.cpp
+++ b/src/KOKKOS/verlet_kokkos.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "verlet_kokkos.h"
#include "neighbor.h"
#include "domain.h"
@@ -42,7 +42,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
VerletKokkos::VerletKokkos(LAMMPS *lmp, int narg, char **arg) :
- Verlet(lmp, narg, arg)
+ Verlet(lmp, narg, arg)
{
atomKK = (AtomKokkos *) atom;
}
diff --git a/src/KOKKOS/verlet_kokkos.h b/src/KOKKOS/verlet_kokkos.h
index 2c7bad1efb..4b64ced567 100644
--- a/src/KOKKOS/verlet_kokkos.h
+++ b/src/KOKKOS/verlet_kokkos.h
@@ -33,7 +33,7 @@ class VerletKokkos : public Verlet {
void run(int);
protected:
-
+
void force_clear();
};
diff --git a/src/KSPACE/ewald.cpp b/src/KSPACE/ewald.cpp
index 386523c364..f3a4188de9 100644
--- a/src/KSPACE/ewald.cpp
+++ b/src/KSPACE/ewald.cpp
@@ -18,11 +18,11 @@
triclinic added by Stan Moore (SNL)
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "stdlib.h"
-#include "stdio.h"
-#include "string.h"
-#include "math.h"
+#include <mpi.h>
+#include <stdlib.h>
+#include <stdio.h>
+#include <string.h>
+#include <math.h>
#include "ewald.h"
#include "atom.h"
#include "comm.h"
@@ -86,7 +86,7 @@ void Ewald::init()
}
// error check
-
+
triclinic_check();
if (domain->dimension == 2)
error->all(FLERR,"Cannot use Ewald with 2d simulation");
@@ -252,19 +252,19 @@ void Ewald::setup()
kmax = MAX(kxmax,kymax);
kmax = MAX(kmax,kzmax);
kmax3d = 4*kmax*kmax*kmax + 6*kmax*kmax + 3*kmax;
-
+
double gsqxmx = unitk[0]*unitk[0]*kxmax*kxmax;
double gsqymx = unitk[1]*unitk[1]*kymax*kymax;
double gsqzmx = unitk[2]*unitk[2]*kzmax*kzmax;
gsqmx = MAX(gsqxmx,gsqymx);
gsqmx = MAX(gsqmx,gsqzmx);
-
+
kxmax_orig = kxmax;
kymax_orig = kymax;
kzmax_orig = kzmax;
// scale lattice vectors for triclinic skew
-
+
if (triclinic) {
double tmp[3];
tmp[0] = kxmax/xprd;
@@ -274,7 +274,7 @@ void Ewald::setup()
kxmax = MAX(1,static_cast<int>(tmp[0]));
kymax = MAX(1,static_cast<int>(tmp[1]));
kzmax = MAX(1,static_cast<int>(tmp[2]));
-
+
kmax = MAX(kxmax,kymax);
kmax = MAX(kmax,kzmax);
kmax3d = 4*kmax*kmax*kmax + 6*kmax*kmax + 3*kmax;
@@ -285,7 +285,7 @@ void Ewald::setup()
kxmax = kx_ewald;
kymax = ky_ewald;
kzmax = kz_ewald;
-
+
kxmax_orig = kxmax;
kymax_orig = kymax;
kzmax_orig = kzmax;
@@ -354,18 +354,18 @@ void Ewald::compute(int eflag, int vflag)
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = evflag_atom = eflag_global = vflag_global =
eflag_atom = vflag_atom = 0;
-
- // if atom count has changed, update qsum and qsqsum
+
+ // if atom count has changed, update qsum and qsqsum
if (atom->natoms != natoms_original) {
qsum_qsq();
natoms_original = atom->natoms;
}
-
+
// return if there are no charges
-
+
if (qsqsum == 0.0) return;
-
+
// extend size of per-atom arrays if necessary
if (atom->nlocal > nmax) {
@@ -1012,7 +1012,7 @@ void Ewald::coeffs()
}
/* ----------------------------------------------------------------------
- pre-compute coefficients for each Ewald K-vector for a triclinic
+ pre-compute coefficients for each Ewald K-vector for a triclinic
system
------------------------------------------------------------------------- */
@@ -1395,7 +1395,7 @@ void Ewald::slabcorr_groups(int groupbit_A, int groupbit_B, int AA_flag)
if (!((mask[i] & groupbit_A) && (mask[i] & groupbit_B)))
if (AA_flag) continue;
- if (mask[i] & groupbit_A) {
+ if (mask[i] & groupbit_A) {
qsum_A += q[i];
dipole_A += q[i]*x[i][2];
dipole_r2_A += q[i]*x[i][2]*x[i][2];
diff --git a/src/KSPACE/ewald_disp.cpp b/src/KSPACE/ewald_disp.cpp
index 2f0874cf11..c1a8d81e00 100644
--- a/src/KSPACE/ewald_disp.cpp
+++ b/src/KSPACE/ewald_disp.cpp
@@ -15,11 +15,11 @@
Contributing authors: Pieter in 't Veld (SNL), Stan Moore (SNL)
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "string.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "math.h"
+#include <mpi.h>
+#include <string.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
#include "ewald_disp.h"
#include "math_vector.h"
#include "math_const.h"
@@ -195,8 +195,8 @@ void EwaldDisp::init()
//Try Newton Solver
//Use old method to get guess
g_ewald = (1.35 - 0.15*log(accuracy))/ *cutoff;
-
- double g_ewald_new =
+
+ double g_ewald_new =
NewtonSolve(g_ewald,(*cutoff),natoms,shape_det(domain->h),b2);
if (g_ewald_new > 0.0) g_ewald = g_ewald_new;
else error->warning(FLERR,"Ewald/disp Newton solver failed, "
@@ -205,7 +205,7 @@ void EwaldDisp::init()
//Try Newton Solver
//Use old method to get guess
g_ewald = (1.35 - 0.15*log(accuracy))/ *cutoff;
- double g_ewald_new =
+ double g_ewald_new =
NewtonSolve(g_ewald,(*cutoff),natoms,shape_det(domain->h),M2);
if (g_ewald_new > 0.0) g_ewald = g_ewald_new;
else error->warning(FLERR,"Ewald/disp Newton solver failed, "
@@ -289,7 +289,7 @@ void EwaldDisp::setup()
compute RMS accuracy for a dimension
------------------------------------------------------------------------- */
-double EwaldDisp::rms(int km, double prd, bigint natoms,
+double EwaldDisp::rms(int km, double prd, bigint natoms,
double q2, double b2, double M2)
{
double value = 0.0;
@@ -930,7 +930,7 @@ void EwaldDisp::compute_energy()
if (func[0]) { // 1/r
sum[0] += *(ke++)*(cek->re*cek->re+cek->im*cek->im);
if (func[3]) cek_coul = cek;
- ++cek;
+ ++cek;
}
if (func[1]) { // geometric 1/r^6
sum[1] += *(ke++)*(cek->re*cek->re+cek->im*cek->im); ++cek; }
@@ -1161,7 +1161,7 @@ void EwaldDisp::compute_virial_dipole()
++cek;
}
if (func[1]) { // geometric 1/r^6
- ke++;
+ ke++;
++cek;
}
if (func[2]) { // arithmetic 1/r^6
@@ -1404,7 +1404,7 @@ void EwaldDisp::compute_slabcorr()
double ffact = qscale * (-4.0*MY_PI/volume);
double **f = atom->f;
- for (int i = 0; i < nlocal; i++)
+ for (int i = 0; i < nlocal; i++)
f[i][2] += ffact * q[i]*(dipole_all - qsum*x[i][2]);
// add on torque corrections
@@ -1423,7 +1423,7 @@ void EwaldDisp::compute_slabcorr()
Newton solver used to find g_ewald for LJ systems
------------------------------------------------------------------------- */
-double EwaldDisp::NewtonSolve(double x, double Rc,
+double EwaldDisp::NewtonSolve(double x, double Rc,
bigint natoms, double vol, double b2)
{
double dx,tol;
@@ -1474,7 +1474,7 @@ double EwaldDisp::f(double x, double Rc, bigint natoms, double vol, double b2)
Calculate numerical derivative f'(x)
------------------------------------------------------------------------- */
-double EwaldDisp::derivf(double x, double Rc,
+double EwaldDisp::derivf(double x, double Rc,
bigint natoms, double vol, double b2)
{
double h = 0.000001; //Derivative step-size
diff --git a/src/KSPACE/fft3d.cpp b/src/KSPACE/fft3d.cpp
index 50ed97fa93..a0896ed22d 100644
--- a/src/KSPACE/fft3d.cpp
+++ b/src/KSPACE/fft3d.cpp
@@ -19,10 +19,10 @@
Paul Coffman (IBM) added MPI collectives remap
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "math.h"
+#include <mpi.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
#include "fft3d.h"
#include "remap.h"
diff --git a/src/KSPACE/fft3d.h b/src/KSPACE/fft3d.h
index 34a7bcf9d6..ed3b597f33 100644
--- a/src/KSPACE/fft3d.h
+++ b/src/KSPACE/fft3d.h
@@ -314,10 +314,10 @@ struct fft_plan_3d {
// function prototypes
-extern "C" {
+extern "C" {
void fft_3d(FFT_DATA *, FFT_DATA *, int, struct fft_plan_3d *);
struct fft_plan_3d *fft_3d_create_plan(MPI_Comm, int, int, int,
- int, int, int, int, int,
+ int, int, int, int, int,
int, int, int, int, int, int, int,
int, int, int *, int);
void fft_3d_destroy_plan(struct fft_plan_3d *);
diff --git a/src/KSPACE/fft3d_wrap.cpp b/src/KSPACE/fft3d_wrap.cpp
index fb5d3e3d2b..b9a6f0ae46 100644
--- a/src/KSPACE/fft3d_wrap.cpp
+++ b/src/KSPACE/fft3d_wrap.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
+#include <mpi.h>
#include "fft3d_wrap.h"
#include "error.h"
diff --git a/src/KSPACE/fix_tune_kspace.cpp b/src/KSPACE/fix_tune_kspace.cpp
index 9c7552f20c..2dbed26941 100644
--- a/src/KSPACE/fix_tune_kspace.cpp
+++ b/src/KSPACE/fix_tune_kspace.cpp
@@ -15,8 +15,8 @@
Contributing author: Paul Crozier (SNL)
------------------------------------------------------------------------- */
-#include "string.h"
-#include "stdlib.h"
+#include <string.h>
+#include <stdlib.h>
#include "fix_tune_kspace.h"
#include "update.h"
#include "domain.h"
@@ -84,9 +84,9 @@ int FixTuneKspace::setmask()
void FixTuneKspace::init()
{
- if (!force->kspace)
+ if (!force->kspace)
error->all(FLERR,"Cannot use fix tune/kspace without a kspace style");
- if (!force->pair)
+ if (!force->pair)
error->all(FLERR,"Cannot use fix tune/kspace without a pair style");
double old_acc = force->kspace->accuracy/force->kspace->two_charge_force;
@@ -219,7 +219,7 @@ void FixTuneKspace::store_old_kspace_settings()
update the pair style if necessary, preserving the settings
------------------------------------------------------------------------- */
-void FixTuneKspace::update_pair_style(char *new_pair_style,
+void FixTuneKspace::update_pair_style(char *new_pair_style,
double pair_cut_coul)
{
int itmp;
@@ -254,7 +254,7 @@ void FixTuneKspace::update_pair_style(char *new_pair_style,
update the kspace style if necessary
------------------------------------------------------------------------- */
-void FixTuneKspace::update_kspace_style(char *new_kspace_style,
+void FixTuneKspace::update_kspace_style(char *new_kspace_style,
char *new_acc_str)
{
// create kspace style char string
diff --git a/src/KSPACE/fix_tune_kspace.h b/src/KSPACE/fix_tune_kspace.h
index b99b7a0851..3311bd1d43 100644
--- a/src/KSPACE/fix_tune_kspace.h
+++ b/src/KSPACE/fix_tune_kspace.h
@@ -20,7 +20,7 @@ FixStyle(tune/kspace,FixTuneKspace)
#ifndef LMP_FIX_TUNE_KSPACE_H
#define LMP_FIX_TUNE_KSPACE_H
-#include "stdio.h"
+#include <stdio.h>
#include "fix.h"
namespace LAMMPS_NS {
diff --git a/src/KSPACE/gridcomm.cpp b/src/KSPACE/gridcomm.cpp
index 1ae7849a7a..ba08c9be26 100644
--- a/src/KSPACE/gridcomm.cpp
+++ b/src/KSPACE/gridcomm.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
+#include <mpi.h>
#include "gridcomm.h"
#include "comm.h"
#include "kspace.h"
@@ -27,7 +27,7 @@ using namespace LAMMPS_NS;
GridComm::GridComm(LAMMPS *lmp, MPI_Comm gcomm, int forward, int reverse,
int ixlo, int ixhi, int iylo, int iyhi, int izlo, int izhi,
int oxlo, int oxhi, int oylo, int oyhi, int ozlo, int ozhi,
- int pxlo, int pxhi, int pylo, int pyhi, int pzlo, int pzhi)
+ int pxlo, int pxhi, int pylo, int pyhi, int pzlo, int pzhi)
: Pointers(lmp)
{
gridcomm = gcomm;
@@ -74,9 +74,9 @@ GridComm::GridComm(LAMMPS *lmp, MPI_Comm gcomm, int forward, int reverse,
GridComm::GridComm(LAMMPS *lmp, MPI_Comm gcomm, int forward, int reverse,
int ixlo, int ixhi, int iylo, int iyhi, int izlo, int izhi,
int oxlo, int oxhi, int oylo, int oyhi, int ozlo, int ozhi,
- int oxlo_max, int oxhi_max, int oylo_max, int oyhi_max,
+ int oxlo_max, int oxhi_max, int oylo_max, int oyhi_max,
int ozlo_max, int ozhi_max,
- int pxlo, int pxhi, int pylo, int pyhi, int pzlo, int pzhi)
+ int pxlo, int pxhi, int pylo, int pyhi, int pzlo, int pzhi)
: Pointers(lmp)
{
gridcomm = gcomm;
@@ -194,7 +194,7 @@ int GridComm::ghost_overlap()
if (ghostyhi > inyhi-inylo+1) nearest = 1;
if (ghostzlo > inzhi-inzlo+1) nearest = 1;
if (ghostzhi > inzhi-inzlo+1) nearest = 1;
-
+
int nearest_all;
MPI_Allreduce(&nearest,&nearest_all,1,MPI_INT,MPI_MIN,gridcomm);
@@ -230,14 +230,14 @@ void GridComm::setup()
while (notdone) {
if (nswap == maxswap) {
maxswap += SWAPDELTA;
- swap = (Swap *)
+ swap = (Swap *)
memory->srealloc(swap,maxswap*sizeof(Swap),"Commgrid:swap");
}
swap[nswap].sendproc = procxlo;
swap[nswap].recvproc = procxhi;
sendplanes = MIN(sendlast-sendfirst+1,ghostxlo-nsent);
- swap[nswap].npack =
+ swap[nswap].npack =
indices(swap[nswap].packlist,
sendfirst,sendfirst+sendplanes-1,inylo,inyhi,inzlo,inzhi);
@@ -246,7 +246,7 @@ void GridComm::setup()
&recvplanes,1,MPI_INT,procxhi,0,gridcomm,MPI_STATUS_IGNORE);
else recvplanes = sendplanes;
- swap[nswap].nunpack =
+ swap[nswap].nunpack =
indices(swap[nswap].unpacklist,
recvfirst,recvfirst+recvplanes-1,inylo,inyhi,inzlo,inzhi);
@@ -272,14 +272,14 @@ void GridComm::setup()
while (notdone) {
if (nswap == maxswap) {
maxswap += 1;
- swap = (Swap *)
+ swap = (Swap *)
memory->srealloc(swap,maxswap*sizeof(Swap),"Commgrid:swap");
}
swap[nswap].sendproc = procxhi;
swap[nswap].recvproc = procxlo;
sendplanes = MIN(sendlast-sendfirst+1,ghostxhi-nsent);
- swap[nswap].npack =
+ swap[nswap].npack =
indices(swap[nswap].packlist,
sendlast-sendplanes+1,sendlast,inylo,inyhi,inzlo,inzhi);
@@ -288,7 +288,7 @@ void GridComm::setup()
&recvplanes,1,MPI_INT,procxlo,0,gridcomm,MPI_STATUS_IGNORE);
else recvplanes = sendplanes;
- swap[nswap].nunpack =
+ swap[nswap].nunpack =
indices(swap[nswap].unpacklist,
recvlast-recvplanes+1,recvlast,inylo,inyhi,inzlo,inzhi);
@@ -314,14 +314,14 @@ void GridComm::setup()
while (notdone) {
if (nswap == maxswap) {
maxswap += SWAPDELTA;
- swap = (Swap *)
+ swap = (Swap *)
memory->srealloc(swap,maxswap*sizeof(Swap),"Commgrid:swap");
}
swap[nswap].sendproc = procylo;
swap[nswap].recvproc = procyhi;
sendplanes = MIN(sendlast-sendfirst+1,ghostylo-nsent);
- swap[nswap].npack =
+ swap[nswap].npack =
indices(swap[nswap].packlist,
outxlo,outxhi,sendfirst,sendfirst+sendplanes-1,inzlo,inzhi);
@@ -330,7 +330,7 @@ void GridComm::setup()
&recvplanes,1,MPI_INT,procyhi,0,gridcomm,MPI_STATUS_IGNORE);
else recvplanes = sendplanes;
- swap[nswap].nunpack =
+ swap[nswap].nunpack =
indices(swap[nswap].unpacklist,
outxlo,outxhi,recvfirst,recvfirst+recvplanes-1,inzlo,inzhi);
@@ -356,14 +356,14 @@ void GridComm::setup()
while (notdone) {
if (nswap == maxswap) {
maxswap += 1;
- swap = (Swap *)
+ swap = (Swap *)
memory->srealloc(swap,maxswap*sizeof(Swap),"Commgrid:swap");
}
swap[nswap].sendproc = procyhi;
swap[nswap].recvproc = procylo;
sendplanes = MIN(sendlast-sendfirst+1,ghostyhi-nsent);
- swap[nswap].npack =
+ swap[nswap].npack =
indices(swap[nswap].packlist,
outxlo,outxhi,sendlast-sendplanes+1,sendlast,inzlo,inzhi);
@@ -372,7 +372,7 @@ void GridComm::setup()
&recvplanes,1,MPI_INT,procylo,0,gridcomm,MPI_STATUS_IGNORE);
else recvplanes = sendplanes;
- swap[nswap].nunpack =
+ swap[nswap].nunpack =
indices(swap[nswap].unpacklist,
outxlo,outxhi,recvlast-recvplanes+1,recvlast,inzlo,inzhi);
@@ -398,14 +398,14 @@ void GridComm::setup()
while (notdone) {
if (nswap == maxswap) {
maxswap += SWAPDELTA;
- swap = (Swap *)
+ swap = (Swap *)
memory->srealloc(swap,maxswap*sizeof(Swap),"Commgrid:swap");
}
swap[nswap].sendproc = proczlo;
swap[nswap].recvproc = proczhi;
sendplanes = MIN(sendlast-sendfirst+1,ghostzlo-nsent);
- swap[nswap].npack =
+ swap[nswap].npack =
indices(swap[nswap].packlist,
outxlo,outxhi,outylo,outyhi,sendfirst,sendfirst+sendplanes-1);
@@ -414,7 +414,7 @@ void GridComm::setup()
&recvplanes,1,MPI_INT,proczhi,0,gridcomm,MPI_STATUS_IGNORE);
else recvplanes = sendplanes;
- swap[nswap].nunpack =
+ swap[nswap].nunpack =
indices(swap[nswap].unpacklist,
outxlo,outxhi,outylo,outyhi,recvfirst,recvfirst+recvplanes-1);
@@ -440,14 +440,14 @@ void GridComm::setup()
while (notdone) {
if (nswap == maxswap) {
maxswap += 1;
- swap = (Swap *)
+ swap = (Swap *)
memory->srealloc(swap,maxswap*sizeof(Swap),"Commgrid:swap");
}
swap[nswap].sendproc = proczhi;
swap[nswap].recvproc = proczlo;
sendplanes = MIN(sendlast-sendfirst+1,ghostzhi-nsent);
- swap[nswap].npack =
+ swap[nswap].npack =
indices(swap[nswap].packlist,
outxlo,outxhi,outylo,outyhi,sendlast-sendplanes+1,sendlast);
@@ -456,7 +456,7 @@ void GridComm::setup()
&recvplanes,1,MPI_INT,proczlo,0,gridcomm,MPI_STATUS_IGNORE);
else recvplanes = sendplanes;
- swap[nswap].nunpack =
+ swap[nswap].nunpack =
indices(swap[nswap].unpacklist,
outxlo,outxhi,outylo,outyhi,recvlast-recvplanes+1,recvlast);
@@ -490,7 +490,7 @@ void GridComm::setup()
void GridComm::forward_comm(KSpace *kspace, int which)
{
for (int m = 0; m < nswap; m++) {
- if (swap[m].sendproc == me)
+ if (swap[m].sendproc == me)
kspace->pack_forward(which,buf2,swap[m].npack,swap[m].packlist);
else
kspace->pack_forward(which,buf1,swap[m].npack,swap[m].packlist);
@@ -502,7 +502,7 @@ void GridComm::forward_comm(KSpace *kspace, int which)
swap[m].sendproc,0,gridcomm);
MPI_Wait(&request,MPI_STATUS_IGNORE);
}
-
+
kspace->unpack_forward(which,buf2,swap[m].nunpack,swap[m].unpacklist);
}
}
@@ -515,7 +515,7 @@ void GridComm::forward_comm(KSpace *kspace, int which)
void GridComm::reverse_comm(KSpace *kspace, int which)
{
for (int m = nswap-1; m >= 0; m--) {
- if (swap[m].recvproc == me)
+ if (swap[m].recvproc == me)
kspace->pack_reverse(which,buf2,swap[m].nunpack,swap[m].unpacklist);
else
kspace->pack_reverse(which,buf1,swap[m].nunpack,swap[m].unpacklist);
@@ -527,7 +527,7 @@ void GridComm::reverse_comm(KSpace *kspace, int which)
swap[m].recvproc,0,gridcomm);
MPI_Wait(&request,MPI_STATUS_IGNORE);
}
-
+
kspace->unpack_reverse(which,buf2,swap[m].npack,swap[m].packlist);
}
}
@@ -538,7 +538,7 @@ void GridComm::reverse_comm(KSpace *kspace, int which)
outzlo_max:outzhi_max)
------------------------------------------------------------------------- */
-int GridComm::indices(int *&list,
+int GridComm::indices(int *&list,
int xlo, int xhi, int ylo, int yhi, int zlo, int zhi)
{
int nmax = (xhi-xlo+1) * (yhi-ylo+1) * (zhi-zlo+1);
diff --git a/src/KSPACE/msm.cpp b/src/KSPACE/msm.cpp
index f4ec380068..92ed86338c 100644
--- a/src/KSPACE/msm.cpp
+++ b/src/KSPACE/msm.cpp
@@ -15,11 +15,11 @@
Contributing authors: Paul Crozier, Stan Moore, Stephen Bond, (all SNL)
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "string.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "math.h"
+#include <mpi.h>
+#include <string.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
#include "msm.h"
#include "atom.h"
#include "comm.h"
@@ -148,7 +148,7 @@ void MSM::init()
triclinic_check();
if (domain->dimension == 2)
error->all(FLERR,"Cannot (yet) use MSM with 2d simulation");
- if (comm->style != 0)
+ if (comm->style != 0)
error->universe_all(FLERR,"MSM can only currently be used with "
"comm_style brick");
@@ -165,7 +165,7 @@ void MSM::init()
if (order%2 != 0) error->all(FLERR,"MSM order must be 4, 6, 8, or 10");
- if (sizeof(FFT_SCALAR) != 8)
+ if (sizeof(FFT_SCALAR) != 8)
error->all(FLERR,"Cannot (yet) use single precision with MSM "
"(remove -DFFT_SINGLE from Makefile and recompile)");
@@ -359,7 +359,7 @@ void MSM::setup()
double ay = a;
double az = a;
- // transform the interaction sphere in box coords to an
+ // transform the interaction sphere in box coords to an
// ellipsoid in lamda (0-1) coords to
// get the direct sum interaction limits for a triclinic system
@@ -408,7 +408,7 @@ void MSM::setup()
else
boxlo = domain->boxlo_lamda;
- // ghost grid points depend on direct sum interaction limits,
+ // ghost grid points depend on direct sum interaction limits,
// so need to recompute local grid
set_grid_local();
@@ -457,17 +457,17 @@ void MSM::compute(int eflag, int vflag)
}
}
- // if atom count has changed, update qsum and qsqsum
+ // if atom count has changed, update qsum and qsqsum
if (atom->natoms != natoms_original) {
qsum_qsq();
natoms_original = atom->natoms;
}
-
+
// return if there are no charges
-
+
if (qsqsum == 0.0) return;
-
+
// invoke allocate_peratom() if needed for first time
if (vflag_atom && !peratom_allocate_flag) {
@@ -500,7 +500,7 @@ void MSM::compute(int eflag, int vflag)
particle_map();
make_rho();
- // all procs reverse communicate charge density values from
+ // all procs reverse communicate charge density values from
// their ghost grid points
// to fully sum contribution in their 3d grid
@@ -3136,7 +3136,7 @@ void MSM::get_g_direct()
for (ix = nxlo_direct; ix <= nxhi_direct; ix++) {
xdiff = ix/delxinv[n];
- // transform grid point pair-wise distance from lamda (0-1) coords to box coords
+ // transform grid point pair-wise distance from lamda (0-1) coords to box coords
if (triclinic) {
tmp[0] = xdiff;
diff --git a/src/KSPACE/msm.h b/src/KSPACE/msm.h
index ef12e460ce..6a0b7d0eeb 100644
--- a/src/KSPACE/msm.h
+++ b/src/KSPACE/msm.h
@@ -21,7 +21,7 @@ KSpaceStyle(msm,MSM)
#define LMP_MSM_H
#include "lmptype.h"
-#include "mpi.h"
+#include <mpi.h>
#include "kspace.h"
@@ -62,8 +62,8 @@ class MSM : public KSpace {
int nlower,nupper;
int peratom_allocate_flag;
int levels;
-
- MPI_Comm *world_levels;
+
+ MPI_Comm *world_levels;
double ****qgrid;
double ****egrid;
@@ -85,7 +85,7 @@ class MSM : public KSpace {
class GridComm **cg_peratom;
class GridComm *cg_all;
class GridComm *cg_peratom_all;
-
+
int current_level;
int **part2grid; // storage for particle -> grid mapping
@@ -221,7 +221,7 @@ The box size has apparently blown up.
E: Out of range atoms - cannot compute MSM
-One or more atoms are attempting to map their charge to a MSM grid point
+One or more atoms are attempting to map their charge to a MSM grid point
that is not owned by a processor. This is likely for one of two
reasons, both of them bad. First, it may mean that an atom near the
boundary of a processor's sub-domain has moved more than 1/2 the
diff --git a/src/KSPACE/msm_cg.cpp b/src/KSPACE/msm_cg.cpp
index 30dcbeb3f6..e7000c26d9 100644
--- a/src/KSPACE/msm_cg.cpp
+++ b/src/KSPACE/msm_cg.cpp
@@ -15,11 +15,11 @@
Contributing authors: Paul Crozier, Stan Moore, Stephen Bond, (all SNL)
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <mpi.h>
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "atom.h"
#include "gridcomm.h"
#include "domain.h"
diff --git a/src/KSPACE/msm_cg.h b/src/KSPACE/msm_cg.h
index 47b95dcc8e..2f68e46461 100644
--- a/src/KSPACE/msm_cg.h
+++ b/src/KSPACE/msm_cg.h
@@ -66,7 +66,7 @@ The box size has apparently blown up.
E: Out of range atoms - cannot compute MSM
-One or more atoms are attempting to map their charge to a MSM grid point
+One or more atoms are attempting to map their charge to a MSM grid point
that is not owned by a processor. This is likely for one of two
reasons, both of them bad. First, it may mean that an atom near the
boundary of a processor's sub-domain has moved more than 1/2 the
diff --git a/src/KSPACE/pair_born_coul_long.cpp b/src/KSPACE/pair_born_coul_long.cpp
index 35b8b517e5..15bcd1081b 100644
--- a/src/KSPACE/pair_born_coul_long.cpp
+++ b/src/KSPACE/pair_born_coul_long.cpp
@@ -15,10 +15,10 @@
Contributing author: Ahmed Ismail (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_born_coul_long.h"
#include "atom.h"
#include "comm.h"
@@ -381,7 +381,7 @@ void PairBornCoulLong::init_style()
g_ewald = force->kspace->g_ewald;
neighbor->request(this,instance_me);
-
+
// setup force tables
if (ncoultablebits) init_tables(cut_coul,NULL);
diff --git a/src/KSPACE/pair_born_coul_msm.cpp b/src/KSPACE/pair_born_coul_msm.cpp
index 50779abb00..6ed120cdc5 100644
--- a/src/KSPACE/pair_born_coul_msm.cpp
+++ b/src/KSPACE/pair_born_coul_msm.cpp
@@ -15,10 +15,10 @@
Contributing author: Stan Moore (SNL), Paul Crozier (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_born_coul_msm.h"
#include "atom.h"
#include "comm.h"
@@ -204,8 +204,8 @@ void PairBornCoulMSM::compute(int eflag, int vflag)
for (i = 0; i < 3; i++) virial[i] += force->pair->eng_coul/3.0;
for (int i = 0; i < nmax; i++) {
f[i][0] += ftmp[i][0];
- f[i][1] += ftmp[i][1];
- f[i][2] += ftmp[i][2];
+ f[i][1] += ftmp[i][1];
+ f[i][2] += ftmp[i][2];
}
}
}
diff --git a/src/KSPACE/pair_buck_coul_long.cpp b/src/KSPACE/pair_buck_coul_long.cpp
index 08d3ebf3d7..683e5bf004 100644
--- a/src/KSPACE/pair_buck_coul_long.cpp
+++ b/src/KSPACE/pair_buck_coul_long.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_buck_coul_long.h"
#include "atom.h"
#include "comm.h"
@@ -125,7 +125,7 @@ void PairBuckCoulLong::compute(int eflag, int vflag)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- r2inv = 1.0/rsq;
+ r2inv = 1.0/rsq;
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq) {
r = sqrt(rsq);
@@ -251,7 +251,7 @@ void PairBuckCoulLong::settings(int narg, char **arg)
void PairBuckCoulLong::coeff(int narg, char **arg)
{
- if (narg < 5 || narg > 6)
+ if (narg < 5 || narg > 6)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
@@ -360,7 +360,7 @@ void PairBuckCoulLong::init_style()
g_ewald = force->kspace->g_ewald;
neighbor->request(this,instance_me);
-
+
// setup force tables
if (ncoultablebits) init_tables(cut_coul,NULL);
diff --git a/src/KSPACE/pair_buck_coul_msm.cpp b/src/KSPACE/pair_buck_coul_msm.cpp
index 370845e384..e33bdc839c 100644
--- a/src/KSPACE/pair_buck_coul_msm.cpp
+++ b/src/KSPACE/pair_buck_coul_msm.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_buck_coul_msm.h"
#include "atom.h"
#include "comm.h"
@@ -200,8 +200,8 @@ void PairBuckCoulMSM::compute(int eflag, int vflag)
for (i = 0; i < 3; i++) virial[i] += force->pair->eng_coul/3.0;
for (int i = 0; i < nmax; i++) {
f[i][0] += ftmp[i][0];
- f[i][1] += ftmp[i][1];
- f[i][2] += ftmp[i][2];
+ f[i][1] += ftmp[i][1];
+ f[i][2] += ftmp[i][2];
}
}
}
diff --git a/src/KSPACE/pair_buck_long_coul_long.cpp b/src/KSPACE/pair_buck_long_coul_long.cpp
index 3b86921854..52d250fbe1 100644
--- a/src/KSPACE/pair_buck_long_coul_long.cpp
+++ b/src/KSPACE/pair_buck_long_coul_long.cpp
@@ -15,10 +15,10 @@
Contributing author: Pieter J. in 't Veld (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "math_vector.h"
#include "pair_buck_long_coul_long.h"
#include "atom.h"
@@ -86,17 +86,17 @@ void PairBuckLongCoulLong::settings(int narg, char **arg)
options(arg,6);
options(++arg,1);
- if (!comm->me && ewald_order == ((1<<1) | (1<<6)))
+ if (!comm->me && ewald_order == ((1<<1) | (1<<6)))
error->warning(FLERR,"Using largest cutoff for buck/long/coul/long");
- if (!*(++arg))
+ if (!*(++arg))
error->all(FLERR,"Cutoffs missing in pair_style buck/long/coul/long");
- if (ewald_off & (1<<6))
+ if (ewald_off & (1<<6))
error->all(FLERR,"LJ6 off not supported in pair_style buck/long/coul/long");
- if (!((ewald_order^ewald_off) & (1<<1)))
+ if (!((ewald_order^ewald_off) & (1<<1)))
error->all(FLERR,
"Coulomb cut not supported in pair_style buck/long/coul/coul");
cut_buck_global = force->numeric(FLERR,*(arg++));
- if (narg == 4 && ((ewald_order & 0x42) == 0x42))
+ if (narg == 4 && ((ewald_order & 0x42) == 0x42))
error->all(FLERR,"Only one cutoff allowed when requesting all long");
if (narg == 4) cut_coul = force->numeric(FLERR,*arg);
else cut_coul = cut_buck_global;
@@ -176,7 +176,7 @@ void *PairBuckLongCoulLong::extract(const char *id, int &dim)
const char *ids[] = {
"B", "ewald_order", "ewald_cut", "ewald_mix", "cut_coul", "cut_LJ", NULL};
void *ptrs[] = {
- buck_c, &ewald_order, &cut_coul, &mix_flag, &cut_coul, &cut_buck_global,
+ buck_c, &ewald_order, &cut_coul, &mix_flag, &cut_coul, &cut_buck_global,
NULL};
int i;
@@ -192,7 +192,7 @@ void *PairBuckLongCoulLong::extract(const char *id, int &dim)
void PairBuckLongCoulLong::coeff(int narg, char **arg)
{
- if (narg < 5 || narg > 6)
+ if (narg < 5 || narg > 6)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
diff --git a/src/KSPACE/pair_coul_long.cpp b/src/KSPACE/pair_coul_long.cpp
index db46fed213..c1cd14523e 100644
--- a/src/KSPACE/pair_coul_long.cpp
+++ b/src/KSPACE/pair_coul_long.cpp
@@ -15,10 +15,10 @@
Contributing author: Paul Crozier (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_coul_long.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/KSPACE/pair_coul_msm.cpp b/src/KSPACE/pair_coul_msm.cpp
index e27714f59d..62daee9a13 100644
--- a/src/KSPACE/pair_coul_msm.cpp
+++ b/src/KSPACE/pair_coul_msm.cpp
@@ -15,10 +15,10 @@
Contributing authors: Stan Moore (SNL), Paul Crozier (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_coul_msm.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/KSPACE/pair_lj_charmm_coul_long.cpp b/src/KSPACE/pair_lj_charmm_coul_long.cpp
index ea357604d4..2c709a3ae0 100644
--- a/src/KSPACE/pair_lj_charmm_coul_long.cpp
+++ b/src/KSPACE/pair_lj_charmm_coul_long.cpp
@@ -15,10 +15,10 @@
Contributing author: Paul Crozier (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_lj_charmm_coul_long.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/KSPACE/pair_lj_charmm_coul_msm.cpp b/src/KSPACE/pair_lj_charmm_coul_msm.cpp
index a06863fd87..e99071f4ef 100644
--- a/src/KSPACE/pair_lj_charmm_coul_msm.cpp
+++ b/src/KSPACE/pair_lj_charmm_coul_msm.cpp
@@ -15,10 +15,10 @@
Contributing authors: Paul Crozier (SNL), Stan Moore (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_lj_charmm_coul_msm.h"
#include "atom.h"
#include "comm.h"
@@ -37,7 +37,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-PairLJCharmmCoulMSM::PairLJCharmmCoulMSM(LAMMPS *lmp) :
+PairLJCharmmCoulMSM::PairLJCharmmCoulMSM(LAMMPS *lmp) :
PairLJCharmmCoulLong(lmp)
{
ewaldflag = pppmflag = 0;
@@ -135,9 +135,9 @@ void PairLJCharmmCoulMSM::compute(int eflag, int vflag)
if (!ncoultablebits || rsq <= tabinnersq) {
r = sqrt(rsq);
prefactor = qqrd2e * qtmp*q[j]/r;
- egamma = 1.0 - (r/cut_coul)*force->kspace->gamma(r/cut_coul);
- fgamma = 1.0 + (rsq/cut_coulsq)*force->kspace->dgamma(r/cut_coul);
- forcecoul = prefactor * fgamma;
+ egamma = 1.0 - (r/cut_coul)*force->kspace->gamma(r/cut_coul);
+ fgamma = 1.0 + (rsq/cut_coulsq)*force->kspace->dgamma(r/cut_coul);
+ forcecoul = prefactor * fgamma;
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
} else {
union_int_float_t rsq_lookup;
@@ -240,8 +240,8 @@ void PairLJCharmmCoulMSM::compute(int eflag, int vflag)
for (i = 0; i < 3; i++) virial[i] += force->pair->eng_coul/3.0;
for (int i = 0; i < nmax; i++) {
f[i][0] += ftmp[i][0];
- f[i][1] += ftmp[i][1];
- f[i][2] += ftmp[i][2];
+ f[i][1] += ftmp[i][1];
+ f[i][2] += ftmp[i][2];
}
}
}
@@ -321,9 +321,9 @@ void PairLJCharmmCoulMSM::compute_outer(int eflag, int vflag)
if (!ncoultablebits || rsq <= tabinnersq) {
r = sqrt(rsq);
prefactor = qqrd2e * qtmp*q[j]/r;
- egamma = 1.0 - (r/cut_coul)*force->kspace->gamma(r/cut_coul);
- fgamma = 1.0 + (rsq/cut_coulsq)*force->kspace->dgamma(r/cut_coul);
- forcecoul = prefactor * (fgamma - 1.0);
+ egamma = 1.0 - (r/cut_coul)*force->kspace->gamma(r/cut_coul);
+ fgamma = 1.0 + (rsq/cut_coulsq)*force->kspace->dgamma(r/cut_coul);
+ forcecoul = prefactor * (fgamma - 1.0);
if (rsq > cut_in_off_sq) {
if (rsq < cut_in_on_sq) {
rsw = (r - cut_in_off)/cut_in_diff;
@@ -412,7 +412,7 @@ void PairLJCharmmCoulMSM::compute_outer(int eflag, int vflag)
if (vflag) {
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq) {
- forcecoul = prefactor * fgamma;
+ forcecoul = prefactor * fgamma;
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
} else {
table = vtable[itable] + fraction*dvtable[itable];
diff --git a/src/KSPACE/pair_lj_cut_coul_long.cpp b/src/KSPACE/pair_lj_cut_coul_long.cpp
index c113aea83a..866db6ba65 100644
--- a/src/KSPACE/pair_lj_cut_coul_long.cpp
+++ b/src/KSPACE/pair_lj_cut_coul_long.cpp
@@ -15,10 +15,10 @@
Contributing author: Paul Crozier (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_lj_cut_coul_long.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/KSPACE/pair_lj_cut_coul_msm.cpp b/src/KSPACE/pair_lj_cut_coul_msm.cpp
index f9fc9be3fc..e3b3f58fcb 100644
--- a/src/KSPACE/pair_lj_cut_coul_msm.cpp
+++ b/src/KSPACE/pair_lj_cut_coul_msm.cpp
@@ -15,10 +15,10 @@
Contributing authors: Stan Moore (SNL), Paul Crozier (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_lj_cut_coul_msm.h"
#include "atom.h"
#include "comm.h"
@@ -228,8 +228,8 @@ void PairLJCutCoulMSM::compute(int eflag, int vflag)
for (i = 0; i < 3; i++) virial[i] += force->pair->eng_coul/3.0;
for (int i = 0; i < nmax; i++) {
f[i][0] += ftmp[i][0];
- f[i][1] += ftmp[i][1];
- f[i][2] += ftmp[i][2];
+ f[i][1] += ftmp[i][1];
+ f[i][2] += ftmp[i][2];
}
}
}
diff --git a/src/KSPACE/pair_lj_cut_tip4p_long.cpp b/src/KSPACE/pair_lj_cut_tip4p_long.cpp
index 657d83b752..6e855e41f0 100644
--- a/src/KSPACE/pair_lj_cut_tip4p_long.cpp
+++ b/src/KSPACE/pair_lj_cut_tip4p_long.cpp
@@ -16,10 +16,10 @@
simpler force assignment added by Rolf Isele-Holder (Aachen University)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_lj_cut_tip4p_long.h"
#include "angle.h"
#include "atom.h"
diff --git a/src/KSPACE/pair_lj_long_coul_long.cpp b/src/KSPACE/pair_lj_long_coul_long.cpp
index 06e77482d2..3675ea76dc 100644
--- a/src/KSPACE/pair_lj_long_coul_long.cpp
+++ b/src/KSPACE/pair_lj_long_coul_long.cpp
@@ -13,14 +13,14 @@
/* ----------------------------------------------------------------------
Contributing author: Pieter J. in 't Veld (SNL)
- Tabulation for long-range dispersion added by Wayne Mitchell (Loyola
+ Tabulation for long-range dispersion added by Wayne Mitchell (Loyola
University New Orleans)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "math_vector.h"
#include "pair_lj_long_coul_long.h"
#include "atom.h"
@@ -57,7 +57,7 @@ PairLJLongCoulLong::PairLJLongCoulLong(LAMMPS *lmp) : Pair(lmp)
fdisptable = NULL;
qdist = 0.0;
}
-
+
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
@@ -87,18 +87,18 @@ void PairLJLongCoulLong::settings(int narg, char **arg)
options(++arg, 1);
if (!comm->me && ewald_order == ((1<<1) | (1<<6)))
error->warning(FLERR,"Using largest cutoff for lj/long/coul/long");
- if (!*(++arg))
+ if (!*(++arg))
error->all(FLERR,"Cutoffs missing in pair_style lj/long/coul/long");
- if (!((ewald_order^ewald_off) & (1<<1)))
+ if (!((ewald_order^ewald_off) & (1<<1)))
error->all(FLERR,
"Coulomb cut not supported in pair_style lj/long/coul/long");
cut_lj_global = force->numeric(FLERR,*(arg++));
- if (narg == 4 && ((ewald_order & 0x42) == 0x42))
+ if (narg == 4 && ((ewald_order & 0x42) == 0x42))
error->all(FLERR,"Only one cutoff allowed when requesting all long");
if (narg == 4) cut_coul = force->numeric(FLERR,*arg);
else cut_coul = cut_lj_global;
- if (allocated) {
+ if (allocated) {
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
@@ -279,12 +279,12 @@ void PairLJLongCoulLong::init_style()
error->all(FLERR,"Pair style requires a KSpace style");
if (force->kspace) g_ewald = force->kspace->g_ewald;
if (force->kspace) g_ewald_6 = force->kspace->g_ewald_6;
-
+
// setup force tables
-
+
if (ncoultablebits) init_tables(cut_coul,cut_respa);
if (ndisptablebits) init_tables_disp(cut_lj_global);
-
+
}
/* ----------------------------------------------------------------------
@@ -598,7 +598,7 @@ void PairLJLongCoulLong::compute(int eflag, int vflag)
}
}
}
-
+
else force_lj = evdwl = 0.0;
fpair = (force_coul+force_lj)*r2inv;
@@ -808,7 +808,7 @@ void PairLJLongCoulLong::compute_outer(int eflag, int vflag)
evdwl = ecoul = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = 0;
-
+
double **x = atom->x, *x0 = x[0];
double **f = atom->f, *f0 = f[0], *fi = f0;
double *q = atom->q;
@@ -818,7 +818,7 @@ void PairLJLongCoulLong::compute_outer(int eflag, int vflag)
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
double qqrd2e = force->qqrd2e;
-
+
int i, j, order1 = ewald_order&(1<<1), order6 = ewald_order&(1<<6);
int *ineigh, *ineighn, *jneigh, *jneighn, typei, typej, ni, respa_flag;
double qi = 0.0, qri = 0.0;
@@ -827,16 +827,16 @@ void PairLJLongCoulLong::compute_outer(int eflag, int vflag)
double g2 = g_ewald_6*g_ewald_6, g6 = g2*g2*g2, g8 = g6*g2;
double respa_lj = 0.0, respa_coul = 0.0, frespa = 0.0;
vector xi, d;
-
+
double cut_in_off = cut_respa[2];
double cut_in_on = cut_respa[3];
-
+
double cut_in_diff = cut_in_on - cut_in_off;
double cut_in_off_sq = cut_in_off*cut_in_off;
double cut_in_on_sq = cut_in_on*cut_in_on;
-
+
ineighn = (ineigh = listouter->ilist)+listouter->inum;
-
+
for (; ineigh<ineighn; ++ineigh) { // loop over my atoms
i = *ineigh; fi = f0+3*i;
if (order1) qri = (qi = q[i])*qqrd2e; // initialize constants
@@ -845,20 +845,20 @@ void PairLJLongCoulLong::compute_outer(int eflag, int vflag)
cutsqi = cutsq[typei]; cut_ljsqi = cut_ljsq[typei];
memcpy(xi, x0+(i+(i<<1)), sizeof(vector));
jneighn = (jneigh = listouter->firstneigh[i])+listouter->numneigh[i];
-
+
for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
j = *jneigh;
ni = sbmask(j);
j &= NEIGHMASK;
-
+
{ register double *xj = x0+(j+(j<<1));
d[0] = xi[0] - xj[0]; // pair vector
d[1] = xi[1] - xj[1];
d[2] = xi[2] - xj[2]; }
-
+
if ((rsq = vec_dot(d, d)) >= cutsqi[typej = type[j]]) continue;
r2inv = 1.0/rsq;
-
+
frespa = 1.0; // check whether and how to compute respa corrections
respa_coul = 0;
respa_lj = 0;
@@ -867,7 +867,7 @@ void PairLJLongCoulLong::compute_outer(int eflag, int vflag)
register double rsw = (sqrt(rsq)-cut_in_off)/cut_in_diff;
frespa = 1-rsw*rsw*(3.0-2.0*rsw);
}
-
+
if (order1 && (rsq < cut_coulsq)) { // coulombic
if (!ncoultablebits || rsq <= tabinnersq) { // series real space
register double r = sqrt(rsq), s = qri*q[j];
@@ -908,7 +908,7 @@ void PairLJLongCoulLong::compute_outer(int eflag, int vflag)
}
}
}
-
+
else force_coul = respa_coul = ecoul = 0.0;
if (rsq < cut_ljsqi[typej]) { // lennard-jones
@@ -964,9 +964,9 @@ void PairLJLongCoulLong::compute_outer(int eflag, int vflag)
}
}
else force_lj = respa_lj = evdwl = 0.0;
-
+
fpair = (force_coul+force_lj)*r2inv;
-
+
if (newton_pair || j < nlocal) {
register double *fj = f0+(j+(j<<1)), f;
fi[0] += f = d[0]*fpair; fj[0] -= f;
@@ -978,7 +978,7 @@ void PairLJLongCoulLong::compute_outer(int eflag, int vflag)
fi[1] += d[1]*fpair;
fi[2] += d[2]*fpair;
}
-
+
if (evflag) {
fvirial = (force_coul + force_lj + respa_coul + respa_lj)*r2inv;
ev_tally(i,j,nlocal,newton_pair,
diff --git a/src/KSPACE/pair_lj_long_coul_long.h b/src/KSPACE/pair_lj_long_coul_long.h
index c1628e3132..22704c79fa 100644
--- a/src/KSPACE/pair_lj_long_coul_long.h
+++ b/src/KSPACE/pair_lj_long_coul_long.h
@@ -19,7 +19,7 @@ PairStyle(lj/long/coul/long,PairLJLongCoulLong)
#ifndef LMP_PAIR_LJ_LONG_COUL_LONG_H
#define LMP_PAIR_LJ_LONG_COUL_LONG_H
-
+
#include "pair.h"
namespace LAMMPS_NS {
diff --git a/src/KSPACE/pair_lj_long_tip4p_long.cpp b/src/KSPACE/pair_lj_long_tip4p_long.cpp
index 712d9c35b2..b8ce8ece4c 100755
--- a/src/KSPACE/pair_lj_long_tip4p_long.cpp
+++ b/src/KSPACE/pair_lj_long_tip4p_long.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -16,10 +16,10 @@
Rolf Isele-Holder (Aachen University)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_lj_long_tip4p_long.h"
#include "angle.h"
#include "atom.h"
@@ -48,7 +48,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-PairLJLongTIP4PLong::PairLJLongTIP4PLong(LAMMPS *lmp) :
+PairLJLongTIP4PLong::PairLJLongTIP4PLong(LAMMPS *lmp) :
PairLJLongCoulLong(lmp)
{
dispersionflag = tip4pflag = 1;
@@ -90,7 +90,7 @@ void PairLJLongTIP4PLong::compute(int eflag, int vflag)
double *x1,*x2;
int *ilist,*jlist,*numneigh,**firstneigh;
double rsq;
-
+
evdwl = ecoul = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
@@ -133,7 +133,7 @@ void PairLJLongTIP4PLong::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@@ -180,7 +180,7 @@ void PairLJLongTIP4PLong::compute(int eflag, int vflag)
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
-
+
if (rsq < cut_ljsq[itype][jtype]) { // lj
r2inv = 1.0/rsq;
if (order6) { // long-range lj
@@ -198,7 +198,7 @@ void PairLJLongTIP4PLong::compute(int eflag, int vflag)
register double f = special_lj[ni], t = rn*(1.0-f);
forcelj = f*(rn *= rn)*lj1i[jtype]-
g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq+t*lj2i[jtype];
- if (eflag)
+ if (eflag)
evdwl = f*rn*lj3i[jtype]-g6*((a2+1.0)*a2+0.5)*x2+t*lj4i[jtype];
}
}
@@ -245,12 +245,12 @@ void PairLJLongTIP4PLong::compute(int eflag, int vflag)
evdwl,0.0,forcelj,delx,dely,delz);
}
-
+
// adjust rsq and delxyz for off-site O charge(s)
// ADDITIONAL REQEUST REQUIRED HERE!!!!!
if (rsq < cut_coulsqplus) {
- if (itype == typeO || jtype == typeO) {
+ if (itype == typeO || jtype == typeO) {
if (jtype == typeO) {
if (hneigh[j][0] < 0) {
hneigh[j][0] = jH1 = atom->map(tag[j] + 1);
@@ -278,7 +278,7 @@ void PairLJLongTIP4PLong::compute(int eflag, int vflag)
}
// test current rsq against cutoff and compute Coulombic force
-
+
if (rsq < cut_coulsq && order1) {
r2inv = 1.0 / rsq;
if (!ncoultablebits || rsq <= tabinnersq) {
@@ -290,7 +290,7 @@ void PairLJLongTIP4PLong::compute(int eflag, int vflag)
prefactor = qqrd2e * qtmp*q[j]/r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
if (factor_coul < 1.0) {
- forcecoul -= (1.0-factor_coul)*prefactor;
+ forcecoul -= (1.0-factor_coul)*prefactor;
}
} else {
union_int_float_t rsq_lookup;
@@ -408,7 +408,7 @@ void PairLJLongTIP4PLong::compute(int eflag, int vflag)
fH[0] = 0.5 * alpha * fd[0];
fH[1] = 0.5 * alpha * fd[1];
- fH[2] = 0.5 * alpha * fd[2];
+ fH[2] = 0.5 * alpha * fd[2];
f[j][0] += fO[0];
f[j][1] += fO[1];
@@ -447,7 +447,7 @@ void PairLJLongTIP4PLong::compute(int eflag, int vflag)
}
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
} else ecoul = 0.0;
-
+
if (evflag) ev_tally_tip4p(key,vlist,v,ecoul,alpha);
}
}
@@ -512,7 +512,7 @@ void PairLJLongTIP4PLong::compute_inner()
ilist = listinner->ilist;
numneigh = listinner->numneigh;
firstneigh = listinner->firstneigh;
-
+
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@@ -557,9 +557,9 @@ void PairLJLongTIP4PLong::compute_inner()
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
-
+
if (rsq < cut_ljsq[itype][jtype] && rsq < cut_out_off_sq ) { // lj
- r2inv = 1.0/rsq;
+ r2inv = 1.0/rsq;
register double rn = r2inv*r2inv*r2inv;
if (ni == 0) forcelj = rn*(rn*lj1i[jtype]-lj2i[jtype]);
else { // special case
@@ -581,12 +581,12 @@ void PairLJLongTIP4PLong::compute_inner()
f[j][2] -= delz*forcelj;
}
-
+
// adjust rsq and delxyz for off-site O charge(s)
// ADDITIONAL REQEUST REQUIRED HERE!!!!!
if (rsq < cut_coulsqplus && order1) {
- if (itype == typeO || jtype == typeO) {
+ if (itype == typeO || jtype == typeO) {
if (jtype == typeO) {
if (hneigh[j][0] < 0) {
hneigh[j][0] = jH1 = atom->map(tag[j] + 1);
@@ -614,7 +614,7 @@ void PairLJLongTIP4PLong::compute_inner()
}
// test current rsq against cutoff and compute Coulombic force
-
+
if (rsq < cut_coulsq && rsq < cut_out_off_sq) {
r2inv = 1.0 / rsq;
qri = qqrd2e*qtmp;
@@ -688,7 +688,7 @@ void PairLJLongTIP4PLong::compute_inner()
fH[0] = 0.5 * alpha * fd[0];
fH[1] = 0.5 * alpha * fd[1];
- fH[2] = 0.5 * alpha * fd[2];
+ fH[2] = 0.5 * alpha * fd[2];
f[j][0] += fO[0];
f[j][1] += fO[1];
@@ -755,7 +755,7 @@ void PairLJLongTIP4PLong::compute_middle()
ilist = listmiddle->ilist;
numneigh = listmiddle->numneigh;
firstneigh = listmiddle->firstneigh;
-
+
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@@ -800,9 +800,9 @@ void PairLJLongTIP4PLong::compute_middle()
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
-
+
if (rsq < cut_ljsq[itype][jtype] && rsq >= cut_in_off_sq && rsq <= cut_out_off_sq ) { // lj
- r2inv = 1.0/rsq;
+ r2inv = 1.0/rsq;
register double rn = r2inv*r2inv*r2inv;
if (ni == 0) forcelj = rn*(rn*lj1i[jtype]-lj2i[jtype]);
else { // special case
@@ -828,12 +828,12 @@ void PairLJLongTIP4PLong::compute_middle()
f[j][2] -= delz*forcelj;
}
-
+
// adjust rsq and delxyz for off-site O charge(s)
// ADDITIONAL REQEUST REQUIRED HERE!!!!!
if (rsq < cut_coulsqplus && order1) {
- if (itype == typeO || jtype == typeO) {
+ if (itype == typeO || jtype == typeO) {
if (jtype == typeO) {
if (hneigh[j][0] < 0) {
hneigh[j][0] = jH1 = atom->map(tag[j] + 1);
@@ -861,7 +861,7 @@ void PairLJLongTIP4PLong::compute_middle()
}
// test current rsq against cutoff and compute Coulombic force
-
+
if (rsq < cut_coulsq && rsq >= cut_in_off_sq && rsq <= cut_out_off_sq) {
r2inv = 1.0 / rsq;
qri = qqrd2e*qtmp;
@@ -939,7 +939,7 @@ void PairLJLongTIP4PLong::compute_middle()
fH[0] = 0.5 * alpha * fd[0];
fH[1] = 0.5 * alpha * fd[1];
- fH[2] = 0.5 * alpha * fd[2];
+ fH[2] = 0.5 * alpha * fd[2];
f[j][0] += fO[0];
f[j][1] += fO[1];
@@ -974,7 +974,7 @@ void PairLJLongTIP4PLong::compute_outer(int eflag, int vflag)
int *ilist,*jlist,*numneigh,**firstneigh;
double rsq,qri;
int respa_flag;
-
+
evdwl = ecoul = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
@@ -1016,7 +1016,7 @@ void PairLJLongTIP4PLong::compute_outer(int eflag, int vflag)
double cut_in_off = cut_respa[2];
double cut_in_on = cut_respa[3];
-
+
double cut_in_diff = cut_in_on - cut_in_off;
double cut_in_off_sq = cut_in_off*cut_in_off;
double cut_in_on_sq = cut_in_on*cut_in_on;
@@ -1025,7 +1025,7 @@ void PairLJLongTIP4PLong::compute_outer(int eflag, int vflag)
ilist = listouter->ilist;
numneigh = listouter->numneigh;
firstneigh = listouter->firstneigh;
-
+
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@@ -1072,7 +1072,7 @@ void PairLJLongTIP4PLong::compute_outer(int eflag, int vflag)
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
-
+
respa_coul = 0;
respa_lj = 0;
if (rsq < cut_ljsq[itype][jtype]) { // lj
@@ -1141,7 +1141,7 @@ void PairLJLongTIP4PLong::compute_outer(int eflag, int vflag)
f[j][0] -= delx*forcelj;
f[j][1] -= dely*forcelj;
f[j][2] -= delz*forcelj;
-
+
if (evflag) {
fvirial = forcelj + respa_lj*r2inv;
ev_tally(i,j,nlocal,newton_pair,
@@ -1149,12 +1149,12 @@ void PairLJLongTIP4PLong::compute_outer(int eflag, int vflag)
}
}
-
+
// adjust rsq and delxyz for off-site O charge(s)
// ADDITIONAL REQEUST REQUIRED HERE!!!!!
if (rsq < cut_coulsqplus) {
- if (itype == typeO || jtype == typeO) {
+ if (itype == typeO || jtype == typeO) {
if (jtype == typeO) {
if (hneigh[j][0] < 0) {
hneigh[j][0] = jH1 = atom->map(tag[j] + 1);
@@ -1229,7 +1229,7 @@ void PairLJLongTIP4PLong::compute_outer(int eflag, int vflag)
ecoul = qiqj*(etable[k]+f*detable[k]-t.f);
}
}
- }
+ }
cforce = forcecoul * r2inv;
fvirial = (forcecoul + respa_coul) * r2inv;
@@ -1342,7 +1342,7 @@ void PairLJLongTIP4PLong::compute_outer(int eflag, int vflag)
fH[0] = 0.5 * alpha * fd[0];
fH[1] = 0.5 * alpha * fd[1];
- fH[2] = 0.5 * alpha * fd[2];
+ fH[2] = 0.5 * alpha * fd[2];
f[j][0] += fO[0];
f[j][1] += fO[1];
@@ -1368,7 +1368,7 @@ void PairLJLongTIP4PLong::compute_outer(int eflag, int vflag)
fH[0] = 0.5 * alpha * fd[0];
fH[1] = 0.5 * alpha * fd[1];
- fH[2] = 0.5 * alpha * fd[2];
+ fH[2] = 0.5 * alpha * fd[2];
domain->closest_image(x[j],x[jH1],xH1);
domain->closest_image(x[j],x[jH2],xH2);
@@ -1384,7 +1384,7 @@ void PairLJLongTIP4PLong::compute_outer(int eflag, int vflag)
vlist[n++] = jH1;
vlist[n++] = jH2;
}
-
+
if (evflag) ev_tally_tip4p(key,vlist,v,ecoul,alpha);
}
}
@@ -1404,12 +1404,12 @@ void PairLJLongTIP4PLong::settings(int narg, char **arg)
ewald_order = 0;
options(arg, 6);
options(++arg, 1);
- if (!comm->me && ewald_order&(1<<6))
+ if (!comm->me && ewald_order&(1<<6))
error->warning(FLERR,"Mixing forced for lj coefficients");
- if (!comm->me && ewald_order==((1<<1)|(1<<6)))
+ if (!comm->me && ewald_order==((1<<1)|(1<<6)))
error->warning(FLERR,
"Using largest cutoff for pair_style lj/long/tip4p/long");
- if (!((ewald_order^ewald_off)&(1<<1)))
+ if (!((ewald_order^ewald_off)&(1<<1)))
error->all(FLERR,
"Coulomb cut not supported in pair_style lj/long/tip4p/long");
typeO = force->inumeric(FLERR,arg[1]);
@@ -1422,8 +1422,8 @@ void PairLJLongTIP4PLong::settings(int narg, char **arg)
cut_lj_global = force->numeric(FLERR,arg[6]);
if (narg == 8) cut_coul = cut_lj_global;
else cut_coul = force->numeric(FLERR,arg[7]);
-
-
+
+
// reset cutoffs that have been explicitly set
if (allocated) {
@@ -1442,7 +1442,7 @@ void PairLJLongTIP4PLong::init_style()
{
if (atom->tag_enable == 0)
error->all(FLERR,"Pair style lj/long/tip4p/long requires atom IDs");
- if (!force->newton_pair)
+ if (!force->newton_pair)
error->all(FLERR,"Pair style lj/long/tip4p/long requires newton pair on");
if (!atom->q_flag)
error->all(FLERR,"Pair style lj/long/tip4p/long requires atom attribute q");
@@ -1573,10 +1573,10 @@ void *PairLJLongTIP4PLong::extract(const char *str, int &dim)
if (strcmp(str,"cut_coul") == 0) return (void *) &cut_coul;
const char *ids[] = {
- "B", "sigma", "epsilon", "ewald_order", "ewald_cut", "cut_coul",
+ "B", "sigma", "epsilon", "ewald_order", "ewald_cut", "cut_coul",
"ewald_mix", "cut_LJ", NULL};
void *ptrs[] = {
- lj4, sigma, epsilon, &ewald_order, &cut_coul, &cut_coul,
+ lj4, sigma, epsilon, &ewald_order, &cut_coul, &cut_coul,
&mix_flag, &cut_lj_global, NULL};
int i;
@@ -1587,7 +1587,7 @@ void *PairLJLongTIP4PLong::extract(const char *str, int &dim)
if (strcmp(ids[i],str) == 0)
return ptrs[i];
-
+
++i;
}
return NULL;
diff --git a/src/KSPACE/pair_lj_long_tip4p_long.h b/src/KSPACE/pair_lj_long_tip4p_long.h
index ef929d198e..ef86e4ed80 100755
--- a/src/KSPACE/pair_lj_long_tip4p_long.h
+++ b/src/KSPACE/pair_lj_long_tip4p_long.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/KSPACE/pair_tip4p_long.cpp b/src/KSPACE/pair_tip4p_long.cpp
index fbe146ecf2..0753a3f34d 100644
--- a/src/KSPACE/pair_tip4p_long.cpp
+++ b/src/KSPACE/pair_tip4p_long.cpp
@@ -16,10 +16,10 @@
simpler force assignment added by Rolf Isele-Holder (Aachen University)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_tip4p_long.h"
#include "angle.h"
#include "atom.h"
diff --git a/src/KSPACE/pppm.cpp b/src/KSPACE/pppm.cpp
index 434667a302..99bae3f41b 100644
--- a/src/KSPACE/pppm.cpp
+++ b/src/KSPACE/pppm.cpp
@@ -18,11 +18,11 @@
triclinic added by Stan Moore (SNL)
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "string.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "math.h"
+#include <mpi.h>
+#include <string.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
#include "pppm.h"
#include "atom.h"
#include "comm.h"
@@ -67,7 +67,7 @@ enum{FORWARD_IK,FORWARD_AD,FORWARD_IK_PERATOM,FORWARD_AD_PERATOM};
PPPM::PPPM(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg)
{
if (narg < 1) error->all(FLERR,"Illegal kspace_style pppm command");
-
+
pppmflag = 1;
group_group_enable = 1;
@@ -91,7 +91,7 @@ PPPM::PPPM(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg)
vg = NULL;
fkx = fky = fkz = NULL;
- sf_precoeff1 = sf_precoeff2 = sf_precoeff3 =
+ sf_precoeff1 = sf_precoeff2 = sf_precoeff3 =
sf_precoeff4 = sf_precoeff5 = sf_precoeff6 = NULL;
density_A_brick = density_B_brick = NULL;
@@ -182,7 +182,7 @@ void PPPM::init()
"slab correction");
if (domain->dimension == 2) error->all(FLERR,
"Cannot use PPPM with 2d simulation");
- if (comm->style != 0)
+ if (comm->style != 0)
error->universe_all(FLERR,"PPPM can only currently be used with "
"comm_style brick");
@@ -304,7 +304,7 @@ void PPPM::init()
order--;
iteration++;
}
-
+
if (order < minorder) error->all(FLERR,"PPPM order < minimum allowed order");
if (!overlap_allowed && cgtmp->ghost_overlap())
error->all(FLERR,"PPPM grid stencil extends "
@@ -623,11 +623,11 @@ void PPPM::compute(int eflag, int vflag)
qsum_qsq();
natoms_original = atom->natoms;
}
-
+
// return if there are no charges
-
+
if (qsqsum == 0.0) return;
-
+
// convert atoms from box to lamda coords
if (triclinic == 0) boxlo = domain->boxlo;
@@ -673,7 +673,7 @@ void PPPM::compute(int eflag, int vflag)
// extra per-atom energy/virial communication
if (evflag_atom) {
- if (differentiation_flag == 1 && vflag_atom)
+ if (differentiation_flag == 1 && vflag_atom)
cg_peratom->forward_comm(this,FORWARD_AD_PERATOM);
else if (differentiation_flag == 0)
cg_peratom->forward_comm(this,FORWARD_IK_PERATOM);
@@ -1073,7 +1073,7 @@ void PPPM::set_grid_global()
}
// scale grid for triclinic skew
-
+
if (triclinic) {
double tmp[3];
tmp[0] = nx_pppm/xprd;
@@ -1165,7 +1165,7 @@ double PPPM::compute_qopt()
{
double qopt = 0.0;
double *prd = domain->prd;
-
+
const double xprd = prd[0];
const double yprd = prd[1];
const double zprd = prd[2];
@@ -1452,7 +1452,7 @@ void PPPM::set_grid_local()
nzhi_in = nzhi_out = nz_pppm - 1;
nzhi_out = MIN(nzhi_out,nz_pppm-1);
}
-
+
// decomposition of FFT mesh
// global indices range from 0 to N-1
// proc owns entire x-dimension, clumps of columns in y,z dimensions
@@ -2772,7 +2772,7 @@ void PPPM::unpack_reverse(int flag, FFT_SCALAR *buf, int nlist, int *list)
FFT_SCALAR *dest = &density_brick[nzlo_out][nylo_out][nxlo_out];
for (int i = 0; i < nlist; i++)
dest[list[i]] += buf[i];
- }
+ }
}
/* ----------------------------------------------------------------------
@@ -3349,7 +3349,7 @@ void PPPM::poisson_groups(int AA_flag)
}
// triclinic system
-
+
if (triclinic) {
poisson_groups_triclinic();
return;
@@ -3464,7 +3464,7 @@ void PPPM::slabcorr_groups(int groupbit_A, int groupbit_B, int AA_flag)
if (!((mask[i] & groupbit_A) && (mask[i] & groupbit_B)))
if (AA_flag) continue;
- if (mask[i] & groupbit_A) {
+ if (mask[i] & groupbit_A) {
qsum_A += q[i];
dipole_A += q[i]*x[i][2];
dipole_r2_A += q[i]*x[i][2]*x[i][2];
diff --git a/src/KSPACE/pppm.h b/src/KSPACE/pppm.h
index 508d47a33f..b543c5fd3d 100644
--- a/src/KSPACE/pppm.h
+++ b/src/KSPACE/pppm.h
@@ -21,7 +21,7 @@ KSpaceStyle(pppm,PPPM)
#define LMP_PPPM_H
#include "lmptype.h"
-#include "mpi.h"
+#include <mpi.h>
#ifdef FFT_SINGLE
typedef float FFT_SCALAR;
@@ -104,7 +104,7 @@ class PPPM : public KSpace {
int typeH,typeO; // atom types of TIP4P water H and O atoms
double qdist; // distance from O site to negative charge
double alpha; // geometric factor
-
+
void set_grid_global();
void set_grid_local();
void adjust_gewald();
@@ -124,19 +124,19 @@ class PPPM : public KSpace {
virtual void compute_gf_ik();
virtual void compute_gf_ad();
void compute_sf_precoeff();
-
+
virtual void particle_map();
virtual void make_rho();
virtual void brick2fft();
-
+
virtual void poisson();
virtual void poisson_ik();
virtual void poisson_ad();
-
+
virtual void fieldforce();
virtual void fieldforce_ik();
virtual void fieldforce_ad();
-
+
virtual void poisson_peratom();
virtual void fieldforce_peratom();
void procs2grid2d(int,int,int,int *, int*);
diff --git a/src/KSPACE/pppm_cg.cpp b/src/KSPACE/pppm_cg.cpp
index 21dd09cae1..f07f38b4be 100644
--- a/src/KSPACE/pppm_cg.cpp
+++ b/src/KSPACE/pppm_cg.cpp
@@ -15,10 +15,10 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <mpi.h>
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "atom.h"
#include "gridcomm.h"
@@ -193,7 +193,7 @@ void PPPMCG::compute(int eflag, int vflag)
// extra per-atom energy/virial communication
if (evflag_atom) {
- if (differentiation_flag == 1 && vflag_atom)
+ if (differentiation_flag == 1 && vflag_atom)
cg_peratom->forward_comm(this,FORWARD_AD_PERATOM);
else if (differentiation_flag == 0)
cg_peratom->forward_comm(this,FORWARD_IK_PERATOM);
diff --git a/src/KSPACE/pppm_disp.cpp b/src/KSPACE/pppm_disp.cpp
index 802d2a7d32..538f9de28c 100755
--- a/src/KSPACE/pppm_disp.cpp
+++ b/src/KSPACE/pppm_disp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -16,11 +16,11 @@
Paul Crozier (SNL)
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "string.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "math.h"
+#include <mpi.h>
+#include <string.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
#include "pppm_disp.h"
#include "math_const.h"
#include "atom.h"
@@ -71,7 +71,7 @@ PPPMDisp::PPPMDisp(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg)
triclinic_support = 0;
pppmflag = dispersionflag = 1;
accuracy_relative = fabs(force->numeric(FLERR,arg[0]));
-
+
nfactors = 3;
factors = new int[nfactors];
factors[0] = 2;
@@ -89,52 +89,52 @@ PPPMDisp::PPPMDisp(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg)
density_brick = vdx_brick = vdy_brick = vdz_brick = NULL;
density_fft = NULL;
- u_brick = v0_brick = v1_brick = v2_brick = v3_brick =
+ u_brick = v0_brick = v1_brick = v2_brick = v3_brick =
v4_brick = v5_brick = NULL;
density_brick_g = vdx_brick_g = vdy_brick_g = vdz_brick_g = NULL;
density_fft_g = NULL;
- u_brick_g = v0_brick_g = v1_brick_g = v2_brick_g = v3_brick_g =
+ u_brick_g = v0_brick_g = v1_brick_g = v2_brick_g = v3_brick_g =
v4_brick_g = v5_brick_g = NULL;
density_brick_a0 = vdx_brick_a0 = vdy_brick_a0 = vdz_brick_a0 = NULL;
density_fft_a0 = NULL;
- u_brick_a0 = v0_brick_a0 = v1_brick_a0 = v2_brick_a0 = v3_brick_a0 =
+ u_brick_a0 = v0_brick_a0 = v1_brick_a0 = v2_brick_a0 = v3_brick_a0 =
v4_brick_a0 = v5_brick_a0 = NULL;
density_brick_a1 = vdx_brick_a1 = vdy_brick_a1 = vdz_brick_a1 = NULL;
density_fft_a1 = NULL;
- u_brick_a1 = v0_brick_a1 = v1_brick_a1 = v2_brick_a1 = v3_brick_a1 =
+ u_brick_a1 = v0_brick_a1 = v1_brick_a1 = v2_brick_a1 = v3_brick_a1 =
v4_brick_a1 = v5_brick_a1 = NULL;
density_brick_a2 = vdx_brick_a2 = vdy_brick_a2 = vdz_brick_a2 = NULL;
density_fft_a2 = NULL;
- u_brick_a2 = v0_brick_a2 = v1_brick_a2 = v2_brick_a2 = v3_brick_a2 =
+ u_brick_a2 = v0_brick_a2 = v1_brick_a2 = v2_brick_a2 = v3_brick_a2 =
v4_brick_a2 = v5_brick_a2 = NULL;
density_brick_a3 = vdx_brick_a3 = vdy_brick_a3 = vdz_brick_a3 = NULL;
density_fft_a3 = NULL;
- u_brick_a3 = v0_brick_a3 = v1_brick_a3 = v2_brick_a3 = v3_brick_a3 =
+ u_brick_a3 = v0_brick_a3 = v1_brick_a3 = v2_brick_a3 = v3_brick_a3 =
v4_brick_a3 = v5_brick_a3 = NULL;
density_brick_a4 = vdx_brick_a4 = vdy_brick_a4 = vdz_brick_a4 = NULL;
density_fft_a4 = NULL;
- u_brick_a4 = v0_brick_a4 = v1_brick_a4 = v2_brick_a4 = v3_brick_a4 =
+ u_brick_a4 = v0_brick_a4 = v1_brick_a4 = v2_brick_a4 = v3_brick_a4 =
v4_brick_a4 = v5_brick_a4 = NULL;
density_brick_a5 = vdx_brick_a5 = vdy_brick_a5 = vdz_brick_a5 = NULL;
density_fft_a5 = NULL;
- u_brick_a5 = v0_brick_a5 = v1_brick_a5 = v2_brick_a5 = v3_brick_a5 =
+ u_brick_a5 = v0_brick_a5 = v1_brick_a5 = v2_brick_a5 = v3_brick_a5 =
v4_brick_a5 = v5_brick_a5 = NULL;
density_brick_a6 = vdx_brick_a6 = vdy_brick_a6 = vdz_brick_a6 = NULL;
density_fft_a6 = NULL;
- u_brick_a6 = v0_brick_a6 = v1_brick_a6 = v2_brick_a6 = v3_brick_a6 =
+ u_brick_a6 = v0_brick_a6 = v1_brick_a6 = v2_brick_a6 = v3_brick_a6 =
v4_brick_a6 = v5_brick_a6 = NULL;
density_brick_none = vdx_brick_none = vdy_brick_none = vdz_brick_none = NULL;
density_fft_none = NULL;
- u_brick_none = v0_brick_none = v1_brick_none = v2_brick_none = v3_brick_none =
+ u_brick_none = v0_brick_none = v1_brick_none = v2_brick_none = v3_brick_none =
v4_brick_none = v5_brick_none = NULL;
greensfn = NULL;
@@ -150,9 +150,9 @@ PPPMDisp::PPPMDisp(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg)
fkx_6 = fky_6 = fkz_6 = NULL;
fkx2_6 = fky2_6 = fkz2_6 = NULL;
- sf_precoeff1 = sf_precoeff2 = sf_precoeff3 = sf_precoeff4 =
+ sf_precoeff1 = sf_precoeff2 = sf_precoeff3 = sf_precoeff4 =
sf_precoeff5 = sf_precoeff6 = NULL;
- sf_precoeff1_6 = sf_precoeff2_6 = sf_precoeff3_6 = sf_precoeff4_6 =
+ sf_precoeff1_6 = sf_precoeff2_6 = sf_precoeff3_6 = sf_precoeff4_6 =
sf_precoeff5_6 = sf_precoeff6_6 = NULL;
gf_b = NULL;
@@ -179,7 +179,7 @@ PPPMDisp::PPPMDisp(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg)
}
/* ----------------------------------------------------------------------
- free all memory
+ free all memory
------------------------------------------------------------------------- */
PPPMDisp::~PPPMDisp()
@@ -199,7 +199,7 @@ PPPMDisp::~PPPMDisp()
}
/* ----------------------------------------------------------------------
- called once before run
+ called once before run
------------------------------------------------------------------------- */
void PPPMDisp::init()
@@ -212,18 +212,18 @@ void PPPMDisp::init()
triclinic_check();
if (domain->dimension == 2)
error->all(FLERR,"Cannot use PPPMDisp with 2d simulation");
- if (comm->style != 0)
+ if (comm->style != 0)
error->universe_all(FLERR,"PPPMDisp can only currently be used with "
"comm_style brick");
if (slabflag == 0 && domain->nonperiodic > 0)
error->all(FLERR,"Cannot use nonperiodic boundaries with PPPMDisp");
if (slabflag == 1) {
- if (domain->xperiodic != 1 || domain->yperiodic != 1 ||
+ if (domain->xperiodic != 1 || domain->yperiodic != 1 ||
domain->boundary[2][0] != 1 || domain->boundary[2][1] != 1)
error->all(FLERR,"Incorrect boundaries with slab PPPMDisp");
}
-
+
if (order > MAXORDER || order_6 > MAXORDER) {
char str[128];
sprintf(str,"PPPMDisp coulomb order cannot be greater than %d",MAXORDER);
@@ -233,7 +233,7 @@ void PPPMDisp::init()
// free all arrays previously allocated
deallocate();
- deallocate_peratom();
+ deallocate_peratom();
// check whether cutoff and pair style are set
@@ -251,7 +251,7 @@ void PPPMDisp::init()
cutoff_lj = *p_cutoff_lj;
double tmp2;
- MPI_Allreduce(&cutoff, &tmp2,1,MPI_DOUBLE,MPI_SUM,world);
+ MPI_Allreduce(&cutoff, &tmp2,1,MPI_DOUBLE,MPI_SUM,world);
// check out which types of potentials will have to be calculated
@@ -266,7 +266,7 @@ void PPPMDisp::init()
case 1:
k = 0; break;
case 6:
- if ((ewald_mix==GEOMETRIC || ewald_mix==SIXTHPOWER ||
+ if ((ewald_mix==GEOMETRIC || ewald_mix==SIXTHPOWER ||
mixflag == 1) && mixflag!= 2) { k = 1; break; }
else if (ewald_mix==ARITHMETIC && mixflag!=2) { k = 2; break; }
else if (mixflag == 2) { k = 3; break; }
@@ -277,7 +277,7 @@ void PPPMDisp::init()
}
function[k] = 1;
}
-
+
// warn, if function[0] is not set but charge attribute is set!
@@ -303,14 +303,14 @@ void PPPMDisp::init()
scale = 1.0;
qqrd2e = force->qqrd2e;
natoms_original = atom->natoms;
-
+
if (function[0]) qsum_qsq();
// if kspace is TIP4P, extract TIP4P params from pair style
// bond/angle are not yet init(), so insure equilibrium request is valid
qdist = 0.0;
-
+
if (tip4pflag) {
int itmp;
double *p_qdist = (double *) force->pair->extract("qdist",itmp);
@@ -328,10 +328,10 @@ void PPPMDisp::init()
if (force->angle == NULL || force->bond == NULL)
error->all(FLERR,"Bond and angle potentials must be defined for TIP4P");
- if (typeA < 1 || typeA > atom->nangletypes ||
+ if (typeA < 1 || typeA > atom->nangletypes ||
force->angle->setflag[typeA] == 0)
error->all(FLERR,"Bad TIP4P angle type for PPPMDisp/TIP4P");
- if (typeB < 1 || typeB > atom->nbondtypes ||
+ if (typeB < 1 || typeB > atom->nbondtypes ||
force->bond->setflag[typeB] == 0)
error->all(FLERR,"Bad TIP4P bond type for PPPMDisp/TIP4P");
double theta = force->angle->equilibrium_angle(typeA);
@@ -353,7 +353,7 @@ void PPPMDisp::init()
if (!gewaldflag_6) g_ewald_6 = 1;
// set accuracy (force units) from accuracy_relative or accuracy_absolute
-
+
if (accuracy_absolute >= 0.0) accuracy = accuracy_absolute;
else accuracy = accuracy_relative * two_charge_force;
@@ -370,7 +370,7 @@ void PPPMDisp::init()
iteration++;
// set grid for dispersion interaction and coulomb interactions
-
+
set_grid();
if (nx_pppm >= OFFSET || ny_pppm >= OFFSET || nz_pppm >= OFFSET)
@@ -408,13 +408,13 @@ void PPPMDisp::init()
if (cgtmp) delete cgtmp;
// adjust g_ewald
-
+
if (!gewaldflag) adjust_gewald();
// calculate the final accuracy
-
+
double acc = final_accuracy();
-
+
// print stats
int ngrid_max,nfft_both_max;
@@ -427,7 +427,7 @@ void PPPMDisp::init()
#else
const char fft_prec[] = "double";
#endif
-
+
if (screen) {
fprintf(screen," Coulomb G vector (1/distance)= %g\n",g_ewald);
fprintf(screen," Coulomb grid = %d %d %d\n",nx_pppm,ny_pppm,nz_pppm);
@@ -467,7 +467,7 @@ void PPPMDisp::init()
iteration++;
set_grid_6();
-
+
if (nx_pppm_6 >= OFFSET || ny_pppm_6 >= OFFSET || nz_pppm_6 >= OFFSET)
error->all(FLERR,"PPPMDisp Dispersion grid is too large");
@@ -497,14 +497,14 @@ void PPPMDisp::init()
order_6--;
}
- if (order_6 < minorder)
+ if (order_6 < minorder)
error->all(FLERR,"Dispersion PPPMDisp order has been "
"reduced below minorder");
if (cgtmp) delete cgtmp;
// adjust g_ewald_6
- if (!gewaldflag_6 && accuracy_kspace_6 == accuracy_real_6)
+ if (!gewaldflag_6 && accuracy_kspace_6 == accuracy_real_6)
adjust_gewald_6();
// calculate the final accuracy
@@ -525,7 +525,7 @@ void PPPMDisp::init()
#else
const char fft_prec[] = "double";
#endif
-
+
if (screen) {
fprintf(screen," Dispersion G vector (1/distance)= %g\n",g_ewald_6);
fprintf(screen," Dispersion grid = %d %d %d\n",
@@ -577,7 +577,7 @@ void PPPMDisp::init()
cg->setup();
if (differentiation_flag == 1)
compute_sf_precoeff(nx_pppm, ny_pppm, nz_pppm, order,
- nxlo_fft, nylo_fft, nzlo_fft,
+ nxlo_fft, nylo_fft, nzlo_fft,
nxhi_fft, nyhi_fft, nzhi_fft,
sf_precoeff1, sf_precoeff2, sf_precoeff3,
sf_precoeff4, sf_precoeff5, sf_precoeff6);
@@ -589,7 +589,7 @@ void PPPMDisp::init()
cg_6->setup();
if (differentiation_flag == 1)
compute_sf_precoeff(nx_pppm_6, ny_pppm_6, nz_pppm_6, order_6,
- nxlo_fft_6, nylo_fft_6, nzlo_fft_6,
+ nxlo_fft_6, nylo_fft_6, nzlo_fft_6,
nxhi_fft_6, nyhi_fft_6, nzhi_fft_6,
sf_precoeff1_6, sf_precoeff2_6, sf_precoeff3_6,
sf_precoeff4_6, sf_precoeff5_6, sf_precoeff6_6);
@@ -598,7 +598,7 @@ void PPPMDisp::init()
}
/* ----------------------------------------------------------------------
- adjust PPPM coeffs, called initially and whenever volume has changed
+ adjust PPPM coeffs, called initially and whenever volume has changed
------------------------------------------------------------------------- */
void PPPMDisp::setup()
@@ -607,11 +607,11 @@ void PPPMDisp::setup()
if (slabflag == 0 && domain->nonperiodic > 0)
error->all(FLERR,"Cannot use nonperiodic boundaries with PPPMDisp");
if (slabflag == 1) {
- if (domain->xperiodic != 1 || domain->yperiodic != 1 ||
+ if (domain->xperiodic != 1 || domain->yperiodic != 1 ||
domain->boundary[2][0] != 1 || domain->boundary[2][1] != 1)
error->all(FLERR,"Incorrect boundaries with slab PPPMDisp");
}
-
+
double *prd;
// volume-dependent factors
@@ -843,9 +843,9 @@ void PPPMDisp::setup_grid()
if (function[0]) {
compute_gf_denom(gf_b, order);
compute_rho_coeff(rho_coeff, drho_coeff, order);
- if (differentiation_flag == 1)
+ if (differentiation_flag == 1)
compute_sf_precoeff(nx_pppm, ny_pppm, nz_pppm, order,
- nxlo_fft, nylo_fft, nzlo_fft,
+ nxlo_fft, nylo_fft, nzlo_fft,
nxhi_fft, nyhi_fft, nzhi_fft,
sf_precoeff1, sf_precoeff2, sf_precoeff3,
sf_precoeff4, sf_precoeff5, sf_precoeff6);
@@ -855,7 +855,7 @@ void PPPMDisp::setup_grid()
compute_rho_coeff(rho_coeff_6, drho_coeff_6, order_6);
if (differentiation_flag == 1)
compute_sf_precoeff(nx_pppm_6, ny_pppm_6, nz_pppm_6, order_6,
- nxlo_fft_6, nylo_fft_6, nzlo_fft_6,
+ nxlo_fft_6, nylo_fft_6, nzlo_fft_6,
nxhi_fft_6, nyhi_fft_6, nzhi_fft_6,
sf_precoeff1_6, sf_precoeff2_6, sf_precoeff3_6,
sf_precoeff4_6, sf_precoeff5_6, sf_precoeff6_6);
@@ -867,7 +867,7 @@ void PPPMDisp::setup_grid()
}
/* ----------------------------------------------------------------------
- compute the PPPM long-range force, energy, virial
+ compute the PPPM long-range force, energy, virial
------------------------------------------------------------------------- */
void PPPMDisp::compute(int eflag, int vflag)
@@ -877,7 +877,7 @@ void PPPMDisp::compute(int eflag, int vflag)
// convert atoms from box to lamda coords
if (eflag || vflag) ev_setup(eflag,vflag);
- else evflag = evflag_atom = eflag_global = vflag_global =
+ else evflag = evflag_atom = eflag_global = vflag_global =
eflag_atom = vflag_atom = 0;
if (evflag_atom && !peratom_allocate_flag) {
@@ -892,7 +892,7 @@ void PPPMDisp::compute(int eflag, int vflag)
}
peratom_allocate_flag = 1;
}
-
+
if (triclinic == 0) boxlo = domain->boxlo;
else {
boxlo = domain->boxlo_lamda;
@@ -906,7 +906,7 @@ void PPPMDisp::compute(int eflag, int vflag)
if (function[1] + function[2] + function[3]) memory->destroy(part2grid_6);
nmax = atom->nmax;
if (function[0]) memory->create(part2grid,nmax,3,"pppm/disp:part2grid");
- if (function[1] + function[2] + function[3])
+ if (function[1] + function[2] + function[3])
memory->create(part2grid_6,nmax,3,"pppm/disp:part2grid_6");
}
@@ -933,23 +933,23 @@ void PPPMDisp::compute(int eflag, int vflag)
make_rho_c();
cg->reverse_comm(this,REVERSE_RHO);
-
+
brick2fft(nxlo_in, nylo_in, nzlo_in, nxhi_in, nyhi_in, nzhi_in,
- density_brick, density_fft, work1,remap);
-
+ density_brick, density_fft, work1,remap);
+
if (differentiation_flag == 1) {
poisson_ad(work1, work2, density_fft, fft1, fft2,
nx_pppm, ny_pppm, nz_pppm, nfft,
nxlo_fft, nylo_fft, nzlo_fft, nxhi_fft, nyhi_fft, nzhi_fft,
nxlo_in, nylo_in, nzlo_in, nxhi_in, nyhi_in, nzhi_in,
- energy_1, greensfn,
+ energy_1, greensfn,
virial_1, vg,vg2,
u_brick, v0_brick, v1_brick, v2_brick, v3_brick, v4_brick, v5_brick);
cg->forward_comm(this,FORWARD_AD);
- fieldforce_c_ad();
+ fieldforce_c_ad();
if (vflag_atom) cg_peratom->forward_comm(this, FORWARD_AD_PERATOM);
@@ -958,14 +958,14 @@ void PPPMDisp::compute(int eflag, int vflag)
nx_pppm, ny_pppm, nz_pppm, nfft,
nxlo_fft, nylo_fft, nzlo_fft, nxhi_fft, nyhi_fft, nzhi_fft,
nxlo_in, nylo_in, nzlo_in, nxhi_in, nyhi_in, nzhi_in,
- energy_1, greensfn,
+ energy_1, greensfn,
fkx, fky, fkz,fkx2, fky2, fkz2,
vdx_brick, vdy_brick, vdz_brick, virial_1, vg,vg2,
u_brick, v0_brick, v1_brick, v2_brick, v3_brick, v4_brick, v5_brick);
cg->forward_comm(this, FORWARD_IK);
- fieldforce_c_ik();
+ fieldforce_c_ik();
if (evflag_atom) cg_peratom->forward_comm(this, FORWARD_IK_PERATOM);
}
@@ -983,14 +983,14 @@ void PPPMDisp::compute(int eflag, int vflag)
brick2fft(nxlo_in_6, nylo_in_6, nzlo_in_6, nxhi_in_6, nyhi_in_6, nzhi_in_6,
density_brick_g, density_fft_g, work1_6,remap_6);
-
+
if (differentiation_flag == 1) {
poisson_ad(work1_6, work2_6, density_fft_g, fft1_6, fft2_6,
nx_pppm_6, ny_pppm_6, nz_pppm_6, nfft_6,
nxlo_fft_6, nylo_fft_6, nzlo_fft_6, nxhi_fft_6, nyhi_fft_6, nzhi_fft_6,
nxlo_in_6, nylo_in_6, nzlo_in_6, nxhi_in_6, nyhi_in_6, nzhi_in_6,
- energy_6, greensfn_6,
+ energy_6, greensfn_6,
virial_6, vg_6, vg2_6,
u_brick_g, v0_brick_g, v1_brick_g, v2_brick_g, v3_brick_g, v4_brick_g, v5_brick_g);
@@ -1005,13 +1005,13 @@ void PPPMDisp::compute(int eflag, int vflag)
nx_pppm_6, ny_pppm_6, nz_pppm_6, nfft_6,
nxlo_fft_6, nylo_fft_6, nzlo_fft_6, nxhi_fft_6, nyhi_fft_6, nzhi_fft_6,
nxlo_in_6, nylo_in_6, nzlo_in_6, nxhi_in_6, nyhi_in_6, nzhi_in_6,
- energy_6, greensfn_6,
+ energy_6, greensfn_6,
fkx_6, fky_6, fkz_6,fkx2_6, fky2_6, fkz2_6,
vdx_brick_g, vdy_brick_g, vdz_brick_g, virial_6, vg_6, vg2_6,
u_brick_g, v0_brick_g, v1_brick_g, v2_brick_g, v3_brick_g, v4_brick_g, v5_brick_g);
-
+
cg_6->forward_comm(this,FORWARD_IK_G);
-
+
fieldforce_g_ik();
@@ -1036,7 +1036,7 @@ void PPPMDisp::compute(int eflag, int vflag)
nx_pppm_6, ny_pppm_6, nz_pppm_6, nfft_6,
nxlo_fft_6, nylo_fft_6, nzlo_fft_6, nxhi_fft_6, nyhi_fft_6, nzhi_fft_6,
nxlo_in_6, nylo_in_6, nzlo_in_6, nxhi_in_6, nyhi_in_6, nzhi_in_6,
- energy_6, greensfn_6,
+ energy_6, greensfn_6,
virial_6, vg_6, vg2_6,
u_brick_a3, v0_brick_a3, v1_brick_a3, v2_brick_a3, v3_brick_a3, v4_brick_a3, v5_brick_a3);
poisson_2s_ad(density_fft_a0, density_fft_a6,
@@ -1056,12 +1056,12 @@ void PPPMDisp::compute(int eflag, int vflag)
if (evflag_atom) cg_peratom_6->forward_comm(this, FORWARD_AD_PERATOM_A);
} else {
-
+
poisson_ik(work1_6, work2_6, density_fft_a3, fft1_6, fft2_6,
nx_pppm_6, ny_pppm_6, nz_pppm_6, nfft_6,
nxlo_fft_6, nylo_fft_6, nzlo_fft_6, nxhi_fft_6, nyhi_fft_6, nzhi_fft_6,
nxlo_in_6, nylo_in_6, nzlo_in_6, nxhi_in_6, nyhi_in_6, nzhi_in_6,
- energy_6, greensfn_6,
+ energy_6, greensfn_6,
fkx_6, fky_6, fkz_6,fkx2_6, fky2_6, fkz2_6,
vdx_brick_a3, vdy_brick_a3, vdz_brick_a3, virial_6, vg_6, vg2_6,
u_brick_a3, v0_brick_a3, v1_brick_a3, v2_brick_a3, v3_brick_a3, v4_brick_a3, v5_brick_a3);
@@ -1134,7 +1134,7 @@ void PPPMDisp::compute(int eflag, int vflag)
fieldforce_none_ik();
- if (evflag_atom)
+ if (evflag_atom)
cg_peratom_6->forward_comm(this, FORWARD_IK_PERATOM_NONE);
}
if (evflag_atom) fieldforce_none_peratom();
@@ -1156,10 +1156,10 @@ void PPPMDisp::compute(int eflag, int vflag)
energy_1 = energy_all;
MPI_Allreduce(&energy_6,&energy_all,1,MPI_DOUBLE,MPI_SUM,world);
energy_6 = energy_all;
-
+
energy_1 *= 0.5*volume;
energy_6 *= 0.5*volume;
-
+
energy_1 -= g_ewald*qsqsum/MY_PIS +
MY_PI2*qsum*qsum / (g_ewald*g_ewald*volume);
energy_6 += - MY_PI*MY_PIS/(6*volume)*pow(g_ewald_6,3)*csumij +
@@ -1199,7 +1199,7 @@ void PPPMDisp::compute(int eflag, int vflag)
}
}
}
-
+
if (vflag_atom) {
if (function[1] + function[2] + function[3]) {
int tmp;
@@ -1218,7 +1218,7 @@ void PPPMDisp::compute(int eflag, int vflag)
if (function[1] + function[2] + function[3]) energy += energy_6;
// convert atoms back from lamda to box coords
-
+
if (triclinic) domain->lamda2x(atom->nlocal);
}
@@ -1262,7 +1262,7 @@ void PPPMDisp::init_coeffs() // local pair coeffs
if (function[3] && !converged) {
error->all(FLERR,"Matrix factorization to split dispersion coefficients failed");
}
- // determine number of used eigenvalues
+ // determine number of used eigenvalues
// based on maximum allowed number or cutoff criterion
// sort eigenvalues according to their size with bubble sort
double t;
@@ -1361,9 +1361,9 @@ void PPPMDisp::init_coeffs() // local pair coeffs
}
if (function[2]) { // arithmetic 1/r^6
//cannot use epsilon, because this has not been set yet
- double **epsilon = (double **) force->pair->extract("epsilon",tmp);
+ double **epsilon = (double **) force->pair->extract("epsilon",tmp);
//cannot use sigma, because this has not been set yet
- double **sigma = (double **) force->pair->extract("sigma",tmp);
+ double **sigma = (double **) force->pair->extract("sigma",tmp);
if (!(epsilon&&sigma))
error->all(FLERR,"Epsilon or sigma reference not set by pair style in PPPMDisp");
double eps_i, sigma_i, sigma_n, *bi = B = new double[7*n+7];
@@ -1420,7 +1420,7 @@ int PPPMDisp::qr_alg(double **A, double **Q, int n)
bn1 = A[n-2][n-1];
d = (an1-an)/2;
mue = an + d - copysign(1.,d)*sqrt(d*d + bn1*bn1);
- for (int i = 0; i < n; i++)
+ for (int i = 0; i < n; i++)
A[i][i] -= mue;
// perform a QR factorization for a tridiagonal matrix A
@@ -1440,19 +1440,19 @@ int PPPMDisp::qr_alg(double **A, double **Q, int n)
count = count + 1;
if (count == countmax) break;
}
-
+
// free allocated memory
memory->destroy(Qi);
memory->destroy(A0);
memory->destroy(C);
memory->destroy(D);
memory->destroy(E);
-
+
return converged;
}
/* ----------------------------------------------------------------------
- Transform a Matrix to Hessenberg form (for symmetric Matrices, the
+ Transform a Matrix to Hessenberg form (for symmetric Matrices, the
result will be a tridiagonal matrix)
------------------------------------------------------------------------- */
@@ -1542,7 +1542,7 @@ void PPPMDisp::mmult(double** A, double** B, double** C, int n)
for (int j = 0; j < n; j++)
C[i][j] = 0.0;
- // perform matrix multiplication
+ // perform matrix multiplication
for (int i = 0; i < n; i++)
for (int j = 0; j < n; j++)
for (int k = 0; k < n; k++)
@@ -1571,7 +1571,7 @@ int PPPMDisp::check_convergence(double** A,double** Q,double** A0,
for (int j = 0; j < n; j++)
Bmax = (Bmax>A0[i][j])?Bmax:A0[i][j]; //max(Bmax,A0[i][j]);
double epsabs = eps*Bmax;
-
+
// reconstruct the original matrix
// store the diagonal elements in D
for (int i = 0; i < n; i++)
@@ -1604,7 +1604,7 @@ int PPPMDisp::check_convergence(double** A,double** Q,double** A0,
}
/* ----------------------------------------------------------------------
- allocate memory that depends on # of K-vectors and order
+ allocate memory that depends on # of K-vectors and order
------------------------------------------------------------------------- */
void PPPMDisp::allocate()
@@ -1924,7 +1924,7 @@ void PPPMDisp::allocate()
nxlo_out_6,nxhi_out_6,nylo_out_6,nyhi_out_6,nzlo_out_6,nzhi_out_6,
procneigh[0][0],procneigh[0][1],procneigh[1][0],
procneigh[1][1],procneigh[2][0],procneigh[2][1]);
- }
+ }
if (function[3]) {
memory->create(work1_6,2*nfft_both_6,"pppm/disp:work1_6");
@@ -2009,7 +2009,7 @@ void PPPMDisp::allocate()
/* ----------------------------------------------------------------------
allocate memory that depends on # of K-vectors and order
- for per atom calculations
+ for per atom calculations
------------------------------------------------------------------------- */
void PPPMDisp::allocate_peratom()
@@ -2095,7 +2095,7 @@ void PPPMDisp::allocate_peratom()
}
if (function[2]) {
-
+
if ( differentiation_flag != 1 ) {
memory->create3d_offset(u_brick_a0,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
nxlo_out_6,nxhi_out_6,"pppm/disp:u_brick_a0");
@@ -2221,7 +2221,7 @@ void PPPMDisp::allocate_peratom()
procneigh[0][0],procneigh[0][1],procneigh[1][0],
procneigh[1][1],procneigh[2][0],procneigh[2][1]);
- }
+ }
if (function[3]) {
@@ -2264,7 +2264,7 @@ void PPPMDisp::allocate_peratom()
/* ----------------------------------------------------------------------
- deallocate memory that depends on # of K-vectors and order
+ deallocate memory that depends on # of K-vectors and order
------------------------------------------------------------------------- */
void PPPMDisp::deallocate()
@@ -2316,7 +2316,7 @@ void PPPMDisp::deallocate()
memory->destroy(density_fft_a3);
density_brick_a3 = vdx_brick_a3 = vdy_brick_a3 = vdz_brick_a3 = NULL;
density_fft_a3 = NULL;
-
+
memory->destroy3d_offset(density_brick_a4,nzlo_out_6,nylo_out_6,nxlo_out_6);
memory->destroy3d_offset(vdx_brick_a4,nzlo_out_6,nylo_out_6,nxlo_out_6);
memory->destroy3d_offset(vdy_brick_a4,nzlo_out_6,nylo_out_6,nxlo_out_6);
@@ -2411,7 +2411,7 @@ void PPPMDisp::deallocate()
memory->destroy(gf_b_6);
memory->destroy2d_offset(rho1d_6,-order_6/2);
memory->destroy2d_offset(rho_coeff_6,(1-order_6)/2);
- memory->destroy2d_offset(drho1d_6,-order_6/2);
+ memory->destroy2d_offset(drho1d_6,-order_6/2);
memory->destroy2d_offset(drho_coeff_6,(1-order_6)/2);
gf_b_6 = NULL;
rho1d_6 = rho_coeff_6 = drho1d_6 = drho_coeff_6 = NULL;
@@ -2436,7 +2436,7 @@ void PPPMDisp::deallocate()
/* ----------------------------------------------------------------------
deallocate memory that depends on # of K-vectors and order
- for per atom calculations
+ for per atom calculations
------------------------------------------------------------------------- */
void PPPMDisp::deallocate_peratom()
@@ -2496,7 +2496,7 @@ void PPPMDisp::deallocate_peratom()
memory->destroy3d_offset(v4_brick_a3, nzlo_out_6, nylo_out_6, nxlo_out_6);
memory->destroy3d_offset(v5_brick_a3, nzlo_out_6, nylo_out_6, nxlo_out_6);
u_brick_a3 = v0_brick_a3 = v1_brick_a3 = v2_brick_a3 = v3_brick_a3 = v4_brick_a3 = v5_brick_a3 = NULL;
-
+
memory->destroy3d_offset(u_brick_a4, nzlo_out_6, nylo_out_6, nxlo_out_6);
memory->destroy3d_offset(v0_brick_a4, nzlo_out_6, nylo_out_6, nxlo_out_6);
memory->destroy3d_offset(v1_brick_a4, nzlo_out_6, nylo_out_6, nxlo_out_6);
@@ -2505,7 +2505,7 @@ void PPPMDisp::deallocate_peratom()
memory->destroy3d_offset(v4_brick_a4, nzlo_out_6, nylo_out_6, nxlo_out_6);
memory->destroy3d_offset(v5_brick_a4, nzlo_out_6, nylo_out_6, nxlo_out_6);
u_brick_a4 = v0_brick_a4 = v1_brick_a4 = v2_brick_a4 = v3_brick_a4 = v4_brick_a4 = v5_brick_a4 = NULL;
-
+
memory->destroy3d_offset(u_brick_a5, nzlo_out_6, nylo_out_6, nxlo_out_6);
memory->destroy3d_offset(v0_brick_a5, nzlo_out_6, nylo_out_6, nxlo_out_6);
memory->destroy3d_offset(v1_brick_a5, nzlo_out_6, nylo_out_6, nxlo_out_6);
@@ -2555,7 +2555,7 @@ void PPPMDisp::set_grid()
double yprd = domain->yprd;
double zprd = domain->zprd;
double zprd_slab = zprd*slab_volfactor;
-
+
// make initial g_ewald estimate
// based on desired accuracy and real space cutoff
// fluid-occupied volume used to estimate real-space error
@@ -2566,20 +2566,20 @@ void PPPMDisp::set_grid()
if (!gewaldflag) {
g_ewald = accuracy*sqrt(natoms*cutoff*xprd*yprd*zprd) / (2.0*q2);
- if (g_ewald >= 1.0)
+ if (g_ewald >= 1.0)
error->all(FLERR,"KSpace accuracy too large to estimate G vector");
g_ewald = sqrt(-log(g_ewald)) / cutoff;
- }
+ }
// set optimal nx_pppm,ny_pppm,nz_pppm based on order and accuracy
// nz_pppm uses extended zprd_slab instead of zprd
// reduce it until accuracy target is met
if (!gridflag) {
- h = h_x = h_y = h_z = 4.0/g_ewald;
+ h = h_x = h_y = h_z = 4.0/g_ewald;
int count = 0;
while (1) {
-
+
// set grid dimension
nx_pppm = static_cast<int> (xprd/h_x);
ny_pppm = static_cast<int> (yprd/h_y);
@@ -2607,7 +2607,7 @@ void PPPMDisp::set_grid()
nzhi_fft = (me_z+1)*nz_pppm/npez_fft - 1;
double qopt = compute_qopt();
-
+
double dfkspace = sqrt(qopt/natoms)*q2/(xprd*yprd*zprd_slab);
count++;
@@ -2619,7 +2619,7 @@ void PPPMDisp::set_grid()
h_x = h_y = h_z = h;
}
}
-
+
// boost grid size until it is factorable
while (!factorable(nx_pppm)) nx_pppm++;
@@ -2628,7 +2628,7 @@ void PPPMDisp::set_grid()
}
/* ----------------------------------------------------------------------
- set the FFT parameters
+ set the FFT parameters
------------------------------------------------------------------------- */
void PPPMDisp::set_fft_parameters(int& nx_p,int& ny_p,int& nz_p,
@@ -2653,9 +2653,9 @@ void PPPMDisp::set_fft_parameters(int& nx_p,int& ny_p,int& nz_p,
nylo_i = static_cast<int> (comm->ysplit[comm->myloc[1]] * ny_p);
nyhi_i = static_cast<int> (comm->ysplit[comm->myloc[1]+1] * ny_p) - 1;
- nzlo_i = static_cast<int>
+ nzlo_i = static_cast<int>
(comm->zsplit[comm->myloc[2]] * nz_p/slab_volfactor);
- nzhi_i = static_cast<int>
+ nzhi_i = static_cast<int>
(comm->zsplit[comm->myloc[2]+1] * nz_p/slab_volfactor) - 1;
@@ -2710,26 +2710,26 @@ void PPPMDisp::set_fft_parameters(int& nx_p,int& ny_p,int& nz_p,
dist[1] = cuthalf/domain->prd[1];
dist[2] = cuthalf/domain->prd[2];
}
-
+
int nlo,nhi;
-
- nlo = static_cast<int> ((sublo[0]-dist[0]-boxlo[0]) *
+
+ nlo = static_cast<int> ((sublo[0]-dist[0]-boxlo[0]) *
nx_p/xprd + sft) - OFFSET;
- nhi = static_cast<int> ((subhi[0]+dist[0]-boxlo[0]) *
+ nhi = static_cast<int> ((subhi[0]+dist[0]-boxlo[0]) *
nx_p/xprd + sft) - OFFSET;
nxlo_o = nlo + nlow;
nxhi_o = nhi + nupp;
- nlo = static_cast<int> ((sublo[1]-dist[1]-boxlo[1]) *
+ nlo = static_cast<int> ((sublo[1]-dist[1]-boxlo[1]) *
ny_p/yprd + sft) - OFFSET;
- nhi = static_cast<int> ((subhi[1]+dist[1]-boxlo[1]) *
+ nhi = static_cast<int> ((subhi[1]+dist[1]-boxlo[1]) *
ny_p/yprd + sft) - OFFSET;
nylo_o = nlo + nlow;
nyhi_o = nhi + nupp;
- nlo = static_cast<int> ((sublo[2]-dist[2]-boxlo[2]) *
+ nlo = static_cast<int> ((sublo[2]-dist[2]-boxlo[2]) *
nz_p/zprd_slab + sft) - OFFSET;
- nhi = static_cast<int> ((subhi[2]+dist[2]-boxlo[2]) *
+ nhi = static_cast<int> ((subhi[2]+dist[2]-boxlo[2]) *
nz_p/zprd_slab + sft) - OFFSET;
nzlo_o = nlo + nlow;
nzhi_o = nhi + nupp;
@@ -2745,7 +2745,7 @@ void PPPMDisp::set_fft_parameters(int& nx_p,int& ny_p,int& nz_p,
nzhi_i = nz_p - 1;
nzhi_o = nz_p - 1;
}
-
+
// decomposition of FFT mesh
// global indices range from 0 to N-1
// proc owns entire x-dimension, clump of columns in y,z dimensions
@@ -2792,7 +2792,7 @@ void PPPMDisp::set_fft_parameters(int& nx_p,int& ny_p,int& nz_p,
/* ----------------------------------------------------------------------
check if all factors of n are in list of factors
- return 1 if yes, 0 if no
+ return 1 if yes, 0 if no
------------------------------------------------------------------------- */
int PPPMDisp::factorable(int n)
@@ -2813,25 +2813,25 @@ int PPPMDisp::factorable(int n)
}
/* ----------------------------------------------------------------------
- pre-compute Green's function denominator expansion coeffs, Gamma(2n)
+ pre-compute Green's function denominator expansion coeffs, Gamma(2n)
------------------------------------------------------------------------- */
void PPPMDisp::adjust_gewald()
{
-
+
// Use Newton solver to find g_ewald
double dx;
-
+
// Begin algorithm
-
+
for (int i = 0; i < LARGE; i++) {
- dx = f() / derivf();
+ dx = f() / derivf();
g_ewald -= dx; //Update g_ewald
if (fabs(f()) < SMALL) return;
}
-
+
// Failed to converge
-
+
char str[128];
sprintf(str, "Could not compute g_ewald");
error->all(FLERR, str);
@@ -2852,12 +2852,12 @@ double PPPMDisp::f()
double zprd_slab = zprd*slab_volfactor;
bigint natoms = atom->natoms;
- df_rspace = 2.0*q2*exp(-g_ewald*g_ewald*cutoff*cutoff) /
+ df_rspace = 2.0*q2*exp(-g_ewald*g_ewald*cutoff*cutoff) /
sqrt(natoms*cutoff*xprd*yprd*zprd);
-
+
double qopt = compute_qopt();
df_kspace = sqrt(qopt/natoms)*q2/(xprd*yprd*zprd_slab);
-
+
return df_rspace - df_kspace;
}
@@ -2865,21 +2865,21 @@ double PPPMDisp::f()
Calculate numerical derivative f'(x) using forward difference
[f(x + h) - f(x)] / h
------------------------------------------------------------------------- */
-
+
double PPPMDisp::derivf()
-{
+{
double h = 0.000001; //Derivative step-size
double df,f1,f2,g_ewald_old;
-
+
f1 = f();
g_ewald_old = g_ewald;
g_ewald += h;
f2 = f();
g_ewald = g_ewald_old;
df = (f2 - f1)/h;
-
+
return df;
-}
+}
/* ----------------------------------------------------------------------
Calculate the final estimator for the accuracy
@@ -2894,7 +2894,7 @@ double PPPMDisp::final_accuracy()
double zprd = domain->zprd;
double zprd_slab = zprd*slab_volfactor;
bigint natoms = atom->natoms;
- df_rspace = 2.0*q2 * exp(-g_ewald*g_ewald*cutoff*cutoff) /
+ df_rspace = 2.0*q2 * exp(-g_ewald*g_ewald*cutoff*cutoff) /
sqrt(natoms*cutoff*xprd*yprd*zprd);
double qopt = compute_qopt();
@@ -2999,8 +2999,8 @@ double PPPMDisp::compute_qopt_ik()
for (k = nxlo_fft; k <= nxhi_fft; k++) {
kper = k - nx_pppm*(2*k/nx_pppm);
-
- sqk = pow(unitkx*kper,2.0) + pow(unitky*lper,2.0) +
+
+ sqk = pow(unitkx*kper,2.0) + pow(unitky*lper,2.0) +
pow(unitkz*mper,2.0);
if (sqk != 0.0) {
@@ -3085,12 +3085,12 @@ double PPPMDisp::compute_qopt_ad()
for (k = nxlo_fft; k <= nxhi_fft; k++) {
kper = k - nx_pppm*(2*k/nx_pppm);
-
- sqk = pow(unitkx*kper,2.0) + pow(unitky*lper,2.0) +
+
+ sqk = pow(unitkx*kper,2.0) + pow(unitky*lper,2.0) +
pow(unitkz*mper,2.0);
if (sqk != 0.0) {
-
+
sum1 = 0.0;
sum2 = 0.0;
sum3 = 0.0;
@@ -3175,8 +3175,8 @@ double PPPMDisp::compute_qopt_6_ik()
for (k = nxlo_fft_6; k <= nxhi_fft_6; k++) {
kper = k - nx_pppm_6*(2*k/nx_pppm_6);
-
- sqk = pow(unitkx*kper,2.0) + pow(unitky*lper,2.0) +
+
+ sqk = pow(unitkx*kper,2.0) + pow(unitky*lper,2.0) +
pow(unitkz*mper,2.0);
if (sqk != 0.0) {
@@ -3268,12 +3268,12 @@ double PPPMDisp::compute_qopt_6_ad()
for (k = nxlo_fft_6; k <= nxhi_fft_6; k++) {
kper = k - nx_pppm_6*(2*k/nx_pppm_6);
-
- sqk = pow(unitkx*kper,2.0) + pow(unitky*lper,2.0) +
+
+ sqk = pow(unitkx*kper,2.0) + pow(unitky*lper,2.0) +
pow(unitkz*mper,2.0);
if (sqk != 0.0) {
-
+
sum1 = 0.0;
sum2 = 0.0;
sum3 = 0.0;
@@ -3333,11 +3333,11 @@ void PPPMDisp::set_grid_6()
while (!factorable(nx_pppm_6)) nx_pppm_6++;
while (!factorable(ny_pppm_6)) ny_pppm_6++;
while (!factorable(nz_pppm_6)) nz_pppm_6++;
-
+
}
/* ----------------------------------------------------------------------
- Calculate the sum of the squared dispersion coefficients and other
+ Calculate the sum of the squared dispersion coefficients and other
related quantities required for the calculations
------------------------------------------------------------------------- */
@@ -3346,17 +3346,17 @@ void PPPMDisp::calc_csum()
csumij = 0.0;
csum = 0.0;
- int ntypes = atom->ntypes;
+ int ntypes = atom->ntypes;
int i,j,k;
delete [] cii;
cii = new double[ntypes +1];
for (i = 0; i<=ntypes; i++) cii[i] = 0.0;
- delete [] csumi;
+ delete [] csumi;
csumi = new double[ntypes +1];
- for (i = 0; i<=ntypes; i++) csumi[i] = 0.0;
+ for (i = 0; i<=ntypes; i++) csumi[i] = 0.0;
int *neach = new int[ntypes+1];
- for (i = 0; i<=ntypes; i++) neach[i] = 0;
+ for (i = 0; i<=ntypes; i++) neach[i] = 0;
//the following variables are needed to distinguish between arithmetic
// and geometric mixing
@@ -3412,7 +3412,7 @@ void PPPMDisp::calc_csum()
d1 = neach_all[i]*B[i];
d2 = neach_all[j]*B[j];
csumij += d1*d2;
- //csumij += neach_all[i]*neach_all[j]*B[i]*B[j];
+ //csumij += neach_all[i]*neach_all[j]*B[i]*B[j];
}
}
}
@@ -3440,7 +3440,7 @@ void PPPMDisp::calc_csum()
}
}
}
- }
+ }
delete [] neach;
delete [] neach_all;
@@ -3490,10 +3490,10 @@ double PPPMDisp::f_6()
bigint natoms = atom->natoms;
df_rspace = lj_rspace_error();
-
+
double qopt = compute_qopt_6();
df_kspace = sqrt(qopt/natoms)*csum/(xprd*yprd*zprd_slab);
-
+
return df_rspace - df_kspace;
}
@@ -3501,21 +3501,21 @@ double PPPMDisp::f_6()
Calculate numerical derivative f'(x) using forward difference
[f(x + h) - f(x)] / h
------------------------------------------------------------------------- */
-
+
double PPPMDisp::derivf_6()
-{
+{
double h = 0.000001; //Derivative step-size
double df,f1,f2,g_ewald_old;
-
+
f1 = f_6();
g_ewald_old = g_ewald_6;
g_ewald_6 += h;
f2 = f_6();
g_ewald_6 = g_ewald_old;
df = (f2 - f1)/h;
-
+
return df;
-}
+}
/* ----------------------------------------------------------------------
@@ -3530,13 +3530,13 @@ void PPPMDisp::set_init_g6()
// make initial g_ewald estimate
// based on desired error and real space cutoff
-
+
// compute initial value for df_real with g_ewald_6 = 1/cutoff_lj
// if df_real > 0, repeat divide g_ewald_6 by 2 until df_real < 0
// else, repeat multiply g_ewald_6 by 2 until df_real > 0
// perform bisection for the last two values of
double df_real;
- double g_ewald_old;
+ double g_ewald_old;
double gmin, gmax;
// check if there is a user defined accuracy
@@ -3608,7 +3608,7 @@ void PPPMDisp::set_n_pppm_6()
// decrease grid spacing untill required precision is obtained
int count = 0;
while(1) {
-
+
// set grid dimension
nx_pppm_6 = static_cast<int> (xprd/h_x);
ny_pppm_6 = static_cast<int> (yprd/h_y);
@@ -3636,7 +3636,7 @@ void PPPMDisp::set_n_pppm_6()
nzhi_fft_6 = (me_z+1)*nz_pppm_6/npez_fft - 1;
double qopt = compute_qopt_6();
-
+
double df_kspace = sqrt(qopt/natoms)*csum/(xprd*yprd*zprd_slab);
count++;
@@ -3673,7 +3673,7 @@ double PPPMDisp::lj_rspace_error()
/* ----------------------------------------------------------------------
Compyute the modified (hockney-eastwood) coulomb green function
- ---------------------------------------------------------------------- */
+ ---------------------------------------------------------------------- */
void PPPMDisp::compute_gf()
{
@@ -3738,7 +3738,7 @@ void PPPMDisp::compute_gf()
if (sqk != 0.0) {
numerator = 4.0*MY_PI/sqk;
- denominator = gf_denom(snx2,sny2,snz2, gf_b, order);
+ denominator = gf_denom(snx2,sny2,snz2, gf_b, order);
greensfn[n++] = numerator*sx*sy*sz*wx*wy*wz/denominator;
} else greensfn[n++] = 0.0;
}
@@ -3748,10 +3748,10 @@ void PPPMDisp::compute_gf()
/* ----------------------------------------------------------------------
compute self force coefficients for ad-differentiation scheme
- and Coulomb interaction
+ and Coulomb interaction
------------------------------------------------------------------------- */
-void PPPMDisp::compute_sf_precoeff(int nxp, int nyp, int nzp, int ord,
+void PPPMDisp::compute_sf_precoeff(int nxp, int nyp, int nzp, int ord,
int nxlo_ft, int nylo_ft, int nzlo_ft,
int nxhi_ft, int nyhi_ft, int nzhi_ft,
double *sf_pre1, double *sf_pre2, double *sf_pre3,
@@ -3795,7 +3795,7 @@ void PPPMDisp::compute_sf_precoeff(int nxp, int nyp, int nzp, int ord,
for (k = nxlo_ft; k <= nxhi_ft; k++) {
kper = k - nxp*(2*k/nxp);
-
+
sum1 = sum2 = sum3 = sum4 = sum5 = sum6 = 0.0;
for (i = -nb; i <= nb; i++) {
@@ -3824,7 +3824,7 @@ void PPPMDisp::compute_sf_precoeff(int nxp, int nyp, int nzp, int ord,
if (argy != 0.0) wy1[i+2] = pow(sin(argy)/argy,ord);
argy = 0.5*qy2*yprd/nyp;
if (argy != 0.0) wy2[i+2] = pow(sin(argy)/argy,ord);
-
+
qz0 = unitkz*(mper+nzp*i);
qz1 = unitkz*(mper+nzp*(i+1));
qz2 = unitkz*(mper+nzp*(i+2));
@@ -3838,7 +3838,7 @@ void PPPMDisp::compute_sf_precoeff(int nxp, int nyp, int nzp, int ord,
argz = 0.5*qz2*zprd_slab/nzp;
if (argz != 0.0) wz2[i+2] = pow(sin(argz)/argz,ord);
}
-
+
for (nx = 0; nx <= 4; nx++) {
for (ny = 0; ny <= 4; ny++) {
for (nz = 0; nz <= 4; nz++) {
@@ -3859,7 +3859,7 @@ void PPPMDisp::compute_sf_precoeff(int nxp, int nyp, int nzp, int ord,
}
}
}
-
+
// store values
sf_pre1[n] = sum1;
@@ -3922,7 +3922,7 @@ void PPPMDisp::compute_gf_6()
argz = 0.5*qz*zprd_slab/nz_pppm_6;
if (argz != 0.0) wz = pow(sin(argz)/argz,order_6);
wz *= wz;
-
+
for (l = nylo_fft_6; l <= nyhi_fft_6; l++) {
lper = l - ny_pppm_6*(2*l/ny_pppm_6);
qy = unitky*lper;
@@ -3944,11 +3944,11 @@ void PPPMDisp::compute_gf_6()
argx = 0.5*qx*xprd/nx_pppm_6;
if (argx != 0.0) wx = pow(sin(argx)/argx,order_6);
wx *= wx;
-
+
sqk = pow(qx,2.0) + pow(qy,2.0) + pow(qz,2.0);
if (sqk != 0.0) {
- denominator = gf_denom(snx2,sny2,snz2, gf_b_6, order_6);
+ denominator = gf_denom(snx2,sny2,snz2, gf_b_6, order_6);
rtsqk = sqrt(sqk);
term = (1-2*sqk*inv2ew*inv2ew)*sx*sy*sz +
2*sqk*rtsqk*inv2ew*inv2ew*inv2ew*rtpi*erfc(rtsqk*inv2ew);
@@ -3961,7 +3961,7 @@ void PPPMDisp::compute_gf_6()
/* ----------------------------------------------------------------------
compute self force coefficients for ad-differentiation scheme
- and Coulomb interaction
+ and Coulomb interaction
------------------------------------------------------------------------- */
void PPPMDisp::compute_sf_coeff()
{
@@ -4017,7 +4017,7 @@ void PPPMDisp::compute_sf_coeff()
/* ----------------------------------------------------------------------
compute self force coefficients for ad-differentiation scheme
- and Dispersion interaction
+ and Dispersion interaction
------------------------------------------------------------------------- */
void PPPMDisp::compute_sf_coeff_6()
@@ -4051,9 +4051,9 @@ void PPPMDisp::compute_sf_coeff_6()
}
}
-
+
// perform multiplication with prefactors
-
+
double prex, prey, prez;
prex = prey = prez = MY_PI/volume;
prex *= nx_pppm_6/xprd;
@@ -4065,9 +4065,9 @@ void PPPMDisp::compute_sf_coeff_6()
sf_coeff_6[3] *= prey*2;
sf_coeff_6[4] *= prez;
sf_coeff_6[5] *= prez*2;
-
+
// communicate values with other procs
-
+
double tmp[6];
MPI_Allreduce(sf_coeff_6,tmp,6,MPI_DOUBLE,MPI_SUM,world);
for (n = 0; n < 6; n++) sf_coeff_6[n] = tmp[n];
@@ -4083,7 +4083,7 @@ void PPPMDisp::compute_sf_coeff_6()
j=-inf l=0
= -(z*z)**n /(2n-1)! * (d/dx)**(2n-1) cot(x) at z = sin(x)
- gf_b = denominator expansion coeffs
+ gf_b = denominator expansion coeffs
------------------------------------------------------------------------- */
double PPPMDisp::gf_denom(double x, double y, double z, double *g_b, int ord)
@@ -4100,18 +4100,18 @@ double PPPMDisp::gf_denom(double x, double y, double z, double *g_b, int ord)
}
/* ----------------------------------------------------------------------
- pre-compute Green's function denominator expansion coeffs, Gamma(2n)
+ pre-compute Green's function denominator expansion coeffs, Gamma(2n)
------------------------------------------------------------------------- */
void PPPMDisp::compute_gf_denom(double* gf, int ord)
{
int k,l,m;
-
+
for (l = 1; l < ord; l++) gf[l] = 0.0;
gf[0] = 1.0;
-
+
for (m = 1; m < ord; m++) {
- for (l = m; l > 0; l--)
+ for (l = m; l > 0; l--)
gf[l] = 4.0 * (gf[l]*(l-m)*(l-m-0.5)-gf[l-1]*(l-m-1)*(l-m-1));
gf[0] = 4.0 * (gf[0]*(l-m)*(l-m-0.5));
}
@@ -4123,7 +4123,7 @@ void PPPMDisp::compute_gf_denom(double* gf, int ord)
}
/* ----------------------------------------------------------------------
- ghost-swap to accumulate full density in brick decomposition
+ ghost-swap to accumulate full density in brick decomposition
remap density from 3d brick decomposition to FFTdecomposition
for coulomb interaction or dispersion interaction with geometric
mixing
@@ -4151,7 +4151,7 @@ void PPPMDisp::brick2fft(int nxlo_i, int nylo_i, int nzlo_i,
/* ----------------------------------------------------------------------
- ghost-swap to accumulate full density in brick decomposition
+ ghost-swap to accumulate full density in brick decomposition
remap density from 3d brick decomposition to FFTdecomposition
for dispersion with arithmetic mixing rule
------------------------------------------------------------------------- */
@@ -4188,7 +4188,7 @@ void PPPMDisp::brick2fft_a()
}
/* ----------------------------------------------------------------------
- ghost-swap to accumulate full density in brick decomposition
+ ghost-swap to accumulate full density in brick decomposition
remap density from 3d brick decomposition to FFTdecomposition
for dispersion with special case
------------------------------------------------------------------------- */
@@ -4205,7 +4205,7 @@ void PPPMDisp::brick2fft_none()
n = 0;
for (iz = nzlo_in_6; iz <= nzhi_in_6; iz++)
for (iy = nylo_in_6; iy <= nyhi_in_6; iy++)
- for (ix = nxlo_in_6; ix <= nxhi_in_6; ix++)
+ for (ix = nxlo_in_6; ix <= nxhi_in_6; ix++)
density_fft_none[k][n++] = density_brick_none[k][iz][iy][ix];
}
@@ -4216,7 +4216,7 @@ void PPPMDisp::brick2fft_none()
/* ----------------------------------------------------------------------
find center grid pt for each of my particles
check that full stencil for the particle will fit in my 3d brick
- store central grid pt indices in part2grid array
+ store central grid pt indices in part2grid array
------------------------------------------------------------------------- */
void PPPMDisp::particle_map(double delx, double dely, double delz,
@@ -4234,7 +4234,7 @@ void PPPMDisp::particle_map(double delx, double dely, double delz,
int flag = 0;
for (int i = 0; i < nlocal; i++) {
-
+
// (nx,ny,nz) = global coords of grid pt to "lower left" of charge
// current particle coord can be outside global and local box
// add/subtract OFFSET to avoid int(-0.75) = 0 when want it to be -1
@@ -4272,7 +4272,7 @@ void PPPMDisp::particle_map_c(double delx, double dely, double delz,
create discretized "density" on section of global grid due to my particles
density(x,y,z) = charge "density" at grid points of my 3d brick
(nxlo:nxhi,nylo:nyhi,nzlo:nzhi) is extent of my brick (including ghosts)
- in global grid
+ in global grid
------------------------------------------------------------------------- */
void PPPMDisp::make_rho_c()
@@ -4410,7 +4410,7 @@ void PPPMDisp::make_rho_a()
int type;
double **x = atom->x;
int nlocal = atom->nlocal;
-
+
for (int i = 0; i < nlocal; i++) {
//do the following for all 4 grids
@@ -4470,7 +4470,7 @@ void PPPMDisp::make_rho_none()
int type;
double **x = atom->x;
int nlocal = atom->nlocal;
-
+
for (int i = 0; i < nlocal; i++) {
//do the following for all 4 grids
@@ -4506,7 +4506,7 @@ void PPPMDisp::make_rho_none()
------------------------------------------------------------------------- */
void PPPMDisp::poisson_ik(FFT_SCALAR* wk1, FFT_SCALAR* wk2,
- FFT_SCALAR* dfft, LAMMPS_NS::FFT3d* ft1,LAMMPS_NS::FFT3d* ft2,
+ FFT_SCALAR* dfft, LAMMPS_NS::FFT3d* ft1,LAMMPS_NS::FFT3d* ft2,
int nx_p, int ny_p, int nz_p, int nft,
int nxlo_ft, int nylo_ft, int nzlo_ft,
int nxhi_ft, int nyhi_ft, int nzhi_ft,
@@ -4525,7 +4525,7 @@ void PPPMDisp::poisson_ik(FFT_SCALAR* wk1, FFT_SCALAR* wk2,
int i,j,k,n;
double eng;
- // transform charge/dispersion density (r -> k)
+ // transform charge/dispersion density (r -> k)
n = 0;
for (i = 0; i < nft; i++) {
wk1[n++] = dfft[i];
@@ -4551,7 +4551,7 @@ void PPPMDisp::poisson_ik(FFT_SCALAR* wk1, FFT_SCALAR* wk2,
} else {
n = 0;
for (i = 0; i < nft; i++) {
- egy +=
+ egy +=
s2 * gfn[i] * (wk1[n]*wk1[n] + wk1[n+1]*wk1[n+1]);
n += 2;
}
@@ -4650,7 +4650,7 @@ void PPPMDisp::poisson_ik(FFT_SCALAR* wk1, FFT_SCALAR* wk2,
------------------------------------------------------------------------- */
void PPPMDisp::poisson_ad(FFT_SCALAR* wk1, FFT_SCALAR* wk2,
- FFT_SCALAR* dfft, LAMMPS_NS::FFT3d* ft1,LAMMPS_NS::FFT3d* ft2,
+ FFT_SCALAR* dfft, LAMMPS_NS::FFT3d* ft1,LAMMPS_NS::FFT3d* ft2,
int nx_p, int ny_p, int nz_p, int nft,
int nxlo_ft, int nylo_ft, int nzlo_ft,
int nxhi_ft, int nyhi_ft, int nzhi_ft,
@@ -4666,7 +4666,7 @@ void PPPMDisp::poisson_ad(FFT_SCALAR* wk1, FFT_SCALAR* wk2,
int i,j,k,n;
double eng;
- // transform charge/dispersion density (r -> k)
+ // transform charge/dispersion density (r -> k)
n = 0;
for (i = 0; i < nft; i++) {
wk1[n++] = dfft[i];
@@ -4692,7 +4692,7 @@ void PPPMDisp::poisson_ad(FFT_SCALAR* wk1, FFT_SCALAR* wk2,
} else {
n = 0;
for (i = 0; i < nft; i++) {
- egy +=
+ egy +=
s2 * gfn[i] * (wk1[n]*wk1[n] + wk1[n+1]*wk1[n+1]);
n += 2;
}
@@ -4740,7 +4740,7 @@ void PPPMDisp::poisson_ad(FFT_SCALAR* wk1, FFT_SCALAR* wk2,
Fourier Transform for per atom virial calculations
------------------------------------------------------------------------- */
-void PPPMDisp:: poisson_peratom(FFT_SCALAR* wk1, FFT_SCALAR* wk2, LAMMPS_NS::FFT3d* ft2,
+void PPPMDisp:: poisson_peratom(FFT_SCALAR* wk1, FFT_SCALAR* wk2, LAMMPS_NS::FFT3d* ft2,
double** vcoeff, double** vcoeff2, int nft,
int nxlo_i, int nylo_i, int nzlo_i,
int nxhi_i, int nyhi_i, int nzhi_i,
@@ -4756,7 +4756,7 @@ void PPPMDisp:: poisson_peratom(FFT_SCALAR* wk1, FFT_SCALAR* wk2, LAMMPS_NS::FFT
n += 2;
}
- ft2->compute(wk2,wk2,-1);
+ ft2->compute(wk2,wk2,-1);
n = 0;
for (k = nzlo_i; k <= nzhi_i; k++)
@@ -4767,7 +4767,7 @@ void PPPMDisp:: poisson_peratom(FFT_SCALAR* wk1, FFT_SCALAR* wk2, LAMMPS_NS::FFT
}
//v2 & v3 term
-
+
n = 0;
for (i = 0; i < nft; i++) {
wk2[n] = wk1[n]*vcoeff[i][2] - wk1[n+1]*vcoeff2[i][0];
@@ -4775,7 +4775,7 @@ void PPPMDisp:: poisson_peratom(FFT_SCALAR* wk1, FFT_SCALAR* wk2, LAMMPS_NS::FFT
n += 2;
}
- ft2->compute(wk2,wk2,-1);
+ ft2->compute(wk2,wk2,-1);
n = 0;
for (k = nzlo_i; k <= nzhi_i; k++)
@@ -4786,7 +4786,7 @@ void PPPMDisp:: poisson_peratom(FFT_SCALAR* wk1, FFT_SCALAR* wk2, LAMMPS_NS::FFT
}
//v4 & v5 term
-
+
n = 0;
for (i = 0; i < nft; i++) {
wk2[n] = wk1[n]*vcoeff2[i][1] - wk1[n+1]*vcoeff2[i][2];
@@ -4794,7 +4794,7 @@ void PPPMDisp:: poisson_peratom(FFT_SCALAR* wk1, FFT_SCALAR* wk2, LAMMPS_NS::FFT
n += 2;
}
- ft2->compute(wk2,wk2,-1);
+ ft2->compute(wk2,wk2,-1);
n = 0;
for (k = nzlo_i; k <= nzhi_i; k++)
@@ -4802,12 +4802,12 @@ void PPPMDisp:: poisson_peratom(FFT_SCALAR* wk1, FFT_SCALAR* wk2, LAMMPS_NS::FFT
for (i = nxlo_i; i <= nxhi_i; i++) {
v4_pa[k][j][i] = wk2[n++];
v5_pa[k][j][i] = wk2[n++];
- }
-
+ }
+
}
/* ----------------------------------------------------------------------
- Poisson solver for one mesh with 2 different dispersion densities
+ Poisson solver for one mesh with 2 different dispersion densities
for ik scheme
------------------------------------------------------------------------- */
@@ -4827,14 +4827,14 @@ void PPPMDisp::poisson_2s_ik(FFT_SCALAR* dfft_1, FFT_SCALAR* dfft_2,
// transform charge/dispersion density (r -> k)
// only one tansform required when energies and pressures do not
- // need to be calculated
+ // need to be calculated
if (eflag_global + vflag_global == 0) {
n = 0;
for (i = 0; i < nfft_6; i++) {
work1_6[n++] = dfft_1[i];
work1_6[n++] = dfft_2[i];
}
-
+
fft1_6->compute(work1_6,work1_6,1);
}
// two transforms are required when energies and pressures are
@@ -4864,7 +4864,7 @@ void PPPMDisp::poisson_2s_ik(FFT_SCALAR* dfft_1, FFT_SCALAR* dfft_2,
} else {
n = 0;
for (i = 0; i < nfft_6; i++) {
- energy_6 +=
+ energy_6 +=
2 * s2 * greensfn_6[i] * (work1_6[n]*work2_6[n+1] - work1_6[n+1]*work2_6[n]);
n += 2;
}
@@ -4897,7 +4897,7 @@ void PPPMDisp::poisson_2s_ik(FFT_SCALAR* dfft_1, FFT_SCALAR* dfft_2,
}
fft2_6->compute(work2_6,work2_6,-1);
-
+
n = 0;
for (k = nzlo_in_6; k <= nzhi_in_6; k++)
for (j = nylo_in_6; j <= nyhi_in_6; j++)
@@ -4949,7 +4949,7 @@ void PPPMDisp::poisson_2s_ik(FFT_SCALAR* dfft_1, FFT_SCALAR* dfft_2,
}
//Per-atom energy
-
+
if (eflag_atom) {
n = 0;
for (i = 0; i < nfft_6; i++) {
@@ -4957,9 +4957,9 @@ void PPPMDisp::poisson_2s_ik(FFT_SCALAR* dfft_1, FFT_SCALAR* dfft_2,
work2_6[n+1] = work1_6[n+1];
n += 2;
}
-
- fft2_6->compute(work2_6,work2_6,-1);
-
+
+ fft2_6->compute(work2_6,work2_6,-1);
+
n = 0;
for (k = nzlo_in_6; k <= nzhi_in_6; k++)
for (j = nylo_in_6; j <= nyhi_in_6; j++)
@@ -4967,7 +4967,7 @@ void PPPMDisp::poisson_2s_ik(FFT_SCALAR* dfft_1, FFT_SCALAR* dfft_2,
u_pa_1[k][j][i] = work2_6[n++];
u_pa_2[k][j][i] = work2_6[n++];
}
- }
+ }
if (vflag_atom) poisson_2s_peratom(v0_pa_1, v1_pa_1, v2_pa_1, v3_pa_1, v4_pa_1, v5_pa_1,
v0_pa_2, v1_pa_2, v2_pa_2, v3_pa_2, v4_pa_2, v5_pa_2);
@@ -4975,7 +4975,7 @@ void PPPMDisp::poisson_2s_ik(FFT_SCALAR* dfft_1, FFT_SCALAR* dfft_2,
/* ----------------------------------------------------------------------
- Poisson solver for one mesh with 2 different dispersion densities
+ Poisson solver for one mesh with 2 different dispersion densities
for ik scheme
------------------------------------------------------------------------- */
@@ -4992,14 +4992,14 @@ void PPPMDisp::poisson_none_ik(int n1, int n2,FFT_SCALAR* dfft_1, FFT_SCALAR* df
// transform charge/dispersion density (r -> k)
// only one tansform required when energies and pressures do not
- // need to be calculated
+ // need to be calculated
if (eflag_global + vflag_global == 0) {
n = 0;
for (i = 0; i < nfft_6; i++) {
work1_6[n++] = dfft_1[i];
work1_6[n++] = dfft_2[i];
}
-
+
fft1_6->compute(work1_6,work1_6,1);
}
@@ -5014,7 +5014,7 @@ void PPPMDisp::poisson_none_ik(int n1, int n2,FFT_SCALAR* dfft_1, FFT_SCALAR* df
work1_6[n] = ZEROF;
work2_6[n++] = dfft_2[i];
}
-
+
fft1_6->compute(work1_6,work1_6,1);
fft1_6->compute(work2_6,work2_6,1);
@@ -5032,7 +5032,7 @@ void PPPMDisp::poisson_none_ik(int n1, int n2,FFT_SCALAR* dfft_1, FFT_SCALAR* df
} else {
n = 0;
for (i = 0; i < nfft_6; i++) {
- energy_6 +=
+ energy_6 +=
s2 * greensfn_6[i] * (B[n1]*(work1_6[n]*work1_6[n] + work1_6[n+1]*work1_6[n+1]) + B[n2]*(work2_6[n]*work2_6[n] + work2_6[n+1]*work2_6[n+1]));
n += 2;
}
@@ -5065,7 +5065,7 @@ void PPPMDisp::poisson_none_ik(int n1, int n2,FFT_SCALAR* dfft_1, FFT_SCALAR* df
}
fft2_6->compute(work2_6,work2_6,-1);
-
+
n = 0;
for (k = nzlo_in_6; k <= nzhi_in_6; k++)
for (j = nylo_in_6; j <= nyhi_in_6; j++)
@@ -5117,7 +5117,7 @@ void PPPMDisp::poisson_none_ik(int n1, int n2,FFT_SCALAR* dfft_1, FFT_SCALAR* df
}
//Per-atom energy
-
+
if (eflag_atom) {
n = 0;
for (i = 0; i < nfft_6; i++) {
@@ -5125,9 +5125,9 @@ void PPPMDisp::poisson_none_ik(int n1, int n2,FFT_SCALAR* dfft_1, FFT_SCALAR* df
work2_6[n+1] = work1_6[n+1];
n += 2;
}
-
- fft2_6->compute(work2_6,work2_6,-1);
-
+
+ fft2_6->compute(work2_6,work2_6,-1);
+
n = 0;
for (k = nzlo_in_6; k <= nzhi_in_6; k++)
for (j = nylo_in_6; j <= nyhi_in_6; j++)
@@ -5135,7 +5135,7 @@ void PPPMDisp::poisson_none_ik(int n1, int n2,FFT_SCALAR* dfft_1, FFT_SCALAR* df
u_pa[n1][k][j][i] = B[n1]*work2_6[n++];
u_pa[n2][k][j][i] = B[n2]*work2_6[n++];
}
- }
+ }
if (vflag_atom) poisson_none_peratom(n1,n2,
v0_pa[n1], v1_pa[n1], v2_pa[n1], v3_pa[n1], v4_pa[n1], v5_pa[n1],
@@ -5143,7 +5143,7 @@ void PPPMDisp::poisson_none_ik(int n1, int n2,FFT_SCALAR* dfft_1, FFT_SCALAR* df
}
/* ----------------------------------------------------------------------
- Poisson solver for one mesh with 2 different dispersion densities
+ Poisson solver for one mesh with 2 different dispersion densities
for ad scheme
------------------------------------------------------------------------- */
@@ -5161,14 +5161,14 @@ void PPPMDisp::poisson_2s_ad(FFT_SCALAR* dfft_1, FFT_SCALAR* dfft_2,
// transform charge/dispersion density (r -> k)
// only one tansform required when energies and pressures do not
- // need to be calculated
+ // need to be calculated
if (eflag_global + vflag_global == 0) {
n = 0;
for (i = 0; i < nfft_6; i++) {
work1_6[n++] = dfft_1[i];
work1_6[n++] = dfft_2[i];
}
-
+
fft1_6->compute(work1_6,work1_6,1);
}
// two transforms are required when energies and pressures are
@@ -5198,7 +5198,7 @@ void PPPMDisp::poisson_2s_ad(FFT_SCALAR* dfft_1, FFT_SCALAR* dfft_2,
} else {
n = 0;
for (i = 0; i < nfft_6; i++) {
- energy_6 +=
+ energy_6 +=
2 * s2 * greensfn_6[i] * (work1_6[n]*work2_6[n+1] - work1_6[n+1]*work2_6[n]);
n += 2;
}
@@ -5223,23 +5223,23 @@ void PPPMDisp::poisson_2s_ad(FFT_SCALAR* dfft_1, FFT_SCALAR* dfft_2,
work2_6[n+1] = work1_6[n+1];
n += 2;
}
-
- fft2_6->compute(work2_6,work2_6,-1);
-
+
+ fft2_6->compute(work2_6,work2_6,-1);
+
n = 0;
for (k = nzlo_in_6; k <= nzhi_in_6; k++)
for (j = nylo_in_6; j <= nyhi_in_6; j++)
for (i = nxlo_in_6; i <= nxhi_in_6; i++) {
u_pa_1[k][j][i] = work2_6[n++];
u_pa_2[k][j][i] = work2_6[n++];
- }
+ }
if (vflag_atom) poisson_2s_peratom(v0_pa_1, v1_pa_1, v2_pa_1, v3_pa_1, v4_pa_1, v5_pa_1,
v0_pa_2, v1_pa_2, v2_pa_2, v3_pa_2, v4_pa_2, v5_pa_2);
}
/* ----------------------------------------------------------------------
- Poisson solver for one mesh with 2 different dispersion densities
+ Poisson solver for one mesh with 2 different dispersion densities
for ad scheme
------------------------------------------------------------------------- */
@@ -5255,14 +5255,14 @@ void PPPMDisp::poisson_none_ad(int n1, int n2, FFT_SCALAR* dfft_1, FFT_SCALAR* d
// transform charge/dispersion density (r -> k)
// only one tansform required when energies and pressures do not
- // need to be calculated
+ // need to be calculated
if (eflag_global + vflag_global == 0) {
n = 0;
for (i = 0; i < nfft_6; i++) {
work1_6[n++] = dfft_1[i];
work1_6[n++] = dfft_2[i];
}
-
+
fft1_6->compute(work1_6,work1_6,1);
}
// two transforms are required when energies and pressures are
@@ -5292,7 +5292,7 @@ void PPPMDisp::poisson_none_ad(int n1, int n2, FFT_SCALAR* dfft_1, FFT_SCALAR* d
} else {
n = 0;
for (i = 0; i < nfft_6; i++) {
- energy_6 +=
+ energy_6 +=
s2 * greensfn_6[i] * (B[n1]*(work1_6[n]*work1_6[n] + work1_6[n+1]*work1_6[n+1]) + B[n2]*(work2_6[n]*work2_6[n] + work2_6[n+1]*work2_6[n+1]));
n += 2;
}
@@ -5317,16 +5317,16 @@ void PPPMDisp::poisson_none_ad(int n1, int n2, FFT_SCALAR* dfft_1, FFT_SCALAR* d
work2_6[n+1] = work1_6[n+1];
n += 2;
}
-
- fft2_6->compute(work2_6,work2_6,-1);
-
+
+ fft2_6->compute(work2_6,work2_6,-1);
+
n = 0;
for (k = nzlo_in_6; k <= nzhi_in_6; k++)
for (j = nylo_in_6; j <= nyhi_in_6; j++)
for (i = nxlo_in_6; i <= nxhi_in_6; i++) {
u_pa_1[k][j][i] = B[n1]*work2_6[n++];
u_pa_2[k][j][i] = B[n2]*work2_6[n++];
- }
+ }
if (vflag_atom) poisson_none_peratom(n1,n2,
v0_pa[n1], v1_pa[n1], v2_pa[n1], v3_pa[n1], v4_pa[n1], v5_pa[n1],
@@ -5351,9 +5351,9 @@ void PPPMDisp::poisson_2s_peratom(FFT_SCALAR*** v0_pa_1, FFT_SCALAR*** v1_pa_1,
work2_6[n+1] = work1_6[n+1]*vg_6[i][0];
n += 2;
}
-
- fft2_6->compute(work2_6,work2_6,-1);
-
+
+ fft2_6->compute(work2_6,work2_6,-1);
+
n = 0;
for (k = nzlo_in_6; k <= nzhi_in_6; k++)
for (j = nylo_in_6; j <= nyhi_in_6; j++)
@@ -5361,18 +5361,18 @@ void PPPMDisp::poisson_2s_peratom(FFT_SCALAR*** v0_pa_1, FFT_SCALAR*** v1_pa_1,
v0_pa_1[k][j][i] = work2_6[n++];
v0_pa_2[k][j][i] = work2_6[n++];
}
-
- //Compute second virial term v1
-
+
+ //Compute second virial term v1
+
n = 0;
for (i = 0; i < nfft_6; i++) {
work2_6[n] = work1_6[n]*vg_6[i][1];
work2_6[n+1] = work1_6[n+1]*vg_6[i][1];
n += 2;
}
-
- fft2_6->compute(work2_6,work2_6,-1);
-
+
+ fft2_6->compute(work2_6,work2_6,-1);
+
n = 0;
for (k = nzlo_in_6; k <= nzhi_in_6; k++)
for (j = nylo_in_6; j <= nyhi_in_6; j++)
@@ -5380,18 +5380,18 @@ void PPPMDisp::poisson_2s_peratom(FFT_SCALAR*** v0_pa_1, FFT_SCALAR*** v1_pa_1,
v1_pa_1[k][j][i] = work2_6[n++];
v1_pa_2[k][j][i] = work2_6[n++];
}
-
+
//Compute third virial term v2
-
+
n = 0;
for (i = 0; i < nfft_6; i++) {
work2_6[n] = work1_6[n]*vg_6[i][2];
work2_6[n+1] = work1_6[n+1]*vg_6[i][2];
n += 2;
}
-
- fft2_6->compute(work2_6,work2_6,-1);
-
+
+ fft2_6->compute(work2_6,work2_6,-1);
+
n = 0;
for (k = nzlo_in_6; k <= nzhi_in_6; k++)
for (j = nylo_in_6; j <= nyhi_in_6; j++)
@@ -5401,16 +5401,16 @@ void PPPMDisp::poisson_2s_peratom(FFT_SCALAR*** v0_pa_1, FFT_SCALAR*** v1_pa_1,
}
//Compute fourth virial term v3
-
+
n = 0;
for (i = 0; i < nfft_6; i++) {
work2_6[n] = work1_6[n]*vg2_6[i][0];
work2_6[n+1] = work1_6[n+1]*vg2_6[i][0];
n += 2;
}
-
- fft2_6->compute(work2_6,work2_6,-1);
-
+
+ fft2_6->compute(work2_6,work2_6,-1);
+
n = 0;
for (k = nzlo_in_6; k <= nzhi_in_6; k++)
for (j = nylo_in_6; j <= nyhi_in_6; j++)
@@ -5420,16 +5420,16 @@ void PPPMDisp::poisson_2s_peratom(FFT_SCALAR*** v0_pa_1, FFT_SCALAR*** v1_pa_1,
}
//Compute fifth virial term v4
-
+
n = 0;
for (i = 0; i < nfft_6; i++) {
work2_6[n] = work1_6[n]*vg2_6[i][1];
work2_6[n+1] = work1_6[n+1]*vg2_6[i][1];
n += 2;
}
-
- fft2_6->compute(work2_6,work2_6,-1);
-
+
+ fft2_6->compute(work2_6,work2_6,-1);
+
n = 0;
for (k = nzlo_in_6; k <= nzhi_in_6; k++)
for (j = nylo_in_6; j <= nyhi_in_6; j++)
@@ -5437,18 +5437,18 @@ void PPPMDisp::poisson_2s_peratom(FFT_SCALAR*** v0_pa_1, FFT_SCALAR*** v1_pa_1,
v4_pa_1[k][j][i] = work2_6[n++];
v4_pa_2[k][j][i] = work2_6[n++];
}
-
+
//Compute last virial term v5
-
+
n = 0;
for (i = 0; i < nfft_6; i++) {
work2_6[n] = work1_6[n]*vg2_6[i][2];
work2_6[n+1] = work1_6[n+1]*vg2_6[i][2];
n += 2;
}
-
- fft2_6->compute(work2_6,work2_6,-1);
-
+
+ fft2_6->compute(work2_6,work2_6,-1);
+
n = 0;
for (k = nzlo_in_6; k <= nzhi_in_6; k++)
for (j = nylo_in_6; j <= nyhi_in_6; j++)
@@ -5462,7 +5462,7 @@ void PPPMDisp::poisson_2s_peratom(FFT_SCALAR*** v0_pa_1, FFT_SCALAR*** v1_pa_1,
Fourier Transform for per atom virial calculations
------------------------------------------------------------------------- */
-void PPPMDisp::poisson_none_peratom(int n1, int n2,
+void PPPMDisp::poisson_none_peratom(int n1, int n2,
FFT_SCALAR*** v0_pa_1, FFT_SCALAR*** v1_pa_1, FFT_SCALAR*** v2_pa_1,
FFT_SCALAR*** v3_pa_1, FFT_SCALAR*** v4_pa_1, FFT_SCALAR*** v5_pa_1,
FFT_SCALAR*** v0_pa_2, FFT_SCALAR*** v1_pa_2, FFT_SCALAR*** v2_pa_2,
@@ -5477,9 +5477,9 @@ void PPPMDisp::poisson_none_peratom(int n1, int n2,
work2_6[n+1] = work1_6[n+1]*vg_6[i][0];
n += 2;
}
-
- fft2_6->compute(work2_6,work2_6,-1);
-
+
+ fft2_6->compute(work2_6,work2_6,-1);
+
n = 0;
for (k = nzlo_in_6; k <= nzhi_in_6; k++)
for (j = nylo_in_6; j <= nyhi_in_6; j++)
@@ -5487,18 +5487,18 @@ void PPPMDisp::poisson_none_peratom(int n1, int n2,
v0_pa_1[k][j][i] = B[n1]*work2_6[n++];
v0_pa_2[k][j][i] = B[n2]*work2_6[n++];
}
-
- //Compute second virial term v1
-
+
+ //Compute second virial term v1
+
n = 0;
for (i = 0; i < nfft_6; i++) {
work2_6[n] = work1_6[n]*vg_6[i][1];
work2_6[n+1] = work1_6[n+1]*vg_6[i][1];
n += 2;
}
-
- fft2_6->compute(work2_6,work2_6,-1);
-
+
+ fft2_6->compute(work2_6,work2_6,-1);
+
n = 0;
for (k = nzlo_in_6; k <= nzhi_in_6; k++)
for (j = nylo_in_6; j <= nyhi_in_6; j++)
@@ -5506,18 +5506,18 @@ void PPPMDisp::poisson_none_peratom(int n1, int n2,
v1_pa_1[k][j][i] = B[n1]*work2_6[n++];
v1_pa_2[k][j][i] = B[n2]*work2_6[n++];
}
-
+
//Compute third virial term v2
-
+
n = 0;
for (i = 0; i < nfft_6; i++) {
work2_6[n] = work1_6[n]*vg_6[i][2];
work2_6[n+1] = work1_6[n+1]*vg_6[i][2];
n += 2;
}
-
- fft2_6->compute(work2_6,work2_6,-1);
-
+
+ fft2_6->compute(work2_6,work2_6,-1);
+
n = 0;
for (k = nzlo_in_6; k <= nzhi_in_6; k++)
for (j = nylo_in_6; j <= nyhi_in_6; j++)
@@ -5527,16 +5527,16 @@ void PPPMDisp::poisson_none_peratom(int n1, int n2,
}
//Compute fourth virial term v3
-
+
n = 0;
for (i = 0; i < nfft_6; i++) {
work2_6[n] = work1_6[n]*vg2_6[i][0];
work2_6[n+1] = work1_6[n+1]*vg2_6[i][0];
n += 2;
}
-
- fft2_6->compute(work2_6,work2_6,-1);
-
+
+ fft2_6->compute(work2_6,work2_6,-1);
+
n = 0;
for (k = nzlo_in_6; k <= nzhi_in_6; k++)
for (j = nylo_in_6; j <= nyhi_in_6; j++)
@@ -5546,16 +5546,16 @@ void PPPMDisp::poisson_none_peratom(int n1, int n2,
}
//Compute fifth virial term v4
-
+
n = 0;
for (i = 0; i < nfft_6; i++) {
work2_6[n] = work1_6[n]*vg2_6[i][1];
work2_6[n+1] = work1_6[n+1]*vg2_6[i][1];
n += 2;
}
-
- fft2_6->compute(work2_6,work2_6,-1);
-
+
+ fft2_6->compute(work2_6,work2_6,-1);
+
n = 0;
for (k = nzlo_in_6; k <= nzhi_in_6; k++)
for (j = nylo_in_6; j <= nyhi_in_6; j++)
@@ -5563,18 +5563,18 @@ void PPPMDisp::poisson_none_peratom(int n1, int n2,
v4_pa_1[k][j][i] = B[n1]*work2_6[n++];
v4_pa_2[k][j][i] = B[n2]*work2_6[n++];
}
-
+
//Compute last virial term v5
-
+
n = 0;
for (i = 0; i < nfft_6; i++) {
work2_6[n] = work1_6[n]*vg2_6[i][2];
work2_6[n+1] = work1_6[n+1]*vg2_6[i][2];
n += 2;
}
-
- fft2_6->compute(work2_6,work2_6,-1);
-
+
+ fft2_6->compute(work2_6,work2_6,-1);
+
n = 0;
for (k = nzlo_in_6; k <= nzhi_in_6; k++)
for (j = nylo_in_6; j <= nyhi_in_6; j++)
@@ -5583,9 +5583,9 @@ void PPPMDisp::poisson_none_peratom(int n1, int n2,
v5_pa_2[k][j][i] = B[n2]*work2_6[n++];
}
}
-
+
/* ----------------------------------------------------------------------
- interpolate from grid to get electric field & force on my particles
+ interpolate from grid to get electric field & force on my particles
for ik scheme
------------------------------------------------------------------------- */
@@ -5644,7 +5644,7 @@ void PPPMDisp::fieldforce_c_ik()
}
/* ----------------------------------------------------------------------
interpolate from grid to get electric field & force on my particles
- for ad scheme
+ for ad scheme
------------------------------------------------------------------------- */
void PPPMDisp::fieldforce_c_ad()
@@ -5733,7 +5733,7 @@ void PPPMDisp::fieldforce_c_ad()
}
/* ----------------------------------------------------------------------
- interpolate from grid to get electric field & force on my particles
+ interpolate from grid to get electric field & force on my particles
------------------------------------------------------------------------- */
void PPPMDisp::fieldforce_c_peratom()
@@ -5773,7 +5773,7 @@ void PPPMDisp::fieldforce_c_peratom()
for (l = nlower; l <= nupper; l++) {
mx = l+nx;
x0 = y0*rho1d[0][l];
- if (eflag_atom) u_pa += x0*u_brick[mz][my][mx];
+ if (eflag_atom) u_pa += x0*u_brick[mz][my][mx];
if (vflag_atom) {
v0 += x0*v0_brick[mz][my][mx];
v1 += x0*v1_brick[mz][my][mx];
@@ -5804,7 +5804,7 @@ void PPPMDisp::fieldforce_c_peratom()
/* ----------------------------------------------------------------------
interpolate from grid to get dispersion field & force on my particles
- for geometric mixing rule
+ for geometric mixing rule
------------------------------------------------------------------------- */
void PPPMDisp::fieldforce_g_ik()
@@ -5901,7 +5901,7 @@ void PPPMDisp::fieldforce_g_ad()
int nlocal = atom->nlocal;
-
+
for (i = 0; i < nlocal; i++) {
nx = part2grid_6[i][0];
ny = part2grid_6[i][1];
@@ -6001,7 +6001,7 @@ void PPPMDisp::fieldforce_g_peratom()
for (l = nlower_6; l <= nupper_6; l++) {
mx = l+nx;
x0 = y0*rho1d_6[0][l];
- if (eflag_atom) u_pa += x0*u_brick_g[mz][my][mx];
+ if (eflag_atom) u_pa += x0*u_brick_g[mz][my][mx];
if (vflag_atom) {
v0 += x0*v0_brick_g[mz][my][mx];
v1 += x0*v1_brick_g[mz][my][mx];
@@ -6402,22 +6402,22 @@ void PPPMDisp::fieldforce_a_peratom()
lj5 = B[7*type+1]*0.5;
lj6 = B[7*type]*0.5;
-
- if (eflag_atom)
- eatom[i] += u_pa0*lj0 + u_pa1*lj1 + u_pa2*lj2 +
+
+ if (eflag_atom)
+ eatom[i] += u_pa0*lj0 + u_pa1*lj1 + u_pa2*lj2 +
u_pa3*lj3 + u_pa4*lj4 + u_pa5*lj5 + u_pa6*lj6;
if (vflag_atom) {
- vatom[i][0] += v00*lj0 + v01*lj1 + v02*lj2 + v03*lj3 +
+ vatom[i][0] += v00*lj0 + v01*lj1 + v02*lj2 + v03*lj3 +
v04*lj4 + v05*lj5 + v06*lj6;
- vatom[i][1] += v10*lj0 + v11*lj1 + v12*lj2 + v13*lj3 +
+ vatom[i][1] += v10*lj0 + v11*lj1 + v12*lj2 + v13*lj3 +
v14*lj4 + v15*lj5 + v16*lj6;
- vatom[i][2] += v20*lj0 + v21*lj1 + v22*lj2 + v23*lj3 +
+ vatom[i][2] += v20*lj0 + v21*lj1 + v22*lj2 + v23*lj3 +
v24*lj4 + v25*lj5 + v26*lj6;
- vatom[i][3] += v30*lj0 + v31*lj1 + v32*lj2 + v33*lj3 +
+ vatom[i][3] += v30*lj0 + v31*lj1 + v32*lj2 + v33*lj3 +
v34*lj4 + v35*lj5 + v36*lj6;
- vatom[i][4] += v40*lj0 + v41*lj1 + v42*lj2 + v43*lj3 +
+ vatom[i][4] += v40*lj0 + v41*lj1 + v42*lj2 + v43*lj3 +
v44*lj4 + v45*lj5 + v46*lj6;
- vatom[i][5] += v50*lj0 + v51*lj1 + v52*lj2 + v53*lj3 +
+ vatom[i][5] += v50*lj0 + v51*lj1 + v52*lj2 + v53*lj3 +
v54*lj4 + v55*lj5 + v56*lj6;
}
}
@@ -6563,7 +6563,7 @@ void PPPMDisp::fieldforce_none_ad()
x0 = drho1d_6[0][l]*rho1d_6[1][m]*rho1d_6[2][n];
y0 = rho1d_6[0][l]*drho1d_6[1][m]*rho1d_6[2][n];
z0 = rho1d_6[0][l]*rho1d_6[1][m]*drho1d_6[2][n];
-
+
for (k = 0; k < nsplit; k++) {
ekx[k] += x0*u_brick_none[k][mz][my][mx];
eky[k] += y0*u_brick_none[k][mz][my][mx];
@@ -6625,7 +6625,7 @@ void PPPMDisp::fieldforce_none_peratom()
int i,k,l,m,n,nx,ny,nz,mx,my,mz;
FFT_SCALAR dx,dy,dz,x0,y0,z0;
FFT_SCALAR *u_pa,*v0,*v1,*v2,*v3,*v4,*v5;
-
+
u_pa = new FFT_SCALAR[nsplit];
v0 = new FFT_SCALAR[nsplit];
v1 = new FFT_SCALAR[nsplit];
@@ -6656,9 +6656,9 @@ void PPPMDisp::fieldforce_none_peratom()
dz = nz+shiftone_6 - (x[i][2]-boxlo[2])*delzinv_6;
compute_rho1d(dx,dy,dz, order_6, rho_coeff_6, rho1d_6);
- for (k = 0; k < nsplit; k++)
+ for (k = 0; k < nsplit; k++)
u_pa[k] = v0[k] = v1[k] = v2[k] = v3[k] = v4[k] = v5[k] = ZEROF;
-
+
for (n = nlower_6; n <= nupper_6; n++) {
mz = n+nz;
z0 = rho1d_6[2][n];
@@ -6689,7 +6689,7 @@ void PPPMDisp::fieldforce_none_peratom()
type = atom->type[i];
for (k = 0; k < nsplit; k++) {
lj = B[nsplit*type + k]*0.5;
-
+
if (eflag_atom) {
eatom[i] += u_pa[k]*lj;
}
@@ -7845,7 +7845,7 @@ void PPPMDisp::unpack_reverse(int flag, FFT_SCALAR *buf, int nlist, int *list)
}
/* ----------------------------------------------------------------------
- map nprocs to NX by NY grid as PX by PY procs - return optimal px,py
+ map nprocs to NX by NY grid as PX by PY procs - return optimal px,py
------------------------------------------------------------------------- */
void PPPMDisp::procs2grid2d(int nprocs, int nx, int ny, int *px, int *py)
@@ -7869,7 +7869,7 @@ void PPPMDisp::procs2grid2d(int nprocs, int nx, int ny, int *px, int *py)
boxy = ny/ipy;
if (ny % ipy) boxy++;
surf = boxx + boxy;
- if (surf < bestsurf ||
+ if (surf < bestsurf ||
(surf == bestsurf && boxx*boxy > bestboxx*bestboxy)) {
bestsurf = surf;
bestboxx = boxx;
@@ -7884,11 +7884,11 @@ void PPPMDisp::procs2grid2d(int nprocs, int nx, int ny, int *px, int *py)
/* ----------------------------------------------------------------------
charge assignment into rho1d
- dx,dy,dz = distance of particle from "lower left" grid point
+ dx,dy,dz = distance of particle from "lower left" grid point
------------------------------------------------------------------------- */
void PPPMDisp::compute_rho1d(const FFT_SCALAR &dx, const FFT_SCALAR &dy,
- const FFT_SCALAR &dz, int ord,
+ const FFT_SCALAR &dz, int ord,
FFT_SCALAR **rho_c, FFT_SCALAR **r1d)
{
int k,l;
@@ -7914,7 +7914,7 @@ void PPPMDisp::compute_rho1d(const FFT_SCALAR &dx, const FFT_SCALAR &dy,
------------------------------------------------------------------------- */
void PPPMDisp::compute_drho1d(const FFT_SCALAR &dx, const FFT_SCALAR &dy,
- const FFT_SCALAR &dz, int ord,
+ const FFT_SCALAR &dz, int ord,
FFT_SCALAR **drho_c, FFT_SCALAR **dr1d)
{
int k,l;
@@ -7950,10 +7950,10 @@ void PPPMDisp::compute_drho1d(const FFT_SCALAR &dx, const FFT_SCALAR &dy,
| 0 otherwise
---
a coeffients are packed into the array rho_coeff to eliminate zeros
- rho_coeff(l,((k+mod(n+1,2))/2) = a(l,k)
+ rho_coeff(l,((k+mod(n+1,2))/2) = a(l,k)
------------------------------------------------------------------------- */
-void PPPMDisp::compute_rho_coeff(FFT_SCALAR **coeff , FFT_SCALAR **dcoeff,
+void PPPMDisp::compute_rho_coeff(FFT_SCALAR **coeff , FFT_SCALAR **dcoeff,
int ord)
{
int j,k,l,m;
@@ -7962,10 +7962,10 @@ void PPPMDisp::compute_rho_coeff(FFT_SCALAR **coeff , FFT_SCALAR **dcoeff,
FFT_SCALAR **a;
memory->create2d_offset(a,ord,-ord,ord,"pppm/disp:a");
- for (k = -ord; k <= ord; k++)
+ for (k = -ord; k <= ord; k++)
for (l = 0; l < ord; l++)
a[l][k] = 0.0;
-
+
a[0][0] = 1.0;
for (j = 1; j < ord; j++) {
for (k = -j; k <= j; k += 2) {
@@ -7976,7 +7976,7 @@ void PPPMDisp::compute_rho_coeff(FFT_SCALAR **coeff , FFT_SCALAR **dcoeff,
s += powf(0.5,(float) l+1) *
(a[l][k-1] + powf(-1.0,(float) l) * a[l][k+1]) / (l+1);
#else
- s += pow(0.5,(double) l+1) *
+ s += pow(0.5,(double) l+1) *
(a[l][k-1] + pow(-1.0,(double) l) * a[l][k+1]) / (l+1);
#endif
}
@@ -8128,7 +8128,7 @@ int PPPMDisp::timing_3d(int n, double &time3d)
if (function[3]) mixing = nsplit_alloc/2;
if (function[0]) for (int i = 0; i < 2*nfft_both; i++) work1[i] = ZEROF;
- if (function[1] + function[2] + function[3])
+ if (function[1] + function[2] + function[3])
for (int i = 0; i < 2*nfft_both_6; i++) work1_6[i] = ZEROF;
@@ -8153,7 +8153,7 @@ int PPPMDisp::timing_3d(int n, double &time3d)
MPI_Barrier(world);
time1 = MPI_Wtime();
-
+
if (function[1] + function[2] + function[3]) {
for (int i = 0; i < n; i++) {
fft1_6->compute(work1_6,work1_6,1);
@@ -8174,7 +8174,7 @@ int PPPMDisp::timing_3d(int n, double &time3d)
}
/* ----------------------------------------------------------------------
- memory usage of local arrays
+ memory usage of local arrays
------------------------------------------------------------------------- */
double PPPMDisp::memory_usage()
@@ -8192,22 +8192,22 @@ double PPPMDisp::memory_usage()
if (function[3]) mixing = nsplit_alloc;
if (function[0]) {
- int nbrick = (nxhi_out-nxlo_out+1) * (nyhi_out-nylo_out+1) *
+ int nbrick = (nxhi_out-nxlo_out+1) * (nyhi_out-nylo_out+1) *
(nzhi_out-nzlo_out+1);
bytes += (1 + diff + per) * nbrick * sizeof(FFT_SCALAR); //brick memory
bytes += 6 * nfft_both * sizeof(double); // vg
bytes += nfft_both * sizeof(double); // greensfn
- bytes += nfft_both * 3 * sizeof(FFT_SCALAR); // density_FFT, work1, work2
+ bytes += nfft_both * 3 * sizeof(FFT_SCALAR); // density_FFT, work1, work2
bytes += cg->memory_usage();
}
if (function[1] + function[2] + function[3]) {
- int nbrick = (nxhi_out_6-nxlo_out_6+1) * (nyhi_out_6-nylo_out_6+1) *
+ int nbrick = (nxhi_out_6-nxlo_out_6+1) * (nyhi_out_6-nylo_out_6+1) *
(nzhi_out_6-nzlo_out_6+1);
bytes += (1 + diff + per ) * nbrick * sizeof(FFT_SCALAR) * mixing; // density_brick + vd_brick + per atom bricks
bytes += 6 * nfft_both_6 * sizeof(double); // vg
bytes += nfft_both_6 * sizeof(double); // greensfn
- bytes += nfft_both_6 * (mixing + 2) * sizeof(FFT_SCALAR); // density_FFT, work1, work2
+ bytes += nfft_both_6 * (mixing + 2) * sizeof(FFT_SCALAR); // density_FFT, work1, work2
bytes += cg_6->memory_usage();
}
return bytes;
diff --git a/src/KSPACE/pppm_disp.h b/src/KSPACE/pppm_disp.h
index 90da7eb392..ae07ea9e07 100755
--- a/src/KSPACE/pppm_disp.h
+++ b/src/KSPACE/pppm_disp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -21,7 +21,7 @@ KSpaceStyle(pppm/disp,PPPMDisp)
#define LMP_PPPM_DISP_H
#include "lmptype.h"
-#include "mpi.h"
+#include <mpi.h>
#ifdef FFT_SINGLE
typedef float FFT_SCALAR;
@@ -79,7 +79,7 @@ Variables needed for calculating the 1/r and 1/r^6 potential
double delxinv,delyinv,delzinv,delvolinv;
double delxinv_6,delyinv_6,delzinv_6,delvolinv_6;
-
+
double shift,shiftone;
int nxlo_in,nylo_in,nzlo_in,nxhi_in,nyhi_in,nzhi_in;
int nxlo_out,nylo_out,nzlo_out,nxhi_out,nyhi_out,nzhi_out;
@@ -171,9 +171,9 @@ Variables needed for calculating the 1/r and 1/r^6 potential
double *gf_b;
double *gf_b_6;
- double *sf_precoeff1, *sf_precoeff2, *sf_precoeff3, *sf_precoeff4,
+ double *sf_precoeff1, *sf_precoeff2, *sf_precoeff3, *sf_precoeff4,
*sf_precoeff5, *sf_precoeff6;
- double *sf_precoeff1_6, *sf_precoeff2_6, *sf_precoeff3_6,
+ double *sf_precoeff1_6, *sf_precoeff2_6, *sf_precoeff3_6,
*sf_precoeff4_6, *sf_precoeff5_6, *sf_precoeff6_6;
FFT_SCALAR **rho1d,**rho_coeff;
FFT_SCALAR **drho1d, **drho_coeff;
@@ -248,9 +248,9 @@ Variables needed for calculating the 1/r and 1/r^6 potential
double diffpr(double, double, double, double, double **);
void compute_gf_denom(double*, int);
double gf_denom(double, double, double, double*, int);
-
- void compute_sf_precoeff(int, int, int, int,
+
+ void compute_sf_precoeff(int, int, int, int,
int, int, int,
int, int, int,
double*, double*, double*,
@@ -281,7 +281,7 @@ Variables needed for calculating the 1/r and 1/r^6 potential
virtual void brick2fft_none();
virtual void poisson_ik(FFT_SCALAR *, FFT_SCALAR *,
- FFT_SCALAR *, LAMMPS_NS::FFT3d *,LAMMPS_NS::FFT3d *,
+ FFT_SCALAR *, LAMMPS_NS::FFT3d *,LAMMPS_NS::FFT3d *,
int, int, int, int, int, int, int,
int, int, int, int, int, int,
int, int, int, double&, double *,
@@ -292,7 +292,7 @@ Variables needed for calculating the 1/r and 1/r^6 potential
FFT_SCALAR ***, FFT_SCALAR ***, FFT_SCALAR ***);
virtual void poisson_ad(FFT_SCALAR*, FFT_SCALAR*,
- FFT_SCALAR*, LAMMPS_NS::FFT3d*,LAMMPS_NS::FFT3d*,
+ FFT_SCALAR*, LAMMPS_NS::FFT3d*,LAMMPS_NS::FFT3d*,
int, int, int, int,
int, int, int, int, int, int,
int, int, int, int, int, int,
@@ -301,7 +301,7 @@ Variables needed for calculating the 1/r and 1/r^6 potential
FFT_SCALAR***, FFT_SCALAR***, FFT_SCALAR***, FFT_SCALAR***,
FFT_SCALAR***, FFT_SCALAR***, FFT_SCALAR***);
- virtual void poisson_peratom(FFT_SCALAR*, FFT_SCALAR*, LAMMPS_NS::FFT3d*,
+ virtual void poisson_peratom(FFT_SCALAR*, FFT_SCALAR*, LAMMPS_NS::FFT3d*,
double**, double**, int,
int, int, int, int, int, int,
FFT_SCALAR***, FFT_SCALAR***, FFT_SCALAR***,
@@ -325,7 +325,7 @@ Variables needed for calculating the 1/r and 1/r^6 potential
FFT_SCALAR***, FFT_SCALAR***, FFT_SCALAR***);
virtual void poisson_none_ad(int, int, FFT_SCALAR *, FFT_SCALAR *,
- FFT_SCALAR ***, FFT_SCALAR ***,
+ FFT_SCALAR ***, FFT_SCALAR ***,
FFT_SCALAR ****, FFT_SCALAR ****, FFT_SCALAR ****,
FFT_SCALAR ****, FFT_SCALAR ****, FFT_SCALAR ****);
virtual void poisson_none_ik(int, int, FFT_SCALAR *, FFT_SCALAR *,
@@ -352,9 +352,9 @@ Variables needed for calculating the 1/r and 1/r^6 potential
virtual void fieldforce_none_ad();
virtual void fieldforce_none_peratom();
void procs2grid2d(int,int,int,int *, int*);
- void compute_rho1d(const FFT_SCALAR &, const FFT_SCALAR &,
+ void compute_rho1d(const FFT_SCALAR &, const FFT_SCALAR &,
const FFT_SCALAR &, int, FFT_SCALAR **, FFT_SCALAR **);
- void compute_drho1d(const FFT_SCALAR &, const FFT_SCALAR &,
+ void compute_drho1d(const FFT_SCALAR &, const FFT_SCALAR &,
const FFT_SCALAR &, int, FFT_SCALAR **, FFT_SCALAR **);
void compute_rho_coeff(FFT_SCALAR **,FFT_SCALAR **, int);
void slabcorr(int);
diff --git a/src/KSPACE/pppm_disp_tip4p.cpp b/src/KSPACE/pppm_disp_tip4p.cpp
index c021e3dcc0..a44e524e9c 100755
--- a/src/KSPACE/pppm_disp_tip4p.cpp
+++ b/src/KSPACE/pppm_disp_tip4p.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -16,7 +16,7 @@
Rolf Isele-Holder (Aachen University)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pppm_disp_tip4p.h"
#include "pppm_disp.h"
#include "atom.h"
@@ -63,7 +63,7 @@ void PPPMDispTIP4P::init()
/* ----------------------------------------------------------------------
find center grid pt for each of my particles
check that full stencil for the particle will fit in my 3d brick
- store central grid pt indices in part2grid array
+ store central grid pt indices in part2grid array
------------------------------------------------------------------------- */
void PPPMDispTIP4P::particle_map_c(double delx, double dely, double delz,
@@ -84,7 +84,7 @@ void PPPMDispTIP4P::particle_map_c(double delx, double dely, double delz,
int flag = 0;
for (int i = 0; i < nlocal; i++) {
if (type[i] == typeO) {
- find_M(i,iH1,iH2,xM);
+ find_M(i,iH1,iH2,xM);
xi = xM;
} else xi = x[i];
@@ -107,7 +107,7 @@ void PPPMDispTIP4P::particle_map_c(double delx, double dely, double delz,
nz+nlow < nzlo || nz+nup > nzhi)
flag = 1;
}
-
+
if (flag) error->one(FLERR,"Out of range atoms - cannot compute PPPM");
}
@@ -115,7 +115,7 @@ void PPPMDispTIP4P::particle_map_c(double delx, double dely, double delz,
create discretized "density" on section of global grid due to my particles
density(x,y,z) = charge "density" at grid points of my 3d brick
(nxlo:nxhi,nylo:nyhi,nzlo:nzhi) is extent of my brick (including ghosts)
- in global grid
+ in global grid
------------------------------------------------------------------------- */
void PPPMDispTIP4P::make_rho_c()
@@ -134,14 +134,14 @@ void PPPMDispTIP4P::make_rho_c()
// (dx,dy,dz) = distance to "lower left" grid pt
// (mx,my,mz) = global coords of moving stencil pt
- int *type = atom->type;
+ int *type = atom->type;
double *q = atom->q;
double **x = atom->x;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (type[i] == typeO) {
- find_M(i,iH1,iH2,xM);
+ find_M(i,iH1,iH2,xM);
xi = xM;
} else xi = x[i];
@@ -171,7 +171,7 @@ void PPPMDispTIP4P::make_rho_c()
}
/* ----------------------------------------------------------------------
- interpolate from grid to get electric field & force on my particles
+ interpolate from grid to get electric field & force on my particles
for ik differentiation
------------------------------------------------------------------------- */
@@ -199,7 +199,7 @@ void PPPMDispTIP4P::fieldforce_c_ik()
for (i = 0; i < nlocal; i++) {
if (type[i] == typeO) {
- find_M(i,iH1,iH2,xM);
+ find_M(i,iH1,iH2,xM);
xi = xM;
} else xi = x[i];
@@ -260,7 +260,7 @@ void PPPMDispTIP4P::fieldforce_c_ik()
/* ----------------------------------------------------------------------
interpolate from grid to get electric field & force on my particles
- for ad scheme
+ for ad scheme
------------------------------------------------------------------------- */
void PPPMDispTIP4P::fieldforce_c_ad()
@@ -287,7 +287,7 @@ void PPPMDispTIP4P::fieldforce_c_ad()
double hx_inv = nx_pppm/xprd;
double hy_inv = ny_pppm/yprd;
double hz_inv = nz_pppm/zprd_slab;
-
+
// loop over my charges, interpolate electric field from nearby grid points
@@ -305,7 +305,7 @@ void PPPMDispTIP4P::fieldforce_c_ad()
for (i = 0; i < nlocal; i++) {
if (type[i] == typeO) {
- find_M(i,iH1,iH2,xM);
+ find_M(i,iH1,iH2,xM);
xi = xM;
} else xi = x[i];
@@ -315,7 +315,7 @@ void PPPMDispTIP4P::fieldforce_c_ad()
dx = nx+shiftone - (xi[0]-boxlo[0])*delxinv;
dy = ny+shiftone - (xi[1]-boxlo[1])*delyinv;
dz = nz+shiftone - (xi[2]-boxlo[2])*delzinv;
-
+
compute_rho1d(dx,dy,dz, order, rho_coeff, rho1d);
compute_drho1d(dx,dy,dz, order, drho_coeff, drho1d);
@@ -336,7 +336,7 @@ void PPPMDispTIP4P::fieldforce_c_ad()
ekx *= hx_inv;
eky *= hy_inv;
ekz *= hz_inv;
-
+
// convert E-field to force and substract self forces
const double qfactor = force->qqrd2e * scale;
@@ -383,7 +383,7 @@ void PPPMDispTIP4P::fieldforce_c_ad()
/* ----------------------------------------------------------------------
- interpolate from grid to get electric field & force on my particles
+ interpolate from grid to get electric field & force on my particles
------------------------------------------------------------------------- */
void PPPMDispTIP4P::fieldforce_c_peratom()
@@ -408,7 +408,7 @@ void PPPMDispTIP4P::fieldforce_c_peratom()
for (i = 0; i < nlocal; i++) {
if (type[i] == typeO) {
- find_M(i,iH1,iH2,xM);
+ find_M(i,iH1,iH2,xM);
xi = xM;
} else xi = x[i];
@@ -431,7 +431,7 @@ void PPPMDispTIP4P::fieldforce_c_peratom()
for (l = nlower; l <= nupper; l++) {
mx = l+nx;
x0 = y0*rho1d[0][l];
- if (eflag_atom) u_pa += x0*u_brick[mz][my][mx];
+ if (eflag_atom) u_pa += x0*u_brick[mz][my][mx];
if (vflag_atom) {
v0 += x0*v0_brick[mz][my][mx];
v1 += x0*v1_brick[mz][my][mx];
@@ -502,7 +502,7 @@ void PPPMDispTIP4P::find_M(int i, int &iH1, int &iH2, double *xM)
if (atom->type[iH1] != typeH || atom->type[iH2] != typeH)
error->one(FLERR,"TIP4P hydrogen has incorrect atom type");
- double **x = atom->x;
+ double **x = atom->x;
double delx1 = x[iH1][0] - x[i][0];
double dely1 = x[iH1][1] - x[i][1];
diff --git a/src/KSPACE/pppm_disp_tip4p.h b/src/KSPACE/pppm_disp_tip4p.h
index 9a5e56660d..7b3c24db8b 100755
--- a/src/KSPACE/pppm_disp_tip4p.h
+++ b/src/KSPACE/pppm_disp_tip4p.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -40,7 +40,7 @@ class PPPMDispTIP4P : public PPPMDisp {
virtual void fieldforce_c_peratom();
private:
- void find_M(int, int &, int &, double *);
+ void find_M(int, int &, int &, double *);
};
}
diff --git a/src/KSPACE/pppm_stagger.cpp b/src/KSPACE/pppm_stagger.cpp
index 1a117c3bca..8cb71f3e6f 100755
--- a/src/KSPACE/pppm_stagger.cpp
+++ b/src/KSPACE/pppm_stagger.cpp
@@ -15,11 +15,11 @@
Contributing author: Stan Moore (Sandia)
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "string.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "math.h"
+#include <mpi.h>
+#include <string.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
#include "pppm_stagger.h"
#include "atom.h"
#include "gridcomm.h"
@@ -51,7 +51,7 @@ enum{FORWARD_IK,FORWARD_AD,FORWARD_IK_PERATOM,FORWARD_AD_PERATOM};
/* ---------------------------------------------------------------------- */
-PPPMStagger::PPPMStagger(LAMMPS *lmp, int narg, char **arg) :
+PPPMStagger::PPPMStagger(LAMMPS *lmp, int narg, char **arg) :
PPPM(lmp, narg, arg)
{
if (narg < 1) error->all(FLERR,"Illegal kspace_style pppm/stagger command");
@@ -160,7 +160,7 @@ void PPPMStagger::compute(int eflag, int vflag)
particle_map();
make_rho();
-
+
// all procs communicate density values from their ghost cells
// to fully sum contribution in their 3d bricks
// remap from 3d decomposition to FFT decomposition
@@ -177,14 +177,14 @@ void PPPMStagger::compute(int eflag, int vflag)
// all procs communicate E-field values
// to fill ghost cells surrounding their 3d bricks
-
+
if (differentiation_flag == 1) cg->forward_comm(this,FORWARD_AD);
else cg->forward_comm(this,FORWARD_IK);
// extra per-atom energy/virial communication
if (evflag_atom) {
- if (differentiation_flag == 1 && vflag_atom)
+ if (differentiation_flag == 1 && vflag_atom)
cg_peratom->forward_comm(this,FORWARD_AD_PERATOM);
else if (differentiation_flag == 0)
cg_peratom->forward_comm(this,FORWARD_IK_PERATOM);
@@ -228,7 +228,7 @@ void PPPMStagger::compute(int eflag, int vflag)
if (vflag_global) {
double virial_all[6];
MPI_Allreduce(virial,virial_all,6,MPI_DOUBLE,MPI_SUM,world);
- for (i = 0; i < 6; i++)
+ for (i = 0; i < 6; i++)
virial[i] = 0.5*qscale*volume*virial_all[i]/float(nstagger);
}
diff --git a/src/KSPACE/pppm_stagger.h b/src/KSPACE/pppm_stagger.h
index ca981072d7..c096d3b0ac 100755
--- a/src/KSPACE/pppm_stagger.h
+++ b/src/KSPACE/pppm_stagger.h
@@ -43,7 +43,7 @@ class PPPMStagger : public PPPM {
virtual void compute_gf_denom();
virtual void compute_gf_ik();
virtual void compute_gf_ad();
-
+
virtual void particle_map();
virtual void make_rho();
virtual void fieldforce_ik();
diff --git a/src/KSPACE/pppm_tip4p.cpp b/src/KSPACE/pppm_tip4p.cpp
index f3c6d3c9a4..6742a0b14d 100644
--- a/src/KSPACE/pppm_tip4p.cpp
+++ b/src/KSPACE/pppm_tip4p.cpp
@@ -15,7 +15,7 @@
Contributing authors: Amalie Frischknecht and Ahmed Ismail (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pppm_tip4p.h"
#include "atom.h"
#include "domain.h"
@@ -296,7 +296,7 @@ void PPPMTIP4P::fieldforce_ad()
for (i = 0; i < nlocal; i++) {
if (type[i] == typeO) {
- find_M(i,iH1,iH2,xM);
+ find_M(i,iH1,iH2,xM);
xi = xM;
} else xi = x[i];
@@ -306,7 +306,7 @@ void PPPMTIP4P::fieldforce_ad()
dx = nx+shiftone - (xi[0]-boxlo[0])*delxinv;
dy = ny+shiftone - (xi[1]-boxlo[1])*delyinv;
dz = nz+shiftone - (xi[2]-boxlo[2])*delzinv;
-
+
compute_rho1d(dx,dy,dz);
compute_drho1d(dx,dy,dz);
@@ -327,7 +327,7 @@ void PPPMTIP4P::fieldforce_ad()
ekx *= hx_inv;
eky *= hy_inv;
ekz *= hz_inv;
-
+
// convert E-field to force and substract self forces
const double qfactor = qqrd2e * scale;
@@ -375,7 +375,7 @@ void PPPMTIP4P::fieldforce_ad()
/* ----------------------------------------------------------------------
- interpolate from grid to get electric field & force on my particles
+ interpolate from grid to get electric field & force on my particles
------------------------------------------------------------------------- */
void PPPMTIP4P::fieldforce_peratom()
@@ -401,7 +401,7 @@ void PPPMTIP4P::fieldforce_peratom()
for (i = 0; i < nlocal; i++) {
if (type[i] == typeO) {
- find_M(i,iH1,iH2,xM);
+ find_M(i,iH1,iH2,xM);
xi = xM;
} else xi = x[i];
@@ -424,7 +424,7 @@ void PPPMTIP4P::fieldforce_peratom()
for (l = nlower; l <= nupper; l++) {
mx = l+nx;
x0 = y0*rho1d[0][l];
- if (eflag_atom) u_pa += x0*u_brick[mz][my][mx];
+ if (eflag_atom) u_pa += x0*u_brick[mz][my][mx];
if (vflag_atom) {
v0 += x0*v0_brick[mz][my][mx];
v1 += x0*v1_brick[mz][my][mx];
diff --git a/src/KSPACE/remap.cpp b/src/KSPACE/remap.cpp
index 115bcc25b8..86522f3f2f 100644
--- a/src/KSPACE/remap.cpp
+++ b/src/KSPACE/remap.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdio.h"
-#include "stdlib.h"
+#include <stdio.h>
+#include <stdlib.h>
#include "remap.h"
#define PACK_DATA FFT_SCALAR
@@ -64,7 +64,7 @@ void remap_3d(FFT_SCALAR *in, FFT_SCALAR *out, FFT_SCALAR *buf,
{
// use point-to-point communication
- if (!plan->usecollective) {
+ if (!plan->usecollective) {
int i,isend,irecv;
FFT_SCALAR *scratch;
@@ -111,7 +111,7 @@ void remap_3d(FFT_SCALAR *in, FFT_SCALAR *out, FFT_SCALAR *buf,
// use All2Allv collective for remap communication
- } else {
+ } else {
if (plan->commringlen > 0) {
int isend,irecv;
@@ -124,9 +124,9 @@ void remap_3d(FFT_SCALAR *in, FFT_SCALAR *out, FFT_SCALAR *buf,
for (int i=0;i<plan->nrecv;i++)
recvBufferSize += plan->recv_size[i];
- FFT_SCALAR *packedSendBuffer
+ FFT_SCALAR *packedSendBuffer
= (FFT_SCALAR *) malloc(sizeof(FFT_SCALAR) * sendBufferSize);
- FFT_SCALAR *packedRecvBuffer
+ FFT_SCALAR *packedRecvBuffer
= (FFT_SCALAR *) malloc(sizeof(FFT_SCALAR) * recvBufferSize);
int *sendcnts = (int *) malloc(sizeof(int) * plan->commringlen);
@@ -454,14 +454,14 @@ struct remap_plan_3d *remap_3d_create_plan(
// create sub-comm rank list
- if (plan->usecollective) {
+ if (plan->usecollective) {
plan->commringlist = NULL;
// merge recv and send rank lists
- // ask Steve Plimpton about method to more accurately determine
+ // ask Steve Plimpton about method to more accurately determine
// maximum number of procs contributing to pencil
- int maxcommsize = nprocs;
+ int maxcommsize = nprocs;
int *commringlist = (int *) malloc(maxcommsize*sizeof(int));
int commringlen = 0;
diff --git a/src/KSPACE/remap_wrap.cpp b/src/KSPACE/remap_wrap.cpp
index d790e9e7c0..8ea2918d7f 100644
--- a/src/KSPACE/remap_wrap.cpp
+++ b/src/KSPACE/remap_wrap.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
+#include <mpi.h>
#include "remap_wrap.h"
#include "error.h"
diff --git a/src/MANYBODY/fix_qeq_comb.cpp b/src/MANYBODY/fix_qeq_comb.cpp
index 877ff1c292..a05211ab64 100644
--- a/src/MANYBODY/fix_qeq_comb.cpp
+++ b/src/MANYBODY/fix_qeq_comb.cpp
@@ -15,10 +15,10 @@
Contributing authors: Ray Shan (Sandia, tnshan@sandia.gov)
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <mpi.h>
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_comb.h"
#include "pair_comb3.h"
#include "fix_qeq_comb.h"
@@ -290,7 +290,7 @@ double FixQEQComb::memory_usage()
}
/* ---------------------------------------------------------------------- */
-int FixQEQComb::pack_forward_comm(int n, int *list, double *buf,
+int FixQEQComb::pack_forward_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
diff --git a/src/MANYBODY/fix_qeq_comb.h b/src/MANYBODY/fix_qeq_comb.h
index 0ce0767dd1..d627ef669b 100644
--- a/src/MANYBODY/fix_qeq_comb.h
+++ b/src/MANYBODY/fix_qeq_comb.h
@@ -20,7 +20,7 @@ FixStyle(qeq/comb,FixQEQComb)
#ifndef LMP_FIX_QEQ_COMB_H
#define LMP_FIX_QEQ_COMB_H
-#include "stdio.h"
+#include <stdio.h>
#include "fix.h"
namespace LAMMPS_NS {
diff --git a/src/MANYBODY/pair_adp.cpp b/src/MANYBODY/pair_adp.cpp
index 5cb861b563..ce1c382da9 100644
--- a/src/MANYBODY/pair_adp.cpp
+++ b/src/MANYBODY/pair_adp.cpp
@@ -16,10 +16,10 @@
Chandra Veer Singh (Cornell)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_adp.h"
#include "atom.h"
#include "force.h"
@@ -934,7 +934,7 @@ void PairADP::grab(FILE *fp, int n, double *list)
/* ---------------------------------------------------------------------- */
-int PairADP::pack_forward_comm(int n, int *list, double *buf,
+int PairADP::pack_forward_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
diff --git a/src/MANYBODY/pair_airebo.cpp b/src/MANYBODY/pair_airebo.cpp
index f3a7be5a2d..d38440a1ff 100644
--- a/src/MANYBODY/pair_airebo.cpp
+++ b/src/MANYBODY/pair_airebo.cpp
@@ -17,11 +17,11 @@
Marcel Fallet & Steve Stuart (Clemson), Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
-#include "mpi.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <mpi.h>
#include "pair_airebo.h"
#include "atom.h"
#include "neighbor.h"
@@ -4196,7 +4196,7 @@ double PairAIREBO::memory_usage()
for (int i = 0; i < comm->nthreads; i++)
bytes += ipage[i].size();
-
+
bytes += 2*maxlocal * sizeof(double);
return bytes;
}
diff --git a/src/MANYBODY/pair_airebo.h b/src/MANYBODY/pair_airebo.h
index 8a6e52fead..b929621bd3 100644
--- a/src/MANYBODY/pair_airebo.h
+++ b/src/MANYBODY/pair_airebo.h
@@ -22,7 +22,7 @@ PairStyle(airebo,PairAIREBO)
#include "pair.h"
#include "my_page.h"
-#include "math.h"
+#include <math.h>
#include "math_const.h"
namespace LAMMPS_NS {
diff --git a/src/MANYBODY/pair_bop.cpp b/src/MANYBODY/pair_bop.cpp
index 20febf3a37..037f893ea5 100644
--- a/src/MANYBODY/pair_bop.cpp
+++ b/src/MANYBODY/pair_bop.cpp
@@ -32,11 +32,11 @@
Rules"_http://lammps.sandia.gov/open_source.html
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
-#include "mpi.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <mpi.h>
#include "pair_bop.h"
#include "atom.h"
#include "neighbor.h"
@@ -49,7 +49,7 @@
#include "neigh_request.h"
#include "memory.h"
#include "error.h"
-#include "ctype.h"
+#include <ctype.h>
using namespace LAMMPS_NS;
@@ -779,14 +779,14 @@ void PairBOP::gneigh()
max_check3++;
}
}
-
+
BOP_index[i]=neigh_total;
BOP_index3[i]=neigh_total3;
BOP_total[i]=max_check;
BOP_total3[i]=max_check3;
neigh_total+=max_check;
neigh_total3+=max_check3;
-
+
if(max_check>maxneigh||max_check3>maxneigh3){
maxneigh=max_check;
maxneigh3=max_check3;
@@ -901,9 +901,9 @@ void PairBOP::gneigh()
for(jj=0;jj<nlisti;jj++) {
temp_ij=BOP_index[i]+jj;
j=iilist[neigh_index[temp_ij]];
-
+
jtype = map[type[j]]+1;
-
+
if(itype==jtype)
i12=itype-1;
else if(itype<jtype)
@@ -1231,7 +1231,7 @@ double PairBOP::sigmaBo(int itmp, int jtmp)
ilist = list->ilist;
firstneigh = list->firstneigh;
MPI_Comm_rank(world,&me);
-
+
if(nb_sg==0) {
nb_sg=(maxneigh)*(maxneigh/2);
}
@@ -1246,7 +1246,7 @@ double PairBOP::sigmaBo(int itmp, int jtmp)
} else {
i=itmp;
}
-
+
i_tag=tag[i];
itype = map[type[i]]+1;
@@ -1467,7 +1467,7 @@ double PairBOP::sigmaBo(int itmp, int jtmp)
r_jk=rij[temp_jk];
}
}
-
+
sig_flag=0;
for(nsearch=0;nsearch<nSigBk;nsearch++) {
ncmp=itypeSigBk[nsearch];
@@ -1579,7 +1579,7 @@ double PairBOP::sigmaBo(int itmp, int jtmp)
//1st CC is Eq. 11 (c) for i atom where j & k=neighbor of i
AA=AA+gfactorsq*betaS_ik*betaS_ik;
-
+
//agpdpr1 is derivative of AA w.r.t. Beta(rik)
//app1 is derivative of AA w.r.t. cos(theta_jik)
@@ -1706,8 +1706,8 @@ double PairBOP::sigmaBo(int itmp, int jtmp)
*dis_jk[1]*r_ij*r_ij)/(r_ij*r_ij*r_jk*r_jk);
dcA_ijk[2][1]=(-dis_ij[2]*r_ij*r_jk-cosAng_ijk
*dis_jk[2]*r_ij*r_ij)/(r_ij*r_ij*r_jk*r_jk);
- }
- } else {
+ }
+ } else {
if(neigh_flag[temp_jkp]) {
pass_jkp=1;
dis_jkp[0]=disij[0][temp_jkp];
@@ -1734,8 +1734,8 @@ double PairBOP::sigmaBo(int itmp, int jtmp)
dcA_ijk[0][1]=dcAng[ang_ijk][0][ngjk];
dcA_ijk[1][1]=dcAng[ang_ijk][1][ngjk];
dcA_ijk[2][1]=dcAng[ang_ijk][2][ngjk];
- }
- }
+ }
+ }
if(pass_jkp==1) {
amean=cosAng_ijk;
if(amean<-1.0) amean=-1.0;
@@ -1792,7 +1792,7 @@ double PairBOP::sigmaBo(int itmp, int jtmp)
ngkj=0;
}
ang_ikj=cos_index[k]+nikj;
-
+
cosAng_ikj=cosAng[ang_ikj];
dcA_ikj[0][0]=dcAng[ang_ikj][0][ngki];
dcA_ikj[1][0]=dcAng[ang_ikj][1][ngki];
@@ -2133,7 +2133,7 @@ double PairBOP::sigmaBo(int itmp, int jtmp)
}
}
}
-
+
// j and k are different neighbors of i and k' is a neighbor k not equal to i
for(ltmp=0;ltmp<nlistk;ltmp++) {
@@ -2198,7 +2198,7 @@ double PairBOP::sigmaBo(int itmp, int jtmp)
dBetaS_kkp=dBetaS[temp_kkp];
}
}
- if(pass_kkp==1) {
+ if(pass_kkp==1) {
sig_flag=0;
for(nsearch=0;nsearch<nSigBk;nsearch++) {
ncmp=itypeSigBk[nsearch];
@@ -2252,7 +2252,7 @@ double PairBOP::sigmaBo(int itmp, int jtmp)
dcA_ikkp[1][1]=dcAng[ang_ikkp][1][ngli];
dcA_ikkp[2][1]=dcAng[ang_ikkp][2][ngli];
}
-
+
nb_kkp=nb_t;
nb_t++;
if(nb_t>nb_sg) {
@@ -2301,7 +2301,7 @@ double PairBOP::sigmaBo(int itmp, int jtmp)
//where j , k =neighbor of i & k' =neighbor of k
CC=CC+gfactor*rfactor;
-
+
//agpdpr1 is derivative of CC 3rd term w.r.t. Beta(r_ik)
//agpdpr2 is derivative of CC 3rd term w.r.t. Beta(r_kk')
//app1 is derivative of CC 3rd term w.r.t. cos(theta_jik)
@@ -2353,7 +2353,7 @@ double PairBOP::sigmaBo(int itmp, int jtmp)
kp=jlist[ni_jkp];
kptype = map[type[kp]]+1;
kplist=firstneigh[kp];
-
+
same_kkpk=0;
same_jkpj=0;
nlistkp=BOP_total[kp];
@@ -2705,7 +2705,7 @@ double PairBOP::sigmaBo(int itmp, int jtmp)
*(betaS_kkp+small2);
rfactor=pow(rfactor0,2.0/3.0);
drfactor=2.0/3.0*pow(rfactor0,-1.0/3.0);
-
+
//EE is Eq. 25(notes)
EE=EE+gfactor*rfactor;
@@ -2786,7 +2786,7 @@ double PairBOP::sigmaBo(int itmp, int jtmp)
temp_jk=BOP_index[j]+ktmp;
ni_jk=neigh_index[temp_jk];
k=jlist[ni_jk];
-
+
klist=firstneigh[k];
ktype=map[type[k]]+1;
nlistk=BOP_total[k];
@@ -2889,7 +2889,7 @@ double PairBOP::sigmaBo(int itmp, int jtmp)
dcA_ijk[2][1]=dcAng[ang_ijk][2][ngk];
}
}
- if(pass_jk==1) {
+ if(pass_jk==1) {
nb_jk=nb_t;
nb_t++;
if(nb_t>nb_sg) {
@@ -3171,11 +3171,11 @@ double PairBOP::sigmaBo(int itmp, int jtmp)
gfactor=gfactor1*gfactor2*gfactor3;
rfactorrt=betaS_jk*betaS_jkp;
rfactor=rfactorrt*rfactorrt;
-
+
//2nd DD is Eq. 11 (c) for j atom where i , k & k'=neighbor of j
DD=DD+2.0*gfactor*rfactor;
-
+
//agpdpr1 is derivative of DD w.r.t. Beta(r_jk)
//agpdpr2 is derivative of DD w.r.t. Beta(r_jk')
//app1 is derivative of DD w.r.t. cos(theta_ijk)
@@ -3222,7 +3222,7 @@ double PairBOP::sigmaBo(int itmp, int jtmp)
app2*dcA_ijkp[2][1]
+app3*dcA_kjkp[2][1]
+agpdpr2*dis_jkp[2];
-
+
}
}
}
@@ -3397,11 +3397,11 @@ double PairBOP::sigmaBo(int itmp, int jtmp)
gfactor=gfactorsq*gfactorsq2;
rfactorrt=betaS_jk*betaS_kkp;
rfactor=rfactorrt*rfactorrt;
-
+
//3rd DD is Eq. 11 (c) for j atom where i & k=neighbor of j & k'=neighbor of k
DD=DD+gfactor*rfactor;
-
+
//agpdpr1 is derivative of DD 3rd term w.r.t. Beta(r_jk)
//agpdpr2 is derivative of DD 3rd term w.r.t. Beta(r_kk')
//app1 is derivative of DD 3rd term w.r.t. cos(theta_ijk)
@@ -3454,7 +3454,7 @@ double PairBOP::sigmaBo(int itmp, int jtmp)
sigB=0.0;
sig_flag=1;
}
- if(sig_flag==0){
+ if(sig_flag==0){
if(sigma_a[iij]==0){
if(sig_flag==0) {
if(AA<0.0)
@@ -3684,7 +3684,7 @@ double PairBOP::sigmaBo(int itmp, int jtmp)
//This loop is to ensure there is not an error for atoms with no neighbors (deposition)
// sigB is the final expression for (a) Eq. 6 and (b) Eq. 11
-
+
if(nb_t==0) {
if(j>i) {
bt_sg[0].dSigB1[0]=bndtmp1*dis_ij[0];
@@ -3764,11 +3764,11 @@ double PairBOP::sigmaBo(int itmp, int jtmp)
part2=1.0-part1*EE1/part0;
part3=dsigB1*part1/part0;
part4=part3/part0*EE1;
-
+
// sigB is the final expression for (a) Eq. 6 and (b) Eq. 11
sigB=dsigB1*part2;
-
+
pp1=2.0*betaS_ij;
xtmp[0]=x[bt_j][0]-x[bt_i][0];
xtmp[1]=x[bt_j][1]-x[bt_i][1];
@@ -4674,7 +4674,7 @@ double PairBOP::PiBo(int itmp, int jtmp)
+2.0*cosAng_ijkp*(1.0-cosSq);
angFactor4=2.0*angFactor*angFactor-(1.0-cosSq)*(1.0-cosSq1);
betaCapSum=.5*betaCapSq1*betaCapSq2;
-
+
//4th BB is 4th term of Eq. 38 (a) where i , k and k' =neighbors j
BB=BB+betaCapSum*angFactor4;
@@ -5036,12 +5036,12 @@ void PairBOP::read_table(char *filename)
}
}
}
- if(nws==3) {
+ if(nws==3) {
sscanf(s,"%d %d %d",&nr,&ntheta,&nBOt);
npower=2;
if(ntheta<=10) npower=ntheta;
}
- else {
+ else {
sscanf(s,"%d %d",&nr,&nBOt);
ntheta=0;
npower=3;
@@ -5077,7 +5077,7 @@ void PairBOP::read_table(char *filename)
memory->create(gfunc5,bop_types,bop_types,bop_types,ntheta,"BOP:gfunc5");
memory->create(gfunc6,bop_types,bop_types,bop_types,ntheta,"BOP:gfunc6");
memory->create(gpara,bop_types,bop_types,bop_types,npower+1,"BOP:gpara");
-
+
allocate();
if (me == 0) {
FILE *fp = force->open_potential(filename);
@@ -5115,7 +5115,7 @@ void PairBOP::read_table(char *filename)
for(j=0;j<bop_types;j++)
for(k=j;k<bop_types;k++) {
if(npower<=2) {
- for(m=0;m<ntheta;m++) {
+ for(m=0;m<ntheta;m++) {
fgets(s,MAXLINE,fp);
sscanf(s,"%lf%lf%lf%lf%lf",&gfunc[j][i][k][n],&gfunc[j][i][k][n+1]
,&gfunc[j][i][k][n+2],&gfunc[j][i][k][n+3],&gfunc[j][i][k][n+4]);
@@ -5372,11 +5372,11 @@ void PairBOP::read_table(char *filename)
gfunc4[j][i][k][ntheta-1]=gfunc1[j][i][k][m]/dtheta;
gfunc5[j][i][k][ntheta-1]=2.0*gfunc2[j][i][k][m]/dtheta;
gfunc6[j][i][k][ntheta-1]=3.0*gfunc3[j][i][k][m]/dtheta;
- }
- }
- }
- }
- }
+ }
+ }
+ }
+ }
+ }
for(i=0;i<bop_types;i++) {
for(j=0;j<bop_types;j++) {
for(k=0;k<j;k++) {
@@ -5393,11 +5393,11 @@ void PairBOP::read_table(char *filename)
} else {
for(n=0;n<npower+1;n++) {
gpara[j][i][k][n]=gpara[k][i][j][n];
- }
- }
- }
- }
- }
+ }
+ }
+ }
+ }
+ }
fclose(fp);
}
MPI_Bcast(&rdBO,1,MPI_DOUBLE,0,world);
@@ -5736,7 +5736,7 @@ double PairBOP::memory_usage()
bytes += bop_types*bop_types*bop_types*ntheta *sizeof(double);
} else {
bytes += bop_types*bop_types*bop_types*npower+1 *sizeof(double);
- }
+ }
return bytes;
}
diff --git a/src/MANYBODY/pair_bop.h b/src/MANYBODY/pair_bop.h
index ed8d1fdc27..28be43fc72 100644
--- a/src/MANYBODY/pair_bop.h
+++ b/src/MANYBODY/pair_bop.h
@@ -26,7 +26,7 @@ PairStyle(bop,PairBOP)
#define LMP_PAIR_BOP_H
#include "pair.h"
-#include "time.h"
+#include <time.h>
#include "update.h"
namespace LAMMPS_NS {
@@ -91,7 +91,7 @@ class PairBOP : public Pair {
double *sigma_rc,*pi_rc,*phi_rc,*r1,*sigma_beta0;
double *pi_beta0,*phi0,*sigma_n,*pi_n,*phi_m;
double *sigma_nc,*pi_nc,*phi_nc;
- double *pro,*sigma_delta,*sigma_c,*sigma_a;
+ double *pro,*sigma_delta,*sigma_c,*sigma_a;
double *sigma_f,*sigma_k,*small3;
double small1,small2,small3g,small4,small5,small6,small7;
double which,alpha,alpha1,beta1,gamma1,alpha2,beta2,alpha3;
diff --git a/src/MANYBODY/pair_comb.cpp b/src/MANYBODY/pair_comb.cpp
index 26ff69d564..083e63e960 100644
--- a/src/MANYBODY/pair_comb.cpp
+++ b/src/MANYBODY/pair_comb.cpp
@@ -18,10 +18,10 @@
and Aidan Thompson's Tersoff code in LAMMPS
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_comb.h"
#include "atom.h"
#include "comm.h"
@@ -73,7 +73,7 @@ PairComb::PairComb(LAMMPS *lmp) : Pair(lmp)
phin = NULL;
dphin = NULL;
erpaw = NULL;
-
+
sht_num = NULL;
sht_first = NULL;
@@ -2002,7 +2002,7 @@ void PairComb::Over_cor(Param *param, double rsq1, int NCoi,
/* ---------------------------------------------------------------------- */
-int PairComb::pack_forward_comm(int n, int *list, double *buf,
+int PairComb::pack_forward_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
diff --git a/src/MANYBODY/pair_comb3.cpp b/src/MANYBODY/pair_comb3.cpp
index 2d1a782070..255e8a54c4 100644
--- a/src/MANYBODY/pair_comb3.cpp
+++ b/src/MANYBODY/pair_comb3.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -17,10 +17,10 @@
Dundar Yilmaz (dundar.yilmaz@zirve.edu.tr)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_comb3.h"
#include "atom.h"
#include "comm.h"
@@ -56,7 +56,7 @@ PairComb3::PairComb3(LAMMPS *lmp) : Pair(lmp)
bbij = NULL;
map = NULL;
esm = NULL;
-
+
nelements = 0;
elements = NULL;
nparams = 0;
@@ -151,11 +151,11 @@ void PairComb3::allocate()
memory->create(cutghost,n+1,n+1,"pair:cutghost");
map = new int[n+1];
- esm = new double[n];
+ esm = new double[n];
}
/* ----------------------------------------------------------------------
- global settings
+ global settings
------------------------------------------------------------------------- */
void PairComb3::settings(int narg, char **arg)
@@ -227,7 +227,7 @@ void PairComb3::coeff(int narg, char **arg)
}
// read potential file and initialize potential parameters
-
+
read_file(arg[2]);
setup();
@@ -334,7 +334,7 @@ void PairComb3::read_lib()
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
ccutoff[0] = atof(words[0]);
ccutoff[1] = atof(words[1]);
- ccutoff[2] = atof(words[2]);
+ ccutoff[2] = atof(words[2]);
ccutoff[3] = atof(words[3]);
ccutoff[4] = atof(words[4]);
ccutoff[5] = atof(words[5]);
@@ -345,12 +345,12 @@ void PairComb3::read_lib()
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
ch_a[0] = atof(words[0]);
ch_a[1] = atof(words[1]);
- ch_a[2] = atof(words[2]);
+ ch_a[2] = atof(words[2]);
ch_a[3] = atof(words[3]);
ch_a[4] = atof(words[4]);
ch_a[5] = atof(words[5]);
ch_a[6] = atof(words[6]);
-
+
fgets(s,maxlib,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
@@ -358,7 +358,7 @@ void PairComb3::read_lib()
nsplpcn = atoi(words[0]);
nsplrad = atoi(words[1]);
nspltor = atoi(words[2]);
-
+
fgets(s,maxlib,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
@@ -366,7 +366,7 @@ void PairComb3::read_lib()
maxx = atoi(words[0]);
maxy = atoi(words[1]);
maxz = atoi(words[2]);
-
+
fgets(s,maxlib,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
@@ -375,7 +375,7 @@ void PairComb3::read_lib()
maxyc = atoi(words[1]);
maxconj = atoi(words[2]);
- for (l=0; l<nsplpcn; l++) {
+ for (l=0; l<nsplpcn; l++) {
fgets(s,maxlib,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
@@ -384,7 +384,7 @@ void PairComb3::read_lib()
vmaxxcn[l] = atof(words[2]);
dvmaxxcn[l] = atof(words[3]);
}
-
+
fgets(s,maxlib,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
@@ -392,7 +392,7 @@ void PairComb3::read_lib()
ntab = atoi(words[0]);
for (i=0; i<ntab+1; i++){
- fgets(s,maxlib,fp);
+ fgets(s,maxlib,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -401,14 +401,14 @@ void PairComb3::read_lib()
ddpang[i] = atof(words[3]);
}
- for (l=0; l<nsplpcn; l++)
+ for (l=0; l<nsplpcn; l++)
for (i=0; i<maxx+1; i++)
for (j=0; j<maxy+1; j++)
- for (k=0; k<maxz+1; k++) {
- fgets(s,maxlib,fp);
+ for (k=0; k<maxz+1; k++) {
+ fgets(s,maxlib,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
- while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
+ while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
ll = atoi(words[0])-1;
ii = atoi(words[1]);
jj = atoi(words[2]);
@@ -422,8 +422,8 @@ void PairComb3::read_lib()
for (l=0; l<nsplpcn; l++)
for (i=0; i<maxx; i++)
for (j=0; j<maxy; j++)
- for (k=0; k<maxz; k++) {
- fgets(s,maxlib,fp);
+ for (k=0; k<maxz; k++) {
+ fgets(s,maxlib,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -432,7 +432,7 @@ void PairComb3::read_lib()
jj = atoi(words[2]);
kk = atoi(words[3]);
for(iii=0; iii<2; iii++) {
- fgets(s,maxlib,fp);
+ fgets(s,maxlib,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -443,11 +443,11 @@ void PairComb3::read_lib()
}
}
- for (l=0; l<nsplrad; l++)
+ for (l=0; l<nsplrad; l++)
for (i=0; i<maxxc+1; i++)
for (j=0; j<maxyc+1; j++)
- for (k=0; k<maxconj; k++) {
- fgets(s,maxlib,fp);
+ for (k=0; k<maxconj; k++) {
+ fgets(s,maxlib,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -464,8 +464,8 @@ void PairComb3::read_lib()
for (l=0; l<nsplrad; l++)
for (i=0; i<maxxc; i++)
for (j=0; j<maxyc; j++)
- for (k=0; k<maxconj-1; k++) {
- fgets(s,maxlib,fp);
+ for (k=0; k<maxconj-1; k++) {
+ fgets(s,maxlib,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -484,12 +484,12 @@ void PairComb3::read_lib()
}
}
}
-
+
for (l=0; l<nspltor; l++)
for (i=0; i<maxxc+1; i++)
for (j=0; j<maxyc+1; j++)
- for (k=0; k<maxconj; k++) {
- fgets(s,maxlib,fp);
+ for (k=0; k<maxconj; k++) {
+ fgets(s,maxlib,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -502,12 +502,12 @@ void PairComb3::read_lib()
tor_gridy[ll][ii][jj][kk] = atof(words[6]);
tor_gridz[ll][ii][jj][kk] = atof(words[7]);
}
-
+
for (l=0; l<nspltor; l++)
for (i=0; i<maxxc; i++)
for (j=0; j<maxyc; j++)
- for (k=0; k<maxconj-1; k++) {
- fgets(s,maxlib,fp);
+ for (k=0; k<maxconj-1; k++) {
+ fgets(s,maxlib,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -526,9 +526,9 @@ void PairComb3::read_lib()
}
}
}
-
+
fclose(fp);
- }
+ }
k = 0;
for (i=0; i<4; i++)
@@ -559,30 +559,30 @@ void PairComb3::read_lib()
MPI_Bcast(&maxxc,1,MPI_INT,0,world);
MPI_Bcast(&maxyc,1,MPI_INT,0,world);
MPI_Bcast(&maxconj,1,MPI_INT,0,world);
- MPI_Bcast(&maxxcn,4,MPI_INT,0,world);
+ MPI_Bcast(&maxxcn,4,MPI_INT,0,world);
MPI_Bcast(&vmaxxcn,4,MPI_DOUBLE,0,world);
MPI_Bcast(&dvmaxxcn,4,MPI_DOUBLE,0,world);
MPI_Bcast(&ntab,1,MPI_INT,0,world);
MPI_Bcast(&pang[0],20001,MPI_DOUBLE,0,world);
MPI_Bcast(&dpang[0],20001,MPI_DOUBLE,0,world);
MPI_Bcast(&ddpang[0],20001,MPI_DOUBLE,0,world);
- MPI_Bcast(&pcn_grid[0][0][0][0],500,MPI_DOUBLE,0,world);
+ MPI_Bcast(&pcn_grid[0][0][0][0],500,MPI_DOUBLE,0,world);
MPI_Bcast(&pcn_gridx[0][0][0][0],500,MPI_DOUBLE,0,world);
MPI_Bcast(&pcn_gridy[0][0][0][0],500,MPI_DOUBLE,0,world);
MPI_Bcast(&pcn_gridz[0][0][0][0],500,MPI_DOUBLE,0,world);
- MPI_Bcast(&pcn_cubs[0][0][0][0][0],16384,MPI_DOUBLE,0,world);
+ MPI_Bcast(&pcn_cubs[0][0][0][0][0],16384,MPI_DOUBLE,0,world);
- MPI_Bcast(&rad_grid[0][0][0][0],825,MPI_DOUBLE,0,world);
+ MPI_Bcast(&rad_grid[0][0][0][0],825,MPI_DOUBLE,0,world);
MPI_Bcast(&rad_gridx[0][0][0][0],825,MPI_DOUBLE,0,world);
MPI_Bcast(&rad_gridy[0][0][0][0],825,MPI_DOUBLE,0,world);
MPI_Bcast(&rad_gridz[0][0][0][0],825,MPI_DOUBLE,0,world);
- MPI_Bcast(&rad_spl[0][0][0][0][0],30720,MPI_DOUBLE,0,world);
+ MPI_Bcast(&rad_spl[0][0][0][0][0],30720,MPI_DOUBLE,0,world);
MPI_Bcast(&tor_grid[0][0][0][0],275,MPI_DOUBLE,0,world);
MPI_Bcast(&tor_gridx[0][0][0][0],275,MPI_DOUBLE,0,world);
MPI_Bcast(&tor_gridy[0][0][0][0],275,MPI_DOUBLE,0,world);
MPI_Bcast(&tor_gridz[0][0][0][0],275,MPI_DOUBLE,0,world);
- MPI_Bcast(&tor_spl[0][0][0][0][0],10240,MPI_DOUBLE,0,world);
+ MPI_Bcast(&tor_spl[0][0][0][0][0],10240,MPI_DOUBLE,0,world);
MPI_Bcast(&iin2[0][0],32,MPI_INT,0,world);
MPI_Bcast(&iin3[0][0],192,MPI_INT,0,world);
@@ -665,7 +665,7 @@ void PairComb3::read_file(char *file)
nwords = 0;
words[nwords++] = strtok(line," \t\n\r\f");
- while ((nwords <= params_per_line)
+ while ((nwords <= params_per_line)
&& (words[nwords++] = strtok(NULL," \t\n\r\f"))) {
continue;
}
@@ -673,7 +673,7 @@ void PairComb3::read_file(char *file)
// ielement,jelement,kelement = 1st args
// if all 3 args are in element list, then parse this line
// else skip to next line
-
+
for (ielement = 0; ielement < nelements; ielement++)
if (strcmp(words[0],elements[ielement]) == 0) break;
if (ielement == nelements) continue;
@@ -706,8 +706,8 @@ void PairComb3::read_file(char *file)
params[nparams].powerm = atof(words[11]);
params[nparams].veps = atof(words[12]);
params[nparams].vsig = atof(words[13]);
- params[nparams].paaa = atof(words[14]);
- params[nparams].pbbb = atof(words[15]);
+ params[nparams].paaa = atof(words[14]);
+ params[nparams].pbbb = atof(words[15]);
params[nparams].lami = atof(words[16]);
params[nparams].alfi = atof(words[17]);
params[nparams].powern = atof(words[18]);
@@ -737,7 +737,7 @@ void PairComb3::read_file(char *file)
params[nparams].alpha2 = atof(words[42]);
params[nparams].bigB2 = atof(words[43]);
params[nparams].alpha3 = atof(words[44]);
- params[nparams].bigB3 = atof(words[45]);
+ params[nparams].bigB3 = atof(words[45]);
params[nparams].lambda = atof(words[46]);
params[nparams].bigA = atof(words[47]);
params[nparams].beta = atof(words[48]);
@@ -770,25 +770,25 @@ void PairComb3::read_file(char *file)
// parameter sanity checks
- if (params[nparams].lambda < 0.0 || params[nparams].powern < 0.0 ||
- params[nparams].beta < 0.0 || params[nparams].alpha1 < 0.0 ||
- params[nparams].bigB1< 0.0 || params[nparams].bigA< 0.0 ||
+ if (params[nparams].lambda < 0.0 || params[nparams].powern < 0.0 ||
+ params[nparams].beta < 0.0 || params[nparams].alpha1 < 0.0 ||
+ params[nparams].bigB1< 0.0 || params[nparams].bigA< 0.0 ||
params[nparams].bigB2< 0.0 || params[nparams].alpha2 <0.0 ||
params[nparams].bigB3< 0.0 || params[nparams].alpha3 <0.0 ||
params[nparams].bigr < 0.0 || params[nparams].bigd < 0.0 ||
params[nparams].bigd > params[nparams].bigr ||
params[nparams].powerm - params[nparams].powermint != 0.0 ||
params[nparams].addrepr < 0.0 || params[nparams].powermint < 1.0 ||
- params[nparams].QL > 0.0 || params[nparams].QU < 0.0 ||
+ params[nparams].QL > 0.0 || params[nparams].QU < 0.0 ||
params[nparams].DL < 0.0 || params[nparams].DU > 0.0 ||
- params[nparams].pcross < 0.0 ||
- params[nparams].esm < 0.0 || params[nparams].veps < 0.0 ||
- params[nparams].vsig < 0.0 || params[nparams].vdwflag < 0.0
+ params[nparams].pcross < 0.0 ||
+ params[nparams].esm < 0.0 || params[nparams].veps < 0.0 ||
+ params[nparams].vsig < 0.0 || params[nparams].vdwflag < 0.0
)
error->all(FLERR,"Illegal COMB3 parameter");
nparams++;
- }
+ }
delete [] words;
}
@@ -811,7 +811,7 @@ void PairComb3::setup()
for (k = 0; k < nelements; k++) {
n = -1;
for (m = 0; m < nparams; m++) {
- if (i == params[m].ielement && j == params[m].jelement &&
+ if (i == params[m].ielement && j == params[m].jelement &&
k == params[m].kelement) {
if (n >= 0) error->all(FLERR,"Potential file has duplicate entry");
n = m;
@@ -833,14 +833,14 @@ void PairComb3::setup()
params[m].Qo = (params[m].QU+params[m].QL)/2.0; // (A22)
params[m].dQ = (params[m].QU-params[m].QL)/2.0; // (A21)
- params[m].aB = 1.0 /
+ params[m].aB = 1.0 /
(1.0-pow(fabs(params[m].Qo/params[m].dQ),10)); // (A20)
params[m].bB = pow(fabs(params[m].aB),0.1)/params[m].dQ; // (A19)
params[m].nD = log(params[m].DU/(params[m].DU-params[m].DL))/
log(params[m].QU/(params[m].QU-params[m].QL));
params[m].bD = (pow((params[m].DL-params[m].DU),(1.0/params[m].nD)))/
(params[m].QU-params[m].QL);
-
+
params[m].lcut = params[m].coulcut;
params[m].lcutsq = params[m].lcut*params[m].lcut;
}
@@ -855,7 +855,7 @@ void PairComb3::setup()
}
chicut1 = 7.0;
chicut2 = cutmax;
-}
+}
/* ---------------------------------------------------------------------- */
@@ -917,22 +917,22 @@ void PairComb3::Short_neigh()
rsq1 = vec3_dot(delrj,delrj);
jtype = map[type[j]];
iparam_ij = elem2param[itype][jtype][jtype];
-
+
if (rsq1 > cutmin) continue;
neighptrj[nj++] = j;
rr1 = sqrt(rsq1);
- NCo[i] += comb_fc(rr1,¶ms[iparam_ij]) * params[iparam_ij].pcross;
-
+ NCo[i] += comb_fc(rr1,¶ms[iparam_ij]) * params[iparam_ij].pcross;
+
icontrol = params[iparam_ij].jelementgp;
-
+
if( icontrol == 1)
- xcctmp[i] += comb_fc(rr1,¶ms[iparam_ij]) * params[iparam_ij].pcross;
- if (icontrol == 2)
- xchtmp[i] += comb_fc(rr1,¶ms[iparam_ij]) * params[iparam_ij].pcross;
+ xcctmp[i] += comb_fc(rr1,¶ms[iparam_ij]) * params[iparam_ij].pcross;
+ if (icontrol == 2)
+ xchtmp[i] += comb_fc(rr1,¶ms[iparam_ij]) * params[iparam_ij].pcross;
if (icontrol == 3)
- xcotmp[i] += comb_fc(rr1,¶ms[iparam_ij]) * params[iparam_ij].pcross;
-
+ xcotmp[i] += comb_fc(rr1,¶ms[iparam_ij]) * params[iparam_ij].pcross;
+
}
sht_first[i] = neighptrj;
@@ -960,21 +960,21 @@ void PairComb3::compute(int eflag, int vflag)
int *ilist,*jlist,*numneigh,**firstneigh,mr1,mr2,mr3,inty,nj;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,rsq1,rsq2,rsq3,iq,jq,yaself;
- double eng_tmp,vionij,fvionij,sr1,sr2,sr3;
+ double eng_tmp,vionij,fvionij,sr1,sr2,sr3;
double zeta_ij,prefac_ij1,prefac_ij2,prefac_ij3,prefac_ij4,prefac_ij5;
double zeta_ji,prefac_ji1,prefac_ji2,prefac_ji3,prefac_ji4,prefac_ji5;
double delrj[3],delrk[3],fi[3],fj[3],fk[3],fl[3];
double ep6p_ij,ep6p_ji,fip6p[3],fjp6p[3],fkp6p[3],flp6p[3];
double potal,fac11,fac11e;
tagint itag, jtag;
-
+
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
tagint *tag = atom->tag;
int *type = atom->type;
double **x = atom->x;
double **f = atom->f;
- double *q = atom->q;
+ double *q = atom->q;
// coordination terms
double xcn, ycn;
@@ -986,7 +986,7 @@ void PairComb3::compute(int eflag, int vflag)
int iparam_jil, iparam_ijl, iparam_ki, iparam_lj;
int iparam_jl, iparam_ik, iparam_km, iparam_lp;
double kconjug, lconjug, kradtot, lradtot;
- double delrl[3], delrm[3], delrp[3], ddprx[3], srmu;
+ double delrl[3], delrm[3], delrp[3], ddprx[3], srmu;
double zet_addi,zet_addj;
evdwl = eng_tmp = 0.0;
@@ -1001,7 +1001,7 @@ void PairComb3::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
- yaself = vionij = fvionij = fpair = 0.0;
+ yaself = vionij = fvionij = fpair = 0.0;
// self energy correction term: potal
potal_calc(potal,fac11,fac11e);
@@ -1031,7 +1031,7 @@ void PairComb3::compute(int eflag, int vflag)
if (x[j][2] < x[i][2]) continue;
if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
- }
+ }
jtype = map[type[j]];
jq = q[j];
@@ -1047,7 +1047,7 @@ void PairComb3::compute(int eflag, int vflag)
if (rsq > params[iparam_ij].lcutsq) continue;
tri_point(rsq, mr1, mr2, mr3, sr1, sr2, sr3);
-
+
dipole_init(¶ms[iparam_ij],¶ms[iparam_ji],fac11,delrj,
rsq,mr1,mr2,mr3,sr1,sr2,sr3,iq,jq,i,j);
}
@@ -1064,7 +1064,7 @@ void PairComb3::compute(int eflag, int vflag)
iq = q[i];
nj = 0;
iparam_i = elem2param[itype][itype][itype];
-
+
// self energy, only on i atom
yaself = self(¶ms[iparam_i],iq);
@@ -1073,7 +1073,7 @@ void PairComb3::compute(int eflag, int vflag)
yaself += dipole_self(¶ms[iparam_i],i);
if (evflag) ev_tally(i,i,nlocal,0,0.0,yaself,0.0,0.0,0.0,0.0);
-
+
// two-body interactions (long:R + A, short: only R)
jlist = firstneigh[i];
@@ -1095,7 +1095,7 @@ void PairComb3::compute(int eflag, int vflag)
if (x[j][2] < x[i][2]) continue;
if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
- }
+ }
jtype = map[type[j]];
jq = q[j];
@@ -1126,12 +1126,12 @@ void PairComb3::compute(int eflag, int vflag)
if (evflag)
ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair,delx,dely,delz);
-
+
// Q-dependent: Coulombic, field, polarization
// 1/r energy and forces
- direct(¶ms[iparam_ij], ¶ms[iparam_ji],
- mr1, mr2, mr3, rsq, sr1, sr2, sr3, iq, jq,
+ direct(¶ms[iparam_ij], ¶ms[iparam_ji],
+ mr1, mr2, mr3, rsq, sr1, sr2, sr3, iq, jq,
fac11, fac11e, eng_tmp, fvionij, i, j);
vionij = eng_tmp;
@@ -1150,7 +1150,7 @@ void PairComb3::compute(int eflag, int vflag)
f[j][2] -= delz*fvionij;
// sums up long range Q-dependent energies (excluding dipole)
- if (evflag)
+ if (evflag)
ev_tally(i,j,nlocal,newton_pair,0.0,vionij,fvionij,delx,dely,delz);
// polarization field
@@ -1161,7 +1161,7 @@ void PairComb3::compute(int eflag, int vflag)
vionij = eng_tmp;
// sums up dipole energies
- if (evflag)
+ if (evflag)
ev_tally(i,j,nlocal,newton_pair,0.0,vionij,fvionij,delx,dely,delz);
// sums up dipole forces
@@ -1171,15 +1171,15 @@ void PairComb3::compute(int eflag, int vflag)
f[j][0] -= (ddprx[0] + delx*fvionij);
f[j][1] -= (ddprx[1] + dely*fvionij);
f[j][2] -= (ddprx[2] + delz*fvionij);
- }
-
+ }
+
if (rsq > params[iparam_ij].cutsq) continue;
repulsive(¶ms[iparam_ij], ¶ms[iparam_ji], rsq,
fpair, eflag, eng_tmp, iq, jq);
evdwl = eng_tmp;
-
+
// repulsion is pure two-body, sums up pair repulsive forces
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
@@ -1187,7 +1187,7 @@ void PairComb3::compute(int eflag, int vflag)
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
-
+
if (evflag)
ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair,delx,dely,delz);
}
@@ -1213,13 +1213,13 @@ void PairComb3::compute(int eflag, int vflag)
rsq1 = vec3_dot(delrj,delrj);
if (rsq1 > params[iparam_ij].cutsq) continue;
nj ++;
-
+
// this Qj for q-dependent BSi
jq = q[j];
-
+
// accumulate bondorder zeta for each i-j interaction via k and l loops
- zeta_ij = 0.0;
- bbtor = 0.0;
+ zeta_ij = 0.0;
+ bbtor = 0.0;
kconjug = 0.0;
for (kk = 0; kk < sht_jnum; kk++) { // kk is neighbor of ii
@@ -1235,7 +1235,7 @@ void PairComb3::compute(int eflag, int vflag)
delrk[1] = x[k][1] - ytmp;
delrk[2] = x[k][2] - ztmp;
rsq2 = vec3_dot(delrk,delrk);
-
+
if (rsq2 > params[iparam_ik].cutsq) continue;
// 3-body zeta in bond order
@@ -1260,13 +1260,13 @@ void PairComb3::compute(int eflag, int vflag)
if(srmu > 0.1) {
for (ll = 0; ll < sht_lnum; ll++) { // ll is neighbor of jj
- l = sht_llist[ll];
+ l = sht_llist[ll];
- if(l==i || l==j || l==k) continue;
+ if(l==i || l==j || l==k) continue;
ltype = map[type[l]];
- delrl[0] = x[l][0] - x[j][0];
+ delrl[0] = x[l][0] - x[j][0];
delrl[1] = x[l][1] - x[j][1];
delrl[2] = x[l][2] - x[j][2];
rsq3 = vec3_dot(delrl,delrl);
@@ -1274,20 +1274,20 @@ void PairComb3::compute(int eflag, int vflag)
if (rsq3 > params[iparam_jl].cutsq) continue;
- iparam_ikl = elem2param[itype][ktype][ltype];
+ iparam_ikl = elem2param[itype][ktype][ltype];
torindx = params[iparam_ij].tor_flag;
bbtor += bbtor1(torindx, ¶ms[iparam_ikl],¶ms[iparam_jl],
rsq1,rsq2,rsq3,delrj,delrk,delrl,srmu);
}
}
}
- }
+ }
- zeta_ji = 0.0;
+ zeta_ji = 0.0;
lconjug = 0.0;
- for (ll = 0; ll < sht_lnum; ll++) {
- l = sht_llist[ll];
+ for (ll = 0; ll < sht_lnum; ll++) {
+ l = sht_llist[ll];
if (l == i) continue;
ltype = map[type[l]];
@@ -1321,7 +1321,7 @@ void PairComb3::compute(int eflag, int vflag)
lcn=NCo[l];
lconjug += rad_init(rsq2,¶ms[iparam_lj],j,lradtot,lcn);
}
- }
+ }
force_zeta(¶ms[iparam_ij], ¶ms[iparam_ji],
rsq1, xcn, ycn, zeta_ij, zeta_ji, fpair,
@@ -1362,14 +1362,14 @@ void PairComb3::compute(int eflag, int vflag)
delrk[2] = x[k][2] - ztmp;
rsq2 = vec3_dot(delrk,delrk);
if (rsq2 > params[iparam_ik].cutsq) continue;
-
+
// BO-dependent 3-body E & F
attractive(¶ms[iparam_ijk], ¶ms[iparam_jik],¶ms[iparam_ikj],
prefac_ij1, prefac_ij2, prefac_ij3, prefac_ij4, prefac_ij5,
rsq1,rsq2,delrj,delrk,fi,fj,fk,i,xcn);
ep6p_ij = ep6p(¶ms[iparam_ijk],¶ms[iparam_ikj],rsq1,rsq2,delrj,delrk,zet_addi);
- fp6p(¶ms[iparam_ijk],¶ms[iparam_ikj],rsq1,rsq2,delrj,delrk,fip6p,fjp6p,fkp6p);
+ fp6p(¶ms[iparam_ijk],¶ms[iparam_ikj],rsq1,rsq2,delrj,delrk,fip6p,fjp6p,fkp6p);
// Sums up i-j-k forces: LP contribution
for (im = 0; im < 3; im++) {
@@ -1392,19 +1392,19 @@ void PairComb3::compute(int eflag, int vflag)
if(srmu > 0.1) {
for (ll = 0; ll < sht_lnum; ll++) { // ll is neighbor of jj
- l = sht_llist[ll];
- if (l==i||l==j||l==k) continue;
+ l = sht_llist[ll];
+ if (l==i||l==j||l==k) continue;
ltype = map[type[l]];
- delrl[0] = x[l][0] - x[j][0];
+ delrl[0] = x[l][0] - x[j][0];
delrl[1] = x[l][1] - x[j][1];
delrl[2] = x[l][2] - x[j][2];
rsq3 = vec3_dot(delrl,delrl);
-
+
iparam_jl = elem2param[jtype][ltype][ltype];
if (rsq3 > params[iparam_jl].cutsq) continue;
- iparam_ikl = elem2param[itype][ktype][ltype];
+ iparam_ikl = elem2param[itype][ktype][ltype];
torindx = params[iparam_ij].tor_flag;
tor_force(torindx, ¶ms[iparam_ikl], ¶ms[iparam_jl],srmu,
rsq1,rsq2,rsq3,delrj,delrk,delrl);
@@ -1420,13 +1420,13 @@ void PairComb3::compute(int eflag, int vflag)
}
if( params[iparam_ijk].rad_flag>=1 &&
- params[iparam_ijk].ielementgp==1 &&
+ params[iparam_ijk].ielementgp==1 &&
params[iparam_ijk].kelementgp==1) {
iparam_ki = elem2param[ktype][itype][itype];
kcn=NCo[k];
double rik=sqrt(rsq2);
kradtot = -comb_fc(rik,¶ms[iparam_ki])*params[iparam_ki].pcross+kcn;
-
+
rad_forceik(¶ms[iparam_ki],rsq2,delrk,kconjug,kradtot);
for (im = 0; im < 3; im++) {
@@ -1437,11 +1437,11 @@ void PairComb3::compute(int eflag, int vflag)
if (fabs(radtmp) > 1.0e-12) {
for (mm = 0; mm < sht_mnum; mm++) { // mm is neighbor of kk
m = sht_mlist[mm];
- if (m == k) continue;
+ if (m == k) continue;
mtype = map[type[m]];
- delrm[0] = x[m][0] - x[k][0];
+ delrm[0] = x[m][0] - x[k][0];
delrm[1] = x[m][1] - x[k][1];
delrm[2] = x[m][2] - x[k][2];
rsq3 = vec3_dot(delrm,delrm);
@@ -1461,7 +1461,7 @@ void PairComb3::compute(int eflag, int vflag)
}
}
- if (evflag)
+ if (evflag)
ev_tally(i,j,nlocal,newton_pair,ep6p_ij,0.0,0.0,0.0,0.0,0.0);
if (vflag_atom)
v_tally3(i,j,k,fj,fk,delrj,delrk);
@@ -1481,7 +1481,7 @@ void PairComb3::compute(int eflag, int vflag)
iparam_jli = elem2param[jtype][ltype][itype];
iparam_ijl = elem2param[itype][jtype][ltype];
iparam_jl = elem2param[jtype][ltype][ltype];
- delrk[0] = x[l][0] - x[j][0];
+ delrk[0] = x[l][0] - x[j][0];
delrk[1] = x[l][1] - x[j][1];
delrk[2] = x[l][2] - x[j][2];
@@ -1495,9 +1495,9 @@ void PairComb3::compute(int eflag, int vflag)
// BO-independent 3-body j-i-l LP and BB correction and forces
ep6p_ji = ep6p(¶ms[iparam_jil],¶ms[iparam_jli],rsq1,rsq2,delrl,delrk,zet_addj);
- fp6p(¶ms[iparam_jil],¶ms[iparam_jli],rsq1,rsq2,delrl,delrk,fjp6p,fip6p,flp6p);
+ fp6p(¶ms[iparam_jil],¶ms[iparam_jli],rsq1,rsq2,delrl,delrk,fjp6p,fip6p,flp6p);
- if (evflag)
+ if (evflag)
ev_tally(j,i,nlocal,newton_pair,ep6p_ji,0.0,0.0,0.0,0.0,0.0);
// BO-dependent 3-body E & F
@@ -1513,9 +1513,9 @@ void PairComb3::compute(int eflag, int vflag)
f[i][im] += fi[im];
f[l][im] += fl[im];
}
-
+
// radical i-j-l-p: apply to all CC,CO,OC bonds
- if( params[iparam_jil].rad_flag >= 1 &&
+ if( params[iparam_jil].rad_flag >= 1 &&
params[iparam_jil].ielementgp == 1 &&
params[iparam_jil].kelementgp == 1 ) {
iparam_lj = elem2param[ltype][jtype][jtype];
@@ -1533,10 +1533,10 @@ void PairComb3::compute(int eflag, int vflag)
if (fabs(radtmp)>1.0e-12) {
for (pp = 0; pp < sht_pnum; pp++) { // pp is neighbor of ll
p = sht_plist[pp];
- if (p == l) continue;
+ if (p == l) continue;
ptype = map[type[p]];
- delrp[0] = x[p][0] - x[l][0];
+ delrp[0] = x[p][0] - x[l][0];
delrp[1] = x[p][1] - x[l][1];
delrp[2] = x[p][2] - x[l][2];
rsq3 = vec3_dot(delrp,delrp);
@@ -1558,7 +1558,7 @@ void PairComb3::compute(int eflag, int vflag)
if (vflag_atom)
v_tally3(j,i,l,fi,fl,delrl,delrk);
- }
+ }
}
}
@@ -1568,7 +1568,7 @@ void PairComb3::compute(int eflag, int vflag)
/* ---------------------------------------------------------------------- */
-void PairComb3::repulsive(Param *parami, Param *paramj, double rsq,
+void PairComb3::repulsive(Param *parami, Param *paramj, double rsq,
double &fforce,int eflag, double &eng, double iq, double jq)
{
double r,tmp_fc,tmp_fc_d,Di,Dj;
@@ -1595,14 +1595,14 @@ void PairComb3::repulsive(Param *parami, Param *paramj, double rsq,
LamDiLamDj = exp(0.5*(parami->lami*Di+paramj->lami*Dj)-rlm1*r);
caj = bigA * LamDiLamDj;
- fforce = -caj * fcdA;
+ fforce = -caj * fcdA;
- // additional repulsion
+ // additional repulsion
vrcs = 1.0; fvrcs = 0.0;
- if (romi != 0.0 && r < addr) {
+ if (romi != 0.0 && r < addr) {
vrcs += romi * pow((1.0-r/addr),2.0);
- fvrcs = romi * 2.0 * (r/addr-1.0)/addr;
+ fvrcs = romi * 2.0 * (r/addr-1.0)/addr;
fforce = fforce*vrcs - caj * tmp_fc * vrcs * fvrcs;
}
fforce /= r;
@@ -1613,7 +1613,7 @@ void PairComb3::repulsive(Param *parami, Param *paramj, double rsq,
/* ---------------------------------------------------------------------- */
-double PairComb3::zeta(Param *parami, Param *paramj, double rsqij,
+double PairComb3::zeta(Param *parami, Param *paramj, double rsqij,
double rsqik, double *delrij, double *delrik, int i, double xcn)
{
double rij,rik,costheta,arg,ex_delr,rlm3;
@@ -1634,7 +1634,7 @@ double PairComb3::zeta(Param *parami, Param *paramj, double rsqij,
/* ---------------------------------------------------------------------- */
-void PairComb3::selfp6p(Param *parami, Param *paramj, double rsq,
+void PairComb3::selfp6p(Param *parami, Param *paramj, double rsq,
double &eng, double &force)
{
double r,comtti,comttj,fcj,fcj_d;
@@ -1676,7 +1676,7 @@ double PairComb3::ep6p(Param *paramj, Param *paramk, double rsqij, double rsqik,
fcj = comb_fc(rij,paramj);
fck = comb_fc(rik,paramk);
- rmu = costheta;
+ rmu = costheta;
rmu2 = rmu *rmu; rmu3 = rmu2*rmu; rmu4 = rmu3*rmu;
rmu5 = rmu4*rmu; rmu6 = rmu5*rmu;
lp0 = pplp0;
@@ -1693,7 +1693,7 @@ double PairComb3::ep6p(Param *paramj, Param *paramk, double rsqij, double rsqik,
/*---------------------------------------------------------------------- */
void PairComb3::fp6p(Param *paramij,Param *paramik, double rsqij, double rsqik,
- double *delrij, double *delrik, double *drilp,
+ double *delrij, double *delrik, double *drilp,
double *drjlp, double *drklp)
{
double pplp0 = paramij->p6p0;
@@ -1705,17 +1705,17 @@ void PairComb3::fp6p(Param *paramij,Param *paramik, double rsqij, double rsqik,
double lp0,lp1,lp2,lp3,lp4,lp5,lp6;
double lp1_d,lp2_d,lp3_d,lp4_d,lp5_d,lp6_d;
double rmu2, rmu3, rmu4, rmu5, rmu6;
-
+
ffj1 = 0.0, ffj2 = 0.0;
ffk1 = 0.0, ffk2 = 0.0;
rij = sqrt(rsqij); rik = sqrt(rsqik);
- costheta = vec3_dot(delrij,delrik) / (rij*rik);
+ costheta = vec3_dot(delrij,delrik) / (rij*rik);
fcj = comb_fc(rij,paramij);
fck = comb_fc(rik,paramik);
fcj_d = comb_fc_d(rij,paramij);
fck_d = comb_fc_d(rik,paramik);
- rmu = costheta;
+ rmu = costheta;
rmu2 = rmu *rmu; rmu3 = rmu2*rmu;
rmu4 = rmu3*rmu; rmu5 = rmu4*rmu; rmu6 = rmu5*rmu;
@@ -1734,38 +1734,38 @@ void PairComb3::fp6p(Param *paramij,Param *paramik, double rsqij, double rsqik,
lp6_d = pplp6*6.0*rmu5;
comtt = lp0 + lp1 + lp2 + lp3 + lp4 + lp5 + lp6;
comtt_d = lp1_d + lp2_d + lp3_d + lp4_d + lp5_d + lp6_d;
-
+
com4k = fcj * fck_d * comtt;
com5 = fcj * fck * comtt_d;
- com5k = fck * comtt * fcj_d;
+ com5k = fck * comtt * fcj_d;
- ffj1 = 0.5*(-com5/(rij*rik));
- ffj2 = 0.5*(com5*rmu/rsqij-com5k/rij);
+ ffj1 = 0.5*(-com5/(rij*rik));
+ ffj2 = 0.5*(com5*rmu/rsqij-com5k/rij);
ffk1 = ffj1;
ffk2 = 0.5*(-com4k/rik+com5*rmu/rsqik);
// j-atom
- vec3_scale(ffj1,delrik,drjlp);
+ vec3_scale(ffj1,delrik,drjlp);
vec3_scaleadd(ffj2,delrij,drjlp,drjlp);
-
+
// k-atom
vec3_scale(ffk1,delrij,drklp);
vec3_scaleadd(ffk2,delrik,drklp,drklp);
-
- // i-atom
- vec3_add(drjlp,drklp,drilp);
+
+ // i-atom
+ vec3_add(drjlp,drklp,drilp);
vec3_scale(-1.0,drilp,drilp);
}
/* ---------------------------------------------------------------------- */
-void PairComb3::force_zeta(Param *parami, Param *paramj, double rsq,
- double xcn, double ycn, double &zeta_ij, double &zeta_ji, double &fforce,
+void PairComb3::force_zeta(Param *parami, Param *paramj, double rsq,
+ double xcn, double ycn, double &zeta_ij, double &zeta_ji, double &fforce,
double &prefac_ij1, double &prefac_ij2, double &prefac_ij3,
double &prefac_ij4, double &prefac_ij5,
- double &prefac_ji1, double &prefac_ji2, double &prefac_ji3,
+ double &prefac_ji1, double &prefac_ji2, double &prefac_ji3,
double &prefac_ji4, double &prefac_ji5,
- int eflag, double &eng, double iq, double jq,
+ int eflag, double &eng, double iq, double jq,
int i, int j, int nj, double bbtor, double kconjug, double lconjug)
{
double r,att_eng,att_force,bij; // att_eng is -cbj
@@ -1817,10 +1817,10 @@ void PairComb3::force_zeta(Param *parami, Param *paramj, double rsq,
// combines com6 & com7 below
if ( parami->rad_flag>0 || parami->tor_flag!=0 ) {
- prefac_ij2-=pradx;
+ prefac_ij2-=pradx;
prefac_ji2-=prady;
}
-
+
// eng = attraction energy
if (eflag) eng = 1.0*bij*att_eng;
}
@@ -1865,7 +1865,7 @@ double PairComb3::comb_fccc_d(double xcn)
{
double cut1 = ccutoff[0];
double cut2 = ccutoff[1];
-
+
if (xcn <= cut1) return 0.0;
if (xcn >= cut2) return 0.0;
return -MY_PI2/(cut2-cut1)*sin(MY_PI*(xcn-cut1)/(cut2-cut1));
@@ -1889,7 +1889,7 @@ double PairComb3::comb_fcch_d(double xcn)
{
double cut1 = ccutoff[2];
double cut2 = ccutoff[3];
-
+
if (xcn <= cut1) return 0.0;
if (xcn >= cut2) return 0.0;
return -MY_PI2/(cut2-cut1)*sin(MY_PI*(xcn-cut1)/(cut2-cut1));
@@ -1924,7 +1924,7 @@ double PairComb3::comb_fccch_d(double xcn)
double PairComb3::comb_fcsw(double rsq)
{
double r = sqrt(rsq);
-
+
if (r <= chicut1) return 1.0;
if (r >= chicut2) return 0.0;
return 0.5*(1.0 + cos(MY_PI*(r-chicut1)/(chicut2-chicut1)));
@@ -1937,23 +1937,23 @@ double PairComb3::self(Param *param, double qi)
double self_tmp, cmin, cmax, qmin, qmax;
double s1=param->chi, s2=param->dj, s3=param->dk, s4=param->dl;
- self_tmp = 0.0;
+ self_tmp = 0.0;
qmin = param->qmin;
qmax = param->qmax;
cmin = cmax = 100.0;
-
+
self_tmp = qi*(s1+qi*(s2+qi*(s3+qi*s4)));
if (qi < qmin) self_tmp += cmin * pow((qi-qmin),4);
if (qi > qmax) self_tmp += cmax * pow((qi-qmax),4);
-
+
return self_tmp;
}
/* ---------------------------------------------------------------------- */
-void PairComb3::comb_fa(double r, Param *parami, Param *paramj, double iq,
+void PairComb3::comb_fa(double r, Param *parami, Param *paramj, double iq,
double jq, double &att_eng, double &att_force)
{
double Bsi;
@@ -1993,8 +1993,8 @@ void PairComb3::comb_fa(double r, Param *parami, Param *paramj, double iq,
/* ---------------------------------------------------------------------- */
-void PairComb3::comb_bij_d(double zet, Param *param, double r, int i,
- double &tbij, double &tbij1, double &tbij2,
+void PairComb3::comb_bij_d(double zet, Param *param, double r, int i,
+ double &tbij, double &tbij1, double &tbij2,
double &tbij3, double &tbij4, double &tbij5, double xcn)
{
double pcorn,dpcorn,dxccij,dxchij,dxcoij;
@@ -2006,7 +2006,7 @@ void PairComb3::comb_bij_d(double zet, Param *param, double r, int i,
zetang=zeta;
pow_n=param->powern;
- zeta = pow(zetang,pow_n)+pcorn;
+ zeta = pow(zetang,pow_n)+pcorn;
tmp_tbij=pow_n*pow(zetang,(pow_n-1.0));
if ((1.0 + zeta) < 0.1 ){
@@ -2014,13 +2014,13 @@ void PairComb3::comb_bij_d(double zet, Param *param, double r, int i,
tbij = pow(1.0 + zeta, -0.5/pow_n);
tbij1=0.0;
}
- else if (zeta > param->c1) {
+ else if (zeta > param->c1) {
tbij = pow(zeta,-0.5/pow_n);
tbij1 = -0.5/pow_n*pow(zeta,(-0.5/pow_n-1.0));
} else if (zeta > param->c2) {
tbij = pow(zeta,-0.5/pow_n)-0.5/pow_n*pow(zeta,(-0.5/pow_n-1.0));
tbij1 = -0.5/pow_n/zeta;
- } else if (fabs(zeta) < param->c4) {
+ } else if (fabs(zeta) < param->c4) {
tbij = 1.0;
tbij1 = 0.0;
} else if (fabs(zeta) < param->c3) {
@@ -2031,10 +2031,10 @@ void PairComb3::comb_bij_d(double zet, Param *param, double r, int i,
tbij1 = -0.5/pow_n * pow(1.0 + zeta,(-1.0-0.5/pow_n));
}
- tbij2 = tbij1 * dpcorn;
+ tbij2 = tbij1 * dpcorn;
tbij3 = tbij1 * dxccij;
tbij4 = tbij1 * dxchij;
- tbij5 = tbij1 * dxcoij;
+ tbij5 = tbij1 * dxcoij;
tbij1 = tbij1 * tmp_tbij;
}
@@ -2042,7 +2042,7 @@ void PairComb3::comb_bij_d(double zet, Param *param, double r, int i,
/* ---------------------------------------------------------------------- */
void PairComb3::coord(Param *param, double r, int i,
- double &pcorn, double &dpcorn, double &dxccij,
+ double &pcorn, double &dpcorn, double &dxccij,
double &dxchij, double &dxcoij, double xcn)
{
int ixmin,iymin,izmin;
@@ -2077,7 +2077,7 @@ void PairComb3::coord(Param *param, double r, int i,
if(xcocn > maxz) xcocn = maxz;
double xcntritot=xcccn+xchcn+xcocn;
-
+
if(xcntritot > maxxcn[tri_flag-1]) {
pcorn = vmaxxcn[tri_flag-1]+(xcntot-maxxcn[tri_flag-1])*dvmaxxcn[tri_flag-1];
dxccij = dxchij = dxcoij = dvmaxxcn[tri_flag-1];
@@ -2090,7 +2090,7 @@ void PairComb3::coord(Param *param, double r, int i,
fabs(float(iymin)-xchcn)>1.0e-8 ||
fabs(float(izmin)-xcocn)>1.0e-8) {
cntri_int(tri_flag,xcccn,xchcn,xcocn,ixmin,iymin,izmin,
- pcorn,dxccij,dxchij,dxcoij,param);
+ pcorn,dxccij,dxchij,dxcoij,param);
}
else {
pcorn = pcn_grid[tri_flag-1][ixmin][iymin][izmin];
@@ -2107,8 +2107,8 @@ void PairComb3::coord(Param *param, double r, int i,
/* ---------------------------------------------------------------------- */
-void PairComb3::cntri_int(int tri_flag, double xval, double yval,
- double zval, int ixmin, int iymin, int izmin, double &vval,
+void PairComb3::cntri_int(int tri_flag, double xval, double yval,
+ double zval, int ixmin, int iymin, int izmin, double &vval,
double &dvalx, double &dvaly, double &dvalz, Param *param)
{
double x;
@@ -2121,7 +2121,7 @@ void PairComb3::cntri_int(int tri_flag, double xval, double yval,
*pow(xval,iin3[j][0])*pow(yval,iin3[j][1])
*pow(zval,iin3[j][2]);
vval += x;
- if(xval>1.0e-8) {dvalx += x*iin3[j][0]/xval;}
+ if(xval>1.0e-8) {dvalx += x*iin3[j][0]/xval;}
if(yval>1.0e-8) {dvaly += x*iin3[j][1]/yval;}
if(zval>1.0e-8) {dvalz += x*iin3[j][2]/zval;}
}
@@ -2131,11 +2131,11 @@ void PairComb3::cntri_int(int tri_flag, double xval, double yval,
double PairComb3::comb_gijk(double costheta, Param *param, double nco_tmp)
{
- double rmu1 = costheta;
- double rmu2 = rmu1*rmu1;
+ double rmu1 = costheta;
+ double rmu2 = rmu1*rmu1;
double rmu3 = rmu2*rmu1;
- double rmu4 = rmu3*rmu1;
- double rmu5 = rmu4*rmu1;
+ double rmu4 = rmu3*rmu1;
+ double rmu5 = rmu4*rmu1;
double rmu6 = rmu5*rmu1;
double co6 = param->pcos6*rmu6;
double co5 = param->pcos5*rmu5;
@@ -2154,10 +2154,10 @@ double PairComb3::comb_gijk(double costheta, Param *param, double nco_tmp)
qtheta = comb_fccc(nco_tmp);
astep = 2.0/ntab;
rrmu = (rmu1+1.0)/astep;
- k = int(rrmu);
+ k = int(rrmu);
gmu1 = co6+co5+co4+co3+co2+co1+co0;
gmu2 = pang[k]+(pang[k+1]-pang[k])*(rrmu-k);
- gmu = gmu2+qtheta*(gmu1-gmu2);
+ gmu = gmu2+qtheta*(gmu1-gmu2);
return gmu*pcross;
} else if (param->ang_flag==2){
@@ -2172,7 +2172,7 @@ double PairComb3::comb_gijk(double costheta, Param *param, double nco_tmp)
qtheta = comb_fccch(nco_tmp);
gmu1 = co6+co5+co4+co3+co2+co1+co0;
gmu2 = ch6+ch5+ch4+ch3+ch2+ch1+ch0;
- gmu = gmu2+qtheta*(gmu1-gmu2);
+ gmu = gmu2+qtheta*(gmu1-gmu2);
return gmu*pcross;
} else {
gmu = co6+co5+co4+co3+co2+co1+co0;
@@ -2185,10 +2185,10 @@ double PairComb3::comb_gijk(double costheta, Param *param, double nco_tmp)
void PairComb3::comb_gijk_d(double costheta, Param *param, double nco_tmp,
double &gijk_d, double &com3jk)
{
- double rmu1 = costheta;
- double rmu2 = rmu1*rmu1;
+ double rmu1 = costheta;
+ double rmu2 = rmu1*rmu1;
double rmu3 = rmu2*rmu1;
- double rmu4 = rmu3*rmu1;
+ double rmu4 = rmu3*rmu1;
double rmu5 = rmu4*rmu1;
double rmu6 = rmu5*rmu1;
double co6 = param->pcos6; //*rmu5*6.0;
@@ -2206,7 +2206,7 @@ void PairComb3::comb_gijk_d(double costheta, Param *param, double nco_tmp,
int k;
qtheta = comb_fccc(nco_tmp);
dqtheta = comb_fccc_d(nco_tmp);
-
+
astep = 2.0/ntab;
rrmu = (rmu1+1.0)/astep;
k = int(rrmu);
@@ -2230,7 +2230,7 @@ void PairComb3::comb_gijk_d(double costheta, Param *param, double nco_tmp,
double ch0 = ch_a[0];
qtheta = comb_fccch(nco_tmp);
dqtheta = comb_fccch_d(nco_tmp);
-
+
gmu1 =rmu6*co6+rmu5*co5+rmu4*co4
+rmu3*co3+rmu2*co2+rmu1*co1+co0;
dgmu1 =6.0*rmu5*co6+5.0*rmu4*co5+4.0*rmu3*co4
@@ -2251,9 +2251,9 @@ void PairComb3::comb_gijk_d(double costheta, Param *param, double nco_tmp,
/*------------------------------------------------------------------------- */
-void PairComb3::attractive(Param *parami, Param *paramj , Param *paramk, double prefac_ij1,
- double prefac_ij2, double prefac_ij3, double prefac_ij4,
- double prefac_ij5, double rsqij, double rsqik, double *delrij,
+void PairComb3::attractive(Param *parami, Param *paramj , Param *paramk, double prefac_ij1,
+ double prefac_ij2, double prefac_ij3, double prefac_ij4,
+ double prefac_ij5, double rsqij, double rsqik, double *delrij,
double *delrik, double *fi, double *fj,double *fk, int i, double xcn)
{
double rij_hat[3],rik_hat[3];
@@ -2262,7 +2262,7 @@ void PairComb3::attractive(Param *parami, Param *paramj , Param *paramk, double
rij = sqrt(rsqij);
rijinv = 1.0/rij;
vec3_scale(rijinv,delrij,rij_hat);
-
+
rik = sqrt(rsqik);
rikinv = 1.0/rik;
vec3_scale(rikinv,delrik,rik_hat);
@@ -2276,7 +2276,7 @@ void PairComb3::attractive(Param *parami, Param *paramj , Param *paramk, double
void PairComb3::comb_zetaterm_d(double prefac_ij1, double prefac_ij2,
double prefac_ij3, double prefac_ij4, double prefac_ij5,
- double *rij_hat, double rij, double *rik_hat, double rik, double *dri,
+ double *rij_hat, double rij, double *rik_hat, double rik, double *dri,
double *drj, double *drk, Param *parami, Param *paramj, Param *paramk, double xcn)
{
double gijk,gijk_d,ex_delr,ex_delr_d,fc_k,cos_theta,tmp,rlm3;
@@ -2294,7 +2294,7 @@ void PairComb3::comb_zetaterm_d(double prefac_ij1, double prefac_ij2,
dfc_k = comb_fc_d(rik,paramk);
rlm3 = parami->beta;
tmp = pow(rlm3*(rij-rik),mint);
-
+
if (tmp > 69.0776) ex_delr = 1.e30;
else if (tmp < -69.0776) ex_delr = 0.0;
else ex_delr = exp(tmp);
@@ -2311,11 +2311,11 @@ void PairComb3::comb_zetaterm_d(double prefac_ij1, double prefac_ij2,
if(parami->kelementgp==2) {com6 = prefac_ij4*pcrossk*dfc_k;}
if(parami->kelementgp==3) {com6 = prefac_ij5*pcrossk*dfc_k;}
if(parami->rad_flag>=1 || parami->tor_flag!=0)
- {com6+=prefac_ij2*pcrossk*dfc_k;}
+ {com6+=prefac_ij2*pcrossk*dfc_k;}
} else {
com6 = prefac_ij2*pcrossi*dfc_k;
}
-
+
if (parami->ang_flag==1 || parami->ang_flag==2) {
com3j = com3jk*ex_delr*pcrossk*pcrossj*fc_k*dfc_i;
com3k = com3jk*ex_delr*pcrossk*pcrossk*fc_k*dfc_k;
@@ -2338,18 +2338,18 @@ void PairComb3::comb_zetaterm_d(double prefac_ij1, double prefac_ij2,
vec3_scaleadd(fc_k*gijk*ex_delr_d,rij_hat,drj,drj); // com3 cont'd
vec3_scaleadd(com3j,rij_hat,drj,drj); // com3j
vec3_scale(prefac_ij1,drj,drj);
-
+
vec3_scale(dfc_k*gijk*ex_delr,rik_hat,drk); // com1
vec3_scaleadd(fc_k*gijk_d*ex_delr,dcosdrk,drk,drk); // com2
vec3_scaleadd(-fc_k*gijk*ex_delr_d,rik_hat,drk,drk); // com3 cont'd
- vec3_scaleadd(com3k,rik_hat,drk,drk); // com3k
+ vec3_scaleadd(com3k,rik_hat,drk,drk); // com3k
vec3_scale(prefac_ij1,drk,drk);
vec3_scaleadd(com6,rik_hat,drk,drk); // com6
}
/* ---------------------------------------------------------------------- */
-void PairComb3::costheta_d(double *rij_hat, double rij, double *rik_hat,
+void PairComb3::costheta_d(double *rij_hat, double rij, double *rik_hat,
double rik, double *dri, double *drj, double *drk)
{
double cos_theta = vec3_dot(rij_hat,rik_hat);
@@ -2365,7 +2365,7 @@ void PairComb3::costheta_d(double *rij_hat, double rij, double *rik_hat,
/* ---------------------------------------------------------------------- */
void PairComb3::tables()
-
+
{
int i,j,k,m, nntypes, ncoul,nnbuf, ncoul_lim, inty, itype, jtype;
int iparam_i, iparam_ij, iparam_ji;
@@ -2375,19 +2375,19 @@ void PairComb3::tables()
double afbshift, dafbshift, exp2ershift;
int n = nelements;
-
- dra = 0.001;
- drin = 0.100;
+
+ dra = 0.001;
+ drin = 0.100;
drbuf = 0.100;
- nnbuf = int(drbuf/dra) +1;
+ nnbuf = int(drbuf/dra) +1;
rc = cutmax;
alf = 0.20;
nmax = atom->nmax;
-
+
nntypes = int((n+1)*n/2.0)+1;
ncoul = int((rc-drin)/dra)+ nnbuf;
ncoul_lim = int(ncoul * 1.20);
-
+
// allocate arrays
memory->create(intype,n,n,"pair:intype");
memory->create(erpaw,ncoul_lim,3,"pair:erpaw");
@@ -2411,11 +2411,11 @@ void PairComb3::tables()
"pair:sht_first");
// set interaction number: 0-0=0, 1-1=1, 0-1=1-0=2
-
+
m = 0; k = n;
for (i = 0; i < n; i++) {
for (j = 0; j < n; j++) {
- if (j == i) {
+ if (j == i) {
intype[i][j] = m;
m += 1;
} else if (j != i && j > i) {
@@ -2426,26 +2426,26 @@ void PairComb3::tables()
}
}
}
-
+
// default arrays to zero
-
+
for (i = 0; i < ncoul; i ++) {
for (j = 0; j < nntypes; j ++) {
- fafb[i][j] = 0.0;
- dfafb[i][j] = 0.0;
- ddfafb[i][j] = 0.0;
- phin[i][j] = 0.0;
+ fafb[i][j] = 0.0;
+ dfafb[i][j] = 0.0;
+ ddfafb[i][j] = 0.0;
+ phin[i][j] = 0.0;
dphin[i][j] = 0.0;
- afb[i][j] = 0.0;
+ afb[i][j] = 0.0;
dafb[i][j] = 0.0;
}
}
// direct 1/r energy with Slater 1S orbital overlap
-
+
for (i = 0; i < n; i++) {
if (map[i+1] < 0) continue;
- r = drin - dra;
+ r = drin - dra;
itype = map[i+1];
iparam_i = elem2param[itype][itype][itype];
z = params[iparam_i].esm;
@@ -2455,7 +2455,7 @@ void PairComb3::tables()
if (comm->me == 0 && screen)
fprintf(screen," element[%d] = %-2s, z = %g\n",i+1,elements[map[i+1]],z);
-
+
for (j = 0; j < ncoul; j++) {
exp2er = exp(-2.0 * z * r);
phin[j][i] = 1.0 - exp2er * (1.0 + 2.0 * z * r * (1.0 + z * r));
@@ -2470,7 +2470,7 @@ void PairComb3::tables()
if (map[i+1] < 0) continue;
for (j = 0; j < n; j ++) {
if (map[j+1] < 0) continue;
- r = drin - dra;
+ r = drin - dra;
if (j == i) {
itype = map[i+1];
inty = intype[itype][itype];
@@ -2478,23 +2478,23 @@ void PairComb3::tables()
z = params[iparam_i].esm;
zrc = z * rc;
exp2ersh = exp(-2.0 * zrc);
- fafash = -exp2ersh * (1.0 / rc +
+ fafash = -exp2ersh * (1.0 / rc +
z * (11.0/8.0 + 3.0/4.0*zrc + zrc*zrc/6.0));
dfafash = exp2ersh * (1.0/(rc*rc) + 2.0*z/rc +
z*z*(2.0 + 7.0/6.0*zrc + zrc*zrc/3.0));
for (k = 0; k < ncoul; k ++) {
- zr = z * r;
+ zr = z * r;
exp2er = exp(-2.0*zr);
- F1 = -exp2er * (1.0 / r +
+ F1 = -exp2er * (1.0 / r +
z * (11.0/8.0 + 3.0/4.0*zr + zr*zr/6.0));
dF1 = exp2er * (1.0/(r*r) + 2.0*z/r +
z*z*(2.0 + 7.0/6.0*zr + zr*zr/3.0));
- ddF1 = -exp2er * (2.0/(r*r*r) + 4.0*z/(r*r) + 4.0*z*z/r +
+ ddF1 = -exp2er * (2.0/(r*r*r) + 4.0*z/(r*r) + 4.0*z*z/r +
z*z*z/3.0*(17.0/2.0 + 5.0*zr + 2.0*zr*zr));
fafb[k][inty] = F1-fafash-(r-rc)*dfafash;
dfafb[k][inty] = -(dF1 - dfafash);
ddfafb[k][inty] = ddF1;
- r += dra;
+ r += dra;
}
} else if (j != i) {
itype = map[i+1];
@@ -2508,20 +2508,20 @@ void PairComb3::tables()
eb3 = eb*eb*eb;
E1 = ea*eb3*eb/((ea+eb)*(ea+eb)*(ea-eb)*(ea-eb));
E2 = eb*ea3*ea/((ea+eb)*(ea+eb)*(eb-ea)*(eb-ea));
- E3 = (3.0*ea*ea*eb3*eb-eb3*eb3) /
+ E3 = (3.0*ea*ea*eb3*eb-eb3*eb3) /
((ea+eb)*(ea+eb)*(ea+eb)*(ea-eb)*(ea-eb)*(ea-eb));
- E4 = (3.0*eb*eb*ea3*ea-ea3*ea3) /
+ E4 = (3.0*eb*eb*ea3*ea-ea3*ea3) /
((ea+eb)*(ea+eb)*(ea+eb)*(eb-ea)*(eb-ea)*(eb-ea));
exp2earsh = exp(-2.0*ea*rc);
exp2ebrsh = exp(-2.0*eb*rc);
fafbsh = -exp2earsh*(E1 + E3/rc)-exp2ebrsh*(E2 + E4/rc);
- dfafbsh =
+ dfafbsh =
exp2earsh*(2.0*ea*(E1+E3/rc)+E3/(rc*rc)) +
exp2ebrsh*(2.0*eb*(E2+E4/rc)+E4/(rc*rc));
for (k = 0; k < ncoul; k ++) {
exp2ear = exp(-2.0*ea*r);
exp2ebr = exp(-2.0*eb*r);
- fafb[k][inty] =
+ fafb[k][inty] =
- exp2ear*(E1+E3/r) - exp2ebr*(E2+E4/r)
- fafbsh - (r-rc) * dfafbsh;
dfafb[k][inty] = -(exp2ear*(2.0*ea*(E1+E3/r) + E3/(r*r))
@@ -2530,9 +2530,9 @@ void PairComb3::tables()
+2.0*E3/(r*r*r))
-exp2ebr*(4.0*eb*eb*(E2+E4/r)+4.0*eb*E4/(r*r)
+2.0*E4/(r*r*r));
- r += dra;
+ r += dra;
}
- }
+ }
}
}
@@ -2540,7 +2540,7 @@ void PairComb3::tables()
r = dra * (i-1) + drin;
erpaw[i][0] = erfc(r*alf);
erpaw[i][1] = exp(-r*r*alf*alf);
- }
+ }
// end wolf summation
// van der Waals
@@ -2552,8 +2552,8 @@ void PairComb3::tables()
vrc = new double[13];
rrc = new double[13];
- cc2 = new double[nntypes];
- cc3 = new double[nntypes];
+ cc2 = new double[nntypes];
+ cc3 = new double[nntypes];
memory->create(rvdw,2,nntypes,"pair:rvdw");
vrc[0] = rc;
@@ -2568,8 +2568,8 @@ void PairComb3::tables()
jtype = jj;
inty = intype[itype][jtype];
iparam_ij = elem2param[itype][jtype][jtype];
-
- // parameter check: eps > 0
+
+ // parameter check: eps > 0
if(params[iparam_ij].vdwflag > 0) {
if(params[iparam_ij].vdwflag==1){
@@ -2578,7 +2578,7 @@ void PairComb3::tables()
else {
rvdw[0][inty] = params[iparam_ij].bigr - params[iparam_ij].bigd;
}
-
+
rvdw[1][inty] = params[iparam_ij].vsig * 0.950;
// radius check: outer radius vs. sigma
@@ -2625,11 +2625,11 @@ void PairComb3::tables()
vepst = params[iparam_ij].veps;
vsigt = vsigt*vsigt*vsigt*vsigt*vsigt*vsigt;
- if(params[iparam_ij].vdwflag>0) {
+ if(params[iparam_ij].vdwflag>0) {
if(r <= rvdw[0][inty]) {
vvdw[k][inty] = 0.0;
vdvdw[k][inty] = 0.0;
- }
+ }
else if ( r > rvdw[0][inty] && r <= rvdw[1][inty]) {
drcc = r-rvdw[0][inty];
vvdw[k][inty] = drcc*drcc*(drcc*cc3[inty]+cc2[inty]);
@@ -2646,7 +2646,7 @@ void PairComb3::tables()
vvdw[k][inty]=0.0;
vdvdw[k][inty]=0.0;
}
- r += dra;
+ r += dra;
}
}
}
@@ -2664,11 +2664,11 @@ void PairComb3::potal_calc(double &calc1, double &calc2, double &calc3)
{
double alf,rcoul,esucon;
int m;
-
+
rcoul = 0.0;
for (m = 0; m < nparams; m++)
if (params[m].lcut > rcoul) rcoul = params[m].lcut;
-
+
alf = 0.20;
esucon = force->qqr2e;
@@ -2680,7 +2680,7 @@ void PairComb3::potal_calc(double &calc1, double &calc2, double &calc3)
/* ---------------------------------------------------------------------- */
-void PairComb3::tri_point(double rsq, int &mr1, int &mr2,
+void PairComb3::tri_point(double rsq, int &mr1, int &mr2,
int &mr3, double &sr1, double &sr2, double &sr3)
{
double r, rin, dr, dd, rr1, rridr, rridr2;
@@ -2710,7 +2710,7 @@ void PairComb3::tri_point(double rsq, int &mr1, int &mr2,
/* ---------------------------------------------------------------------- */
void PairComb3::vdwaals(int inty, int mr1, int mr2, int mr3, double rsq,
- double sr1, double sr2, double sr3,
+ double sr1, double sr2, double sr3,
double &eng, double &fforce)
{
double r = sqrt(rsq);
@@ -2721,9 +2721,9 @@ void PairComb3::vdwaals(int inty, int mr1, int mr2, int mr3, double rsq,
/* ---------------------------------------------------------------------- */
-void PairComb3::direct(Param *parami, Param *paramj, int mr1,
- int mr2, int mr3, double rsq, double sr1, double sr2, double sr3,
- double iq, double jq, double fac11, double fac11e,
+void PairComb3::direct(Param *parami, Param *paramj, int mr1,
+ int mr2, int mr3, double rsq, double sr1, double sr2, double sr3,
+ double iq, double jq, double fac11, double fac11e,
double &pot_tmp, double &for_tmp, int i, int j)
{
double r,erfcc,fafbnl,potij,esucon;
@@ -2755,7 +2755,7 @@ void PairComb3::direct(Param *parami, Param *paramj, int mr1,
icurl=1;
curlij1=curli;
}
-
+
if(jelegp==2 && curlj>curlji0) {
jcurl=1;
curlji1=curlj;
@@ -2764,7 +2764,7 @@ void PairComb3::direct(Param *parami, Param *paramj, int mr1,
if(icurl==1 || jcurl ==1) {
xcoij = xcotmp[i];
xcoji = xcotmp[j];
- fcp1j = comb_fc_d(r,parami);
+ fcp1j = comb_fc_d(r,parami);
if(icurl==1) {
curli=curlij1+(curlij0-curlij1)*comb_fc_curl(xcoij,parami);
@@ -2787,7 +2787,7 @@ void PairComb3::direct(Param *parami, Param *paramj, int mr1,
sme1j = jq*curli*(afbj-fafbnl)*esucon;
sme1 = sme1n + sme1j;
sme2 = (potij + fafbnl * esucon) * iq * jq;
- pot_tmp = 1.0 * (sme1+sme2);
+ pot_tmp = 1.0 * (sme1+sme2);
// 1/r force (wrt r)
@@ -2828,15 +2828,15 @@ void PairComb3::field(Param *parami, Param *paramj, double rsq, double iq,
r4 = r3 * r;
r5 = r4 * r;
rc = parami->lcut;
- rc2 = rc * rc;
+ rc2 = rc * rc;
rc3 = rc*rc*rc;
rc4 = rc3 * rc;
rc5 = rc4 * rc;
- cmi1 = parami->cmn1;
+ cmi1 = parami->cmn1;
cmi2 = parami->cmn2;
- cmj1 = paramj->cmn1;
+ cmj1 = paramj->cmn1;
cmj2 = paramj->cmn2;
- pcmi1 = parami->pcmn1;
+ pcmi1 = parami->pcmn1;
pcmi2 = parami->pcmn2;
rf3i = r3/(pow(r3,2)+pow(pcmi1,3));
@@ -2881,7 +2881,7 @@ double PairComb3::rad_init(double rsq2,Param *param,int i,
/* ---------------------------------------------------------------------- */
-void PairComb3::rad_calc(double r, Param *parami, Param *paramj,
+void PairComb3::rad_calc(double r, Param *parami, Param *paramj,
double kconjug, double lconjug, int i, int j, double xcn, double ycn)
{
int ixmin, iymin, izmin;
@@ -2893,16 +2893,16 @@ void PairComb3::rad_calc(double r, Param *parami, Param *paramj,
yrad = -comb_fc(r,paramj)*paramj->pcross + ycn;
zcon = 1.0 + pow(kconjug,2) + pow(lconjug,2);
- if(xrad < 0.0) xrad = 0.0;
+ if(xrad < 0.0) xrad = 0.0;
if(yrad < 0.0) yrad = 0.0;
if(zcon < 1.0) zcon = 1.0;
- if(xrad > maxxc) xrad = maxxc;
+ if(xrad > maxxc) xrad = maxxc;
if(yrad > maxyc) yrad = maxyc;
if(zcon > maxconj) zcon = maxconj;
ixmin = int(xrad+1.0e-12);
iymin = int(yrad+1.0e-12);
izmin = int(zcon+1.0e-12);
- radindx=parami->rad_flag-1;
+ radindx=parami->rad_flag-1;
if (fabs(float(ixmin)-xrad)>1.0e-8 ||
fabs(float(iymin)-yrad)>1.0e-8 ||
fabs(float(izmin)-zcon)>1.0e-8) {
@@ -2923,14 +2923,14 @@ void PairComb3::rad_calc(double r, Param *parami, Param *paramj,
/* ---------------------------------------------------------------------- */
-void PairComb3::rad_int(int radindx,double xrad, double yrad, double zcon, int l,
- int m, int n, double &vrad, double &pradx, double &prady,
+void PairComb3::rad_int(int radindx,double xrad, double yrad, double zcon, int l,
+ int m, int n, double &vrad, double &pradx, double &prady,
double &pradz)
{
int j;
double x;
- vrad = pradx = prady = pradz = 0.0;
- if(l >= maxxc-1) { l=maxxc-1;}
+ vrad = pradx = prady = pradz = 0.0;
+ if(l >= maxxc-1) { l=maxxc-1;}
if(m >= maxyc-1) { m=maxyc-1; }
if(n >= maxconj-1) { n=maxconj-1;}
@@ -2938,7 +2938,7 @@ void PairComb3::rad_int(int radindx,double xrad, double yrad, double zcon, int l
x = rad_spl[radindx][l][m][n-1][j] * pow(xrad,iin3[j][0])
* pow(yrad,iin3[j][1]) * pow(zcon,iin3[j][2]);
vrad += x;
- if(xrad > 1.0e-8) pradx += x*iin3[j][0]/xrad;
+ if(xrad > 1.0e-8) pradx += x*iin3[j][0]/xrad;
if(yrad > 1.0e-8) prady += x*iin3[j][1]/yrad;
if(zcon > 1.0e-8) pradz += x*iin3[j][2]/zcon;
}
@@ -2975,14 +2975,14 @@ void PairComb3::rad_forceik(Param *paramk, double rsq2, double *delrk,
}
for (nm=0; nm<3; nm++) {
- fi_rad[nm] = fktmp[nm];
- fk_rad[nm] = -fktmp[nm];
+ fi_rad[nm] = fktmp[nm];
+ fk_rad[nm] = -fktmp[nm];
}
}
/* ---------------------------------------------------------------------- */
-void PairComb3::rad_force(Param *paramm, double rsq3,
+void PairComb3::rad_force(Param *paramm, double rsq3,
double *delrm, double dpradk)
{
int nm;
@@ -2998,7 +2998,7 @@ void PairComb3::rad_force(Param *paramm, double rsq3,
fcp1m = comb_fc_d(rkm, paramm);
- comkm = dpradk * fcp1m * paramm->pcross;
+ comkm = dpradk * fcp1m * paramm->pcross;
ffmm2 = -comkm/rkm;
for (nm=0; nm<3; nm++) {
@@ -3013,8 +3013,8 @@ void PairComb3::rad_force(Param *paramm, double rsq3,
/* ---------------------------------------------------------------------- */
-double PairComb3::bbtor1(int torindx, Param *paramk, Param *paraml,
- double rsq1, double rsq2, double rsq3, double *delrj,
+double PairComb3::bbtor1(int torindx, Param *paramk, Param *paraml,
+ double rsq1, double rsq2, double rsq3, double *delrj,
double *delrk, double *delrl, double srmu)
{
double rmul, rij, rik, rjl;
@@ -3031,7 +3031,7 @@ double PairComb3::bbtor1(int torindx, Param *paramk, Param *paraml,
if(rmul > 0.1 ) {
double fc1k, fc1l, TT1, TT2, rmut, btt, tork[3], torl[3];
- fc1k = comb_fc(rik,paramk);
+ fc1k = comb_fc(rik,paramk);
fc1l = comb_fc(rjl,paraml);
TT1 = rik*rjl*rij*rij*srmu*rmul;
@@ -3043,16 +3043,16 @@ double PairComb3::bbtor1(int torindx, Param *paramk, Param *paraml,
torl[2] = delrj[0]*delrl[1] - delrj[1]*delrl[0];
TT2 = vec3_dot(tork,torl);
rmut = pow((TT2/TT1),2);
- if(torindx>=1) {
+ if(torindx>=1) {
btt = 1.0 - rmut;
- return btt * fc1k * fc1l;
+ return btt * fc1k * fc1l;
}
else {
- btt=paramk->ptork1-TT2/TT1;
- btt=paramk->ptork2*pow(btt,2);
- return btt * fc1k * fc1l;
+ btt=paramk->ptork1-TT2/TT1;
+ btt=paramk->ptork2*pow(btt,2);
+ return btt * fc1k * fc1l;
}
-
+
} else {
return 0.0;
}
@@ -3060,7 +3060,7 @@ double PairComb3::bbtor1(int torindx, Param *paramk, Param *paraml,
/* ---------------------------------------------------------------------- */
-void PairComb3::tor_calc(double r, Param *parami, Param *paramj,
+void PairComb3::tor_calc(double r, Param *parami, Param *paramj,
double kconjug, double lconjug, int i, int j, double xcn, double ycn)
{
int ixmin, iymin, izmin;
@@ -3091,7 +3091,7 @@ void PairComb3::tor_calc(double r, Param *parami, Param *paramj,
iymin = int(ytor+1.0e-12);
izmin = int(zcon+1.0e-12);
- torindx=torindx-1;
+ torindx=torindx-1;
if (fabs(float(ixmin)-xtor)>1.0e-8 ||
fabs(float(iymin)-ytor)>1.0e-8 ||
@@ -3130,7 +3130,7 @@ void PairComb3::tor_int(int torindx,double xtor, double ytor, double zcon, int l
* pow(ytor,iin3[j][1]) * pow(zcon,iin3[j][2]);
vtor += x;
- if(xtor > 1.0e-8 ) dtorx += x*iin3[j][0]/xtor;
+ if(xtor > 1.0e-8 ) dtorx += x*iin3[j][0]/xtor;
if(ytor > 1.0e-8 ) dtory += x*iin3[j][1]/ytor;
if(zcon > 1.0e-8 ) dtorz += x*iin3[j][2]/zcon;
}
@@ -3138,7 +3138,7 @@ void PairComb3::tor_int(int torindx,double xtor, double ytor, double zcon, int l
/* ---------------------------------------------------------------------- */
-void PairComb3::tor_force(int torindx, Param *paramk, Param *paraml,
+void PairComb3::tor_force(int torindx, Param *paramk, Param *paraml,
double srmu, double rsq1,double rsq2, double rsq3,
double *delrj, double *delrk, double *delrl)
{
@@ -3190,11 +3190,11 @@ void PairComb3::tor_force(int torindx, Param *paramk, Param *paraml,
dt2djl[0] = delrj[1]*tork[2] - delrj[2]*tork[1];
dt2djl[1] = delrj[2]*tork[0] - delrj[0]*tork[2];
dt2djl[2] = delrj[0]*tork[1] - delrj[1]*tork[0];
- dt2dij[0] = -delrk[2]*torl[1] + delrl[2]*tork[1]
+ dt2dij[0] = -delrk[2]*torl[1] + delrl[2]*tork[1]
+ delrk[1]*torl[2] - delrl[1]*tork[2];
- dt2dij[1] = -delrk[0]*torl[2] + delrl[0]*tork[2]
+ dt2dij[1] = -delrk[0]*torl[2] + delrl[0]*tork[2]
+ delrk[2]*torl[0] - delrl[2]*tork[0];
- dt2dij[2] = -delrk[1]*torl[0] + delrl[1]*tork[0]
+ dt2dij[2] = -delrk[1]*torl[0] + delrl[1]*tork[0]
+ delrk[0]*torl[1] - delrl[0]*tork[1];
rmut = TT2/TT1;
@@ -3207,7 +3207,7 @@ void PairComb3::tor_force(int torindx, Param *paramk, Param *paraml,
btt=paramk->ptork1-rmut;
btt=paramk->ptork2*pow(btt,2);
AA = -2.0 * ptorr * paramk->ptork2 *
- (paramk->ptork1-rmut) * fc1k * fc1l /TT1;
+ (paramk->ptork1-rmut) * fc1k * fc1l /TT1;
}
AA2 = AA * TT2;
@@ -3216,10 +3216,10 @@ void PairComb3::tor_force(int torindx, Param *paramk, Param *paraml,
tfij[2] = -dt1djl*AA2/rij/rjl;
tfij[3] = AA2/rij/rij - dt1djl*AA2*rmul/rij/rij;
tfik[0] = tfij[0];
- tfik[1] = (AA2/rik - btt*ptorr*fc1l*fcp1k)/rik -
+ tfik[1] = (AA2/rik - btt*ptorr*fc1l*fcp1k)/rik -
dt1dik*AA2*rmu/rik/rik;
tfjl[0] = tfij[2];
- tfjl[1] = (AA2/rjl - btt*ptorr*fc1k*fcp1l)/rjl -
+ tfjl[1] = (AA2/rjl - btt*ptorr*fc1k*fcp1l)/rjl -
dt1djl*AA2*rmul/rjl/rjl;
tjx[0] = tfij[0]*delrk[0] - tfij[1]*delrj[0];
@@ -3278,7 +3278,7 @@ double PairComb3::combqeq(double *qf_fix, int &igroup)
double potal,fac11,fac11e;
int sht_jnum,*sht_jlist;
tagint itag, jtag;
-
+
double **x = atom->x;
double *q = atom->q;
tagint *tag = atom->tag;
@@ -3332,7 +3332,7 @@ double PairComb3::combqeq(double *qf_fix, int &igroup)
sht_jlist = sht_first[i];
sht_jnum = sht_num[i];
-
+
// two-body interactions
for (jj = 0; jj < jnum; jj++) {
@@ -3354,7 +3354,7 @@ double PairComb3::combqeq(double *qf_fix, int &igroup)
iparam_ji = elem2param[jtype][itype][itype];
// long range q-dependent
-
+
if (rsq1 > params[iparam_ij].lcutsq) continue;
// polynomial three-point interpolation
@@ -3364,7 +3364,7 @@ double PairComb3::combqeq(double *qf_fix, int &igroup)
qfo_direct(¶ms[iparam_ij],¶ms[iparam_ji],
mr1,mr2,mr3,rsq1,sr1,sr2,sr3,fac11e,fqij,fqji,
iq,jq,i,j);
-
+
fqi += fqij; qf[j] += fqji;
// field correction to self energy and charge force
@@ -3406,17 +3406,17 @@ double PairComb3::combqeq(double *qf_fix, int &igroup)
// charge force in Aij and Bij
qfo_short(¶ms[iparam_ij],¶ms[iparam_ji],
rsq1,iq,jq,fqij,fqji,i,j,nj);
-
+
fqi += fqij; qf[j] += fqji;
}
qf[i] += fqi;
- }
- }
-
+ }
+ }
+
comm->reverse_comm_pair(this);
// sum charge force on each node and return it
-
+
double eneg = 0.0;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
@@ -3443,13 +3443,13 @@ double PairComb3::qfo_self(Param *param, double qi)
double s3 = param->dk;
double s4 = param->dl;
- self_d = 0.0;
+ self_d = 0.0;
qmin = param->qmin;
qmax = param->qmax;
cmin = cmax = 100.0;
self_d = s1+qi*(2.0*s2+qi*(3.0*s3+qi*4.0*s4));
-
+
if (qi < qmin) self_d += 4.0 * cmin * pow((qi-qmin),3);
if (qi > qmax) self_d += 4.0 * cmax * pow((qi-qmax),3);
@@ -3458,8 +3458,8 @@ double PairComb3::qfo_self(Param *param, double qi)
/* ---------------------------------------------------------------------- */
-void PairComb3::qfo_direct(Param *parami, Param *paramj, int mr1,
- int mr2, int mr3, double rsq, double sr1, double sr2,
+void PairComb3::qfo_direct(Param *parami, Param *paramj, int mr1,
+ int mr2, int mr3, double rsq, double sr1, double sr2,
double sr3, double fac11e, double &fqij, double &fqji,
double iq, double jq, int i, int j)
{
@@ -3494,7 +3494,7 @@ void PairComb3::qfo_direct(Param *parami, Param *paramj, int mr1,
if(icurl==1 || jcurl ==1) {
double xcoij= xcotmp[i];
double xcoji= xcotmp[j];
-
+
if(icurl==1) {
curli=curlij1+(curlij0-curlij1)*comb_fc_curl(xcoij,parami);
}
@@ -3562,7 +3562,7 @@ void PairComb3::qfo_field(Param *parami, Param *paramj, double rsq,
/* ---------------------------------------------------------------------- */
void PairComb3::qfo_dipole(double fac11, int mr1, int mr2, int mr3,
- int inty, double rsq, double *delrj, double sr1, double sr2,
+ int inty, double rsq, double *delrj, double sr1, double sr2,
double sr3, double &fqij, double &fqji, int i, int j)
{
double erfcc, erfcd, dvdrr, dfafbnl, smf2;
@@ -3629,7 +3629,7 @@ void PairComb3::qfo_short(Param *parami, Param *paramj, double rsq,
Bsi = parami->aB - pow(QOchi,10); // YYBsin
dBsi = -parami->bB * 10.0 * pow(QOchi,9.0); // YYBsiqp
}
-
+
if (jq < paramj->QL-0.2) {
jq = paramj->QL-0.2;
Dj = paramj->DL;
@@ -3644,7 +3644,7 @@ void PairComb3::qfo_short(Param *parami, Param *paramj, double rsq,
Bsj = paramj->aB - pow(QOchj,10); // YYBsij
dBsj = -paramj->bB * 10.0 * pow(QOchj,9.0); // YYBsiqpj
}
-
+
LamDiLamDj = exp(0.5*(parami->lami*Di+paramj->lami*Dj)-rlm1*r);
caj = 0.5 * tmp_fc * parami->bigA * LamDiLamDj;
@@ -3669,7 +3669,7 @@ void PairComb3::qfo_short(Param *parami, Param *paramj, double rsq,
/* ---------------------------------------------------------------------- */
void PairComb3::dipole_init(Param *parami, Param *paramj, double fac11,
- double *delrj, double rsq, int mr1, int mr2, int mr3, double sr1,
+ double *delrj, double rsq, int mr1, int mr2, int mr3, double sr1,
double sr2, double sr3, double iq, double jq, int i, int j)
{
double erfcc, erfcd, dvdrr, dfafbnl, smf2, phinn, phinj, efn, efj;
@@ -3679,7 +3679,7 @@ void PairComb3::dipole_init(Param *parami, Param *paramj, double fac11,
int inti = parami->ielement;
int intj = paramj->ielement;
int inty = intype[inti][intj];
-
+
for(nm=0; nm<3; nm++) Qext[nm] = 0.0;
r = sqrt(rsq);
@@ -3710,7 +3710,7 @@ void PairComb3::dipole_init(Param *parami, Param *paramj, double fac11,
for (nm=0; nm<3; nm++) {
dpl[i][nm] += (Qext[nm]/esucon + delrj[nm]*efn + poln[nm])*parami->polz*0.50;
dpl[j][nm] += (Qext[nm]/esucon - delrj[nm]*efj + polj[nm])*paramj->polz*0.50;
- }
+ }
}
@@ -3730,10 +3730,10 @@ double PairComb3::dipole_self(Param *parami, int i)
/* ---------------------------------------------------------------------- */
-void PairComb3::dipole_calc(Param *parami, Param *paramj, double fac11,
+void PairComb3::dipole_calc(Param *parami, Param *paramj, double fac11,
double delx, double dely, double delz, double rsq,
- int mr1, int mr2, int mr3, double sr1, double sr2, double sr3,
- double iq, double jq, int i, int j, double &vionij,
+ int mr1, int mr2, int mr3, double sr1, double sr2, double sr3,
+ double iq, double jq, int i, int j, double &vionij,
double &fvionij, double *ddprx)
{
double erfcc, erfcd, dvdrr, dfafbnl, ef, phinn, phinj, efn, efj;
@@ -3745,7 +3745,7 @@ void PairComb3::dipole_calc(Param *parami, Param *paramj, double fac11,
int inti = parami->ielement;
int intj = paramj->ielement;
int inty = intype[inti][intj];
-
+
r = sqrt(rsq);
r3 = r * rsq;
esucon = force->qqr2e;
@@ -3803,7 +3803,7 @@ void PairComb3::dipole_calc(Param *parami, Param *paramj, double fac11,
dcoef = rct * (phinn+phinj);
for (nm = 0; nm < 3; nm ++) {
- ddprx[nm] = dcoef * (ddpr*delr1[nm] - tmurn*dpl[j][nm] - tmurj*dpl[i][nm])
+ ddprx[nm] = dcoef * (ddpr*delr1[nm] - tmurn*dpl[j][nm] - tmurj*dpl[i][nm])
+ demuTmu * delr1[nm];
}
@@ -3863,7 +3863,7 @@ double PairComb3::switching_d(double rr)
/* ---------------------------------------------------------------------- */
-int PairComb3::pack_forward_comm(int n, int *list, double *buf,
+int PairComb3::pack_forward_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
@@ -3881,15 +3881,15 @@ int PairComb3::pack_forward_comm(int n, int *list, double *buf,
}
}
return m;
-}
-
+}
+
/* ---------------------------------------------------------------------- */
-
+
void PairComb3::unpack_forward_comm(int n, int first, double *buf)
-{
+{
int i,m,last;
-
- m = 0;
+
+ m = 0;
last = first + n ;
if (pack_flag == 1) {
for (i = first; i < last; i++)
@@ -3898,16 +3898,16 @@ void PairComb3::unpack_forward_comm(int n, int first, double *buf)
for (i = first; i < last; i++)
NCo[i] = buf[m++];
}
-}
+}
/* ---------------------------------------------------------------------- */
int PairComb3::pack_reverse_comm(int n, int first, double *buf)
{
int i,m,last;
-
+
m = 0;
- last = first + n;
+ last = first + n;
if (pack_flag == 1) {
for (i = first; i < last; i++)
buf[m++] = qf[i];
@@ -3916,15 +3916,15 @@ int PairComb3::pack_reverse_comm(int n, int first, double *buf)
buf[m++] = NCo[i];
}
return m;
-}
-
+}
+
/* ---------------------------------------------------------------------- */
-
+
void PairComb3::unpack_reverse_comm(int n, int *list, double *buf)
-{
+{
int i,j,m;
- m = 0;
+ m = 0;
if (pack_flag == 1) {
for (i = 0; i < n; i++) {
j = list[i];
@@ -3936,10 +3936,10 @@ void PairComb3::unpack_reverse_comm(int n, int *list, double *buf)
NCo[j] += buf[m++];
}
}
-}
+}
/* ----------------------------------------------------------------------
- memory usage of local atom-based arrays
+ memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double PairComb3::memory_usage()
diff --git a/src/MANYBODY/pair_comb3.h b/src/MANYBODY/pair_comb3.h
index e525fa416a..94490e00b5 100644
--- a/src/MANYBODY/pair_comb3.h
+++ b/src/MANYBODY/pair_comb3.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -54,7 +54,7 @@ class PairComb3 : public Pair {
double chi,dj,dk,dl,dm,esm,cmn1,cmn2,pcmn1,pcmn2;
double coulcut, lcut, lcutsq;
double veps, vsig, pcna, pcnb, pcnc, pcnd, polz, curl, pcross;
- double paaa, pbbb;
+ double paaa, pbbb;
double curlcut1, curlcut2, curl0;
};
@@ -76,7 +76,7 @@ class PairComb3 : public Pair {
// Short range neighbor list
void Short_neigh();
int pgsize, oneatom;
- int *sht_num, **sht_first;
+ int *sht_num, **sht_first;
MyPage<int> *ipage;
// loop up tables and flags
@@ -93,7 +93,7 @@ class PairComb3 : public Pair {
int cflag;
int nsplpcn,nsplrad,nspltor;
int maxx,maxy,maxz,maxxc,maxyc,maxconj;
- int maxxcn[4];
+ int maxxcn[4];
double vmaxxcn[4],dvmaxxcn[4];
int ntab;
double iin2[16][2],iin3[64][3];
@@ -111,11 +111,11 @@ class PairComb3 : public Pair {
double ddpang[20001];
//coordination spline arrays
- double pcn_grid[4][5][5][5];
+ double pcn_grid[4][5][5][5];
double pcn_gridx[4][5][5][5];
double pcn_gridy[4][5][5][5];
double pcn_gridz[4][5][5][5];
- double pcn_cubs[4][4][4][4][64];
+ double pcn_cubs[4][4][4][4][64];
//coordination spline arrays
double rad_grid[3][5][5][11];
@@ -125,7 +125,7 @@ class PairComb3 : public Pair {
double rad_spl[3][4][4][10][64];
//torsion spline arrays
- double tor_grid[1][5][5][11];
+ double tor_grid[1][5][5][11];
double tor_gridx[1][5][5][11];
double tor_gridy[1][5][5][11];
double tor_gridz[1][5][5][11];
@@ -152,11 +152,11 @@ class PairComb3 : public Pair {
// short range terms
void attractive(Param *, Param *, Param *, double, double, double, double,
- double, double, double, double *, double *, double *,
+ double, double, double, double *, double *, double *,
double *, double *, int, double);
- virtual void comb_fa(double, Param *, Param *, double, double,
+ virtual void comb_fa(double, Param *, Param *, double, double,
double &, double &);
- virtual void repulsive(Param *, Param *,double, double &, int,
+ virtual void repulsive(Param *, Param *,double, double &, int,
double &, double, double);
// bond order terms
@@ -166,17 +166,17 @@ class PairComb3 : public Pair {
double zeta(Param *, Param *, double, double, double *, double *, int, double);
void comb_bij_d(double, Param *, double, int, double &,
double &, double &, double &, double &, double &, double);
- void coord(Param *, double, int, double &, double &,
+ void coord(Param *, double, int, double &, double &,
double &, double &, double &, double);
- void comb_zetaterm_d(double, double, double, double, double,
- double *, double, double *, double, double *, double *,
+ void comb_zetaterm_d(double, double, double, double, double,
+ double *, double, double *, double, double *, double *,
double *, Param *, Param *, Param *, double);
void costheta_d(double *, double, double *, double,
double *, double *, double *);
- void force_zeta(Param *, Param *, double, double, double, double &,
- double &, double &, double &, double &, double &, double &,
- double &, double &, double &, double &, double &, double &,
- int, double &, double,double, int, int, int,
+ void force_zeta(Param *, Param *, double, double, double, double &,
+ double &, double &, double &, double &, double &, double &,
+ double &, double &, double &, double &, double &, double &,
+ int, double &, double,double, int, int, int,
double , double , double);
void cntri_int(int, double, double, double, int, int, int,
double &, double &, double &, double &, Param *);
@@ -184,14 +184,14 @@ class PairComb3 : public Pair {
// Legendre polynomials
void selfp6p(Param *, Param *, double, double &, double &);
double ep6p(Param *, Param *, double, double, double *, double * ,double &);
- void fp6p(Param *, Param *, double, double, double *, double *, double *,
+ void fp6p(Param *, Param *, double, double, double *, double *, double *,
double *, double *);
// long range q-dependent terms
double self(Param *, double);
void tables();
void potal_calc(double &, double &, double &);
- void tri_point(double, int &, int &, int &, double &, double &,
+ void tri_point(double, int &, int &, int &, double &, double &,
double &);
void vdwaals(int,int,int,int,double,double,double,double,
double &, double &);
@@ -206,7 +206,7 @@ class PairComb3 : public Pair {
// radical terms
double rad_init(double, Param *, int, double &, double);
- void rad_calc(double, Param *, Param *, double, double, int,
+ void rad_calc(double, Param *, Param *, double, double, int,
int, double, double);
void rad_int(int , double, double, double, int, int, int,
double &, double &, double &, double &);
@@ -214,27 +214,27 @@ class PairComb3 : public Pair {
void rad_force(Param *, double, double *, double);
// torsion terms
- double bbtor1(int, Param *, Param *, double, double, double,
+ double bbtor1(int, Param *, Param *, double, double, double,
double *, double *, double *, double); //modified by TAO
- void tor_calc(double, Param *, Param *, double, double, int,
+ void tor_calc(double, Param *, Param *, double, double, int,
int, double, double);
void tor_int(int , double, double, double, int, int, int,
double &, double &, double &, double &);
- void tor_force(int, Param *, Param *, double, double, double,
+ void tor_force(int, Param *, Param *, double, double, double,
double, double *, double *, double *); //modified by TAO
// charge force terms
double qfo_self(Param *, double);
- void qfo_short(Param *, Param *, double, double, double,
+ void qfo_short(Param *, Param *, double, double, double,
double &, double &, int, int, int);
- void qfo_direct(Param *, Param *, int, int, int, double,
- double, double, double, double, double &, double &,
+ void qfo_direct(Param *, Param *, int, int, int, double,
+ double, double, double, double, double &, double &,
double, double, int, int);
void qfo_field(Param *, Param *,double,double ,double ,double &, double &);
- void qfo_dipole(double, int, int, int, int, double, double *, double,
+ void qfo_dipole(double, int, int, int, int, double, double *, double,
double, double, double &, double &, int, int);
void qsolve(double *);
-
+
// dipole - polarization terms
double dipole_self(Param *, int);
void dipole_init(Param *, Param *, double, double *, double,
diff --git a/src/MANYBODY/pair_eam.cpp b/src/MANYBODY/pair_eam.cpp
index 5b832d0ab4..dc6727e1d5 100644
--- a/src/MANYBODY/pair_eam.cpp
+++ b/src/MANYBODY/pair_eam.cpp
@@ -15,10 +15,10 @@
Contributing authors: Stephen Foiles (SNL), Murray Daw (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_eam.h"
#include "atom.h"
#include "force.h"
@@ -815,7 +815,7 @@ double PairEAM::single(int i, int j, int itype, int jtype,
/* ---------------------------------------------------------------------- */
-int PairEAM::pack_forward_comm(int n, int *list, double *buf,
+int PairEAM::pack_forward_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
diff --git a/src/MANYBODY/pair_eam.h b/src/MANYBODY/pair_eam.h
index ca97175704..a941b95402 100644
--- a/src/MANYBODY/pair_eam.h
+++ b/src/MANYBODY/pair_eam.h
@@ -20,7 +20,7 @@ PairStyle(eam,PairEAM)
#ifndef LMP_PAIR_EAM_H
#define LMP_PAIR_EAM_H
-#include "stdio.h"
+#include <stdio.h>
#include "pair.h"
namespace LAMMPS_NS {
diff --git a/src/MANYBODY/pair_eam_alloy.cpp b/src/MANYBODY/pair_eam_alloy.cpp
index 13336ef823..8d040f0d39 100644
--- a/src/MANYBODY/pair_eam_alloy.cpp
+++ b/src/MANYBODY/pair_eam_alloy.cpp
@@ -15,9 +15,9 @@
Contributing authors: Stephen Foiles (SNL), Murray Daw (SNL)
------------------------------------------------------------------------- */
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_eam_alloy.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/MANYBODY/pair_eam_fs.cpp b/src/MANYBODY/pair_eam_fs.cpp
index 16f017c64b..b929920449 100644
--- a/src/MANYBODY/pair_eam_fs.cpp
+++ b/src/MANYBODY/pair_eam_fs.cpp
@@ -15,9 +15,9 @@
Contributing authors: Tim Lau (MIT)
------------------------------------------------------------------------- */
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_eam_fs.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/MANYBODY/pair_eim.cpp b/src/MANYBODY/pair_eim.cpp
index 196e899534..c25f3d92e6 100644
--- a/src/MANYBODY/pair_eim.cpp
+++ b/src/MANYBODY/pair_eim.cpp
@@ -15,10 +15,10 @@
Contributing author: Xiaowang Zhou (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_eim.h"
#include "atom.h"
#include "force.h"
@@ -1084,7 +1084,7 @@ double PairEIM::funccoul(int i, int j, double r)
/* ---------------------------------------------------------------------- */
-int PairEIM::pack_forward_comm(int n, int *list, double *buf,
+int PairEIM::pack_forward_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
diff --git a/src/MANYBODY/pair_eim.h b/src/MANYBODY/pair_eim.h
index 92261bb394..9b2d518a2a 100644
--- a/src/MANYBODY/pair_eim.h
+++ b/src/MANYBODY/pair_eim.h
@@ -20,7 +20,7 @@ PairStyle(eim,PairEIM)
#ifndef LMP_PAIR_EIM_H
#define LMP_PAIR_EIM_H
-#include "stdio.h"
+#include <stdio.h>
#include "pair.h"
namespace LAMMPS_NS {
diff --git a/src/MANYBODY/pair_lcbop.cpp b/src/MANYBODY/pair_lcbop.cpp
index 464f50cacb..fde0342dcc 100644
--- a/src/MANYBODY/pair_lcbop.cpp
+++ b/src/MANYBODY/pair_lcbop.cpp
@@ -16,11 +16,11 @@
based on pair_airebo by Ase Henry (MIT)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
-#include "mpi.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <mpi.h>
#include "pair_lcbop.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/MANYBODY/pair_lcbop.h b/src/MANYBODY/pair_lcbop.h
index 6acd3a2f46..c099c7c4a1 100644
--- a/src/MANYBODY/pair_lcbop.h
+++ b/src/MANYBODY/pair_lcbop.h
@@ -22,7 +22,7 @@ PairStyle(lcbop,PairLCBOP)
#include "pair.h"
#include "my_page.h"
-#include "math.h"
+#include <math.h>
#include "math_const.h"
namespace LAMMPS_NS {
diff --git a/src/MANYBODY/pair_nb3b_harmonic.cpp b/src/MANYBODY/pair_nb3b_harmonic.cpp
index a98bacd274..cd9b2ccd0d 100644
--- a/src/MANYBODY/pair_nb3b_harmonic.cpp
+++ b/src/MANYBODY/pair_nb3b_harmonic.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -16,10 +16,10 @@
(based on Stillinger-Weber pair style)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_nb3b_harmonic.h"
#include "atom.h"
#include "neighbor.h"
@@ -37,7 +37,7 @@ using namespace LAMMPS_NS;
#define MAXLINE 1024
#define DELTA 4
#define SMALL 0.001
-#define PI 3.141592653589793238462643383279
+#define PI 3.141592653589793238462643383279
/* ---------------------------------------------------------------------- */
@@ -170,7 +170,7 @@ void PairNb3bHarmonic::allocate()
}
/* ----------------------------------------------------------------------
- global settings
+ global settings
------------------------------------------------------------------------- */
void PairNb3bHarmonic::settings(int narg, char **arg)
@@ -226,7 +226,7 @@ void PairNb3bHarmonic::coeff(int narg, char **arg)
}
// read potential file and initialize potential parameters
-
+
read_file(arg[2]);
setup();
@@ -388,7 +388,7 @@ void PairNb3bHarmonic::read_file(char *file)
params[nparams].cutoff = atof(words[5]);
if (params[nparams].k_theta < 0.0 || params[nparams].theta0 < 0.0 ||
- params[nparams].cutoff < 0.0)
+ params[nparams].cutoff < 0.0)
error->all(FLERR,"Illegal nb3b/harmonic parameter");
nparams++;
@@ -416,7 +416,7 @@ void PairNb3bHarmonic::setup()
for (k = 0; k < nelements; k++) {
n = -1;
for (m = 0; m < nparams; m++) {
- if (i == params[m].ielement && j == params[m].jelement &&
+ if (i == params[m].ielement && j == params[m].jelement &&
k == params[m].kelement) {
if (n >= 0) error->all(FLERR,"Potential file has duplicate entry");
n = m;
@@ -430,7 +430,7 @@ void PairNb3bHarmonic::setup()
// set cutsq using shortcut to reduce neighbor list for accelerated
// calculations. cut must remain unchanged as it is a potential parameter
- // (cut = a*sigma)
+ // (cut = a*sigma)
for (m = 0; m < nparams; m++) {
@@ -448,12 +448,12 @@ void PairNb3bHarmonic::setup()
rtmp = sqrt(params[m].cutsq);
if (rtmp > cutmax) cutmax = rtmp;
}
-}
+}
/* ---------------------------------------------------------------------- */
-void PairNb3bHarmonic::threebody(Param *paramij, Param *paramik,
+void PairNb3bHarmonic::threebody(Param *paramij, Param *paramik,
Param *paramijk,
double rsq1, double rsq2,
double *delr1, double *delr2,
@@ -463,32 +463,32 @@ void PairNb3bHarmonic::threebody(Param *paramij, Param *paramik,
double r1,r2,c,s,a,a11,a12,a22;
// angle (cos and sin)
-
+
r1 = sqrt(rsq1);
r2 = sqrt(rsq2);
-
+
c = delr1[0]*delr2[0] + delr1[1]*delr2[1] + delr1[2]*delr2[2];
c /= r1*r2;
-
+
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
-
+
s = sqrt(1.0 - c*c);
if (s < SMALL) s = SMALL;
s = 1.0/s;
-
+
// force & energy
-
+
dtheta = acos(c) - paramijk->theta0;
tk = paramijk->k_theta * dtheta;
-
+
if (eflag) eng = tk*dtheta;
-
+
a = -2.0 * tk * s;
a11 = a*c / rsq1;
a12 = -a / (r1*r2);
a22 = a*c / rsq2;
-
+
fj[0] = a11*delr1[0] + a12*delr2[0];
fj[1] = a11*delr1[1] + a12*delr2[1];
fj[2] = a11*delr1[2] + a12*delr2[2];
diff --git a/src/MANYBODY/pair_nb3b_harmonic.h b/src/MANYBODY/pair_nb3b_harmonic.h
index 1469c91444..064fd2c6c0 100644
--- a/src/MANYBODY/pair_nb3b_harmonic.h
+++ b/src/MANYBODY/pair_nb3b_harmonic.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -40,7 +40,7 @@ class PairNb3bHarmonic : public Pair {
double cut,cutsq;
int ielement,jelement,kelement;
};
-
+
double cutmax; // max cutoff for all elements
int nelements; // # of unique elements
char **elements; // names of unique elements
diff --git a/src/MANYBODY/pair_polymorphic.cpp b/src/MANYBODY/pair_polymorphic.cpp
index b9d3755e6c..0d35872046 100755
--- a/src/MANYBODY/pair_polymorphic.cpp
+++ b/src/MANYBODY/pair_polymorphic.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -16,10 +16,10 @@
Based on pair_tersoff by Aidan Thompson (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_polymorphic.h"
#include "atom.h"
#include "neighbor.h"
@@ -280,7 +280,7 @@ void PairPolymorphic::compute(int eflag, int vflag)
costheta = (delr1[0]*delr2[0] + delr1[1]*delr2[1] +
delr1[2]*delr2[2]) / (r1*r2);
- iparam_ijk = elem3param[jel][iel][kel];
+ iparam_ijk = elem3param[jel][iel][kel];
TripletParameters & trip = tripletParameters[iparam_ijk];
wfac= (q.W)->value(r2);
@@ -331,7 +331,7 @@ void PairPolymorphic::compute(int eflag, int vflag)
iparam_ijk = elem3param[jel][iel][kel];
TripletParameters & trip = tripletParameters[iparam_ijk];
-
+
attractive(&q,&trip,prefactor,r1,r2,delr1,delr2,fi,fj,fk);
f[i][0] += fi[0];
@@ -366,7 +366,7 @@ void PairPolymorphic::allocate()
}
/* ----------------------------------------------------------------------
- global settings
+ global settings
------------------------------------------------------------------------- */
void PairPolymorphic::settings(int narg, char **arg)
@@ -459,8 +459,8 @@ void PairPolymorphic::coeff(int narg, char **arg)
// type_map = atom type to element in potential file
if (type_map) { delete [] type_map; }
type_map = new int[ntypes+1];
- for (int i = 0; i < ntypes+1; i++) {
- type_map[i] = -1;
+ for (int i = 0; i < ntypes+1; i++) {
+ type_map[i] = -1;
}
// elements = list of requested element names (ntypes long)
char** elements = new char*[ntypes];
@@ -479,7 +479,7 @@ void PairPolymorphic::coeff(int narg, char **arg)
setup();
if (elements)
- for (int i = 0; i < ntypes; i++)
+ for (int i = 0; i < ntypes; i++)
if (elements[i]) delete [] elements[i];
delete [] elements;
@@ -547,7 +547,7 @@ void PairPolymorphic::read_file(char *file, char** elements)
break;
}
}
- if (j == nelements)
+ if (j == nelements)
error->all(FLERR,"Element not defined in potential file");
}
if (comm->me == 0) { printf("\n"); }
@@ -586,42 +586,42 @@ void PairPolymorphic::read_file(char *file, char** elements)
read_line(fp,line);
ptr = strtok(line," \t\n\r\f"); // 1st token
strcpy(ftype,ptr);
- p.U = create_function(ftype,fp);
+ p.U = create_function(ftype,fp);
}
for (int i = 0; i < npair; i++) { // V
PairParameters & p = pairParameters[i];
read_line(fp,line);
ptr = strtok(line," \t\n\r\f"); // 1st token
strcpy(ftype,ptr);
- p.V = create_function(ftype,fp);
+ p.V = create_function(ftype,fp);
}
for (int i = 0; i < npair; i++) { // W
PairParameters & p = pairParameters[i];
read_line(fp,line);
ptr = strtok(line," \t\n\r\f"); // 1st token
strcpy(ftype,ptr);
- p.W = create_function(ftype,fp);
+ p.W = create_function(ftype,fp);
}
for (int i = 0; i < npair; i++) { // P
PairParameters & p = pairParameters[i];
read_line(fp,line);
ptr = strtok(line," \t\n\r\f"); // 1st token
strcpy(ftype,ptr);
- p.P = create_function(ftype,fp);
+ p.P = create_function(ftype,fp);
}
for (int i = 0; i < ntriple; i++) { // G
TripletParameters & p = tripletParameters[i];
read_line(fp,line);
ptr = strtok(line," \t\n\r\f"); // 1st token
strcpy(ftype,ptr);
- p.G = create_function(ftype,fp);
+ p.G = create_function(ftype,fp);
}
for (int i = 0; i < npair; i++) { // F
PairParameters & p = pairParameters[i];
read_line(fp,line);
ptr = strtok(line," \t\n\r\f"); // 1st token
strcpy(ftype,ptr);
- p.F = create_function(ftype,fp);
+ p.F = create_function(ftype,fp);
}
if (comm->me == 0) { fclose(fp); }
}
@@ -633,11 +633,11 @@ C1function * PairPolymorphic::create_function(char* ftype, FILE* fp)
char * ptr;
if (strcmp(ftype,"spline")==0) { // N, min, max, values
C1tabularFunction * f = new C1tabularFunction();
- ptr = strtok(NULL," \t\n\r\f");
+ ptr = strtok(NULL," \t\n\r\f");
int n = atof(ptr);
- ptr = strtok(NULL," \t\n\r\f");
+ ptr = strtok(NULL," \t\n\r\f");
double xmin = atof(ptr);
- ptr = strtok(NULL," \t\n\r\f");
+ ptr = strtok(NULL," \t\n\r\f");
double xmax = atof(ptr);
double * table = new double[n];
read_array(fp,n,table);
@@ -646,28 +646,28 @@ C1function * PairPolymorphic::create_function(char* ftype, FILE* fp)
return f;
}
else if (strcmp(ftype,"constant") == 0) {
- ptr = strtok(NULL," \t\n\r\f");
+ ptr = strtok(NULL," \t\n\r\f");
double c = atof(ptr);
return new C1constant(c);
}
else if (strcmp(ftype,"exponential") == 0) {
- ptr = strtok(NULL," \t\n\r\f");
+ ptr = strtok(NULL," \t\n\r\f");
double c = atof(ptr);
- ptr = strtok(NULL," \t\n\r\f");
+ ptr = strtok(NULL," \t\n\r\f");
double lambda = atof(ptr);
return new C1exponential(c,lambda);
}
else if (strcmp(ftype,"sine") == 0) {
- ptr = strtok(NULL," \t\n\r\f");
+ ptr = strtok(NULL," \t\n\r\f");
double c = atof(ptr);
- ptr = strtok(NULL," \t\n\r\f");
+ ptr = strtok(NULL," \t\n\r\f");
double w = atof(ptr);
return new C1sine(c,w);
}
else if (strcmp(ftype,"cosine") == 0) {
- ptr = strtok(NULL," \t\n\r\f");
+ ptr = strtok(NULL," \t\n\r\f");
double c = atof(ptr);
- ptr = strtok(NULL," \t\n\r\f");
+ ptr = strtok(NULL," \t\n\r\f");
double w = atof(ptr);
return new C1cosine(c,w);
}
@@ -717,7 +717,7 @@ void PairPolymorphic::attractive(PairParameters *p, TripletParameters *trip,
rijinv = 1.0/rij;
vec3_scale(rijinv,delrij,rij_hat);
-
+
rikinv = 1.0/rik;
vec3_scale(rikinv,delrik,rik_hat);
diff --git a/src/MANYBODY/pair_polymorphic.h b/src/MANYBODY/pair_polymorphic.h
index 8e7950263c..901fdaecc0 100755
--- a/src/MANYBODY/pair_polymorphic.h
+++ b/src/MANYBODY/pair_polymorphic.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -26,7 +26,7 @@ namespace LAMMPS_NS {
//===========================================
class C1function {
- public:
+ public:
C1function(){};
virtual ~C1function() {};
virtual double value(double x)=0;
@@ -34,7 +34,7 @@ class C1function {
};
//===========================================
class C1constant : public C1function {
- public:
+ public:
C1constant(double C): C_(C) {};
C1constant(): C_(0) {};
virtual double value(double x) { return C_; }
@@ -44,7 +44,7 @@ class C1constant : public C1function {
};
//===========================================
class C1exponential : public C1function {
- public:
+ public:
C1exponential(double C, double lambda): C_(C),lambda_(lambda) {};
C1exponential(): C_(0),lambda_(0) {};
virtual double value(double x) { return C_*exp(lambda_*x); }
@@ -54,7 +54,7 @@ class C1exponential : public C1function {
};
//===========================================
class C1sine : public C1function {
- public:
+ public:
C1sine(double C, double lambda): C_(C),lambda_(lambda) {};
C1sine(): C_(0),lambda_(0) {};
virtual double value(double x) { return C_*sin(lambda_*x); }
@@ -64,7 +64,7 @@ class C1sine : public C1function {
};
//===========================================
class C1cosine : public C1function {
- public:
+ public:
C1cosine(double C, double lambda): C_(C),lambda_(lambda) {};
C1cosine(): C_(0),lambda_(0) {};
virtual double value(double x) { return C_*cos(lambda_*x); }
@@ -115,7 +115,7 @@ class C1tabularFunction : public C1function {
{
resize(n);
xmin = x1;
- xmax = x2;
+ xmax = x2;
memcpy(ys,values,n*sizeof(double));
initialize();
}
@@ -256,11 +256,11 @@ class PairPolymorphic : public Pair {
bool eta; // global indicator
int nx,nr,ng; // table sizes
double maxX;
-
+
// parameter sets
PairParameters * pairParameters; // for I-J interaction
TripletParameters * tripletParameters; // for I-J-K interaction
-
+
char **elements; // names of unique elements
int **elem2param; // map: element pairs to parameters
int ***elem3param; // map: element triplets to parameters
@@ -291,7 +291,7 @@ class PairPolymorphic : public Pair {
return x[0]*y[0] + x[1]*y[1] + x[2]*y[2];
}
- inline void vec3_add(const double x[3], const double y[3],
+ inline void vec3_add(const double x[3], const double y[3],
double * const z) const {
z[0] = x[0]+y[0]; z[1] = x[1]+y[1]; z[2] = x[2]+y[2];
}
@@ -301,7 +301,7 @@ class PairPolymorphic : public Pair {
y[0] = k*x[0]; y[1] = k*x[1]; y[2] = k*x[2];
}
- inline void vec3_scaleadd(const double k, const double x[3],
+ inline void vec3_scaleadd(const double k, const double x[3],
const double y[3], double * const z) const {
z[0] = k*x[0]+y[0];
z[1] = k*x[1]+y[1];
diff --git a/src/MANYBODY/pair_sw.cpp b/src/MANYBODY/pair_sw.cpp
index 5cdd8f778e..700d0b3a83 100755
--- a/src/MANYBODY/pair_sw.cpp
+++ b/src/MANYBODY/pair_sw.cpp
@@ -15,10 +15,10 @@
Contributing author: Aidan Thompson (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_sw.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/MANYBODY/pair_tersoff.cpp b/src/MANYBODY/pair_tersoff.cpp
index 44712e691e..e5d34f07a5 100755
--- a/src/MANYBODY/pair_tersoff.cpp
+++ b/src/MANYBODY/pair_tersoff.cpp
@@ -15,10 +15,10 @@
Contributing author: Aidan Thompson (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_tersoff.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/MANYBODY/pair_tersoff_mod.cpp b/src/MANYBODY/pair_tersoff_mod.cpp
index 558e96de37..6cbf418dbe 100644
--- a/src/MANYBODY/pair_tersoff_mod.cpp
+++ b/src/MANYBODY/pair_tersoff_mod.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -13,13 +13,13 @@
/* ----------------------------------------------------------------------
Contributing author: Aidan Thompson (SNL) - original Tersoff implementation
- Vitaly Dozhdikov (JIHT of RAS) - MOD addition
+ Vitaly Dozhdikov (JIHT of RAS) - MOD addition
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_tersoff_mod.h"
#include "atom.h"
#include "neighbor.h"
@@ -162,15 +162,15 @@ void PairTersoffMOD::read_file(char *file)
params[nparams].c4 = atof(words[18]);
params[nparams].c5 = atof(words[19]);
- // currently only allow m exponent of 1
+ // currently only allow m exponent of 1
params[nparams].powermint = int(params[nparams].powerm);
if (
- params[nparams].lam3 < 0.0 || params[nparams].powern < 0.0 ||
- params[nparams].beta < 0.0 || params[nparams].lam2 < 0.0 ||
+ params[nparams].lam3 < 0.0 || params[nparams].powern < 0.0 ||
+ params[nparams].beta < 0.0 || params[nparams].lam2 < 0.0 ||
params[nparams].bigb < 0.0 || params[nparams].bigr < 0.0 ||
- params[nparams].bigd < 0.0 ||
+ params[nparams].bigd < 0.0 ||
params[nparams].bigd > params[nparams].bigr ||
params[nparams].lam3 < 0.0 || params[nparams].biga < 0.0 ||
params[nparams].powerm - params[nparams].powermint != 0.0 ||
@@ -201,7 +201,7 @@ void PairTersoffMOD::setup()
for (k = 0; k < nelements; k++) {
n = -1;
for (m = 0; m < nparams; m++) {
- if (i == params[m].ielement && j == params[m].jelement &&
+ if (i == params[m].ielement && j == params[m].jelement &&
k == params[m].kelement) {
if (n >= 0) error->all(FLERR,"Potential file has duplicate entry");
n = m;
@@ -227,7 +227,7 @@ void PairTersoffMOD::setup()
cutmax = 0.0;
for (m = 0; m < nparams; m++)
if (params[m].cut > cutmax) cutmax = params[m].cut;
-}
+}
/* ---------------------------------------------------------------------- */
@@ -238,7 +238,7 @@ double PairTersoffMOD::zeta(Param *param, double rsqij, double rsqik,
rij = sqrt(rsqij);
rik = sqrt(rsqik);
- costheta = (delrij[0]*delrik[0] + delrij[1]*delrik[1] +
+ costheta = (delrij[0]*delrik[0] + delrij[1]*delrik[1] +
delrij[2]*delrik[2]) / (rij*rik);
if (param->powermint == 3) arg = pow(param->lam3 * (rij-rik),3.0);
@@ -247,7 +247,7 @@ double PairTersoffMOD::zeta(Param *param, double rsqij, double rsqik,
if (arg > 69.0776) ex_delr = 1.e30;
else if (arg < -69.0776) ex_delr = 0.0;
else ex_delr = exp(arg);
-
+
return ters_fc(rik,param) * ters_gijk_mod(costheta,param) * ex_delr;
}
@@ -257,10 +257,10 @@ double PairTersoffMOD::ters_fc(double r, Param *param)
{
double ters_R = param->bigr;
double ters_D = param->bigd;
-
+
if (r < ters_R-ters_D) return 1.0;
if (r > ters_R+ters_D) return 0.0;
- return 0.5*(1.0 - 1.125*sin(MY_PI2*(r - ters_R)/ters_D) -
+ return 0.5*(1.0 - 1.125*sin(MY_PI2*(r - ters_R)/ters_D) -
0.125*sin(3*MY_PI2*(r - ters_R)/ters_D));
}
@@ -270,10 +270,10 @@ double PairTersoffMOD::ters_fc_d(double r, Param *param)
{
double ters_R = param->bigr;
double ters_D = param->bigd;
-
+
if (r < ters_R-ters_D) return 0.0;
if (r > ters_R+ters_D) return 0.0;
- return -(0.375*MY_PI4/ters_D) * (3*cos(MY_PI2*(r - ters_R)/ters_D) +
+ return -(0.375*MY_PI4/ters_D) * (3*cos(MY_PI2*(r - ters_R)/ters_D) +
cos(3*MY_PI2*(r - ters_R)/ters_D));
}
@@ -295,9 +295,9 @@ double PairTersoffMOD::ters_bij_d(double zeta, Param *param)
if (tmp > param->ca1) return -0.5*(param->powern/param->powern_del)*
pow(tmp,-0.5*(param->powern/param->powern_del)) / zeta;
if (tmp < param->ca4) return 0.0;
-
+
double tmp_n = pow(tmp,param->powern);
- return -0.5 *(param->powern/param->powern_del)*
+ return -0.5 *(param->powern/param->powern_del)*
pow(1.0+tmp_n, -1.0-(1.0/(2.0*param->powern_del)))*tmp_n / zeta;
}
diff --git a/src/MANYBODY/pair_tersoff_mod.h b/src/MANYBODY/pair_tersoff_mod.h
index fc9ac66877..d11fdf1dbb 100644
--- a/src/MANYBODY/pair_tersoff_mod.h
+++ b/src/MANYBODY/pair_tersoff_mod.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -18,7 +18,7 @@ PairStyle(tersoff/mod,PairTersoffMOD)
#else
#ifndef LMP_PAIR_TERSOFF_MOD_H
-#define LMP_PAIR_TERSOFF_MOD_H
+#define LMP_PAIR_TERSOFF_MOD_H
#include "pair_tersoff.h"
@@ -28,7 +28,7 @@ class PairTersoffMOD : public PairTersoff {
public:
PairTersoffMOD(class LAMMPS *);
~PairTersoffMOD() {}
-
+
protected:
void read_file(char *);
virtual void setup();
@@ -54,7 +54,7 @@ class PairTersoffMOD : public PairTersoff {
const double ters_c5 = param->c5;
const double tmp_h = (param->h - costheta)*(param->h - costheta);
- return ters_c1 + (ters_c2*tmp_h/(ters_c3 + tmp_h)) *
+ return ters_c1 + (ters_c2*tmp_h/(ters_c3 + tmp_h)) *
(1.0 + ters_c4*exp(-ters_c5*tmp_h));
}
@@ -68,9 +68,9 @@ class PairTersoffMOD : public PairTersoff {
const double g1 = (param->h - costheta)/(ters_c3 + tmp_h);
const double g2 = exp(-ters_c5*tmp_h);
- return -2.0*ters_c2*g1*((1 + ters_c4*g2)*(1 + g1*(costheta - param->h)) -
+ return -2.0*ters_c2*g1*((1 + ters_c4*g2)*(1 + g1*(costheta - param->h)) -
tmp_h*ters_c4*ters_c5*g2);
- }
+ }
};
}
diff --git a/src/MANYBODY/pair_tersoff_zbl.cpp b/src/MANYBODY/pair_tersoff_zbl.cpp
index 95c3dd711c..b900283ca3 100644
--- a/src/MANYBODY/pair_tersoff_zbl.cpp
+++ b/src/MANYBODY/pair_tersoff_zbl.cpp
@@ -16,10 +16,10 @@
David Farrell (NWU) - ZBL addition
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_tersoff_zbl.h"
#include "atom.h"
#include "update.h"
diff --git a/src/MANYBODY/pair_vashishta.cpp b/src/MANYBODY/pair_vashishta.cpp
index c8e6d65dc0..7c2e8c4c09 100755
--- a/src/MANYBODY/pair_vashishta.cpp
+++ b/src/MANYBODY/pair_vashishta.cpp
@@ -16,10 +16,10 @@
Aidan Thompson (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_vashishta.h"
#include "atom.h"
#include "neighbor.h"
@@ -496,7 +496,7 @@ void PairVashishta::setup()
params[m].lam1inv = 1.0/params[m].lambda1;
params[m].lam4inv = 1.0/params[m].lambda4;
params[m].zizj = params[m].zi*params[m].zj * force->qqr2e;
- // note that bigd does not have 1/2 factor
+ // note that bigd does not have 1/2 factor
params[m].mbigd = params[m].bigd;
params[m].heta = params[m].bigh*params[m].eta;
params[m].big2b = 2.0*params[m].bigb;
@@ -513,14 +513,14 @@ void PairVashishta::setup()
exp(-params[m].lam1rc);
params[m].vrcc3 = params[m].mbigd*params[m].rc4inv *
exp(-params[m].lam4rc);
- params[m].vrc = params[m].bigh*params[m].rceta +
- params[m].vrcc2 - params[m].vrcc3 -
+ params[m].vrc = params[m].bigh*params[m].rceta +
+ params[m].vrcc2 - params[m].vrcc3 -
params[m].bigw*params[m].rc6inv;
- params[m].dvrc =
- params[m].vrcc3 * (4.0*params[m].rcinv+params[m].lam4inv)
+ params[m].dvrc =
+ params[m].vrcc3 * (4.0*params[m].rcinv+params[m].lam4inv)
+ params[m].big6w * params[m].rc6inv * params[m].rcinv
- - params[m].heta * params[m].rceta*params[m].rcinv
+ - params[m].heta * params[m].rceta*params[m].rcinv
- params[m].vrcc2 * (params[m].rcinv+params[m].lam1inv);
params[m].c0 = params[m].cut*params[m].dvrc - params[m].vrc;
}
@@ -551,11 +551,11 @@ void PairVashishta::twobody(Param *param, double rsq, double &fforce,
vc2 = param->zizj * exp(-lam1r)/r;
vc3 = param->mbigd * r4inv*exp(-lam4r);
- fforce = (param->dvrc*r
+ fforce = (param->dvrc*r
- (4.0*vc3 + lam4r*vc3+param->big6w*r6inv
- param->heta*reta - vc2 - lam1r*vc2)
) * rinvsq;
- if (eflag) eng = param->bigh*reta
+ if (eflag) eng = param->bigh*reta
+ vc2 - vc3 - param->bigw*r6inv
- r*param->dvrc + param->c0;
}
diff --git a/src/MC/fix_atom_swap.cpp b/src/MC/fix_atom_swap.cpp
index fe20ce389d..7cdee69c39 100644
--- a/src/MC/fix_atom_swap.cpp
+++ b/src/MC/fix_atom_swap.cpp
@@ -16,10 +16,10 @@
Alexander Stukowski
------------------------------------------------------------------------- */
-#include "math.h"
-#include "float.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <float.h>
+#include <stdlib.h>
+#include <string.h>
#include "fix_atom_swap.h"
#include "atom.h"
#include "atom_vec.h"
@@ -61,7 +61,7 @@ FixAtomSwap::FixAtomSwap(LAMMPS *lmp, int narg, char **arg) :
if (narg < 10) error->all(FLERR,"Illegal fix atom/swap command");
dynamic_group_allow = 1;
-
+
vector_flag = 1;
size_vector = 2;
global_freq = 1;
@@ -75,9 +75,9 @@ FixAtomSwap::FixAtomSwap(LAMMPS *lmp, int narg, char **arg) :
nevery = force->inumeric(FLERR,arg[3]);
ncycles = force->inumeric(FLERR,arg[4]);
- seed = force->inumeric(FLERR,arg[5]);
+ seed = force->inumeric(FLERR,arg[5]);
double temperature = force->numeric(FLERR,arg[6]);
- beta = 1.0/(force->boltz*temperature);
+ beta = 1.0/(force->boltz*temperature);
if (ncycles < 0) error->all(FLERR,"Illegal fix atom/swap command");
if (seed <= 0) error->all(FLERR,"Illegal fix atom/swap command");
@@ -85,7 +85,7 @@ FixAtomSwap::FixAtomSwap(LAMMPS *lmp, int narg, char **arg) :
memory->create(type_list,atom->ntypes,"atom/swap:type_list");
memory->create(mu,atom->ntypes+1,"atom/swap:mu");
for (int i = 1; i <= atom->ntypes; i++) mu[i] = 0.0;
-
+
// read options from end of input line
options(narg-7,&arg[7]);
@@ -97,7 +97,7 @@ FixAtomSwap::FixAtomSwap(LAMMPS *lmp, int narg, char **arg) :
// random number generator, not the same for all procs
random_unequal = new RanPark(lmp,seed);
-
+
// set up reneighboring
force_reneighbor = 1;
@@ -128,13 +128,13 @@ void FixAtomSwap::options(int narg, char **arg)
{
if (narg < 0) error->all(FLERR,"Illegal fix atom/swap command");
- regionflag = 0;
+ regionflag = 0;
conserve_ke_flag = 1;
semi_grand_flag = 0;
nswaptypes = 0;
nmutypes = 0;
- iregion = -1;
-
+ iregion = -1;
+
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"region") == 0) {
@@ -208,7 +208,7 @@ int FixAtomSwap::setmask()
/* ---------------------------------------------------------------------- */
void FixAtomSwap::init()
-{
+{
char *id_pe = (char *) "thermo_pe";
int ipe = modify->find_compute(id_pe);
c_pe = modify->compute[ipe];
@@ -217,7 +217,7 @@ void FixAtomSwap::init()
if (nswaptypes < 2)
error->all(FLERR,"Must specify at least 2 types in fix atom/swap command");
-
+
if (semi_grand_flag) {
if (nswaptypes != nmutypes)
error->all(FLERR,"Need nswaptypes mu values in fix atom/swap command");
@@ -227,7 +227,7 @@ void FixAtomSwap::init()
if (nmutypes != 0)
error->all(FLERR,"Mu not allowed when not using semi-grand in fix atom/swap command");
}
-
+
for (int iswaptype = 0; iswaptype < nswaptypes; iswaptype++)
if (type_list[iswaptype] <= 0 || type_list[iswaptype] > atom->ntypes)
error->all(FLERR,"Invalid atom type in fix atom/swap command");
@@ -261,15 +261,15 @@ void FixAtomSwap::init()
}
}
}
-
+
memory->create(sqrt_mass_ratio,atom->ntypes+1,atom->ntypes+1,"atom/swap:sqrt_mass_ratio");
for (int itype = 1; itype <= atom->ntypes; itype++)
for (int jtype = 1; jtype <= atom->ntypes; jtype++)
sqrt_mass_ratio[itype][jtype] = sqrt(atom->mass[itype]/atom->mass[jtype]);
-
+
// check to see if itype and jtype cutoffs are the same
// if not, reneighboring will be needed between swaps
-
+
double **cutsq = force->pair->cutsq;
unequal_cutoffs = false;
for (int iswaptype = 0; iswaptype < nswaptypes; iswaptype++)
@@ -277,10 +277,10 @@ void FixAtomSwap::init()
for (int ktype = 1; ktype <= atom->ntypes; ktype++)
if (cutsq[type_list[iswaptype]][ktype] != cutsq[type_list[jswaptype]][ktype])
unequal_cutoffs = true;
-
+
// check that no swappable atoms are in atom->firstgroup
// swapping such an atom might not leave firstgroup atoms first
-
+
if (atom->firstgroup >= 0) {
int *mask = atom->mask;
int firstgroupbit = group->bitmask[atom->firstgroup];
@@ -288,7 +288,7 @@ void FixAtomSwap::init()
int flag = 0;
for (int i = 0; i < atom->nlocal; i++)
if ((mask[i] == groupbit) && (mask[i] && firstgroupbit)) flag = 1;
-
+
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
@@ -306,7 +306,7 @@ void FixAtomSwap::pre_exchange()
// just return if should not be called on this timestep
if (next_reneighbor != update->ntimestep) return;
-
+
if (domain->triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
comm->exchange();
@@ -314,9 +314,9 @@ void FixAtomSwap::pre_exchange()
if (domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
if (modify->n_pre_neighbor) modify->pre_neighbor();
neighbor->build();
-
+
energy_stored = energy_full();
-
+
int nsuccess = 0;
if (semi_grand_flag) {
update_semi_grand_atoms_list();
@@ -325,7 +325,7 @@ void FixAtomSwap::pre_exchange()
update_swap_atoms_list();
for (int i = 0; i < ncycles; i++) nsuccess += attempt_swap();
}
-
+
nswap_attempts += ncycles;
nswap_successes += nsuccess;
@@ -355,7 +355,7 @@ int FixAtomSwap::attempt_semi_grand()
}
atom->type[i] = jtype;
}
-
+
if (unequal_cutoffs) {
if (domain->triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
@@ -367,19 +367,19 @@ int FixAtomSwap::attempt_semi_grand()
} else {
comm->forward_comm_fix(this);
}
-
+
if (force->kspace) force->kspace->qsum_qsq();
double energy_after = energy_full();
int success = 0;
- if (i >= 0)
- if (random_unequal->uniform() <
+ if (i >= 0)
+ if (random_unequal->uniform() <
exp(-beta*(energy_after - energy_before
+ mu[jtype] - mu[itype]))) success = 1;
-
+
int success_all = 0;
MPI_Allreduce(&success,&success_all,1,MPI_INT,MPI_MAX,world);
-
+
if (success_all) {
update_semi_grand_atoms_list();
energy_stored = energy_after;
@@ -397,7 +397,7 @@ int FixAtomSwap::attempt_semi_grand()
}
if (force->kspace) force->kspace->qsum_qsq();
energy_stored = energy_before;
-
+
if (unequal_cutoffs) {
if (domain->triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
@@ -409,7 +409,7 @@ int FixAtomSwap::attempt_semi_grand()
} else {
comm->forward_comm_fix(this);
}
- }
+ }
return 0;
}
@@ -420,14 +420,14 @@ int FixAtomSwap::attempt_semi_grand()
int FixAtomSwap::attempt_swap()
{
if ((niswap == 0) || (njswap == 0)) return 0;
-
+
double energy_before = energy_stored;
int i = pick_i_swap_atom();
int j = pick_j_swap_atom();
int itype = type_list[0];
int jtype = type_list[1];
-
+
if (i >= 0) {
atom->type[i] = jtype;
if (atom->q_flag) atom->q[i] = qtype[1];
@@ -436,7 +436,7 @@ int FixAtomSwap::attempt_swap()
atom->type[j] = itype;
if (atom->q_flag) atom->q[j] = qtype[0];
}
-
+
if (unequal_cutoffs) {
if (domain->triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
@@ -448,10 +448,10 @@ int FixAtomSwap::attempt_swap()
} else {
comm->forward_comm_fix(this);
}
-
+
double energy_after = energy_full();
- if (random_equal->uniform() <
+ if (random_equal->uniform() <
exp(beta*(energy_before - energy_after))) {
update_swap_atoms_list();
energy_stored = energy_after;
@@ -478,7 +478,7 @@ int FixAtomSwap::attempt_swap()
if (atom->q_flag) atom->q[j] = qtype[1];
}
energy_stored = energy_before;
-
+
if (unequal_cutoffs) {
if (domain->triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
@@ -499,13 +499,13 @@ int FixAtomSwap::attempt_swap()
------------------------------------------------------------------------- */
double FixAtomSwap::energy_full()
-{
+{
int eflag = 1;
int vflag = 0;
if (modify->n_pre_neighbor) modify->pre_neighbor();
if (modify->n_pre_force) modify->pre_force(vflag);
-
+
if (force->pair) force->pair->compute(eflag,vflag);
if (atom->molecular) {
@@ -516,10 +516,10 @@ double FixAtomSwap::energy_full()
}
if (force->kspace) force->kspace->compute(eflag,vflag);
-
+
if (modify->n_post_force) modify->post_force(vflag);
if (modify->n_end_of_step) modify->end_of_step();
-
+
update->eflag_global = update->ntimestep;
double total_energy = c_pe->compute_scalar();
@@ -582,7 +582,7 @@ void FixAtomSwap::update_semi_grand_atoms_list()
{
int nlocal = atom->nlocal;
double **x = atom->x;
-
+
if (nlocal > atom_swap_nmax) {
memory->sfree(local_swap_atom_list);
atom_swap_nmax = atom->nmax;
@@ -591,9 +591,9 @@ void FixAtomSwap::update_semi_grand_atoms_list()
}
nswap_local = 0;
-
+
if (regionflag) {
-
+
for (int i = 0; i < nlocal; i++) {
if (domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2]) == 1) {
if (atom->mask[i] & groupbit) {
@@ -637,7 +637,7 @@ void FixAtomSwap::update_swap_atoms_list()
int nlocal = atom->nlocal;
int *type = atom->type;
double **x = atom->x;
-
+
if (nlocal > atom_swap_nmax) {
memory->sfree(local_swap_iatom_list);
memory->sfree(local_swap_jatom_list);
@@ -650,9 +650,9 @@ void FixAtomSwap::update_swap_atoms_list()
niswap_local = 0;
njswap_local = 0;
-
+
if (regionflag) {
-
+
for (int i = 0; i < nlocal; i++) {
if (domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2]) == 1) {
if (atom->mask[i] & groupbit) {
@@ -684,7 +684,7 @@ void FixAtomSwap::update_swap_atoms_list()
MPI_Allreduce(&niswap_local,&niswap,1,MPI_INT,MPI_SUM,world);
MPI_Scan(&niswap_local,&niswap_before,1,MPI_INT,MPI_SUM,world);
niswap_before -= niswap_local;
-
+
MPI_Allreduce(&njswap_local,&njswap,1,MPI_INT,MPI_SUM,world);
MPI_Scan(&njswap_local,&njswap_before,1,MPI_INT,MPI_SUM,world);
njswap_before -= njswap_local;
@@ -698,7 +698,7 @@ int FixAtomSwap::pack_forward_comm(int n, int *list, double *buf, int pbc_flag,
int *type = atom->type;
double *q = atom->q;
-
+
m = 0;
if (atom->q_flag) {
@@ -725,7 +725,7 @@ void FixAtomSwap::unpack_forward_comm(int n, int first, double *buf)
int *type = atom->type;
double *q = atom->q;
-
+
m = 0;
last = first + n;
@@ -791,7 +791,7 @@ void FixAtomSwap::restart(char *buf)
seed = static_cast<int> (list[n++]);
random_equal->reset(seed);
-
+
seed = static_cast<int> (list[n++]);
random_unequal->reset(seed);
diff --git a/src/MC/fix_atom_swap.h b/src/MC/fix_atom_swap.h
index 464c6a7239..066b0a3c8a 100644
--- a/src/MC/fix_atom_swap.h
+++ b/src/MC/fix_atom_swap.h
@@ -20,7 +20,7 @@ FixStyle(atom/swap,FixAtomSwap)
#ifndef LMP_FIX_MCSWAP_H
#define LMP_FIX_MCSWAP_H
-#include "stdio.h"
+#include <stdio.h>
#include "fix.h"
namespace LAMMPS_NS {
@@ -65,12 +65,12 @@ class FixAtomSwap : public Fix {
int nswaptypes,nmutypes;
int *type_list;
double *mu;
-
+
double nswap_attempts;
double nswap_successes;
bool unequal_cutoffs;
-
+
int atom_swap_nmax;
double beta;
double *qtype;
@@ -82,7 +82,7 @@ class FixAtomSwap : public Fix {
class RanPark *random_equal;
class RanPark *random_unequal;
-
+
class Compute *c_pe;
void options(int, char **);
diff --git a/src/MC/fix_bond_break.cpp b/src/MC/fix_bond_break.cpp
index bede607d76..8e48f633e0 100755
--- a/src/MC/fix_bond_break.cpp
+++ b/src/MC/fix_bond_break.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "mpi.h"
-#include "string.h"
-#include "stdlib.h"
+#include <math.h>
+#include <mpi.h>
+#include <string.h>
+#include <stdlib.h>
#include "fix_bond_break.h"
#include "update.h"
#include "respa.h"
@@ -402,7 +402,7 @@ void FixBondBreak::check_ghosts()
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
- if (flagall)
+ if (flagall)
error->all(FLERR,"Fix bond/break needs ghost atoms from further away");
lastcheck = update->ntimestep;
}
@@ -465,7 +465,7 @@ void FixBondBreak::update_topology()
if (influenced) rebuild_special_one(i);
}
-
+
int newton_bond = force->newton_bond;
int all;
@@ -829,7 +829,7 @@ void FixBondBreak::print_bb()
/* ---------------------------------------------------------------------- */
-void FixBondBreak::print_copy(const char *str, tagint m,
+void FixBondBreak::print_copy(const char *str, tagint m,
int n1, int n2, int n3, int *v)
{
printf("%s %i: %d %d %d nspecial: ",str,m,n1,n2,n3);
diff --git a/src/MC/fix_bond_break.h b/src/MC/fix_bond_break.h
index 51f926ce93..ba0e0f63b6 100755
--- a/src/MC/fix_bond_break.h
+++ b/src/MC/fix_bond_break.h
@@ -71,7 +71,7 @@ class FixBondBreak : public Fix {
void break_impropers(int, tagint, tagint);
void rebuild_special_one(int);
int dedup(int, int, tagint *);
-
+
// DEBUG
void print_bb();
diff --git a/src/MC/fix_bond_create.cpp b/src/MC/fix_bond_create.cpp
index 7b4e8a03db..6db8644cac 100755
--- a/src/MC/fix_bond_create.cpp
+++ b/src/MC/fix_bond_create.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "mpi.h"
-#include "string.h"
-#include "stdlib.h"
+#include <math.h>
+#include <mpi.h>
+#include <string.h>
+#include <stdlib.h>
#include "fix_bond_create.h"
#include "update.h"
#include "respa.h"
@@ -222,19 +222,19 @@ void FixBondCreate::init()
if (atype && force->angle) {
angleflag = 1;
- if (atype > atom->nangletypes)
+ if (atype > atom->nangletypes)
error->all(FLERR,"Fix bond/create angle type is invalid");
} else angleflag = 0;
if (dtype && force->dihedral) {
dihedralflag = 1;
- if (dtype > atom->ndihedraltypes)
+ if (dtype > atom->ndihedraltypes)
error->all(FLERR,"Fix bond/create dihedral type is invalid");
} else dihedralflag = 0;
if (itype && force->improper) {
improperflag = 1;
- if (itype > atom->nimpropertypes)
+ if (itype > atom->nimpropertypes)
error->all(FLERR,"Fix bond/create improper type is invalid");
} else improperflag = 0;
@@ -294,7 +294,7 @@ void FixBondCreate::setup(int vflag)
bondcount[i]++;
if (newton_bond) {
m = atom->map(bond_atom[i][j]);
- if (m < 0)
+ if (m < 0)
error->one(FLERR,"Fix bond/create needs ghost atoms "
"from further away");
bondcount[m]++;
@@ -605,7 +605,7 @@ void FixBondCreate::check_ghosts()
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
- if (flagall)
+ if (flagall)
error->all(FLERR,"Fix bond/create needs ghost atoms from further away");
lastcheck = update->ntimestep;
}
@@ -729,7 +729,7 @@ void FixBondCreate::rebuild_special_one(int m)
cn2 = cn1;
for (i = 0; i < cn1; i++) {
n = atom->map(copy[i]);
- if (n < 0)
+ if (n < 0)
error->one(FLERR,"Fix bond/create needs ghost atoms from further away");
slist = special[n];
n1 = nspecial[n][0];
@@ -748,7 +748,7 @@ void FixBondCreate::rebuild_special_one(int m)
cn3 = cn2;
for (i = cn1; i < cn2; i++) {
n = atom->map(copy[i]);
- if (n < 0)
+ if (n < 0)
error->one(FLERR,"Fix bond/create needs ghost atoms from further away");
slist = special[n];
n1 = nspecial[n][0];
@@ -842,7 +842,7 @@ void FixBondCreate::create_angles(int m)
for (i = 0; i < n1; i++) {
i2 = s1list[i];
i2local = atom->map(i2);
- if (i2local < 0)
+ if (i2local < 0)
error->one(FLERR,"Fix bond/create needs ghost atoms from further away");
s2list = special[i2local];
n2 = nspecial[i2local][0];
@@ -923,7 +923,7 @@ void FixBondCreate::create_dihedrals(int m)
i3 = s2list[j];
if (force->newton_bond && i2 > i3) continue;
i3local = atom->map(i3);
- if (i3local < 0)
+ if (i3local < 0)
error->one(FLERR,"Fix bond/create needs ghost atoms from further away");
s3list = special[i3local];
n3 = nspecial[i3local][0];
@@ -962,7 +962,7 @@ void FixBondCreate::create_dihedrals(int m)
i1 = s2list[i];
if (force->newton_bond && i2 > i1) continue;
i1local = atom->map(i1);
- if (i1local < 0)
+ if (i1local < 0)
error->one(FLERR,"Fix bond/create needs ghost atoms from further away");
s3list = special[i1local];
n3 = nspecial[i1local][0];
@@ -1012,7 +1012,7 @@ void FixBondCreate::create_dihedrals(int m)
for (i = 0; i < n1; i++) {
i2 = s1list[i];
i2local = atom->map(i2);
- if (i2local < 0)
+ if (i2local < 0)
error->one(FLERR,"Fix bond/create needs ghost atoms from further away");
s2list = special[i2local];
n2 = nspecial[i2local][0];
@@ -1021,7 +1021,7 @@ void FixBondCreate::create_dihedrals(int m)
i3 = s2list[j];
if (i3 == i1) continue;
i3local = atom->map(i3);
- if (i3local < 0)
+ if (i3local < 0)
error->one(FLERR,"Fix bond/create needs ghost atoms from further away");
s3list = special[i3local];
n3 = nspecial[i3local][0];
@@ -1138,7 +1138,7 @@ void FixBondCreate::create_impropers(int m)
for (i = 0; i < n2; i++) {
i1 = s2list[i];
i1local = atom->map(i1);
- if (i1local < 0)
+ if (i1local < 0)
error->one(FLERR,"Fix bond/create needs ghost atoms from further away");
s1list = special[i1local];
n1 = nspecial[i1local][0];
@@ -1410,7 +1410,7 @@ void FixBondCreate::print_bb()
printf("\n");
printf("TAG " TAGINT_FORMAT ": %d ndihedrals: ",atom->tag[i],atom->num_dihedral[i]);
for (int j = 0; j < atom->num_dihedral[i]; j++) {
- printf(" " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT " "
+ printf(" " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT " "
TAGINT_FORMAT ",", atom->dihedral_atom1[i][j],
atom->dihedral_atom2[i][j],atom->dihedral_atom3[i][j],
atom->dihedral_atom4[i][j]);
@@ -1418,7 +1418,7 @@ void FixBondCreate::print_bb()
printf("\n");
printf("TAG " TAGINT_FORMAT ": %d nimpropers: ",atom->tag[i],atom->num_improper[i]);
for (int j = 0; j < atom->num_improper[i]; j++) {
- printf(" " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT " "
+ printf(" " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT " "
TAGINT_FORMAT ",",atom->improper_atom1[i][j],
atom->improper_atom2[i][j],atom->improper_atom3[i][j],
atom->improper_atom4[i][j]);
@@ -1435,7 +1435,7 @@ void FixBondCreate::print_bb()
/* ---------------------------------------------------------------------- */
-void FixBondCreate::print_copy(const char *str, tagint m,
+void FixBondCreate::print_copy(const char *str, tagint m,
int n1, int n2, int n3, int *v)
{
printf("%s " TAGINT_FORMAT ": %d %d %d nspecial: ",str,m,n1,n2,n3);
diff --git a/src/MC/fix_bond_create.h b/src/MC/fix_bond_create.h
index 707b754067..403b1ae340 100755
--- a/src/MC/fix_bond_create.h
+++ b/src/MC/fix_bond_create.h
@@ -71,7 +71,7 @@ class FixBondCreate : public Fix {
class RanMars *random;
class NeighList *list;
-
+
int countflag,commflag;
int nlevels_respa;
int nangles,ndihedrals,nimpropers;
diff --git a/src/MC/fix_bond_swap.cpp b/src/MC/fix_bond_swap.cpp
index 448c164159..0c36cecb30 100644
--- a/src/MC/fix_bond_swap.cpp
+++ b/src/MC/fix_bond_swap.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "fix_bond_swap.h"
#include "atom.h"
#include "force.h"
@@ -652,7 +652,7 @@ int FixBondSwap::modify_param(int narg, char **arg)
strcpy(id_temp,arg[1]);
int icompute = modify->find_compute(id_temp);
- if (icompute < 0)
+ if (icompute < 0)
error->all(FLERR,"Could not find fix_modify temperature ID");
temperature = modify->compute[icompute];
diff --git a/src/MC/fix_gcmc.cpp b/src/MC/fix_gcmc.cpp
index d41e3ef325..a9c7ad439c 100644
--- a/src/MC/fix_gcmc.cpp
+++ b/src/MC/fix_gcmc.cpp
@@ -15,9 +15,9 @@
Contributing author: Paul Crozier, Aidan Thompson (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "fix_gcmc.h"
#include "atom.h"
#include "atom_vec.h"
@@ -62,11 +62,11 @@ FixGCMC::FixGCMC(LAMMPS *lmp, int narg, char **arg) :
{
if (narg < 11) error->all(FLERR,"Illegal fix gcmc command");
- if (atom->molecular == 2)
+ if (atom->molecular == 2)
error->all(FLERR,"Fix gcmc does not (yet) work with atom_style template");
dynamic_group_allow = 1;
-
+
vector_flag = 1;
size_vector = 8;
global_freq = 1;
@@ -103,17 +103,17 @@ FixGCMC::FixGCMC(LAMMPS *lmp, int narg, char **arg) :
// random number generator, not the same for all procs
random_unequal = new RanPark(lmp,seed);
-
+
// error checks on region and its extent being inside simulation box
- region_xlo = region_xhi = region_ylo = region_yhi =
+ region_xlo = region_xhi = region_ylo = region_yhi =
region_zlo = region_zhi = 0.0;
if (regionflag) {
if (domain->regions[iregion]->bboxflag == 0)
error->all(FLERR,"Fix gcmc region does not support a bounding box");
if (domain->regions[iregion]->dynamic_check())
error->all(FLERR,"Fix gcmc region cannot be dynamic");
-
+
region_xlo = domain->regions[iregion]->extent_xlo;
region_xhi = domain->regions[iregion]->extent_xhi;
region_ylo = domain->regions[iregion]->extent_ylo;
@@ -127,7 +127,7 @@ FixGCMC::FixGCMC(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,"Fix gcmc region extends outside simulation box");
// estimate region volume using MC trials
-
+
double coord[3];
int inside = 0;
int attempts = 10000000;
@@ -135,7 +135,7 @@ FixGCMC::FixGCMC(LAMMPS *lmp, int narg, char **arg) :
coord[0] = region_xlo + random_equal->uniform() * (region_xhi-region_xlo);
coord[1] = region_ylo + random_equal->uniform() * (region_yhi-region_ylo);
coord[2] = region_zlo + random_equal->uniform() * (region_zhi-region_zlo);
- if (domain->regions[iregion]->match(coord[0],coord[1],coord[2]) != 0)
+ if (domain->regions[iregion]->match(coord[0],coord[1],coord[2]) != 0)
inside++;
}
@@ -214,10 +214,10 @@ void FixGCMC::options(int narg, char **arg)
mode = ATOM;
max_rotation_angle = 10*MY_PI/180;
- regionflag = 0;
- iregion = -1;
+ regionflag = 0;
+ iregion = -1;
region_volume = 0;
- max_region_attempts = 1000;
+ max_region_attempts = 1000;
molecule_group = 0;
molecule_group_bit = 0;
molecule_group_inversebit = 0;
@@ -300,7 +300,7 @@ void FixGCMC::options(int narg, char **arg)
if (iarg+2 > narg) error->all(FLERR,"Illegal fix gcmc command");
if (ngroups >= ngroupsmax) {
ngroupsmax = ngroups+1;
- groupstrings = (char **)
+ groupstrings = (char **)
memory->srealloc(groupstrings,
ngroupsmax*sizeof(char *),
"fix_gcmc:groupstrings");
@@ -316,7 +316,7 @@ void FixGCMC::options(int narg, char **arg)
ngrouptypesmax = ngrouptypes+1;
grouptypes = (int*) memory->srealloc(grouptypes,ngrouptypesmax*sizeof(int),
"fix_gcmc:grouptypes");
- grouptypestrings = (char**)
+ grouptypestrings = (char**)
memory->srealloc(grouptypestrings,
ngrouptypesmax*sizeof(char *),
"fix_gcmc:grouptypestrings");
@@ -351,11 +351,11 @@ FixGCMC::~FixGCMC()
memory->destroy(atom_coord);
memory->destroy(coords);
memory->destroy(imageflags);
-
+
delete [] idshake;
if (ngroups > 0) {
- for (int igroup = 0; igroup < ngroups; igroup++)
+ for (int igroup = 0; igroup < ngroups; igroup++)
delete [] groupstrings[igroup];
memory->sfree(groupstrings);
}
@@ -363,7 +363,7 @@ FixGCMC::~FixGCMC()
if (ngrouptypes > 0) {
memory->destroy(grouptypes);
memory->destroy(grouptypebits);
- for (int igroup = 0; igroup < ngrouptypes; igroup++)
+ for (int igroup = 0; igroup < ngrouptypes; igroup++)
delete [] grouptypestrings[igroup];
memory->sfree(grouptypestrings);
}
@@ -381,14 +381,14 @@ int FixGCMC::setmask()
/* ---------------------------------------------------------------------- */
void FixGCMC::init()
-{
+{
triclinic = domain->triclinic;
// decide whether to switch to the full_energy option
if (!full_flag) {
- if ((force->kspace) ||
+ if ((force->kspace) ||
(force->pair == NULL) ||
(force->pair->single_enable == 0) ||
(force->pair_match("hybrid",0)) ||
@@ -396,11 +396,11 @@ void FixGCMC::init()
(triclinic == 1)
) {
full_flag = true;
- if (comm->me == 0)
+ if (comm->me == 0)
error->warning(FLERR,"Fix gcmc using full_energy option");
}
}
-
+
if (full_flag) {
char *id_pe = (char *) "thermo_pe";
int ipe = modify->find_compute(id_pe);
@@ -445,7 +445,7 @@ void FixGCMC::init()
"All mol IDs should be set for fix gcmc group atoms");
}
- if (((mode == MOLECULE) && (atom->molecule_flag == 0)) ||
+ if (((mode == MOLECULE) && (atom->molecule_flag == 0)) ||
((mode == MOLECULE) && (!atom->tag_enable || !atom->map_style)))
error->all(FLERR,
"Fix gcmc molecule command requires that "
@@ -481,14 +481,14 @@ void FixGCMC::init()
group_arg[3] = (char *) "all";
group->assign(4,group_arg);
exclusion_group = group->find(group_arg[0]);
- if (exclusion_group == -1)
+ if (exclusion_group == -1)
error->all(FLERR,"Could not find fix gcmc exclusion group ID");
exclusion_group_bit = group->bitmask[exclusion_group];
-
+
// neighbor list exclusion setup
// turn off interactions between group all and the exclusion group
-
- int narg = 4;
+
+ int narg = 4;
char **arg = new char*[narg];;
arg[0] = (char *) "exclude";
arg[1] = (char *) "group";
@@ -499,7 +499,7 @@ void FixGCMC::init()
delete [] group_arg;
delete [] arg;
}
-
+
// create a new group for temporary use with selected molecules
if (mode == MOLECULE) {
@@ -514,17 +514,17 @@ void FixGCMC::init()
group_arg[2] = digits;
group->assign(3,group_arg);
molecule_group = group->find(group_arg[0]);
- if (molecule_group == -1)
+ if (molecule_group == -1)
error->all(FLERR,"Could not find fix gcmc rotation group ID");
molecule_group_bit = group->bitmask[molecule_group];
molecule_group_inversebit = molecule_group_bit ^ ~0;
delete [] group_arg[0];
delete [] group_arg;
}
-
- // get all of the needed molecule data if mode == MOLECULE,
+
+ // get all of the needed molecule data if mode == MOLECULE,
// otherwise just get the gas mass
-
+
if (mode == MOLECULE) {
onemols[imol]->compute_mass();
@@ -535,15 +535,15 @@ void FixGCMC::init()
onemols[imol]->x[i][1] -= onemols[imol]->com[1];
onemols[imol]->x[i][2] -= onemols[imol]->com[2];
}
-
+
} else gas_mass = atom->mass[ngcmc_type];
-
+
if (gas_mass <= 0.0)
error->all(FLERR,"Illegal fix gcmc gas mass <= 0");
-
+
// check that no deletable atoms are in atom->firstgroup
// deleting such an atom would not leave firstgroup atoms first
-
+
if (atom->firstgroup >= 0) {
int *mask = atom->mask;
int firstgroupbit = group->bitmask[atom->firstgroup];
@@ -551,14 +551,14 @@ void FixGCMC::init()
int flag = 0;
for (int i = 0; i < atom->nlocal; i++)
if ((mask[i] == groupbit) && (mask[i] && firstgroupbit)) flag = 1;
-
+
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
if (flagall)
error->all(FLERR,"Cannot do GCMC on atoms in atom_modify first group");
}
-
+
// compute beta, lambda, sigma, and the zz factor
beta = 1.0/(force->boltz*reservoir_temperature);
@@ -568,17 +568,17 @@ void FixGCMC::init()
sigma = sqrt(force->boltz*reservoir_temperature*tfac_insert/gas_mass/force->mvv2e);
zz = exp(beta*chemical_potential)/(pow(lambda,3.0));
if (pressure_flag) zz = pressure*fugacity_coeff*beta/force->nktv2p;
-
- imagezero = ((imageint) IMGMAX << IMG2BITS) |
+
+ imagezero = ((imageint) IMGMAX << IMG2BITS) |
((imageint) IMGMAX << IMGBITS) | IMGMAX;
// construct group bitmask for all new atoms
// aggregated over all group keywords
-
+
groupbitall = 1 | groupbit;
for (int igroup = 0; igroup < ngroups; igroup++) {
int jgroup = group->find(groupstrings[igroup]);
- if (jgroup == -1)
+ if (jgroup == -1)
error->all(FLERR,"Could not find specified fix gcmc group ID");
groupbitall |= group->bitmask[jgroup];
}
@@ -590,7 +590,7 @@ void FixGCMC::init()
memory->create(grouptypebits,ngrouptypes,"fix_gcmc:grouptypebits");
for (int igroup = 0; igroup < ngrouptypes; igroup++) {
int jgroup = group->find(grouptypestrings[igroup]);
- if (jgroup == -1)
+ if (jgroup == -1)
error->all(FLERR,"Could not find specified fix gcmc group ID");
grouptypebits[igroup] = group->bitmask[jgroup];
}
@@ -668,9 +668,9 @@ void FixGCMC::pre_exchange()
atom->nghost = 0;
comm->borders();
if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
-
+
} else {
-
+
if (mode == MOLECULE) {
for (int i = 0; i < ncycles; i++) {
int random_int_fraction =
@@ -705,11 +705,11 @@ void FixGCMC::pre_exchange()
void FixGCMC::attempt_atomic_translation()
{
ntranslation_attempts += 1.0;
-
+
if (ngas == 0) return;
int i = pick_random_gas_atom();
-
+
int success = 0;
if (i >= 0) {
double **x = atom->x;
@@ -723,7 +723,7 @@ void FixGCMC::attempt_atomic_translation()
ry = 2*random_unequal->uniform() - 1.0;
rz = 2*random_unequal->uniform() - 1.0;
rsq = rx*rx + ry*ry + rz*rz;
- }
+ }
coord[0] = x[i][0] + displace*rx;
coord[1] = x[i][1] + displace*ry;
coord[2] = x[i][2] + displace*rz;
@@ -735,17 +735,17 @@ void FixGCMC::attempt_atomic_translation()
ry = 2*random_unequal->uniform() - 1.0;
rz = 2*random_unequal->uniform() - 1.0;
rsq = rx*rx + ry*ry + rz*rz;
- }
+ }
coord[0] = x[i][0] + displace*rx;
coord[1] = x[i][1] + displace*ry;
coord[2] = x[i][2] + displace*rz;
}
}
- if (!domain->inside_nonperiodic(coord))
+ if (!domain->inside_nonperiodic(coord))
error->one(FLERR,"Fix gcmc put atom outside box");
double energy_after = energy(i,ngcmc_type,-1,coord);
- if (random_unequal->uniform() <
+ if (random_unequal->uniform() <
exp(beta*(energy_before - energy_after))) {
x[i][0] = coord[0];
x[i][1] = coord[1];
@@ -777,13 +777,13 @@ void FixGCMC::attempt_atomic_deletion()
ndeletion_attempts += 1.0;
if (ngas == 0) return;
-
+
int i = pick_random_gas_atom();
int success = 0;
if (i >= 0) {
double deletion_energy = energy(i,ngcmc_type,-1,atom->x[i]);
- if (random_unequal->uniform() <
+ if (random_unequal->uniform() <
ngas*exp(beta*deletion_energy)/(zz*volume)) {
atom->avec->copy(atom->nlocal-1,i,1);
atom->nlocal--;
@@ -854,7 +854,7 @@ void FixGCMC::attempt_atomic_insertion()
int proc_flag = 0;
if (triclinic == 0) {
domain->remap(coord);
- if (!domain->inside(coord))
+ if (!domain->inside(coord))
error->one(FLERR,"Fix gcmc put atom outside box");
if (coord[0] >= sublo[0] && coord[0] < subhi[0] &&
coord[1] >= sublo[1] && coord[1] < subhi[1] &&
@@ -926,7 +926,7 @@ void FixGCMC::attempt_molecule_translation()
if (translation_molecule == -1) return;
double energy_before_sum = molecule_energy(translation_molecule);
-
+
double **x = atom->x;
double rx,ry,rz;
double com_displace[3],coord[3];
@@ -940,7 +940,7 @@ void FixGCMC::attempt_molecule_translation()
com_displace[0] = displace*rx;
com_displace[1] = displace*ry;
com_displace[2] = displace*rz;
-
+
int nlocal = atom->nlocal;
if (regionflag) {
int *mask = atom->mask;
@@ -964,7 +964,7 @@ void FixGCMC::attempt_molecule_translation()
ry = 2*random_equal->uniform() - 1.0;
rz = 2*random_equal->uniform() - 1.0;
rsq = rx*rx + ry*ry + rz*rz;
- }
+ }
coord[0] = com[0] + displace*rx;
coord[1] = com[1] + displace*ry;
coord[2] = com[2] + displace*rz;
@@ -980,7 +980,7 @@ void FixGCMC::attempt_molecule_translation()
coord[0] = x[i][0] + com_displace[0];
coord[1] = x[i][1] + com_displace[1];
coord[2] = x[i][2] + com_displace[2];
- if (!domain->inside_nonperiodic(coord))
+ if (!domain->inside_nonperiodic(coord))
error->one(FLERR,"Fix gcmc put atom outside box");
energy_after += energy(i,atom->type[i],translation_molecule,coord);
}
@@ -989,7 +989,7 @@ void FixGCMC::attempt_molecule_translation()
double energy_after_sum = 0.0;
MPI_Allreduce(&energy_after,&energy_after_sum,1,MPI_DOUBLE,MPI_SUM,world);
- if (random_equal->uniform() <
+ if (random_equal->uniform() <
exp(beta*(energy_before_sum - energy_after_sum))) {
for (int i = 0; i < nlocal; i++) {
if (atom->molecule[i] == translation_molecule) {
@@ -1020,7 +1020,7 @@ void FixGCMC::attempt_molecule_rotation()
tagint rotation_molecule = pick_random_gas_molecule();
if (rotation_molecule == -1) return;
-
+
double energy_before_sum = molecule_energy(rotation_molecule);
int nlocal = atom->nlocal;
@@ -1065,7 +1065,7 @@ void FixGCMC::attempt_molecule_rotation()
xtmp[0] -= com[0];
xtmp[1] -= com[1];
xtmp[2] -= com[2];
- MathExtra::matvec(rotmat,xtmp,atom_coord[n]);
+ MathExtra::matvec(rotmat,xtmp,atom_coord[n]);
atom_coord[n][0] += com[0];
atom_coord[n][1] += com[1];
atom_coord[n][2] += com[2];
@@ -1073,7 +1073,7 @@ void FixGCMC::attempt_molecule_rotation()
xtmp[1] = atom_coord[n][1];
xtmp[2] = atom_coord[n][2];
domain->remap(xtmp);
- if (!domain->inside(xtmp))
+ if (!domain->inside(xtmp))
error->one(FLERR,"Fix gcmc put atom outside box");
energy_after += energy(i,atom->type[i],rotation_molecule,xtmp);
n++;
@@ -1083,7 +1083,7 @@ void FixGCMC::attempt_molecule_rotation()
double energy_after_sum = 0.0;
MPI_Allreduce(&energy_after,&energy_after_sum,1,MPI_DOUBLE,MPI_SUM,world);
- if (random_equal->uniform() <
+ if (random_equal->uniform() <
exp(beta*(energy_before_sum - energy_after_sum))) {
int n = 0;
for (int i = 0; i < nlocal; i++) {
@@ -1115,13 +1115,13 @@ void FixGCMC::attempt_molecule_deletion()
ndeletion_attempts += 1.0;
if (ngas == 0) return;
-
+
tagint deletion_molecule = pick_random_gas_molecule();
if (deletion_molecule == -1) return;
double deletion_energy_sum = molecule_energy(deletion_molecule);
- if (random_equal->uniform() <
+ if (random_equal->uniform() <
ngas*exp(beta*deletion_energy_sum)/(zz*volume*natoms_per_molecule)) {
int i = 0;
while (i < atom->nlocal) {
@@ -1150,19 +1150,19 @@ void FixGCMC::attempt_molecule_insertion()
double com_coord[3];
if (regionflag) {
int region_attempt = 0;
- com_coord[0] = region_xlo + random_equal->uniform() *
+ com_coord[0] = region_xlo + random_equal->uniform() *
(region_xhi-region_xlo);
- com_coord[1] = region_ylo + random_equal->uniform() *
+ com_coord[1] = region_ylo + random_equal->uniform() *
(region_yhi-region_ylo);
- com_coord[2] = region_zlo + random_equal->uniform() *
+ com_coord[2] = region_zlo + random_equal->uniform() *
(region_zhi-region_zlo);
while (domain->regions[iregion]->match(com_coord[0],com_coord[1],
com_coord[2]) == 0) {
- com_coord[0] = region_xlo + random_equal->uniform() *
+ com_coord[0] = region_xlo + random_equal->uniform() *
(region_xhi-region_xlo);
- com_coord[1] = region_ylo + random_equal->uniform() *
+ com_coord[1] = region_ylo + random_equal->uniform() *
(region_yhi-region_ylo);
- com_coord[2] = region_zlo + random_equal->uniform() *
+ com_coord[2] = region_zlo + random_equal->uniform() *
(region_zhi-region_zlo);
region_attempt++;
if (region_attempt >= max_region_attempts) return;
@@ -1177,11 +1177,11 @@ void FixGCMC::attempt_molecule_insertion()
lamda[0] = random_equal->uniform();
lamda[1] = random_equal->uniform();
lamda[2] = random_equal->uniform();
-
+
// wasteful, but necessary
-
+
if (lamda[0] == 1.0) lamda[0] = 0.0;
- if (lamda[1] == 1.0) lamda[1] = 0.0;
+ if (lamda[1] == 1.0) lamda[1] = 0.0;
if (lamda[2] == 1.0) lamda[2] = 0.0;
domain->lamda2x(lamda,com_coord);
@@ -1204,7 +1204,7 @@ void FixGCMC::attempt_molecule_insertion()
MathExtra::norm3(r);
MathExtra::axisangle_to_quat(r,theta,quat);
MathExtra::quat_to_mat(quat,rotmat);
-
+
double insertion_energy = 0.0;
bool procflag[natoms_per_molecule];
@@ -1222,7 +1222,7 @@ void FixGCMC::attempt_molecule_insertion()
xtmp[1] = atom_coord[i][1];
xtmp[2] = atom_coord[i][2];
domain->remap(xtmp);
- if (!domain->inside(xtmp))
+ if (!domain->inside(xtmp))
error->one(FLERR,"Fix gcmc put atom outside box");
procflag[i] = false;
@@ -1253,28 +1253,28 @@ void FixGCMC::attempt_molecule_insertion()
MPI_DOUBLE,MPI_SUM,world);
if (random_equal->uniform() < zz*volume*natoms_per_molecule*
- exp(-beta*insertion_energy_sum)/(ngas + natoms_per_molecule)) {
+ exp(-beta*insertion_energy_sum)/(ngas + natoms_per_molecule)) {
tagint maxmol = 0;
for (int i = 0; i < atom->nlocal; i++) maxmol = MAX(maxmol,atom->molecule[i]);
tagint maxmol_all;
MPI_Allreduce(&maxmol,&maxmol_all,1,MPI_LMP_TAGINT,MPI_MAX,world);
maxmol_all++;
- if (maxmol_all >= MAXTAGINT)
+ if (maxmol_all >= MAXTAGINT)
error->all(FLERR,"Fix gcmc ran out of available molecule IDs");
tagint maxtag = 0;
for (int i = 0; i < atom->nlocal; i++) maxtag = MAX(maxtag,atom->tag[i]);
tagint maxtag_all;
MPI_Allreduce(&maxtag,&maxtag_all,1,MPI_LMP_TAGINT,MPI_MAX,world);
-
+
int nlocalprev = atom->nlocal;
-
+
double vnew[3];
vnew[0] = random_equal->gaussian()*sigma;
vnew[1] = random_equal->gaussian()*sigma;
vnew[2] = random_equal->gaussian()*sigma;
-
+
for (int i = 0; i < natoms_per_molecule; i++) {
if (procflag[i]) {
atom->avec->create_atom(onemols[imol]->type[i],atom_coord[i]);
@@ -1298,13 +1298,13 @@ void FixGCMC::attempt_molecule_insertion()
atom->v[m][0] = vnew[0];
atom->v[m][1] = vnew[1];
atom->v[m][2] = vnew[2];
-
+
atom->add_molecule_atom(onemols[imol],i,m,maxtag_all);
modify->create_attribute(m);
}
}
- if (shakeflag)
+ if (shakeflag)
fixshake->set_molecule(nlocalprev,maxtag_all,imol,com_coord,vnew,quat);
atom->natoms += natoms_per_molecule;
@@ -1328,22 +1328,22 @@ void FixGCMC::attempt_molecule_insertion()
void FixGCMC::attempt_atomic_translation_full()
{
ntranslation_attempts += 1.0;
-
+
if (ngas == 0) return;
double energy_before = energy_stored;
-
+
int i = pick_random_gas_atom();
double **x = atom->x;
double xtmp[3];
-
+
xtmp[0] = xtmp[1] = xtmp[2] = 0.0;
-
+
tagint tmptag = -1;
-
+
if (i >= 0) {
-
+
double rsq = 1.1;
double rx,ry,rz;
rx = ry = rz = 0.0;
@@ -1353,7 +1353,7 @@ void FixGCMC::attempt_atomic_translation_full()
ry = 2*random_unequal->uniform() - 1.0;
rz = 2*random_unequal->uniform() - 1.0;
rsq = rx*rx + ry*ry + rz*rz;
- }
+ }
coord[0] = x[i][0] + displace*rx;
coord[1] = x[i][1] + displace*ry;
coord[2] = x[i][2] + displace*rz;
@@ -1365,13 +1365,13 @@ void FixGCMC::attempt_atomic_translation_full()
ry = 2*random_unequal->uniform() - 1.0;
rz = 2*random_unequal->uniform() - 1.0;
rsq = rx*rx + ry*ry + rz*rz;
- }
+ }
coord[0] = x[i][0] + displace*rx;
coord[1] = x[i][1] + displace*ry;
coord[2] = x[i][2] + displace*rz;
}
}
- if (!domain->inside_nonperiodic(coord))
+ if (!domain->inside_nonperiodic(coord))
error->one(FLERR,"Fix gcmc put atom outside box");
xtmp[0] = x[i][0];
xtmp[1] = x[i][1];
@@ -1379,33 +1379,33 @@ void FixGCMC::attempt_atomic_translation_full()
x[i][0] = coord[0];
x[i][1] = coord[1];
x[i][2] = coord[2];
-
+
tmptag = atom->tag[i];
}
-
+
double energy_after = energy_full();
-
- if (random_equal->uniform() <
+
+ if (random_equal->uniform() <
exp(beta*(energy_before - energy_after))) {
energy_stored = energy_after;
ntranslation_successes += 1.0;
} else {
-
+
tagint tmptag_all;
MPI_Allreduce(&tmptag,&tmptag_all,1,MPI_LMP_TAGINT,MPI_MAX,world);
-
+
double xtmp_all[3];
MPI_Allreduce(&xtmp,&xtmp_all,3,MPI_DOUBLE,MPI_SUM,world);
-
+
for (int i = 0; i < atom->nlocal; i++) {
- if (tmptag_all == atom->tag[i]) {
+ if (tmptag_all == atom->tag[i]) {
x[i][0] = xtmp_all[0];
x[i][1] = xtmp_all[1];
x[i][2] = xtmp_all[2];
}
}
energy_stored = energy_before;
- }
+ }
update_gas_atoms_list();
}
@@ -1420,7 +1420,7 @@ void FixGCMC::attempt_atomic_deletion_full()
ndeletion_attempts += 1.0;
if (ngas == 0) return;
-
+
double energy_before = energy_stored;
const int i = pick_random_gas_atom();
@@ -1437,16 +1437,16 @@ void FixGCMC::attempt_atomic_deletion_full()
if (force->kspace) force->kspace->qsum_qsq();
double energy_after = energy_full();
- if (random_equal->uniform() <
+ if (random_equal->uniform() <
ngas*exp(beta*(energy_before - energy_after))/(zz*volume)) {
if (i >= 0) {
atom->avec->copy(atom->nlocal-1,i,1);
- atom->nlocal--;
+ atom->nlocal--;
}
atom->natoms--;
- if (atom->map_style) atom->map_init();
- ndeletion_successes += 1.0;
- energy_stored = energy_after;
+ if (atom->map_style) atom->map_init();
+ ndeletion_successes += 1.0;
+ energy_stored = energy_after;
} else {
if (i >= 0) {
atom->mask[i] = tmpmask;
@@ -1467,7 +1467,7 @@ void FixGCMC::attempt_atomic_insertion_full()
ninsertion_attempts += 1.0;
double energy_before = energy_stored;
-
+
double coord[3];
if (regionflag) {
int region_attempt = 0;
@@ -1501,11 +1501,11 @@ void FixGCMC::attempt_atomic_insertion_full()
domain->lamda2x(lamda,coord);
}
}
-
+
int proc_flag = 0;
if (triclinic == 0) {
domain->remap(coord);
- if (!domain->inside(coord))
+ if (!domain->inside(coord))
error->one(FLERR,"Fix gcmc put atom outside box");
if (coord[0] >= sublo[0] && coord[0] < subhi[0] &&
coord[1] >= sublo[1] && coord[1] < subhi[1] &&
@@ -1522,7 +1522,7 @@ void FixGCMC::attempt_atomic_insertion_full()
// add to groups
// optionally add to type-based groups
-
+
atom->mask[m] = groupbitall;
for (int igroup = 0; igroup < ngrouptypes; igroup++) {
if (ngcmc_type == grouptypes[igroup])
@@ -1545,7 +1545,7 @@ void FixGCMC::attempt_atomic_insertion_full()
comm->borders();
if (force->kspace) force->kspace->qsum_qsq();
double energy_after = energy_full();
-
+
if (random_equal->uniform() <
zz*volume*exp(beta*(energy_before - energy_after))/(ngas+1)) {
@@ -1573,7 +1573,7 @@ void FixGCMC::attempt_molecule_translation_full()
if (translation_molecule == -1) return;
double energy_before = energy_stored;
-
+
double **x = atom->x;
double rx,ry,rz;
double com_displace[3],coord[3];
@@ -1587,7 +1587,7 @@ void FixGCMC::attempt_molecule_translation_full()
com_displace[0] = displace*rx;
com_displace[1] = displace*ry;
com_displace[2] = displace*rz;
-
+
int nlocal = atom->nlocal;
if (regionflag) {
int *mask = atom->mask;
@@ -1611,7 +1611,7 @@ void FixGCMC::attempt_molecule_translation_full()
ry = 2*random_equal->uniform() - 1.0;
rz = 2*random_equal->uniform() - 1.0;
rsq = rx*rx + ry*ry + rz*rz;
- }
+ }
coord[0] = com[0] + displace*rx;
coord[1] = com[1] + displace*ry;
coord[2] = com[2] + displace*rz;
@@ -1620,7 +1620,7 @@ void FixGCMC::attempt_molecule_translation_full()
com_displace[1] = displace*ry;
com_displace[2] = displace*rz;
}
-
+
for (int i = 0; i < nlocal; i++) {
if (atom->molecule[i] == translation_molecule) {
x[i][0] += com_displace[0];
@@ -1633,7 +1633,7 @@ void FixGCMC::attempt_molecule_translation_full()
double energy_after = energy_full();
- if (random_equal->uniform() <
+ if (random_equal->uniform() <
exp(beta*(energy_before - energy_after))) {
ntranslation_successes += 1.0;
energy_stored = energy_after;
@@ -1658,10 +1658,10 @@ void FixGCMC::attempt_molecule_rotation_full()
nrotation_attempts += 1.0;
if (ngas == 0) return;
-
+
tagint rotation_molecule = pick_random_gas_molecule();
if (rotation_molecule == -1) return;
-
+
double energy_before = energy_stored;
int nlocal = atom->nlocal;
@@ -1703,14 +1703,14 @@ void FixGCMC::attempt_molecule_rotation_full()
if (mask[i] & molecule_group_bit) {
atom_coord[n][0] = x[i][0];
atom_coord[n][1] = x[i][1];
- atom_coord[n][2] = x[i][2];
- image_orig[n] = image[i];
+ atom_coord[n][2] = x[i][2];
+ image_orig[n] = image[i];
double xtmp[3];
domain->unmap(x[i],image[i],xtmp);
xtmp[0] -= com[0];
xtmp[1] -= com[1];
xtmp[2] -= com[2];
- MathExtra::matvec(rotmat,xtmp,x[i]);
+ MathExtra::matvec(rotmat,xtmp,x[i]);
x[i][0] += com[0];
x[i][1] += com[1];
x[i][2] += com[2];
@@ -1721,13 +1721,13 @@ void FixGCMC::attempt_molecule_rotation_full()
n++;
}
}
-
+
double energy_after = energy_full();
- if (random_equal->uniform() <
+ if (random_equal->uniform() <
exp(beta*(energy_before - energy_after))) {
nrotation_successes += 1.0;
- energy_stored = energy_after;
+ energy_stored = energy_after;
} else {
energy_stored = energy_before;
int n = 0;
@@ -1752,12 +1752,12 @@ void FixGCMC::attempt_molecule_deletion_full()
ndeletion_attempts += 1.0;
if (ngas == 0) return;
-
+
tagint deletion_molecule = pick_random_gas_molecule();
if (deletion_molecule == -1) return;
double energy_before = energy_stored;
-
+
int m = 0;
double q_tmp[natoms_per_molecule];
int tmpmask[atom->nlocal];
@@ -1774,7 +1774,7 @@ void FixGCMC::attempt_molecule_deletion_full()
}
}
if (force->kspace) force->kspace->qsum_qsq();
- double energy_after = energy_full();
+ double energy_after = energy_full();
// energy_before corrected by energy_intra
@@ -1803,7 +1803,7 @@ void FixGCMC::attempt_molecule_deletion_full()
atom->q[i] = q_tmp[m];
m++;
}
- }
+ }
}
if (force->kspace) force->kspace->qsum_qsq();
}
@@ -1817,7 +1817,7 @@ void FixGCMC::attempt_molecule_insertion_full()
{
double lamda[3];
ninsertion_attempts += 1.0;
-
+
double energy_before = energy_stored;
tagint maxmol = 0;
@@ -1825,33 +1825,33 @@ void FixGCMC::attempt_molecule_insertion_full()
tagint maxmol_all;
MPI_Allreduce(&maxmol,&maxmol_all,1,MPI_LMP_TAGINT,MPI_MAX,world);
maxmol_all++;
- if (maxmol_all >= MAXTAGINT)
+ if (maxmol_all >= MAXTAGINT)
error->all(FLERR,"Fix gcmc ran out of available molecule IDs");
int insertion_molecule = maxmol_all;
-
+
tagint maxtag = 0;
for (int i = 0; i < atom->nlocal; i++) maxtag = MAX(maxtag,atom->tag[i]);
tagint maxtag_all;
MPI_Allreduce(&maxtag,&maxtag_all,1,MPI_LMP_TAGINT,MPI_MAX,world);
int nlocalprev = atom->nlocal;
-
+
double com_coord[3];
if (regionflag) {
int region_attempt = 0;
- com_coord[0] = region_xlo + random_equal->uniform() *
+ com_coord[0] = region_xlo + random_equal->uniform() *
(region_xhi-region_xlo);
- com_coord[1] = region_ylo + random_equal->uniform() *
+ com_coord[1] = region_ylo + random_equal->uniform() *
(region_yhi-region_ylo);
- com_coord[2] = region_zlo + random_equal->uniform() *
+ com_coord[2] = region_zlo + random_equal->uniform() *
(region_zhi-region_zlo);
while (domain->regions[iregion]->match(com_coord[0],com_coord[1],
com_coord[2]) == 0) {
- com_coord[0] = region_xlo + random_equal->uniform() *
+ com_coord[0] = region_xlo + random_equal->uniform() *
(region_xhi-region_xlo);
- com_coord[1] = region_ylo + random_equal->uniform() *
+ com_coord[1] = region_ylo + random_equal->uniform() *
(region_yhi-region_ylo);
- com_coord[2] = region_zlo + random_equal->uniform() *
+ com_coord[2] = region_zlo + random_equal->uniform() *
(region_zhi-region_zlo);
region_attempt++;
if (region_attempt >= max_region_attempts) return;
@@ -1866,18 +1866,18 @@ void FixGCMC::attempt_molecule_insertion_full()
lamda[0] = random_equal->uniform();
lamda[1] = random_equal->uniform();
lamda[2] = random_equal->uniform();
-
+
// wasteful, but necessary
-
+
if (lamda[0] == 1.0) lamda[0] = 0.0;
- if (lamda[1] == 1.0) lamda[1] = 0.0;
+ if (lamda[1] == 1.0) lamda[1] = 0.0;
if (lamda[2] == 1.0) lamda[2] = 0.0;
domain->lamda2x(lamda,com_coord);
}
}
-
+
// generate point in unit cube
// then restrict to unit sphere
@@ -1899,7 +1899,7 @@ void FixGCMC::attempt_molecule_insertion_full()
vnew[0] = random_equal->gaussian()*sigma;
vnew[1] = random_equal->gaussian()*sigma;
vnew[2] = random_equal->gaussian()*sigma;
-
+
for (int i = 0; i < natoms_per_molecule; i++) {
double xtmp[3];
MathExtra::matvec(rotmat,onemols[imol]->x[i],xtmp);
@@ -1911,7 +1911,7 @@ void FixGCMC::attempt_molecule_insertion_full()
imageint imagetmp = imagezero;
domain->remap(xtmp,imagetmp);
- if (!domain->inside(xtmp))
+ if (!domain->inside(xtmp))
error->one(FLERR,"Fix gcmc put atom outside box");
int proc_flag = 0;
@@ -1953,7 +1953,7 @@ void FixGCMC::attempt_molecule_insertion_full()
}
}
- if (shakeflag)
+ if (shakeflag)
fixshake->set_molecule(nlocalprev,maxtag_all,imol,com_coord,vnew,quat);
atom->natoms += natoms_per_molecule;
@@ -1974,8 +1974,8 @@ void FixGCMC::attempt_molecule_insertion_full()
double deltaphi = zz*volume*natoms_per_molecule*
exp(beta*(energy_before - (energy_after - energy_intra)))/(ngas + natoms_per_molecule);
- if (random_equal->uniform() < deltaphi) {
-
+ if (random_equal->uniform() < deltaphi) {
+
ninsertion_successes += 1.0;
energy_stored = energy_after;
@@ -1986,7 +1986,7 @@ void FixGCMC::attempt_molecule_insertion_full()
atom->ndihedrals -= onemols[imol]->ndihedrals;
atom->nimpropers -= onemols[imol]->nimpropers;
atom->natoms -= natoms_per_molecule;
-
+
energy_stored = energy_before;
int i = 0;
while (i < atom->nlocal) {
@@ -2042,7 +2042,7 @@ double FixGCMC::energy(int i, int itype, tagint imolecule, double *coord)
}
/* ----------------------------------------------------------------------
- compute the energy of the given gas molecule in its current position
+ compute the energy of the given gas molecule in its current position
sum across all procs that own atoms of the given molecule
------------------------------------------------------------------------- */
@@ -2056,7 +2056,7 @@ double FixGCMC::molecule_energy(tagint gas_molecule_id)
double mol_energy_sum = 0.0;
MPI_Allreduce(&mol_energy,&mol_energy_sum,1,MPI_DOUBLE,MPI_SUM,world);
-
+
return mol_energy_sum;
}
@@ -2065,7 +2065,7 @@ double FixGCMC::molecule_energy(tagint gas_molecule_id)
------------------------------------------------------------------------- */
double FixGCMC::energy_full()
-{
+{
if (triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
comm->exchange();
@@ -2076,9 +2076,9 @@ double FixGCMC::energy_full()
neighbor->build();
int eflag = 1;
int vflag = 0;
-
+
if (modify->n_pre_force) modify->pre_force(vflag);
-
+
if (force->pair) force->pair->compute(eflag,vflag);
if (atom->molecular) {
@@ -2089,13 +2089,13 @@ double FixGCMC::energy_full()
}
if (force->kspace) force->kspace->compute(eflag,vflag);
-
+
if (modify->n_post_force) modify->post_force(vflag);
if (modify->n_end_of_step) modify->end_of_step();
-
+
update->eflag_global = update->ntimestep;
double total_energy = c_pe->compute_scalar();
-
+
return total_energy;
}
@@ -2132,7 +2132,7 @@ tagint FixGCMC::pick_random_gas_molecule()
tagint gas_molecule_id_all = 0;
MPI_Allreduce(&gas_molecule_id,&gas_molecule_id_all,1,
MPI_LMP_TAGINT,MPI_MAX,world);
-
+
return gas_molecule_id_all;
}
@@ -2142,9 +2142,9 @@ tagint FixGCMC::pick_random_gas_molecule()
void FixGCMC::toggle_intramolecular(int i)
{
if (atom->avec->bonds_allow)
- for (int m = 0; m < atom->num_bond[i]; m++)
+ for (int m = 0; m < atom->num_bond[i]; m++)
atom->bond_type[i][m] = -atom->bond_type[i][m];
-
+
if (atom->avec->angles_allow)
for (int m = 0; m < atom->num_angle[i]; m++)
atom->angle_type[i][m] = -atom->angle_type[i][m];
@@ -2152,12 +2152,12 @@ void FixGCMC::toggle_intramolecular(int i)
if (atom->avec->dihedrals_allow)
for (int m = 0; m < atom->num_dihedral[i]; m++)
atom->dihedral_type[i][m] = -atom->dihedral_type[i][m];
-
+
if (atom->avec->impropers_allow)
for (int m = 0; m < atom->num_improper[i]; m++)
atom->improper_type[i][m] = -atom->improper_type[i][m];
}
-
+
/* ----------------------------------------------------------------------
update the list of gas atoms
------------------------------------------------------------------------- */
@@ -2168,7 +2168,7 @@ void FixGCMC::update_gas_atoms_list()
int *mask = atom->mask;
tagint *molecule = atom->molecule;
double **x = atom->x;
-
+
if (nlocal > gcmc_nmax) {
memory->sfree(local_gas_list);
gcmc_nmax = atom->nmax;
@@ -2177,11 +2177,11 @@ void FixGCMC::update_gas_atoms_list()
}
ngas_local = 0;
-
+
if (regionflag) {
-
+
if (mode == MOLECULE) {
-
+
tagint maxmol = 0;
for (int i = 0; i < nlocal; i++) maxmol = MAX(maxmol,molecule[i]);
tagint maxmol_all;
@@ -2204,7 +2204,7 @@ void FixGCMC::update_gas_atoms_list()
comy[imolecule] = com[1];
comz[imolecule] = com[2];
}
-
+
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
if (domain->regions[iregion]->match(comx[molecule[i]],
@@ -2214,7 +2214,7 @@ void FixGCMC::update_gas_atoms_list()
}
}
}
-
+
} else {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
diff --git a/src/MC/fix_gcmc.h b/src/MC/fix_gcmc.h
index ece963c7c9..668ce5a1ed 100644
--- a/src/MC/fix_gcmc.h
+++ b/src/MC/fix_gcmc.h
@@ -20,7 +20,7 @@ FixStyle(gcmc,FixGCMC)
#ifndef LMP_FIX_GCMC_H
#define LMP_FIX_GCMC_H
-#include "stdio.h"
+#include <stdio.h>
#include "fix.h"
namespace LAMMPS_NS {
@@ -74,7 +74,7 @@ class FixGCMC : public Fix {
bool pressure_flag; // true if user specified reservoir pressure
bool charge_flag; // true if user specified atomic charge
bool full_flag; // true if doing full system energy calculations
-
+
int natoms_per_molecule; // number of atoms in each gas molecule
int groupbitall; // group bitmask for inserted atoms
@@ -82,8 +82,8 @@ class FixGCMC : public Fix {
char** groupstrings; // list of group-ids for inserted atoms
int ngrouptypes; // number of type-based group-ids for inserted atoms
char** grouptypestrings; // list of type-based group-ids for inserted atoms
- int* grouptypebits; // list of type-based group bitmasks
- int* grouptypes; // list of type-based group types
+ int* grouptypebits; // list of type-based group bitmasks
+ int* grouptypes; // list of type-based group types
double ntranslation_attempts;
double ntranslation_successes;
double nrotation_attempts;
@@ -119,7 +119,7 @@ class FixGCMC : public Fix {
class RanPark *random_equal;
class RanPark *random_unequal;
-
+
class Atom *model_atom;
class Molecule **onemols;
@@ -130,7 +130,7 @@ class FixGCMC : public Fix {
int shakeflag;
char *idshake;
int triclinic; // 0 = orthog box, 1 = triclinic
-
+
class Compute *c_pe;
void options(int, char **);
@@ -254,7 +254,7 @@ Self-explanatory.
E: Illegal fix gcmc gas mass <= 0
-The computed mass of the designated gas molecule or atom type was less
+The computed mass of the designated gas molecule or atom type was less
than or equal to zero.
E: Cannot do gcmc on atoms in atom_modify first group
diff --git a/src/MC/fix_tfmc.cpp b/src/MC/fix_tfmc.cpp
index fb8bd19e77..a59542e890 100755
--- a/src/MC/fix_tfmc.cpp
+++ b/src/MC/fix_tfmc.cpp
@@ -16,10 +16,10 @@
------------------------------------------------------------------------- */
#include "fix_tfmc.h"
-#include "mpi.h"
-#include "string.h"
-#include "math.h"
-#include "float.h"
+#include <mpi.h>
+#include <string.h>
+#include <math.h>
+#include <float.h>
#include "atom.h"
#include "force.h"
#include "update.h"
@@ -43,11 +43,11 @@ FixTFMC::FixTFMC(LAMMPS *lmp, int narg, char **arg) :
// although we are not doing MD, we would like to use tfMC as an MD "drop in"
time_integrate = 1;
-
+
d_max = force->numeric(FLERR,arg[3]);
T_set = force->numeric(FLERR,arg[4]);
seed = force->inumeric(FLERR,arg[5]);
-
+
if (d_max <= 0) error->all(FLERR,"Fix tfmc displacement length must be > 0");
if (T_set <= 0) error->all(FLERR,"Fix tfmc temperature must be > 0");
if (seed <= 0) error->all(FLERR,"Illegal fix tfmc random seed");
@@ -76,16 +76,16 @@ FixTFMC::FixTFMC(LAMMPS *lmp, int narg, char **arg) :
// error checks
if (comflag)
if (xflag < 0 || xflag > 1 || yflag < 0 || yflag > 1 ||
- zflag < 0 || zflag > 1)
+ zflag < 0 || zflag > 1)
error->all(FLERR,"Illegal fix tfmc command");
- if (xflag + yflag + zflag == 0)
+ if (xflag + yflag + zflag == 0)
comflag = 0;
if (rotflag) {
xd = NULL;
nmax = -1;
}
-
+
random_num = new RanMars(lmp,seed + comm->me);
}
@@ -125,7 +125,7 @@ void FixTFMC::init()
// obtain lowest mass in the system
// We do this here, in init(), rather than in initial_integrate().
- // This might seem somewhat odd: after all, another atom could be added with a
+ // This might seem somewhat odd: after all, another atom could be added with a
// mass smaller than mass_min (in the case of a per-particle mass), so mass_min
// should change during the run. However, this would imply that the overall
// meaning of the input Delta is not very well-defined, because its meaning
@@ -174,7 +174,7 @@ void FixTFMC::initial_integrate(int vflag)
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
- // in case we wish to track (and zero) the com movement
+ // in case we wish to track (and zero) the com movement
if (comflag) {
xcm_d[0] = 0.0;
xcm_d[1] = 0.0;
@@ -249,11 +249,11 @@ void FixTFMC::initial_integrate(int vflag)
tagint *image = atom->image;
group->xcm(igroup,masstotal,cm);
- // to zero rotations, we can employ the same principles the
- // velocity command uses to zero the angular momentum. of course,
- // there is no (conserved) momentum in MC, but we can substitute
+ // to zero rotations, we can employ the same principles the
+ // velocity command uses to zero the angular momentum. of course,
+ // there is no (conserved) momentum in MC, but we can substitute
// "velocities" by a displacement vector and proceed from there.
- // this of course requires "forking" group->angmom(), which is
+ // this of course requires "forking" group->angmom(), which is
// what we do here.
double p[3];
diff --git a/src/MC/pair_dsmc.cpp b/src/MC/pair_dsmc.cpp
index 444c49f25d..7aa0237a91 100644
--- a/src/MC/pair_dsmc.cpp
+++ b/src/MC/pair_dsmc.cpp
@@ -15,10 +15,10 @@
Contributing authors: Paul Crozier (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_dsmc.h"
#include "atom.h"
#include "comm.h"
@@ -28,7 +28,7 @@
#include "domain.h"
#include "update.h"
#include "random_mars.h"
-#include "limits.h"
+#include <limits.h>
using namespace LAMMPS_NS;
diff --git a/src/MEAM/pair_meam.cpp b/src/MEAM/pair_meam.cpp
index f3fbe0a70d..a350c66a96 100644
--- a/src/MEAM/pair_meam.cpp
+++ b/src/MEAM/pair_meam.cpp
@@ -15,10 +15,10 @@
Contributing author: Greg Wagner (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_meam.h"
#include "atom.h"
#include "force.h"
@@ -730,7 +730,7 @@ void PairMEAM::read_files(char *globalfile, char *userfile)
/* ---------------------------------------------------------------------- */
-int PairMEAM::pack_forward_comm(int n, int *list, double *buf,
+int PairMEAM::pack_forward_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,k,m;
diff --git a/src/MISC/compute_msd_nongauss.cpp b/src/MISC/compute_msd_nongauss.cpp
index c5b22a4595..4639fa7916 100644
--- a/src/MISC/compute_msd_nongauss.cpp
+++ b/src/MISC/compute_msd_nongauss.cpp
@@ -15,7 +15,7 @@
Contributing authors: Rob Hoy
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "compute_msd_nongauss.h"
#include "atom.h"
#include "update.h"
diff --git a/src/MISC/compute_ti.cpp b/src/MISC/compute_ti.cpp
index f24cb1c950..02f1608505 100644
--- a/src/MISC/compute_ti.cpp
+++ b/src/MISC/compute_ti.cpp
@@ -15,9 +15,9 @@
Contributing author: Sai Jayaraman (University of Notre Dame)
------------------------------------------------------------------------- */
-#include "mpi.h"
+#include <mpi.h>
#include "atom.h"
-#include "string.h"
+#include <string.h>
#include "compute_ti.h"
#include "update.h"
#include "modify.h"
@@ -42,7 +42,7 @@ ComputeTI::ComputeTI(LAMMPS *lmp, int narg, char **arg) :
peflag = 1;
peratom_flag = 1;
- peatomflag = 1;
+ peatomflag = 1;
scalar_flag = 1;
extscalar = 1;
timeflag = 1;
@@ -166,7 +166,7 @@ double ComputeTI::compute_scalar()
for (int m = 0; m < nterms; m++) {
int total_flag = 0;
- if ((ihi[m]-ilo[m])==atom->ntypes) total_flag = 1;
+ if ((ihi[m]-ilo[m])==atom->ntypes) total_flag = 1;
eng = 0.0;
value1 = input->variable->compute_equal(ivar1[m]);
value2 = input->variable->compute_equal(ivar2[m]);
@@ -176,26 +176,26 @@ double ComputeTI::compute_scalar()
if (total_flag) {
eng = pptr[m]->eng_vdwl + pptr[m]->eng_coul;
MPI_Allreduce(&eng,&engall,1,MPI_DOUBLE,MPI_SUM,world);
- }
- else {
+ }
+ else {
int npair = nlocal;
double *eatom = pptr[m]->eatom;
-
+
if (force->newton_pair) npair += atom->nghost;
- for (int i = 0; i < npair; i++)
- if ((ilo[m]<=type[i])&(ihi[m]>=type[i])) eng += eatom[i];
+ for (int i = 0; i < npair; i++)
+ if ((ilo[m]<=type[i])&(ihi[m]>=type[i])) eng += eatom[i];
MPI_Allreduce(&eng,&engall,1,MPI_DOUBLE,MPI_SUM,world);
}
dUdl += engall/value1 * value2;
-
+
} else if (which[m] == TAIL) {
double vol = domain->xprd*domain->yprd*domain->zprd;
- if (total_flag)
+ if (total_flag)
eng = force->pair->etail / vol;
else {
- eng = 0;
+ eng = 0;
for (int it = 1; it <= atom->ntypes; it++) {
- int jt;
+ int jt;
if ((it >= ilo[m])&&(it <=ihi[m])) jt = it;
else jt = ilo[m];
for (; jt <=ihi[m];jt++) {
@@ -203,28 +203,28 @@ double ComputeTI::compute_scalar()
force->pair->init_one(it,jt);
eng += force->pair->etail_ij;
}
- if (it !=jt) eng += force->pair->etail_ij;
+ if (it !=jt) eng += force->pair->etail_ij;
}
}
- eng /= vol;
+ eng /= vol;
}
dUdl += eng/value1 * value2;
-
+
} else if (which[m] == KSPACE) {
- if (total_flag)
+ if (total_flag)
eng = force->kspace->energy;
- else {
+ else {
double *eatom = force->kspace->eatom;
for(int i = 0; i < nlocal; i++)
- if ((ilo[m]<=type[i])&(ihi[m]>=type[i]))
- eng += eatom[i];
+ if ((ilo[m]<=type[i])&(ihi[m]>=type[i]))
+ eng += eatom[i];
MPI_Allreduce(&eng,&engall,1,MPI_DOUBLE,MPI_SUM,world);
eng = engall;
}
dUdl += eng/value1 * value2;
}
}
-
+
scalar = dUdl;
return scalar;
}
diff --git a/src/MISC/compute_ti.h b/src/MISC/compute_ti.h
index d6c054fd07..d1557a436e 100644
--- a/src/MISC/compute_ti.h
+++ b/src/MISC/compute_ti.h
@@ -35,7 +35,7 @@ class ComputeTI : public Compute {
int nterms;
int *which;
int *ivar1,*ivar2;
- int *ilo, *ihi;
+ int *ilo, *ihi;
char **var1,**var2;
class Pair **pptr;
char **pstyle;
diff --git a/src/MISC/fix_deposit.cpp b/src/MISC/fix_deposit.cpp
index 7aa3f72ce0..bfac27fa52 100644
--- a/src/MISC/fix_deposit.cpp
+++ b/src/MISC/fix_deposit.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "fix_deposit.h"
#include "atom.h"
#include "atom_vec.h"
@@ -107,17 +107,17 @@ FixDeposit::FixDeposit(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,"Fix deposit molecule must have coordinates");
if (onemols[i]->typeflag == 0)
error->all(FLERR,"Fix deposit molecule must have atom types");
- if (ntype+onemols[i]->ntypes <= 0 ||
+ if (ntype+onemols[i]->ntypes <= 0 ||
ntype+onemols[i]->ntypes > atom->ntypes)
error->all(FLERR,"Invalid atom type in fix deposit mol command");
-
+
if (atom->molecular == 2 && onemols != atom->avec->onemols)
error->all(FLERR,"Fix deposit molecule template ID must be same "
"as atom_style template ID");
onemols[i]->check_attributes(0);
// fix deposit uses geoemetric center of molecule for insertion
-
+
onemols[i]->compute_center();
}
}
@@ -253,7 +253,7 @@ void FixDeposit::init()
// for finite size spherical particles:
// warn if near < 2 * maxrad of existing and inserted particles
// since may lead to overlaps
- // if inserted molecule does not define diameters,
+ // if inserted molecule does not define diameters,
// use AtomVecSphere::create_atom() default radius = 0.5
if (atom->radius_flag) {
@@ -482,7 +482,7 @@ void FixDeposit::pre_exchange()
domain->x2lamda(coords[m],lamda);
newcoord = lamda;
} else newcoord = coords[m];
-
+
flag = 0;
if (newcoord[0] >= sublo[0] && newcoord[0] < subhi[0] &&
newcoord[1] >= sublo[1] && newcoord[1] < subhi[1] &&
@@ -496,7 +496,7 @@ void FixDeposit::pre_exchange()
if (comm->mysplit[2][1] == 1.0 &&
newcoord[0] >= sublo[0] && newcoord[0] < subhi[0] &&
newcoord[1] >= sublo[1] && newcoord[1] < subhi[1]) flag = 1;
- }
+ }
} else if (dimension == 2 && newcoord[1] >= domain->boxhi[1]) {
if (comm->layout != LAYOUT_TILED) {
if (comm->myloc[1] == comm->procgrid[1]-1 &&
@@ -524,7 +524,7 @@ void FixDeposit::pre_exchange()
atom->v[n][0] = vnew[0];
atom->v[n][1] = vnew[1];
atom->v[n][2] = vnew[2];
- if (mode == MOLECULE)
+ if (mode == MOLECULE)
atom->add_molecule_atom(onemols[imol],m,n,maxtag_all);
modify->create_attribute(n);
}
@@ -668,9 +668,9 @@ void FixDeposit::options(int narg, char **arg)
if (mode != MOLECULE) error->all(FLERR,"Illegal fix deposit command");
if (iarg+nmol+1 > narg) error->all(FLERR,"Illegal fix deposit command");
molfrac[0] = force->numeric(FLERR,arg[iarg+1]);
- for (int i = 1; i < nmol; i++)
+ for (int i = 1; i < nmol; i++)
molfrac[i] = molfrac[i-1] + force->numeric(FLERR,arg[iarg+i+1]);
- if (molfrac[nmol-1] < 1.0-EPSILON || molfrac[nmol-1] > 1.0+EPSILON)
+ if (molfrac[nmol-1] < 1.0-EPSILON || molfrac[nmol-1] > 1.0+EPSILON)
error->all(FLERR,"Illegal fix deposit command");
molfrac[nmol-1] = 1.0;
iarg += nmol+1;
@@ -711,13 +711,13 @@ void FixDeposit::options(int narg, char **arg)
globalflag = 0;
lo = force->numeric(FLERR,arg[iarg+1]);
hi = force->numeric(FLERR,arg[iarg+2]);
- deltasq = force->numeric(FLERR,arg[iarg+3]) *
+ deltasq = force->numeric(FLERR,arg[iarg+3]) *
force->numeric(FLERR,arg[iarg+3]);
iarg += 4;
} else if (strcmp(arg[iarg],"near") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix deposit command");
- nearsq = force->numeric(FLERR,arg[iarg+1]) *
+ nearsq = force->numeric(FLERR,arg[iarg+1]) *
force->numeric(FLERR,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"attempt") == 0) {
diff --git a/src/MISC/fix_deposit.h b/src/MISC/fix_deposit.h
index 81c555a660..ea047bd518 100644
--- a/src/MISC/fix_deposit.h
+++ b/src/MISC/fix_deposit.h
@@ -20,7 +20,7 @@ FixStyle(deposit,FixDeposit)
#ifndef LMP_FIX_DEPOSIT_H
#define LMP_FIX_DEPOSIT_H
-#include "stdio.h"
+#include <stdio.h>
#include "fix.h"
namespace LAMMPS_NS {
diff --git a/src/MISC/fix_efield.cpp b/src/MISC/fix_efield.cpp
index c472bf9f16..85ed926834 100644
--- a/src/MISC/fix_efield.cpp
+++ b/src/MISC/fix_efield.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -16,9 +16,9 @@
Stan Moore (Sandia) for dipole terms
------------------------------------------------------------------------- */
-#include "math.h"
-#include "string.h"
-#include "stdlib.h"
+#include <math.h>
+#include <string.h>
+#include <stdlib.h>
#include "fix_efield.h"
#include "atom.h"
#include "update.h"
@@ -149,14 +149,14 @@ void FixEfield::init()
qflag = muflag = 0;
if (atom->q_flag) qflag = 1;
if (atom->mu_flag && atom->torque_flag) muflag = 1;
- if (!qflag && !muflag)
+ if (!qflag && !muflag)
error->all(FLERR,"Fix efield requires atom attribute q or mu");
// check variables
if (xstr) {
xvar = input->variable->find(xstr);
- if (xvar < 0)
+ if (xvar < 0)
error->all(FLERR,"Variable name for fix efield does not exist");
if (input->variable->equalstyle(xvar)) xstyle = EQUAL;
else if (input->variable->atomstyle(xvar)) xstyle = ATOM;
@@ -164,7 +164,7 @@ void FixEfield::init()
}
if (ystr) {
yvar = input->variable->find(ystr);
- if (yvar < 0)
+ if (yvar < 0)
error->all(FLERR,"Variable name for fix efield does not exist");
if (input->variable->equalstyle(yvar)) ystyle = EQUAL;
else if (input->variable->atomstyle(yvar)) ystyle = ATOM;
@@ -172,7 +172,7 @@ void FixEfield::init()
}
if (zstr) {
zvar = input->variable->find(zstr);
- if (zvar < 0)
+ if (zvar < 0)
error->all(FLERR,"Variable name for fix efield does not exist");
if (input->variable->equalstyle(zvar)) zstyle = EQUAL;
else if (input->variable->atomstyle(zvar)) zstyle = ATOM;
@@ -180,7 +180,7 @@ void FixEfield::init()
}
if (estr) {
evar = input->variable->find(estr);
- if (evar < 0)
+ if (evar < 0)
error->all(FLERR,"Variable name for fix efield does not exist");
if (input->variable->atomstyle(evar)) estyle = ATOM;
else error->all(FLERR,"Variable for fix efield is invalid style");
@@ -295,7 +295,7 @@ void FixEfield::post_force(int vflag)
f[i][0] += fx;
f[i][1] += fy;
f[i][2] += fz;
-
+
domain->unmap(x[i],image[i],unwrap);
fsum[0] -= fx*unwrap[0]+fy*unwrap[1]+fz*unwrap[2];
fsum[1] += fx;
@@ -412,7 +412,7 @@ double FixEfield::memory_usage()
double bytes = 0.0;
if (varflag == ATOM) bytes = atom->nmax*4 * sizeof(double);
return bytes;
-}
+}
/* ----------------------------------------------------------------------
return energy added by fix
diff --git a/src/MISC/fix_efield.h b/src/MISC/fix_efield.h
index 48466b3250..93272ba9bf 100644
--- a/src/MISC/fix_efield.h
+++ b/src/MISC/fix_efield.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/MISC/fix_evaporate.cpp b/src/MISC/fix_evaporate.cpp
index 8eca5c6015..873227449d 100644
--- a/src/MISC/fix_evaporate.cpp
+++ b/src/MISC/fix_evaporate.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "fix_evaporate.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/MISC/fix_gld.cpp b/src/MISC/fix_gld.cpp
index 998d7f4ebe..0266d2501c 100644
--- a/src/MISC/fix_gld.cpp
+++ b/src/MISC/fix_gld.cpp
@@ -12,13 +12,13 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
- Contributing authors: Stephen Bond (SNL) and
- Andrew Baczewski (Michigan State/SNL)
+ Contributing authors: Stephen Bond (SNL) and
+ Andrew Baczewski (Michigan State/SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <string.h>
#include "fix_gld.h"
#include "math_extra.h"
#include "atom.h"
@@ -129,8 +129,8 @@ FixGLD::FixGLD(LAMMPS *lmp, int narg, char **arg) :
while (iarg < narg) {
if (strcmp(arg[iarg],"zero") == 0) {
- if (iarg+2 > narg) {
- error->all(FLERR, "Illegal fix gld command");
+ if (iarg+2 > narg) {
+ error->all(FLERR, "Illegal fix gld command");
}
if (strcmp(arg[iarg+1],"no") == 0) {
} else if (strcmp(arg[iarg+1],"yes") == 0) {
@@ -139,11 +139,11 @@ FixGLD::FixGLD(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,"Illegal fix gld command");
}
iarg += 2;
- }
+ }
else if (strcmp(arg[iarg],"frozen") == 0) {
if (iarg+2 > narg) {
error->all(FLERR, "Illegal fix gld command");
- }
+ }
if (strcmp(arg[iarg+1],"no") == 0) {
} else if (strcmp(arg[iarg+1],"yes") == 0) {
freezeflag = 1;
@@ -157,7 +157,7 @@ FixGLD::FixGLD(LAMMPS *lmp, int narg, char **arg) :
}
}
}
- } else {
+ } else {
error->all(FLERR, "Illegal fix gld command");
}
iarg += 2;
@@ -233,7 +233,7 @@ void FixGLD::initial_integrate(int vflag)
double *rmass = atom->rmass;
double *mass = atom->mass;
int *type = atom->type;
- int *mask = atom->mask;
+ int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
@@ -271,19 +271,19 @@ void FixGLD::initial_integrate(int vflag)
double rmult = sqrt(2.0*kT*ck/dtv)*(1.-theta)/ftm2v;
// random force
-#ifdef GLD_GAUSSIAN_DISTRO
+#ifdef GLD_GAUSSIAN_DISTRO
fran[0] = rmult*random->gaussian();
- fran[1] = rmult*random->gaussian();
- fran[2] = rmult*random->gaussian();
-#endif
-
-#ifdef GLD_UNIFORM_DISTRO
+ fran[1] = rmult*random->gaussian();
+ fran[2] = rmult*random->gaussian();
+#endif
+
+#ifdef GLD_UNIFORM_DISTRO
rmult *= sqrt(12.0); // correct variance of uniform distribution
fran[0] = rmult*(random->uniform() - 0.5);
fran[1] = rmult*(random->uniform() - 0.5);
fran[2] = rmult*(random->uniform() - 0.5);
#endif
-
+
// sum of random forces
fsum[0] += fran[0];
fsum[1] += fran[1];
@@ -358,7 +358,7 @@ void FixGLD::initial_integrate(int vflag)
s_gld[i][k] += fran[0];
s_gld[i][k+1] += fran[1];
s_gld[i][k+2] += fran[2];
-
+
icoeff += 1;
}
@@ -465,7 +465,7 @@ void FixGLD::final_integrate_respa(int ilevel, int iloop)
/* ----------------------------------------------------------------------
Called when a change to the target temperature is requested mid-run
-------------------------------------------------------------------------- */
+------------------------------------------------------------------------- */
void FixGLD::reset_target(double t_new)
{
@@ -486,10 +486,10 @@ void FixGLD::reset_dt()
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
-
+
double FixGLD::memory_usage()
{
- double bytes = atom->nmax*3*prony_terms*sizeof(double);
+ double bytes = atom->nmax*3*prony_terms*sizeof(double);
return bytes;
}
@@ -542,8 +542,8 @@ int FixGLD::unpack_exchange(int nlocal, double *buf)
/* ----------------------------------------------------------------------
- Pack extended variables assoc. w/ atom i into buffer for
- writing to a restart file
+ Pack extended variables assoc. w/ atom i into buffer for
+ writing to a restart file
------------------------------------------------------------------------- */
int FixGLD::pack_restart(int i, double *buf)
@@ -582,7 +582,7 @@ void FixGLD::unpack_restart(int nlocal, int nth)
}
/* ----------------------------------------------------------------------
- Returns the number of items in atomic restart data associated with
+ Returns the number of items in atomic restart data associated with
local atom nlocal. Used in determining the total extra data stored by
fixes on a given processor.
------------------------------------------------------------------------- */
@@ -603,7 +603,7 @@ int FixGLD::maxsize_restart()
}
/* ----------------------------------------------------------------------
- Initializes the extended variables to equilibrium distribution
+ Initializes the extended variables to equilibrium distribution
at t_start.
------------------------------------------------------------------------- */
diff --git a/src/MISC/fix_gld.h b/src/MISC/fix_gld.h
index 7270da4634..abb3286544 100644
--- a/src/MISC/fix_gld.h
+++ b/src/MISC/fix_gld.h
@@ -47,7 +47,7 @@ class FixGLD : public Fix {
int size_restart(int);
int maxsize_restart();
void init_s_gld();
-
+
protected:
double dtv,dtf;
double *step_respa;
diff --git a/src/MISC/fix_oneway.cpp b/src/MISC/fix_oneway.cpp
index 2f25b714b0..758beed553 100644
--- a/src/MISC/fix_oneway.cpp
+++ b/src/MISC/fix_oneway.cpp
@@ -15,7 +15,7 @@
Contributing author: Axel Kohlmeyer (ICTP, Italy)
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "fix_oneway.h"
#include "atom.h"
#include "domain.h"
diff --git a/src/MISC/fix_orient_fcc.cpp b/src/MISC/fix_orient_fcc.cpp
index efcffdd1e5..df41981f3d 100644
--- a/src/MISC/fix_orient_fcc.cpp
+++ b/src/MISC/fix_orient_fcc.cpp
@@ -15,10 +15,10 @@
Contributing authors: Koenraad Janssens and David Olmsted (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "string.h"
-#include "stdlib.h"
-#include "mpi.h"
+#include <math.h>
+#include <string.h>
+#include <stdlib.h>
+#include <mpi.h>
#include "fix_orient_fcc.h"
#include "atom.h"
#include "update.h"
diff --git a/src/MISC/fix_thermal_conductivity.cpp b/src/MISC/fix_thermal_conductivity.cpp
index ceec08a921..b465188fbb 100644
--- a/src/MISC/fix_thermal_conductivity.cpp
+++ b/src/MISC/fix_thermal_conductivity.cpp
@@ -16,10 +16,10 @@
for swapping atoms of different masses
------------------------------------------------------------------------- */
-#include "math.h"
-#include "mpi.h"
-#include "string.h"
-#include "stdlib.h"
+#include <math.h>
+#include <mpi.h>
+#include <string.h>
+#include <stdlib.h>
#include "fix_thermal_conductivity.h"
#include "atom.h"
#include "force.h"
diff --git a/src/MISC/fix_ttm.cpp b/src/MISC/fix_ttm.cpp
index f3e25d5ff0..f5157139ba 100644
--- a/src/MISC/fix_ttm.cpp
+++ b/src/MISC/fix_ttm.cpp
@@ -16,10 +16,10 @@
Carolyn Phillips (University of Michigan)
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "math.h"
-#include "string.h"
-#include "stdlib.h"
+#include <mpi.h>
+#include <math.h>
+#include <string.h>
+#include <stdlib.h>
#include "fix_ttm.h"
#include "atom.h"
#include "force.h"
diff --git a/src/MISC/fix_viscosity.cpp b/src/MISC/fix_viscosity.cpp
index d875f8e9c8..2b8807c605 100644
--- a/src/MISC/fix_viscosity.cpp
+++ b/src/MISC/fix_viscosity.cpp
@@ -16,10 +16,10 @@
for swapping atoms of different masses
------------------------------------------------------------------------- */
-#include "math.h"
-#include "mpi.h"
-#include "string.h"
-#include "stdlib.h"
+#include <math.h>
+#include <mpi.h>
+#include <string.h>
+#include <stdlib.h>
#include "fix_viscosity.h"
#include "atom.h"
#include "domain.h"
@@ -73,7 +73,7 @@ FixViscosity::FixViscosity(LAMMPS *lmp, int narg, char **arg) :
if (strcmp(arg[iarg],"swap") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix viscosity command");
nswap = force->inumeric(FLERR,arg[iarg+1]);
- if (nswap <= 0)
+ if (nswap <= 0)
error->all(FLERR,"Fix viscosity swap value must be positive");
iarg += 2;
} else if (strcmp(arg[iarg],"vtarget") == 0) {
diff --git a/src/MISC/pair_nm_cut.cpp b/src/MISC/pair_nm_cut.cpp
index b8bbb57dfe..f0c9806fb8 100644
--- a/src/MISC/pair_nm_cut.cpp
+++ b/src/MISC/pair_nm_cut.cpp
@@ -15,10 +15,10 @@
Contributing Author: Julien Devemy (ICCF)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_nm_cut.h"
#include "atom.h"
#include "comm.h"
@@ -114,8 +114,8 @@ void PairNMCut::compute(int eflag, int vflag)
rminv = pow(r2inv,mm[itype][jtype]/2.0);
rninv = pow(r2inv,nn[itype][jtype]/2.0);
- forcenm = e0nm[itype][jtype]*nm[itype][jtype] *
- (r0n[itype][jtype]/pow(r,nn[itype][jtype]) -
+ forcenm = e0nm[itype][jtype]*nm[itype][jtype] *
+ (r0n[itype][jtype]/pow(r,nn[itype][jtype]) -
r0m[itype][jtype]/pow(r,mm[itype][jtype]));
fpair = factor_lj*forcenm*r2inv;
@@ -129,8 +129,8 @@ void PairNMCut::compute(int eflag, int vflag)
}
if (eflag) {
- evdwl = e0nm[itype][jtype] *
- (mm[itype][jtype]*r0n[itype][jtype]*rninv -
+ evdwl = e0nm[itype][jtype] *
+ (mm[itype][jtype]*r0n[itype][jtype]*rninv -
nn[itype][jtype]*r0m[itype][jtype]*rminv) - offset[itype][jtype];
evdwl *= factor_lj;
}
@@ -241,11 +241,11 @@ double PairNMCut::init_one(int i, int j)
nm[i][j] = nn[i][j]*mm[i][j];
e0nm[i][j] = e0[i][j]/(nn[i][j]-mm[i][j]);
r0n[i][j] = pow(r0[i][j],nn[i][j]);
- r0m[i][j] = pow(r0[i][j],mm[i][j]);
+ r0m[i][j] = pow(r0[i][j],mm[i][j]);
if (offset_flag) {
- offset[i][j] = e0nm[i][j] *
- ((mm[i][j]*r0n[i][j] / pow(cut[i][j],nn[i][j])) -
+ offset[i][j] = e0nm[i][j] *
+ ((mm[i][j]*r0n[i][j] / pow(cut[i][j],nn[i][j])) -
(nn[i][j]*r0m[i][j] / pow(cut[i][j],mm[i][j])));
} else offset[i][j] = 0.0;
@@ -282,9 +282,9 @@ double PairNMCut::init_one(int i, int j)
double rrr1 = pow(r0[i][j],nn[i][j])*(1-nn[i][j]);
double rrr2 = pow(r0[i][j],mm[i][j])*(1-mm[i][j]);
- etail_ij = 2.0*MY_PI*all[0]*all[1]*e0nm[i][j] *
+ etail_ij = 2.0*MY_PI*all[0]*all[1]*e0nm[i][j] *
(rr1*pow(cut[i][j],p1)-rr2*pow(cut[i][j],p2));
- ptail_ij = 2.0*MY_PI*all[0]*all[1]*e0nm[i][j] *
+ ptail_ij = 2.0*MY_PI*all[0]*all[1]*e0nm[i][j] *
nn[i][j]*mm[i][j]*(rrr1*pow(cut[i][j],p1)-rrr2*pow(cut[i][j],p2));
}
@@ -408,14 +408,14 @@ double PairNMCut::single(int i, int j, int itype, int jtype,
r2inv = 1.0/rsq;
r = sqrt(rsq);
- forcenm = e0nm[itype][jtype]*nm[itype][jtype] *
- (r0n[itype][jtype]/pow(r,nn[itype][jtype]) -
+ forcenm = e0nm[itype][jtype]*nm[itype][jtype] *
+ (r0n[itype][jtype]/pow(r,nn[itype][jtype]) -
r0m[itype][jtype]/pow(r,mm[itype][jtype]));
fforce = factor_lj*forcenm*r2inv;
- phinm = e0nm[itype][jtype] *
- (mm[itype][jtype] * r0n[itype][jtype]/pow(r,nn[itype][jtype]) -
- nn[itype][jtype]*r0m[itype][jtype] /pow(r,mm[itype][jtype])) -
+ phinm = e0nm[itype][jtype] *
+ (mm[itype][jtype] * r0n[itype][jtype]/pow(r,nn[itype][jtype]) -
+ nn[itype][jtype]*r0m[itype][jtype] /pow(r,mm[itype][jtype])) -
offset[itype][jtype];
return factor_lj*phinm;
}
diff --git a/src/MISC/pair_nm_cut_coul_cut.cpp b/src/MISC/pair_nm_cut_coul_cut.cpp
index 33bddb5223..61326ee1eb 100644
--- a/src/MISC/pair_nm_cut_coul_cut.cpp
+++ b/src/MISC/pair_nm_cut_coul_cut.cpp
@@ -15,10 +15,10 @@
Contributing Author: Julien Devemy (ICCF)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_nm_cut_coul_cut.h"
#include "atom.h"
#include "comm.h"
@@ -126,8 +126,8 @@ void PairNMCutCoulCut::compute(int eflag, int vflag)
r = sqrt(rsq);
rminv = pow(r2inv,mm[itype][jtype]/2.0);
rninv = pow(r2inv,nn[itype][jtype]/2.0);
- forcenm = e0nm[itype][jtype]*nm[itype][jtype] *
- (r0n[itype][jtype]/pow(r,nn[itype][jtype]) -
+ forcenm = e0nm[itype][jtype]*nm[itype][jtype] *
+ (r0n[itype][jtype]/pow(r,nn[itype][jtype]) -
r0m[itype][jtype]/pow(r,mm[itype][jtype]));
} else forcenm = 0.0;
@@ -147,10 +147,10 @@ void PairNMCutCoulCut::compute(int eflag, int vflag)
ecoul = factor_coul * qqrd2e * qtmp*q[j]*sqrt(r2inv);
else ecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
- evdwl = e0nm[itype][jtype]*(mm[itype][jtype] *
- r0n[itype][jtype]*rninv -
- nn[itype][jtype] *
- r0m[itype][jtype]*rminv) -
+ evdwl = e0nm[itype][jtype]*(mm[itype][jtype] *
+ r0n[itype][jtype]*rninv -
+ nn[itype][jtype] *
+ r0m[itype][jtype]*rminv) -
offset[itype][jtype];
evdwl *= factor_lj;
} else evdwl = 0.0;
@@ -289,11 +289,11 @@ double PairNMCutCoulCut::init_one(int i, int j)
nm[i][j] = nn[i][j]*mm[i][j];
e0nm[i][j] = e0[i][j]/(nn[i][j]-mm[i][j]);
r0n[i][j] = pow(r0[i][j],nn[i][j]);
- r0m[i][j] = pow(r0[i][j],mm[i][j]);
+ r0m[i][j] = pow(r0[i][j],mm[i][j]);
if (offset_flag) {
offset[i][j] = e0nm[i][j] *
- ((mm[i][j]*r0n[i][j] / pow(cut_lj[i][j],nn[i][j])) -
+ ((mm[i][j]*r0n[i][j] / pow(cut_lj[i][j],nn[i][j])) -
(nn[i][j]*r0m[i][j] / pow(cut_lj[i][j],mm[i][j])));
} else offset[i][j] = 0.0;
@@ -332,9 +332,9 @@ double PairNMCutCoulCut::init_one(int i, int j)
double rrr1 = pow(r0[i][j],nn[i][j])*(1-nn[i][j]);
double rrr2 = pow(r0[i][j],mm[i][j])*(1-mm[i][j]);
- etail_ij = 2.0*MY_PI*all[0]*all[1]*e0nm[i][j] *
+ etail_ij = 2.0*MY_PI*all[0]*all[1]*e0nm[i][j] *
(rr1*pow(cut_lj[i][j],p1)-rr2*pow(cut_lj[i][j],p2));
- ptail_ij = 2.0*MY_PI*all[0]*all[1]*e0nm[i][j] *
+ ptail_ij = 2.0*MY_PI*all[0]*all[1]*e0nm[i][j] *
nn[i][j]*mm[i][j]*(rrr1*pow(cut_lj[i][j],p1)-rrr2*pow(cut_lj[i][j],p2));
}
@@ -469,8 +469,8 @@ double PairNMCutCoulCut::single(int i, int j, int itype, int jtype,
else forcecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
r = sqrt(rsq);
- forcenm = e0nm[itype][jtype]*nm[itype][jtype] *
- (r0n[itype][jtype]/pow(r,nn[itype][jtype]) -
+ forcenm = e0nm[itype][jtype]*nm[itype][jtype] *
+ (r0n[itype][jtype]/pow(r,nn[itype][jtype]) -
r0m[itype][jtype]/pow(r,mm[itype][jtype]));
} else forcenm = 0.0;
fforce = (factor_coul*forcecoul + factor_lj*forcenm) * r2inv;
@@ -481,8 +481,8 @@ double PairNMCutCoulCut::single(int i, int j, int itype, int jtype,
eng += factor_coul*phicoul;
}
if (rsq < cut_ljsq[itype][jtype]) {
- phinm = e0nm[itype][jtype] *
- (mm[itype][jtype]*r0n[itype][jtype]/pow(r,nn[itype][jtype]) -
+ phinm = e0nm[itype][jtype] *
+ (mm[itype][jtype]*r0n[itype][jtype]/pow(r,nn[itype][jtype]) -
nn[itype][jtype]*r0m[itype][jtype]/pow(r,mm[itype][jtype])) -
offset[itype][jtype];
eng += factor_lj*phinm;
diff --git a/src/MISC/pair_nm_cut_coul_long.cpp b/src/MISC/pair_nm_cut_coul_long.cpp
index b613b584c2..0cd12ac035 100644
--- a/src/MISC/pair_nm_cut_coul_long.cpp
+++ b/src/MISC/pair_nm_cut_coul_long.cpp
@@ -15,10 +15,10 @@
Contributing Author: Julien Devemy (ICCF)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_nm_cut_coul_long.h"
#include "atom.h"
#include "comm.h"
@@ -165,8 +165,8 @@ void PairNMCutCoulLong::compute(int eflag, int vflag)
r = sqrt(rsq);
rminv = pow(r2inv,mm[itype][jtype]/2.0);
rninv = pow(r2inv,nn[itype][jtype]/2.0);
- forcenm = e0nm[itype][jtype]*nm[itype][jtype] *
- (r0n[itype][jtype]/pow(r,nn[itype][jtype]) -
+ forcenm = e0nm[itype][jtype]*nm[itype][jtype] *
+ (r0n[itype][jtype]/pow(r,nn[itype][jtype]) -
r0m[itype][jtype]/pow(r,mm[itype][jtype]));
} else forcenm = 0.0;
@@ -193,8 +193,8 @@ void PairNMCutCoulLong::compute(int eflag, int vflag)
} else ecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
- evdwl = e0nm[itype][jtype] *
- (mm[itype][jtype]*r0n[itype][jtype]*rninv -
+ evdwl = e0nm[itype][jtype] *
+ (mm[itype][jtype]*r0n[itype][jtype]*rninv -
nn[itype][jtype]*r0m[itype][jtype]*rminv) - offset[itype][jtype];
evdwl *= factor_lj;
} else evdwl = 0.0;
@@ -337,11 +337,11 @@ double PairNMCutCoulLong::init_one(int i, int j)
nm[i][j] = nn[i][j]*mm[i][j];
e0nm[i][j] = e0[i][j]/(nn[i][j]-mm[i][j]);
r0n[i][j] = pow(r0[i][j],nn[i][j]);
- r0m[i][j] = pow(r0[i][j],mm[i][j]);
+ r0m[i][j] = pow(r0[i][j],mm[i][j]);
if (offset_flag) {
- offset[i][j] = e0nm[i][j] *
- ((mm[i][j]*r0n[i][j] / pow(cut_lj[i][j],nn[i][j])) -
+ offset[i][j] = e0nm[i][j] *
+ ((mm[i][j]*r0n[i][j] / pow(cut_lj[i][j],nn[i][j])) -
(nn[i][j]*r0m[i][j] / pow(cut_lj[i][j],mm[i][j])));
} else offset[i][j] = 0.0;
@@ -381,7 +381,7 @@ double PairNMCutCoulLong::init_one(int i, int j)
etail_ij = 2.0*MY_PI*all[0]*all[1]*e0nm[i][j] *
(rr1*pow(cut_lj[i][j],p1)-rr2*pow(cut_lj[i][j],p2));
- ptail_ij = 2.0*MY_PI*all[0]*all[1]*e0nm[i][j]*nn[i][j]*mm[i][j] *
+ ptail_ij = 2.0*MY_PI*all[0]*all[1]*e0nm[i][j]*nn[i][j]*mm[i][j] *
(rrr1*pow(cut_lj[i][j],p1)-rrr2*pow(cut_lj[i][j],p2));
}
@@ -545,8 +545,8 @@ double PairNMCutCoulLong::single(int i, int j, int itype, int jtype,
if (rsq < cut_ljsq[itype][jtype]) {
r = sqrt(rsq);
- forcenm = e0nm[itype][jtype]*nm[itype][jtype] *
- (r0n[itype][jtype]/pow(r,nn[itype][jtype]) -
+ forcenm = e0nm[itype][jtype]*nm[itype][jtype] *
+ (r0n[itype][jtype]/pow(r,nn[itype][jtype]) -
r0m[itype][jtype]/pow(r,mm[itype][jtype]));
} else forcenm = 0.0;
@@ -565,8 +565,8 @@ double PairNMCutCoulLong::single(int i, int j, int itype, int jtype,
}
if (rsq < cut_ljsq[itype][jtype]) {
- phinm = e0nm[itype][jtype] *
- (mm[itype][jtype]*r0n[itype][jtype]/pow(r,nn[itype][jtype]) -
+ phinm = e0nm[itype][jtype] *
+ (mm[itype][jtype]*r0n[itype][jtype]/pow(r,nn[itype][jtype]) -
nn[itype][jtype]*r0m[itype][jtype]/pow(r,mm[itype][jtype])) -
offset[itype][jtype];
eng += factor_lj*phinm;
diff --git a/src/MOLECULE/angle_charmm.cpp b/src/MOLECULE/angle_charmm.cpp
index 228ea1c601..c2d44b26dd 100644
--- a/src/MOLECULE/angle_charmm.cpp
+++ b/src/MOLECULE/angle_charmm.cpp
@@ -15,8 +15,8 @@
Contributing author: Paul Crozier (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdlib.h>
#include "angle_charmm.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/MOLECULE/angle_charmm.h b/src/MOLECULE/angle_charmm.h
index 738ec69e11..fa27866be3 100644
--- a/src/MOLECULE/angle_charmm.h
+++ b/src/MOLECULE/angle_charmm.h
@@ -20,7 +20,7 @@ AngleStyle(charmm,AngleCharmm)
#ifndef LMP_ANGLE_CHARMM_H
#define LMP_ANGLE_CHARMM_H
-#include "stdio.h"
+#include <stdio.h>
#include "angle.h"
namespace LAMMPS_NS {
diff --git a/src/MOLECULE/angle_cosine.cpp b/src/MOLECULE/angle_cosine.cpp
index f43c7bc6e9..135d4bbf8f 100644
--- a/src/MOLECULE/angle_cosine.cpp
+++ b/src/MOLECULE/angle_cosine.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdlib.h>
#include "angle_cosine.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/MOLECULE/angle_cosine.h b/src/MOLECULE/angle_cosine.h
index 7e06aa150f..a6581f11bd 100644
--- a/src/MOLECULE/angle_cosine.h
+++ b/src/MOLECULE/angle_cosine.h
@@ -20,7 +20,7 @@ AngleStyle(cosine,AngleCosine)
#ifndef LMP_ANGLE_COSINE_H
#define LMP_ANGLE_COSINE_H
-#include "stdio.h"
+#include <stdio.h>
#include "angle.h"
namespace LAMMPS_NS {
diff --git a/src/MOLECULE/angle_cosine_delta.cpp b/src/MOLECULE/angle_cosine_delta.cpp
index 08124142e5..fe482eb3eb 100644
--- a/src/MOLECULE/angle_cosine_delta.cpp
+++ b/src/MOLECULE/angle_cosine_delta.cpp
@@ -15,8 +15,8 @@
Contributing author: Axel Kohlmeyer (Temple U), akohlmey at gmail.com
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdlib.h>
#include "angle_cosine_delta.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/MOLECULE/angle_cosine_delta.h b/src/MOLECULE/angle_cosine_delta.h
index 70fdf315ee..b29064e35e 100644
--- a/src/MOLECULE/angle_cosine_delta.h
+++ b/src/MOLECULE/angle_cosine_delta.h
@@ -20,7 +20,7 @@ AngleStyle(cosine/delta,AngleCosineDelta)
#ifndef LMP_ANGLE_COSINE_DELTA_H
#define LMP_ANGLE_COSINE_DELTA_H
-#include "stdio.h"
+#include <stdio.h>
#include "angle_cosine_squared.h"
namespace LAMMPS_NS {
diff --git a/src/MOLECULE/angle_cosine_periodic.cpp b/src/MOLECULE/angle_cosine_periodic.cpp
index 8198f3d4b4..dbd93b3b7b 100644
--- a/src/MOLECULE/angle_cosine_periodic.cpp
+++ b/src/MOLECULE/angle_cosine_periodic.cpp
@@ -15,8 +15,8 @@
Contributing author: Tod A Pascal (Caltech)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdlib.h>
#include "angle_cosine_periodic.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/MOLECULE/angle_cosine_periodic.h b/src/MOLECULE/angle_cosine_periodic.h
index f9485539f0..9b7f062272 100644
--- a/src/MOLECULE/angle_cosine_periodic.h
+++ b/src/MOLECULE/angle_cosine_periodic.h
@@ -20,7 +20,7 @@ AngleStyle(cosine/periodic, AngleCosinePeriodic)
#ifndef LMP_ANGLE_PERIODIC_H
#define LMP_ANGLE_PERIODIC_H
-#include "stdio.h"
+#include <stdio.h>
#include "angle.h"
namespace LAMMPS_NS {
diff --git a/src/MOLECULE/angle_cosine_squared.cpp b/src/MOLECULE/angle_cosine_squared.cpp
index 578d641de3..6d073f156e 100644
--- a/src/MOLECULE/angle_cosine_squared.cpp
+++ b/src/MOLECULE/angle_cosine_squared.cpp
@@ -15,8 +15,8 @@
Contributing author: Naveen Michaud-Agrawal (Johns Hopkins U)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdlib.h>
#include "angle_cosine_squared.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/MOLECULE/angle_cosine_squared.h b/src/MOLECULE/angle_cosine_squared.h
index a9f6572c47..b9f79f923f 100644
--- a/src/MOLECULE/angle_cosine_squared.h
+++ b/src/MOLECULE/angle_cosine_squared.h
@@ -20,7 +20,7 @@ AngleStyle(cosine/squared,AngleCosineSquared)
#ifndef LMP_ANGLE_COSINE_SQUARED_H
#define LMP_ANGLE_COSINE_SQUARED_H
-#include "stdio.h"
+#include <stdio.h>
#include "angle.h"
namespace LAMMPS_NS {
diff --git a/src/MOLECULE/angle_harmonic.cpp b/src/MOLECULE/angle_harmonic.cpp
index 4fdf42ed49..cffc3182dd 100644
--- a/src/MOLECULE/angle_harmonic.cpp
+++ b/src/MOLECULE/angle_harmonic.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdlib.h>
#include "angle_harmonic.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/MOLECULE/angle_harmonic.h b/src/MOLECULE/angle_harmonic.h
index 0731980f44..177e7cbadb 100644
--- a/src/MOLECULE/angle_harmonic.h
+++ b/src/MOLECULE/angle_harmonic.h
@@ -20,7 +20,7 @@ AngleStyle(harmonic,AngleHarmonic)
#ifndef LMP_ANGLE_HARMONIC_H
#define LMP_ANGLE_HARMONIC_H
-#include "stdio.h"
+#include <stdio.h>
#include "angle.h"
namespace LAMMPS_NS {
diff --git a/src/MOLECULE/angle_table.cpp b/src/MOLECULE/angle_table.cpp
index cf8b62cc9b..9dd9925725 100644
--- a/src/MOLECULE/angle_table.cpp
+++ b/src/MOLECULE/angle_table.cpp
@@ -15,9 +15,9 @@
Contributing author: Chuanfu Luo (luochuanfu@gmail.com)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "angle_table.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/MOLECULE/angle_table.h b/src/MOLECULE/angle_table.h
index 99f547052e..cb04aa6125 100644
--- a/src/MOLECULE/angle_table.h
+++ b/src/MOLECULE/angle_table.h
@@ -20,7 +20,7 @@ AngleStyle(table,AngleTable)
#ifndef LMP_ANGLE_TABLE_H
#define LMP_ANGLE_TABLE_H
-#include "stdio.h"
+#include <stdio.h>
#include "angle.h"
namespace LAMMPS_NS {
diff --git a/src/MOLECULE/atom_vec_angle.cpp b/src/MOLECULE/atom_vec_angle.cpp
index 8241c693aa..7053f0eb30 100644
--- a/src/MOLECULE/atom_vec_angle.cpp
+++ b/src/MOLECULE/atom_vec_angle.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdlib.h"
+#include <stdlib.h>
#include "atom_vec_angle.h"
#include "atom.h"
#include "comm.h"
@@ -865,7 +865,7 @@ int AtomVecAngle::pack_data_hybrid(int i, double *buf)
void AtomVecAngle::write_data(FILE *fp, int n, double **buf)
{
for (int i = 0; i < n; i++)
- fprintf(fp,TAGINT_FORMAT " " TAGINT_FORMAT
+ fprintf(fp,TAGINT_FORMAT " " TAGINT_FORMAT
" %d %-1.16e %-1.16e %-1.16e %d %d %d\n",
(tagint) ubuf(buf[i][0]).i,(tagint) ubuf(buf[i][1]).i,
(int) ubuf(buf[i][2]).i,
diff --git a/src/MOLECULE/atom_vec_bond.cpp b/src/MOLECULE/atom_vec_bond.cpp
index f53c71736e..bae924c28a 100644
--- a/src/MOLECULE/atom_vec_bond.cpp
+++ b/src/MOLECULE/atom_vec_bond.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdlib.h"
+#include <stdlib.h>
#include "atom_vec_bond.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/MOLECULE/atom_vec_full.cpp b/src/MOLECULE/atom_vec_full.cpp
index 006917ce49..ba85a1280b 100644
--- a/src/MOLECULE/atom_vec_full.cpp
+++ b/src/MOLECULE/atom_vec_full.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdlib.h"
+#include <stdlib.h>
#include "atom_vec_full.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/MOLECULE/atom_vec_molecular.cpp b/src/MOLECULE/atom_vec_molecular.cpp
index 3e347af5c9..23786d7641 100644
--- a/src/MOLECULE/atom_vec_molecular.cpp
+++ b/src/MOLECULE/atom_vec_molecular.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdlib.h"
+#include <stdlib.h>
#include "atom_vec_molecular.h"
#include "atom.h"
#include "comm.h"
@@ -918,7 +918,7 @@ void AtomVecMolecular::create_atom(int itype, double *coord)
initialize other atom quantities
------------------------------------------------------------------------- */
-void AtomVecMolecular::data_atom(double *coord, imageint imagetmp,
+void AtomVecMolecular::data_atom(double *coord, imageint imagetmp,
char **values)
{
int nlocal = atom->nlocal;
@@ -1002,7 +1002,7 @@ int AtomVecMolecular::pack_data_hybrid(int i, double *buf)
void AtomVecMolecular::write_data(FILE *fp, int n, double **buf)
{
for (int i = 0; i < n; i++)
- fprintf(fp,TAGINT_FORMAT " " TAGINT_FORMAT
+ fprintf(fp,TAGINT_FORMAT " " TAGINT_FORMAT
" %d %-1.16e %-1.16e %-1.16e %d %d %d\n",
(tagint) ubuf(buf[i][0]).i,(tagint) ubuf(buf[i][1]).i,
(int) ubuf(buf[i][2]).i,
diff --git a/src/MOLECULE/atom_vec_template.cpp b/src/MOLECULE/atom_vec_template.cpp
index 546b442825..5d3b0a3264 100644
--- a/src/MOLECULE/atom_vec_template.cpp
+++ b/src/MOLECULE/atom_vec_template.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
-#include "stdlib.h"
+#include <string.h>
+#include <stdlib.h>
#include "atom_vec_template.h"
#include "atom.h"
#include "molecule.h"
@@ -750,7 +750,7 @@ void AtomVecTemplate::data_atom(double *coord, imageint imagetmp, char **values)
if (molindex[nlocal] < 0 || molindex[nlocal] >= nset)
error->one(FLERR,"Invalid template index in Atoms section of data file");
- if (molatom[nlocal] < 0 ||
+ if (molatom[nlocal] < 0 ||
molatom[nlocal] >= onemols[molindex[nlocal]]->natoms)
error->one(FLERR,"Invalid template atom in Atoms section of data file");
@@ -826,7 +826,7 @@ int AtomVecTemplate::pack_data_hybrid(int i, double *buf)
void AtomVecTemplate::write_data(FILE *fp, int n, double **buf)
{
for (int i = 0; i < n; i++)
- fprintf(fp,TAGINT_FORMAT " " TAGINT_FORMAT
+ fprintf(fp,TAGINT_FORMAT " " TAGINT_FORMAT
" %d %d %d %-1.16e %-1.16e %-1.16e %d %d %d\n",
(tagint) ubuf(buf[i][0]).i,(tagint) ubuf(buf[i][1]).i,
(int) ubuf(buf[i][2]).i,(int) ubuf(buf[i][3]).i,
diff --git a/src/MOLECULE/bond_fene.cpp b/src/MOLECULE/bond_fene.cpp
index e72fbaa40a..66c5c08174 100644
--- a/src/MOLECULE/bond_fene.cpp
+++ b/src/MOLECULE/bond_fene.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdlib.h>
#include "bond_fene.h"
#include "atom.h"
#include "neighbor.h"
@@ -85,7 +85,7 @@ void BondFENE::compute(int eflag, int vflag)
if (rlogarg < 0.1) {
char str[128];
- sprintf(str,"FENE bond too long: " BIGINT_FORMAT " "
+ sprintf(str,"FENE bond too long: " BIGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT " %g",
update->ntimestep,atom->tag[i1],atom->tag[i2],sqrt(rsq));
error->warning(FLERR,str,0);
@@ -242,7 +242,7 @@ void BondFENE::write_data(FILE *fp)
/* ---------------------------------------------------------------------- */
-double BondFENE::single(int type, double rsq, int i, int j,
+double BondFENE::single(int type, double rsq, int i, int j,
double &fforce)
{
double r0sq = r0[type] * r0[type];
diff --git a/src/MOLECULE/bond_fene.h b/src/MOLECULE/bond_fene.h
index 3ad7fa95fa..6124478567 100644
--- a/src/MOLECULE/bond_fene.h
+++ b/src/MOLECULE/bond_fene.h
@@ -20,7 +20,7 @@ BondStyle(fene,BondFENE)
#ifndef LMP_BOND_FENE_H
#define LMP_BOND_FENE_H
-#include "stdio.h"
+#include <stdio.h>
#include "bond.h"
namespace LAMMPS_NS {
diff --git a/src/MOLECULE/bond_fene_expand.cpp b/src/MOLECULE/bond_fene_expand.cpp
index 6f616b98dd..f65632cc3f 100644
--- a/src/MOLECULE/bond_fene_expand.cpp
+++ b/src/MOLECULE/bond_fene_expand.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdlib.h>
#include "bond_fene_expand.h"
#include "atom.h"
#include "neighbor.h"
@@ -90,7 +90,7 @@ void BondFENEExpand::compute(int eflag, int vflag)
if (rlogarg < 0.1) {
char str[128];
- sprintf(str,"FENE bond too long: " BIGINT_FORMAT " "
+ sprintf(str,"FENE bond too long: " BIGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT " %g",
update->ntimestep,atom->tag[i1],atom->tag[i2],sqrt(rsq));
error->warning(FLERR,str,0);
diff --git a/src/MOLECULE/bond_fene_expand.h b/src/MOLECULE/bond_fene_expand.h
index 0d2f535cb8..1971c6f428 100644
--- a/src/MOLECULE/bond_fene_expand.h
+++ b/src/MOLECULE/bond_fene_expand.h
@@ -20,7 +20,7 @@ BondStyle(fene/expand,BondFENEExpand)
#ifndef LMP_BOND_FENE_EXPAND_H
#define LMP_BOND_FENE_EXPAND_H
-#include "stdio.h"
+#include <stdio.h>
#include "bond.h"
namespace LAMMPS_NS {
diff --git a/src/MOLECULE/bond_harmonic.cpp b/src/MOLECULE/bond_harmonic.cpp
index 573e610238..8c5663bf79 100644
--- a/src/MOLECULE/bond_harmonic.cpp
+++ b/src/MOLECULE/bond_harmonic.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdlib.h>
#include "bond_harmonic.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/MOLECULE/bond_harmonic.h b/src/MOLECULE/bond_harmonic.h
index 4c72352895..7c7125b04c 100644
--- a/src/MOLECULE/bond_harmonic.h
+++ b/src/MOLECULE/bond_harmonic.h
@@ -20,7 +20,7 @@ BondStyle(harmonic,BondHarmonic)
#ifndef LMP_BOND_HARMONIC_H
#define LMP_BOND_HARMONIC_H
-#include "stdio.h"
+#include <stdio.h>
#include "bond.h"
namespace LAMMPS_NS {
diff --git a/src/MOLECULE/bond_morse.cpp b/src/MOLECULE/bond_morse.cpp
index 03af2dd1c6..da2717899a 100644
--- a/src/MOLECULE/bond_morse.cpp
+++ b/src/MOLECULE/bond_morse.cpp
@@ -15,8 +15,8 @@
Contributing author: Jeff Greathouse (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdlib.h>
#include "bond_morse.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/MOLECULE/bond_morse.h b/src/MOLECULE/bond_morse.h
index f19b05f5df..74379c91ee 100644
--- a/src/MOLECULE/bond_morse.h
+++ b/src/MOLECULE/bond_morse.h
@@ -20,7 +20,7 @@ BondStyle(morse,BondMorse)
#ifndef LMP_BOND_MORSE_H
#define LMP_BOND_MORSE_H
-#include "stdio.h"
+#include <stdio.h>
#include "bond.h"
namespace LAMMPS_NS {
diff --git a/src/MOLECULE/bond_nonlinear.cpp b/src/MOLECULE/bond_nonlinear.cpp
index 0ed5f0f4e8..9da2993c54 100644
--- a/src/MOLECULE/bond_nonlinear.cpp
+++ b/src/MOLECULE/bond_nonlinear.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdlib.h>
#include "bond_nonlinear.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/MOLECULE/bond_nonlinear.h b/src/MOLECULE/bond_nonlinear.h
index c7c7c27b22..5d2448b112 100644
--- a/src/MOLECULE/bond_nonlinear.h
+++ b/src/MOLECULE/bond_nonlinear.h
@@ -20,7 +20,7 @@ BondStyle(nonlinear,BondNonlinear)
#ifndef LMP_BOND_NONLINEAR_H
#define LMP_BOND_NONLINEAR_H
-#include "stdio.h"
+#include <stdio.h>
#include "bond.h"
namespace LAMMPS_NS {
diff --git a/src/MOLECULE/bond_quartic.cpp b/src/MOLECULE/bond_quartic.cpp
index 84a82c9bb4..c92048b2ca 100755
--- a/src/MOLECULE/bond_quartic.cpp
+++ b/src/MOLECULE/bond_quartic.cpp
@@ -15,8 +15,8 @@
Contributing authors: Chris Lorenz and Mark Stevens (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdlib.h>
#include "bond_quartic.h"
#include "atom.h"
#include "neighbor.h"
@@ -236,7 +236,7 @@ void BondQuartic::init_style()
if (force->angle || force->dihedral || force->improper)
error->all(FLERR,
"Bond style quartic cannot be used with 3,4-body interactions");
- if (atom->molecular == 2)
+ if (atom->molecular == 2)
error->all(FLERR,
"Bond style quartic cannot be used with atom style template");
diff --git a/src/MOLECULE/bond_quartic.h b/src/MOLECULE/bond_quartic.h
index 9788626f13..21bd7f00b4 100644
--- a/src/MOLECULE/bond_quartic.h
+++ b/src/MOLECULE/bond_quartic.h
@@ -20,7 +20,7 @@ BondStyle(quartic,BondQuartic)
#ifndef LMP_BOND_QUARTIC_H
#define LMP_BOND_QUARTIC_H
-#include "stdio.h"
+#include <stdio.h>
#include "bond.h"
namespace LAMMPS_NS {
diff --git a/src/MOLECULE/bond_table.cpp b/src/MOLECULE/bond_table.cpp
index 99d0bb2ab5..fc42faeeea 100644
--- a/src/MOLECULE/bond_table.cpp
+++ b/src/MOLECULE/bond_table.cpp
@@ -15,9 +15,9 @@
Contributing author: Chuanfu Luo (luochuanfu@gmail.com)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "bond_table.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/MOLECULE/bond_table.h b/src/MOLECULE/bond_table.h
index 91d78461d1..8b84b1b66d 100644
--- a/src/MOLECULE/bond_table.h
+++ b/src/MOLECULE/bond_table.h
@@ -20,7 +20,7 @@ BondStyle(table,BondTable)
#ifndef LMP_BOND_TABLE_H
#define LMP_BOND_TABLE_H
-#include "stdio.h"
+#include <stdio.h>
#include "bond.h"
namespace LAMMPS_NS {
diff --git a/src/MOLECULE/dihedral_charmm.cpp b/src/MOLECULE/dihedral_charmm.cpp
index 5e8fef6442..8b6909f1ad 100644
--- a/src/MOLECULE/dihedral_charmm.cpp
+++ b/src/MOLECULE/dihedral_charmm.cpp
@@ -15,9 +15,9 @@
Contributing author: Paul Crozier (SNL)
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "math.h"
-#include "stdlib.h"
+#include <mpi.h>
+#include <math.h>
+#include <stdlib.h>
#include "dihedral_charmm.h"
#include "atom.h"
#include "comm.h"
@@ -149,8 +149,8 @@ void DihedralCharmm::compute(int eflag, int vflag)
MPI_Comm_rank(world,&me);
if (screen) {
char str[128];
- sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " "
- TAGINT_FORMAT " " TAGINT_FORMAT " "
+ sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT,
me,update->ntimestep,
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
diff --git a/src/MOLECULE/dihedral_charmm.h b/src/MOLECULE/dihedral_charmm.h
index 6ebb4f977a..4116469904 100644
--- a/src/MOLECULE/dihedral_charmm.h
+++ b/src/MOLECULE/dihedral_charmm.h
@@ -20,7 +20,7 @@ DihedralStyle(charmm,DihedralCharmm)
#ifndef LMP_DIHEDRAL_CHARMM_H
#define LMP_DIHEDRAL_CHARMM_H
-#include "stdio.h"
+#include <stdio.h>
#include "dihedral.h"
namespace LAMMPS_NS {
diff --git a/src/MOLECULE/dihedral_harmonic.cpp b/src/MOLECULE/dihedral_harmonic.cpp
index 865500cfdc..f9ea31ac7c 100644
--- a/src/MOLECULE/dihedral_harmonic.cpp
+++ b/src/MOLECULE/dihedral_harmonic.cpp
@@ -15,9 +15,9 @@
Contributing author: Paul Crozier (SNL)
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "math.h"
-#include "stdlib.h"
+#include <mpi.h>
+#include <math.h>
+#include <stdlib.h>
#include "dihedral_harmonic.h"
#include "atom.h"
#include "comm.h"
@@ -136,8 +136,8 @@ void DihedralHarmonic::compute(int eflag, int vflag)
MPI_Comm_rank(world,&me);
if (screen) {
char str[128];
- sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " "
- TAGINT_FORMAT " " TAGINT_FORMAT " "
+ sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT,
me,update->ntimestep,
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
diff --git a/src/MOLECULE/dihedral_harmonic.h b/src/MOLECULE/dihedral_harmonic.h
index 40ebdf26a0..db8789675d 100644
--- a/src/MOLECULE/dihedral_harmonic.h
+++ b/src/MOLECULE/dihedral_harmonic.h
@@ -20,7 +20,7 @@ DihedralStyle(harmonic,DihedralHarmonic)
#ifndef LMP_DIHEDRAL_HARMONIC_H
#define LMP_DIHEDRAL_HARMONIC_H
-#include "stdio.h"
+#include <stdio.h>
#include "dihedral.h"
namespace LAMMPS_NS {
diff --git a/src/MOLECULE/dihedral_helix.cpp b/src/MOLECULE/dihedral_helix.cpp
index f6fb9f3298..b0565e29fb 100644
--- a/src/MOLECULE/dihedral_helix.cpp
+++ b/src/MOLECULE/dihedral_helix.cpp
@@ -16,9 +16,9 @@
Mark Stevens (Sandia)
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "math.h"
-#include "stdlib.h"
+#include <mpi.h>
+#include <math.h>
+#include <stdlib.h>
#include "dihedral_helix.h"
#include "atom.h"
#include "neighbor.h"
@@ -164,8 +164,8 @@ void DihedralHelix::compute(int eflag, int vflag)
MPI_Comm_rank(world,&me);
if (screen) {
char str[128];
- sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " "
- TAGINT_FORMAT " " TAGINT_FORMAT " "
+ sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT,
me,update->ntimestep,
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
diff --git a/src/MOLECULE/dihedral_helix.h b/src/MOLECULE/dihedral_helix.h
index c9cd014c56..61aef1d2ec 100644
--- a/src/MOLECULE/dihedral_helix.h
+++ b/src/MOLECULE/dihedral_helix.h
@@ -20,7 +20,7 @@ DihedralStyle(helix,DihedralHelix)
#ifndef LMP_DIHEDRAL_HELIX_H
#define LMP_DIHEDRAL_HELIX_H
-#include "stdio.h"
+#include <stdio.h>
#include "dihedral.h"
namespace LAMMPS_NS {
diff --git a/src/MOLECULE/dihedral_multi_harmonic.cpp b/src/MOLECULE/dihedral_multi_harmonic.cpp
index 48f4f2b45f..0842595fba 100644
--- a/src/MOLECULE/dihedral_multi_harmonic.cpp
+++ b/src/MOLECULE/dihedral_multi_harmonic.cpp
@@ -15,8 +15,8 @@
Contributing author: Mathias Puetz (SNL) and friends
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdlib.h>
#include "dihedral_multi_harmonic.h"
#include "atom.h"
#include "neighbor.h"
@@ -155,8 +155,8 @@ void DihedralMultiHarmonic::compute(int eflag, int vflag)
MPI_Comm_rank(world,&me);
if (screen) {
char str[128];
- sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " "
- TAGINT_FORMAT " " TAGINT_FORMAT " "
+ sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT,
me,update->ntimestep,
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
diff --git a/src/MOLECULE/dihedral_multi_harmonic.h b/src/MOLECULE/dihedral_multi_harmonic.h
index b77f85ddff..8f40b56a5f 100644
--- a/src/MOLECULE/dihedral_multi_harmonic.h
+++ b/src/MOLECULE/dihedral_multi_harmonic.h
@@ -20,7 +20,7 @@ DihedralStyle(multi/harmonic,DihedralMultiHarmonic)
#ifndef LMP_DIHEDRAL_MULTI_HARMONIC_H
#define LMP_DIHEDRAL_MULTI_HARMONIC_H
-#include "stdio.h"
+#include <stdio.h>
#include "dihedral.h"
namespace LAMMPS_NS {
diff --git a/src/MOLECULE/dihedral_opls.cpp b/src/MOLECULE/dihedral_opls.cpp
index b85f0d36f7..609fac74bd 100644
--- a/src/MOLECULE/dihedral_opls.cpp
+++ b/src/MOLECULE/dihedral_opls.cpp
@@ -15,8 +15,8 @@
Contributing author: Mark Stevens (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdlib.h>
#include "dihedral_opls.h"
#include "atom.h"
#include "comm.h"
@@ -164,8 +164,8 @@ void DihedralOPLS::compute(int eflag, int vflag)
MPI_Comm_rank(world,&me);
if (screen) {
char str[128];
- sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " "
- TAGINT_FORMAT " " TAGINT_FORMAT " "
+ sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT,
me,update->ntimestep,
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
diff --git a/src/MOLECULE/dihedral_opls.h b/src/MOLECULE/dihedral_opls.h
index 106dbe2431..0a127d3ac1 100644
--- a/src/MOLECULE/dihedral_opls.h
+++ b/src/MOLECULE/dihedral_opls.h
@@ -20,7 +20,7 @@ DihedralStyle(opls,DihedralOPLS)
#ifndef LMP_DIHEDRAL_OPLS_H
#define LMP_DIHEDRAL_OPLS_H
-#include "stdio.h"
+#include <stdio.h>
#include "dihedral.h"
namespace LAMMPS_NS {
diff --git a/src/MOLECULE/improper_cvff.cpp b/src/MOLECULE/improper_cvff.cpp
index fde5738c51..28b3612c78 100644
--- a/src/MOLECULE/improper_cvff.cpp
+++ b/src/MOLECULE/improper_cvff.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "math.h"
-#include "stdlib.h"
+#include <mpi.h>
+#include <math.h>
+#include <stdlib.h>
#include "improper_cvff.h"
#include "atom.h"
#include "comm.h"
@@ -150,8 +150,8 @@ void ImproperCvff::compute(int eflag, int vflag)
MPI_Comm_rank(world,&me);
if (screen) {
char str[128];
- sprintf(str,"Improper problem: %d " BIGINT_FORMAT " "
- TAGINT_FORMAT " " TAGINT_FORMAT " "
+ sprintf(str,"Improper problem: %d " BIGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT,
me,update->ntimestep,
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
diff --git a/src/MOLECULE/improper_cvff.h b/src/MOLECULE/improper_cvff.h
index 7717fe7b64..8e997e3ff4 100644
--- a/src/MOLECULE/improper_cvff.h
+++ b/src/MOLECULE/improper_cvff.h
@@ -20,7 +20,7 @@ ImproperStyle(cvff,ImproperCvff)
#ifndef LMP_IMPROPER_CVFF_H
#define LMP_IMPROPER_CVFF_H
-#include "stdio.h"
+#include <stdio.h>
#include "improper.h"
namespace LAMMPS_NS {
diff --git a/src/MOLECULE/improper_harmonic.cpp b/src/MOLECULE/improper_harmonic.cpp
index c11601347b..56ddce6f5b 100644
--- a/src/MOLECULE/improper_harmonic.cpp
+++ b/src/MOLECULE/improper_harmonic.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "math.h"
-#include "stdlib.h"
+#include <mpi.h>
+#include <math.h>
+#include <stdlib.h>
#include "improper_harmonic.h"
#include "atom.h"
#include "comm.h"
@@ -124,8 +124,8 @@ void ImproperHarmonic::compute(int eflag, int vflag)
MPI_Comm_rank(world,&me);
if (screen) {
char str[128];
- sprintf(str,"Improper problem: %d " BIGINT_FORMAT " "
- TAGINT_FORMAT " " TAGINT_FORMAT " "
+ sprintf(str,"Improper problem: %d " BIGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT,
me,update->ntimestep,
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
diff --git a/src/MOLECULE/improper_harmonic.h b/src/MOLECULE/improper_harmonic.h
index c4c606b557..b5132ab7ff 100644
--- a/src/MOLECULE/improper_harmonic.h
+++ b/src/MOLECULE/improper_harmonic.h
@@ -20,7 +20,7 @@ ImproperStyle(harmonic,ImproperHarmonic)
#ifndef LMP_IMPROPER_HARMONIC_H
#define LMP_IMPROPER_HARMONIC_H
-#include "stdio.h"
+#include <stdio.h>
#include "improper.h"
namespace LAMMPS_NS {
diff --git a/src/MOLECULE/improper_umbrella.cpp b/src/MOLECULE/improper_umbrella.cpp
index 28b3fe8924..14551e6c5c 100644
--- a/src/MOLECULE/improper_umbrella.cpp
+++ b/src/MOLECULE/improper_umbrella.cpp
@@ -15,9 +15,9 @@
Contributing author: Tod A Pascal (Caltech)
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "math.h"
-#include "stdlib.h"
+#include <mpi.h>
+#include <math.h>
+#include <stdlib.h>
#include "improper_umbrella.h"
#include "atom.h"
#include "comm.h"
@@ -128,8 +128,8 @@ void ImproperUmbrella::compute(int eflag, int vflag)
MPI_Comm_rank(world,&me);
if (screen) {
char str[128];
- sprintf(str,"Improper problem: %d " BIGINT_FORMAT " "
- TAGINT_FORMAT " " TAGINT_FORMAT " "
+ sprintf(str,"Improper problem: %d " BIGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT,
me,update->ntimestep,
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
diff --git a/src/MOLECULE/improper_umbrella.h b/src/MOLECULE/improper_umbrella.h
index 1103303747..f590a63c32 100644
--- a/src/MOLECULE/improper_umbrella.h
+++ b/src/MOLECULE/improper_umbrella.h
@@ -20,7 +20,7 @@ ImproperStyle(umbrella,ImproperUmbrella)
#ifndef LMP_IMPROPER_UMBRELLA_H
#define LMP_IMPROPER_UMBRELLA_H
-#include "stdio.h"
+#include <stdio.h>
#include "improper.h"
namespace LAMMPS_NS {
diff --git a/src/MOLECULE/pair_hbond_dreiding_lj.cpp b/src/MOLECULE/pair_hbond_dreiding_lj.cpp
index cfb2dfeb57..af54c9bdfa 100644
--- a/src/MOLECULE/pair_hbond_dreiding_lj.cpp
+++ b/src/MOLECULE/pair_hbond_dreiding_lj.cpp
@@ -15,10 +15,10 @@
Contributing author: Tod A Pascal (Caltech)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_hbond_dreiding_lj.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/MOLECULE/pair_hbond_dreiding_morse.cpp b/src/MOLECULE/pair_hbond_dreiding_morse.cpp
index f0b31b1baf..ab793405dd 100644
--- a/src/MOLECULE/pair_hbond_dreiding_morse.cpp
+++ b/src/MOLECULE/pair_hbond_dreiding_morse.cpp
@@ -15,10 +15,10 @@
Contributing author: Tod A Pascal (Caltech)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_hbond_dreiding_morse.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp b/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp
index 89f4350335..0d08a672ad 100644
--- a/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp
+++ b/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp
@@ -15,10 +15,10 @@
Contributing author: Paul Crozier (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_lj_charmm_coul_charmm.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.cpp b/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.cpp
index 19a44f2878..3421f88eb3 100644
--- a/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.cpp
+++ b/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "string.h"
+#include <math.h>
+#include <string.h>
#include "pair_lj_charmm_coul_charmm_implicit.h"
#include "atom.h"
#include "force.h"
diff --git a/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp b/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp
index 3ba9ee7edb..0f5a1f68d1 100644
--- a/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp
+++ b/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp
@@ -15,9 +15,9 @@
Contributing author: Pavel Elkind (Gothenburg University)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_lj_cut_tip4p_cut.h"
#include "atom.h"
#include "force.h"
@@ -31,7 +31,7 @@
#include "memory.h"
#include "error.h"
-using namespace LAMMPS_NS;
+using namespace LAMMPS_NS;
using namespace MathConst;
/* ---------------------------------------------------------------------- */
@@ -488,7 +488,7 @@ void PairLJCutTIP4PCut::init_style()
error->all(FLERR,"Must use a bond style with TIP4P potential");
if (force->angle == NULL)
error->all(FLERR,"Must use an angle style with TIP4P potential");
-
+
neighbor->request(this,instance_me);
// set alpha parameter
@@ -525,14 +525,14 @@ double PairLJCutTIP4PCut::init_one(int i, int j)
double ratio = sigma[i][j] / cut_lj[i][j];
offset[i][j] = 4.0 * epsilon[i][j] * (pow(ratio,12.0) - pow(ratio,6.0));
} else offset[i][j] = 0.0;
-
+
cut_ljsq[j][i] = cut_ljsq[i][j];
lj1[j][i] = lj1[i][j];
lj2[j][i] = lj2[i][j];
lj3[j][i] = lj3[i][j];
lj4[j][i] = lj4[i][j];
offset[j][i] = offset[i][j];
-
+
// compute I,J contribution to long-range tail correction
// count total # of atoms of type I and J via Allreduce
@@ -562,15 +562,15 @@ double PairLJCutTIP4PCut::init_one(int i, int j)
// check that LJ epsilon = 0.0 for water H
// set LJ cutoff to 0.0 for any interaction involving water H
// so LJ term isn't calculated in compute()
-
+
if ((i == typeH && epsilon[i][i] != 0.0) ||
(j == typeH && epsilon[j][j] != 0.0))
error->all(FLERR,"Water H epsilon must be 0.0 for "
"pair style lj/cut/tip4p/cut");
-
+
if (i == typeH || j == typeH)
cut_ljsq[j][i] = cut_ljsq[i][j] = 0.0;
-
+
return cut;
}
diff --git a/src/MOLECULE/pair_tip4p_cut.cpp b/src/MOLECULE/pair_tip4p_cut.cpp
index f6a0d0bb43..47aa773047 100644
--- a/src/MOLECULE/pair_tip4p_cut.cpp
+++ b/src/MOLECULE/pair_tip4p_cut.cpp
@@ -15,8 +15,8 @@
Contributing author: Pavel Elkind (Gothenburg University)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdlib.h>
#include "pair_tip4p_cut.h"
#include "atom.h"
#include "force.h"
@@ -30,7 +30,7 @@
#include "memory.h"
#include "error.h"
-using namespace LAMMPS_NS;
+using namespace LAMMPS_NS;
using namespace MathConst;
/* ---------------------------------------------------------------------- */
@@ -419,7 +419,7 @@ void PairTIP4PCut::init_style()
error->all(FLERR,"Must use a bond style with TIP4P potential");
if (force->angle == NULL)
error->all(FLERR,"Must use an angle style with TIP4P potential");
-
+
neighbor->request(this,instance_me);
// set alpha parameter
diff --git a/src/MPIIO/dump_atom_mpiio.cpp b/src/MPIIO/dump_atom_mpiio.cpp
index 8ac03829ee..a44297f141 100644
--- a/src/MPIIO/dump_atom_mpiio.cpp
+++ b/src/MPIIO/dump_atom_mpiio.cpp
@@ -15,7 +15,7 @@
Contributing author: Paul Coffman (IBM)
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "dump_atom_mpiio.h"
#include "domain.h"
#include "atom.h"
diff --git a/src/MPIIO/dump_cfg_mpiio.cpp b/src/MPIIO/dump_cfg_mpiio.cpp
index 285eb038b4..50683ecf64 100644
--- a/src/MPIIO/dump_cfg_mpiio.cpp
+++ b/src/MPIIO/dump_cfg_mpiio.cpp
@@ -15,9 +15,9 @@
Contributing author: Paul Coffman (IBM)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "dump_cfg_mpiio.h"
#include "atom.h"
#include "domain.h"
@@ -290,7 +290,7 @@ void DumpCFGMPIIO::write_header(bigint n)
else if (unwrapflag == 1) scale = UNWRAPEXPAND;
char str[64];
-
+
sprintf(str,"Number of particles = %s\n",BIGINT_FORMAT);
headerSize += sprintf(((char*)&((char*)headerBuffer)[headerSize]),str,n);
headerSize += sprintf(((char*)&((char*)headerBuffer)[headerSize]),"A = %g Angstrom (basic length-scale)\n",scale);
@@ -372,24 +372,24 @@ int DumpCFGMPIIO::convert_string_omp(int n, double *mybuf)
mpifh_buffer_line_per_thread[tid] = (char *) realloc(mpifh_buffer_line_per_thread[tid],(mpifhStringCountPerThread[tid]+DUMP_BUF_CHUNK_SIZE) * sizeof(char));
bufLength[tid] = (mpifhStringCountPerThread[tid]+DUMP_BUF_CHUNK_SIZE) * sizeof(char);
}
- for (int j = 0; j < size_one; j++) {
+ for (int j = 0; j < size_one; j++) {
if (j == 0) {
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),"%f \n",(mybuf[bufOffset[tid]+m]));
} else if (j == 1) {
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),"%s \n",typenames[(int) mybuf[bufOffset[tid]+m]]);
} else if (j >= 2) {
- if (vtype[j] == INT)
+ if (vtype[j] == INT)
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),vformat[j],static_cast<int> (mybuf[bufOffset[tid]+m]));
- else if (vtype[j] == DOUBLE)
+ else if (vtype[j] == DOUBLE)
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),vformat[j],mybuf[bufOffset[tid]+m]);
- else if (vtype[j] == STRING)
+ else if (vtype[j] == STRING)
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),vformat[j],typenames[(int) mybuf[bufOffset[tid]+m]]);
- else if (vtype[j] == BIGINT)
+ else if (vtype[j] == BIGINT)
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),vformat[j],static_cast<bigint> (mybuf[bufOffset[tid]+m]));
}
m++;
} // for j
- mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),"\n");
+ mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),"\n");
} // for i
} // wrap flag
else if (unwrapflag == 1) {
@@ -398,7 +398,7 @@ int DumpCFGMPIIO::convert_string_omp(int n, double *mybuf)
mpifh_buffer_line_per_thread[tid] = (char *) realloc(mpifh_buffer_line_per_thread[tid],(mpifhStringCountPerThread[tid]+DUMP_BUF_CHUNK_SIZE) * sizeof(char));
bufLength[tid] = (mpifhStringCountPerThread[tid]+DUMP_BUF_CHUNK_SIZE) * sizeof(char);
}
- for (int j = 0; j < size_one; j++) {
+ for (int j = 0; j < size_one; j++) {
double unwrap_coord;
if (j == 0) {
//offset += sprintf(&sbuf[offset],"%f \n",mybuf[m]);
@@ -411,39 +411,39 @@ int DumpCFGMPIIO::convert_string_omp(int n, double *mybuf)
//offset += sprintf(&sbuf[offset],vformat[j],unwrap_coord);
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),vformat[j],unwrap_coord);
} else if (j >= 5 ) {
- if (vtype[j] == INT)
- //offset +=
+ if (vtype[j] == INT)
+ //offset +=
// sprintf(&sbuf[offset],vformat[j],static_cast<int> (mybuf[m]));
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),vformat[j],static_cast<int> (mybuf[bufOffset[tid]+m]));
- else if (vtype[j] == DOUBLE)
+ else if (vtype[j] == DOUBLE)
// offset += sprintf(&sbuf[offset],vformat[j],mybuf[m]);
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),vformat[j],mybuf[bufOffset[tid]+m]);
- else if (vtype[j] == STRING)
- // offset +=
+ else if (vtype[j] == STRING)
+ // offset +=
// sprintf(&sbuf[offset],vformat[j],typenames[(int) mybuf[m]]);
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),vformat[j],typenames[(int) mybuf[bufOffset[tid]+m]]);
- else if (vtype[j] == BIGINT)
- // offset +=
+ else if (vtype[j] == BIGINT)
+ // offset +=
// sprintf(&sbuf[offset],vformat[j],static_cast<bigint> (mybuf[m]));
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),vformat[j],static_cast<bigint> (mybuf[bufOffset[tid]+m]));
}
m++;
} // for j
- mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),"\n");
+ mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),"\n");
} // for i
} // unwrap flag
} // pragma omp parallel
-
+
#pragma omp barrier
mpifhStringCount = 0;
for (i=0;i<nthreads;i++) {
mpifhStringCount += mpifhStringCountPerThread[i];
}
-
+
memory->destroy(bufOffset);
memory->destroy(bufRange);
memory->destroy(bufLength);
-
+
if (mpifhStringCount > 0) {
if (mpifhStringCount > maxsbuf) {
if (mpifhStringCount > MAXSMALLINT) return -1;
@@ -452,19 +452,19 @@ int DumpCFGMPIIO::convert_string_omp(int n, double *mybuf)
}
sbuf[0] = '\0';
}
-
+
for (int i=0;i<nthreads;i++) {
strcat(sbuf,mpifh_buffer_line_per_thread[i]);
free(mpifh_buffer_line_per_thread[i]);
}
-
+
memory->destroy(mpifhStringCountPerThread);
free(mpifh_buffer_line_per_thread);
-
+
} // else omp
return mpifhStringCount;
-
+
}
#endif
diff --git a/src/MPIIO/dump_custom_mpiio.cpp b/src/MPIIO/dump_custom_mpiio.cpp
index baf74222cc..1cfb0ab81b 100644
--- a/src/MPIIO/dump_custom_mpiio.cpp
+++ b/src/MPIIO/dump_custom_mpiio.cpp
@@ -15,9 +15,9 @@
Contributing author: Paul Coffman (IBM)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "dump_custom_mpiio.h"
#include "atom.h"
#include "force.h"
diff --git a/src/MPIIO/dump_xyz_mpiio.cpp b/src/MPIIO/dump_xyz_mpiio.cpp
index 3c6d0b7d7d..f673d2e9d4 100644
--- a/src/MPIIO/dump_xyz_mpiio.cpp
+++ b/src/MPIIO/dump_xyz_mpiio.cpp
@@ -15,9 +15,9 @@
Contributing author: Paul Coffman (IBM)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "dump_xyz_mpiio.h"
#include "atom.h"
#include "force.h"
diff --git a/src/MPIIO/restart_mpiio.cpp b/src/MPIIO/restart_mpiio.cpp
index b769a58a8a..8ad1dccdca 100644
--- a/src/MPIIO/restart_mpiio.cpp
+++ b/src/MPIIO/restart_mpiio.cpp
@@ -15,10 +15,10 @@
Contributing author: Paul Coffman (IBM)
------------------------------------------------------------------------- */
-#include "mpi.h"
+#include <mpi.h>
#include "restart_mpiio.h"
#include "error.h"
-#include "limits.h"
+#include <limits.h>
using namespace LAMMPS_NS;
diff --git a/src/OPT/pair_eam_opt.cpp b/src/OPT/pair_eam_opt.cpp
index 1f20db29a2..66b2e7283c 100644
--- a/src/OPT/pair_eam_opt.cpp
+++ b/src/OPT/pair_eam_opt.cpp
@@ -19,8 +19,8 @@
Vincent Natoli, Stone Ridge Technology
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdlib.h>
#include "pair_eam_opt.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/OPT/pair_lj_charmm_coul_long_opt.cpp b/src/OPT/pair_lj_charmm_coul_long_opt.cpp
index 136b9fc64d..b98dd36dd1 100644
--- a/src/OPT/pair_lj_charmm_coul_long_opt.cpp
+++ b/src/OPT/pair_lj_charmm_coul_long_opt.cpp
@@ -18,8 +18,8 @@
Vincent Natoli, Stone Ridge Technology
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdlib.h>
#include "pair_lj_charmm_coul_long_opt.h"
#include "atom.h"
#include "force.h"
diff --git a/src/OPT/pair_lj_cut_coul_long_opt.cpp b/src/OPT/pair_lj_cut_coul_long_opt.cpp
index 2ff5fc7bd6..140d4d023a 100644
--- a/src/OPT/pair_lj_cut_coul_long_opt.cpp
+++ b/src/OPT/pair_lj_cut_coul_long_opt.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_lj_cut_coul_long_opt.h"
#include "atom.h"
#include "force.h"
diff --git a/src/OPT/pair_lj_cut_opt.cpp b/src/OPT/pair_lj_cut_opt.cpp
index 170a3aa728..0812a56f01 100644
--- a/src/OPT/pair_lj_cut_opt.cpp
+++ b/src/OPT/pair_lj_cut_opt.cpp
@@ -18,7 +18,7 @@
Vincent Natoli, Stone Ridge Technology
------------------------------------------------------------------------- */
-#include "stdlib.h"
+#include <stdlib.h>
#include "pair_lj_cut_opt.h"
#include "atom.h"
#include "force.h"
diff --git a/src/OPT/pair_lj_cut_tip4p_long_opt.cpp b/src/OPT/pair_lj_cut_tip4p_long_opt.cpp
index e045eeec75..2cca32baec 100644
--- a/src/OPT/pair_lj_cut_tip4p_long_opt.cpp
+++ b/src/OPT/pair_lj_cut_tip4p_long_opt.cpp
@@ -15,7 +15,7 @@
OPT version: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_lj_cut_tip4p_long_opt.h"
#include "atom.h"
#include "domain.h"
diff --git a/src/OPT/pair_lj_long_coul_long_opt.cpp b/src/OPT/pair_lj_long_coul_long_opt.cpp
index 538abb051e..9004e5c93c 100644
--- a/src/OPT/pair_lj_long_coul_long_opt.cpp
+++ b/src/OPT/pair_lj_long_coul_long_opt.cpp
@@ -15,7 +15,7 @@
OPT version: Wayne Mitchell (Loyola University New Orleans)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_lj_long_coul_long_opt.h"
#include "atom.h"
#include "force.h"
@@ -43,11 +43,11 @@ PairLJLongCoulLongOpt::PairLJLongCoulLongOpt(LAMMPS *lmp) : PairLJLongCoulLong(l
void PairLJLongCoulLongOpt::compute(int eflag, int vflag)
{
-
+
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
int order1 = ewald_order&(1<<1), order6 = ewald_order&(1<<6);
-
+
if (order6) {
if (order1) {
if (!ndisptablebits) {
@@ -289,11 +289,11 @@ void PairLJLongCoulLongOpt::compute(int eflag, int vflag)
void PairLJLongCoulLongOpt::compute_outer(int eflag, int vflag)
{
-
+
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
int order1 = ewald_order&(1<<1), order6 = ewald_order&(1<<6);
-
+
if (order6) {
if (order1) {
if (!ndisptablebits) {
@@ -540,7 +540,7 @@ void PairLJLongCoulLongOpt::eval()
{
double evdwl,ecoul,fpair;
evdwl = ecoul = 0.0;
-
+
double **x = atom->x, *x0 = x[0];
double **f = atom->f, *f0 = f[0], *fi = f0;
double *q = atom->q;
@@ -549,7 +549,7 @@ void PairLJLongCoulLongOpt::eval()
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
double qqrd2e = force->qqrd2e;
-
+
int i, j;
int *ineigh, *ineighn, *jneigh, *jneighn, typei, typej, ni;
double qi = 0.0, qri = 0.0;
@@ -557,9 +557,9 @@ void PairLJLongCoulLongOpt::eval()
double rsq, r2inv, force_coul, force_lj;
double g2 = g_ewald_6*g_ewald_6, g6 = g2*g2*g2, g8 = g6*g2;
vector xi, d;
-
+
ineighn = (ineigh = list->ilist)+list->inum;
-
+
for (; ineigh<ineighn; ++ineigh) { // loop over my atoms
i = *ineigh; fi = f0+3*i;
if (ORDER1) qri = (qi = q[i])*qqrd2e; // initialize constants
@@ -568,20 +568,20 @@ void PairLJLongCoulLongOpt::eval()
cutsqi = cutsq[typei]; cut_ljsqi = cut_ljsq[typei];
memcpy(xi, x0+(i+(i<<1)), sizeof(vector));
jneighn = (jneigh = list->firstneigh[i])+list->numneigh[i];
-
+
for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
j = *jneigh;
ni = sbmask(j);
j &= NEIGHMASK;
-
+
{ register double *xj = x0+(j+(j<<1));
d[0] = xi[0] - xj[0]; // pair vector
d[1] = xi[1] - xj[1];
d[2] = xi[2] - xj[2]; }
-
+
if ((rsq = vec_dot(d, d)) >= cutsqi[typej = type[j]]) continue;
r2inv = 1.0/rsq;
-
+
if (ORDER1 && (rsq < cut_coulsq)) { // coulombic
if (!CTABLE || rsq <= tabinnersq) { // series real space
register double r = sqrt(rsq), x = g_ewald*r;
@@ -614,7 +614,7 @@ void PairLJLongCoulLongOpt::eval()
}
}
else force_coul = ecoul = 0.0;
-
+
if (rsq < cut_ljsqi[typej]) { // lj
if (ORDER6) { // long-range lj
if(!LJTABLE || rsq <= tabinnerdispsq) { // series real space
@@ -667,9 +667,9 @@ void PairLJLongCoulLongOpt::eval()
}
}
else force_lj = evdwl = 0.0;
-
+
fpair = (force_coul+force_lj)*r2inv;
-
+
if (NEWTON_PAIR || j < nlocal) {
register double *fj = f0+(j+(j<<1)), f;
fi[0] += f = d[0]*fpair; fj[0] -= f;
@@ -681,12 +681,12 @@ void PairLJLongCoulLongOpt::eval()
fi[1] += d[1]*fpair;
fi[2] += d[2]*fpair;
}
-
+
if (EVFLAG) ev_tally(i,j,nlocal,NEWTON_PAIR,
evdwl,ecoul,fpair,d[0],d[1],d[2]);
}
}
-
+
if (vflag_fdotr) virial_fdotr_compute();
}
@@ -699,7 +699,7 @@ void PairLJLongCoulLongOpt::eval_outer()
{
double evdwl,ecoul,fvirial,fpair;
evdwl = ecoul = 0.0;
-
+
double **x = atom->x, *x0 = x[0];
double **f = atom->f, *f0 = f[0], *fi = f0;
double *q = atom->q;
@@ -709,7 +709,7 @@ void PairLJLongCoulLongOpt::eval_outer()
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
double qqrd2e = force->qqrd2e;
-
+
int i, j;
int *ineigh, *ineighn, *jneigh, *jneighn, typei, typej, ni, respa_flag;
double qi = 0.0, qri = 0.0;
@@ -718,16 +718,16 @@ void PairLJLongCoulLongOpt::eval_outer()
double g2 = g_ewald_6*g_ewald_6, g6 = g2*g2*g2, g8 = g6*g2;
double respa_lj = 0.0, respa_coul = 0.0, frespa = 0.0;
vector xi, d;
-
+
double cut_in_off = cut_respa[2];
double cut_in_on = cut_respa[3];
-
+
double cut_in_diff = cut_in_on - cut_in_off;
double cut_in_off_sq = cut_in_off*cut_in_off;
double cut_in_on_sq = cut_in_on*cut_in_on;
-
+
ineighn = (ineigh = listouter->ilist)+listouter->inum;
-
+
for (; ineigh<ineighn; ++ineigh) { // loop over my atoms
i = *ineigh; fi = f0+3*i;
if (ORDER1) qri = (qi = q[i])*qqrd2e; // initialize constants
@@ -736,20 +736,20 @@ void PairLJLongCoulLongOpt::eval_outer()
cutsqi = cutsq[typei]; cut_ljsqi = cut_ljsq[typei];
memcpy(xi, x0+(i+(i<<1)), sizeof(vector));
jneighn = (jneigh = listouter->firstneigh[i])+listouter->numneigh[i];
-
+
for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
j = *jneigh;
ni = sbmask(j);
j &= NEIGHMASK;
-
+
{ register double *xj = x0+(j+(j<<1));
d[0] = xi[0] - xj[0]; // pair vector
d[1] = xi[1] - xj[1];
d[2] = xi[2] - xj[2]; }
-
+
if ((rsq = vec_dot(d, d)) >= cutsqi[typej = type[j]]) continue;
r2inv = 1.0/rsq;
-
+
frespa = 1.0; // check whether and how to compute respa corrections
respa_coul = 0;
respa_lj = 0;
@@ -758,7 +758,7 @@ void PairLJLongCoulLongOpt::eval_outer()
register double rsw = (sqrt(rsq)-cut_in_off)/cut_in_diff;
frespa = 1-rsw*rsw*(3.0-2.0*rsw);
}
-
+
if (ORDER1 && (rsq < cut_coulsq)) { // coulombic
if (!CTABLE || rsq <= tabinnersq) { // series real space
register double r = sqrt(rsq), s = qri*q[j];
@@ -799,7 +799,7 @@ void PairLJLongCoulLongOpt::eval_outer()
}
}
}
-
+
else force_coul = respa_coul = ecoul = 0.0;
if (rsq < cut_ljsqi[typej]) { // lennard-jones
@@ -855,9 +855,9 @@ void PairLJLongCoulLongOpt::eval_outer()
}
}
else force_lj = respa_lj = evdwl = 0.0;
-
+
fpair = (force_coul+force_lj)*r2inv;
-
+
if (NEWTON_PAIR || j < nlocal) {
register double *fj = f0+(j+(j<<1)), f;
fi[0] += f = d[0]*fpair; fj[0] -= f;
@@ -869,7 +869,7 @@ void PairLJLongCoulLongOpt::eval_outer()
fi[1] += d[1]*fpair;
fi[2] += d[2]*fpair;
}
-
+
if (EVFLAG) {
fvirial = (force_coul + force_lj + respa_coul + respa_lj)*r2inv;
ev_tally(i,j,nlocal,newton_pair,
diff --git a/src/OPT/pair_morse_opt.cpp b/src/OPT/pair_morse_opt.cpp
index 6fcb9843a6..e63fbd0938 100644
--- a/src/OPT/pair_morse_opt.cpp
+++ b/src/OPT/pair_morse_opt.cpp
@@ -18,8 +18,8 @@
Vincent Natoli, Stone Ridge Technology
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdlib.h>
#include "pair_morse_opt.h"
#include "atom.h"
#include "force.h"
diff --git a/src/PERI/atom_vec_peri.cpp b/src/PERI/atom_vec_peri.cpp
index a5fafb04a0..3e6a72289a 100644
--- a/src/PERI/atom_vec_peri.cpp
+++ b/src/PERI/atom_vec_peri.cpp
@@ -15,9 +15,9 @@
Contributing author: Mike Parks (SNL)
------------------------------------------------------------------------- */
-#include "float.h"
-#include "stdlib.h"
-#include "string.h"
+#include <float.h>
+#include <stdlib.h>
+#include <string.h>
#include "atom_vec_peri.h"
#include "atom.h"
#include "comm.h"
@@ -877,7 +877,7 @@ int AtomVecPeri::pack_data_hybrid(int i, double *buf)
void AtomVecPeri::write_data(FILE *fp, int n, double **buf)
{
for (int i = 0; i < n; i++)
- fprintf(fp,TAGINT_FORMAT
+ fprintf(fp,TAGINT_FORMAT
" %d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d\n",
(tagint) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).i,
buf[i][2],buf[i][3],buf[i][4],buf[i][5],buf[i][6],
@@ -912,7 +912,7 @@ int AtomVecPeri::property_atom(char *name)
index maps to data specific to this atom style
------------------------------------------------------------------------- */
-void AtomVecPeri::pack_property_atom(int index, double *buf,
+void AtomVecPeri::pack_property_atom(int index, double *buf,
int nvalues, int groupbit)
{
int *mask = atom->mask;
diff --git a/src/PERI/compute_damage_atom.cpp b/src/PERI/compute_damage_atom.cpp
index 7a8cbfd3dd..cf8cf35cd3 100644
--- a/src/PERI/compute_damage_atom.cpp
+++ b/src/PERI/compute_damage_atom.cpp
@@ -15,7 +15,7 @@
Contributing author: Mike Parks (SNL)
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "compute_damage_atom.h"
#include "atom.h"
#include "update.h"
@@ -102,13 +102,13 @@ void ComputeDamageAtom::compute_peratom()
damage_temp = 0.0;
for (jj = 0; jj < jnum; jj++) {
if (partner[i][jj] == 0) continue;
-
+
// look up local index of this partner particle
// skip if particle is "lost"
-
+
j = atom->map(partner[i][jj]);
if (j < 0) continue;
-
+
damage_temp += vfrac[j];
}
diff --git a/src/PERI/compute_dilatation_atom.cpp b/src/PERI/compute_dilatation_atom.cpp
index 366c5bcda9..20993fab47 100644
--- a/src/PERI/compute_dilatation_atom.cpp
+++ b/src/PERI/compute_dilatation_atom.cpp
@@ -15,7 +15,7 @@
Contributing author: Rezwanur Rahman, John Foster (UTSA)
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "compute_dilatation_atom.h"
#include "atom.h"
#include "update.h"
@@ -72,8 +72,8 @@ void ComputeDilatationAtom::init()
if (force->pair_match("peri/lps",1)) isLPS = 1;
if (force->pair_match("peri/ves",1)) isVES = 1;
if (force->pair_match("peri/eps",1)) isEPS = 1;
-
- if (isPMB)
+
+ if (isPMB)
error->all(FLERR,"Compute dilatation/atom cannot be used "
"with this pair style");
diff --git a/src/PERI/compute_dilatation_atom.h b/src/PERI/compute_dilatation_atom.h
index 9aac567760..a247cc9291 100644
--- a/src/PERI/compute_dilatation_atom.h
+++ b/src/PERI/compute_dilatation_atom.h
@@ -27,8 +27,8 @@ namespace LAMMPS_NS {
class ComputeDilatationAtom : public Compute {
friend class PairPeriPMB;
friend class PairPeriLPS;
- friend class PairPeriVES;
- friend class PairPeriEPS;
+ friend class PairPeriVES;
+ friend class PairPeriEPS;
public:
ComputeDilatationAtom(class LAMMPS *, int, char **);
~ComputeDilatationAtom();
diff --git a/src/PERI/compute_plasticity_atom.cpp b/src/PERI/compute_plasticity_atom.cpp
index ac089fe7a6..2c47f18b1f 100644
--- a/src/PERI/compute_plasticity_atom.cpp
+++ b/src/PERI/compute_plasticity_atom.cpp
@@ -15,7 +15,7 @@
Contributing author: Rezwanur Rahman, John Foster (UTSA)
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "compute_plasticity_atom.h"
#include "atom.h"
#include "update.h"
@@ -36,7 +36,7 @@ ComputePlasticityAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 3) error->all(FLERR,"Illegal compute plasticity/atom command");
-
+
if (!force->pair_match("peri/eps",1))
error->all(FLERR,"Compute plasticity/atom cannot be used "
"with this pair style");
diff --git a/src/PERI/fix_peri_neigh.cpp b/src/PERI/fix_peri_neigh.cpp
index a26507ae54..a84ce31609 100644
--- a/src/PERI/fix_peri_neigh.cpp
+++ b/src/PERI/fix_peri_neigh.cpp
@@ -15,7 +15,7 @@
Contributing authors: Mike Parks (SNL), Ezwanur Rahman, J.T. Foster (UTSA)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "fix_peri_neigh.h"
#include "pair_peri_pmb.h"
#include "pair_peri_lps.h"
@@ -47,7 +47,7 @@ FixPeriNeigh::FixPeriNeigh(LAMMPS *lmp,int narg, char **arg) :
if (force->pair_match("peri/lps",1)) isLPS = 1;
if (force->pair_match("peri/ves",1)) isVES = 1;
if (force->pair_match("peri/eps",1)) isEPS = 1;
-
+
restart_global = 1;
restart_peratom = 1;
first = 1;
@@ -225,7 +225,7 @@ void FixPeriNeigh::setup(int vflag)
memory->destroy(deviatorextention);
memory->destroy(deviatorBackextention);
memory->destroy(deviatorPlasticextension);
- memory->destroy(lambdaValue);
+ memory->destroy(lambdaValue);
memory->destroy(r0);
memory->destroy(npartner);
@@ -235,7 +235,7 @@ void FixPeriNeigh::setup(int vflag)
deviatorBackextention = NULL;
deviatorPlasticextension = NULL;
lambdaValue = NULL;
- r0 = NULL;
+ r0 = NULL;
grow_arrays(atom->nmax);
// create partner list and r0 values from neighbor list
@@ -270,11 +270,11 @@ void FixPeriNeigh::setup(int vflag)
if (rsq <= cutsq[itype][jtype]) {
partner[i][npartner[i]] = tag[j];
if (isVES)
- deviatorextention[i][npartner[i]] =
+ deviatorextention[i][npartner[i]] =
deviatorBackextention[i][npartner[i]] = 0.0;
if (isEPS)
deviatorPlasticextension[i][npartner[i]] = 0.0;
- r0[i][npartner[i]] = sqrt(rsq);
+ r0[i][npartner[i]] = sqrt(rsq);
npartner[i]++;
vinter[i] += vfrac[j];
}
@@ -332,7 +332,7 @@ void FixPeriNeigh::setup(int vflag)
double delx0 = xtmp0 - x0[j][0];
double dely0 = ytmp0 - x0[j][1];
double delz0 = ztmp0 - x0[j][2];
-
+
double rsq0 = delx0*delx0 + dely0*dely0 + delz0*delz0;
jtype = type[j];
@@ -347,8 +347,8 @@ void FixPeriNeigh::setup(int vflag)
// for PMB, influence = 1.0, otherwise invoke influence function
- if (isPMB)
- wvolume[i] += 1.0 * rsq0 * vfrac[j] * vfrac_scale;
+ if (isPMB)
+ wvolume[i] += 1.0 * rsq0 * vfrac[j] * vfrac_scale;
else if (isLPS)
wvolume[i] += pairlps->influence_function(delx0,dely0,delz0) *
rsq0 * vfrac[j] * vfrac_scale;
@@ -357,7 +357,7 @@ void FixPeriNeigh::setup(int vflag)
rsq0 * vfrac[j] * vfrac_scale;
else if (isEPS)
wvolume[i] += paireps->influence_function(delx0,dely0,delz0) *
- rsq0 * vfrac[j] * vfrac_scale;
+ rsq0 * vfrac[j] * vfrac_scale;
}
}
@@ -391,7 +391,7 @@ void FixPeriNeigh::setup(int vflag)
------------------------------------------------------------------------- */
double FixPeriNeigh::memory_usage()
-{
+{
int nmax = atom->nmax;
int bytes = nmax * sizeof(int);
bytes += nmax*maxpartner * sizeof(tagint);
@@ -399,14 +399,14 @@ double FixPeriNeigh::memory_usage()
if (isVES) {
bytes += nmax*maxpartner * sizeof(double);
bytes += nmax*maxpartner * sizeof(double);
- }
+ }
if (isEPS) {
bytes += nmax*maxpartner * sizeof(double);
bytes += nmax * sizeof(double);
- }
+ }
bytes += nmax * sizeof(double);
bytes += nmax * sizeof(double);
- return bytes;
+ return bytes;
}
/* ----------------------------------------------------------------------
@@ -426,7 +426,7 @@ void FixPeriNeigh::grow_arrays(int nmax)
if (isEPS) memory->grow(deviatorPlasticextension,nmax,maxpartner,
"peri_neigh:deviatorPlasticextension");
memory->grow(r0,nmax,maxpartner,"peri_neigh:r0");
- if (isEPS) memory->grow(lambdaValue,nmax,"peri_neigh:lambdaValue");
+ if (isEPS) memory->grow(lambdaValue,nmax,"peri_neigh:lambdaValue");
memory->grow(vinter,nmax,"peri_neigh:vinter");
memory->grow(wvolume,nmax,"peri_neigh:wvolume");
}
@@ -443,7 +443,7 @@ void FixPeriNeigh::copy_arrays(int i, int j, int delflag)
if (isVES) {
deviatorextention[j][m] = deviatorextention[i][m];
deviatorBackextention[j][m] = deviatorBackextention[i][m];
- }
+ }
if (isEPS)
deviatorPlasticextension[j][m] = deviatorPlasticextension[i][m];
r0[j][m] = r0[i][m];
@@ -469,14 +469,14 @@ int FixPeriNeigh::pack_exchange(int i, double *buf)
if (isVES) {
buf[m++] = deviatorextention[i][n];
buf[m++] = deviatorBackextention[i][n];
- }
+ }
if (isEPS) buf[m++] = deviatorPlasticextension[i][n];
buf[m++] = r0[i][n];
}
if (isVES) buf[0] = m/4;
else if (isEPS) buf[0] = m/3;
else buf[0] = m/2;
- if (isEPS) buf[m++] = lambdaValue[i];
+ if (isEPS) buf[m++] = lambdaValue[i];
buf[m++] = vinter[i];
buf[m++] = wvolume[i];
return m;
@@ -492,12 +492,12 @@ int FixPeriNeigh::unpack_exchange(int nlocal, double *buf)
npartner[nlocal] = static_cast<int> (buf[m++]);
for (int n = 0; n < npartner[nlocal]; n++) {
partner[nlocal][n] = static_cast<tagint> (buf[m++]);
- if (isVES) {
+ if (isVES) {
deviatorextention[nlocal][n] = buf[m++];
deviatorBackextention[nlocal][n] = buf[m++];
}
if (isEPS) deviatorPlasticextension[nlocal][n] = buf[m++];
- r0[nlocal][n] = buf[m++];
+ r0[nlocal][n] = buf[m++];
}
if (isEPS) lambdaValue[nlocal] = buf[m++];
vinter[nlocal] = buf[m++];
@@ -580,17 +580,17 @@ int FixPeriNeigh::pack_restart(int i, double *buf)
buf[m++] = npartner[i];
for (int n = 0; n < npartner[i]; n++) {
buf[m++] = partner[i][n];
- if (isVES) {
+ if (isVES) {
buf[m++] = deviatorextention[i][n];
buf[m++] = deviatorBackextention[i][n];
- }
+ }
if (isEPS) buf[m++] = deviatorPlasticextension[i][n];
buf[m++] = r0[i][n];
}
if (isEPS) buf[m++] = lambdaValue[i];
buf[m++] = vinter[i];
buf[m++] = wvolume[i];
- return m;
+ return m;
}
/* ----------------------------------------------------------------------
@@ -611,16 +611,16 @@ void FixPeriNeigh::unpack_restart(int nlocal, int nth)
npartner[nlocal] = static_cast<int> (extra[nlocal][m++]);
for (int n = 0; n < npartner[nlocal]; n++) {
partner[nlocal][n] = static_cast<tagint> (extra[nlocal][m++]);
- if (isVES) {
+ if (isVES) {
deviatorextention[nlocal][n] = extra[nlocal][m++];
deviatorBackextention[nlocal][n] = extra[nlocal][m++];
- }
+ }
if (isEPS) deviatorPlasticextension[nlocal][n] = extra[nlocal][m++];
r0[nlocal][n] = extra[nlocal][m++];
}
if (isEPS) lambdaValue[nlocal] = extra[nlocal][m++];
vinter[nlocal] = extra[nlocal][m++];
- wvolume[nlocal] = extra[nlocal][m++];
+ wvolume[nlocal] = extra[nlocal][m++];
}
/* ----------------------------------------------------------------------
@@ -631,7 +631,7 @@ int FixPeriNeigh::maxsize_restart()
{
if (isVES) return 4*maxpartner + 4;
if (isEPS) return 3*maxpartner + 5;
- return 2*maxpartner + 4;
+ return 2*maxpartner + 4;
}
/* ----------------------------------------------------------------------
@@ -642,5 +642,5 @@ int FixPeriNeigh::size_restart(int nlocal)
{
if (isVES) return 4*npartner[nlocal] + 4;
if (isEPS) return 3*npartner[nlocal] + 5;
- return 2*npartner[nlocal] + 4;
+ return 2*npartner[nlocal] + 4;
}
diff --git a/src/PERI/fix_peri_neigh.h b/src/PERI/fix_peri_neigh.h
index 30d3d81436..79006ab541 100644
--- a/src/PERI/fix_peri_neigh.h
+++ b/src/PERI/fix_peri_neigh.h
@@ -63,13 +63,13 @@ class FixPeriNeigh : public Fix {
int maxpartner; // max # of peridynamic neighs for any atom
int *npartner; // # of neighbors for each atom
tagint **partner; // neighs for each atom, stored as global IDs
- double **deviatorextention; // Deviatoric extention
- double **deviatorBackextention; // Deviatoric back extention
- double **deviatorPlasticextension; // Deviatoric plastic extension
+ double **deviatorextention; // Deviatoric extention
+ double **deviatorBackextention; // Deviatoric back extention
+ double **deviatorPlasticextension; // Deviatoric plastic extension
double *lambdaValue;
double **r0; // initial distance to partners
double **r1; // instanteneous distance to partners
- double *thetaValue; // dilatation
+ double *thetaValue; // dilatation
double *vinter; // sum of vfrac for bonded neighbors
double *wvolume; // weighted volume of particle
int isPMB,isLPS,isVES,isEPS; // which flavor of PD
diff --git a/src/PERI/pair_peri_eps.cpp b/src/PERI/pair_peri_eps.cpp
index 1d9361a362..ecf6f0a3fa 100644
--- a/src/PERI/pair_peri_eps.cpp
+++ b/src/PERI/pair_peri_eps.cpp
@@ -15,9 +15,9 @@
Contributing author: Rezwanur Rahman, John Foster (UTSA)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_peri_eps.h"
#include "atom.h"
#include "domain.h"
@@ -108,7 +108,7 @@ void PairPeriEPS::compute(int eflag, int vflag)
double *s0 = atom->s0;
double **x0 = atom->x0;
double **r0 = ((FixPeriNeigh *) modify->fix[ifix_peri])->r0;
- double **deviatorPlasticextension =
+ double **deviatorPlasticextension =
((FixPeriNeigh *) modify->fix[ifix_peri])->deviatorPlasticextension;
tagint **partner = ((FixPeriNeigh *) modify->fix[ifix_peri])->partner;
int *npartner = ((FixPeriNeigh *) modify->fix[ifix_peri])->npartner;
@@ -146,7 +146,7 @@ void PairPeriEPS::compute(int eflag, int vflag)
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
-
+
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
@@ -204,10 +204,10 @@ void PairPeriEPS::compute(int eflag, int vflag)
}
// grow bond forces array if necessary
-
+
int maxpartner = 0;
for (i = 0; i < nlocal; i++) maxpartner = MAX(maxpartner,npartner[i]);
-
+
if (atom->nmax > nmax) {
memory->destroy(s0_new);
@@ -215,21 +215,21 @@ void PairPeriEPS::compute(int eflag, int vflag)
nmax = atom->nmax;
memory->create(s0_new,nmax,"pair:s0_new");
memory->create(theta,nmax,"pair:theta");
-
+
}
-
+
// ******** temp array to store Plastic extension *********** ///
// create on heap to reduce stack use and to allow for faster zeroing
double **deviatorPlasticExtTemp;
memory->create(deviatorPlasticExtTemp,nlocal,maxpartner,"pair:plastext");
memset(&(deviatorPlasticExtTemp[0][0]),0,sizeof(double)*nlocal*maxpartner);
// ******** temp array to store Plastic extension *********** ///
-
-
+
+
// compute the dilatation on each particle
compute_dilatation();
-
+
// communicate dilatation (theta) of each particle
comm->forward_comm_pair(this);
@@ -268,27 +268,27 @@ void PairPeriEPS::compute(int eflag, int vflag)
itype = type[i];
jnum = npartner[i];
first = true;
-
+
double yieldStress = m_yieldstress[itype][itype];
double horizon = cut[itype][itype];
double tdnorm = compute_DeviatoricForceStateNorm(i);
- double pointwiseYieldvalue = 25.0 * yieldStress *
+ double pointwiseYieldvalue = 25.0 * yieldStress *
yieldStress / 8 / M_PI / pow(horizon,5);
-
-
+
+
double fsurf = (tdnorm * tdnorm)/2 - pointwiseYieldvalue;
bool elastic = true;
double alphavalue = (15 * shearmodulus[itype][itype]) /wvolume[i];
-
-
+
+
if (fsurf>0) {
elastic = false;
deltalambda = ((tdnorm /sqrt(2.0 * pointwiseYieldvalue)) - 1.0) / alphavalue;
double templambda = lambdaValue[i];
lambdaValue[i] = templambda + deltalambda;
- }
+ }
for (jj = 0; jj < jnum; jj++) {
if (partner[i][jj] == 0) continue;
@@ -320,7 +320,7 @@ void PairPeriEPS::compute(int eflag, int vflag)
if (fabs(dr) < 2.2204e-016) {
dr = 0.0;
- }
+ }
// scale vfrac[j] if particle j near the horizon
@@ -328,35 +328,35 @@ void PairPeriEPS::compute(int eflag, int vflag)
vfrac_scale = (-1.0/(2*half_lc))*(r0[i][jj]) +
(1.0 + ((delta - half_lc)/(2*half_lc) ) );
else vfrac_scale = 1.0;
-
+
omega_plus = influence_function(-1.0*delx0,-1.0*dely0,-1.0*delz0);
omega_minus = influence_function(delx0,dely0,delz0);
-
- //Elastic Part
+
+ //Elastic Part
rk = ((3.0 * bulkmodulus[itype][itype]) * ( (omega_plus * theta[i] / wvolume[i]) +
( omega_minus * theta[j] / wvolume[j] ) ) ) * r0[i][jj];
-
+
if (r > 0.0) fbond = -((rk/r) * vfrac[j] * vfrac_scale);
else fbond = 0.0;
-
+
//Plastic part
-
+
double deviatoric_extension = dr - (theta[i]* r0[i][jj] / 3.0);
edpNp1 = deviatorPlasticextension[i][jj];
-
+
double tdtrialValue = ( 15 * shearmodulus[itype][itype]) *
- ( (omega_plus / wvolume[i]) + (omega_minus / wvolume[j]) ) *
- (deviatoric_extension - edpNp1);
-
+ ( (omega_plus / wvolume[i]) + (omega_minus / wvolume[j]) ) *
+ (deviatoric_extension - edpNp1);
+
if(elastic) {
rkNew = tdtrialValue;
}
else {
rkNew = (sqrt(2.0*pointwiseYieldvalue) * tdtrialValue) / tdnorm;
deviatorPlasticExtTemp[i][jj] = edpNp1 + rkNew * deltalambda;
- }
-
-
+ }
+
+
if (r > 0.0) fbondElastoPlastic = -((rkNew/r) * vfrac[j] * vfrac_scale);
else fbondElastoPlastic = 0.0;
@@ -364,17 +364,17 @@ void PairPeriEPS::compute(int eflag, int vflag)
// total Force state: elastic + plastic
fbondFinal=fbond+fbondElastoPlastic;
fbond=fbondFinal;
-
-
+
+
f[i][0] += delx*fbond;
f[i][1] += dely*fbond;
f[i][2] += delz*fbond;
-
+
// since I-J is double counted, set newton off & use 1/2 factor and I,I
if (eflag) evdwl = (0.5 * 15 * shearmodulus[itype][itype]/wvolume[i] *
- omega_plus * (deviatoric_extension - edpNp1) *
+ omega_plus * (deviatoric_extension - edpNp1) *
(deviatoric_extension-edpNp1)) * vfrac[j] * vfrac_scale;
if (evflag) ev_tally(i,i,nlocal,0,0.5*evdwl,0.0,
0.5*fbond*vfrac[i],delx,dely,delz);
@@ -395,13 +395,13 @@ void PairPeriEPS::compute(int eflag, int vflag)
(alpha[itype][jtype] * stretch));
first = false;
- }
+ }
}
// store new s0
memcpy(s0,s0_new,sizeof(double)*nlocal);
-
+
memcpy(&(deviatorPlasticextension[0][0]),
&(deviatorPlasticExtTemp[0][0]),
sizeof(double)*nlocal*maxpartner);
@@ -502,7 +502,7 @@ void PairPeriEPS::init_style()
{
// error checks
- if (!atom->peri_flag)
+ if (!atom->peri_flag)
error->all(FLERR,"Pair style peri requires atom style peri");
if (atom->map_style == 0)
error->all(FLERR,"Pair peri requires an atom map, see atom_modify");
@@ -607,7 +607,7 @@ double PairPeriEPS::influence_function(double xi_x, double xi_y, double xi_z)
{
double r = sqrt(xi_x*xi_x + xi_y*xi_y + xi_z*xi_z);
double omega;
-
+
if (fabs(r) < 2.2204e-016)
error->one(FLERR,"Divide by 0 in influence function");
omega = 1.0/r;
@@ -726,11 +726,11 @@ double PairPeriEPS::compute_DeviatoricForceStateNorm(int i)
tagint **partner = ((FixPeriNeigh *) modify->fix[ifix_peri])->partner;
int *npartner = ((FixPeriNeigh *) modify->fix[ifix_peri])->npartner;
double *wvolume = ((FixPeriNeigh *) modify->fix[ifix_peri])->wvolume;
- double **deviatorPlasticextension =
+ double **deviatorPlasticextension =
((FixPeriNeigh *) modify->fix[ifix_peri])->deviatorPlasticextension;
int periodic = domain->xperiodic || domain->yperiodic || domain->zperiodic;
-
+
// compute the dilatation theta
xtmp = x[i][0];
@@ -749,7 +749,7 @@ double PairPeriEPS::compute_DeviatoricForceStateNorm(int i)
if (j < 0) {
partner[i][jj] = 0;
continue;
- }
+ }
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
@@ -762,10 +762,10 @@ double PairPeriEPS::compute_DeviatoricForceStateNorm(int i)
r = sqrt(rsq);
dr = r - r0[i][jj];
if (fabs(dr) < 2.2204e-016) dr = 0.0;
-
+
// scale vfrac[j] if particle j near the horizon
double vfrac_scale;
-
+
jtype = type[j];
double delta = cut[itype][jtype];
@@ -775,21 +775,21 @@ double PairPeriEPS::compute_DeviatoricForceStateNorm(int i)
vfrac_scale = (-1.0/(2*half_lc))*(r0[i][jj]) +
(1.0 + ((delta - half_lc)/(2*half_lc) ) );
else vfrac_scale = 1.0;
-
+
double ed = dr - (theta[i] * r0[i][jj])/3;
double edPNP1 = deviatorPlasticextension[i][jj];
jtype = type[j];
delta = cut[itype][jtype];
-
+
double omega_plus = influence_function(-1.0*delx0,-1.0*dely0,-1.0*delz0);
double omega_minus = influence_function(delx0,dely0,delz0);
-
+
tdtrial = ( 15 * shearmodulus[itype][itype]) *
((omega_plus * theta[i] / wvolume[i]) +
( omega_minus * theta[j] / wvolume[j] ) ) * (ed - edPNP1);
-
- norm += tdtrial * tdtrial * vfrac[j] * vfrac_scale;
+
+ norm += tdtrial * tdtrial * vfrac[j] * vfrac_scale;
}
return sqrt(norm);
}
diff --git a/src/PERI/pair_peri_lps.cpp b/src/PERI/pair_peri_lps.cpp
index 00c7f3dc3f..7b2ccec92c 100644
--- a/src/PERI/pair_peri_lps.cpp
+++ b/src/PERI/pair_peri_lps.cpp
@@ -15,9 +15,9 @@
Contributing author: Mike Parks (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_peri_lps.h"
#include "atom.h"
#include "domain.h"
@@ -285,7 +285,7 @@ void PairPeriLPS::compute(int eflag, int vflag)
omega_plus = influence_function(-1.0*delx0,-1.0*dely0,-1.0*delz0);
omega_minus = influence_function(delx0,dely0,delz0);
-
+
rk = ( (3.0 * bulkmodulus[itype][itype]) -
(5.0 * shearmodulus[itype][itype]) ) * vfrac[j] * vfrac_scale *
( (omega_plus * theta[i] / wvolume[i]) +
@@ -303,8 +303,8 @@ void PairPeriLPS::compute(int eflag, int vflag)
// since I-J is double counted, set newton off & use 1/2 factor and I,I
double deviatoric_extension = dr - (theta[i]* r0[i][jj] / 3.0);
-
-
+
+
if (eflag) evdwl = 0.5 * 15 * (shearmodulus[itype][itype]/wvolume[i]) *
omega_plus*(deviatoric_extension * deviatoric_extension) *
vfrac[j] * vfrac_scale;
@@ -326,7 +326,7 @@ void PairPeriLPS::compute(int eflag, int vflag)
(alpha[itype][jtype] * stretch));
first = false;
- }
+ }
}
// store new s0
diff --git a/src/PERI/pair_peri_pmb.cpp b/src/PERI/pair_peri_pmb.cpp
index 2b68a25227..bc971cb244 100644
--- a/src/PERI/pair_peri_pmb.cpp
+++ b/src/PERI/pair_peri_pmb.cpp
@@ -15,10 +15,10 @@
Contributing author: Mike Parks (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "float.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <float.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_peri_pmb.h"
#include "atom.h"
#include "domain.h"
@@ -359,7 +359,7 @@ void PairPeriPMB::init_style()
{
// error checks
- if (!atom->peri_flag)
+ if (!atom->peri_flag)
error->all(FLERR,"Pair style peri requires atom style peri");
if (atom->map_style == 0)
error->all(FLERR,"Pair peri requires an atom map, see atom_modify");
diff --git a/src/PERI/pair_peri_ves.cpp b/src/PERI/pair_peri_ves.cpp
index 12c0768500..c34fb87e20 100644
--- a/src/PERI/pair_peri_ves.cpp
+++ b/src/PERI/pair_peri_ves.cpp
@@ -15,9 +15,9 @@
Contributing authors: Rezwanur Rahman, J.T. Foster (UTSA)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_peri_ves.h"
#include "atom.h"
#include "domain.h"
@@ -111,9 +111,9 @@ void PairPeriVES::compute(int eflag, int vflag)
double *s0 = atom->s0;
double **x0 = atom->x0;
double **r0 = ((FixPeriNeigh *) modify->fix[ifix_peri])->r0;
- double **deviatorextention =
+ double **deviatorextention =
((FixPeriNeigh *) modify->fix[ifix_peri])->deviatorextention;
- double **deviatorBackextention =
+ double **deviatorBackextention =
((FixPeriNeigh *) modify->fix[ifix_peri])->deviatorBackextention;
tagint **partner = ((FixPeriNeigh *) modify->fix[ifix_peri])->partner;
int *npartner = ((FixPeriNeigh *) modify->fix[ifix_peri])->npartner;
@@ -258,7 +258,7 @@ void PairPeriVES::compute(int eflag, int vflag)
itype = type[i];
jnum = npartner[i];
first = true;
-
+
for (jj = 0; jj < jnum; jj++) {
if (partner[i][jj] == 0) continue;
j = atom->map(partner[i][jj]);
@@ -299,7 +299,7 @@ void PairPeriVES::compute(int eflag, int vflag)
omega_plus = influence_function(-1.0*delx0,-1.0*dely0,-1.0*delz0);
omega_minus = influence_function(delx0,dely0,delz0);
-
+
rk = ( (3.0 * bulkmodulus[itype][itype]) * vfrac[j] * vfrac_scale *
( (omega_plus * theta[i] / wvolume[i]) +
( omega_minus * theta[j] / wvolume[j] ) ) ) * r0[i][jj];
@@ -309,37 +309,37 @@ void PairPeriVES::compute(int eflag, int vflag)
// for viscoelasticity
lambdai=m_lambdai[itype][itype];
- double taui = m_taubi[itype][itype];
+ double taui = m_taubi[itype][itype];
double c1 = taui/timestepsize;
decay=exp(-1.0/c1);
betai=1.-c1*(1.-decay);
- double deviatoric_extension =
+ double deviatoric_extension =
dr - (theta[i]* r0[i][jj] / 3.0);
deltaed = deviatoric_extension-deviatorextention[i][jj];
-
+
// back extention at current step
- edbNp1 = deviatorextention[i][jj]*(1-decay) +
+ edbNp1 = deviatorextention[i][jj]*(1-decay) +
deviatorBackextention[i][jj]*decay+betai*deltaed;
- rkNew = ((1-lambdai)*15.0) *
+ rkNew = ((1-lambdai)*15.0) *
( shearmodulus[itype][itype] * vfrac[j] * vfrac_scale ) *
- ( (omega_plus / wvolume[i]) + (omega_minus / wvolume[j]) ) *
+ ( (omega_plus / wvolume[i]) + (omega_minus / wvolume[j]) ) *
deviatoric_extension;
- rkNew += (lambdai*15.0) *
+ rkNew += (lambdai*15.0) *
( shearmodulus[itype][itype] * vfrac[j] * vfrac_scale ) *
- ( (omega_plus / wvolume[i]) + (omega_minus / wvolume[j]) ) *
+ ( (omega_plus / wvolume[i]) + (omega_minus / wvolume[j]) ) *
(deviatoric_extension-edbNp1);
if (r > 0.0) fbondViscoElastic = -(rkNew/r);
else fbondViscoElastic = 0.0;
- // total Force: elastic + viscoelastic
+ // total Force: elastic + viscoelastic
fbondFinal=fbond+fbondViscoElastic;
fbond=fbondFinal;
-
+
f[i][0] += delx*fbond;
f[i][1] += dely*fbond;
f[i][2] += delz*fbond;
@@ -347,10 +347,10 @@ void PairPeriVES::compute(int eflag, int vflag)
// since I-J is double counted, set newton off & use 1/2 factor and I,I
if (eflag) evdwl = ((0.5 * 15 * (1 - lambdai) * shearmodulus[itype][itype]/wvolume[i] *
- omega_plus * deviatoric_extension *
- deviatoric_extension) +
+ omega_plus * deviatoric_extension *
+ deviatoric_extension) +
(0.5 * 15 * lambdai * shearmodulus[itype][itype]/wvolume[i] *
- omega_plus * (deviatoric_extension-edbNp1) *
+ omega_plus * (deviatoric_extension-edbNp1) *
(deviatoric_extension-edbNp1))) * vfrac[j] * vfrac_scale;
if (evflag) ev_tally(i,i,nlocal,0,0.5*evdwl,0.0,
0.5*fbond*vfrac[i],delx,dely,delz);
@@ -375,7 +375,7 @@ void PairPeriVES::compute(int eflag, int vflag)
(alpha[itype][jtype] * stretch));
first = false;
- }
+ }
}
// store new s0
@@ -482,7 +482,7 @@ void PairPeriVES::init_style()
{
// error checks
- if (!atom->peri_flag)
+ if (!atom->peri_flag)
error->all(FLERR,"Pair style peri requires atom style peri");
if (atom->map_style == 0)
error->all(FLERR,"Pair peri requires an atom map, see atom_modify");
diff --git a/src/PERI/pair_peri_ves.h b/src/PERI/pair_peri_ves.h
index 6c39e98e65..8aae426510 100644
--- a/src/PERI/pair_peri_ves.h
+++ b/src/PERI/pair_peri_ves.h
@@ -27,7 +27,7 @@ namespace LAMMPS_NS {
class PairPeriVES : public Pair {
public:
double *theta;
- double *elastic_energy;
+ double *elastic_energy;
PairPeriVES(class LAMMPS *);
virtual ~PairPeriVES();
@@ -45,8 +45,8 @@ class PairPeriVES : public Pair {
void read_restart_settings(FILE *) {}
double memory_usage();
double influence_function(double, double, double);
- void compute_dilatation();
-
+ void compute_dilatation();
+
protected:
int ifix_peri;
diff --git a/src/POEMS/fix_poems.cpp b/src/POEMS/fix_poems.cpp
index 47e96f7192..e4888df9d3 100644
--- a/src/POEMS/fix_poems.cpp
+++ b/src/POEMS/fix_poems.cpp
@@ -17,11 +17,11 @@
Kurt Anderson (anderk5@rpi.edu)
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "math.h"
-#include "stdio.h"
-#include "string.h"
-#include "stdlib.h"
+#include <mpi.h>
+#include <math.h>
+#include <stdio.h>
+#include <string.h>
+#include <stdlib.h>
#include "workspace.h"
#include "fix_poems.h"
#include "atom.h"
@@ -165,7 +165,7 @@ FixPOEMS::FixPOEMS(LAMMPS *lmp, int narg, char **arg) :
tagint itmp;
MPI_Allreduce(&maxmol_tag,&itmp,1,MPI_LMP_TAGINT,MPI_MAX,world);
- if (itmp+1 > MAXSMALLINT)
+ if (itmp+1 > MAXSMALLINT)
error->all(FLERR,"Too many molecules for fix poems");
int maxmol = (int) itmp;
@@ -208,7 +208,7 @@ FixPOEMS::FixPOEMS(LAMMPS *lmp, int narg, char **arg) :
if (natom2body[i] > MAXBODY) flag = 1;
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
- if (flagall)
+ if (flagall)
error->all(FLERR,"Atom in too many rigid bodies - boost MAXBODY");
// create all nbody-length arrays
@@ -1057,7 +1057,7 @@ void FixPOEMS::jointbuild()
bodyflag[jlist[i][1]]++;
}
for (i = 0; i < nbody; i++)
- if (bodyflag[i] > 2)
+ if (bodyflag[i] > 2)
error->all(FLERR,"Tree structure in joint connections");
delete [] bodyflag;
diff --git a/src/PYTHON/python.cpp b/src/PYTHON/python.cpp
index 607181a1ec..c9947f3521 100644
--- a/src/PYTHON/python.cpp
+++ b/src/PYTHON/python.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "Python.h"
+#include <Python.h>
#include "python.h"
#include "force.h"
#include "input.h"
@@ -75,7 +75,7 @@ void Python::command(int narg, char **arg)
if (noutput) {
str = input->variable->pythonstyle(pfuncs[ifunc].ovarname,
pfuncs[ifunc].name);
- if (!str)
+ if (!str)
error->all(FLERR,"Python variable does not match Python function");
}
@@ -185,7 +185,7 @@ void Python::command(int narg, char **arg)
PyObject *pModule = (PyObject *) pyMain;
PyObject *pFunc = PyObject_GetAttrString(pModule,pfuncs[ifunc].name);
if (!pFunc) error->all(FLERR,"Could not find Python function");
- if (!PyCallable_Check(pFunc))
+ if (!PyCallable_Check(pFunc))
error->all(FLERR,"Python function is not callable");
pfuncs[ifunc].pFunc = (void *) pFunc;
@@ -216,28 +216,28 @@ void Python::invoke_function(int ifunc, char *result)
if (itype == INT) {
if (pfuncs[ifunc].ivarflag[i]) {
str = input->variable->retrieve(pfuncs[ifunc].svalue[i]);
- if (!str)
+ if (!str)
error->all(FLERR,"Could not evaluate Python function input variable");
pValue = PyInt_FromLong(atoi(str));
} else pValue = PyInt_FromLong(pfuncs[ifunc].ivalue[i]);
} else if (itype == DOUBLE) {
if (pfuncs[ifunc].ivarflag[i]) {
str = input->variable->retrieve(pfuncs[ifunc].svalue[i]);
- if (!str)
+ if (!str)
error->all(FLERR,"Could not evaluate Python function input variable");
pValue = PyFloat_FromDouble(atof(str));
} else pValue = PyFloat_FromDouble(pfuncs[ifunc].dvalue[i]);
} else if (itype == STRING) {
if (pfuncs[ifunc].ivarflag[i]) {
str = input->variable->retrieve(pfuncs[ifunc].svalue[i]);
- if (!str)
+ if (!str)
error->all(FLERR,"Could not evaluate Python function input variable");
pValue = PyString_FromString(str);
} else pValue = PyString_FromString(pfuncs[ifunc].svalue[i]);
} else if (itype == PTR) {
pValue = PyCObject_FromVoidPtr((void *) lmp,NULL);
}
- PyTuple_SetItem(pArgs,i,pValue);
+ PyTuple_SetItem(pArgs,i,pValue);
}
// call the Python function
@@ -297,7 +297,7 @@ int Python::create_entry(char *name)
if (ifunc < 0) {
ifunc = nfunc;
nfunc++;
- pfuncs = (PyFunc *)
+ pfuncs = (PyFunc *)
memory->srealloc(pfuncs,nfunc*sizeof(struct PyFunc),"python:pfuncs");
int n = strlen(name) + 1;
pfuncs[ifunc].name = new char[n];
@@ -306,10 +306,10 @@ int Python::create_entry(char *name)
pfuncs[ifunc].ninput = ninput;
pfuncs[ifunc].noutput = noutput;
-
+
if (!format && ninput+noutput)
error->all(FLERR,"Invalid python command");
- else if (format && strlen(format) != ninput+noutput)
+ else if (format && strlen(format) != ninput+noutput)
error->all(FLERR,"Invalid python command");
// process inputs as values or variables
@@ -361,12 +361,12 @@ int Python::create_entry(char *name)
} else if (type == 'p') {
pfuncs[ifunc].ivarflag[i] = 0;
pfuncs[ifunc].itype[i] = PTR;
- if (strcmp(istr[i],"SELF") != 0)
+ if (strcmp(istr[i],"SELF") != 0)
error->all(FLERR,"Invalid python command");
} else error->all(FLERR,"Invalid python command");
}
-
+
// process output as value or variable
pfuncs[ifunc].ovarname = NULL;
diff --git a/src/PYTHON/python.h b/src/PYTHON/python.h
index 55525c266b..d1622728ac 100644
--- a/src/PYTHON/python.h
+++ b/src/PYTHON/python.h
@@ -34,7 +34,7 @@ class Python : protected Pointers {
char **istr;
char *ostr,*format;
void *pyMain;
-
+
struct PyFunc {
char *name;
int ninput,noutput;
diff --git a/src/QEQ/fix_qeq.cpp b/src/QEQ/fix_qeq.cpp
index 96e7a036b9..0c322634db 100644
--- a/src/QEQ/fix_qeq.cpp
+++ b/src/QEQ/fix_qeq.cpp
@@ -16,10 +16,10 @@
Based on fix qeq/reax by H. Metin Aktulga
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "fix_qeq.h"
#include "atom.h"
#include "comm.h"
@@ -49,7 +49,7 @@ FixQEq::FixQEq(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 8) error->all(FLERR,"Illegal fix qeq command");
-
+
nevery = force->inumeric(FLERR,arg[3]);
cutoff = force->numeric(FLERR,arg[4]);
tolerance = force->numeric(FLERR,arg[5]);
@@ -101,7 +101,7 @@ FixQEq::FixQEq(LAMMPS *lmp, int narg, char **arg) :
s_hist = t_hist = NULL;
grow_arrays(atom->nmax);
atom->add_callback(0);
-
+
for( int i = 0; i < atom->nmax; i++ )
for (int j = 0; j < nprev; ++j )
s_hist[i][j] = t_hist[i][j] = atom->q[i];
@@ -618,7 +618,7 @@ double FixQEq::parallel_dot( double *v1, double *v2, int n)
if (atom->mask[i] & groupbit)
my_dot += v1[i] * v2[i];
}
-
+
MPI_Allreduce( &my_dot, &res, 1, MPI_DOUBLE, MPI_SUM, world );
return res;
diff --git a/src/QEQ/fix_qeq_dynamic.cpp b/src/QEQ/fix_qeq_dynamic.cpp
index 42f9cd324d..8e8247e121 100644
--- a/src/QEQ/fix_qeq_dynamic.cpp
+++ b/src/QEQ/fix_qeq_dynamic.cpp
@@ -15,10 +15,10 @@
Contributing author: Ray Shan (Sandia)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "fix_qeq_dynamic.h"
#include "atom.h"
#include "comm.h"
@@ -39,8 +39,8 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-FixQEqDynamic::FixQEqDynamic(LAMMPS *lmp, int narg, char **arg) :
- FixQEq(lmp, narg, arg)
+FixQEqDynamic::FixQEqDynamic(LAMMPS *lmp, int narg, char **arg) :
+ FixQEq(lmp, narg, arg)
{
qdamp = 0.10;
qstep = 0.02;
@@ -76,7 +76,7 @@ void FixQEqDynamic::init()
neighbor->requests[irequest]->half = 1;
neighbor->requests[irequest]->full = 0;
- if (tolerance < 1e-4)
+ if (tolerance < 1e-4)
if (comm->me == 0)
error->warning(FLERR,"Fix qeq/dynamic tolerance may be too small"
" for damped dynamics");
diff --git a/src/QEQ/fix_qeq_point.cpp b/src/QEQ/fix_qeq_point.cpp
index d7dcb0d9a4..9af70a445a 100644
--- a/src/QEQ/fix_qeq_point.cpp
+++ b/src/QEQ/fix_qeq_point.cpp
@@ -15,10 +15,10 @@
Contributing author: Ray Shan (Sandia)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "fix_qeq_point.h"
#include "atom.h"
#include "comm.h"
@@ -45,7 +45,7 @@ FixQEqPoint::FixQEqPoint(LAMMPS *lmp, int narg, char **arg) :
void FixQEqPoint::init()
{
- if (!atom->q_flag)
+ if (!atom->q_flag)
error->all(FLERR,"Fix qeq/point requires atom attribute q");
ngroup = group->count(igroup);
diff --git a/src/QEQ/fix_qeq_shielded.cpp b/src/QEQ/fix_qeq_shielded.cpp
index 7c7ca6d155..661dd73f7b 100644
--- a/src/QEQ/fix_qeq_shielded.cpp
+++ b/src/QEQ/fix_qeq_shielded.cpp
@@ -15,10 +15,10 @@
Contributing author: Ray Shan (Sandia)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "fix_qeq_shielded.h"
#include "atom.h"
#include "comm.h"
@@ -45,7 +45,7 @@ FixQEqShielded::FixQEqShielded(LAMMPS *lmp, int narg, char **arg) :
void FixQEqShielded::init()
{
- if (!atom->q_flag)
+ if (!atom->q_flag)
error->all(FLERR,"Fix qeq/shielded requires atom attribute q");
ngroup = group->count(igroup);
@@ -64,7 +64,7 @@ void FixQEqShielded::init()
int i;
for (i = 1; i <= ntypes; i++) {
- if (gamma[i] == 0.0)
+ if (gamma[i] == 0.0)
error->all(FLERR,"Invalid param file for fix qeq/shielded");
}
@@ -219,7 +219,7 @@ void FixQEqShielded::compute_H()
/* ---------------------------------------------------------------------- */
double FixQEqShielded::calculate_H( double r, double gamma )
-{
+{
double Taper, denom;
Taper = Tap[7] * r + Tap[6];
diff --git a/src/QEQ/fix_qeq_slater.cpp b/src/QEQ/fix_qeq_slater.cpp
index 36b3b2c65f..ad1c652100 100644
--- a/src/QEQ/fix_qeq_slater.cpp
+++ b/src/QEQ/fix_qeq_slater.cpp
@@ -15,10 +15,10 @@
Contributing author: Ray Shan (Sandia)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "fix_qeq_slater.h"
#include "atom.h"
#include "comm.h"
@@ -42,8 +42,8 @@ using namespace FixConst;
/* ---------------------------------------------------------------------- */
-FixQEqSlater::FixQEqSlater(LAMMPS *lmp, int narg, char **arg) :
- FixQEq(lmp, narg, arg)
+FixQEqSlater::FixQEqSlater(LAMMPS *lmp, int narg, char **arg) :
+ FixQEq(lmp, narg, arg)
{
alpha = 0.20;
@@ -64,7 +64,7 @@ FixQEqSlater::FixQEqSlater(LAMMPS *lmp, int narg, char **arg) :
void FixQEqSlater::init()
{
- if (!atom->q_flag)
+ if (!atom->q_flag)
error->all(FLERR,"Fix qeq/slater requires atom attribute q");
ngroup = group->count(igroup);
@@ -78,7 +78,7 @@ void FixQEqSlater::init()
int ntypes = atom->ntypes;
for (int i = 1; i <= ntypes; i++) {
- if (zeta[i] == 0.0)
+ if (zeta[i] == 0.0)
error->all(FLERR,"Invalid param file for fix qeq/slater");
}
@@ -106,7 +106,7 @@ void FixQEqSlater::extract_streitz()
gamma = (double *) pair->extract("gamma",tmp);
zeta = (double *) pair->extract("zeta",tmp);
zcore = (double *) pair->extract("zcore",tmp);
- if (chi == NULL || eta == NULL || gamma == NULL
+ if (chi == NULL || eta == NULL || gamma == NULL
|| zeta == NULL || zcore == NULL)
error->all(FLERR,
"Fix qeq/slater could not extract params from pair coul/streitz");
@@ -230,7 +230,7 @@ void FixQEqSlater::compute_H()
/* ---------------------------------------------------------------------- */
-double FixQEqSlater::calculate_H(double zei, double zej, double zj,
+double FixQEqSlater::calculate_H(double zei, double zej, double zj,
double r, double &zjtmp)
{
double rinv = 1.0/r;
@@ -283,7 +283,7 @@ double FixQEqSlater::calculate_H(double zei, double zej, double zj,
/* ---------------------------------------------------------------------- */
-double FixQEqSlater::calculate_H_wolf(double zei, double zej, double zj,
+double FixQEqSlater::calculate_H_wolf(double zei, double zej, double zj,
double r, double &zjtmp)
{
double rinv = 1.0/r;
@@ -339,14 +339,14 @@ double FixQEqSlater::calculate_H_wolf(double zei, double zej, double zj,
((zei+zej)*(zei+zej)*(zei+zej)*(zej-zei)*(zej-zei)*(zej-zei));
eshift = -exp2zirsh*(e1+e3/rc) - exp2zjrsh*(e2+e4/rc);
- ci_fifj = -exp2zir*(e1+e3/r) - exp2zjr*(e2+e4/r)
+ ci_fifj = -exp2zir*(e1+e3/r) - exp2zjr*(e2+e4/r)
- eshift - (r-rc)*fshift;
}
etmp1 = erfcr/r - erfcrc/rc;
etmp2 = 1.00 * (ci_jfi - ci_fifj);
etmp3 = 0.50 * (etmp1 + ci_fifj);
-
+
zjtmp += qqrd2e * zj * etmp2;
return qqrd2e * etmp3;
diff --git a/src/REAX/fix_reax_bonds.cpp b/src/REAX/fix_reax_bonds.cpp
index 7efc20f82d..2574d991ae 100644
--- a/src/REAX/fix_reax_bonds.cpp
+++ b/src/REAX/fix_reax_bonds.cpp
@@ -19,8 +19,8 @@
#error LAMMPS_BIGBIG is not supported by the REAX package
#endif
-#include "stdlib.h"
-#include "string.h"
+#include <stdlib.h>
+#include <string.h>
#include "fix_reax_bonds.h"
#include "pair_reax_fortran.h"
#include "atom.h"
diff --git a/src/REAX/fix_reax_bonds.h b/src/REAX/fix_reax_bonds.h
index 9bb1743f95..dc7c6d389e 100644
--- a/src/REAX/fix_reax_bonds.h
+++ b/src/REAX/fix_reax_bonds.h
@@ -20,7 +20,7 @@ FixStyle(reax/bonds,FixReaxBonds)
#ifndef LMP_FIX_REAX_BONDS_H
#define LMP_FIX_REAX_BONDS_H
-#include "stdio.h"
+#include <stdio.h>
#include "fix.h"
namespace LAMMPS_NS {
diff --git a/src/REAX/pair_reax.cpp b/src/REAX/pair_reax.cpp
index e3674cb401..642bf78d91 100644
--- a/src/REAX/pair_reax.cpp
+++ b/src/REAX/pair_reax.cpp
@@ -20,11 +20,11 @@
and Ardi Van Duin's original ReaxFF code
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <mpi.h>
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_reax.h"
#include "pair_reax_fortran.h"
#include "atom.h"
@@ -626,7 +626,7 @@ double PairREAX::init_one(int i, int j)
/* ---------------------------------------------------------------------- */
-int PairREAX::pack_forward_comm(int n, int *list, double *buf,
+int PairREAX::pack_forward_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
diff --git a/src/REPLICA/compute_event_displace.cpp b/src/REPLICA/compute_event_displace.cpp
index 7f1db90481..7ff803459e 100644
--- a/src/REPLICA/compute_event_displace.cpp
+++ b/src/REPLICA/compute_event_displace.cpp
@@ -15,10 +15,10 @@
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <mpi.h>
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "compute_event_displace.h"
#include "atom.h"
#include "domain.h"
diff --git a/src/REPLICA/fix_event.cpp b/src/REPLICA/fix_event.cpp
index 77cb2dc314..f3276178e2 100644
--- a/src/REPLICA/fix_event.cpp
+++ b/src/REPLICA/fix_event.cpp
@@ -15,8 +15,8 @@
Contributing author: Mike Brown (SNL), Aidan Thompson (SNL)
------------------------------------------------------------------------- */
-#include "stdlib.h"
-#include "string.h"
+#include <stdlib.h>
+#include <string.h>
#include "fix_event.h"
#include "atom.h"
#include "update.h"
diff --git a/src/REPLICA/fix_event_prd.cpp b/src/REPLICA/fix_event_prd.cpp
index 57db1e17b7..863caa64f2 100644
--- a/src/REPLICA/fix_event_prd.cpp
+++ b/src/REPLICA/fix_event_prd.cpp
@@ -15,8 +15,8 @@
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
-#include "stdlib.h"
-#include "string.h"
+#include <stdlib.h>
+#include <string.h>
#include "fix_event_prd.h"
#include "atom.h"
#include "update.h"
diff --git a/src/REPLICA/fix_event_tad.cpp b/src/REPLICA/fix_event_tad.cpp
index aed1d75437..b2d74855fa 100644
--- a/src/REPLICA/fix_event_tad.cpp
+++ b/src/REPLICA/fix_event_tad.cpp
@@ -15,8 +15,8 @@
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
-#include "stdlib.h"
-#include "string.h"
+#include <stdlib.h>
+#include <string.h>
#include "fix_event_tad.h"
#include "atom.h"
#include "update.h"
diff --git a/src/REPLICA/fix_neb.cpp b/src/REPLICA/fix_neb.cpp
index e254339da5..c66fa2dd04 100644
--- a/src/REPLICA/fix_neb.cpp
+++ b/src/REPLICA/fix_neb.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <mpi.h>
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "fix_neb.h"
#include "universe.h"
#include "update.h"
diff --git a/src/REPLICA/neb.cpp b/src/REPLICA/neb.cpp
index 6e5399ba82..68d2af8bd9 100644
--- a/src/REPLICA/neb.cpp
+++ b/src/REPLICA/neb.cpp
@@ -15,11 +15,11 @@
// due to OpenMPI bug which sets INT64_MAX via its mpi.h
// before lmptype.h can set flags to insure it is done correctly
-#include "lmptype.h"
-#include "mpi.h"
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include "lmptype.h"
+#include <mpi.h>
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "neb.h"
#include "universe.h"
#include "atom.h"
@@ -418,11 +418,11 @@ void NEB::readfile(char *file, int flag)
for (i = 0; i < nchunk; i++) {
next = strchr(buf,'\n');
-
+
values[0] = strtok(buf," \t\n\r\f");
for (j = 1; j < nwords; j++)
values[j] = strtok(NULL," \t\n\r\f");
-
+
// adjust atom coord based on replica fraction
// for flag = 0, interpolate for intermediate and final replicas
// for flag = 1, replace existing coord with new coord
diff --git a/src/REPLICA/neb.h b/src/REPLICA/neb.h
index 08ab5c989b..00719dcc95 100644
--- a/src/REPLICA/neb.h
+++ b/src/REPLICA/neb.h
@@ -20,7 +20,7 @@ CommandStyle(neb,NEB)
#ifndef LMP_NEB_H
#define LMP_NEB_H
-#include "stdio.h"
+#include <stdio.h>
#include "pointers.h"
namespace LAMMPS_NS {
diff --git a/src/REPLICA/prd.cpp b/src/REPLICA/prd.cpp
index 57aaf485f4..fcdfa67ccc 100644
--- a/src/REPLICA/prd.cpp
+++ b/src/REPLICA/prd.cpp
@@ -19,11 +19,11 @@
// due to OpenMPI bug which sets INT64_MAX via its mpi.h
// before lmptype.h can set flags to insure it is done correctly
-#include "lmptype.h"
-#include "mpi.h"
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include "lmptype.h"
+#include <mpi.h>
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "prd.h"
#include "universe.h"
#include "update.h"
@@ -431,12 +431,12 @@ void PRD::command(int narg, char **arg)
if (me_universe == 0) {
if (universe->uscreen)
fprintf(universe->uscreen,
- "Loop time of %g on %d procs for %d steps with " BIGINT_FORMAT
+ "Loop time of %g on %d procs for %d steps with " BIGINT_FORMAT
" atoms\n",
timer->get_wall(Timer::TOTAL),nprocs_universe,nsteps,atom->natoms);
if (universe->ulogfile)
fprintf(universe->ulogfile,
- "Loop time of %g on %d procs for %d steps with " BIGINT_FORMAT
+ "Loop time of %g on %d procs for %d steps with " BIGINT_FORMAT
" atoms\n",
timer->get_wall(Timer::TOTAL),nprocs_universe,nsteps,atom->natoms);
}
@@ -695,7 +695,7 @@ void PRD::share_event(int ireplica, int flag, int decrement)
if (flag != 2) delta *= universe->nworlds;
if (delta > 0 && flag != 2) delta -= decrement;
delta += corr_adjust;
-
+
// delta passed to store_event_prd() should make its clock update
// be consistent with clock in main PRD loop
// don't change the clock or timestep if this is a restart
diff --git a/src/REPLICA/tad.cpp b/src/REPLICA/tad.cpp
index 0f46867f99..25043a0f8a 100644
--- a/src/REPLICA/tad.cpp
+++ b/src/REPLICA/tad.cpp
@@ -19,11 +19,11 @@
// due to OpenMPI bug which sets INT64_MAX via its mpi.h
// before lmptype.h can set flags to insure it is done correctly
-#include "lmptype.h"
-#include "mpi.h"
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include "lmptype.h"
+#include <mpi.h>
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "tad.h"
#include "universe.h"
#include "update.h"
@@ -104,14 +104,14 @@ void TAD::command(int narg, char **arg)
char *id_compute = new char[strlen(arg[6])+1];
strcpy(id_compute,arg[6]);
-
+
// quench minimizer is set by min_style command
// NEB minimizer is set by options, default = quickmin
int n = strlen(update->minimize_style) + 1;
min_style = new char[n];
strcpy(min_style,update->minimize_style);
-
+
options(narg-7,&arg[7]);
// total # of timesteps must be multiple of t_event
@@ -396,12 +396,12 @@ void TAD::command(int narg, char **arg)
if (me_universe == 0) {
if (universe->uscreen)
fprintf(universe->uscreen,
- "Loop time of %g on %d procs for %d steps with " BIGINT_FORMAT
+ "Loop time of %g on %d procs for %d steps with " BIGINT_FORMAT
" atoms\n",
timer->get_wall(Timer::TOTAL),nprocs_universe,nsteps,atom->natoms);
- if (universe->ulogfile)
+ if (universe->ulogfile)
fprintf(universe->ulogfile,
- "Loop time of %g on %d procs for %d steps with " BIGINT_FORMAT
+ "Loop time of %g on %d procs for %d steps with " BIGINT_FORMAT
" atoms\n",
timer->get_wall(Timer::TOTAL),nprocs_universe,nsteps,atom->natoms);
}
diff --git a/src/REPLICA/temper.cpp b/src/REPLICA/temper.cpp
index 8771ab5375..17c2c30fca 100644
--- a/src/REPLICA/temper.cpp
+++ b/src/REPLICA/temper.cpp
@@ -15,9 +15,9 @@
Contributing author: Mark Sears (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "temper.h"
#include "universe.h"
#include "domain.h"
diff --git a/src/REPLICA/verlet_split.cpp b/src/REPLICA/verlet_split.cpp
index dbb2660eb5..5985c756ad 100644
--- a/src/REPLICA/verlet_split.cpp
+++ b/src/REPLICA/verlet_split.cpp
@@ -15,7 +15,7 @@
Contributing authors: Yuxing Peng and Chris Knight (U Chicago)
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "verlet_split.h"
#include "universe.h"
#include "neighbor.h"
@@ -52,7 +52,7 @@ VerletSplit::VerletSplit(LAMMPS *lmp, int narg, char **arg) :
if (universe->procs_per_world[0] % universe->procs_per_world[1])
error->universe_all(FLERR,"Verlet/split requires Rspace partition "
"size be multiple of Kspace partition size");
- if (comm->style != 0)
+ if (comm->style != 0)
error->universe_all(FLERR,"Verlet/split can only currently be used with "
"comm_style brick");
@@ -217,7 +217,7 @@ VerletSplit::~VerletSplit()
void VerletSplit::init()
{
- if (comm->style != 0)
+ if (comm->style != 0)
error->universe_all(FLERR,"Verlet/split can only currently be used with "
"comm_style brick");
if (!force->kspace && comm->me == 0)
diff --git a/src/RIGID/compute_erotate_rigid.cpp b/src/RIGID/compute_erotate_rigid.cpp
index 336f988ee9..2b156b5ca9 100644
--- a/src/RIGID/compute_erotate_rigid.cpp
+++ b/src/RIGID/compute_erotate_rigid.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "string.h"
+#include <mpi.h>
+#include <string.h>
#include "compute_erotate_rigid.h"
#include "update.h"
#include "force.h"
@@ -52,7 +52,7 @@ ComputeERotateRigid::~ComputeERotateRigid()
void ComputeERotateRigid::init()
{
irfix = modify->find_fix(rfix);
- if (irfix < 0)
+ if (irfix < 0)
error->all(FLERR,"Fix ID for compute erotate/rigid does not exist");
int flag = 1;
diff --git a/src/RIGID/compute_ke_rigid.cpp b/src/RIGID/compute_ke_rigid.cpp
index 671e17f69b..7bd2a032c9 100644
--- a/src/RIGID/compute_ke_rigid.cpp
+++ b/src/RIGID/compute_ke_rigid.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "string.h"
+#include <mpi.h>
+#include <string.h>
#include "compute_ke_rigid.h"
#include "update.h"
#include "force.h"
diff --git a/src/RIGID/fix_rattle.cpp b/src/RIGID/fix_rattle.cpp
index 59fa6ed359..f07e5fe252 100644
--- a/src/RIGID/fix_rattle.cpp
+++ b/src/RIGID/fix_rattle.cpp
@@ -15,11 +15,11 @@
Contributing author: Peter Wirnsberger (University of Cambridge)
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
-#include "stdio.h"
+#include <mpi.h>
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
+#include <stdio.h>
#include "fix_rattle.h"
#include "atom.h"
#include "atom_vec.h"
@@ -79,7 +79,7 @@ FixRattle::FixRattle(LAMMPS *lmp, int narg, char **arg) :
/* ---------------------------------------------------------------------- */
FixRattle::~FixRattle()
-{
+{
memory->destroy(vp);
}
@@ -89,11 +89,11 @@ int FixRattle::setmask()
{
int mask = 0;
mask |= PRE_NEIGHBOR;
- mask |= POST_FORCE;
+ mask |= POST_FORCE;
mask |= POST_FORCE_RESPA;
mask |= FINAL_INTEGRATE;
mask |= FINAL_INTEGRATE_RESPA;
- if (RATTLE_DEBUG) mask |= END_OF_STEP;
+ if (RATTLE_DEBUG) mask |= END_OF_STEP;
return mask;
}
@@ -149,10 +149,10 @@ void FixRattle::post_force(int vflag)
int m;
for (int i = 0; i < nlist; i++) {
m = list[i];
- if (shake_flag[m] == 2) vrattle2(m);
- else if (shake_flag[m] == 3) vrattle3(m);
- else if (shake_flag[m] == 4) vrattle4(m);
- else vrattle3angle(m);
+ if (shake_flag[m] == 2) vrattle2(m);
+ else if (shake_flag[m] == 3) vrattle3(m);
+ else if (shake_flag[m] == 4) vrattle4(m);
+ else vrattle3angle(m);
}
}
@@ -231,7 +231,7 @@ void FixRattle::vrattle3angle(int m)
domain->minimum_image(r02);
domain->minimum_image(r12);
- // v01,v02,v12 = velocity differences
+ // v01,v02,v12 = velocity differences
MathExtra::sub3(vp[i1],vp[i0],vp01);
MathExtra::sub3(vp[i2],vp[i0],vp02);
MathExtra::sub3(vp[i2],vp[i1],vp12);
@@ -252,7 +252,7 @@ void FixRattle::vrattle3angle(int m)
a[0][1] = (imass[0] ) * MathExtra::dot3(r01,r02);
a[0][2] = (-imass[1] ) * MathExtra::dot3(r01,r12);
a[1][0] = a[0][1];
- a[1][1] = (imass[0] + imass[2]) * MathExtra::dot3(r02,r02);
+ a[1][1] = (imass[0] + imass[2]) * MathExtra::dot3(r02,r02);
a[1][2] = (imass[2] ) * MathExtra::dot3(r02,r12);
a[2][0] = a[0][2];
a[2][1] = a[1][2];
@@ -268,15 +268,15 @@ void FixRattle::vrattle3angle(int m)
// add corrections to the velocities if processor owns atom
if (i0 < nlocal) {
- for (int k=0; k<3; k++)
+ for (int k=0; k<3; k++)
v[i0][k] -= imass[0]* ( l[0] * r01[k] + l[1] * r02[k] );
- }
+ }
if (i1 < nlocal) {
- for (int k=0; k<3; k++)
+ for (int k=0; k<3; k++)
v[i1][k] -= imass[1] * ( -l[0] * r01[k] + l[2] * r12[k] );
}
if (i2 < nlocal) {
- for (int k=0; k<3; k++)
+ for (int k=0; k<3; k++)
v[i2][k] -= imass[2] * ( -l[1] * r02[k] - l[2] * r12[k] );
}
}
@@ -309,16 +309,16 @@ void FixRattle::vrattle2(int m)
}
// Lagrange multiplier: exact solution
- double l01 = - MathExtra::dot3(r01,vp01) /
+ double l01 = - MathExtra::dot3(r01,vp01) /
(MathExtra::dot3(r01,r01) * (imass[0] + imass[1]));
// add corrections to the velocities if the process owns this atom
if (i0 < nlocal) {
- for (int k=0; k<3; k++)
+ for (int k=0; k<3; k++)
v[i0][k] -= imass[0] * l01 * r01[k];
- }
+ }
if (i1 < nlocal) {
- for (int k=0; k<3; k++)
+ for (int k=0; k<3; k++)
v[i1][k] -= imass[1] * (-l01) * r01[k];
}
}
@@ -339,7 +339,7 @@ void FixRattle::vrattle3(int m)
// r01,r02 = distance vec between atoms, with PBC
MathExtra::sub3(x[i1],x[i0],r01);
MathExtra::sub3(x[i2],x[i0],r02);
-
+
domain->minimum_image(r01);
domain->minimum_image(r02);
@@ -372,15 +372,15 @@ void FixRattle::vrattle3(int m)
// add corrections to the velocities if the process owns this atom
if (i0 < nlocal) {
- for (int k=0; k<3; k++)
+ for (int k=0; k<3; k++)
v[i0][k] -= imass[0] * ( l[0] * r01[k] + l[1] * r02[k] );
- }
- if (i1 < nlocal)
+ }
+ if (i1 < nlocal)
for (int k=0; k<3; k++) {
v[i1][k] -= imass[1] * ( -l[0] * r01[k] );
}
if (i2 < nlocal) {
- for (int k=0; k<3; k++)
+ for (int k=0; k<3; k++)
v[i2][k] -= imass[2] * ( -l[1] * r02[k] );
}
}
@@ -447,26 +447,26 @@ void FixRattle::vrattle4(int m)
// add corrections to the velocities if the process owns this atom
if (i0 < nlocal) {
- for (int k=0; k<3; k++)
+ for (int k=0; k<3; k++)
v[i0][k] -= imass[0] * ( l[0] * r01[k] + l[1] * r02[k] + l[2] * r03[k]);
- }
+ }
if (i1 < nlocal) {
- for (int k=0; k<3; k++)
- v[i1][k] -= imass[1] * (-l[0] * r01[k]);
+ for (int k=0; k<3; k++)
+ v[i1][k] -= imass[1] * (-l[0] * r01[k]);
}
if (i2 < nlocal) {
- for (int k=0; k<3; k++)
+ for (int k=0; k<3; k++)
v[i2][k] -= imass[2] * ( -l[1] * r02[k]);
}
if (i3 < nlocal) {
- for (int k=0; k<3; k++)
- v[i3][k] -= imass[3] * ( -l[2] * r03[k]);
+ for (int k=0; k<3; k++)
+ v[i3][k] -= imass[3] * ( -l[2] * r03[k]);
}
}
/* ---------------------------------------------------------------------- */
-void FixRattle::solve2x2exactly(const double a[][2],
+void FixRattle::solve2x2exactly(const double a[][2],
const double c[], double l[])
{
double determ, determinv;
@@ -485,24 +485,24 @@ void FixRattle::solve2x2exactly(const double a[][2],
/* ---------------------------------------------------------------------- */
-void FixRattle::solve3x3exactly(const double a[][3],
+void FixRattle::solve3x3exactly(const double a[][3],
const double c[], double l[])
{
double ai[3][3];
double determ, determinv;
-
+
// calculate the determinant of the matrix
- determ = a[0][0]*a[1][1]*a[2][2] + a[0][1]*a[1][2]*a[2][0] +
- a[0][2]*a[1][0]*a[2][1] - a[0][0]*a[1][2]*a[2][1] -
+ determ = a[0][0]*a[1][1]*a[2][2] + a[0][1]*a[1][2]*a[2][0] +
+ a[0][2]*a[1][0]*a[2][1] - a[0][0]*a[1][2]*a[2][1] -
a[0][1]*a[1][0]*a[2][2] - a[0][2]*a[1][1]*a[2][0];
-
+
// check if matrix is actually invertible
if (determ == 0.0) error->one(FLERR,"RATTLE determinant = 0.0");
// calculate the inverse 3x3 matrix: A^(-1) = (ai_jk)
determinv = 1.0/determ;
ai[0][0] = determinv * (a[1][1]*a[2][2] - a[1][2]*a[2][1]);
- ai[0][1] = -determinv * (a[0][1]*a[2][2] - a[0][2]*a[2][1]);
+ ai[0][1] = -determinv * (a[0][1]*a[2][2] - a[0][2]*a[2][1]);
ai[0][2] = determinv * (a[0][1]*a[1][2] - a[0][2]*a[1][1]);
ai[1][0] = -determinv * (a[1][0]*a[2][2] - a[1][2]*a[2][0]);
ai[1][1] = determinv * (a[0][0]*a[2][2] - a[0][2]*a[2][0]);
@@ -514,9 +514,9 @@ void FixRattle::solve3x3exactly(const double a[][3],
// calculate the solution: (l01, l02, l12)^T = A^(-1) * c
for (int i=0; i<3; i++) {
l[i] = 0;
- for (int j=0; j<3; j++)
+ for (int j=0; j<3; j++)
l[i] += ai[i][j] * c[j];
- }
+ }
}
/* ---------------------------------------------------------------------- */
@@ -632,7 +632,7 @@ int FixRattle::pack_forward_comm(int n, int *list, double *buf,
break;
}
return m;
-}
+}
/* ---------------------------------------------------------------------- */
@@ -686,7 +686,7 @@ void FixRattle::coordinate_constraints_end_of_step() {
/* ----------------------------------------------------------------------
DEBUGGING methods
- The functions below allow you to check whether the
+ The functions below allow you to check whether the
coordinate and velocity constraints are satisfied at the
end of the timestep
only enabled if RATTLE_DEBUG is set to 1 at top of file
@@ -698,7 +698,7 @@ void FixRattle::end_of_step()
// communicate velocities and coordinates (x and v)
if (nprocs > 1) {
comm_mode = V;
- comm->forward_comm_fix(this);
+ comm->forward_comm_fix(this);
comm_mode = X;
comm->forward_comm_fix(this);
}
@@ -716,9 +716,9 @@ bool FixRattle::check_constraints(double **v, bool checkr, bool checkv)
int i=0;
while (i < nlist && ret) {
m = list[i];
- if (shake_flag[m] == 2) ret = check2(v,m,checkr,checkv);
- else if (shake_flag[m] == 3) ret = check3(v,m,checkr,checkv);
- else if (shake_flag[m] == 4) ret = check4(v,m,checkr,checkv);
+ if (shake_flag[m] == 2) ret = check2(v,m,checkr,checkv);
+ else if (shake_flag[m] == 3) ret = check3(v,m,checkr,checkv);
+ else if (shake_flag[m] == 4) ret = check4(v,m,checkr,checkv);
else ret = check3angle(v,m,checkr,checkv);
i++;
}
@@ -733,7 +733,7 @@ bool FixRattle::check2(double **v, int m, bool checkr, bool checkv)
double r01[3],v01[3];
const double tol = tolerance;
double bond1 = bond_distance[shake_type[m][0]];
-
+
tagint i0 = atom->map(shake_atom[m][0]);
tagint i1 = atom->map(shake_atom[m][1]);
@@ -742,12 +742,12 @@ bool FixRattle::check2(double **v, int m, bool checkr, bool checkv)
MathExtra::sub3(v[i1],v[i0],v01);
stat = !(checkr && (fabs(sqrt(MathExtra::dot3(r01,r01)) - bond1) > tol));
- if (!stat)
+ if (!stat)
error->one(FLERR,"RATTLE coordinate constraints are not satisfied "
"up to desired tolerance");
stat = !(checkv && (fabs(MathExtra::dot3(r01,v01)) > tol));
- if (!stat)
+ if (!stat)
error->one(FLERR,"RATTLE velocity constraints are not satisfied "
"up to desired tolerance");
return stat;
@@ -763,14 +763,14 @@ bool FixRattle::check3(double **v, int m, bool checkr, bool checkv)
const double tol = tolerance;
double bond1 = bond_distance[shake_type[m][0]];
double bond2 = bond_distance[shake_type[m][1]];
-
+
i0 = atom->map(shake_atom[m][0]);
i1 = atom->map(shake_atom[m][1]);
i2 = atom->map(shake_atom[m][2]);
MathExtra::sub3(x[i1],x[i0],r01);
MathExtra::sub3(x[i2],x[i0],r02);
-
+
domain->minimum_image(r01);
domain->minimum_image(r02);
@@ -779,13 +779,13 @@ bool FixRattle::check3(double **v, int m, bool checkr, bool checkv)
stat = !(checkr && (fabs(sqrt(MathExtra::dot3(r01,r01)) - bond1) > tol ||
fabs(sqrt(MathExtra::dot3(r02,r02))-bond2) > tol));
- if (!stat)
+ if (!stat)
error->one(FLERR,"RATTLE coordinate constraints are not satisfied "
"up to desired tolerance");
- stat = !(checkv && (fabs(MathExtra::dot3(r01,v01)) > tol ||
+ stat = !(checkv && (fabs(MathExtra::dot3(r01,v01)) > tol ||
fabs(MathExtra::dot3(r02,v02)) > tol));
- if (!stat)
+ if (!stat)
error->one(FLERR,"RATTLE velocity constraints are not satisfied "
"up to desired tolerance");
return stat;
@@ -819,17 +819,17 @@ bool FixRattle::check4(double **v, int m, bool checkr, bool checkv)
MathExtra::sub3(v[i2],v[i0],v02);
MathExtra::sub3(v[i3],v[i0],v03);
- stat = !(checkr && (fabs(sqrt(MathExtra::dot3(r01,r01)) - bond1) > tol ||
- fabs(sqrt(MathExtra::dot3(r02,r02))-bond2) > tol ||
+ stat = !(checkr && (fabs(sqrt(MathExtra::dot3(r01,r01)) - bond1) > tol ||
+ fabs(sqrt(MathExtra::dot3(r02,r02))-bond2) > tol ||
fabs(sqrt(MathExtra::dot3(r03,r03))-bond3) > tol));
- if (!stat)
+ if (!stat)
error->one(FLERR,"RATTLE coordinate constraints are not satisfied "
"up to desired tolerance");
- stat = !(checkv && (fabs(MathExtra::dot3(r01,v01)) > tol ||
- fabs(MathExtra::dot3(r02,v02)) > tol ||
+ stat = !(checkv && (fabs(MathExtra::dot3(r01,v01)) > tol ||
+ fabs(MathExtra::dot3(r02,v02)) > tol ||
fabs(MathExtra::dot3(r03,v03)) > tol));
- if (!stat)
+ if (!stat)
error->one(FLERR,"RATTLE velocity constraints are not satisfied "
"up to desired tolerance");
return stat;
@@ -862,17 +862,17 @@ bool FixRattle::check3angle(double **v, int m, bool checkr, bool checkv)
MathExtra::sub3(v[i2],v[i0],v02);
MathExtra::sub3(v[i2],v[i1],v12);
- stat = !(checkr && (fabs(sqrt(MathExtra::dot3(r01,r01)) - bond1) > tol ||
- fabs(sqrt(MathExtra::dot3(r02,r02))-bond2) > tol ||
+ stat = !(checkr && (fabs(sqrt(MathExtra::dot3(r01,r01)) - bond1) > tol ||
+ fabs(sqrt(MathExtra::dot3(r02,r02))-bond2) > tol ||
fabs(sqrt(MathExtra::dot3(r12,r12))-bond12) > tol));
- if (!stat)
+ if (!stat)
error->one(FLERR,"RATTLE coordinate constraints are not satisfied "
"up to desired tolerance");
- stat = !(checkv && (fabs(MathExtra::dot3(r01,v01)) > tol ||
- fabs(MathExtra::dot3(r02,v02)) > tol ||
+ stat = !(checkv && (fabs(MathExtra::dot3(r01,v01)) > tol ||
+ fabs(MathExtra::dot3(r02,v02)) > tol ||
fabs(MathExtra::dot3(r12,v12)) > tol));
- if (!stat)
+ if (!stat)
error->one(FLERR,"RATTLE velocity constraints are not satisfied "
"up to desired tolerance");
return stat;
diff --git a/src/RIGID/fix_rigid.cpp b/src/RIGID/fix_rigid.cpp
index 2f7cc31f15..32917a53d7 100644
--- a/src/RIGID/fix_rigid.cpp
+++ b/src/RIGID/fix_rigid.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "fix_rigid.h"
#include "math_extra.h"
#include "atom.h"
@@ -132,7 +132,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
tagint itmp;
MPI_Allreduce(&maxmol_tag,&itmp,1,MPI_LMP_TAGINT,MPI_MAX,world);
- if (itmp+1 > MAXSMALLINT)
+ if (itmp+1 > MAXSMALLINT)
error->all(FLERR,"Too many molecules for fix rigid");
maxmol = (int) itmp;
@@ -251,7 +251,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
}
// number of linear rigid bodies is counted later
- nlinear = 0;
+ nlinear = 0;
// parse optional args
@@ -270,12 +270,12 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
pcouple = NONE;
pstyle = ANISO;
dimension = domain->dimension;
-
+
for (int i = 0; i < 3; i++) {
p_start[i] = p_stop[i] = p_period[i] = 0.0;
p_flag[i] = 0;
}
-
+
while (iarg < narg) {
if (strcmp(arg[iarg],"force") == 0) {
if (iarg+5 > narg) error->all(FLERR,"Illegal fix rigid command");
@@ -341,7 +341,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"langevin") == 0) {
if (iarg+5 > narg) error->all(FLERR,"Illegal fix rigid command");
- if (strcmp(style,"rigid") != 0 && strcmp(style,"rigid/nve") != 0 &&
+ if (strcmp(style,"rigid") != 0 && strcmp(style,"rigid/nve") != 0 &&
strcmp(style,"rigid/omp") != 0 && strcmp(style,"rigid/nve/omp") != 0)
error->all(FLERR,"Illegal fix rigid command");
langflag = 1;
@@ -357,7 +357,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"temp") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix rigid command");
if (strcmp(style,"rigid/nvt") != 0 && strcmp(style,"rigid/npt") != 0 &&
- strcmp(style,"rigid/nvt/omp") != 0 &&
+ strcmp(style,"rigid/nvt/omp") != 0 &&
strcmp(style,"rigid/npt/omp") != 0)
error->all(FLERR,"Illegal fix rigid command");
tstat_flag = 1;
@@ -369,13 +369,13 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"iso") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix rigid command");
if (strcmp(style,"rigid/npt") != 0 && strcmp(style,"rigid/nph") != 0 &&
- strcmp(style,"rigid/npt/omp") != 0 &&
+ strcmp(style,"rigid/npt/omp") != 0 &&
strcmp(style,"rigid/nph/omp") != 0)
error->all(FLERR,"Illegal fix rigid command");
pcouple = XYZ;
p_start[0] = p_start[1] = p_start[2] = force->numeric(FLERR,arg[iarg+1]);
p_stop[0] = p_stop[1] = p_stop[2] = force->numeric(FLERR,arg[iarg+2]);
- p_period[0] = p_period[1] = p_period[2] =
+ p_period[0] = p_period[1] = p_period[2] =
force->numeric(FLERR,arg[iarg+3]);
p_flag[0] = p_flag[1] = p_flag[2] = 1;
if (dimension == 2) {
@@ -387,12 +387,12 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"aniso") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix rigid command");
if (strcmp(style,"rigid/npt") != 0 && strcmp(style,"rigid/nph") != 0 &&
- strcmp(style,"rigid/npt/omp") != 0 &&
+ strcmp(style,"rigid/npt/omp") != 0 &&
strcmp(style,"rigid/nph/omp") != 0)
error->all(FLERR,"Illegal fix rigid command");
p_start[0] = p_start[1] = p_start[2] = force->numeric(FLERR,arg[iarg+1]);
p_stop[0] = p_stop[1] = p_stop[2] = force->numeric(FLERR,arg[iarg+2]);
- p_period[0] = p_period[1] = p_period[2] =
+ p_period[0] = p_period[1] = p_period[2] =
force->numeric(FLERR,arg[iarg+3]);
p_flag[0] = p_flag[1] = p_flag[2] = 1;
if (dimension == 2) {
@@ -404,7 +404,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"x") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix rigid command");
if (strcmp(style,"rigid/npt") != 0 && strcmp(style,"rigid/nph") != 0 &&
- strcmp(style,"rigid/npt/omp") != 0 &&
+ strcmp(style,"rigid/npt/omp") != 0 &&
strcmp(style,"rigid/nph/omp") != 0)
error->all(FLERR,"Illegal fix rigid command");
p_start[0] = force->numeric(FLERR,arg[iarg+1]);
@@ -416,7 +416,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"y") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix rigid command");
if (strcmp(style,"rigid/npt") != 0 && strcmp(style,"rigid/nph") != 0 &&
- strcmp(style,"rigid/npt/omp") != 0 &&
+ strcmp(style,"rigid/npt/omp") != 0 &&
strcmp(style,"rigid/nph/omp") != 0)
error->all(FLERR,"Illegal fix rigid command");
p_start[1] = force->numeric(FLERR,arg[iarg+1]);
@@ -428,7 +428,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"z") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix rigid command");
if (strcmp(style,"rigid/npt") != 0 && strcmp(style,"rigid/nph") != 0 &&
- strcmp(style,"rigid/npt/omp") != 0 &&
+ strcmp(style,"rigid/npt/omp") != 0 &&
strcmp(style,"rigid/nph/omp") != 0)
error->all(FLERR,"Illegal fix rigid command");
p_start[2] = force->numeric(FLERR,arg[iarg+1]);
@@ -448,7 +448,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
iarg += 2;
} else if (strcmp(arg[iarg],"dilate") == 0) {
- if (iarg+2 > narg)
+ if (iarg+2 > narg)
error->all(FLERR,"Illegal fix rigid npt/nph command");
if (strcmp(arg[iarg+1],"all") == 0) allremap = 1;
else {
@@ -466,8 +466,8 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"tparam") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix rigid command");
- if (strcmp(style,"rigid/nvt") != 0 && strcmp(style,"rigid/npt") != 0 &&
- strcmp(style,"rigid/nvt/omp") != 0 &&
+ if (strcmp(style,"rigid/nvt") != 0 && strcmp(style,"rigid/npt") != 0 &&
+ strcmp(style,"rigid/nvt/omp") != 0 &&
strcmp(style,"rigid/npt/omp") != 0)
error->all(FLERR,"Illegal fix rigid command");
t_chain = force->inumeric(FLERR,arg[iarg+1]);
@@ -477,8 +477,8 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"pchain") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix rigid command");
- if (strcmp(style,"rigid/npt") != 0 && strcmp(style,"rigid/nph") != 0 &&
- strcmp(style,"rigid/npt/omp") != 0 &&
+ if (strcmp(style,"rigid/npt") != 0 && strcmp(style,"rigid/nph") != 0 &&
+ strcmp(style,"rigid/npt/omp") != 0 &&
strcmp(style,"rigid/nph/omp") != 0)
error->all(FLERR,"Illegal fix rigid command");
p_chain = force->inumeric(FLERR,arg[iarg+1]);
@@ -495,16 +495,16 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
} else error->all(FLERR,"Illegal fix rigid command");
}
-
+
// set pstat_flag
pstat_flag = 0;
- for (int i = 0; i < 3; i++)
+ for (int i = 0; i < 3; i++)
if (p_flag[i]) pstat_flag = 1;
if (pcouple == XYZ || (dimension == 2 && pcouple == XY)) pstyle = ISO;
else pstyle = ANISO;
-
+
// initialize Marsaglia RNG with processor-unique seed
if (langflag) random = new RanMars(lmp,seed + me);
@@ -1035,7 +1035,7 @@ void FixRigid::final_integrate_respa(int ilevel, int iloop)
xcmimage flags are relative to xcm so that body can be unwrapped
if don't do this, would need xcm to move with true image flags
then a body could end up very far away from box
- set_xv() will then compute huge displacements every step to
+ set_xv() will then compute huge displacements every step to
reset coords of all body atoms to be back inside the box,
ditto for triclinic box flip, which causes numeric problems
------------------------------------------------------------------------- */
@@ -1089,7 +1089,7 @@ int FixRigid::dof(int tgroup)
// cannot count DOF correctly unless setup_bodies_static() has been called
if (!setupflag) {
- if (comm->me == 0)
+ if (comm->me == 0)
error->warning(FLERR,"Cannot count rigid body degrees-of-freedom "
"before bodies are initialized");
return 0;
@@ -1668,7 +1668,7 @@ void FixRigid::setup_bodies_static()
// set rigid body image flags to default values
for (ibody = 0; ibody < nbody; ibody++)
- imagebody[ibody] = ((imageint) IMGMAX << IMG2BITS) |
+ imagebody[ibody] = ((imageint) IMGMAX << IMG2BITS) |
((imageint) IMGMAX << IMGBITS) | IMGMAX;
// overwrite masstotal, center-of-mass, image flags with file values
@@ -2122,7 +2122,7 @@ void FixRigid::setup_bodies_dynamic()
vxcm vycm vzcm lx ly lz ix iy iz
------------------------------------------------------------------------- */
-void FixRigid::readfile(int which, double *vec,
+void FixRigid::readfile(int which, double *vec,
double **array1, double **array2, double **array3,
imageint *ivec, int *inbody)
{
@@ -2131,7 +2131,7 @@ void FixRigid::readfile(int which, double *vec,
FILE *fp;
char *eof,*start,*next,*buf;
char line[MAXLINE];
-
+
if (me == 0) {
fp = fopen(infile,"r");
if (fp == NULL) {
@@ -2170,7 +2170,7 @@ void FixRigid::readfile(int which, double *vec,
if (nwords != ATTRIBUTE_PERBODY)
error->all(FLERR,"Incorrect rigid body format in fix rigid file");
-
+
// loop over lines of rigid body attributes
// tokenize the line into values
// id = rigid body ID
@@ -2180,19 +2180,19 @@ void FixRigid::readfile(int which, double *vec,
for (int i = 0; i < nchunk; i++) {
next = strchr(buf,'\n');
-
+
values[0] = strtok(buf," \t\n\r\f");
for (j = 1; j < nwords; j++)
values[j] = strtok(NULL," \t\n\r\f");
-
+
id = atoi(values[0]);
if (rstyle == MOLECULE) {
- if (id <= 0 || id > maxmol)
+ if (id <= 0 || id > maxmol)
error->all(FLERR,"Invalid rigid body ID in fix rigid file");
id = mol2body[id];
} else id--;
- if (id < 0 || id >= nbody)
+ if (id < 0 || id >= nbody)
error->all(FLERR,"Invalid rigid body ID in fix rigid file");
inbody[id] = 1;
@@ -2210,8 +2210,8 @@ void FixRigid::readfile(int which, double *vec,
xbox = atoi(values[17]);
ybox = atoi(values[18]);
zbox = atoi(values[19]);
- ivec[id] = ((imageint) (xbox + IMGMAX) & IMGMASK) |
- (((imageint) (ybox + IMGMAX) & IMGMASK) << IMGBITS) |
+ ivec[id] = ((imageint) (xbox + IMGMAX) & IMGMASK) |
+ (((imageint) (ybox + IMGMAX) & IMGMASK) << IMGBITS) |
(((imageint) (zbox + IMGMAX) & IMGMASK) << IMG2BITS);
} else {
array1[id][0] = atof(values[5]);
@@ -2224,7 +2224,7 @@ void FixRigid::readfile(int which, double *vec,
buf = next + 1;
}
-
+
nread += nchunk;
}
@@ -2557,7 +2557,7 @@ double FixRigid::extract_ke()
{
double ke = 0.0;
for (int i = 0; i < nbody; i++)
- ke += masstotal[i] *
+ ke += masstotal[i] *
(vcm[i][0]*vcm[i][0] + vcm[i][1]*vcm[i][1] + vcm[i][2]*vcm[i][2]);
return 0.5*ke;
diff --git a/src/RIGID/fix_rigid.h b/src/RIGID/fix_rigid.h
index 50314bd792..94692da367 100644
--- a/src/RIGID/fix_rigid.h
+++ b/src/RIGID/fix_rigid.h
@@ -39,7 +39,7 @@ class FixRigid : public Fix {
void write_restart_file(char *);
virtual double compute_scalar();
virtual int modify_param(int, char **) {return 0;}
-
+
double memory_usage();
void grow_arrays(int);
void copy_arrays(int, int, int);
@@ -58,7 +58,7 @@ class FixRigid : public Fix {
double extract_ke();
double extract_erotational();
double compute_array(int, int);
-
+
protected:
int me,nprocs;
double dtv,dtf,dtq;
@@ -121,14 +121,14 @@ class FixRigid : public Fix {
int pstat_flag; // NPT settings
double p_start[3],p_stop[3];
double p_period[3],p_freq[3];
- int p_flag[3];
+ int p_flag[3];
int pcouple,pstyle;
int p_chain;
int allremap; // remap all atoms
int dilate_group_bit; // mask for dilation group
char *id_dilate; // group name to dilate
-
+
class RanMars *random;
class AtomVecEllipsoid *avec_ellipsoid;
class AtomVecLine *avec_line;
@@ -142,7 +142,7 @@ class FixRigid : public Fix {
void set_v();
void setup_bodies_static();
void setup_bodies_dynamic();
- void readfile(int, double *, double **, double **, double **,
+ void readfile(int, double *, double **, double **, double **,
imageint *, int *);
};
diff --git a/src/RIGID/fix_rigid_nh.cpp b/src/RIGID/fix_rigid_nh.cpp
index 5bed48f3d5..6a1476ba35 100644
--- a/src/RIGID/fix_rigid_nh.cpp
+++ b/src/RIGID/fix_rigid_nh.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -17,9 +17,9 @@
Miller et al., J Chem Phys. 116, 8649-8659 (2002)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <string.h>
#include "fix_rigid_nh.h"
#include "math_extra.h"
#include "atom.h"
@@ -50,12 +50,12 @@ FixRigidNH::FixRigidNH(LAMMPS *lmp, int narg, char **arg) :
FixRigid(lmp, narg, arg)
{
// error checks: could be moved up to FixRigid
-
- if ((p_flag[0] == 1 && p_period[0] <= 0.0) ||
- (p_flag[1] == 1 && p_period[1] <= 0.0) ||
- (p_flag[2] == 1 && p_period[2] <= 0.0))
+
+ if ((p_flag[0] == 1 && p_period[0] <= 0.0) ||
+ (p_flag[1] == 1 && p_period[1] <= 0.0) ||
+ (p_flag[2] == 1 && p_period[2] <= 0.0))
error->all(FLERR,"Fix rigid npt/nph period must be > 0.0");
-
+
if (dimension == 2 && p_flag[2])
error->all(FLERR,"Invalid fix rigid npt/nph command for a 2d simulation");
if (dimension == 2 && (pcouple == YZ || pcouple == XZ))
@@ -83,7 +83,7 @@ FixRigidNH::FixRigidNH(LAMMPS *lmp, int narg, char **arg) :
if (p_flag[2] && domain->zperiodic == 0)
error->all(FLERR,
"Cannot use fix rigid npt/nph on a non-periodic dimension");
-
+
if (pcouple == XYZ && dimension == 3 &&
(p_start[0] != p_start[1] || p_start[0] != p_start[2] ||
p_stop[0] != p_stop[1] || p_stop[0] != p_stop[2] ||
@@ -113,39 +113,39 @@ FixRigidNH::FixRigidNH(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,"Fix rigid nvt/npt/nph damping parameters must be > 0.0");
// memory allocation and initialization
-
+
memory->create(conjqm,nbody,4,"rigid_nh:conjqm");
if (tstat_flag || pstat_flag) {
allocate_chain();
allocate_order();
}
-
+
if (tstat_flag) {
eta_t[0] = eta_r[0] = 0.0;
eta_dot_t[0] = eta_dot_r[0] = 0.0;
f_eta_t[0] = f_eta_r[0] = 0.0;
-
+
for (int i = 1; i < t_chain; i++) {
eta_t[i] = eta_r[i] = 0.0;
eta_dot_t[i] = eta_dot_r[i] = 0.0;
}
}
-
+
if (pstat_flag) {
epsilon_dot[0] = epsilon_dot[1] = epsilon_dot[2] = 0.0;
eta_b[0] = eta_dot_b[0] = f_eta_b[0] = 0.0;
- for (int i = 1; i < p_chain; i++)
+ for (int i = 1; i < p_chain; i++)
eta_b[i] = eta_dot_b[i] = 0.0;
}
// rigid body pointers
-
+
nrigidfix = 0;
rfix = NULL;
vol0 = 0.0;
t0 = 1.0;
-
+
tcomputeflag = 0;
pcomputeflag = 0;
}
@@ -159,16 +159,16 @@ FixRigidNH::~FixRigidNH()
deallocate_chain();
deallocate_order();
}
-
+
if (rfix) delete [] rfix;
if (tcomputeflag) {
modify->delete_compute(id_temp);
delete [] id_temp;
}
-
+
// delete pressure if fix created it
-
+
if (pstat_flag) {
if (pcomputeflag) modify->delete_compute(id_press);
delete [] id_press;
@@ -182,7 +182,7 @@ int FixRigidNH::setmask()
int mask = 0;
mask = FixRigid::setmask();
if (tstat_flag || pstat_flag) mask |= THERMO_ENERGY;
-
+
return mask;
}
@@ -202,25 +202,25 @@ void FixRigidNH::init()
}
// initialize thermostats
- // set timesteps, constants
+ // set timesteps, constants
// store Yoshida-Suzuki integrator parameters
-
+
dtv = update->dt;
dtf = 0.5 * update->dt * force->ftm2v;
dtq = 0.5 * update->dt;
-
+
boltz = force->boltz;
nktv2p = force->nktv2p;
mvv2e = force->mvv2e;
-
+
if (force->kspace) kspace_flag = 1;
else kspace_flag = 0;
- nf_t = dimension * nbody;
+ nf_t = dimension * nbody;
if (dimension == 3) {
nf_r = dimension * nbody;
for (int ibody = 0; ibody < nbody; ibody++)
- for (int k = 0; k < domain->dimension; k++)
+ for (int k = 0; k < domain->dimension; k++)
if (fabs(inertia[ibody][k]) < EPSILON) nf_r--;
} else if (dimension == 2) {
nf_r = nbody;
@@ -228,12 +228,12 @@ void FixRigidNH::init()
if (fabs(inertia[ibody][2]) < EPSILON) nf_r--;
}
- g_f = nf_t + nf_r;
+ g_f = nf_t + nf_r;
onednft = 1.0 + (double)(dimension) / (double)g_f;
onednfr = (double) (dimension) / (double)g_f;
// see Table 1 in Kamberaj et al
-
+
if (tstat_flag || pstat_flag) {
if (t_order == 3) {
w[0] = 1.0 / (2.0 - pow(2.0, 1.0/3.0));
@@ -249,30 +249,30 @@ void FixRigidNH::init()
}
int icompute;
- if (tcomputeflag) {
+ if (tcomputeflag) {
icompute = modify->find_compute(id_temp);
- if (icompute < 0)
+ if (icompute < 0)
error->all(FLERR,"Temperature ID for fix rigid nvt/npt/nph does not exist");
temperature = modify->compute[icompute];
}
if (pstat_flag) {
- if (domain->triclinic)
+ if (domain->triclinic)
error->all(FLERR,"Fix rigid npt/nph does not yet allow triclinic box");
-
+
// ensure no conflict with fix deform
for (int i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"deform") == 0) {
int *dimflag = ((FixDeform *) modify->fix[i])->dimflag;
- if ((p_flag[0] && dimflag[0]) || (p_flag[1] && dimflag[1]) ||
+ if ((p_flag[0] && dimflag[0]) || (p_flag[1] && dimflag[1]) ||
(p_flag[2] && dimflag[2]))
error->all(FLERR,"Cannot use fix rigid npt/nph and fix deform on "
"same component of stress tensor");
}
// set frequency
-
+
p_freq_max = 0.0;
p_freq_max = MAX(p_freq[0],p_freq[1]);
p_freq_max = MAX(p_freq_max,p_freq[2]);
@@ -289,10 +289,10 @@ void FixRigidNH::init()
// set pressure compute ptr
icompute = modify->find_compute(id_press);
- if (icompute < 0)
+ if (icompute < 0)
error->all(FLERR,"Pressure ID for fix rigid npt/nph does not exist");
pressure = modify->compute[icompute];
-
+
// detect if any rigid fixes exist so rigid bodies move on remap
// rfix[] = indices to each fix rigid
// this will include self
@@ -317,7 +317,7 @@ void FixRigidNH::init()
void FixRigidNH::setup(int vflag)
{
FixRigid::setup(vflag);
-
+
double mbody[3];
akin_t = akin_r = 0.0;
for (int ibody = 0; ibody < nbody; ibody++) {
@@ -328,17 +328,17 @@ void FixRigidNH::setup(int vflag)
conjqm[ibody][1] *= 2.0;
conjqm[ibody][2] *= 2.0;
conjqm[ibody][3] *= 2.0;
-
+
if (tstat_flag || pstat_flag) {
- akin_t += masstotal[ibody]*(vcm[ibody][0]*vcm[ibody][0] +
+ akin_t += masstotal[ibody]*(vcm[ibody][0]*vcm[ibody][0] +
vcm[ibody][1]*vcm[ibody][1] + vcm[ibody][2]*vcm[ibody][2]);
- akin_r += angmom[ibody][0]*omega[ibody][0] +
+ akin_r += angmom[ibody][0]*omega[ibody][0] +
angmom[ibody][1]*omega[ibody][1] + angmom[ibody][2]*omega[ibody][2];
}
}
// compute target temperature
-
+
if (tstat_flag) compute_temp_target();
else if (pstat_flag) {
t0 = temperature->compute_scalar();
@@ -352,8 +352,8 @@ void FixRigidNH::setup(int vflag)
// compute target pressure
// compute current pressure
// trigger virial computation on next timestep
-
- if (pstat_flag) {
+
+ if (pstat_flag) {
if (pstyle == ISO) {
temperature->compute_scalar();
pressure->compute_scalar();
@@ -364,9 +364,9 @@ void FixRigidNH::setup(int vflag)
couple();
pressure->addstep(update->ntimestep+1);
}
-
+
// initialize thermostat/barostat settings
-
+
double kt, t_mass, tb_mass;
kt = boltz * t_target;
@@ -374,7 +374,7 @@ void FixRigidNH::setup(int vflag)
t_mass = kt / (t_freq*t_freq);
q_t[0] = nf_t * t_mass;
q_r[0] = nf_r * t_mass;
- for (int i = 1; i < t_chain; i++)
+ for (int i = 1; i < t_chain; i++)
q_t[i] = q_r[i] = t_mass;
for (int i = 1; i < t_chain; i++) {
@@ -382,16 +382,16 @@ void FixRigidNH::setup(int vflag)
f_eta_r[i] = (q_r[i-1] * eta_dot_r[i-1] * eta_dot_r[i-1] - kt)/q_r[i];
}
}
-
+
// initial forces on barostat thermostat variables
-
+
if (pstat_flag) {
for (int i = 0; i < 3; i++)
if (p_flag[i]) {
epsilon_mass[i] = (g_f + dimension) * kt / (p_freq[i]*p_freq[i]);
epsilon[i] = log(vol0)/dimension;
- }
-
+ }
+
tb_mass = kt / (p_freq_max * p_freq_max);
q_b[0] = dimension * dimension * tb_mass;
for (int i = 1; i < p_chain; i++) {
@@ -399,9 +399,9 @@ void FixRigidNH::setup(int vflag)
f_eta_b[i] = (q_b[i] * eta_dot_b[i-1] * eta_dot_b[i-1] - kt)/q_b[i];
}
}
-
+
// update order/timestep dependent coefficients
-
+
if (tstat_flag || pstat_flag) {
for (int i = 0; i < t_order; i++) {
wdti1[i] = w[i] * dtv / t_iter;
@@ -410,7 +410,7 @@ void FixRigidNH::setup(int vflag)
}
}
- if (pstat_flag) {
+ if (pstat_flag) {
compute_press_target();
nh_epsilon_dot();
}
@@ -426,7 +426,7 @@ void FixRigidNH::initial_integrate(int vflag)
double tmp,scale_r,scale_t[3],scale_v[3];
double dtfm,mbody[3],tbody[3],fquat[4];
double dtf2 = dtf * 2.0;
-
+
// compute scale variables
scale_t[0] = scale_t[1] = scale_t[2] = 1.0;
@@ -439,7 +439,7 @@ void FixRigidNH::initial_integrate(int vflag)
scale_t[0] = scale_t[1] = scale_t[2] = tmp;
tmp = exp(-dtq * eta_dot_r[0]);
scale_r = tmp;
- }
+ }
if (pstat_flag) {
akin_t = akin_r = 0.0;
@@ -455,28 +455,28 @@ void FixRigidNH::initial_integrate(int vflag)
tmp = dtq * epsilon_dot[2];
scale_v[2] = dtv * exp(tmp) * maclaurin_series(tmp);
}
-
+
// update xcm, vcm, quat, conjqm and angmom
for (int ibody = 0; ibody < nbody; ibody++) {
-
+
// step 1.1 - update vcm by 1/2 step
-
+
dtfm = dtf / masstotal[ibody];
vcm[ibody][0] += dtfm * fcm[ibody][0] * fflag[ibody][0];
vcm[ibody][1] += dtfm * fcm[ibody][1] * fflag[ibody][1];
vcm[ibody][2] += dtfm * fcm[ibody][2] * fflag[ibody][2];
-
+
if (tstat_flag || pstat_flag) {
vcm[ibody][0] *= scale_t[0];
vcm[ibody][1] *= scale_t[1];
vcm[ibody][2] *= scale_t[2];
-
+
tmp = vcm[ibody][0]*vcm[ibody][0] + vcm[ibody][1]*vcm[ibody][1] +
vcm[ibody][2]*vcm[ibody][2];
akin_t += masstotal[ibody]*tmp;
}
-
+
// step 1.2 - update xcm by full step
if (!pstat_flag) {
@@ -488,56 +488,56 @@ void FixRigidNH::initial_integrate(int vflag)
xcm[ibody][1] += scale_v[1] * vcm[ibody][1];
xcm[ibody][2] += scale_v[2] * vcm[ibody][2];
}
-
+
// step 1.3 - apply torque (body coords) to quaternion momentum
-
+
torque[ibody][0] *= tflag[ibody][0];
torque[ibody][1] *= tflag[ibody][1];
torque[ibody][2] *= tflag[ibody][2];
-
+
MathExtra::transpose_matvec(ex_space[ibody],ey_space[ibody],ez_space[ibody],
torque[ibody],tbody);
MathExtra::quatvec(quat[ibody],tbody,fquat);
-
+
conjqm[ibody][0] += dtf2 * fquat[0];
conjqm[ibody][1] += dtf2 * fquat[1];
conjqm[ibody][2] += dtf2 * fquat[2];
conjqm[ibody][3] += dtf2 * fquat[3];
-
+
if (tstat_flag || pstat_flag) {
conjqm[ibody][0] *= scale_r;
conjqm[ibody][1] *= scale_r;
conjqm[ibody][2] *= scale_r;
conjqm[ibody][3] *= scale_r;
}
-
+
// step 1.4 to 1.13 - use no_squish rotate to update p and q
-
+
MathExtra::no_squish_rotate(3,conjqm[ibody],quat[ibody],inertia[ibody],dtq);
MathExtra::no_squish_rotate(2,conjqm[ibody],quat[ibody],inertia[ibody],dtq);
MathExtra::no_squish_rotate(1,conjqm[ibody],quat[ibody],inertia[ibody],dtv);
MathExtra::no_squish_rotate(2,conjqm[ibody],quat[ibody],inertia[ibody],dtq);
MathExtra::no_squish_rotate(3,conjqm[ibody],quat[ibody],inertia[ibody],dtq);
-
+
// update exyz_space
// transform p back to angmom
// update angular velocity
-
+
MathExtra::q_to_exyz(quat[ibody],ex_space[ibody],ey_space[ibody],
ez_space[ibody]);
MathExtra::invquatvec(quat[ibody],conjqm[ibody],mbody);
MathExtra::matvec(ex_space[ibody],ey_space[ibody],ez_space[ibody],
mbody,angmom[ibody]);
-
+
angmom[ibody][0] *= 0.5;
angmom[ibody][1] *= 0.5;
angmom[ibody][2] *= 0.5;
-
+
MathExtra::angmom_to_omega(angmom[ibody],ex_space[ibody],ey_space[ibody],
ez_space[ibody],inertia[ibody],omega[ibody]);
-
+
if (tstat_flag || pstat_flag) {
- akin_r += angmom[ibody][0]*omega[ibody][0] +
+ akin_r += angmom[ibody][0]*omega[ibody][0] +
angmom[ibody][1]*omega[ibody][1] + angmom[ibody][2]*omega[ibody][2];
}
}
@@ -550,7 +550,7 @@ void FixRigidNH::initial_integrate(int vflag)
compute_temp_target();
nhc_temp_integrate();
}
-
+
// update thermostat chains coupled with barostat
// refer to update_nhcb() in Kamberaj et al.
@@ -571,14 +571,14 @@ void FixRigidNH::initial_integrate(int vflag)
// from quarternion and omega
set_xv();
-
+
// remap simulation box by full step
// redo KSpace coeffs since volume has changed
if (pstat_flag) {
remap();
if (kspace_flag) force->kspace->setup();
- }
+ }
}
/* ---------------------------------------------------------------------- */
@@ -592,7 +592,7 @@ void FixRigidNH::final_integrate()
double dtf2 = dtf * 2.0;
// compute scale variables
-
+
scale_t[0] = scale_t[1] = scale_t[2] = 1.0;
scale_r = 1.0;
@@ -600,25 +600,25 @@ void FixRigidNH::final_integrate()
tmp = exp(-1.0 * dtq * eta_dot_t[0]);
scale_t[0] = scale_t[1] = scale_t[2] = tmp;
scale_r = exp(-1.0 * dtq * eta_dot_r[0]);
- }
-
+ }
+
if (pstat_flag) {
scale_t[0] *= exp(-dtq * (epsilon_dot[0] + mtk_term2));
scale_t[1] *= exp(-dtq * (epsilon_dot[1] + mtk_term2));
scale_t[2] *= exp(-dtq * (epsilon_dot[2] + mtk_term2));
scale_r *= exp(-dtq * (pdim * mtk_term2));
-
+
// reset akin_t and akin_r, to be accumulated for use in nh_epsilon_dot()
akin_t = akin_r = 0.0;
}
-
+
// sum over atoms to get force and torque on rigid body
-
+
double **x = atom->x;
double **f = atom->f;
int nlocal = atom->nlocal;
-
+
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
@@ -632,7 +632,7 @@ void FixRigidNH::final_integrate()
double xunwrap,yunwrap,zunwrap,dx,dy,dz;
for (ibody = 0; ibody < nbody; ibody++)
for (i = 0; i < 6; i++) sum[ibody][i] = 0.0;
-
+
for (i = 0; i < nlocal; i++) {
if (body[i] < 0) continue;
ibody = body[i];
@@ -640,7 +640,7 @@ void FixRigidNH::final_integrate()
sum[ibody][0] += f[i][0];
sum[ibody][1] += f[i][1];
sum[ibody][2] += f[i][2];
-
+
xbox = (xcmimage[i] & IMGMASK) - IMGMAX;
ybox = (xcmimage[i] >> IMGBITS & IMGMASK) - IMGMAX;
zbox = (xcmimage[i] >> IMG2BITS) - IMGMAX;
@@ -658,12 +658,12 @@ void FixRigidNH::final_integrate()
dx = xunwrap - xcm[ibody][0];
dy = yunwrap - xcm[ibody][1];
dz = zunwrap - xcm[ibody][2];
-
+
sum[ibody][3] += dy*f[i][2] - dz*f[i][1];
sum[ibody][4] += dz*f[i][0] - dx*f[i][2];
sum[ibody][5] += dx*f[i][1] - dy*f[i][0];
}
-
+
// extended particles add their torque to torque of body
if (extended) {
@@ -682,7 +682,7 @@ void FixRigidNH::final_integrate()
}
MPI_Allreduce(sum[0],all[0],6*nbody,MPI_DOUBLE,MPI_SUM,world);
-
+
// update vcm and angmom
// include Langevin thermostat forces
// fflag,tflag = 0 for some dimensions in 2d
@@ -696,35 +696,35 @@ void FixRigidNH::final_integrate()
torque[ibody][2] = all[ibody][5] + langextra[ibody][5];
// update vcm by 1/2 step
-
+
dtfm = dtf / masstotal[ibody];
if (tstat_flag || pstat_flag) {
vcm[ibody][0] *= scale_t[0];
vcm[ibody][1] *= scale_t[1];
vcm[ibody][2] *= scale_t[2];
}
-
+
vcm[ibody][0] += dtfm * fcm[ibody][0] * fflag[ibody][0];
vcm[ibody][1] += dtfm * fcm[ibody][1] * fflag[ibody][1];
vcm[ibody][2] += dtfm * fcm[ibody][2] * fflag[ibody][2];
-
+
if (pstat_flag) {
tmp = vcm[ibody][0]*vcm[ibody][0] + vcm[ibody][1]*vcm[ibody][1] +
vcm[ibody][2]*vcm[ibody][2];
akin_t += masstotal[ibody]*tmp;
}
-
+
// update conjqm, then transform to angmom, set velocity again
// virial is already setup from initial_integrate
-
+
torque[ibody][0] *= tflag[ibody][0];
torque[ibody][1] *= tflag[ibody][1];
torque[ibody][2] *= tflag[ibody][2];
-
+
MathExtra::transpose_matvec(ex_space[ibody],ey_space[ibody],
ez_space[ibody],torque[ibody],tbody);
MathExtra::quatvec(quat[ibody],tbody,fquat);
-
+
if (tstat_flag || pstat_flag) {
conjqm[ibody][0] = scale_r * conjqm[ibody][0] + dtf2 * fquat[0];
conjqm[ibody][1] = scale_r * conjqm[ibody][1] + dtf2 * fquat[1];
@@ -740,17 +740,17 @@ void FixRigidNH::final_integrate()
MathExtra::invquatvec(quat[ibody],conjqm[ibody],mbody);
MathExtra::matvec(ex_space[ibody],ey_space[ibody],ez_space[ibody],
mbody,angmom[ibody]);
-
+
angmom[ibody][0] *= 0.5;
angmom[ibody][1] *= 0.5;
- angmom[ibody][2] *= 0.5;
-
+ angmom[ibody][2] *= 0.5;
+
MathExtra::angmom_to_omega(angmom[ibody],ex_space[ibody],ey_space[ibody],
ez_space[ibody],inertia[ibody],omega[ibody]);
-
+
if (pstat_flag) {
- akin_r += angmom[ibody][0]*omega[ibody][0] +
- angmom[ibody][1]*omega[ibody][1] +
+ akin_r += angmom[ibody][0]*omega[ibody][0] +
+ angmom[ibody][1]*omega[ibody][1] +
angmom[ibody][2]*omega[ibody][2];
}
}
@@ -765,7 +765,7 @@ void FixRigidNH::final_integrate()
// compute current and target pressures
// update epsilon dot using akin_t and akin_r
-
+
if (pstat_flag) {
if (pstyle == ISO) {
temperature->compute_scalar();
@@ -789,68 +789,68 @@ void FixRigidNH::nhc_temp_integrate()
{
int i,j,k;
double kt,gfkt_t,gfkt_r,tmp,ms,s,s2;
-
+
kt = boltz * t_target;
gfkt_t = nf_t * kt;
gfkt_r = nf_r * kt;
// update thermostat masses
-
+
double t_mass = boltz * t_target / (t_freq * t_freq);
q_t[0] = nf_t * t_mass;
q_r[0] = nf_r * t_mass;
for (i = 1; i < t_chain; i++)
q_t[i] = q_r[i] = t_mass;
-
+
// update force of thermostats coupled to particles
-
+
f_eta_t[0] = (akin_t * mvv2e - gfkt_t) / q_t[0];
f_eta_r[0] = (akin_r * mvv2e - gfkt_r) / q_r[0];
-
+
// multiple timestep iteration
-
+
for (i = 0; i < t_iter; i++) {
for (j = 0; j < t_order; j++) {
-
+
// update thermostat velocities half step
-
+
eta_dot_t[t_chain-1] += wdti2[j] * f_eta_t[t_chain-1];
eta_dot_r[t_chain-1] += wdti2[j] * f_eta_r[t_chain-1];
-
+
for (k = 1; k < t_chain; k++) {
tmp = wdti4[j] * eta_dot_t[t_chain-k];
ms = maclaurin_series(tmp);
s = exp(-1.0 * tmp);
s2 = s * s;
- eta_dot_t[t_chain-k-1] = eta_dot_t[t_chain-k-1] * s2 +
+ eta_dot_t[t_chain-k-1] = eta_dot_t[t_chain-k-1] * s2 +
wdti2[j] * f_eta_t[t_chain-k-1] * s * ms;
-
+
tmp = wdti4[j] * eta_dot_r[t_chain-k];
ms = maclaurin_series(tmp);
s = exp(-1.0 * tmp);
s2 = s * s;
- eta_dot_r[t_chain-k-1] = eta_dot_r[t_chain-k-1] * s2 +
+ eta_dot_r[t_chain-k-1] = eta_dot_r[t_chain-k-1] * s2 +
wdti2[j] * f_eta_r[t_chain-k-1] * s * ms;
}
-
+
// update thermostat positions a full step
-
+
for (k = 0; k < t_chain; k++) {
eta_t[k] += wdti1[j] * eta_dot_t[k];
eta_r[k] += wdti1[j] * eta_dot_r[k];
}
-
- // update thermostat forces
-
+
+ // update thermostat forces
+
for (k = 1; k < t_chain; k++) {
f_eta_t[k] = q_t[k-1] * eta_dot_t[k-1] * eta_dot_t[k-1] - kt;
f_eta_t[k] /= q_t[k];
f_eta_r[k] = q_r[k-1] * eta_dot_r[k-1] * eta_dot_r[k-1] - kt;
f_eta_r[k] /= q_r[k];
}
-
+
// update thermostat velocities a full step
-
+
for (k = 0; k < t_chain-1; k++) {
tmp = wdti4[j] * eta_dot_t[k+1];
ms = maclaurin_series(tmp);
@@ -859,7 +859,7 @@ void FixRigidNH::nhc_temp_integrate()
eta_dot_t[k] = eta_dot_t[k] * s2 + wdti2[j] * f_eta_t[k] * s * ms;
tmp = q_t[k] * eta_dot_t[k] * eta_dot_t[k] - kt;
f_eta_t[k+1] = tmp / q_t[k+1];
-
+
tmp = wdti4[j] * eta_dot_r[k+1];
ms = maclaurin_series(tmp);
s = exp(-1.0 * tmp);
@@ -868,7 +868,7 @@ void FixRigidNH::nhc_temp_integrate()
tmp = q_r[k] * eta_dot_r[k] * eta_dot_r[k] - kt;
f_eta_r[k+1] = tmp / q_r[k+1];
}
-
+
eta_dot_t[t_chain-1] += wdti2[j] * f_eta_t[t_chain-1];
eta_dot_r[t_chain-1] += wdti2[j] * f_eta_r[t_chain-1];
}
@@ -883,9 +883,9 @@ void FixRigidNH::nhc_press_integrate()
double tmp,s,s2,ms,kecurrent;
double kt = boltz * t_target;
double lkt_press = kt;
-
+
// update thermostat masses
-
+
double tb_mass = kt / (p_freq_max * p_freq_max);
q_b[0] = dimension * dimension * tb_mass;
for (int i = 1; i < p_chain; i++) {
@@ -893,11 +893,11 @@ void FixRigidNH::nhc_press_integrate()
f_eta_b[i] = q_b[i-1] * eta_dot_b[i-1] * eta_dot_b[i-1] - kt;
f_eta_b[i] /= q_b[i];
}
-
+
// update forces acting on thermostat
-
+
kecurrent = 0.0;
- for (i = 0; i < 3; i++)
+ for (i = 0; i < 3; i++)
if (p_flag[i]) {
epsilon_mass[i] = (g_f + dimension) * kt / (p_freq[i] * p_freq[i]);
kecurrent += epsilon_mass[i] * epsilon_dot[i] * epsilon_dot[i];
@@ -907,37 +907,37 @@ void FixRigidNH::nhc_press_integrate()
f_eta_b[0] = (kecurrent - lkt_press) / q_b[0];
// multiple timestep iteration
-
+
for (i = 0; i < t_iter; i++) {
for (j = 0; j < t_order; j++) {
// update thermostat velocities a half step
-
+
eta_dot_b[p_chain-1] += wdti2[j] * f_eta_b[p_chain-1];
-
+
for (k = 1; k < p_chain; k++) {
tmp = wdti4[j] * eta_dot_b[p_chain-k];
ms = maclaurin_series(tmp);
s = exp(-0.5 * tmp);
s2 = s * s;
- eta_dot_b[p_chain-k-1] = eta_dot_b[p_chain-k-1] * s2 +
+ eta_dot_b[p_chain-k-1] = eta_dot_b[p_chain-k-1] * s2 +
wdti2[j] * f_eta_b[p_chain-k-1] * s * ms;
}
-
+
// update thermostat positions
-
+
for (k = 0; k < p_chain; k++)
eta_b[k] += wdti1[j] * eta_dot_b[k];
-
+
// update thermostat forces
-
+
for (k = 1; k < p_chain; k++) {
f_eta_b[k] = q_b[k-1] * eta_dot_b[k-1] * eta_dot_b[k-1] - kt;
f_eta_b[k] /= q_b[k];
}
// update thermostat velocites a full step
-
+
for (k = 0; k < p_chain-1; k++) {
tmp = wdti4[j] * eta_dot_b[k+1];
ms = maclaurin_series(tmp);
@@ -947,13 +947,13 @@ void FixRigidNH::nhc_press_integrate()
tmp = q_b[k] * eta_dot_b[k] * eta_dot_b[k] - kt;
f_eta_b[k+1] = tmp / q_b[k+1];
}
-
+
eta_dot_b[p_chain-1] += wdti2[j] * f_eta_b[p_chain-1];
}
}
}
-/* ----------------------------------------------------------------------
+/* ----------------------------------------------------------------------
compute kinetic energy in the extended Hamiltonian
conserved quantity = sum of returned energy and potential energy
-----------------------------------------------------------------------*/
@@ -963,24 +963,24 @@ double FixRigidNH::compute_scalar()
const double kt = boltz * t_target;
double energy;
int i;
-
+
energy = FixRigid::compute_scalar();
-
+
if (tstat_flag) {
-
+
// thermostat chain energy: from equation 12 in Kameraj et al (JCP 2005)
energy += kt * (nf_t * eta_t[0] + nf_r * eta_r[0]);
-
- for (i = 1; i < t_chain; i++)
+
+ for (i = 1; i < t_chain; i++)
energy += kt * (eta_t[i] + eta_r[i]);
-
+
for (i = 0; i < t_chain; i++) {
energy += 0.5 * q_t[i] * (eta_dot_t[i] * eta_dot_t[i]);
energy += 0.5 * q_r[i] * (eta_dot_r[i] * eta_dot_r[i]);
}
}
-
+
if (pstat_flag) {
// using equation 22 in Kameraj et al for H_NPT
@@ -990,7 +990,7 @@ double FixRigidNH::compute_scalar()
if (p_flag[i])
e += epsilon_mass[i] * epsilon_dot[i] * epsilon_dot[i];
energy += e*(0.5/pdim);
-
+
double vol;
if (dimension == 2) vol = domain->xprd * domain->yprd;
else vol = domain->xprd * domain->yprd * domain->zprd;
@@ -1003,7 +1003,7 @@ double FixRigidNH::compute_scalar()
energy += 0.5 * q_b[i] * (eta_dot_b[i] * eta_dot_b[i]);
}
}
-
+
return energy;
}
@@ -1012,7 +1012,7 @@ double FixRigidNH::compute_scalar()
void FixRigidNH::couple()
{
double *tensor = pressure->vector;
-
+
if (pstyle == ISO) {
p_current[0] = p_current[1] = p_current[2] = pressure->scalar;
} else if (pcouple == XYZ) {
@@ -1043,30 +1043,30 @@ void FixRigidNH::remap()
{
int i;
double oldlo,oldhi,ctr,expfac;
-
+
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
-
+
// epsilon is not used, except for book-keeping
-
+
for (i = 0; i < 3; i++) epsilon[i] += dtq * epsilon_dot[i];
-
+
// convert pertinent atoms and rigid bodies to lamda coords
-
+
if (allremap) domain->x2lamda(nlocal);
else {
for (i = 0; i < nlocal; i++)
if (mask[i] & dilate_group_bit)
domain->x2lamda(x[i],x[i]);
}
-
+
if (nrigidfix)
for (i = 0; i < nrigidfix; i++)
modify->fix[rfix[i]]->deform(0);
-
+
// reset global and local box to new size/shape
-
+
for (i = 0; i < 3; i++) {
if (p_flag[i]) {
oldlo = domain->boxlo[i];
@@ -1080,16 +1080,16 @@ void FixRigidNH::remap()
domain->set_global_box();
domain->set_local_box();
-
+
// convert pertinent atoms and rigid bodies back to box coords
-
+
if (allremap) domain->lamda2x(nlocal);
else {
for (i = 0; i < nlocal; i++)
if (mask[i] & dilate_group_bit)
domain->lamda2x(x[i],x[i]);
}
-
+
if (nrigidfix)
for (i = 0; i< nrigidfix; i++)
modify->fix[rfix[i]]->deform(1);
@@ -1103,7 +1103,7 @@ void FixRigidNH::compute_temp_target()
{
double delta = update->ntimestep - update->beginstep;
if (delta != 0.0) delta /= update->endstep - update->beginstep;
-
+
t_target = t_start + delta * (t_stop-t_start);
}
@@ -1115,7 +1115,7 @@ void FixRigidNH::compute_press_target()
{
double delta = update->ntimestep - update->beginstep;
if (delta != 0.0) delta /= update->endstep - update->beginstep;
-
+
p_hydro = 0.0;
for (int i = 0; i < 3; i++)
if (p_flag[i]) {
@@ -1138,9 +1138,9 @@ void FixRigidNH::nh_epsilon_dot()
else volume = domain->xprd*domain->yprd*domain->zprd;
// MTK terms
-
+
mtk_term1 = (akin_t + akin_r) * mvv2e / g_f;
-
+
scale = exp(-1.0 * dtq * eta_dot_b[0]);
for (i = 0; i < 3; i++)
@@ -1150,7 +1150,7 @@ void FixRigidNH::nh_epsilon_dot()
epsilon_dot[i] += dtq * f_epsilon;
epsilon_dot[i] *= scale;
}
-
+
mtk_term2 = 0.0;
for (i = 0; i < 3; i++)
if (p_flag[i]) mtk_term2 += epsilon_dot[i];
@@ -1158,15 +1158,15 @@ void FixRigidNH::nh_epsilon_dot()
}
/* ----------------------------------------------------------------------
- pack entire state of Fix into one write
+ pack entire state of Fix into one write
------------------------------------------------------------------------- */
void FixRigidNH::write_restart(FILE *fp)
{
if (tstat_flag == 0 && pstat_flag == 0) return;
-
+
int nsize = 2; // tstat_flag and pstat_flag
-
+
if (tstat_flag) {
nsize += 1; // t_chain
nsize += 4*t_chain; // eta_t, eta_r, eta_dot_t, eta_dot_r
@@ -1176,12 +1176,12 @@ void FixRigidNH::write_restart(FILE *fp)
nsize += 7; // p_chain, epsilon(3) and epsilon_dot(3)
nsize += 2*p_chain;
}
-
+
double *list;
memory->create(list,nsize,"rigid_nh:list");
-
+
int n = 0;
-
+
list[n++] = tstat_flag;
if (tstat_flag) {
list[n++] = t_chain;
@@ -1192,7 +1192,7 @@ void FixRigidNH::write_restart(FILE *fp)
list[n++] = eta_dot_r[i];
}
}
-
+
list[n++] = pstat_flag;
if (pstat_flag) {
list[n++] = epsilon[0];
@@ -1201,25 +1201,25 @@ void FixRigidNH::write_restart(FILE *fp)
list[n++] = epsilon_dot[0];
list[n++] = epsilon_dot[1];
list[n++] = epsilon_dot[2];
-
+
list[n++] = p_chain;
for (int i = 0; i < p_chain; i++) {
list[n++] = eta_b[i];
list[n++] = eta_dot_b[i];
}
}
-
+
if (comm->me == 0) {
int size = (nsize)*sizeof(double);
fwrite(&size,sizeof(int),1,fp);
fwrite(list,sizeof(double),nsize,fp);
}
-
+
memory->destroy(list);
}
/* ----------------------------------------------------------------------
- use state info from restart file to restart the Fix
+ use state info from restart file to restart the Fix
------------------------------------------------------------------------- */
void FixRigidNH::restart(char *buf)
@@ -1227,7 +1227,7 @@ void FixRigidNH::restart(char *buf)
int n = 0;
double *list = (double *) buf;
int flag = static_cast<int> (list[n++]);
-
+
if (flag) {
int m = static_cast<int> (list[n++]);
if (tstat_flag && m == t_chain) {
@@ -1248,7 +1248,7 @@ void FixRigidNH::restart(char *buf)
epsilon_dot[0] = list[n++];
epsilon_dot[1] = list[n++];
epsilon_dot[2] = list[n++];
-
+
int m = static_cast<int> (list[n++]);
if (pstat_flag && m == p_chain) {
for (int i = 0; i < p_chain; i++) {
@@ -1335,7 +1335,7 @@ void FixRigidNH::allocate_chain()
f_eta_t = new double[t_chain];
f_eta_r = new double[t_chain];
}
-
+
if (pstat_flag) {
q_b = new double[p_chain];
eta_b = new double[p_chain];
@@ -1375,7 +1375,7 @@ void FixRigidNH::deallocate_chain()
delete [] f_eta_t;
delete [] f_eta_r;
}
-
+
if (pstat_flag) {
delete [] q_b;
delete [] eta_b;
diff --git a/src/RIGID/fix_rigid_nh.h b/src/RIGID/fix_rigid_nh.h
index 64bfa37f90..684579b8af 100644
--- a/src/RIGID/fix_rigid_nh.h
+++ b/src/RIGID/fix_rigid_nh.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -32,26 +32,26 @@ class FixRigidNH : public FixRigid {
void write_restart(FILE *);
void restart(char *buf);
void reset_target(double);
-
+
protected:
double **conjqm; // conjugate quaternion momentum
double boltz,nktv2p,mvv2e; // boltzman constant, conversion factors
int nf_t,nf_r; // trans/rot degrees of freedom
- double onednft,onednfr; // factors 1 + dimension/trans(rot)
+ double onednft,onednfr; // factors 1 + dimension/trans(rot)
// degrees of freedom
double *w,*wdti1,*wdti2,*wdti4; // Yoshida-Suzuki coefficients
double *q_t,*q_r; // trans/rot thermostat masses
double *eta_t,*eta_r; // trans/rot thermostat positions
double *eta_dot_t,*eta_dot_r; // trans/rot thermostat velocities
double *f_eta_t,*f_eta_r; // trans/rot thermostat forces
-
+
double epsilon_mass[3], *q_b; // baro/thermo masses
double epsilon[3],*eta_b; // baro/thermo positions
double epsilon_dot[3],*eta_dot_b; // baro/thermo velocities
double *f_eta_b; // thermo forces
double akin_t,akin_r; // translational/rotational kinetic energies
-
+
int kspace_flag; // 1 if KSpace invoked, 0 if not
int nrigidfix; // number of rigid fixes
int *rfix; // indicies of rigid fixes
@@ -61,9 +61,9 @@ class FixRigidNH : public FixRigid {
int pdim,g_f; // number of barostatted dims, total DoFs
double p_hydro; // hydrostatic target pressure
double p_freq_max; // maximum barostat frequency
-
+
double mtk_term1,mtk_term2; // Martyna-Tobias-Klein corrections
-
+
double t_current,t_target;
double p_current[3],p_target[3];
@@ -72,7 +72,7 @@ class FixRigidNH : public FixRigid {
int tcomputeflag,pcomputeflag;
void couple();
- void remap();
+ void remap();
void nhc_temp_integrate();
void nhc_press_integrate();
diff --git a/src/RIGID/fix_rigid_nh_small.cpp b/src/RIGID/fix_rigid_nh_small.cpp
index 39d778cba5..5708bb6602 100644
--- a/src/RIGID/fix_rigid_nh_small.cpp
+++ b/src/RIGID/fix_rigid_nh_small.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -17,9 +17,9 @@
Miller et al., J Chem Phys. 116, 8649-8659 (2002)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <string.h>
#include "fix_rigid_nh_small.h"
#include "math_extra.h"
#include "atom.h"
@@ -51,16 +51,16 @@ enum{FULL_BODY,INITIAL,FINAL,FORCE_TORQUE,VCM_ANGMOM,XCM_MASS,ITENSOR,DOF};
FixRigidNHSmall::FixRigidNHSmall(LAMMPS *lmp, int narg, char **arg) :
FixRigidSmall(lmp, narg, arg)
-{
+{
// error checks
-
- if ((p_flag[0] == 1 && p_period[0] <= 0.0) ||
- (p_flag[1] == 1 && p_period[1] <= 0.0) ||
- (p_flag[2] == 1 && p_period[2] <= 0.0))
+
+ if ((p_flag[0] == 1 && p_period[0] <= 0.0) ||
+ (p_flag[1] == 1 && p_period[1] <= 0.0) ||
+ (p_flag[2] == 1 && p_period[2] <= 0.0))
error->all(FLERR,"Fix rigid/small npt/nph period must be > 0.0");
dimension = domain->dimension;
-
+
if (dimension == 2 && p_flag[2])
error->all(FLERR,"Invalid fix rigid/small npt/nph command "
"for a 2d simulation");
@@ -98,7 +98,7 @@ FixRigidNHSmall::FixRigidNHSmall(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,
"Cannot use fix rigid/small npt/nph on a "
"non-periodic dimension");
-
+
if (pcouple == XYZ && dimension == 3 &&
(p_start[0] != p_start[1] || p_start[0] != p_start[2] ||
p_stop[0] != p_stop[1] || p_stop[0] != p_stop[2] ||
@@ -129,38 +129,38 @@ FixRigidNHSmall::FixRigidNHSmall(LAMMPS *lmp, int narg, char **arg) :
"must be > 0.0");
// memory allocation and initialization
-
+
if (tstat_flag || pstat_flag) {
allocate_chain();
allocate_order();
}
-
+
if (tstat_flag) {
eta_t[0] = eta_r[0] = 0.0;
eta_dot_t[0] = eta_dot_r[0] = 0.0;
f_eta_t[0] = f_eta_r[0] = 0.0;
-
+
for (int i = 1; i < t_chain; i++) {
eta_t[i] = eta_r[i] = 0.0;
eta_dot_t[i] = eta_dot_r[i] = 0.0;
}
}
-
+
if (pstat_flag) {
epsilon_dot[0] = epsilon_dot[1] = epsilon_dot[2] = 0.0;
eta_b[0] = eta_dot_b[0] = f_eta_b[0] = 0.0;
- for (int i = 1; i < p_chain; i++)
+ for (int i = 1; i < p_chain; i++)
eta_b[i] = eta_dot_b[i] = 0.0;
}
// rigid body pointers
-
+
nrigidfix = 0;
rfix = NULL;
vol0 = 0.0;
t0 = 1.0;
-
+
tcomputeflag = 0;
pcomputeflag = 0;
}
@@ -173,16 +173,16 @@ FixRigidNHSmall::~FixRigidNHSmall()
deallocate_chain();
deallocate_order();
}
-
+
if (rfix) delete [] rfix;
if (tcomputeflag) {
modify->delete_compute(id_temp);
delete [] id_temp;
}
-
+
// delete pressure if fix created it
-
+
if (pstat_flag) {
if (pcomputeflag) modify->delete_compute(id_press);
delete [] id_press;
@@ -196,7 +196,7 @@ int FixRigidNHSmall::setmask()
int mask = 0;
mask = FixRigidSmall::setmask();
if (tstat_flag || pstat_flag) mask |= THERMO_ENERGY;
-
+
return mask;
}
@@ -216,13 +216,13 @@ void FixRigidNHSmall::init()
}
// initialize thermostats
- // set timesteps, constants
+ // set timesteps, constants
// store Yoshida-Suzuki integrator parameters
-
+
dtv = update->dt;
dtf = 0.5 * update->dt * force->ftm2v;
dtq = 0.5 * update->dt;
-
+
boltz = force->boltz;
nktv2p = force->nktv2p;
mvv2e = force->mvv2e;
@@ -231,7 +231,7 @@ void FixRigidNHSmall::init()
else kspace_flag = 0;
// see Table 1 in Kamberaj et al
-
+
if (tstat_flag || pstat_flag) {
if (t_order == 3) {
w[0] = 1.0 / (2.0 - pow(2.0, 1.0/3.0));
@@ -247,30 +247,30 @@ void FixRigidNHSmall::init()
}
int icompute;
- if (tcomputeflag) {
+ if (tcomputeflag) {
icompute = modify->find_compute(id_temp);
- if (icompute < 0)
+ if (icompute < 0)
error->all(FLERR,"Temperature ID for fix rigid nvt/npt/nph does not exist");
temperature = modify->compute[icompute];
}
if (pstat_flag) {
- if (domain->triclinic)
+ if (domain->triclinic)
error->all(FLERR,"Fix rigid npt/nph does not yet allow triclinic box");
-
+
// ensure no conflict with fix deform
for (int i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"deform") == 0) {
int *dimflag = ((FixDeform *) modify->fix[i])->dimflag;
- if ((p_flag[0] && dimflag[0]) || (p_flag[1] && dimflag[1]) ||
+ if ((p_flag[0] && dimflag[0]) || (p_flag[1] && dimflag[1]) ||
(p_flag[2] && dimflag[2]))
error->all(FLERR,"Cannot use fix rigid npt/nph and fix deform on "
"same component of stress tensor");
}
// set frequency
-
+
p_freq_max = 0.0;
p_freq_max = MAX(p_freq[0],p_freq[1]);
p_freq_max = MAX(p_freq_max,p_freq[2]);
@@ -287,10 +287,10 @@ void FixRigidNHSmall::init()
// set pressure compute ptr
icompute = modify->find_compute(id_press);
- if (icompute < 0)
+ if (icompute < 0)
error->all(FLERR,"Pressure ID for fix rigid npt/nph does not exist");
pressure = modify->compute[icompute];
-
+
// detect if any rigid fixes exist so rigid bodies move on remap
// rfix[] = indices to each fix rigid
// this will include self
@@ -317,13 +317,13 @@ void FixRigidNHSmall::setup(int vflag)
FixRigidSmall::setup(vflag);
// total translational and rotational degrees of freedom
-
- nf_t = dimension * nlocal_body;
+
+ nf_t = dimension * nlocal_body;
if (dimension == 3) {
nf_r = dimension * nlocal_body;
for (int ibody = 0; ibody < nlocal_body; ibody++) {
Body *b = &body[ibody];
- for (int k = 0; k < dimension; k++)
+ for (int k = 0; k < dimension; k++)
if (fabs(b->inertia[k]) < EPSILON) nf_r--;
}
} else if (dimension == 2) {
@@ -341,10 +341,10 @@ void FixRigidNHSmall::setup(int vflag)
nf_t = nfall[0];
nf_r = nfall[1];
- g_f = nf_t + nf_r;
+ g_f = nf_t + nf_r;
onednft = 1.0 + (double)(dimension) / (double)g_f;
onednfr = (double) (dimension) / (double)g_f;
-
+
double mbody[3];
akin_t = akin_r = 0.0;
for (int ibody = 0; ibody < nlocal_body; ibody++) {
@@ -356,7 +356,7 @@ void FixRigidNHSmall::setup(int vflag)
b->conjqm[1] *= 2.0;
b->conjqm[2] *= 2.0;
b->conjqm[3] *= 2.0;
-
+
if (tstat_flag || pstat_flag) {
akin_t += b->mass*(b->vcm[0]*b->vcm[0] + b->vcm[1]*b->vcm[1] +
b->vcm[2]*b->vcm[2]);
@@ -364,9 +364,9 @@ void FixRigidNHSmall::setup(int vflag)
b->angmom[2]*b->omega[2];
}
}
-
+
// accumulate translational and rotational kinetic energies
-
+
if (tstat_flag || pstat_flag) {
double ke[2],keall[2];
ke[0] = akin_t;
@@ -375,9 +375,9 @@ void FixRigidNHSmall::setup(int vflag)
akin_t = keall[0];
akin_r = keall[1];
}
-
+
// compute target temperature
-
+
if (tstat_flag) compute_temp_target();
else if (pstat_flag) {
t0 = temperature->compute_scalar();
@@ -391,10 +391,10 @@ void FixRigidNHSmall::setup(int vflag)
// compute target pressure
// compute current pressure
// trigger virial computation on next timestep
-
- if (pstat_flag) {
+
+ if (pstat_flag) {
compute_press_target();
-
+
if (pstyle == ISO) {
temperature->compute_scalar();
pressure->compute_scalar();
@@ -406,9 +406,9 @@ void FixRigidNHSmall::setup(int vflag)
couple();
pressure->addstep(update->ntimestep+1);
}
-
+
// initialize thermostat/barostat settings
-
+
double kt, t_mass, tb_mass;
kt = boltz * t_target;
@@ -416,7 +416,7 @@ void FixRigidNHSmall::setup(int vflag)
t_mass = kt / (t_freq*t_freq);
q_t[0] = nf_t * t_mass;
q_r[0] = nf_r * t_mass;
- for (int i = 1; i < t_chain; i++)
+ for (int i = 1; i < t_chain; i++)
q_t[i] = q_r[i] = t_mass;
for (int i = 1; i < t_chain; i++) {
@@ -424,16 +424,16 @@ void FixRigidNHSmall::setup(int vflag)
f_eta_r[i] = (q_r[i-1] * eta_dot_r[i-1] * eta_dot_r[i-1] - kt)/q_r[i];
}
}
-
+
// initial forces on barostat thermostat variables
-
+
if (pstat_flag) {
for (int i = 0; i < 3; i++)
if (p_flag[i]) {
epsilon_mass[i] = (g_f + dimension) * kt / (p_freq[i]*p_freq[i]);
epsilon[i] = log(vol0)/dimension;
- }
-
+ }
+
tb_mass = kt / (p_freq_max * p_freq_max);
q_b[0] = dimension * dimension * tb_mass;
for (int i = 1; i < p_chain; i++) {
@@ -441,9 +441,9 @@ void FixRigidNHSmall::setup(int vflag)
f_eta_b[i] = (q_b[i] * eta_dot_b[i-1] * eta_dot_b[i-1] - kt)/q_b[i];
}
}
-
+
// update order/timestep dependent coefficients
-
+
if (tstat_flag || pstat_flag) {
for (int i = 0; i < t_order; i++) {
wdti1[i] = w[i] * dtv / t_iter;
@@ -452,7 +452,7 @@ void FixRigidNHSmall::setup(int vflag)
}
}
- if (pstat_flag) {
+ if (pstat_flag) {
compute_press_target();
nh_epsilon_dot();
}
@@ -468,7 +468,7 @@ void FixRigidNHSmall::initial_integrate(int vflag)
double tmp,scale_r,scale_t[3],scale_v[3];
double dtfm,mbody[3],tbody[3],fquat[4];
double dtf2 = dtf * 2.0;
-
+
// compute scale variables
scale_t[0] = scale_t[1] = scale_t[2] = 1.0;
@@ -480,7 +480,7 @@ void FixRigidNHSmall::initial_integrate(int vflag)
scale_t[0] = scale_t[1] = scale_t[2] = tmp;
tmp = exp(-dtq * eta_dot_r[0]);
scale_r = tmp;
- }
+ }
if (pstat_flag) {
scale_t[0] *= exp(-dtq * (epsilon_dot[0] + mtk_term2));
@@ -495,25 +495,25 @@ void FixRigidNHSmall::initial_integrate(int vflag)
tmp = dtq * epsilon_dot[2];
scale_v[2] = dtv * exp(tmp) * maclaurin_series(tmp);
}
-
+
// update xcm, vcm, quat, conjqm and angmom
for (int ibody = 0; ibody < nlocal_body; ibody++) {
Body *b = &body[ibody];
-
+
// step 1.1 - update vcm by 1/2 step
-
+
dtfm = dtf / b->mass;
b->vcm[0] += dtfm * b->fcm[0];
b->vcm[1] += dtfm * b->fcm[1];
b->vcm[2] += dtfm * b->fcm[2];
-
+
if (tstat_flag || pstat_flag) {
b->vcm[0] *= scale_t[0];
b->vcm[1] *= scale_t[1];
b->vcm[2] *= scale_t[2];
}
-
+
// step 1.2 - update xcm by full step
if (!pstat_flag) {
@@ -525,51 +525,51 @@ void FixRigidNHSmall::initial_integrate(int vflag)
b->xcm[1] += scale_v[1] * b->vcm[1];
b->xcm[2] += scale_v[2] * b->vcm[2];
}
-
+
// step 1.3 - apply torque (body coords) to quaternion momentum
-
+
MathExtra::transpose_matvec(b->ex_space,b->ey_space,b->ez_space,
b->torque,tbody);
MathExtra::quatvec(b->quat,tbody,fquat);
-
+
b->conjqm[0] += dtf2 * fquat[0];
b->conjqm[1] += dtf2 * fquat[1];
b->conjqm[2] += dtf2 * fquat[2];
b->conjqm[3] += dtf2 * fquat[3];
-
+
if (tstat_flag || pstat_flag) {
b->conjqm[0] *= scale_r;
b->conjqm[1] *= scale_r;
b->conjqm[2] *= scale_r;
b->conjqm[3] *= scale_r;
}
-
+
// step 1.4 to 1.13 - use no_squish rotate to update p and q
-
+
no_squish_rotate(3,b->conjqm,b->quat,b->inertia,dtq);
no_squish_rotate(2,b->conjqm,b->quat,b->inertia,dtq);
no_squish_rotate(1,b->conjqm,b->quat,b->inertia,dtv);
no_squish_rotate(2,b->conjqm,b->quat,b->inertia,dtq);
no_squish_rotate(3,b->conjqm,b->quat,b->inertia,dtq);
-
+
// update exyz_space
// transform p back to angmom
// update angular velocity
-
+
MathExtra::q_to_exyz(b->quat,b->ex_space,b->ey_space,
b->ez_space);
MathExtra::invquatvec(b->quat,b->conjqm,mbody);
MathExtra::matvec(b->ex_space,b->ey_space,b->ez_space,
mbody,b->angmom);
-
+
b->angmom[0] *= 0.5;
b->angmom[1] *= 0.5;
b->angmom[2] *= 0.5;
-
+
MathExtra::angmom_to_omega(b->angmom,b->ex_space,b->ey_space,
b->ez_space,b->inertia,b->omega);
}
-
+
// forward communicate updated info of all bodies
commflag = INITIAL;
@@ -581,13 +581,13 @@ void FixRigidNHSmall::initial_integrate(int vflag)
akin_t = akin_r = 0.0;
for (int ibody = 0; ibody < nlocal_body; ibody++) {
- Body *b = &body[ibody];
+ Body *b = &body[ibody];
akin_t += b->mass*(b->vcm[0]*b->vcm[0] + b->vcm[1]*b->vcm[1] +
b->vcm[2]*b->vcm[2]);
akin_r += b->angmom[0]*b->omega[0] + b->angmom[1]*b->omega[1] +
b->angmom[2]*b->omega[2];
}
-
+
double ke[2],keall[2];
ke[0] = akin_t;
ke[1] = akin_r;
@@ -604,7 +604,7 @@ void FixRigidNHSmall::initial_integrate(int vflag)
compute_temp_target();
nhc_temp_integrate();
}
-
+
// update thermostat chains coupled with barostat
// refer to update_nhcb() in Kamberaj et al.
@@ -625,14 +625,14 @@ void FixRigidNHSmall::initial_integrate(int vflag)
// from quarternion and omega
set_xv();
-
+
// remap simulation box by full step
// redo KSpace coeffs since volume has changed
if (pstat_flag) {
remap();
if (kspace_flag) force->kspace->setup();
- }
+ }
}
/* ---------------------------------------------------------------------- */
@@ -646,7 +646,7 @@ void FixRigidNHSmall::final_integrate()
double dtf2 = dtf * 2.0;
// compute scale variables
-
+
scale_t[0] = scale_t[1] = scale_t[2] = 1.0;
scale_r = 1.0;
@@ -654,21 +654,21 @@ void FixRigidNHSmall::final_integrate()
tmp = exp(-1.0 * dtq * eta_dot_t[0]);
scale_t[0] = scale_t[1] = scale_t[2] = tmp;
scale_r = exp(-1.0 * dtq * eta_dot_r[0]);
- }
-
+ }
+
if (pstat_flag) {
scale_t[0] *= exp(-dtq * (epsilon_dot[0] + mtk_term2));
scale_t[1] *= exp(-dtq * (epsilon_dot[1] + mtk_term2));
scale_t[2] *= exp(-dtq * (epsilon_dot[2] + mtk_term2));
scale_r *= exp(-dtq * (pdim * mtk_term2));
}
-
+
// sum over atoms to get force and torque on rigid body
-
+
double **x = atom->x;
double **f = atom->f;
int nlocal = atom->nlocal;
-
+
double dx,dy,dz;
double unwrap[3];
double *xcm,*fcm,*tcm;
@@ -700,7 +700,7 @@ void FixRigidNHSmall::final_integrate()
tcm[1] += dz*f[i][0] - dx*f[i][2];
tcm[2] += dx*f[i][1] - dy*f[i][0];
}
-
+
// extended particles add their torque to torque of body
if (extended) {
@@ -737,7 +737,7 @@ void FixRigidNHSmall::final_integrate()
tcm[2] += langextra[ibody][5];
}
}
-
+
// update vcm and angmom
// include Langevin thermostat forces
// fflag,tflag = 0 for some dimensions in 2d
@@ -760,11 +760,11 @@ void FixRigidNHSmall::final_integrate()
// update conjqm, then transform to angmom, set velocity again
// virial is already setup from initial_integrate
-
+
MathExtra::transpose_matvec(b->ex_space,b->ey_space,
b->ez_space,b->torque,tbody);
MathExtra::quatvec(b->quat,tbody,fquat);
-
+
if (tstat_flag || pstat_flag) {
b->conjqm[0] = scale_r * b->conjqm[0] + dtf2 * fquat[0];
b->conjqm[1] = scale_r * b->conjqm[1] + dtf2 * fquat[1];
@@ -779,11 +779,11 @@ void FixRigidNHSmall::final_integrate()
MathExtra::invquatvec(b->quat,b->conjqm,mbody);
MathExtra::matvec(b->ex_space,b->ey_space,b->ez_space,mbody,b->angmom);
-
+
b->angmom[0] *= 0.5;
b->angmom[1] *= 0.5;
- b->angmom[2] *= 0.5;
-
+ b->angmom[2] *= 0.5;
+
MathExtra::angmom_to_omega(b->angmom,b->ex_space,b->ey_space,
b->ez_space,b->inertia,b->omega);
}
@@ -799,13 +799,13 @@ void FixRigidNHSmall::final_integrate()
akin_t = akin_r = 0.0;
for (int ibody = 0; ibody < nlocal_body; ibody++) {
- Body *b = &body[ibody];
+ Body *b = &body[ibody];
akin_t += b->mass*(b->vcm[0]*b->vcm[0] + b->vcm[1]*b->vcm[1] +
b->vcm[2]*b->vcm[2]);
akin_r += b->angmom[0]*b->omega[0] + b->angmom[1]*b->omega[1] +
b->angmom[2]*b->omega[2];
}
-
+
double ke[2],keall[2];
ke[0] = akin_t;
ke[1] = akin_r;
@@ -824,7 +824,7 @@ void FixRigidNHSmall::final_integrate()
// compute current and target pressures
// update epsilon dot using akin_t and akin_r
-
+
if (pstat_flag) {
if (pstyle == ISO) {
temperature->compute_scalar();
@@ -848,68 +848,68 @@ void FixRigidNHSmall::nhc_temp_integrate()
{
int i,j,k;
double kt,gfkt_t,gfkt_r,tmp,ms,s,s2;
-
+
kt = boltz * t_target;
gfkt_t = nf_t * kt;
gfkt_r = nf_r * kt;
// update thermostat masses
-
+
double t_mass = boltz * t_target / (t_freq * t_freq);
q_t[0] = nf_t * t_mass;
q_r[0] = nf_r * t_mass;
for (i = 1; i < t_chain; i++)
q_t[i] = q_r[i] = t_mass;
-
+
// update force of thermostats coupled to particles
-
+
f_eta_t[0] = (akin_t * mvv2e - gfkt_t) / q_t[0];
f_eta_r[0] = (akin_r * mvv2e - gfkt_r) / q_r[0];
-
+
// multiple timestep iteration
-
+
for (i = 0; i < t_iter; i++) {
for (j = 0; j < t_order; j++) {
-
+
// update thermostat velocities half step
-
+
eta_dot_t[t_chain-1] += wdti2[j] * f_eta_t[t_chain-1];
eta_dot_r[t_chain-1] += wdti2[j] * f_eta_r[t_chain-1];
-
+
for (k = 1; k < t_chain; k++) {
tmp = wdti4[j] * eta_dot_t[t_chain-k];
ms = maclaurin_series(tmp);
s = exp(-1.0 * tmp);
s2 = s * s;
- eta_dot_t[t_chain-k-1] = eta_dot_t[t_chain-k-1] * s2 +
+ eta_dot_t[t_chain-k-1] = eta_dot_t[t_chain-k-1] * s2 +
wdti2[j] * f_eta_t[t_chain-k-1] * s * ms;
-
+
tmp = wdti4[j] * eta_dot_r[t_chain-k];
ms = maclaurin_series(tmp);
s = exp(-1.0 * tmp);
s2 = s * s;
- eta_dot_r[t_chain-k-1] = eta_dot_r[t_chain-k-1] * s2 +
+ eta_dot_r[t_chain-k-1] = eta_dot_r[t_chain-k-1] * s2 +
wdti2[j] * f_eta_r[t_chain-k-1] * s * ms;
}
-
+
// update thermostat positions a full step
-
+
for (k = 0; k < t_chain; k++) {
eta_t[k] += wdti1[j] * eta_dot_t[k];
eta_r[k] += wdti1[j] * eta_dot_r[k];
}
-
- // update thermostat forces
-
+
+ // update thermostat forces
+
for (k = 1; k < t_chain; k++) {
f_eta_t[k] = q_t[k-1] * eta_dot_t[k-1] * eta_dot_t[k-1] - kt;
f_eta_t[k] /= q_t[k];
f_eta_r[k] = q_r[k-1] * eta_dot_r[k-1] * eta_dot_r[k-1] - kt;
f_eta_r[k] /= q_r[k];
}
-
+
// update thermostat velocities a full step
-
+
for (k = 0; k < t_chain-1; k++) {
tmp = wdti4[j] * eta_dot_t[k+1];
ms = maclaurin_series(tmp);
@@ -918,7 +918,7 @@ void FixRigidNHSmall::nhc_temp_integrate()
eta_dot_t[k] = eta_dot_t[k] * s2 + wdti2[j] * f_eta_t[k] * s * ms;
tmp = q_t[k] * eta_dot_t[k] * eta_dot_t[k] - kt;
f_eta_t[k+1] = tmp / q_t[k+1];
-
+
tmp = wdti4[j] * eta_dot_r[k+1];
ms = maclaurin_series(tmp);
s = exp(-1.0 * tmp);
@@ -927,7 +927,7 @@ void FixRigidNHSmall::nhc_temp_integrate()
tmp = q_r[k] * eta_dot_r[k] * eta_dot_r[k] - kt;
f_eta_r[k+1] = tmp / q_r[k+1];
}
-
+
eta_dot_t[t_chain-1] += wdti2[j] * f_eta_t[t_chain-1];
eta_dot_r[t_chain-1] += wdti2[j] * f_eta_r[t_chain-1];
}
@@ -942,9 +942,9 @@ void FixRigidNHSmall::nhc_press_integrate()
double tmp,s,s2,ms,kecurrent;
double kt = boltz * t_target;
double lkt_press = kt;
-
+
// update thermostat masses
-
+
double tb_mass = kt / (p_freq_max * p_freq_max);
q_b[0] = dimension * dimension * tb_mass;
for (int i = 1; i < p_chain; i++) {
@@ -952,11 +952,11 @@ void FixRigidNHSmall::nhc_press_integrate()
f_eta_b[i] = q_b[i-1] * eta_dot_b[i-1] * eta_dot_b[i-1] - kt;
f_eta_b[i] /= q_b[i];
}
-
+
// update forces acting on thermostat
-
+
kecurrent = 0.0;
- for (i = 0; i < 3; i++)
+ for (i = 0; i < 3; i++)
if (p_flag[i]) {
epsilon_mass[i] = (g_f + dimension) * kt / (p_freq[i] * p_freq[i]);
kecurrent += epsilon_mass[i] * epsilon_dot[i] * epsilon_dot[i];
@@ -966,37 +966,37 @@ void FixRigidNHSmall::nhc_press_integrate()
f_eta_b[0] = (kecurrent - lkt_press) / q_b[0];
// multiple timestep iteration
-
+
for (i = 0; i < t_iter; i++) {
for (j = 0; j < t_order; j++) {
// update thermostat velocities a half step
-
+
eta_dot_b[p_chain-1] += wdti2[j] * f_eta_b[p_chain-1];
-
+
for (k = 1; k < p_chain; k++) {
tmp = wdti4[j] * eta_dot_b[p_chain-k];
ms = maclaurin_series(tmp);
s = exp(-0.5 * tmp);
s2 = s * s;
- eta_dot_b[p_chain-k-1] = eta_dot_b[p_chain-k-1] * s2 +
+ eta_dot_b[p_chain-k-1] = eta_dot_b[p_chain-k-1] * s2 +
wdti2[j] * f_eta_b[p_chain-k-1] * s * ms;
}
-
+
// update thermostat positions
-
+
for (k = 0; k < p_chain; k++)
eta_b[k] += wdti1[j] * eta_dot_b[k];
-
+
// update thermostat forces
-
+
for (k = 1; k < p_chain; k++) {
f_eta_b[k] = q_b[k-1] * eta_dot_b[k-1] * eta_dot_b[k-1] - kt;
f_eta_b[k] /= q_b[k];
}
// update thermostat velocites a full step
-
+
for (k = 0; k < p_chain-1; k++) {
tmp = wdti4[j] * eta_dot_b[k+1];
ms = maclaurin_series(tmp);
@@ -1006,13 +1006,13 @@ void FixRigidNHSmall::nhc_press_integrate()
tmp = q_b[k] * eta_dot_b[k] * eta_dot_b[k] - kt;
f_eta_b[k+1] = tmp / q_b[k+1];
}
-
+
eta_dot_b[p_chain-1] += wdti2[j] * f_eta_b[p_chain-1];
}
}
}
-/* ----------------------------------------------------------------------
+/* ----------------------------------------------------------------------
compute kinetic energy in the extended Hamiltonian
conserved quantity = sum of returned energy and potential energy
-----------------------------------------------------------------------*/
@@ -1022,22 +1022,22 @@ double FixRigidNHSmall::compute_scalar()
int i,k;
double kt = boltz * t_target;
double energy,ke_t,ke_q,tmp,Pkq[4];
-
+
double *vcm,*quat;
-
+
// compute the kinetic parts of H_NVE in Kameraj et al (JCP 2005, pp 224114)
-
+
// translational and rotational kinetic energies
ke_t = 0.0;
ke_q = 0.0;
-
+
for (int i = 0; i < nlocal_body; i++) {
vcm = body[i].vcm;
quat = body[i].quat;
ke_t += body[i].mass * (vcm[0]*vcm[0] + vcm[1]*vcm[1] +
vcm[2]*vcm[2]);
-
+
for (k = 1; k < 4; k++) {
if (k == 1) {
Pkq[0] = -quat[1];
@@ -1053,43 +1053,43 @@ double FixRigidNHSmall::compute_scalar()
Pkq[0] = -quat[3];
Pkq[1] = quat[2];
Pkq[2] = -quat[1];
- Pkq[3] = quat[0];
+ Pkq[3] = quat[0];
}
-
+
tmp = body[i].conjqm[0]*Pkq[0] + body[i].conjqm[1]*Pkq[1] +
body[i].conjqm[2]*Pkq[2] + body[i].conjqm[3]*Pkq[3];
tmp *= tmp;
-
+
if (fabs(body[i].inertia[k-1]) < 1e-6) tmp = 0.0;
- else tmp /= (8.0 * body[i].inertia[k-1]);
+ else tmp /= (8.0 * body[i].inertia[k-1]);
ke_q += tmp;
}
}
-
+
double ke[2],keall[2];
ke[0] = ke_t;
ke[1] = ke_q;
MPI_Allreduce(ke,keall,2,MPI_DOUBLE,MPI_SUM,world);
ke_t = keall[0];
ke_q = keall[1];
-
+
energy = (ke_t + ke_q) * mvv2e;
-
+
if (tstat_flag) {
-
+
// thermostat chain energy: from equation 12 in Kameraj et al (JCP 2005)
energy += kt * (nf_t * eta_t[0] + nf_r * eta_r[0]);
-
- for (i = 1; i < t_chain; i++)
+
+ for (i = 1; i < t_chain; i++)
energy += kt * (eta_t[i] + eta_r[i]);
-
+
for (i = 0; i < t_chain; i++) {
energy += 0.5 * q_t[i] * (eta_dot_t[i] * eta_dot_t[i]);
energy += 0.5 * q_r[i] * (eta_dot_r[i] * eta_dot_r[i]);
}
}
-
+
if (pstat_flag) {
// using equation 22 in Kameraj et al for H_NPT
@@ -1099,7 +1099,7 @@ double FixRigidNHSmall::compute_scalar()
if (p_flag[i])
e += epsilon_mass[i] * epsilon_dot[i] * epsilon_dot[i];
energy += e*(0.5/pdim);
-
+
double vol;
if (dimension == 2) vol = domain->xprd * domain->yprd;
else vol = domain->xprd * domain->yprd * domain->zprd;
@@ -1112,7 +1112,7 @@ double FixRigidNHSmall::compute_scalar()
energy += 0.5 * q_b[i] * (eta_dot_b[i] * eta_dot_b[i]);
}
}
-
+
return energy;
}
@@ -1121,7 +1121,7 @@ double FixRigidNHSmall::compute_scalar()
void FixRigidNHSmall::couple()
{
double *tensor = pressure->vector;
-
+
if (pstyle == ISO) {
p_current[0] = p_current[1] = p_current[2] = pressure->scalar;
} else if (pcouple == XYZ) {
@@ -1152,30 +1152,30 @@ void FixRigidNHSmall::remap()
{
int i;
double oldlo,oldhi,ctr,expfac;
-
+
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
-
+
// epsilon is not used, except for book-keeping
-
+
for (i = 0; i < 3; i++) epsilon[i] += dtq * epsilon_dot[i];
-
+
// convert pertinent atoms and rigid bodies to lamda coords
-
+
if (allremap) domain->x2lamda(nlocal);
else {
for (i = 0; i < nlocal; i++)
if (mask[i] & dilate_group_bit)
domain->x2lamda(x[i],x[i]);
}
-
+
if (nrigidfix)
for (i = 0; i < nrigidfix; i++)
modify->fix[rfix[i]]->deform(0);
-
+
// reset global and local box to new size/shape
-
+
for (i = 0; i < 3; i++) {
if (p_flag[i]) {
oldlo = domain->boxlo[i];
@@ -1189,16 +1189,16 @@ void FixRigidNHSmall::remap()
domain->set_global_box();
domain->set_local_box();
-
+
// convert pertinent atoms and rigid bodies back to box coords
-
+
if (allremap) domain->lamda2x(nlocal);
else {
for (i = 0; i < nlocal; i++)
if (mask[i] & dilate_group_bit)
domain->lamda2x(x[i],x[i]);
}
-
+
if (nrigidfix)
for (i = 0; i< nrigidfix; i++)
modify->fix[rfix[i]]->deform(1);
@@ -1212,7 +1212,7 @@ void FixRigidNHSmall::compute_temp_target()
{
double delta = update->ntimestep - update->beginstep;
if (delta != 0.0) delta /= update->endstep - update->beginstep;
-
+
t_target = t_start + delta * (t_stop-t_start);
}
@@ -1224,7 +1224,7 @@ void FixRigidNHSmall::compute_press_target()
{
double delta = update->ntimestep - update->beginstep;
if (delta != 0.0) delta /= update->endstep - update->beginstep;
-
+
p_hydro = 0.0;
for (int i = 0; i < 3; i++)
if (p_flag[i]) {
@@ -1247,9 +1247,9 @@ void FixRigidNHSmall::nh_epsilon_dot()
else volume = domain->xprd*domain->yprd*domain->zprd;
// MTK terms
-
+
mtk_term1 = (akin_t + akin_r) * mvv2e / g_f;
-
+
scale = exp(-1.0 * dtq * eta_dot_b[0]);
for (i = 0; i < 3; i++)
@@ -1259,7 +1259,7 @@ void FixRigidNHSmall::nh_epsilon_dot()
epsilon_dot[i] += dtq * f_epsilon;
epsilon_dot[i] *= scale;
}
-
+
mtk_term2 = 0.0;
for (i = 0; i < 3; i++)
if (p_flag[i]) mtk_term2 += epsilon_dot[i];
@@ -1267,15 +1267,15 @@ void FixRigidNHSmall::nh_epsilon_dot()
}
/* ----------------------------------------------------------------------
- pack entire state of Fix into one write
+ pack entire state of Fix into one write
------------------------------------------------------------------------- */
void FixRigidNHSmall::write_restart(FILE *fp)
{
if (tstat_flag == 0 && pstat_flag == 0) return;
-
+
int nsize = 2; // tstat_flag and pstat_flag
-
+
if (tstat_flag) {
nsize += 1; // t_chain
nsize += 4*t_chain; // eta_t, eta_r, eta_dot_t, eta_dot_r
@@ -1285,12 +1285,12 @@ void FixRigidNHSmall::write_restart(FILE *fp)
nsize += 7; // p_chain, epsilon(3) and epsilon_dot(3)
nsize += 2*p_chain;
}
-
+
double *list;
memory->create(list,nsize,"rigid_nh:list");
-
+
int n = 0;
-
+
list[n++] = tstat_flag;
if (tstat_flag) {
list[n++] = t_chain;
@@ -1301,7 +1301,7 @@ void FixRigidNHSmall::write_restart(FILE *fp)
list[n++] = eta_dot_r[i];
}
}
-
+
list[n++] = pstat_flag;
if (pstat_flag) {
list[n++] = epsilon[0];
@@ -1310,25 +1310,25 @@ void FixRigidNHSmall::write_restart(FILE *fp)
list[n++] = epsilon_dot[0];
list[n++] = epsilon_dot[1];
list[n++] = epsilon_dot[2];
-
+
list[n++] = p_chain;
for (int i = 0; i < p_chain; i++) {
list[n++] = eta_b[i];
list[n++] = eta_dot_b[i];
}
}
-
+
if (comm->me == 0) {
int size = (nsize)*sizeof(double);
fwrite(&size,sizeof(int),1,fp);
fwrite(list,sizeof(double),nsize,fp);
}
-
+
memory->destroy(list);
}
/* ----------------------------------------------------------------------
- use state info from restart file to restart the Fix
+ use state info from restart file to restart the Fix
------------------------------------------------------------------------- */
void FixRigidNHSmall::restart(char *buf)
@@ -1336,7 +1336,7 @@ void FixRigidNHSmall::restart(char *buf)
int n = 0;
double *list = (double *) buf;
int flag = static_cast<int> (list[n++]);
-
+
if (flag) {
int m = static_cast<int> (list[n++]);
if (tstat_flag && m == t_chain) {
@@ -1357,7 +1357,7 @@ void FixRigidNHSmall::restart(char *buf)
epsilon_dot[0] = list[n++];
epsilon_dot[1] = list[n++];
epsilon_dot[2] = list[n++];
-
+
int m = static_cast<int> (list[n++]);
if (pstat_flag && m == p_chain) {
for (int i = 0; i < p_chain; i++) {
@@ -1444,7 +1444,7 @@ void FixRigidNHSmall::allocate_chain()
f_eta_t = new double[t_chain];
f_eta_r = new double[t_chain];
}
-
+
if (pstat_flag) {
q_b = new double[p_chain];
eta_b = new double[p_chain];
@@ -1484,7 +1484,7 @@ void FixRigidNHSmall::deallocate_chain()
delete [] f_eta_t;
delete [] f_eta_r;
}
-
+
if (pstat_flag) {
delete [] q_b;
delete [] eta_b;
diff --git a/src/RIGID/fix_rigid_nh_small.h b/src/RIGID/fix_rigid_nh_small.h
index aed112a632..f771b8c41b 100644
--- a/src/RIGID/fix_rigid_nh_small.h
+++ b/src/RIGID/fix_rigid_nh_small.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -32,11 +32,11 @@ class FixRigidNHSmall : public FixRigidSmall {
void write_restart(FILE *);
void restart(char *buf);
void reset_target(double);
-
+
protected:
double boltz,nktv2p,mvv2e; // boltzman constant, conversion factors
- int dimension; // # of dimensions
+ int dimension; // # of dimensions
int nf_t,nf_r; // trans/rot degrees of freedom
double onednft,onednfr; // factors 1 + dimension/trans(rot) degrees of freedom
double *w,*wdti1,*wdti2,*wdti4; // Yoshida-Suzuki coefficients
@@ -44,13 +44,13 @@ class FixRigidNHSmall : public FixRigidSmall {
double *eta_t,*eta_r; // trans/rot thermostat positions
double *eta_dot_t,*eta_dot_r; // trans/rot thermostat velocities
double *f_eta_t,*f_eta_r; // trans/rot thermostat forces
-
+
double epsilon_mass[3], *q_b; // baro/thermo masses
double epsilon[3],*eta_b; // baro/thermo positions
double epsilon_dot[3],*eta_dot_b; // baro/thermo velocities
double *f_eta_b; // thermo forces
double akin_t,akin_r; // translational/rotational kinetic energies
-
+
int kspace_flag; // 1 if KSpace invoked, 0 if not
int nrigidfix; // number of rigid fixes
int *rfix; // indicies of rigid fixes
@@ -60,18 +60,18 @@ class FixRigidNHSmall : public FixRigidSmall {
int pdim,g_f; // number of barostatted dims, total DoFs
double p_hydro; // hydrostatic target pressure
double p_freq_max; // maximum barostat frequency
-
+
double mtk_term1,mtk_term2; // Martyna-Tobias-Klein corrections
double t_target,t_current;
double t_freq;
-
+
char *id_temp,*id_press;
class Compute *temperature,*pressure;
int tcomputeflag,pcomputeflag;
void couple();
- void remap();
+ void remap();
void nhc_temp_integrate();
void nhc_press_integrate();
diff --git a/src/RIGID/fix_rigid_nph.cpp b/src/RIGID/fix_rigid_nph.cpp
index 663511553b..c0aa3b7040 100644
--- a/src/RIGID/fix_rigid_nph.cpp
+++ b/src/RIGID/fix_rigid_nph.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -17,7 +17,7 @@
Miller et al., J Chem Phys. 116, 8649-8659 (2002)
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "fix_rigid_nph.h"
#include "domain.h"
#include "modify.h"
@@ -29,14 +29,14 @@ using namespace LAMMPS_NS;
FixRigidNPH::FixRigidNPH(LAMMPS *lmp, int narg, char **arg) :
FixRigidNH(lmp, narg, arg)
-{
+{
// other setting are made by parent
scalar_flag = 1;
restart_global = 1;
box_change_size = 1;
extscalar = 1;
-
+
// error checks
if (pstat_flag == 0)
@@ -65,15 +65,15 @@ FixRigidNPH::FixRigidNPH(LAMMPS *lmp, int narg, char **arg) :
char **newarg = new char*[3];
newarg[0] = id_temp;
newarg[1] = (char *) "all";
- newarg[2] = (char *) "temp";
+ newarg[2] = (char *) "temp";
modify->add_compute(3,newarg);
delete [] newarg;
tcomputeflag = 1;
-
+
// create a new compute pressure style
// id = fix-ID + press, compute group = all
// pass id_temp as 4th arg to pressure constructor
-
+
n = strlen(id) + 7;
id_press = new char[n];
strcpy(id_press,id);
diff --git a/src/RIGID/fix_rigid_nph.h b/src/RIGID/fix_rigid_nph.h
index 58054c17a7..836c357d8f 100644
--- a/src/RIGID/fix_rigid_nph.h
+++ b/src/RIGID/fix_rigid_nph.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/RIGID/fix_rigid_nph_small.cpp b/src/RIGID/fix_rigid_nph_small.cpp
index f7eef13791..4e3e54766f 100644
--- a/src/RIGID/fix_rigid_nph_small.cpp
+++ b/src/RIGID/fix_rigid_nph_small.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -17,7 +17,7 @@
Miller et al., J Chem Phys. 116, 8649-8659 (2002)
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "fix_rigid_nph_small.h"
#include "domain.h"
#include "modify.h"
@@ -29,24 +29,24 @@ using namespace LAMMPS_NS;
FixRigidNPHSmall::FixRigidNPHSmall(LAMMPS *lmp, int narg, char **arg) :
FixRigidNHSmall(lmp, narg, arg)
-{
+{
// other setting are made by parent
scalar_flag = 1;
restart_global = 1;
box_change_size = 1;
extscalar = 1;
-
+
// error checks
if (pstat_flag == 0)
error->all(FLERR,"Pressure control must be used with fix nph/small");
if (tstat_flag == 1)
error->all(FLERR,"Temperature control must not be used with fix nph/small");
- if (p_start[0] < 0.0 || p_start[1] < 0.0 || p_start[2] < 0.0 ||
+ if (p_start[0] < 0.0 || p_start[1] < 0.0 || p_start[2] < 0.0 ||
p_stop[0] < 0.0 || p_stop[1] < 0.0 || p_stop[2] < 0.0)
error->all(FLERR,"Target pressure for fix rigid/nph cannot be < 0.0");
-
+
// convert input periods to frequency
p_freq[0] = p_freq[1] = p_freq[2] = 0.0;
@@ -68,15 +68,15 @@ FixRigidNPHSmall::FixRigidNPHSmall(LAMMPS *lmp, int narg, char **arg) :
char **newarg = new char*[3];
newarg[0] = id_temp;
newarg[1] = (char *) "all";
- newarg[2] = (char *) "temp";
+ newarg[2] = (char *) "temp";
modify->add_compute(3,newarg);
delete [] newarg;
tcomputeflag = 1;
-
+
// create a new compute pressure style
// id = fix-ID + press, compute group = all
// pass id_temp as 4th arg to pressure constructor
-
+
n = strlen(id) + 7;
id_press = new char[n];
strcpy(id_press,id);
diff --git a/src/RIGID/fix_rigid_nph_small.h b/src/RIGID/fix_rigid_nph_small.h
index 8dae871a82..073fbee5eb 100644
--- a/src/RIGID/fix_rigid_nph_small.h
+++ b/src/RIGID/fix_rigid_nph_small.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/RIGID/fix_rigid_npt.cpp b/src/RIGID/fix_rigid_npt.cpp
index 2e88ab34b0..24e12e41c2 100644
--- a/src/RIGID/fix_rigid_npt.cpp
+++ b/src/RIGID/fix_rigid_npt.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -17,7 +17,7 @@
Miller et al., J Chem Phys. 116, 8649-8659 (2002)
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "fix_rigid_npt.h"
#include "domain.h"
#include "modify.h"
@@ -29,14 +29,14 @@ using namespace LAMMPS_NS;
FixRigidNPT::FixRigidNPT(LAMMPS *lmp, int narg, char **arg) :
FixRigidNH(lmp, narg, arg)
-{
+{
// other setting are made by parent
scalar_flag = 1;
restart_global = 1;
box_change_size = 1;
extscalar = 1;
-
+
// error checks
if (tstat_flag == 0 || pstat_flag == 0)
@@ -49,7 +49,7 @@ FixRigidNPT::FixRigidNPT(LAMMPS *lmp, int narg, char **arg) :
if (t_chain < 1) error->all(FLERR,"Illegal fix rigid/npt command");
if (t_iter < 1) error->all(FLERR,"Illegal fix rigid/npt command");
- if (t_order != 3 && t_order != 5)
+ if (t_order != 3 && t_order != 5)
error->all(FLERR,"Fix rigid/npt temperature order must be 3 or 5");
// convert input periods to frequency
@@ -75,15 +75,15 @@ FixRigidNPT::FixRigidNPT(LAMMPS *lmp, int narg, char **arg) :
char **newarg = new char*[3];
newarg[0] = id_temp;
newarg[1] = (char *) "all";
- newarg[2] = (char *) "temp";
+ newarg[2] = (char *) "temp";
modify->add_compute(3,newarg);
delete [] newarg;
tcomputeflag = 1;
-
+
// create a new compute pressure style
// id = fix-ID + press, compute group = all
// pass id_temp as 4th arg to pressure constructor
-
+
n = strlen(id) + 7;
id_press = new char[n];
strcpy(id_press,id);
diff --git a/src/RIGID/fix_rigid_npt.h b/src/RIGID/fix_rigid_npt.h
index 73881dc193..09efecdae8 100644
--- a/src/RIGID/fix_rigid_npt.h
+++ b/src/RIGID/fix_rigid_npt.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/RIGID/fix_rigid_npt_small.cpp b/src/RIGID/fix_rigid_npt_small.cpp
index 472cccf85a..551ef50ca9 100644
--- a/src/RIGID/fix_rigid_npt_small.cpp
+++ b/src/RIGID/fix_rigid_npt_small.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -17,7 +17,7 @@
Miller et al., J Chem Phys. 116, 8649-8659 (2002)
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "fix_rigid_npt_small.h"
#include "domain.h"
#include "modify.h"
@@ -29,21 +29,21 @@ using namespace LAMMPS_NS;
FixRigidNPTSmall::FixRigidNPTSmall(LAMMPS *lmp, int narg, char **arg) :
FixRigidNHSmall(lmp, narg, arg)
-{
+{
// other setting are made by parent
scalar_flag = 1;
restart_global = 1;
box_change_size = 1;
extscalar = 1;
-
+
// error checks
if (tstat_flag == 0 || pstat_flag == 0)
error->all(FLERR,"Did not set temp or press for fix rigid/npt/small");
if (t_start <= 0.0 || t_stop <= 0.0)
error->all(FLERR,"Target temperature for fix rigid/npt/small cannot be 0.0");
- if (p_start[0] < 0.0 || p_start[1] < 0.0 || p_start[2] < 0.0 ||
+ if (p_start[0] < 0.0 || p_start[1] < 0.0 || p_start[2] < 0.0 ||
p_stop[0] < 0.0 || p_stop[1] < 0.0 || p_stop[2] < 0.0)
error->all(FLERR,"Target pressure for fix rigid/npt/small cannot be < 0.0");
@@ -53,7 +53,7 @@ FixRigidNPTSmall::FixRigidNPTSmall(LAMMPS *lmp, int narg, char **arg) :
if (t_chain < 1) error->all(FLERR,"Fix rigid npt/small t_chain should not be less than 1");
if (t_iter < 1) error->all(FLERR,"Fix rigid npt/small t_chain should not be less than 1");
- if (t_order != 3 && t_order != 5)
+ if (t_order != 3 && t_order != 5)
error->all(FLERR,"Fix rigid npt/small t_order must be 3 or 5");
// convert input periods to frequency
@@ -79,15 +79,15 @@ FixRigidNPTSmall::FixRigidNPTSmall(LAMMPS *lmp, int narg, char **arg) :
char **newarg = new char*[3];
newarg[0] = id_temp;
newarg[1] = (char *) "all";
- newarg[2] = (char *) "temp";
+ newarg[2] = (char *) "temp";
modify->add_compute(3,newarg);
delete [] newarg;
tcomputeflag = 1;
-
+
// create a new compute pressure style
// id = fix-ID + press, compute group = all
// pass id_temp as 4th arg to pressure constructor
-
+
n = strlen(id) + 7;
id_press = new char[n];
strcpy(id_press,id);
diff --git a/src/RIGID/fix_rigid_npt_small.h b/src/RIGID/fix_rigid_npt_small.h
index fd762e7dbb..82bac2780e 100644
--- a/src/RIGID/fix_rigid_npt_small.h
+++ b/src/RIGID/fix_rigid_npt_small.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/RIGID/fix_rigid_nve.cpp b/src/RIGID/fix_rigid_nve.cpp
index 6cde617e59..731940b648 100644
--- a/src/RIGID/fix_rigid_nve.cpp
+++ b/src/RIGID/fix_rigid_nve.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/RIGID/fix_rigid_nve.h b/src/RIGID/fix_rigid_nve.h
index 98e1e00574..22039eaf09 100644
--- a/src/RIGID/fix_rigid_nve.h
+++ b/src/RIGID/fix_rigid_nve.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/RIGID/fix_rigid_nve_small.cpp b/src/RIGID/fix_rigid_nve_small.cpp
index fdea05db09..25ec723464 100644
--- a/src/RIGID/fix_rigid_nve_small.cpp
+++ b/src/RIGID/fix_rigid_nve_small.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/RIGID/fix_rigid_nve_small.h b/src/RIGID/fix_rigid_nve_small.h
index db9485cbf5..f534a3efa8 100644
--- a/src/RIGID/fix_rigid_nve_small.h
+++ b/src/RIGID/fix_rigid_nve_small.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/RIGID/fix_rigid_nvt.cpp b/src/RIGID/fix_rigid_nvt.cpp
index 0f5593777c..f7723d03c8 100644
--- a/src/RIGID/fix_rigid_nvt.cpp
+++ b/src/RIGID/fix_rigid_nvt.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -26,13 +26,13 @@ using namespace LAMMPS_NS;
FixRigidNVT::FixRigidNVT(LAMMPS *lmp, int narg, char **arg) :
FixRigidNH(lmp, narg, arg)
-{
+{
// other settings are made by parent
scalar_flag = 1;
restart_global = 1;
extscalar = 1;
-
+
// error checking
// convert input period to frequency
@@ -45,6 +45,6 @@ FixRigidNVT::FixRigidNVT(LAMMPS *lmp, int narg, char **arg) :
if (t_chain < 1) error->all(FLERR,"Illegal fix rigid/nvt command");
if (t_iter < 1) error->all(FLERR,"Illegal fix rigid/nvt command");
- if (t_order != 3 && t_order != 5)
- error->all(FLERR,"Fix rigid/nvt temperature order must be 3 or 5");
+ if (t_order != 3 && t_order != 5)
+ error->all(FLERR,"Fix rigid/nvt temperature order must be 3 or 5");
}
diff --git a/src/RIGID/fix_rigid_nvt.h b/src/RIGID/fix_rigid_nvt.h
index 293b4abec3..11091125ae 100644
--- a/src/RIGID/fix_rigid_nvt.h
+++ b/src/RIGID/fix_rigid_nvt.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/RIGID/fix_rigid_nvt_small.cpp b/src/RIGID/fix_rigid_nvt_small.cpp
index f21f7168ac..42fd31537b 100644
--- a/src/RIGID/fix_rigid_nvt_small.cpp
+++ b/src/RIGID/fix_rigid_nvt_small.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -26,13 +26,13 @@ using namespace LAMMPS_NS;
FixRigidNVTSmall::FixRigidNVTSmall(LAMMPS *lmp, int narg, char **arg) :
FixRigidNHSmall(lmp, narg, arg)
-{
+{
// other settings are made by parent
scalar_flag = 1;
restart_global = 1;
extscalar = 1;
-
+
// error checking
// convert input period to frequency
@@ -45,6 +45,6 @@ FixRigidNVTSmall::FixRigidNVTSmall(LAMMPS *lmp, int narg, char **arg) :
if (t_chain < 1) error->all(FLERR,"Fix rigid nvt/small t_chain should not be less than 1");
if (t_iter < 1) error->all(FLERR,"Fix rigid nvt/small t_iter should not be less than 1");
- if (t_order != 3 && t_order != 5)
- error->all(FLERR,"Fix rigid nvt/small t_order must be 3 or 5");
+ if (t_order != 3 && t_order != 5)
+ error->all(FLERR,"Fix rigid nvt/small t_order must be 3 or 5");
}
diff --git a/src/RIGID/fix_rigid_nvt_small.h b/src/RIGID/fix_rigid_nvt_small.h
index 62d550ac28..5fd0ce290a 100644
--- a/src/RIGID/fix_rigid_nvt_small.h
+++ b/src/RIGID/fix_rigid_nvt_small.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp
index fb9c0b42e8..d1263ff0a7 100644
--- a/src/RIGID/fix_rigid_small.cpp
+++ b/src/RIGID/fix_rigid_small.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "fix_rigid_small.h"
#include "math_extra.h"
#include "atom.h"
@@ -101,7 +101,7 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
// parse args for rigid body specification
if (narg < 4) error->all(FLERR,"Illegal fix rigid/small command");
- if (strcmp(arg[3],"molecule") != 0)
+ if (strcmp(arg[3],"molecule") != 0)
error->all(FLERR,"Illegal fix rigid/small command");
if (atom->molecule_flag == 0)
@@ -188,7 +188,7 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"temp") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix rigid/small command");
- if (strcmp(style,"rigid/nvt/small") != 0 &&
+ if (strcmp(style,"rigid/nvt/small") != 0 &&
strcmp(style,"rigid/npt/small") != 0)
error->all(FLERR,"Illegal fix rigid command");
tstat_flag = 1;
@@ -199,13 +199,13 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"iso") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix rigid/small command");
- if (strcmp(style,"rigid/npt/small") != 0 &&
+ if (strcmp(style,"rigid/npt/small") != 0 &&
strcmp(style,"rigid/nph/small") != 0)
error->all(FLERR,"Illegal fix rigid/small command");
pcouple = XYZ;
p_start[0] = p_start[1] = p_start[2] = force->numeric(FLERR,arg[iarg+1]);
p_stop[0] = p_stop[1] = p_stop[2] = force->numeric(FLERR,arg[iarg+2]);
- p_period[0] = p_period[1] = p_period[2] =
+ p_period[0] = p_period[1] = p_period[2] =
force->numeric(FLERR,arg[iarg+3]);
p_flag[0] = p_flag[1] = p_flag[2] = 1;
if (domain->dimension == 2) {
@@ -216,12 +216,12 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"aniso") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix rigid/small command");
- if (strcmp(style,"rigid/npt/small") != 0 &&
+ if (strcmp(style,"rigid/npt/small") != 0 &&
strcmp(style,"rigid/nph/small") != 0)
error->all(FLERR,"Illegal fix rigid/small command");
p_start[0] = p_start[1] = p_start[2] = force->numeric(FLERR,arg[iarg+1]);
p_stop[0] = p_stop[1] = p_stop[2] = force->numeric(FLERR,arg[iarg+2]);
- p_period[0] = p_period[1] = p_period[2] =
+ p_period[0] = p_period[1] = p_period[2] =
force->numeric(FLERR,arg[iarg+3]);
p_flag[0] = p_flag[1] = p_flag[2] = 1;
if (domain->dimension == 2) {
@@ -265,7 +265,7 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
iarg += 2;
} else if (strcmp(arg[iarg],"dilate") == 0) {
- if (iarg+2 > narg)
+ if (iarg+2 > narg)
error->all(FLERR,"Illegal fix rigid/small nvt/npt/nph command");
if (strcmp(arg[iarg+1],"all") == 0) allremap = 1;
else {
@@ -283,7 +283,7 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"tparam") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix rigid/small command");
- if (strcmp(style,"rigid/nvt/small") != 0 &&
+ if (strcmp(style,"rigid/nvt/small") != 0 &&
strcmp(style,"rigid/npt/small") != 0)
error->all(FLERR,"Illegal fix rigid/small command");
t_chain = force->numeric(FLERR,arg[iarg+1]);
@@ -293,7 +293,7 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"pchain") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix rigid/small command");
- if (strcmp(style,"rigid/npt/small") != 0 &&
+ if (strcmp(style,"rigid/npt/small") != 0 &&
strcmp(style,"rigid/nph/small") != 0)
error->all(FLERR,"Illegal fix rigid/small command");
p_chain = force->numeric(FLERR,arg[iarg+1]);
@@ -313,7 +313,7 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,"Fix rigid/small molecule must have atom types");
// fix rigid/small uses center, masstotal, COM, inertia of molecule
-
+
onemols[i]->compute_center();
onemols[i]->compute_mass();
onemols[i]->compute_com();
@@ -324,7 +324,7 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
// set pstat_flag
pstat_flag = 0;
- for (int i = 0; i < 3; i++)
+ for (int i = 0; i < 3; i++)
if (p_flag[i]) pstat_flag = 1;
if (pcouple == XYZ || (domain->dimension == 2 && pcouple == XY)) pstyle = ISO;
@@ -445,7 +445,7 @@ FixRigidSmall::~FixRigidSmall()
// delete locally stored arrays
memory->sfree(body);
-
+
memory->destroy(bodyown);
memory->destroy(bodytag);
memory->destroy(atom2body);
@@ -736,7 +736,7 @@ void FixRigidSmall::post_force(int vflag)
langextra[ibody][0] = gamma1*vcm[0] + gamma2*(random->uniform()-0.5);
langextra[ibody][1] = gamma1*vcm[1] + gamma2*(random->uniform()-0.5);
langextra[ibody][2] = gamma1*vcm[2] + gamma2*(random->uniform()-0.5);
-
+
gamma1 = -1.0 / t_period / ftm2v;
gamma2 = tsqrt * sqrt(24.0*boltz/t_period/dt/mvv2e) / ftm2v;
langextra[ibody][3] = inertia[0]*gamma1*omega[0] +
@@ -833,7 +833,7 @@ void FixRigidSmall::final_integrate()
}
// update vcm and angmom, recompute omega
-
+
for (int ibody = 0; ibody < nlocal_body; ibody++) {
Body *b = &body[ibody];
@@ -900,10 +900,10 @@ void FixRigidSmall::final_integrate_respa(int ilevel, int iloop)
(2) change in imagebody due to xcm remap
xcmimage flags are always -1,0,-1 so that body can be unwrapped
around in-box xcm and stay close to simulation box
- if just inferred unwrapped from atom image flags,
+ if just inferred unwrapped from atom image flags,
then a body could end up very far away
when unwrapped by true image flags
- then set_xv() will compute huge displacements every step to reset coords of
+ then set_xv() will compute huge displacements every step to reset coords of
all the body atoms to be back inside the box, ditto for triclinic box flip
note: so just want to avoid that numeric probem?
------------------------------------------------------------------------- */
@@ -913,7 +913,7 @@ void FixRigidSmall::pre_neighbor()
for (int ibody = 0; ibody < nlocal_body; ibody++) {
Body *b = &body[ibody];
domain->remap(b->xcm,b->image);
- }
+ }
nghost_body = 0;
commflag = FULL_BODY;
@@ -967,7 +967,7 @@ int FixRigidSmall::dof(int tgroup)
// cannot count DOF correctly unless setup_bodies_static() has been called
if (!setupflag) {
- if (comm->me == 0)
+ if (comm->me == 0)
error->warning(FLERR,"Cannot count rigid body degrees-of-freedom "
"before bodies are fully initialized");
return 0;
@@ -1472,10 +1472,10 @@ void FixRigidSmall::create_bodies()
flag = 0;
for (i = 0; i < n; i++)
- if (bbox[i][0] == bbox[i][1] && bbox[i][2] == bbox[i][3] &&
+ if (bbox[i][0] == bbox[i][1] && bbox[i][2] == bbox[i][3] &&
bbox[i][4] == bbox[i][5]) flag = 1;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
- if (flagall)
+ if (flagall)
error->all(FLERR,"One or more rigid bodies are a single particle");
// ctr = center pt of each rigid body my atoms are part of
@@ -1855,7 +1855,7 @@ void FixRigidSmall::setup_bodies_static()
// set rigid body image flags to default values
for (ibody = 0; ibody < nlocal_body; ibody++)
- body[ibody].image = ((imageint) IMGMAX << IMG2BITS) |
+ body[ibody].image = ((imageint) IMGMAX << IMG2BITS) |
((imageint) IMGMAX << IMGBITS) | IMGMAX;
// overwrite masstotal, center-of-mass, image flags with file values
@@ -2330,7 +2330,7 @@ void FixRigidSmall::readfile(int which, double **array, int *inbody)
FILE *fp;
char *eof,*start,*next,*buf;
char line[MAXLINE];
-
+
// create local hash with key/value pairs
// key = mol ID of bodies my atoms own
// value = index into local body array
@@ -2353,7 +2353,7 @@ void FixRigidSmall::readfile(int which, double **array, int *inbody)
while (1) {
eof = fgets(line,MAXLINE,fp);
- if (eof == NULL)
+ if (eof == NULL)
error->one(FLERR,"Unexpected end of fix rigid/small file");
start = &line[strspn(line," \t\n\v\f\r")];
if (*start != '\0' && *start != '#') break;
@@ -2381,7 +2381,7 @@ void FixRigidSmall::readfile(int which, double **array, int *inbody)
if (nwords != ATTRIBUTE_PERBODY)
error->all(FLERR,"Incorrect rigid body format in fix rigid/small file");
-
+
// loop over lines of rigid body attributes
// tokenize the line into values
// id = rigid body ID = mol-ID
@@ -2390,13 +2390,13 @@ void FixRigidSmall::readfile(int which, double **array, int *inbody)
for (int i = 0; i < nchunk; i++) {
next = strchr(buf,'\n');
-
+
values[0] = strtok(buf," \t\n\r\f");
for (j = 1; j < nwords; j++)
values[j] = strtok(NULL," \t\n\r\f");
id = ATOTAGINT(values[0]);
- if (id <= 0 || id > maxmol)
+ if (id <= 0 || id > maxmol)
error->all(FLERR,"Invalid rigid body ID in fix rigid/small file");
if (hash->find(id) == hash->end()) {
buf = next + 1;
@@ -2419,8 +2419,8 @@ void FixRigidSmall::readfile(int which, double **array, int *inbody)
xbox = atoi(values[17]);
ybox = atoi(values[18]);
zbox = atoi(values[19]);
- body[m].image = ((imageint) (xbox + IMGMAX) & IMGMASK) |
- (((imageint) (ybox + IMGMAX) & IMGMASK) << IMGBITS) |
+ body[m].image = ((imageint) (xbox + IMGMAX) & IMGMASK) |
+ (((imageint) (ybox + IMGMAX) & IMGMASK) << IMGBITS) |
(((imageint) (zbox + IMGMAX) & IMGMASK) << IMG2BITS);
} else {
array[m][0] = atof(values[5]);
@@ -2433,7 +2433,7 @@ void FixRigidSmall::readfile(int which, double **array, int *inbody)
buf = next + 1;
}
-
+
nread += nchunk;
}
@@ -2555,7 +2555,7 @@ void FixRigidSmall::write_restart_file(char *file)
static_cast<int> (buf[i][18]),
static_cast<int> (buf[i][19]));
}
-
+
} else {
MPI_Recv(&tmp,0,MPI_INT,0,0,world,MPI_STATUS_IGNORE);
MPI_Rsend(&buf[0][0],sendrow*ncol,MPI_DOUBLE,0,0,world);
@@ -3212,11 +3212,11 @@ void FixRigidSmall::reset_atom2body()
if (iowner == -1) {
char str[128];
sprintf(str,
- "Rigid body atoms " TAGINT_FORMAT " " TAGINT_FORMAT
+ "Rigid body atoms " TAGINT_FORMAT " " TAGINT_FORMAT
" missing on proc %d at step " BIGINT_FORMAT,
atom->tag[i],bodytag[i],comm->me,update->ntimestep);
error->one(FLERR,str);
-
+
}
atom2body[i] = bodyown[iowner];
}
@@ -3353,7 +3353,7 @@ double FixRigidSmall::extract_erotational()
double erotate = 0.0;
for (int i = 0; i < nlocal_body; i++) {
- // for Iw^2 rotational term, need wbody = angular velocity in body frame
+ // for Iw^2 rotational term, need wbody = angular velocity in body frame
// not omega = angular velocity in space frame
inertia = body[i].inertia;
@@ -3393,7 +3393,7 @@ double FixRigidSmall::compute_scalar()
vcm = body[i].vcm;
t += body[i].mass * (vcm[0]*vcm[0] + vcm[1]*vcm[1] + vcm[2]*vcm[2]);
- // for Iw^2 rotational term, need wbody = angular velocity in body frame
+ // for Iw^2 rotational term, need wbody = angular velocity in body frame
// not omega = angular velocity in space frame
inertia = body[i].inertia;
@@ -3481,7 +3481,7 @@ void FixRigidSmall::check(int flag)
for (int i = atom->nlocal; i < atom->nlocal + atom->nghost; i++) {
if (bodyown[i] >= 0) {
- if (bodyown[i] < nlocal_body ||
+ if (bodyown[i] < nlocal_body ||
bodyown[i] >= nlocal_body+nghost_body) {
printf("Values %d %d: %d %d %d\n",
i,atom->tag[i],bodyown[i],nlocal_body,nghost_body);
@@ -3500,7 +3500,7 @@ void FixRigidSmall::check(int flag)
printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag);
errorx->one(FLERR,"BAD III");
}
- if (bodytag[body[i].ilocal] != atom->tag[body[i].ilocal] ||
+ if (bodytag[body[i].ilocal] != atom->tag[body[i].ilocal] ||
bodyown[body[i].ilocal] != i) {
printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag);
errorx->one(FLERR,"BAD JJJ");
@@ -3508,7 +3508,7 @@ void FixRigidSmall::check(int flag)
}
for (int i = nlocal_body; i < nlocal_body + nghost_body; i++) {
- if (body[i].ilocal < atom->nlocal ||
+ if (body[i].ilocal < atom->nlocal ||
body[i].ilocal >= atom->nlocal + atom->nghost) {
printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag);
errorx->one(FLERR,"BAD KKK");
diff --git a/src/RIGID/fix_rigid_small.h b/src/RIGID/fix_rigid_small.h
index 5d6c2fe363..96c8f4e4dc 100644
--- a/src/RIGID/fix_rigid_small.h
+++ b/src/RIGID/fix_rigid_small.h
@@ -155,12 +155,12 @@ class FixRigidSmall : public Fix {
class RanMars *random; // RNG
int tstat_flag,pstat_flag; // 0/1 = no/yes thermostat/barostat
-
+
int t_chain,t_iter,t_order;
double p_start[3],p_stop[3];
double p_period[3],p_freq[3];
- int p_flag[3];
+ int p_flag[3];
int pcouple,pstyle;
int p_chain;
diff --git a/src/RIGID/fix_shake.cpp b/src/RIGID/fix_shake.cpp
index d82445560a..18811eee6a 100644
--- a/src/RIGID/fix_shake.cpp
+++ b/src/RIGID/fix_shake.cpp
@@ -11,11 +11,11 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
-#include "stdio.h"
+#include <mpi.h>
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
+#include <stdio.h>
#include "fix_shake.h"
#include "atom.h"
#include "atom_vec.h"
@@ -355,7 +355,7 @@ void FixShake::init()
// set equilibrium angle distances
int nlocal = atom->nlocal;
-
+
for (i = 1; i <= atom->nangletypes; i++) {
if (angle_flag[i] == 0) continue;
if (force->angle == NULL)
@@ -436,7 +436,7 @@ void FixShake::setup(int vflag)
// half timestep constraint on pre-step, full timestep thereafter
if (strstr(update->integrate_style,"verlet")) {
- respa = 0;
+ respa = 0;
dtv = update->dt;
dtfsq = 0.5 * update->dt * update->dt * force->ftm2v;
FixShake::post_force(vflag);
@@ -444,7 +444,7 @@ void FixShake::setup(int vflag)
} else {
respa = 1;
- dtv = step_respa[0];
+ dtv = step_respa[0];
dtf_innerhalf = 0.5 * step_respa[0] * force->ftm2v;
dtf_inner = dtf_innerhalf;
@@ -499,7 +499,7 @@ void FixShake::pre_neighbor()
atom2 = atom->map(shake_atom[i][1]);
if (atom1 == -1 || atom2 == -1) {
char str[128];
- sprintf(str,"Shake atoms " TAGINT_FORMAT " " TAGINT_FORMAT
+ sprintf(str,"Shake atoms " TAGINT_FORMAT " " TAGINT_FORMAT
" missing on proc %d at step " BIGINT_FORMAT,
shake_atom[i][0],shake_atom[i][1],me,update->ntimestep);
error->one(FLERR,str);
@@ -511,7 +511,7 @@ void FixShake::pre_neighbor()
atom3 = atom->map(shake_atom[i][2]);
if (atom1 == -1 || atom2 == -1 || atom3 == -1) {
char str[128];
- sprintf(str,"Shake atoms "
+ sprintf(str,"Shake atoms "
TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT
" missing on proc %d at step " BIGINT_FORMAT,
shake_atom[i][0],shake_atom[i][1],shake_atom[i][2],
@@ -526,8 +526,8 @@ void FixShake::pre_neighbor()
atom4 = atom->map(shake_atom[i][3]);
if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) {
char str[128];
- sprintf(str,"Shake atoms "
- TAGINT_FORMAT " " TAGINT_FORMAT " "
+ sprintf(str,"Shake atoms "
+ TAGINT_FORMAT " " TAGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT
" missing on proc %d at step " BIGINT_FORMAT,
shake_atom[i][0],shake_atom[i][1],
@@ -570,7 +570,7 @@ void FixShake::post_force(int vflag)
else if (shake_flag[m] == 4) shake4(m);
else shake3angle(m);
}
-
+
// store vflag for coordinate_constraints_end_of_step()
vflag_post_force = vflag;
@@ -670,7 +670,7 @@ void FixShake::find_clusters()
tagint tagprev;
double massone;
tagint *buf;
-
+
if (me == 0 && screen) {
if (!rattle) fprintf(screen,"Finding SHAKE clusters ...\n");
else fprintf(screen,"Finding RATTLE clusters ...\n");
@@ -685,7 +685,7 @@ void FixShake::find_clusters()
double *rmass = atom->rmass;
int **nspecial = atom->nspecial;
tagint **special = atom->special;
-
+
int *molindex = atom->molindex;
int *molatom = atom->molatom;
@@ -956,7 +956,7 @@ void FixShake::find_clusters()
comm->ring(size,sizeof(tagint),buf,2,ring_nshake,buf);
// store partner info returned to me
-
+
m = 0;
while (m < size) {
i = atom->map(buf[m]);
@@ -2289,7 +2289,7 @@ int FixShake::bondtype_findset(int i, tagint n1, tagint n2, int setflag)
tagint *batom = atommols[imol]->bond_atom[iatom];
btype = atommols[imol]->bond_type[iatom];
nbonds = atommols[imol]->num_bond[iatom];
-
+
for (m = 0; m < nbonds; m++) {
if (n1 == tag[i] && n2 == batom[m]+tagprev) break;
if (n1 == batom[m]+tagprev && n2 == tag[i]) break;
@@ -2346,7 +2346,7 @@ int FixShake::angletype_findset(int i, tagint n1, tagint n2, int setflag)
tagint *aatom3 = atommols[imol]->angle_atom3[iatom];
atype = atommols[imol]->angle_type[iatom];
nangles = atommols[imol]->num_angle[iatom];
-
+
for (m = 0; m < nangles; m++) {
if (n1 == aatom1[m]+tagprev && n2 == aatom3[m]+tagprev) break;
if (n1 == aatom3[m]+tagprev && n2 == aatom1[m]+tagprev) break;
@@ -2456,7 +2456,7 @@ void FixShake::update_arrays(int i, int atom_offset)
shake_atom[i][0] += atom_offset;
shake_atom[i][1] += atom_offset;
shake_atom[i][2] += atom_offset;
- } else if (flag == 2) {
+ } else if (flag == 2) {
shake_atom[i][0] += atom_offset;
shake_atom[i][1] += atom_offset;
} else if (flag == 3) {
@@ -2602,7 +2602,7 @@ int FixShake::unpack_exchange(int nlocal, double *buf)
/* ---------------------------------------------------------------------- */
-int FixShake::pack_forward_comm(int n, int *list, double *buf,
+int FixShake::pack_forward_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
@@ -2691,7 +2691,7 @@ void FixShake::coordinate_constraints_end_of_step() {
dtfsq = 0.5 * update->dt * update->dt * force->ftm2v;
FixShake::post_force(vflag_post_force);
if (!rattle) dtfsq = update->dt * update->dt * force->ftm2v;
- }
+ }
else {
dtf_innerhalf = 0.5 * step_respa[0] * force->ftm2v;
dtf_inner = dtf_innerhalf;
diff --git a/src/RIGID/fix_shake.h b/src/RIGID/fix_shake.h
index 049971ca4c..564d2fa96e 100644
--- a/src/RIGID/fix_shake.h
+++ b/src/RIGID/fix_shake.h
@@ -61,7 +61,7 @@ class FixShake : public Fix {
int max_iter; // max # of SHAKE iterations
int output_every; // SHAKE stat output every so often
bigint next_output; // timestep for next output
-
+
// settings from input command
int *bond_flag,*angle_flag; // bond/angle types to constrain
int *type_flag; // constrain bonds to these types
diff --git a/src/SHOCK/fix_append_atoms.cpp b/src/SHOCK/fix_append_atoms.cpp
index 310fc82633..e14d88aad9 100644
--- a/src/SHOCK/fix_append_atoms.cpp
+++ b/src/SHOCK/fix_append_atoms.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "string.h"
-#include "stdlib.h"
+#include <math.h>
+#include <string.h>
+#include <stdlib.h>
#include "fix_append_atoms.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/SHOCK/fix_msst.cpp b/src/SHOCK/fix_msst.cpp
index c6d4978513..42b8358602 100644
--- a/src/SHOCK/fix_msst.cpp
+++ b/src/SHOCK/fix_msst.cpp
@@ -17,9 +17,9 @@
See Reed, Fried, Joannopoulos, Phys Rev Lett, 90, 235503 (2003)
------------------------------------------------------------------------- */
-#include "string.h"
-#include "stdlib.h"
-#include "math.h"
+#include <string.h>
+#include <stdlib.h>
+#include <math.h>
#include "fix_msst.h"
#include "atom.h"
#include "force.h"
diff --git a/src/SHOCK/fix_nphug.cpp b/src/SHOCK/fix_nphug.cpp
index 78079dbb64..36500100cd 100644
--- a/src/SHOCK/fix_nphug.cpp
+++ b/src/SHOCK/fix_nphug.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
-#include "stdlib.h"
+#include <string.h>
+#include <stdlib.h>
#include "fix_nphug.h"
#include "modify.h"
#include "error.h"
@@ -21,10 +21,10 @@
#include "force.h"
#include "domain.h"
#include "group.h"
-#include "math.h"
+#include <math.h>
#include "memory.h"
#include "comm.h"
-#include "math.h"
+#include <math.h>
using namespace LAMMPS_NS;
using namespace FixConst;
diff --git a/src/SHOCK/fix_wall_piston.cpp b/src/SHOCK/fix_wall_piston.cpp
index 9217a24f6f..443b2670cb 100644
--- a/src/SHOCK/fix_wall_piston.cpp
+++ b/src/SHOCK/fix_wall_piston.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "string.h"
-#include "stdlib.h"
+#include <math.h>
+#include <string.h>
+#include <stdlib.h>
#include "fix_wall_piston.h"
#include "atom.h"
#include "modify.h"
diff --git a/src/SNAP/compute_sna_atom.cpp b/src/SNAP/compute_sna_atom.cpp
index 128eca00a9..1f7c943719 100644
--- a/src/SNAP/compute_sna_atom.cpp
+++ b/src/SNAP/compute_sna_atom.cpp
@@ -5,14 +5,14 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "sna.h"
-#include "string.h"
-#include "stdlib.h"
+#include <string.h>
+#include <stdlib.h>
#include "compute_sna_atom.h"
#include "atom.h"
#include "update.h"
@@ -39,7 +39,7 @@ ComputeSNAAtom::ComputeSNAAtom(LAMMPS *lmp, int narg, char **arg) :
int ntypes = atom->ntypes;
int nargmin = 6+2*ntypes;
-
+
if (narg < nargmin) error->all(FLERR,"Illegal compute sna/atom command");
// default values
@@ -50,7 +50,7 @@ ComputeSNAAtom::ComputeSNAAtom(LAMMPS *lmp, int narg, char **arg) :
// offset by 1 to match up with types
- memory->create(radelem,ntypes+1,"sna/atom:radelem");
+ memory->create(radelem,ntypes+1,"sna/atom:radelem");
memory->create(wjelem,ntypes+1,"sna/atom:wjelem");
rcutfac = atof(arg[3]);
@@ -83,19 +83,19 @@ ComputeSNAAtom::ComputeSNAAtom(LAMMPS *lmp, int narg, char **arg) :
while (iarg < narg) {
if (strcmp(arg[iarg],"diagonal") == 0) {
- if (iarg+2 > narg)
+ if (iarg+2 > narg)
error->all(FLERR,"Illegal compute sna/atom command");
diagonalstyle = atoi(arg[iarg+1]);
if (diagonalstyle < 0 || diagonalstyle > 3)
error->all(FLERR,"Illegal compute sna/atom command");
iarg += 2;
} else if (strcmp(arg[iarg],"rmin0") == 0) {
- if (iarg+2 > narg)
+ if (iarg+2 > narg)
error->all(FLERR,"Illegal compute sna/atom command");
rmin0 = atof(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"switchflag") == 0) {
- if (iarg+2 > narg)
+ if (iarg+2 > narg)
error->all(FLERR,"Illegal compute sna/atom command");
switchflag = atoi(arg[iarg+1]);
iarg += 2;
@@ -121,7 +121,7 @@ ComputeSNAAtom::ComputeSNAAtom(LAMMPS *lmp, int narg, char **arg) :
nmax = 0;
njmax = 0;
sna = NULL;
-
+
}
/* ---------------------------------------------------------------------- */
@@ -139,10 +139,10 @@ ComputeSNAAtom::~ComputeSNAAtom()
void ComputeSNAAtom::init()
{
- if (force->pair == NULL)
+ if (force->pair == NULL)
error->all(FLERR,"Compute sna/atom requires a pair style be defined");
- if (cutmax > force->pair->cutforce)
+ if (cutmax > force->pair->cutforce)
error->all(FLERR,"Compute sna/atom cutoff is longer than pairwise cutoff");
// need an occasional full neighbor list
@@ -223,7 +223,7 @@ void ComputeSNAAtom::compute_peratom()
const int jnum = numneigh[i];
// insure rij, inside, and typej are of size jnum
-
+
snaptr[tid]->grow_rij(jnum);
// rij[][3] = displacements between atom I and those neighbors
@@ -234,7 +234,7 @@ void ComputeSNAAtom::compute_peratom()
for (int jj = 0; jj < jnum; jj++) {
int j = jlist[jj];
j &= NEIGHMASK;
-
+
const double delx = xtmp - x[j][0];
const double dely = ytmp - x[j][1];
const double delz = ztmp - x[j][2];
@@ -265,7 +265,7 @@ void ComputeSNAAtom::compute_peratom()
}
/* ----------------------------------------------------------------------
- memory usage
+ memory usage
------------------------------------------------------------------------- */
double ComputeSNAAtom::memory_usage()
diff --git a/src/SNAP/compute_sna_atom.h b/src/SNAP/compute_sna_atom.h
index ff5471d03d..af62d7cf3b 100644
--- a/src/SNAP/compute_sna_atom.h
+++ b/src/SNAP/compute_sna_atom.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -21,7 +21,7 @@ ComputeStyle(sna/atom,ComputeSNAAtom)
#define LMP_COMPUTE_SNA_ATOM_H
#include "compute.h"
-
+
namespace LAMMPS_NS {
class ComputeSNAAtom : public Compute {
diff --git a/src/SNAP/compute_snad_atom.cpp b/src/SNAP/compute_snad_atom.cpp
index 5b5d4728ed..8767ca1745 100644
--- a/src/SNAP/compute_snad_atom.cpp
+++ b/src/SNAP/compute_snad_atom.cpp
@@ -5,14 +5,14 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "sna.h"
-#include "string.h"
-#include "stdlib.h"
+#include <string.h>
+#include <stdlib.h>
#include "compute_snad_atom.h"
#include "atom.h"
#include "update.h"
@@ -69,14 +69,14 @@ ComputeSNADAtom::ComputeSNADAtom(LAMMPS *lmp, int narg, char **arg) :
cutsq[i][j] = cutsq[j][i] = cut*cut;
}
}
-
+
// process optional args
int iarg = nargmin;
while (iarg < narg) {
if (strcmp(arg[iarg],"diagonal") == 0) {
- if (iarg+2 > narg)
+ if (iarg+2 > narg)
error->all(FLERR,"Illegal compute snad/atom command");
diagonalstyle = atof(arg[iarg+1]);
if (diagonalstyle < 0 || diagonalstyle > 3)
@@ -88,7 +88,7 @@ ComputeSNADAtom::ComputeSNADAtom(LAMMPS *lmp, int narg, char **arg) :
rmin0 = atof(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"switchflag") == 0) {
- if (iarg+2 > narg)
+ if (iarg+2 > narg)
error->all(FLERR,"Illegal compute snad/atom command");
switchflag = atoi(arg[iarg+1]);
iarg += 2;
@@ -132,11 +132,11 @@ ComputeSNADAtom::~ComputeSNADAtom()
void ComputeSNADAtom::init()
{
- if (force->pair == NULL)
+ if (force->pair == NULL)
error->all(FLERR,"Compute snad/atom requires a pair style be defined");
// TODO: Not sure what to do with this error check since cutoff radius is not
// a single number
- //if (sqrt(cutsq) > force->pair->cutforce)
+ //if (sqrt(cutsq) > force->pair->cutforce)
//error->all(FLERR,"Compute snad/atom cutoff is longer than pairwise cutoff");
// need an occasional full neighbor list
@@ -241,12 +241,12 @@ void ComputeSNADAtom::compute_peratom()
for (int jj = 0; jj < jnum; jj++) {
int j = jlist[jj];
j &= NEIGHMASK;
-
+
const double delx = x[j][0] - xtmp;
const double dely = x[j][1] - ytmp;
const double delz = x[j][2] - ztmp;
const double rsq = delx*delx + dely*dely + delz*delz;
- int jtype = type[j];
+ int jtype = type[j];
if (rsq < cutsq[itype][jtype]&&rsq>1e-20) {
snaptr[tid]->rij[ninside][0] = delx;
snaptr[tid]->rij[ninside][1] = dely;
@@ -300,7 +300,7 @@ int ComputeSNADAtom::pack_reverse_comm(int n, int first, double *buf)
m = 0;
last = first + n;
- for (i = first; i < last; i++)
+ for (i = first; i < last; i++)
for (icoeff = 0; icoeff < size_peratom_cols; icoeff++)
buf[m++] = snad[i][icoeff];
return comm_reverse;
@@ -321,7 +321,7 @@ void ComputeSNADAtom::unpack_reverse_comm(int n, int *list, double *buf)
}
/* ----------------------------------------------------------------------
- memory usage
+ memory usage
------------------------------------------------------------------------- */
double ComputeSNADAtom::memory_usage()
diff --git a/src/SNAP/compute_snad_atom.h b/src/SNAP/compute_snad_atom.h
index 6dbd310e44..31f5bf252d 100644
--- a/src/SNAP/compute_snad_atom.h
+++ b/src/SNAP/compute_snad_atom.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -21,7 +21,7 @@ ComputeStyle(snad/atom,ComputeSNADAtom)
#define LMP_COMPUTE_SNAD_ATOM_H
#include "compute.h"
-
+
namespace LAMMPS_NS {
class ComputeSNADAtom : public Compute {
diff --git a/src/SNAP/compute_snav_atom.cpp b/src/SNAP/compute_snav_atom.cpp
index 6394321eb4..cbe53821b8 100644
--- a/src/SNAP/compute_snav_atom.cpp
+++ b/src/SNAP/compute_snav_atom.cpp
@@ -5,14 +5,14 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "sna.h"
-#include "string.h"
-#include "stdlib.h"
+#include <string.h>
+#include <stdlib.h>
#include "compute_snav_atom.h"
#include "atom.h"
#include "update.h"
@@ -78,19 +78,19 @@ ComputeSNAVAtom::ComputeSNAVAtom(LAMMPS *lmp, int narg, char **arg) :
while (iarg < narg) {
if (strcmp(arg[iarg],"diagonal") == 0) {
- if (iarg+2 > narg)
+ if (iarg+2 > narg)
error->all(FLERR,"Illegal compute snav/atom command");
diagonalstyle = atof(arg[iarg+1]);
if (diagonalstyle < 0 || diagonalstyle > 3)
error->all(FLERR,"Illegal compute snav/atom command");
iarg += 2;
} else if (strcmp(arg[iarg],"rmin0") == 0) {
- if (iarg+2 > narg)
+ if (iarg+2 > narg)
error->all(FLERR,"Illegal compute snav/atom command");
rmin0 = atof(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"switchflag") == 0) {
- if (iarg+2 > narg)
+ if (iarg+2 > narg)
error->all(FLERR,"Illegal compute snav/atom command");
switchflag = atoi(arg[iarg+1]);
iarg += 2;
@@ -135,11 +135,11 @@ delete [] snaptr;
void ComputeSNAVAtom::init()
{
- if (force->pair == NULL)
+ if (force->pair == NULL)
error->all(FLERR,"Compute snav/atom requires a pair style be defined");
// TODO: Not sure what to do with this error check since cutoff radius is not
// a single number
- //if (sqrt(cutsq) > force->pair->cutforce)
+ //if (sqrt(cutsq) > force->pair->cutforce)
// error->all(FLERR,"Compute snav/atom cutoff is longer than pairwise cutoff");
// need an occasional full neighbor list
@@ -244,7 +244,7 @@ void ComputeSNAVAtom::compute_peratom()
for (int jj = 0; jj < jnum; jj++) {
int j = jlist[jj];
j &= NEIGHMASK;
-
+
const double delx = x[j][0] - xtmp;
const double dely = x[j][1] - ytmp;
const double delz = x[j][2] - ztmp;
@@ -277,7 +277,7 @@ void ComputeSNAVAtom::compute_peratom()
double *snavi = snav[i]+typeoffset;
double *snavj = snav[j]+typeoffset;
-
+
for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
snavi[icoeff] += snaptr[tid]->dbvec[icoeff][0]*xtmp;
snavi[icoeff+ncoeff] += snaptr[tid]->dbvec[icoeff][1]*ytmp;
@@ -310,7 +310,7 @@ int ComputeSNAVAtom::pack_reverse_comm(int n, int first, double *buf)
m = 0;
last = first + n;
- for (i = first; i < last; i++)
+ for (i = first; i < last; i++)
for (icoeff = 0; icoeff < size_peratom_cols; icoeff++)
buf[m++] = snav[i][icoeff];
return comm_reverse;
@@ -331,7 +331,7 @@ void ComputeSNAVAtom::unpack_reverse_comm(int n, int *list, double *buf)
}
/* ----------------------------------------------------------------------
- memory usage
+ memory usage
------------------------------------------------------------------------- */
double ComputeSNAVAtom::memory_usage()
diff --git a/src/SNAP/compute_snav_atom.h b/src/SNAP/compute_snav_atom.h
index 0c4d1cf788..0252be7059 100644
--- a/src/SNAP/compute_snav_atom.h
+++ b/src/SNAP/compute_snav_atom.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -21,7 +21,7 @@ ComputeStyle(snav/atom,ComputeSNAVAtom)
#define LMP_COMPUTE_SNAV_ATOM_H
#include "compute.h"
-
+
namespace LAMMPS_NS {
class ComputeSNAVAtom : public Compute {
diff --git a/src/SNAP/pair_snap.cpp b/src/SNAP/pair_snap.cpp
index 39962b210f..d3f132bd04 100644
--- a/src/SNAP/pair_snap.cpp
+++ b/src/SNAP/pair_snap.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_snap.h"
#include "atom.h"
#include "atom_vec.h"
@@ -104,7 +104,7 @@ PairSNAP::PairSNAP(LAMMPS *lmp) : Pair(lmp)
PairSNAP::~PairSNAP()
{
if (nelements) {
- for (int i = 0; i < nelements; i++)
+ for (int i = 0; i < nelements; i++)
delete[] elements[i];
delete[] elements;
memory->destroy(radelem);
@@ -121,7 +121,7 @@ PairSNAP::~PairSNAP()
double timeave[5];
double timeave_mpi[5];
double timemax_mpi[5];
-
+
for (int i = 0; i < 5; i++) {
time[i] = 0;
timeave[i] = 0;
@@ -135,7 +135,7 @@ PairSNAP::~PairSNAP()
MPI_Reduce(timeave, timeave_mpi, 5, MPI_DOUBLE, MPI_SUM, 0, world);
MPI_Reduce(time, timemax_mpi, 5, MPI_DOUBLE, MPI_MAX, 0, world);
#endif
-
+
for (int tid = 0; tid<nthreads; tid++)
delete sna[tid];
delete [] sna;
@@ -197,7 +197,7 @@ void PairSNAP::compute_regular(int eflag, int vflag)
jnum = numneigh[i];
// insure rij, inside, wj, and rcutij are of size jnum
-
+
snaptr->grow_rij(jnum);
// rij[][3] = displacements between atom I and those neighbors
@@ -216,7 +216,7 @@ void PairSNAP::compute_regular(int eflag, int vflag)
rsq = delx*delx + dely*dely + delz*delz;
int jtype = type[j];
int jelem = map[jtype];
-
+
if (rsq < cutsq[itype][jtype]&&rsq>1e-20) {
snaptr->rij[ninside][0] = delx;
snaptr->rij[ninside][1] = dely;
@@ -229,7 +229,7 @@ void PairSNAP::compute_regular(int eflag, int vflag)
}
// compute Ui, Zi, and Bi for atom I
-
+
snaptr->compute_ui(ninside);
snaptr->compute_zi();
if (!gammaoneflag) {
@@ -257,7 +257,7 @@ void PairSNAP::compute_regular(int eflag, int vflag)
for (int k = 1; k <= ncoeff; k++) {
double bgb;
- if (gammaoneflag)
+ if (gammaoneflag)
bgb = coeffi[k];
else bgb = coeffi[k]*
gamma*pow(snaptr->bvec[k-1],gamma-1.0);
@@ -281,7 +281,7 @@ void PairSNAP::compute_regular(int eflag, int vflag)
}
if (eflag) {
-
+
// evdwl = energy of atom I, sum over coeffs_k * Bi_k
evdwl = coeffi[0];
@@ -297,7 +297,7 @@ void PairSNAP::compute_regular(int eflag, int vflag)
}
}
-
+
if (vflag_fdotr) virial_fdotr_compute();
}
@@ -573,7 +573,7 @@ void PairSNAP::compute_optimized(int eflag, int vflag)
for (k = 1; k <= ncoeff; k++) {
double bgb;
- if (gammaoneflag)
+ if (gammaoneflag)
bgb = coeffi[k];
else bgb = coeffi[k]*
gamma*pow(sna[tid]->bvec[k-1],gamma-1.0);
@@ -1306,8 +1306,8 @@ void PairSNAP::settings(int narg, char **arg)
// optimization flags set
if (!use_optimized)
- if (nthreads > 1 ||
- use_shared_arrays ||
+ if (nthreads > 1 ||
+ use_shared_arrays ||
do_load_balance ||
schedule_user)
error->all(FLERR,"Illegal pair_style command");
@@ -1327,7 +1327,7 @@ void PairSNAP::coeff(int narg, char **arg)
if (!allocated) allocate();
if (nelements) {
- for (int i = 0; i < nelements; i++)
+ for (int i = 0; i < nelements; i++)
delete[] elements[i];
delete[] elements;
memory->destroy(radelem);
@@ -1461,7 +1461,7 @@ void PairSNAP::init_style()
double PairSNAP::init_one(int i, int j)
{
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
- return (radelem[map[i]] +
+ return (radelem[map[i]] +
radelem[map[j]])*rcutfac;
}
@@ -1505,7 +1505,7 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename)
if ((ptr = strchr(line,'#'))) *ptr = '\0';
nwords = atom->count_words(line);
}
- if (nwords != 2)
+ if (nwords != 2)
error->all(FLERR,"Incorrect format in SNAP coefficient file");
// words = ptrs to all words in line
@@ -1520,20 +1520,20 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename)
int nelemfile = atoi(words[0]);
ncoeff = atoi(words[1])-1;
- // Set up element lists
+ // Set up element lists
memory->create(radelem,nelements,"pair:radelem");
memory->create(wjelem,nelements,"pair:wjelem");
memory->create(coeffelem,nelements,ncoeff+1,"pair:coeffelem");
int *found = new int[nelements];
- for (int ielem = 0; ielem < nelements; ielem++)
+ for (int ielem = 0; ielem < nelements; ielem++)
found[ielem] = 0;
// Loop over elements in the SNAP coefficient file
for (int ielemfile = 0; ielemfile < nelemfile; ielemfile++) {
-
+
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fpcoeff);
if (ptr == NULL) {
@@ -1542,13 +1542,13 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename)
} else n = strlen(line) + 1;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
- if (eof)
+ if (eof)
error->all(FLERR,"Incorrect format in SNAP coefficient file");
MPI_Bcast(&n,1,MPI_INT,0,world);
MPI_Bcast(line,n,MPI_CHAR,0,world);
nwords = atom->count_words(line);
- if (nwords != 3)
+ if (nwords != 3)
error->all(FLERR,"Incorrect format in SNAP coefficient file");
iword = 0;
@@ -1569,7 +1569,7 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename)
if (strcmp(elemtmp,elements[ielem]) == 0) break;
if (ielem == nelements) {
if (comm->me == 0)
- for (int icoeff = 0; icoeff <= ncoeff; icoeff++)
+ for (int icoeff = 0; icoeff <= ncoeff; icoeff++)
ptr = fgets(line,MAXLINE,fpcoeff);
continue;
}
@@ -1578,7 +1578,7 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename)
if (found[ielem]) {
if (comm->me == 0)
- for (int icoeff = 0; icoeff <= ncoeff; icoeff++)
+ for (int icoeff = 0; icoeff <= ncoeff; icoeff++)
ptr = fgets(line,MAXLINE,fpcoeff);
continue;
}
@@ -1589,13 +1589,13 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename)
if (comm->me == 0) {
- if (screen) fprintf(screen,"SNAP Element = %s, Radius %g, Weight %g \n",
+ if (screen) fprintf(screen,"SNAP Element = %s, Radius %g, Weight %g \n",
elements[ielem], radelem[ielem], wjelem[ielem]);
- if (logfile) fprintf(logfile,"SNAP Element = %s, Radius %g, Weight %g \n",
+ if (logfile) fprintf(logfile,"SNAP Element = %s, Radius %g, Weight %g \n",
elements[ielem], radelem[ielem], wjelem[ielem]);
}
- for (int icoeff = 0; icoeff <= ncoeff; icoeff++) {
+ for (int icoeff = 0; icoeff <= ncoeff; icoeff++) {
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fpcoeff);
if (ptr == NULL) {
@@ -1605,20 +1605,20 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename)
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
- if (eof)
+ if (eof)
error->all(FLERR,"Incorrect format in SNAP coefficient file");
MPI_Bcast(&n,1,MPI_INT,0,world);
MPI_Bcast(line,n,MPI_CHAR,0,world);
nwords = atom->count_words(line);
- if (nwords != 1)
+ if (nwords != 1)
error->all(FLERR,"Incorrect format in SNAP coefficient file");
iword = 0;
words[iword] = strtok(line,"' \t\n\r\f");
coeffelem[ielem][icoeff] = atof(words[0]);
-
+
}
}
@@ -1667,7 +1667,7 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename)
nwords = atom->count_words(line);
if (nwords == 0) continue;
- if (nwords != 2)
+ if (nwords != 2)
error->all(FLERR,"Incorrect format in SNAP parameter file");
// words = ptrs to all words in line
diff --git a/src/SNAP/sna.cpp b/src/SNAP/sna.cpp
index 00e2b9df74..65a23671a4 100644
--- a/src/SNAP/sna.cpp
+++ b/src/SNAP/sna.cpp
@@ -16,11 +16,11 @@
------------------------------------------------------------------------- */
#include "sna.h"
-#include "math.h"
+#include <math.h>
#include "math_const.h"
#include "math_extra.h"
-#include "string.h"
-#include "stdlib.h"
+#include <string.h>
+#include <stdlib.h>
#include "openmp_snap.h"
#include "memory.h"
@@ -51,11 +51,11 @@ using namespace MathConst;
m2 = beta+b or 2*beta = 2*m2 - j2
m = gamma+c 2*gamma = 2*m - j
- in this way:
+ in this way:
- -a <= alpha <= a
- -b <= beta <= b
- -c <= gamma <= c
+ -a <= alpha <= a
+ -b <= beta <= b
+ -c <= gamma <= c
becomes:
@@ -65,10 +65,10 @@ using namespace MathConst;
and the requirement that
a+b+c be integral implies that
- j1+j2+j must be even.
+ j1+j2+j must be even.
The requirement that:
-
- gamma = alpha+beta
+
+ gamma = alpha+beta
becomes:
@@ -88,7 +88,7 @@ using namespace MathConst;
0 <= ma, mb <= j.
For the bispectrum components B(J1,J2,J) we convert to:
-
+
j1 = 2*J1
j2 = 2*J2
j = 2*J
@@ -101,8 +101,8 @@ using namespace MathConst;
|j1-j2| <= j <= j1+j2, for j1+j2+j even integer
- or
-
+ or
+
j = |j1-j2|, |j1-j2|+2,...,j1+j2-2,j1+j2
[1] Albert Bartok-Partay, "Gaussian Approximation..."
@@ -291,7 +291,7 @@ void SNA::grow_rij(int newnmax)
memory->destroy(rcutij);
memory->create(rij, nmax, 3, "pair:rij");
memory->create(inside, nmax, "pair:inside");
- memory->create(wj, nmax, "pair:wj");
+ memory->create(wj, nmax, "pair:wj");
memory->create(rcutij, nmax, "pair:rcutij");
}
}
@@ -304,7 +304,7 @@ void SNA::compute_ui(int jnum)
double rsq, r, x, y, z, z0, theta0;
// utot(j,ma,mb) = 0 for all j,ma,ma
- // utot(j,ma,ma) = 1 for all j,ma
+ // utot(j,ma,ma) = 1 for all j,ma
// for j in neighbors of i:
// compute r0 = (x,y,z,z0)
// utot(j,ma,mb) += u(r0;j,ma,mb) for all j,ma,mb
@@ -344,7 +344,7 @@ void SNA::compute_ui_omp(int jnum, int sub_threads)
double rsq, r, x, y, z, z0, theta0;
// utot(j,ma,mb) = 0 for all j,ma,ma
- // utot(j,ma,ma) = 1 for all j,ma
+ // utot(j,ma,ma) = 1 for all j,ma
// for j in neighbors of i:
// compute r0 = (x,y,z,z0)
// utot(j,ma,mb) += u(r0;j,ma,mb) for all j,ma,mb
@@ -412,7 +412,7 @@ void SNA::compute_zi()
for(int ma = 0; ma <= j; ma++) {
zarray_r[j1][j2][j][ma][mb] = 0.0;
zarray_i[j1][j2][j][ma][mb] = 0.0;
-
+
for(int ma1 = MAX(0, (2 * ma - j - j2 + j1) / 2);
ma1 <= MIN(j1, (2 * ma - j + j2 + j1) / 2); ma1++) {
sumb1_r = 0.0;
@@ -424,10 +424,10 @@ void SNA::compute_zi()
mb1 <= MIN(j1, (2 * mb - j + j2 + j1) / 2); mb1++) {
mb2 = (2 * mb - j - (2 * mb1 - j1) + j2) / 2;
- sumb1_r += cgarray[j1][j2][j][mb1][mb2] *
+ sumb1_r += cgarray[j1][j2][j][mb1][mb2] *
(uarraytot_r[j1][ma1][mb1] * uarraytot_r[j2][ma2][mb2] -
uarraytot_i[j1][ma1][mb1] * uarraytot_i[j2][ma2][mb2]);
- sumb1_i += cgarray[j1][j2][j][mb1][mb2] *
+ sumb1_i += cgarray[j1][j2][j][mb1][mb2] *
(uarraytot_r[j1][ma1][mb1] * uarraytot_i[j2][ma2][mb2] +
uarraytot_i[j1][ma1][mb1] * uarraytot_r[j2][ma2][mb2]);
} // end loop over mb1
@@ -829,7 +829,7 @@ void SNA::compute_dbidrj()
double sumzdu_r[3];
double** jjjzarray_r;
double** jjjzarray_i;
- double jjjmambzarray_r;
+ double jjjmambzarray_r;
double jjjmambzarray_i;
#ifdef TIMING_INFO
@@ -1182,21 +1182,21 @@ void SNA::compute_uarray(double x, double y, double z,
rootpq = rootpqarray[j - ma][j - mb];
uarray_r[j][ma][mb] +=
rootpq *
- (a_r * uarray_r[j - 1][ma][mb] +
+ (a_r * uarray_r[j - 1][ma][mb] +
a_i * uarray_i[j - 1][ma][mb]);
uarray_i[j][ma][mb] +=
rootpq *
- (a_r * uarray_i[j - 1][ma][mb] -
+ (a_r * uarray_i[j - 1][ma][mb] -
a_i * uarray_r[j - 1][ma][mb]);
rootpq = rootpqarray[ma + 1][j - mb];
uarray_r[j][ma + 1][mb] =
-rootpq *
- (b_r * uarray_r[j - 1][ma][mb] +
+ (b_r * uarray_r[j - 1][ma][mb] +
b_i * uarray_i[j - 1][ma][mb]);
uarray_i[j][ma + 1][mb] =
-rootpq *
- (b_r * uarray_i[j - 1][ma][mb] -
+ (b_r * uarray_i[j - 1][ma][mb] -
b_i * uarray_r[j - 1][ma][mb]);
}
}
@@ -1216,7 +1216,7 @@ void SNA::compute_uarray(double x, double y, double z,
} else {
uarray_r[j][j-ma][j-mb] = -uarray_r[j][ma][mb];
uarray_i[j][j-ma][j-mb] = uarray_i[j][ma][mb];
- }
+ }
}
}
}
@@ -1254,21 +1254,21 @@ void SNA::compute_uarray_omp(double x, double y, double z,
rootpq = rootpqarray[j - ma][j - mb];
uarray_r[j][ma][mb] +=
rootpq *
- (a_r * uarray_r[j - 1][ma][mb] +
+ (a_r * uarray_r[j - 1][ma][mb] +
a_i * uarray_i[j - 1][ma][mb]);
uarray_i[j][ma][mb] +=
rootpq *
- (a_r * uarray_i[j - 1][ma][mb] -
+ (a_r * uarray_i[j - 1][ma][mb] -
a_i * uarray_r[j - 1][ma][mb]);
rootpq = rootpqarray[ma + 1][j - mb];
uarray_r[j][ma + 1][mb] =
-rootpq *
- (b_r * uarray_r[j - 1][ma][mb] +
+ (b_r * uarray_r[j - 1][ma][mb] +
b_i * uarray_i[j - 1][ma][mb]);
uarray_i[j][ma + 1][mb] =
-rootpq *
- (b_r * uarray_i[j - 1][ma][mb] -
+ (b_r * uarray_i[j - 1][ma][mb] -
b_i * uarray_r[j - 1][ma][mb]);
}
}
@@ -1284,21 +1284,21 @@ void SNA::compute_uarray_omp(double x, double y, double z,
rootpq = rootpqarray[j - ma][mb];
uarray_r[j][ma][mb] +=
rootpq *
- (b_r * uarray_r[j - 1][ma][mb - 1] -
+ (b_r * uarray_r[j - 1][ma][mb - 1] -
b_i * uarray_i[j - 1][ma][mb - 1]);
uarray_i[j][ma][mb] +=
rootpq *
- (b_r * uarray_i[j - 1][ma][mb - 1] +
+ (b_r * uarray_i[j - 1][ma][mb - 1] +
b_i * uarray_r[j - 1][ma][mb - 1]);
rootpq = rootpqarray[ma + 1][mb];
uarray_r[j][ma + 1][mb] =
rootpq *
- (a_r * uarray_r[j - 1][ma][mb - 1] -
+ (a_r * uarray_r[j - 1][ma][mb - 1] -
a_i * uarray_i[j - 1][ma][mb - 1]);
uarray_i[j][ma + 1][mb] =
rootpq *
- (a_r * uarray_i[j - 1][ma][mb - 1] +
+ (a_r * uarray_i[j - 1][ma][mb - 1] +
a_i * uarray_r[j - 1][ma][mb - 1]);
}
}
@@ -1776,7 +1776,7 @@ void SNA::init_clebsch_gordan()
sum = 0.0;
- for (int z = MAX(0, MAX(-(j - j2 + aa2)
+ for (int z = MAX(0, MAX(-(j - j2 + aa2)
/ 2, -(j - j1 - bb2) / 2));
z <= MIN((j1 + j2 - j) / 2,
MIN((j1 - aa2) / 2, (j2 + bb2) / 2));
@@ -1807,7 +1807,7 @@ void SNA::init_clebsch_gordan()
}
/* ----------------------------------------------------------------------
- pre-compute table of sqrt[p/m2], p, q = 1,twojmax
+ pre-compute table of sqrt[p/m2], p, q = 1,twojmax
the p = 0, q = 0 entries are allocated and skipped for convenience.
------------------------------------------------------------------------- */
diff --git a/src/SNAP/sna.h b/src/SNAP/sna.h
index 260d4bfe35..ccc37866d5 100644
--- a/src/SNAP/sna.h
+++ b/src/SNAP/sna.h
@@ -122,9 +122,9 @@ private:
void compute_duarray(double, double, double,
double, double, double, double, double);
- // if number of atoms are small use per atom arrays
+ // if number of atoms are small use per atom arrays
// for twojmax arrays, rij, inside, bvec
- // this will increase the memory footprint considerably,
+ // this will increase the memory footprint considerably,
// but allows parallel filling and reuse of these arrays
int use_shared_arrays;
diff --git a/src/SRD/fix_srd.cpp b/src/SRD/fix_srd.cpp
index 52c0abd560..35eb21254c 100644
--- a/src/SRD/fix_srd.cpp
+++ b/src/SRD/fix_srd.cpp
@@ -15,9 +15,9 @@
Contributing authors: Jeremy Lechman (SNL), Pieter in 't Veld (BASF)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "string.h"
-#include "stdlib.h"
+#include <math.h>
+#include <string.h>
+#include <stdlib.h>
#include "fix_srd.h"
#include "math_extra.h"
#include "atom.h"
@@ -185,9 +185,9 @@ FixSRD::FixSRD(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
iarg += 2;
} else if (strcmp(arg[iarg],"rescale") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix srd command");
- if (strcmp(arg[iarg+1],"no") == 0)
+ if (strcmp(arg[iarg+1],"no") == 0)
rescale_rotate = rescale_collide = 0;
- else if (strcmp(arg[iarg+1],"yes") == 0)
+ else if (strcmp(arg[iarg+1],"yes") == 0)
rescale_rotate = rescale_collide = 1;
else if (strcmp(arg[iarg+1],"rotate") == 0) {
rescale_rotate = 1;
@@ -337,7 +337,7 @@ void FixSRD::init()
error->all(FLERR,"Fix srd no-slip requires atom attribute torque");
if (initflag && update->dt != dt_big)
error->all(FLERR,"Cannot change timestep once fix srd is setup");
- if (comm->style != 0)
+ if (comm->style != 0)
error->universe_all(FLERR,"Fix srd can only currently be used with "
"comm_style brick");
@@ -745,7 +745,7 @@ void FixSRD::post_force(int vflag)
if (ix < 0 || ix >= nbin2x || iy < 0 || iy >= nbin2y ||
iz < 0 || iz >= nbin2z) {
if (screen) {
- fprintf(screen,"SRD particle " TAGINT_FORMAT
+ fprintf(screen,"SRD particle " TAGINT_FORMAT
" on step " BIGINT_FORMAT "\n",
atom->tag[i],update->ntimestep);
fprintf(screen,"v = %g %g %g\n",v[i][0],v[i][1],v[i][2]);
@@ -961,7 +961,7 @@ void FixSRD::reset_velocities()
if (dimension == 3) axis = irandom / 2;
vsq = 0.0;
- for (j = binhead[i]; j >= 0; j = binnext[j]) {
+ for (j = binhead[i]; j >= 0; j = binnext[j]) {
if (axis == 0) {
u[0] = v[j][0]-vave[0];
u[1] = sign ? v[j][2]-vave[2] : vave[2]-v[j][2];
@@ -983,7 +983,7 @@ void FixSRD::reset_velocities()
if (n > 1) vbin[i].value[0] = vsq;
}
-
+
if (shifts[shiftflag].commflag) xbin_comm(shiftflag,1);
if (tstat) {
@@ -1009,11 +1009,11 @@ void FixSRD::reset_velocities()
// tbin = thermal temperature of particles in bin
// scale = scale factor for thermal velocity
-
+
tbin = vbin[i].value[0]/(n-dof_tstat) * tfactor;
scale = sqrt(temperature_srd/tbin);
vsq = 0.0;
- for (j = binhead[i]; j >= 0; j = binnext[j]) {
+ for (j = binhead[i]; j >= 0; j = binnext[j]) {
u[0] = (v[j][0] - vave[0]) * scale;
u[1] = (v[j][1] - vave[1]) * scale;
u[2] = (v[j][2] - vave[2]) * scale;
@@ -1246,7 +1246,7 @@ void FixSRD::xbin_unpack(double *buf, BinAve *vbin, int n, int *list, int nval)
int m = 0;
for (int i = 0; i < n; i++) {
j = list[i];
- for (k = 0; k < nval; k++)
+ for (k = 0; k < nval; k++)
vbin[j].value[k] += buf[m++];
}
}
@@ -1339,7 +1339,7 @@ void FixSRD::collisions_single()
if (type != WALL) {
sprintf(str,
"SRD particle " TAGINT_FORMAT " started "
- "inside big particle " TAGINT_FORMAT
+ "inside big particle " TAGINT_FORMAT
" on step " BIGINT_FORMAT " bounce %d",
atom->tag[i],atom->tag[j],update->ntimestep,ibounce+1);
if (insideflag == INSIDE_ERROR) error->one(FLERR,str);
@@ -1498,7 +1498,7 @@ void FixSRD::collisions_multi()
if (type != WALL) {
sprintf(str,
"SRD particle " TAGINT_FORMAT " started "
- "inside big particle " TAGINT_FORMAT
+ "inside big particle " TAGINT_FORMAT
" on step " BIGINT_FORMAT " bounce %d",
atom->tag[i],atom->tag[j],update->ntimestep,ibounce+1);
if (insideflag == INSIDE_ERROR) error->one(FLERR,str);
@@ -2505,7 +2505,7 @@ int FixSRD::update_srd(int i, double dt, double *xscoll, double *vsnew,
xs[2] < srdlo[2] || xs[2] > srdhi[2]) {
if (screen) {
error->warning(FLERR,"Fix srd particle moved outside valid domain");
- fprintf(screen," particle " TAGINT_FORMAT
+ fprintf(screen," particle " TAGINT_FORMAT
" on proc %d at timestep " BIGINT_FORMAT,
atom->tag[i],me,update->ntimestep);
fprintf(screen," xnew %g %g %g\n",xs[0],xs[1],xs[2]);
@@ -4007,7 +4007,7 @@ void FixSRD::print_collision(int i, int j, int ibounce,
double **v = atom->v;
if (type != WALL) {
- printf("COLLISION between SRD " TAGINT_FORMAT
+ printf("COLLISION between SRD " TAGINT_FORMAT
" and BIG " TAGINT_FORMAT "\n",atom->tag[i],atom->tag[j]);
printf(" bounce # = %d\n",ibounce+1);
printf(" local indices: %d %d\n",i,j);
diff --git a/src/SRD/fix_wall_srd.cpp b/src/SRD/fix_wall_srd.cpp
index d192b55c4a..95ec8e796a 100644
--- a/src/SRD/fix_wall_srd.cpp
+++ b/src/SRD/fix_wall_srd.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdlib.h"
-#include "string.h"
+#include <stdlib.h>
+#include <string.h>
#include "fix_wall_srd.h"
#include "atom.h"
#include "modify.h"
diff --git a/src/STUBS/mpi.c b/src/STUBS/mpi.c
index 38174bb1de..202e19bcfd 100644
--- a/src/STUBS/mpi.c
+++ b/src/STUBS/mpi.c
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -13,12 +13,12 @@
/* Single-processor "stub" versions of MPI routines */
-#include "stdlib.h"
-#include "string.h"
-#include "stdio.h"
-#include "stdint.h"
+#include <stdlib.h>
+#include <string.h>
+#include <stdio.h>
+#include <stdint.h>
#include <sys/time.h>
-#include "mpi.h"
+#include <mpi.h>
/* data structure for double/int */
@@ -250,7 +250,7 @@ int MPI_Waitall(int n, MPI_Request *request, MPI_Status *status)
/* ---------------------------------------------------------------------- */
-int MPI_Waitany(int count, MPI_Request *request, int *index,
+int MPI_Waitany(int count, MPI_Request *request, int *index,
MPI_Status *status)
{
printf("MPI Stub WARNING: Should not wait on message from self\n");
@@ -306,7 +306,7 @@ MPI_Comm MPI_Comm_f2c(MPI_Fint comm) { return comm; };
//* ---------------------------------------------------------------------- */
-int MPI_Comm_group(MPI_Comm comm, MPI_Group *group)
+int MPI_Comm_group(MPI_Comm comm, MPI_Group *group)
{
*group = comm;
return 0;
@@ -314,7 +314,7 @@ int MPI_Comm_group(MPI_Comm comm, MPI_Group *group)
/* ---------------------------------------------------------------------- */
-int MPI_Comm_create(MPI_Comm comm, MPI_Group group, MPI_Comm *newcomm)
+int MPI_Comm_create(MPI_Comm comm, MPI_Group group, MPI_Comm *newcomm)
{
*newcomm = group;
return 0;
@@ -371,7 +371,7 @@ int MPI_Cart_rank(MPI_Comm comm, int *coords, int *rank)
/* store size of user datatype in extra lists */
-int MPI_Type_contiguous(int count, MPI_Datatype oldtype,
+int MPI_Type_contiguous(int count, MPI_Datatype oldtype,
MPI_Datatype *newtype)
{
if (nextra_datatype == MAXEXTRA_DATATYPE) return -1;
@@ -384,7 +384,7 @@ int MPI_Type_contiguous(int count, MPI_Datatype oldtype,
/* ---------------------------------------------------------------------- */
-/* set value of user datatype to internal negative index,
+/* set value of user datatype to internal negative index,
based on match of ptr */
int MPI_Type_commit(MPI_Datatype *datatype)
@@ -556,7 +556,7 @@ int MPI_Gatherv(void *sendbuf, int sendcount, MPI_Datatype sendtype,
/* copy values from data1 to data2 */
-int MPI_Scatter(void *sendbuf, int sendcount, MPI_Datatype sendtype,
+int MPI_Scatter(void *sendbuf, int sendcount, MPI_Datatype sendtype,
void *recvbuf, int recvcount, MPI_Datatype recvtype,
int root, MPI_Comm comm)
{
diff --git a/src/STUBS/mpi.h b/src/STUBS/mpi.h
index 1344de76df..01a4b85173 100644
--- a/src/STUBS/mpi.h
+++ b/src/STUBS/mpi.h
@@ -14,7 +14,7 @@
#ifndef MPI_STUBS
#define MPI_STUBS
-#include "stdlib.h"
+#include <stdlib.h>
/* use C bindings for MPI interface */
@@ -64,7 +64,7 @@ extern "C" {
#define MPI_MAX_PROCESSOR_NAME 128
-typedef void MPI_User_function(void *invec, void *inoutvec,
+typedef void MPI_User_function(void *invec, void *inoutvec,
int *len, MPI_Datatype *datatype);
/* MPI data structs */
@@ -127,7 +127,7 @@ int MPI_Cart_shift(MPI_Comm comm, int direction, int displ,
int *source, int *dest);
int MPI_Cart_rank(MPI_Comm comm, int *coords, int *rank);
-int MPI_Type_contiguous(int count, MPI_Datatype oldtype,
+int MPI_Type_contiguous(int count, MPI_Datatype oldtype,
MPI_Datatype *newtype);
int MPI_Type_commit(MPI_Datatype *datatype);
int MPI_Type_free(MPI_Datatype *datatype);
@@ -158,8 +158,8 @@ int MPI_Gather(void *sendbuf, int sendcount, MPI_Datatype sendtype,
int MPI_Gatherv(void *sendbuf, int sendcount, MPI_Datatype sendtype,
void *recvbuf, int *recvcounts, int *displs,
MPI_Datatype recvtype, int root, MPI_Comm comm);
-int MPI_Scatter(void *sendbuf, int sendcount, MPI_Datatype sendtype,
- void *recvbuf, int recvcount, MPI_Datatype recvtype,
+int MPI_Scatter(void *sendbuf, int sendcount, MPI_Datatype sendtype,
+ void *recvbuf, int recvcount, MPI_Datatype recvtype,
int root, MPI_Comm comm);
int MPI_Scatterv(void *sendbuf, int *sendcounts, int *displs,
MPI_Datatype sendtype, void *recvbuf, int recvcount,
diff --git a/src/USER-ATC/fix_atc.cpp b/src/USER-ATC/fix_atc.cpp
index b13719add3..0dc10e1773 100644
--- a/src/USER-ATC/fix_atc.cpp
+++ b/src/USER-ATC/fix_atc.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -35,11 +35,11 @@
#include "ATC_CouplingMomentumEnergy.h"
#include "LammpsInterface.h"
// other
-#include "stdio.h"
-#include "string.h"
+#include <stdio.h>
+#include <string.h>
#include <sstream>
-using namespace LAMMPS_NS;
+using namespace LAMMPS_NS;
using namespace FixConst;
using std::string;
@@ -64,7 +64,7 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
// Set LAMMPS pointer on LammpsInterface
ATC::LammpsInterface::instance()->set_lammps(lmp);
- /*! \page man_fix_atc fix atc command
+ /*! \page man_fix_atc fix atc command
\section syntax
fix <fixID> <group> atc <type> <parameter_file>
- fixID = name of fix
@@ -87,10 +87,10 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
fix do Verlet integration and the /post-processing does not.
After instantiating this fix, several other fix_modify commands will be
needed to set up the problem, e.g. define the finite element mesh and
- prescribe initial and boundary conditions.
+ prescribe initial and boundary conditions.
The following coupling example is typical, but non-exhaustive:\n
-
+
<TT>
# ... commands to create and initialize the MD system \n
@@ -121,7 +121,7 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
# initial fix to designate post-processing and the group to apply it to \n
# no material file is allowed nor required \n
fix AtC internal atc hardy \n \n
- # for hardy fix, specific kernel function (function type and range) to
+ # for hardy fix, specific kernel function (function type and range) to
# be used as a localization function \n
fix AtC kernel quartic_sphere 10.0 \n \n
# create a uniform 1 x 1 x 1 mesh that covers region contain the group \n
@@ -149,7 +149,7 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
... \n\n
</TT>
- Note coupling and post-processing can be combined in the same simulations
+ Note coupling and post-processing can be combined in the same simulations
using separate fixes.
\n
For detailed exposition of the theory and algorithms please see:\n
@@ -158,7 +158,7 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
Special Issue of Computer Methods and Applied Mechanics (2008) 197:3351. \n
- Zimmerman, JA; Webb, EB; Hoyt, JJ;. Jones, RE; Klein, PA; Bammann, DJ,
<VAR> Calculation of stress in atomistic simulation. </VAR>
- Special Issue of Modelling and Simulation in Materials Science and
+ Special Issue of Modelling and Simulation in Materials Science and
Engineering (2004), 12:S319. \n
- Zimmerman, JA; Jones, RE; Templeton, JA,
<VAR> A material frame approach for evaluating continuum variables in
@@ -179,17 +179,17 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
Journal of Chemical Physics (2013), 139:054115. \n
Please refer to the standard
- finite element (FE) texts, e.g. T.J.R Hughes <VAR> The finite element
+ finite element (FE) texts, e.g. T.J.R Hughes <VAR> The finite element
method </VAR>, Dover 2003, for the basics of FE simulation.
\section restrictions
- Thermal and two_temperature (coupling) types use a Verlet time-integration
+ Thermal and two_temperature (coupling) types use a Verlet time-integration
algorithm.
- The hardy type does not contain its own time-integrator and must be used
+ The hardy type does not contain its own time-integrator and must be used
with a separate fix that does contain one, e.g. nve, nvt, etc.
- Currently,
- - the coupling is restricted to thermal physics
+ Currently,
+ - the coupling is restricted to thermal physics
- the FE computations are done in serial on each processor.
\section related
@@ -279,7 +279,7 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
- \ref man_remove_species
- \ref man_remove_molecule
- Note: a set of example input files with the attendant material files are
+ Note: a set of example input files with the attendant material files are
included with this package
\section default
none
@@ -297,7 +297,7 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
try {
// Postprocessing
- if (strcmp(arg[3],"field")==0)
+ if (strcmp(arg[3],"field")==0)
{
if (atomCount == 0) {
if (me==0) printf("ATC: can't construct transfer, no atoms in group \n");
@@ -308,8 +308,8 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
atc_ = new ATC::ATC_TransferPartitionOfUnity(groupName,
array_atom,
this);
- }
- else {
+ }
+ else {
if (me==0) printf("ATC: constructing shape function field estimate with parameter file %s\n",arg[4]);
string matParamFile = arg[4];
atc_ = new ATC::ATC_TransferPartitionOfUnity(groupName,
@@ -317,7 +317,7 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
matParamFile);
}
}
- else if (strcmp(arg[3],"hardy")==0)
+ else if (strcmp(arg[3],"hardy")==0)
{
if (atomCount == 0) {
if (me==0) printf("ATC: Can't construct transfer, no atoms in group \n");
@@ -328,8 +328,8 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
atc_ = new ATC::ATC_TransferKernel(groupName,
array_atom,
this);
- }
- else {
+ }
+ else {
if (me==0) printf("ATC: constructing kernel field estimate with parameter file %s\n",arg[4]);
string matParamFile = arg[4];
atc_ = new ATC::ATC_TransferKernel(groupName,
@@ -338,7 +338,7 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
}
}
// PhysicsTypes
- else if (strcmp(arg[3],"thermal")==0)
+ else if (strcmp(arg[3],"thermal")==0)
{
string matParamFile = arg[4];
if (me==0) printf("ATC: constructing thermal coupling with parameter file %s\n",arg[4]);
@@ -346,7 +346,7 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
array_atom, this,
matParamFile);
}
- else if (strcmp(arg[3],"two_temperature")==0)
+ else if (strcmp(arg[3],"two_temperature")==0)
{
string matParamFile = arg[4];
if (me==0) printf("ATC: constructing two_temperature coupling with parameter file %s\n",arg[4]);
@@ -354,7 +354,7 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
array_atom, this,
matParamFile, ATC::TWO_TEMPERATURE);
}
- else if (strcmp(arg[3],"drift_diffusion")==0)
+ else if (strcmp(arg[3],"drift_diffusion")==0)
{
string matParamFile = arg[4];
if (me==0) printf("ATC: constructing drift_diffusion coupling with parameter file %s\n",arg[4]);
@@ -362,7 +362,7 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
array_atom, this,
matParamFile, ATC::DRIFT_DIFFUSION);
}
- else if (strcmp(arg[3],"drift_diffusion-equilibrium")==0)
+ else if (strcmp(arg[3],"drift_diffusion-equilibrium")==0)
{
string matParamFile = arg[4];
if (me==0) printf("ATC: constructing drift_diffusion-equilibrium coupling with parameter file %s\n",arg[4]);
@@ -370,7 +370,7 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
array_atom, this,
matParamFile, ATC::DRIFT_DIFFUSION_EQUILIBRIUM);
}
- else if (strcmp(arg[3],"drift_diffusion-schrodinger")==0)
+ else if (strcmp(arg[3],"drift_diffusion-schrodinger")==0)
{
string matParamFile = arg[4];
if (me==0) printf("ATC: constructing drift_diffusion-schrodinger coupling with parameter file %s\n",arg[4]);
@@ -378,7 +378,7 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
array_atom, this,
matParamFile, ATC::DRIFT_DIFFUSION_SCHRODINGER);
}
- else if (strcmp(arg[3],"drift_diffusion-schrodinger-slice")==0)
+ else if (strcmp(arg[3],"drift_diffusion-schrodinger-slice")==0)
{
string matParamFile = arg[4];
if (me==0) printf("Constructing ATC transfer (drift_diffusion-schrodinger-slice) with parameter file %s\n",arg[4]);
@@ -386,7 +386,7 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
array_atom, this,
matParamFile, ATC::DRIFT_DIFFUSION_SCHRODINGER_SLICE);
}
- else if (strcmp(arg[3],"convective_drift_diffusion")==0)
+ else if (strcmp(arg[3],"convective_drift_diffusion")==0)
{
string matParamFile = arg[4];
if (me==0) printf("ATC: constructing convective_drift_diffusion coupling with parameter file %s\n",arg[4]);
@@ -394,7 +394,7 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
array_atom, this,
matParamFile, ATC::CONVECTIVE_DRIFT_DIFFUSION);
}
- else if (strcmp(arg[3],"convective_drift_diffusion-equilibrium")==0)
+ else if (strcmp(arg[3],"convective_drift_diffusion-equilibrium")==0)
{
string matParamFile = arg[4];
if (me==0) printf("ATC: constructing convective_drift_diffusion-equilibrium coupling with parameter file %s\n",arg[4]);
@@ -402,7 +402,7 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
array_atom, this,
matParamFile, ATC::CONVECTIVE_DRIFT_DIFFUSION_EQUILIBRIUM);
}
- else if (strcmp(arg[3],"convective_drift_diffusion-schrodinger")==0)
+ else if (strcmp(arg[3],"convective_drift_diffusion-schrodinger")==0)
{
string matParamFile = arg[4];
if (me==0) printf("ATC: constructing convective_drift_diffusion-schrodinger coupling with parameter file %s\n",arg[4]);
@@ -410,7 +410,7 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
array_atom, this,
matParamFile, ATC::CONVECTIVE_DRIFT_DIFFUSION_SCHRODINGER);
}
- else if (strcmp(arg[3],"elastic")==0)
+ else if (strcmp(arg[3],"elastic")==0)
{
string matParamFile = arg[4];
if (me==0) printf("ATC: constructing elastic coupling with parameter file %s\n",arg[4]);
@@ -419,7 +419,7 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
matParamFile,
ATC::ELASTIC);
}
- else if (strcmp(arg[3],"electrostatic")==0)
+ else if (strcmp(arg[3],"electrostatic")==0)
{
string matParamFile = arg[4];
if (me==0) printf("ATC: constructing electrostatic mechanical coupling with parameter file %s\n",arg[4]);
@@ -429,7 +429,7 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
ATC::ELASTIC,
ATC::ELECTROSTATIC);
}
- else if (strcmp(arg[3],"electrostatic-equilibrium")==0)
+ else if (strcmp(arg[3],"electrostatic-equilibrium")==0)
{
string matParamFile = arg[4];
if (me==0) printf("ATC: constructing equilibrium electrostatic coupling with parameter file %s\n",arg[4]);
@@ -439,7 +439,7 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
ATC::ELASTIC,
ATC::ELECTROSTATIC_EQUILIBRIUM);
}
- else if (strcmp(arg[3],"shear")==0)
+ else if (strcmp(arg[3],"shear")==0)
{
string matParamFile = arg[4];
if (me==0) printf("ATC: constructing viscous/shear coupling with parameter file %s\n",arg[4]);
@@ -464,7 +464,7 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
array_atom, this,
matParamFile, ATC::FEM_EFIELD);
}
- else if (strcmp(arg[3],"thermo_elastic")==0)
+ else if (strcmp(arg[3],"thermo_elastic")==0)
{
string matParamFile = arg[4];
if (me==0) printf("ATC: constructing thermo-mechanical coupling with parameter file %s\n",arg[4]);
@@ -472,7 +472,7 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
array_atom, this,
matParamFile);
}
- else
+ else
{
lmp->error->all(FLERR,"Unknown physics type in ATC");
}
@@ -485,9 +485,9 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
lmp->atom->add_callback(0);
// we write our own restart file
- restart_global = 0;
-
-
+ restart_global = 0;
+
+
// Set output computation data based on transfer info
scalar_flag = atc_->scalar_flag();
@@ -503,13 +503,13 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
peratom_flag = atc_->peratom_flag();
size_peratom_cols = atc_->size_peratom_cols();
peratom_freq = atc_->peratom_freq();
-
+
// set comm size needed by this fix
- comm_forward = atc_->comm_forward();
+ comm_forward = atc_->comm_forward();
// call this fix every step
- nevery = 1;
+ nevery = 1;
}
/*----------------------------------------------------------------------- */
@@ -545,7 +545,7 @@ int FixATC::setmask()
int FixATC::modify_param(int narg, char** arg)
{
- bool match;
+ bool match;
// pass on to transfer layer
try {
@@ -701,15 +701,15 @@ void FixATC::unpack_restart(int nlocal, int nth){
/* ----------------------------------------------------------------------
maxsize of any atom's restart data
------------------------------------------------------------------------- */
-
+
int FixATC::maxsize_restart(){
return 0;
}
-
+
/* ----------------------------------------------------------------------
size of atom nlocal's restart data
------------------------------------------------------------------------- */
-
+
int FixATC::size_restart(int nlocal){
return 0;
}
@@ -719,7 +719,7 @@ int FixATC::size_restart(int nlocal){
------------------------------------------------------------------------- */
void FixATC::write_restart(FILE *fp){
-
+
char ** args = new char*[2];
args[0] = new char[50];
args[1] = new char[50];
@@ -741,7 +741,7 @@ void FixATC::write_restart(FILE *fp){
------------------------------------------------------------------------- */
void FixATC::restart(char *buf){
-
+
char ** args = new char*[2];
args[0] = new char[50];
args[1] = new char[50];
@@ -840,7 +840,7 @@ void FixATC::pre_neighbor()
{
try {
atc_->pre_neighbor();
- comm->forward_comm_fix(this);
+ comm->forward_comm_fix(this);
}
catch (ATC::ATC_Error& atcError) {
ATC::LammpsInterface::instance()->print_msg(atcError.error_description());
@@ -850,9 +850,9 @@ void FixATC::pre_neighbor()
/* ---------------------------------------------------------------------- */
void FixATC::pre_force(int vflag)
{
-
+
try {
- atc_->pre_force();
+ atc_->pre_force();
}
catch (ATC::ATC_Error& atcError) {
ATC::LammpsInterface::instance()->print_msg(atcError.error_description());
@@ -862,9 +862,9 @@ void FixATC::pre_force(int vflag)
/* ---------------------------------------------------------------------- */
void FixATC::post_force(int vflag)
{
-
+
try {
- atc_->post_force();
+ atc_->post_force();
}
catch (ATC::ATC_Error& atcError) {
ATC::LammpsInterface::instance()->print_msg(atcError.error_description());
@@ -912,7 +912,7 @@ void FixATC::min_setup_pre_neighbor()
void FixATC::min_pre_force(int vflag)
{
try {
- atc_->min_pre_force();
+ atc_->min_pre_force();
}
catch (ATC::ATC_Error& atcError) {
ATC::LammpsInterface::instance()->print_msg(atcError.error_description());
@@ -924,7 +924,7 @@ void FixATC::min_pre_force(int vflag)
void FixATC::min_post_force(int vflag)
{
try {
- atc_->min_post_force();
+ atc_->min_post_force();
}
catch (ATC::ATC_Error& atcError) {
ATC::LammpsInterface::instance()->print_msg(atcError.error_description());
@@ -933,17 +933,17 @@ void FixATC::min_post_force(int vflag)
}
/* ---------------------------------------------------------------------- */
-double FixATC::compute_scalar()
+double FixATC::compute_scalar()
{
return atc_->compute_scalar();
}
/* ---------------------------------------------------------------------- */
-double FixATC::compute_vector(int n)
+double FixATC::compute_vector(int n)
{
return atc_->compute_vector(n);
}
/* ---------------------------------------------------------------------- */
-double FixATC::compute_array(int irow, int icol)
+double FixATC::compute_array(int irow, int icol)
{
return atc_->compute_array(irow,icol);
}
diff --git a/src/USER-ATC/fix_atc.h b/src/USER-ATC/fix_atc.h
index dd58becfa2..b87c585e73 100644
--- a/src/USER-ATC/fix_atc.h
+++ b/src/USER-ATC/fix_atc.h
@@ -17,19 +17,19 @@ namespace LAMMPS_NS {
class NeighList;
/**
- * @class FixATC
- * @brief Class for an atom-to-continuum (ATC) Lammps fix.
+ * @class FixATC
+ * @brief Class for an atom-to-continuum (ATC) Lammps fix.
*/
class FixATC : public Fix {
- public:
+ public:
/** constructor & destructor */
FixATC(class LAMMPS *, int, char **);
~FixATC();
/** initialization functions */
void init();
- void init_list(int id, NeighList *ptr) ;
+ void init_list(int id, NeighList *ptr) ;
void setup(int vflag);
void min_setup(int vflag);
@@ -55,32 +55,32 @@ namespace LAMMPS_NS {
void min_setup_pre_exchange();
void min_pre_exchange();
- double memory_usage();
+ double memory_usage();
void grow_arrays(int);
void copy_arrays(int, int, int);
/** pack_exchange called from atom_vec->pack_exchange()
- and packs fix-specific data for a given real (local)
+ and packs fix-specific data for a given real (local)
atom being sent to another processor. */
int pack_exchange(int, double *);
/** unpack_exchange called from atom_vec->unpack_exchange()
- and unpacks fix-specific data for a given real (local)
+ and unpacks fix-specific data for a given real (local)
atom received from another processor. */
int unpack_exchange(int, double *);
/** pack_comm called from comm->forward_comm_fix and
packs fix-specific data for a given ghost atom
from exchange with another proc */
- int pack_forward_comm(int , int *, double *, int, int *);
-
+ int pack_forward_comm(int , int *, double *, int, int *);
+
/** unpack_comm called from comm->forward_comm_fix and
unpacks fix-specific data for a given ghost atom
from exchange with another proc */
void unpack_forward_comm(int, int, double *);
/** pre_neighbor is used to modify fix-specific data
- and is called before neighbor list is built in
+ and is called before neighbor list is built in
neighbor->build(). */
void pre_neighbor();
void setup_pre_neighbor();
diff --git a/src/USER-AWPMD/atom_vec_wavepacket.cpp b/src/USER-AWPMD/atom_vec_wavepacket.cpp
index 525262af0c..33048efba6 100644
--- a/src/USER-AWPMD/atom_vec_wavepacket.cpp
+++ b/src/USER-AWPMD/atom_vec_wavepacket.cpp
@@ -15,9 +15,9 @@
Contributing author: Ilya Valuev (JIHT, Moscow, Russia)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "atom_vec_wavepacket.h"
#include "atom.h"
#include "comm.h"
@@ -908,7 +908,7 @@ void AtomVecWavepacket::create_atom(int itype, double *coord)
AWPMD: 0-tag 1-type 2-q 3-spin 4-eradius 5-etag 6-cs_re 7-cs_im
------------------------------------------------------------------------- */
-void AtomVecWavepacket::data_atom(double *coord, imageint imagetmp,
+void AtomVecWavepacket::data_atom(double *coord, imageint imagetmp,
char **values)
{
int nlocal = atom->nlocal;
@@ -1039,7 +1039,7 @@ int AtomVecWavepacket::pack_data_hybrid(int i, double *buf)
void AtomVecWavepacket::write_data(FILE *fp, int n, double **buf)
{
for (int i = 0; i < n; i++)
- fprintf(fp,TAGINT_FORMAT
+ fprintf(fp,TAGINT_FORMAT
" %d %-1.16e %d %-1.16e %d %-1.16e %-1.16e %-1.16e "
"%-1.16e %-1.16e %d %d %d\n",
(tagint) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).i,
@@ -1128,7 +1128,7 @@ int AtomVecWavepacket::property_atom(char *name)
index maps to data specific to this atom style
------------------------------------------------------------------------- */
-void AtomVecWavepacket::pack_property_atom(int index, double *buf,
+void AtomVecWavepacket::pack_property_atom(int index, double *buf,
int nvalues, int groupbit)
{
int *mask = atom->mask;
diff --git a/src/USER-AWPMD/fix_nve_awpmd.cpp b/src/USER-AWPMD/fix_nve_awpmd.cpp
index c4a3820e6b..3ad425030d 100644
--- a/src/USER-AWPMD/fix_nve_awpmd.cpp
+++ b/src/USER-AWPMD/fix_nve_awpmd.cpp
@@ -15,16 +15,16 @@
Contributing author: Ilya Valuev (JIHT, Moscow, Russia)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <string.h>
#include "fix_nve_awpmd.h"
#include "atom.h"
#include "force.h"
#include "update.h"
#include "respa.h"
#include "error.h"
-#include "math.h"
+#include <math.h>
#include "TCP/wpmd_split.h"
diff --git a/src/USER-AWPMD/pair_awpmd_cut.cpp b/src/USER-AWPMD/pair_awpmd_cut.cpp
index e9ca0352f2..29feb37ca1 100644
--- a/src/USER-AWPMD/pair_awpmd_cut.cpp
+++ b/src/USER-AWPMD/pair_awpmd_cut.cpp
@@ -15,10 +15,10 @@
Contributing author: Ilya Valuev (JIHT, Moscow, Russia)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_awpmd_cut.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-CG-CMM/angle_sdk.cpp b/src/USER-CG-CMM/angle_sdk.cpp
index 87fd7f5439..31136e5cd9 100644
--- a/src/USER-CG-CMM/angle_sdk.cpp
+++ b/src/USER-CG-CMM/angle_sdk.cpp
@@ -17,8 +17,8 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdlib.h>
#include "angle_sdk.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/USER-CG-CMM/angle_sdk.h b/src/USER-CG-CMM/angle_sdk.h
index f4885d5e0d..fbd5461187 100644
--- a/src/USER-CG-CMM/angle_sdk.h
+++ b/src/USER-CG-CMM/angle_sdk.h
@@ -21,7 +21,7 @@ AngleStyle(cg/cmm,AngleSDK)
#ifndef LMP_ANGLE_SDK_H
#define LMP_ANGLE_SDK_H
-#include "stdio.h"
+#include <stdio.h>
#include "angle.h"
namespace LAMMPS_NS {
diff --git a/src/USER-CG-CMM/lj_sdk_common.h b/src/USER-CG-CMM/lj_sdk_common.h
index ddf14eb01f..f8f7a66ce9 100644
--- a/src/USER-CG-CMM/lj_sdk_common.h
+++ b/src/USER-CG-CMM/lj_sdk_common.h
@@ -19,7 +19,7 @@
#ifndef LMP_LJ_SDK_COMMON_H
#define LMP_LJ_SDK_COMMON_H
-#include "string.h"
+#include <string.h>
namespace LAMMPS_NS {
namespace LJSDKParms {
diff --git a/src/USER-CG-CMM/pair_lj_sdk.cpp b/src/USER-CG-CMM/pair_lj_sdk.cpp
index ef53e5db16..1ab93447f4 100644
--- a/src/USER-CG-CMM/pair_lj_sdk.cpp
+++ b/src/USER-CG-CMM/pair_lj_sdk.cpp
@@ -16,10 +16,10 @@
This style is a simplified re-implementation of the CG/CMM pair style
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_lj_sdk.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-CG-CMM/pair_lj_sdk_coul_long.cpp b/src/USER-CG-CMM/pair_lj_sdk_coul_long.cpp
index 591a81fe53..1549acfc28 100644
--- a/src/USER-CG-CMM/pair_lj_sdk_coul_long.cpp
+++ b/src/USER-CG-CMM/pair_lj_sdk_coul_long.cpp
@@ -16,10 +16,10 @@
This style is a simplified re-implementation of the CG/CMM pair style
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_lj_sdk_coul_long.h"
#include "atom.h"
#include "comm.h"
@@ -190,7 +190,7 @@ void PairLJSDKCoulLong::eval()
fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
table = ftable[itable] + fraction*dftable[itable];
forcecoul = qtmp*q[j] * table;
- if (EFLAG) ecoul = qtmp*q[j] *
+ if (EFLAG) ecoul = qtmp*q[j] *
(etable[itable] + fraction*detable[itable]);
if (factor_coul < 1.0) {
table = ctable[itable] + fraction*dctable[itable];
@@ -319,7 +319,7 @@ void PairLJSDKCoulLong::settings(int narg, char **arg)
void PairLJSDKCoulLong::coeff(int narg, char **arg)
{
- if (narg < 5 || narg > 6)
+ if (narg < 5 || narg > 6)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
@@ -394,16 +394,16 @@ double PairLJSDKCoulLong::init_one(int i, int j)
double cut = MAX(cut_lj[i][j],cut_coul);
cut_ljsq[i][j] = cut_lj[i][j] * cut_lj[i][j];
- lj1[i][j] = lj_prefact[ljt] * lj_pow1[ljt] * epsilon[i][j] *
+ lj1[i][j] = lj_prefact[ljt] * lj_pow1[ljt] * epsilon[i][j] *
pow(sigma[i][j],lj_pow1[ljt]);
- lj2[i][j] = lj_prefact[ljt] * lj_pow2[ljt] * epsilon[i][j] *
+ lj2[i][j] = lj_prefact[ljt] * lj_pow2[ljt] * epsilon[i][j] *
pow(sigma[i][j],lj_pow2[ljt]);
lj3[i][j] = lj_prefact[ljt] * epsilon[i][j] * pow(sigma[i][j],lj_pow1[ljt]);
lj4[i][j] = lj_prefact[ljt] * epsilon[i][j] * pow(sigma[i][j],lj_pow2[ljt]);
if (offset_flag) {
double ratio = sigma[i][j] / cut_lj[i][j];
- offset[i][j] = lj_prefact[ljt] * epsilon[i][j] *
+ offset[i][j] = lj_prefact[ljt] * epsilon[i][j] *
(pow(ratio,lj_pow1[ljt]) - pow(ratio,lj_pow2[ljt]));
} else offset[i][j] = 0.0;
diff --git a/src/USER-CG-CMM/pair_lj_sdk_coul_msm.cpp b/src/USER-CG-CMM/pair_lj_sdk_coul_msm.cpp
index 726f089877..ddca927a68 100644
--- a/src/USER-CG-CMM/pair_lj_sdk_coul_msm.cpp
+++ b/src/USER-CG-CMM/pair_lj_sdk_coul_msm.cpp
@@ -16,10 +16,10 @@
This style is a simplified re-implementation of the CG/CMM pair style
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_lj_sdk_coul_msm.h"
#include "atom.h"
#include "comm.h"
@@ -158,7 +158,7 @@ void PairLJSDKCoulMSM::eval_msm()
fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
table = ftable[itable] + fraction*dftable[itable];
forcecoul = qtmp*q[j] * table;
- if (EFLAG) ecoul = qtmp*q[j] *
+ if (EFLAG) ecoul = qtmp*q[j] *
(etable[itable] + fraction*detable[itable]);
if (factor_coul < 1.0) {
table = ctable[itable] + fraction*dctable[itable];
diff --git a/src/USER-CG-CMM/pair_lj_sdk_coul_msm.h b/src/USER-CG-CMM/pair_lj_sdk_coul_msm.h
index d9d086f9ab..be56c0cec3 100644
--- a/src/USER-CG-CMM/pair_lj_sdk_coul_msm.h
+++ b/src/USER-CG-CMM/pair_lj_sdk_coul_msm.h
@@ -36,7 +36,7 @@ class PairLJSDKCoulMSM : public PairLJSDKCoulLong {
virtual void compute(int, int);
virtual double single(int, int, int, int, double, double, double, double &);
virtual void *extract(const char *, int &);
-
+
private:
template <int EVFLAG, int EFLAG, int NEWTON_PAIR> void eval_msm();
diff --git a/src/USER-COLVARS/colvarproxy_lammps.cpp b/src/USER-COLVARS/colvarproxy_lammps.cpp
index 579b24f790..d48e547908 100644
--- a/src/USER-COLVARS/colvarproxy_lammps.cpp
+++ b/src/USER-COLVARS/colvarproxy_lammps.cpp
@@ -1,5 +1,5 @@
-#include "mpi.h"
+#include <mpi.h>
#include "lammps.h"
#include "atom.h"
#include "error.h"
diff --git a/src/USER-CUDA/comm_cuda.cpp b/src/USER-CUDA/comm_cuda.cpp
index bf813c4f8b..a03f873ce2 100644
--- a/src/USER-CUDA/comm_cuda.cpp
+++ b/src/USER-CUDA/comm_cuda.cpp
@@ -19,7 +19,7 @@
#error LAMMPS_BIGBIG not supported by this file
#endif
-#include "mpi.h"
+#include <mpi.h>
#include <cmath>
#include <cstring>
#include <cstdio>
diff --git a/src/USER-CUDA/compute_pe_cuda.cpp b/src/USER-CUDA/compute_pe_cuda.cpp
index 57685e52f3..b8661c9702 100644
--- a/src/USER-CUDA/compute_pe_cuda.cpp
+++ b/src/USER-CUDA/compute_pe_cuda.cpp
@@ -34,7 +34,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
+#include <mpi.h>
#include <cstring>
#include "compute_pe_cuda.h"
#include "atom.h"
diff --git a/src/USER-CUDA/compute_pressure_cuda.cpp b/src/USER-CUDA/compute_pressure_cuda.cpp
index e87264d722..c92e918ad0 100644
--- a/src/USER-CUDA/compute_pressure_cuda.cpp
+++ b/src/USER-CUDA/compute_pressure_cuda.cpp
@@ -34,7 +34,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
+#include <mpi.h>
#include <cstring>
#include <cstdlib>
#include "compute_pressure_cuda.h"
diff --git a/src/USER-CUDA/compute_temp_cuda.cpp b/src/USER-CUDA/compute_temp_cuda.cpp
index 1db65294c6..85afa07258 100644
--- a/src/USER-CUDA/compute_temp_cuda.cpp
+++ b/src/USER-CUDA/compute_temp_cuda.cpp
@@ -34,7 +34,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
+#include <mpi.h>
#include <cstdlib>
#include <cstdio>
#include <cstring>
diff --git a/src/USER-CUDA/compute_temp_partial_cuda.cpp b/src/USER-CUDA/compute_temp_partial_cuda.cpp
index 3de4fbb354..b366c546f6 100644
--- a/src/USER-CUDA/compute_temp_partial_cuda.cpp
+++ b/src/USER-CUDA/compute_temp_partial_cuda.cpp
@@ -34,7 +34,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
+#include <mpi.h>
#include <cstdlib>
#include <cstdio>
#include <cstring>
diff --git a/src/USER-CUDA/cuda.cpp b/src/USER-CUDA/cuda.cpp
index 909b1259e5..995289a792 100644
--- a/src/USER-CUDA/cuda.cpp
+++ b/src/USER-CUDA/cuda.cpp
@@ -65,7 +65,7 @@ Cuda::Cuda(LAMMPS* lmp) : Pointers(lmp)
if (universe->me == 0) {
- if(shared_data.compile_settings.prec_glob != sizeof(CUDA_CFLOAT) / 4)
+ if(shared_data.compile_settings.prec_glob != sizeof(CUDA_CFLOAT) / 4)
printf("\n\n # CUDA WARNING: Compile Settings of cuda and cpp code differ! \n"
" # CUDA WARNING: Global Precision: cuda %i cpp %i\n\n",
shared_data.compile_settings.prec_glob, (int) sizeof(CUDA_CFLOAT) / 4);
@@ -239,7 +239,7 @@ Cuda::~Cuda()
void Cuda::accelerator(int narg, char **arg)
{
- // this error should not happen
+ // this error should not happen
if (device_set) error->all(FLERR,"USER-CUDA device is already activated");
@@ -277,11 +277,11 @@ void Cuda::accelerator(int narg, char **arg)
iarg += 2;
} else if (strcmp(arg[iarg],"thread") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal package cuda command");
- if (strcmp(arg[iarg+1],"auto") == 0)
+ if (strcmp(arg[iarg+1],"auto") == 0)
shared_data.pair.override_block_per_atom = -1;
- else if (strcmp(arg[iarg+1],"tpa") == 0)
+ else if (strcmp(arg[iarg+1],"tpa") == 0)
shared_data.pair.override_block_per_atom = 0;
- else if (strcmp(arg[iarg+1],"bpa") == 0)
+ else if (strcmp(arg[iarg+1],"bpa") == 0)
shared_data.pair.override_block_per_atom = 1;
else error->all(FLERR,"Illegal package cuda command");
iarg += 2;
@@ -299,7 +299,7 @@ void Cuda::accelerator(int narg, char **arg)
} else if (strcmp(arg[iarg],"pinned") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal package cuda command");
pinned = force->inumeric(FLERR,arg[iarg+1]) == 0 ? false : true;
- if ((pinned == false) && (universe->me == 0))
+ if ((pinned == false) && (universe->me == 0))
printf(" #CUDA: Pinned memory is not used for communication\n");
iarg += 2;
} else error->all(FLERR,"Illegal package cuda command");
diff --git a/src/USER-CUDA/domain_cuda.cpp b/src/USER-CUDA/domain_cuda.cpp
index 43b1dc24a3..997a42a681 100644
--- a/src/USER-CUDA/domain_cuda.cpp
+++ b/src/USER-CUDA/domain_cuda.cpp
@@ -15,11 +15,11 @@
Contributing author (triclinic) : Pieter in 't Veld (SNL)
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "stdlib.h"
-#include "string.h"
-#include "stdio.h"
-#include "math.h"
+#include <mpi.h>
+#include <stdlib.h>
+#include <string.h>
+#include <stdio.h>
+#include <math.h>
#include "domain_cuda.h"
#include "style_region.h"
#include "atom.h"
diff --git a/src/USER-CUDA/fft3d_cuda.cpp b/src/USER-CUDA/fft3d_cuda.cpp
index 05994ea6df..42ec4b16ee 100644
--- a/src/USER-CUDA/fft3d_cuda.cpp
+++ b/src/USER-CUDA/fft3d_cuda.cpp
@@ -38,7 +38,7 @@
Contributing authors: Jim Shepherd (GA Tech) added SGI SCSL support
------------------------------------------------------------------------- */
-#include "mpi.h"
+#include <mpi.h>
#include <cstdio>
#include <cstdlib>
#include <cmath>
diff --git a/src/USER-CUDA/fft3d_wrap_cuda.cpp b/src/USER-CUDA/fft3d_wrap_cuda.cpp
index 80fc7b8228..f02c38d831 100644
--- a/src/USER-CUDA/fft3d_wrap_cuda.cpp
+++ b/src/USER-CUDA/fft3d_wrap_cuda.cpp
@@ -34,7 +34,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
+#include <mpi.h>
#include "fft3d_wrap_cuda.h"
#include "error.h"
diff --git a/src/USER-CUDA/fix_aveforce_cuda.cpp b/src/USER-CUDA/fix_aveforce_cuda.cpp
index 917058fa3a..9b4ceaa67c 100644
--- a/src/USER-CUDA/fix_aveforce_cuda.cpp
+++ b/src/USER-CUDA/fix_aveforce_cuda.cpp
@@ -22,7 +22,7 @@
------------------------------------------------------------------------- */
-#include "mpi.h"
+#include <mpi.h>
#include <cstring>
#include <cstdlib>
#include "fix_aveforce_cuda.h"
diff --git a/src/USER-CUDA/fix_shake_cuda.cpp b/src/USER-CUDA/fix_shake_cuda.cpp
index 070274cedd..92274d1d46 100644
--- a/src/USER-CUDA/fix_shake_cuda.cpp
+++ b/src/USER-CUDA/fix_shake_cuda.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
+#include <mpi.h>
#include <cmath>
#include <cstdlib>
#include <cstring>
@@ -2793,7 +2793,7 @@ void FixShakeCuda::post_force_respa(int vflag, int ilevel, int iloop)
/* ---------------------------------------------------------------------- */
-int FixShakeCuda::pack_forward_comm(int n, int* list, double* buf,
+int FixShakeCuda::pack_forward_comm(int n, int* list, double* buf,
int pbc_flag, int* pbc)
{
if(cuda->finished_setup) {
diff --git a/src/USER-CUDA/neighbor_cuda.cpp b/src/USER-CUDA/neighbor_cuda.cpp
index eb46a44b3c..015e85ff07 100644
--- a/src/USER-CUDA/neighbor_cuda.cpp
+++ b/src/USER-CUDA/neighbor_cuda.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "neighbor_cuda.h"
#include "user_cuda.h"
#include "atom.h"
diff --git a/src/USER-CUDA/pair_eam_cuda.cpp b/src/USER-CUDA/pair_eam_cuda.cpp
index f3dcdd16f5..3db0c66cd6 100644
--- a/src/USER-CUDA/pair_eam_cuda.cpp
+++ b/src/USER-CUDA/pair_eam_cuda.cpp
@@ -231,7 +231,7 @@ void PairEAMCuda::array2spline()
/* ---------------------------------------------------------------------- */
-int PairEAMCuda::pack_forward_comm(int n, int* iswap, double* buf,
+int PairEAMCuda::pack_forward_comm(int n, int* iswap, double* buf,
int pbc_flag, int* pbc)
{
Cuda_PairEAMCuda_PackComm(&cuda->shared_data, n, *iswap, buf);
diff --git a/src/USER-CUDA/pair_eam_cuda.h b/src/USER-CUDA/pair_eam_cuda.h
index 27f0f45d27..973fc20a45 100644
--- a/src/USER-CUDA/pair_eam_cuda.h
+++ b/src/USER-CUDA/pair_eam_cuda.h
@@ -57,7 +57,7 @@ class PairEAMCuda : public PairEAM
void init_list(int, class NeighList *);
void init_style();
void array2spline();
- int pack_forward_comm(int n, int *iswap, double *buf,
+ int pack_forward_comm(int n, int *iswap, double *buf,
int pbc_flag, int *pbc);
void unpack_forward_comm(int n, int first, double *buf);
protected:
diff --git a/src/USER-CUDA/pair_gran_hooke_cuda.cpp b/src/USER-CUDA/pair_gran_hooke_cuda.cpp
index 88cf2a2c28..3f60475ad5 100644
--- a/src/USER-CUDA/pair_gran_hooke_cuda.cpp
+++ b/src/USER-CUDA/pair_gran_hooke_cuda.cpp
@@ -197,12 +197,12 @@ void PairGranHookeCuda::init_style()
onerad_dynamic[i] = onerad_frozen[i] = 0.0;
if (ipour >= 0) {
itype = i;
- onerad_dynamic[i] =
+ onerad_dynamic[i] =
*((double *) modify->fix[ipour]->extract("radius",itype));
}
if (idep >= 0) {
itype = i;
- onerad_dynamic[i] =
+ onerad_dynamic[i] =
*((double *) modify->fix[idep]->extract("radius",itype));
}
}
diff --git a/src/USER-CUDA/pair_tersoff_zbl_cuda.cpp b/src/USER-CUDA/pair_tersoff_zbl_cuda.cpp
index 32588ed04a..91dcf6189e 100644
--- a/src/USER-CUDA/pair_tersoff_zbl_cuda.cpp
+++ b/src/USER-CUDA/pair_tersoff_zbl_cuda.cpp
@@ -16,10 +16,10 @@
David Farrell (NWU) - ZBL addition
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_tersoff_zbl_cuda.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-CUDA/pppm_cuda.cpp b/src/USER-CUDA/pppm_cuda.cpp
index d770fa350d..b322c9dd17 100644
--- a/src/USER-CUDA/pppm_cuda.cpp
+++ b/src/USER-CUDA/pppm_cuda.cpp
@@ -38,7 +38,7 @@
Contributing authors: Roy Pollock (LLNL), Paul Crozier (SNL)
------------------------------------------------------------------------- */
-#include "mpi.h"
+#include <mpi.h>
#include <cstring>
#include <cstdio>
#include <cstdlib>
@@ -96,7 +96,7 @@ void printArray(double*** data,int nx, int ny, int nz)
}
/* ---------------------------------------------------------------------- */
-PPPMCuda::PPPMCuda(LAMMPS *lmp, int narg, char **arg) :
+PPPMCuda::PPPMCuda(LAMMPS *lmp, int narg, char **arg) :
PPPMOld(lmp, (narg==2?1:narg), arg)
{
cuda = lmp->cuda;
@@ -209,7 +209,7 @@ void PPPMCuda::init()
// error check
if (domain->dimension == 2) error->all(FLERR,"Cannot use PPPMCuda with 2d simulation");
- if (comm->style != 0)
+ if (comm->style != 0)
error->universe_all(FLERR,"PPPMCuda can only currently be used with "
"comm_style brick");
@@ -695,7 +695,7 @@ void PPPMCuda::compute(int eflag, int vflag)
delete cu_part2grid;
delete [] adev_data_array;
adev_data_array=new dev_array[1];
- cu_part2grid = new cCudaData<int , int , yx >
+ cu_part2grid = new cCudaData<int , int , yx >
((int*)part2grid,adev_data_array, nmax,3);
pppm_device_update(&cuda->shared_data,cu_part2grid->dev_data(),
diff --git a/src/USER-CUDA/pppm_old.cpp b/src/USER-CUDA/pppm_old.cpp
index 22d23c4b58..2cc4c18626 100755
--- a/src/USER-CUDA/pppm_old.cpp
+++ b/src/USER-CUDA/pppm_old.cpp
@@ -16,11 +16,11 @@
per-atom energy/virial & group/group energy/force added by Stan Moore (BYU)
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "string.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "math.h"
+#include <mpi.h>
+#include <string.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
#include "pppm_old.h"
#include "math_const.h"
#include "atom.h"
diff --git a/src/USER-CUDA/pppm_old.h b/src/USER-CUDA/pppm_old.h
index b849a4e3fc..57a92e1202 100644
--- a/src/USER-CUDA/pppm_old.h
+++ b/src/USER-CUDA/pppm_old.h
@@ -21,7 +21,7 @@ KSpaceStyle(pppm/old,PPPMOld)
#define LMP_PPPM_OLD_H
#include "lmptype.h"
-#include "mpi.h"
+#include <mpi.h>
#ifdef FFT_SINGLE
typedef float FFT_SCALAR;
diff --git a/src/USER-CUDA/verlet_cuda.cpp b/src/USER-CUDA/verlet_cuda.cpp
index 2a216b5b46..f382117567 100644
--- a/src/USER-CUDA/verlet_cuda.cpp
+++ b/src/USER-CUDA/verlet_cuda.cpp
@@ -53,7 +53,7 @@
#include <ctime>
#include <cmath>
#ifdef _OPENMP
-#include "omp.h"
+#include <omp.h>
#endif
using namespace LAMMPS_NS;
diff --git a/src/USER-DIFFRACTION/compute_saed.cpp b/src/USER-DIFFRACTION/compute_saed.cpp
index e275b5eb1a..fc76a8f867 100644
--- a/src/USER-DIFFRACTION/compute_saed.cpp
+++ b/src/USER-DIFFRACTION/compute_saed.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -15,9 +15,9 @@
Contributing authors: Shawn Coleman & Douglas Spearot (Arkansas)
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "math.h"
-#include "stdlib.h"
+#include <mpi.h>
+#include <math.h>
+#include <stdlib.h>
#include "math_const.h"
#include "compute_saed.h"
#include "compute_saed_consts.h"
@@ -29,8 +29,8 @@
#include "citeme.h"
#include "memory.h"
#include "error.h"
-#include "stdio.h"
-#include "string.h"
+#include <stdio.h>
+#include <string.h>
using namespace LAMMPS_NS;
using namespace MathConst;
@@ -61,16 +61,16 @@ ComputeSAED::ComputeSAED(LAMMPS *lmp, int narg, char **arg) :
me = comm->me;
// Checking errors specific to the compute
- if (dimension == 2)
+ if (dimension == 2)
error->all(FLERR,"Compute SAED does not work with 2d structures");
- if (narg < 4+ntypes)
+ if (narg < 4+ntypes)
error->all(FLERR,"Illegal Compute SAED Command");
- if (triclinic == 1)
- error->all(FLERR,"Compute SAED does not work with triclinic structures");
-
+ if (triclinic == 1)
+ error->all(FLERR,"Compute SAED does not work with triclinic structures");
+
vector_flag = 1;
extvector = 0;
-
+
// Store radiation wavelength
lambda = atof(arg[3]);
if (lambda < 0)
@@ -82,7 +82,7 @@ ComputeSAED::ComputeSAED(LAMMPS *lmp, int narg, char **arg) :
for (int i = 0; i < ntypes; i++){
ztype[i] = SAEDmaxType + 1;
}
- for (int i=0; i<ntypes; i++) {
+ for (int i=0; i<ntypes; i++) {
for(int j = 0; j < SAEDmaxType; j++){
if (strcasecmp(arg[iarg],SAEDtypeList[j]) == 0) {
ztype[i] = j;
@@ -99,40 +99,40 @@ ComputeSAED::ComputeSAED(LAMMPS *lmp, int narg, char **arg) :
c[0] = 1; c[1] = 1; c[2] = 1;
dR_Ewald = 0.01 / 2;
manual = false;
- double manual_double=0;
+ double manual_double=0;
echo = false;
// Process optional args
while (iarg < narg) {
-
+
if (strcmp(arg[iarg],"Kmax") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal Compute SAED Command");
Kmax = atof(arg[iarg+1]);
- if (Kmax / 2 < 0 || Kmax / 2 > 6)
+ if (Kmax / 2 < 0 || Kmax / 2 > 6)
error->all(FLERR,"Compute SAED: |K|max/2 must be between 0 and 6 ");
iarg += 2;
-
+
} else if (strcmp(arg[iarg],"Zone") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal Compute SAED Command");
Zone[0] = atof(arg[iarg+1]);
Zone[1] = atof(arg[iarg+2]);
Zone[2] = atof(arg[iarg+3]);
iarg += 4;
-
+
} else if (strcmp(arg[iarg],"c") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal Compute SAED Command");
c[0] = atof(arg[iarg+1]);
c[1] = atof(arg[iarg+2]);
c[2] = atof(arg[iarg+3]);
- if (c[0] < 0 || c[1] < 0 || c[2] < 0)
- error->all(FLERR,"Compute SAED: dKs must be greater than 0");
+ if (c[0] < 0 || c[1] < 0 || c[2] < 0)
+ error->all(FLERR,"Compute SAED: dKs must be greater than 0");
iarg += 4;
-
+
} else if (strcmp(arg[iarg],"dR_Ewald") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal Compute SAED Command");
dR_Ewald = atof(arg[iarg+1]);
- if (dR_Ewald < 0)
- error->all(FLERR,"Compute SAED: dR_Ewald slice must be greater than 0");
+ if (dR_Ewald < 0)
+ error->all(FLERR,"Compute SAED: dR_Ewald slice must be greater than 0");
iarg += 2;
} else if (strcmp(arg[iarg],"echo") == 0) {
@@ -141,41 +141,41 @@ ComputeSAED::ComputeSAED(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"manual") == 0) {
manual = true;
- manual_double = 1;
- iarg += 1;
-
+ manual_double = 1;
+ iarg += 1;
+
} else error->all(FLERR,"Illegal Compute SAED Command");
}
-
+
// Zone flag to capture entire recrocal space volume
if ( (Zone[0] == 0) && (Zone[1] == 0) && (Zone[2] == 0) ){
} else {
- R_Ewald = (1 / lambda);
- double Rnorm = R_Ewald/ sqrt(Zone[0] * Zone[0] +
+ R_Ewald = (1 / lambda);
+ double Rnorm = R_Ewald/ sqrt(Zone[0] * Zone[0] +
Zone[1] * Zone[1] + Zone[2]* Zone[2]);
- Zone[0] = Zone[0] * Rnorm;
- Zone[1] = Zone[1] * Rnorm;
- Zone[2] = Zone[2] * Rnorm;
+ Zone[0] = Zone[0] * Rnorm;
+ Zone[1] = Zone[1] * Rnorm;
+ Zone[2] = Zone[2] * Rnorm;
}
// Procedure to determine how many rows are needed given the constraints on 2theta
- // Calculating spacing between reciprical lattice points
+ // Calculating spacing between reciprical lattice points
// Using distance based on periodic repeating distance
- if (!manual) {
+ if (!manual) {
if (!periodicity[0] && !periodicity[1] && !periodicity[2])
error->all(FLERR,"Compute SAED must have at least one periodic boundary unless manual spacing specified");
double *prd;
- double ave_inv = 0.0;
+ double ave_inv = 0.0;
prd = domain->prd;
if (periodicity[0]){
- prd_inv[0] = 1 / prd[0];
+ prd_inv[0] = 1 / prd[0];
ave_inv += prd_inv[0];
- }
+ }
if (periodicity[1]){
prd_inv[1] = 1 / prd[1];
ave_inv += prd_inv[1];
- }
+ }
if (periodicity[2]){
prd_inv[2] = 1 / prd[2];
ave_inv += prd_inv[2];
@@ -184,34 +184,34 @@ ComputeSAED::ComputeSAED(LAMMPS *lmp, int narg, char **arg) :
// Using the average inverse dimensions for non-periodic direction
ave_inv = ave_inv / (periodicity[0] + periodicity[1] + periodicity[2]);
if (!periodicity[0]){
- prd_inv[0] = ave_inv;
- }
+ prd_inv[0] = ave_inv;
+ }
if (!periodicity[1]){
prd_inv[1] = ave_inv;
- }
+ }
if (!periodicity[2]){
prd_inv[2] = ave_inv;
}
}
- // Use manual mapping of reciprocal lattice
+ // Use manual mapping of reciprocal lattice
if (manual) {
for (int i=0; i<3; i++) {
prd_inv[i] = 1.0;
}
- }
-
+ }
+
// Find reprical spacing and integer dimensions
for (int i=0; i<3; i++) {
dK[i] = prd_inv[i]*c[i];
Knmax[i] = ceil(Kmax / dK[i]);
}
-
+
// Finding the intersection of the reciprical space and Ewald sphere
int n = 0;
double dinv2, r2, EmdR2, EpdR2;
double K[3];
-
+
// Zone flag to capture entire recrocal space volume
if ( (Zone[0] == 0) && (Zone[1] == 0) && (Zone[2] == 0) ){
for (int k = -Knmax[2]; k <= Knmax[2]; k++) {
@@ -222,9 +222,9 @@ ComputeSAED::ComputeSAED(LAMMPS *lmp, int narg, char **arg) :
K[2] = k * dK[2];
dinv2 = (K[0] * K[0] + K[1] * K[1] + K[2] * K[2]);
if (dinv2 < Kmax * Kmax) n++;
- }
+ }
}
- }
+ }
} else {
for (int k = -Knmax[2]; k <= Knmax[2]; k++) {
for (int j = -Knmax[1]; j <= Knmax[1]; j++) {
@@ -238,14 +238,14 @@ ComputeSAED::ComputeSAED(LAMMPS *lmp, int narg, char **arg) :
for (int m=0; m<3; m++)
r2 += pow(K[m] - Zone[m],2.0);
EmdR2 = pow(R_Ewald - dR_Ewald,2);
- EpdR2 = pow(R_Ewald + dR_Ewald,2);
+ EpdR2 = pow(R_Ewald + dR_Ewald,2);
if ( (r2 > EmdR2 ) && (r2 < EpdR2 ) ) {
n++;
}
}
- }
+ }
}
- }
+ }
}
if (me == 0) {
@@ -254,13 +254,13 @@ ComputeSAED::ComputeSAED(LAMMPS *lmp, int narg, char **arg) :
fprintf(screen,"Reciprocal point spacing in k1,k2,k3 = %g %g %g\n-----\n",
dK[0], dK[1], dK[2]);
}
- }
+ }
nRows = n;
size_vector = n;
memory->create(vector,size_vector,"saed:vector");
memory->create(store_tmp,3*size_vector,"saed:store_tmp");
-
+
// Create vector of variables to be passed to fix ave/time/saed
saed_var[0] = lambda;
@@ -291,7 +291,7 @@ void ComputeSAED::init()
double dinv2, r2, EmdR2, EpdR2;
double K[3];
int n = 0;
-
+
// Zone 0 0 0 flag to capture entire recrocal space volume
if ( (Zone[0] == 0) && (Zone[1] == 0) && (Zone[2] == 0) ){
for (int k = -Knmax[2]; k <= Knmax[2]; k++) {
@@ -307,8 +307,8 @@ void ComputeSAED::init()
store_tmp[3*n+2] = k;
n++;
}
- }
- }
+ }
+ }
}
} else {
for (int k = -Knmax[2]; k <= Knmax[2]; k++) {
@@ -323,7 +323,7 @@ void ComputeSAED::init()
for (int m=0; m<3; m++)
r2 += pow(K[m] - Zone[m],2.0);
EmdR2 = pow(R_Ewald - dR_Ewald,2);
- EpdR2 = pow(R_Ewald + dR_Ewald,2);
+ EpdR2 = pow(R_Ewald + dR_Ewald,2);
if ( (r2 > EmdR2 ) && (r2 < EpdR2 ) ) {
store_tmp[3*n] = i;
store_tmp[3*n+1] = j;
@@ -332,8 +332,8 @@ void ComputeSAED::init()
}
}
}
- }
- }
+ }
+ }
}
if (n != nRows) error->all(FLERR,"Compute SAED Nrows inconsistent");
@@ -379,7 +379,7 @@ void ComputeSAED::compute_vector()
typelocal[nlocalgroup]=type[ii];
nlocalgroup++;
}
- }
+ }
/*
double *x = new double [3*nlocal];
@@ -397,10 +397,10 @@ void ComputeSAED::compute_vector()
// determining paramater set to use based on maximum S = sin(theta)/lambda
double Smax = Kmax / 2;
-
+
int offset = 0; // offset the ASFSAED matrix for appropriate value
if (Smax <= 2) offset = 0;
- if (Smax > 2) offset = 10;
+ if (Smax > 2) offset = 10;
// Setting up OMP
#if defined(_OPENMP)
@@ -429,7 +429,7 @@ void ComputeSAED::compute_vector()
double K[3];
double dinv2 = 0.0;
double dinv = 0.0;
- double SinTheta_lambda = 0.0;
+ double SinTheta_lambda = 0.0;
double inners = 0.0;
#if defined(_OPENMP)
@@ -442,11 +442,11 @@ void ComputeSAED::compute_vector()
K[0] = i * dK[0];
K[1] = j * dK[1];
K[2] = k * dK[2];
-
+
dinv2 = (K[0] * K[0] + K[1] * K[1] + K[2] * K[2]);
dinv = sqrt(dinv2);
SinTheta_lambda = 0.5*dinv;
-
+
Fatom1 = 0.0;
Fatom2 = 0.0;
@@ -508,14 +508,14 @@ void ComputeSAED::compute_vector()
bytes += 3.0 * nlocalgroup * sizeof(double); // xlocal
bytes += nlocalgroup * sizeof(int); // typelocal
bytes += 3.0 * nRows * sizeof(int); // store_temp
-
+
if (me == 0 && echo) {
if (screen)
fprintf(screen," 100%% \nTime ellapsed during compute_saed = %0.2f sec using %0.2f Mbytes/processor\n-----\n", t2-t0, bytes/1024.0/1024.0);
}
delete [] xlocal;
- delete [] typelocal;
+ delete [] typelocal;
delete [] scratch;
delete [] Fvec;
}
@@ -532,7 +532,7 @@ double ComputeSAED::memory_usage()
bytes += 3.0 * nlocalgroup * sizeof(double); // xlocal
bytes += nlocalgroup * sizeof(int); // typelocal
bytes += 3.0 * nRows * sizeof(int); // store_temp
-
+
return bytes;
}
diff --git a/src/USER-DIFFRACTION/compute_saed.h b/src/USER-DIFFRACTION/compute_saed.h
index 0118b64811..89e57f5097 100644
--- a/src/USER-DIFFRACTION/compute_saed.h
+++ b/src/USER-DIFFRACTION/compute_saed.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -31,7 +31,7 @@ class ComputeSAED : public Compute {
void init();
void compute_vector();
double memory_usage();
-//testing
+//testing
double saed_var[10];
private:
diff --git a/src/USER-DIFFRACTION/compute_saed_consts.h b/src/USER-DIFFRACTION/compute_saed_consts.h
index 3d62829c89..0cce0abfc2 100644
--- a/src/USER-DIFFRACTION/compute_saed_consts.h
+++ b/src/USER-DIFFRACTION/compute_saed_consts.h
@@ -16,20 +16,20 @@
/*
The paramaters for analytical approximation of the atomic scattering factors
-used for electron diffraction are gathered from the resources:
+used for electron diffraction are gathered from the resources:
-Colliex C et al 2004 Electron diffraction International Tables for
-Crystallography Volume C: Mathematical, Physical, and Chemical Tables
+Colliex C et al 2004 Electron diffraction International Tables for
+Crystallography Volume C: Mathematical, Physical, and Chemical Tables
ed E Prince (Norwell, MA: Kluwer) pp 259429
-Peng L-M, Ren G, Dudarev S L and Whelan MJ 1996 Robust parameterization of
-elastic and absorptive electron atomic scattering factors
+Peng L-M, Ren G, Dudarev S L and Whelan MJ 1996 Robust parameterization of
+elastic and absorptive electron atomic scattering factors
Acta Crystallogr.A 52 25776
*/
#define SAEDmaxType 98
-// list of element types associated with atomic scattering factor constants
+// list of element types associated with atomic scattering factor constants
static const char *SAEDtypeList[SAEDmaxType] = {
"H", "He", "Li", "Be", "B",
"C", "N", "O", "F", "Ne",
diff --git a/src/USER-DIFFRACTION/compute_xrd.cpp b/src/USER-DIFFRACTION/compute_xrd.cpp
index ffd1f1c9dd..5d30cfc877 100644
--- a/src/USER-DIFFRACTION/compute_xrd.cpp
+++ b/src/USER-DIFFRACTION/compute_xrd.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -16,9 +16,9 @@
Updated: 06/17/2015-2
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "math.h"
-#include "stdlib.h"
+#include <mpi.h>
+#include <math.h>
+#include <stdlib.h>
#include "math_const.h"
#include "compute_xrd.h"
#include "compute_xrd_consts.h"
@@ -30,8 +30,8 @@
#include "citeme.h"
#include "memory.h"
#include "error.h"
-#include "stdio.h"
-#include "string.h"
+#include <stdio.h>
+#include <string.h>
using namespace LAMMPS_NS;
using namespace MathConst;
@@ -62,11 +62,11 @@ ComputeXRD::ComputeXRD(LAMMPS *lmp, int narg, char **arg) :
me = comm->me;
// Checking errors
- if (dimension == 2)
+ if (dimension == 2)
error->all(FLERR,"Compute XRD does not work with 2d structures");
- if (narg < 4+ntypes)
+ if (narg < 4+ntypes)
error->all(FLERR,"Illegal Compute XRD Command");
- if (triclinic == 1)
+ if (triclinic == 1)
error->all(FLERR,"Compute XRD does not work with triclinic structures");
array_flag = 1;
@@ -78,12 +78,12 @@ ComputeXRD::ComputeXRD(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,"Compute SAED: Wavelength must be greater than zero");
// Define atom types for atomic scattering factor coefficients
- int iarg = 4;
+ int iarg = 4;
ztype = new int[ntypes];
for (int i = 0; i < ntypes; i++){
ztype[i] = XRDmaxType + 1;
}
- for (int i = 0; i < ntypes; i++) {
+ for (int i = 0; i < ntypes; i++) {
for(int j = 0; j < XRDmaxType; j++){
if (strcasecmp(arg[iarg],XRDtypeList[j]) == 0) {
ztype[i] = j;
@@ -96,7 +96,7 @@ ComputeXRD::ComputeXRD(LAMMPS *lmp, int narg, char **arg) :
// Set defaults for optional args
Min2Theta = 1;
- Max2Theta = 179;
+ Max2Theta = 179;
radflag = 1;
c[0] = 1; c[1] = 1; c[2] = 1;
LP = 1;
@@ -114,11 +114,11 @@ ComputeXRD::ComputeXRD(LAMMPS *lmp, int narg, char **arg) :
Max2Theta = Max2Theta * MY_PI / 180;
radflag = 0;
}
- if (Min2Theta <= 0)
+ if (Min2Theta <= 0)
error->all(FLERR,"Minimum 2theta value must be greater than zero");
- if (Max2Theta >= MY_PI )
+ if (Max2Theta >= MY_PI )
error->all(FLERR,"Maximum 2theta value must be less than 180 degrees");
- if (Max2Theta-Min2Theta <= 0)
+ if (Max2Theta-Min2Theta <= 0)
error->all(FLERR,"Two-theta range must be greater than zero");
iarg += 3;
@@ -127,16 +127,16 @@ ComputeXRD::ComputeXRD(LAMMPS *lmp, int narg, char **arg) :
c[0] = atof(arg[iarg+1]);
c[1] = atof(arg[iarg+2]);
c[2] = atof(arg[iarg+3]);
- if (c[0] < 0 || c[1] < 0 || c[2] < 0)
- error->all(FLERR,"Compute XRD: c's must be greater than 0");
+ if (c[0] < 0 || c[1] < 0 || c[2] < 0)
+ error->all(FLERR,"Compute XRD: c's must be greater than 0");
iarg += 4;
-
+
} else if (strcmp(arg[iarg],"LP") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal Compute XRD Command");
LP = atof(arg[iarg+1]);
- if (!(LP == 1 || LP == 0))
- error->all(FLERR,"Compute XRD: LP must have value of 0 or 1");
+ if (!(LP == 1 || LP == 0))
+ error->all(FLERR,"Compute XRD: LP must have value of 0 or 1");
iarg += 2;
} else if (strcmp(arg[iarg],"echo") == 0) {
@@ -145,31 +145,31 @@ ComputeXRD::ComputeXRD(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"manual") == 0) {
manual = true;
- iarg += 1;
-
+ iarg += 1;
+
} else error->all(FLERR,"Illegal Compute XRD Command");
}
-
+
Kmax = 2 * sin(Max2Theta) / lambda;
-
- // Calculating spacing between reciprocal lattice points
+
+ // Calculating spacing between reciprocal lattice points
// Using distance based on periodic repeating distance
- if (!manual) {
+ if (!manual) {
if (!periodicity[0] && !periodicity[1] && !periodicity[2])
error->all(FLERR,"Compute SAED must have at least one periodic boundary unless manual spacing specified");
double *prd;
- double ave_inv = 0.0;
+ double ave_inv = 0.0;
prd = domain->prd;
if (periodicity[0]){
- prd_inv[0] = 1 / prd[0];
+ prd_inv[0] = 1 / prd[0];
ave_inv += prd_inv[0];
- }
+ }
if (periodicity[1]){
prd_inv[1] = 1 / prd[1];
ave_inv += prd_inv[1];
- }
+ }
if (periodicity[2]){
prd_inv[2] = 1 / prd[2];
ave_inv += prd_inv[2];
@@ -178,35 +178,35 @@ ComputeXRD::ComputeXRD(LAMMPS *lmp, int narg, char **arg) :
// Using the average inverse dimensions for non-periodic direction
ave_inv = ave_inv / (periodicity[0] + periodicity[1] + periodicity[2]);
if (!periodicity[0]){
- prd_inv[0] = ave_inv;
- }
+ prd_inv[0] = ave_inv;
+ }
if (!periodicity[1]){
prd_inv[1] = ave_inv;
- }
+ }
if (!periodicity[2]){
prd_inv[2] = ave_inv;
}
}
- // Use manual mapping of reciprocal lattice
+ // Use manual mapping of reciprocal lattice
if (manual) {
for (int i=0; i<3; i++) {
prd_inv[i] = 1.0;
}
- }
-
+ }
+
// Find reciprocal spacing and integer dimensions
for (int i=0; i<3; i++) {
dK[i] = prd_inv[i]*c[i];
Knmax[i] = ceil(Kmax / dK[i]);
- }
-
+ }
+
// Finding the intersection of the reciprocal space and Ewald sphere
int nRows = 0;
double dinv2= 0.0;
double ang = 0.0;
double K[3];
-
+
// Procedure to determine how many rows are needed given the constraints on 2theta
for (int i = -Knmax[0]; i <= Knmax[0]; i++) {
for (int j = -Knmax[1]; j <= Knmax[1]; j++) {
@@ -221,22 +221,22 @@ ComputeXRD::ComputeXRD(LAMMPS *lmp, int narg, char **arg) :
nRows++;
}
}
- }
+ }
}
- }
-
+ }
+
size_array_rows = nRows;
size_array_cols = 2;
-
+
if (me == 0) {
if (screen && echo) {
fprintf(screen,"-----\nCompute XRD id:%s, # of atoms:%d, # of relp:%d\n",id,natoms,nRows);
fprintf(screen,"Reciprocal point spacing in k1,k2,k3 = %g %g %g\n-----\n",
dK[0], dK[1], dK[2]);
}
- }
-
+ }
+
memory->create(array,size_array_rows,size_array_cols,"xrd:array");
memory->create(store_tmp,3*size_array_rows,"xrd:store_tmp");
}
@@ -287,7 +287,7 @@ void ComputeXRD::init()
}
}
}
- if (n != size_array_rows)
+ if (n != size_array_rows)
error->all(FLERR,"Compute XRD compute_array() rows mismatch");
}
@@ -307,7 +307,7 @@ void ComputeXRD::compute_array()
double *Fvec = new double[2*size_array_rows]; // Strct factor (real & imaginary)
// -- Note: array rows correspond to different RELP
-
+
ntypes = atom->ntypes;
int nlocal = atom->nlocal;
int *type = atom->type;
@@ -333,7 +333,7 @@ void ComputeXRD::compute_array()
typelocal[nlocalgroup]=type[ii];
nlocalgroup++;
}
- }
+ }
// Setting up OMP
#if defined(_OPENMP)
@@ -387,14 +387,14 @@ void ComputeXRD::compute_array()
K[0] = i * dK[0];
K[1] = j * dK[1];
K[2] = k * dK[2];
-
+
dinv2 = (K[0] * K[0] + K[1] * K[1] + K[2] * K[2]);
dinv = sqrt(dinv2);
SinTheta_lambda = 0.5*dinv;
- SinTheta = SinTheta_lambda * lambda;
+ SinTheta = SinTheta_lambda * lambda;
ang = asin( SinTheta );
Cos2Theta = cos( 2 * ang);
- CosTheta = cos( ang );
+ CosTheta = cos( ang );
Fatom1 = 0.0;
Fatom2 = 0.0;
@@ -433,7 +433,7 @@ void ComputeXRD::compute_array()
}
m++;
}
- }
+ }
} // End of pragma omp for region
} else {
@@ -447,11 +447,11 @@ void ComputeXRD::compute_array()
K[0] = i * dK[0];
K[1] = j * dK[1];
K[2] = k * dK[2];
-
+
dinv2 = (K[0] * K[0] + K[1] * K[1] + K[2] * K[2]);
dinv = sqrt(dinv2);
SinTheta_lambda = 0.5*dinv;
-
+
Fatom1 = 0.0;
Fatom2 = 0.0;
@@ -489,7 +489,7 @@ void ComputeXRD::compute_array()
}
}
} // End of pragma omp for region
- } // End of if LP=1 check
+ } // End of if LP=1 check
delete [] f;
} // End of pragma omp parallel region
@@ -511,7 +511,7 @@ void ComputeXRD::compute_array()
bytes += 3.0 * nlocalgroup * sizeof(double); // xlocal
bytes += nlocalgroup * sizeof(int); // typelocal
bytes += 3.0 * size_array_rows * sizeof(int); // store_temp
-
+
if (me == 0 && echo) {
if (screen)
fprintf(screen," 100%% \nTime ellapsed during compute_xrd = %0.2f sec using %0.2f Mbytes/processor\n-----\n", t2-t0, bytes/1024.0/1024.0);
@@ -535,7 +535,7 @@ double ComputeXRD::memory_usage()
bytes += nlocalgroup * sizeof(int); // typelocal
bytes += ntypes * sizeof(double); // f
bytes += 3.0 * size_array_rows * sizeof(int); // store_temp
-
+
return bytes;
}
diff --git a/src/USER-DIFFRACTION/compute_xrd.h b/src/USER-DIFFRACTION/compute_xrd.h
index d3df948adc..92a59fcf23 100644
--- a/src/USER-DIFFRACTION/compute_xrd.h
+++ b/src/USER-DIFFRACTION/compute_xrd.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -37,7 +37,7 @@ class ComputeXRD : public Compute {
int *ztype; // Atomic number of the different atom types
double Min2Theta; // Minimum 2theta value (input in 2theta rad)
double Max2Theta; // Maximum 2theta value (input in 2theta rad)
- double Kmax; // Maximum reciprocal distance to explore
+ double Kmax; // Maximum reciprocal distance to explore
double c[3]; // Resolution parameters for reciprocal space explored
int Knmax[3]; // maximum integer value for K points in each dimension
double dK[3]; // Parameters controlling resolution of reciprocal space explored
@@ -45,13 +45,13 @@ class ComputeXRD : public Compute {
int LP; // Switch to turn on Lorentz-Polarization factor 1=on
bool echo; // echo compute_array progress
bool manual; // Turn on manual recpiprocal map
-
+
int ntypes;
int nlocalgroup;
double lambda; // Radiation wavelenght (distance units)
int radflag;
int *store_tmp;
-
+
};
}
diff --git a/src/USER-DIFFRACTION/compute_xrd_consts.h b/src/USER-DIFFRACTION/compute_xrd_consts.h
index e3f2a0ca67..1ca0d6bd66 100644
--- a/src/USER-DIFFRACTION/compute_xrd_consts.h
+++ b/src/USER-DIFFRACTION/compute_xrd_consts.h
@@ -16,49 +16,49 @@
/*
The paramaters for analytical approximation of the atomic scattering factors
-used for x-ray diffraction are gathered from the resources:
+used for x-ray diffraction are gathered from the resources:
-Brown P J, Fox A G, Maslen E N, O’Keefe M A and Willis B T M 2004 Intensity
-of diffraction intensities International Tables for Crystallography
-Volume C: Mathematical, Physical, and Chemical Tables
+Brown P J, Fox A G, Maslen E N, O’Keefe M A and Willis B T M 2004 Intensity
+of diffraction intensities International Tables for Crystallography
+Volume C: Mathematical, Physical, and Chemical Tables
ed E Prince (Norwell, MA: Kluwer Academic Publishers) pp 55495
Fox A G, O’Keefe M A and Tabbernor M A 1989 Relativistic Hartree Fock
-x-ray and electron atomic scattering factors at high angles
+x-ray and electron atomic scattering factors at high angles
Acta Crystallogr. A 45 78693
*/
#define XRDmaxType 210
static const char *XRDtypeList[XRDmaxType] = {
- "H", "He1-", "He", "Li", "Li1+",
- "Be", "Be2+", "B", "C", "Cval",
- "N", "O", "O1-", "F", "F1-",
- "Ne", "Na", "Na1+", "Mg", "Mg2+",
- "Al", "Al3+", "Si", "Sival", "Si4+",
- "P", "S", "Cl", "Cl1-", "Ar",
- "K", "Ca", "Ca2+", "Sc", "Sc3+",
- "Ti", "Ti2+", "Ti3+", "Ti4+", "V",
- "V2+", "V3+", "V5+", "Cr", "Cr2+",
- "Cr3+", "Mn", "Mn2+", "Mn3+", "Mn4+",
- "Fe", "Fe2+", "Fe3+", "Co", "Co2+",
- "Co", "Ni", "Ni2+", "Ni3+", "Cu",
- "Cu1+", "Cu2+", "Zn", "Zn2+", "Ga",
- "Ga3+", "Ge", "Ge4+", "As", "Se",
- "Br", "Br1-", "Kr", "Rb", "Rb1+",
- "Sr", "Sr2+", "Y", "Y3+", "Zr",
- "Zr4+", "Nb", "Nb3+", "Nb5+", "Mo",
- "Mo3+", "Mo5+", "Mo6+", "Tc", "Ru",
- "Ru3+", "Ru4+", "Rh", "Rh3+", "Rh4+",
- "Pd", "Pd2+", "Pd4+", "Ag", "Ag1+",
- "Ag2+", "Cd", "Cd2+", "In", "In3+",
- "Sn", "Sn2+", "Sn4+", "Sb", "Sb3+",
- "Sb5+", "Te", "I", "I1-", "Xe",
- "Cs", "Cs1+", "Ba", "Ba2+", "La",
- "La3+", "Ce", "Ce3+", "Ce4+", "Pr",
- "Pr3+", "Pr4+", "Nd", "Nd3+", "Pm",
- "Pm3+", "Sm", "Sm3+", "Eu", "Eu2+",
- "Eu3+", "Gd", "Gd3+", "Tb", "Tb3+",
+ "H", "He1-", "He", "Li", "Li1+",
+ "Be", "Be2+", "B", "C", "Cval",
+ "N", "O", "O1-", "F", "F1-",
+ "Ne", "Na", "Na1+", "Mg", "Mg2+",
+ "Al", "Al3+", "Si", "Sival", "Si4+",
+ "P", "S", "Cl", "Cl1-", "Ar",
+ "K", "Ca", "Ca2+", "Sc", "Sc3+",
+ "Ti", "Ti2+", "Ti3+", "Ti4+", "V",
+ "V2+", "V3+", "V5+", "Cr", "Cr2+",
+ "Cr3+", "Mn", "Mn2+", "Mn3+", "Mn4+",
+ "Fe", "Fe2+", "Fe3+", "Co", "Co2+",
+ "Co", "Ni", "Ni2+", "Ni3+", "Cu",
+ "Cu1+", "Cu2+", "Zn", "Zn2+", "Ga",
+ "Ga3+", "Ge", "Ge4+", "As", "Se",
+ "Br", "Br1-", "Kr", "Rb", "Rb1+",
+ "Sr", "Sr2+", "Y", "Y3+", "Zr",
+ "Zr4+", "Nb", "Nb3+", "Nb5+", "Mo",
+ "Mo3+", "Mo5+", "Mo6+", "Tc", "Ru",
+ "Ru3+", "Ru4+", "Rh", "Rh3+", "Rh4+",
+ "Pd", "Pd2+", "Pd4+", "Ag", "Ag1+",
+ "Ag2+", "Cd", "Cd2+", "In", "In3+",
+ "Sn", "Sn2+", "Sn4+", "Sb", "Sb3+",
+ "Sb5+", "Te", "I", "I1-", "Xe",
+ "Cs", "Cs1+", "Ba", "Ba2+", "La",
+ "La3+", "Ce", "Ce3+", "Ce4+", "Pr",
+ "Pr3+", "Pr4+", "Nd", "Nd3+", "Pm",
+ "Pm3+", "Sm", "Sm3+", "Eu", "Eu2+",
+ "Eu3+", "Gd", "Gd3+", "Tb", "Tb3+",
"Dy", "Dy3+", "Ho", "Ho3+", "Er",
"Er3+", "Tm", "Tm3+", "Yb", "Yb2+",
"Yb3+", "Lu", "Lu3+", "Hf", "Hf4+",
@@ -82,425 +82,425 @@ static const double ASFXRD[XRDmaxType][9] = {
B3, A4, B4, C
*/
{0.489918, 20.6593, 0.262003, 7.74039, 0.196767,
- 49.5519, 0.049879, 2.20159, 0.001305},
+ 49.5519, 0.049879, 2.20159, 0.001305},
{0.897661, 53.1368, 0.565616, 15.187, 0.415815,
- 186.576, 0.116973, 3.56709, 0.002389},
+ 186.576, 0.116973, 3.56709, 0.002389},
{ 0.8734, 9.1037, 0.6309, 3.3568, 0.3112,
- 22.9276, 0.178, 0.9821, 0.0064},
+ 22.9276, 0.178, 0.9821, 0.0064},
{ 1.1282, 3.9546, 0.7508, 1.0524, 0.6175,
- 85.3905, 0.4653, 68.261, 0.0377},
+ 85.3905, 0.4653, 68.261, 0.0377},
{ 0.6968, 4.6237, 0.7888, 1.9557, 0.3414,
- 0.6316, 0.7029, 0.542, 0.0167},
+ 0.6316, 0.7029, 0.542, 0.0167},
{ 1.5919, 43.6427, 1.1278, 1.8623, 0.5391,
- 103.483, 0.7029, 0.542, 0.0385},
+ 103.483, 0.7029, 0.542, 0.0385},
{ 6.2603, 0.0027, 0.8849, 0.8313, 0.7993,
- 2.2758, 0.1647, 5.1146, -6.1092},
+ 2.2758, 0.1647, 5.1146, -6.1092},
{ 2.0545, 23.2185, 1.3326, 1.021, 1.0979,
- 60.3498, 0.7068, 0.1403, -0.1932},
+ 60.3498, 0.7068, 0.1403, -0.1932},
{ 2.31, 20.8439, 1.02, 10.2075, 1.5886,
- 0.5687, 0.865, 51.6512, 0.2156},
+ 0.5687, 0.865, 51.6512, 0.2156},
{ 2.26069, 22.6907, 1.56165, 0.656665, 1.05075,
- 9.75618, 0.839259, 55.5949, 0.286977},
+ 9.75618, 0.839259, 55.5949, 0.286977},
{ 12.2126, 0.0057, 3.1322, 9.8933, 2.0125,
- 28.9975, 1.1663, 0.5826, -11.529},
+ 28.9975, 1.1663, 0.5826, -11.529},
{ 3.0485, 13.2771, 2.2868, 5.7011, 1.5463,
- 0.3239, 0.867, 32.9089, 0.2508},
+ 0.3239, 0.867, 32.9089, 0.2508},
{ 4.1916, 12.8573, 1.63969, 4.17236, 1.52673,
- -47.0179, 20.307, -0.01404, 21.9412},
+ -47.0179, 20.307, -0.01404, 21.9412},
{ 3.5392, 10.2825, 2.6412, 4.2944, 1.517,
- 0.2615, 1.0243, 26.1476, 0.2776},
+ 0.2615, 1.0243, 26.1476, 0.2776},
{ 3.6322, 5.27756, 3.51057, 14.7353, 1.26064,
- 0.442258, 0.940706, 47.3437, 0.653396},
+ 0.442258, 0.940706, 47.3437, 0.653396},
{ 3.9553, 8.4042, 3.1125, 3.4262, 1.4546,
- 0.2306, 1.1251, 21.7184, 0.3515},
+ 0.2306, 1.1251, 21.7184, 0.3515},
{ 4.7626, 3.285, 3.1736, 8.8422, 1.2674,
- 0.3136, 1.1128, 129.424, 0.676},
+ 0.3136, 1.1128, 129.424, 0.676},
{ 3.2565, 2.6671, 3.9362, 6.1153, 1.3998,
- 0.2001, 1.0032, 14.039, 0.404},
+ 0.2001, 1.0032, 14.039, 0.404},
{ 5.4204, 2.8275, 2.1735, 79.2611, 1.2269,
- 0.3808, 2.3073, 7.1937, 0.8584},
+ 0.3808, 2.3073, 7.1937, 0.8584},
{ 3.4988, 2.1676, 3.8378, 4.7542, 1.3284,
- 0.185, 0.8497, 10.1411, 0.4853},
+ 0.185, 0.8497, 10.1411, 0.4853},
{ 6.4202, 3.0387, 1.9002, 0.7426, 1.5936,
- 31.5472, 1.9646, 85.0886, 1.1151},
+ 31.5472, 1.9646, 85.0886, 1.1151},
{ 4.17448, 1.93816, 3.3876, 4.14553, 1.20296,
- 0.228753, 0.528137, 8.28524, 0.706786},
+ 0.228753, 0.528137, 8.28524, 0.706786},
{ 6.2915, 2.4386, 3.0353, 32.3337, 1.9891,
- 0.6785, 1.541, 81.6937, 1.1407},
+ 0.6785, 1.541, 81.6937, 1.1407},
{ 5.66269, 2.6652, 3.07164, 38.6634, 2.62446,
- 0.916946, 1.3932, 93.5458, 1.24707},
+ 0.916946, 1.3932, 93.5458, 1.24707},
{ 4.43918, 1.64167, 3.20345, 3.43757, 1.19453,
- 0.2149, 0.41653, 6.65365, 0.746297},
+ 0.2149, 0.41653, 6.65365, 0.746297},
{ 6.4345, 1.9067, 4.1791, 27.157, 1.78,
- 0.526, 1.4908, 68.1645, 1.1149},
+ 0.526, 1.4908, 68.1645, 1.1149},
{ 6.9053, 1.4679, 5.2034, 22.2151, 1.4379,
- 0.2536, 1.5863, 56.172, 0.8669},
+ 0.2536, 1.5863, 56.172, 0.8669},
{ 11.4604, 0.0104, 7.1964, 1.1662, 6.2556,
- 18.5194, 1.6455, 47.7784, -9.5574},
+ 18.5194, 1.6455, 47.7784, -9.5574},
{ 18.2915, 0.0066, 7.2084, 1.1717, 6.5337,
- 19.5424, 2.3386, 60.4486, -16.378},
+ 19.5424, 2.3386, 60.4486, -16.378},
{ 7.4845, 0.9072, 6.7723, 14.8407, 0.6539,
- 43.8983, 1.6442, 33.3929, 1.4445},
+ 43.8983, 1.6442, 33.3929, 1.4445},
{ 8.2186, 12.7949, 7.4398, 0.7748, 1.0519,
- 213.187, 0.8659, 41.6841, 1.4228},
+ 213.187, 0.8659, 41.6841, 1.4228},
{ 8.6266, 10.4421, 7.3873, 0.6599, 1.5899,
- 85.7484, 1.0211, 178.437, 1.3751},
+ 85.7484, 1.0211, 178.437, 1.3751},
{ 15.6348, -0.0074, 7.9518, 0.6089, 8.4372,
- 10.3116, 0.8537, 25.9905, -14.875},
+ 10.3116, 0.8537, 25.9905, -14.875},
{ 9.189, 9.0213, 7.3679, 0.5729, 1.6409,
- 136.108, 1.468, 51.3531, 1.3329},
+ 136.108, 1.468, 51.3531, 1.3329},
{ 13.4008, 0.29854, 8.0273, 7.9629, 1.65943,
- -0.28604, 1.57936, 16.0662, -6.6667},
+ -0.28604, 1.57936, 16.0662, -6.6667},
{ 9.7595, 7.8508, 7.3558, 0.5, 1.6991,
- 35.6338, 1.9021, 116.105, 1.2807},
+ 35.6338, 1.9021, 116.105, 1.2807},
{ 9.11423, 7.5243, 7.62174, 0.457585, 2.2793,
- 19.5361, 0.087899, 61.6558, 0.897155},
+ 19.5361, 0.087899, 61.6558, 0.897155},
{ 17.7344, 0.22061, 8.73816, 7.04716, 5.25691,
- -0.15762, 1.92134, 15.9768, -14.652},
+ -0.15762, 1.92134, 15.9768, -14.652},
{ 19.5114, 0.178847, 8.23473, 6.67018, 2.01341,
- -0.29263, 1.5208, 12.9464, -13.28},
+ -0.29263, 1.5208, 12.9464, -13.28},
{ 10.2971, 6.8657, 7.3511, 0.4385, 2.0703,
- 26.8938, 2.0571, 102.478, 1.2199},
+ 26.8938, 2.0571, 102.478, 1.2199},
{ 10.106, 6.8818, 7.3541, 0.4409, 2.2884,
- 20.3004, 0.0223, 115.122, 1.2298},
+ 20.3004, 0.0223, 115.122, 1.2298},
{ 9.43141, 6.39535, 7.7419, 0.383349, 2.15343,
- 15.1908, 0.016865, 63.969, 0.656565},
+ 15.1908, 0.016865, 63.969, 0.656565},
{ 15.6887, 0.679003, 8.14208, 5.40135, 2.03081,
- 9.97278, -9.576, 0.940464, 1.7143},
+ 9.97278, -9.576, 0.940464, 1.7143},
{ 10.6406, 6.1038, 7.3537, 0.392, 3.324,
- 20.2626, 1.4922, 98.7399, 1.1832},
+ 20.2626, 1.4922, 98.7399, 1.1832},
{ 9.54034, 5.66078, 7.7509, 0.344261, 3.58274,
- 13.3075, 0.509107, 32.4224, 0.616898},
+ 13.3075, 0.509107, 32.4224, 0.616898},
{ 9.6809, 5.59463, 7.81136, 0.334393, 2.87603,
- 12.8288, 0.113575, 32.8761, 0.518275},
+ 12.8288, 0.113575, 32.8761, 0.518275},
{ 11.2819, 5.3409, 7.3573, 0.3432, 3.0193,
- 17.8674, 2.2441, 83.7543, 1.0896},
+ 17.8674, 2.2441, 83.7543, 1.0896},
{ 10.8061, 5.2796, 7.362, 0.3435, 3.5268,
- 14.343, 0.2184, 41.3235, 1.0874},
+ 14.343, 0.2184, 41.3235, 1.0874},
{ 9.84521, 4.91797, 7.87194, 0.294393, 3.56531,
- 10.8171, 0.323613, 24.1281, 0.393974},
+ 10.8171, 0.323613, 24.1281, 0.393974},
{ 9.96253, 4.8485, 7.97057, 0.283303, 2.76067,
- 10.4852, 0.054447, 27.573, 0.251877},
+ 10.4852, 0.054447, 27.573, 0.251877},
{ 11.7695, 4.7611, 7.3573, 0.3072, 3.5222,
- 15.3535, 2.3045, 76.8805, 1.0369},
+ 15.3535, 2.3045, 76.8805, 1.0369},
{ 11.0424, 4.6538, 7.374, 0.3053, 4.1346,
- 12.0546, 0.4399, 31.2809, 1.0097},
+ 12.0546, 0.4399, 31.2809, 1.0097},
{ 11.1764, 4.6147, 7.3863, 0.3005, 3.3948,
- 11.6729, 0.0724, 38.5566, 0.9707},
+ 11.6729, 0.0724, 38.5566, 0.9707},
{ 12.2841, 4.2791, 7.3409, 0.2784, 4.0034,
- 13.5359, 2.3488, 71.1692, 1.0118},
+ 13.5359, 2.3488, 71.1692, 1.0118},
{ 11.2296, 4.1231, 7.3883, 0.2726, 4.7393,
- 10.2443, 0.7108, 25.6466, 0.9324},
+ 10.2443, 0.7108, 25.6466, 0.9324},
{ 10.338, 3.90969, 7.88173, 0.238668, 4.76795,
- 8.35583, 0.725591, 18.3491, 0.286667},
+ 8.35583, 0.725591, 18.3491, 0.286667},
{ 12.8376, 3.8785, 7.292, 0.2565, 4.4438,
- 12.1763, 2.38, 66.3421, 1.0341},
+ 12.1763, 2.38, 66.3421, 1.0341},
{ 11.4166, 3.6766, 7.4005, 0.2449, 5.3442,
- 8.873, 0.9773, 22.1626, 0.8614},
+ 8.873, 0.9773, 22.1626, 0.8614},
{ 10.7806, 3.5477, 7.75868, 0.22314, 5.22746,
- 7.64468, 0.847114, 16.9673, 0.386044},
+ 7.64468, 0.847114, 16.9673, 0.386044},
{ 13.338, 3.5828, 7.1676, 0.247, 5.6158,
- 11.3966, 1.6735, 64.8126, 1.191},
+ 11.3966, 1.6735, 64.8126, 1.191},
{ 11.9475, 3.3669, 7.3573, 0.2274, 6.2455,
- 8.6625, 1.5578, 25.8487, 0.89},
+ 8.6625, 1.5578, 25.8487, 0.89},
{ 11.8168, 3.37484, 7.11181, 0.244078, 5.78135,
- 7.9876, 1.14523, 19.897, 1.14431},
+ 7.9876, 1.14523, 19.897, 1.14431},
{ 14.0743, 3.2655, 7.0318, 0.2333, 5.1652,
- 10.3163, 2.41, 58.7097, 1.3041},
+ 10.3163, 2.41, 58.7097, 1.3041},
{ 11.9719, 2.9946, 7.3862, 0.2031, 6.4668,
- 7.0826, 1.394, 18.0995, 0.7807},
+ 7.0826, 1.394, 18.0995, 0.7807},
{ 15.2354, 3.0669, 6.7006, 0.2412, 4.3591,
- 10.7805, 2.9623, 61.4135, 1.7189},
+ 10.7805, 2.9623, 61.4135, 1.7189},
{ 12.692, 2.81262, 6.69883, 0.22789, 6.06692,
- 6.36441, 1.0066, 14.4122, 1.53545},
+ 6.36441, 1.0066, 14.4122, 1.53545},
{ 16.0816, 2.8509, 6.3747, 0.2516, 3.7068,
- 11.4468, 3.683, 54.7625, 2.1313},
+ 11.4468, 3.683, 54.7625, 2.1313},
{ 12.9172, 2.53718, 6.70003, 0.205855, 6.06791,
- 5.47913, 0.859041, 11.603, 1.45572},
+ 5.47913, 0.859041, 11.603, 1.45572},
{ 16.6723, 2.6345, 6.0701, 0.2647, 3.4313,
- 12.9479, 4.2779, 47.7972, 2.531},
+ 12.9479, 4.2779, 47.7972, 2.531},
{ 17.0006, 2.4098, 5.8196, 0.2726, 3.9731,
- 15.2372, 4.3543, 43.8163, 2.8409},
+ 15.2372, 4.3543, 43.8163, 2.8409},
{ 17.1789, 2.1723, 5.2358, 16.5796, 5.6377,
- 0.2609, 3.9851, 41.4328, 2.9557},
+ 0.2609, 3.9851, 41.4328, 2.9557},
{ 17.1718, 2.2059, 6.3338, 19.3345, 5.5754,
- 0.2871, 3.7272, 58.1535, 3.1776},
+ 0.2871, 3.7272, 58.1535, 3.1776},
{ 17.3555, 1.9384, 6.7286, 16.5623, 5.5493,
- 0.2261, 3.5375, 39.3972, 2.825},
+ 0.2261, 3.5375, 39.3972, 2.825},
{ 17.1784, 1.7888, 9.6435, 17.3151, 5.1399,
- 0.2748, 1.5292, 164.934, 3.4873},
+ 0.2748, 1.5292, 164.934, 3.4873},
{ 17.5816, 1.7139, 7.6598, 14.7957, 5.8981,
- 0.1603, 2.7817, 31.2087, 2.0782},
+ 0.1603, 2.7817, 31.2087, 2.0782},
{ 17.5663, 1.5564, 9.8184, 14.0988, 5.422,
- 0.1664, 2.6694, 132.376, 2.5064},
+ 0.1664, 2.6694, 132.376, 2.5064},
{ 18.0874, 1.4907, 8.1373, 12.6963, 2.5654,
- -24.5651, 34.193, -0.0138, 41.4025},
+ -24.5651, 34.193, -0.0138, 41.4025},
{ 17.776, 1.4029, 10.2946, 12.8006, 5.72629,
- 0.125599, 3.26588, 104.354, 1.91213},
+ 0.125599, 3.26588, 104.354, 1.91213},
{ 17.9268, 1.35417, 9.1531, 11.2145, 1.76795,
- -22.6599, 33.108, -0.01319, 40.2602},
+ -22.6599, 33.108, -0.01319, 40.2602},
{ 17.8765, 1.27618, 10.948, 11.916, 5.41732,
- 0.117622, 3.65721, 87.6627, 2.06929},
+ 0.117622, 3.65721, 87.6627, 2.06929},
{ 18.1668, 1.2148, 10.0562, 10.1483, 1.01118,
- 21.6054, -2.6479, -0.10276, 9.41454},
+ 21.6054, -2.6479, -0.10276, 9.41454},
{ 17.6142, 1.18865, 12.0144, 11.766, 4.04183,
- 0.204785, 3.53346, 69.7957, 3.75591},
+ 0.204785, 3.53346, 69.7957, 3.75591},
{ 19.8812, 0.019175, 18.0653, 1.13305, 11.0177,
- 10.1621, 1.94715, 28.3389, -12.912},
+ 10.1621, 1.94715, 28.3389, -12.912},
{ 17.9163, 1.12446, 13.3417, 0.028781, 10.799,
- 9.28206, 0.337905, 25.7228, -6.3934},
+ 9.28206, 0.337905, 25.7228, -6.3934},
{ 3.7025, 0.2772, 17.2356, 1.0958, 12.8876,
- 11.004, 3.7429, 61.6584, 4.3875},
+ 11.004, 3.7429, 61.6584, 4.3875},
{ 21.1664, 0.014734, 18.2017, 1.03031, 11.7423,
- 9.53659, 2.30951, 26.6307, -14.421},
+ 9.53659, 2.30951, 26.6307, -14.421},
{ 21.0149, 0.014345, 18.0992, 1.02238, 11.4632,
- 8.78809, 0.740625, 23.3452, -14.316},
+ 8.78809, 0.740625, 23.3452, -14.316},
{ 17.8871, 1.03649, 11.175, 8.48061, 6.57891,
- 0.058881, 0, 0, 0.344941},
+ 0.058881, 0, 0, 0.344941},
{ 19.1301, 0.864132, 11.0948, 8.14487, 4.64901,
- 21.5707, 2.71263, 86.8472, 5.40428},
+ 21.5707, 2.71263, 86.8472, 5.40428},
{ 19.2674, 0.80852, 12.9182, 8.43467, 4.86337,
- 24.7997, 1.56756, 94.2928, 5.37814},
+ 24.7997, 1.56756, 94.2928, 5.37814},
{ 18.5638, 0.847329, 13.2885, 8.37164, 9.32602,
- 0.017662, 3.00964, 22.887, -3.1892},
+ 0.017662, 3.00964, 22.887, -3.1892},
{ 18.5003, 0.844582, 13.1787, 8.12534, 4.71304,
- 0.36495, 2.18535, 20.8504, 1.42357},
+ 0.36495, 2.18535, 20.8504, 1.42357},
{ 19.2957, 0.751536, 14.3501, 8.21758, 4.73425,
- 25.8749, 1.28918, 98.6062, 5.328},
+ 25.8749, 1.28918, 98.6062, 5.328},
{ 18.8785, 0.764252, 14.1259, 7.84438, 3.32515,
- 21.2487, -6.1989, -0.01036, 11.8678},
+ 21.2487, -6.1989, -0.01036, 11.8678},
{ 18.8545, 0.760825, 13.9806, 7.62436, 2.53464,
- 19.3317, -5.6526, -0.0102, 11.2835},
+ 19.3317, -5.6526, -0.0102, 11.2835},
{ 19.3319, 0.698655, 15.5017, 7.98929, 5.29537,
- 25.2052, 0.605844, 76.8986, 5.26593},
+ 25.2052, 0.605844, 76.8986, 5.26593},
{ 19.1701, 0.696219, 15.2096, 7.55573, 4.32234,
- 22.5057, 0, 0, 5.2916},
+ 22.5057, 0, 0, 5.2916},
{ 19.2493, 0.683839, 14.79, 7.14833, 2.89289,
- 17.9144, -7.9492, 0.005127, 13.0174},
+ 17.9144, -7.9492, 0.005127, 13.0174},
{ 19.2808, 0.6446, 16.6885, 7.4726, 4.8045,
- 24.6605, 1.0463, 99.8156, 5.179},
+ 24.6605, 1.0463, 99.8156, 5.179},
{ 19.1812, 0.646179, 15.9719, 7.19123, 5.27475,
- 21.7326, 0.357534, 66.1147, 5.21572},
+ 21.7326, 0.357534, 66.1147, 5.21572},
{ 19.1643, 0.645643, 16.2456, 7.18544, 4.3709,
- 21.4072, 0, 0, 5.21404},
+ 21.4072, 0, 0, 5.21404},
{ 19.2214, 0.5946, 17.6444, 6.9089, 4.461,
- 24.7008, 1.6029, 87.4825, 5.0694},
+ 24.7008, 1.6029, 87.4825, 5.0694},
{ 19.1514, 0.597922, 17.2535, 6.80639, 4.47128,
- 20.2521, 0, 0, 5.11937},
+ 20.2521, 0, 0, 5.11937},
{ 19.1624, 0.5476, 18.5596, 6.3776, 4.2948,
- 25.8499, 2.0396, 92.8029, 4.9391},
+ 25.8499, 2.0396, 92.8029, 4.9391},
{ 19.1045, 0.551522, 18.1108, 6.3247, 3.78897,
- 17.3595, 0, 0, 4.99635},
+ 17.3595, 0, 0, 4.99635},
{ 19.1889, 5.8303, 19.1005, 0.5031, 4.4585,
- 26.8909, 2.4663, 83.9571, 4.7821},
+ 26.8909, 2.4663, 83.9571, 4.7821},
{ 19.1094, 0.5036, 19.0548, 5.8378, 4.5648,
- 23.3752, 0.487, 62.2061, 4.7861},
+ 23.3752, 0.487, 62.2061, 4.7861},
{ 18.9333, 5.764, 19.7131, 0.4655, 3.4182,
- 14.0049, 0.0193, -0.7583, 3.9182},
+ 14.0049, 0.0193, -0.7583, 3.9182},
{ 19.6418, 5.3034, 19.0455, 0.4607, 5.0371,
- 27.9074, 2.6827, 75.2825, 4.5909},
+ 27.9074, 2.6827, 75.2825, 4.5909},
{ 18.9755, 0.467196, 18.933, 5.22126, 5.10789,
- 19.5902, 0.288753, 55.5113, 4.69626},
+ 19.5902, 0.288753, 55.5113, 4.69626},
{ 19.8685, 5.44853, 19.0302, 0.467973, 2.41253,
- 14.1259, 0, 0, 4.69263},
+ 14.1259, 0, 0, 4.69263},
{ 19.9644, 4.81742, 19.0138, 0.420885, 6.14487,
- 28.5284, 2.5239, 70.8403, 4.352},
+ 28.5284, 2.5239, 70.8403, 4.352},
{ 20.1472, 4.347, 18.9949, 0.3814, 7.5138,
- 27.766, 2.2735, 66.8776, 4.0712},
+ 27.766, 2.2735, 66.8776, 4.0712},
{ 20.2332, 4.3579, 18.997, 0.3815, 7.8069,
- 29.5259, 2.8868, 84.9304, 4.0714},
+ 29.5259, 2.8868, 84.9304, 4.0714},
{ 20.2933, 3.9282, 19.0298, 0.344, 8.9767,
- 26.4659, 1.99, 64.2658, 3.7118},
+ 26.4659, 1.99, 64.2658, 3.7118},
{ 20.3892, 3.569, 19.1062, 0.3107, 10.662,
- 24.3879, 1.4953, 213.904, 3.3352},
+ 24.3879, 1.4953, 213.904, 3.3352},
{ 20.3524, 3.552, 19.1278, 0.3086, 10.2821,
- 23.7128, 0.9615, 59.4565, 3.2791},
+ 23.7128, 0.9615, 59.4565, 3.2791},
{ 20.3361, 3.216, 19.297, 0.2756, 10.888,
- 20.2073, 2.6959, 167.202, 2.7731},
+ 20.2073, 2.6959, 167.202, 2.7731},
{ 20.1807, 3.21367, 19.1136, 0.28331, 10.9054,
- 20.0558, 0.77634, 51.746, 3.02902},
+ 20.0558, 0.77634, 51.746, 3.02902},
{ 20.578, 2.94817, 19.599, 0.244475, 11.3727,
- 18.7726, 3.28719, 133.124, 2.14678},
+ 18.7726, 3.28719, 133.124, 2.14678},
{ 20.2489, 2.9207, 19.3763, 0.250698, 11.6323,
- 17.8211, 0.336048, 54.9453, 2.4086},
+ 17.8211, 0.336048, 54.9453, 2.4086},
{ 21.1671, 2.81219, 19.7695, 0.226836, 11.8513,
- 17.6083, 3.33049, 127.113, 1.86264},
+ 17.6083, 3.33049, 127.113, 1.86264},
{ 20.8036, 2.77691, 19.559, 0.23154, 11.9369,
- 16.5408, 0.612376, 43.1692, 2.09013},
+ 16.5408, 0.612376, 43.1692, 2.09013},
{ 20.3235, 2.65941, 19.8186, 0.21885, 12.1233,
- 15.7992, 0.144583, 62.2355, 1.5918},
+ 15.7992, 0.144583, 62.2355, 1.5918},
{ 22.044, 2.77393, 19.6697, 0.222087, 12.3856,
- 16.7669, 2.82428, 143.644, 2.0583},
+ 16.7669, 2.82428, 143.644, 2.0583},
{ 21.3727, 2.6452, 19.7491, 0.214299, 12.1329,
- 15.323, 0.97518, 36.4065, 1.77132},
+ 15.323, 0.97518, 36.4065, 1.77132},
{ 20.9413, 2.54467, 20.0539, 0.202481, 12.4668,
- 14.8137, 0.296689, 45.4643, 1.24285},
+ 14.8137, 0.296689, 45.4643, 1.24285},
{ 22.6845, 2.66248, 19.6847, 0.210628, 12.774,
- 15.885, 2.85137, 137.903, 1.98486},
+ 15.885, 2.85137, 137.903, 1.98486},
{ 21.961, 2.52722, 19.9339, 0.199237, 12.12,
- 14.1783, 1.51031, 30.8717, 1.47588},
+ 14.1783, 1.51031, 30.8717, 1.47588},
{ 23.3405, 2.5627, 19.6095, 0.202088, 13.1235,
- 15.1009, 2.87516, 132.721, 2.02876},
+ 15.1009, 2.87516, 132.721, 2.02876},
{ 22.5527, 2.4174, 20.1108, 0.185769, 12.0671,
- 13.1275, 2.07492, 27.4491, 1.19499},
+ 13.1275, 2.07492, 27.4491, 1.19499},
{ 24.0042, 2.47274, 19.4258, 0.196451, 13.4396,
- 14.3996, 2.89604, 128.007, 2.20963},
+ 14.3996, 2.89604, 128.007, 2.20963},
{ 23.1504, 2.31641, 20.2599, 0.174081, 11.9202,
- 12.1571, 2.71488, 24.8242, 0.954586},
+ 12.1571, 2.71488, 24.8242, 0.954586},
{ 24.6274, 2.3879, 19.0886, 0.1942, 13.7603,
- 13.7546, 2.9227, 123.174, 2.5745},
+ 13.7546, 2.9227, 123.174, 2.5745},
{ 24.0063, 2.27783, 19.9504, 0.17353, 11.8034,
- 11.6096, 3.87243, 26.5156, 1.36389},
+ 11.6096, 3.87243, 26.5156, 1.36389},
{ 23.7497, 2.22258, 20.3745, 0.16394, 11.8509,
- 11.311, 3.26503, 22.9966, 0.759344},
+ 11.311, 3.26503, 22.9966, 0.759344},
{ 25.0709, 2.25341, 19.0798, 0.181951, 13.8518,
- 12.9331, 3.54545, 101.398, 2.4196},
+ 12.9331, 3.54545, 101.398, 2.4196},
{ 24.3466, 2.13553, 20.4208, 0.155525, 11.8708,
- 10.5782, 3.7149, 21.7029, 0.645089},
+ 10.5782, 3.7149, 21.7029, 0.645089},
{ 25.8976, 2.24256, 18.2185, 0.196143, 14.3167,
- 12.6648, 2.95354, 115.362, 3.58324},
+ 12.6648, 2.95354, 115.362, 3.58324},
{ 24.9559, 2.05601, 20.3271, 0.149525, 12.2471,
- 10.0499, 3.773, 21.2773, 0.691967},
+ 10.0499, 3.773, 21.2773, 0.691967},
{ 26.507, 2.1802, 17.6383, 0.202172, 14.5596,
- 12.1899, 2.96577, 111.874, 4.29728},
+ 12.1899, 2.96577, 111.874, 4.29728},
{ 25.5395, 1.9804, 20.2861, 0.143384, 11.9812,
- 9.34972, 4.50073, 19.581, 0.68969},
+ 9.34972, 4.50073, 19.581, 0.68969},
{ 26.9049, 2.07051, 17.294, 0.19794, 14.5583,
- 11.4407, 3.63837, 92.6566, 4.56796},
+ 11.4407, 3.63837, 92.6566, 4.56796},
{ 26.1296, 1.91072, 20.0994, 0.139358, 11.9788,
- 8.80018, 4.93676, 18.5908, 0.852795},
+ 8.80018, 4.93676, 18.5908, 0.852795},
{ 27.6563, 2.07356, 16.4285, 0.223545, 14.9779,
- 11.3604, 2.98233, 105.703, 5.92046},
+ 11.3604, 2.98233, 105.703, 5.92046},
{ 26.722, 1.84659, 19.7748, 0.13729, 12.1506,
- 8.36225, 5.17379, 17.8974, 1.17613},
+ 8.36225, 5.17379, 17.8974, 1.17613},
{ 28.1819, 2.02859, 15.8851, 0.238849, 15.1542,
- 10.9975, 2.98706, 102.961, 1.63929},
+ 10.9975, 2.98706, 102.961, 1.63929},
{ 27.3083, 1.78711, 19.332, 0.136974, 12.3339,
- 7.96778, 5.38348, 17.2922, 1.63929},
+ 7.96778, 5.38348, 17.2922, 1.63929},
{ 28.6641, 1.9889, 15.4345, 0.257119, 15.3087,
- 10.6647, 2.98963, 100.417, 7.56672},
+ 10.6647, 2.98963, 100.417, 7.56672},
{ 28.1209, 1.78503, 17.6817, 0.15997, 13.3335,
- 8.18304, 5.14657, 20.39, 3.70983},
+ 8.18304, 5.14657, 20.39, 3.70983},
{ 27.8917, 1.73272, 18.7614, 0.13879, 12.6072,
- 7.64412, 5.47647, 16.8153, 2.26001},
+ 7.64412, 5.47647, 16.8153, 2.26001},
{ 28.9476, 1.90182, 15.2208, 9.98519, 15.1,
- 0.261033, 3.71601, 84.3298, 7.97628},
+ 0.261033, 3.71601, 84.3298, 7.97628},
{ 28.4628, 1.68216, 18.121, 0.142292, 12.8429,
- 7.33727, 5.59415, 16.3535, 2.97573},
+ 7.33727, 5.59415, 16.3535, 2.97573},
{ 29.144, 1.83262, 15.1726, 9.5999, 14.7586,
- 0.275116, 4.30013, 72.029, 8.58154},
+ 0.275116, 4.30013, 72.029, 8.58154},
{ 28.8131, 1.59136, 18.4601, 0.128903, 12.7285,
- 6.76232, 5.59927, 14.0366, 2.39699},
+ 6.76232, 5.59927, 14.0366, 2.39699},
{ 29.2024, 1.77333, 15.2293, 9.37046, 14.5135,
- 0.295977, 4.76492, 63.3644, 9.24354},
+ 0.295977, 4.76492, 63.3644, 9.24354},
{ 29.1587, 1.50711, 18.8407, 0.116741, 12.8268,
- 6.31524, 5.38695, 12.4244, 1.78555},
+ 6.31524, 5.38695, 12.4244, 1.78555},
{ 29.0818, 1.72029, 15.43, 9.2259, 14.4327,
- 0.321703, 5.11982, 57.056, 9.8875},
+ 0.321703, 5.11982, 57.056, 9.8875},
{ 29.4936, 1.42755, 19.3763, 0.104621, 13.0544,
- 5.93667, 5.06412, 11.1972, 1.01074},
+ 5.93667, 5.06412, 11.1972, 1.01074},
{ 28.7621, 1.67191, 15.7189, 9.09227, 14.5564,
- 0.3505, 5.44174, 52.0861, 10.472},
+ 0.3505, 5.44174, 52.0861, 10.472},
{ 28.1894, 1.62903, 16.155, 8.97948, 14.9305,
- 0.382661, 5.67589, 48.1647, 11.0005},
+ 0.382661, 5.67589, 48.1647, 11.0005},
{ 30.419, 1.37113, 15.2637, 6.84706, 14.7458,
- 0.165191, 5.06795, 18.003, 6.49804},
+ 0.165191, 5.06795, 18.003, 6.49804},
{ 27.3049, 1.59279, 16.7296, 8.86553, 15.6115,
- 0.417916, 5.83377, 45.0011, 11.4722},
+ 0.417916, 5.83377, 45.0011, 11.4722},
{ 30.4156, 1.34323, 15.862, 7.10909, 13.6145,
- 0.204633, 5.82008, 20.3254, 8.27903},
+ 0.204633, 5.82008, 20.3254, 8.27903},
{ 30.7058, 1.30923, 15.5512, 6.71983, 14.2326,
- 0.167252, 5.53672, 17.4911, 6.96824},
+ 0.167252, 5.53672, 17.4911, 6.96824},
{ 27.0059, 1.51293, 17.7639, 8.81174, 15.7131,
- 0.424593, 5.7837, 38.6103, 11.6883},
+ 0.424593, 5.7837, 38.6103, 11.6883},
{ 29.8429, 1.32927, 16.7224, 7.38979, 13.2153,
- 0.263297, 6.35234, 22.9426, 9.85329},
+ 0.263297, 6.35234, 22.9426, 9.85329},
{ 30.9612, 1.24813, 15.9829, 6.60834, 13.7348,
- 0.16864, 5.92034, 16.9392, 7.39534},
+ 0.16864, 5.92034, 16.9392, 7.39534},
{ 16.8819, 0.4611, 18.5913, 8.6216, 25.5582,
- 1.4826, 5.86, 36.3956, 12.0658},
+ 1.4826, 5.86, 36.3956, 12.0658},
{ 28.0109, 1.35321, 17.8204, 7.7395, 14.3359,
- 0.356752, 6.58077, 26.4043, 11.2299},
+ 0.356752, 6.58077, 26.4043, 11.2299},
{ 30.6886, 1.2199, 16.9029, 6.82872, 12.7801,
- 0.212867, 6.52354, 18.659, 9.0968},
+ 0.212867, 6.52354, 18.659, 9.0968},
{ 20.6809, 0.545, 19.0417, 8.4484, 21.6575,
- 1.5729, 5.9676, 38.3246, 12.6089},
+ 1.5729, 5.9676, 38.3246, 12.6089},
{ 25.0853, 1.39507, 18.4973, 7.65105, 16.8883,
- 0.443378, 6.48216, 28.2262, 12.0205},
+ 0.443378, 6.48216, 28.2262, 12.0205},
{ 29.5641, 1.21152, 18.06, 7.05639, 12.8374,
- 0.284738, 6.89912, 20.7482, 10.6268},
+ 0.284738, 6.89912, 20.7482, 10.6268},
{ 27.5446, 0.65515, 19.1584, 8.70751, 15.538,
- 1.96347, 5.52593, 45.8149, 13.1746},
+ 1.96347, 5.52593, 45.8149, 13.1746},
{ 21.3985, 1.4711, 20.4723, 0.517394, 18.7478,
- 7.43463, 6.82847, 28.8482, 12.5258},
+ 7.43463, 6.82847, 28.8482, 12.5258},
{ 30.8695, 1.1008, 18.3481, 6.53852, 11.9328,
- 0.219074, 7.00574, 17.2114, 9.8027},
+ 0.219074, 7.00574, 17.2114, 9.8027},
{ 31.0617, 0.6902, 13.0637, 2.3576, 18.442,
- 8.618, 5.9696, 47.2579, 13.4118},
+ 8.618, 5.9696, 47.2579, 13.4118},
{ 21.7886, 1.3366, 19.5682, 0.488383, 19.1406,
- 6.7727, 7.01107, 23.8132, 12.4734},
+ 6.7727, 7.01107, 23.8132, 12.4734},
{ 32.1244, 1.00566, 18.8003, 6.10926, 12.0175,
- 0.147041, 6.96886, 14.714, 8.08428},
+ 0.147041, 6.96886, 14.714, 8.08428},
{ 33.3689, 0.704, 12.951, 2.9238, 16.5877,
- 8.7937, 6.4692, 48.0093, 13.5782},
+ 8.7937, 6.4692, 48.0093, 13.5782},
{ 21.8053, 1.2356, 19.5026, 6.24149, 19.1053,
- 0.469999, 7.10295, 20.3185, 12.4711},
+ 0.469999, 7.10295, 20.3185, 12.4711},
{ 33.5364, 0.91654, 25.0946, 0.39042, 19.2497,
- 5.71414, 6.91555, 12.8285, 6.7994},
+ 5.71414, 6.91555, 12.8285, 6.7994},
{ 34.6726, 0.700999, 15.4733, 3.55078, 13.1138,
- 9.55642, 7.02588, 47.0045, 13.677},
+ 9.55642, 7.02588, 47.0045, 13.677},
{ 35.3163, 0.68587, 19.0211, 3.97458, 9.49887,
- 11.3824, 7.42518, 45.4715, 13.7108},
+ 11.3824, 7.42518, 45.4715, 13.7108},
{ 35.5631, 0.6631, 21.2816, 4.0691, 8.0037,
- 14.0422, 7.4433, 44.2473, 13.6905},
+ 14.0422, 7.4433, 44.2473, 13.6905},
{ 35.9299, 0.646453, 23.0547, 4.17619, 12.1439,
- 23.1052, 2.11253, 150.645, 13.7247},
+ 23.1052, 2.11253, 150.645, 13.7247},
{ 35.763, 0.616341, 22.9064, 3.87135, 12.4739,
- 19.9887, 3.21097, 142.325, 13.6211},
+ 19.9887, 3.21097, 142.325, 13.6211},
{ 35.215, 0.604909, 21.67, 3.5767, 7.91342,
- 12.601, 7.65078, 29.8436, 13.5431},
+ 12.601, 7.65078, 29.8436, 13.5431},
{ 35.6597, 0.589092, 23.1032, 3.65155, 12.5977,
- 18.599, 4.08655, 117.02, 13.5266},
+ 18.599, 4.08655, 117.02, 13.5266},
{ 35.1736, 0.579689, 22.1112, 3.41437, 8.19216,
- 12.9187, 7.05545, 25.9443, 13.4637},
+ 12.9187, 7.05545, 25.9443, 13.4637},
{ 35.5645, 0.563359, 23.4219, 3.46204, 12.7473,
- 17.8309, 4.80703, 99.1722, 13.4314},
+ 17.8309, 4.80703, 99.1722, 13.4314},
{ 35.1007, 0.555054, 22.4418, 3.24498, 9.78554,
- 13.4661, 5.29444, 23.9533, 13.376},
+ 13.4661, 5.29444, 23.9533, 13.376},
{ 35.8847, 0.547751, 23.2948, 3.41519, 14.1891,
- 16.9235, 4.17287, 105.251, 13.4287},
+ 16.9235, 4.17287, 105.251, 13.4287},
{ 36.0228, 0.5293, 23.4128, 3.3253, 14.9491,
- 16.0927, 4.188, 100.613, 13.3966},
+ 16.0927, 4.188, 100.613, 13.3966},
{ 35.5747, 0.52048, 22.5259, 3.12293, 12.2165,
- 12.7148, 5.37073, 26.3394, 13.3092},
+ 12.7148, 5.37073, 26.3394, 13.3092},
{ 35.3715, 0.516598, 22.5326, 3.05053, 12.0291,
- 12.5723, 4.7984, 23.4582, 13.2671},
+ 12.5723, 4.7984, 23.4582, 13.2671},
{ 34.8509, 0.507079, 22.7584, 2.8903, 14.0099,
- 13.1767, 1.21457, 25.2017, 13.1665},
+ 13.1767, 1.21457, 25.2017, 13.1665},
{ 36.1874, 0.511929, 23.5964, 3.25396, 15.6402,
- 15.3622, 4.1855, 97.4908, 13.3573},
+ 15.3622, 4.1855, 97.4908, 13.3573},
{ 35.7074, 0.502322, 22.613, 3.03807, 12.9898,
- 12.1449, 5.43227, 25.4928, 13.2544},
+ 12.1449, 5.43227, 25.4928, 13.2544},
{ 35.5103, 0.498626, 22.5787, 2.96627, 12.7766,
- 11.9484, 4.92159, 22.7502, 13.2116},
+ 11.9484, 4.92159, 22.7502, 13.2116},
{ 35.0136, 0.48981, 22.7286, 2.81099, 14.3884,
- 12.33, 1.75669, 22.6581, 13.113},
+ 12.33, 1.75669, 22.6581, 13.113},
{ 36.5254, 0.499384, 23.8083, 3.26371, 16.7707,
- 14.9455, 3.47947, 105.98, 13.3812},
+ 14.9455, 3.47947, 105.98, 13.3812},
{ 35.84, 0.484938, 22.7169, 2.96118, 13.5807,
- 11.5331, 5.66016, 24.3992, 13.1991},
+ 11.5331, 5.66016, 24.3992, 13.1991},
{ 35.6493, 0.481422, 22.646, 2.8902, 13.3595,
- 11.316, 5.18831, 21.8301, 13.1555},
+ 11.316, 5.18831, 21.8301, 13.1555},
{ 35.1736, 0.473204, 22.7181, 2.73848, 14.7635,
- 11.553, 2.28678, 20.9303, 13.0582},
+ 11.553, 2.28678, 20.9303, 13.0582},
{ 36.6706, 0.483629, 24.0992, 3.20647, 17.3415,
- 14.3136, 3.49331, 102.273, 13.3592},
+ 14.3136, 3.49331, 102.273, 13.3592},
{ 36.6488, 0.465154, 24.4096, 3.08997, 17.399,
- 13.4346, 4.21665, 88.4834, 13.2887},
+ 13.4346, 4.21665, 88.4834, 13.2887},
{ 36.7881, 0.451018, 24.7736, 3.04619, 17.8919,
- 12.8946, 4.23284, 86.003, 13.2754},
+ 12.8946, 4.23284, 86.003, 13.2754},
{ 36.9185, 0.437533, 25.1995, 3.00775, 18.3317,
- 12.4044, 4.24391, 83.7881, 13.2674},
+ 12.4044, 4.24391, 83.7881, 13.2674},
};
#endif
diff --git a/src/USER-DIFFRACTION/fix_saed_vtk.cpp b/src/USER-DIFFRACTION/fix_saed_vtk.cpp
index 984c4a87e5..30ecc900e8 100644
--- a/src/USER-DIFFRACTION/fix_saed_vtk.cpp
+++ b/src/USER-DIFFRACTION/fix_saed_vtk.cpp
@@ -16,8 +16,8 @@
Incorporating SAED: Shawn Coleman (Arkansas)
------------------------------------------------------------------------- */
-#include "stdlib.h"
-#include "string.h"
+#include <stdlib.h>
+#include <string.h>
#include "fix_saed_vtk.h"
#include "update.h"
#include "modify.h"
@@ -29,7 +29,7 @@
#include "memory.h"
#include "error.h"
#include "force.h"
-#include "math.h"
+#include <math.h>
#include "domain.h"
using namespace LAMMPS_NS;
@@ -67,7 +67,7 @@ FixSAEDVTK::FixSAEDVTK(LAMMPS *lmp, int narg, char **arg) :
if (nvalues != 1) error->all(FLERR,"Illegal fix saed/vtk command");
options(narg,arg);
-
+
which = 0;
ids = NULL;
@@ -90,9 +90,9 @@ FixSAEDVTK::FixSAEDVTK(LAMMPS *lmp, int narg, char **arg) :
delete [] suffix;
int icompute = modify->find_compute(ids);
- if (icompute < 0)
+ if (icompute < 0)
error->all(FLERR,"Compute ID for fix saed/vtk does not exist");
-
+
Compute *compute = modify->compute[icompute];
// Check that specified compute is for SAED
@@ -118,9 +118,9 @@ FixSAEDVTK::FixSAEDVTK(LAMMPS *lmp, int narg, char **arg) :
// Standard error check for fix/ave/time
if (compute->vector_flag == 0)
error->all(FLERR,"Fix saed/vtk compute does not calculate a vector");
- if (compute->extvector != 0)
- error->all(FLERR,"Illegal fix saed/vtk command");
-
+ if (compute->extvector != 0)
+ error->all(FLERR,"Illegal fix saed/vtk command");
+
nrows = compute->size_vector;
nvalues++;
iarg++;
@@ -154,7 +154,7 @@ FixSAEDVTK::FixSAEDVTK(LAMMPS *lmp, int narg, char **arg) :
size_vector = nrows;
if (nOutput == 0) {
-
+
// SAED specific paramaters needed
int *periodicity = domain->periodicity;
// Zone flag to capture entire recrocal space volume
@@ -184,7 +184,7 @@ FixSAEDVTK::FixSAEDVTK(LAMMPS *lmp, int narg, char **arg) :
prd_inv[2] = 1 / prd[2];
ave_inv += prd_inv[2];
}
-
+
// Using the average inverse dimensions for non-periodic direction
ave_inv = ave_inv / (periodicity[0] + periodicity[1] + periodicity[2]);
if (!periodicity[0]){
@@ -197,12 +197,12 @@ FixSAEDVTK::FixSAEDVTK(LAMMPS *lmp, int narg, char **arg) :
prd_inv[2] = ave_inv;
}
- // Use manual mapping of reciprocal lattice
+ // Use manual mapping of reciprocal lattice
if (manual) {
for (int i=0; i<3; i++) {
prd_inv[i] = 1.0;
}
- }
+ }
// Find integer dimensions of the reciprocal lattice box bounds
if ( (Zone[0] == 0) && (Zone[1] == 0) && (Zone[2] == 0) ){
@@ -210,13 +210,13 @@ FixSAEDVTK::FixSAEDVTK(LAMMPS *lmp, int narg, char **arg) :
dK[i] = prd_inv[i]*c[i];
Knmax[i] = ceil(Kmax / dK[i]);
Knmin[i] = -Knmax[i];
- }
+ }
} else {
for (int i=0; i<3; i++) {
Knmax[i] = -10000;
Knmin[i] = 10000;
- }
+ }
double dinv2 = 0.0;
double r = 0.0;
double K[3];
@@ -224,8 +224,8 @@ FixSAEDVTK::FixSAEDVTK(LAMMPS *lmp, int narg, char **arg) :
for (int i=0; i<3; i++) {
dK[i] = prd_inv[i]*c[i];
Ksearch[i] = ceil(Kmax / dK[i]);
- }
-
+ }
+
for (int k = -Ksearch[2]; k <= Ksearch[2]; k++) {
for (int j = -Ksearch[1]; j <= Ksearch[1]; j++) {
for (int i = -Ksearch[0]; i <= Ksearch[0]; i++) {
@@ -237,21 +237,21 @@ FixSAEDVTK::FixSAEDVTK(LAMMPS *lmp, int narg, char **arg) :
r=0.0;
for (int m=0; m<3; m++) r += pow(K[m] - Zone[m],2.0);
- r = sqrt(r);
+ r = sqrt(r);
if ( (r > (R_Ewald - dR_Ewald) ) && (r < (R_Ewald + dR_Ewald) ) ){
-
+
if ( i < Knmin[0] ) Knmin[0] = i;
if ( j < Knmin[1] ) Knmin[1] = j;
- if ( k < Knmin[2] ) Knmin[2] = k;
-
+ if ( k < Knmin[2] ) Knmin[2] = k;
+
if ( i > Knmax[0] ) Knmax[0] = i;
if ( j > Knmax[1] ) Knmax[1] = j;
- if ( k > Knmax[2] ) Knmax[2] = k;
+ if ( k > Knmax[2] ) Knmax[2] = k;
}
}
- }
+ }
}
- }
+ }
}
// Finding dimensions for vtk files
@@ -306,7 +306,7 @@ void FixSAEDVTK::init()
{
// set current indices for all computes,fixes,variables
-
+
int icompute = modify->find_compute(ids);
if (icompute < 0)
error->all(FLERR,"Compute ID for fix saed/vtk does not exist");
@@ -347,7 +347,7 @@ void FixSAEDVTK::invoke_vector(bigint ntimestep)
int icompute = modify->find_compute(ids);
if (icompute < 0)
error->all(FLERR,"Compute ID for fix saed/vtk does not exist");
-
+
if (irepeat == 0)
for (int i = 0; i < nrows; i++)
vector[i] = 0.0;
@@ -367,7 +367,7 @@ void FixSAEDVTK::invoke_vector(bigint ntimestep)
}
double *vector = compute->vector;
-
+
// done if irepeat < nrepeat
// else reset irepeat and nvalid
@@ -405,8 +405,8 @@ void FixSAEDVTK::invoke_vector(bigint ntimestep)
vector_total[i] += vector[i];
if (window_limit) vector_total[i] -= vector_list[iwindow][i];
vector_list[iwindow][i] = vector[i];
- }
-
+ }
+
iwindow++;
if (iwindow == nwindow) {
iwindow = 0;
@@ -420,7 +420,7 @@ void FixSAEDVTK::invoke_vector(bigint ntimestep)
if (fp && me == 0) {
if (nOutput > 0) {
- fclose(fp);
+ fclose(fp);
char nName [128];
sprintf(nName,"%s.%d.vtk",filename,nOutput);
@@ -443,9 +443,9 @@ void FixSAEDVTK::invoke_vector(bigint ntimestep)
fprintf(fp,"POINT_DATA %d\n", Dim[0] * Dim[1] * Dim[2] );
fprintf(fp,"SCALARS intensity float\n");
fprintf(fp,"LOOKUP_TABLE default\n");
-
+
filepos = ftell(fp);
-
+
if (overwrite) fseek(fp,filepos,SEEK_SET);
// Finding the intersection of the reciprical space and Ewald sphere
@@ -509,7 +509,7 @@ void FixSAEDVTK::invoke_vector(bigint ntimestep)
}
}
}
- nOutput++;
+ nOutput++;
}
/* ----------------------------------------------------------------------
@@ -543,7 +543,7 @@ void FixSAEDVTK::options(int narg, char **arg)
if (strcmp(arg[iarg],"file") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix saed/vtk command");
if (me == 0) {
-
+
nOutput = 0;
int n = strlen(arg[iarg+1]) + 1;
filename = new char[n];
@@ -557,7 +557,7 @@ void FixSAEDVTK::options(int narg, char **arg)
char str[128];
sprintf(str,"Cannot open fix saed/vtk file %s",nName);
error->one(FLERR,str);
- }
+ }
}
iarg += 2;
} else if (strcmp(arg[iarg],"ave") == 0) {
diff --git a/src/USER-DIFFRACTION/fix_saed_vtk.h b/src/USER-DIFFRACTION/fix_saed_vtk.h
index a421112688..b8cee21c35 100644
--- a/src/USER-DIFFRACTION/fix_saed_vtk.h
+++ b/src/USER-DIFFRACTION/fix_saed_vtk.h
@@ -20,7 +20,7 @@ FixStyle(saed/vtk,FixSAEDVTK)
#ifndef LMP_FIX_SAED_VTK_H
#define LMP_FIX_SAED_VTK_H
-#include "stdio.h"
+#include <stdio.h>
#include "fix.h"
namespace LAMMPS_NS {
@@ -60,7 +60,7 @@ class FixSAEDVTK : public Fix {
void options(int, char **);
bigint nextvalid();
-
+
class ComputeSAED *compute_saed;
double Zone[3]; // Zone axis to view SAED
@@ -77,7 +77,7 @@ class FixSAEDVTK : public Fix {
double prd_inv[3]; // Inverse spacing of unit cell
char *filename; // user-specified file
- int nOutput;
+ int nOutput;
int Dim[3];
bool manual; // Turn on manual recpiprocal map
diff --git a/src/USER-DRUDE/compute_temp_drude.cpp b/src/USER-DRUDE/compute_temp_drude.cpp
index 97d264647d..99578e65e0 100644
--- a/src/USER-DRUDE/compute_temp_drude.cpp
+++ b/src/USER-DRUDE/compute_temp_drude.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "stdlib.h"
-#include "string.h"
+#include <mpi.h>
+#include <stdlib.h>
+#include <string.h>
#include "compute_temp_drude.h"
#include "atom.h"
#include "update.h"
@@ -67,9 +67,9 @@ void ComputeTempDrude::init()
int ifix;
for (ifix = 0; ifix < modify->nfix; ifix++)
if (strcmp(modify->fix[ifix]->style,"drude") == 0) break;
- if (ifix == modify->nfix) error->all(FLERR, "compute temp/drude requires fix drude");
+ if (ifix == modify->nfix) error->all(FLERR, "compute temp/drude requires fix drude");
fix_drude = (FixDrude *) modify->fix[ifix];
-
+
if (!comm->ghost_velocity)
error->all(FLERR,"compute temp/drude requires ghost velocities. Use comm_modify vel yes");
}
@@ -143,7 +143,7 @@ int ComputeTempDrude::modify_param(int narg, char **arg)
void ComputeTempDrude::compute_vector()
{
invoked_vector = update->ntimestep;
-
+
int nlocal = atom->nlocal;
int *mask = atom->mask;
int *type = atom->type;
@@ -159,12 +159,12 @@ void ComputeTempDrude::compute_vector()
double *vcore, *vdrude;
double kineng_core_loc = 0., kineng_drude_loc = 0.;
for (int i=0; i<nlocal; i++){
- if (groupbit & mask[i] && drudetype[type[i]] != DRUDE_TYPE){
+ if (groupbit & mask[i] && drudetype[type[i]] != DRUDE_TYPE){
if (drudetype[type[i]] == NOPOL_TYPE) {
ecore = 0.;
vcore = v[i];
if (temperature) temperature->remove_bias(i, vcore);
- for (int k=0; k<dim; k++) ecore += vcore[k]*vcore[k];
+ for (int k=0; k<dim; k++) ecore += vcore[k]*vcore[k];
if (temperature) temperature->restore_bias(i, vcore);
if (rmass) mcore = rmass[i];
else mcore = mass[type[i]];
@@ -202,7 +202,7 @@ void ComputeTempDrude::compute_vector()
}
}
}
-
+
if (dynamic) dof_compute();
kineng_core_loc *= 0.5 * mvv2e;
kineng_drude_loc *= 0.5 * mvv2e;
diff --git a/src/USER-DRUDE/fix_drude.cpp b/src/USER-DRUDE/fix_drude.cpp
index 46b49707df..7f37b89eff 100644
--- a/src/USER-DRUDE/fix_drude.cpp
+++ b/src/USER-DRUDE/fix_drude.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
-#include "stdlib.h"
+#include <string.h>
+#include <stdlib.h>
#include "fix_drude.h"
#include "atom.h"
#include "comm.h"
@@ -51,7 +51,7 @@ FixDrude::FixDrude(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR, "Illegal fix drude command");
}
- drudeid = NULL;
+ drudeid = NULL;
grow_arrays(atom->nmax);
atom->add_callback(0);
atom->add_callback(1);
@@ -107,7 +107,7 @@ void FixDrude::build_drudeid(){
std::vector<tagint> drude_vec; // list of my Drudes' tags
std::vector<tagint> core_drude_vec;
partner_set = new std::set<tagint>[nlocal]; // Temporary sets of bond partner tags
-
+
sptr = this;
// Build list of my atoms' bond partners
for (int i=0; i<nlocal; i++){
@@ -124,7 +124,7 @@ void FixDrude::build_drudeid(){
4, ring_build_partner, NULL, 1);
// Build the list of my Drudes' tags
- // The only bond partners of a Drude particle is its core,
+ // The only bond partners of a Drude particle is its core,
// so fill drudeid for my Drudes.
for (int i=0; i<nlocal; i++){
if (drudetype[type[i]] == DRUDE_TYPE){
@@ -135,9 +135,9 @@ void FixDrude::build_drudeid(){
// At this point each of my Drudes knows its core.
// Send my list of Drudes to other procs and myself
// so that each core finds its Drude.
- comm->ring(drude_vec.size(), sizeof(tagint),
- (char *) drude_vec.data(),
- 3, ring_search_drudeid, NULL, 1);
+ comm->ring(drude_vec.size(), sizeof(tagint),
+ (char *) drude_vec.data(),
+ 3, ring_search_drudeid, NULL, 1);
delete [] partner_set;
}
@@ -159,7 +159,7 @@ void FixDrude::ring_search_drudeid(int size, char *cbuf){
tagint *last = first + size;
std::set<tagint> drude_set(first, last);
std::set<tagint>::iterator it;
-
+
for (int i=0; i<nlocal; i++) {
if (drudetype[type[i]] != CORE_TYPE || drudeid[i] > 0) continue;
for (it = partner_set[i].begin(); it != partner_set[i].end(); it++) { // Drude-core are 1-2 neighbors
@@ -286,14 +286,14 @@ void FixDrude::rebuild_special(){
int nspecmax, nspecmax_old, nspecmax_loc;
nspecmax_loc = 0;
for (int i=0; i<nlocal; i++) {
- if (nspecmax_loc < nspecial[i][2]) nspecmax_loc = nspecial[i][2];
+ if (nspecmax_loc < nspecial[i][2]) nspecmax_loc = nspecial[i][2];
}
MPI_Allreduce(&nspecmax_loc, &nspecmax_old, 1, MPI_INT, MPI_MAX, world);
if (comm->me == 0) {
if (screen) fprintf(screen, "Old max number of 1-2 to 1-4 neighbors: %d\n", nspecmax_old);
if (logfile) fprintf(logfile, "Old max number of 1-2 to 1-4 neighbors: %d\n", nspecmax_old);
}
-
+
// Build lists of drude and core-drude pairs
std::vector<tagint> drude_vec, core_drude_vec, core_special_vec;
for (int i=0; i<nlocal; i++) {
@@ -306,17 +306,17 @@ void FixDrude::rebuild_special(){
}
// Remove Drude particles from the special lists of each proc
comm->ring(drude_vec.size(), sizeof(tagint),
- (char *) drude_vec.data(),
+ (char *) drude_vec.data(),
9, ring_remove_drude, NULL, 1);
// Add back Drude particles in the lists just after their core
comm->ring(core_drude_vec.size(), sizeof(tagint),
- (char *) core_drude_vec.data(),
+ (char *) core_drude_vec.data(),
10, ring_add_drude, NULL, 1);
-
+
// Check size of special list
nspecmax_loc = 0;
for (int i=0; i<nlocal; i++) {
- if (nspecmax_loc < nspecial[i][2]) nspecmax_loc = nspecial[i][2];
+ if (nspecmax_loc < nspecial[i][2]) nspecmax_loc = nspecial[i][2];
}
MPI_Allreduce(&nspecmax_loc, &nspecmax, 1, MPI_INT, MPI_MAX, world);
if (comm->me == 0) {
@@ -341,7 +341,7 @@ void FixDrude::rebuild_special(){
}
// Copy core's list into their drude list
comm->ring(core_special_vec.size(), sizeof(tagint),
- (char *) core_special_vec.data(),
+ (char *) core_special_vec.data(),
11, ring_copy_drude, NULL, 1);
}
@@ -385,7 +385,7 @@ void FixDrude::ring_remove_drude(int size, char *cbuf){
* particle if they have one.
------------------------------------------------------------------------- */
void FixDrude::ring_add_drude(int size, char *cbuf){
- // Assume special array size is big enough
+ // Assume special array size is big enough
// Add all particle just after their core in the special list
Atom *atom = sptr->atom;
int nlocal = atom->nlocal;
@@ -394,7 +394,7 @@ void FixDrude::ring_add_drude(int size, char *cbuf){
int *type = atom->type;
tagint *drudeid = sptr->drudeid;
int *drudetype = sptr->drudetype;
-
+
tagint *first = (tagint *) cbuf;
tagint *last = first + size;
std::map<tagint, tagint> core_drude_map;
@@ -406,7 +406,7 @@ void FixDrude::ring_add_drude(int size, char *cbuf){
core_drude_map[core_tag] = *it;
it++;
}
-
+
for (int i=0; i<nlocal; i++) {
if (drudetype[type[i]] == DRUDE_TYPE) continue;
if (core_drude_map.count(atom->tag[i]) > 0) { // I identify myself as a core, add my own drude
@@ -449,11 +449,11 @@ void FixDrude::ring_copy_drude(int size, char *cbuf){
int *type = atom->type;
tagint *drudeid = sptr->drudeid;
int *drudetype = sptr->drudetype;
-
+
tagint *first = (tagint *) cbuf;
tagint *last = first + size;
std::map<tagint, tagint*> core_special_map;
-
+
tagint *it = first;
while (it < last) {
tagint core_tag = *it;
@@ -462,7 +462,7 @@ void FixDrude::ring_copy_drude(int size, char *cbuf){
it += 2;
it += (int) *it;
}
-
+
for (int i=0; i<nlocal; i++) {
if (drudetype[type[i]] != DRUDE_TYPE) continue;
if (core_special_map.count(drudeid[i]) > 0) { // My core is in this list, copy its special info
@@ -482,8 +482,8 @@ void FixDrude::ring_copy_drude(int size, char *cbuf){
}
}
-/* ----------------------------------------------------------------------
- * Set drudeid when a new atom is created,
+/* ----------------------------------------------------------------------
+ * Set drudeid when a new atom is created,
* special list must be up-to-date
* ----------------------------------------------------------------------*/
void FixDrude::set_arrays(int i){
diff --git a/src/USER-DRUDE/fix_drude_transform.cpp b/src/USER-DRUDE/fix_drude_transform.cpp
index 3edcdc01ca..adbfd324df 100644
--- a/src/USER-DRUDE/fix_drude_transform.cpp
+++ b/src/USER-DRUDE/fix_drude_transform.cpp
@@ -12,7 +12,7 @@
------------------------------------------------------------------------- */
/** Fix Drude Transform ******************************************************/
-#include "math.h"
+#include <math.h>
#include "fix_drude_transform.h"
#include "atom.h"
#include "domain.h"
@@ -38,11 +38,11 @@ FixDrudeTransform<inverse>::FixDrudeTransform(LAMMPS *lmp, int narg, char **arg)
/* ---------------------------------------------------------------------- */
template <bool inverse>
-FixDrudeTransform<inverse>::~FixDrudeTransform()
+FixDrudeTransform<inverse>::~FixDrudeTransform()
{
if (mcoeff) delete [] mcoeff;
}
-
+
/* ---------------------------------------------------------------------- */
template <bool inverse>
void FixDrudeTransform<inverse>::init()
@@ -50,7 +50,7 @@ void FixDrudeTransform<inverse>::init()
int ifix;
for (ifix = 0; ifix < modify->nfix; ifix++)
if (strcmp(modify->fix[ifix]->style,"drude") == 0) break;
- if (ifix == modify->nfix) error->all(FLERR, "fix drude/transform requires fix drude");
+ if (ifix == modify->nfix) error->all(FLERR, "fix drude/transform requires fix drude");
fix_drude = (FixDrude *) modify->fix[ifix];
}
@@ -73,7 +73,7 @@ void FixDrudeTransform<inverse>::setup(int) {
double * rmass = atom->rmass, * mass = atom->mass;
tagint * drudeid = fix_drude->drudeid;
int * drudetype = fix_drude->drudetype;
-
+
if (!rmass) {
if (!mcoeff) mcoeff = new double[ntypes+1];
double mcoeff_loc[ntypes+1];
@@ -183,7 +183,7 @@ void FixDrudeTransform<inverse>::real_to_reduced()
v[icore][k] += coeff * v[idrude][k];
f[icore][k] += f[idrude][k];
f[idrude][k] -= coeff * f[icore][k];
- }
+ }
}
}
fix_drude->is_reduced = true;
@@ -208,7 +208,7 @@ void FixDrudeTransform<inverse>::reduced_to_real()
if (mask[i] & groupbit && drudetype[type[i]] != NOPOL_TYPE) {
int j = (int) drudeid[i]; // local index of drude partner because drudeid is in reduced form
if (drudetype[type[i]] == DRUDE_TYPE && j < nlocal) continue;
-
+
if (drudetype[type[i]] == DRUDE_TYPE) {
idrude = i;
icore = j;
@@ -241,7 +241,7 @@ void FixDrudeTransform<inverse>::reduced_to_real()
v[idrude][k] += v[icore][k];
f[idrude][k] += coeff * f[icore][k];
f[icore][k] -= f[idrude][k];
- }
+ }
}
}
for (int i=0; i<nlocal; i++) {
diff --git a/src/USER-DRUDE/fix_langevin_drude.cpp b/src/USER-DRUDE/fix_langevin_drude.cpp
index 041e7b79ae..119328a1dd 100644
--- a/src/USER-DRUDE/fix_langevin_drude.cpp
+++ b/src/USER-DRUDE/fix_langevin_drude.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
-#include "stdlib.h"
-#include "math.h"
+#include <string.h>
+#include <stdlib.h>
+#include <math.h>
#include "fix_langevin_drude.h"
#include "atom.h"
#include "force.h"
@@ -50,7 +50,7 @@ FixLangevinDrude::FixLangevinDrude(LAMMPS *lmp, int narg, char **arg) :
size_vector = 6;
comm_reverse = 3;
//extscalar = 1;
-
+
// core temperature
tstr_core = NULL;
if (strstr(arg[3],"v_") == arg[3]) {
@@ -64,7 +64,7 @@ FixLangevinDrude::FixLangevinDrude(LAMMPS *lmp, int narg, char **arg) :
tstyle_core = CONSTANT;
}
t_period_core = force->numeric(FLERR,arg[4]);
- int seed_core = force->inumeric(FLERR,arg[5]);
+ int seed_core = force->inumeric(FLERR,arg[5]);
// drude temperature
tstr_drude = NULL;
@@ -80,21 +80,21 @@ FixLangevinDrude::FixLangevinDrude(LAMMPS *lmp, int narg, char **arg) :
}
t_period_drude = force->numeric(FLERR,arg[7]);
int seed_drude = force->inumeric(FLERR,arg[8]);
-
+
// error checks
if (t_period_core <= 0.0)
error->all(FLERR,"Fix langevin/drude period must be > 0.0");
if (seed_core <= 0) error->all(FLERR,"Illegal langevin/drude seed");
if (t_period_drude <= 0.0)
error->all(FLERR,"Fix langevin/drude period must be > 0.0");
- if (seed_drude <= 0) error->all(FLERR,"Illegal langevin/drude seed");
+ if (seed_drude <= 0) error->all(FLERR,"Illegal langevin/drude seed");
random_core = new RanMars(lmp,seed_core);
random_drude = new RanMars(lmp,seed_drude);
-
+
int iarg = 9;
zero = 0;
- while (iarg < narg) {
+ while (iarg < narg) {
if (strcmp(arg[iarg],"zero") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix langevin/drude command");
if (strcmp(arg[iarg+1],"no") == 0) zero = 0;
@@ -155,7 +155,7 @@ void FixLangevinDrude::init()
int ifix;
for (ifix = 0; ifix < modify->nfix; ifix++)
if (strcmp(modify->fix[ifix]->style,"drude") == 0) break;
- if (ifix == modify->nfix) error->all(FLERR, "fix langevin/drude requires fix drude");
+ if (ifix == modify->nfix) error->all(FLERR, "fix langevin/drude requires fix drude");
fix_drude = (FixDrude *) modify->fix[ifix];
}
@@ -171,7 +171,7 @@ void FixLangevinDrude::setup(int vflag)
if (zero) {
int *mask = atom->mask;
int nlocal = atom->nlocal;
- int *drudetype = fix_drude->drudetype;
+ int *drudetype = fix_drude->drudetype;
int *type = atom->type;
bigint ncore_loc = 0;
for (int i=0; i<nlocal; i++)
@@ -222,7 +222,7 @@ void FixLangevinDrude::post_force(int /*vflag*/)
double *rmass = atom->rmass;
double ftm2v = force->ftm2v, mvv2e = force->mvv2e;
double kb = force->boltz, dt = update->dt;
-
+
int *drudetype = fix_drude->drudetype;
tagint *drudeid = fix_drude->drudeid;
double vdrude[3], vcore[3]; // velocities in reduced representation
@@ -230,7 +230,7 @@ void FixLangevinDrude::post_force(int /*vflag*/)
double Ccore, Cdrude, Gcore, Gdrude;
double fcoresum[3], fcoreloc[3];
int dim = domain->dimension;
-
+
// Compute target core temperature
if (tstyle_core == CONSTANT)
t_target_core = t_start_core; // + delta * (t_stop-t_start_core);
@@ -254,7 +254,7 @@ void FixLangevinDrude::post_force(int /*vflag*/)
"negative drude temperature");
modify->addstep_compute(update->ntimestep + nevery);
}
-
+
// Clear ghost forces
// They have already been communicated if needed
for (int i = nlocal; i < nall; i++) {
@@ -271,7 +271,7 @@ void FixLangevinDrude::post_force(int /*vflag*/)
if (rmass)
mi = rmass[i];
else
- mi = mass[type[i]];
+ mi = mass[type[i]];
Gcore = mi / t_period_core / ftm2v;
Ccore = sqrt(2.0 * Gcore * kb * t_target_core / dt / ftm2v / mvv2e);
if (temperature) temperature->remove_bias(i, v[i]);
@@ -283,21 +283,21 @@ void FixLangevinDrude::post_force(int /*vflag*/)
if (temperature) temperature->restore_bias(i, v[i]);
} else {
if (drudetype[type[i]] == DRUDE_TYPE) continue; // do with the core
-
+
int j = atom->map(drudeid[i]);
double mi, mj, mtot, mu; // i is core, j is drude
if (rmass) {
mi = rmass[i];
mj = rmass[j];
} else {
- mi = mass[type[i]];
+ mi = mass[type[i]];
mj = mass[type[j]];
- }
+ }
mtot = mi + mj;
mu = mi * mj / mtot;
mi /= mtot;
mj /= mtot;
-
+
Gcore = mtot / t_period_core / ftm2v;
Gdrude = mu / t_period_drude / ftm2v;
Ccore = sqrt(2.0 * Gcore * kb * t_target_core / dt / ftm2v / mvv2e);
@@ -309,14 +309,14 @@ void FixLangevinDrude::post_force(int /*vflag*/)
}
for (int k=0; k<dim; k++) {
// TODO check whether a fix_modify temp can subtract a bias velocity
- vcore[k] = mi * v[i][k] + mj * v[j][k];
+ vcore[k] = mi * v[i][k] + mj * v[j][k];
vdrude[k] = v[j][k] - v[i][k];
-
+
fcore[k] = Ccore * random_core->gaussian() - Gcore * vcore[k];
fdrude[k] = Cdrude * random_drude->gaussian() - Gdrude * vdrude[k];
-
+
if (zero) fcoreloc[k] += fcore[k];
-
+
f[i][k] += mi * fcore[k] - fdrude[k];
f[j][k] += mj * fcore[k] + fdrude[k];
@@ -329,7 +329,7 @@ void FixLangevinDrude::post_force(int /*vflag*/)
}
}
}
-
+
if(zero) { // Remove the drift
MPI_Allreduce(fcoreloc, fcoresum, dim, MPI_DOUBLE, MPI_SUM, world);
for (int k=0; k<dim; k++) fcoresum[k] /= ncore;
@@ -345,9 +345,9 @@ void FixLangevinDrude::post_force(int /*vflag*/)
mi = rmass[i];
mj = rmass[j];
} else {
- mi = mass[type[i]];
+ mi = mass[type[i]];
mj = mass[type[j]];
- }
+ }
mtot = mi + mj;
mi /= mtot;
mj /= mtot;
diff --git a/src/USER-DRUDE/pair_lj_cut_thole_long.cpp b/src/USER-DRUDE/pair_lj_cut_thole_long.cpp
index d517eb7932..ef3747e7b3 100644
--- a/src/USER-DRUDE/pair_lj_cut_thole_long.cpp
+++ b/src/USER-DRUDE/pair_lj_cut_thole_long.cpp
@@ -15,10 +15,10 @@
Contributing author: Paul Crozier (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_lj_cut_thole_long.h"
#include "atom.h"
#include "comm.h"
@@ -115,7 +115,7 @@ void PairLJCutTholeLong::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
@@ -133,7 +133,7 @@ void PairLJCutTholeLong::compute(int eflag, int vflag)
di_closest = domain->closest_image(i, di);
if (drudetype[type[i]] == CORE_TYPE)
dqi = -q[di];
- else
+ else
dqi = qi;
}
@@ -179,7 +179,7 @@ void PairLJCutTholeLong::compute(int eflag, int vflag)
forcecoul -= (1.0-factor_coul)*prefactor;
}
}
-
+
if (drudetype[type[i]] != NOPOL_TYPE &&
drudetype[type[j]] != NOPOL_TYPE){
if (j != di_closest){
@@ -242,7 +242,7 @@ void PairLJCutTholeLong::compute(int eflag, int vflag)
}
}
}
-
+
if (vflag_fdotr) virial_fdotr_compute();
}
@@ -320,7 +320,7 @@ void PairLJCutTholeLong::coeff(int narg, char **arg)
double epsilon_one = force->numeric(FLERR,arg[2]);
double sigma_one = force->numeric(FLERR,arg[3]);
double polar_one = force->numeric(FLERR,arg[4]);
- double thole_one = thole_global;
+ double thole_one = thole_global;
if (narg >=6) thole_one = force->numeric(FLERR,arg[5]);
double cut_lj_one = cut_lj_global;
@@ -650,7 +650,7 @@ double PairLJCutTholeLong::single(int i, int j, int itype, int jtype,
factor_f = 0.5*(2. + (exp_asr * (-2. - asr * (2. + asr))))
- factor_coul;
forcecoul += factor_f * dcoul;
- factor_e = 0.5*(2. - (exp_asr * (2. + asr))) - factor_coul;
+ factor_e = 0.5*(2. - (exp_asr * (2. + asr))) - factor_coul;
}
}
} else forcecoul = 0.0;
diff --git a/src/USER-DRUDE/pair_thole.cpp b/src/USER-DRUDE/pair_thole.cpp
index 5840dbc51b..13b1265a7e 100644
--- a/src/USER-DRUDE/pair_thole.cpp
+++ b/src/USER-DRUDE/pair_thole.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_thole.h"
#include "atom.h"
#include "comm.h"
@@ -213,7 +213,7 @@ void PairThole::settings(int narg, char **arg)
void PairThole::coeff(int narg, char **arg)
{
- if (narg < 3 || narg > 5)
+ if (narg < 3 || narg > 5)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
@@ -222,7 +222,7 @@ void PairThole::coeff(int narg, char **arg)
force->bounds(arg[1],atom->ntypes,jlo,jhi);
double polar_one = force->numeric(FLERR,arg[2]);
- double thole_one = thole_global;
+ double thole_one = thole_global;
double cut_one = cut_global;
if (narg >=4) thole_one = force->numeric(FLERR,arg[3]);
if (narg == 5) cut_one = force->numeric(FLERR,arg[4]);
@@ -255,7 +255,7 @@ void PairThole::init_style()
int ifix;
for (ifix = 0; ifix < modify->nfix; ifix++)
if (strcmp(modify->fix[ifix]->style,"drude") == 0) break;
- if (ifix == modify->nfix) error->all(FLERR, "Pair thole requires fix drude");
+ if (ifix == modify->nfix) error->all(FLERR, "Pair thole requires fix drude");
fix_drude = (FixDrude *) modify->fix[ifix];
neighbor->request(this,instance_me);
@@ -401,7 +401,7 @@ double PairThole::single(int i, int j, int itype, int jtype,
dcoul = force->qqrd2e * qi * qj * scale[itype][jtype] * rinv;
factor_f = 0.5*(2. + (exp_asr * (-2. - asr * (2. + asr)))) - factor_coul;
fforce = factor_f * dcoul * r2inv;
- factor_e = 0.5*(2. - (exp_asr * (2. + asr))) - factor_coul;
+ factor_e = 0.5*(2. - (exp_asr * (2. + asr))) - factor_coul;
phicoul = factor_e * dcoul;
}
diff --git a/src/USER-EFF/atom_vec_electron.cpp b/src/USER-EFF/atom_vec_electron.cpp
index 5935c71402..56d61fd74f 100644
--- a/src/USER-EFF/atom_vec_electron.cpp
+++ b/src/USER-EFF/atom_vec_electron.cpp
@@ -15,9 +15,9 @@
Contributing author: Andres Jaramillo-Botero (Caltech)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "atom_vec_electron.h"
#include "atom.h"
#include "comm.h"
@@ -908,7 +908,7 @@ int AtomVecElectron::pack_data_hybrid(int i, double *buf)
void AtomVecElectron::write_data(FILE *fp, int n, double **buf)
{
for (int i = 0; i < n; i++)
- fprintf(fp,TAGINT_FORMAT
+ fprintf(fp,TAGINT_FORMAT
" %d %-1.16e %d %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d\n",
(tagint) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).i,buf[i][2],
(int) ubuf(buf[i][3]).i,buf[i][4],buf[i][5],buf[i][6],buf[i][7],
@@ -992,7 +992,7 @@ int AtomVecElectron::property_atom(char *name)
index maps to data specific to this atom style
------------------------------------------------------------------------- */
-void AtomVecElectron::pack_property_atom(int index, double *buf,
+void AtomVecElectron::pack_property_atom(int index, double *buf,
int nvalues, int groupbit)
{
int *mask = atom->mask;
@@ -1046,7 +1046,7 @@ bigint AtomVecElectron::memory_usage()
if (atom->memcheck("spin")) bytes += memory->usage(spin,nmax);
if (atom->memcheck("eradius")) bytes += memory->usage(eradius,nmax);
if (atom->memcheck("ervel")) bytes += memory->usage(ervel,nmax);
- if (atom->memcheck("erforce"))
+ if (atom->memcheck("erforce"))
bytes += memory->usage(erforce,nmax*comm->nthreads);
return bytes;
diff --git a/src/USER-EFF/compute_ke_atom_eff.cpp b/src/USER-EFF/compute_ke_atom_eff.cpp
index 3c29e801cb..93ad934d6d 100644
--- a/src/USER-EFF/compute_ke_atom_eff.cpp
+++ b/src/USER-EFF/compute_ke_atom_eff.cpp
@@ -15,9 +15,9 @@
Contributing author: Andres Jaramillo-Botero
------------------------------------------------------------------------- */
-#include "math.h"
-#include "string.h"
-#include "stdlib.h"
+#include <math.h>
+#include <string.h>
+#include <stdlib.h>
#include "compute_ke_atom_eff.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-EFF/compute_ke_eff.cpp b/src/USER-EFF/compute_ke_eff.cpp
index 7d3487b69b..80c7192708 100644
--- a/src/USER-EFF/compute_ke_eff.cpp
+++ b/src/USER-EFF/compute_ke_eff.cpp
@@ -15,9 +15,9 @@
Contributing author: Andres Jaramillo-Botero
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "math.h"
-#include "stdlib.h"
+#include <mpi.h>
+#include <math.h>
+#include <stdlib.h>
#include "compute_ke_eff.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-EFF/compute_temp_deform_eff.cpp b/src/USER-EFF/compute_temp_deform_eff.cpp
index 8ff1d6f768..12c72479cb 100644
--- a/src/USER-EFF/compute_temp_deform_eff.cpp
+++ b/src/USER-EFF/compute_temp_deform_eff.cpp
@@ -15,10 +15,10 @@
Contributing author: Andres Jaramillo-Botero (Caltech)
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "math.h"
-#include "string.h"
-#include "stdlib.h"
+#include <mpi.h>
+#include <math.h>
+#include <string.h>
+#include <stdlib.h>
#include "compute_temp_deform_eff.h"
#include "domain.h"
#include "atom.h"
@@ -174,7 +174,7 @@ double ComputeTempDeformEff::compute_scalar()
MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
if (dynamic) dof_compute();
- if (dof < 0.0 && natoms_temp > 0.0)
+ if (dof < 0.0 && natoms_temp > 0.0)
error->all(FLERR,"Temperature compute degrees of freedom < 0");
scalar *= tfactor;
return scalar;
diff --git a/src/USER-EFF/compute_temp_eff.cpp b/src/USER-EFF/compute_temp_eff.cpp
index 2b4e507091..251cdccaca 100644
--- a/src/USER-EFF/compute_temp_eff.cpp
+++ b/src/USER-EFF/compute_temp_eff.cpp
@@ -15,10 +15,10 @@
Contributing author: Andres Jaramillo-Botero (Caltech)
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "math.h"
-#include "string.h"
-#include "stdlib.h"
+#include <mpi.h>
+#include <math.h>
+#include <string.h>
+#include <stdlib.h>
#include "compute_temp_eff.h"
#include "atom.h"
#include "update.h"
@@ -120,7 +120,7 @@ double ComputeTempEff::compute_scalar()
MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
if (dynamic) dof_compute();
- if (dof < 0.0 && natoms_temp > 0.0)
+ if (dof < 0.0 && natoms_temp > 0.0)
error->all(FLERR,"Temperature compute degrees of freedom < 0");
scalar *= tfactor;
return scalar;
diff --git a/src/USER-EFF/compute_temp_region_eff.cpp b/src/USER-EFF/compute_temp_region_eff.cpp
index 3c762e5d7b..1035a3e31b 100644
--- a/src/USER-EFF/compute_temp_region_eff.cpp
+++ b/src/USER-EFF/compute_temp_region_eff.cpp
@@ -15,10 +15,10 @@
Contributing author: Andres Jaramillo-Botero (Caltech)
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "math.h"
-#include "string.h"
-#include "stdlib.h"
+#include <mpi.h>
+#include <math.h>
+#include <string.h>
+#include <stdlib.h>
#include "compute_temp_region_eff.h"
#include "atom.h"
#include "update.h"
@@ -148,7 +148,7 @@ double ComputeTempRegionEff::compute_scalar()
tarray[1] = t;
MPI_Allreduce(tarray,tarray_all,2,MPI_DOUBLE,MPI_SUM,world);
dof = domain->dimension * tarray_all[0] - extra_dof;
- if (dof < 0.0 && tarray_all[0] > 0.0)
+ if (dof < 0.0 && tarray_all[0] > 0.0)
error->all(FLERR,"Temperature compute degrees of freedom < 0");
int one = 0;
diff --git a/src/USER-EFF/fix_langevin_eff.cpp b/src/USER-EFF/fix_langevin_eff.cpp
index dec460da93..f2ca444de2 100644
--- a/src/USER-EFF/fix_langevin_eff.cpp
+++ b/src/USER-EFF/fix_langevin_eff.cpp
@@ -15,10 +15,10 @@
Contributing author: Andres Jaramillo-Botero
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "math.h"
-#include "string.h"
-#include "stdlib.h"
+#include <mpi.h>
+#include <math.h>
+#include <string.h>
+#include <stdlib.h>
#include "fix_langevin_eff.h"
#include "math_extra.h"
#include "atom.h"
diff --git a/src/USER-EFF/fix_nh_eff.cpp b/src/USER-EFF/fix_nh_eff.cpp
index ca38fc7e73..bbf5ac31f0 100644
--- a/src/USER-EFF/fix_nh_eff.cpp
+++ b/src/USER-EFF/fix_nh_eff.cpp
@@ -15,8 +15,8 @@
Contributing author: Andres Jaramillo-Botero (Caltech)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdlib.h>
#include "fix_nh_eff.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/USER-EFF/fix_nph_eff.cpp b/src/USER-EFF/fix_nph_eff.cpp
index e580a3fc73..dc6bfe20d5 100644
--- a/src/USER-EFF/fix_nph_eff.cpp
+++ b/src/USER-EFF/fix_nph_eff.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "fix_nph_eff.h"
#include "modify.h"
#include "error.h"
diff --git a/src/USER-EFF/fix_npt_eff.cpp b/src/USER-EFF/fix_npt_eff.cpp
index baea9a16ea..36a6f87cba 100644
--- a/src/USER-EFF/fix_npt_eff.cpp
+++ b/src/USER-EFF/fix_npt_eff.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "fix_npt_eff.h"
#include "modify.h"
#include "error.h"
diff --git a/src/USER-EFF/fix_nve_eff.cpp b/src/USER-EFF/fix_nve_eff.cpp
index d1aefaa768..09cd81a722 100644
--- a/src/USER-EFF/fix_nve_eff.cpp
+++ b/src/USER-EFF/fix_nve_eff.cpp
@@ -15,17 +15,17 @@
Contributing author: Andres Jaramillo-Botero (Caltech)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "string.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdio.h>
+#include <string.h>
+#include <stdlib.h>
#include "fix_nve_eff.h"
#include "atom.h"
#include "force.h"
#include "update.h"
#include "respa.h"
#include "error.h"
-#include "math.h"
+#include <math.h>
#include "domain.h"
using namespace LAMMPS_NS;
diff --git a/src/USER-EFF/fix_nvt_eff.cpp b/src/USER-EFF/fix_nvt_eff.cpp
index 17e01a31bb..36a9ff3293 100644
--- a/src/USER-EFF/fix_nvt_eff.cpp
+++ b/src/USER-EFF/fix_nvt_eff.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
-#include "math.h"
+#include <string.h>
+#include <math.h>
#include "fix_nvt_eff.h"
#include "group.h"
#include "modify.h"
diff --git a/src/USER-EFF/fix_nvt_sllod_eff.cpp b/src/USER-EFF/fix_nvt_sllod_eff.cpp
index 46b49331b0..1f6dea658f 100644
--- a/src/USER-EFF/fix_nvt_sllod_eff.cpp
+++ b/src/USER-EFF/fix_nvt_sllod_eff.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdlib.h>
#include "fix_nvt_sllod_eff.h"
#include "math_extra.h"
#include "atom.h"
diff --git a/src/USER-EFF/fix_temp_rescale_eff.cpp b/src/USER-EFF/fix_temp_rescale_eff.cpp
index 18ba739e0f..774cd1f2e3 100644
--- a/src/USER-EFF/fix_temp_rescale_eff.cpp
+++ b/src/USER-EFF/fix_temp_rescale_eff.cpp
@@ -15,9 +15,9 @@
Contributing author: Andres Jaramillo-Botero
------------------------------------------------------------------------- */
-#include "string.h"
-#include "stdlib.h"
-#include "math.h"
+#include <string.h>
+#include <stdlib.h>
+#include <math.h>
#include "fix_temp_rescale_eff.h"
#include "atom.h"
#include "force.h"
diff --git a/src/USER-EFF/pair_eff_cut.cpp b/src/USER-EFF/pair_eff_cut.cpp
index d8635c10a9..b12e1f43b3 100644
--- a/src/USER-EFF/pair_eff_cut.cpp
+++ b/src/USER-EFF/pair_eff_cut.cpp
@@ -15,10 +15,10 @@
Contributing author: Andres Jaramillo-Botero
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_eff_cut.h"
#include "pair_eff_inline.h"
#include "atom.h"
@@ -806,11 +806,11 @@ void PairEffCut::settings(int narg, char **arg)
while (iarg < narg) {
if (strcmp(arg[iarg],"limit/eradius") == 0) {
- limit_eradius_flag = 1;
+ limit_eradius_flag = 1;
iarg += 1;
}
else if (strcmp(arg[iarg],"pressure/evirials") == 0) {
- pressure_with_evirials_flag = 1;
+ pressure_with_evirials_flag = 1;
iarg += 1;
}
else if (strcmp(arg[iarg],"ecp") == 0) {
@@ -822,14 +822,14 @@ void PairEffCut::settings(int narg, char **arg)
else if (strcmp(arg[iarg+1],"O") == 0) ecp_type[atype] = 8;
else if (strcmp(arg[iarg+1],"Al") == 0) ecp_type[atype] = 13;
else if (strcmp(arg[iarg+1],"Si") == 0) ecp_type[atype] = 14;
- else error->all(FLERR, "Note: there are no default parameters for this atom ECP\n");
+ else error->all(FLERR, "Note: there are no default parameters for this atom ECP\n");
iarg += 2;
ecp_found = 1;
- }
+ }
}
}
- if (!ecp_found && atom->ecp_flag)
+ if (!ecp_found && atom->ecp_flag)
error->all(FLERR,"Need to specify ECP type on pair_style command");
// Need to introduce 2 new constants w/out changing update.cpp
@@ -921,7 +921,7 @@ void PairEffCut::coeff(int narg, char **arg)
PAULI_CORE_C[ecp_type[ecp]] = force->numeric(FLERR,arg[4]);
PAULI_CORE_D[ecp_type[ecp]] = force->numeric(FLERR,arg[5]);
PAULI_CORE_E[ecp_type[ecp]] = force->numeric(FLERR,arg[6]);
- } else error->all(FLERR,"Illegal pair_coeff command");
+ } else error->all(FLERR,"Illegal pair_coeff command");
}
}
diff --git a/src/USER-FEP/compute_fep.cpp b/src/USER-FEP/compute_fep.cpp
index dd7d29be42..d3c3bf9409 100644
--- a/src/USER-FEP/compute_fep.cpp
+++ b/src/USER-FEP/compute_fep.cpp
@@ -15,10 +15,10 @@
Contributing author: Agilio Padua (Univ Blaise Pascal & CNRS)
------------------------------------------------------------------------- */
-#include "stdlib.h"
-#include "string.h"
-#include "math.h"
-#include "mpi.h"
+#include <stdlib.h>
+#include <string.h>
+#include <math.h>
+#include <mpi.h>
#include "comm.h"
#include "update.h"
#include "atom.h"
@@ -144,7 +144,7 @@ ComputeFEP::ComputeFEP(LAMMPS *lmp, int narg, char **arg) :
else if (strcmp(arg[iarg+1],"yes") == 0) volumeflag = 1;
else error->all(FLERR,"Illegal optional keyword in compute fep");
iarg += 2;
- } else
+ } else
error->all(FLERR,"Illegal optional keyword in compute fep");
}
@@ -220,7 +220,7 @@ void ComputeFEP::init()
if (pair == NULL) error->all(FLERR,"compute fep pair style "
"does not exist");
void *ptr = pair->extract(pert->pparam,pert->pdim);
- if (ptr == NULL)
+ if (ptr == NULL)
error->all(FLERR,"compute fep pair style param not supported");
pert->array = (double **) ptr;
@@ -335,10 +335,10 @@ void ComputeFEP::compute_vector()
}
// accumulate force/energy/virial from /gpu pair styles
- // this is required as to empty the answer queue,
+ // this is required as to empty the answer queue,
// otherwise the force compute on the GPU in the next step would be incorrect
if (fixgpu) fixgpu->post_force(vflag);
-
+
pe1 = compute_epair();
restore_qfev(); // restore charge, force, energy, virial array values
@@ -398,14 +398,14 @@ void ComputeFEP::perturb_params()
if (pert->aparam == CHARGE) { // modify charges
int *atype = atom->type;
- double *q = atom->q;
+ double *q = atom->q;
int *mask = atom->mask;
int natom = atom->nlocal + atom->nghost;
-
+
for (i = 0; i < natom; i++)
if (atype[i] >= pert->ilo && atype[i] <= pert->ihi)
if (mask[i] & groupbit)
- q[i] += delta;
+ q[i] += delta;
}
}
@@ -519,9 +519,9 @@ void ComputeFEP::backup_qfev()
double **f = atom->f;
for (i = 0; i < natom; i++) {
- f_orig[i][0] = f[i][0];
- f_orig[i][1] = f[i][1];
- f_orig[i][2] = f[i][2];
+ f_orig[i][0] = f[i][0];
+ f_orig[i][1] = f[i][1];
+ f_orig[i][2] = f[i][2];
}
eng_vdwl_orig = force->pair->eng_vdwl;
@@ -552,7 +552,7 @@ void ComputeFEP::backup_qfev()
}
if (chgflag) {
- double *q = atom->q;
+ double *q = atom->q;
for (i = 0; i < nall; i++)
q_orig[i] = q[i];
@@ -564,7 +564,7 @@ void ComputeFEP::backup_qfev()
kvirial_orig[3] = force->kspace->virial[3];
kvirial_orig[4] = force->kspace->virial[4];
kvirial_orig[5] = force->kspace->virial[5];
-
+
if (update->eflag_atom) {
double *keatom = force->kspace->eatom;
for (i = 0; i < natom; i++)
@@ -598,9 +598,9 @@ void ComputeFEP::restore_qfev()
double **f = atom->f;
for (i = 0; i < natom; i++) {
- f[i][0] = f_orig[i][0];
- f[i][1] = f_orig[i][1];
- f[i][2] = f_orig[i][2];
+ f[i][0] = f_orig[i][0];
+ f[i][1] = f_orig[i][1];
+ f[i][2] = f_orig[i][2];
}
force->pair->eng_vdwl = eng_vdwl_orig;
@@ -631,7 +631,7 @@ void ComputeFEP::restore_qfev()
}
if (chgflag) {
- double *q = atom->q;
+ double *q = atom->q;
for (i = 0; i < nall; i++)
q[i] = q_orig[i];
@@ -643,7 +643,7 @@ void ComputeFEP::restore_qfev()
force->kspace->virial[3] = kvirial_orig[3];
force->kspace->virial[4] = kvirial_orig[4];
force->kspace->virial[5] = kvirial_orig[5];
-
+
if (update->eflag_atom) {
double *keatom = force->kspace->eatom;
for (i = 0; i < natom; i++)
diff --git a/src/USER-FEP/fix_adapt_fep.cpp b/src/USER-FEP/fix_adapt_fep.cpp
index c033e7c45a..54e90f4c6e 100644
--- a/src/USER-FEP/fix_adapt_fep.cpp
+++ b/src/USER-FEP/fix_adapt_fep.cpp
@@ -15,9 +15,9 @@
Charges by type and after option: Agilio Padua (Univ Blaise Pascal & CNRS)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "string.h"
-#include "stdlib.h"
+#include <math.h>
+#include <string.h>
+#include <stdlib.h>
#include "fix_adapt_fep.h"
#include "atom.h"
#include "update.h"
@@ -123,8 +123,8 @@ FixAdaptFEP::FixAdaptFEP(LAMMPS *lmp, int narg, char **arg) :
adapt[nadapt].aparam = DIAMETER;
diamflag = 1;
} else if (strcmp(arg[iarg+1],"charge") == 0) {
- adapt[nadapt].aparam = CHARGE;
- chgflag = 1;
+ adapt[nadapt].aparam = CHARGE;
+ chgflag = 1;
} else error->all(FLERR,"Illegal fix adapt/fep command");
force->bounds(arg[iarg+2],atom->ntypes,
adapt[nadapt].ilo,adapt[nadapt].ihi);
@@ -289,7 +289,7 @@ void FixAdaptFEP::init()
if (group->dynamic[igroup])
for (int i = 0; i < nadapt; i++)
- if (adapt[i].which == ATOM)
+ if (adapt[i].which == ATOM)
error->all(FLERR,"Cannot use dynamic group with fix adapt/fep atom");
// setup and error checks
@@ -320,7 +320,7 @@ void FixAdaptFEP::init()
if (pair == NULL)
error->all(FLERR, "Fix adapt/fep pair style does not exist");
void *ptr = pair->extract(ad->pparam,ad->pdim);
- if (ptr == NULL)
+ if (ptr == NULL)
error->all(FLERR,"Fix adapt/fep pair style param not supported");
ad->pdim = 2;
@@ -368,7 +368,7 @@ void FixAdaptFEP::init()
}
// fixes that store initial per-atom values
-
+
if (id_fix_diam) {
int ifix = modify->find_fix(id_fix_diam);
if (ifix < 0) error->all(FLERR,"Could not find fix adapt storage fix ID");
@@ -507,7 +507,7 @@ void FixAdaptFEP::change_settings()
}
} else if (ad->aparam == CHARGE) {
int *atype = atom->type;
- double *q = atom->q;
+ double *q = atom->q;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
diff --git a/src/USER-FEP/fix_adapt_fep.h b/src/USER-FEP/fix_adapt_fep.h
index 16a6d4b740..cee19752e4 100644
--- a/src/USER-FEP/fix_adapt_fep.h
+++ b/src/USER-FEP/fix_adapt_fep.h
@@ -27,7 +27,7 @@ namespace LAMMPS_NS {
class FixAdaptFEP : public Fix {
public:
int diamflag; // 1 if atom diameters will vary, for AtomVecGranular
- int chgflag;
+ int chgflag;
FixAdaptFEP(class LAMMPS *, int, char **);
~FixAdaptFEP();
diff --git a/src/USER-FEP/pair_coul_cut_soft.cpp b/src/USER-FEP/pair_coul_cut_soft.cpp
index dbb63f19a2..b82abc1ed1 100644
--- a/src/USER-FEP/pair_coul_cut_soft.cpp
+++ b/src/USER-FEP/pair_coul_cut_soft.cpp
@@ -15,10 +15,10 @@
Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_coul_cut_soft.h"
#include "atom.h"
#include "comm.h"
@@ -179,7 +179,7 @@ void PairCoulCutSoft::settings(int narg, char **arg)
void PairCoulCutSoft::coeff(int narg, char **arg)
{
- if (narg < 3 || narg > 4)
+ if (narg < 3 || narg > 4)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
@@ -357,7 +357,7 @@ double PairCoulCutSoft::single(int i, int j, int itype, int jtype,
denc = sqrt(lam2[itype][jtype] + rsq);
forcecoul = force->qqrd2e * lam1[itype][jtype] * atom->q[i]*atom->q[j] /
(denc*denc*denc);
- } else forcecoul = 0.0;
+ } else forcecoul = 0.0;
fforce = factor_coul*forcecoul;
if (rsq < cutsq[itype][jtype])
diff --git a/src/USER-FEP/pair_coul_long_soft.cpp b/src/USER-FEP/pair_coul_long_soft.cpp
index be1d9a246c..d209628104 100644
--- a/src/USER-FEP/pair_coul_long_soft.cpp
+++ b/src/USER-FEP/pair_coul_long_soft.cpp
@@ -16,10 +16,10 @@
Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_coul_long_soft.h"
#include "atom.h"
#include "comm.h"
@@ -201,7 +201,7 @@ void PairCoulLongSoft::settings(int narg, char **arg)
void PairCoulLongSoft::coeff(int narg, char **arg)
{
- if (narg != 3)
+ if (narg != 3)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
@@ -361,7 +361,7 @@ double PairCoulLongSoft::single(int i, int j, int itype, int jtype,
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
-
+
denc = sqrt(lam2[itype][jtype] + rsq);
prefactor = force->qqrd2e * lam1[itype][jtype] * atom->q[i]*atom->q[j] /
(denc*denc*denc);
@@ -390,6 +390,6 @@ void *PairCoulLongSoft::extract(const char *str, int &dim)
dim = 2;
if (strcmp(str,"scale") == 0) return (void *) scale;
if (strcmp(str,"lambda") == 0) return (void *) lambda;
-
+
return NULL;
}
diff --git a/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp b/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp
index 1f4a2529f5..d2a9a04ba6 100644
--- a/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp
+++ b/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp
@@ -16,10 +16,10 @@
Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_lj_charmm_coul_long_soft.h"
#include "atom.h"
#include "comm.h"
@@ -153,14 +153,14 @@ void PairLJCharmmCoulLongSoft::compute(int eflag, int vflag)
if (rsq < cut_ljsq) {
r4sig6 = rsq*rsq / lj2[itype][jtype];
denlj = lj3[itype][jtype] + rsq*r4sig6;
- forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
+ forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
(48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj));
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
switch2 = 12.0 * (cut_ljsq-rsq) * (rsq-cut_lj_innersq) / denom_lj;
- philj = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
+ philj = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
(1.0/(denlj*denlj) - 1.0/denlj);
forcelj = forcelj*switch1 + philj*switch2;
}
@@ -185,7 +185,7 @@ void PairLJCharmmCoulLongSoft::compute(int eflag, int vflag)
} else ecoul = 0.0;
if (rsq < cut_ljsq) {
- evdwl = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
+ evdwl = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
(1.0/(denlj*denlj) - 1.0/denlj);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
@@ -270,7 +270,7 @@ void PairLJCharmmCoulLongSoft::compute_inner()
r4sig6 = rsq*rsq / lj2[itype][jtype];
denlj = lj3[itype][jtype] + rsq*r4sig6;
- forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
+ forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
(48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj));
fpair = forcecoul + factor_lj*forcelj;
@@ -365,14 +365,14 @@ void PairLJCharmmCoulLongSoft::compute_middle()
r4sig6 = rsq*rsq / lj2[itype][jtype];
denlj = lj3[itype][jtype] + rsq*r4sig6;
- forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
+ forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
(48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj));
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
switch2 = 12.0 * (cut_ljsq-rsq) * (rsq-cut_lj_innersq) / denom_lj;
- philj = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
+ philj = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
(1.0/(denlj*denlj) - 1.0/denlj);
forcelj = forcelj*switch1 + philj*switch2;
}
@@ -497,14 +497,14 @@ void PairLJCharmmCoulLongSoft::compute_outer(int eflag, int vflag)
if (rsq < cut_ljsq && rsq > cut_in_off_sq) {
r4sig6 = rsq*rsq / lj2[itype][jtype];
denlj = lj3[itype][jtype] + rsq*r4sig6;
- forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
+ forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
(48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj));
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
switch2 = 12.0 * (cut_ljsq-rsq) * (rsq-cut_lj_innersq) / denom_lj;
- philj = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
+ philj = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
(1.0/(denlj*denlj) - 1.0/denlj);
forcelj = forcelj*switch1 + philj*switch2;
}
@@ -535,7 +535,7 @@ void PairLJCharmmCoulLongSoft::compute_outer(int eflag, int vflag)
if (rsq < cut_ljsq) {
r4sig6 = rsq*rsq / lj2[itype][jtype];
denlj = lj3[itype][jtype] + rsq*r4sig6;
- evdwl = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
+ evdwl = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
(1.0/(denlj*denlj) - 1.0/denlj);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
@@ -555,27 +555,27 @@ void PairLJCharmmCoulLongSoft::compute_outer(int eflag, int vflag)
if (rsq <= cut_in_off_sq) {
r4sig6 = rsq*rsq / lj2[itype][jtype];
denlj = lj3[itype][jtype] + rsq*r4sig6;
- forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
+ forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
(48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj));
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
switch2 = 12.0 * (cut_ljsq-rsq) * (rsq-cut_lj_innersq) / denom_lj;
- philj = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
+ philj = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
(1.0/(denlj*denlj) - 1.0/denlj);
forcelj = forcelj*switch1 + philj*switch2;
}
} else if (rsq <= cut_in_on_sq) {
r4sig6 = rsq*rsq / lj2[itype][jtype];
denlj = lj3[itype][jtype] + rsq*r4sig6;
- forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
+ forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
(48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj));
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
switch2 = 12.0 * (cut_ljsq-rsq) * (rsq-cut_lj_innersq) / denom_lj;
- philj = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
+ philj = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
(1.0/(denlj*denlj) - 1.0/denlj);
forcelj = forcelj*switch1 + philj*switch2;
}
@@ -971,13 +971,13 @@ double PairLJCharmmCoulLongSoft::single(int i, int j, int itype, int jtype,
if (rsq < cut_ljsq) {
r4sig6 = rsq*rsq / lj2[itype][jtype];
denlj = lj3[itype][jtype] + rsq*r4sig6;
- forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
+ forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
(48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj));
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
switch2 = 12.0 * (cut_ljsq-rsq) * (rsq-cut_lj_innersq) / denom_lj;
- philj = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
+ philj = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
(1.0/(denlj*denlj) - 1.0/denlj);
forcelj = forcelj*switch1 + philj*switch2;
}
@@ -993,7 +993,7 @@ double PairLJCharmmCoulLongSoft::single(int i, int j, int itype, int jtype,
}
if (rsq < cut_ljsq) {
- philj = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
+ philj = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
(1.0/(denlj*denlj) - 1.0/denlj) - offset[itype][jtype];
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
diff --git a/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp b/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp
index e4c3f63b95..631d608afb 100644
--- a/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp
+++ b/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp
@@ -15,10 +15,10 @@
Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_lj_cut_coul_cut_soft.h"
#include "atom.h"
#include "comm.h"
@@ -121,11 +121,11 @@ void PairLJCutCoulCutSoft::compute(int eflag, int vflag)
denc = sqrt(lj4[itype][jtype] + rsq);
forcecoul = qqrd2e * lj1[itype][jtype] * qtmp*q[j] / (denc*denc*denc);
} else forcecoul = 0.0;
-
+
if (rsq < cut_ljsq[itype][jtype]) {
r4sig6 = rsq*rsq / lj2[itype][jtype];
denlj = lj3[itype][jtype] + rsq*r4sig6;
- forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
+ forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
(48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj));
} else forcelj = 0.0;
@@ -145,7 +145,7 @@ void PairLJCutCoulCutSoft::compute(int eflag, int vflag)
ecoul = factor_coul * qqrd2e * lj1[itype][jtype] * qtmp*q[j] / denc;
else ecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
- evdwl = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
+ evdwl = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
(1.0/(denlj*denlj) - 1.0/denlj) - offset[itype][jtype];
evdwl *= factor_lj;
} else evdwl = 0.0;
@@ -225,7 +225,7 @@ void PairLJCutCoulCutSoft::settings(int narg, char **arg)
void PairLJCutCoulCutSoft::coeff(int narg, char **arg)
{
- if (narg < 5 || narg > 7)
+ if (narg < 5 || narg > 7)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
@@ -481,7 +481,7 @@ double PairLJCutCoulCutSoft::single(int i, int j, int itype, int jtype,
if (rsq < cut_ljsq[itype][jtype]) {
r4sig6 = rsq*rsq / lj2[itype][jtype];
denlj = lj3[itype][jtype] + rsq*r4sig6;
- forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
+ forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
(48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj));
} else forcelj = 0.0;
fforce = factor_coul*forcecoul + factor_lj*forcelj;
@@ -492,7 +492,7 @@ double PairLJCutCoulCutSoft::single(int i, int j, int itype, int jtype,
eng += factor_coul*phicoul;
}
if (rsq < cut_ljsq[itype][jtype]) {
- philj = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
+ philj = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
(1.0/(denlj*denlj) - 1.0/denlj) - offset[itype][jtype];
eng += factor_lj*philj;
}
diff --git a/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp b/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp
index 6bb9538023..1b3c2b5ece 100644
--- a/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp
+++ b/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp
@@ -16,10 +16,10 @@
Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_lj_cut_coul_long_soft.h"
#include "atom.h"
#include "comm.h"
@@ -139,10 +139,10 @@ void PairLJCutCoulLongSoft::compute(int eflag, int vflag)
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
-
+
denc = sqrt(lj4[itype][jtype] + rsq);
prefactor = qqrd2e * lj1[itype][jtype] * qtmp*q[j] / (denc*denc*denc);
-
+
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
} else forcecoul = 0.0;
@@ -150,7 +150,7 @@ void PairLJCutCoulLongSoft::compute(int eflag, int vflag)
if (rsq < cut_ljsq[itype][jtype]) {
r4sig6 = rsq*rsq / lj2[itype][jtype];
denlj = lj3[itype][jtype] + rsq*r4sig6;
- forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
+ forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
(48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj));
} else forcelj = 0.0;
@@ -173,7 +173,7 @@ void PairLJCutCoulLongSoft::compute(int eflag, int vflag)
} else ecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
- evdwl = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
+ evdwl = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
(1.0/(denlj*denlj) - 1.0/denlj) - offset[itype][jtype];
evdwl *= factor_lj;
} else evdwl = 0.0;
@@ -254,7 +254,7 @@ void PairLJCutCoulLongSoft::compute_inner()
if (rsq < cut_ljsq[itype][jtype]) {
r4sig6 = rsq*rsq / lj2[itype][jtype];
denlj = lj3[itype][jtype] + rsq*r4sig6;
- forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
+ forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
(48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj));
} else forcelj = 0.0;
@@ -349,7 +349,7 @@ void PairLJCutCoulLongSoft::compute_middle()
if (rsq < cut_ljsq[itype][jtype]) {
r4sig6 = rsq*rsq / lj2[itype][jtype];
denlj = lj3[itype][jtype] + rsq*r4sig6;
- forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
+ forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
(48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj));
} else forcelj = 0.0;
@@ -447,10 +447,10 @@ void PairLJCutCoulLongSoft::compute_outer(int eflag, int vflag)
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
-
+
denc = sqrt(lj4[itype][jtype] + rsq);
fprefactor = qqrd2e * lj1[itype][jtype] * qtmp*q[j] / (denc*denc*denc);
-
+
forcecoul = fprefactor * (erfc + EWALD_F*grij*expm2 - 1.0);
if (rsq > cut_in_off_sq) {
@@ -471,7 +471,7 @@ void PairLJCutCoulLongSoft::compute_outer(int eflag, int vflag)
if (rsq < cut_ljsq[itype][jtype] && rsq > cut_in_off_sq) {
r4sig6 = rsq*rsq / lj2[itype][jtype];
denlj = lj3[itype][jtype] + rsq*r4sig6;
- forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
+ forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
(48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj));
if (rsq < cut_in_on_sq) {
rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff;
@@ -500,7 +500,7 @@ void PairLJCutCoulLongSoft::compute_outer(int eflag, int vflag)
if (rsq < cut_ljsq[itype][jtype]) {
r4sig6 = rsq*rsq / lj2[itype][jtype];
denlj = lj3[itype][jtype] + rsq*r4sig6;
- evdwl = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
+ evdwl = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
(1.0/(denlj*denlj) - 1.0/denlj) - offset[itype][jtype];
evdwl *= factor_lj;
} else evdwl = 0.0;
@@ -515,12 +515,12 @@ void PairLJCutCoulLongSoft::compute_outer(int eflag, int vflag)
if (rsq <= cut_in_off_sq) {
r4sig6 = rsq*rsq / lj2[itype][jtype];
denlj = lj3[itype][jtype] + rsq*r4sig6;
- forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
+ forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
(48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj));
} else if (rsq < cut_in_on_sq) {
r4sig6 = rsq*rsq / lj2[itype][jtype];
denlj = lj3[itype][jtype] + rsq*r4sig6;
- forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
+ forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
(48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj));
}
fpair = forcecoul + factor_lj*forcelj;
@@ -910,11 +910,11 @@ double PairLJCutCoulLongSoft::single(int i, int j, int itype, int jtype,
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
-
+
denc = sqrt(lj4[itype][jtype] + rsq);
prefactor = force->qqrd2e * lj1[itype][jtype] * atom->q[i]*atom->q[j] /
(denc*denc*denc);
-
+
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
} else forcecoul = 0.0;
@@ -922,7 +922,7 @@ double PairLJCutCoulLongSoft::single(int i, int j, int itype, int jtype,
if (rsq < cut_ljsq[itype][jtype]) {
r4sig6 = rsq*rsq / lj2[itype][jtype];
denlj = lj3[itype][jtype] + rsq*r4sig6;
- forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
+ forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
(48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj));
} else forcelj = 0.0;
@@ -937,7 +937,7 @@ double PairLJCutCoulLongSoft::single(int i, int j, int itype, int jtype,
}
if (rsq < cut_ljsq[itype][jtype]) {
- philj = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
+ philj = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
(1.0/(denlj*denlj) - 1.0/denlj) - offset[itype][jtype];
eng += factor_lj*philj;
}
diff --git a/src/USER-FEP/pair_lj_cut_soft.cpp b/src/USER-FEP/pair_lj_cut_soft.cpp
index 95b74d0d1f..7f04158c17 100644
--- a/src/USER-FEP/pair_lj_cut_soft.cpp
+++ b/src/USER-FEP/pair_lj_cut_soft.cpp
@@ -16,10 +16,10 @@
Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_lj_cut_soft.h"
#include "atom.h"
#include "comm.h"
@@ -118,7 +118,7 @@ void PairLJCutSoft::compute(int eflag, int vflag)
r4sig6 = rsq*rsq / lj2[itype][jtype];
denlj = lj3[itype][jtype] + rsq*r4sig6;
- forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
+ forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
(48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj));
fpair = factor_lj*forcelj;
@@ -133,7 +133,7 @@ void PairLJCutSoft::compute(int eflag, int vflag)
}
if (eflag) {
- evdwl = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
+ evdwl = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
(1.0/(denlj*denlj) - 1.0/denlj) - offset[itype][jtype];
evdwl *= factor_lj;
}
@@ -202,7 +202,7 @@ void PairLJCutSoft::compute_inner()
r4sig6 = rsq*rsq / lj2[itype][jtype];
denlj = lj3[itype][jtype] + rsq*r4sig6;
- forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
+ forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
(48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj));
fpair = factor_lj*forcelj;
@@ -285,7 +285,7 @@ void PairLJCutSoft::compute_middle()
r4sig6 = rsq*rsq / lj2[itype][jtype];
denlj = lj3[itype][jtype] + rsq*r4sig6;
- forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
+ forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
(48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj));
fpair = factor_lj*forcelj;
@@ -372,7 +372,7 @@ void PairLJCutSoft::compute_outer(int eflag, int vflag)
r4sig6 = rsq*rsq / lj2[itype][jtype];
denlj = lj3[itype][jtype] + rsq*r4sig6;
- forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
+ forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
(48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj));
fpair = factor_lj*forcelj;
@@ -395,7 +395,7 @@ void PairLJCutSoft::compute_outer(int eflag, int vflag)
if (eflag) {
r4sig6 = rsq*rsq / lj2[itype][jtype];
denlj = lj3[itype][jtype] + rsq*r4sig6;
- evdwl = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
+ evdwl = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
(1.0/(denlj*denlj) - 1.0/denlj) - offset[itype][jtype];
evdwl *= factor_lj;
}
@@ -404,7 +404,7 @@ void PairLJCutSoft::compute_outer(int eflag, int vflag)
if (rsq <= cut_in_off_sq) {
r4sig6 = rsq*rsq / lj2[itype][jtype];
denlj = lj3[itype][jtype] + rsq*r4sig6;
- forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
+ forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
(48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj));
fpair = factor_lj*forcelj;
} else if (rsq < cut_in_on_sq)
@@ -756,13 +756,13 @@ double PairLJCutSoft::single(int i, int j, int itype, int jtype, double rsq,
if (rsq < cutsq[itype][jtype]) {
r4sig6 = rsq*rsq / lj2[itype][jtype];
denlj = lj3[itype][jtype] + rsq*r4sig6;
- forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
+ forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
(48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj));
} else forcelj = 0.0;
fforce = factor_lj*forcelj;
if (rsq < cutsq[itype][jtype]) {
- philj = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
+ philj = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
(1.0/(denlj*denlj) - 1.0/denlj) - offset[itype][jtype];
} else philj = 0.0;
diff --git a/src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp b/src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp
index 0ea6cf7a7f..2edad28bf3 100644
--- a/src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp
+++ b/src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp
@@ -17,10 +17,10 @@
Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_lj_cut_tip4p_long_soft.h"
#include "angle.h"
#include "atom.h"
@@ -183,7 +183,7 @@ void PairLJCutTIP4PLongSoft::compute(int eflag, int vflag)
r4sig6 = rsq*rsq / lj2[itype][jtype];
denlj = lj3[itype][jtype] + rsq*r4sig6;
- forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
+ forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
(48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj));
forcelj *= factor_lj;
@@ -196,7 +196,7 @@ void PairLJCutTIP4PLongSoft::compute(int eflag, int vflag)
f[j][2] -= delz*forcelj;
if (eflag) {
- evdwl = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
+ evdwl = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
(1.0/(denlj*denlj) - 1.0/denlj) - offset[itype][jtype];
evdwl *= factor_lj;
} else evdwl = 0.0;
diff --git a/src/USER-FEP/pair_tip4p_long_soft.cpp b/src/USER-FEP/pair_tip4p_long_soft.cpp
index ef76da4994..027882cfba 100644
--- a/src/USER-FEP/pair_tip4p_long_soft.cpp
+++ b/src/USER-FEP/pair_tip4p_long_soft.cpp
@@ -17,10 +17,10 @@
Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_tip4p_long_soft.h"
#include "angle.h"
#include "atom.h"
diff --git a/src/USER-H5MD/dump_h5md.cpp b/src/USER-H5MD/dump_h5md.cpp
index 4af1e2ed4c..87cec4aef0 100644
--- a/src/USER-H5MD/dump_h5md.cpp
+++ b/src/USER-H5MD/dump_h5md.cpp
@@ -12,11 +12,11 @@
Contributing author: Pierre de Buyl (KU Leuven)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
-#include "limits.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <limits.h>
#include "ch5md.h"
#include "dump_h5md.h"
#include "domain.h"
diff --git a/src/USER-INTEL/fix_intel.cpp b/src/USER-INTEL/fix_intel.cpp
index 8bc3772509..602c20e5db 100644
--- a/src/USER-INTEL/fix_intel.cpp
+++ b/src/USER-INTEL/fix_intel.cpp
@@ -95,11 +95,11 @@ FixIntel::FixIntel(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
iarg += 2;
} else if (strcmp(arg[iarg],"mode") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal package intel command");
- if (strcmp(arg[iarg+1],"single") == 0)
+ if (strcmp(arg[iarg+1],"single") == 0)
_precision_mode = PREC_MODE_SINGLE;
- else if (strcmp(arg[iarg+1],"mixed") == 0)
+ else if (strcmp(arg[iarg+1],"mixed") == 0)
_precision_mode = PREC_MODE_MIXED;
- else if (strcmp(arg[iarg+1],"double") == 0)
+ else if (strcmp(arg[iarg+1],"double") == 0)
_precision_mode = PREC_MODE_DOUBLE;
else error->all(FLERR,"Illegal package intel command");
iarg += 2;
@@ -176,7 +176,7 @@ FixIntel::FixIntel(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
// set OpenMP threads
// nomp is user setting, default = 0
-
+
#if defined(_OPENMP)
#if defined(__INTEL_COMPILER)
kmp_set_blocktime(0);
@@ -232,7 +232,7 @@ FixIntel::~FixIntel()
double *time1 = off_watch_pair();
double *time2 = off_watch_neighbor();
int *overflow = get_off_overflow_flag();
- if (_offload_balance != 0.0 && time1 != NULL && time2 != NULL &&
+ if (_offload_balance != 0.0 && time1 != NULL && time2 != NULL &&
overflow != NULL) {
#pragma offload_transfer target(mic:_cop) \
nocopy(time1,time2,overflow:alloc_if(0) free_if(1))
@@ -315,7 +315,7 @@ void FixIntel::pair_init_check()
#ifdef _LMP_INTEL_OFFLOAD
if (_offload_balance != 0.0) atom->sortfreq = 1;
-
+
if (force->newton_pair == 0)
_offload_noghost = 0;
else if (_offload_ghost == 0)
@@ -327,7 +327,7 @@ void FixIntel::pair_init_check()
double *time1 = off_watch_pair();
double *time2 = off_watch_neighbor();
int *overflow = get_off_overflow_flag();
- if (_offload_balance !=0.0 && time1 != NULL && time2 != NULL &&
+ if (_offload_balance !=0.0 && time1 != NULL && time2 != NULL &&
overflow != NULL) {
#pragma offload_transfer target(mic:_cop) \
nocopy(time1,time2:length(1) alloc_if(1) free_if(0)) \
@@ -419,7 +419,7 @@ void FixIntel::check_neighbor_intel()
if (_offload_balance != 0.0 && neighbor->requests[i]->intel == 0) {
_full_host_list = 1;
_offload_noghost = 0;
- }
+ }
#endif
if (neighbor->requests[i]->skip)
error->all(FLERR, "Cannot yet use hybrid styles with Intel package.");
@@ -532,7 +532,7 @@ void FixIntel::output_timing_data() {
#endif
double ht = timers[TIME_HOST_NEIGHBOR] + timers[TIME_HOST_PAIR] +
timers[TIME_OFFLOAD_WAIT];
- double ct = timers[TIME_OFFLOAD_NEIGHBOR] +
+ double ct = timers[TIME_OFFLOAD_NEIGHBOR] +
timers[TIME_OFFLOAD_PAIR];
double tt = MAX(ht,ct);
if (timers[TIME_OFFLOAD_LATENCY] / tt > 0.07 && _separate_coi == 0)
diff --git a/src/USER-INTEL/fix_intel.h b/src/USER-INTEL/fix_intel.h
index 93716f9afc..18cd76be1d 100644
--- a/src/USER-INTEL/fix_intel.h
+++ b/src/USER-INTEL/fix_intel.h
@@ -31,7 +31,7 @@ namespace LAMMPS_NS {
class IntelData;
template <class flt_t, class acc_t> class IntelBuffers;
-
+
class FixIntel : public Fix {
public:
FixIntel(class LAMMPS *, int, char **);
@@ -49,13 +49,13 @@ class FixIntel : public Fix {
typedef struct { double x,y,z; } lmp_ft;
enum {PREC_MODE_SINGLE, PREC_MODE_MIXED, PREC_MODE_DOUBLE};
-
+
inline int precision() { return _precision_mode; }
- inline IntelBuffers<float,float> * get_single_buffers()
+ inline IntelBuffers<float,float> * get_single_buffers()
{ return _single_buffers; }
- inline IntelBuffers<float,double> * get_mixed_buffers()
+ inline IntelBuffers<float,double> * get_mixed_buffers()
{ return _mixed_buffers; }
- inline IntelBuffers<double,double> * get_double_buffers()
+ inline IntelBuffers<double,double> * get_double_buffers()
{ return _double_buffers; }
protected:
@@ -77,7 +77,7 @@ class FixIntel : public Fix {
inline void add_result_array(IntelBuffers<float,float>::vec3_acc_t *f_in,
float *ev_in, const int offload,
const int eatom = 0, const int vatom = 0);
- inline void get_buffern(const int offload, int &nlocal, int &nall,
+ inline void get_buffern(const int offload, int &nlocal, int &nall,
int &minlocal);
#ifdef _LMP_INTEL_OFFLOAD
@@ -101,7 +101,7 @@ class FixIntel : public Fix {
inline int host_nall() { return _host_nall; }
inline int separate_buffers() { return _separate_buffers; }
inline int offload_noghost() { return _offload_noghost; }
- inline void set_offload_noghost(const int v)
+ inline void set_offload_noghost(const int v)
{ if (_offload_ghost < 0) _offload_noghost = v; }
inline void set_neighbor_host_sizes();
@@ -301,7 +301,7 @@ void FixIntel::add_results(const ft * _noalias const f_in,
const acc_t * _noalias const enull = 0;
int offset = _offload_nlocal;
if (atom->torque) offset *= 2;
- add_oresults(f_in + offset, enull, eatom, vatom,
+ add_oresults(f_in + offset, enull, eatom, vatom,
_offload_min_ghost, _offload_nghost);
}
} else {
@@ -311,7 +311,7 @@ void FixIntel::add_results(const ft * _noalias const f_in,
const acc_t * _noalias const enull = 0;
int offset = _host_used_local;
if (atom->torque) offset *= 2;
- add_oresults(f_in + offset, enull, eatom,
+ add_oresults(f_in + offset, enull, eatom,
vatom, _host_min_ghost, _host_used_ghost);
}
}
@@ -511,7 +511,7 @@ void FixIntel::add_off_results(const ft * _noalias const f_in,
_offload_nall = _offload_nlocal + _offload_nghost;
_offload_nlocal;
}
-
+
int nlocal = atom->nlocal;
// Load balance?
if (_offload_balance < 0.0) {
@@ -625,8 +625,8 @@ pair styles.
E: Cannot yet use hybrid styles with Intel package.
-The hybrid pair style configuration is not yet supported by the Intel
-package. Support is limited to hybrid/overlay or a hybrid style that does
+The hybrid pair style configuration is not yet supported by the Intel
+package. Support is limited to hybrid/overlay or a hybrid style that does
not require a skip list.
W: Leaving a core/node free can improve performance for offload
diff --git a/src/USER-INTEL/intel_buffers.cpp b/src/USER-INTEL/intel_buffers.cpp
index e430a1ebc4..154db19258 100644
--- a/src/USER-INTEL/intel_buffers.cpp
+++ b/src/USER-INTEL/intel_buffers.cpp
@@ -101,7 +101,7 @@ void IntelBuffers<flt_t, acc_t>::free_buffers()
/* ---------------------------------------------------------------------- */
template <class flt_t, class acc_t>
-void IntelBuffers<flt_t, acc_t>::_grow(const int nall, const int nlocal,
+void IntelBuffers<flt_t, acc_t>::_grow(const int nall, const int nlocal,
const int nthreads,
const int offload_end)
{
@@ -129,7 +129,7 @@ void IntelBuffers<flt_t, acc_t>::_grow(const int nall, const int nlocal,
if (lmp->atom->ellipsoid != NULL)
lmp->memory->create(_host_quat, _buf_size, "intel_host_quat");
}
-
+
if (offload_end > 0) {
lmp->memory->create(_off_f, f_stride * _off_threads, "intel_off_f");
const atom_t * const x = get_x();
@@ -252,7 +252,7 @@ void IntelBuffers<flt_t, acc_t>::free_local()
/* ---------------------------------------------------------------------- */
template <class flt_t, class acc_t>
-void IntelBuffers<flt_t, acc_t>::_grow_local(NeighList *list,
+void IntelBuffers<flt_t, acc_t>::_grow_local(NeighList *list,
const int offload_end)
{
free_local();
@@ -341,7 +341,7 @@ void IntelBuffers<flt_t, acc_t>::free_nbor_list()
/* ---------------------------------------------------------------------- */
template <class flt_t, class acc_t>
-void IntelBuffers<flt_t, acc_t>::_grow_nbor_list(NeighList *list,
+void IntelBuffers<flt_t, acc_t>::_grow_nbor_list(NeighList *list,
const int nlocal,
const int offload_end)
{
@@ -449,7 +449,7 @@ void IntelBuffers<flt_t, acc_t>::grow_ccache(const int off_flag,
int *ccachei = _ccachei;
int *ccachej = _ccachej;
- if (ccachex != NULL && ccachey !=NULL && ccachez != NULL &&
+ if (ccachex != NULL && ccachey !=NULL && ccachez != NULL &&
ccachew != NULL && ccachei != NULL && ccachej !=NULL) {
#pragma offload_transfer target(mic:_cop) \
nocopy(ccachex,ccachey:length(vsize) alloc_if(1) free_if(0)) \
diff --git a/src/USER-INTEL/intel_buffers.h b/src/USER-INTEL/intel_buffers.h
index 91dbb790ca..afd7fe46ed 100644
--- a/src/USER-INTEL/intel_buffers.h
+++ b/src/USER-INTEL/intel_buffers.h
@@ -39,16 +39,16 @@ class IntelBuffers {
public:
typedef struct { flt_t x,y,z; int w; } atom_t;
typedef struct { flt_t w,i,j,k; } quat_t;
- typedef struct { flt_t x,y,z,w; } vec3_t;
+ typedef struct { flt_t x,y,z,w; } vec3_t;
typedef struct { flt_t x,y,z,w; } vec4_t;
typedef struct { acc_t x,y,z,w; } vec3_acc_t;
-
+
IntelBuffers(class LAMMPS *lmp_in);
~IntelBuffers();
inline int get_stride(int nall) {
int stride;
- IP_PRE_get_stride(stride, nall, sizeof(vec3_acc_t),
+ IP_PRE_get_stride(stride, nall, sizeof(vec3_acc_t),
lmp->atom->torque);
return stride;
}
@@ -102,7 +102,7 @@ class IntelBuffers {
}
void free_binhead();
-
+
inline void grow_binhead() {
#ifdef _LMP_INTEL_OFFLOAD
if (lmp->neighbor->maxhead > _off_map_maxhead)
@@ -125,7 +125,7 @@ class IntelBuffers {
(INTEL_ONEATOM_FACTOR * INTEL_DATA_ALIGN);
return mn * INTEL_DATA_ALIGN / sizeof(int);
}
-
+
void free_nbor_list();
inline void grow_nbor_list(NeighList *list, const int nlocal,
@@ -144,35 +144,35 @@ class IntelBuffers {
inline int * cnumneigh(const NeighList *list) { return _cnumneigh; }
inline int * get_atombin() { return _atombin; }
- inline atom_t * get_x(const int offload = 1) {
+ inline atom_t * get_x(const int offload = 1) {
#ifdef _LMP_INTEL_OFFLOAD
if (_separate_buffers && offload == 0) return _host_x;
#endif
- return _x;
+ return _x;
}
- inline flt_t * get_q(const int offload = 1) {
+ inline flt_t * get_q(const int offload = 1) {
#ifdef _LMP_INTEL_OFFLOAD
if (_separate_buffers && offload == 0) return _host_q;
#endif
- return _q;
+ return _q;
}
- inline quat_t * get_quat(const int offload = 1) {
+ inline quat_t * get_quat(const int offload = 1) {
#ifdef _LMP_INTEL_OFFLOAD
if (_separate_buffers && offload == 0) return _host_quat;
#endif
- return _quat;
+ return _quat;
}
inline vec3_acc_t * get_f() { return _f; }
inline acc_t * get_ev_global() { return _ev_global; }
inline acc_t * get_ev_global_host() { return _ev_global_host; }
- inline void zero_ev()
+ inline void zero_ev()
{ for (int i = 0; i < 8; i++) _ev_global[i] = _ev_global_host[i] = 0.0; }
inline flt_t ** get_cutneighsq() { return _cutneighsq; }
inline int get_off_threads() { return _off_threads; }
#ifdef _LMP_INTEL_OFFLOAD
- inline void set_off_params(const int n, const int cop,
- const int separate_buffers)
- { _off_threads = n; _cop = cop; _separate_buffers = separate_buffers; }
+ inline void set_off_params(const int n, const int cop,
+ const int separate_buffers)
+ { _off_threads = n; _cop = cop; _separate_buffers = separate_buffers; }
inline vec3_acc_t * get_off_f() { return _off_f; }
#endif
@@ -197,7 +197,7 @@ class IntelBuffers {
}
#ifdef _LMP_INTEL_OFFLOAD
- inline void thr_pack_cop(const int ifrom, const int ito,
+ inline void thr_pack_cop(const int ifrom, const int ito,
const int offset, const bool dotype = false) {
double ** x = lmp->atom->x + offset;
if (dotype == false) {
@@ -219,7 +219,7 @@ class IntelBuffers {
}
}
- inline void thr_pack_host(const int ifrom, const int ito,
+ inline void thr_pack_host(const int ifrom, const int ito,
const int offset) {
double ** x = lmp->atom->x + offset;
for (int i = ifrom; i < ito; i++) {
@@ -229,7 +229,7 @@ class IntelBuffers {
}
}
- inline void pack_sep_from_single(const int host_min_local,
+ inline void pack_sep_from_single(const int host_min_local,
const int used_local,
const int host_min_ghost,
const int used_ghost) {
@@ -295,7 +295,7 @@ class IntelBuffers {
bool _off_list_alloc;
int _need_tag;
#endif
-
+
int _buf_size, _buf_local_size;
_alignvar(acc_t _ev_global[8],64);
_alignvar(acc_t _ev_global_host[8],64);
diff --git a/src/USER-INTEL/intel_preprocess.h b/src/USER-INTEL/intel_preprocess.h
index f4c8b50629..39809cf882 100644
--- a/src/USER-INTEL/intel_preprocess.h
+++ b/src/USER-INTEL/intel_preprocess.h
@@ -298,7 +298,7 @@ inline double MIC_Wtime() {
#define MIC_Wtime MPI_Wtime
#define IP_PRE_pack_separate_buffers(fix, buffers, ago, offload, \
- nlocal, nall)
+ nlocal, nall)
#define IP_PRE_get_transfern(ago, newton, evflag, eflag, vflag, \
buffers, offload, fix, separate_flag, \
@@ -323,7 +323,7 @@ inline double MIC_Wtime() {
}
#define IP_PRE_repack_for_offload(newton, separate_flag, nlocal, nall, \
- f_stride, x, q)
+ f_stride, x, q)
#endif
diff --git a/src/USER-INTEL/neigh_half_bin_intel.cpp b/src/USER-INTEL/neigh_half_bin_intel.cpp
index 8b4fe4c101..ca3f12135d 100644
--- a/src/USER-INTEL/neigh_half_bin_intel.cpp
+++ b/src/USER-INTEL/neigh_half_bin_intel.cpp
@@ -143,7 +143,7 @@ void Neighbor::half_bin_no_newton_intel(NeighList *list)
int host_start = off_end;;
#ifdef _LMP_INTEL_OFFLOAD
if (fix->full_host_list()) host_start = 0;
- if (exclude)
+ if (exclude)
error->all(FLERR, "Exclusion lists not yet supported for Intel offload");
#endif
@@ -214,7 +214,7 @@ void Neighbor::hbnni(const int offload, NeighList *list, void *buffers_in,
#endif
{
int ifrom, ito, tid;
- IP_PRE_omp_range_id_align(ifrom, ito, tid, nall, nthreads,
+ IP_PRE_omp_range_id_align(ifrom, ito, tid, nall, nthreads,
sizeof(ATOM_T));
buffers->thr_pack(ifrom, ito, 0);
}
@@ -492,9 +492,9 @@ void Neighbor::hbnni(const int offload, NeighList *list, void *buffers_in,
ofind_special(which, special, nspecial, i, tag[j], special_flag);
#ifdef _LMP_INTEL_OFFLOAD
if (j >= nlocal) {
- if (j == nall)
+ if (j == nall)
jlist[jj] = nall_offset;
- else if (which > 0)
+ else if (which > 0)
jlist[jj] = (j-ghost_offset) ^ (which << SBBITS);
else jlist[jj]-=ghost_offset;
} else
@@ -571,7 +571,7 @@ void Neighbor::half_bin_newton_intel(NeighList *list)
#ifdef _LMP_INTEL_OFFLOAD
if (fix->full_host_list()) host_start = 0;
offload_noghost = fix->offload_noghost();
- if (exclude)
+ if (exclude)
error->all(FLERR, "Exclusion lists not yet supported for Intel offload");
#endif
@@ -587,7 +587,7 @@ void Neighbor::half_bin_newton_intel(NeighList *list)
0, off_end, fix);
hbni<float,double,1,1>(0, list, fix->get_mixed_buffers(),
host_start, nlocal, fix, off_end);
- } else
+ } else
#endif
{
hbni<float,double,0,1>(1, list, fix->get_mixed_buffers(),
@@ -602,25 +602,25 @@ void Neighbor::half_bin_newton_intel(NeighList *list)
0, off_end, fix);
hbni<double,double,1,1>(0, list, fix->get_double_buffers(),
host_start, nlocal, fix, off_end);
- } else
+ } else
#endif
{
hbni<double,double,0,1>(1, list, fix->get_double_buffers(),
0, off_end, fix);
hbni<double,double,0,1>(0, list, fix->get_double_buffers(),
host_start, nlocal, fix);
- }
+ }
} else {
#ifdef _LMP_INTEL_OFFLOAD
if (offload_noghost) {
- hbni<float,float,1,1>(1, list, fix->get_single_buffers(), 0, off_end,
+ hbni<float,float,1,1>(1, list, fix->get_single_buffers(), 0, off_end,
fix);
hbni<float,float,1,1>(0, list, fix->get_single_buffers(),
host_start, nlocal, fix, off_end);
- } else
+ } else
#endif
{
- hbni<float,float,0,1>(1, list, fix->get_single_buffers(), 0, off_end,
+ hbni<float,float,0,1>(1, list, fix->get_single_buffers(), 0, off_end,
fix);
hbni<float,float,0,1>(0, list, fix->get_single_buffers(),
host_start, nlocal, fix);
@@ -634,7 +634,7 @@ void Neighbor::half_bin_newton_intel(NeighList *list)
0, off_end, fix);
hbni<float,double,1,0>(0, list, fix->get_mixed_buffers(),
host_start, nlocal, fix, off_end);
- } else
+ } else
#endif
{
hbni<float,double,0,0>(1, list, fix->get_mixed_buffers(),
@@ -649,25 +649,25 @@ void Neighbor::half_bin_newton_intel(NeighList *list)
0, off_end, fix);
hbni<double,double,1,0>(0, list, fix->get_double_buffers(),
host_start, nlocal, fix, off_end);
- } else
+ } else
#endif
{
hbni<double,double,0,0>(1, list, fix->get_double_buffers(),
0, off_end, fix);
hbni<double,double,0,0>(0, list, fix->get_double_buffers(),
host_start, nlocal, fix);
- }
+ }
} else {
#ifdef _LMP_INTEL_OFFLOAD
if (offload_noghost) {
- hbni<float,float,1,0>(1, list, fix->get_single_buffers(), 0, off_end,
+ hbni<float,float,1,0>(1, list, fix->get_single_buffers(), 0, off_end,
fix);
hbni<float,float,1,0>(0, list, fix->get_single_buffers(),
host_start, nlocal, fix, off_end);
- } else
+ } else
#endif
{
- hbni<float,float,0,0>(1, list, fix->get_single_buffers(), 0, off_end,
+ hbni<float,float,0,0>(1, list, fix->get_single_buffers(), 0, off_end,
fix);
hbni<float,float,0,0>(0, list, fix->get_single_buffers(),
host_start, nlocal, fix);
@@ -703,7 +703,7 @@ void Neighbor::hbni(const int offload, NeighList *list, void *buffers_in,
#endif
{
int ifrom, ito, tid;
- IP_PRE_omp_range_id_align(ifrom, ito, tid, nall, nthreads,
+ IP_PRE_omp_range_id_align(ifrom, ito, tid, nall, nthreads,
sizeof(ATOM_T));
buffers->thr_pack(ifrom, ito, 0);
}
@@ -717,7 +717,7 @@ void Neighbor::hbni(const int offload, NeighList *list, void *buffers_in,
fix->start_watch(TIME_HOST_NEIGHBOR);
if (INTEL_NBOR_PAD > 1)
pad = INTEL_NBOR_PAD * sizeof(float) / sizeof(flt_t);
- }
+ }
const int pad_width = pad;
if (aend-astart == 0) {
@@ -845,7 +845,7 @@ void Neighbor::hbni(const int offload, NeighList *list, void *buffers_in,
#ifdef _LMP_INTEL_OFFLOAD
int lmin = e_nall, lmax = -1, gmin = e_nall, gmax = -1;
#endif
-
+
const int num = aend - astart;
int tid, ifrom, ito;
IP_PRE_omp_range_id(ifrom, ito, tid, num, nthreads);
@@ -1044,7 +1044,7 @@ void Neighbor::hbni(const int offload, NeighList *list, void *buffers_in,
if (j >= nlocal) {
if (j == e_nall)
jlist[jj] = nall_offset;
- else if (which > 0)
+ else if (which > 0)
jlist[jj] = (j-ghost_offset) ^ (which << SBBITS);
else jlist[jj]-=ghost_offset;
} else
@@ -1121,7 +1121,7 @@ void Neighbor::half_bin_newton_tri_intel(NeighList *list)
#ifdef _LMP_INTEL_OFFLOAD
if (fix->full_host_list()) host_start = 0;
offload_noghost = fix->offload_noghost();
- if (exclude)
+ if (exclude)
error->all(FLERR, "Exclusion lists not yet supported for Intel offload");
#endif
@@ -1137,7 +1137,7 @@ void Neighbor::half_bin_newton_tri_intel(NeighList *list)
0, off_end, fix);
hbnti<float,double,1,1>(0, list, fix->get_mixed_buffers(),
host_start, nlocal, fix, off_end);
- } else
+ } else
#endif
{
hbnti<float,double,0,1>(1, list, fix->get_mixed_buffers(),
@@ -1153,7 +1153,7 @@ void Neighbor::half_bin_newton_tri_intel(NeighList *list)
hbnti<double,double,1,1>(0, list, fix->get_double_buffers(),
host_start, nlocal, fix, off_end);
} else
- #endif
+ #endif
{
hbnti<double,double,0,1>(1, list, fix->get_double_buffers(),
0, off_end, fix);
@@ -1167,7 +1167,7 @@ void Neighbor::half_bin_newton_tri_intel(NeighList *list)
0, off_end, fix);
hbnti<float,float,1,1>(0, list, fix->get_single_buffers(),
host_start, nlocal, fix, off_end);
- } else
+ } else
#endif
{
hbnti<float,float,0,1>(1, list, fix->get_single_buffers(),
@@ -1184,7 +1184,7 @@ void Neighbor::half_bin_newton_tri_intel(NeighList *list)
0, off_end, fix);
hbnti<float,double,1,0>(0, list, fix->get_mixed_buffers(),
host_start, nlocal, fix, off_end);
- } else
+ } else
#endif
{
hbnti<float,double,0,0>(1, list, fix->get_mixed_buffers(),
@@ -1199,7 +1199,7 @@ void Neighbor::half_bin_newton_tri_intel(NeighList *list)
0, off_end, fix);
hbnti<double,double,1,0>(0, list, fix->get_double_buffers(),
host_start, nlocal, fix, off_end);
- } else
+ } else
#endif
{
hbnti<double,double,0,0>(1, list, fix->get_double_buffers(),
@@ -1214,7 +1214,7 @@ void Neighbor::half_bin_newton_tri_intel(NeighList *list)
0, off_end, fix);
hbnti<float,float,1,0>(0, list, fix->get_single_buffers(),
host_start, nlocal, fix, off_end);
- } else
+ } else
#endif
{
hbnti<float,float,0,0>(1, list, fix->get_single_buffers(),
@@ -1253,7 +1253,7 @@ void Neighbor::hbnti(const int offload, NeighList *list, void *buffers_in,
#endif
{
int ifrom, ito, tid;
- IP_PRE_omp_range_id_align(ifrom, ito, tid, nall, nthreads,
+ IP_PRE_omp_range_id_align(ifrom, ito, tid, nall, nthreads,
sizeof(ATOM_T));
buffers->thr_pack(ifrom, ito, 0);
}
@@ -1548,9 +1548,9 @@ void Neighbor::hbnti(const int offload, NeighList *list, void *buffers_in,
ofind_special(which, special, nspecial, i, tag[j], special_flag);
#ifdef _LMP_INTEL_OFFLOAD
if (j >= nlocal) {
- if (j == e_nall)
+ if (j == e_nall)
jlist[jj] = nall_offset;
- else if (which > 0)
+ else if (which > 0)
jlist[jj] = (j-ghost_offset) ^ (which << SBBITS);
else jlist[jj]-=ghost_offset;
} else
@@ -1643,7 +1643,7 @@ void Neighbor::full_bin_intel(NeighList *list)
0, off_end, fix);
fbi<float,double,1,1>(0, list, fix->get_mixed_buffers(),
host_start, nlocal, fix, off_end);
- } else
+ } else
#endif
{
fbi<float,double,0,1>(1, list, fix->get_mixed_buffers(),
@@ -1658,7 +1658,7 @@ void Neighbor::full_bin_intel(NeighList *list)
0, off_end, fix);
fbi<double,double,1,1>(0, list, fix->get_double_buffers(),
host_start, nlocal, fix, off_end);
- } else
+ } else
#endif
{
fbi<double,double,0,1>(1, list, fix->get_double_buffers(),
@@ -1669,14 +1669,14 @@ void Neighbor::full_bin_intel(NeighList *list)
} else {
#ifdef _LMP_INTEL_OFFLOAD
if (offload_noghost) {
- fbi<float,float,1,1>(1, list, fix->get_single_buffers(), 0, off_end,
+ fbi<float,float,1,1>(1, list, fix->get_single_buffers(), 0, off_end,
fix);
fbi<float,float,1,1>(0, list, fix->get_single_buffers(),
host_start, nlocal, fix, off_end);
- } else
+ } else
#endif
{
- fbi<float,float,0,1>(1, list, fix->get_single_buffers(), 0, off_end,
+ fbi<float,float,0,1>(1, list, fix->get_single_buffers(), 0, off_end,
fix);
fbi<float,float,0,1>(0, list, fix->get_single_buffers(),
host_start, nlocal, fix);
@@ -1690,7 +1690,7 @@ void Neighbor::full_bin_intel(NeighList *list)
0, off_end, fix);
fbi<float,double,1,0>(0, list, fix->get_mixed_buffers(),
host_start, nlocal, fix, off_end);
- } else
+ } else
#endif
{
fbi<float,double,0,0>(1, list, fix->get_mixed_buffers(),
@@ -1705,7 +1705,7 @@ void Neighbor::full_bin_intel(NeighList *list)
0, off_end, fix);
fbi<double,double,1,0>(0, list, fix->get_double_buffers(),
host_start, nlocal, fix, off_end);
- } else
+ } else
#endif
{
fbi<double,double,0,0>(1, list, fix->get_double_buffers(),
@@ -1716,14 +1716,14 @@ void Neighbor::full_bin_intel(NeighList *list)
} else {
#ifdef _LMP_INTEL_OFFLOAD
if (offload_noghost) {
- fbi<float,float,1,0>(1, list, fix->get_single_buffers(), 0, off_end,
+ fbi<float,float,1,0>(1, list, fix->get_single_buffers(), 0, off_end,
fix);
fbi<float,float,1,0>(0, list, fix->get_single_buffers(),
host_start, nlocal, fix, off_end);
- } else
+ } else
#endif
{
- fbi<float,float,0,0>(1, list, fix->get_single_buffers(), 0, off_end,
+ fbi<float,float,0,0>(1, list, fix->get_single_buffers(), 0, off_end,
fix);
fbi<float,float,0,0>(0, list, fix->get_single_buffers(),
host_start, nlocal, fix);
@@ -1957,7 +1957,7 @@ void Neighbor::fbi(const int offload, NeighList *list, void *buffers_in,
} else {
if (x[j].z < ztmp) flist = 1;
else if (x[j].z == ztmp && x[j].y < ytmp) flist = 1;
- else if (x[j].z == ztmp && x[j].y == ytmp && x[j].x < xtmp)
+ else if (x[j].z == ztmp && x[j].y == ytmp && x[j].x < xtmp)
flist = 1;
}
if (flist) {
@@ -1980,8 +1980,8 @@ void Neighbor::fbi(const int offload, NeighList *list, void *buffers_in,
neighptr[n++] = j;
} else
neighptr[n++] = j;
- }
-
+ }
+
#ifdef _LMP_INTEL_OFFLOAD
if (j < nlocal) {
if (j < lmin) lmin = j;
diff --git a/src/USER-INTEL/pair_gayberne_intel.cpp b/src/USER-INTEL/pair_gayberne_intel.cpp
index 5eb76d891e..5b3e65bf66 100644
--- a/src/USER-INTEL/pair_gayberne_intel.cpp
+++ b/src/USER-INTEL/pair_gayberne_intel.cpp
@@ -12,7 +12,7 @@
Contributing author: W. Michael Brown (Intel)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_gayberne_intel.h"
#include "math_extra_intel.h"
#include "atom.h"
@@ -85,7 +85,7 @@ void PairGayBerneIntel::compute(int eflag, int vflag,
#endif
{
int ifrom, ito, tid;
- IP_PRE_omp_range_id_align(ifrom, ito, tid, nall, nthreads,
+ IP_PRE_omp_range_id_align(ifrom, ito, tid, nall, nthreads,
sizeof(ATOM_T));
if (ago != 0) buffers->thr_pack(ifrom,ito,ago);
@@ -156,16 +156,16 @@ void PairGayBerneIntel::eval(const int offload, const int vflag,
const int *ellipsoid = atom->ellipsoid;
#ifdef _LMP_INTEL_OFFLOAD
- if (fix->separate_buffers()) {
- fix->start_watch(TIME_PACK);
+ if (fix->separate_buffers()) {
+ fix->start_watch(TIME_PACK);
if (offload) {
#pragma omp parallel default(none) \
shared(buffers,nlocal,nall,bonus,ellipsoid)
- {
- int ifrom, ito, tid;
- int nthreads = comm->nthreads;
- IP_PRE_omp_range_id_align(ifrom, ito, tid, nlocal,
- nthreads, sizeof(ATOM_T));
+ {
+ int ifrom, ito, tid;
+ int nthreads = comm->nthreads;
+ IP_PRE_omp_range_id_align(ifrom, ito, tid, nlocal,
+ nthreads, sizeof(ATOM_T));
if (ago != 0) buffers->thr_pack_cop(ifrom, ito, 0);
for (int i = ifrom; i < ito; i++) {
int qi = ellipsoid[i];
@@ -178,8 +178,8 @@ void PairGayBerneIntel::eval(const int offload, const int vflag,
}
int nghost = nall - nlocal;
if (nghost) {
- IP_PRE_omp_range_align(ifrom, ito, tid, nall - nlocal,
- nthreads, sizeof(ATOM_T));
+ IP_PRE_omp_range_align(ifrom, ito, tid, nall - nlocal,
+ nthreads, sizeof(ATOM_T));
int offset = 0;
ifrom += nlocal;
ito += nlocal;
@@ -197,7 +197,7 @@ void PairGayBerneIntel::eval(const int offload, const int vflag,
}
}
}
- }
+ }
} else {
if (ago != 0) buffers->thr_pack_host(fix->host_min_local(), nlocal, 0);
for (int i = fix->host_min_local(); i < nlocal; i++) {
@@ -220,9 +220,9 @@ void PairGayBerneIntel::eval(const int offload, const int vflag,
quat[i].k = bonus[qi].quat[3];
}
}
- }
- fix->stop_watch(TIME_PACK);
- }
+ }
+ fix->stop_watch(TIME_PACK);
+ }
#endif
// const int * _noalias const ilist = list->ilist;
@@ -268,9 +268,9 @@ void PairGayBerneIntel::eval(const int offload, const int vflag,
} else {
if (INTEL_NBOR_PAD > 1)
pad = INTEL_NBOR_PAD * sizeof(float) / sizeof(flt_t);
- }
+ }
const int pad_width = pad;
-
+
#ifdef _LMP_INTEL_OFFLOAD
int *overflow = fix->get_off_overflow_flag();
double *timer_compute = fix->off_watch_pair();
@@ -300,29 +300,29 @@ void PairGayBerneIntel::eval(const int offload, const int vflag,
#endif
#ifdef _LMP_INTEL_OFFLOAD
- if (separate_flag) {
- if (separate_flag < 3) {
- int all_local = nlocal;
- int ghost_min = overflow[LMP_GHOST_MIN];
- nlocal = overflow[LMP_LOCAL_MAX] + 1;
+ if (separate_flag) {
+ if (separate_flag < 3) {
+ int all_local = nlocal;
+ int ghost_min = overflow[LMP_GHOST_MIN];
+ nlocal = overflow[LMP_LOCAL_MAX] + 1;
int nghost = overflow[LMP_GHOST_MAX] + 1 - ghost_min;
if (nghost < 0) nghost = 0;
nall = nlocal + nghost;
- separate_flag--;
- int flength;
- if (NEWTON_PAIR) flength = nall;
- else flength = nlocal;
- IP_PRE_get_stride(f_stride, flength, sizeof(FORCE_T),
- separate_flag);
+ separate_flag--;
+ int flength;
+ if (NEWTON_PAIR) flength = nall;
+ else flength = nlocal;
+ IP_PRE_get_stride(f_stride, flength, sizeof(FORCE_T),
+ separate_flag);
if (nghost) {
- if (nlocal < all_local || ghost_min > all_local) {
+ if (nlocal < all_local || ghost_min > all_local) {
memmove(x + nlocal, x + ghost_min,
- (nall - nlocal) * sizeof(ATOM_T));
+ (nall - nlocal) * sizeof(ATOM_T));
memmove(quat + nlocal, quat + ghost_min,
- (nall - nlocal) * sizeof(QUAT_T));
+ (nall - nlocal) * sizeof(QUAT_T));
}
}
- }
+ }
x[nall].x = (flt_t)INTEL_BIGP;
x[nall].y = (flt_t)INTEL_BIGP;
x[nall].z = (flt_t)INTEL_BIGP;
@@ -330,7 +330,7 @@ void PairGayBerneIntel::eval(const int offload, const int vflag,
quat[nall].i = (flt_t)0.0;
quat[nall].j = (flt_t)0.0;
quat[nall].k = (flt_t)0.0;
- }
+ }
#endif
acc_t oevdwl, ov0, ov1, ov2, ov3, ov4, ov5;
@@ -462,7 +462,7 @@ void PairGayBerneIntel::eval(const int offload, const int vflag,
ME_transpose_times3(a2, temp, b2);
ME_diag_times3a(shape2, a2, temp);
ME_transpose_times3(a2, temp, g2);
-
+
flt_t tempv_0, tempv_1, tempv_2, tempv2_0, tempv2_1, tempv2_2;
flt_t temp1, temp2, temp3;
@@ -471,13 +471,13 @@ void PairGayBerneIntel::eval(const int offload, const int vflag,
flt_t r = sqrt(rsq_form[jj]);
// compute distance of closest approach
-
+
flt_t g12_0, g12_1, g12_2, g12_3, g12_4, g12_5, g12_6, g12_7, g12_8;
ME_plus3(g1, g2, g12);
flt_t kappa_0, kappa_1, kappa_2;
ME_mldivide3(g12, delx_form[jj], dely_form[jj], delz_form[jj],
kappa, ierror);
-
+
// tempv = G12^-1*r12hat
flt_t inv_r = (flt_t)1.0 / r;
@@ -521,7 +521,7 @@ void PairGayBerneIntel::eval(const int offload, const int vflag,
// force
// compute dUr/dr
- temp1 = ((flt_t)2.0 * varrho12 * varrho - varrho6 * varrho) /
+ temp1 = ((flt_t)2.0 * varrho12 * varrho - varrho6 * varrho) /
sigma;
temp1 = temp1 * (flt_t)24.0 * epsilon;
flt_t u_slj = temp1 * pow(sigma12, (flt_t)3.0) * (flt_t)0.5;
@@ -536,7 +536,7 @@ void PairGayBerneIntel::eval(const int offload, const int vflag,
flt_t dchi_0, dchi_1, dchi_2;
temp1 = ME_dot3(iota, r12hat);
- temp2 = (flt_t)-4.0 / rsq_form[jj] * mu *
+ temp2 = (flt_t)-4.0 / rsq_form[jj] * mu *
pow(chi, (mu - (flt_t)1.0) / mu);
dchi_0 = temp2 * (iota_0 - temp1 * r12hat_0);
dchi_1 = temp2 * (iota_1 - temp1 * r12hat_1);
@@ -650,19 +650,19 @@ void PairGayBerneIntel::eval(const int offload, const int vflag,
temp2 = u_r * chi;
temp3 = chi * eta;
- ttor_0 = (temp1 * dchi_0 + temp2 * deta_0 + temp3 * dUr_0) *
+ ttor_0 = (temp1 * dchi_0 + temp2 * deta_0 + temp3 * dUr_0) *
(flt_t)-1.0;
- ttor_1 = (temp1 * dchi_1 + temp2 * deta_1 + temp3 * dUr_1) *
+ ttor_1 = (temp1 * dchi_1 + temp2 * deta_1 + temp3 * dUr_1) *
(flt_t)-1.0;
- ttor_2 = (temp1 * dchi_2 + temp2 * deta_2 + temp3 * dUr_2) *
+ ttor_2 = (temp1 * dchi_2 + temp2 * deta_2 + temp3 * dUr_2) *
(flt_t)-1.0;
if (NEWTON_PAIR || j < nlocal) {
- rtor_0 = (temp1 * dchi2_0 + temp2 * deta2_0 + temp3 * dUr2_0) *
+ rtor_0 = (temp1 * dchi2_0 + temp2 * deta2_0 + temp3 * dUr2_0) *
(flt_t)-1.0;
- rtor_1 = (temp1 * dchi2_1 + temp2 * deta2_1 + temp3 * dUr2_1) *
+ rtor_1 = (temp1 * dchi2_1 + temp2 * deta2_1 + temp3 * dUr2_1) *
(flt_t)-1.0;
- rtor_2 = (temp1 * dchi2_2 + temp2 * deta2_2 + temp3 * dUr2_2) *
+ rtor_2 = (temp1 * dchi2_2 + temp2 * deta2_2 + temp3 * dUr2_2) *
(flt_t)-1.0;
}
@@ -712,7 +712,7 @@ void PairGayBerneIntel::eval(const int offload, const int vflag,
f[jp].y += rtor_1;
f[jp].z += rtor_2;
}
-
+
if (EVFLAG) {
flt_t ev_pre = (flt_t)0;
if (NEWTON_PAIR || i < nlocal)
@@ -730,7 +730,7 @@ void PairGayBerneIntel::eval(const int offload, const int vflag,
f[j*2].w += (flt_t)0.5 * evdwl;
}
}
-
+
if (vflag == 1) {
ev_pre *= (flt_t)-1.0;
sv0 += ev_pre * delx_form[jj] * fforce_0;
@@ -781,7 +781,7 @@ void PairGayBerneIntel::eval(const int offload, const int vflag,
else
o_range = nlocal;
if (offload == 0) o_range -= minlocal;
- IP_PRE_omp_range_align(iifrom, iito, tid, o_range, nthreads,
+ IP_PRE_omp_range_align(iifrom, iito, tid, o_range, nthreads,
sizeof(FORCE_T));
const int two_iito = iito * 2;
@@ -1060,9 +1060,9 @@ void PairGayBerneIntel::ForceConst<flt_t>::set_ntypes(const int ntypes,
int off_onel = one_length * nthreads;
int tp1sq = ntypes*ntypes;
- if (ospecial_lj != NULL && oijc != NULL && olj34 != NULL &&
- oic != NULL && orsq_form != NULL && odelx_form != NULL &&
- odely_form != NULL && odelz_form != NULL && ojtype_form !=NULL &&
+ if (ospecial_lj != NULL && oijc != NULL && olj34 != NULL &&
+ oic != NULL && orsq_form != NULL && odelx_form != NULL &&
+ odely_form != NULL && odelz_form != NULL && ojtype_form !=NULL &&
ojlist_form !=NULL && cop >= 0) {
#pragma offload_transfer target(mic:cop) \
nocopy(ospecial_lj: length(4) alloc_if(1) free_if(0)) \
diff --git a/src/USER-INTEL/pair_gayberne_intel.h b/src/USER-INTEL/pair_gayberne_intel.h
index 9a4aae6c72..aaed31d567 100644
--- a/src/USER-INTEL/pair_gayberne_intel.h
+++ b/src/USER-INTEL/pair_gayberne_intel.h
@@ -55,9 +55,9 @@ class PairGayBerneIntel : public PairGayBerne {
template <class flt_t>
class ForceConst {
public:
- typedef struct {
- flt_t cutsq, lj1, lj2, offset, sigma, epsilon, lshape;
- int form;
+ typedef struct {
+ flt_t cutsq, lj1, lj2, offset, sigma, epsilon, lshape;
+ int form;
} fc_packed1;
typedef struct { flt_t lj3, lj4; } fc_packed2;
typedef struct { flt_t shape2[4], well[4]; } fc_packed3;
diff --git a/src/USER-INTEL/pair_lj_charmm_coul_long_intel.cpp b/src/USER-INTEL/pair_lj_charmm_coul_long_intel.cpp
index 88a9012c29..7ed23d4dee 100644
--- a/src/USER-INTEL/pair_lj_charmm_coul_long_intel.cpp
+++ b/src/USER-INTEL/pair_lj_charmm_coul_long_intel.cpp
@@ -12,7 +12,7 @@
Contributing author: W. Michael Brown (Intel)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_lj_charmm_coul_long_intel.h"
#include "atom.h"
#include "comm.h"
@@ -52,7 +52,7 @@ PairLJCharmmCoulLongIntel::~PairLJCharmmCoulLongIntel()
void PairLJCharmmCoulLongIntel::compute(int eflag, int vflag)
{
if (fix->precision()==FixIntel::PREC_MODE_MIXED)
- compute<float,double>(eflag, vflag, fix->get_mixed_buffers(),
+ compute<float,double>(eflag, vflag, fix->get_mixed_buffers(),
force_const_single);
else if (fix->precision()==FixIntel::PREC_MODE_DOUBLE)
compute<double,double>(eflag, vflag, fix->get_double_buffers(),
@@ -79,7 +79,7 @@ void PairLJCharmmCoulLongIntel::compute(int eflag, int vflag,
const int host_start = fix->host_start_pair();
const int offload_end = fix->offload_end_pair();
const int ago = neighbor->ago;
-
+
if (ago != 0 && fix->separate_buffers() == 0) {
fix->start_watch(TIME_PACK);
#if defined(_OPENMP)
@@ -87,13 +87,13 @@ void PairLJCharmmCoulLongIntel::compute(int eflag, int vflag,
#endif
{
int ifrom, ito, tid;
- IP_PRE_omp_range_id_align(ifrom, ito, tid, atom->nlocal+atom->nghost,
+ IP_PRE_omp_range_id_align(ifrom, ito, tid, atom->nlocal+atom->nghost,
nthreads, sizeof(ATOM_T));
buffers->thr_pack(ifrom,ito,ago);
}
fix->stop_watch(TIME_PACK);
}
-
+
// -------------------- Regular version
if (evflag || vflag_fdotr) {
int ovflag = 0;
@@ -176,7 +176,7 @@ void PairLJCharmmCoulLongIntel::eval(const int offload, const int vflag,
IP_PRE_get_transfern(ago, NEWTON_PAIR, EVFLAG, EFLAG, vflag,
buffers, offload, fix, separate_flag,
x_size, q_size, ev_size, f_stride);
-
+
int tc;
FORCE_T * _noalias f_start;
acc_t * _noalias ev_global;
@@ -221,7 +221,7 @@ void PairLJCharmmCoulLongIntel::eval(const int offload, const int vflag,
*timer_compute = MIC_Wtime();
#endif
- IP_PRE_repack_for_offload(NEWTON_PAIR, separate_flag, nlocal, nall,
+ IP_PRE_repack_for_offload(NEWTON_PAIR, separate_flag, nlocal, nall,
f_stride, x, q);
acc_t oevdwl, oecoul, ov0, ov1, ov2, ov3, ov4, ov5;
@@ -419,7 +419,7 @@ void PairLJCharmmCoulLongIntel::eval(const int offload, const int vflag,
if (eatom) {
if (NEWTON_PAIR || i < nlocal)
fwtmp += (flt_t)0.5 * evdwl + (flt_t)0.5 * ecoul;
- if (NEWTON_PAIR || j < nlocal)
+ if (NEWTON_PAIR || j < nlocal)
f[j].w += (flt_t)0.5 * evdwl + (flt_t)0.5 * ecoul;
}
}
@@ -442,7 +442,7 @@ void PairLJCharmmCoulLongIntel::eval(const int offload, const int vflag,
#pragma omp barrier
#endif
IP_PRE_fdotr_acc_force(NEWTON_PAIR, EVFLAG, EFLAG, vflag, eatom, nall,
- nlocal, minlocal, nthreads, f_start, f_stride,
+ nlocal, minlocal, nthreads, f_start, f_stride,
x);
} // end of omp parallel region
if (EVFLAG) {
@@ -487,7 +487,7 @@ void PairLJCharmmCoulLongIntel::init_style()
error->all(FLERR,
"The 'package intel' command is required for /intel styles");
fix = static_cast<FixIntel *>(modify->fix[ifix]);
-
+
fix->pair_init_check();
#ifdef _LMP_INTEL_OFFLOAD
_cop = fix->coprocessor_number();
diff --git a/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp b/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp
index 1aed04ed04..427d7be33f 100644
--- a/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp
+++ b/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp
@@ -12,7 +12,7 @@
Contributing author: W. Michael Brown (Intel)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_lj_cut_coul_long_intel.h"
#include "atom.h"
#include "comm.h"
@@ -53,7 +53,7 @@ PairLJCutCoulLongIntel::~PairLJCutCoulLongIntel()
void PairLJCutCoulLongIntel::compute(int eflag, int vflag)
{
if (fix->precision()==FixIntel::PREC_MODE_MIXED)
- compute<float,double>(eflag, vflag, fix->get_mixed_buffers(),
+ compute<float,double>(eflag, vflag, fix->get_mixed_buffers(),
force_const_single);
else if (fix->precision()==FixIntel::PREC_MODE_DOUBLE)
compute<double,double>(eflag, vflag, fix->get_double_buffers(),
@@ -88,13 +88,13 @@ void PairLJCutCoulLongIntel::compute(int eflag, int vflag,
#endif
{
int ifrom, ito, tid;
- IP_PRE_omp_range_id_align(ifrom, ito, tid, atom->nlocal + atom->nghost,
+ IP_PRE_omp_range_id_align(ifrom, ito, tid, atom->nlocal + atom->nghost,
nthreads, sizeof(ATOM_T));
buffers->thr_pack(ifrom,ito,ago);
}
fix->stop_watch(TIME_PACK);
}
-
+
if (evflag || vflag_fdotr) {
int ovflag = 0;
if (vflag_fdotr) ovflag = 2;
@@ -216,7 +216,7 @@ void PairLJCutCoulLongIntel::eval(const int offload, const int vflag,
*timer_compute = MIC_Wtime();
#endif
- IP_PRE_repack_for_offload(NEWTON_PAIR, separate_flag, nlocal, nall,
+ IP_PRE_repack_for_offload(NEWTON_PAIR, separate_flag, nlocal, nall,
f_stride, x, q);
acc_t oevdwl, oecoul, ov0, ov1, ov2, ov3, ov4, ov5;
@@ -389,7 +389,7 @@ void PairLJCutCoulLongIntel::eval(const int offload, const int vflag,
if (eatom) {
if (NEWTON_PAIR || i < nlocal)
fwtmp += (flt_t)0.5 * evdwl + (flt_t)0.5 * ecoul;
- if (NEWTON_PAIR || j < nlocal)
+ if (NEWTON_PAIR || j < nlocal)
f[j].w += (flt_t)0.5 * evdwl + (flt_t)0.5 * ecoul;
}
}
@@ -409,7 +409,7 @@ void PairLJCutCoulLongIntel::eval(const int offload, const int vflag,
#pragma omp barrier
#endif
IP_PRE_fdotr_acc_force(NEWTON_PAIR, EVFLAG, EFLAG, vflag, eatom, nall,
- nlocal, minlocal, nthreads, f_start, f_stride,
+ nlocal, minlocal, nthreads, f_start, f_stride,
x);
} // end of omp parallel region
if (EVFLAG) {
@@ -454,7 +454,7 @@ void PairLJCutCoulLongIntel::init_style()
error->all(FLERR,
"The 'package intel' command is required for /intel styles");
fix = static_cast<FixIntel *>(modify->fix[ifix]);
-
+
fix->pair_init_check();
#ifdef _LMP_INTEL_OFFLOAD
_cop = fix->coprocessor_number();
diff --git a/src/USER-INTEL/pair_lj_cut_intel.cpp b/src/USER-INTEL/pair_lj_cut_intel.cpp
index 9d7e1b0682..a3665b6588 100644
--- a/src/USER-INTEL/pair_lj_cut_intel.cpp
+++ b/src/USER-INTEL/pair_lj_cut_intel.cpp
@@ -12,7 +12,7 @@
Contributing author: W. Michael Brown (Intel)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_lj_cut_intel.h"
#include "atom.h"
#include "comm.h"
@@ -163,7 +163,7 @@ void PairLJCutIntel::eval(const int offload, const int vflag,
*timer_compute = MIC_Wtime();
#endif
- IP_PRE_repack_for_offload(NEWTON_PAIR, separate_flag, nlocal, nall,
+ IP_PRE_repack_for_offload(NEWTON_PAIR, separate_flag, nlocal, nall,
f_stride, x, 0);
acc_t oevdwl, ov0, ov1, ov2, ov3, ov4, ov5;
@@ -277,7 +277,7 @@ void PairLJCutIntel::eval(const int offload, const int vflag,
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
-
+
IP_PRE_ev_tally_atom(EVFLAG, EFLAG, vflag, f, fwtmp);
} // for ii
@@ -285,7 +285,7 @@ void PairLJCutIntel::eval(const int offload, const int vflag,
#pragma omp barrier
#endif
IP_PRE_fdotr_acc_force(NEWTON_PAIR, EVFLAG, EFLAG, vflag, eatom, nall,
- nlocal, minlocal, nthreads, f_start, f_stride,
+ nlocal, minlocal, nthreads, f_start, f_stride,
x);
} // end omp
if (EVFLAG) {
diff --git a/src/USER-INTEL/pair_sw_intel.cpp b/src/USER-INTEL/pair_sw_intel.cpp
index 884d3436d3..0380147abf 100755
--- a/src/USER-INTEL/pair_sw_intel.cpp
+++ b/src/USER-INTEL/pair_sw_intel.cpp
@@ -15,10 +15,10 @@
Contributing author: W. Michael Brown (Intel)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_sw_intel.h"
#include "atom.h"
#include "neighbor.h"
@@ -147,7 +147,7 @@ void PairSWIntel::compute(int eflag, int vflag,
template <int SPQ, int EVFLAG, int EFLAG, class flt_t, class acc_t>
void PairSWIntel::eval(const int offload, const int vflag,
IntelBuffers<flt_t,acc_t> *buffers,
- const ForceConst<flt_t> &fc, const int astart,
+ const ForceConst<flt_t> &fc, const int astart,
const int aend, const int pad_width)
{
const int inum = aend - astart;
@@ -323,10 +323,10 @@ void PairSWIntel::eval(const int offload, const int vflag,
const int jtype = tjtype[jj];
const flt_t rsq1 = trsq[jj];
- const flt_t r1 = sqrt(rsq1);
+ const flt_t r1 = sqrt(rsq1);
const flt_t rinvsq1 = (flt_t)1.0 / rsq1;
const flt_t rainv1 = (flt_t)1.0 / (r1 - p2fi[jtype].cut);
-
+
// two-body interactions, skip half of them
flt_t rp, rq;
if (SPQ == 1) {
@@ -342,7 +342,7 @@ void PairSWIntel::eval(const int offload, const int vflag,
flt_t expsrainv = exp(p2fi[jtype].sigma * rainv1);
if (jj >= ejnumhalf) expsrainv = (flt_t)0.0;
const flt_t fpair = (p2fi[jtype].c1 * rp - p2fi[jtype].c2 * rq +
- (p2fi[jtype].c3 * rp -p2fi[jtype].c4 * rq) *
+ (p2fi[jtype].c3 * rp -p2fi[jtype].c4 * rq) *
rainvsq) * expsrainv * rinvsq1;
fxtmp -= delx * fpair;
@@ -355,7 +355,7 @@ void PairSWIntel::eval(const int offload, const int vflag,
if (EVFLAG) {
if (EFLAG) {
flt_t evdwl;
- evdwl = (p2ei[jtype].c5 * rp - p2ei[jtype].c6 * rq) *
+ evdwl = (p2ei[jtype].c5 * rp - p2ei[jtype].c6 * rq) *
expsrainv;
sevdwl += evdwl;
if (eatom) {
@@ -390,7 +390,7 @@ void PairSWIntel::eval(const int offload, const int vflag,
const flt_t expgsrainv2 = exp(gsrainv2);
const flt_t rinv12 = (flt_t)1.0 / (r1 * r2);
- const flt_t cs = (delx * delr2[0] + dely * delr2[1] +
+ const flt_t cs = (delx * delr2[0] + dely * delr2[1] +
delz * delr2[2]) * rinv12;
const flt_t delcs = cs - p3i[joffset + ktype].costheta;
const flt_t delcssq = delcs*delcs;
@@ -400,11 +400,11 @@ void PairSWIntel::eval(const int offload, const int vflag,
else kfactor = (flt_t)1.0;
const flt_t facexp = expgsrainv1*expgsrainv2*kfactor;
- const flt_t facrad = p3i[joffset + ktype].lambda_epsilon *
+ const flt_t facrad = p3i[joffset + ktype].lambda_epsilon *
facexp * delcssq;
const flt_t frad1 = facrad*gsrainvsq1;
const flt_t frad2 = facrad*gsrainvsq2;
- const flt_t facang = p3i[joffset + ktype].lambda_epsilon2 *
+ const flt_t facang = p3i[joffset + ktype].lambda_epsilon2 *
facexp * delcs;
const flt_t facang12 = rinv12*facang;
const flt_t csfacang = cs*facang;
@@ -420,7 +420,7 @@ void PairSWIntel::eval(const int offload, const int vflag,
fjxtmp += fjx;
fjytmp += fjy;
fjztmp += fjz;
-
+
if (EVFLAG) {
if (EFLAG) {
const flt_t evdwl = facrad * (flt_t)0.5;
@@ -430,7 +430,7 @@ void PairSWIntel::eval(const int offload, const int vflag,
fjtmp += (acc_t)0.33333333 * facrad;
}
}
- IP_PRE_ev_tally_nbor3v(vflag, fjx, fjy, fjz,
+ IP_PRE_ev_tally_nbor3v(vflag, fjx, fjy, fjz,
delx, dely, delz);
}
} // for kk
@@ -441,7 +441,7 @@ void PairSWIntel::eval(const int offload, const int vflag,
if (EFLAG)
if (eatom) f[j].w += fjtmp;
} // for jj
-
+
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
diff --git a/src/USER-INTEL/pair_sw_intel.h b/src/USER-INTEL/pair_sw_intel.h
index 5bd54c5f49..a38dd75cf3 100755
--- a/src/USER-INTEL/pair_sw_intel.h
+++ b/src/USER-INTEL/pair_sw_intel.h
@@ -44,7 +44,7 @@ class PairSWIntel : public PairSW {
const ForceConst<flt_t> &fc);
template <int SPQ, int EVFLAG, int EFLAG, class flt_t, class acc_t>
void eval(const int offload, const int vflag,
- IntelBuffers<flt_t,acc_t> * buffers, const ForceConst<flt_t> &fc,
+ IntelBuffers<flt_t,acc_t> * buffers, const ForceConst<flt_t> &fc,
const int astart, const int aend, const int pad_width);
template <class flt_t, class acc_t>
diff --git a/src/USER-INTEL/verlet_intel.cpp b/src/USER-INTEL/verlet_intel.cpp
index 5d6a36ec46..587b2fbd44 100644
--- a/src/USER-INTEL/verlet_intel.cpp
+++ b/src/USER-INTEL/verlet_intel.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "verlet_intel.h"
#include "neighbor.h"
#include "domain.h"
@@ -159,7 +159,7 @@ void VerletIntel::setup()
sync_mode = 1;
}
}
-
+
if (sync_mode == 1) fix_intel->sync_coprocessor();
#endif
@@ -237,7 +237,7 @@ void VerletIntel::setup_minimal(int flag)
sync_mode = 1;
}
}
-
+
if (sync_mode == 1) fix_intel->sync_coprocessor();
#endif
diff --git a/src/USER-INTEL/verlet_split_intel.cpp b/src/USER-INTEL/verlet_split_intel.cpp
index 806b3652f9..644ebce9fc 100644
--- a/src/USER-INTEL/verlet_split_intel.cpp
+++ b/src/USER-INTEL/verlet_split_intel.cpp
@@ -15,7 +15,7 @@
Contributing authors: Yuxing Peng and Chris Knight (U Chicago)
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "verlet_split_intel.h"
#include "universe.h"
#include "neighbor.h"
@@ -52,7 +52,7 @@ VerletSplitIntel::VerletSplitIntel(LAMMPS *lmp, int narg, char **arg) :
if (universe->procs_per_world[0] % universe->procs_per_world[1])
error->universe_all(FLERR,"Verlet/split requires Rspace partition "
"size be multiple of Kspace partition size");
- if (comm->style != 0)
+ if (comm->style != 0)
error->universe_all(FLERR,"Verlet/split can only currently be used with "
"comm_style brick");
@@ -217,7 +217,7 @@ VerletSplitIntel::~VerletSplitIntel()
void VerletSplitIntel::init()
{
- if (comm->style != 0)
+ if (comm->style != 0)
error->universe_all(FLERR,"Verlet/split can only currently be used with "
"comm_style brick");
if (!force->kspace && comm->me == 0)
diff --git a/src/USER-LB/fix_lb_fluid.cpp b/src/USER-LB/fix_lb_fluid.cpp
index e37ec438f1..5b4463631f 100755
--- a/src/USER-LB/fix_lb_fluid.cpp
+++ b/src/USER-LB/fix_lb_fluid.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -17,11 +17,11 @@
------------------------------------------------------------------------- */
#include "fix_lb_fluid.h"
-#include "math.h"
-#include "mpi.h"
-#include "stdlib.h"
-#include "stdio.h"
-#include "string.h"
+#include <math.h>
+#include <mpi.h>
+#include <stdlib.h>
+#include <stdio.h>
+#include <string.h>
#include "comm.h"
#include "memory.h"
#include "error.h"
@@ -46,17 +46,17 @@ FixLbFluid::FixLbFluid(LAMMPS *lmp, int narg, char **arg) :
//=====================================================================================================
// Sample inputfile call:
// fix # group lb/fluid nevery typeLB viscosity densityinit_real
- //
- // where: nevery: call this fix every nevery timesteps.
+ //
+ // where: nevery: call this fix every nevery timesteps.
// (keep this set to 1 for now).
- // typeLB: there are two different integrators
+ // typeLB: there are two different integrators
// in the code labelled "1" and "2".
- // viscosity: the viscosity of the fluid.
+ // viscosity: the viscosity of the fluid.
// densityinit_real: the density of the fluid.
//
// optional arguments:
// "setArea" type node_area: set the surface area per node associated with a
- // given atom type. By default the surface area
+ // given atom type. By default the surface area
// is set at 1.0*dx_lb^2.
// "setGamma" gamma: specify a user-defined value for the force
// coupling constant, instead of using the default
@@ -67,10 +67,10 @@ FixLbFluid::FixLbFluid(LAMMPS *lmp, int narg, char **arg) :
// "dx" dx_lb: the lattice-Boltzmann grid spacing.
// "dm" dm_lb: the lattice-Boltzmann mass unit.
// "a0" a_0_real: the square of the sound speed in the fluid.
- // "noise" Temperature seed: include noise in the system.
+ // "noise" Temperature seed: include noise in the system.
// Temperature is the temperature for the fluid.
- // seed is the seed for the random number generator.
- // "calcforce" N group: print the force acting on a given group every
+ // seed is the seed for the random number generator.
+ // "calcforce" N group: print the force acting on a given group every
// N timesteps.
// "trilinear": use the trilinear interpolation stencil.
// "read_restart" restart_file: restart a fluid run from restart_file.
@@ -98,7 +98,7 @@ FixLbFluid::FixLbFluid(LAMMPS *lmp, int narg, char **arg) :
typeLB = atoi(arg[4]);
viscosity = atof(arg[5]);
densityinit_real = atof(arg[6]);
-
+
// Default values for optional arguments:
force_diagnostic=0;
noisestress = 0;
@@ -157,7 +157,7 @@ FixLbFluid::FixLbFluid(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,"Illegal fix lb/fluid command: scaleGamma");
Gamma[itype] *= scalefactor;
iarg += 3;
- }
+ }
else if(strcmp(arg[iarg],"dx")==0){
dx_lb = atof(arg[iarg+1]);
iarg += 2;
@@ -188,10 +188,10 @@ FixLbFluid::FixLbFluid(LAMMPS *lmp, int narg, char **arg) :
iarg += 1;
}
else if(strcmp(arg[iarg],"read_restart")==0){
- readrestart = 1;
+ readrestart = 1;
int nlength = strlen(arg[iarg+1]) + 16;
char *filename = new char[nlength];
- strcpy(filename,arg[iarg+1]);
+ strcpy(filename,arg[iarg+1]);
MPI_File_open(world,filename,MPI_MODE_RDONLY,MPI_INFO_NULL,&pFileRead);
delete [] filename;
iarg += 2;
@@ -234,9 +234,9 @@ a z wall velocity without implementing fixed BCs in z");
}else{
initializeLB = &FixLbFluid::initializeLB19;
equilibriumdist = &FixLbFluid::equilibriumdist19;
- update_full = &FixLbFluid::update_full19;
- }
-
+ update_full = &FixLbFluid::update_full19;
+ }
+
//--------------------------------------------------------------------------
// perform initial allocation of atom-based array register
// with Atom class
@@ -248,7 +248,7 @@ a z wall velocity without implementing fixed BCs in z");
for(int i=0; i<atom->nmax; i++)
for(int j=0; j<3; j++)
hydroF[i][j] = 0.0;
-
+
Ng_lb = NULL;
w_lb = NULL;
mg_lb = NULL;
@@ -269,12 +269,12 @@ a z wall velocity without implementing fixed BCs in z");
Fftempz = NULL;
//--------------------------------------------------------------------------
- // Set the lattice Boltzmann dt.
+ // Set the lattice Boltzmann dt.
//--------------------------------------------------------------------------
dt_lb=nevery*(update->dt);
//--------------------------------------------------------------------------
- // Set the lattice Boltzmann dx if it wasn't specified in the
+ // Set the lattice Boltzmann dx if it wasn't specified in the
// input.
//--------------------------------------------------------------------------
if(setdx == 1){
@@ -286,14 +286,14 @@ a z wall velocity without implementing fixed BCs in z");
char str[128];
sprintf(str,"Setting the lattice-Boltzmann dx to %10.6f",dx_lb);
error->message(FLERR,str);
- }
+ }
}
//--------------------------------------------------------------------------
- // If the area per node has not been set by the user, set to the
+ // If the area per node has not been set by the user, set to the
// default value of dx_lb*dx_lb.
//--------------------------------------------------------------------------
if(setGamma == 0){
- if(setArea == 0){
+ if(setArea == 0){
if(comm->me==0){
error->message(FLERR,"Assuming an area per node of dx*dx for all of the MD particles. This should only be used if these all correspond to point particles; otherwise, change using the setArea keyword");
}
@@ -313,7 +313,7 @@ a z wall velocity without implementing fixed BCs in z");
// Check to make sure that the total number of grid points in each direction
// divides evenly among the processors in that direction.
// Shrink-wrapped boundary conditions (which are not permitted by this fix)
- // might cause a problem, so check for this. A full check of the boundary
+ // might cause a problem, so check for this. A full check of the boundary
// conditions is performed in the init routine, rather than here, as it is
// possible to change the BCs between runs.
//--------------------------------------------------------------------------
@@ -346,7 +346,7 @@ a z wall velocity without implementing fixed BCs in z");
sprintf(errormessage,"With dx= %f, and the simulation domain divided by %i processors in the z direction, the simulation domain in the z direction must be a multiple of %f",dx_lb,comm->procgrid[2],comm->procgrid[2]*dx_lb);
error->all(FLERR,errormessage);
}
-
+
//--------------------------------------------------------------------------
// Set the total number of grid points in each direction.
//--------------------------------------------------------------------------
@@ -360,7 +360,7 @@ a z wall velocity without implementing fixed BCs in z");
subNbx= Nbx/comm->procgrid[0] + 2;
subNby= Nby/comm->procgrid[1] + 2;
subNbz= Nbz/comm->procgrid[2] + 2;
-
+
//--------------------------------------------------------------------------
// In order to calculate the fluid forces correctly, need to have atleast
// 5 grid points in each direction per processor.
@@ -382,7 +382,7 @@ a z wall velocity without implementing fixed BCs in z");
}else{
sprintf(str,"Using a lattice-Boltzmann grid of %i by %i by %i total grid points.",Nbx,Nby,Nbz);
}
- error->message(FLERR,str);
+ error->message(FLERR,str);
}
//--------------------------------------------------------------------------
@@ -399,15 +399,15 @@ a z wall velocity without implementing fixed BCs in z");
//--------------------------------------------------------------------------
MPI_Aint lb,sizeofdouble;
MPI_Type_get_extent(MPI_DOUBLE,&lb,&sizeofdouble);
-
+
MPI_Type_vector(subNbz-2,numvel,numvel,MPI_DOUBLE,&oneslice);
MPI_Type_commit(&oneslice);
MPI_Type_create_hvector(subNby-2,1,numvel*subNbz*sizeofdouble,oneslice,&passxf);
MPI_Type_commit(&passxf);
-
+
MPI_Type_create_hvector(subNbx,1,numvel*subNbz*subNby*sizeofdouble,oneslice,&passyf);
MPI_Type_commit(&passyf);
-
+
MPI_Type_free(&oneslice);
MPI_Type_vector(subNby,numvel,numvel*subNbz,MPI_DOUBLE,&oneslice);
MPI_Type_commit(&oneslice);
@@ -420,10 +420,10 @@ a z wall velocity without implementing fixed BCs in z");
MPI_Type_commit(&oneslice);
MPI_Type_create_hvector(subNby+3,1,3*(subNbz+3)*sizeofdouble,oneslice,&passxu);
MPI_Type_commit(&passxu);
-
+
MPI_Type_create_hvector(subNbx+3,1,3*(subNbz+3)*(subNby+3)*sizeofdouble,oneslice,&passyu);
MPI_Type_commit(&passyu);
-
+
MPI_Type_free(&oneslice);
MPI_Type_vector(subNby+3,3,3*(subNbz+3),MPI_DOUBLE,&oneslice);
MPI_Type_commit(&oneslice);
@@ -436,10 +436,10 @@ a z wall velocity without implementing fixed BCs in z");
MPI_Type_commit(&oneslice);
MPI_Type_create_hvector(subNby+3,1,1*(subNbz+3)*sizeofdouble,oneslice,&passxrho);
MPI_Type_commit(&passxrho);
-
+
MPI_Type_create_hvector(subNbx+3,1,1*(subNbz+3)*(subNby+3)*sizeofdouble,oneslice,&passyrho);
MPI_Type_commit(&passyrho);
-
+
MPI_Type_free(&oneslice);
MPI_Type_vector(subNby+3,1,1*(subNbz+3),MPI_DOUBLE,&oneslice);
MPI_Type_commit(&oneslice);
@@ -452,10 +452,10 @@ a z wall velocity without implementing fixed BCs in z");
MPI_Type_commit(&oneslice);
MPI_Type_create_hvector(subNby+3,1,3*(subNbz+3)*sizeofdouble,oneslice,&passxtemp);
MPI_Type_commit(&passxtemp);
-
+
MPI_Type_create_hvector(subNbx+3,1,3*(subNbz+3)*5*sizeofdouble,oneslice,&passytemp);
MPI_Type_commit(&passytemp);
-
+
MPI_Type_free(&oneslice);
MPI_Type_vector(subNby+3,3,3*5,MPI_DOUBLE,&oneslice);
MPI_Type_commit(&oneslice);
@@ -499,7 +499,7 @@ a z wall velocity without implementing fixed BCs in z");
// Rescale the variables to Lattice Boltzmann dimensionless units.
//--------------------------------------------------------------------------
rescale();
-
+
//--------------------------------------------------------------------------
// Initialize the arrays.
//--------------------------------------------------------------------------
@@ -513,7 +513,7 @@ FixLbFluid::~FixLbFluid()
atom->delete_callback(id,0);
memory->destroy(hydroF);
-
+
memory->destroy(Ng_lb);
memory->destroy(w_lb);
memory->destroy(mg_lb);
@@ -537,7 +537,7 @@ FixLbFluid::~FixLbFluid()
memory->destroy(Fftempx);
memory->destroy(Fftempy);
memory->destroy(Fftempz);
-
+
if(noisestress==1){
delete random;
}
@@ -574,8 +574,8 @@ void FixLbFluid::init(void)
if(fabs(dt_lb_now - dt_lb) > 1.0e-12){
error->warning(FLERR,"Timestep has changed between runs with the same lb/fluid. Unphysical results may occur");
- }
-
+ }
+
//--------------------------------------------------------------------------
// Make sure the size of the simulation domain has not changed
// between runs.
@@ -588,11 +588,11 @@ void FixLbFluid::init(void)
if(domain->periodicity[2]==0){
Nbz_now += 1;
}
-
+
if(Nbx_now != Nbx || Nby_now != Nby || Nbz_now != Nbz){
error->all(FLERR,"the simulation domain can not change shape between runs with the same lb/fluid");
}
-
+
//--------------------------------------------------------------------------
// Check to make sure that the chosen LAMMPS boundary types are compatible
// with this fix.
@@ -608,7 +608,7 @@ void FixLbFluid::init(void)
if(domain->boundary[2][0] == 2 || domain->boundary[2][0] == 3){
error->all(FLERR,"the z-direction can not have shrink-wrap boundary conditions");
}
-
+
//--------------------------------------------------------------------------
// Check if the lb/viscous fix is also called:
//--------------------------------------------------------------------------
@@ -630,8 +630,8 @@ void FixLbFluid::init(void)
if(!(groupbit_viscouslb || groupbit_pc || groupbit_rigid_pc_sphere) && comm->me==0){
error->message(FLERR,"Not adding the fluid force to any of the MD particles. To add this force use one of the lb/viscous, lb/pc, or lb/rigid/pc/sphere fixes");
}
-
- // If fix lb/viscous is called for a particular atom, make sure
+
+ // If fix lb/viscous is called for a particular atom, make sure
// lb/pc or lb/rigid/pc/sphere are not:
if(fixviscouslb == 1){
int *mask = atom->mask;
@@ -643,7 +643,7 @@ void FixLbFluid::init(void)
error->one(FLERR,"should not use the lb/viscous command when integrating with the lb/rigid/pc/sphere fix");
}
}
-
+
}
void FixLbFluid::setup(int vflag)
@@ -653,7 +653,7 @@ void FixLbFluid::setup(int vflag)
//--------------------------------------------------------------------------
if(step > 0)
calc_fluidforce();
-}
+}
void FixLbFluid::initial_integrate(int vflag)
{
@@ -668,7 +668,7 @@ void FixLbFluid::initial_integrate(int vflag)
printf(" F_x F_y F_z T_x T_y T_z\n");
printf("-------------------------------------------------------------------------------\n");
}
-
+
if(printfluid > 0 && me == 0){
printf("---------------------------------------------------------------------\n");
printf(" density u_x u_y u_z \n");
@@ -687,8 +687,8 @@ void FixLbFluid::initial_integrate(int vflag)
// distribution function.
//--------------------------------------------------------------------------
(*this.*update_full)();
-
- std::swap(f_lb,fnew);
+
+ std::swap(f_lb,fnew);
//--------------------------------------------------------------------------
// Calculate moments of the distribution function.
@@ -709,7 +709,7 @@ void FixLbFluid::initial_integrate(int vflag)
//--------------------------------------------------------------------------
if(printfluid > 0 && update->ntimestep > 0 && (update->ntimestep % printfluid == 0))
streamout();
-
+
}
void FixLbFluid::post_force(int vflag)
{
@@ -718,10 +718,10 @@ void FixLbFluid::post_force(int vflag)
}
void FixLbFluid::end_of_step()
-{
+{
if(fixviscouslb==0)
calc_fluidforce();
-
+
if(printrestart>0){
if((update->ntimestep)%printrestart == 0){
write_restartfile();
@@ -784,7 +784,7 @@ void FixLbFluid::calc_fluidforce(void)
MPI_Request requests[20];
double forceloc[3],force[3];
double torqueloc[3],torque[3];
-
+
//--------------------------------------------------------------------------
// Zero out arrays
//--------------------------------------------------------------------------
@@ -799,8 +799,8 @@ void FixLbFluid::calc_fluidforce(void)
for(i=0; i<atom->nmax; i++)
for(j=0; j<3; j++)
hydroF[i][j] = 0.0;
-
-
+
+
double unwrap[3];
double dx,dy,dz;
double massone;
@@ -821,7 +821,7 @@ void FixLbFluid::calc_fluidforce(void)
if(rmass) massone = rmass[i];
else massone = mass[type[i]];
-
+
sum[0] += unwrap[0]*massone;
sum[1] += unwrap[1]*massone;
sum[2] += unwrap[2]*massone;
@@ -844,23 +844,23 @@ void FixLbFluid::calc_fluidforce(void)
}else{
peskin_interpolation(i);
}
-
+
if(force_diagnostic > 0 && update->ntimestep > 0 && (update->ntimestep % force_diagnostic == 0)){
if(mask[i] & group->bitmask[igroupforce]){
-
+
domain->unmap(x[i],image[i],unwrap);
dx = unwrap[0] - xcm[0];
dy = unwrap[1] - xcm[1];
dz = unwrap[2] - xcm[2];
-
+
forceloc[0] += hydroF[i][0];
forceloc[1] += hydroF[i][1];
forceloc[2] += hydroF[i][2];
torqueloc[0] += dy*hydroF[i][2] - dz*hydroF[i][1];
torqueloc[1] += dz*hydroF[i][0] - dx*hydroF[i][2];
torqueloc[2] += dx*hydroF[i][1] - dy*hydroF[i][0];
- }
- }
+ }
+ }
}
}
@@ -881,7 +881,7 @@ void FixLbFluid::calc_fluidforce(void)
MPI_Irecv(&Fftempx[3][0][0][0],1,passxtemp,comm->procneigh[0][0],40,world,&requests[8]);
MPI_Irecv(&Fftempx[4][0][0][0],1,passxtemp,comm->procneigh[0][0],50,world,&requests[9]);
MPI_Waitall(10,requests,MPI_STATUS_IGNORE);
-
+
for(j=0; j<subNby+3; j++){
for(k=0; k<subNbz+3; k++){
for(m=0; m<3; m++){
@@ -949,17 +949,17 @@ void FixLbFluid::calc_fluidforce(void)
if(force_diagnostic > 0 && update->ntimestep > 0 && (update->ntimestep % force_diagnostic == 0)){
force[0] = force[1] = force[2] = 0.0;
torque[0] = torque[1] = torque[2] =0.0;
-
- MPI_Allreduce(&forceloc[0],&force[0],3,MPI_DOUBLE,MPI_SUM,world);
+
+ MPI_Allreduce(&forceloc[0],&force[0],3,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(&torqueloc[0],&torque[0],3,MPI_DOUBLE,MPI_SUM,world);
-
+
if(me==0){
printf("%E %E %E %E %E %E\n",force[0],force[1],force[2],
torque[0],torque[1],torque[2]);
}
}
-
+
}
//==========================================================================
// uses the Peskin stencil to perform the velocity, density and
@@ -987,36 +987,36 @@ void FixLbFluid::peskin_interpolation(int i)
//--------------------------------------------------------------------------
//Calculate nearest leftmost grid point.
//Since array indices from 1 to subNb-2 correspond to the
- // local subprocessor domain (not indices from 0), use the
+ // local subprocessor domain (not indices from 0), use the
// ceiling value.
//--------------------------------------------------------------------------
ix = (int)ceil((x[i][0]-domain->sublo[0])/dx_lb);
iy = (int)ceil((x[i][1]-domain->sublo[1])/dx_lb);
iz = (int)ceil((x[i][2]-domain->sublo[2])/dx_lb);
-
+
//--------------------------------------------------------------------------
//Calculate distances to the nearest points.
//--------------------------------------------------------------------------
dx1 = x[i][0] - (domain->sublo[0] + (ix-1)*dx_lb);
dy1 = x[i][1] - (domain->sublo[1] + (iy-1)*dx_lb);
dz1 = x[i][2] - (domain->sublo[2] + (iz-1)*dx_lb);
-
+
// Need to convert these to lattice units:
dx1 = dx1/dx_lb;
dy1 = dy1/dx_lb;
dz1 = dz1/dx_lb;
-
+
unode[0]=0.0; unode[1]=0.0; unode[2]=0.0;
mnode = 0.0;
isten=0;
-
+
//--------------------------------------------------------------------------
// Calculate the interpolation weights, and interpolated values of
// the fluid velocity, and density.
//--------------------------------------------------------------------------
for(ii=-1; ii<3; ii++){
rsq=(-dx1+ii)*(-dx1+ii);
-
+
if(rsq>=4)
weightx=0.0;
else{
@@ -1056,7 +1056,7 @@ void FixLbFluid::peskin_interpolation(int i)
izp = iz+kk;
//The atom is allowed to be within one lattice grid point outside the
- //local processor sub-domain.
+ //local processor sub-domain.
if(ixp < -1 || ixp > (subNbx+1) || iyp < -1 || iyp > (subNby+1) || izp < -1 || izp > (subNbz+1))
error->one(FLERR,"Atom outside local processor simulation domain. Either unstable fluid pararmeters, or \
require more frequent neighborlist rebuilds");
@@ -1065,11 +1065,11 @@ require more frequent neighborlist rebuilds");
error->warning(FLERR,"Atom too close to lower z wall. Unphysical results may occur");
if(domain->periodicity[2] == 0 && comm->myloc[2] == (comm->procgrid[2]-1) && (izp > (subNbz-2) ))
error->warning(FLERR,"Atom too close to upper z wall. Unphysical results may occur");
-
+
if(ixp==-1) ixp=subNbx+2;
if(iyp==-1) iyp=subNby+2;
if(izp==-1) izp=subNbz+2;
-
+
FfP[isten] = weightx*weighty*weightz;
// interpolated velocity based on delta function.
for(k=0; k<3; k++){
@@ -1077,7 +1077,7 @@ require more frequent neighborlist rebuilds");
}
if(setGamma==0)
mnode += density_lb[ixp][iyp][izp]*FfP[isten];
-
+
isten++;
}
}
@@ -1087,14 +1087,14 @@ require more frequent neighborlist rebuilds");
if(rmass) massone = rmass[i];
else massone = mass[type[i]];
- massone = massone/dm_lb;
+ massone = massone/dm_lb;
gammavalue = 2.0*(mnode*massone)*dtoverdtcollision/(mnode+massone);
- }
+ }
else{
gammavalue = Gamma[type[i]];
}
-
+
isten=0;
for(ii=-1; ii<3; ii++)
for(jj=-1; jj<3; jj++)
@@ -1102,7 +1102,7 @@ require more frequent neighborlist rebuilds");
ixp = ix+ii;
iyp = iy+jj;
izp = iz+kk;
-
+
if(ixp==-1) ixp=subNbx+2;
if(iyp==-1) iyp=subNby+2;
if(izp==-1) izp=subNbz+2;
@@ -1111,7 +1111,7 @@ require more frequent neighborlist rebuilds");
for(k=0; k<3; k++){
Ff[ixp][iyp][izp][k] += gammavalue*((v[i][k]*dt_lb/dx_lb)-unode[k])*FfP[isten];
}
-
+
isten++;
}
for(k=0; k<3; k++)
@@ -1142,20 +1142,20 @@ void FixLbFluid::trilinear_interpolation(int i)
//--------------------------------------------------------------------------
// Calculate nearest leftmost grid point.
// Since array indices from 1 to subNb-2 correspond to the
- // local subprocessor domain (not indices from 0), use the
+ // local subprocessor domain (not indices from 0), use the
// ceiling value.
//--------------------------------------------------------------------------
ix = (int)ceil((x[i][0]-domain->sublo[0])/dx_lb);
iy = (int)ceil((x[i][1]-domain->sublo[1])/dx_lb);
iz = (int)ceil((x[i][2]-domain->sublo[2])/dx_lb);
-
+
//--------------------------------------------------------------------------
//Calculate distances to the nearest points.
//--------------------------------------------------------------------------
dx1 = x[i][0] - (domain->sublo[0] + (ix-1)*dx_lb);
dy1 = x[i][1] - (domain->sublo[1] + (iy-1)*dx_lb);
dz1 = x[i][2] - (domain->sublo[2] + (iz-1)*dx_lb);
-
+
//--------------------------------------------------------------------------
// Need to convert these to lattice units:
//--------------------------------------------------------------------------
@@ -1174,13 +1174,13 @@ void FixLbFluid::trilinear_interpolation(int i)
FfP[5] = dx1*(1.-dy1)*dz1;
FfP[6] = dx1*dy1*(1.-dz1);
FfP[7] = dx1*dy1*dz1;
-
+
ixp = (ix+1);
iyp = (iy+1);
izp = (iz+1);
//The atom is allowed to be within one lattice grid point outside the
- //local processor sub-domain.
+ //local processor sub-domain.
if(ix < 0 || ixp > (subNbx+1) || iy < 0 || iyp > (subNby+1) || iz < 0 || izp > (subNbz+1))
error->one(FLERR,"Atom outside local processor simulation domain. Either unstable fluid pararmeters, or \
require more frequent neighborlist rebuilds");
@@ -1188,9 +1188,9 @@ require more frequent neighborlist rebuilds");
if(domain->periodicity[2] == 0 && comm->myloc[2] == 0 && (iz < 1 || izp < 1))
error->warning(FLERR,"Atom too close to lower z wall. Unphysical results may occur");
if(domain->periodicity[2] == 0 && comm->myloc[2] == (comm->procgrid[2]-1) && (izp > (subNbz-2) || iz > (subNbz-2)))
- error->warning(FLERR,"Atom too close to upper z wall. Unphysical results may occur");
-
-
+ error->warning(FLERR,"Atom too close to upper z wall. Unphysical results may occur");
+
+
for (k=0; k<3; k++) { // tri-linearly interpolated velocity at node
unode[k] = u_lb[ix][iy][iz][k]*FfP[0]
+ u_lb[ix][iy][izp][k]*FfP[1]
@@ -1216,13 +1216,13 @@ require more frequent neighborlist rebuilds");
if(rmass) massone = rmass[i];
else massone = mass[type[i]];
- massone = massone/dm_lb;
+ massone = massone/dm_lb;
gammavalue = 2.0*(mnode*massone)*dtoverdtcollision/(mnode+massone);
}else{
gammavalue = Gamma[type[i]];
}
-
+
for(k=0; k<3; k++){
Ff[ix][iy][iz][k] += gammavalue*((v[i][k]*dt_lb/dx_lb)-unode[k])*FfP[0];
@@ -1242,7 +1242,7 @@ require more frequent neighborlist rebuilds");
//==========================================================================
// read in a fluid restart file. This is only used to restart the
-// fluid portion of a LAMMPS simulation.
+// fluid portion of a LAMMPS simulation.
//==========================================================================
void FixLbFluid::read_restartfile(void)
{
@@ -1272,7 +1272,7 @@ void FixLbFluid::read_restartfile(void)
MPI_File_read_all(pFileRead,&f_lb[0][0][0][0],1,realtype,&status);
if(typeLB == 2){
MPI_File_read_all(pFileRead,&feqold[0][0][0][0],1,realtype,&status);
- MPI_File_read_all(pFileRead,&feqoldn[0][0][0][0],1,realtype,&status);
+ MPI_File_read_all(pFileRead,&feqoldn[0][0][0][0],1,realtype,&status);
}
MPI_Type_free(&realtype);
@@ -1282,7 +1282,7 @@ void FixLbFluid::read_restartfile(void)
}
//==========================================================================
-// write a fluid restart file.
+// write a fluid restart file.
//==========================================================================
void FixLbFluid::write_restartfile(void)
{
@@ -1295,7 +1295,7 @@ void FixLbFluid::write_restartfile(void)
char *hfile;
hfile = new char[32];
sprintf(hfile,"FluidRestart_" BIGINT_FORMAT ".dat",update->ntimestep);
-
+
MPI_File_open(world,hfile,MPI_MODE_WRONLY | MPI_MODE_CREATE, MPI_INFO_NULL,&fh);
int realsizes[4] = {subNbx,subNby,subNbz,numvel};
@@ -1317,7 +1317,7 @@ void FixLbFluid::write_restartfile(void)
MPI_File_write_all(fh,&f_lb[0][0][0][0],1,realtype,&status);
if(typeLB == 2){
MPI_File_write_all(fh,&feqold[0][0][0][0],1,realtype,&status);
- MPI_File_write_all(fh,&feqoldn[0][0][0][0],1,realtype,&status);
+ MPI_File_write_all(fh,&feqoldn[0][0][0][0],1,realtype,&status);
}
MPI_Type_free(&realtype);
@@ -1330,22 +1330,22 @@ void FixLbFluid::write_restartfile(void)
//==========================================================================
// rescale the simulation parameters so that dx_lb=dt_lb=dm_lb=1.
// This assumes that all the simulation parameters have been given in
-// terms of distance, time and mass units.
+// terms of distance, time and mass units.
//==========================================================================
void FixLbFluid::rescale(void)
{
vwtp = vwtp*dt_lb/dx_lb;
vwbt = vwbt*dt_lb/dx_lb;
-
+
bodyforcex = bodyforcex*dt_lb*dt_lb/dx_lb;
bodyforcey = bodyforcey*dt_lb*dt_lb/dx_lb;
bodyforcez = bodyforcez*dt_lb*dt_lb/dx_lb;
-
+
tau=(3.0*viscosity/densityinit_real)*dt_lb*dt_lb/dx_lb/dx_lb;
tau /= dt_lb;
if(typeLB==1)
tau = tau + 0.5;
-
+
if(setGamma == 0){
for(int i=0; i<= atom->ntypes; i++){
NodeArea[i] = NodeArea[i]/dx_lb/dx_lb;
@@ -1355,7 +1355,7 @@ void FixLbFluid::rescale(void)
Gamma[i] = Gamma[i]*dt_lb/dm_lb;
}
}
-
+
densityinit = densityinit_real*dx_lb*dx_lb*dx_lb/dm_lb;
a_0 = a_0_real*dt_lb*dt_lb/(dx_lb*dx_lb);
@@ -1529,13 +1529,13 @@ void FixLbFluid::initializeLB15(void)
mg_lb[6][10]=2./3.;mg_lb[6][11]=2./3.;mg_lb[6][12]=2./3.;mg_lb[6][13]=2./3.;mg_lb[6][14]=2./3.;
mg_lb[7][0]=0;mg_lb[7][1]=0;mg_lb[7][2]=0;mg_lb[7][3]=0;mg_lb[7][4]=0;
mg_lb[7][5]=0;mg_lb[7][6]=0;mg_lb[7][7]=1;mg_lb[7][8]=-1;mg_lb[7][9]=1;
- mg_lb[7][10]=-1;mg_lb[7][11]=1;mg_lb[7][12]=-1;mg_lb[7][13]=1;mg_lb[7][14]=-1;
+ mg_lb[7][10]=-1;mg_lb[7][11]=1;mg_lb[7][12]=-1;mg_lb[7][13]=1;mg_lb[7][14]=-1;
mg_lb[8][0]=0;mg_lb[8][1]=0;mg_lb[8][2]=0;mg_lb[8][3]=0;mg_lb[8][4]=0;
mg_lb[8][5]=0;mg_lb[8][6]=0;mg_lb[8][7]=1;mg_lb[8][8]=1;mg_lb[8][9]=-1;
- mg_lb[8][10]=-1;mg_lb[8][11]=-1;mg_lb[8][12]=-1;mg_lb[8][13]=1;mg_lb[8][14]=1;
+ mg_lb[8][10]=-1;mg_lb[8][11]=-1;mg_lb[8][12]=-1;mg_lb[8][13]=1;mg_lb[8][14]=1;
mg_lb[9][0]=0;mg_lb[9][1]=0;mg_lb[9][2]=0;mg_lb[9][3]=0;mg_lb[9][4]=0;
mg_lb[9][5]=0;mg_lb[9][6]=0;mg_lb[9][7]=1;mg_lb[9][8]=-1;mg_lb[9][9]=-1;
- mg_lb[9][10]=1;mg_lb[9][11]=-1;mg_lb[9][12]=1;mg_lb[9][13]=1;mg_lb[9][14]=-1;
+ mg_lb[9][10]=1;mg_lb[9][11]=-1;mg_lb[9][12]=1;mg_lb[9][13]=1;mg_lb[9][14]=-1;
mg_lb[10][0]=0;mg_lb[10][1]=0;mg_lb[10][2]=-1./3.;mg_lb[10][3]=0;mg_lb[10][4]=1./3.;
mg_lb[10][5]=0;mg_lb[10][6]=0;mg_lb[10][7]=2./3.;mg_lb[10][8]=2./3.;mg_lb[10][9]=-2./3.;
mg_lb[10][10]=-2./3.;mg_lb[10][11]=2./3.;mg_lb[10][12]=2./3.;mg_lb[10][13]=-2./3.;mg_lb[10][14]=-2./3.;
@@ -1618,7 +1618,7 @@ void FixLbFluid::initializeLB19(void)
e[9][0] = -1;
e[9][1] = 1;
- e[9][2] = 0;
+ e[9][2] = 0;
e[10][0] = -1;
e[10][1] = -1;
@@ -1710,7 +1710,7 @@ void FixLbFluid::initializeLB19(void)
mg_lb[2][0] = 0.; mg_lb[2][1] = 0.; mg_lb[2][2] = 1.; mg_lb[2][3] = 0.; mg_lb[2][4] =-1.;
mg_lb[2][5] = 0.; mg_lb[2][6] = 0.; mg_lb[2][7] = 1.; mg_lb[2][8] =-1.; mg_lb[2][9] = 1.;
mg_lb[2][10]=-1.; mg_lb[2][11]= 0.; mg_lb[2][12]= 0.; mg_lb[2][13]= 0.; mg_lb[2][14]= 0.;
- mg_lb[2][15]= 1.; mg_lb[2][16]= 1.; mg_lb[2][17]=-1.; mg_lb[2][18]=-1.;
+ mg_lb[2][15]= 1.; mg_lb[2][16]= 1.; mg_lb[2][17]=-1.; mg_lb[2][18]=-1.;
mg_lb[3][0] = 0.; mg_lb[3][1] = 0.; mg_lb[3][2] = 0.; mg_lb[3][3] = 0.; mg_lb[3][4] = 0.;
mg_lb[3][5] = 1.; mg_lb[3][6] =-1.; mg_lb[3][7] = 0.; mg_lb[3][8] = 0.; mg_lb[3][9] = 0.;
@@ -1809,7 +1809,7 @@ void FixLbFluid::initializeLB19(void)
}
//==========================================================================
-// Initialize the equilibrium distribution functions
+// Initialize the equilibrium distribution functions
// (this just uses the initial fluid parameters, and assumes no forces).
//==========================================================================
void FixLbFluid::initialize_feq(void)
@@ -1828,13 +1828,13 @@ void FixLbFluid::initialize_feq(void)
std::fill(&Ff[0][0][0][0],&Ff[0][0][0][0] + (subNbx+3)*(subNby+3)*(subNbz+3)*3,0.0);
std::fill(&Fftempx[0][0][0][0],&Fftempx[0][0][0][0] + 5*(subNby+3)*(subNbz+3)*3,0.0);
std::fill(&Fftempy[0][0][0][0],&Fftempy[0][0][0][0] + (subNbx+3)*5*(subNbz+3)*3,0.0);
- std::fill(&Fftempz[0][0][0][0],&Fftempz[0][0][0][0] + (subNbx+3)*(subNby+3)*5*3,0.0);
+ std::fill(&Fftempz[0][0][0][0],&Fftempz[0][0][0][0] + (subNbx+3)*(subNby+3)*5*3,0.0);
if(readrestart == 0){
step=0;
parametercalc_full();
- (*this.*equilibriumdist)(1,subNbx-1,1,subNby-1,1,subNbz-1);
+ (*this.*equilibriumdist)(1,subNbx-1,1,subNby-1,1,subNbz-1);
for(i=0; i<numrequests; i++)
requests[i]=MPI_REQUEST_NULL;
@@ -1847,23 +1847,23 @@ void FixLbFluid::initialize_feq(void)
MPI_Irecv(&feqn[0][1][1][0],1,passxf,comm->procneigh[0][0],20,world,&requests[5]);
MPI_Isend(&feqn[subNbx-2][1][1][0],1,passxf,comm->procneigh[0][1],20,world,&requests[6]);
MPI_Irecv(&feqn[subNbx-1][1][1][0],1,passxf,comm->procneigh[0][1],10,world,&requests[7]);
- }
+ }
MPI_Waitall(numrequests,requests,MPI_STATUS_IGNORE);
-
+
for(i=0; i<numrequests; i++)
requests[i]=MPI_REQUEST_NULL;
MPI_Isend(&feq[0][1][1][0],1,passyf,comm->procneigh[1][0],15,world,&requests[0]);
- MPI_Irecv(&feq[0][0][1][0],1,passyf,comm->procneigh[1][0],25,world,&requests[1]);
+ MPI_Irecv(&feq[0][0][1][0],1,passyf,comm->procneigh[1][0],25,world,&requests[1]);
MPI_Isend(&feq[0][subNby-2][1][0],1,passyf,comm->procneigh[1][1],25,world,&requests[2]);
MPI_Irecv(&feq[0][subNby-1][1][0],1,passyf,comm->procneigh[1][1],15,world,&requests[3]);
if(typeLB == 2){
MPI_Isend(&feqn[0][1][1][0],1,passyf,comm->procneigh[1][0],10,world,&requests[4]);
- MPI_Irecv(&feqn[0][0][1][0],1,passyf,comm->procneigh[1][0],20,world,&requests[5]);
+ MPI_Irecv(&feqn[0][0][1][0],1,passyf,comm->procneigh[1][0],20,world,&requests[5]);
MPI_Isend(&feqn[0][subNby-2][1][0],1,passyf,comm->procneigh[1][1],20,world,&requests[6]);
MPI_Irecv(&feqn[0][subNby-1][1][0],1,passyf,comm->procneigh[1][1],10,world,&requests[7]);
}
MPI_Waitall(numrequests,requests,MPI_STATUS_IGNORE);
-
+
for(i=0; i<numrequests; i++)
requests[i]=MPI_REQUEST_NULL;
MPI_Isend(&feq[0][0][1][0],1,passzf,comm->procneigh[2][0],15,world,&requests[0]);
@@ -1875,9 +1875,9 @@ void FixLbFluid::initialize_feq(void)
MPI_Irecv(&feqn[0][0][0][0],1,passzf,comm->procneigh[2][0],20,world,&requests[5]);
MPI_Isend(&feqn[0][0][subNbz-2][0],1,passzf,comm->procneigh[2][1],20,world,&requests[6]);
MPI_Irecv(&feqn[0][0][subNbz-1][0],1,passzf,comm->procneigh[2][1],10,world,&requests[7]);
- }
+ }
MPI_Waitall(numrequests,requests,MPI_STATUS_IGNORE);
-
+
//Save feqold.
if(typeLB == 2){
for(i=0; i<subNbx; i++)
@@ -1890,9 +1890,9 @@ void FixLbFluid::initialize_feq(void)
}
}else{
step = 1;
-
+
read_restartfile();
-
+
if(typeLB == 2){
for(i=0; i<8; i++)
requests[i]=MPI_REQUEST_NULL;
@@ -1903,31 +1903,31 @@ void FixLbFluid::initialize_feq(void)
MPI_Isend(&feqoldn[1][1][1][0],1,passxf,comm->procneigh[0][0],10,world,&requests[4]);
MPI_Irecv(&feqoldn[0][1][1][0],1,passxf,comm->procneigh[0][0],20,world,&requests[5]);
MPI_Isend(&feqoldn[subNbx-2][1][1][0],1,passxf,comm->procneigh[0][1],20,world,&requests[6]);
- MPI_Irecv(&feqoldn[subNbx-1][1][1][0],1,passxf,comm->procneigh[0][1],10,world,&requests[7]);
+ MPI_Irecv(&feqoldn[subNbx-1][1][1][0],1,passxf,comm->procneigh[0][1],10,world,&requests[7]);
MPI_Waitall(8,requests,MPI_STATUS_IGNORE);
-
+
for(i=0; i<8; i++)
requests[i]=MPI_REQUEST_NULL;
MPI_Isend(&feqold[0][1][1][0],1,passyf,comm->procneigh[1][0],15,world,&requests[0]);
- MPI_Irecv(&feqold[0][0][1][0],1,passyf,comm->procneigh[1][0],25,world,&requests[1]);
+ MPI_Irecv(&feqold[0][0][1][0],1,passyf,comm->procneigh[1][0],25,world,&requests[1]);
MPI_Isend(&feqold[0][subNby-2][1][0],1,passyf,comm->procneigh[1][1],25,world,&requests[2]);
MPI_Irecv(&feqold[0][subNby-1][1][0],1,passyf,comm->procneigh[1][1],15,world,&requests[3]);
MPI_Isend(&feqoldn[0][1][1][0],1,passyf,comm->procneigh[1][0],10,world,&requests[4]);
- MPI_Irecv(&feqoldn[0][0][1][0],1,passyf,comm->procneigh[1][0],20,world,&requests[5]);
+ MPI_Irecv(&feqoldn[0][0][1][0],1,passyf,comm->procneigh[1][0],20,world,&requests[5]);
MPI_Isend(&feqoldn[0][subNby-2][1][0],1,passyf,comm->procneigh[1][1],20,world,&requests[6]);
MPI_Irecv(&feqoldn[0][subNby-1][1][0],1,passyf,comm->procneigh[1][1],10,world,&requests[7]);
MPI_Waitall(8,requests,MPI_STATUS_IGNORE);
-
+
for(i=0; i<8; i++)
requests[i]=MPI_REQUEST_NULL;
MPI_Isend(&feqold[0][0][1][0],1,passzf,comm->procneigh[2][0],15,world,&requests[0]);
MPI_Irecv(&feqold[0][0][0][0],1,passzf,comm->procneigh[2][0],25,world,&requests[1]);
MPI_Isend(&feqold[0][0][subNbz-2][0],1,passzf,comm->procneigh[2][1],25,world,&requests[2]);
- MPI_Irecv(&feqold[0][0][subNbz-1][0],1,passzf,comm->procneigh[2][1],15,world,&requests[3]);
+ MPI_Irecv(&feqold[0][0][subNbz-1][0],1,passzf,comm->procneigh[2][1],15,world,&requests[3]);
MPI_Isend(&feqoldn[0][0][1][0],1,passzf,comm->procneigh[2][0],10,world,&requests[4]);
MPI_Irecv(&feqoldn[0][0][0][0],1,passzf,comm->procneigh[2][0],20,world,&requests[5]);
MPI_Isend(&feqoldn[0][0][subNbz-2][0],1,passzf,comm->procneigh[2][1],20,world,&requests[6]);
- MPI_Irecv(&feqoldn[0][0][subNbz-1][0],1,passzf,comm->procneigh[2][1],10,world,&requests[7]);
+ MPI_Irecv(&feqoldn[0][0][subNbz-1][0],1,passzf,comm->procneigh[2][1],10,world,&requests[7]);
MPI_Waitall(8,requests,MPI_STATUS_IGNORE);
}
parametercalc_full();
@@ -1952,7 +1952,7 @@ void FixLbFluid::equilibriumdist15(int xstart, int xend, int ystart, int yend, i
double S[2][3],std;
int jj;
-
+
double etacov[15],ghostnoise;
@@ -1971,35 +1971,35 @@ void FixLbFluid::equilibriumdist15(int xstart, int xend, int ystart, int yend, i
// Derivatives.
drhox = (density_lb[iup][j][k] - density_lb[idwn][j][k])/2.0;
- drhoxx = (density_lb[iup][j][k] - 2.0*density_lb[i][j][k] +
+ drhoxx = (density_lb[iup][j][k] - 2.0*density_lb[i][j][k] +
density_lb[idwn][j][k]);
drhoy = (density_lb[i][jup][k] - density_lb[i][jdwn][k])/2.0;
- drhoyy = (density_lb[i][jup][k] - 2.0*density_lb[i][j][k] +
+ drhoyy = (density_lb[i][jup][k] - 2.0*density_lb[i][j][k] +
density_lb[i][jdwn][k]);
drhoz = (density_lb[i][j][kup] - density_lb[i][j][kdwn])/2.0;
- drhozz = (density_lb[i][j][kup] - 2.0*density_lb[i][j][k] +
+ drhozz = (density_lb[i][j][kup] - 2.0*density_lb[i][j][k] +
density_lb[i][j][kdwn]);
// Need one-sided derivatives for the boundary of the domain, if fixed boundary
// conditions are used.
if(domain->periodicity[2]==0){
if(comm->myloc[2]==0 && k==1){
- drhoz = (-3.0*density_lb[i][j][k] + 4.0*density_lb[i][j][k+1] -
+ drhoz = (-3.0*density_lb[i][j][k] + 4.0*density_lb[i][j][k+1] -
density_lb[i][j][k+2])/2.0;
- drhozz = (-density_lb[i][j][k+3] + 4.0*density_lb[i][j][k+2] -
+ drhozz = (-density_lb[i][j][k+3] + 4.0*density_lb[i][j][k+2] -
5.0*density_lb[i][j][k+1] + 2.0*rho);
}
if(comm->myloc[2]==comm->procgrid[2]-1 && k==subNbz-2){
- drhoz = -(-3.0*density_lb[i][j][k] + 4.0*density_lb[i][j][k-1] -
+ drhoz = -(-3.0*density_lb[i][j][k] + 4.0*density_lb[i][j][k-1] -
density_lb[i][j][k-2])/2.0;
- drhozz = (-density_lb[i][j][k-3] + 4.0*density_lb[i][j][k-2] -
+ drhozz = (-density_lb[i][j][k-3] + 4.0*density_lb[i][j][k-2] -
5.0*density_lb[i][j][k-1] + 2.0*rho);
}
}
- grs = drhox*drhox + drhoy*drhoy + drhoz*drhoz;
+ grs = drhox*drhox + drhoy*drhoy + drhoz*drhoz;
p0 = rho*a_0-kappa_lb*rho*(drhoxx + drhoyy + drhozz);
// kappa_lb is the square gradient coeff in the pressure tensor
@@ -2033,7 +2033,7 @@ void FixLbFluid::equilibriumdist15(int xstart, int xend, int ystart, int yend, i
(u_lb[i][j][k][0]*drhoz+u_lb[i][j][k][2]*drhox);
Pyz = kappa_lb*drhoy*drhoz+tau*(1.0/3.0-dPdrho)*
(u_lb[i][j][k][1]*drhoz+u_lb[i][j][k][2]*drhoy);
- }
+ }
Fx_w = Ff[i][j][k][0];
Fy_w = Ff[i][j][k][1];
@@ -2044,29 +2044,29 @@ void FixLbFluid::equilibriumdist15(int xstart, int xend, int ystart, int yend, i
etacov[2] = rho*u_lb[i][j][k][1] + Fy_w*tau + rho*bodyforcey*tau;
etacov[3] = rho*u_lb[i][j][k][2] + Fz_w*tau + rho*bodyforcez*tau;
- etacov[4] = Pxx + rho*u_lb[i][j][k][0]*u_lb[i][j][k][0] -rho/3. +
+ etacov[4] = Pxx + rho*u_lb[i][j][k][0]*u_lb[i][j][k][0] -rho/3. +
tau*(2.0*u_lb[i][j][k][0]*(Fx_w+rho*bodyforcex));
- etacov[5] = Pyy + rho*u_lb[i][j][k][1]*u_lb[i][j][k][1] -rho/3. +
+ etacov[5] = Pyy + rho*u_lb[i][j][k][1]*u_lb[i][j][k][1] -rho/3. +
tau*(2.0*u_lb[i][j][k][1]*(Fy_w+rho*bodyforcey));
- etacov[6] = Pzz + rho*u_lb[i][j][k][2]*u_lb[i][j][k][2] -rho/3. +
+ etacov[6] = Pzz + rho*u_lb[i][j][k][2]*u_lb[i][j][k][2] -rho/3. +
tau*(2.0*u_lb[i][j][k][2]*(Fz_w+rho*bodyforcez));
- etacov[7] = Pxy + rho*u_lb[i][j][k][0]*u_lb[i][j][k][1] +
+ etacov[7] = Pxy + rho*u_lb[i][j][k][0]*u_lb[i][j][k][1] +
tau*(u_lb[i][j][k][0]*(Fy_w+rho*bodyforcey) + (Fx_w+rho*bodyforcex)*u_lb[i][j][k][1]);
- etacov[8] = Pyz + rho*u_lb[i][j][k][1]*u_lb[i][j][k][2] +
+ etacov[8] = Pyz + rho*u_lb[i][j][k][1]*u_lb[i][j][k][2] +
tau*(u_lb[i][j][k][1]*(Fz_w+rho*bodyforcez) + (Fy_w+rho*bodyforcey)*u_lb[i][j][k][2]);
- etacov[9] = Pxz + rho*u_lb[i][j][k][0]*u_lb[i][j][k][2] +
+ etacov[9] = Pxz + rho*u_lb[i][j][k][0]*u_lb[i][j][k][2] +
tau*(u_lb[i][j][k][0]*(Fz_w+rho*bodyforcez) + (Fx_w+rho*bodyforcex)*u_lb[i][j][k][2]);
- etacov[10] = 0.0;
- etacov[11] = 0.0;
+ etacov[10] = 0.0;
+ etacov[11] = 0.0;
etacov[12] = 0.0;
etacov[13] = rho*u_lb[i][j][k][0]*u_lb[i][j][k][1]*u_lb[i][j][k][2];
const double TrP = Pxx+Pyy+Pzz;
etacov[14] = K_0*(rho-TrP);
-
+
for (l=0; l<15; l++) {
feq[i][j][k][l] = 0.0;
- for (int ii=0; ii<15; ii++)
+ for (int ii=0; ii<15; ii++)
feq[i][j][k][l] += w_lb[l]*mg_lb[ii][l]*etacov[ii]*Ng_lb[ii];
if(typeLB == 2){
@@ -2080,7 +2080,7 @@ void FixLbFluid::equilibriumdist15(int xstart, int xend, int ystart, int yend, i
for(jj=0; jj<3; jj++)
S[0][jj] = std*random->gaussian();
for(jj=0; jj<3; jj++)
- S[1][jj] = std*random->gaussian();
+ S[1][jj] = std*random->gaussian();
etacov[4] = (S[0][0]*sqrt(3.0-3.0*a_0));
etacov[5] = ((1.0-3.0*a_0)*S[0][0]/sqrt(3.0-3.0*a_0)+
@@ -2099,15 +2099,15 @@ void FixLbFluid::equilibriumdist15(int xstart, int xend, int ystart, int yend, i
for (l=0; l<15; l++) {
ghostnoise = w_lb[l]*
- (mg_lb[4][l]*etacov[4]*Ng_lb[4] + mg_lb[5][l]*etacov[5]*Ng_lb[5] +
- mg_lb[6][l]*etacov[6]*Ng_lb[6] + mg_lb[7][l]*etacov[7]*Ng_lb[7] +
- mg_lb[8][l]*etacov[8]*Ng_lb[8] + mg_lb[9][l]*etacov[9]*Ng_lb[9] +
+ (mg_lb[4][l]*etacov[4]*Ng_lb[4] + mg_lb[5][l]*etacov[5]*Ng_lb[5] +
+ mg_lb[6][l]*etacov[6]*Ng_lb[6] + mg_lb[7][l]*etacov[7]*Ng_lb[7] +
+ mg_lb[8][l]*etacov[8]*Ng_lb[8] + mg_lb[9][l]*etacov[9]*Ng_lb[9] +
mg_lb[10][l]*etacov[10]*Ng_lb[10] + mg_lb[11][l]*etacov[11]*Ng_lb[11]
+ mg_lb[12][l]*etacov[12]*Ng_lb[12] + mg_lb[13][l]*etacov[13]*Ng_lb[13]
+ mg_lb[14][l]*etacov[14]*Ng_lb[14]);
feq[i][j][k][l] += ghostnoise*noisefactor;
}
- }
+ }
}
}
}
@@ -2131,7 +2131,7 @@ void FixLbFluid::equilibriumdist19(int xstart, int xend, int ystart, int yend, i
double S[2][3],std;
int jj;
-
+
double etacov[19],ghostnoise;
for (i=xstart; i<xend; i++) {
@@ -2149,35 +2149,35 @@ void FixLbFluid::equilibriumdist19(int xstart, int xend, int ystart, int yend, i
// Derivatives.
drhox = (density_lb[iup][j][k] - density_lb[idwn][j][k])/2.0;
- drhoxx = (density_lb[iup][j][k] - 2.0*density_lb[i][j][k] +
+ drhoxx = (density_lb[iup][j][k] - 2.0*density_lb[i][j][k] +
density_lb[idwn][j][k]);
drhoy = (density_lb[i][jup][k] - density_lb[i][jdwn][k])/2.0;
- drhoyy = (density_lb[i][jup][k] - 2.0*density_lb[i][j][k] +
+ drhoyy = (density_lb[i][jup][k] - 2.0*density_lb[i][j][k] +
density_lb[i][jdwn][k]);
drhoz = (density_lb[i][j][kup] - density_lb[i][j][kdwn])/2.0;
- drhozz = (density_lb[i][j][kup] - 2.0*density_lb[i][j][k] +
+ drhozz = (density_lb[i][j][kup] - 2.0*density_lb[i][j][k] +
density_lb[i][j][kdwn]);
// Need one-sided derivatives for the boundary of the domain, if fixed boundary
// conditions are used.
if(domain->periodicity[2]==0){
if(comm->myloc[2]==0 && k==1){
- drhoz = (-3.0*density_lb[i][j][k] + 4.0*density_lb[i][j][k+1] -
+ drhoz = (-3.0*density_lb[i][j][k] + 4.0*density_lb[i][j][k+1] -
density_lb[i][j][k+2])/2.0;
- drhozz = (-density_lb[i][j][k+3] + 4.0*density_lb[i][j][k+2] -
+ drhozz = (-density_lb[i][j][k+3] + 4.0*density_lb[i][j][k+2] -
5.0*density_lb[i][j][k+1] + 2.0*rho);
}
if(comm->myloc[2]==comm->procgrid[2]-1 && k==subNbz-2){
- drhoz = -(-3.0*density_lb[i][j][k] + 4.0*density_lb[i][j][k-1] -
+ drhoz = -(-3.0*density_lb[i][j][k] + 4.0*density_lb[i][j][k-1] -
density_lb[i][j][k-2])/2.0;
- drhozz = (-density_lb[i][j][k-3] + 4.0*density_lb[i][j][k-2] -
+ drhozz = (-density_lb[i][j][k-3] + 4.0*density_lb[i][j][k-2] -
5.0*density_lb[i][j][k-1] + 2.0*rho);
}
}
- grs = drhox*drhox + drhoy*drhoy + drhoz*drhoz;
+ grs = drhox*drhox + drhoy*drhoy + drhoz*drhoz;
p0 = rho*a_0-kappa_lb*rho*(drhoxx + drhoyy + drhozz);
// kappa_lb is the square gradient coeff in the pressure tensor
@@ -2211,7 +2211,7 @@ void FixLbFluid::equilibriumdist19(int xstart, int xend, int ystart, int yend, i
(u_lb[i][j][k][0]*drhoz+u_lb[i][j][k][2]*drhox);
Pyz = kappa_lb*drhoy*drhoz+tau*(1.0/3.0-dPdrho)*
(u_lb[i][j][k][1]*drhoz+u_lb[i][j][k][2]*drhoy);
- }
+ }
Fx_w = Ff[i][j][k][0];
Fy_w = Ff[i][j][k][1];
@@ -2222,20 +2222,20 @@ void FixLbFluid::equilibriumdist19(int xstart, int xend, int ystart, int yend, i
etacov[2] = rho*u_lb[i][j][k][1] + Fy_w*tau + rho*bodyforcey*tau;
etacov[3] = rho*u_lb[i][j][k][2] + Fz_w*tau + rho*bodyforcez*tau;
- etacov[4] = Pxx + rho*u_lb[i][j][k][0]*u_lb[i][j][k][0] -rho/3. +
+ etacov[4] = Pxx + rho*u_lb[i][j][k][0]*u_lb[i][j][k][0] -rho/3. +
tau*(2.0*u_lb[i][j][k][0]*(Fx_w+rho*bodyforcex));
- etacov[5] = Pyy + rho*u_lb[i][j][k][1]*u_lb[i][j][k][1] -rho/3. +
+ etacov[5] = Pyy + rho*u_lb[i][j][k][1]*u_lb[i][j][k][1] -rho/3. +
tau*(2.0*u_lb[i][j][k][1]*(Fy_w+rho*bodyforcey));
- etacov[6] = Pzz + rho*u_lb[i][j][k][2]*u_lb[i][j][k][2] -rho/3. +
+ etacov[6] = Pzz + rho*u_lb[i][j][k][2]*u_lb[i][j][k][2] -rho/3. +
tau*(2.0*u_lb[i][j][k][2]*(Fz_w+rho*bodyforcez));
- etacov[7] = Pxy + rho*u_lb[i][j][k][0]*u_lb[i][j][k][1] +
+ etacov[7] = Pxy + rho*u_lb[i][j][k][0]*u_lb[i][j][k][1] +
tau*(u_lb[i][j][k][0]*(Fy_w+rho*bodyforcey) + (Fx_w+rho*bodyforcex)*u_lb[i][j][k][1]);
- etacov[8] = Pxz + rho*u_lb[i][j][k][0]*u_lb[i][j][k][2] +
+ etacov[8] = Pxz + rho*u_lb[i][j][k][0]*u_lb[i][j][k][2] +
tau*(u_lb[i][j][k][0]*(Fz_w+rho*bodyforcez) + (Fx_w+rho*bodyforcex)*u_lb[i][j][k][2]);
- etacov[9] = Pyz + rho*u_lb[i][j][k][1]*u_lb[i][j][k][2] +
+ etacov[9] = Pyz + rho*u_lb[i][j][k][1]*u_lb[i][j][k][2] +
tau*(u_lb[i][j][k][1]*(Fz_w+rho*bodyforcez) + (Fy_w+rho*bodyforcey)*u_lb[i][j][k][2]);
- etacov[10] = 0.0;
- etacov[11] = 0.0;
+ etacov[10] = 0.0;
+ etacov[11] = 0.0;
etacov[12] = 0.0;
etacov[13] = 0.0;
etacov[14] = 0.0;
@@ -2243,11 +2243,11 @@ void FixLbFluid::equilibriumdist19(int xstart, int xend, int ystart, int yend, i
etacov[16] = 0.0;
etacov[17] = 0.0;
etacov[18] = 0.0;
-
+
for (l=0; l<19; l++) {
feq[i][j][k][l] = 0.0;
- for (int ii=0; ii<19; ii++)
+ for (int ii=0; ii<19; ii++)
feq[i][j][k][l] += w_lb[l]*mg_lb[ii][l]*etacov[ii]*Ng_lb[ii];
if(typeLB == 2){
@@ -2261,7 +2261,7 @@ void FixLbFluid::equilibriumdist19(int xstart, int xend, int ystart, int yend, i
for(jj=0; jj<3; jj++)
S[0][jj] = std*random->gaussian();
for(jj=0; jj<3; jj++)
- S[1][jj] = std*random->gaussian();
+ S[1][jj] = std*random->gaussian();
etacov[4] = (S[0][0]*sqrt(3.0-3.0*a_0));
etacov[5] = ((1.0-3.0*a_0)*S[0][0]/sqrt(3.0-3.0*a_0)+
@@ -2276,12 +2276,12 @@ void FixLbFluid::equilibriumdist19(int xstart, int xend, int ystart, int yend, i
for (l=10; l<19; l++) {
etacov[l] = sqrt(9.0*namp*rho/Ng_lb[l])*random->gaussian();
}
-
+
for (l=0; l<19; l++) {
ghostnoise = w_lb[l]*
- (mg_lb[4][l]*etacov[4]*Ng_lb[4] + mg_lb[5][l]*etacov[5]*Ng_lb[5] +
- mg_lb[6][l]*etacov[6]*Ng_lb[6] + mg_lb[7][l]*etacov[7]*Ng_lb[7] +
- mg_lb[8][l]*etacov[8]*Ng_lb[8] + mg_lb[9][l]*etacov[9]*Ng_lb[9] +
+ (mg_lb[4][l]*etacov[4]*Ng_lb[4] + mg_lb[5][l]*etacov[5]*Ng_lb[5] +
+ mg_lb[6][l]*etacov[6]*Ng_lb[6] + mg_lb[7][l]*etacov[7]*Ng_lb[7] +
+ mg_lb[8][l]*etacov[8]*Ng_lb[8] + mg_lb[9][l]*etacov[9]*Ng_lb[9] +
mg_lb[10][l]*etacov[10]*Ng_lb[10] + mg_lb[11][l]*etacov[11]*Ng_lb[11]
+ mg_lb[12][l]*etacov[12]*Ng_lb[12] + mg_lb[13][l]*etacov[13]*Ng_lb[13]
+ mg_lb[14][l]*etacov[14]*Ng_lb[14] + mg_lb[15][l]*etacov[15]*Ng_lb[15]
@@ -2290,7 +2290,7 @@ void FixLbFluid::equilibriumdist19(int xstart, int xend, int ystart, int yend, i
feq[i][j][k][l] += ghostnoise*noisefactor;
}
}
-
+
}
}
}
@@ -2309,7 +2309,7 @@ void FixLbFluid::parametercalc_full(void)
//--------------------------------------------------------------------------
// send the boundaries of f_lb, as they will be needed later by the update
- // routine, and use these to calculate the density and velocity on the
+ // routine, and use these to calculate the density and velocity on the
// boundary.
//--------------------------------------------------------------------------
for(i=0; i<4; i++)
@@ -2324,7 +2324,7 @@ void FixLbFluid::parametercalc_full(void)
for(i=0; i<4; i++)
requests[i]=MPI_REQUEST_NULL;
MPI_Isend(&f_lb[0][1][1][0],1,passyf,comm->procneigh[1][0],10,world,&requests[0]);
- MPI_Irecv(&f_lb[0][0][1][0],1,passyf,comm->procneigh[1][0],20,world,&requests[1]);
+ MPI_Irecv(&f_lb[0][0][1][0],1,passyf,comm->procneigh[1][0],20,world,&requests[1]);
MPI_Isend(&f_lb[0][subNby-2][1][0],1,passyf,comm->procneigh[1][1],20,world,&requests[2]);
MPI_Irecv(&f_lb[0][subNby-1][1][0],1,passyf,comm->procneigh[1][1],10,world,&requests[3]);
parametercalc_part(0,1,1,subNby-1,1,subNbz-1);
@@ -2340,12 +2340,12 @@ void FixLbFluid::parametercalc_full(void)
parametercalc_part(0,subNbx,0,1,1,subNbz-1);
parametercalc_part(0,subNbx,subNby-1,subNby,1,subNbz-1);
MPI_Waitall(4,requests,MPI_STATUS_IGNORE);
-
+
parametercalc_part(0,subNbx,0,subNby,0,1);
parametercalc_part(0,subNbx,0,subNby,subNbz-1,subNbz);
//--------------------------------------------------------------------------
- // Send the remaining portions of the u array (and density array if Gamma
+ // Send the remaining portions of the u array (and density array if Gamma
// is set the default way).
//--------------------------------------------------------------------------
if(setGamma == 0) numrequests = 12;
@@ -2413,7 +2413,7 @@ void FixLbFluid::parametercalc_full(void)
MPI_Irecv(&density_lb[0][0][subNbz+1],1,passzrho,comm->procneigh[2][1],50,world,&requests2[requestcount+2]);
requestcount=requestcount+3;
}
- }
+ }
MPI_Waitall(requestcount,requests2,MPI_STATUS_IGNORE);
}
@@ -2435,15 +2435,15 @@ void FixLbFluid::parametercalc_part(int xstart, int xend, int ystart, int yend,
u_lb[i][j][k][1]=0.0;
u_lb[i][j][k][2]=0.0;
for (m=0; m<numvel; m++) {
-
+
density_lb[i][j][k] += f_lb[i][j][k][m];
-
+
u_lb[i][j][k][0] += f_lb[i][j][k][m]*e[m][0];
u_lb[i][j][k][1] += f_lb[i][j][k][m]*e[m][1];
u_lb[i][j][k][2] += f_lb[i][j][k][m]*e[m][2];
-
+
}
-
+
//For the on-lattice wall scheme, need to set this velocity to zero.
if(domain->periodicity[2]==0){
if(comm->myloc[2]==0){
@@ -2456,20 +2456,20 @@ void FixLbFluid::parametercalc_part(int xstart, int xend, int ystart, int yend,
u_lb[i][j][k][2]=0.0;
}
}
-
+
}
-
+
u_lb[i][j][k][0]=u_lb[i][j][k][0]/density_lb[i][j][k];
u_lb[i][j][k][1]=u_lb[i][j][k][1]/density_lb[i][j][k];
u_lb[i][j][k][2]=u_lb[i][j][k][2]/density_lb[i][j][k];
}
}
}
-
+
}
//==========================================================================
-// Update the distribution function over a simulation volume specified
+// Update the distribution function over a simulation volume specified
// by xstart,xend; ystart,yend; zstart,zend.
//==========================================================================
void FixLbFluid::update_periodic(int xstart, int xend, int ystart, int yend, int zstart, int zend)
@@ -2480,7 +2480,7 @@ void FixLbFluid::update_periodic(int xstart, int xend, int ystart, int yend, int
for(i=xstart; i<xend; i++)
for(j=ystart; j<yend; j++)
for(k=zstart; k<zend; k++){
-
+
if(typeLB==1){
for(m=0; m<numvel; m++){
imod = i-e[m][0];
@@ -2488,16 +2488,16 @@ void FixLbFluid::update_periodic(int xstart, int xend, int ystart, int yend, int
kmod = k-e[m][2];
fnew[i][j][k][m] = f_lb[imod][jmod][kmod][m] + (feq[imod][jmod][kmod][m]-f_lb[imod][jmod][kmod][m])/tau;
- }
+ }
}else if(typeLB==2){
for(m=0; m<numvel; m++){
imod = i-e[m][0];
jmod = j-e[m][1];
kmod = k-e[m][2];
-
+
fnew[i][j][k][m] = feq[imod][jmod][kmod][m] + (f_lb[imod][jmod][kmod][m] - feq[imod][jmod][kmod][m])*expminusdtovertau;
}
-
+
fnew[i][j][k][0]+=Dcoeff*(feq[i][j][k][0]-feqold[i][j][k][0]);
for(m=1; m<numvel; m++){
imod = i-e[m][0];
@@ -2506,13 +2506,13 @@ void FixLbFluid::update_periodic(int xstart, int xend, int ystart, int yend, int
imodm = i+e[m][0];
jmodm = j+e[m][1];
kmodm = k+e[m][2];
-
+
fnew[i][j][k][m] += Dcoeff*(feq[i][j][k][m] - feqold[imod][jmod][kmod][m]) + (0.5-Dcoeff*(tau+0.5))*
(feqn[imodm][jmodm][kmodm][m] - feqoldn[i][j][k][m] - feqn[i][j][k][m] + feqoldn[imod][jmod][kmod][m]);
}
- }
- }
+ }
+ }
}
//==========================================================================
@@ -2596,8 +2596,8 @@ void FixLbFluid::streamout(void)
for(k=0; k<Nbz; k++){
printf("%16.12f %16.12f %16.12f %16.12f\n",altogether[i][j][k][0]*dm_lb/dx_lb/dx_lb/dx_lb,altogether[i][j][k][1]*dx_lb/dt_lb,altogether[i][j][k][2]*dx_lb/dt_lb,altogether[i][j][k][3]*dx_lb/dt_lb);
}
-
-
+
+
} else {
istart=comm->myloc[0]*(subNbx-2);
jstart=comm->myloc[1]*(subNby-2);
@@ -2631,7 +2631,7 @@ void FixLbFluid::streamout(void)
buf[0][0][1][2]=kend;
MPI_Isend(&buf[0][0][0][0],size,MPI_DOUBLE,0,0,world,&request_send);
- MPI_Wait(&request_send,&status);
+ MPI_Wait(&request_send,&status);
}
}
@@ -2642,7 +2642,7 @@ void FixLbFluid::streamout(void)
//==========================================================================
void FixLbFluid::update_full15(void)
{
-
+
MPI_Request req_send15,req_recv15;
MPI_Request req_send25,req_recv25;
MPI_Request requests[8];
@@ -2662,12 +2662,12 @@ void FixLbFluid::update_full15(void)
}else{
numrequests = 8;
}
-
+
//--------------------------------------------------------------------------
// Fixed z boundary conditions.
//--------------------------------------------------------------------------
- if(domain->periodicity[2]==0){
-
+ if(domain->periodicity[2]==0){
+
for(i=0; i<numrequests; i++)
requests[i]=MPI_REQUEST_NULL;
MPI_Isend(&feq[1][1][1][0],1,passxf,comm->procneigh[0][0],15,world,&requests[0]);
@@ -2687,19 +2687,19 @@ void FixLbFluid::update_full15(void)
for(i=0; i<numrequests; i++)
requests[i]=MPI_REQUEST_NULL;
MPI_Isend(&feq[0][1][1][0],1,passyf,comm->procneigh[1][0],15,world,&requests[0]);
- MPI_Irecv(&feq[0][0][1][0],1,passyf,comm->procneigh[1][0],25,world,&requests[1]);
+ MPI_Irecv(&feq[0][0][1][0],1,passyf,comm->procneigh[1][0],25,world,&requests[1]);
MPI_Isend(&feq[0][subNby-2][1][0],1,passyf,comm->procneigh[1][1],25,world,&requests[2]);
MPI_Irecv(&feq[0][subNby-1][1][0],1,passyf,comm->procneigh[1][1],15,world,&requests[3]);
if(typeLB == 2){
MPI_Isend(&feqn[0][1][1][0],1,passyf,comm->procneigh[1][0],10,world,&requests[4]);
- MPI_Irecv(&feqn[0][0][1][0],1,passyf,comm->procneigh[1][0],20,world,&requests[5]);
+ MPI_Irecv(&feqn[0][0][1][0],1,passyf,comm->procneigh[1][0],20,world,&requests[5]);
MPI_Isend(&feqn[0][subNby-2][1][0],1,passyf,comm->procneigh[1][1],20,world,&requests[6]);
MPI_Irecv(&feqn[0][subNby-1][1][0],1,passyf,comm->procneigh[1][1],10,world,&requests[7]);
}
update_periodic(1,2,2,subNby-2,2,subNbz-2);
update_periodic(subNbx-2,subNbx-1,2,subNby-2,2,subNbz-2);
MPI_Waitall(numrequests,requests,MPI_STATUS_IGNORE);
-
+
for(i=0; i<numrequests; i++)
requests[i]=MPI_REQUEST_NULL;
MPI_Isend(&feq[0][0][1][0],1,passzf,comm->procneigh[2][0],15,world,&requests[0]);
@@ -2711,7 +2711,7 @@ void FixLbFluid::update_full15(void)
MPI_Irecv(&feqn[0][0][0][0],1,passzf,comm->procneigh[2][0],20,world,&requests[5]);
MPI_Isend(&feqn[0][0][subNbz-2][0],1,passzf,comm->procneigh[2][1],20,world,&requests[6]);
MPI_Irecv(&feqn[0][0][subNbz-1][0],1,passzf,comm->procneigh[2][1],10,world,&requests[7]);
- }
+ }
update_periodic(1,subNbx-1,1,2,2,subNbz-2);
update_periodic(1,subNbx-1,subNby-2,subNby-1,2,subNbz-2);
MPI_Waitall(numrequests,requests,MPI_STATUS_IGNORE);
@@ -2728,7 +2728,7 @@ void FixLbFluid::update_full15(void)
imod = i-e[m][0];
jmod = j-e[m][1];
kmod = k-e[m][2];
-
+
fnew[i][j][k][m] = feq[imod][jmod][kmod][m] + (f_lb[imod][jmod][kmod][m]-feq[imod][jmod][kmod][m])*expminusdtovertau;
}
@@ -2739,9 +2739,9 @@ void FixLbFluid::update_full15(void)
imodm = i+e[m][0];
jmodm = j+e[m][1];
kmodm = k+e[m][2];
-
+
if(m==5)
- fnew[i][j][k][m] += Dcoeff*(feq[imod][jmod][kmod][6] - feqold[imod][jmod][kmod][m]) +
+ fnew[i][j][k][m] += Dcoeff*(feq[imod][jmod][kmod][6] - feqold[imod][jmod][kmod][m]) +
(0.5-Dcoeff*(tau+0.5))*(feqoldn[imod][jmod][kmod][m] - feqoldn[imod][jmod][kmod][6] - feqn[imod][jmod][kmod][6]);
else if(m==7)
fnew[i][j][k][m] += Dcoeff*(feq[imod][jmod][kmod][11] - feqold[imod][jmod][kmod][m]) +
@@ -2760,23 +2760,23 @@ void FixLbFluid::update_full15(void)
(0.5-Dcoeff*(tau+0.5))*(feqn[i][j][k][5] - feqoldn[i][j][k][m] - feqn[i][j][k][m] + feqoldn[imod][jmod][kmod][m]);
else if(m==11)
fnew[i][j][k][m] += Dcoeff*(feq[i][j][k][m]-feqold[imod][jmod][kmod][m]) +
- (0.5-Dcoeff*(tau+0.5))*(feqn[i][j][k][7] - feqoldn[i][j][k][m] - feqn[i][j][k][m] + feqoldn[imod][jmod][kmod][m]);
+ (0.5-Dcoeff*(tau+0.5))*(feqn[i][j][k][7] - feqoldn[i][j][k][m] - feqn[i][j][k][m] + feqoldn[imod][jmod][kmod][m]);
else if(m==12)
fnew[i][j][k][m] += Dcoeff*(feq[i][j][k][m]-feqold[imod][jmod][kmod][m]) +
- (0.5-Dcoeff*(tau+0.5))*(feqn[i][j][k][8] - feqoldn[i][j][k][m] - feqn[i][j][k][m] + feqoldn[imod][jmod][kmod][m]);
+ (0.5-Dcoeff*(tau+0.5))*(feqn[i][j][k][8] - feqoldn[i][j][k][m] - feqn[i][j][k][m] + feqoldn[imod][jmod][kmod][m]);
else if(m==13)
fnew[i][j][k][m] += Dcoeff*(feq[i][j][k][m]-feqold[imod][jmod][kmod][m]) +
- (0.5-Dcoeff*(tau+0.5))*(feqn[i][j][k][9] - feqoldn[i][j][k][m] - feqn[i][j][k][m] + feqoldn[imod][jmod][kmod][m]);
+ (0.5-Dcoeff*(tau+0.5))*(feqn[i][j][k][9] - feqoldn[i][j][k][m] - feqn[i][j][k][m] + feqoldn[imod][jmod][kmod][m]);
else if(m==14)
fnew[i][j][k][m] += Dcoeff*(feq[i][j][k][m]-feqold[imod][jmod][kmod][m]) +
- (0.5-Dcoeff*(tau+0.5))*(feqn[i][j][k][10] - feqoldn[i][j][k][m] - feqn[i][j][k][m] + feqoldn[imod][jmod][kmod][m]);
+ (0.5-Dcoeff*(tau+0.5))*(feqn[i][j][k][10] - feqoldn[i][j][k][m] - feqn[i][j][k][m] + feqoldn[imod][jmod][kmod][m]);
else
- fnew[i][j][k][m] += Dcoeff*(feq[i][j][k][m] - feqold[imod][jmod][kmod][m]) +
+ fnew[i][j][k][m] += Dcoeff*(feq[i][j][k][m] - feqold[imod][jmod][kmod][m]) +
(0.5-Dcoeff*(tau+0.5))*(feqn[imodm][jmodm][kmodm][m] - feqoldn[i][j][k][m] - feqn[i][j][k][m] + feqoldn[imod][jmod][kmod][m]);
}
}
- }
+ }
}else{
update_periodic(1,subNbx-1,1,subNby-1,1,2);
}
@@ -2790,7 +2790,7 @@ void FixLbFluid::update_full15(void)
kmod = k-e[m][2];
fnew[i][j][k][m] = feq[imod][jmod][kmod][m] + (f_lb[imod][jmod][kmod][m]-feq[imod][jmod][kmod][m])*expminusdtovertau;
- }
+ }
for(m=0; m<15; m++){
imod = i-e[m][0];
jmod = j-e[m][1];
@@ -2798,9 +2798,9 @@ void FixLbFluid::update_full15(void)
imodm = i+e[m][0];
jmodm = j+e[m][1];
kmodm = k+e[m][2];
-
+
if(m==6)
- fnew[i][j][k][m] += Dcoeff*(feq[imod][jmod][kmod][5] - feqold[imod][jmod][kmod][m]) +
+ fnew[i][j][k][m] += Dcoeff*(feq[imod][jmod][kmod][5] - feqold[imod][jmod][kmod][m]) +
(0.5-Dcoeff*(tau+0.5))*(feqoldn[imod][jmod][kmod][m] - feqoldn[imod][jmod][kmod][5] - feqn[imod][jmod][kmod][5]);
else if(m==11)
fnew[i][j][k][m] += Dcoeff*(feq[imod][jmod][kmod][7] - feqold[imod][jmod][kmod][m]) +
@@ -2819,20 +2819,20 @@ void FixLbFluid::update_full15(void)
(0.5-Dcoeff*(tau+0.5))*(feqn[i][j][k][6] - feqoldn[i][j][k][m] - feqn[i][j][k][m] + feqoldn[imod][jmod][kmod][m]);
else if(m==7)
fnew[i][j][k][m] += Dcoeff*(feq[i][j][k][m] - feqold[imod][jmod][kmod][m]) +
- (0.5-Dcoeff*(tau+0.5))*(feqn[i][j][k][11] - feqoldn[i][j][k][m] - feqn[i][j][k][m] + feqoldn[imod][jmod][kmod][m]);
+ (0.5-Dcoeff*(tau+0.5))*(feqn[i][j][k][11] - feqoldn[i][j][k][m] - feqn[i][j][k][m] + feqoldn[imod][jmod][kmod][m]);
else if(m==8)
fnew[i][j][k][m] += Dcoeff*(feq[i][j][k][m] - feqold[imod][jmod][kmod][m]) +
- (0.5-Dcoeff*(tau+0.5))*(feqn[i][j][k][12] - feqoldn[i][j][k][m] - feqn[i][j][k][m] + feqoldn[imod][jmod][kmod][m]);
+ (0.5-Dcoeff*(tau+0.5))*(feqn[i][j][k][12] - feqoldn[i][j][k][m] - feqn[i][j][k][m] + feqoldn[imod][jmod][kmod][m]);
else if(m==9)
fnew[i][j][k][m] += Dcoeff*(feq[i][j][k][m] - feqold[imod][jmod][kmod][m]) +
- (0.5-Dcoeff*(tau+0.5))*(feqn[i][j][k][13] - feqoldn[i][j][k][m] - feqn[i][j][k][m] + feqoldn[imod][jmod][kmod][m]);
+ (0.5-Dcoeff*(tau+0.5))*(feqn[i][j][k][13] - feqoldn[i][j][k][m] - feqn[i][j][k][m] + feqoldn[imod][jmod][kmod][m]);
else if(m==10)
fnew[i][j][k][m] += Dcoeff*(feq[i][j][k][m] - feqold[imod][jmod][kmod][m]) +
- (0.5-Dcoeff*(tau+0.5))*(feqn[i][j][k][14] - feqoldn[i][j][k][m] - feqn[i][j][k][m] + feqoldn[imod][jmod][kmod][m]);
+ (0.5-Dcoeff*(tau+0.5))*(feqn[i][j][k][14] - feqoldn[i][j][k][m] - feqn[i][j][k][m] + feqoldn[imod][jmod][kmod][m]);
else
- fnew[i][j][k][m] += Dcoeff*(feq[i][j][k][m] - feqold[imod][jmod][kmod][m]) +
+ fnew[i][j][k][m] += Dcoeff*(feq[i][j][k][m] - feqold[imod][jmod][kmod][m]) +
(0.5-Dcoeff*(tau+0.5))*(feqn[imodm][jmodm][kmodm][m] - feqoldn[i][j][k][m] - feqn[i][j][k][m] + feqoldn[imod][jmod][kmod][m]);
-
+
}
}
}
@@ -2841,17 +2841,17 @@ void FixLbFluid::update_full15(void)
update_periodic(1,subNbx-1,1,subNby-1,subNbz-2,subNbz-1);
}
}
-
+
req_send15=MPI_REQUEST_NULL;
req_recv25=MPI_REQUEST_NULL;
req_send25=MPI_REQUEST_NULL;
req_recv15=MPI_REQUEST_NULL;
-
+
if(comm->myloc[2]==0){
MPI_Isend(&fnew[0][0][1][0],1,passzf,comm->procneigh[2][0],15,world,&req_send15);
MPI_Irecv(&fnew[0][0][0][0],1,passzf,comm->procneigh[2][0],25,world,&req_recv25);
}
-
+
if(comm->myloc[2]==comm->procgrid[2]-1){
MPI_Isend(&fnew[0][0][subNbz-2][0],1,passzf,comm->procneigh[2][1],25,world,&req_send25);
MPI_Irecv(&fnew[0][0][subNbz-1][0],1,passzf,comm->procneigh[2][1],15,world,&req_recv15);
@@ -2859,18 +2859,18 @@ void FixLbFluid::update_full15(void)
if(comm->myloc[2]==0){
MPI_Wait(&req_send15,&status);
MPI_Wait(&req_recv25,&status);
-
+
for(i=1;i<subNbx-1;i++){
for(j=1;j<subNby-1;j++){
k=1;
if(typeLB == 1){
fnew[i][j][k][5]=fnew[i][j][k-1][6];
- tmp1=fnew[i][j][k-1][11]+fnew[i][j][k-1][12]+fnew[i][j][k-1][13]+fnew[i][j][k-1][14];
+ tmp1=fnew[i][j][k-1][11]+fnew[i][j][k-1][12]+fnew[i][j][k-1][13]+fnew[i][j][k-1][14];
}
else{
fnew[i][j][k][5]=fnew[i][j][k-1][6] + (0.5-Dcoeff*(tau+0.5))*feqn[i][j][k+1][5];
- tmp1=fnew[i][j][k-1][11]+fnew[i][j][k-1][12]+fnew[i][j][k-1][13]+fnew[i][j][k-1][14] +
- (0.5-Dcoeff*(tau+0.5))*(feqn[i-1][j-1][k+1][7] + feqn[i+1][j-1][k+1][8] +
+ tmp1=fnew[i][j][k-1][11]+fnew[i][j][k-1][12]+fnew[i][j][k-1][13]+fnew[i][j][k-1][14] +
+ (0.5-Dcoeff*(tau+0.5))*(feqn[i-1][j-1][k+1][7] + feqn[i+1][j-1][k+1][8] +
feqn[i+1][j+1][k+1][9] + feqn[i-1][j+1][k+1][10]);
}
@@ -2888,7 +2888,7 @@ void FixLbFluid::update_full15(void)
rb=fnew[i][j][k][0]+fnew[i][j][k][1]+fnew[i][j][k][2]+fnew[i][j][k][3]+fnew[i][j][k][4]+
fnew[i][j][k][5]+fnew[i][j][k][6]+tmp1+fnew[i][j][k][11]+fnew[i][j][k][12]+
fnew[i][j][k][13]+fnew[i][j][k][14];
-
+
fnew[i][j][k][7] += 0.25*rb*vwbt;
fnew[i][j][k][8] += 0.25*rb*vwbt;
fnew[i][j][k][9] += -0.25*rb*vwbt;
@@ -2900,22 +2900,22 @@ void FixLbFluid::update_full15(void)
if(comm->myloc[2]==comm->procgrid[2]-1){
MPI_Wait(&req_send25,&status);
MPI_Wait(&req_recv15,&status);
-
+
for(i=1;i<subNbx-1;i++){
for(j=1;j<subNby-1;j++){
k=subNbz-2;
-
+
if(typeLB == 1){
fnew[i][j][k][6]=fnew[i][j][k+1][5];
tmp1=fnew[i][j][k+1][7]+fnew[i][j][k+1][8]+fnew[i][j][k+1][9]+fnew[i][j][k+1][10];
}
else{
fnew[i][j][k][6]=fnew[i][j][k+1][5] + (0.5-Dcoeff*(tau+0.5))*feqn[i][j][k-1][6];
- tmp1=fnew[i][j][k+1][7]+fnew[i][j][k+1][8]+fnew[i][j][k+1][9]+fnew[i][j][k+1][10] +
- (0.5-Dcoeff*(tau+0.5))*(feqn[i-1][j-1][k-1][11] + feqn[i+1][j-1][k-1][12] +
+ tmp1=fnew[i][j][k+1][7]+fnew[i][j][k+1][8]+fnew[i][j][k+1][9]+fnew[i][j][k+1][10] +
+ (0.5-Dcoeff*(tau+0.5))*(feqn[i-1][j-1][k-1][11] + feqn[i+1][j-1][k-1][12] +
feqn[i+1][j+1][k-1][13] + feqn[i-1][j+1][k-1][14]);
}
-
+
fnew[i][j][k][11]=-0.25*(fnew[i][j][k][1]+fnew[i][j][k][2]-fnew[i][j][k][3]-
fnew[i][j][k][4]+2.0*fnew[i][j][k][7]-2.0*fnew[i][j][k][9]-tmp1);
fnew[i][j][k][12]=0.25*(fnew[i][j][k][1]-fnew[i][j][k][2]-fnew[i][j][k][3]+
@@ -2925,19 +2925,19 @@ void FixLbFluid::update_full15(void)
fnew[i][j][k][14]=-0.25*(fnew[i][j][k][1]-fnew[i][j][k][2]-fnew[i][j][k][3]+
fnew[i][j][k][4]-2.0*fnew[i][j][k][8]+2.0*fnew[i][j][k][10]-tmp1);
-
+
rb=fnew[i][j][k][0]+fnew[i][j][k][1]+fnew[i][j][k][2]+fnew[i][j][k][3]+fnew[i][j][k][4]+
fnew[i][j][k][5]+fnew[i][j][k][6]+fnew[i][j][k][7]+fnew[i][j][k][8]+fnew[i][j][k][9]+
fnew[i][j][k][10]+tmp1;
-
+
fnew[i][j][k][11] += 0.25*rb*vwtp;
fnew[i][j][k][12] += 0.25*rb*vwtp;
fnew[i][j][k][13] += -0.25*rb*vwtp;
fnew[i][j][k][14] += -0.25*rb*vwtp;
}
- }
+ }
}
-
+
//--------------------------------------------------------------------------
// Periodic z boundary conditions.
//--------------------------------------------------------------------------
@@ -2961,12 +2961,12 @@ void FixLbFluid::update_full15(void)
for(i=0; i<numrequests; i++)
requests[i]=MPI_REQUEST_NULL;
MPI_Isend(&feq[0][1][1][0],1,passyf,comm->procneigh[1][0],15,world,&requests[0]);
- MPI_Irecv(&feq[0][0][1][0],1,passyf,comm->procneigh[1][0],25,world,&requests[1]);
+ MPI_Irecv(&feq[0][0][1][0],1,passyf,comm->procneigh[1][0],25,world,&requests[1]);
MPI_Isend(&feq[0][subNby-2][1][0],1,passyf,comm->procneigh[1][1],25,world,&requests[2]);
MPI_Irecv(&feq[0][subNby-1][1][0],1,passyf,comm->procneigh[1][1],15,world,&requests[3]);
if(typeLB == 2){
MPI_Isend(&feqn[0][1][1][0],1,passyf,comm->procneigh[1][0],10,world,&requests[4]);
- MPI_Irecv(&feqn[0][0][1][0],1,passyf,comm->procneigh[1][0],20,world,&requests[5]);
+ MPI_Irecv(&feqn[0][0][1][0],1,passyf,comm->procneigh[1][0],20,world,&requests[5]);
MPI_Isend(&feqn[0][subNby-2][1][0],1,passyf,comm->procneigh[1][1],20,world,&requests[6]);
MPI_Irecv(&feqn[0][subNby-1][1][0],1,passyf,comm->procneigh[1][1],10,world,&requests[7]);
}
@@ -2985,15 +2985,15 @@ void FixLbFluid::update_full15(void)
MPI_Irecv(&feqn[0][0][0][0],1,passzf,comm->procneigh[2][0],20,world,&requests[5]);
MPI_Isend(&feqn[0][0][subNbz-2][0],1,passzf,comm->procneigh[2][1],20,world,&requests[6]);
MPI_Irecv(&feqn[0][0][subNbz-1][0],1,passzf,comm->procneigh[2][1],10,world,&requests[7]);
- }
+ }
update_periodic(1,subNbx-1,1,2,2,subNbz-2);
update_periodic(1,subNbx-1,subNby-2,subNby-1,2,subNbz-2);
MPI_Waitall(numrequests,requests,MPI_STATUS_IGNORE);
-
+
update_periodic(1,subNbx-1,1,subNby-1,1,2);
update_periodic(1,subNbx-1,1,subNby-1,subNbz-2,subNbz-1);
}
-
+
}
//==========================================================================
@@ -3002,7 +3002,7 @@ void FixLbFluid::update_full15(void)
//==========================================================================
void FixLbFluid::update_full19(void)
{
-
+
MPI_Request req_send15,req_recv15;
MPI_Request req_send25,req_recv25;
MPI_Request requests[8];
@@ -3013,7 +3013,7 @@ void FixLbFluid::update_full19(void)
int i,j,k,m;
int imod,jmod,kmod;
int imodm,jmodm,kmodm;
-
+
//--------------------------------------------------------------------------
// If using the standard LB integrator, do not need to send info about feqn.
//--------------------------------------------------------------------------
@@ -3022,12 +3022,12 @@ void FixLbFluid::update_full19(void)
}else{
numrequests = 8;
}
-
+
//--------------------------------------------------------------------------
// Fixed z boundary conditions.
//--------------------------------------------------------------------------
- if(domain->periodicity[2]==0){
-
+ if(domain->periodicity[2]==0){
+
for(i=0; i<numrequests; i++)
requests[i]=MPI_REQUEST_NULL;
MPI_Isend(&feq[1][1][1][0],1,passxf,comm->procneigh[0][0],15,world,&requests[0]);
@@ -3042,23 +3042,23 @@ void FixLbFluid::update_full19(void)
}
update_periodic(2,subNbx-2,2,subNby-2,2,subNbz-2);
MPI_Waitall(numrequests,requests,MPI_STATUS_IGNORE);
-
+
for(i=0; i<numrequests; i++)
requests[i]=MPI_REQUEST_NULL;
MPI_Isend(&feq[0][1][1][0],1,passyf,comm->procneigh[1][0],15,world,&requests[0]);
- MPI_Irecv(&feq[0][0][1][0],1,passyf,comm->procneigh[1][0],25,world,&requests[1]);
+ MPI_Irecv(&feq[0][0][1][0],1,passyf,comm->procneigh[1][0],25,world,&requests[1]);
MPI_Isend(&feq[0][subNby-2][1][0],1,passyf,comm->procneigh[1][1],25,world,&requests[2]);
MPI_Irecv(&feq[0][subNby-1][1][0],1,passyf,comm->procneigh[1][1],15,world,&requests[3]);
if(typeLB == 2){
MPI_Isend(&feqn[0][1][1][0],1,passyf,comm->procneigh[1][0],10,world,&requests[4]);
- MPI_Irecv(&feqn[0][0][1][0],1,passyf,comm->procneigh[1][0],20,world,&requests[5]);
+ MPI_Irecv(&feqn[0][0][1][0],1,passyf,comm->procneigh[1][0],20,world,&requests[5]);
MPI_Isend(&feqn[0][subNby-2][1][0],1,passyf,comm->procneigh[1][1],20,world,&requests[6]);
MPI_Irecv(&feqn[0][subNby-1][1][0],1,passyf,comm->procneigh[1][1],10,world,&requests[7]);
}
update_periodic(1,2,2,subNby-2,2,subNbz-2);
update_periodic(subNbx-2,subNbx-1,2,subNby-2,2,subNbz-2);
MPI_Waitall(numrequests,requests,MPI_STATUS_IGNORE);
-
+
for(i=0; i<numrequests; i++)
requests[i]=MPI_REQUEST_NULL;
MPI_Isend(&feq[0][0][1][0],1,passzf,comm->procneigh[2][0],15,world,&requests[0]);
@@ -3070,11 +3070,11 @@ void FixLbFluid::update_full19(void)
MPI_Irecv(&feqn[0][0][0][0],1,passzf,comm->procneigh[2][0],20,world,&requests[5]);
MPI_Isend(&feqn[0][0][subNbz-2][0],1,passzf,comm->procneigh[2][1],20,world,&requests[6]);
MPI_Irecv(&feqn[0][0][subNbz-1][0],1,passzf,comm->procneigh[2][1],10,world,&requests[7]);
- }
+ }
update_periodic(1,subNbx-1,1,2,2,subNbz-2);
update_periodic(1,subNbx-1,subNby-2,subNby-1,2,subNbz-2);
MPI_Waitall(numrequests,requests,MPI_STATUS_IGNORE);
-
+
if(typeLB==1){
update_periodic(1,subNbx-1,1,subNby-1,1,2);
update_periodic(1,subNbx-1,1,subNby-1,subNbz-2,subNbz-1);
@@ -3087,10 +3087,10 @@ void FixLbFluid::update_full19(void)
imod = i-e[m][0];
jmod = j-e[m][1];
kmod = k-e[m][2];
-
+
fnew[i][j][k][m] = feq[imod][jmod][kmod][m] + (f_lb[imod][jmod][kmod][m]-feq[imod][jmod][kmod][m])*expminusdtovertau;
}
-
+
for(m=0; m<19; m++){
imod = i-e[m][0];
jmod = j-e[m][1];
@@ -3098,9 +3098,9 @@ void FixLbFluid::update_full19(void)
imodm = i+e[m][0];
jmodm = j+e[m][1];
kmodm = k+e[m][2];
-
+
if(m==5)
- fnew[i][j][k][m] += Dcoeff*(feq[imod][jmod][kmod][6] - feqold[imod][jmod][kmod][m]) +
+ fnew[i][j][k][m] += Dcoeff*(feq[imod][jmod][kmod][6] - feqold[imod][jmod][kmod][m]) +
(0.5-Dcoeff*(tau+0.5))*(feqoldn[imod][jmod][kmod][m] - feqoldn[imod][jmod][kmod][6] - feqn[imod][jmod][kmod][6]);
else if(m==11)
fnew[i][j][k][m] += Dcoeff*(feq[imod][jmod][kmod][12] - feqold[imod][jmod][kmod][m]) +
@@ -3130,11 +3130,11 @@ void FixLbFluid::update_full19(void)
fnew[i][j][k][m] += Dcoeff*(feq[i][j][k][m] - feqold[imod][jmod][kmod][m]) +
(0.5-Dcoeff*(tau+0.5))*(feqn[i][j][k][17] - feqoldn[i][j][k][m] - feqn[i][j][k][m] + feqoldn[imod][jmod][kmod][m]);
else
- fnew[i][j][k][m] += Dcoeff*(feq[i][j][k][m] - feqold[imod][jmod][kmod][m]) +
+ fnew[i][j][k][m] += Dcoeff*(feq[i][j][k][m] - feqold[imod][jmod][kmod][m]) +
(0.5-Dcoeff*(tau+0.5))*(feqn[imodm][jmodm][kmodm][m] - feqoldn[i][j][k][m] - feqn[i][j][k][m] + feqoldn[imod][jmod][kmod][m]);
}
}
- }
+ }
}else{
update_periodic(1,subNbx-1,1,subNby-1,1,2);
}
@@ -3146,9 +3146,9 @@ void FixLbFluid::update_full19(void)
imod = i-e[m][0];
jmod = j-e[m][1];
kmod = k-e[m][2];
-
+
fnew[i][j][k][m] = feq[imod][jmod][kmod][m] + (f_lb[imod][jmod][kmod][m]-feq[imod][jmod][kmod][m])*expminusdtovertau;
- }
+ }
for(m=0; m<19; m++){
imod = i-e[m][0];
jmod = j-e[m][1];
@@ -3156,40 +3156,40 @@ void FixLbFluid::update_full19(void)
imodm = i+e[m][0];
jmodm = j+e[m][1];
kmodm = k+e[m][2];
-
+
if(m==6)
- fnew[i][j][k][m] += Dcoeff*(feq[imod][jmod][kmod][5] - feqold[imod][jmod][kmod][m]) +
+ fnew[i][j][k][m] += Dcoeff*(feq[imod][jmod][kmod][5] - feqold[imod][jmod][kmod][m]) +
(0.5-Dcoeff*(tau+0.5))*(feqoldn[imod][jmod][kmod][m] - feqoldn[imod][jmod][kmod][5] - feqn[imod][jmod][kmod][5]);
else if(m==12)
- fnew[i][j][k][m] += Dcoeff*(feq[imod][jmod][kmod][11] - feqold[imod][jmod][kmod][m]) +
+ fnew[i][j][k][m] += Dcoeff*(feq[imod][jmod][kmod][11] - feqold[imod][jmod][kmod][m]) +
(0.5-Dcoeff*(tau+0.5))*(feqoldn[imod][jmod][kmod][m] - feqoldn[imod][jmod][kmod][11] - feqn[imod][jmod][kmod][11]);
else if(m==14)
- fnew[i][j][k][m] += Dcoeff*(feq[imod][jmod][kmod][13] - feqold[imod][jmod][kmod][m]) +
+ fnew[i][j][k][m] += Dcoeff*(feq[imod][jmod][kmod][13] - feqold[imod][jmod][kmod][m]) +
(0.5-Dcoeff*(tau+0.5))*(feqoldn[imod][jmod][kmod][m] - feqoldn[imod][jmod][kmod][13] - feqn[imod][jmod][kmod][13]);
else if(m==16)
- fnew[i][j][k][m] += Dcoeff*(feq[imod][jmod][kmod][15] - feqold[imod][jmod][kmod][m]) +
+ fnew[i][j][k][m] += Dcoeff*(feq[imod][jmod][kmod][15] - feqold[imod][jmod][kmod][m]) +
(0.5-Dcoeff*(tau+0.5))*(feqoldn[imod][jmod][kmod][m] - feqoldn[imod][jmod][kmod][15] - feqn[imod][jmod][kmod][15]);
else if(m==18)
- fnew[i][j][k][m] += Dcoeff*(feq[imod][jmod][kmod][17] - feqold[imod][jmod][kmod][m]) +
+ fnew[i][j][k][m] += Dcoeff*(feq[imod][jmod][kmod][17] - feqold[imod][jmod][kmod][m]) +
(0.5-Dcoeff*(tau+0.5))*(feqoldn[imod][jmod][kmod][m] - feqoldn[imod][jmod][kmod][17] - feqn[imod][jmod][kmod][17]);
else if(m==5)
fnew[i][j][k][m] += Dcoeff*(feq[i][j][k][m] - feqold[imod][jmod][kmod][m]) +
- (0.5-Dcoeff*(tau+0.5))*(feqn[i][j][k][6] - feqoldn[i][j][k][m] - feqn[i][j][k][m] + feqoldn[imod][jmod][kmod][m]);
+ (0.5-Dcoeff*(tau+0.5))*(feqn[i][j][k][6] - feqoldn[i][j][k][m] - feqn[i][j][k][m] + feqoldn[imod][jmod][kmod][m]);
else if(m==11)
fnew[i][j][k][m] += Dcoeff*(feq[i][j][k][m] - feqold[imod][jmod][kmod][m]) +
- (0.5-Dcoeff*(tau+0.5))*(feqn[i][j][k][12] - feqoldn[i][j][k][m] - feqn[i][j][k][m] + feqoldn[imod][jmod][kmod][m]);
+ (0.5-Dcoeff*(tau+0.5))*(feqn[i][j][k][12] - feqoldn[i][j][k][m] - feqn[i][j][k][m] + feqoldn[imod][jmod][kmod][m]);
else if(m==13)
fnew[i][j][k][m] += Dcoeff*(feq[i][j][k][m] - feqold[imod][jmod][kmod][m]) +
- (0.5-Dcoeff*(tau+0.5))*(feqn[i][j][k][14] - feqoldn[i][j][k][m] - feqn[i][j][k][m] + feqoldn[imod][jmod][kmod][m]);
+ (0.5-Dcoeff*(tau+0.5))*(feqn[i][j][k][14] - feqoldn[i][j][k][m] - feqn[i][j][k][m] + feqoldn[imod][jmod][kmod][m]);
else if(m==15)
fnew[i][j][k][m] += Dcoeff*(feq[i][j][k][m] - feqold[imod][jmod][kmod][m]) +
(0.5-Dcoeff*(tau+0.5))*(feqn[i][j][k][16] - feqoldn[i][j][k][m] - feqn[i][j][k][m] + feqoldn[imod][jmod][kmod][m]);
else if(m==17)
fnew[i][j][k][m] += Dcoeff*(feq[i][j][k][m] - feqold[imod][jmod][kmod][m]) +
- (0.5-Dcoeff*(tau+0.5))*(feqn[i][j][k][18] - feqoldn[i][j][k][m] - feqn[i][j][k][m] + feqoldn[imod][jmod][kmod][m]);
+ (0.5-Dcoeff*(tau+0.5))*(feqn[i][j][k][18] - feqoldn[i][j][k][m] - feqn[i][j][k][m] + feqoldn[imod][jmod][kmod][m]);
else
- fnew[i][j][k][m] += Dcoeff*(feq[i][j][k][m] - feqold[imod][jmod][kmod][m]) +
- (0.5-Dcoeff*(tau+0.5))*(feqn[imodm][jmodm][kmodm][m] - feqoldn[i][j][k][m] - feqn[i][j][k][m] + feqoldn[imod][jmod][kmod][m]);
+ fnew[i][j][k][m] += Dcoeff*(feq[i][j][k][m] - feqold[imod][jmod][kmod][m]) +
+ (0.5-Dcoeff*(tau+0.5))*(feqn[imodm][jmodm][kmodm][m] - feqoldn[i][j][k][m] - feqn[i][j][k][m] + feqoldn[imod][jmod][kmod][m]);
}
}
}
@@ -3198,17 +3198,17 @@ void FixLbFluid::update_full19(void)
update_periodic(1,subNbx-1,1,subNby-1,subNbz-2,subNbz-1);
}
}
-
+
req_send15=MPI_REQUEST_NULL;
req_recv25=MPI_REQUEST_NULL;
req_send25=MPI_REQUEST_NULL;
req_recv15=MPI_REQUEST_NULL;
-
+
if(comm->myloc[2]==0){
MPI_Isend(&fnew[0][0][1][0],1,passzf,comm->procneigh[2][0],15,world,&req_send15);
MPI_Irecv(&fnew[0][0][0][0],1,passzf,comm->procneigh[2][0],25,world,&req_recv25);
}
-
+
if(comm->myloc[2]==comm->procgrid[2]-1){
MPI_Isend(&fnew[0][0][subNbz-2][0],1,passzf,comm->procneigh[2][1],25,world,&req_send25);
MPI_Irecv(&fnew[0][0][subNbz-1][0],1,passzf,comm->procneigh[2][1],15,world,&req_recv15);
@@ -3216,11 +3216,11 @@ void FixLbFluid::update_full19(void)
if(comm->myloc[2]==0){
MPI_Wait(&req_send15,&status);
MPI_Wait(&req_recv25,&status);
-
+
for(i=1;i<subNbx-1;i++){
for(j=1;j<subNby-1;j++){
k=1;
-
+
if(typeLB == 1){
fnew[i][j][k][5]=fnew[i][j][k-1][6];
tmp1=fnew[i][j][k-1][12]+fnew[i][j][k-1][14]+fnew[i][j][k-1][16]+fnew[i][j][k-1][18];
@@ -3228,36 +3228,36 @@ void FixLbFluid::update_full19(void)
else{
fnew[i][j][k][5]=fnew[i][j][k-1][6] + (0.5-Dcoeff*(tau+0.5))*feqn[i][j][k+1][5];
tmp1=fnew[i][j][k-1][12]+fnew[i][j][k-1][14]+fnew[i][j][k-1][16]+fnew[i][j][k-1][18] +
- (0.5-Dcoeff*(tau+0.5))*(feqn[i-1][j][k+1][11] + feqn[i+1][j][k+1][13] +
- feqn[i][j-1][k+1][15] + feqn[i][j+1][k+1][17]);
+ (0.5-Dcoeff*(tau+0.5))*(feqn[i-1][j][k+1][11] + feqn[i+1][j][k+1][13] +
+ feqn[i][j-1][k+1][15] + feqn[i][j+1][k+1][17]);
}
-
+
tmp2=fnew[i][j][k][3]+fnew[i][j][k][9]+fnew[i][j][k][10]+fnew[i][j][k][14]-
fnew[i][j][k][1]-fnew[i][j][k][7]-fnew[i][j][k][8]-fnew[i][j][k][12];
-
+
rb=fnew[i][j][k][0]+fnew[i][j][k][1]+fnew[i][j][k][2]+fnew[i][j][k][3]+fnew[i][j][k][4]+
fnew[i][j][k][5]+fnew[i][j][k][6]+fnew[i][j][k][7]+fnew[i][j][k][8]+fnew[i][j][k][9]+
fnew[i][j][k][10]+fnew[i][j][k][12]+fnew[i][j][k][14]+fnew[i][j][k][16]+fnew[i][j][k][18]+tmp1;
-
+
tmp3=rb*vwbt-fnew[i][j][k][2]+fnew[i][j][k][4]-fnew[i][j][k][7]+fnew[i][j][k][8]-fnew[i][j][k][9]+
fnew[i][j][k][10]-fnew[i][j][k][16]+fnew[i][j][k][18];
-
+
fnew[i][j][k][11] = 0.25*(tmp1+2.0*tmp2);
fnew[i][j][k][13] = 0.25*(tmp1-2.0*tmp2);
fnew[i][j][k][15] = 0.25*(tmp1+2.0*tmp3);
fnew[i][j][k][17] = 0.25*(tmp1-2.0*tmp3);
}
}
-
+
}
if(comm->myloc[2]==comm->procgrid[2]-1){
MPI_Wait(&req_send25,&status);
MPI_Wait(&req_recv15,&status);
-
+
for(i=1;i<subNbx-1;i++){
for(j=1;j<subNby-1;j++){
k=subNbz-2;
-
+
if(typeLB == 1){
fnew[i][j][k][6]=fnew[i][j][k+1][5];
tmp1=fnew[i][j][k+1][11]+fnew[i][j][k+1][13]+fnew[i][j][k+1][15]+fnew[i][j][k+1][17];
@@ -3265,33 +3265,33 @@ void FixLbFluid::update_full19(void)
else{
fnew[i][j][k][6]=fnew[i][j][k+1][5] + (0.5-Dcoeff*(tau+0.5))*feqn[i][j][k-1][6];
tmp1=fnew[i][j][k+1][11]+fnew[i][j][k+1][13]+fnew[i][j][k+1][15]+fnew[i][j][k+1][17] +
- (0.5-Dcoeff*(tau+0.5))*(feqn[i-1][j][k-1][12] + feqn[i+1][j][k-1][14] +
+ (0.5-Dcoeff*(tau+0.5))*(feqn[i-1][j][k-1][12] + feqn[i+1][j][k-1][14] +
feqn[i][j-1][k-1][16] + feqn[i][j+1][k-1][18]);
}
-
+
tmp2=fnew[i][j][k][3]+fnew[i][j][k][9]+fnew[i][j][k][10]+fnew[i][j][k][13]-fnew[i][j][k][1]-
fnew[i][j][k][7]-fnew[i][j][k][8]-fnew[i][j][k][11];
-
+
rb=fnew[i][j][k][0]+fnew[i][j][k][1]+fnew[i][j][k][2]+fnew[i][j][k][3]+fnew[i][j][k][4]+
fnew[i][j][k][5]+fnew[i][j][k][6]+fnew[i][j][k][7]+fnew[i][j][k][8]+fnew[i][j][k][9]+
fnew[i][j][k][10]+fnew[i][j][k][11]+fnew[i][j][k][13]+fnew[i][j][k][15]+fnew[i][j][k][17]+tmp1;
-
+
tmp3=rb*vwtp-fnew[i][j][k][2]+fnew[i][j][k][4]-fnew[i][j][k][7]+fnew[i][j][k][8]-fnew[i][j][k][9]+
fnew[i][j][k][10]-fnew[i][j][k][15]+fnew[i][j][k][17];
-
+
fnew[i][j][k][12] = 0.25*(tmp1+2.0*tmp2);
fnew[i][j][k][14] = 0.25*(tmp1-2.0*tmp2);
fnew[i][j][k][16] = 0.25*(tmp1+2.0*tmp3);
fnew[i][j][k][18] = 0.25*(tmp1-2.0*tmp3);
}
- }
+ }
}
-
+
//--------------------------------------------------------------------------
// Periodic z boundary conditions.
//--------------------------------------------------------------------------
}else {
-
+
for(i=0; i<numrequests; i++)
requests[i]=MPI_REQUEST_NULL;
MPI_Isend(&feq[1][1][1][0],1,passxf,comm->procneigh[0][0],15,world,&requests[0]);
@@ -3306,23 +3306,23 @@ void FixLbFluid::update_full19(void)
}
update_periodic(2,subNbx-2,2,subNby-2,2,subNbz-2);
MPI_Waitall(numrequests,requests,MPI_STATUS_IGNORE);
-
+
for(i=0; i<numrequests; i++)
requests[i]=MPI_REQUEST_NULL;
MPI_Isend(&feq[0][1][1][0],1,passyf,comm->procneigh[1][0],15,world,&requests[0]);
- MPI_Irecv(&feq[0][0][1][0],1,passyf,comm->procneigh[1][0],25,world,&requests[1]);
+ MPI_Irecv(&feq[0][0][1][0],1,passyf,comm->procneigh[1][0],25,world,&requests[1]);
MPI_Isend(&feq[0][subNby-2][1][0],1,passyf,comm->procneigh[1][1],25,world,&requests[2]);
MPI_Irecv(&feq[0][subNby-1][1][0],1,passyf,comm->procneigh[1][1],15,world,&requests[3]);
if(typeLB == 2){
MPI_Isend(&feqn[0][1][1][0],1,passyf,comm->procneigh[1][0],10,world,&requests[4]);
- MPI_Irecv(&feqn[0][0][1][0],1,passyf,comm->procneigh[1][0],20,world,&requests[5]);
+ MPI_Irecv(&feqn[0][0][1][0],1,passyf,comm->procneigh[1][0],20,world,&requests[5]);
MPI_Isend(&feqn[0][subNby-2][1][0],1,passyf,comm->procneigh[1][1],20,world,&requests[6]);
MPI_Irecv(&feqn[0][subNby-1][1][0],1,passyf,comm->procneigh[1][1],10,world,&requests[7]);
}
update_periodic(1,2,2,subNby-2,2,subNbz-2);
update_periodic(subNbx-2,subNbx-1,2,subNby-2,2,subNbz-2);
MPI_Waitall(numrequests,requests,MPI_STATUS_IGNORE);
-
+
for(i=0; i<numrequests; i++)
requests[i]=MPI_REQUEST_NULL;
MPI_Isend(&feq[0][0][1][0],1,passzf,comm->procneigh[2][0],15,world,&requests[0]);
@@ -3334,15 +3334,15 @@ void FixLbFluid::update_full19(void)
MPI_Irecv(&feqn[0][0][0][0],1,passzf,comm->procneigh[2][0],20,world,&requests[5]);
MPI_Isend(&feqn[0][0][subNbz-2][0],1,passzf,comm->procneigh[2][1],20,world,&requests[6]);
MPI_Irecv(&feqn[0][0][subNbz-1][0],1,passzf,comm->procneigh[2][1],10,world,&requests[7]);
- }
+ }
update_periodic(1,subNbx-1,1,2,2,subNbz-2);
update_periodic(1,subNbx-1,subNby-2,subNby-1,2,subNbz-2);
MPI_Waitall(numrequests,requests,MPI_STATUS_IGNORE);
-
+
update_periodic(1,subNbx-1,1,subNby-1,1,2);
update_periodic(1,subNbx-1,1,subNby-1,subNbz-2,subNbz-1);
}
-
+
}
diff --git a/src/USER-LB/fix_lb_fluid.h b/src/USER-LB/fix_lb_fluid.h
index 98bb650477..8d81648e47 100755
--- a/src/USER-LB/fix_lb_fluid.h
+++ b/src/USER-LB/fix_lb_fluid.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
For more info, see the README file in the top-level LAMMPS directory.
@@ -15,7 +15,7 @@
FixStyle(lb/fluid,FixLbFluid)
-#else
+#else
#ifndef LMP_FIX_LB_FLUID_H
#define LMP_FIX_LB_FLUID_H
@@ -57,7 +57,7 @@ public:
double dm_lb,dx_lb,dt_lb; // Lattice units for mass, distance, time.
int Nbx,Nby,Nbz; // Total # of x,y,z grid points.
- int subNbx,subNby,subNbz; // # of x,y,z, grid points (including buffer)
+ int subNbx,subNby,subNbz; // # of x,y,z, grid points (including buffer)
// on local processor.
int me, nprocs; // MPI variables: processor ID, # of processors
MPI_Datatype oneslice; // MPI datatypes to pass arrays.
@@ -66,9 +66,9 @@ public:
MPI_Datatype passxrho,passyrho,passzrho;
MPI_Datatype passxtemp,passytemp,passztemp;
- double kB,densityinit,a_0; // Boltzmann constant, initial density,
+ double kB,densityinit,a_0; // Boltzmann constant, initial density,
// and a_0 all in lattice units.
- double *Gamma;
+ double *Gamma;
double *NodeArea;
int setGamma,setArea;
double **hydroF;
@@ -78,21 +78,21 @@ public:
double ***density_lb; // fluid density
double ****u_lb; // fluid velocity
double ****f_lb; // distributions
- double ****fnew; // used in the calculation of the new
+ double ****fnew; // used in the calculation of the new
// distributions.
double ****feq; // equilibrium distributions
- double ****feqold; // equilibrium distributions from previous
+ double ****feqold; // equilibrium distributions from previous
// timestep
double ****feqn; // equilibrium distributions without noise.
- double ****feqoldn; // equilibrium distributions from previous
+ double ****feqoldn; // equilibrium distributions from previous
// timestep without noise.
double ****Ff; // Force from the MD particles on the fluid.
double ****Fftempx;
double ****Fftempy;
double ****Fftempz;
- double *Ng_lb; // Lattice Boltzmann variables.
+ double *Ng_lb; // Lattice Boltzmann variables.
double *w_lb;
double **mg_lb;
int **e;
@@ -110,28 +110,28 @@ public:
double ****altogether2;
double bodyforcex,bodyforcey,bodyforcez; // Body Forces acting on the fluid (default=0)
- double vwtp,vwbt; // Velocities of the z walls in the y
- // direction. (must have fixed boundary
+ double vwtp,vwbt; // Velocities of the z walls in the y
+ // direction. (must have fixed boundary
// conditions in z)
- int noisestress; // 1 to include noise in the system,
+ int noisestress; // 1 to include noise in the system,
// 0 otherwise.
double namp,noisefactor;
int seed;
class RanMars *random;
- int force_diagnostic; // 1 to print out the force action on a group
+ int force_diagnostic; // 1 to print out the force action on a group
// of particles, 0 otherwise.
- int igroupforce; // the group for which the force is to be
+ int igroupforce; // the group for which the force is to be
// printed.
- int typeLB;
-
- int trilinear_stencil; // 1 to use the trilinear stencil, 0 to use the
+ int typeLB;
+
+ int trilinear_stencil; // 1 to use the trilinear stencil, 0 to use the
// peskin stencil.
int readrestart; // 1 to read in data from a restart file.
- MPI_File pFileRead;
+ MPI_File pFileRead;
int printrestart; // 1 to write data to a restart file.
MPI_File pFileWrite;
@@ -164,4 +164,4 @@ public:
}
#endif
#endif
-
+
diff --git a/src/USER-LB/fix_lb_momentum.cpp b/src/USER-LB/fix_lb_momentum.cpp
index 63c89fe040..18d98edda8 100755
--- a/src/USER-LB/fix_lb_momentum.cpp
+++ b/src/USER-LB/fix_lb_momentum.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -18,8 +18,8 @@
Contributing author: Naveen Michaud-Agrawal (Johns Hopkins U)
------------------------------------------------------------------------- */
-#include "stdlib.h"
-#include "string.h"
+#include <stdlib.h>
+#include <string.h>
#include "fix_lb_momentum.h"
#include "atom.h"
#include "domain.h"
@@ -63,7 +63,7 @@ FixLbMomentum::FixLbMomentum(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,"Illegal fix lb/momentum command");
if (linear)
- if (xflag < 0 || xflag > 1 || yflag < 0 || yflag > 1 ||
+ if (xflag < 0 || xflag > 1 || yflag < 0 || yflag > 1 ||
zflag < 0 || zflag > 1) error->all(FLERR,"Illegal fix lb/momentum command");
// cannot have 0 atoms in group
@@ -74,7 +74,7 @@ FixLbMomentum::FixLbMomentum(LAMMPS *lmp, int narg, char **arg) :
for(int ifix=0; ifix<modify->nfix; ifix++)
if(strcmp(modify->fix[ifix]->style,"lb/fluid")==0)
fix_lb_fluid = (FixLbFluid *)modify->fix[ifix];
-
+
}
@@ -146,7 +146,7 @@ void FixLbMomentum::end_of_step()
}
MPI_Allreduce(&masslbloc,&masslb,1,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(&momentumlbloc[0],&momentumlb[0],3,MPI_DOUBLE,MPI_SUM,world);
-
+
momentumlb[0] *= dm_lb*dx_lb/dt_lb;
momentumlb[1] *= dm_lb*dx_lb/dt_lb;
momentumlb[2] *= dm_lb*dx_lb/dt_lb;
@@ -156,7 +156,7 @@ void FixLbMomentum::end_of_step()
vcmtotal[0] = (masstotal*vcm[0] + momentumlb[0])/(masslb + masstotal);
vcmtotal[1] = (masstotal*vcm[1] + momentumlb[1])/(masslb + masstotal);
vcmtotal[2] = (masstotal*vcm[2] + momentumlb[2])/(masslb + masstotal);
-
+
//Subtract vcm from the particles.
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
@@ -200,7 +200,7 @@ void FixLbMomentum::end_of_step()
u_lb[i][j][k][0]*ucmy*ucmz+ucmx*u_lb[i][j][k][1]*u_lb[i][j][k][2]-
ucmx*u_lb[i][j][k][1]*ucmz-ucmx*ucmy*u_lb[i][j][k][2]+
ucmx*ucmy*ucmz);
- etacov[14]=0.0;
+ etacov[14]=0.0;
}else{
etacov[0] = 0.0;
etacov[1] = rho*ucmx;
@@ -212,8 +212,8 @@ void FixLbMomentum::end_of_step()
etacov[7]=rho*(u_lb[i][j][k][0]*ucmy+u_lb[i][j][k][1]*ucmx-ucmx*ucmy);
etacov[8]=rho*(u_lb[i][j][k][0]*ucmz+u_lb[i][j][k][2]*ucmx-ucmx*ucmz);
etacov[9]=rho*(u_lb[i][j][k][1]*ucmz+u_lb[i][j][k][2]*ucmy-ucmy*ucmz);
- etacov[10] = 0.0;
- etacov[11] = 0.0;
+ etacov[10] = 0.0;
+ etacov[11] = 0.0;
etacov[12] = 0.0;
etacov[13] = 0.0;
etacov[14] = 0.0;
@@ -221,13 +221,13 @@ void FixLbMomentum::end_of_step()
etacov[16] = 0.0;
etacov[17] = 0.0;
etacov[18] = 0.0;
- }
+ }
for(int l=0; l<numvel; l++)
for(int ii=0; ii<numvel; ii++){
f_lb[i][j][k][l] -= w_lb[l]*mg_lb[ii][l]*etacov[ii]*Ng_lb[ii];
- }
-
+ }
+
if(typeLB == 2){
double ****feqold = fix_lb_fluid->feqold;
@@ -243,7 +243,7 @@ void FixLbMomentum::end_of_step()
u_old[0] = u_old[0]/density_old;
u_old[1] = u_old[1]/density_old;
u_old[2] = u_old[2]/density_old;
-
+
if(numvel==15){
etacov[0]=0.0;
etacov[1]=density_old*ucmx;
@@ -262,7 +262,7 @@ void FixLbMomentum::end_of_step()
u_old[0]*ucmy*ucmz+ucmx*u_old[1]*u_old[2]-
ucmx*u_old[1]*ucmz-ucmx*ucmy*u_old[2]+
ucmx*ucmy*ucmz);
- etacov[14]=0.0;
+ etacov[14]=0.0;
}else{
etacov[0] = 0.0;
etacov[1] = density_old*ucmx;
@@ -274,8 +274,8 @@ void FixLbMomentum::end_of_step()
etacov[7] = density_old*(u_lb[i][j][k][0]*ucmy+u_lb[i][j][k][1]*ucmx-ucmx*ucmy);
etacov[8] = density_old*(u_lb[i][j][k][0]*ucmz+u_lb[i][j][k][2]*ucmx-ucmx*ucmz);
etacov[9] = density_old*(u_lb[i][j][k][1]*ucmz+u_lb[i][j][k][2]*ucmy-ucmy*ucmz);
- etacov[10] = 0.0;
- etacov[11] = 0.0;
+ etacov[10] = 0.0;
+ etacov[11] = 0.0;
etacov[12] = 0.0;
etacov[13] = 0.0;
etacov[14] = 0.0;
@@ -284,13 +284,13 @@ void FixLbMomentum::end_of_step()
etacov[17] = 0.0;
etacov[18] = 0.0;
}
-
+
for(int l=0; l<numvel; l++)
for(int ii=0; ii<numvel; ii++){
feqold[i][j][k][l] -= w_lb[l]*mg_lb[ii][l]*etacov[ii]*Ng_lb[ii];
feqoldn[i][j][k][l] -= w_lb[l]*mg_lb[ii][l]*etacov[ii]*Ng_lb[ii];
}
- }
+ }
}
}
diff --git a/src/USER-LB/fix_lb_momentum.h b/src/USER-LB/fix_lb_momentum.h
index a4277c0232..51c9f6f4a4 100755
--- a/src/USER-LB/fix_lb_momentum.h
+++ b/src/USER-LB/fix_lb_momentum.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-LB/fix_lb_pc.cpp b/src/USER-LB/fix_lb_pc.cpp
index c8c518f039..9ea1afc2ea 100755
--- a/src/USER-LB/fix_lb_pc.cpp
+++ b/src/USER-LB/fix_lb_pc.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -15,9 +15,9 @@
Contributing authors: Frances Mackay, Santtu Ollila, Colin Denniston (UWO)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <string.h>
#include "fix_lb_pc.h"
#include "atom.h"
#include "force.h"
@@ -29,7 +29,7 @@
#include "domain.h"
#include "fix_lb_fluid.h"
#include "modify.h"
-#include "mpi.h"
+#include <mpi.h>
#include "group.h"
using namespace LAMMPS_NS;
@@ -64,7 +64,7 @@ FixLbPC::FixLbPC(LAMMPS *lmp, int narg, char **arg) :
}
if(groupbit_lb_fluid == 0)
- error->all(FLERR,"the lb/fluid fix must also be used if using the lb/pc fix");
+ error->all(FLERR,"the lb/fluid fix must also be used if using the lb/pc fix");
int *mask = atom->mask;
int nlocal = atom->nlocal;
@@ -72,7 +72,7 @@ FixLbPC::FixLbPC(LAMMPS *lmp, int narg, char **arg) :
if((mask[j] & groupbit) && !(mask[j] & groupbit_lb_fluid))
error->one(FLERR,"can only use the lb/pc fix for an atom if also using the lb/fluid fix for that atom");
}
-
+
}
/* ---------------------------------------------------------------------- */
@@ -80,7 +80,7 @@ FixLbPC::FixLbPC(LAMMPS *lmp, int narg, char **arg) :
FixLbPC::~FixLbPC() {
atom->delete_callback(id,0);
-
+
memory->destroy(force_old);
memory->destroy(up);
memory->destroy(up_old);
@@ -108,7 +108,7 @@ void FixLbPC::init()
double dt_lb = fix_lb_fluid->dt_lb;
MPI_Comm_rank(world,&me);
-
+
dtv = update->dt;
dtf = update->dt * force->ftm2v;
@@ -121,7 +121,7 @@ void FixLbPC::init()
void FixLbPC::initial_integrate(int vflag) {
double dtfm;
-
+
double **x = atom->x;
double dx[3];
double **v = atom->v;
@@ -144,13 +144,13 @@ void FixLbPC::initial_integrate(int vflag) {
force_old[i][2] = f[i][2];
}
-
+
if(rmass){
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dtfm = dtf/rmass[i];
- expminusdttimesgamma = exp(-dtv*Gamma_MD[type[i]]/rmass[i]);
-
+ expminusdttimesgamma = exp(-dtv*Gamma_MD[type[i]]/rmass[i]);
+
dx[0] = dtv*v[i][0] + 0.5*(f[i][0]*force->ftm2v - Gamma_MD[type[i]]*(v[i][0]-up[i][0]))*dtv*dtv/rmass[i];
dx[1] = dtv*v[i][1] + 0.5*(f[i][1]*force->ftm2v - Gamma_MD[type[i]]*(v[i][1]-up[i][1]))*dtv*dtv/rmass[i];
dx[2] = dtv*v[i][2] + 0.5*(f[i][2]*force->ftm2v - Gamma_MD[type[i]]*(v[i][2]-up[i][2]))*dtv*dtv/rmass[i];
@@ -158,20 +158,20 @@ void FixLbPC::initial_integrate(int vflag) {
x[i][0] += dx[0];
x[i][1] += dx[1];
x[i][2] += dx[2];
-
+
// Approximation for v
if(Gamma_MD[type[i]] == 0.0){
v[i][0] += f[i][0]*dtfm;
v[i][1] += f[i][1]*dtfm;
v[i][2] += f[i][2]*dtfm;
}else{
- v[i][0] = (v[i][0]-up[i][0]-f[i][0]*force->ftm2v/Gamma_MD[type[i]])*expminusdttimesgamma +
+ v[i][0] = (v[i][0]-up[i][0]-f[i][0]*force->ftm2v/Gamma_MD[type[i]])*expminusdttimesgamma +
f[i][0]*force->ftm2v/Gamma_MD[type[i]] + up[i][0];
- v[i][1] = (v[i][1]-up[i][1]-f[i][1]*force->ftm2v/Gamma_MD[type[i]])*expminusdttimesgamma +
+ v[i][1] = (v[i][1]-up[i][1]-f[i][1]*force->ftm2v/Gamma_MD[type[i]])*expminusdttimesgamma +
f[i][1]*force->ftm2v/Gamma_MD[type[i]] + up[i][1];
- v[i][2] = (v[i][2]-up[i][2]-f[i][2]*force->ftm2v/Gamma_MD[type[i]])*expminusdttimesgamma +
+ v[i][2] = (v[i][2]-up[i][2]-f[i][2]*force->ftm2v/Gamma_MD[type[i]])*expminusdttimesgamma +
f[i][2]*force->ftm2v/Gamma_MD[type[i]] + up[i][2];
- }
+ }
}
}
@@ -180,7 +180,7 @@ void FixLbPC::initial_integrate(int vflag) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dtfm = dtf/mass[type[i]];
- expminusdttimesgamma = exp(-dtv*Gamma_MD[type[i]]/mass[type[i]]);
+ expminusdttimesgamma = exp(-dtv*Gamma_MD[type[i]]/mass[type[i]]);
dx[0] = dtv*v[i][0] + 0.5*(f[i][0]*force->ftm2v - Gamma_MD[type[i]]*(v[i][0]-up[i][0]))*dtv*dtv/mass[type[i]];
dx[1] = dtv*v[i][1] + 0.5*(f[i][1]*force->ftm2v - Gamma_MD[type[i]]*(v[i][1]-up[i][1]))*dtv*dtv/mass[type[i]];
@@ -189,18 +189,18 @@ void FixLbPC::initial_integrate(int vflag) {
x[i][0] += dx[0];
x[i][1] += dx[1];
x[i][2] += dx[2];
-
+
// Approximation for v
if(Gamma_MD[type[i]] == 0.0){
v[i][0] += f[i][0]*dtfm;
v[i][1] += f[i][1]*dtfm;
v[i][2] += f[i][2]*dtfm;
}else{
- v[i][0] = (v[i][0]-up[i][0]-f[i][0]*force->ftm2v/Gamma_MD[type[i]])*expminusdttimesgamma +
+ v[i][0] = (v[i][0]-up[i][0]-f[i][0]*force->ftm2v/Gamma_MD[type[i]])*expminusdttimesgamma +
f[i][0]*force->ftm2v/Gamma_MD[type[i]] + up[i][0];
- v[i][1] = (v[i][1]-up[i][1]-f[i][1]*force->ftm2v/Gamma_MD[type[i]])*expminusdttimesgamma +
+ v[i][1] = (v[i][1]-up[i][1]-f[i][1]*force->ftm2v/Gamma_MD[type[i]])*expminusdttimesgamma +
f[i][1]*force->ftm2v/Gamma_MD[type[i]] + up[i][1];
- v[i][2] = (v[i][2]-up[i][2]-f[i][2]*force->ftm2v/Gamma_MD[type[i]])*expminusdttimesgamma +
+ v[i][2] = (v[i][2]-up[i][2]-f[i][2]*force->ftm2v/Gamma_MD[type[i]])*expminusdttimesgamma +
f[i][2]*force->ftm2v/Gamma_MD[type[i]] + up[i][2];
}
}
@@ -222,14 +222,14 @@ void FixLbPC::final_integrate()
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
compute_up();
-
+
if(rmass){
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dtfm = dtf/rmass[i];
expminusdttimesgamma = exp(-dtv*Gamma_MD[type[i]]/rmass[i]);
DMDcoeff = (dtv - rmass[i]*(1.0-expminusdttimesgamma)/Gamma_MD[type[i]]);
-
+
if(Gamma_MD[type[i]] == 0.0){
v[i][0] += 0.5*(f[i][0] - force_old[i][0])*dtfm;
v[i][1] += 0.5*(f[i][1] - force_old[i][1])*dtfm;
@@ -239,7 +239,7 @@ void FixLbPC::final_integrate()
v[i][1] += DMDcoeff*((f[i][1] - force_old[i][1])*force->ftm2v/Gamma_MD[type[i]] + up[i][1] - up_old[i][1])/dtv;
v[i][2] += DMDcoeff*((f[i][2] - force_old[i][2])*force->ftm2v/Gamma_MD[type[i]] + up[i][2] - up_old[i][2])/dtv;
}
-
+
}
}
@@ -250,7 +250,7 @@ void FixLbPC::final_integrate()
dtfm = dtf/mass[type[i]];
expminusdttimesgamma = exp(-dtv*Gamma_MD[type[i]]/mass[type[i]]);
DMDcoeff = (dtv - mass[type[i]]*(1.0-expminusdttimesgamma)/Gamma_MD[type[i]]);
-
+
if(Gamma_MD[type[i]] == 0.0){
v[i][0] += 0.5*(f[i][0] - force_old[i][0])*dtfm;
v[i][1] += 0.5*(f[i][1] - force_old[i][1])*dtfm;
@@ -259,7 +259,7 @@ void FixLbPC::final_integrate()
v[i][0] += DMDcoeff*((f[i][0] - force_old[i][0])*force->ftm2v/Gamma_MD[type[i]] + up[i][0] - up_old[i][0])/dtv;
v[i][1] += DMDcoeff*((f[i][1] - force_old[i][1])*force->ftm2v/Gamma_MD[type[i]] + up[i][1] - up_old[i][1])/dtv;
v[i][2] += DMDcoeff*((f[i][2] - force_old[i][2])*force->ftm2v/Gamma_MD[type[i]] + up[i][2] - up_old[i][2])/dtv;
- }
+ }
}
}
@@ -359,18 +359,18 @@ int FixLbPC::unpack_exchange(int nlocal, double *buf)
double dt_lb = fix_lb_fluid->dt_lb;
double FfP[64];
int trilinear_stencil = fix_lb_fluid->trilinear_stencil;
-
+
for(i=0; i<nlocal; i++){
if(mask[i] & groupbit){
//Calculate nearest leftmost grid point.
//Since array indices from 1 to subNb-2 correspond to the
- // local subprocessor domain (not indices from 0), use the
+ // local subprocessor domain (not indices from 0), use the
// ceiling value.
ix = (int)ceil((x[i][0]-domain->sublo[0])/dx_lb);
iy = (int)ceil((x[i][1]-domain->sublo[1])/dx_lb);
iz = (int)ceil((x[i][2]-domain->sublo[2])/dx_lb);
-
+
//Calculate distances to the nearest points.
dx1 = x[i][0] - (domain->sublo[0] + (ix-1)*dx_lb);
dy1 = x[i][1] - (domain->sublo[1] + (iy-1)*dx_lb);
@@ -380,13 +380,13 @@ int FixLbPC::unpack_exchange(int nlocal, double *buf)
dx1 = dx1/dx_lb;
dy1 = dy1/dx_lb;
dz1 = dz1/dx_lb;
-
+
up[i][0]=0.0; up[i][1]=0.0; up[i][2]=0.0;
if(trilinear_stencil==0){
isten=0;
for(ii=-1; ii<3; ii++){
rsq=(-dx1+ii)*(-dx1+ii);
-
+
if(rsq>=4)
weightx=0.0;
else{
@@ -424,12 +424,12 @@ int FixLbPC::unpack_exchange(int nlocal, double *buf)
ixp = ix+ii;
iyp = iy+jj;
izp = iz+kk;
-
-
+
+
if(ixp==-1) ixp=subNbx+2;
if(iyp==-1) iyp=subNby+2;
if(izp==-1) izp=subNbz+2;
-
+
FfP[isten] = weightx*weighty*weightz;
// interpolated velocity based on delta function.
for(k=0; k<3; k++){
@@ -447,11 +447,11 @@ int FixLbPC::unpack_exchange(int nlocal, double *buf)
FfP[5] = dx1*(1.-dy1)*dz1;
FfP[6] = dx1*dy1*(1.-dz1);
FfP[7] = dx1*dy1*dz1;
-
+
ixp = (ix+1);
iyp = (iy+1);
izp = (iz+1);
-
+
for (k=0; k<3; k++) { // tri-linearly interpolated velocity at node
up[i][k] = u_lb[ix][iy][iz][k]*FfP[0]
+ u_lb[ix][iy][izp][k]*FfP[1]
@@ -460,9 +460,9 @@ int FixLbPC::unpack_exchange(int nlocal, double *buf)
+ u_lb[ixp][iy][iz][k]*FfP[4]
+ u_lb[ixp][iy][izp][k]*FfP[5]
+ u_lb[ixp][iyp][iz][k]*FfP[6]
- + u_lb[ixp][iyp][izp][k]*FfP[7];
+ + u_lb[ixp][iyp][izp][k]*FfP[7];
}
- }
+ }
for(k=0; k<3; k++)
up[i][k] = up[i][k]*dx_lb/dt_lb;
diff --git a/src/USER-LB/fix_lb_pc.h b/src/USER-LB/fix_lb_pc.h
index 1804810afd..7d0be65e60 100755
--- a/src/USER-LB/fix_lb_pc.h
+++ b/src/USER-LB/fix_lb_pc.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -52,7 +52,7 @@ namespace LAMMPS_NS {
double **up_old;
void compute_up(void);
- class FixLbFluid *fix_lb_fluid;
+ class FixLbFluid *fix_lb_fluid;
};
}
diff --git a/src/USER-LB/fix_lb_rigid_pc_sphere.cpp b/src/USER-LB/fix_lb_rigid_pc_sphere.cpp
index c031d1b782..54637ce349 100755
--- a/src/USER-LB/fix_lb_rigid_pc_sphere.cpp
+++ b/src/USER-LB/fix_lb_rigid_pc_sphere.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -16,10 +16,10 @@
Based on fix_rigid (version from 2008).
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "fix_lb_rigid_pc_sphere.h"
#include "atom.h"
#include "atom_vec.h"
@@ -54,7 +54,7 @@ FixLbRigidPCSphere::FixLbRigidPCSphere(LAMMPS *lmp, int narg, char **arg) :
// perform initial allocation of atom-based arrays
// register with Atom class
-
+
body = NULL;
up = NULL;
grow_arrays(atom->nmax);
@@ -62,12 +62,12 @@ FixLbRigidPCSphere::FixLbRigidPCSphere(LAMMPS *lmp, int narg, char **arg) :
// by default assume all of the particles interact with the fluid.
inner_nodes = 0;
-
+
// parse command-line args
// set nbody and body[i] for each atom
if (narg < 4) error->all(FLERR,"Illegal fix lb/rigid/pc/sphere command");
-
+
// single rigid body
// nbody = 1
// all atoms in fix group are part of body
@@ -108,7 +108,7 @@ FixLbRigidPCSphere::FixLbRigidPCSphere(LAMMPS *lmp, int narg, char **arg) :
tagint itmp;
MPI_Allreduce(&maxmol_tag,&itmp,1,MPI_LMP_TAGINT,MPI_MAX,world);
- if (itmp+1 > MAXSMALLINT)
+ if (itmp+1 > MAXSMALLINT)
error->all(FLERR,"Too many molecules for fix lb/rigid/pc/sphere");
int maxmol = (int) itmp;
@@ -145,14 +145,14 @@ FixLbRigidPCSphere::FixLbRigidPCSphere(LAMMPS *lmp, int narg, char **arg) :
if (narg < 5) error->all(FLERR,"Illegal fix lb/rigid/pc/sphere command");
nbody = atoi(arg[4]);
if (nbody <= 0) error->all(FLERR,"Illegal fix lb/rigid/pc/sphere command");
- if (narg < 5+nbody)
+ if (narg < 5+nbody)
error->all(FLERR,"Illegal fix lb/rigid/pc/sphere command");
iarg = 5 + nbody;
int *igroups = new int[nbody];
for (ibody = 0; ibody < nbody; ibody++) {
igroups[ibody] = group->find(arg[5+ibody]);
- if (igroups[ibody] == -1)
+ if (igroups[ibody] == -1)
error->all(FLERR,"Could not find fix lb/rigid/pc/sphere group ID");
}
@@ -172,13 +172,13 @@ FixLbRigidPCSphere::FixLbRigidPCSphere(LAMMPS *lmp, int narg, char **arg) :
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
- if (flagall)
+ if (flagall)
error->all(FLERR,"One or more atoms belong to multiple rigid bodies");
delete [] igroups;
}else error->all(FLERR,"Illegal fix lb/rigid/pc/sphere command");
-
+
// error check on nbody
if (nbody == 0) error->all(FLERR,"No rigid bodies defined");
@@ -286,7 +286,7 @@ FixLbRigidPCSphere::FixLbRigidPCSphere(LAMMPS *lmp, int narg, char **arg) :
iarg += 5;
// specify if certain particles are inside the rigid spherical body,
- // and therefore should not
+ // and therefore should not
} else if(strcmp(arg[iarg],"innerNodes")==0){
inner_nodes = 1;
igroupinner = group->find(arg[iarg+1]);
@@ -315,7 +315,7 @@ FixLbRigidPCSphere::FixLbRigidPCSphere(LAMMPS *lmp, int narg, char **arg) :
// nrigid[n] = # of atoms in Nth rigid body
// error if one or zero atoms
-
+
int *ncount = new int[nbody];
for (ibody = 0; ibody < nbody; ibody++) ncount[ibody] = 0;
@@ -323,9 +323,9 @@ FixLbRigidPCSphere::FixLbRigidPCSphere(LAMMPS *lmp, int narg, char **arg) :
for (i = 0; i < nlocal; i++)
if (body[i] >= 0) ncount[body[i]]++;
-
+
MPI_Allreduce(ncount,nrigid,nbody,MPI_INT,MPI_SUM,world);
-
+
//count the number of atoms in the shell.
if(inner_nodes == 1){
int *mask = atom->mask;
@@ -335,7 +335,7 @@ FixLbRigidPCSphere::FixLbRigidPCSphere(LAMMPS *lmp, int narg, char **arg) :
if(body[i] >= 0) ncount[body[i]]++;
}
}
-
+
MPI_Allreduce(ncount,nrigid_shell,nbody,MPI_INT,MPI_SUM,world);
}else {
for(ibody=0; ibody < nbody; ibody++) nrigid_shell[ibody]=nrigid[ibody];
@@ -351,14 +351,14 @@ FixLbRigidPCSphere::FixLbRigidPCSphere(LAMMPS *lmp, int narg, char **arg) :
// set here, so image value will persist from run to run
for (ibody = 0; ibody < nbody; ibody++)
- imagebody[ibody] = ((imageint) IMGMAX << IMG2BITS) |
+ imagebody[ibody] = ((imageint) IMGMAX << IMG2BITS) |
((imageint) IMGMAX << IMGBITS) | IMGMAX;
// print statistics
int nsum = 0;
for (ibody = 0; ibody < nbody; ibody++) nsum += nrigid[ibody];
-
+
if (comm->me == 0) {
if (screen) fprintf(screen,"%d rigid bodies with %d atoms\n",nbody,nsum);
if (logfile) fprintf(logfile,"%d rigid bodies with %d atoms\n",nbody,nsum);
@@ -374,7 +374,7 @@ FixLbRigidPCSphere::FixLbRigidPCSphere(LAMMPS *lmp, int narg, char **arg) :
if(groupbit_lb_fluid == 0)
error->all(FLERR,"the lb/fluid fix must also be used if using the lb/rigid/pc/sphere fix");
-
+
int *mask = atom->mask;
if(inner_nodes == 1){
for(int j=0; j<nlocal; j++){
@@ -384,15 +384,15 @@ FixLbRigidPCSphere::FixLbRigidPCSphere(LAMMPS *lmp, int narg, char **arg) :
// If inner nodes are present, which should not interact with the fluid, make
// sure these are not used by the lb/fluid fix to apply a force to the fluid.
if((mask[j] & groupbit) && (mask[j] & groupbit_lb_fluid) && (mask[j] & group->bitmask[igroupinner]))
- error->one(FLERR,"the inner nodes specified in lb/rigid/pc/sphere should not be included in the lb/fluid fix");
+ error->one(FLERR,"the inner nodes specified in lb/rigid/pc/sphere should not be included in the lb/fluid fix");
}
}else{
for(int j=0; j<nlocal; j++){
if((mask[j] & groupbit) && !(mask[j] & groupbit_lb_fluid))
error->one(FLERR,"use the innerNodes keyword in the lb/rigid/pc/sphere fix for atoms which do not interact with the lb/fluid");
}
- }
-
+ }
+
}
/* ---------------------------------------------------------------------- */
@@ -402,12 +402,12 @@ FixLbRigidPCSphere::~FixLbRigidPCSphere()
// unregister callbacks to this fix from Atom class
atom->delete_callback(id,0);
-
+
// delete locally stored arrays
-
+
memory->destroy(body);
memory->destroy(up);
-
+
// delete nbody-length arrays
memory->destroy(nrigid);
@@ -474,7 +474,7 @@ void FixLbRigidPCSphere::init()
double **x = atom->x;
imageint *image = atom->image;
double *rmass = atom->rmass;
- double *mass = atom->mass;
+ double *mass = atom->mass;
int *periodicity = domain->periodicity;
double xprd = domain->xprd;
double yprd = domain->yprd;
@@ -500,14 +500,14 @@ void FixLbRigidPCSphere::init()
}
if(extended)
error->warning(FLERR,"Fix lb/rigid/pc/sphere assumes point particles");
-
+
// compute masstotal & center-of-mass of each rigid body
for (ibody = 0; ibody < nbody; ibody++)
for (i = 0; i < 6; i++) sum[ibody][i] = 0.0;
int xbox,ybox,zbox;
double massone,xunwrap,yunwrap,zunwrap;
-
+
for (i = 0; i < nlocal; i++) {
if (body[i] < 0) continue;
ibody = body[i];
@@ -539,9 +539,9 @@ void FixLbRigidPCSphere::init()
sum[ibody][4] += massone;
}
}
-
+
MPI_Allreduce(sum[0],all[0],6*nbody,MPI_DOUBLE,MPI_SUM,world);
-
+
for (ibody = 0; ibody < nbody; ibody++) {
masstotal[ibody] = all[ibody][3];
masstotal_shell[ibody] = all[ibody][4];
@@ -564,25 +564,25 @@ void FixLbRigidPCSphere::init()
if(inner_nodes == 1){
if(!(mask[i] & group->bitmask[igroupinner])){
ibody = body[i];
-
+
xbox = (image[i] & IMGMASK) - IMGMAX;
ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
zbox = (image[i] >> IMG2BITS) - IMGMAX;
-
+
xunwrap = x[i][0] + xbox*xprd;
yunwrap = x[i][1] + ybox*yprd;
zunwrap = x[i][2] + zbox*zprd;
-
+
dx = xunwrap - xcm[ibody][0];
dy = yunwrap - xcm[ibody][1];
dz = zunwrap - xcm[ibody][2];
-
+
sum[ibody][0] += dx*dx + dy*dy + dz*dz;
sum[ibody][1] += Gamma[type[i]];
}
}else{
ibody = body[i];
-
+
xbox = (image[i] & IMGMASK) - IMGMAX;
ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
zbox = (image[i] >> IMG2BITS) - IMGMAX;
@@ -606,7 +606,7 @@ void FixLbRigidPCSphere::init()
sphereradius[ibody] = sqrt(all[ibody][0]/nrigid_shell[ibody]);
Gamma_MD[ibody] = all[ibody][1]*dm_lb/dt_lb/nrigid_shell[ibody];
}
-
+
// Check that all atoms in the rigid body have the same value of gamma.
double eps = 1.0e-7;
for (i=0; i<nlocal; i++){
@@ -622,11 +622,11 @@ void FixLbRigidPCSphere::init()
ibody = body[i];
if(Gamma_MD[ibody]*dt_lb/dm_lb - Gamma[type[i]] > eps)
- error->one(FLERR,"All atoms in a rigid body must have the same gamma value");
+ error->one(FLERR,"All atoms in a rigid body must have the same gamma value");
}
}
-
+
// remap the xcm of each body back into simulation box if needed
// only really necessary the 1st time a run is performed
@@ -642,7 +642,7 @@ void FixLbRigidPCSphere::init()
}
if (ndof > 0.0) tfactor = force->mvv2e / (ndof * force->boltz);
else tfactor = 0.0;
-
+
}
/* ---------------------------------------------------------------------- */
@@ -650,7 +650,7 @@ void FixLbRigidPCSphere::setup(int vflag)
{
int i,n,ibody;
double massone;
-
+
// vcm = velocity of center-of-mass of each rigid body
// fcm = force on center-of-mass of each rigid body
@@ -671,7 +671,7 @@ void FixLbRigidPCSphere::setup(int vflag)
for (ibody = 0; ibody < nbody; ibody++)
for (i = 0; i < 6; i++) sum[ibody][i] = 0.0;
-
+
for (i = 0; i < nlocal; i++) {
if (body[i] < 0) continue;
ibody = body[i];
@@ -685,7 +685,7 @@ void FixLbRigidPCSphere::setup(int vflag)
sum[ibody][4] += f[i][1];
sum[ibody][5] += f[i][2];
}
-
+
MPI_Allreduce(sum[0],all[0],6*nbody,MPI_DOUBLE,MPI_SUM,world);
for (ibody = 0; ibody < nbody; ibody++) {
@@ -707,13 +707,13 @@ void FixLbRigidPCSphere::setup(int vflag)
for (i = 0; i < nlocal; i++) {
if (body[i] < 0) continue;
ibody = body[i];
-
+
domain->unmap(x[i],image[i],unwrap);
-
+
dx = unwrap[0] - xcm[ibody][0];
dy = unwrap[1] - xcm[ibody][1];
dz = unwrap[2] - xcm[ibody][2];
-
+
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
@@ -783,13 +783,13 @@ void FixLbRigidPCSphere::initial_integrate(int vflag)
for (ibody = 0; ibody < nbody; ibody++)
for (i = 0; i < 6; i++) sum[ibody][i] = 0.0;
// Store the fluid velocity at the center of mass
-
+
for (i = 0; i < nlocal; i++) {
if (body[i] < 0) continue;
ibody = body[i];
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
-
+
if(inner_nodes == 1){
if(!(mask[i] & group->bitmask[igroupinner])){
sum[ibody][0] += up[i][0]*massone;
@@ -800,7 +800,7 @@ void FixLbRigidPCSphere::initial_integrate(int vflag)
sum[ibody][0] += up[i][0]*massone;
sum[ibody][1] += up[i][1]*massone;
sum[ibody][2] += up[i][2]*massone;
- }
+ }
}
MPI_Allreduce(sum[0],all[0],6*nbody,MPI_DOUBLE,MPI_SUM,world);
@@ -819,7 +819,7 @@ void FixLbRigidPCSphere::initial_integrate(int vflag)
ibody = body[i];
domain->unmap(x[i],image[i],unwrap);
-
+
dx = unwrap[0] - xcm[ibody][0];
dy = unwrap[1] - xcm[ibody][1];
dz = unwrap[2] - xcm[ibody][2];
@@ -872,7 +872,7 @@ void FixLbRigidPCSphere::initial_integrate(int vflag)
torque_old[ibody][2] = torque[ibody][2];
torque_fluid_old[ibody][0] = torque_fluid[ibody][0];
torque_fluid_old[ibody][1] = torque_fluid[ibody][1];
- torque_fluid_old[ibody][2] = torque_fluid[ibody][2];
+ torque_fluid_old[ibody][2] = torque_fluid[ibody][2];
ucm_old[ibody][0] = ucm[ibody][0];
ucm_old[ibody][1] = ucm[ibody][1];
ucm_old[ibody][2] = ucm[ibody][2];
@@ -899,7 +899,7 @@ void FixLbRigidPCSphere::initial_integrate(int vflag)
force_factor = force->ftm2v/Gamma_MD[ibody]/nrigid_shell[ibody];
if(fflag[ibody][0]==1){
- vcm[ibody][0] = expminusdttimesgamma*(vcm[ibody][0] - ucm[ibody][0] - fcm[ibody][0]*force_factor)
+ vcm[ibody][0] = expminusdttimesgamma*(vcm[ibody][0] - ucm[ibody][0] - fcm[ibody][0]*force_factor)
+ ucm[ibody][0] + fcm[ibody][0]*force_factor;
}
if(fflag[ibody][1]==1){
@@ -918,19 +918,19 @@ void FixLbRigidPCSphere::initial_integrate(int vflag)
if(tflag[ibody][0]==1){
omega[ibody][0] = expminusdttimesgamma*(omega[ibody][0] - (3.0/(2.0*nrigid_shell[ibody]*sphereradius[ibody]*sphereradius[ibody]*Gamma_MD[ibody]))*
- (force->ftm2v*torque[ibody][0] + torque_fluid[ibody][0])) +
+ (force->ftm2v*torque[ibody][0] + torque_fluid[ibody][0])) +
(3.0/(2.0*nrigid_shell[ibody]*sphereradius[ibody]*sphereradius[ibody]*Gamma_MD[ibody]))*
(force->ftm2v*torque[ibody][0] + torque_fluid[ibody][0]);
}
if(tflag[ibody][1]==1){
omega[ibody][1] = expminusdttimesgamma*(omega[ibody][1] - (3.0/(2.0*nrigid_shell[ibody]*sphereradius[ibody]*sphereradius[ibody]*Gamma_MD[ibody]))*
- (force->ftm2v*torque[ibody][1] + torque_fluid[ibody][1])) +
+ (force->ftm2v*torque[ibody][1] + torque_fluid[ibody][1])) +
(3.0/(2.0*nrigid_shell[ibody]*sphereradius[ibody]*sphereradius[ibody]*Gamma_MD[ibody]))*
(force->ftm2v*torque[ibody][1] + torque_fluid[ibody][1]);
}
if(tflag[ibody][2]==1){
omega[ibody][2] = expminusdttimesgamma*(omega[ibody][2] - (3.0/(2.0*nrigid_shell[ibody]*sphereradius[ibody]*sphereradius[ibody]*Gamma_MD[ibody]))*
- (force->ftm2v*torque[ibody][2] + torque_fluid[ibody][2])) +
+ (force->ftm2v*torque[ibody][2] + torque_fluid[ibody][2])) +
(3.0/(2.0*nrigid_shell[ibody]*sphereradius[ibody]*sphereradius[ibody]*Gamma_MD[ibody]))*
(force->ftm2v*torque[ibody][2] + torque_fluid[ibody][2]);
}
@@ -941,7 +941,7 @@ void FixLbRigidPCSphere::initial_integrate(int vflag)
if (vflag) v_setup(vflag);
else evflag = 0;
- set_xv();
+ set_xv();
}
@@ -961,7 +961,7 @@ void FixLbRigidPCSphere::final_integrate()
double *mass = atom->mass;
int *type = atom->type;
int nlocal = atom->nlocal;
-
+
double unwrap[3];
double dx,dy,dz;
@@ -969,7 +969,7 @@ void FixLbRigidPCSphere::final_integrate()
for (ibody = 0; ibody < nbody; ibody++)
for (i = 0; i < 6; i++) sum[ibody][i] = 0.0;
-
+
for (i = 0; i < nlocal; i++) {
if (body[i] < 0) continue;
ibody = body[i];
@@ -977,13 +977,13 @@ void FixLbRigidPCSphere::final_integrate()
sum[ibody][0] += f[i][0];
sum[ibody][1] += f[i][1];
sum[ibody][2] += f[i][2];
-
+
domain->unmap(x[i],image[i],unwrap);
-
+
dx = unwrap[0] - xcm[ibody][0];
dy = unwrap[1] - xcm[ibody][1];
dz = unwrap[2] - xcm[ibody][2];
-
+
sum[ibody][3] += dy*f[i][2] - dz*f[i][1];
sum[ibody][4] += dz*f[i][0] - dx*f[i][2];
sum[ibody][5] += dx*f[i][1] - dy*f[i][0];
@@ -991,7 +991,7 @@ void FixLbRigidPCSphere::final_integrate()
MPI_Allreduce(sum[0],all[0],6*nbody,MPI_DOUBLE,MPI_SUM,world);
- //Compute the correction to the velocity and angular momentum due to the non-fluid forces:
+ //Compute the correction to the velocity and angular momentum due to the non-fluid forces:
for (ibody = 0; ibody < nbody; ibody++) {
fcm[ibody][0] = all[ibody][0];
fcm[ibody][1] = all[ibody][1];
@@ -1002,11 +1002,11 @@ void FixLbRigidPCSphere::final_integrate()
expminusdttimesgamma = exp(-dtv*Gamma_MD[ibody]*nrigid_shell[ibody]/masstotal[ibody]);
DMDcoeff= (dtv - (masstotal[ibody]/nrigid_shell[ibody])*(1.0-expminusdttimesgamma)/Gamma_MD[ibody]);
-
+
vcm[ibody][0] += fflag[ibody][0]*DMDcoeff*force->ftm2v*(fcm[ibody][0]-fcm_old[ibody][0])/Gamma_MD[ibody]/dtv/nrigid_shell[ibody];
vcm[ibody][1] += fflag[ibody][1]*DMDcoeff*force->ftm2v*(fcm[ibody][1]-fcm_old[ibody][1])/Gamma_MD[ibody]/dtv/nrigid_shell[ibody];
vcm[ibody][2] += fflag[ibody][2]*DMDcoeff*force->ftm2v*(fcm[ibody][2]-fcm_old[ibody][2])/Gamma_MD[ibody]/dtv/nrigid_shell[ibody];
-
+
torque_factor = 5.0*Gamma_MD[ibody]*nrigid_shell[ibody]/(3.0*masstotal[ibody]);
expminusdttimesgamma = exp(-dtv*torque_factor);
DMDcoeff = (dtv - (1.0-expminusdttimesgamma)/torque_factor);
@@ -1035,34 +1035,34 @@ void FixLbRigidPCSphere::final_integrate()
else massone = mass[type[i]];
domain->unmap(x[i],image[i],unwrap);
-
+
dx = unwrap[0] - xcm[ibody][0];
dy = unwrap[1] - xcm[ibody][1];
- dz = unwrap[2] - xcm[ibody][2];
+ dz = unwrap[2] - xcm[ibody][2];
if(inner_nodes == 1){
if(!(mask[i] & group->bitmask[igroupinner])){
sum[ibody][0] += up[i][0]*massone;
sum[ibody][1] += up[i][1]*massone;
- sum[ibody][2] += up[i][2]*massone;
- sum[ibody][3] += Gamma_MD[ibody]*(dy * ((up[i][2]-vcm[ibody][2])) -
+ sum[ibody][2] += up[i][2]*massone;
+ sum[ibody][3] += Gamma_MD[ibody]*(dy * ((up[i][2]-vcm[ibody][2])) -
dz * ((up[i][1]-vcm[ibody][1])));
- sum[ibody][4] += Gamma_MD[ibody]*(dz * ((up[i][0]-vcm[ibody][0])) -
+ sum[ibody][4] += Gamma_MD[ibody]*(dz * ((up[i][0]-vcm[ibody][0])) -
dx * ((up[i][2]-vcm[ibody][2])));
- sum[ibody][5] += Gamma_MD[ibody]*(dx * ((up[i][1]-vcm[ibody][1])) -
- dy * ((up[i][0]-vcm[ibody][0])));
+ sum[ibody][5] += Gamma_MD[ibody]*(dx * ((up[i][1]-vcm[ibody][1])) -
+ dy * ((up[i][0]-vcm[ibody][0])));
}
}else{
sum[ibody][0] += up[i][0]*massone;
sum[ibody][1] += up[i][1]*massone;
sum[ibody][2] += up[i][2]*massone;
- sum[ibody][3] += Gamma_MD[ibody]*(dy * ((up[i][2]-vcm[ibody][2])) -
+ sum[ibody][3] += Gamma_MD[ibody]*(dy * ((up[i][2]-vcm[ibody][2])) -
dz * ((up[i][1]-vcm[ibody][1])));
- sum[ibody][4] += Gamma_MD[ibody]*(dz * ((up[i][0]-vcm[ibody][0])) -
+ sum[ibody][4] += Gamma_MD[ibody]*(dz * ((up[i][0]-vcm[ibody][0])) -
dx * ((up[i][2]-vcm[ibody][2])));
- sum[ibody][5] += Gamma_MD[ibody]*(dx * ((up[i][1]-vcm[ibody][1])) -
+ sum[ibody][5] += Gamma_MD[ibody]*(dx * ((up[i][1]-vcm[ibody][1])) -
dy * ((up[i][0]-vcm[ibody][0])));
- }
+ }
}
MPI_Allreduce(sum[0],all[0],6*nbody,MPI_DOUBLE,MPI_SUM,world);
@@ -1080,7 +1080,7 @@ void FixLbRigidPCSphere::final_integrate()
expminusdttimesgamma = exp(-dtv*Gamma_MD[ibody]*nrigid_shell[ibody]/masstotal[ibody]);
DMDcoeff= (dtv - (masstotal[ibody]/nrigid_shell[ibody])*(1.0-expminusdttimesgamma)/Gamma_MD[ibody]);
-
+
vcm[ibody][0] += DMDcoeff*fflag[ibody][0]*(ucm[ibody][0]-ucm_old[ibody][0])/dtv;
vcm[ibody][1] += DMDcoeff*fflag[ibody][1]*(ucm[ibody][1]-ucm_old[ibody][1])/dtv;
vcm[ibody][2] += DMDcoeff*fflag[ibody][2]*(ucm[ibody][2]-ucm_old[ibody][2])/dtv;
@@ -1094,7 +1094,7 @@ void FixLbRigidPCSphere::final_integrate()
omega[ibody][1] += tflag[ibody][1]*(3.0/(2.0*nrigid_shell[ibody]*sphereradius[ibody]*sphereradius[ibody]*Gamma_MD[ibody]))*
DMDcoeff*(torque_fluid[ibody][1] - torque_fluid_old[ibody][1])/dtv;
omega[ibody][2] += tflag[ibody][2]*(3.0/(2.0*nrigid_shell[ibody]*sphereradius[ibody]*sphereradius[ibody]*Gamma_MD[ibody]))*
- DMDcoeff*(torque_fluid[ibody][2] - torque_fluid_old[ibody][2])/dtv;
+ DMDcoeff*(torque_fluid[ibody][2] - torque_fluid_old[ibody][2])/dtv;
}
set_v();
@@ -1119,7 +1119,7 @@ void FixLbRigidPCSphere::set_v()
double **v = atom->v;
double **f = atom->f;
double *rmass = atom->rmass;
- double *mass = atom->mass;
+ double *mass = atom->mass;
int *type = atom->type;
imageint *image = atom->image;
int nlocal = atom->nlocal;
@@ -1142,7 +1142,7 @@ void FixLbRigidPCSphere::set_v()
xunwrap = x[i][0] + xbox*xprd;
yunwrap = x[i][1] + ybox*yprd;
zunwrap = x[i][2] + zbox*zprd;
-
+
dx = xunwrap - xcm[ibody][0];
dy = yunwrap - xcm[ibody][1];
dz = zunwrap - xcm[ibody][2];
@@ -1169,7 +1169,7 @@ void FixLbRigidPCSphere::set_v()
else massone = mass[type[i]];
fc0 = massone*(v[i][0] - v0)/dtf - f[i][0] + Gamma_MD[ibody]*(v0-up[i][0]);
fc1 = massone*(v[i][1] - v1)/dtf - f[i][1] + Gamma_MD[ibody]*(v1-up[i][1]);
- fc2 = massone*(v[i][2] - v2)/dtf - f[i][2] + Gamma_MD[ibody]*(v2-up[i][2]);
+ fc2 = massone*(v[i][2] - v2)/dtf - f[i][2] + Gamma_MD[ibody]*(v2-up[i][2]);
xbox = (image[i] & IMGMASK) - IMGMAX;
ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
@@ -1211,7 +1211,7 @@ void FixLbRigidPCSphere::set_xv()
double **v = atom->v;
double **f = atom->f;
double *rmass = atom->rmass;
- double *mass = atom->mass;
+ double *mass = atom->mass;
int *type = atom->type;
imageint *image = atom->image;
int nlocal = atom->nlocal;
@@ -1222,9 +1222,9 @@ void FixLbRigidPCSphere::set_xv()
double xunwrap,yunwrap,zunwrap;
double dx,dy,dz;
-
+
// set x and v of each atom
-
+
for (int i = 0; i < nlocal; i++) {
if (body[i] < 0) continue;
ibody = body[i];
@@ -1236,7 +1236,7 @@ void FixLbRigidPCSphere::set_xv()
xunwrap = x[i][0] + xbox*xprd;
yunwrap = x[i][1] + ybox*yprd;
zunwrap = x[i][2] + zbox*zprd;
-
+
dx = xunwrap - xcm_old[ibody][0];
dy = yunwrap - xcm_old[ibody][1];
dz = zunwrap - xcm_old[ibody][2];
@@ -1299,7 +1299,7 @@ void FixLbRigidPCSphere::set_xv()
else massone = mass[type[i]];
fc0 = massone*(v[i][0] - v0)/dtf - f[i][0] + Gamma_MD[ibody]*(v0-up[i][0]);
fc1 = massone*(v[i][1] - v1)/dtf - f[i][1] + Gamma_MD[ibody]*(v1-up[i][1]);
- fc2 = massone*(v[i][2] - v2)/dtf - f[i][2] + Gamma_MD[ibody]*(v2-up[i][2]);
+ fc2 = massone*(v[i][2] - v2)/dtf - f[i][2] + Gamma_MD[ibody]*(v2-up[i][2]);
vr[0] = 0.5*x0*fc0;
vr[1] = 0.5*x1*fc1;
@@ -1323,7 +1323,7 @@ void FixLbRigidPCSphere::set_xv()
due to 1st definition of rigid body or due to box flip
if don't do this, then atoms of a body which drifts far away
from a triclinic box will be remapped back into box
- with huge displacements when the box tilt changes via set_x()
+ with huge displacements when the box tilt changes via set_x()
------------------------------------------------------------------------- */
void FixLbRigidPCSphere::pre_neighbor()
@@ -1333,7 +1333,7 @@ void FixLbRigidPCSphere::pre_neighbor()
for (int ibody = 0; ibody < nbody; ibody++) {
original = imagebody[ibody];
domain->remap(xcm[ibody],imagebody[ibody]);
-
+
if (original == imagebody[ibody]) remapflag[ibody][3] = 0;
else {
oldimage = original & IMGMASK;
@@ -1386,7 +1386,7 @@ void FixLbRigidPCSphere::pre_neighbor()
}
}
/* ----------------------------------------------------------------------
- count # of degrees-of-freedom removed by fix_rigid for atoms in igroup
+ count # of degrees-of-freedom removed by fix_rigid for atoms in igroup
------------------------------------------------------------------------- */
int FixLbRigidPCSphere::dof(int igroup)
@@ -1423,7 +1423,7 @@ int FixLbRigidPCSphere::dof(int igroup)
}
/* ----------------------------------------------------------------------
- memory usage of local atom-based arrays
+ memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double FixLbRigidPCSphere::memory_usage()
@@ -1434,10 +1434,10 @@ double FixLbRigidPCSphere::memory_usage()
bytes += maxvatom*6 * sizeof(double);
return bytes;
-}
+}
/* ----------------------------------------------------------------------
- allocate local atom-based arrays
+ allocate local atom-based arrays
------------------------------------------------------------------------- */
void FixLbRigidPCSphere::grow_arrays(int nmax)
@@ -1449,7 +1449,7 @@ void FixLbRigidPCSphere::grow_arrays(int nmax)
}
/* ----------------------------------------------------------------------
- copy values within local atom-based arrays
+ copy values within local atom-based arrays
------------------------------------------------------------------------- */
void FixLbRigidPCSphere::copy_arrays(int i, int j, int delflag)
@@ -1474,7 +1474,7 @@ void FixLbRigidPCSphere::set_arrays(int i)
}
/* ----------------------------------------------------------------------
- pack values in local atom-based arrays for exchange with another proc
+ pack values in local atom-based arrays for exchange with another proc
------------------------------------------------------------------------- */
int FixLbRigidPCSphere::pack_exchange(int i, double *buf)
@@ -1488,7 +1488,7 @@ int FixLbRigidPCSphere::pack_exchange(int i, double *buf)
}
/* ----------------------------------------------------------------------
- unpack values in local atom-based arrays from exchange with another proc
+ unpack values in local atom-based arrays from exchange with another proc
------------------------------------------------------------------------- */
int FixLbRigidPCSphere::unpack_exchange(int nlocal, double *buf)
@@ -1520,16 +1520,16 @@ double FixLbRigidPCSphere::compute_scalar()
double t = 0.0;
for (int i = 0; i < nbody; i++) {
- t += masstotal[i] * (fflag[i][0]*vcm[i][0]*vcm[i][0] +
+ t += masstotal[i] * (fflag[i][0]*vcm[i][0]*vcm[i][0] +
fflag[i][1]*vcm[i][1]*vcm[i][1] + \
fflag[i][2]*vcm[i][2]*vcm[i][2]);
-
+
// wbody = angular velocity in body frame
-
+
inertia = 2.0*masstotal[i]*sphereradius[i]*sphereradius[i]/5.0;
-
+
t += tflag[i][0]*inertia*omega[i][0]*omega[i][0] +
- tflag[i][1]*inertia*omega[i][1]*omega[i][1] +
+ tflag[i][1]*inertia*omega[i][1]*omega[i][1] +
tflag[i][2]*inertia*omega[i][2]*omega[i][2];
}
@@ -1582,22 +1582,22 @@ double FixLbRigidPCSphere::compute_array(int i, int j)
//Calculate nearest leftmost grid point.
//Since array indices from 1 to subNb-2 correspond to the
- // local subprocessor domain (not indices from 0), use the
+ // local subprocessor domain (not indices from 0), use the
// ceiling value.
ix = (int)ceil((x[i][0]-domain->sublo[0])/dx_lb);
iy = (int)ceil((x[i][1]-domain->sublo[1])/dx_lb);
iz = (int)ceil((x[i][2]-domain->sublo[2])/dx_lb);
-
+
//Calculate distances to the nearest points.
dx1 = x[i][0] - (domain->sublo[0] + (ix-1)*dx_lb);
dy1 = x[i][1] - (domain->sublo[1] + (iy-1)*dx_lb);
dz1 = x[i][2] - (domain->sublo[2] + (iz-1)*dx_lb);
-
+
// Need to convert these to lattice units:
dx1 = dx1/dx_lb;
dy1 = dy1/dx_lb;
dz1 = dz1/dx_lb;
-
+
up[i][0]=0.0; up[i][1]=0.0; up[i][2]=0.0;
@@ -1605,7 +1605,7 @@ double FixLbRigidPCSphere::compute_array(int i, int j)
isten=0;
for(ii=-1; ii<3; ii++){
rsq=(-dx1+ii)*(-dx1+ii);
-
+
if(rsq>=4)
weightx=0.0;
else{
@@ -1648,7 +1648,7 @@ double FixLbRigidPCSphere::compute_array(int i, int j)
if(ixp==-1) ixp=subNbx+2;
if(iyp==-1) iyp=subNby+2;
if(izp==-1) izp=subNbz+2;
-
+
FfP[isten] = weightx*weighty*weightz;
// interpolated velocity based on delta function.
for(k=0; k<3; k++){
@@ -1666,11 +1666,11 @@ double FixLbRigidPCSphere::compute_array(int i, int j)
FfP[5] = dx1*(1.-dy1)*dz1;
FfP[6] = dx1*dy1*(1.-dz1);
FfP[7] = dx1*dy1*dz1;
-
+
ixp = (ix+1);
iyp = (iy+1);
izp = (iz+1);
-
+
for (k=0; k<3; k++) { // tri-linearly interpolated velocity at node
up[i][k] = u_lb[ix][iy][iz][k]*FfP[0]
+ u_lb[ix][iy][izp][k]*FfP[1]
@@ -1679,13 +1679,13 @@ double FixLbRigidPCSphere::compute_array(int i, int j)
+ u_lb[ixp][iy][iz][k]*FfP[4]
+ u_lb[ixp][iy][izp][k]*FfP[5]
+ u_lb[ixp][iyp][iz][k]*FfP[6]
- + u_lb[ixp][iyp][izp][k]*FfP[7];
+ + u_lb[ixp][iyp][izp][k]*FfP[7];
}
- }
+ }
for(k=0; k<3; k++)
up[i][k] = up[i][k]*dx_lb/dt_lb;
}
}
-
+
}
diff --git a/src/USER-LB/fix_lb_rigid_pc_sphere.h b/src/USER-LB/fix_lb_rigid_pc_sphere.h
index 0ce7e9b833..be7e9ee253 100755
--- a/src/USER-LB/fix_lb_rigid_pc_sphere.h
+++ b/src/USER-LB/fix_lb_rigid_pc_sphere.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -90,7 +90,7 @@ class FixLbRigidPCSphere : public Fix {
double tfactor; // scale factor on temperature of rigid bodies
int inner_nodes; // ==1 if certain particle are inside the rigid
- // body and should not interact with the fluid.
+ // body and should not interact with the fluid.
// ==0 otherwise.
int igroupinner; // specifies the particles which are inside the
// spherical rigid body, and do not interact with
@@ -98,7 +98,7 @@ class FixLbRigidPCSphere : public Fix {
void set_xv();
void set_v();
-
+
void compute_up();
class FixLbFluid *fix_lb_fluid;
diff --git a/src/USER-LB/fix_lb_viscous.cpp b/src/USER-LB/fix_lb_viscous.cpp
index 03beb57f3d..d0157272a8 100755
--- a/src/USER-LB/fix_lb_viscous.cpp
+++ b/src/USER-LB/fix_lb_viscous.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -15,9 +15,9 @@
Contributing authors: Frances Mackay, Santtu Ollila, Colin Denniston (UWO)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "fix_lb_viscous.h"
#include "atom.h"
#include "update.h"
@@ -38,7 +38,7 @@ FixLbViscous::FixLbViscous(LAMMPS *lmp, int narg, char **arg) :
if (narg < 3) error->all(FLERR,"Illegal fix lb/viscous command");
int groupbit_lb_fluid = 0;
-
+
for(int ifix=0; ifix<modify->nfix; ifix++)
if(strcmp(modify->fix[ifix]->style,"lb/fluid")==0){
fix_lb_fluid = (FixLbFluid *)modify->fix[ifix];
@@ -52,9 +52,9 @@ FixLbViscous::FixLbViscous(LAMMPS *lmp, int narg, char **arg) :
int nlocal = atom->nlocal;
for(int j=0; j<nlocal; j++){
if((mask[j] & groupbit) && !(mask[j] & groupbit_lb_fluid))
- error->one(FLERR,"to apply a fluid force onto an atom, the lb/fluid fix must be used for that atom.");
+ error->one(FLERR,"to apply a fluid force onto an atom, the lb/fluid fix must be used for that atom.");
}
-
+
}
diff --git a/src/USER-LB/fix_lb_viscous.h b/src/USER-LB/fix_lb_viscous.h
index 3a6569fac7..51cecc293b 100755
--- a/src/USER-LB/fix_lb_viscous.h
+++ b/src/USER-LB/fix_lb_viscous.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -40,7 +40,7 @@ class FixLbViscous : public Fix {
int nlevels_respa;
private:
- class FixLbFluid *fix_lb_fluid;
+ class FixLbFluid *fix_lb_fluid;
};
}
diff --git a/src/USER-MGPT/mgpt_linalg.cpp b/src/USER-MGPT/mgpt_linalg.cpp
index 185b61e1c7..94a4e21ea6 100644
--- a/src/USER-MGPT/mgpt_linalg.cpp
+++ b/src/USER-MGPT/mgpt_linalg.cpp
@@ -94,7 +94,7 @@ static void transprod_generic(const double * restrict A,
C[i*lda+(j+1)] = s;
}
}
-
+
static void transtrace3_generic(const double * restrict A,
const double * restrict B0,double * restrict tout0,
const double * restrict B1,double * restrict tout1,
@@ -146,7 +146,7 @@ mgpt_linalg::mgpt_linalg() {
tr_trace = transtrace3_error;
single = 0;
}
-
+
mgpt_linalg::mgpt_linalg(int n,int single_precision) {
mgpt_linalg::matrix_size = n;
diff --git a/src/USER-MGPT/mgpt_readpot.cpp b/src/USER-MGPT/mgpt_readpot.cpp
index bfbb15ddcb..144c661b05 100644
--- a/src/USER-MGPT/mgpt_readpot.cpp
+++ b/src/USER-MGPT/mgpt_readpot.cpp
@@ -39,7 +39,7 @@ static double fl(double r,int mode,double rp,double p1,double al,double r0,doubl
term = pow(rp/r, p1);
else
term = exp(-p1*(pow(r/rp, pn) - 1.0)/pn);
-
+
if (r <= r0) return term;
double quan = al*(r/r0 - 1.0)*(r/r0 - 1.0);
if(mode <= 2)
@@ -102,7 +102,7 @@ static void getparmindata(const char *potin_file,int nvol[1],double vol0[1],doub
__FILE__,__LINE__,
metal,ipot,mode,
metalx,ipotx,modex);
- exit(1);
+ exit(1);
}
}
@@ -129,7 +129,7 @@ static void getparmindata(const char *potin_file,int nvol[1],double vol0[1],doub
__FILE__,__LINE__,potin_file);
exit(1);
}
-
+
if(0) {
printf("Before sort:\n");
for(int i = 0; i<n; i++)
@@ -196,7 +196,7 @@ void potdata::readpot(const char *parmin_file,const char *potin_file,const doubl
if(0) {
printf("getparmindata() ==> nvol = %d, vol0 = %.6f, x0= %.6f, x1 = %.6f, dx = %.6f\n",
nvol,vol0,x0,x1,dx);
- }
+ }
} else {
/* Two-line version, reparse this line, and read second line */
sscanf(line,"%lf %lf %lf %lf",&x0,&x1,&dx,&vol0);
@@ -375,7 +375,7 @@ void potdata::readpot(const char *parmin_file,const char *potin_file,const doubl
double alp = al,alm = al;
if(mode == 2 || mode == 4 || mode == 6) alm = 125.0;
al = alp;
-
+
double r = r0 + j*(r1-r0)/(nr-1);
double rrws = r/rws;
@@ -386,7 +386,7 @@ void potdata::readpot(const char *parmin_file,const char *potin_file,const doubl
double v2a = vatab[i]*fl2*fl2;
double v2b = vbtab[i]*fl2;
double fscr = 1.0;
-
+
if(bscreen == 1 && rrws >= r0rws) {
double arg = rrws/r0rwstab[i];
double arg1 = arg - 1.0;
@@ -402,7 +402,7 @@ void potdata::readpot(const char *parmin_file,const char *potin_file,const doubl
dp=2.0*al*al*arg*arg13/(1.+al*arg12);
}
fscr = f*f;
- }
+ }
double vpair_tmp = vpairtab[i*nr+j];
vpairtab[i*nr+j] = vpairtab[i*nr+j]*fscr + v2a - v2b;
@@ -421,7 +421,7 @@ void potdata::readpot(const char *parmin_file,const char *potin_file,const doubl
}
-
+
}
}
fclose(in);
@@ -488,10 +488,10 @@ void potdata::readpot(const char *parmin_file,const char *potin_file,const doubl
if(1) {
printf("%% READPOT PARAMETERS:\n");
-
+
printf("%% ddl = %15.5e %15.5e %15.5e %15.5e\n",ddl[1],ddl[2],ddl[3],ddl[4]);
printf("%% anorm3 = %15.5e anorm4 = %15.5e\n",anorm3,anorm4);
-
+
printf("%% x = %15.5e pn = %15.5e\n",x,pn);
printf("%% va = %15.5e dva = %15.5e\n",va,dva);
printf("%% vb = %15.5e dvb = %15.5e\n",vb,dvb);
diff --git a/src/USER-MGPT/mgpt_readpot.h b/src/USER-MGPT/mgpt_readpot.h
index c8a7a806d1..c19ea40774 100644
--- a/src/USER-MGPT/mgpt_readpot.h
+++ b/src/USER-MGPT/mgpt_readpot.h
@@ -30,7 +30,7 @@ struct potdata {
double (*vpair_spline)[4],(*dvpair_spline)[4];
double r0,r1;
int nr;
-
+
double mass,rcrit,rmax;
int lang,lmax;
@@ -64,7 +64,7 @@ struct potdata2 {
double (*vpair)[4][4],(*dvpair)[4][4];
double r0,r1,T0,T1;
int nr,nt;
-
+
potdata *potlist;
double mass,rcrit,rmax;
diff --git a/src/USER-MGPT/mgpt_splinetab.cpp b/src/USER-MGPT/mgpt_splinetab.cpp
index 22df495f9e..7cff0e6e2b 100644
--- a/src/USER-MGPT/mgpt_splinetab.cpp
+++ b/src/USER-MGPT/mgpt_splinetab.cpp
@@ -40,7 +40,7 @@ void makespline(int ntab,int stride,double tab[],double C[][4]) {
double h_left,h_right,d;
int i,j;
-
+
/* Second order second derivative approximation
at end points. */
h_left =
@@ -58,7 +58,7 @@ void makespline(int ntab,int stride,double tab[],double C[][4]) {
A[j+2][0] = 1.0; A[j+2][1] = 2.0; A[j+2][2] = -1.0; y[j+2] = -d;
A[j+3][0] = 2.0; A[j+3][1] = 2.0; A[j+3][2] = -2.0; y[j+3] = 2.0*d;
}
-
+
j = 3*(ntab-2);
d = tab[stride*(ntab-1)] - tab[stride*(ntab-2)];
A[j+1][0] = 1.0; A[j+1][1] = 1.0; A[j+1][2] = 1.0; y[j+1] = d;
@@ -82,9 +82,9 @@ void evalcubic(double p[4],double x,double *y,double *dy,double *d2y) {
t1 = p[2] + x*p[3];
t2 = p[1] + x*t1;
-
+
t3 = t1 + x*p[3];
-
+
*y = p[0] + x*t2;
*dy = (t2 + x*t3);
*d2y = 2.0*(t3 + x*p[3]);
@@ -115,9 +115,9 @@ void evalspline(int n,double x0,double x1,double C[][4],
} else {
t1 = p[2] + xhat*p[3];
t2 = p[1] + xhat*t1;
-
+
t3 = t1 + xhat*p[3];
-
+
*y = p[0] + xhat*t2;
*dy = (t2 + xhat*t3)*dxinv;
*d2y = 2.0*(t3 + xhat*p[3])*(dxinv*dxinv);
diff --git a/src/USER-MGPT/mgpt_splinetab.h b/src/USER-MGPT/mgpt_splinetab.h
index e719f34218..05c9dbcafb 100644
--- a/src/USER-MGPT/mgpt_splinetab.h
+++ b/src/USER-MGPT/mgpt_splinetab.h
@@ -24,11 +24,11 @@
Given a table of ntab data points tab, assumed to be sampled
on an equidistant grid, compute coefficients of interpolating
cubic polynimials, one per interval (i.e. ntab-1 polynomials).
-
+
Input point i is located at tab[i*stride].
-
+
Coefficients of output polynomial j are at C[j][0..3];
-
+
The piecewise polynimials form a C^2 function which
approximates the input function to fourth order.
diff --git a/src/USER-MGPT/pair_mgpt.cpp b/src/USER-MGPT/pair_mgpt.cpp
index 596e66f488..83524107c8 100644
--- a/src/USER-MGPT/pair_mgpt.cpp
+++ b/src/USER-MGPT/pair_mgpt.cpp
@@ -12,7 +12,7 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
- Contributing authors: Tomas Oppelstrup, LLNL (oppelstrup2@llnl.gov)
+ Contributing authors: Tomas Oppelstrup, LLNL (oppelstrup2@llnl.gov)
and John Moriarty, LLNL (moriarty2@llnl.gov)
Fast MGPT algorithm developed by Tomas Oppelstrup (2015) based on the
@@ -62,7 +62,7 @@ static double gettime(int x = 0) {
const double x = 1.0 / CLOCKS_PER_SEC;
return clock() * x;
*/
-
+
//const double invfreq = 1.0 / 2394.108e6;
/*
const double invfreq = 1.0 / 700e6;
@@ -147,12 +147,12 @@ void PairMGPT::make_bond(const double xx[][3],int i,int j,bond_data *bptr) {
hamltn_5_raw(rrij[0],rrij[1],rrij[2],
bptr->H.m ,bptr->Hx.m,
bptr->Hy.m,bptr->Hz.m,&bptr->fl_deriv_sum);
- } else {
+ } else {
hamltn_7_raw(rrij[0],rrij[1],rrij[2],
bptr->H.m ,bptr->Hx.m,
bptr->Hy.m,bptr->Hz.m,&bptr->fl_deriv_sum);
}
-
+
t1 = gettime();
t_make_b2 += t1-t0;
n_make_b2++;
@@ -274,10 +274,10 @@ PairMGPT::triplet_data *PairMGPT::get_triplet(const double xx[][3],int i,int j,i
}
-double PairMGPT::numderiv3t(double xx[][3],int i,int j,int k,int p) {
+double PairMGPT::numderiv3t(double xx[][3],int i,int j,int k,int p) {
static bond_data Bij,Bjk,Bki;
const double delta = 1e-5;
-
+
const double xsave = xx[i][p];
double e1,e2;
@@ -301,10 +301,10 @@ double PairMGPT::numderiv3t(double xx[][3],int i,int j,int k,int p) {
return (e1 - e2)/(2.0*delta);
}
-double PairMGPT::numderiv3v(double xx[][3],int i,int j,int k,int p,int ipert) {
+double PairMGPT::numderiv3v(double xx[][3],int i,int j,int k,int p,int ipert) {
static bond_data Bij,Bik;
const double delta = 1e-5;
-
+
const double xsave = xx[ipert][p];
double e1,e2;
@@ -325,10 +325,10 @@ double PairMGPT::numderiv3v(double xx[][3],int i,int j,int k,int p,int ipert) {
}
-double PairMGPT::numderiv4(double xx[][3],int i,int j,int k,int m,int p) {
+double PairMGPT::numderiv4(double xx[][3],int i,int j,int k,int m,int p) {
static bond_data Bij,Bjk,Bkm,Bmi;
const double delta = 1e-5;
-
+
const double xsave = xx[i][p];
double e1,e2;
@@ -365,14 +365,14 @@ void PairMGPT::force_debug_3t(double xx[][3],
dfi[0] = dfix; dfi[1] = dfiy; dfi[2] = dfiz;
dfj[0] = dfjx; dfj[1] = dfjy; dfj[2] = dfjz;
dfk[0] = dfkx; dfk[1] = dfky; dfk[2] = dfkz;
-
+
for(int p = 0; p<3; p++) {
/* Compute numerical derivatives by displacing atoms i,j,k */
double ndfi,ndfj,ndfk;
ndfi = -numderiv3t(xx,i,j,k,p);
ndfj = -numderiv3t(xx,j,k,i,p);
ndfk = -numderiv3t(xx,k,i,j,p);
-
+
if((fabs(dfi[p] - ndfi) > dtol &&
fabs(dfi[p] - ndfi) > dtol*fabs(ndfi)) ||
(fabs(dfj[p] - ndfj) > dtol &&
@@ -382,7 +382,7 @@ void PairMGPT::force_debug_3t(double xx[][3],
printf("Force error in T12 & T23 & T31 :: i,j,k = %d,%d,%d\n",i0,j0,k0);
printf(" dE/d%c[i] = %20.10e %20.10e\n", 'x'+p,ndfi, dfi[p]);
printf(" dE/d%c[j] = %20.10e %20.10e\n", 'x'+p,ndfj, dfj[p]);
- printf(" dE/d%c[k] = %20.10e %20.10e\n", 'x'+p,ndfk, dfk[p]);
+ printf(" dE/d%c[k] = %20.10e %20.10e\n", 'x'+p,ndfk, dfk[p]);
printf("\n");
}
}
@@ -398,14 +398,14 @@ void PairMGPT::force_debug_3v(double xx[][3],
dfi[0] = dfix; dfi[1] = dfiy; dfi[2] = dfiz;
dfj[0] = dfjx; dfj[1] = dfjy; dfj[2] = dfjz;
dfk[0] = dfkx; dfk[1] = dfky; dfk[2] = dfkz;
-
+
for(int p = 0; p<3; p++) {
/* Compute numerical derivatives by displacing atoms i,j,k */
double ndfi,ndfj,ndfk;
ndfi = -numderiv3v(xx,i,j,k,p,i0);
ndfj = -numderiv3v(xx,i,j,k,p,j0);
ndfk = -numderiv3v(xx,i,j,k,p,k0);
-
+
if((fabs(dfi[p] - ndfi) > dtol &&
fabs(dfi[p] - ndfi) > dtol*fabs(ndfi)) ||
(fabs(dfj[p] - ndfj) > dtol &&
@@ -415,7 +415,7 @@ void PairMGPT::force_debug_3v(double xx[][3],
printf("Force error in T12 :: i,j,k = %d,%d,%d\n",i0,j0,k0);
printf(" dE/d%c[i] = %20.10e %20.10e\n", 'x'+p,ndfi, dfi[p]);
printf(" dE/d%c[j] = %20.10e %20.10e\n", 'x'+p,ndfj, dfj[p]);
- printf(" dE/d%c[k] = %20.10e %20.10e\n", 'x'+p,ndfk, dfk[p]);
+ printf(" dE/d%c[k] = %20.10e %20.10e\n", 'x'+p,ndfk, dfk[p]);
printf("\n");
}
}
@@ -434,7 +434,7 @@ void PairMGPT::force_debug_4(double xx[][3],
dfj[0] = dfjx; dfj[1] = dfjy; dfj[2] = dfjz;
dfk[0] = dfkx; dfk[1] = dfky; dfk[2] = dfkz;
dfm[0] = dfmx; dfm[1] = dfmy; dfm[2] = dfmz;
-
+
const int ii0[] = {i0,j0,k0,m0},ii[] = {i,j,k,m,i,j,k};
for(int p = 0; p<3; p++) {
@@ -466,7 +466,7 @@ void PairMGPT::force_debug_4(double xx[][3],
printf("Force error in T31 & T64 :: i,j,k,m = %d,%d,%d,%d\n",i0,j0,k0,m0);
printf(" dE/d%c[i] = %20.10e %20.10e\n", 'x'+p,ndfi, dfi[p]);
printf(" dE/d%c[j] = %20.10e %20.10e\n", 'x'+p,ndfj, dfj[p]);
- printf(" dE/d%c[k] = %20.10e %20.10e\n", 'x'+p,ndfk, dfk[p]);
+ printf(" dE/d%c[k] = %20.10e %20.10e\n", 'x'+p,ndfk, dfk[p]);
printf(" dE/d%c[m] = %20.10e %20.10e\n", 'x'+p,ndfm, dfm[p]);
printf("\n");
}
@@ -519,7 +519,7 @@ void PairMGPT::force_debug_4(double xx[][3],
dfj##coord = ( ( sij)*trd1##coord + (-sjk)*trd2##coord ) * (ve / anorm4); \
dfk##coord = ( ( sjk)*trd2##coord + (-skm)*trd4##coord ) * (ve / anorm4); \
dfm##coord = ( ( sim)*trd3##coord + ( skm)*trd4##coord ) * (ve / anorm4); \
- } while(0)
+ } while(0)
#define dfix_update_4b(coord) \
@@ -592,7 +592,7 @@ void PairMGPT::compute_x(const int *nnei,const int * const *nlist,
int evflag,int newton_pair) {
Hash<bond_data,Doublet> bond_hash(100000);
int i,j,k,m,ix,jx,kx,mx,itag,jtag,p;
-
+
double e_single,e_pair,e_triplet,e_triplet_c,e_quad;
double volvir2;
@@ -709,7 +709,7 @@ void PairMGPT::compute_x(const int *nnei,const int * const *nlist,
if(triclinic) {
double E[3][3],EX[3][3];
int cyc[] = {0,1,2,0,1};
-
+
ss = (double (*)[3]) memory->smalloc(sizeof(double [3]) * ntot,
"mgpt: local reduced coordinate vector.");
@@ -739,7 +739,7 @@ void PairMGPT::compute_x(const int *nnei,const int * const *nlist,
}
} else
ss = xx;
-
+
nneitot = 0;
for(ix = 0; ix<ntot; ix++) {
for(p = 0; p<3; p++) {
@@ -773,7 +773,7 @@ void PairMGPT::compute_x(const int *nnei,const int * const *nlist,
printf("Can not handle triclinic box yet\n");
error->all(__FILE__,__LINE__,"Can not handle triclinic cell with mgpt yet.");
}
-
+
/*
for(i = 0; i<nloc; i++) {
printf("Atom %3d:: %10.3f %10.3f %10.3f\n",
@@ -788,13 +788,13 @@ void PairMGPT::compute_x(const int *nnei,const int * const *nlist,
first[i+1] = first[i];
const int c1 = c1_outside(ss[i],triclinic,alpha);
-
+
tx0 = gettime();
for(jx = 0; jx<nnei[i]; jx++) {
fjx = fjy = fjz = 0.0;
j = NIDX( nlist[i][jx] );
-
+
rij2 = 0.0;
for(p = 0; p<3; p++) {
double t = xx[i][p] - xx[j][p];
@@ -813,14 +813,14 @@ void PairMGPT::compute_x(const int *nnei,const int * const *nlist,
splinepot.eval_pot(rij,&de_pair,&df);
de_pair = de_pair * e_scale * w2;
df = df / rij * w2;
-
+
if(pair_energies == 0) de_pair = 0.0;
e_pair = e_pair + de_pair;
c_p++;
-
+
if(pair_forces == 0) df = 0.0;
-
+
if(volpres_flag && pair_energies) {
double dvir;
splinepot.eval_vir(rij,&dvir);
@@ -834,40 +834,40 @@ void PairMGPT::compute_x(const int *nnei,const int * const *nlist,
vatom[j][pp] -= 0.5 * rhoinv*e_scale*dvir*w2;
}
}
-
+
double drijx = xx[j][0] - xx[i][0];
double drijy = xx[j][1] - xx[i][1];
double drijz = xx[j][2] - xx[i][2];
-
+
fix = fix + df*drijx;
fjx = fjx - df*drijx;
-
+
fiy = fiy + df*drijy;
fjy = fjy - df*drijy;
-
+
fiz = fiz + df*drijz;
fjz = fjz - df*drijz;
-
+
if(evflag) {
//ev_tally(i,j,nloc,newton_pair,de_pair,0.0,df,-drijx,-drijy,-drijz);
/* To fix stress-per-atom scaling, and sign */
ev_tally(i,j,nloc,newton_pair,de_pair,0.0,-df * e_scale,-drijx,-drijy,-drijz);
}
-
+
ff[j][0] += fjx * e_scale;
ff[j][1] += fjy * e_scale;
ff[j][2] += fjz * e_scale;
-
+
}
}
}
-
+
if(rij2 < rcut2_bond && c2_outside(ss[i],ss[j],triclinic,alpha) == 0) {
/*
Add j to short neighbor list for i.
- Insert j to keep list sorted.
+ Insert j to keep list sorted.
*/
-
+
p = first[i+1]-1;
while(p >= first[i] && nlist_short[p] > j) {
nlist_short[p+1] = nlist_short[p];
@@ -880,13 +880,13 @@ void PairMGPT::compute_x(const int *nnei,const int * const *nlist,
nneitot,i);
error->one(__FILE__,__LINE__,"Shit! Short list full\n");
}
-
+
}
}
ff[i][0] += fix * e_scale;
ff[i][1] += fiy * e_scale;
- ff[i][2] += fiz * e_scale;
+ ff[i][2] += fiz * e_scale;
tx1 = gettime();
tpair += tx1-tx0;
@@ -916,27 +916,27 @@ void PairMGPT::compute_x(const int *nnei,const int * const *nlist,
fjx = fjy = fjz = 0.0;
j = nlist_short[jx];
-
+
for(kx = first[i]; kx<jx; kx++) {
fkx = fky = fkz = 0.0;
k = nlist_short[kx];
-
+
/*
Search lists of j and k, and see if
1) j is in k-list (closed triplet)
2) j and k have a common neighbor (closed quadruplet)
*/
-
+
c_ij = c_ki = 1;
-
+
const int sij = (i < j) ? 1 : -1;
const int sjk = (j < k) ? 1 : -1;
const int ski = (k < i) ? 1 : -1;
-
-
+
+
T12 = T23 = T31 = 0;
-
+
mj = first[j];
/*
Since i is in the j-list, and i > k and the list
@@ -946,7 +946,7 @@ void PairMGPT::compute_x(const int *nnei,const int * const *nlist,
if(mj < first[j+1] && nlist_short[mj] == k) {
/* Closed triplet */
c_jk = 1;
-
+
if(j > i) continue; /* Require k<j<i for closed triplets */
} else {
/* Open triplet */
@@ -954,13 +954,13 @@ void PairMGPT::compute_x(const int *nnei,const int * const *nlist,
}
tx0 = gettime();
-
+
w3 = get_weight(triclinic,ss[i],ss[j],ss[k]);
int triplet_defer;
if(w3 > 0.0) {
triplet_defer = 0;
-
+
dvir_ij = dvir_jk = dvir_ki = 0.0;
if(c_ij && c_jk)
T12 = get_triplet(xx,j,i,k,&bond_hash,&T12work,&dvir_ij,&dvir_jk);
@@ -968,7 +968,7 @@ void PairMGPT::compute_x(const int *nnei,const int * const *nlist,
T23 = get_triplet(xx,k,i,j,&bond_hash,&T23work,&dvir_ki,&dvir_jk);
if(c_ij && c_ki)
T31 = get_triplet(xx,i,j,k,&bond_hash,&T31work,&dvir_ij,&dvir_ki);
-
+
if(evflag) {
fsave[0][0] = fix; fsave[0][1] = fiy; fsave[0][2] = fiz;
fsave[1][0] = fjx; fsave[1][1] = fjy; fsave[1][2] = fjz;
@@ -977,14 +977,14 @@ void PairMGPT::compute_x(const int *nnei,const int * const *nlist,
fjx = fjy = fjz = 0.0;
fkx = fky = fkz = 0.0;
}
-
- tr0 = tr1 = tr2 = tr3 = 0.0;
+
+ tr0 = tr1 = tr2 = tr3 = 0.0;
double xvir3t,xvir3v;
xvir3t = xvir3v = 0.0;
if(T12 && T23) {
bond_data *bki = bond_hash.Lookup(Doublet(k,i));
-
+
if(three_body_energies && evflag) {
tr0 = transtrace(T12->H1H2,bki->H);
double dvir = ((dvir_ij + dvir_jk + bki->fl_deriv_sum)*splinepot.vc +
@@ -993,7 +993,7 @@ void PairMGPT::compute_x(const int *nnei,const int * const *nlist,
xvir3t = xvir3t + dvir;
}
mcount2++;
-
+
{
const double vc = splinepot.vc;
tr_trace3(&(bki->H.m[1][0]),
@@ -1009,7 +1009,7 @@ void PairMGPT::compute_x(const int *nnei,const int * const *nlist,
tr_trace3(&(T12->H1H2.m[1][0]),
&(bki->Hx.m[1][0]),&utr3x.d,
&(bki->Hy.m[1][0]),&utr3y.d,
- &(bki->Hz.m[1][0]),&utr3z.d);
+ &(bki->Hz.m[1][0]),&utr3z.d);
if(linalg.single) {
trd1x = utr1x.f; trd2x = utr2x.f; trd3x = utr3x.f;
@@ -1018,17 +1018,17 @@ void PairMGPT::compute_x(const int *nnei,const int * const *nlist,
} else {
trd1x = utr1x.d; trd2x = utr2x.d; trd3x = utr3x.d;
trd1y = utr1y.d; trd2y = utr2y.d; trd3y = utr3y.d;
- trd1z = utr1z.d; trd2z = utr2z.d; trd3z = utr3z.d;
+ trd1z = utr1z.d; trd2z = utr2z.d; trd3z = utr3z.d;
}
dfix = ( (-sij)*trd1x + ( ski)*trd3x ) * (vc / anorm3);
dfjx = ( ( sij)*trd1x + (-sjk)*trd2x ) * (vc / anorm3);
dfkx = ( ( sjk)*trd2x + (-ski)*trd3x ) * (vc / anorm3);
-
+
dfiy = ( (-sij)*trd1y + ( ski)*trd3y ) * (vc / anorm3);
dfjy = ( ( sij)*trd1y + (-sjk)*trd2y ) * (vc / anorm3);
dfky = ( ( sjk)*trd2y + (-ski)*trd3y ) * (vc / anorm3);
-
+
dfiz = ( (-sij)*trd1z + ( ski)*trd3z ) * (vc / anorm3);
dfjz = ( ( sij)*trd1z + (-sjk)*trd2z ) * (vc / anorm3);
dfkz = ( ( sjk)*trd2z + (-ski)*trd3z ) * (vc / anorm3);
@@ -1039,11 +1039,11 @@ void PairMGPT::compute_x(const int *nnei,const int * const *nlist,
dfix,dfiy,dfiz,
dfjx,dfjy,dfjz,
dfkx,dfky,dfkz);
-
+
if(three_body_forces)
accumulate_forces_3(w3);
}
-
+
if(T12 != 0) {
//printf("T12 i,j,k = %d,%d,%d\n",i,j,k);
mcount++;
@@ -1054,7 +1054,7 @@ void PairMGPT::compute_x(const int *nnei,const int * const *nlist,
vir3v = vir3v + dvir;
xvir3v = xvir3v + dvir;
}
-
+
{
const double vd = splinepot.vd;
@@ -1079,23 +1079,23 @@ void PairMGPT::compute_x(const int *nnei,const int * const *nlist,
dfix = 2.0*(-sij)*trd1x * (vd / anorm4);
dfkx = 2.0*( sjk)*trd2x * (vd / anorm4);
dfjx = -(dfix + dfkx);
-
+
dfiy = 2.0*(-sij)*trd1y * (vd / anorm4);
dfky = 2.0*( sjk)*trd2y * (vd / anorm4);
dfjy = -(dfiy + dfky);
-
+
dfiz = 2.0*(-sij)*trd1z * (vd / anorm4);
dfkz = 2.0*( sjk)*trd2z * (vd / anorm4);
dfjz = -(dfiz + dfkz);
}
-
+
if(triplet_debug) /* Compare forces to numerical derivatives */
force_debug_3v(xx,i,j,k, j,i,k,
dfix,dfiy,dfiz,
dfjx,dfjy,dfjz,
dfkx,dfky,dfkz);
-
-
+
+
if(three_body_forces)
accumulate_forces_3(w3);
}
@@ -1110,10 +1110,10 @@ void PairMGPT::compute_x(const int *nnei,const int * const *nlist,
vir3v = vir3v + dvir;
xvir3v = xvir3v + dvir;
}
-
+
{
const double vd = splinepot.vd;
-
+
tr_trace3(&(T23->H1H2.m[1][0]),
&(T23->H1xH2.m[1][0]),&utr1x.d,
&(T23->H1yH2.m[1][0]),&utr1y.d,
@@ -1135,11 +1135,11 @@ void PairMGPT::compute_x(const int *nnei,const int * const *nlist,
dfix = 2.0*( ski)*trd1x * (vd / anorm4);
dfjx = 2.0*(-sjk)*trd2x * (vd / anorm4);
dfkx = -(dfix + dfjx);
-
+
dfiy = 2.0*( ski)*trd1y * (vd / anorm4);
dfjy = 2.0*(-sjk)*trd2y * (vd / anorm4);
dfky = -(dfiy + dfjy);
-
+
dfiz = 2.0*( ski)*trd1z * (vd / anorm4);
dfjz = 2.0*(-sjk)*trd2z * (vd / anorm4);
dfkz = -(dfiz + dfjz);
@@ -1150,10 +1150,10 @@ void PairMGPT::compute_x(const int *nnei,const int * const *nlist,
dfix,dfiy,dfiz,
dfjx,dfjy,dfjz,
dfkx,dfky,dfkz);
-
+
if(three_body_forces)
accumulate_forces_3(w3);
-
+
}
if(T31 != 0) {
@@ -1166,10 +1166,10 @@ void PairMGPT::compute_x(const int *nnei,const int * const *nlist,
vir3v = vir3v + dvir;
xvir3v = xvir3v + dvir;
}
-
+
{
const double vd = splinepot.vd;
-
+
tr_trace3(&(T31->H1H2.m[1][0]),
&(T31->H1xH2.m[1][0]),&utr1x.d,
&(T31->H1yH2.m[1][0]),&utr1y.d,
@@ -1191,36 +1191,36 @@ void PairMGPT::compute_x(const int *nnei,const int * const *nlist,
dfjx = 2.0*( sij)*trd1x * (vd / anorm4);
dfkx = 2.0*(-ski)*trd2x * (vd / anorm4);
dfix = -(dfjx + dfkx);
-
+
dfjy = 2.0*( sij)*trd1y * (vd / anorm4);
dfky = 2.0*(-ski)*trd2y * (vd / anorm4);
dfiy = -(dfjy + dfky);
-
+
dfjz = 2.0*( sij)*trd1z * (vd / anorm4);
dfkz = 2.0*(-ski)*trd2z * (vd / anorm4);
dfiz = -(dfjz + dfkz);
-
+
}
-
+
if(triplet_debug) /* Compare forces to numerical derivatives */
force_debug_3v(xx,i,j,k, i,j,k,
dfix,dfiy,dfiz,
dfjx,dfjy,dfjz,
dfkx,dfky,dfkz);
-
+
if(three_body_forces)
accumulate_forces_3(w3);
}
-
+
v33 = tr0 / anorm3;
v43 = (tr1 + tr2 + tr3) / anorm4;
double de_triplet = (splinepot.vc*v33 + splinepot.vd*v43) * e_scale * w3;
e_triplet = e_triplet + de_triplet;
e_triplet_c = e_triplet_c + splinepot.vc*v33 * e_scale * w3;
c_t++;
-
+
//printf("xxxx %6d %6d %6d :: %20.10e\n",1,2,3,de_triplet);
-
+
if(evflag) {
double drji[3],drki[3];
double fj[3] = {fjx,fjy,fjz},fk[3] = {fkx,fky,fkz};
@@ -1231,7 +1231,7 @@ void PairMGPT::compute_x(const int *nnei,const int * const *nlist,
fj[p] *= e_scale;
fk[p] *= e_scale;
}
-
+
ev_tally3(i,j,k,de_triplet,0.0,fj,fk,drji,drki);
if(volpres_flag && vflag_atom) {
@@ -1243,23 +1243,23 @@ void PairMGPT::compute_x(const int *nnei,const int * const *nlist,
vatom[k][pp] += dvir;
}
}
-
+
fix = fix+fsave[0][0]; fiy = fiy+fsave[0][1]; fiz = fiz+fsave[0][2];
fjx = fjx+fsave[1][0]; fjy = fjy+fsave[1][1]; fjz = fjz+fsave[1][2];
fkx = fkx+fsave[2][0]; fky = fky+fsave[2][1]; fkz = fkz+fsave[2][2];
- }
-
+ }
+
tx1 = gettime();
ttriplet += tx1 - tx0;
nttriplet++;
} else {
triplet_defer = 1;
}
-
+
if(four_body_energies || four_body_forces)
if(j < i) { /* Search for quadruplet */
tx0 = gettime();
-
+
mj = first[j];
mk = first[k];
/*
@@ -1267,7 +1267,7 @@ void PairMGPT::compute_x(const int *nnei,const int * const *nlist,
and lists are sorted, so the loop terminates.
*/
while(nlist_short[mj] < i && nlist_short[mk] < i) {
-
+
if(mj >= first[j+1] || mk >= first[k+1]) {
printf("Illegal quad...\n"
" j=%d first[j]=%d first[j+1]=%d mj=%d\n"
@@ -1276,20 +1276,20 @@ void PairMGPT::compute_x(const int *nnei,const int * const *nlist,
k,first[k],first[k+1],mk);
error->one(__FILE__,__LINE__,"Shit, brkoen quad loop");
}
-
+
if(nlist_short[mj] == nlist_short[mk]) {
/* Closed quadruplet */
m = nlist_short[mj];
c_jm = c_km = 1;
-
+
const int sim = (i < m) ? 1 : -1;
const int sjm = (j < m) ? 1 : -1;
const int skm = (k < m) ? 1 : -1;
-
+
w4 = get_weight(triclinic,ss[i],ss[j],ss[k],ss[m]);
-
+
if(w4 > 0.0) {
-
+
/* Alrady know ij,jk,ki,jm,km bonds. Look for im bond. */
mi = first[i];
while(mi < first[i+1] && nlist_short[mi] < m) mi = mi + 1;
@@ -1297,9 +1297,9 @@ void PairMGPT::compute_x(const int *nnei,const int * const *nlist,
c_im = 1;
else
c_im = 0;
-
+
if(c_im == 0 || c_jk == 0 || (c_jk && c_im && m < k)) {
-
+
if(triplet_defer) {
dvir_ij = dvir_jk = dvir_ki = 0.0;
if(c_ij && c_jk)
@@ -1310,8 +1310,8 @@ void PairMGPT::compute_x(const int *nnei,const int * const *nlist,
T31 = get_triplet(xx,i,j,k,&bond_hash,&T31work,&dvir_ij,&dvir_ki);
triplet_defer = 0;
}
-
-
+
+
fmx = fmy = fmz = 0.0;
double xvir4 = 0.0;
@@ -1325,10 +1325,10 @@ void PairMGPT::compute_x(const int *nnei,const int * const *nlist,
fkx = fky = fkz = 0.0;
fmx = fmy = fmz = 0.0;
}
-
+
tr1 = tr2 = tr3 = 0.0;
-
- dvir_im = dvir_jm = dvir_km = 0.0;
+
+ dvir_im = dvir_jm = dvir_km = 0.0;
T45 = T56 = T64 = 0;
if(T12 != 0 && c_km && c_im)
T45 = get_triplet(xx,m,i,k,&bond_hash,&T45work,&dvir_im,&dvir_km);
@@ -1336,7 +1336,7 @@ void PairMGPT::compute_x(const int *nnei,const int * const *nlist,
T56 = get_triplet(xx,m,i,j,&bond_hash,&T56work,&dvir_im,&dvir_jm);
if(T31 != 0 && c_jm && c_km)
T64 = get_triplet(xx,m,j,k,&bond_hash,&T64work,&dvir_jm,&dvir_km);
-
+
if(T12 != 0 && T45 != 0) {
if(four_body_energies && evflag) {
tr1 = transtrace(T12->H1H2,T45->H1H2);
@@ -1346,26 +1346,26 @@ void PairMGPT::compute_x(const int *nnei,const int * const *nlist,
xvir4 = xvir4 + dvir;
}
qcount++;
-
+
{
const double ve = splinepot.ve;
-
+
trd_update_4(T12,T45);
dfix_update_4a(x);
dfix_update_4a(y);
dfix_update_4a(z);
}
-
+
if(quad_debug) /* Compare forces to numerical derivatives */
force_debug_4(xx,i,j,k,m, i,j,k,m,
dfix,dfiy,dfiz , dfjx,dfjy,dfjz,
dfkx,dfky,dfkz , dfmx,dfmy,dfmz);
-
+
if(four_body_forces)
accumulate_forces_4(w4);
}
-
+
if(T23 != 0 && T56 != 0) {
if(four_body_energies && evflag) {
tr2 = transtrace(T23->H1H2,T56->H1H2);
@@ -1375,25 +1375,25 @@ void PairMGPT::compute_x(const int *nnei,const int * const *nlist,
xvir4 = xvir4 + dvir;
}
qcount++;
-
+
{
const double ve = splinepot.ve;
-
+
trd_update_4(T23,T56);
dfix_update_4b(x);
dfix_update_4b(y);
dfix_update_4b(z);
}
-
+
if(quad_debug) /* Compare forces to numerical derivatives */
force_debug_4(xx,i,j,k,m, i,m,j,k,
dfix,dfiy,dfiz , dfjx,dfjy,dfjz,
dfkx,dfky,dfkz , dfmx,dfmy,dfmz);
-
+
if(four_body_forces)
accumulate_forces_4(w4);
-
+
}
if(T31 != 0 && T64 != 0) {
@@ -1405,10 +1405,10 @@ void PairMGPT::compute_x(const int *nnei,const int * const *nlist,
xvir4 = xvir4 + dvir;
}
qcount++;
-
+
{
const double ve = splinepot.ve;
-
+
/* X */
trd_update_4(T31,T64);
@@ -1416,16 +1416,16 @@ void PairMGPT::compute_x(const int *nnei,const int * const *nlist,
dfix_update_4c(y);
dfix_update_4c(z);
}
-
+
if(quad_debug) /* Compare forces to numerical derivatives */
force_debug_4(xx,i,j,k,m, i,j,m,k,
dfix,dfiy,dfiz , dfjx,dfjy,dfjz,
dfkx,dfky,dfkz , dfmx,dfmy,dfmz);
-
+
if(four_body_forces)
accumulate_forces_4(w4);
}
-
+
double de_quad = splinepot.ve*(tr1 + tr2 + tr3)/anorm4 * e_scale * w4;
e_quad = e_quad + de_quad;
if((T12 && T45) ||
@@ -1447,9 +1447,9 @@ void PairMGPT::compute_x(const int *nnei,const int * const *nlist,
fj[p] *= e_scale;
fk[p] *= e_scale;
}
-
+
ev_tally4(i,j,k,m,de_quad,fi,fj,fk,drim,drjm,drkm);
-
+
if(volpres_flag && vflag_atom) {
//virial[i] = virial[i] - vir4 * rhoinv*e_scale;
double dvir = -xvir4 * rhoinv*e_scale * (1.0/4.0);
@@ -1465,12 +1465,12 @@ void PairMGPT::compute_x(const int *nnei,const int * const *nlist,
fjx = fjx+fsave[1][0]; fjy = fjy+fsave[1][1]; fjz = fjz+fsave[1][2];
fkx = fkx+fsave[2][0]; fky = fky+fsave[2][1]; fkz = fkz+fsave[2][2];
fmx = fmx+fsave[3][0]; fmy = fmy+fsave[3][1]; fmz = fmz+fsave[3][2];
- }
-
+ }
+
ff[m][0] += fmx * e_scale;
ff[m][1] += fmy * e_scale;
ff[m][2] += fmz * e_scale;
-
+
}
}
mj = mj + 1;
@@ -1480,32 +1480,32 @@ void PairMGPT::compute_x(const int *nnei,const int * const *nlist,
} else {
mk = mk + 1;
}
-
+
}
tx1 = gettime();
tquad += tx1 - tx0;
ntquad++;
ntquaditer++;
}
-
-
+
+
ff[k][0] += fkx * e_scale;
ff[k][1] += fky * e_scale;
ff[k][2] += fkz * e_scale;
-
+
}
#undef transtrace
-
+
ff[j][0] += fjx * e_scale;
ff[j][1] += fjy * e_scale;
ff[j][2] += fjz * e_scale;
-
+
}
-
+
ff[i][0] += fix * e_scale;
ff[i][1] += fiy * e_scale;
ff[i][2] += fiz * e_scale;
-
+
if(single_energies == 1 && i < nloc) {
const double evol0 = splinepot.evol0;
if(eflag_global) {
@@ -1519,14 +1519,14 @@ void PairMGPT::compute_x(const int *nnei,const int * const *nlist,
}
}
-
+
}
-
+
tx0 = gettime();
for(i = 0; i<ntot; i++)
for(p = 0; p<3; p++)
atom->f[i][p] = atom->f[i][p] + ff[i][p];
-
+
memory->sfree(nlist_short);
memory->sfree(first);
if(ss != xx) memory->sfree(ss);
@@ -1535,7 +1535,7 @@ void PairMGPT::compute_x(const int *nnei,const int * const *nlist,
tx1 = gettime();
tmem += tx1-tx0;
ntmem++;
-
+
t1 = gettime(1);
//printf("compute_x: c_p = %d c_t = %d c_q = %d\n",c_p,c_t,c_q);
@@ -1565,7 +1565,7 @@ void PairMGPT::compute_x(const int *nnei,const int * const *nlist,
make_t_adj = t_make_t - adj*n_make,
make_b2_adj = t_make_b2 - adj*n_make_b2,
trace_adj = t_trace - adj*n_trace;
-
+
printf("mgpt engy = %10.3fms\n",(t1-t0)*1e3);
printf(" mem = %10.3fms n = %8.0f adj = %10.3fms one = %10.3fns\n",
tmem*1e3,ntmem,memadj*1e3,memadj/ntmem*1e9);
@@ -1592,7 +1592,7 @@ void PairMGPT::compute_x(const int *nnei,const int * const *nlist,
printf("mcount (transpose + trace for triplet) = %.0f , %.0f qcount = %.0f lmax = %d\n",
mcount,mcount2,qcount,lmax);
-
+
printf("nbc=%.0f tbl=%.3fms tbm=%.3fms one tbl=%.3fns one tbm=%.3fns\n",
nbc,(tbl-adj*nbc)*1e3,(tbm-adj*nbc)*1e3,(tbl/nbc-adj)*1e9,
(tbm/nbc-adj)*1e9);
@@ -1605,9 +1605,9 @@ void PairMGPT::compute_x(const int *nnei,const int * const *nlist,
printf("Bonds : nsearch=%d maxlen=%d avg.len=%.3f\n",
bond_hash.NSearch(),bond_hash.MaxLength(),
bond_hash.NStep()/(double) bond_hash.NSearch());
-
+
printf("compute_x: c_p = %d c_t = %d c_q = %d\n",c_p,c_t,c_q);
-
+
printf("@@ Total number of trace3 calls is %d, total number of make_triplet is %.1f\n",
ntr_calls,n_make);
@@ -1650,21 +1650,21 @@ void PairMGPT::compute_x(const int *nnei,const int * const *nlist,
if(pair_energies) // Virial correction for pair energy
for(i = 0; i<3; i++)
virial[i] = virial[i] + rhoinv*e_scale*volvir2;
-
+
if(three_body_energies) // Virial correction for three body enegries
for(i = 0; i<3; i++) {
//virial[i] = virial[i] - pot_input_vol*(e_triplet_c*pc + (e_triplet-e_triplet_c)*pd);
virial[i] = virial[i] - (vir3v + vir3t) * rhoinv*e_scale;
}
-
+
if(four_body_energies) // Virial correction for four body enegries
for(i = 0; i<3; i++) {
//virial[i] = virial[i] - pot_input_vol*e_quad*pe;
virial[i] = virial[i] - vir4 * rhoinv*e_scale;
}
-
+
}
-
+
*e_s = e_single;
*e_p = e_pair;
*e_t = e_triplet;
@@ -1675,7 +1675,7 @@ void PairMGPT::compute(int eflag, int vflag)
{
if(eflag || vflag) ev_setup(eflag, vflag);
else evflag = vflag_fdotr = eflag_global = vflag_global = eflag_atom = vflag_atom = 0;
-
+
int newton_pair = force->newton_pair;
double e_s,e_p,e_t,e_q;
@@ -1690,7 +1690,7 @@ void PairMGPT::compute(int eflag, int vflag)
printf("This is a problem. MGPT requires tag_enable flag to be on. Exiting...\n");
exit(1);
}
-
+
compute_x(listfull->numneigh,listfull->firstneigh,&e_s,&e_p,&e_t,&e_q,evflag,newton_pair);
if(0) { // Stupid force calculation / verification
@@ -1727,11 +1727,11 @@ void PairMGPT::compute(int eflag, int vflag)
double **atom_f_save = atom->f;
atom->f = ffptr;
-
+
for(int p = 0; p<3; p++) {
double xsave = atom->x[i][p];
const double delta = 1e-3;
-
+
atom->x[i][p] = xsave + delta;
for(int jj = 0; jj<3*nmax; jj++) ffwork[jj] = 0.0;
compute_x(listfull->numneigh,
@@ -1747,7 +1747,7 @@ void PairMGPT::compute(int eflag, int vflag)
double e2 = e_s + e_p + e_t + e_q;
ffloc[3*ii+p] = -(e1-e2)/(2*delta);
-
+
atom->x[i][p] = xsave;
}
@@ -1762,7 +1762,7 @@ void PairMGPT::compute(int eflag, int vflag)
printf(" Boundary %20.10e %20.10e %20.10e\n",
ffloc2[3*ii+0],ffloc2[3*ii+1],ffloc2[3*ii+2]);
}
-
+
delete[] ffloc2;
delete[] ffloc;
@@ -1781,7 +1781,7 @@ void PairMGPT::compute(int eflag, int vflag)
}
printf("\n\n");
}
-
+
if(vflag_fdotr) {
//printf("##### Using virial_compute!!!\n");
virial_fdotr_compute();
@@ -1803,7 +1803,7 @@ void PairMGPT::allocate()
}
/* ----------------------------------------------------------------------
- global settings
+ global settings
------------------------------------------------------------------------- */
void PairMGPT::settings(int narg, char **arg)
{
@@ -1821,27 +1821,27 @@ void PairMGPT::coeff(int narg, char **arg)
if(narg < 5)
error->all(__FILE__,__LINE__,
"Not enough arguments for mgpt (MGPT) pair coefficients.");
-
+
if(!allocated) allocate();
-
+
// Make sure I,J args are * *
if(strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0)
error->all(__FILE__,__LINE__,"Incorrect args for pair coefficients");
-
+
double vol;
if(sscanf(arg[4], "%lg", &vol) != 1 || vol <= 0.0)
error->all(__FILE__,__LINE__,"Invalid volume in mgpt (MGPT) pair coefficients.");
-
+
volpres_flag = 1;
single_precision = 0;
-
+
/* Parse arguments */ {
int volpres_tag = 0,precision_tag = 0,nbody_tag = 0;
int iarg = 5;
while (iarg < narg) {
if(strcmp(arg[iarg],"volpress") == 0) { /* Volumetric pressure flag */
- if (iarg+2 > narg)
+ if (iarg+2 > narg)
error->all(FLERR,"Incorrect args for pair coefficients");
if(strcmp(arg[iarg+1],"yes") == 0) volpres_flag = 1;
else if(strcmp(arg[iarg+1],"no") == 0) volpres_flag = 0;
@@ -1856,7 +1856,7 @@ void PairMGPT::coeff(int narg, char **arg)
iarg += 2;
if(comm->me == 0) printf("* volpress: volpres_flag = %d [%s %s]\n",volpres_flag,arg[iarg-2],arg[iarg-1]);
} else if(strcmp(arg[iarg],"nbody") == 0) {
- if (iarg+2 > narg)
+ if (iarg+2 > narg)
error->all(FLERR,"Incorrect args for pair coefficients");
if(strspn(arg[iarg+1],"1234") == strlen(arg[iarg+1])) {
nbody_flag = 0;
@@ -1877,7 +1877,7 @@ void PairMGPT::coeff(int narg, char **arg)
nbody_tag = 1;
iarg += 2;
} else if(strcmp(arg[iarg],"precision") == 0) {
- if (iarg+2 > narg)
+ if (iarg+2 > narg)
error->all(FLERR,"Incorrect args for pair coefficients");
if(strcmp(arg[iarg+1],"single") == 0) single_precision = 1;
else if(strcmp(arg[iarg+1],"double") == 0) single_precision = 0;
@@ -1898,13 +1898,13 @@ void PairMGPT::coeff(int narg, char **arg)
" precision {single|double} , default = double\n"
" nbody {[1234,]*} , default = whichever terms potential require\n"
"The invalid argument is \"%s\".\n",__FILE__,__LINE__,arg[iarg]);
- error->all(__FILE__,__LINE__,line);
+ error->all(__FILE__,__LINE__,line);
}
}
-
+
if(comm->me == 0)
printf("Volumetric pressure is %s.\n",volpres_flag ? "on" : "off");
-
+
if(comm->me == 0) {
FILE *parmin_fp = force->open_potential(arg[2]);
FILE *potin_fp = force->open_potential(arg[3]);
@@ -1926,7 +1926,7 @@ void PairMGPT::coeff(int narg, char **arg)
nbody_default -= (1<<2); // No 3-body contributions
if(splinepot.ve == 0.0 && splinepot.dve == 0.0)
nbody_default -= (1<<3); // No 4-body contributions
-
+
if(nbody_tag == 0) nbody_flag = nbody_default;
if(nbody_flag != nbody_default) {
@@ -1936,9 +1936,9 @@ void PairMGPT::coeff(int narg, char **arg)
}
}
}
-
+
MPI_Bcast(&nbody_flag,sizeof(nbody_flag),MPI_BYTE,0,world);
-
+
/*
Broadcast structure to all processes. In receiving
processes, pointes will be screwed up. We allocate
@@ -1963,15 +1963,15 @@ void PairMGPT::coeff(int narg, char **arg)
del0.m[i+1][j+1] = 0.0;
del0.m[i+1][i+1] = 1.0;
}
-
+
/* Set matrix param, cutoff, LAMMPS param */
Matrix::sz = lmax;
-
+
rcrit = splinepot.rcrit;
rmax = splinepot.rmax;
cutoff = rmax;
if(rcrit > rmax) cutoff = rcrit;
-
+
// Set LAMMPS pair interaction flags.
for(int i = 1; i <= atom->ntypes; i++) {
for(int j = 1; j <= atom->ntypes; j++) {
@@ -1980,11 +1980,11 @@ void PairMGPT::coeff(int narg, char **arg)
cutghost[i][j] = cutoff;
}
}
-
+
// Set atomic mass.
for(int i = 1; i <= atom->ntypes; i++)
atom->set_mass(i, splinepot.mass);
-
+
// Initialize linear algebra routines.
linalg = mgpt_linalg(lmax,single_precision);
if(comm->me == 0)
@@ -2006,14 +2006,14 @@ void PairMGPT::init_style()
neighbor->requests[irequest_full]->half = 0;
neighbor->requests[irequest_full]->full = 1;
neighbor->requests[irequest_full]->ghost = 1;
-
+
// Also need half neighbor list.
int irequest_half = neighbor->request(this);
neighbor->requests[irequest_half]->id = 2;
neighbor->requests[irequest_half]->half = 0;
neighbor->requests[irequest_half]->half_from_full = 1;
neighbor->requests[irequest_half]->otherlist = irequest_full;
-
+
}
/* ----------------------------------------------------------------------
@@ -2089,7 +2089,7 @@ void PairMGPT::fl_deriv_new(double r,double ri,double xhat,double yhat,double zh
fl_rp = t_rp_ti;
fl_p1 = t_p1_ti;
-
+
if (r <= r0) {
fl_0 = t;
fl_x = tx;
@@ -2186,7 +2186,7 @@ void PairMGPT::hamltn_5_raw(const double xin,const double yin,const double zin,
double M [8][8],double Mx[8][8],
double My[8][8],double Mz[8][8],
double *fl_deriv_sum_p) {
-
+
const double r = sqrt(xin*xin + yin*yin + zin*zin),ri = 1.0/r;
const double x = xin*ri,y = yin*ri,z = zin*ri;
@@ -2194,7 +2194,7 @@ void PairMGPT::hamltn_5_raw(const double xin,const double yin,const double zin,
// call delndd(x,y,z)
const double x2 = x*x,y2 = y*y,z2 = z*z;
const double xy = x*y,xz = x*z,yz = y*z;
-
+
const double sr3 = sqrt(3.0),sr3i = 1.0/sr3;
const double frac_1_3 = 1.0/3.0,frac_2_3 = 2.0/3.0,frac_4_3 = 4.0/3.0;
@@ -2203,7 +2203,7 @@ void PairMGPT::hamltn_5_raw(const double xin,const double yin,const double zin,
const double w2 = ddl_2 - ddl_3;
const double w0 = ddl_2;
-
+
//del4
double gsl_1 ,gsl_2 ,gsl_3 ,gsl_4 ,gsl_5;
double gsl_1x,gsl_2x,gsl_3x,gsl_4x,gsl_5x;
@@ -2239,7 +2239,7 @@ void PairMGPT::hamltn_5_raw(const double xin,const double yin,const double zin,
gsl_5x = sr3*y;
gsl_5y = sr3*x;
gsl_5z = 0.0;
-
+
// Compute bond length potential
fl_deriv_new(r,ri,x,y,z,fl,fl_x,fl_y,fl_z , fl_rp,fl_p1,fl_r0,fl_al);
fl_ri = fl*ri;
@@ -2249,7 +2249,7 @@ void PairMGPT::hamltn_5_raw(const double xin,const double yin,const double zin,
fl_r0*splinepot.dr00 + fl_al*splinepot.dal;
// del2
-
+
//del2.m[1][1] = z2 - 2.0/3.0;
dl2 = z2 - frac_2_3;
dl2x = 0.0;
@@ -2361,7 +2361,7 @@ void PairMGPT::hamltn_7_raw(const double xin,const double yin,const double zin,
double M [8][8],double Mx[8][8],
double My[8][8],double Mz[8][8],
double *fl_deriv_sum_p) {
-
+
const double r = sqrt(xin*xin + yin*yin + zin*zin),ri = 1.0/r;
const double x = xin*ri,y = yin*ri,z = zin*ri;
@@ -2370,7 +2370,7 @@ void PairMGPT::hamltn_7_raw(const double xin,const double yin,const double zin,
const double x2 = x*x,y2 = y*y,z2 = z*z;
const double xy = x*y,xz = x*z,yz = y*z;
const double x4 = x2*x2,y4 = y2*y2;
-
+
//const double sr3 = sqrt(3.0);//,sr3i = 1.0/sr3;
//const double frac_1_3 = 1.0/3.0,frac_2_3 = 2.0/3.0,frac_4_3 = 4.0/3.0;
@@ -2396,7 +2396,7 @@ void PairMGPT::hamltn_7_raw(const double xin,const double yin,const double zin,
const double w2 = 0.625*(ddl_2 - ddl_4);
const double w0 = 0.625*ddl_2 + 0.375*ddl_4;
-
+
//del6
double gsl_1 ,gsl_2 ,gsl_3 ,gsl_4 ,gsl_5 ,gsl_6, gsl_7;
double gsl_1x,gsl_2x,gsl_3x,gsl_4x,gsl_5x,gsl_6x,gsl_7x;
@@ -2452,11 +2452,11 @@ void PairMGPT::hamltn_7_raw(const double xin,const double yin,const double zin,
gsl_7y = 3.0*sr0625*(x2 - y2);
gsl_7z = 0.0;
-
+
// Compute bond length potential
fl_deriv_new(r,ri,x,y,z,fl,fl_x,fl_y,fl_z , fl_rp,fl_p1,fl_r0,fl_al);
fl_ri = fl*ri;
-
+
*fl_deriv_sum_p =
fl_rp*splinepot.drp + fl_p1*splinepot.dp1 +
fl_r0*splinepot.dr00 + fl_al*splinepot.dal;
@@ -2734,7 +2734,7 @@ void PairMGPT::hamltn_7_raw(const double xin,const double yin,const double zin,
//del2f.m[4][4] = 0.0;
- dl2 = 0.0;
+ dl2 = 0.0;
dl2x = 0.0;
dl2y = 0.0;
dl2z = 0.0;
@@ -2804,7 +2804,7 @@ void PairMGPT::hamltn_7_raw(const double xin,const double yin,const double zin,
dl4x = 8.0*x*y2;
dl4y = 8.0*x2*y;
dl4z = -8.0*t1*z;
-
+
MAKE_ELEMENT_7(5,5);
@@ -2885,7 +2885,7 @@ void PairMGPT::hamltn_7_raw(const double xin,const double yin,const double zin,
/************************************************************************/
/* ----------------------------------------------------------------------
- * Fast Model Generalized Pseudopotential Theory (MGPT) interatomic
+ * Fast Model Generalized Pseudopotential Theory (MGPT) interatomic
* potential routine.
*
* Copyright (2015) Lawrence Livermore National Security, LLC.
@@ -2894,8 +2894,8 @@ void PairMGPT::hamltn_7_raw(const double xin,const double yin,const double zin,
* (moriarty2@llnl.gov)
* LLNL-CODE-674031 All rights reserved.
*
- * This program is free software; you can redistribute it and/or modify it
- * under the terms of the GNU General Public License (as published by the
+ * This program is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU General Public License (as published by the
* Free Software Foundation) version 2, dated June 1991.
*
* This program is distributed in the hope that it will be useful, but
diff --git a/src/USER-MGPT/pair_mgpt.h b/src/USER-MGPT/pair_mgpt.h
index 5e5740f391..94c66fb603 100644
--- a/src/USER-MGPT/pair_mgpt.h
+++ b/src/USER-MGPT/pair_mgpt.h
@@ -12,7 +12,7 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
- Contributing authors: Tomas Oppelstrup, LLNL (oppelstrup2@llnl.gov)
+ Contributing authors: Tomas Oppelstrup, LLNL (oppelstrup2@llnl.gov)
and John Moriarty, LLNL (moriarty2@llnl.gov)
Fast MGPT algorithm developed by Tomas Oppelstrup (2015) based on the
@@ -55,7 +55,7 @@ public:
public:
Doublet(const Doublet &t) : i(t.i),j(t.j) {}
Doublet(int ii,int jj) : i(ii < jj ? ii:jj),j(ii < jj ? jj : ii) {}
-
+
Doublet operator=(const Doublet &t) {
i = t.i;
j = t.j;
@@ -66,9 +66,9 @@ public:
}
int hash() const { return i*333331 + j*331; }
};
-
+
template<typename T,typename K> class Hash {
-
+
class Link {
public:
T data;
@@ -90,7 +90,7 @@ public:
::operator delete(((void **) ptr)[-1]);
}
};
-
+
int isprime(int x) {
if(x%2 == 0)
return 0;
@@ -103,13 +103,13 @@ public:
return 1;
}
}
-
+
int size,used;
Link **table;
-
+
int maxlength,nstep,nsearch;
public:
-
+
class Iterator {
Hash &H;
int idx;
@@ -131,7 +131,7 @@ public:
K *key() { return &p->key; }
T *data() { return &p->data; }
Link *link() { return p; }
-
+
int operator==(const Iterator &a) {
return idx==a.idx && p==a.p;
}
@@ -139,23 +139,23 @@ public:
return !(*this == a);
}
};
-
+
Hash(int sz) {
while(!isprime(sz)) sz = sz + 1;
size = sz;
used = 0;
-
-
+
+
table = new Link *[size];
for(int i = 0; i<size; i++)
table[i] = 0;
-
+
/* Counters for statistics */
maxlength = 0;
nstep = 0;
nsearch = 0;
}
-
+
~Hash() {
for(int i = 0; i<size; i++) {
Link *p = table[i];
@@ -170,7 +170,7 @@ public:
Iterator begin() { return Iterator(*this); }
Iterator end() { return Iterator(*this,size,0); }
-
+
int Size() { return size; }
int Used() { return used; }
int NSearch() { return nsearch; }
@@ -183,7 +183,7 @@ public:
printf("(1) Damn... key = %d, idx = %d, size = %d\n",key.hash(),idx,size);
exit(1);
}
-
+
used = used + 1;
if(1) {
table[idx] = new Link(key,table[idx]);
@@ -191,7 +191,7 @@ public:
} else { /* This is for threading... and incomplete */
typedef Link *LinkPtr;
LinkPtr ptr = table[idx],last = 0,dataptr = new Link(key,0);
-
+
while(ptr != 0) {
last = ptr;
ptr = ptr->next;
@@ -225,7 +225,7 @@ public:
last->next = p->next;
delete p;
}
-
+
if(count > maxlength)
maxlength = count;
nsearch = nsearch + 1;
@@ -240,25 +240,25 @@ public:
printf("(3) Damn... key = %d, idx = %d, size = %d\n",key.hash(),idx,size);
exit(1);
}
-
-
+
+
p = table[idx];
while(p != 0 && !(p->key == key)) {
p = p->next;
count = count + 1;
}
-
+
if(count > maxlength)
maxlength = count;
nsearch = nsearch + 1;
nstep = nstep + count;
-
+
if(p != 0) p->hits++;
-
+
return (p == 0) ? 0 : &p->data;
}
};
-
+
public:
PairMGPT(class LAMMPS *);
~PairMGPT();
@@ -268,17 +268,17 @@ public:
void init_style();
void init_list(int, class NeighList *);
double init_one(int, int);
-
+
private:
-
+
void read_files(const char* parminFile, const char* potinFile, double vol);
void allocate();
-
+
struct Matrix {
static int sz;
-
+
double m[8][8];
-
+
int align_check() {
return ((((unsigned long long int) m) & 31) > 0);
}
@@ -323,7 +323,7 @@ public:
Matrix P;
for(int i = 1; i<=sz; i++)
for(int j = 0; j<=sz; j++)
- P.m[i][j] = m[i][j] * x;
+ P.m[i][j] = m[i][j] * x;
return P;
}
Matrix operator/(double x) const {
@@ -399,7 +399,7 @@ public:
triplet_data *get_triplet(const double xx[][3],int i,int j,int k,
Hash<bond_data,Doublet> *bhash,triplet_data *twork,
double *dvir_ij_p,double *dvir_ik_p);
-
+
int c1_outside(const double a[3],
int triclinic,const double alpha[3]) {
const double stol = 1e-5;
@@ -410,16 +410,16 @@ public:
if(cog < domain->sublo_lamda[p]-0.5*rmax*alpha[p]-stol) return 1;
if(cog > domain->subhi_lamda[p]+0.5*rmax*alpha[p]+stol) return 1;
}
-
+
} else {
double rout = 0.0;
-
-
+
+
for(int p = 0; p<3; p++) {
double cog = a[p];
if(cog < domain->sublo[p]-0.5*rmax-stol) return 1;
if(cog > domain->subhi[p]+0.5*rmax+stol) return 1;
-
+
if(cog < domain->sublo[p]-stol) {
double t = cog - (domain->sublo[p]-stol);
rout = rout + t*t;
@@ -427,9 +427,9 @@ public:
double t = cog - (domain->subhi[p]+stol);
rout = rout + t*t;
}
-
+
}
-
+
if(rout > 0.25*rmax*rmax)
return 1;
}
@@ -439,7 +439,7 @@ public:
int c2_outside(const double a[3],const double b[3],
int triclinic,const double alpha[3]) {
const double stol = 1e-5;
-
+
if(triclinic) {
for(int p = 0; p<3; p++) {
double cog = 0.5*(a[p] + b[p]);
@@ -453,7 +453,7 @@ public:
double cog = 0.5*(a[p] + b[p]);
if(cog < domain->sublo[p]-0.5*rcrit-stol) return 1;
if(cog > domain->subhi[p]+0.5*rcrit+stol) return 1;
-
+
if(cog < domain->sublo[p]-stol) {
double t = cog - (domain->sublo[p]-stol);
rout = rout + t*t;
@@ -461,9 +461,9 @@ public:
double t = cog - (domain->subhi[p]+stol);
rout = rout + t*t;
}
-
+
}
-
+
if(rout > 0.25*rcrit*rcrit)
return 1;
}
@@ -478,7 +478,7 @@ public:
*s1 = triclinic ? domain->subhi_lamda : domain->subhi;
double weight = 1.0;
const double stol = 1e-5;
-
+
for(int p = 0; p<3; p++) {
double cog = 0.0,q,w,n = 0.0;
if(a != 0) { cog = cog + a[p]; n = n + 1; }
@@ -486,10 +486,10 @@ public:
if(c != 0) { cog = cog + c[p]; n = n + 1; }
if(d != 0) { cog = cog + d[p]; n = n + 1; }
cog = cog * (1.0/n);
-
+
if(cog < 0.5*(s0[p]+s1[p])) q = cog - s0[p];
else q = s1[p] - cog;
-
+
w = q*(0.5/stol) + 0.5;
if(w > 1.0) w = 1.0;
if(w < 0.0) w = 0.0;
@@ -497,21 +497,21 @@ public:
}
return weight;
}
-
+
void force_debug_3t(double xx[][3],
int i0,int j0,int k0,
int i ,int j ,int k ,
double dfix,double dfiy,double dfiz,
double dfjx,double dfjy,double dfjz,
double dfkx,double dfky,double dfkz);
-
+
void force_debug_3v(double xx[][3],
int i0,int j0,int k0,
int i ,int j ,int k ,
double dfix,double dfiy,double dfiz,
double dfjx,double dfjy,double dfjz,
double dfkx,double dfky,double dfkz);
-
+
void force_debug_4(double xx[][3],
int i0,int j0,int k0,int m0,
int i ,int j ,int k ,int m ,
@@ -519,14 +519,14 @@ public:
double dfjx,double dfjy,double dfjz,
double dfkx,double dfky,double dfkz,
double dfmx,double dfmy,double dfmz);
-
+
double numderiv3t(double xx[][3],int i,int j,int k,int p);
double numderiv3v(double xx[][3],int i,int j,int k,int p,int ipert);
double numderiv4(double xx[][3],int i,int j,int k,int m,int p);
void compute_x(const int *nnei,const int * const *nlist,
double *e_s,double *e_p,double *e_t,double *e_q,
int evflag,int newton_pair);
-
+
/* Reimplementation of bond matrix computation */
void fl_deriv_new(double r,double ri,double xhat,double yhat,double zhat,
double &fl_0,double &fl_x,double &fl_y,double &fl_z,
@@ -554,7 +554,7 @@ public:
}
return h;
}
-
+
/// This function calculates the trace of the matrix product of ha and hb.
inline double trace(const Matrix& ha, const Matrix& hb) const {
double zquan = 0.0;
@@ -571,7 +571,7 @@ public:
inline void transprod(const Matrix& a,const Matrix& b,Matrix &c) const
{
int i,j,k;
-
+
if(lmax == 5) {
const int n = 5;
for(i = 1; i<=n; i++)
@@ -616,12 +616,12 @@ public:
{
int i,k;
double s = 0.0;
-
+
if(linalg.single)
return transtrace_s((const float (*)[8]) &a.m[1][0],(const float (*)[8]) &b.m[1][0]);
//printf("Calling transtrace... That is shit\n");
-
+
if(lmax == 5) {
const int n = 5;
for(i = 1; i<=n; i++)
@@ -640,7 +640,7 @@ public:
}
return s;
}
-
+
double cutoff;
//double vpair[601];
//double ktan[601];
@@ -651,32 +651,32 @@ public:
double rcrit;
//double evol0, pvol0, pot_input_vol;
//double epsr, epsa;
-
+
int thrion;
int fourion;
-
+
//int mode;
double ddl[5];
int lmax, lang;
Matrix del0;
double anorm3, anorm4;
-
+
// Flag indicating whether volumetric pressure should be used.
// Volumetric pressure means that terms emanating from the
// derivative of the energy with respect to the potential atomic
// volume parameter is included.
int volpres_flag,nbody_flag;
-
+
potdata splinepot;
};
-
+
}
#endif
#endif
/* ----------------------------------------------------------------------
- * Fast Model Generalized Pseudopotential Theory (MGPT) interatomic
+ * Fast Model Generalized Pseudopotential Theory (MGPT) interatomic
* potential routine.
*
* Copyright (2015) Lawrence Livermore National Security, LLC.
diff --git a/src/USER-MISC/angle_cosine_shift.cpp b/src/USER-MISC/angle_cosine_shift.cpp
index a144118cb2..8e7c67fd70 100644
--- a/src/USER-MISC/angle_cosine_shift.cpp
+++ b/src/USER-MISC/angle_cosine_shift.cpp
@@ -15,8 +15,8 @@
Contributing author: Carsten Svaneborg, science@zqex.dk
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdlib.h>
#include "angle_cosine_shift.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/USER-MISC/angle_cosine_shift.h b/src/USER-MISC/angle_cosine_shift.h
index 03002fbfe2..b8ab74ee43 100644
--- a/src/USER-MISC/angle_cosine_shift.h
+++ b/src/USER-MISC/angle_cosine_shift.h
@@ -20,7 +20,7 @@ AngleStyle(cosine/shift,AngleCosineShift)
#ifndef LMP_ANGLE_COSINE_SHIFT_H
#define LMP_ANGLE_COSINE_SHIFT_H
-#include "stdio.h"
+#include <stdio.h>
#include "angle.h"
namespace LAMMPS_NS {
diff --git a/src/USER-MISC/angle_cosine_shift_exp.cpp b/src/USER-MISC/angle_cosine_shift_exp.cpp
index 2941293be7..e19b9e20ef 100644
--- a/src/USER-MISC/angle_cosine_shift_exp.cpp
+++ b/src/USER-MISC/angle_cosine_shift_exp.cpp
@@ -15,8 +15,8 @@
Contributing author: Carsten Svaneborg, science@zqex.dk
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdlib.h>
#include "angle_cosine_shift_exp.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/USER-MISC/angle_cosine_shift_exp.h b/src/USER-MISC/angle_cosine_shift_exp.h
index b37d292a70..4db9e1f696 100644
--- a/src/USER-MISC/angle_cosine_shift_exp.h
+++ b/src/USER-MISC/angle_cosine_shift_exp.h
@@ -18,7 +18,7 @@ AngleStyle(cosine/shift/exp,AngleCosineShiftExp)
#ifndef LMP_ANGLE_COSINE_SHIFT_EXP_H
#define LMP_ANGLE_COSINE_SHIFT_EXP_H
-#include "stdio.h"
+#include <stdio.h>
#include "angle.h"
namespace LAMMPS_NS {
diff --git a/src/USER-MISC/angle_dipole.cpp b/src/USER-MISC/angle_dipole.cpp
index 2d1b7eb3ef..25d5f6187b 100644
--- a/src/USER-MISC/angle_dipole.cpp
+++ b/src/USER-MISC/angle_dipole.cpp
@@ -15,8 +15,8 @@
Contributing author: Mario Orsi (U Southampton), orsimario@gmail.com
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdlib.h>
#include "angle_dipole.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/USER-MISC/angle_dipole.h b/src/USER-MISC/angle_dipole.h
index f4ea4a88bf..347eecfca4 100644
--- a/src/USER-MISC/angle_dipole.h
+++ b/src/USER-MISC/angle_dipole.h
@@ -20,7 +20,7 @@ AngleStyle(dipole,AngleDipole)
#ifndef LMP_ANGLE_DIPOLE_H
#define LMP_ANGLE_DIPOLE_H
-#include "stdio.h"
+#include <stdio.h>
#include "angle.h"
namespace LAMMPS_NS {
diff --git a/src/USER-MISC/angle_fourier.cpp b/src/USER-MISC/angle_fourier.cpp
index f067141b9a..dee6ed1301 100644
--- a/src/USER-MISC/angle_fourier.cpp
+++ b/src/USER-MISC/angle_fourier.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -16,8 +16,8 @@
[ based on angle_cosine_squared.cpp Naveen Michaud-Agrawal (Johns Hopkins U)]
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdlib.h>
#include "angle_fourier.h"
#include "atom.h"
#include "neighbor.h"
@@ -218,7 +218,7 @@ void AngleFourier::write_restart(FILE *fp)
}
/* ----------------------------------------------------------------------
- proc 0 reads coeffs from restart file, bcasts them
+ proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void AngleFourier::read_restart(FILE *fp)
@@ -272,7 +272,7 @@ double AngleFourier::single(int type, int i1, int i2, int i3)
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
double c2 = 2.0*c*c-1.0;
-
+
double eng = k[type]*(C0[type]+C1[type]*c+C2[type]*c2);
return eng;
}
diff --git a/src/USER-MISC/angle_fourier.h b/src/USER-MISC/angle_fourier.h
index 43291777a9..da5c96479f 100644
--- a/src/USER-MISC/angle_fourier.h
+++ b/src/USER-MISC/angle_fourier.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -20,7 +20,7 @@ AngleStyle(fourier,AngleFourier)
#ifndef ANGLE_FOURIER_H
#define ANGLE_FOURIER_H
-#include "stdio.h"
+#include <stdio.h>
#include "angle.h"
namespace LAMMPS_NS {
diff --git a/src/USER-MISC/angle_fourier_simple.cpp b/src/USER-MISC/angle_fourier_simple.cpp
index cfe5681314..63991f320e 100644
--- a/src/USER-MISC/angle_fourier_simple.cpp
+++ b/src/USER-MISC/angle_fourier_simple.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -16,8 +16,8 @@
[ based on angle_cosine_squared.cpp Naveen Michaud-Agrawal (Johns Hopkins U)]
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdlib.h>
#include "angle_fourier_simple.h"
#include "atom.h"
#include "neighbor.h"
@@ -225,7 +225,7 @@ void AngleFourierSimple::write_restart(FILE *fp)
}
/* ----------------------------------------------------------------------
- proc 0 reads coeffs from restart file, bcasts them
+ proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void AngleFourierSimple::read_restart(FILE *fp)
diff --git a/src/USER-MISC/angle_fourier_simple.h b/src/USER-MISC/angle_fourier_simple.h
index 2222d5e419..ca160f185d 100644
--- a/src/USER-MISC/angle_fourier_simple.h
+++ b/src/USER-MISC/angle_fourier_simple.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -20,7 +20,7 @@ AngleStyle(fourier/simple,AngleFourierSimple)
#ifndef ANGLE_FOURIER_SIMPLE_H
#define ANGLE_FOURIER_SIMPLE_H
-#include "stdio.h"
+#include <stdio.h>
#include "angle.h"
namespace LAMMPS_NS {
diff --git a/src/USER-MISC/angle_quartic.cpp b/src/USER-MISC/angle_quartic.cpp
index cb0072373e..a1a3e4cf3f 100644
--- a/src/USER-MISC/angle_quartic.cpp
+++ b/src/USER-MISC/angle_quartic.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -16,8 +16,8 @@
[ based on angle_harmonic.cpp]
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdlib.h>
#include "angle_quartic.h"
#include "atom.h"
#include "neighbor.h"
@@ -112,7 +112,7 @@ void AngleQuartic::compute(int eflag, int vflag)
dtheta = acos(c) - theta0[type];
dtheta2 = dtheta * dtheta;
dtheta3 = dtheta2 * dtheta;
- tk = 2.0 * k2[type] * dtheta + 3.0 * k3[type] * dtheta2 +
+ tk = 2.0 * k2[type] * dtheta + 3.0 * k3[type] * dtheta2 +
4.0 * k4[type] * dtheta3;
if (eflag) {
@@ -225,7 +225,7 @@ void AngleQuartic::write_restart(FILE *fp)
}
/* ----------------------------------------------------------------------
- proc 0 reads coeffs from restart file, bcasts them
+ proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void AngleQuartic::read_restart(FILE *fp)
diff --git a/src/USER-MISC/angle_quartic.h b/src/USER-MISC/angle_quartic.h
index b98443cf78..8844ad111d 100644
--- a/src/USER-MISC/angle_quartic.h
+++ b/src/USER-MISC/angle_quartic.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -20,7 +20,7 @@ AngleStyle(quartic,AngleQuartic)
#ifndef LMP_ANGLE_QUARTIC_H
#define LMP_ANGLE_QUARTIC_H
-#include "stdio.h"
+#include <stdio.h>
#include "angle.h"
namespace LAMMPS_NS {
diff --git a/src/USER-MISC/bond_harmonic_shift.cpp b/src/USER-MISC/bond_harmonic_shift.cpp
index d9a5bbc4f9..6f1b67e245 100644
--- a/src/USER-MISC/bond_harmonic_shift.cpp
+++ b/src/USER-MISC/bond_harmonic_shift.cpp
@@ -15,8 +15,8 @@
Contributing author: Carsten Svaneborg, science@zqex.dk
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdlib.h>
#include "bond_harmonic_shift.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/USER-MISC/bond_harmonic_shift.h b/src/USER-MISC/bond_harmonic_shift.h
index a9aabf96ec..95dc091a62 100644
--- a/src/USER-MISC/bond_harmonic_shift.h
+++ b/src/USER-MISC/bond_harmonic_shift.h
@@ -20,7 +20,7 @@ BondStyle(harmonic/shift,BondHarmonicShift)
#ifndef LMP_BOND_HARMONIC_SHIFT_H
#define LMP_BOND_HARMONIC_SHIFT_H
-#include "stdio.h"
+#include <stdio.h>
#include "bond.h"
namespace LAMMPS_NS {
diff --git a/src/USER-MISC/bond_harmonic_shift_cut.cpp b/src/USER-MISC/bond_harmonic_shift_cut.cpp
index 07bea4a861..1a1be16999 100644
--- a/src/USER-MISC/bond_harmonic_shift_cut.cpp
+++ b/src/USER-MISC/bond_harmonic_shift_cut.cpp
@@ -15,8 +15,8 @@
Contributing author: Carsten Svaneborg, science@zqex.dk
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdlib.h>
#include "bond_harmonic_shift_cut.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/USER-MISC/bond_harmonic_shift_cut.h b/src/USER-MISC/bond_harmonic_shift_cut.h
index e743641601..9b2587936e 100644
--- a/src/USER-MISC/bond_harmonic_shift_cut.h
+++ b/src/USER-MISC/bond_harmonic_shift_cut.h
@@ -20,7 +20,7 @@ BondStyle(harmonic/shift/cut,BondHarmonicShiftCut)
#ifndef LMP_BOND_HARMONIC_SHIFT_CUT_H
#define LMP_BOND_HARMONIC_SHIFT_CUT_H
-#include "stdio.h"
+#include <stdio.h>
#include "bond.h"
namespace LAMMPS_NS {
diff --git a/src/USER-MISC/compute_ackland_atom.cpp b/src/USER-MISC/compute_ackland_atom.cpp
index 064e14ef93..7a60117bb8 100644
--- a/src/USER-MISC/compute_ackland_atom.cpp
+++ b/src/USER-MISC/compute_ackland_atom.cpp
@@ -16,7 +16,7 @@
Copyright (C) 2007
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "compute_ackland_atom.h"
#include "atom.h"
#include "update.h"
@@ -246,7 +246,7 @@ void ComputeAcklandAtom::compute_peratom()
double delta_bcc = delta_cp + 1.0;
int chi56m4 = chi[5]+chi[6]-chi[4];
- // note that chi[7] presumed zero
+ // note that chi[7] presumed zero
if (chi56m4 != 0) delta_bcc = 0.35*chi[4]/(double)chi56m4;
double delta_fcc = 0.61*(fabs((double)(chi[0]+chi[1]-6))
@@ -258,7 +258,7 @@ void ComputeAcklandAtom::compute_peratom()
// Identification of the local structure according to the reference
- if (delta_bcc >= 0.1 && delta_cp >= 0.1 && delta_fcc >= 0.1
+ if (delta_bcc >= 0.1 && delta_cp >= 0.1 && delta_fcc >= 0.1
&& delta_hcp >= 0.1) structure[i] = UNKNOWN;
// not part of Ackland-Jones 2006; included for backward compatibility
diff --git a/src/USER-MISC/compute_basal_atom.cpp b/src/USER-MISC/compute_basal_atom.cpp
index cf90b50d8a..d323e20a10 100644
--- a/src/USER-MISC/compute_basal_atom.cpp
+++ b/src/USER-MISC/compute_basal_atom.cpp
@@ -16,7 +16,7 @@
Copyright (C) 2013
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "compute_basal_atom.h"
#include "atom.h"
#include "update.h"
@@ -164,7 +164,7 @@ void ComputeBasalAtom::compute_peratom()
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
-
+
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
@@ -172,7 +172,7 @@ void ComputeBasalAtom::compute_peratom()
if (rsq < cutsq) {
distsq[n] = rsq;
nearest[n++] = j;
- }
+ }
}
// Select 6 nearest neighbors
@@ -220,7 +220,7 @@ void ComputeBasalAtom::compute_peratom()
if (norm_k <= 0.) {continue;}
bond_angle = (x_ij*x_ik + y_ij*y_ik + z_ij*z_ik) / (norm_j*norm_k);
//find all bond angles that are about 180 degrees
- if (-1. <= bond_angle && bond_angle < -0.945) {
+ if (-1. <= bond_angle && bond_angle < -0.945) {
x3[chi[0]] = x_ik - x_ij;
y3[chi[0]] = y_ik - y_ij;
z3[chi[0]] = z_ik - z_ij;
@@ -416,7 +416,7 @@ void ComputeBasalAtom::compute_peratom()
else BPV[i][0] = BPV[i][1] = BPV[i][2] = 0.0;
//normalize BPV:
- double Mag = sqrt(BPV[i][0]*BPV[i][0] +
+ double Mag = sqrt(BPV[i][0]*BPV[i][0] +
BPV[i][1]*BPV[i][1] + BPV[i][2]*BPV[i][2]);
if (Mag > 0){
BPV[i][0] = BPV[i][0]/Mag;
diff --git a/src/USER-MISC/compute_temp_rotate.cpp b/src/USER-MISC/compute_temp_rotate.cpp
index 02cc87c4b9..574db8757c 100644
--- a/src/USER-MISC/compute_temp_rotate.cpp
+++ b/src/USER-MISC/compute_temp_rotate.cpp
@@ -15,9 +15,9 @@
Contributing author: Laurent Joly (U Lyon, France), ljoly.ulyon@gmail.com
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "stdlib.h"
-#include "string.h"
+#include <mpi.h>
+#include <stdlib.h>
+#include <string.h>
#include "compute_temp_rotate.h"
#include "atom.h"
#include "update.h"
@@ -142,7 +142,7 @@ double ComputeTempRotate::compute_scalar()
MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
if (dynamic) dof_compute();
- if (dof < 0.0 && natoms_temp > 0.0)
+ if (dof < 0.0 && natoms_temp > 0.0)
error->all(FLERR,"Temperature compute degrees of freedom < 0");
scalar *= tfactor;
return scalar;
diff --git a/src/USER-MISC/dihedral_cosine_shift_exp.cpp b/src/USER-MISC/dihedral_cosine_shift_exp.cpp
index 8ce119d40a..8706b5fb1a 100644
--- a/src/USER-MISC/dihedral_cosine_shift_exp.cpp
+++ b/src/USER-MISC/dihedral_cosine_shift_exp.cpp
@@ -15,9 +15,9 @@
Contributing author: Carsten Svaneborg, science@zqex.dk
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "math.h"
-#include "stdlib.h"
+#include <mpi.h>
+#include <math.h>
+#include <stdlib.h>
#include "dihedral_cosine_shift_exp.h"
#include "atom.h"
#include "comm.h"
@@ -136,8 +136,8 @@ void DihedralCosineShiftExp::compute(int eflag, int vflag)
MPI_Comm_rank(world,&me);
if (screen) {
char str[128];
- sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " "
- TAGINT_FORMAT " " TAGINT_FORMAT " "
+ sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT,
me,update->ntimestep,
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
diff --git a/src/USER-MISC/dihedral_cosine_shift_exp.h b/src/USER-MISC/dihedral_cosine_shift_exp.h
index ff0843ab18..819fd769cb 100644
--- a/src/USER-MISC/dihedral_cosine_shift_exp.h
+++ b/src/USER-MISC/dihedral_cosine_shift_exp.h
@@ -20,7 +20,7 @@ DihedralStyle(cosine/shift/exp,DihedralCosineShiftExp)
#ifndef LMP_DIHEDRAL_COSINE_SHIFT_EXP_H
#define LMP_DIHEDRAL_COSINE_SHIFT_EXP_H
-#include "stdio.h"
+#include <stdio.h>
#include "dihedral.h"
namespace LAMMPS_NS {
diff --git a/src/USER-MISC/dihedral_fourier.cpp b/src/USER-MISC/dihedral_fourier.cpp
index 3656a43e26..93e818183d 100644
--- a/src/USER-MISC/dihedral_fourier.cpp
+++ b/src/USER-MISC/dihedral_fourier.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -16,9 +16,9 @@
[ based on dihedral_charmm.cpp Paul Crozier (SNL) ]
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "math.h"
-#include "stdlib.h"
+#include <mpi.h>
+#include <math.h>
+#include <stdlib.h>
#include "dihedral_fourier.h"
#include "atom.h"
#include "comm.h"
@@ -73,7 +73,7 @@ void DihedralFourier::compute(int eflag, int vflag)
double edihedral,f1[3],f2[3],f3[3],f4[3];
double ax,ay,az,bx,by,bz,rasq,rbsq,rgsq,rg,rginv,ra2inv,rb2inv,rabinv;
double df,df1_,ddf1_,fg,hg,fga,hgb,gaa,gbb;
- double dtfx,dtfy,dtfz,dtgx,dtgy,dtgz,dthx,dthy,dthz;
+ double dtfx,dtfy,dtfz,dtgx,dtgy,dtgz,dthx,dthy,dthz;
double c,s,p_,sx2,sy2,sz2;
if (eflag || vflag) ev_setup(eflag,vflag);
@@ -143,8 +143,8 @@ void DihedralFourier::compute(int eflag, int vflag)
MPI_Comm_rank(world,&me);
if (screen) {
char str[128];
- sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " "
- TAGINT_FORMAT " " TAGINT_FORMAT " "
+ sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT,
me,update->ntimestep,
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
@@ -173,7 +173,7 @@ void DihedralFourier::compute(int eflag, int vflag)
m = multiplicity[type][j];
p_ = 1.0;
ddf1_ = df1_ = 0.0;
-
+
for (i = 0; i < m; i++) {
ddf1_ = p_*c - df1_*s;
df1_ = p_*s + df1_*c;
@@ -184,13 +184,13 @@ void DihedralFourier::compute(int eflag, int vflag)
df1_ = df1_*cos_shift[type][j] - ddf1_*sin_shift[type][j];
df1_ *= -m;
p_ += 1.0;
-
+
if (m == 0) {
p_ = 1.0 + cos_shift[type][j];
df1_ = 0.0;
}
- if (eflag) edihedral += k[type][j] * p_;
+ if (eflag) edihedral += k[type][j] * p_;
df += (-k[type][j] * df1_);
}
@@ -282,7 +282,7 @@ void DihedralFourier::allocate()
k[i] = shift[i] = cos_shift[i] = sin_shift[i] = 0;
multiplicity[i] = 0;
}
-
+
memory->create(setflag,n+1,"dihedral:setflag");
for (int i = 1; i <= n; i++) setflag[i] = 0;
}
@@ -320,8 +320,8 @@ void DihedralFourier::coeff(int narg, char **arg)
k[i] = new double [nterms_one];
multiplicity[i] = new int [nterms_one];
shift[i] = new double [nterms_one];
- cos_shift[i] = new double [nterms_one];
- sin_shift[i] = new double [nterms_one];
+ cos_shift[i] = new double [nterms_one];
+ sin_shift[i] = new double [nterms_one];
for (int j = 0; j<nterms_one; j++) {
int offset = 1+3*j;
k_one = force->numeric(FLERR,arg[offset+1]);
@@ -341,7 +341,7 @@ void DihedralFourier::coeff(int narg, char **arg)
}
/* ----------------------------------------------------------------------
- proc 0 writes out coeffs to restart file
+ proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void DihedralFourier::write_restart(FILE *fp)
@@ -357,7 +357,7 @@ void DihedralFourier::write_restart(FILE *fp)
}
/* ----------------------------------------------------------------------
- proc 0 reads coeffs from restart file, bcasts them
+ proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void DihedralFourier::read_restart(FILE *fp)
@@ -369,7 +369,7 @@ void DihedralFourier::read_restart(FILE *fp)
MPI_Bcast(&nterms[1],atom->ndihedraltypes,MPI_INT,0,world);
- // allocate
+ // allocate
for (int i=1; i<=atom->ndihedraltypes; i++) {
k[i] = new double [nterms[i]];
multiplicity[i] = new int [nterms[i]];
diff --git a/src/USER-MISC/dihedral_fourier.h b/src/USER-MISC/dihedral_fourier.h
index 734812c8b4..4229f494c2 100644
--- a/src/USER-MISC/dihedral_fourier.h
+++ b/src/USER-MISC/dihedral_fourier.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -20,7 +20,7 @@ DihedralStyle(fourier,DihedralFourier)
#ifndef LMP_DIHEDRAL_FOURIER_H
#define LMP_DIHEDRAL_FOURIER_H
-#include "stdio.h"
+#include <stdio.h>
#include "dihedral.h"
namespace LAMMPS_NS {
diff --git a/src/USER-MISC/dihedral_nharmonic.cpp b/src/USER-MISC/dihedral_nharmonic.cpp
index 5789f88402..67b363f552 100644
--- a/src/USER-MISC/dihedral_nharmonic.cpp
+++ b/src/USER-MISC/dihedral_nharmonic.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -16,8 +16,8 @@
[ based on dihedral_multi_harmonic.cpp Mathias Puetz (SNL) and friends ]
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdlib.h>
#include "dihedral_nharmonic.h"
#include "atom.h"
#include "neighbor.h"
@@ -155,8 +155,8 @@ void DihedralNHarmonic::compute(int eflag, int vflag)
MPI_Comm_rank(world,&me);
if (screen) {
char str[128];
- sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " "
- TAGINT_FORMAT " " TAGINT_FORMAT " "
+ sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT,
me,update->ntimestep,
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
@@ -296,7 +296,7 @@ void DihedralNHarmonic::coeff(int narg, char **arg)
}
/* ----------------------------------------------------------------------
- proc 0 writes out coeffs to restart file
+ proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void DihedralNHarmonic::write_restart(FILE *fp)
@@ -307,22 +307,22 @@ void DihedralNHarmonic::write_restart(FILE *fp)
}
/* ----------------------------------------------------------------------
- proc 0 reads coeffs from restart file, bcasts them
+ proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void DihedralNHarmonic::read_restart(FILE *fp)
{
allocate();
- if (comm->me == 0)
+ if (comm->me == 0)
fread(&nterms[1],sizeof(int),atom->ndihedraltypes,fp);
MPI_Bcast(&nterms[1],atom->ndihedraltypes,MPI_INT,0,world);
- // allocate
+ // allocate
for(int i = 1; i <= atom->ndihedraltypes; i++)
a[i] = new double [nterms[i]];
-
+
if (comm->me == 0) {
for(int i = 1; i <= atom->ndihedraltypes; i++)
fread(a[i],sizeof(double),nterms[i],fp);
diff --git a/src/USER-MISC/dihedral_nharmonic.h b/src/USER-MISC/dihedral_nharmonic.h
index a705c0ff45..c347f37cbd 100644
--- a/src/USER-MISC/dihedral_nharmonic.h
+++ b/src/USER-MISC/dihedral_nharmonic.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -20,7 +20,7 @@ DihedralStyle(nharmonic,DihedralNHarmonic)
#ifndef DIHEDRAL_NHARMONIC_H
#define DIHEDRAL_NHARMONIC_H
-#include "stdio.h"
+#include <stdio.h>
#include "dihedral.h"
namespace LAMMPS_NS {
diff --git a/src/USER-MISC/dihedral_quadratic.cpp b/src/USER-MISC/dihedral_quadratic.cpp
index 40e1d7f3c3..3a5eac6fa0 100644
--- a/src/USER-MISC/dihedral_quadratic.cpp
+++ b/src/USER-MISC/dihedral_quadratic.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -16,8 +16,8 @@
[ based on dihedral_helix.cpp Paul Crozier (SNL) ]
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdlib.h>
#include "dihedral_quadratic.h"
#include "atom.h"
#include "neighbor.h"
@@ -162,8 +162,8 @@ void DihedralQuadratic::compute(int eflag, int vflag)
MPI_Comm_rank(world,&me);
if (screen) {
char str[128];
- sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " "
- TAGINT_FORMAT " " TAGINT_FORMAT " "
+ sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT,
me,update->ntimestep,
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
@@ -197,7 +197,7 @@ void DihedralQuadratic::compute(int eflag, int vflag)
pd = - 2.0 * p * siinv;
p = p * dphi;
- if (eflag) edihedral = p;
+ if (eflag) edihedral = p;
a = pd;
c = c * a;
@@ -293,7 +293,7 @@ void DihedralQuadratic::coeff(int narg, char **arg)
// require k >= 0
if (k_one < 0.0)
error->all(FLERR,"Incorrect coefficient arg for dihedral coefficients");
-
+
int count = 0;
for (int i = ilo; i <= ihi; i++) {
k[i] = k_one;
@@ -306,7 +306,7 @@ void DihedralQuadratic::coeff(int narg, char **arg)
}
/* ----------------------------------------------------------------------
- proc 0 writes out coeffs to restart file
+ proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void DihedralQuadratic::write_restart(FILE *fp)
@@ -316,7 +316,7 @@ void DihedralQuadratic::write_restart(FILE *fp)
}
/* ----------------------------------------------------------------------
- proc 0 reads coeffs from restart file, bcasts them
+ proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void DihedralQuadratic::read_restart(FILE *fp)
@@ -329,7 +329,7 @@ void DihedralQuadratic::read_restart(FILE *fp)
}
MPI_Bcast(&k[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&phi0[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
-
+
for (int i = 1; i <= atom->ndihedraltypes; i++) setflag[i] = 1;
}
diff --git a/src/USER-MISC/dihedral_quadratic.h b/src/USER-MISC/dihedral_quadratic.h
index bc4e032c00..638efac668 100644
--- a/src/USER-MISC/dihedral_quadratic.h
+++ b/src/USER-MISC/dihedral_quadratic.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -20,7 +20,7 @@ DihedralStyle(quadratic,DihedralQuadratic)
#ifndef LMP_DIHEDRAL_QUADRATIC_H
#define LMP_DIHEDRAL_QUADRATIC_H
-#include "stdio.h"
+#include <stdio.h>
#include "dihedral.h"
namespace LAMMPS_NS {
diff --git a/src/USER-MISC/dihedral_table.cpp b/src/USER-MISC/dihedral_table.cpp
index befaffc363..4e3b05bc4b 100644
--- a/src/USER-MISC/dihedral_table.cpp
+++ b/src/USER-MISC/dihedral_table.cpp
@@ -1300,7 +1300,7 @@ void DihedralTable::compute_table(Table *tb)
tb->e[i]= cyc_lin(tb->phifile,tb->efile,tb->ninput,MY_2PI,phi);
}
// In the linear case, if the user did not specify the forces, then we
- // must generate the "f" array. Do this using linear interpolation
+ // must generate the "f" array. Do this using linear interpolation
// of the e array (which itself was generated above)
for (int i = 0; i < tablength; i++) {
int im1 = i-1; if (im1 < 0) im1 += tablength;
diff --git a/src/USER-MISC/fix_addtorque.cpp b/src/USER-MISC/fix_addtorque.cpp
index db90b7b21c..0e1ffaf0e1 100644
--- a/src/USER-MISC/fix_addtorque.cpp
+++ b/src/USER-MISC/fix_addtorque.cpp
@@ -15,8 +15,8 @@
Contributing author: Laurent Joly (U Lyon, France), ljoly.ulyon@gmail.com
------------------------------------------------------------------------- */
-#include "string.h"
-#include "stdlib.h"
+#include <string.h>
+#include <stdlib.h>
#include "fix_addtorque.h"
#include "atom.h"
#include "update.h"
@@ -109,21 +109,21 @@ void FixAddTorque::init()
if (xstr) {
xvar = input->variable->find(xstr);
- if (xvar < 0)
+ if (xvar < 0)
error->all(FLERR,"Variable name for fix addtorque does not exist");
if (input->variable->equalstyle(xvar)) xstyle = EQUAL;
else error->all(FLERR,"Variable for fix addtorque is invalid style");
}
if (ystr) {
yvar = input->variable->find(ystr);
- if (yvar < 0)
+ if (yvar < 0)
error->all(FLERR,"Variable name for fix addtorque does not exist");
if (input->variable->equalstyle(yvar)) ystyle = EQUAL;
else error->all(FLERR,"Variable for fix addtorque is invalid style");
}
if (zstr) {
zvar = input->variable->find(zstr);
- if (zvar < 0)
+ if (zvar < 0)
error->all(FLERR,"Variable name for fix addtorque does not exist");
if (input->variable->equalstyle(zvar)) zstyle = EQUAL;
else error->all(FLERR,"Variable for fix addtorque is invalid style");
diff --git a/src/USER-MISC/fix_ave_correlate_long.cpp b/src/USER-MISC/fix_ave_correlate_long.cpp
index 03fdd13675..3811eabcf3 100644
--- a/src/USER-MISC/fix_ave_correlate_long.cpp
+++ b/src/USER-MISC/fix_ave_correlate_long.cpp
@@ -21,10 +21,10 @@
see J. Chem. Phys. 133, 154103 (2010)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
-#include "unistd.h"
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
+#include <unistd.h>
#include "fix_ave_correlate_long.h"
#include "update.h"
#include "modify.h"
@@ -114,7 +114,7 @@ FixAveCorrelateLong::FixAveCorrelateLong(LAMMPS * lmp, int narg, char **arg):
while (iarg < narg) {
if (strcmp(arg[iarg],"type") == 0) {
- if (iarg+2 > narg)
+ if (iarg+2 > narg)
error->all(FLERR,"Illegal fix ave/correlate/long command");
if (strcmp(arg[iarg+1],"auto") == 0) type = AUTO;
else if (strcmp(arg[iarg+1],"upper") == 0) type = UPPER;
@@ -125,27 +125,27 @@ FixAveCorrelateLong::FixAveCorrelateLong(LAMMPS * lmp, int narg, char **arg):
else error->all(FLERR,"Illegal fix ave/correlate/long command");
iarg += 2;
} else if (strcmp(arg[iarg],"start") == 0) {
- if (iarg+2 > narg)
+ if (iarg+2 > narg)
error->all(FLERR,"Illegal fix ave/correlate/long command");
startstep = force->inumeric(FLERR,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"ncorr") == 0) {
- if (iarg+2 > narg)
+ if (iarg+2 > narg)
error->all(FLERR,"Illegal fix ave/correlate/long command");
numcorrelators = force->inumeric(FLERR,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"nlen") == 0) {
- if (iarg+2 > narg)
+ if (iarg+2 > narg)
error->all(FLERR,"Illegal fix ave/correlate/long command");
p = force->inumeric(FLERR,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"ncount") == 0) {
- if (iarg+2 > narg)
+ if (iarg+2 > narg)
error->all(FLERR,"Illegal fix ave/correlate/long command");
m = force->inumeric(FLERR,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"file") == 0) {
- if (iarg+2 > narg)
+ if (iarg+2 > narg)
error->all(FLERR,"Illegal fix ave/correlate/long command");
if (me == 0) {
fp = fopen(arg[iarg+1],"w");
@@ -160,7 +160,7 @@ FixAveCorrelateLong::FixAveCorrelateLong(LAMMPS * lmp, int narg, char **arg):
overwrite = 1;
iarg += 1;
} else if (strcmp(arg[iarg],"title1") == 0) {
- if (iarg+2 > narg)
+ if (iarg+2 > narg)
error->all(FLERR,"Illegal fix ave/correlate/long command");
delete [] title1;
int n = strlen(arg[iarg+1]) + 1;
@@ -168,7 +168,7 @@ FixAveCorrelateLong::FixAveCorrelateLong(LAMMPS * lmp, int narg, char **arg):
strcpy(title1,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"title2") == 0) {
- if (iarg+2 > narg)
+ if (iarg+2 > narg)
error->all(FLERR,"Illegal fix ave/correlate/long command");
delete [] title2;
int n = strlen(arg[iarg+1]) + 1;
@@ -309,7 +309,7 @@ FixAveCorrelateLong::FixAveCorrelateLong(LAMMPS * lmp, int narg, char **arg):
}
for (int i=0;i<length;i++) t[i]=0.0;
- for (int i=0;i<npair;i++)
+ for (int i=0;i<npair;i++)
for (int j=0;j<length;j++) f[i][j]=0.0;
@@ -336,11 +336,11 @@ FixAveCorrelateLong::~FixAveCorrelateLong()
memory->destroy(values);
memory->destroy(shift);
memory->destroy(shift2);
- memory->destroy(correlation);
- memory->destroy(accumulator);
- memory->destroy(accumulator2);
- memory->destroy(ncorrelation);
- memory->destroy(naccumulator);
+ memory->destroy(correlation);
+ memory->destroy(accumulator);
+ memory->destroy(accumulator2);
+ memory->destroy(ncorrelation);
+ memory->destroy(naccumulator);
memory->destroy(insertindex);
memory->destroy(t);
memory->destroy(f);
@@ -412,7 +412,7 @@ void FixAveCorrelateLong::end_of_step()
// error check if timestep was reset in an invalid manner
bigint ntimestep = update->ntimestep;
- if (ntimestep < nvalid_last || ntimestep > nvalid)
+ if (ntimestep < nvalid_last || ntimestep > nvalid)
error->all(FLERR,"Invalid timestep reset for fix ave/correlate/long");
if (ntimestep != nvalid) return;
nvalid_last = nvalid;
@@ -622,7 +622,7 @@ void FixAveCorrelateLong::add(const int i, const double w, const unsigned int k)
/* ----------------------------------------------------------------------
Add 2 scalar values to the cross-correlator k of pair i
------------------------------------------------------------------------- */
-void FixAveCorrelateLong::add(const int i, const double wA, const double wB,
+void FixAveCorrelateLong::add(const int i, const double wA, const double wB,
const unsigned int k) {
if (k == numcorrelators) return;
if (k > kmax) kmax=k;
@@ -687,7 +687,7 @@ bigint FixAveCorrelateLong::nextvalid()
/* ----------------------------------------------------------------------
- memory_usage
+ memory_usage
------------------------------------------------------------------------- */
double FixAveCorrelateLong::memory_usage() {
// shift: npair x numcorrelators x p
@@ -698,11 +698,11 @@ double FixAveCorrelateLong::memory_usage() {
// ncorrelation: numcorrelators x p
// naccumulator: numcorrelators
// insertindex: numcorrelators
- // t: numcorrelators x p
+ // t: numcorrelators x p
// f: npair x numcorrelators x p
double bytes = (4*npair*numcorrelators*p + 2*npair*numcorrelators
+ numcorrelators*p)*sizeof(double)
- + numcorrelators*p*sizeof(unsigned long int)
+ + numcorrelators*p*sizeof(unsigned long int)
+ 2*numcorrelators*sizeof(unsigned int);
return bytes;
}
@@ -720,7 +720,7 @@ void FixAveCorrelateLong::write_restart(FILE *fp) {
memory->create(list,nsize,"correlator:list");
list[n++]=npair;
list[n++]=numcorrelators;
- list[n++]=p;
+ list[n++]=p;
list[n++]=m;
list[n++]=nvalid;
list[n++]=nvalid_last;
@@ -740,7 +740,7 @@ void FixAveCorrelateLong::write_restart(FILE *fp) {
list[n++]=insertindex[i];
}
- int size = n*sizeof(double);
+ int size = n*sizeof(double);
fwrite(&size,sizeof(int),1,fp);
fwrite(list,sizeof(double),n,fp);
memory->destroy(list);
@@ -754,17 +754,17 @@ void FixAveCorrelateLong::write_restart(FILE *fp) {
void FixAveCorrelateLong::restart(char *buf)
{
int n = 0;
- double *list = (double *) buf;
+ double *list = (double *) buf;
int npairin = static_cast<int> (list[n++]);
- int numcorrelatorsin = static_cast<int> (list[n++]);
- int pin = static_cast<int> (list[n++]);
- int min = static_cast<int> (list[n++]);
- nvalid = static_cast<int> (list[n++]);
- nvalid_last = static_cast<int> (list[n++]);
+ int numcorrelatorsin = static_cast<int> (list[n++]);
+ int pin = static_cast<int> (list[n++]);
+ int min = static_cast<int> (list[n++]);
+ nvalid = static_cast<int> (list[n++]);
+ nvalid_last = static_cast<int> (list[n++]);
if ((npairin!=npair) || (numcorrelatorsin!=numcorrelators)
|| (pin!=p) || (min!=m))
- error->all(FLERR,"Fix ave/correlate/long: restart and input data are different");
+ error->all(FLERR,"Fix ave/correlate/long: restart and input data are different");
for (int i=0;i<npair;i++)
for (int j=0;j<numcorrelators;j++) {
@@ -777,7 +777,7 @@ void FixAveCorrelateLong::restart(char *buf)
accumulator2[i][j] = list[n++];
}
for (int i=0;i<numcorrelators;i++) {
- for (int j=0;j<p;j++)
+ for (int j=0;j<p;j++)
ncorrelation[i][j] = static_cast<unsigned long int>(list[n++]);
naccumulator[i] = static_cast<unsigned int> (list[n++]);
insertindex[i] = static_cast<unsigned int> (list[n++]);
diff --git a/src/USER-MISC/fix_ave_correlate_long.h b/src/USER-MISC/fix_ave_correlate_long.h
index 49e840e890..d5354ebf5e 100644
--- a/src/USER-MISC/fix_ave_correlate_long.h
+++ b/src/USER-MISC/fix_ave_correlate_long.h
@@ -20,7 +20,7 @@ FixStyle(ave/correlate/long,FixAveCorrelateLong)
#ifndef LMP_FIX_AVE_CORRELATE_LONG_H
#define LMP_FIX_AVE_CORRELATE_LONG_H
-#include "stdio.h"
+#include <stdio.h>
#include "fix.h"
namespace LAMMPS_NS {
@@ -37,19 +37,19 @@ class FixAveCorrelateLong : public Fix {
void write_restart(FILE *);
void restart(char *);
double memory_usage();
-
+
double *t; // Time steps for result arrays
double **f; // Result arrays
unsigned int npcorr;
private:
// NOT OPTIMAL: shift2 and accumulator2 only needed in cross-correlations
- double ***shift, *** shift2;
+ double ***shift, *** shift2;
double ***correlation;
double **accumulator, **accumulator2;
- unsigned long int **ncorrelation;
- unsigned int *naccumulator;
- unsigned int *insertindex;
+ unsigned long int **ncorrelation;
+ unsigned int *naccumulator;
+ unsigned int *insertindex;
unsigned int numcorrelators; // Recommended 20
unsigned int p; // Points per correlator (recommended 16)
@@ -75,7 +75,7 @@ class FixAveCorrelateLong : public Fix {
void accumulate();
void evaluate();
bigint nextvalid();
-
+
void add(const int i, const double w, const unsigned int k = 0);
void add(const int i, const double wA, const double wB, const unsigned int k = 0);
diff --git a/src/USER-MISC/fix_ave_spatial_sphere.cpp b/src/USER-MISC/fix_ave_spatial_sphere.cpp
index bf82173be2..d26908bc38 100644
--- a/src/USER-MISC/fix_ave_spatial_sphere.cpp
+++ b/src/USER-MISC/fix_ave_spatial_sphere.cpp
@@ -15,9 +15,9 @@
Adapted from fix ave/spatial by Niall Jackson <niall.jackson@gmail.com>
------------------------------------------------------------------------- */
-#include "stdlib.h"
-#include "string.h"
-#include "unistd.h"
+#include <stdlib.h>
+#include <string.h>
+#include <unistd.h>
#include "fix_ave_spatial_sphere.h"
#include "atom.h"
#include "update.h"
@@ -55,17 +55,17 @@ enum{ONE,RUNNING,WINDOW};
FixAveSpatialSphere::FixAveSpatialSphere(LAMMPS* lmp, int narg, char** arg) :
Fix(lmp, narg, arg) {
-
+
if (narg < 12) error->all(FLERR, "Illegal fix ave/spatial/sphere command");
-
+
MPI_Comm_rank(world, &me);
-
+
nevery= force->inumeric(FLERR, arg[3]);
nrepeat= force->inumeric(FLERR, arg[4]);
nfreq= force->inumeric(FLERR, arg[5]);
-
+
global_freq= nfreq;
-
+
for (int iarg = 6; iarg < 9; ++iarg) {
int dim= iarg-6;
origin_ids[dim]= NULL;
@@ -104,11 +104,11 @@ FixAveSpatialSphere::FixAveSpatialSphere(LAMMPS* lmp, int narg, char** arg) :
if(origin_type[dim] == COMPUTE) {
int icompute= modify->find_compute(origin_ids[dim]);
- if(icompute < 0)
+ if(icompute < 0)
error->all(FLERR,
"Compute ID for fix ave/spatial/sphere does not exist");
- if(origin_index[dim] == 0 &&
+ if(origin_index[dim] == 0 &&
modify->compute[icompute]->scalar_flag != 0)
error->all(FLERR,"Compute for fix ave/spatial/sphere does not calculate a scalar");
else if(origin_index[dim] && modify->compute[icompute]->vector_flag == 0)
@@ -127,14 +127,14 @@ FixAveSpatialSphere::FixAveSpatialSphere(LAMMPS* lmp, int narg, char** arg) :
origin[dim]= force->numeric(FLERR, arg[iarg]);
}
}
-
+
//the extrema of the radius
r_min= force->numeric(FLERR, arg[9]);
r_max= force->numeric(FLERR, arg[10]);
-
+
//and finally, the number of spherical bins
nbins= force->inumeric(FLERR, arg[11]);
-
+
if (r_min >= r_max) {
error->all(FLERR, "r_min must be less than r_max in fix ave/spatial/sphere");
}
@@ -142,17 +142,17 @@ FixAveSpatialSphere::FixAveSpatialSphere(LAMMPS* lmp, int narg, char** arg) :
if (nbins <= 0) {
error->all(FLERR, "nbins must be positive in fix ave/spatial/sphere");
}
-
+
int iarg= 12;
which= new int[narg-12];
argindex= new int[narg-12];
ids= new char*[narg-12];
value2index= new int[narg-12];
nvalues= 0;
-
+
while(iarg < narg) {
ids[nvalues]= NULL;
-
+
if(strcmp(arg[iarg], "vx") == 0) {
which[nvalues] = V;
argindex[nvalues++]= 0;
@@ -183,12 +183,12 @@ FixAveSpatialSphere::FixAveSpatialSphere(LAMMPS* lmp, int narg, char** arg) :
if(arg[iarg][0] == 'c') which[nvalues] = COMPUTE;
else if(arg[iarg][0] == 'f') which[nvalues] = FIX;
else if(arg[iarg][0] == 'v') which[nvalues] = VARIABLE;
-
+
//strip the v_/c_/f_ off the front of the variable name
int n= strlen(arg[iarg]);
char *suffix= new char[n];
strcpy(suffix, &arg[iarg][2]);
-
+
//does the variable name contain a [?
//(in other words, is this an array element?)
char *ptr= strchr(suffix, '[');
@@ -203,7 +203,7 @@ FixAveSpatialSphere::FixAveSpatialSphere(LAMMPS* lmp, int narg, char** arg) :
} else {
argindex[nvalues]= 0;
}
-
+
//store the name of the variable
n= strlen(suffix)+1;
ids[nvalues]= new char[n];
@@ -212,10 +212,10 @@ FixAveSpatialSphere::FixAveSpatialSphere(LAMMPS* lmp, int narg, char** arg) :
//tidy up the array we allocated earlier
delete[] suffix;
} else break;
-
+
iarg++;
}
-
+
//process the optional arguments
normflag= ALL; //normalise the average right at the end
scaleflag= LATTICE; // lattice units are the default
@@ -228,7 +228,7 @@ FixAveSpatialSphere::FixAveSpatialSphere(LAMMPS* lmp, int narg, char** arg) :
char *title1= NULL;
char *title2= NULL;
char *title3= NULL;
-
+
while (iarg < narg) {
if (strcmp(arg[iarg],"norm") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/spatial/sphere command");
@@ -303,7 +303,7 @@ FixAveSpatialSphere::FixAveSpatialSphere(LAMMPS* lmp, int narg, char** arg) :
iarg += 2;
} else error->all(FLERR,"Illegal fix ave/spatial/sphere command");
}
-
+
//setup and error checking
if (nevery <= 0 || nrepeat <= 0 || nfreq <= 0)
error->all(FLERR,"Illegal fix ave/spatial/sphere command");
@@ -311,7 +311,7 @@ FixAveSpatialSphere::FixAveSpatialSphere(LAMMPS* lmp, int narg, char** arg) :
error->all(FLERR,"Illegal fix ave/spatial/sphere command");
if (ave != RUNNING && overwrite)
error->all(FLERR,"Illegal fix ave/spatial/sphere command");
-
+
//setup the variables that we need to average
for (int i = 0; i < nvalues; i++) {
if (which[i] == COMPUTE) {
@@ -367,7 +367,7 @@ FixAveSpatialSphere::FixAveSpatialSphere(LAMMPS* lmp, int narg, char** arg) :
no_change_box= 1;
}
}
-
+
if(scaleflag == LATTICE) {
scale= domain->lattice->xlattice;
if(domain->lattice->xlattice != domain->lattice->ylattice
@@ -379,7 +379,7 @@ FixAveSpatialSphere::FixAveSpatialSphere(LAMMPS* lmp, int narg, char** arg) :
} else {
scale= 1.0;
}
-
+
//apply the scaling factors
origin[0]*= scale;
origin[1]*= scale;
@@ -390,7 +390,7 @@ FixAveSpatialSphere::FixAveSpatialSphere(LAMMPS* lmp, int narg, char** arg) :
r_maxsq= r_max*r_max;
deltar= (r_max-r_min)/nbins;
inv_deltar= 1.0/deltar;
-
+
//print file comment lines
if (fp && me == 0) {
if (title1) {
@@ -401,7 +401,7 @@ FixAveSpatialSphere::FixAveSpatialSphere(LAMMPS* lmp, int narg, char** arg) :
for (int i= 0; i < 3; ++i) {
if(origin_type[i] == CONSTANT) fprintf(fp,"%g",origin[i]);
else fprintf(fp,"%s",arg[i+6]);
-
+
if(i != 2) fprintf(fp, ", ");
else fprintf(fp, ")");
}
@@ -424,13 +424,13 @@ FixAveSpatialSphere::FixAveSpatialSphere(LAMMPS* lmp, int narg, char** arg) :
delete [] title1;
delete [] title2;
delete [] title3;
-
+
//this fix produces a global array
array_flag= 1;
size_array_rows= BIG;
size_array_cols= 1 + 1 + nvalues;
extarray= 0; //intensive value (don't divide by N when we output this)
-
+
//initialization of remaining variables
irepeat= 0;
iwindow= window_limit= 0;
@@ -446,7 +446,7 @@ FixAveSpatialSphere::FixAveSpatialSphere(LAMMPS* lmp, int narg, char** arg) :
count_list= NULL;
values_one= values_many= values_sum= values_total= NULL;
values_list= NULL;
-
+
//nvalid = next step on which end_of_step does something
nvalid= nextvalid();
//make every compute update itself on step nvalid
@@ -505,11 +505,11 @@ void FixAveSpatialSphere::init()
//set up the region and check it's valid
if(regionflag) {
int iregion= domain->find_region(idregion);
- if(iregion == -1)
+ if(iregion == -1)
error->all(FLERR,"Region ID for fix ave/spatial/sphere does not exist");
region = domain->regions[iregion];
}
-
+
// set indices and check validity of all computes,fixes,variables
// check that fix frequency is acceptable
@@ -552,8 +552,8 @@ void FixAveSpatialSphere::init()
} else value2index[m] = -1;
}
-
-
+
+
// need to reset nvalid if nvalid < ntimestep b/c minimize was performed
if (nvalid < update->ntimestep) {
irepeat = 0;
@@ -583,7 +583,7 @@ void FixAveSpatialSphere::end_of_step()
//update region if necessary
if (regionflag) region->prematch();
-
+
//zero out arrays that accumulate over many samples
if(irepeat == 0) {
for(int m= 0; m < nbins; m++) {
@@ -594,23 +594,23 @@ void FixAveSpatialSphere::end_of_step()
//if in reduced units, we need to update the bin volumes
if (scaleflag == REDUCED && domain->box_change) set_bin_volumes();
-
+
//zero out arrays for one sample
for(int m= 0; m < nbins; m++) {
count_one[m]= 0.0;
for (int i= 0; i < nvalues; i++) values_one[m][i]= 0.0;
}
-
+
//bin each atom
int *mask= atom->mask;
int nlocal= atom->nlocal;
-
+
if (nlocal > maxatom) {
maxatom= atom->nmax;
memory->destroy(bin);
memory->create(bin,maxatom,"ave/spatial/sphere:bin");
}
-
+
// perform the computation for one sample
// accumulate results of attributes,computes,fixes,variables to local copy
// sum within each bin, only include atoms in fix group
@@ -621,11 +621,11 @@ void FixAveSpatialSphere::end_of_step()
//each atom gets either the number of the bin into which
//it fits, or -1
bin_atoms();
-
+
for(int m= 0; m < nvalues; m++) {
int n= value2index[m];
int j= argindex[m];
-
+
if(which[m] == V || which[m] == F) {
double **attribute;
if(which[m] == V) attribute= atom->v;
@@ -696,7 +696,7 @@ void FixAveSpatialSphere::end_of_step()
values_one[bin[i]][m] += varatom[i];
}
}
-
+
// process a single sample
// if normflag = ALL, accumulate values,count separately to many
// if normflag = SAMPLE, one = value/count, accumulate one to many
@@ -720,7 +720,7 @@ void FixAveSpatialSphere::end_of_step()
count_sum[m] += count_many[m];
}
}
-
+
// done if irepeat < nrepeat
// else reset irepeat and nvalid
irepeat++;
@@ -729,14 +729,14 @@ void FixAveSpatialSphere::end_of_step()
modify->addstep_compute(nvalid);
return;
}
-
+
irepeat++;
if (irepeat < nrepeat) {
nvalid += nevery;
modify->addstep_compute(nvalid);
return;
}
-
+
irepeat = 0;
nvalid = ntimestep+nfreq - (nrepeat-1)*nevery;
modify->addstep_compute(nvalid);
@@ -745,7 +745,7 @@ void FixAveSpatialSphere::end_of_step()
// if normflag = ALL, final is total value / total count
// if normflag = SAMPLE, final is sum of ave / repeat
// exception is densities: normalized by repeat, not total count
-
+
double repeat = nrepeat;
double mv2d = force->mv2d;
if (normflag == ALL) {
@@ -810,7 +810,7 @@ void FixAveSpatialSphere::end_of_step()
if (window_limit) norm = nwindow;
else norm = iwindow;
}
-
+
// output result to file
if (fp && me == 0) {
@@ -852,21 +852,21 @@ void FixAveSpatialSphere::setup_bins()
memory->grow(values_many,nbins,nvalues,"ave/spatial/sphere:values_many");
memory->grow(values_sum,nbins,nvalues,"ave/spatial/sphere:values_sum");
memory->grow(values_total,nbins,nvalues,"ave/spatial/sphere:values_total");
-
+
//the count and value lists are only relevant for windowed averaging
if(ave == WINDOW) {
memory->create(count_list,nwindow,nbins,"ave/spatial/sphere:count_list");
memory->create(values_list,nwindow,nbins,nvalues,
"ave/spatial/sphere:values_list");
}
-
+
//reinitialize the regrown count and values
for(int m= 0; m < nbins; m++) {
for(int i= 0; i < nvalues; i++) values_total[m][i]= 0.0;
count_total[m]= 0.0;
}
}
-
+
//set the bin coordinates
for(int i= 0; i < nbins; i++)
coord[i]= r_min + (i+0.5)*deltar;
@@ -904,7 +904,7 @@ void FixAveSpatialSphere::set_bin_volumes()
assign atoms to bins
------------------------------------------------------------------------- */
-void FixAveSpatialSphere::bin_atoms()
+void FixAveSpatialSphere::bin_atoms()
{
//update the origin coordinates if necessary
//unscale the existing coordinates
@@ -938,7 +938,7 @@ void FixAveSpatialSphere::bin_atoms()
double **x= atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
-
+
double *prd,*prd_half;
//deal with the periodic boundary conditions
if(domain->periodicity[0] || domain->periodicity[1] || domain->periodicity[2]) {
@@ -950,16 +950,16 @@ void FixAveSpatialSphere::bin_atoms()
prd_half= domain->prd_half;
}
}
-
+
double rsq, tmp;
-
+
if(!regionflag) {
if(scaleflag == REDUCED) {
//convert the atomic coordinates into reduced coordinates
domain->x2lamda(nlocal);
}
for(int i= 0; i < nlocal; i++) {
- if(mask[i] & groupbit) {
+ if(mask[i] & groupbit) {
rsq= 0.0;
for(int dim= 0; dim < 3; dim++) {
tmp= x[i][dim] - origin[dim];
diff --git a/src/USER-MISC/fix_ave_spatial_sphere.h b/src/USER-MISC/fix_ave_spatial_sphere.h
index ea752f2e3e..1ac550c5e0 100644
--- a/src/USER-MISC/fix_ave_spatial_sphere.h
+++ b/src/USER-MISC/fix_ave_spatial_sphere.h
@@ -22,7 +22,7 @@ FixStyle(ave/spatial/sphere,FixAveSpatialSphere)
#ifndef LMP_FIX_AVE_SPATIAL_SPHERE_H
#define LMP_FIX_AVE_SPATIAL_SPHERE_H
-#include "stdio.h"
+#include <stdio.h>
#include "fix.h"
namespace LAMMPS_NS {
@@ -37,13 +37,13 @@ class FixAveSpatialSphere : public Fix {
void end_of_step();
double memory_usage();
double compute_array(int,int);
-
+
private:
int me; //rank of the MPI Process
int nfreq; //fix nfreq parameter
int nrepeat; //fix nrepeat parameter
bigint nvalid; //the next timestep on which I'll be invoked
-
+
//controls for various optional behaviours
int normflag; //what type of normalisation to do
int norm;
@@ -57,9 +57,9 @@ class FixAveSpatialSphere : public Fix {
int ave; //averaging mode
int nwindow; //number of averaging windows
int iwindow; //current window
- int window_limit;
+ int window_limit;
int overwrite; //continuously overwrite the output (requires ave running)
-
+
//used to keep track of which per-atom values we deal with
int nvalues; //number of variables to average
int *argindex; //if the variable is an array, this is the offset in that array
@@ -68,7 +68,7 @@ class FixAveSpatialSphere : public Fix {
char **ids; //names of the variables
int maxvar; //current size of the varatom array
double* varatom; //contains the peratom values of a variable
-
+
//details of the sphere and the bins
int maxbin; //current number of bins in memory (relevant if box changes)
int nbins; //number of spherical bins
@@ -86,17 +86,17 @@ class FixAveSpatialSphere : public Fix {
double r_min, r_minsq; //minimum radius, and its square
double r_max, r_maxsq; //maximum radius, and its square
double deltar, inv_deltar; //radial width of a bin, and its inverse (and their squares)
-
+
void setup_bins(); //create the bin arrays
void set_bin_volumes(); //calculate the volume of each bin
void bin_atoms(); //put the atom into bins based on their coordinates
bigint nextvalid(); //return the next timestep on which this is invoked
-
+
//NEED TO BE CATEGORISED
int irepeat;
double **count_list;
double ***values_list;
-
+
};
}
diff --git a/src/USER-MISC/fix_gle.cpp b/src/USER-MISC/fix_gle.cpp
index 95f868f95f..40d1047648 100644
--- a/src/USER-MISC/fix_gle.cpp
+++ b/src/USER-MISC/fix_gle.cpp
@@ -16,10 +16,10 @@
Axel Kohylmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "math.h"
-#include "string.h"
-#include "stdlib.h"
+#include <mpi.h>
+#include <math.h>
+#include <string.h>
+#include <stdlib.h>
#include "fix_gle.h"
#include "math_extra.h"
#include "atom.h"
@@ -82,11 +82,11 @@ void StabCholesky(int n, const double* MMt, double* M)
for (k=0; k<i; ++k) D[i]-=L[midx(n,i,k)]*L[midx(n,i,k)]*D[k];
}
- for(i=0; i<n; ++i)
+ for(i=0; i<n; ++i)
{
-#ifdef GLE_DEBUG
- if (D[i]<0) fprintf(stderr,"GLE Cholesky: Negative diagonal term %le, has been set to zero.\n", D[i]);
-#endif
+#ifdef GLE_DEBUG
+ if (D[i]<0) fprintf(stderr,"GLE Cholesky: Negative diagonal term %le, has been set to zero.\n", D[i]);
+#endif
D[i]=(D[i]>0.?sqrt(D[i]):0.);
}
diff --git a/src/USER-MISC/fix_ipi.cpp b/src/USER-MISC/fix_ipi.cpp
index 07dbeb2500..f9b0b519ac 100644
--- a/src/USER-MISC/fix_ipi.cpp
+++ b/src/USER-MISC/fix_ipi.cpp
@@ -15,10 +15,10 @@
Contributing author: Michele Ceriotti (EPFL), Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "stdio.h"
-#include "string.h"
-#include "stdlib.h"
+#include <mpi.h>
+#include <stdio.h>
+#include <string.h>
+#include <stdlib.h>
#include "fix_ipi.h"
#include "atom.h"
#include "force.h"
@@ -32,7 +32,7 @@
#include "neighbor.h"
#include "domain.h"
#include "compute_pressure.h"
-#include "errno.h"
+#include <errno.h>
using namespace LAMMPS_NS;
using namespace FixConst;
diff --git a/src/USER-MISC/fix_pimd.cpp b/src/USER-MISC/fix_pimd.cpp
index 75662a8207..bba6b2e2be 100644
--- a/src/USER-MISC/fix_pimd.cpp
+++ b/src/USER-MISC/fix_pimd.cpp
@@ -16,14 +16,14 @@
Purpose Quantum Path Integral Algorithm for Quantum Chemistry
Copyright Voth Group @ University of Chicago
Authors Chris Knight & Yuxing Peng (yuxing at uchicago.edu)
-
+
Updated Oct-01-2011
Version 1.0
------------------------------------------------------------------------- */
-#include "math.h"
-#include "string.h"
-#include "stdlib.h"
+#include <math.h>
+#include <string.h>
+#include <stdlib.h>
#include "fix_pimd.h"
#include "universe.h"
#include "comm.h"
@@ -42,7 +42,7 @@ enum{PIMD,NMPIMD,CMD};
/* ---------------------------------------------------------------------- */
FixPIMD::FixPIMD(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
-{
+{
method = PIMD;
fmass = 1.0;
nhc_temp = 298.15;
@@ -80,57 +80,57 @@ FixPIMD::FixPIMD(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
}
else error->universe_all(arg[i],i+1,"Unkown keyword for fix pimd");
}
-
+
/* Initiation */
-
+
max_nsend = 0;
tag_send = NULL;
buf_send = NULL;
-
+
max_nlocal = 0;
buf_recv = NULL;
buf_beads = NULL;
-
+
size_plan = 0;
plan_send = plan_recv = NULL;
-
+
M_x2xp = M_xp2x = M_f2fp = M_fp2f = NULL;
lam = NULL;
mode_index = NULL;
mass = NULL;
-
+
array_atom = NULL;
nhc_eta = NULL;
nhc_eta_dot = NULL;
nhc_eta_dotdot = NULL;
nhc_eta_mass = NULL;
-
+
size_peratom_cols = 12 * nhc_nchain + 3;
-
+
nhc_offset_one_1 = 3 * nhc_nchain;
nhc_offset_one_2 = 3 * nhc_nchain +3;
nhc_size_one_1 = sizeof(double) * nhc_offset_one_1;
nhc_size_one_2 = sizeof(double) * nhc_offset_one_2;
-
+
restart_peratom = 1;
peratom_flag = 1;
peratom_freq = 1;
-
+
global_freq = 1;
thermo_energy = 1;
vector_flag = 1;
size_vector = 2;
extvector = 1;
comm_forward = 3;
-
+
atom->add_callback(0); // Call LAMMPS to allocate memory for per-atom array
atom->add_callback(1); // Call LAMMPS to re-assign restart-data for per-atom array
-
+
grow_arrays(atom->nmax);
-
+
// some initilizations
-
+
nhc_ready = false;
}
@@ -153,53 +153,53 @@ void FixPIMD::init()
error->all(FLERR,"Fix pimd requires an atom map, see atom_modify");
if(universe->me==0 && screen) fprintf(screen,"Fix pimd initializing Path-Integral ...\n");
-
+
// prepare the constants
-
+
np = universe->nworlds;
inverse_np = 1.0 / np;
-
- /* The first solution for the force constant, using SI units
-
+
+ /* The first solution for the force constant, using SI units
+
const double Boltzmann = 1.3806488E-23; // SI unit: J/K
const double Plank = 6.6260755E-34; // SI unit: m^2 kg / s
-
+
double hbar = Plank / ( 2.0 * M_PI ) * sp;
double beta = 1.0 / ( Boltzmann * input.nh_temp);
-
+
// - P / ( beta^2 * hbar^2) SI unit: s^-2
double _fbond = -1.0 / (beta*beta*hbar*hbar) * input.nbeads;
-
+
// convert the units: s^-2 -> (kcal/mol) / (g/mol) / (A^2)
fbond = _fbond * 4.184E+26;
-
+
*/
-
+
/* The current solution, using LAMMPS internal real units */
-
- const double Boltzmann = force->boltz;
- const double Plank = force->hplanck;
-
+
+ const double Boltzmann = force->boltz;
+ const double Plank = force->hplanck;
+
double hbar = Plank / ( 2.0 * M_PI );
- double beta = 1.0 / (Boltzmann * nhc_temp);
+ double beta = 1.0 / (Boltzmann * nhc_temp);
double _fbond = 1.0 * np / (beta*beta*hbar*hbar) ;
-
+
omega_np = sqrt(np) / (hbar * beta) * sqrt(force->mvv2e);
fbond = - _fbond * force->mvv2e;
-
+
if(universe->me==0)
printf("Fix pimd -P/(beta^2 * hbar^2) = %20.7lE (kcal/mol/A^2)\n\n", fbond);
-
+
dtv = update->dt;
dtf = 0.5 * update->dt * force->ftm2v;
-
+
comm_init();
-
+
mass = new double [atom->ntypes+1];
-
+
if(method==CMD || method==NMPIMD) nmpimd_init();
else for(int i=1; i<=atom->ntypes; i++) mass[i] = atom->mass[i] / np * fmass;
-
+
if(!nhc_ready) nhc_init();
}
@@ -208,7 +208,7 @@ void FixPIMD::init()
void FixPIMD::setup(int vflag)
{
if(universe->me==0 && screen) fprintf(screen,"Setting up Path-Integral ...\n");
-
+
post_force(vflag);
}
@@ -232,22 +232,22 @@ void FixPIMD::final_integrate()
void FixPIMD::post_force(int flag)
{
for(int i=0; i<atom->nlocal; i++) for(int j=0; j<3; j++) atom->f[i][j] /= np;
-
+
comm_exec(atom->x);
spring_force();
-
+
if(method==CMD || method==NMPIMD)
{
/* forward comm for the force on ghost atoms */
-
- nmpimd_fill(atom->f);
-
+
+ nmpimd_fill(atom->f);
+
/* inter-partition comm */
-
+
comm_exec(atom->f);
-
+
/* normal-mode transform */
-
+
nmpimd_transform(buf_beads, atom->f, M_f2fp[universe->iworld]);
}
}
@@ -263,50 +263,50 @@ void FixPIMD::nhc_init()
double mass0 = KT * tau * tau;
int max = 3 * atom->nlocal;
-
- for(int i=0; i<max; i++)
+
+ for(int i=0; i<max; i++)
{
- for(int ichain=0; ichain<nhc_nchain; ichain++)
+ for(int ichain=0; ichain<nhc_nchain; ichain++)
{
nhc_eta[i][ichain] = 0.0;
nhc_eta_dot[i][ichain] = 0.0;
nhc_eta_dot[i][ichain] = 0.0;
nhc_eta_dotdot[i][ichain] = 0.0;
nhc_eta_mass[i][ichain] = mass0;
- if((method==CMD || method==NMPIMD) && universe->iworld==0) ; else nhc_eta_mass[i][ichain] *= fmass;
+ if((method==CMD || method==NMPIMD) && universe->iworld==0) ; else nhc_eta_mass[i][ichain] *= fmass;
}
-
+
nhc_eta_dot[i][nhc_nchain] = 0.0;
-
+
for(int ichain=1; ichain<nhc_nchain; ichain++)
- nhc_eta_dotdot[i][ichain] = (nhc_eta_mass[i][ichain-1] * nhc_eta_dot[i][ichain-1]
+ nhc_eta_dotdot[i][ichain] = (nhc_eta_mass[i][ichain-1] * nhc_eta_dot[i][ichain-1]
* nhc_eta_dot[i][ichain-1] * force->mvv2e - KT) / nhc_eta_mass[i][ichain];
}
// Zero NH acceleration for CMD
-
- if(method==CMD && universe->iworld==0) for(int i=0; i<max; i++)
+
+ if(method==CMD && universe->iworld==0) for(int i=0; i<max; i++)
for(int ichain=0; ichain<nhc_nchain; ichain++) nhc_eta_dotdot[i][ichain] = 0.0;
-
+
nhc_ready = true;
}
/* ---------------------------------------------------------------------- */
void FixPIMD::nhc_update_x()
-{
+{
int n = atom->nlocal;
double **x = atom->x;
double **v = atom->v;
-
+
if(method==CMD || method==NMPIMD)
{
- nmpimd_fill(atom->v);
+ nmpimd_fill(atom->v);
comm_exec(atom->v);
-
+
/* borrow the space of atom->f to store v in cartisian */
-
- v = atom->f;
+
+ v = atom->f;
nmpimd_transform(buf_beads, v, M_xp2x[universe->iworld]);
}
@@ -326,7 +326,7 @@ void FixPIMD::nhc_update_v()
int *type = atom->type;
double **v = atom->v;
double **f = atom->f;
-
+
for(int i=0; i<n; i++)
{
double dtfm = dtf / mass[type[i]];
@@ -334,36 +334,36 @@ void FixPIMD::nhc_update_v()
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
}
-
+
t_sys = 0.0;
if(method==CMD && universe->iworld==0) return;
-
+
double expfac;
int nmax = 3 * atom->nlocal;
double KT = force->boltz * nhc_temp;
double kecurrent, t_current;
-
+
double dthalf = 0.5 * update->dt;
double dt4 = 0.25 * update->dt;
double dt8 = 0.125 * update->dt;
-
- for(int i=0; i<nmax; i++)
+
+ for(int i=0; i<nmax; i++)
{
int iatm = i/3;
int idim = i%3;
-
- double *vv = v[iatm];
-
+
+ double *vv = v[iatm];
+
kecurrent = mass[type[iatm]] * vv[idim]* vv[idim] * force->mvv2e;
t_current = kecurrent / force->boltz;
-
+
double *eta = nhc_eta[i];
double *eta_dot = nhc_eta_dot[i];
double *eta_dotdot = nhc_eta_dotdot[i];
-
+
eta_dotdot[0] = (kecurrent - KT) / nhc_eta_mass[i][0];
- for(int ichain=nhc_nchain-1; ichain>0; ichain--)
+ for(int ichain=nhc_nchain-1; ichain>0; ichain--)
{
expfac = exp(-dt8 * eta_dot[ichain+1]);
eta_dot[ichain] *= expfac;
@@ -377,7 +377,7 @@ void FixPIMD::nhc_update_v()
eta_dot[0] *= expfac;
// Update particle velocities half-step
-
+
double factor_eta = exp(-dthalf * eta_dot[0]);
vv[idim] *= factor_eta;
@@ -385,14 +385,14 @@ void FixPIMD::nhc_update_v()
kecurrent = force->boltz * t_current;
eta_dotdot[0] = (kecurrent - KT) / nhc_eta_mass[i][0];
- for(int ichain=0; ichain<nhc_nchain; ichain++)
+ for(int ichain=0; ichain<nhc_nchain; ichain++)
eta[ichain] += dthalf * eta_dot[ichain];
eta_dot[0] *= expfac;
eta_dot[0] += eta_dotdot[0] * dt4;
eta_dot[0] *= expfac;
- for(int ichain=1; ichain<nhc_nchain; ichain++)
+ for(int ichain=1; ichain<nhc_nchain; ichain++)
{
expfac = exp(-dt8 * eta_dot[ichain+1]);
eta_dot[ichain] *= expfac;
@@ -401,10 +401,10 @@ void FixPIMD::nhc_update_v()
eta_dot[ichain] += eta_dotdot[ichain] * dt4;
eta_dot[ichain] *= expfac;
}
-
- t_sys += t_current;
+
+ t_sys += t_current;
}
-
+
t_sys /= nmax;
}
@@ -418,54 +418,54 @@ void FixPIMD::nmpimd_init()
memory->create(M_xp2x, np, np, "fix_feynman:M_xp2x");
memory->create(M_f2fp, np, np, "fix_feynman:M_f2fp");
memory->create(M_fp2f, np, np, "fix_feynman:M_fp2f");
-
+
lam = (double*) memory->smalloc(sizeof(double)*np, "FixPIMD::lam");
// Set up eigenvalues
-
+
lam[0] = 0.0;
if(np%2==0) lam[np-1] = 4.0 * np;
-
+
for(int i=2; i<=np/2; i++)
{
lam[2*i-3] = lam[2*i-2] = 2.0 * np * (1.0 - 1.0 *cos(2.0*M_PI*(i-1)/np));
}
-
+
// Set up eigenvectors for non-degenerated modes
-
+
for(int i=0; i<np; i++)
{
M_x2xp[0][i] = 1.0 / np;
if(np%2==0) M_x2xp[np-1][i] = 1.0 / np * pow(-1.0, i);
}
-
+
// Set up eigenvectors for degenerated modes
-
+
for(int i=0; i<(np-1)/2; i++) for(int j=0; j<np; j++)
{
M_x2xp[2*i+1][j] = sqrt(2.0) * cos ( 2.0 * M_PI * (i+1) * j / np) / np;
M_x2xp[2*i+2][j] = - sqrt(2.0) * sin ( 2.0 * M_PI * (i+1) * j / np) / np;
}
-
+
// Set up Ut
-
- for(int i=0; i<np; i++)
+
+ for(int i=0; i<np; i++)
for(int j=0; j<np; j++)
{
- M_xp2x[i][j] = M_x2xp[j][i] * np;
+ M_xp2x[i][j] = M_x2xp[j][i] * np;
M_f2fp[i][j] = M_x2xp[i][j] * np;
M_fp2f[i][j] = M_xp2x[i][j];
}
-
+
// Set up masses
-
+
int iworld = universe->iworld;
-
+
for(int i=1; i<=atom->ntypes; i++)
{
mass[i] = atom->mass[i];
- if(iworld)
+ if(iworld)
{
mass[i] *= lam[iworld];
mass[i] *= fmass;
@@ -487,10 +487,10 @@ void FixPIMD::nmpimd_transform(double** src, double** des, double *vector)
{
int n = atom->nlocal;
int m = 0;
-
+
for(int i=0; i<n; i++) for(int d=0; d<3; d++)
{
- des[i][d] = 0.0;
+ des[i][d] = 0.0;
for(int j=0; j<np; j++) { des[i][d] += (src[j][m] * vector[j]); }
m++;
}
@@ -508,9 +508,9 @@ void FixPIMD::spring_force()
int* type = atom->type;
int nlocal = atom->nlocal;
- double* xlast = buf_beads[x_last];
+ double* xlast = buf_beads[x_last];
double* xnext = buf_beads[x_next];
-
+
for(int i=0; i<nlocal; i++)
{
double delx1 = xlast[0] - x[i][0];
@@ -524,17 +524,17 @@ void FixPIMD::spring_force()
double delz2 = xnext[2] - x[i][2];
xnext += 3;
domain->minimum_image(delx2, dely2, delz2);
-
+
double ff = fbond * _mass[type[i]];
-
+
double dx = delx1+delx2;
double dy = dely1+dely2;
double dz = delz1+delz2;
-
+
f[i][0] -= (dx) * ff;
f[i][1] -= (dy) * ff;
f[i][2] -= (dz) * ff;
-
+
spring_energy += (dx*dx+dy*dy+dz*dz);
}
}
@@ -550,26 +550,26 @@ void FixPIMD::comm_init()
delete [] plan_send;
delete [] plan_recv;
}
-
- if(method == PIMD)
+
+ if(method == PIMD)
{
size_plan = 2;
plan_send = new int [2];
plan_recv = new int [2];
mode_index = new int [2];
-
+
int rank_last = universe->me - comm->nprocs;
- int rank_next = universe->me + comm->nprocs;
+ int rank_next = universe->me + comm->nprocs;
if(rank_last<0) rank_last += universe->nprocs;
if(rank_next>=universe->nprocs) rank_next -= universe->nprocs;
-
+
plan_send[0] = rank_next; plan_send[1] = rank_last;
plan_recv[0] = rank_last; plan_recv[1] = rank_next;
-
+
mode_index[0] = 0; mode_index[1] = 1;
x_last = 1; x_next = 0;
}
- else
+ else
{
size_plan = np - 1;
plan_send = new int [size_plan];
@@ -580,23 +580,23 @@ void FixPIMD::comm_init()
{
plan_send[i] = universe->me + comm->nprocs * (i+1);
if(plan_send[i]>=universe->nprocs) plan_send[i] -= universe->nprocs;
-
+
plan_recv[i] = universe->me - comm->nprocs * (i+1);
if(plan_recv[i]<0) plan_recv[i] += universe->nprocs;
mode_index[i]=(universe->iworld+i+1)%(universe->nworlds);
}
-
+
x_next = (universe->iworld+1+universe->nworlds)%(universe->nworlds);
x_last = (universe->iworld-1+universe->nworlds)%(universe->nworlds);
}
-
+
if(buf_beads)
{
for(int i=0; i<np; i++) if(buf_beads[i]) delete [] buf_beads[i];
delete [] buf_beads;
}
-
+
buf_beads = new double* [np];
for(int i=0; i<np; i++) buf_beads[i] = NULL;
}
@@ -606,51 +606,51 @@ void FixPIMD::comm_init()
void FixPIMD::comm_exec(double **ptr)
{
int nlocal = atom->nlocal;
-
+
if(nlocal > max_nlocal)
{
max_nlocal = nlocal+200;
int size = sizeof(double) * max_nlocal * 3;
buf_recv = (double*) memory->srealloc(buf_recv, size, "FixPIMD:x_recv");
-
- for(int i=0; i<np; i++)
+
+ for(int i=0; i<np; i++)
buf_beads[i] = (double*) memory->srealloc(buf_beads[i], size, "FixPIMD:x_beads[i]");
}
-
+
// copy local positions
-
+
memcpy(buf_beads[universe->iworld], &(ptr[0][0]), sizeof(double)*nlocal*3);
-
+
// go over comm plans
-
+
for(int iplan = 0; iplan<size_plan; iplan++)
- {
+ {
// sendrecv nlocal
-
+
int nsend;
-
- MPI_Sendrecv( &(nlocal), 1, MPI_INT, plan_send[iplan], 0,
+
+ MPI_Sendrecv( &(nlocal), 1, MPI_INT, plan_send[iplan], 0,
&(nsend), 1, MPI_INT, plan_recv[iplan], 0, universe->uworld, MPI_STATUS_IGNORE);
-
+
// allocate arrays
-
+
if(nsend > max_nsend)
{
max_nsend = nsend+200;
tag_send = (int*) memory->srealloc(tag_send, sizeof(int)*max_nsend, "FixPIMD:tag_send");
buf_send = (double*) memory->srealloc(buf_send, sizeof(double)*max_nsend*3, "FixPIMD:x_send");
}
-
- // send tags
-
- MPI_Sendrecv( atom->tag, nlocal, MPI_INT, plan_send[iplan], 0,
+
+ // send tags
+
+ MPI_Sendrecv( atom->tag, nlocal, MPI_INT, plan_send[iplan], 0,
tag_send, nsend, MPI_INT, plan_recv[iplan], 0, universe->uworld, MPI_STATUS_IGNORE);
// wrap positions
-
+
double *wrap_ptr = buf_send;
int ncpy = sizeof(double)*3;
-
+
for(int i=0; i<nsend; i++)
{
int index = atom->map(tag_send[i]);
@@ -658,27 +658,27 @@ void FixPIMD::comm_exec(double **ptr)
if(index<0)
{
char error_line[256];
-
+
sprintf(error_line, "Atom " TAGINT_FORMAT " is missing at world [%d] "
"rank [%d] required by rank [%d] (" TAGINT_FORMAT ", "
TAGINT_FORMAT ", " TAGINT_FORMAT ").\n",tag_send[i],
universe->iworld, comm->me, plan_recv[iplan],
atom->tag[0], atom->tag[1], atom->tag[2]);
-
+
error->universe_one(FLERR,error_line);
}
-
+
memcpy(wrap_ptr, ptr[index], ncpy);
wrap_ptr += 3;
}
-
- // sendrecv x
-
- MPI_Sendrecv( buf_send, nsend*3, MPI_DOUBLE, plan_recv[iplan], 0,
+
+ // sendrecv x
+
+ MPI_Sendrecv( buf_send, nsend*3, MPI_DOUBLE, plan_recv[iplan], 0,
buf_recv, nlocal*3, MPI_DOUBLE, plan_send[iplan], 0, universe->uworld, MPI_STATUS_IGNORE);
-
+
// copy x
-
+
memcpy(buf_beads[mode_index[iplan]], buf_recv, sizeof(double)*nlocal*3);
}
}
@@ -691,14 +691,14 @@ int FixPIMD::pack_forward_comm(int n, int *list, double *buf,
int i,j,m;
m = 0;
-
+
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = comm_ptr[j][0];
buf[m++] = comm_ptr[j][1];
buf[m++] = comm_ptr[j][2];
}
-
+
return m;
}
@@ -736,10 +736,10 @@ void FixPIMD::grow_arrays(int nmax)
int count = nmax*3;
memory->grow(array_atom, nmax, size_peratom_cols, "FixPIMD::array_atom");
- memory->grow(nhc_eta, count, nhc_nchain, "FixPIMD::nh_eta");
- memory->grow(nhc_eta_dot, count, nhc_nchain+1, "FixPIMD::nh_eta_dot");
+ memory->grow(nhc_eta, count, nhc_nchain, "FixPIMD::nh_eta");
+ memory->grow(nhc_eta_dot, count, nhc_nchain+1, "FixPIMD::nh_eta_dot");
memory->grow(nhc_eta_dotdot, count, nhc_nchain, "FixPIMD::nh_eta_dotdot");
- memory->grow(nhc_eta_mass, count, nhc_nchain, "FixPIMD::nh_eta_mass");
+ memory->grow(nhc_eta_mass, count, nhc_nchain, "FixPIMD::nh_eta_mass");
}
/* ---------------------------------------------------------------------- */
@@ -748,7 +748,7 @@ void FixPIMD::copy_arrays(int i, int j, int delflag)
{
int i_pos = i*3;
int j_pos = j*3;
-
+
memcpy(nhc_eta [j_pos], nhc_eta [i_pos], nhc_size_one_1);
memcpy(nhc_eta_dot [j_pos], nhc_eta_dot [i_pos], nhc_size_one_2);
memcpy(nhc_eta_dotdot[j_pos], nhc_eta_dotdot[i_pos], nhc_size_one_1);
@@ -759,14 +759,14 @@ void FixPIMD::copy_arrays(int i, int j, int delflag)
int FixPIMD::pack_exchange(int i, double *buf)
{
- int offset=0;
+ int offset=0;
int pos = i * 3;
-
+
memcpy(buf+offset, nhc_eta[pos], nhc_size_one_1); offset += nhc_offset_one_1;
memcpy(buf+offset, nhc_eta_dot[pos], nhc_size_one_2); offset += nhc_offset_one_2;
memcpy(buf+offset, nhc_eta_dotdot[pos], nhc_size_one_1); offset += nhc_offset_one_1;
memcpy(buf+offset, nhc_eta_mass[pos], nhc_size_one_1); offset += nhc_offset_one_1;
-
+
return size_peratom_cols;
}
@@ -776,12 +776,12 @@ int FixPIMD::unpack_exchange(int nlocal, double *buf)
{
int offset=0;
int pos = nlocal*3;
-
+
memcpy(nhc_eta[pos], buf+offset, nhc_size_one_1); offset += nhc_offset_one_1;
memcpy(nhc_eta_dot[pos], buf+offset, nhc_size_one_2); offset += nhc_offset_one_2;
memcpy(nhc_eta_dotdot[pos], buf+offset, nhc_size_one_1); offset += nhc_offset_one_1;
memcpy(nhc_eta_mass[pos], buf+offset, nhc_size_one_1); offset += nhc_offset_one_1;
-
+
return size_peratom_cols;
}
@@ -797,8 +797,8 @@ int FixPIMD::pack_restart(int i, double *buf)
memcpy(buf+offset, nhc_eta_dot[pos], nhc_size_one_2); offset += nhc_offset_one_2;
memcpy(buf+offset, nhc_eta_dotdot[pos], nhc_size_one_1); offset += nhc_offset_one_1;
memcpy(buf+offset, nhc_eta_mass[pos], nhc_size_one_1); offset += nhc_offset_one_1;
-
- return size_peratom_cols+1;
+
+ return size_peratom_cols+1;
}
/* ---------------------------------------------------------------------- */
@@ -808,18 +808,18 @@ void FixPIMD::unpack_restart(int nlocal, int nth)
double **extra = atom->extra;
// skip to Nth set of extra values
-
+
int m = 0;
for (int i=0; i<nth; i++) m += static_cast<int> (extra[nlocal][m]);
m++;
-
+
int pos = nlocal * 3;
-
+
memcpy(nhc_eta[pos], extra[nlocal]+m, nhc_size_one_1); m += nhc_offset_one_1;
memcpy(nhc_eta_dot[pos], extra[nlocal]+m, nhc_size_one_2); m += nhc_offset_one_2;
memcpy(nhc_eta_dotdot[pos], extra[nlocal]+m, nhc_size_one_1); m += nhc_offset_one_1;
memcpy(nhc_eta_mass[pos], extra[nlocal]+m, nhc_size_one_1); m += nhc_offset_one_1;
-
+
nhc_ready = true;
}
@@ -840,7 +840,7 @@ int FixPIMD::size_restart(int nlocal)
/* ---------------------------------------------------------------------- */
double FixPIMD::compute_vector(int n)
-{
+{
if(n==0) { return spring_energy; }
if(n==1) { return t_sys; }
return 0.0;
diff --git a/src/USER-MISC/fix_pimd.h b/src/USER-MISC/fix_pimd.h
index 37ea652dfe..411fa42c81 100644
--- a/src/USER-MISC/fix_pimd.h
+++ b/src/USER-MISC/fix_pimd.h
@@ -27,15 +27,15 @@ namespace LAMMPS_NS {
class FixPIMD : public Fix {
public:
FixPIMD(class LAMMPS *, int, char **);
-
+
int setmask();
-
+
void init();
void setup(int);
void post_force(int);
void initial_integrate(int);
void final_integrate();
-
+
double memory_usage();
void grow_arrays(int);
void copy_arrays(int,int,int);
@@ -46,63 +46,63 @@ class FixPIMD : public Fix {
int maxsize_restart();
int size_restart(int);
double compute_vector(int);
-
+
int pack_forward_comm(int, int*, double *, int, int*);
void unpack_forward_comm(int, int, double *);
-
+
int method;
int np;
double inverse_np;
-
+
/* ring-polymer model */
-
+
double omega_np, fbond, spring_energy, sp;
int x_last, x_next;
-
+
void spring_force();
-
+
/* fictious mass */
-
+
double fmass, *mass;
-
+
/* inter-partition communication */
-
+
int max_nsend;
int* tag_send;
double *buf_send;
-
+
int max_nlocal;
double *buf_recv, **buf_beads;
-
+
int size_plan;
int *plan_send, *plan_recv;
double **comm_ptr;
-
+
void comm_init();
void comm_exec(double **);
-
+
/* normal-mode operations */
-
+
double *lam, **M_x2xp, **M_xp2x, **M_f2fp, **M_fp2f;
int *mode_index;
void nmpimd_init();
void nmpimd_fill(double**);
void nmpimd_transform(double**, double**, double*);
-
+
/* Nose-hoover chain integration */
-
+
int nhc_offset_one_1, nhc_offset_one_2;
int nhc_size_one_1, nhc_size_one_2;
int nhc_nchain;
bool nhc_ready;
double nhc_temp, dtv, dtf, t_sys;
-
+
double **nhc_eta; /* coordinates of NH chains for ring-polymer beads */
double **nhc_eta_dot; /* velocities of NH chains */
double **nhc_eta_dotdot; /* acceleration of NH chains */
double **nhc_eta_mass; /* mass of NH chains */
-
+
void nhc_init();
void nhc_update_v();
void nhc_update_x();
diff --git a/src/USER-MISC/fix_smd.cpp b/src/USER-MISC/fix_smd.cpp
index d8b4f1b9fb..3f6ca3f58a 100644
--- a/src/USER-MISC/fix_smd.cpp
+++ b/src/USER-MISC/fix_smd.cpp
@@ -16,9 +16,9 @@
based on fix spring by: Paul Crozier (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "fix_smd.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-MISC/fix_srp.cpp b/src/USER-MISC/fix_srp.cpp
index 08224d2950..fb4bd4e5ab 100644
--- a/src/USER-MISC/fix_srp.cpp
+++ b/src/USER-MISC/fix_srp.cpp
@@ -15,8 +15,8 @@
Contributing authors: Timothy Sirk (ARL), Pieter in't Veld (BASF)
------------------------------------------------------------------------- */
-#include "string.h"
-#include "stdlib.h"
+#include <string.h>
+#include <stdlib.h>
#include "fix_srp.h"
#include "atom.h"
#include "force.h"
@@ -49,22 +49,22 @@ FixSRP::FixSRP(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
// per-atom array width 2
peratom_flag = 1;
- size_peratom_cols = 2;
+ size_peratom_cols = 2;
- // initial allocation of atom-based array
+ // initial allocation of atom-based array
// register with Atom class
array = NULL;
- grow_arrays(atom->nmax);
+ grow_arrays(atom->nmax);
- // extends pack_exchange()
+ // extends pack_exchange()
atom->add_callback(0);
atom->add_callback(1); // restart
- atom->add_callback(2);
+ atom->add_callback(2);
- // zero
- for (int i = 0; i < atom->nmax; i++)
- for (int m = 0; m < 3; m++)
- array[i][m] = 0.0;
+ // zero
+ for (int i = 0; i < atom->nmax; i++)
+ for (int m = 0; m < 3; m++)
+ array[i][m] = 0.0;
// assume setup of fix is needed to insert particles
// is true if reading from datafile
@@ -72,7 +72,7 @@ FixSRP::FixSRP(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
// might be true if reading from restart
// a restart file written during the run has bond particles as per atom data
// a restart file written after the run does not have bond particles
- setup = 1;
+ setup = 1;
}
/* ---------------------------------------------------------------------- */
@@ -106,7 +106,7 @@ void FixSRP::init()
error->all(FLERR,"Cannot use pair srp without pair_style hybrid");
// the highest numbered atom type should be reserved for bond particles (bptype)
- // set bptype, unless it will be read from restart
+ // set bptype, unless it will be read from restart
if(!restart_reset) bptype = atom->ntypes;
// check if bptype is already in use
@@ -118,24 +118,24 @@ void FixSRP::init()
if(!restart_reset)
error->all(FLERR,"Fix SRP requires an extra atom type");
else
- setup = 0;
+ setup = 0;
}
-
+
// setup neigh exclusions for diff atom types
// bond particles do not interact with other types
// type bptype only interacts with itself
char* arg1[4];
- arg1[0] = (char *) "exclude";
- arg1[1] = (char *) "type";
+ arg1[0] = (char *) "exclude";
+ arg1[1] = (char *) "type";
char c0[20];
char c1[20];
for(int z = 1; z < bptype; z++)
{
sprintf(c0, "%d", z);
- arg1[2] = c0;
+ arg1[2] = c0;
sprintf(c1, "%d", bptype);
- arg1[3] = c1;
+ arg1[3] = c1;
neighbor->modify_params(4, arg1);
}
}
@@ -192,19 +192,19 @@ void FixSRP::setup_pre_force(int zz)
xone[1] = (xold[i][1] + xold[j][1])*0.5;
xone[2] = (xold[i][2] + xold[j][2])*0.5;
- // record longest bond
+ // record longest bond
// this used to set ghost cutoff
delx = xold[j][0] - xold[i][0];
dely = xold[j][1] - xold[i][1];
delz = xold[j][2] - xold[i][2];
rsq = delx*delx + dely*dely + delz*delz;
- if(rsq > rsqold) rsqold = rsq;
+ if(rsq > rsqold) rsqold = rsq;
// make one particle for each bond
// i is local
// if newton bond, always make particle
// if j is local, always make particle
- // if j is ghost, decide from tag
+ // if j is ghost, decide from tag
if( force->newton_bond || j < nlocal || tagold[i] > tagold[j] ){
atom->natoms += 1;
@@ -246,7 +246,7 @@ void FixSRP::setup_pre_force(int zz)
// ghost atoms must be present for bonds on edge of neighbor cutoff
// extend cutghost slightly more than half of the longest bond
MPI_Allreduce(&rsqold,&rsqmax,1,MPI_DOUBLE,MPI_MAX,world);
- rmax = sqrt(rsqmax);
+ rmax = sqrt(rsqmax);
double cutneighmax_srp = neighbor->cutneighmax + 0.51*rmax;
// find smallest cutghost
@@ -262,7 +262,7 @@ void FixSRP::setup_pre_force(int zz)
sprintf(str, "Extending ghost comm cutoff. New %f, old %f.", cutneighmax_srp, cutghostmin);
error->message(FLERR,str);
}
- // cutghost updated by comm->setup
+ // cutghost updated by comm->setup
comm->cutghostuser = cutneighmax_srp;
}
@@ -270,7 +270,7 @@ void FixSRP::setup_pre_force(int zz)
// move owned to new procs
// get ghosts
// build neigh lists again
-
+
// if triclinic, lambda coords needed for pbc, exchange, borders
if (domain->triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
@@ -290,7 +290,7 @@ void FixSRP::setup_pre_force(int zz)
// new atom counts
nlocal = atom->nlocal;
nall = atom->nlocal + atom->nghost;
- // zero all forces
+ // zero all forces
for(int i = 0; i < nall; i++)
for(int n = 0; n < 3; n++)
atom->f[i][n] = 0.0;
@@ -308,7 +308,7 @@ void FixSRP::setup_pre_force(int zz)
void FixSRP::pre_exchange()
{
- // update ghosts
+ // update ghosts
comm->forward_comm();
// reassign bond particle coordinates to midpoint of bonds
@@ -328,7 +328,7 @@ void FixSRP::pre_exchange()
if(j < 0) error->all(FLERR,"Fix SRP failed to map atom");
j = domain->closest_image(ii,j);
- // position of bond particle ii
+ // position of bond particle ii
atom->x[ii][0] = (x[i][0] + x[j][0])*0.5;
atom->x[ii][1] = (x[i][1] + x[j][1])*0.5;
atom->x[ii][2] = (x[i][2] + x[j][2])*0.5;
@@ -374,7 +374,7 @@ void FixSRP::copy_arrays(int i, int j, int delflag)
void FixSRP::set_arrays(int i)
{
array[i][0] = -1;
- array[i][1] = -1;
+ array[i][1] = -1;
}
/* ----------------------------------------------------------------------
@@ -438,9 +438,9 @@ int FixSRP::unpack_border(int n, int first, double *buf)
void FixSRP::post_run()
{
// all bond particles are removed after each run
- // useful for write_data and write_restart commands
+ // useful for write_data and write_restart commands
// since those commands occur between runs
-
+
bigint natoms_previous = atom->natoms;
int nlocal = atom->nlocal;
int* dlist;
@@ -508,7 +508,7 @@ void FixSRP::post_run()
comm->borders();
// change back to box coordinates
if (domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
-}
+}
/* ----------------------------------------------------------------------
pack values in local atom-based arrays for restart file
@@ -518,7 +518,7 @@ int FixSRP::pack_restart(int i, double *buf)
{
int m = 0;
buf[m++] = 3;
- buf[m++] = array[i][0];
+ buf[m++] = array[i][0];
buf[m++] = array[i][1];
return m;
}
@@ -527,17 +527,17 @@ int FixSRP::pack_restart(int i, double *buf)
unpack values from atom->extra array to restart the fix
------------------------------------------------------------------------- */
-void FixSRP::unpack_restart(int nlocal, int nth)
+void FixSRP::unpack_restart(int nlocal, int nth)
{
double **extra = atom->extra;
// skip to Nth set of extra values
- int m = 0;
+ int m = 0;
for (int i = 0; i < nth; i++){
m += static_cast<int> (extra[nlocal][m]);
}
- m++;
+ m++;
array[nlocal][0] = extra[nlocal][m++];
array[nlocal][1] = extra[nlocal][m++];
@@ -561,7 +561,7 @@ int FixSRP::size_restart(int nlocal)
}
/* ----------------------------------------------------------------------
- pack global state of Fix
+ pack global state of Fix
------------------------------------------------------------------------- */
void FixSRP::write_restart(FILE *fp)
diff --git a/src/USER-MISC/fix_srp.h b/src/USER-MISC/fix_srp.h
index 859b0020b0..5315d506d7 100644
--- a/src/USER-MISC/fix_srp.h
+++ b/src/USER-MISC/fix_srp.h
@@ -20,7 +20,7 @@ FixStyle(SRP,FixSRP)
#ifndef LMP_FIX_SRP_H
#define LMP_FIX_SRP_H
-#include "stdio.h"
+#include <stdio.h>
#include "fix.h"
namespace LAMMPS_NS {
@@ -43,7 +43,7 @@ class FixSRP : public Fix {
int unpack_exchange(int, double *);
int pack_border(int, int *, double *);
int unpack_border(int, int, double *);
- void post_run();
+ void post_run();
int pack_restart(int, double*);
void unpack_restart(int, int);
diff --git a/src/USER-MISC/fix_ti_rs.cpp b/src/USER-MISC/fix_ti_rs.cpp
index d5036eb520..1090fc02d0 100755
--- a/src/USER-MISC/fix_ti_rs.cpp
+++ b/src/USER-MISC/fix_ti_rs.cpp
@@ -12,14 +12,14 @@
------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------
- Contributing authors:
+ Contributing authors:
Rodrigo Freitas (Unicamp/Brazil) - rodrigohb@gmail.com
Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br
------------------------------------------------------------------------- */
-
-#include "stdlib.h"
-#include "string.h"
-#include "math.h"
+
+#include <stdlib.h>
+#include <string.h>
+#include <math.h>
#include "fix_ti_rs.h"
#include "atom.h"
#include "update.h"
@@ -34,7 +34,7 @@ using namespace FixConst;
// Class constructor initialize all variables.
-FixTIRS::FixTIRS(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
+FixTIRS::FixTIRS(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
{
// Checking the input information.
if (narg < 7 || narg > 9) error->all(FLERR,"Illegal fix ti/rs command");
@@ -48,10 +48,10 @@ FixTIRS::FixTIRS(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
// Time variables.
t_switch = force->bnumeric(FLERR,arg[5]);
t_equil = force->bnumeric(FLERR,arg[6]);
- t0 = update->ntimestep;
+ t0 = update->ntimestep;
if (t_switch <= 0) error->all(FLERR,"Illegal fix ti/rs command");
if (t_equil <= 0) error->all(FLERR,"Illegal fix ti/rs command");
-
+
// Coupling parameter limits and initialization.
l_initial = force->numeric(FLERR,arg[3]);
l_final = force->numeric(FLERR,arg[4]);
@@ -68,7 +68,7 @@ FixTIRS::FixTIRS(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
/* ---------------------------------------------------------------------- */
-FixTIRS::~FixTIRS()
+FixTIRS::~FixTIRS()
{
// unregister callbacks to this fix from Atom class
atom->delete_callback(id,0);
@@ -77,7 +77,7 @@ FixTIRS::~FixTIRS()
/* ---------------------------------------------------------------------- */
-int FixTIRS::setmask()
+int FixTIRS::setmask()
{
int mask = 0;
mask |= INITIAL_INTEGRATE;
@@ -95,7 +95,7 @@ void FixTIRS::init()
/* ---------------------------------------------------------------------- */
-void FixTIRS::setup(int vflag)
+void FixTIRS::setup(int vflag)
{
if (strstr(update->integrate_style,"verlet"))
post_force(vflag);
@@ -116,7 +116,7 @@ void FixTIRS::min_setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixTIRS::post_force(int vflag)
+void FixTIRS::post_force(int vflag)
{
int *mask = atom->mask;
@@ -126,7 +126,7 @@ void FixTIRS::post_force(int vflag)
// Scaling forces.
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
- f[i][0] = lambda * f[i][0];
+ f[i][0] = lambda * f[i][0];
f[i][1] = lambda * f[i][1];
f[i][2] = lambda * f[i][2];
}
@@ -149,7 +149,7 @@ void FixTIRS::min_post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixTIRS::initial_integrate(int vflag)
+void FixTIRS::initial_integrate(int vflag)
{
// Update the coupling parameter value.
const bigint t = update->ntimestep - (t0+t_equil);
@@ -181,7 +181,7 @@ double FixTIRS::switch_func(double t)
{
if (sf == 2) return l_initial / (1 + t * (l_initial/l_final - 1));
if (sf == 3) return l_initial / (1 + log2(1+t) * (l_initial/l_final - 1));
-
+
// Default option is sf = 1.
return l_initial + (l_final - l_initial) * t;
}
diff --git a/src/USER-MISC/fix_ti_rs.h b/src/USER-MISC/fix_ti_rs.h
index 6b5124f711..0aee21a872 100755
--- a/src/USER-MISC/fix_ti_rs.h
+++ b/src/USER-MISC/fix_ti_rs.h
@@ -12,7 +12,7 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
- Contributing authors:
+ Contributing authors:
Rodrigo Freitas (Unicamp/Brazil) - rodrigohb@gmail.com
Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br
------------------------------------------------------------------------- */
diff --git a/src/USER-MISC/fix_ti_spring.cpp b/src/USER-MISC/fix_ti_spring.cpp
index 3d10312720..edb6a7b2ca 100755
--- a/src/USER-MISC/fix_ti_spring.cpp
+++ b/src/USER-MISC/fix_ti_spring.cpp
@@ -12,13 +12,13 @@
------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------
- Contributing authors:
+ Contributing authors:
Rodrigo Freitas (Unicamp/Brazil) - rodrigohb@gmail.com
Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br
------------------------------------------------------------------------- */
-#include "stdlib.h"
-#include "string.h"
+#include <stdlib.h>
+#include <string.h>
#include "fix_ti_spring.h"
#include "atom.h"
#include "update.h"
@@ -28,13 +28,13 @@
#include "error.h"
#include "force.h"
-using namespace LAMMPS_NS;
-using namespace FixConst;
+using namespace LAMMPS_NS;
+using namespace FixConst;
/* ---------------------------------------------------------------------- */
-FixTISpring::FixTISpring(LAMMPS *lmp, int narg, char **arg) :
- Fix(lmp, narg, arg)
+FixTISpring::FixTISpring(LAMMPS *lmp, int narg, char **arg) :
+ Fix(lmp, narg, arg)
{
if (narg < 6 || narg > 8)
error->all(FLERR,"Illegal fix ti/spring command");
@@ -84,11 +84,11 @@ FixTISpring::FixTISpring(LAMMPS *lmp, int narg, char **arg) :
if (narg > 6) {
if (strcmp(arg[6], "function") == 0) sf = force->inumeric(FLERR,arg[7]);
else error->all(FLERR,"Illegal fix ti/spring switching function");
- if ((sf!=1) && (sf!=2))
+ if ((sf!=1) && (sf!=2))
error->all(FLERR,"Illegal fix ti/spring switching function");
}
- lambda = switch_func(0);
- dlambda = dswitch_func(0);
+ lambda = switch_func(0);
+ dlambda = dswitch_func(0);
espring = 0.0;
}
@@ -196,8 +196,8 @@ void FixTISpring::min_post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixTISpring::initial_integrate(int vflag)
-{
+void FixTISpring::initial_integrate(int vflag)
+{
// Update the coupling parameter value.
const bigint t = update->ntimestep - (t0+t_equil);
const double r_switch = 1.0/t_switch;
@@ -211,7 +211,7 @@ void FixTISpring::initial_integrate(int vflag)
lambda = switch_func(1.0 - (t - t_switch - t_equil)*r_switch);
dlambda = - dswitch_func(1.0 - (t - t_switch - t_equil)*r_switch);
}
-}
+}
/* ----------------------------------------------------------------------
energy of stretched springs
@@ -311,11 +311,11 @@ void FixTISpring::unpack_restart(int nlocal, int nth)
double **extra = atom->extra;
// skip to Nth set of extra values
-
+
int m = 0;
for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]);
m++;
-
+
xoriginal[nlocal][0] = extra[nlocal][m++];
xoriginal[nlocal][1] = extra[nlocal][m++];
xoriginal[nlocal][2] = extra[nlocal][m++];
@@ -343,7 +343,7 @@ int FixTISpring::size_restart(int nlocal)
Switching function.
------------------------------------------------------------------------- */
-double FixTISpring::switch_func(double t)
+double FixTISpring::switch_func(double t)
{
if (sf == 1) return t;
@@ -356,7 +356,7 @@ double FixTISpring::switch_func(double t)
Switching function derivative.
------------------------------------------------------------------------- */
-double FixTISpring::dswitch_func(double t)
+double FixTISpring::dswitch_func(double t)
{
if(sf == 1) return 1.0/t_switch;
diff --git a/src/USER-MISC/fix_ti_spring.h b/src/USER-MISC/fix_ti_spring.h
index a5ff1fb677..bce3421627 100755
--- a/src/USER-MISC/fix_ti_spring.h
+++ b/src/USER-MISC/fix_ti_spring.h
@@ -12,7 +12,7 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
- Contributing authors:
+ Contributing authors:
Rodrigo Freitas (Unicamp/Brazil) - rodrigohb@gmail.com
Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br
------------------------------------------------------------------------- */
@@ -44,7 +44,7 @@ class FixTISpring : public Fix {
void initial_integrate(int);
double compute_scalar();
double compute_vector(int);
-
+
double memory_usage();
void grow_arrays(int);
void copy_arrays(int, int, int);
diff --git a/src/USER-MISC/fix_ttm_mod.cpp b/src/USER-MISC/fix_ttm_mod.cpp
index 3a6aafe700..f54c21532b 100644
--- a/src/USER-MISC/fix_ttm_mod.cpp
+++ b/src/USER-MISC/fix_ttm_mod.cpp
@@ -18,10 +18,10 @@
------------------------------------------------------------------------- */
#include "lmptype.h"
-#include "mpi.h"
-#include "math.h"
-#include "string.h"
-#include "stdlib.h"
+#include <mpi.h>
+#include <math.h>
+#include <string.h>
+#include <stdlib.h>
#include "fix_ttm_mod.h"
#include "atom.h"
#include "force.h"
@@ -69,7 +69,7 @@ FixTTMMod::FixTTMMod(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (lmp->citeme) lmp->citeme->add(cite_fix_ttm_mod);
-
+
if (narg < 9) error->all(FLERR,"Illegal fix ttm/mod command");
vector_flag = 1;
size_vector = 2;
@@ -611,7 +611,7 @@ void FixTTMMod::end_of_step()
int num_inner_timesteps = 1;
double inner_dt = update->dt;
double stability_criterion = 0.0;
-
+
for (int ixnode = 0; ixnode < nxnodes; ixnode++)
for (int iynode = 0; iynode < nynodes; iynode++)
for (int iznode = 0; iznode < nznodes; iznode++)
@@ -623,7 +623,7 @@ void FixTTMMod::end_of_step()
for (int iznode = 0; iznode < nznodes; iznode++)
T_electron[ixnode][iynode][iznode] =
T_electron_first[ixnode][iynode][iznode];
-
+
stability_criterion = 1.0 -
2.0*inner_dt/el_specific_heat *
(el_thermal_conductivity*(1.0/dx/dx + 1.0/dy/dy + 1.0/dz/dz));
@@ -705,7 +705,7 @@ void FixTTMMod::end_of_step()
T_electron_old[ixnode][iynode][iznode];
if ((T_electron[ixnode][iynode][iznode] > 0.0) && (T_electron[ixnode][iynode][iznode] < electron_temperature_min))
T_electron[ixnode][iynode][iznode] = T_electron[ixnode][iynode][iznode] + 0.5*(electron_temperature_min - T_electron[ixnode][iynode][iznode]);
-
+
if (el_properties(T_electron[ixnode][iynode][iznode]).el_thermal_conductivity > el_thermal_conductivity)
el_thermal_conductivity = el_properties(T_electron[ixnode][iynode][iznode]).el_thermal_conductivity;
if ((T_electron[ixnode][iynode][iznode] > 0.0) && (el_properties(T_electron[ixnode][iynode][iznode]).el_heat_capacity < el_specific_heat))
@@ -715,7 +715,7 @@ void FixTTMMod::end_of_step()
stability_criterion = 1.0 -
2.0*inner_dt/el_specific_heat *
(el_thermal_conductivity*(1.0/dx/dx + 1.0/dy/dy + 1.0/dz/dz));
-
+
} while (stability_criterion < 0.0);
// output nodal temperatures for current timestep
if ((nfileevery) && !(update->ntimestep % nfileevery)) {
diff --git a/src/USER-MISC/improper_cossq.cpp b/src/USER-MISC/improper_cossq.cpp
index 8eabd57d61..77033381e9 100644
--- a/src/USER-MISC/improper_cossq.cpp
+++ b/src/USER-MISC/improper_cossq.cpp
@@ -16,9 +16,9 @@
gvog@chemeng.ntua.gr
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "math.h"
-#include "stdlib.h"
+#include <mpi.h>
+#include <math.h>
+#include <stdlib.h>
#include "improper_cossq.h"
#include "atom.h"
#include "comm.h"
@@ -109,8 +109,8 @@ void ImproperCossq::compute(int eflag, int vflag)
MPI_Comm_rank(world,&me);
if (screen) {
char str[128];
- sprintf(str,"Improper problem: %d " BIGINT_FORMAT " "
- TAGINT_FORMAT " " TAGINT_FORMAT " "
+ sprintf(str,"Improper problem: %d " BIGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT,
me,update->ntimestep,
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
diff --git a/src/USER-MISC/improper_cossq.h b/src/USER-MISC/improper_cossq.h
index 3eca800dbe..266e317977 100644
--- a/src/USER-MISC/improper_cossq.h
+++ b/src/USER-MISC/improper_cossq.h
@@ -20,7 +20,7 @@ ImproperStyle(cossq,ImproperCossq)
#ifndef LMP_IMPROPER_COSSQ_H
#define LMP_IMPROPER_COSSQ_H
-#include "stdio.h"
+#include <stdio.h>
#include "improper.h"
namespace LAMMPS_NS {
diff --git a/src/USER-MISC/improper_fourier.cpp b/src/USER-MISC/improper_fourier.cpp
index f3fe065d6e..ea5f78662e 100644
--- a/src/USER-MISC/improper_fourier.cpp
+++ b/src/USER-MISC/improper_fourier.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -16,10 +16,10 @@
[ based on improper_umbrella.cpp Tod A Pascal (Caltech) ]
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <mpi.h>
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "improper_fourier.h"
#include "atom.h"
#include "comm.h"
@@ -92,18 +92,18 @@ void ImproperFourier::compute(int eflag, int vflag)
vb3z = x[i4][2] - x[i1][2];
addone(i1,i2,i3,i4, type,evflag,eflag,
- vb1x, vb1y, vb1z,
- vb2x, vb2y, vb2z,
+ vb1x, vb1y, vb1z,
+ vb2x, vb2y, vb2z,
vb3x, vb3y, vb3z);
if ( all[type] ) {
addone(i1,i4,i2,i3, type,evflag,eflag,
vb3x, vb3y, vb3z,
- vb1x, vb1y, vb1z,
- vb2x, vb2y, vb2z);
+ vb1x, vb1y, vb1z,
+ vb2x, vb2y, vb2z);
addone(i1,i3,i4,i2, type,evflag,eflag,
- vb2x, vb2y, vb2z,
+ vb2x, vb2y, vb2z,
vb3x, vb3y, vb3z,
- vb1x, vb1y, vb1z);
+ vb1x, vb1y, vb1z);
}
}
}
@@ -156,8 +156,8 @@ void ImproperFourier::addone(const int &i1,const int &i2,const int &i3,const int
MPI_Comm_rank(world,&me);
if (screen) {
char str[128];
- sprintf(str,"Improper problem: %d " BIGINT_FORMAT " "
- TAGINT_FORMAT " " TAGINT_FORMAT " "
+ sprintf(str,"Improper problem: %d " BIGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT,
me,update->ntimestep,
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
@@ -308,7 +308,7 @@ void ImproperFourier::coeff(int narg, char **arg)
}
/* ----------------------------------------------------------------------
- proc 0 writes out coeffs to restart file
+ proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void ImproperFourier::write_restart(FILE *fp)
@@ -321,7 +321,7 @@ void ImproperFourier::write_restart(FILE *fp)
}
/* ----------------------------------------------------------------------
- proc 0 reads coeffs from restart file, bcasts them
+ proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void ImproperFourier::read_restart(FILE *fp)
diff --git a/src/USER-MISC/improper_fourier.h b/src/USER-MISC/improper_fourier.h
index 0d2a798c1f..903b9a12b6 100644
--- a/src/USER-MISC/improper_fourier.h
+++ b/src/USER-MISC/improper_fourier.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -20,7 +20,7 @@ ImproperStyle(fourier,ImproperFourier)
#ifndef LMP_IMPROPER_FOURIER_H
#define LMP_IMPROPER_FOURIER_H
-#include "stdio.h"
+#include <stdio.h>
#include "improper.h"
namespace LAMMPS_NS {
diff --git a/src/USER-MISC/improper_ring.cpp b/src/USER-MISC/improper_ring.cpp
index 2d6f510446..4134b4b172 100644
--- a/src/USER-MISC/improper_ring.cpp
+++ b/src/USER-MISC/improper_ring.cpp
@@ -36,9 +36,9 @@
of j.
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "math.h"
-#include "stdlib.h"
+#include <mpi.h>
+#include <math.h>
+#include <stdlib.h>
#include "improper_ring.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-MISC/improper_ring.h b/src/USER-MISC/improper_ring.h
index a578e4d17e..cdb2907c65 100644
--- a/src/USER-MISC/improper_ring.h
+++ b/src/USER-MISC/improper_ring.h
@@ -20,7 +20,7 @@ ImproperStyle(ring,ImproperRing)
#ifndef LMP_IMPROPER_RING_H
#define LMP_IMPROPER_RING_H
-#include "stdio.h"
+#include <stdio.h>
#include "improper.h"
namespace LAMMPS_NS {
diff --git a/src/USER-MISC/pair_cdeam.cpp b/src/USER-MISC/pair_cdeam.cpp
index 6723911900..91ef598de8 100644
--- a/src/USER-MISC/pair_cdeam.cpp
+++ b/src/USER-MISC/pair_cdeam.cpp
@@ -17,10 +17,10 @@
Germany Department of Materials Science
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_cdeam.h"
#include "atom.h"
#include "force.h"
@@ -494,7 +494,7 @@ void PairCDEAM::read_h_coeff(char *filename)
/* ---------------------------------------------------------------------- */
-int PairCDEAM::pack_forward_comm(int n, int *list, double *buf,
+int PairCDEAM::pack_forward_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
diff --git a/src/USER-MISC/pair_coul_diel.cpp b/src/USER-MISC/pair_coul_diel.cpp
index a846aa53c6..1913e48b67 100644
--- a/src/USER-MISC/pair_coul_diel.cpp
+++ b/src/USER-MISC/pair_coul_diel.cpp
@@ -14,10 +14,10 @@
Contributiong authors: Arben Jusufi, Axel Kohlmeyer (Temple U.)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_coul_diel.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-MISC/pair_edip.cpp b/src/USER-MISC/pair_edip.cpp
index c6eceb0cac..2994da2683 100755
--- a/src/USER-MISC/pair_edip.cpp
+++ b/src/USER-MISC/pair_edip.cpp
@@ -21,11 +21,11 @@
Phys. Rev. B 58, 2539 (1998)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "float.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <float.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_edip.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/USER-MISC/pair_gauss_cut.cpp b/src/USER-MISC/pair_gauss_cut.cpp
index e277f9865d..0df6734849 100644
--- a/src/USER-MISC/pair_gauss_cut.cpp
+++ b/src/USER-MISC/pair_gauss_cut.cpp
@@ -15,10 +15,10 @@
Contributing authors: Arben Jusufi, Axel Kohlmeyer (Temple U.)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_gauss_cut.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-MISC/pair_list.cpp b/src/USER-MISC/pair_list.cpp
index 2895b8216b..5f05392631 100644
--- a/src/USER-MISC/pair_list.cpp
+++ b/src/USER-MISC/pair_list.cpp
@@ -80,7 +80,7 @@ PairList::~PairList()
void PairList::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
- else evflag = vflag_fdotr = eflag_global =
+ else evflag = vflag_fdotr = eflag_global =
vflag_global = eflag_atom = vflag_atom = 0;
const int nlocal = atom->nlocal;
@@ -138,7 +138,7 @@ void PairList::compute(int eflag, int vflag)
const double r = sqrt(rsq);
const double dr = par.parm.morse.r0 - r;
const double dexp = exp(par.parm.morse.alpha * dr);
- fpair = 2.0*par.parm.morse.d0*par.parm.morse.alpha
+ fpair = 2.0*par.parm.morse.d0*par.parm.morse.alpha
* (dexp*dexp - dexp) / r;
if (eflag_either)
@@ -148,11 +148,11 @@ void PairList::compute(int eflag, int vflag)
const double r6inv = r2inv*r2inv*r2inv;
const double sig6 = mypow(par.parm.lj126.sigma,6);
- fpair = 24.0*par.parm.lj126.epsilon*r6inv
+ fpair = 24.0*par.parm.lj126.epsilon*r6inv
* (2.0*sig6*sig6*r6inv - sig6) * r2inv;
if (eflag_either)
- epair = 4.0*par.parm.lj126.epsilon*r6inv
+ epair = 4.0*par.parm.lj126.epsilon*r6inv
* (sig6*sig6*r6inv - sig6) - par.offset;
}
@@ -169,7 +169,7 @@ void PairList::compute(int eflag, int vflag)
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,epair,0.0,fpair,dx,dy,dz);
- }
+ }
}
if (vflag_fdotr) virial_fdotr_compute();
@@ -236,7 +236,7 @@ void PairList::settings(int narg, char **arg)
// skip empty lines
if (!ptr) continue;
-
+
// skip comment lines starting with #
if (*ptr == '#') continue;
diff --git a/src/USER-MISC/pair_list.h b/src/USER-MISC/pair_list.h
index 4059b0ef29..4802194158 100644
--- a/src/USER-MISC/pair_list.h
+++ b/src/USER-MISC/pair_list.h
@@ -46,7 +46,7 @@ class PairList : public Pair {
struct morse_p { double d0, alpha, r0; };
struct lj126_p { double epsilon, sigma; };
- union parm_u {
+ union parm_u {
struct harm_p harm;
struct morse_p morse;
struct lj126_p lj126;
@@ -57,7 +57,7 @@ class PairList : public Pair {
double cutsq; // cutoff**2 for this pair
double offset; // energy offset
union parm_u parm; // parameters for style
- } list_parm_t;
+ } list_parm_t;
protected:
double cut_global; // global cutoff distance
@@ -77,7 +77,7 @@ class PairList : public Pair {
E: Not all pairs processed in pair_style list
Not all interacting pairs for which coefficients were found. This can be intentional
-and then you need to set the 'nocheck' option. If not, it usually means that the
+and then you need to set the 'nocheck' option. If not, it usually means that the
communication cutoff is too small. This can be ameliorated by either increasing
the cutoff in the pair_style command or the communication cutoff.
diff --git a/src/USER-MISC/pair_lj_sf.cpp b/src/USER-MISC/pair_lj_sf.cpp
index 6138d0b847..69a7efcfde 100644
--- a/src/USER-MISC/pair_lj_sf.cpp
+++ b/src/USER-MISC/pair_lj_sf.cpp
@@ -15,9 +15,9 @@
Contributing author: Laurent Joly (U Lyon), ljoly.ulyon@gmail.com
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
#include "pair_lj_sf.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-MISC/pair_lj_sf_dipole_sf.cpp b/src/USER-MISC/pair_lj_sf_dipole_sf.cpp
index 58d7f4d61d..48e23d5833 100755
--- a/src/USER-MISC/pair_lj_sf_dipole_sf.cpp
+++ b/src/USER-MISC/pair_lj_sf_dipole_sf.cpp
@@ -15,8 +15,8 @@
Contributing author: Mario Orsi (U Southampton), orsimario@gmail.com
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdlib.h>
#include "pair_lj_sf_dipole_sf.h"
#include "atom.h"
#include "neighbor.h"
@@ -26,7 +26,7 @@
#include "memory.h"
#include "error.h"
#include "update.h"
-#include "string.h"
+#include <string.h>
using namespace LAMMPS_NS;
diff --git a/src/USER-MISC/pair_meam_spline.cpp b/src/USER-MISC/pair_meam_spline.cpp
index 26cd70509d..cb6ddbd2ae 100644
--- a/src/USER-MISC/pair_meam_spline.cpp
+++ b/src/USER-MISC/pair_meam_spline.cpp
@@ -25,10 +25,10 @@
* 24-Sep-11 - AS: Adapted code to new interface of Error::one() function.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_meam_spline.h"
#include "atom.h"
#include "force.h"
@@ -526,7 +526,7 @@ double PairMEAMSpline::init_one(int i, int j)
/* ---------------------------------------------------------------------- */
-int PairMEAMSpline::pack_forward_comm(int n, int *list, double *buf,
+int PairMEAMSpline::pack_forward_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int* list_iter = list;
diff --git a/src/USER-MISC/pair_meam_sw_spline.cpp b/src/USER-MISC/pair_meam_sw_spline.cpp
index 30613afab6..8ae9a3b7d9 100644
--- a/src/USER-MISC/pair_meam_sw_spline.cpp
+++ b/src/USER-MISC/pair_meam_sw_spline.cpp
@@ -23,10 +23,10 @@
* 01-Aug-12 - RER: First code version.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_meam_sw_spline.h"
#include "atom.h"
#include "force.h"
@@ -562,7 +562,7 @@ double PairMEAMSWSpline::init_one(int i, int j)
/* ---------------------------------------------------------------------- */
-int PairMEAMSWSpline::pack_forward_comm(int n, int *list, double *buf,
+int PairMEAMSWSpline::pack_forward_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int* list_iter = list;
@@ -735,16 +735,16 @@ void PairMEAMSWSpline::SplineFunction::writeGnuplot(const char* filename, const
}
/* ----------------------------------------------------------------------
- * Spline-based Modified Embedded Atom Method plus
+ * Spline-based Modified Embedded Atom Method plus
* Stillinger-Weber (MEAM+SW) potential routine.
*
* Copyright (2012) Lawrence Livermore National Security, LLC.
* Produced at the Lawrence Livermore National Laboratory.
* Written by Robert E. Rudd (<robert.rudd@llnl.gov>).
- * Based on the spline-based MEAM routine written by
+ * Based on the spline-based MEAM routine written by
* Alexander Stukowski (<alex@stukowski.com>).
* LLNL-CODE-588032 All rights reserved.
- *
+ *
* The spline-based MEAM+SW format was first devised and used to develop
* potentials for bcc transition metals by Jeremy Nicklas, Michael Fellinger,
* and Hyoungki Park at The Ohio State University.
@@ -800,7 +800,7 @@ void PairMEAMSWSpline::SplineFunction::writeGnuplot(const char* filename, const
* the Program is not restricted, and the output from the Program is covered
* only if its contents constitute a work based on the Program (independent of
* having been made by running the Program). Whether that is true depends on
- * what the Program does.
+ * what the Program does.
*
* 1. You may copy and distribute verbatim copies of the Program's source
* code as you receive it, in any medium, provided that you conspicuously and
@@ -916,10 +916,10 @@ void PairMEAMSWSpline::SplineFunction::writeGnuplot(const char* filename, const
* for enforcing compliance by third parties to this License.
*
* 7. If, as a consequence of a court judgment or allegation of patent
- * infringement or for any other reason (not limited to patent
- * issues), conditions are imposed on you (whether by court
- * order, agreement or otherwise) that contradict the conditions
- * of this License, they do not excuse you from the conditions
+ * infringement or for any other reason (not limited to patent
+ * issues), conditions are imposed on you (whether by court
+ * order, agreement or otherwise) that contradict the conditions
+ * of this License, they do not excuse you from the conditions
* of this License. If you cannot distribute so as to satisfy
* simultaneously your obligations under this License and any other pertinent
* obligations, then as a consequence you may not distribute the Program at
@@ -996,5 +996,5 @@ void PairMEAMSWSpline::SplineFunction::writeGnuplot(const char* filename, const
* PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
* POSSIBILITY OF SUCH DAMAGES.
*
- * END OF TERMS AND CONDITIONS
+ * END OF TERMS AND CONDITIONS
------------------------------------------------------------------------- */
diff --git a/src/USER-MISC/pair_meam_sw_spline.h b/src/USER-MISC/pair_meam_sw_spline.h
index 383104df4b..9398619b63 100644
--- a/src/USER-MISC/pair_meam_sw_spline.h
+++ b/src/USER-MISC/pair_meam_sw_spline.h
@@ -245,13 +245,13 @@ protected:
#endif
/* ----------------------------------------------------------------------
- * Spline-based Modified Embedded Atom Method plus
+ * Spline-based Modified Embedded Atom Method plus
* Stillinger-Weber (MEAM+SW) potential routine.
*
* Copyright (2012) Lawrence Livermore National Security, LLC.
* Produced at the Lawrence Livermore National Laboratory.
* Written by Robert E. Rudd (<robert.rudd@llnl.gov>).
- * Based on the spline MEAM routine written by Alexander Stukowski
+ * Based on the spline MEAM routine written by Alexander Stukowski
* (<alex@stukowski.com>).
* LLNL-CODE-588032 All rights reserved.
*
@@ -310,7 +310,7 @@ protected:
* the Program is not restricted, and the output from the Program is covered
* only if its contents constitute a work based on the Program (independent of
* having been made by running the Program). Whether that is true depends on
- * what the Program does.
+ * what the Program does.
*
* 1. You may copy and distribute verbatim copies of the Program's source
* code as you receive it, in any medium, provided that you conspicuously and
@@ -426,10 +426,10 @@ protected:
* for enforcing compliance by third parties to this License.
*
* 7. If, as a consequence of a court judgment or allegation of patent
- * infringement or for any other reason (not limited to patent
- * issues), conditions are imposed on you (whether by court
- * order, agreement or otherwise) that contradict the conditions
- * of this License, they do not excuse you from the conditions
+ * infringement or for any other reason (not limited to patent
+ * issues), conditions are imposed on you (whether by court
+ * order, agreement or otherwise) that contradict the conditions
+ * of this License, they do not excuse you from the conditions
* of this License. If you cannot distribute so as to satisfy
* simultaneously your obligations under this License and any other pertinent
* obligations, then as a consequence you may not distribute the Program at
@@ -506,5 +506,5 @@ protected:
* PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
* POSSIBILITY OF SUCH DAMAGES.
*
- * END OF TERMS AND CONDITIONS
+ * END OF TERMS AND CONDITIONS
------------------------------------------------------------------------- */
diff --git a/src/USER-MISC/pair_srp.cpp b/src/USER-MISC/pair_srp.cpp
index c79ef490d5..e607c8e86f 100644
--- a/src/USER-MISC/pair_srp.cpp
+++ b/src/USER-MISC/pair_srp.cpp
@@ -10,7 +10,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-
+
/* ----------------------------------------------------------------------
Contributing authors: Timothy Sirk (ARL), Pieter in't Veld (BASF)
@@ -25,26 +25,26 @@ There is an example script for this package in examples/USER/srp.
Please contact Timothy Sirk for questions (tim.sirk@us.army.mil).
------------------------------------------------------------------------- */
-#include "stdlib.h"
-#include "pair_srp.h"
-#include "atom.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "memory.h"
-#include "error.h"
-#include "domain.h"
+#include <stdlib.h>
+#include "pair_srp.h"
+#include "atom.h"
+#include "comm.h"
+#include "force.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "memory.h"
+#include "error.h"
+#include "domain.h"
#include "modify.h"
#include "fix.h"
#include "fix_srp.h"
#include "thermo.h"
#include "output.h"
-#include "string.h"
+#include <string.h>
#include "citeme.h"
-
-using namespace LAMMPS_NS;
-
+
+using namespace LAMMPS_NS;
+
#define SMALL 1.0e-10
#define BIG 1e10
#define ONETWOBIT 0x40000000
@@ -65,10 +65,10 @@ static int srp_instance = 0;
set size of pair comms in constructor
---------------------------------------------------------------------- */
-PairSRP::PairSRP(LAMMPS *lmp) : Pair(lmp)
+PairSRP::PairSRP(LAMMPS *lmp) : Pair(lmp)
{
- writedata = 1;
-
+ writedata = 1;
+
if (lmp->citeme) lmp->citeme->add(cite_srp);
nextra = 1;
@@ -77,8 +77,8 @@ PairSRP::PairSRP(LAMMPS *lmp) : Pair(lmp)
fix_id[0] = '0' + srp_instance / 10;
fix_id[1] = '0' + srp_instance % 10;
++srp_instance;
-}
-
+}
+
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
@@ -102,19 +102,19 @@ void PairSRP::allocate()
maxcount = 0;
}
-/* ----------------------------------------------------------------------
- free
- ------------------------------------------------------------------------- */
-
-PairSRP::~PairSRP()
-{
- if (allocated)
- {
- memory->destroy(setflag);
- memory->destroy(cutsq);
- memory->destroy(cut);
- memory->destroy(a0);
- memory->destroy(segment);
+/* ----------------------------------------------------------------------
+ free
+ ------------------------------------------------------------------------- */
+
+PairSRP::~PairSRP()
+{
+ if (allocated)
+ {
+ memory->destroy(setflag);
+ memory->destroy(cutsq);
+ memory->destroy(cut);
+ memory->destroy(a0);
+ memory->destroy(segment);
}
// check nfix in case all fixes have already been deleted
@@ -122,24 +122,24 @@ PairSRP::~PairSRP()
free(fix_id);
}
-/* ----------------------------------------------------------------------
- compute bond-bond repulsions
- ------------------------------------------------------------------------- */
-
-void PairSRP::compute(int eflag, int vflag)
+/* ----------------------------------------------------------------------
+ compute bond-bond repulsions
+ ------------------------------------------------------------------------- */
+
+void PairSRP::compute(int eflag, int vflag)
{
- // setup energy and virial
- if (eflag || vflag)
- ev_setup(eflag, vflag);
- else
- evflag = vflag_fdotr = 0;
-
- double **x = atom->x;
- double **f = atom->f;
- int nlocal = atom->nlocal;
- int nall = nlocal + atom->nghost;
- int i0, i1, j0, j1;
+ // setup energy and virial
+ if (eflag || vflag)
+ ev_setup(eflag, vflag);
+ else
+ evflag = vflag_fdotr = 0;
+
+ double **x = atom->x;
+ double **f = atom->f;
+ int nlocal = atom->nlocal;
+ int nall = nlocal + atom->nghost;
+ int i0, i1, j0, j1;
int i,j,ii,jj,inum,jnum;
double dijsq, dij;
@@ -155,8 +155,8 @@ void PairSRP::compute(int eflag, int vflag)
double fx, fy, fz;
evdwl = 0.0;
- // mapping global to local for atoms inside bond particles
- // exclude 1-2 neighs if requested
+ // mapping global to local for atoms inside bond particles
+ // exclude 1-2 neighs if requested
if (neighbor->ago == 0){
remapBonds(nall);
if(exclude) onetwoexclude(ilist, inum, jlist, numneigh, firstneigh);
@@ -164,9 +164,9 @@ void PairSRP::compute(int eflag, int vflag)
// this pair style only used with hybrid
// due to exclusions
- // each atom i is type bptype
- // each neigh j is type bptype
-
+ // each atom i is type bptype
+ // each neigh j is type bptype
+
// using midpoint distance option
if(midpoint){
@@ -194,18 +194,18 @@ void PairSRP::compute(int eflag, int vflag)
// midpt dist bond 0 and 1
dx = 0.5*(x[i0][0] - x[i1][0] + x[j0][0] - x[j1][0]);
- dy = 0.5*(x[i0][1] - x[i1][1] + x[j0][1] - x[j1][1]);
- dz = 0.5*(x[i0][2] - x[i1][2] + x[j0][2] - x[j1][2]);
+ dy = 0.5*(x[i0][1] - x[i1][1] + x[j0][1] - x[j1][1]);
+ dz = 0.5*(x[i0][2] - x[i1][2] + x[j0][2] - x[j1][2]);
dijsq = dx*dx + dy*dy + dz*dz;
if (dijsq < cutsq[bptype][bptype]){
dij = sqrt(dijsq);
- if (dij < SMALL)
+ if (dij < SMALL)
continue; // dij can be 0.0 with soft potentials
wd = 1.0 - dij / cut[bptype][bptype];
- fpair = 0.5 * a0[bptype][bptype] * wd / dij; // 0.5 factor for lever rule
+ fpair = 0.5 * a0[bptype][bptype] * wd / dij; // 0.5 factor for lever rule
// force for bond 0, beads 0,1
//force between bonds
@@ -245,10 +245,10 @@ void PairSRP::compute(int eflag, int vflag)
}
}
}
- }
+ }
else{
// using min distance option
-
+
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
@@ -275,13 +275,13 @@ void PairSRP::compute(int eflag, int vflag)
if (dijsq < cutsq[bptype][bptype]){
- dij = sqrt(dijsq);
+ dij = sqrt(dijsq);
if (dij < SMALL)
continue; // dij can be 0.0 with soft potentials
wd = 1.0 - dij / cut[bptype][bptype];
- fpair = a0[bptype][bptype] * wd / dij;
+ fpair = a0[bptype][bptype] * wd / dij;
// force for bond 0, beads 0,1
lever0 = 0.5 + ti; // assign force according to lever rule
@@ -365,7 +365,7 @@ void PairSRP::settings(int narg, char **arg)
int iarg = 3;
// default exclude 1-2
// scaling for 1-2, etc not supported
- exclude = 1;
+ exclude = 1;
while (iarg < narg) {
if (strcmp(arg[iarg],"exclude") == 0) {
@@ -393,7 +393,7 @@ void PairSRP::settings(int narg, char **arg)
}
/* ----------------------------------------------------------------------
- set coeffs
+ set coeffs
------------------------------------------------------------------------- */
void PairSRP::coeff(int narg, char **arg)
@@ -460,7 +460,7 @@ void PairSRP::init_style()
// bond particles do not contribute to energy or virial
// bond particles do not belong to group all
- // but thermo normalization is by nall
+ // but thermo normalization is by nall
// therefore should turn off normalization
int me;
MPI_Comm_rank(world,&me);
@@ -468,7 +468,7 @@ void PairSRP::init_style()
arg1[0] = (char *) "norm";
arg1[1] = (char *) "no";
output->thermo->modify_params(2, arg1);
- if (me == 0)
+ if (me == 0)
error->message(FLERR,"Thermo normalization turned off by pair srp");
neighbor->request(this,instance_me);
@@ -488,13 +488,13 @@ double PairSRP::init_one(int i, int j)
return cut[i][j];
}
-
-/* ----------------------------------------------------------------------
+
+/* ----------------------------------------------------------------------
find min distance for bonds i0/j0 and i1/j1
- ------------------------------------------------------------------------- */
+ ------------------------------------------------------------------------- */
inline void PairSRP::getMinDist(double** &x, double &dx, double &dy, double &dz, double &ti, double &tj, int &i0, int &j0, int &i1, int &j1)
-{
- // move these outside the loop
+{
+ // move these outside the loop
double diffx0, diffy0, diffz0, diffx1, diffy1, diffz1, dPx, dPy, dPz, RiRi, RiRj, RjRj;
double denom, termx0, termy0, termz0, num0, termx1, termy1, termz1, num1;
@@ -504,7 +504,7 @@ inline void PairSRP::getMinDist(double** &x, double &dx, double &dy, double &dz,
diffz0 = x[j0][2] - x[i0][2];
// compute midpt dist from 1st atom, 2nd bond
- diffx1 = x[j1][0] - x[i1][0];
+ diffx1 = x[j1][0] - x[i1][0];
diffy1 = x[j1][1] - x[i1][1];
diffz1 = x[j1][2] - x[i1][2];
@@ -520,22 +520,22 @@ inline void PairSRP::getMinDist(double** &x, double &dx, double &dy, double &dz,
denom = RiRj*RiRj - RiRi*RjRj;
// handle case of parallel lines
- // reduce to midpt distance
- if (fabs(denom) < SMALL){
+ // reduce to midpt distance
+ if (fabs(denom) < SMALL){
if(denom < 0) denom = -BIG;
else denom = BIG;
- }
+ }
- // calc ti
+ // calc ti
termx0 = RiRj*diffx1 - RjRj*diffx0;
termy0 = RiRj*diffy1 - RjRj*diffy0;
termz0 = RiRj*diffz1 - RjRj*diffz0;
num0 = dPx*termx0 + dPy*termy0 + dPz*termz0;
ti = num0 / denom;
- if (ti > 0.5) ti = 0.5;
- if (ti < -0.5) ti = -0.5;
-
- // calc tj
+ if (ti > 0.5) ti = 0.5;
+ if (ti < -0.5) ti = -0.5;
+
+ // calc tj
termx1 = RiRj*diffx0 - RiRi*diffx1;
termy1 = RiRj*diffy0 - RiRi*diffy1;
termz1 = RiRj*diffz0 - RiRi*diffz1;
@@ -543,28 +543,28 @@ inline void PairSRP::getMinDist(double** &x, double &dx, double &dy, double &dz,
tj = -num1/ denom;
if (tj > 0.5) tj = 0.5;
if (tj < -0.5) tj = -0.5;
-
- // min dist
+
+ // min dist
dx = dPx - ti*diffx0 + tj*diffx1;
dy = dPy - ti*diffy0 + tj*diffy1;
dz = dPz - ti*diffz0 + tj*diffz1;
-}
+}
-/* --------------------------------------------------------
+/* --------------------------------------------------------
map global id of atoms in stored by each bond particle
- ------------------------------------------------------- */
+ ------------------------------------------------------- */
inline void PairSRP::remapBonds(int &nall)
{
if(nall > maxcount){
- memory->grow(segment, nall, 2, "pair:segment");
+ memory->grow(segment, nall, 2, "pair:segment");
maxcount = nall;
}
// loop over all bond particles
// each bond paricle holds two bond atoms
// map global ids of bond atoms to local ids
- // might not be able to map both bond atoms of j, if j is outside neighcut
- // these are not on neighlist, so are not used
+ // might not be able to map both bond atoms of j, if j is outside neighcut
+ // these are not on neighlist, so are not used
int tmp;
srp = f_srp->array_atom;
@@ -581,18 +581,18 @@ inline void PairSRP::remapBonds(int &nall)
}
}
-/* --------------------------------------------------------
+/* --------------------------------------------------------
add exclusions for 1-2 neighs, if requested
-more complex exclusions or scaling probably not needed
- ------------------------------------------------------- */
+more complex exclusions or scaling probably not needed
+ ------------------------------------------------------- */
inline void PairSRP::onetwoexclude(int* &ilist, int &inum, int* &jlist, int* &numneigh, int** &firstneigh)
{
int i0, i1, j0, j1;
int i,j,ii,jj,jnum;
// encode neighs with exclusions
- // only need 1-2 info for normal uses of srp
- // add 1-3, etc later if ever needed
+ // only need 1-2 info for normal uses of srp
+ // add 1-3, etc later if ever needed
for (ii = 0; ii < inum; ii++) {
@@ -611,7 +611,7 @@ inline void PairSRP::onetwoexclude(int* &ilist, int &inum, int* &jlist, int* &nu
i1 = segment[j][0];
j1 = segment[j][1];
- // check for a 1-2 neigh
+ // check for a 1-2 neigh
if(i0 == i1 || i0 == j1 || i1 == j0 || j0 == j1){
j |= ONETWOBIT;
jlist[jj] = j;
@@ -640,7 +640,7 @@ void PairSRP::write_data_all(FILE *fp)
for (int j = i; j <= atom->ntypes; j++)
fprintf(fp,"%d %d %g %g\n",i,j,a0[i][j],cut[i][j]);
}
-
+
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
diff --git a/src/USER-MISC/pair_srp.h b/src/USER-MISC/pair_srp.h
index ecd352cdeb..95cc5a5c94 100644
--- a/src/USER-MISC/pair_srp.h
+++ b/src/USER-MISC/pair_srp.h
@@ -44,9 +44,9 @@ class PairSRP : public Pair {
inline void onetwoexclude(int* &, int &, int* &, int* &, int** &);
inline void remapBonds(int &);
void allocate();
- void getMinDist(double** &, double &, double &, double &, double &,
+ void getMinDist(double** &, double &, double &, double &, double &,
double &, int &, int &, int &, int &);
- bool min, midpoint;
+ bool min, midpoint;
double **cut;
double **a0;
double **srp;
diff --git a/src/USER-MISC/pair_tersoff_table.cpp b/src/USER-MISC/pair_tersoff_table.cpp
index c5865c0a99..59c19d9a11 100644
--- a/src/USER-MISC/pair_tersoff_table.cpp
+++ b/src/USER-MISC/pair_tersoff_table.cpp
@@ -20,10 +20,10 @@
1) Tersoff, Phys. Rev. B 39, 5566 (1988)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_tersoff_table.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/USER-MOLFILE/reader_molfile.cpp b/src/USER-MOLFILE/reader_molfile.cpp
index 2e3aa89506..15735ab92a 100644
--- a/src/USER-MOLFILE/reader_molfile.cpp
+++ b/src/USER-MOLFILE/reader_molfile.cpp
@@ -15,9 +15,9 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "string.h"
-#include "stdlib.h"
-#include "math.h"
+#include <string.h>
+#include <stdlib.h>
+#include <math.h>
#include "reader_molfile.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/dihedral_charmm_omp.cpp b/src/USER-OMP/dihedral_charmm_omp.cpp
index 311ef73e3b..95cab754c3 100644
--- a/src/USER-OMP/dihedral_charmm_omp.cpp
+++ b/src/USER-OMP/dihedral_charmm_omp.cpp
@@ -15,8 +15,8 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "math.h"
+#include <mpi.h>
+#include <math.h>
#include "dihedral_charmm_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/dihedral_class2_omp.cpp b/src/USER-OMP/dihedral_class2_omp.cpp
index b4d1080cea..edf3e972d2 100644
--- a/src/USER-OMP/dihedral_class2_omp.cpp
+++ b/src/USER-OMP/dihedral_class2_omp.cpp
@@ -15,7 +15,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "dihedral_class2_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp b/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp
index 57a4561629..fe99d52cb7 100644
--- a/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp
+++ b/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp
@@ -15,7 +15,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "dihedral_cosine_shift_exp_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/dihedral_fourier_omp.cpp b/src/USER-OMP/dihedral_fourier_omp.cpp
index 29d18c9fca..9c93f2ad30 100644
--- a/src/USER-OMP/dihedral_fourier_omp.cpp
+++ b/src/USER-OMP/dihedral_fourier_omp.cpp
@@ -15,7 +15,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "dihedral_fourier_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/dihedral_harmonic_omp.cpp b/src/USER-OMP/dihedral_harmonic_omp.cpp
index 79daf186cb..2e0a1cf554 100644
--- a/src/USER-OMP/dihedral_harmonic_omp.cpp
+++ b/src/USER-OMP/dihedral_harmonic_omp.cpp
@@ -15,7 +15,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "dihedral_harmonic_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/dihedral_helix_omp.cpp b/src/USER-OMP/dihedral_helix_omp.cpp
index 316fbfcb3f..7dd1e8f8a4 100644
--- a/src/USER-OMP/dihedral_helix_omp.cpp
+++ b/src/USER-OMP/dihedral_helix_omp.cpp
@@ -15,7 +15,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "dihedral_helix_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/dihedral_multi_harmonic_omp.cpp b/src/USER-OMP/dihedral_multi_harmonic_omp.cpp
index e43c75d539..06565e7b50 100644
--- a/src/USER-OMP/dihedral_multi_harmonic_omp.cpp
+++ b/src/USER-OMP/dihedral_multi_harmonic_omp.cpp
@@ -15,7 +15,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "dihedral_multi_harmonic_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/dihedral_nharmonic_omp.cpp b/src/USER-OMP/dihedral_nharmonic_omp.cpp
index 3cf0630736..c698f7c109 100644
--- a/src/USER-OMP/dihedral_nharmonic_omp.cpp
+++ b/src/USER-OMP/dihedral_nharmonic_omp.cpp
@@ -15,7 +15,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "dihedral_nharmonic_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/dihedral_opls_omp.cpp b/src/USER-OMP/dihedral_opls_omp.cpp
index 187bdae3a6..069d6d2dd2 100644
--- a/src/USER-OMP/dihedral_opls_omp.cpp
+++ b/src/USER-OMP/dihedral_opls_omp.cpp
@@ -15,7 +15,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "dihedral_opls_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/dihedral_quadratic_omp.cpp b/src/USER-OMP/dihedral_quadratic_omp.cpp
index 3157e3b40a..3fa580defc 100644
--- a/src/USER-OMP/dihedral_quadratic_omp.cpp
+++ b/src/USER-OMP/dihedral_quadratic_omp.cpp
@@ -15,7 +15,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "dihedral_quadratic_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/ewald_omp.cpp b/src/USER-OMP/ewald_omp.cpp
index 6625a1dcb8..7ab903aab1 100644
--- a/src/USER-OMP/ewald_omp.cpp
+++ b/src/USER-OMP/ewald_omp.cpp
@@ -15,7 +15,7 @@
Contributing authors: Roy Pollock (LLNL), Paul Crozier (SNL)
------------------------------------------------------------------------- */
-#include "mpi.h"
+#include <mpi.h>
#include "ewald_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/fix_gravity_omp.cpp b/src/USER-OMP/fix_gravity_omp.cpp
index fd32a00e58..b853d844f0 100644
--- a/src/USER-OMP/fix_gravity_omp.cpp
+++ b/src/USER-OMP/fix_gravity_omp.cpp
@@ -15,10 +15,10 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "fix_gravity_omp.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-OMP/fix_nh_asphere_omp.cpp b/src/USER-OMP/fix_nh_asphere_omp.cpp
index 4286140a43..d90e907d0e 100644
--- a/src/USER-OMP/fix_nh_asphere_omp.cpp
+++ b/src/USER-OMP/fix_nh_asphere_omp.cpp
@@ -15,9 +15,9 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "string.h"
-#include "stdlib.h"
-#include "math.h"
+#include <string.h>
+#include <stdlib.h>
+#include <math.h>
#include "math_extra.h"
#include "fix_nh_asphere_omp.h"
#include "atom.h"
@@ -79,7 +79,7 @@ void FixNHAsphereOMP::nve_v()
const int nlocal = (igroup == atom->firstgroup) ? atom->nfirst : atom->nlocal;
int i;
- // standard nve_v velocity update. for efficiency the loop is
+ // standard nve_v velocity update. for efficiency the loop is
// merged with FixNHOMP instead of calling it for the COM update.
#if defined(_OPENMP)
@@ -122,7 +122,7 @@ void FixNHAsphereOMP::nve_x()
// update quaternion a full step via Richardson iteration
// returns new normalized quaternion
// principal moments of inertia
-
+
#if defined(_OPENMP)
#pragma omp parallel for default(none) private(i) schedule(static)
#endif
diff --git a/src/USER-OMP/fix_nh_sphere_omp.cpp b/src/USER-OMP/fix_nh_sphere_omp.cpp
index 79d98a6cca..71c5e4b985 100644
--- a/src/USER-OMP/fix_nh_sphere_omp.cpp
+++ b/src/USER-OMP/fix_nh_sphere_omp.cpp
@@ -15,7 +15,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "fix_nh_sphere_omp.h"
#include "atom.h"
#include "atom_vec.h"
@@ -81,7 +81,7 @@ void FixNHSphereOMP::nve_v()
const int nlocal = (igroup == atom->firstgroup) ? atom->nfirst : atom->nlocal;
int i;
- // standard nve_v velocity update. for efficiency the loop is
+ // standard nve_v velocity update. for efficiency the loop is
// merged with FixNHOMP instead of calling it for the COM update.
// update omega for all particles
diff --git a/src/USER-OMP/fix_nph_asphere_omp.cpp b/src/USER-OMP/fix_nph_asphere_omp.cpp
index d9343b3337..3e0a6c9df0 100644
--- a/src/USER-OMP/fix_nph_asphere_omp.cpp
+++ b/src/USER-OMP/fix_nph_asphere_omp.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "fix_nph_asphere_omp.h"
#include "modify.h"
#include "error.h"
diff --git a/src/USER-OMP/fix_nph_omp.cpp b/src/USER-OMP/fix_nph_omp.cpp
index 6d3e33453d..be21da2eed 100644
--- a/src/USER-OMP/fix_nph_omp.cpp
+++ b/src/USER-OMP/fix_nph_omp.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "fix_nph_omp.h"
#include "modify.h"
#include "error.h"
diff --git a/src/USER-OMP/fix_nph_sphere_omp.cpp b/src/USER-OMP/fix_nph_sphere_omp.cpp
index d39bf09582..a5626f9d1c 100644
--- a/src/USER-OMP/fix_nph_sphere_omp.cpp
+++ b/src/USER-OMP/fix_nph_sphere_omp.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "fix_nph_sphere_omp.h"
#include "modify.h"
#include "error.h"
diff --git a/src/USER-OMP/fix_nphug_omp.cpp b/src/USER-OMP/fix_nphug_omp.cpp
index 57bc1fc2a1..7721781769 100644
--- a/src/USER-OMP/fix_nphug_omp.cpp
+++ b/src/USER-OMP/fix_nphug_omp.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
-#include "stdlib.h"
+#include <string.h>
+#include <stdlib.h>
#include "fix_nphug_omp.h"
#include "modify.h"
#include "error.h"
@@ -21,10 +21,10 @@
#include "force.h"
#include "domain.h"
#include "group.h"
-#include "math.h"
+#include <math.h>
#include "memory.h"
#include "comm.h"
-#include "math.h"
+#include <math.h>
using namespace LAMMPS_NS;
using namespace FixConst;
diff --git a/src/USER-OMP/fix_npt_asphere_omp.cpp b/src/USER-OMP/fix_npt_asphere_omp.cpp
index 05bc61f45e..00bafe661a 100644
--- a/src/USER-OMP/fix_npt_asphere_omp.cpp
+++ b/src/USER-OMP/fix_npt_asphere_omp.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "fix_npt_asphere_omp.h"
#include "modify.h"
#include "error.h"
diff --git a/src/USER-OMP/fix_npt_omp.cpp b/src/USER-OMP/fix_npt_omp.cpp
index 2f2d90a2d1..c4af48542a 100644
--- a/src/USER-OMP/fix_npt_omp.cpp
+++ b/src/USER-OMP/fix_npt_omp.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "fix_npt_omp.h"
#include "modify.h"
#include "error.h"
diff --git a/src/USER-OMP/fix_npt_sphere_omp.cpp b/src/USER-OMP/fix_npt_sphere_omp.cpp
index f1959bc29e..6baee93cb4 100644
--- a/src/USER-OMP/fix_npt_sphere_omp.cpp
+++ b/src/USER-OMP/fix_npt_sphere_omp.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "fix_npt_sphere_omp.h"
#include "modify.h"
#include "error.h"
diff --git a/src/USER-OMP/fix_nve_sphere_omp.cpp b/src/USER-OMP/fix_nve_sphere_omp.cpp
index bbe009ecc9..ee58c88cb8 100644
--- a/src/USER-OMP/fix_nve_sphere_omp.cpp
+++ b/src/USER-OMP/fix_nve_sphere_omp.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <string.h>
#include "fix_nve_sphere_omp.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/USER-OMP/fix_nvt_asphere_omp.cpp b/src/USER-OMP/fix_nvt_asphere_omp.cpp
index 68cd4f0df6..23cc2e9581 100644
--- a/src/USER-OMP/fix_nvt_asphere_omp.cpp
+++ b/src/USER-OMP/fix_nvt_asphere_omp.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "fix_nvt_asphere_omp.h"
#include "group.h"
#include "modify.h"
diff --git a/src/USER-OMP/fix_nvt_omp.cpp b/src/USER-OMP/fix_nvt_omp.cpp
index 8f096cd7d3..18d02bff4d 100644
--- a/src/USER-OMP/fix_nvt_omp.cpp
+++ b/src/USER-OMP/fix_nvt_omp.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "fix_nvt_omp.h"
#include "group.h"
#include "modify.h"
diff --git a/src/USER-OMP/fix_nvt_sllod_omp.cpp b/src/USER-OMP/fix_nvt_sllod_omp.cpp
index 0ce946e769..8105e831f7 100644
--- a/src/USER-OMP/fix_nvt_sllod_omp.cpp
+++ b/src/USER-OMP/fix_nvt_sllod_omp.cpp
@@ -15,8 +15,8 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "string.h"
+#include <math.h>
+#include <string.h>
#include "fix_nvt_sllod_omp.h"
#include "math_extra.h"
#include "atom.h"
diff --git a/src/USER-OMP/fix_nvt_sphere_omp.cpp b/src/USER-OMP/fix_nvt_sphere_omp.cpp
index e34b3da5a4..6db9ad849a 100644
--- a/src/USER-OMP/fix_nvt_sphere_omp.cpp
+++ b/src/USER-OMP/fix_nvt_sphere_omp.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "fix_nvt_sphere_omp.h"
#include "group.h"
#include "modify.h"
diff --git a/src/USER-OMP/fix_qeq_comb_omp.cpp b/src/USER-OMP/fix_qeq_comb_omp.cpp
index 7b2be715d3..f8de18498d 100644
--- a/src/USER-OMP/fix_qeq_comb_omp.cpp
+++ b/src/USER-OMP/fix_qeq_comb_omp.cpp
@@ -15,8 +15,8 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "math.h"
+#include <mpi.h>
+#include <math.h>
#include "fix_qeq_comb_omp.h"
#include "fix_omp.h"
#include "atom.h"
@@ -59,7 +59,7 @@ void FixQEQCombOMP::init()
comb = (PairComb *) force->pair_match("comb/omp",1);
if (comb == NULL)
comb = (PairComb *) force->pair_match("comb",1);
- if (comb == NULL)
+ if (comb == NULL)
error->all(FLERR,"Must use pair_style comb or "
"comb/omp with fix qeq/comb/omp");
diff --git a/src/USER-OMP/fix_rigid_nh_omp.cpp b/src/USER-OMP/fix_rigid_nh_omp.cpp
index 0e347eb128..f2d6d8513b 100644
--- a/src/USER-OMP/fix_rigid_nh_omp.cpp
+++ b/src/USER-OMP/fix_rigid_nh_omp.cpp
@@ -57,7 +57,7 @@ typedef struct { double x,y,z; } dbl3_t;
void FixRigidNHOMP::initial_integrate(int vflag)
{
double scale_r,scale_t[3],scale_v[3];
-
+
// compute scale variables
scale_t[0] = scale_t[1] = scale_t[2] = 1.0;
@@ -70,7 +70,7 @@ void FixRigidNHOMP::initial_integrate(int vflag)
scale_t[0] = scale_t[1] = scale_t[2] = tmp;
tmp = exp(-dtq * eta_dot_r[0]);
scale_r = tmp;
- }
+ }
if (pstat_flag) {
akin_t = akin_r = 0.0;
@@ -86,7 +86,7 @@ void FixRigidNHOMP::initial_integrate(int vflag)
tmp = dtq * epsilon_dot[2];
scale_v[2] = dtv * exp(tmp) * maclaurin_series(tmp);
}
-
+
// update xcm, vcm, quat, conjqm and angmom
double akt=0.0, akr=0.0;
int ibody;
@@ -97,24 +97,24 @@ void FixRigidNHOMP::initial_integrate(int vflag)
for (ibody = 0; ibody < nbody; ibody++) {
double mbody[3],tbody[3],fquat[4];
const double dtf2 = dtf * 2.0;
-
+
// step 1.1 - update vcm by 1/2 step
-
+
const double dtfm = dtf / masstotal[ibody];
vcm[ibody][0] += dtfm * fcm[ibody][0] * fflag[ibody][0];
vcm[ibody][1] += dtfm * fcm[ibody][1] * fflag[ibody][1];
vcm[ibody][2] += dtfm * fcm[ibody][2] * fflag[ibody][2];
-
+
if (tstat_flag || pstat_flag) {
vcm[ibody][0] *= scale_t[0];
vcm[ibody][1] *= scale_t[1];
vcm[ibody][2] *= scale_t[2];
-
+
double tmp = vcm[ibody][0]*vcm[ibody][0] + vcm[ibody][1]*vcm[ibody][1] +
vcm[ibody][2]*vcm[ibody][2];
akt += masstotal[ibody]*tmp;
}
-
+
// step 1.2 - update xcm by full step
if (!pstat_flag) {
@@ -126,56 +126,56 @@ void FixRigidNHOMP::initial_integrate(int vflag)
xcm[ibody][1] += scale_v[1] * vcm[ibody][1];
xcm[ibody][2] += scale_v[2] * vcm[ibody][2];
}
-
+
// step 1.3 - apply torque (body coords) to quaternion momentum
-
+
torque[ibody][0] *= tflag[ibody][0];
torque[ibody][1] *= tflag[ibody][1];
torque[ibody][2] *= tflag[ibody][2];
-
+
MathExtra::transpose_matvec(ex_space[ibody],ey_space[ibody],ez_space[ibody],
torque[ibody],tbody);
MathExtra::quatvec(quat[ibody],tbody,fquat);
-
+
conjqm[ibody][0] += dtf2 * fquat[0];
conjqm[ibody][1] += dtf2 * fquat[1];
conjqm[ibody][2] += dtf2 * fquat[2];
conjqm[ibody][3] += dtf2 * fquat[3];
-
+
if (tstat_flag || pstat_flag) {
conjqm[ibody][0] *= scale_r;
conjqm[ibody][1] *= scale_r;
conjqm[ibody][2] *= scale_r;
conjqm[ibody][3] *= scale_r;
}
-
+
// step 1.4 to 1.13 - use no_squish rotate to update p and q
-
+
MathExtra::no_squish_rotate(3,conjqm[ibody],quat[ibody],inertia[ibody],dtq);
MathExtra::no_squish_rotate(2,conjqm[ibody],quat[ibody],inertia[ibody],dtq);
MathExtra::no_squish_rotate(1,conjqm[ibody],quat[ibody],inertia[ibody],dtv);
MathExtra::no_squish_rotate(2,conjqm[ibody],quat[ibody],inertia[ibody],dtq);
MathExtra::no_squish_rotate(3,conjqm[ibody],quat[ibody],inertia[ibody],dtq);
-
+
// update exyz_space
// transform p back to angmom
// update angular velocity
-
+
MathExtra::q_to_exyz(quat[ibody],ex_space[ibody],ey_space[ibody],
ez_space[ibody]);
MathExtra::invquatvec(quat[ibody],conjqm[ibody],mbody);
MathExtra::matvec(ex_space[ibody],ey_space[ibody],ez_space[ibody],
mbody,angmom[ibody]);
-
+
angmom[ibody][0] *= 0.5;
angmom[ibody][1] *= 0.5;
angmom[ibody][2] *= 0.5;
-
+
MathExtra::angmom_to_omega(angmom[ibody],ex_space[ibody],ey_space[ibody],
ez_space[ibody],inertia[ibody],omega[ibody]);
-
+
if (tstat_flag || pstat_flag) {
- akr += angmom[ibody][0]*omega[ibody][0] +
+ akr += angmom[ibody][0]*omega[ibody][0] +
angmom[ibody][1]*omega[ibody][1] + angmom[ibody][2]*omega[ibody][2];
}
} // end of parallel for
@@ -193,7 +193,7 @@ void FixRigidNHOMP::initial_integrate(int vflag)
compute_temp_target();
nhc_temp_integrate();
}
-
+
// update thermostat chains coupled with barostat
// refer to update_nhcb() in Kamberaj et al.
@@ -205,14 +205,14 @@ void FixRigidNHOMP::initial_integrate(int vflag)
if (vflag) v_setup(vflag);
else evflag = 0;
-
+
// remap simulation box by 1/2 step
if (pstat_flag) remap();
-
+
// set coords/orient and velocity/rotation of atoms in rigid bodies
// from quarternion and omega
-
+
if (triclinic)
if (evflag)
set_xv_thr<1,1>();
@@ -230,7 +230,7 @@ void FixRigidNHOMP::initial_integrate(int vflag)
if (pstat_flag) {
remap();
if (kspace_flag) force->kspace->setup();
- }
+ }
}
/* ---------------------------------------------------------------------- */
@@ -240,7 +240,7 @@ void FixRigidNHOMP::final_integrate()
double scale_t[3],scale_r;
// compute scale variables
-
+
scale_t[0] = scale_t[1] = scale_t[2] = 1.0;
scale_r = 1.0;
@@ -248,17 +248,17 @@ void FixRigidNHOMP::final_integrate()
double tmp = exp(-1.0 * dtq * eta_dot_t[0]);
scale_t[0] = scale_t[1] = scale_t[2] = tmp;
scale_r = exp(-1.0 * dtq * eta_dot_r[0]);
- }
-
+ }
+
if (pstat_flag) {
scale_t[0] *= exp(-dtq * (epsilon_dot[0] + mtk_term2));
scale_t[1] *= exp(-dtq * (epsilon_dot[1] + mtk_term2));
scale_t[2] *= exp(-dtq * (epsilon_dot[2] + mtk_term2));
scale_r *= exp(-dtq * (pdim * mtk_term2));
-
+
akin_t = akin_r = 0.0;
}
-
+
double * const * _noalias const x = atom->x;
const dbl3_t * _noalias const f = (dbl3_t *) atom->f[0];
const double * const * const torque_one = atom->torque;
@@ -306,7 +306,7 @@ void FixRigidNHOMP::final_integrate()
// we likely have only a rather number of groups so we loops
// over bodies and thread over all atoms for each of them.
-
+
for (int ib = 0; ib < nbody; ++ib) {
double s0=0.0,s1=0.0,s2=0.0,s3=0.0,s4=0.0,s5=0.0;
int i;
@@ -361,7 +361,7 @@ void FixRigidNHOMP::final_integrate()
#else
const int tid = 0;
#endif
-
+
for (int i = 0; i < nlocal; i++) {
const int ibody = body[i];
if ((ibody < 0) || (ibody % nthreads != tid)) continue;
@@ -423,28 +423,28 @@ void FixRigidNHOMP::final_integrate()
vcm[ibody][1] *= scale_t[1];
vcm[ibody][2] *= scale_t[2];
}
-
+
vcm[ibody][0] += dtfm * fcm[ibody][0] * fflag[ibody][0];
vcm[ibody][1] += dtfm * fcm[ibody][1] * fflag[ibody][1];
vcm[ibody][2] += dtfm * fcm[ibody][2] * fflag[ibody][2];
-
+
if (pstat_flag) {
double tmp = vcm[ibody][0]*vcm[ibody][0] + vcm[ibody][1]*vcm[ibody][1] +
vcm[ibody][2]*vcm[ibody][2];
akt += masstotal[ibody]*tmp;
}
-
+
// update conjqm, then transform to angmom, set velocity again
// virial is already setup from initial_integrate
-
+
torque[ibody][0] *= tflag[ibody][0];
torque[ibody][1] *= tflag[ibody][1];
torque[ibody][2] *= tflag[ibody][2];
-
+
MathExtra::transpose_matvec(ex_space[ibody],ey_space[ibody],
ez_space[ibody],torque[ibody],tbody);
MathExtra::quatvec(quat[ibody],tbody,fquat);
-
+
if (tstat_flag || pstat_flag) {
conjqm[ibody][0] = scale_r * conjqm[ibody][0] + dtf2 * fquat[0];
conjqm[ibody][1] = scale_r * conjqm[ibody][1] + dtf2 * fquat[1];
@@ -460,17 +460,17 @@ void FixRigidNHOMP::final_integrate()
MathExtra::invquatvec(quat[ibody],conjqm[ibody],mbody);
MathExtra::matvec(ex_space[ibody],ey_space[ibody],ez_space[ibody],
mbody,angmom[ibody]);
-
+
angmom[ibody][0] *= 0.5;
angmom[ibody][1] *= 0.5;
- angmom[ibody][2] *= 0.5;
-
+ angmom[ibody][2] *= 0.5;
+
MathExtra::angmom_to_omega(angmom[ibody],ex_space[ibody],ey_space[ibody],
ez_space[ibody],inertia[ibody],omega[ibody]);
-
+
if (pstat_flag) {
- akr += angmom[ibody][0]*omega[ibody][0] +
- angmom[ibody][1]*omega[ibody][1] +
+ akr += angmom[ibody][0]*omega[ibody][0] +
+ angmom[ibody][1]*omega[ibody][1] +
angmom[ibody][2]*omega[ibody][2];
}
} // end of parallel for
@@ -490,13 +490,13 @@ void FixRigidNHOMP::final_integrate()
set_v_thr<0,1>();
else
set_v_thr<0,0>();
-
+
// compute current temperature
if (tcomputeflag) t_current = temperature->compute_scalar();
// compute current and target pressures
// update epsilon dot using akin_t and akin_r
-
+
if (pstat_flag) {
if (pstyle == ISO) {
temperature->compute_scalar();
@@ -523,11 +523,11 @@ void FixRigidNHOMP::remap()
const int nlocal = atom->nlocal;
// epsilon is not used, except for book-keeping
-
+
for (int i = 0; i < 3; i++) epsilon[i] += dtq * epsilon_dot[i];
-
+
// convert pertinent atoms and rigid bodies to lamda coords
-
+
if (allremap) domain->x2lamda(nlocal);
else {
int i;
@@ -538,13 +538,13 @@ void FixRigidNHOMP::remap()
if (mask[i] & dilate_group_bit)
domain->x2lamda(x[i],x[i]);
}
-
+
if (nrigid)
for (int i = 0; i < nrigidfix; i++)
modify->fix[rfix[i]]->deform(0);
-
+
// reset global and local box to new size/shape
-
+
for (int i = 0; i < 3; i++) {
if (p_flag[i]) {
const double oldlo = domain->boxlo[i];
@@ -558,9 +558,9 @@ void FixRigidNHOMP::remap()
domain->set_global_box();
domain->set_local_box();
-
+
// convert pertinent atoms and rigid bodies back to box coords
-
+
if (allremap) domain->lamda2x(nlocal);
else {
int i;
@@ -901,7 +901,7 @@ void FixRigidNHOMP::set_v_thr()
}
}
- // set omega, angmom of each extended particle
+ // set omega, angmom of each extended particle
// XXX: extended particle info not yet multi-threaded
if (extended) {
diff --git a/src/USER-OMP/fix_rigid_nh_omp.h b/src/USER-OMP/fix_rigid_nh_omp.h
index f2902ca333..9210d7e5dc 100644
--- a/src/USER-OMP/fix_rigid_nh_omp.h
+++ b/src/USER-OMP/fix_rigid_nh_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -26,7 +26,7 @@ class FixRigidNHOMP : public FixRigidNH {
virtual void initial_integrate(int);
virtual void final_integrate();
- virtual void remap();
+ virtual void remap();
private: // copied from FixRigidOMP
template <int, int> void set_xv_thr();
diff --git a/src/USER-OMP/fix_rigid_nph_omp.cpp b/src/USER-OMP/fix_rigid_nph_omp.cpp
index bd2ba5f6fb..6aca84c309 100644
--- a/src/USER-OMP/fix_rigid_nph_omp.cpp
+++ b/src/USER-OMP/fix_rigid_nph_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -17,7 +17,7 @@
Miller et al., J Chem Phys. 116, 8649-8659 (2002)
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "fix_rigid_nph_omp.h"
#include "domain.h"
#include "modify.h"
@@ -29,24 +29,24 @@ using namespace LAMMPS_NS;
FixRigidNPHOMP::FixRigidNPHOMP(LAMMPS *lmp, int narg, char **arg) :
FixRigidNHOMP(lmp, narg, arg)
-{
+{
// other setting are made by parent
scalar_flag = 1;
restart_global = 1;
box_change_size = 1;
extscalar = 1;
-
+
// error checks
if (pstat_flag == 0)
error->all(FLERR,"Pressure control must be used with fix nph/omp");
if (tstat_flag == 1)
error->all(FLERR,"Temperature control must not be used with fix nph/omp");
- if (p_start[0] < 0.0 || p_start[1] < 0.0 || p_start[2] < 0.0 ||
+ if (p_start[0] < 0.0 || p_start[1] < 0.0 || p_start[2] < 0.0 ||
p_stop[0] < 0.0 || p_stop[1] < 0.0 || p_stop[2] < 0.0)
error->all(FLERR,"Target pressure for fix rigid/nph/omp cannot be 0.0");
-
+
// convert input periods to frequency
p_freq[0] = p_freq[1] = p_freq[2] = 0.0;
@@ -67,15 +67,15 @@ FixRigidNPHOMP::FixRigidNPHOMP(LAMMPS *lmp, int narg, char **arg) :
char **newarg = new char*[3];
newarg[0] = id_temp;
newarg[1] = (char *) "all";
- newarg[2] = (char *) "temp";
+ newarg[2] = (char *) "temp";
modify->add_compute(3,newarg);
delete [] newarg;
tcomputeflag = 1;
-
+
// create a new compute pressure style
// id = fix-ID + press, compute group = all
// pass id_temp as 4th arg to pressure constructor
-
+
n = strlen(id) + 7;
id_press = new char[n];
strcpy(id_press,id);
diff --git a/src/USER-OMP/fix_rigid_nph_omp.h b/src/USER-OMP/fix_rigid_nph_omp.h
index 31b95fa02f..f64a743fea 100644
--- a/src/USER-OMP/fix_rigid_nph_omp.h
+++ b/src/USER-OMP/fix_rigid_nph_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/fix_rigid_npt_omp.cpp b/src/USER-OMP/fix_rigid_npt_omp.cpp
index 5d41d5f296..23f16c6155 100644
--- a/src/USER-OMP/fix_rigid_npt_omp.cpp
+++ b/src/USER-OMP/fix_rigid_npt_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -17,7 +17,7 @@
Miller et al., J Chem Phys. 116, 8649-8659 (2002)
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "fix_rigid_npt_omp.h"
#include "domain.h"
#include "modify.h"
@@ -29,21 +29,21 @@ using namespace LAMMPS_NS;
FixRigidNPTOMP::FixRigidNPTOMP(LAMMPS *lmp, int narg, char **arg) :
FixRigidNHOMP(lmp, narg, arg)
-{
+{
// other setting are made by parent
scalar_flag = 1;
restart_global = 1;
box_change_size = 1;
extscalar = 1;
-
+
// error checks
if (tstat_flag == 0 || pstat_flag == 0)
error->all(FLERR,"Did not set temp or press for fix rigid/npt/omp");
if (t_start <= 0.0 || t_stop <= 0.0)
error->all(FLERR,"Target temperature for fix rigid/npt/omp cannot be 0.0");
- if (p_start[0] < 0.0 || p_start[1] < 0.0 || p_start[2] < 0.0 ||
+ if (p_start[0] < 0.0 || p_start[1] < 0.0 || p_start[2] < 0.0 ||
p_stop[0] < 0.0 || p_stop[1] < 0.0 || p_stop[2] < 0.0)
error->all(FLERR,"Target pressure for fix rigid/npt/omp cannot be 0.0");
@@ -53,7 +53,7 @@ FixRigidNPTOMP::FixRigidNPTOMP(LAMMPS *lmp, int narg, char **arg) :
if (t_chain < 1) error->all(FLERR,"Illegal fix_modify command");
if (t_iter < 1) error->all(FLERR,"Illegal fix_modify command");
- if (t_order != 3 && t_order != 5)
+ if (t_order != 3 && t_order != 5)
error->all(FLERR,"Fix_modify order must be 3 or 5");
// convert input periods to frequency
@@ -79,15 +79,15 @@ FixRigidNPTOMP::FixRigidNPTOMP(LAMMPS *lmp, int narg, char **arg) :
char **newarg = new char*[3];
newarg[0] = id_temp;
newarg[1] = (char *) "all";
- newarg[2] = (char *) "temp";
+ newarg[2] = (char *) "temp";
modify->add_compute(3,newarg);
delete [] newarg;
tcomputeflag = 1;
-
+
// create a new compute pressure style
// id = fix-ID + press, compute group = all
// pass id_temp as 4th arg to pressure constructor
-
+
n = strlen(id) + 7;
id_press = new char[n];
strcpy(id_press,id);
diff --git a/src/USER-OMP/fix_rigid_npt_omp.h b/src/USER-OMP/fix_rigid_npt_omp.h
index 4f17d0ba55..627b5a8c29 100644
--- a/src/USER-OMP/fix_rigid_npt_omp.h
+++ b/src/USER-OMP/fix_rigid_npt_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/fix_rigid_nve_omp.cpp b/src/USER-OMP/fix_rigid_nve_omp.cpp
index 1da3c29fa7..51ed34fae8 100644
--- a/src/USER-OMP/fix_rigid_nve_omp.cpp
+++ b/src/USER-OMP/fix_rigid_nve_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/fix_rigid_nve_omp.h b/src/USER-OMP/fix_rigid_nve_omp.h
index 464dde528b..eea45ee358 100644
--- a/src/USER-OMP/fix_rigid_nve_omp.h
+++ b/src/USER-OMP/fix_rigid_nve_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/fix_rigid_nvt_omp.cpp b/src/USER-OMP/fix_rigid_nvt_omp.cpp
index 5e367899d9..758dcce9bf 100644
--- a/src/USER-OMP/fix_rigid_nvt_omp.cpp
+++ b/src/USER-OMP/fix_rigid_nvt_omp.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -26,13 +26,13 @@ using namespace LAMMPS_NS;
FixRigidNVTOMP::FixRigidNVTOMP(LAMMPS *lmp, int narg, char **arg) :
FixRigidNHOMP(lmp, narg, arg)
-{
+{
// other settings are made by parent
scalar_flag = 1;
restart_global = 1;
extscalar = 1;
-
+
// error checking
// convert input period to frequency
@@ -46,6 +46,6 @@ FixRigidNVTOMP::FixRigidNVTOMP(LAMMPS *lmp, int narg, char **arg) :
if (t_chain < 1) error->all(FLERR,"Illegal fix_modify command");
if (t_iter < 1) error->all(FLERR,"Illegal fix_modify command");
- if (t_order != 3 && t_order != 5)
- error->all(FLERR,"Fix_modify order must be 3 or 5");
+ if (t_order != 3 && t_order != 5)
+ error->all(FLERR,"Fix_modify order must be 3 or 5");
}
diff --git a/src/USER-OMP/fix_rigid_nvt_omp.h b/src/USER-OMP/fix_rigid_nvt_omp.h
index d083834d82..e1583aa4df 100644
--- a/src/USER-OMP/fix_rigid_nvt_omp.h
+++ b/src/USER-OMP/fix_rigid_nvt_omp.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-OMP/fix_rigid_omp.cpp b/src/USER-OMP/fix_rigid_omp.cpp
index 8e069abfbf..d5bacc0320 100644
--- a/src/USER-OMP/fix_rigid_omp.cpp
+++ b/src/USER-OMP/fix_rigid_omp.cpp
@@ -157,7 +157,7 @@ void FixRigidOMP::final_integrate()
// we likely have only a rather number of groups so we loops
// over bodies and thread over all atoms for each of them.
-
+
for (int ib = 0; ib < nbody; ++ib) {
double s0=0.0,s1=0.0,s2=0.0,s3=0.0,s4=0.0,s5=0.0;
int i;
@@ -212,7 +212,7 @@ void FixRigidOMP::final_integrate()
#else
const int tid = 0;
#endif
-
+
for (int i = 0; i < nlocal; i++) {
const int ibody = body[i];
if ((ibody < 0) || (ibody % nthreads != tid)) continue;
@@ -616,7 +616,7 @@ void FixRigidOMP::set_v_thr()
}
}
- // set omega, angmom of each extended particle
+ // set omega, angmom of each extended particle
// XXX: extended particle info not yet multi-threaded
if (extended) {
diff --git a/src/USER-OMP/fix_rigid_small_omp.cpp b/src/USER-OMP/fix_rigid_small_omp.cpp
index e419bc5227..a260899aef 100644
--- a/src/USER-OMP/fix_rigid_small_omp.cpp
+++ b/src/USER-OMP/fix_rigid_small_omp.cpp
@@ -120,7 +120,7 @@ void FixRigidSmallOMP::final_integrate()
const int nlocal = atom->nlocal;
const int nthreads=comm->nthreads;
int i, ibody;
-
+
#if defined(_OPENMP)
#pragma omp parallel for default(none) private(ibody) schedule(static)
#endif
@@ -139,7 +139,7 @@ void FixRigidSmallOMP::final_integrate()
#if defined(_OPENMP)
#pragma omp parallel default(none) private(i,ibody)
#endif
- {
+ {
#if defined(_OPENMP)
const int tid = omp_get_thread_num();
#else
@@ -149,7 +149,7 @@ void FixRigidSmallOMP::final_integrate()
for (i = 0; i < nlocal; i++) {
ibody = atom2body[i];
if ((ibody < 0) || (ibody % nthreads != tid)) continue;
-
+
Body &b = body[ibody];
double unwrap[3];
@@ -203,7 +203,7 @@ void FixRigidSmallOMP::final_integrate()
}
// update vcm and angmom, recompute omega
-
+
#if defined(_OPENMP)
#pragma omp parallel for default(none) private(ibody) schedule(static)
#endif
@@ -562,7 +562,7 @@ void FixRigidSmallOMP::set_v_thr()
}
}
- // set omega, angmom of each extended particle
+ // set omega, angmom of each extended particle
// XXX: extended particle info not yet multi-threaded
if (extended) {
diff --git a/src/USER-OMP/fix_shear_history_omp.cpp b/src/USER-OMP/fix_shear_history_omp.cpp
index 16f5212acf..a91a129fee 100644
--- a/src/USER-OMP/fix_shear_history_omp.cpp
+++ b/src/USER-OMP/fix_shear_history_omp.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
-#include "stdio.h"
+#include <string.h>
+#include <stdio.h>
#include "fix_shear_history_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/fix_wall_gran_omp.cpp b/src/USER-OMP/fix_wall_gran_omp.cpp
index e131acc0fa..11cc307904 100644
--- a/src/USER-OMP/fix_wall_gran_omp.cpp
+++ b/src/USER-OMP/fix_wall_gran_omp.cpp
@@ -15,7 +15,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "fix_wall_gran_omp.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-OMP/improper_class2_omp.cpp b/src/USER-OMP/improper_class2_omp.cpp
index 2cf71f675c..5e32795371 100644
--- a/src/USER-OMP/improper_class2_omp.cpp
+++ b/src/USER-OMP/improper_class2_omp.cpp
@@ -15,7 +15,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "improper_class2_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/improper_cossq_omp.cpp b/src/USER-OMP/improper_cossq_omp.cpp
index 745591a338..f34941d624 100644
--- a/src/USER-OMP/improper_cossq_omp.cpp
+++ b/src/USER-OMP/improper_cossq_omp.cpp
@@ -15,7 +15,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "improper_cossq_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/improper_cvff_omp.cpp b/src/USER-OMP/improper_cvff_omp.cpp
index 1d252fee5b..cba14226ac 100644
--- a/src/USER-OMP/improper_cvff_omp.cpp
+++ b/src/USER-OMP/improper_cvff_omp.cpp
@@ -15,7 +15,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "improper_cvff_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/improper_fourier_omp.cpp b/src/USER-OMP/improper_fourier_omp.cpp
index 6c32c8e538..9e7912e335 100644
--- a/src/USER-OMP/improper_fourier_omp.cpp
+++ b/src/USER-OMP/improper_fourier_omp.cpp
@@ -15,7 +15,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "improper_fourier_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/improper_harmonic_omp.cpp b/src/USER-OMP/improper_harmonic_omp.cpp
index e323b75e3f..8c1f91ecab 100644
--- a/src/USER-OMP/improper_harmonic_omp.cpp
+++ b/src/USER-OMP/improper_harmonic_omp.cpp
@@ -15,7 +15,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "improper_harmonic_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/improper_ring_omp.cpp b/src/USER-OMP/improper_ring_omp.cpp
index c1737a4f21..bd7593c51a 100644
--- a/src/USER-OMP/improper_ring_omp.cpp
+++ b/src/USER-OMP/improper_ring_omp.cpp
@@ -15,7 +15,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "improper_ring_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/improper_umbrella_omp.cpp b/src/USER-OMP/improper_umbrella_omp.cpp
index f100d3a0a9..9d28e25053 100644
--- a/src/USER-OMP/improper_umbrella_omp.cpp
+++ b/src/USER-OMP/improper_umbrella_omp.cpp
@@ -15,7 +15,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "improper_umbrella_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/msm_cg_omp.cpp b/src/USER-OMP/msm_cg_omp.cpp
index 26926ab775..93379c8d3b 100644
--- a/src/USER-OMP/msm_cg_omp.cpp
+++ b/src/USER-OMP/msm_cg_omp.cpp
@@ -16,11 +16,11 @@
Original MSM class by: Paul Crozier, Stan Moore, Stephen Bond, (all SNL)
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <mpi.h>
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "atom.h"
#include "gridcomm.h"
diff --git a/src/USER-OMP/pair_adp_omp.cpp b/src/USER-OMP/pair_adp_omp.cpp
index ec63dead89..658ef365a3 100644
--- a/src/USER-OMP/pair_adp_omp.cpp
+++ b/src/USER-OMP/pair_adp_omp.cpp
@@ -12,8 +12,8 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "string.h"
+#include <math.h>
+#include <string.h>
#include "pair_adp_omp.h"
#include "atom.h"
diff --git a/src/USER-OMP/pair_airebo_omp.cpp b/src/USER-OMP/pair_airebo_omp.cpp
index f2149088c1..8215e9967d 100644
--- a/src/USER-OMP/pair_airebo_omp.cpp
+++ b/src/USER-OMP/pair_airebo_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_airebo_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_beck_omp.cpp b/src/USER-OMP/pair_beck_omp.cpp
index 3e261aa2fd..e56a0dc7fa 100644
--- a/src/USER-OMP/pair_beck_omp.cpp
+++ b/src/USER-OMP/pair_beck_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_beck_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_born_coul_long_omp.cpp b/src/USER-OMP/pair_born_coul_long_omp.cpp
index 06e6da9d2c..cbb71dfeb5 100644
--- a/src/USER-OMP/pair_born_coul_long_omp.cpp
+++ b/src/USER-OMP/pair_born_coul_long_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_born_coul_long_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_born_coul_msm_omp.cpp b/src/USER-OMP/pair_born_coul_msm_omp.cpp
index bd282cfaa9..8ce564ccfa 100755
--- a/src/USER-OMP/pair_born_coul_msm_omp.cpp
+++ b/src/USER-OMP/pair_born_coul_msm_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_born_coul_msm_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_born_coul_wolf_omp.cpp b/src/USER-OMP/pair_born_coul_wolf_omp.cpp
index 9091332080..bd3e539dd6 100644
--- a/src/USER-OMP/pair_born_coul_wolf_omp.cpp
+++ b/src/USER-OMP/pair_born_coul_wolf_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_born_coul_wolf_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_born_omp.cpp b/src/USER-OMP/pair_born_omp.cpp
index 01fdc1d012..35669cb539 100644
--- a/src/USER-OMP/pair_born_omp.cpp
+++ b/src/USER-OMP/pair_born_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_born_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_brownian_omp.cpp b/src/USER-OMP/pair_brownian_omp.cpp
index 8412644ff3..9ea6a9187b 100644
--- a/src/USER-OMP/pair_brownian_omp.cpp
+++ b/src/USER-OMP/pair_brownian_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_brownian_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_brownian_poly_omp.cpp b/src/USER-OMP/pair_brownian_poly_omp.cpp
index e0124204de..d8cb3bf06e 100644
--- a/src/USER-OMP/pair_brownian_poly_omp.cpp
+++ b/src/USER-OMP/pair_brownian_poly_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_brownian_poly_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_buck_coul_cut_omp.cpp b/src/USER-OMP/pair_buck_coul_cut_omp.cpp
index 054493cc01..ead60d70ac 100644
--- a/src/USER-OMP/pair_buck_coul_cut_omp.cpp
+++ b/src/USER-OMP/pair_buck_coul_cut_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_buck_coul_cut_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_buck_coul_long_omp.cpp b/src/USER-OMP/pair_buck_coul_long_omp.cpp
index 6ab1a851b7..48750f8318 100644
--- a/src/USER-OMP/pair_buck_coul_long_omp.cpp
+++ b/src/USER-OMP/pair_buck_coul_long_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_buck_coul_long_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_buck_coul_msm_omp.cpp b/src/USER-OMP/pair_buck_coul_msm_omp.cpp
index bd59dccf7d..df94efc812 100755
--- a/src/USER-OMP/pair_buck_coul_msm_omp.cpp
+++ b/src/USER-OMP/pair_buck_coul_msm_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_buck_coul_msm_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_buck_long_coul_long_omp.cpp b/src/USER-OMP/pair_buck_long_coul_long_omp.cpp
index 2443b0a61d..87f9e2e321 100644
--- a/src/USER-OMP/pair_buck_long_coul_long_omp.cpp
+++ b/src/USER-OMP/pair_buck_long_coul_long_omp.cpp
@@ -12,7 +12,7 @@
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "math_vector.h"
#include "pair_buck_long_coul_long_omp.h"
#include "atom.h"
diff --git a/src/USER-OMP/pair_buck_omp.cpp b/src/USER-OMP/pair_buck_omp.cpp
index 0b8dbc7f68..826fd78deb 100644
--- a/src/USER-OMP/pair_buck_omp.cpp
+++ b/src/USER-OMP/pair_buck_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_buck_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_cdeam_omp.cpp b/src/USER-OMP/pair_cdeam_omp.cpp
index cb1f201a9e..3bfe74e129 100644
--- a/src/USER-OMP/pair_cdeam_omp.cpp
+++ b/src/USER-OMP/pair_cdeam_omp.cpp
@@ -12,8 +12,8 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "string.h"
+#include <math.h>
+#include <string.h>
#include "pair_cdeam_omp.h"
#include "atom.h"
diff --git a/src/USER-OMP/pair_colloid_omp.cpp b/src/USER-OMP/pair_colloid_omp.cpp
index e3b6472c2a..4c6411f150 100644
--- a/src/USER-OMP/pair_colloid_omp.cpp
+++ b/src/USER-OMP/pair_colloid_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_colloid_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_comb_omp.cpp b/src/USER-OMP/pair_comb_omp.cpp
index a075ee1f6a..c776ff3026 100644
--- a/src/USER-OMP/pair_comb_omp.cpp
+++ b/src/USER-OMP/pair_comb_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_comb_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_coul_cut_omp.cpp b/src/USER-OMP/pair_coul_cut_omp.cpp
index 1478618682..381e7f83c2 100644
--- a/src/USER-OMP/pair_coul_cut_omp.cpp
+++ b/src/USER-OMP/pair_coul_cut_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_coul_cut_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_coul_cut_soft_omp.cpp b/src/USER-OMP/pair_coul_cut_soft_omp.cpp
index da6760902e..af9c9472fa 100644
--- a/src/USER-OMP/pair_coul_cut_soft_omp.cpp
+++ b/src/USER-OMP/pair_coul_cut_soft_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_coul_cut_soft_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_coul_debye_omp.cpp b/src/USER-OMP/pair_coul_debye_omp.cpp
index 47d3dab99e..0d9b117967 100644
--- a/src/USER-OMP/pair_coul_debye_omp.cpp
+++ b/src/USER-OMP/pair_coul_debye_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_coul_debye_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_coul_diel_omp.cpp b/src/USER-OMP/pair_coul_diel_omp.cpp
index b100c5053b..577ba6bf65 100644
--- a/src/USER-OMP/pair_coul_diel_omp.cpp
+++ b/src/USER-OMP/pair_coul_diel_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_coul_diel_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_coul_dsf_omp.cpp b/src/USER-OMP/pair_coul_dsf_omp.cpp
index c85ede20ee..4707fad733 100644
--- a/src/USER-OMP/pair_coul_dsf_omp.cpp
+++ b/src/USER-OMP/pair_coul_dsf_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_coul_dsf_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_coul_long_omp.cpp b/src/USER-OMP/pair_coul_long_omp.cpp
index d77a88198b..dc619913d6 100644
--- a/src/USER-OMP/pair_coul_long_omp.cpp
+++ b/src/USER-OMP/pair_coul_long_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_coul_long_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_coul_long_soft_omp.cpp b/src/USER-OMP/pair_coul_long_soft_omp.cpp
index 1246bb10ae..f44f95717d 100644
--- a/src/USER-OMP/pair_coul_long_soft_omp.cpp
+++ b/src/USER-OMP/pair_coul_long_soft_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_coul_long_soft_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_coul_msm_omp.cpp b/src/USER-OMP/pair_coul_msm_omp.cpp
index 870afb7806..baf9ceefb5 100755
--- a/src/USER-OMP/pair_coul_msm_omp.cpp
+++ b/src/USER-OMP/pair_coul_msm_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_coul_msm_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_coul_wolf_omp.cpp b/src/USER-OMP/pair_coul_wolf_omp.cpp
index bcc19af0fe..c5080bc7de 100644
--- a/src/USER-OMP/pair_coul_wolf_omp.cpp
+++ b/src/USER-OMP/pair_coul_wolf_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_coul_wolf_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_dpd_omp.cpp b/src/USER-OMP/pair_dpd_omp.cpp
index 625d5bc19f..98e5af0d81 100644
--- a/src/USER-OMP/pair_dpd_omp.cpp
+++ b/src/USER-OMP/pair_dpd_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_dpd_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_dpd_tstat_omp.cpp b/src/USER-OMP/pair_dpd_tstat_omp.cpp
index 37b2994e3d..ee697a2e96 100644
--- a/src/USER-OMP/pair_dpd_tstat_omp.cpp
+++ b/src/USER-OMP/pair_dpd_tstat_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_dpd_tstat_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_eam_alloy_omp.cpp b/src/USER-OMP/pair_eam_alloy_omp.cpp
index 40a93c143e..f0c0b5272b 100644
--- a/src/USER-OMP/pair_eam_alloy_omp.cpp
+++ b/src/USER-OMP/pair_eam_alloy_omp.cpp
@@ -15,9 +15,9 @@
Contributing authors: Stephen Foiles (SNL), Murray Daw (SNL)
------------------------------------------------------------------------- */
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_eam_alloy_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_eam_fs_omp.cpp b/src/USER-OMP/pair_eam_fs_omp.cpp
index ec12bcefad..5a104fde6d 100644
--- a/src/USER-OMP/pair_eam_fs_omp.cpp
+++ b/src/USER-OMP/pair_eam_fs_omp.cpp
@@ -15,9 +15,9 @@
Contributing authors: Tim Lau (MIT)
------------------------------------------------------------------------- */
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_eam_fs_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_eam_omp.cpp b/src/USER-OMP/pair_eam_omp.cpp
index cff4daf5ea..6b4ac4363e 100644
--- a/src/USER-OMP/pair_eam_omp.cpp
+++ b/src/USER-OMP/pair_eam_omp.cpp
@@ -12,8 +12,8 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "string.h"
+#include <math.h>
+#include <string.h>
#include "pair_eam_omp.h"
#include "atom.h"
diff --git a/src/USER-OMP/pair_edip_omp.cpp b/src/USER-OMP/pair_edip_omp.cpp
index f86d8ebcbc..7c503ea8aa 100644
--- a/src/USER-OMP/pair_edip_omp.cpp
+++ b/src/USER-OMP/pair_edip_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_edip_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_eim_omp.cpp b/src/USER-OMP/pair_eim_omp.cpp
index 501c282f79..e98c035860 100644
--- a/src/USER-OMP/pair_eim_omp.cpp
+++ b/src/USER-OMP/pair_eim_omp.cpp
@@ -12,8 +12,8 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "string.h"
+#include <math.h>
+#include <string.h>
#include "pair_eim_omp.h"
#include "atom.h"
diff --git a/src/USER-OMP/pair_gauss_cut_omp.cpp b/src/USER-OMP/pair_gauss_cut_omp.cpp
index e80768d5af..ad0eb77963 100644
--- a/src/USER-OMP/pair_gauss_cut_omp.cpp
+++ b/src/USER-OMP/pair_gauss_cut_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_gauss_cut_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_gauss_omp.cpp b/src/USER-OMP/pair_gauss_omp.cpp
index 4d8b477465..062da924e3 100644
--- a/src/USER-OMP/pair_gauss_omp.cpp
+++ b/src/USER-OMP/pair_gauss_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_gauss_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_gayberne_omp.cpp b/src/USER-OMP/pair_gayberne_omp.cpp
index 031b1d4ddd..54e4496f22 100644
--- a/src/USER-OMP/pair_gayberne_omp.cpp
+++ b/src/USER-OMP/pair_gayberne_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_gayberne_omp.h"
#include "math_extra.h"
#include "atom.h"
diff --git a/src/USER-OMP/pair_gran_hertz_history_omp.cpp b/src/USER-OMP/pair_gran_hertz_history_omp.cpp
index d684fde19d..36873a4852 100644
--- a/src/USER-OMP/pair_gran_hertz_history_omp.cpp
+++ b/src/USER-OMP/pair_gran_hertz_history_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_gran_hertz_history_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_gran_hooke_history_omp.cpp b/src/USER-OMP/pair_gran_hooke_history_omp.cpp
index 3da16dea16..545d93cccb 100644
--- a/src/USER-OMP/pair_gran_hooke_history_omp.cpp
+++ b/src/USER-OMP/pair_gran_hooke_history_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_gran_hooke_history_omp.h"
#include "atom.h"
#include "comm.h"
@@ -23,7 +23,7 @@
#include "neigh_list.h"
#include "update.h"
-#include "string.h"
+#include <string.h>
#include "suffix.h"
using namespace LAMMPS_NS;
diff --git a/src/USER-OMP/pair_gran_hooke_omp.cpp b/src/USER-OMP/pair_gran_hooke_omp.cpp
index c4e792708f..3197b7076e 100644
--- a/src/USER-OMP/pair_gran_hooke_omp.cpp
+++ b/src/USER-OMP/pair_gran_hooke_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_gran_hooke_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp b/src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp
index 26c456c170..c22efffb5a 100644
--- a/src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp
+++ b/src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_hbond_dreiding_lj_omp.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp b/src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp
index 557852fb2d..7debe5a68a 100644
--- a/src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp
+++ b/src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_hbond_dreiding_morse_omp.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/USER-OMP/pair_line_lj_omp.cpp b/src/USER-OMP/pair_line_lj_omp.cpp
index 8a9cf0b0d2..144a9f04f2 100644
--- a/src/USER-OMP/pair_line_lj_omp.cpp
+++ b/src/USER-OMP/pair_line_lj_omp.cpp
@@ -15,7 +15,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_line_lj_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj96_cut_omp.cpp b/src/USER-OMP/pair_lj96_cut_omp.cpp
index 451d876a48..e502a93acf 100644
--- a/src/USER-OMP/pair_lj96_cut_omp.cpp
+++ b/src/USER-OMP/pair_lj96_cut_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_lj96_cut_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp b/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp
index b8f9d68807..1333ae2761 100644
--- a/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp
+++ b/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_lj_charmm_coul_charmm_implicit_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp b/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp
index 35f3867c9d..880fa40068 100644
--- a/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp
+++ b/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_lj_charmm_coul_charmm_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp b/src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp
index caaeb8f916..acbf61d9fd 100644
--- a/src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp
+++ b/src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_lj_charmm_coul_long_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.cpp b/src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.cpp
index a1ccbffab4..4953c89a4d 100644
--- a/src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.cpp
+++ b/src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_lj_charmm_coul_long_soft_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp b/src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp
index 2fcfe213a4..c603f0dd3a 100755
--- a/src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp
+++ b/src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_lj_charmm_coul_msm_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp b/src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp
index 1ba825ab8e..98c2b0d578 100644
--- a/src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp
+++ b/src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_lj_class2_coul_cut_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_class2_coul_long_omp.cpp b/src/USER-OMP/pair_lj_class2_coul_long_omp.cpp
index 6b535a59a5..3038332c90 100644
--- a/src/USER-OMP/pair_lj_class2_coul_long_omp.cpp
+++ b/src/USER-OMP/pair_lj_class2_coul_long_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_lj_class2_coul_long_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_class2_omp.cpp b/src/USER-OMP/pair_lj_class2_omp.cpp
index 8c920ab9a8..ffb0ceaa0a 100644
--- a/src/USER-OMP/pair_lj_class2_omp.cpp
+++ b/src/USER-OMP/pair_lj_class2_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_lj_class2_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_cubic_omp.cpp b/src/USER-OMP/pair_lj_cubic_omp.cpp
index 2caf4620a3..1cea0f454a 100644
--- a/src/USER-OMP/pair_lj_cubic_omp.cpp
+++ b/src/USER-OMP/pair_lj_cubic_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_lj_cubic_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp
index 49c7ba128b..1f48b4245e 100644
--- a/src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp
+++ b/src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_lj_cut_coul_cut_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.cpp
index f6db06a51c..f6ba7236a0 100644
--- a/src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.cpp
+++ b/src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_lj_cut_coul_cut_soft_omp.h"
#include "atom.h"
#include "comm.h"
@@ -136,7 +136,7 @@ void PairLJCutCoulCutSoftOMP::eval(int iifrom, int iito, ThrData * const thr)
if (rsq < cut_ljsq[itype][jtype]) {
r4sig6 = rsq*rsq / lj2[itype][jtype];
denlj = lj3[itype][jtype] + rsq*r4sig6;
- forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
+ forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
(48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj));
} else forcelj = 0.0;
@@ -156,7 +156,7 @@ void PairLJCutCoulCutSoftOMP::eval(int iifrom, int iito, ThrData * const thr)
ecoul = factor_coul * qqrd2e * lj1[itype][jtype] * qtmp*q[j] / denc;
else ecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
- evdwl = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
+ evdwl = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
(1.0/(denlj*denlj) - 1.0/denlj) - offset[itype][jtype];
evdwl *= factor_lj;
} else evdwl = 0.0;
diff --git a/src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp
index 405755ecbb..9fc64cf38c 100644
--- a/src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp
+++ b/src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_lj_cut_coul_debye_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_cut_coul_dsf_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_dsf_omp.cpp
index f33ea97e9c..d0b6c1b2dc 100644
--- a/src/USER-OMP/pair_lj_cut_coul_dsf_omp.cpp
+++ b/src/USER-OMP/pair_lj_cut_coul_dsf_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_lj_cut_coul_dsf_omp.h"
#include "atom.h"
#include "comm.h"
@@ -155,7 +155,7 @@ void PairLJCutCoulDSFOMP::eval(int iifrom, int iito, ThrData * const thr)
erfcd = exp(-alpha*alpha*r*r);
t = 1.0 / (1.0 + EWALD_P*alpha*r);
erfcc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * erfcd;
- forcecoul = prefactor * (erfcc/r + 2.0*alpha/MY_PIS * erfcd +
+ forcecoul = prefactor * (erfcc/r + 2.0*alpha/MY_PIS * erfcd +
r*f_shift) * r;
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
} else forcecoul = 0.0;
diff --git a/src/USER-OMP/pair_lj_cut_coul_long_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_long_omp.cpp
index 842b84270c..6746cf9701 100644
--- a/src/USER-OMP/pair_lj_cut_coul_long_omp.cpp
+++ b/src/USER-OMP/pair_lj_cut_coul_long_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_lj_cut_coul_long_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_cut_coul_long_soft_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_long_soft_omp.cpp
index cdfd4a4c2d..5f0a3d57c4 100644
--- a/src/USER-OMP/pair_lj_cut_coul_long_soft_omp.cpp
+++ b/src/USER-OMP/pair_lj_cut_coul_long_soft_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_lj_cut_coul_long_soft_omp.h"
#include "atom.h"
#include "comm.h"
@@ -144,10 +144,10 @@ void PairLJCutCoulLongSoftOMP::eval(int iifrom, int iito, ThrData * const thr)
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
-
+
denc = sqrt(lj4[itype][jtype] + rsq);
prefactor = qqrd2e * lj1[itype][jtype] * qtmp*q[j] / (denc*denc*denc);
-
+
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
} else forcecoul = 0.0;
@@ -155,7 +155,7 @@ void PairLJCutCoulLongSoftOMP::eval(int iifrom, int iito, ThrData * const thr)
if (rsq < cut_ljsq[itype][jtype]) {
r4sig6 = rsq*rsq / lj2[itype][jtype];
denlj = lj3[itype][jtype] + rsq*r4sig6;
- forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
+ forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
(48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj));
} else forcelj = 0.0;
@@ -178,7 +178,7 @@ void PairLJCutCoulLongSoftOMP::eval(int iifrom, int iito, ThrData * const thr)
} else ecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
- evdwl = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
+ evdwl = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
(1.0/(denlj*denlj) - 1.0/denlj) - offset[itype][jtype];
evdwl *= factor_lj;
} else evdwl = 0.0;
diff --git a/src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp
index 4b53b7784b..fba8f552db 100755
--- a/src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp
+++ b/src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_lj_cut_coul_msm_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp b/src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp
index 8c22961c1e..d9fd7ac72e 100755
--- a/src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp
+++ b/src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_lj_cut_dipole_cut_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_cut_omp.cpp b/src/USER-OMP/pair_lj_cut_omp.cpp
index 5804e41119..34754975fb 100644
--- a/src/USER-OMP/pair_lj_cut_omp.cpp
+++ b/src/USER-OMP/pair_lj_cut_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_lj_cut_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_cut_soft_omp.cpp b/src/USER-OMP/pair_lj_cut_soft_omp.cpp
index 92f0cc339f..9147b9aa1c 100644
--- a/src/USER-OMP/pair_lj_cut_soft_omp.cpp
+++ b/src/USER-OMP/pair_lj_cut_soft_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_lj_cut_soft_omp.h"
#include "atom.h"
#include "comm.h"
@@ -126,7 +126,7 @@ void PairLJCutSoftOMP::eval(int iifrom, int iito, ThrData * const thr)
r4sig6 = rsq*rsq / lj2i[jtype];
denlj = lj3i[jtype] + rsq*r4sig6;
- forcelj = lj1i[jtype] * epsi[jtype] *
+ forcelj = lj1i[jtype] * epsi[jtype] *
(48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj));
fpair = factor_lj*forcelj;
@@ -141,7 +141,7 @@ void PairLJCutSoftOMP::eval(int iifrom, int iito, ThrData * const thr)
}
if (EFLAG) {
- evdwl = lj1i[jtype] * 4.0 * epsi[jtype] *
+ evdwl = lj1i[jtype] * 4.0 * epsi[jtype] *
(1.0/(denlj*denlj) - 1.0/denlj) - offseti[jtype];
evdwl *= factor_lj;
}
diff --git a/src/USER-OMP/pair_lj_cut_tip4p_cut_omp.cpp b/src/USER-OMP/pair_lj_cut_tip4p_cut_omp.cpp
index 5bc0165120..3b028fb67b 100644
--- a/src/USER-OMP/pair_lj_cut_tip4p_cut_omp.cpp
+++ b/src/USER-OMP/pair_lj_cut_tip4p_cut_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_lj_cut_tip4p_cut_omp.h"
#include "atom.h"
#include "domain.h"
diff --git a/src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp b/src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp
index 3646c0a2e8..70be3e5228 100644
--- a/src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp
+++ b/src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_lj_cut_tip4p_long_omp.h"
#include "atom.h"
#include "domain.h"
diff --git a/src/USER-OMP/pair_lj_cut_tip4p_long_soft_omp.cpp b/src/USER-OMP/pair_lj_cut_tip4p_long_soft_omp.cpp
index 047b42775d..2d4be0d884 100644
--- a/src/USER-OMP/pair_lj_cut_tip4p_long_soft_omp.cpp
+++ b/src/USER-OMP/pair_lj_cut_tip4p_long_soft_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_lj_cut_tip4p_long_soft_omp.h"
#include "atom.h"
#include "domain.h"
@@ -218,7 +218,7 @@ void PairLJCutTIP4PLongSoftOMP::eval(int iifrom, int iito, ThrData * const thr)
r4sig6 = rsq*rsq / lj2[itype][jtype];
denlj = lj3[itype][jtype] + rsq*r4sig6;
- forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
+ forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
(48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj));
forcelj *= factor_lj;
@@ -231,7 +231,7 @@ void PairLJCutTIP4PLongSoftOMP::eval(int iifrom, int iito, ThrData * const thr)
f[j].z -= delz*forcelj;
if (EFLAG) {
- evdwl = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
+ evdwl = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
(1.0/(denlj*denlj) - 1.0/denlj) - offset[itype][jtype];
evdwl *= factor_lj;
} else evdwl = 0.0;
diff --git a/src/USER-OMP/pair_lj_expand_omp.cpp b/src/USER-OMP/pair_lj_expand_omp.cpp
index 187cc5f78d..e0f64e471e 100644
--- a/src/USER-OMP/pair_lj_expand_omp.cpp
+++ b/src/USER-OMP/pair_lj_expand_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_lj_expand_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp b/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp
index 3e3fbbc9dd..954fbe7cce 100644
--- a/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp
+++ b/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_lj_gromacs_coul_gromacs_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_gromacs_omp.cpp b/src/USER-OMP/pair_lj_gromacs_omp.cpp
index 618e20ab66..84c46886e1 100644
--- a/src/USER-OMP/pair_lj_gromacs_omp.cpp
+++ b/src/USER-OMP/pair_lj_gromacs_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_lj_gromacs_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_long_coul_long_omp.cpp b/src/USER-OMP/pair_lj_long_coul_long_omp.cpp
index 23a2bc3cc4..28d4f229c8 100644
--- a/src/USER-OMP/pair_lj_long_coul_long_omp.cpp
+++ b/src/USER-OMP/pair_lj_long_coul_long_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_lj_long_coul_long_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp b/src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp
index 4c86ce7d33..f04e6380c8 100644
--- a/src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp
+++ b/src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_lj_long_tip4p_long_omp.h"
#include "atom.h"
#include "comm.h"
@@ -1158,7 +1158,7 @@ void PairLJLongTIP4PLongOMP::eval_inner(int iifrom, int iito, ThrData * const th
jtype = type[j];
if (rsq < cut_ljsq[itype][jtype] && rsq < cut_out_off_sq ) { // lj
- r2inv = 1.0/rsq;
+ r2inv = 1.0/rsq;
register double rn = r2inv*r2inv*r2inv;
if (ni == 0) forcelj = rn*(rn*lj1i[jtype]-lj2i[jtype]);
else { // special case
@@ -1397,7 +1397,7 @@ void PairLJLongTIP4PLongOMP::eval_middle(int iifrom, int iito, ThrData * const t
jtype = type[j];
if (rsq < cut_ljsq[itype][jtype] && rsq >= cut_in_off_sq && rsq <= cut_out_off_sq ) { // lj
- r2inv = 1.0/rsq;
+ r2inv = 1.0/rsq;
register double rn = r2inv*r2inv*r2inv;
if (ni == 0) forcelj = rn*(rn*lj1i[jtype]-lj2i[jtype]);
else { // special case
diff --git a/src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp b/src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp
index c86a1f6c0e..f388009bd8 100644
--- a/src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp
+++ b/src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_lj_sdk_coul_long_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_sdk_coul_msm_omp.cpp b/src/USER-OMP/pair_lj_sdk_coul_msm_omp.cpp
index 95013932e8..9d991d5812 100644
--- a/src/USER-OMP/pair_lj_sdk_coul_msm_omp.cpp
+++ b/src/USER-OMP/pair_lj_sdk_coul_msm_omp.cpp
@@ -13,7 +13,7 @@
This style is a simplified re-implementation of the CG/CMM pair style
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_lj_sdk_coul_msm_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_sdk_omp.cpp b/src/USER-OMP/pair_lj_sdk_omp.cpp
index ca32528ee0..36e170046d 100644
--- a/src/USER-OMP/pair_lj_sdk_omp.cpp
+++ b/src/USER-OMP/pair_lj_sdk_omp.cpp
@@ -13,7 +13,7 @@
This style is a simplified re-implementation of the CG/CMM pair style
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_lj_sdk_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp b/src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp
index 572c775467..67afbbeefe 100755
--- a/src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp
+++ b/src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_lj_sf_dipole_sf_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_sf_omp.cpp b/src/USER-OMP/pair_lj_sf_omp.cpp
index c1bdbcc93e..bd9d5220b8 100644
--- a/src/USER-OMP/pair_lj_sf_omp.cpp
+++ b/src/USER-OMP/pair_lj_sf_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_lj_sf_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_smooth_linear_omp.cpp b/src/USER-OMP/pair_lj_smooth_linear_omp.cpp
index 6ad61b0dbf..9017ac740f 100644
--- a/src/USER-OMP/pair_lj_smooth_linear_omp.cpp
+++ b/src/USER-OMP/pair_lj_smooth_linear_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_lj_smooth_linear_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_smooth_omp.cpp b/src/USER-OMP/pair_lj_smooth_omp.cpp
index d2eee11102..9bf15035bd 100644
--- a/src/USER-OMP/pair_lj_smooth_omp.cpp
+++ b/src/USER-OMP/pair_lj_smooth_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_lj_smooth_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lubricate_omp.cpp b/src/USER-OMP/pair_lubricate_omp.cpp
index 3da80c8c5a..1c622f5641 100644
--- a/src/USER-OMP/pair_lubricate_omp.cpp
+++ b/src/USER-OMP/pair_lubricate_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_lubricate_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lubricate_poly_omp.cpp b/src/USER-OMP/pair_lubricate_poly_omp.cpp
index abe27b7434..f2e873ea45 100644
--- a/src/USER-OMP/pair_lubricate_poly_omp.cpp
+++ b/src/USER-OMP/pair_lubricate_poly_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_lubricate_poly_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_meam_spline_omp.cpp b/src/USER-OMP/pair_meam_spline_omp.cpp
index ebe576e59b..98e1541319 100644
--- a/src/USER-OMP/pair_meam_spline_omp.cpp
+++ b/src/USER-OMP/pair_meam_spline_omp.cpp
@@ -12,8 +12,8 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "string.h"
+#include <math.h>
+#include <string.h>
#include "pair_meam_spline_omp.h"
#include "atom.h"
diff --git a/src/USER-OMP/pair_morse_omp.cpp b/src/USER-OMP/pair_morse_omp.cpp
index b27829d897..8aca4ef98f 100644
--- a/src/USER-OMP/pair_morse_omp.cpp
+++ b/src/USER-OMP/pair_morse_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_morse_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_nb3b_harmonic_omp.cpp b/src/USER-OMP/pair_nb3b_harmonic_omp.cpp
index d86d1eadf5..199cbc9337 100644
--- a/src/USER-OMP/pair_nb3b_harmonic_omp.cpp
+++ b/src/USER-OMP/pair_nb3b_harmonic_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_nb3b_harmonic_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_nm_cut_coul_cut_omp.cpp b/src/USER-OMP/pair_nm_cut_coul_cut_omp.cpp
index f4fa780c60..38af84d1f7 100644
--- a/src/USER-OMP/pair_nm_cut_coul_cut_omp.cpp
+++ b/src/USER-OMP/pair_nm_cut_coul_cut_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_nm_cut_coul_cut_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_nm_cut_coul_long_omp.cpp b/src/USER-OMP/pair_nm_cut_coul_long_omp.cpp
index c5e7ebd621..bbcdfb26c3 100644
--- a/src/USER-OMP/pair_nm_cut_coul_long_omp.cpp
+++ b/src/USER-OMP/pair_nm_cut_coul_long_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_nm_cut_coul_long_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_nm_cut_omp.cpp b/src/USER-OMP/pair_nm_cut_omp.cpp
index a988633acf..ea2d0fa7f5 100644
--- a/src/USER-OMP/pair_nm_cut_omp.cpp
+++ b/src/USER-OMP/pair_nm_cut_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_nm_cut_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_peri_lps_omp.cpp b/src/USER-OMP/pair_peri_lps_omp.cpp
index 92b7037127..4876e6b15f 100644
--- a/src/USER-OMP/pair_peri_lps_omp.cpp
+++ b/src/USER-OMP/pair_peri_lps_omp.cpp
@@ -12,8 +12,8 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "float.h"
+#include <math.h>
+#include <float.h>
#include "pair_peri_lps_omp.h"
#include "fix.h"
#include "fix_peri_neigh.h"
diff --git a/src/USER-OMP/pair_peri_pmb_omp.cpp b/src/USER-OMP/pair_peri_pmb_omp.cpp
index 8895b3ba6c..1c14ff753c 100644
--- a/src/USER-OMP/pair_peri_pmb_omp.cpp
+++ b/src/USER-OMP/pair_peri_pmb_omp.cpp
@@ -12,8 +12,8 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "float.h"
+#include <math.h>
+#include <float.h>
#include "pair_peri_pmb_omp.h"
#include "fix.h"
#include "fix_peri_neigh.h"
diff --git a/src/USER-OMP/pair_resquared_omp.cpp b/src/USER-OMP/pair_resquared_omp.cpp
index c38070304d..a1364133d0 100644
--- a/src/USER-OMP/pair_resquared_omp.cpp
+++ b/src/USER-OMP/pair_resquared_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_resquared_omp.h"
#include "math_extra.h"
#include "atom.h"
diff --git a/src/USER-OMP/pair_soft_omp.cpp b/src/USER-OMP/pair_soft_omp.cpp
index 51cac9106b..9a926652a8 100644
--- a/src/USER-OMP/pair_soft_omp.cpp
+++ b/src/USER-OMP/pair_soft_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_soft_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_sw_omp.cpp b/src/USER-OMP/pair_sw_omp.cpp
index d9547d0bd7..ba7eeacae1 100644
--- a/src/USER-OMP/pair_sw_omp.cpp
+++ b/src/USER-OMP/pair_sw_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_sw_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_table_omp.cpp b/src/USER-OMP/pair_table_omp.cpp
index f8c6a9f186..d584061648 100644
--- a/src/USER-OMP/pair_table_omp.cpp
+++ b/src/USER-OMP/pair_table_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_table_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_tersoff_mod_omp.cpp b/src/USER-OMP/pair_tersoff_mod_omp.cpp
index 907bb9e078..403a61147b 100644
--- a/src/USER-OMP/pair_tersoff_mod_omp.cpp
+++ b/src/USER-OMP/pair_tersoff_mod_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_tersoff_mod_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_tersoff_omp.cpp b/src/USER-OMP/pair_tersoff_omp.cpp
index ff0f41b282..71d00108df 100644
--- a/src/USER-OMP/pair_tersoff_omp.cpp
+++ b/src/USER-OMP/pair_tersoff_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_tersoff_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_tersoff_table_omp.cpp b/src/USER-OMP/pair_tersoff_table_omp.cpp
index ece331abd9..9de9ee5708 100644
--- a/src/USER-OMP/pair_tersoff_table_omp.cpp
+++ b/src/USER-OMP/pair_tersoff_table_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_tersoff_table_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_tersoff_zbl_omp.cpp b/src/USER-OMP/pair_tersoff_zbl_omp.cpp
index b92378d50d..f5c08741ce 100644
--- a/src/USER-OMP/pair_tersoff_zbl_omp.cpp
+++ b/src/USER-OMP/pair_tersoff_zbl_omp.cpp
@@ -16,10 +16,10 @@
David Farrell (NWU) - ZBL addition
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_tersoff_zbl_omp.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-OMP/pair_tip4p_cut_omp.cpp b/src/USER-OMP/pair_tip4p_cut_omp.cpp
index 72c582acb8..2b125fde7f 100644
--- a/src/USER-OMP/pair_tip4p_cut_omp.cpp
+++ b/src/USER-OMP/pair_tip4p_cut_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_tip4p_cut_omp.h"
#include "atom.h"
#include "domain.h"
diff --git a/src/USER-OMP/pair_tip4p_long_omp.cpp b/src/USER-OMP/pair_tip4p_long_omp.cpp
index 3476ed5928..96ebc64a90 100644
--- a/src/USER-OMP/pair_tip4p_long_omp.cpp
+++ b/src/USER-OMP/pair_tip4p_long_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_tip4p_long_omp.h"
#include "atom.h"
#include "domain.h"
diff --git a/src/USER-OMP/pair_tip4p_long_soft_omp.cpp b/src/USER-OMP/pair_tip4p_long_soft_omp.cpp
index f693e0a06a..ac3bcfc393 100644
--- a/src/USER-OMP/pair_tip4p_long_soft_omp.cpp
+++ b/src/USER-OMP/pair_tip4p_long_soft_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_tip4p_long_soft_omp.h"
#include "atom.h"
#include "domain.h"
@@ -260,7 +260,7 @@ void PairTIP4PLongSoftOMP::eval(int iifrom, int iito, ThrData * const thr)
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
denc = sqrt(lam2[itype][jtype] + rsq);
- prefactor = qqrd2e * lam1[itype][jtype]
+ prefactor = qqrd2e * lam1[itype][jtype]
* qtmp*q[j] / (denc*denc*denc);
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
diff --git a/src/USER-OMP/pair_tri_lj_omp.cpp b/src/USER-OMP/pair_tri_lj_omp.cpp
index 3e1e1fe93f..94b84316bd 100644
--- a/src/USER-OMP/pair_tri_lj_omp.cpp
+++ b/src/USER-OMP/pair_tri_lj_omp.cpp
@@ -15,7 +15,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_tri_lj_omp.h"
#include "math_extra.h"
#include "atom.h"
diff --git a/src/USER-OMP/pair_vashishta_omp.cpp b/src/USER-OMP/pair_vashishta_omp.cpp
index f89b2ad184..679eceab50 100644
--- a/src/USER-OMP/pair_vashishta_omp.cpp
+++ b/src/USER-OMP/pair_vashishta_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_vashishta_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_yukawa_colloid_omp.cpp b/src/USER-OMP/pair_yukawa_colloid_omp.cpp
index c3c73fab58..cc05fc9155 100644
--- a/src/USER-OMP/pair_yukawa_colloid_omp.cpp
+++ b/src/USER-OMP/pair_yukawa_colloid_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_yukawa_colloid_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_yukawa_omp.cpp b/src/USER-OMP/pair_yukawa_omp.cpp
index 9bb0dea9c3..c705446f05 100644
--- a/src/USER-OMP/pair_yukawa_omp.cpp
+++ b/src/USER-OMP/pair_yukawa_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_yukawa_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_zbl_omp.cpp b/src/USER-OMP/pair_zbl_omp.cpp
index 281ee52acb..1d69487eb2 100644
--- a/src/USER-OMP/pair_zbl_omp.cpp
+++ b/src/USER-OMP/pair_zbl_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_zbl_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/respa_omp.cpp b/src/USER-OMP/respa_omp.cpp
index e3e425a77f..d925088eda 100644
--- a/src/USER-OMP/respa_omp.cpp
+++ b/src/USER-OMP/respa_omp.cpp
@@ -15,8 +15,8 @@
Contributing authors: Mark Stevens (SNL), Paul Crozier (SNL)
------------------------------------------------------------------------- */
-#include "stdlib.h"
-#include "string.h"
+#include <stdlib.h>
+#include <string.h>
#include "respa_omp.h"
#include "neighbor.h"
#include "domain.h"
diff --git a/src/USER-PHONON/fix_phonon.cpp b/src/USER-PHONON/fix_phonon.cpp
index b0d09c146f..db20eab300 100644
--- a/src/USER-PHONON/fix_phonon.cpp
+++ b/src/USER-PHONON/fix_phonon.cpp
@@ -23,7 +23,7 @@
konglt@sjtu.edu.cn; konglt@gmail.com
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "fix_phonon.h"
#include "atom.h"
#include "compute.h"
@@ -64,7 +64,7 @@ FixPhonon::FixPhonon(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
MPI_Comm_rank(world,&me);
MPI_Comm_size(world,&nprocs);
-
+
if (narg < 8) error->all(FLERR,"Illegal fix phonon command: number of arguments < 8");
nevery = force->inumeric(FLERR, arg[3]); // Calculate this fix every n steps!
@@ -85,7 +85,7 @@ FixPhonon::FixPhonon(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
strcpy(prefix, arg[7]);
logfile = new char[n+4];
sprintf(logfile,"%s.log",prefix);
-
+
int sdim = sysdim = domain->dimension;
int iarg = 8;
nasr = 20;
@@ -165,10 +165,10 @@ FixPhonon::FixPhonon(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
memory->create(RIloc,ngroup,(sysdim+1),"fix_phonon:RIloc");
memory->create(RIall,ngroup,(sysdim+1),"fix_phonon:RIall");
memory->create(Rsort,ngroup, sysdim, "fix_phonon:Rsort");
-
+
memory->create(Rnow, MAX(1,mynpt),fft_dim,"fix_phonon:Rnow");
memory->create(Rsum, MAX(1,mynpt),fft_dim,"fix_phonon:Rsum");
-
+
memory->create(basis,nucell, sysdim, "fix_phonon:basis");
// because of hermit, only nearly half of q points are stored
@@ -216,7 +216,7 @@ FixPhonon::FixPhonon(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
fflush(flog);
}
surf2tag.clear();
-
+
// default temperature is from thermo
TempSum = new double[sysdim];
id_temp = new char[12];
@@ -268,7 +268,7 @@ FixPhonon::~FixPhonon()
// destroy FFT
delete fft;
memory->sfree(fft_data);
-
+
// clear map info
tag2surf.clear();
surf2tag.clear();
@@ -346,7 +346,7 @@ void FixPhonon::end_of_step()
idx = tag2surf[itag];
domain->unmap(x[i], image[i], xcur);
-
+
for (idim = 0; idim < sysdim; ++idim) RIloc[nfind][idim] = xcur[idim];
RIloc[nfind++][sysdim] = double(idx);
}
@@ -540,13 +540,13 @@ void FixPhonon::readmap()
for (int i = 0; i < atom->nlocal; ++i){
if (atom->mask[i] & groupbit) tag_loc[nfind++] = atom->tag[i];
}
-
+
// gather IDs on local proc
displs[0] = 0;
for (int i = 0; i < nprocs; ++i) recvcnts[i] = 0;
MPI_Allgather(&nfind,1,MPI_INT,recvcnts,1,MPI_INT,world);
for (int i = 1; i < nprocs; ++i) displs[i] = displs[i-1] + recvcnts[i-1];
-
+
MPI_Allgatherv(tag_loc,nfind,MPI_LMP_TAGINT,tag_all,recvcnts,displs,MPI_INT,world);
for (int i = 0; i < ngroup; ++i){
itag = tag_all[i];
@@ -567,24 +567,24 @@ void FixPhonon::readmap()
error->all(FLERR,line);
}
- if (fgets(line,MAXLINE,fp) == NULL)
+ if (fgets(line,MAXLINE,fp) == NULL)
error->all(FLERR,"Error while reading header of mapping file!");
nx = force->inumeric(FLERR, strtok(line, " \n\t\r\f"));
ny = force->inumeric(FLERR, strtok(NULL, " \n\t\r\f"));
nz = force->inumeric(FLERR, strtok(NULL, " \n\t\r\f"));
nucell = force->inumeric(FLERR, strtok(NULL, " \n\t\r\f"));
ntotal = nx*ny*nz;
- if (ntotal*nucell != ngroup)
+ if (ntotal*nucell != ngroup)
error->all(FLERR,"FFT mesh and number of atoms in group mismatch!");
-
+
// second line of mapfile is comment
- if (fgets(line,MAXLINE,fp) == NULL)
+ if (fgets(line,MAXLINE,fp) == NULL)
error->all(FLERR,"Error while reading comment of mapping file!");
int ix, iy, iz, iu;
// the remaining lines carry the mapping info
for (int i = 0; i < ngroup; ++i){
- if (fgets(line,MAXLINE,fp) == NULL) {info = 1; break;}
+ if (fgets(line,MAXLINE,fp) == NULL) {info = 1; break;}
ix = force->inumeric(FLERR, strtok(line, " \n\t\r\f"));
iy = force->inumeric(FLERR, strtok(NULL, " \n\t\r\f"));
iz = force->inumeric(FLERR, strtok(NULL, " \n\t\r\f"));
@@ -592,7 +592,7 @@ void FixPhonon::readmap()
itag = force->inumeric(FLERR, strtok(NULL, " \n\t\r\f"));
// check if index is in correct range
- if (ix < 0 || ix >= nx || iy < 0 || iy >= ny ||
+ if (ix < 0 || ix >= nx || iy < 0 || iy >= ny ||
iz < 0 || iz >= nz || iu < 0 || iu >= nucell) {info = 2; break;}
// 1 <= itag <= natoms
if (itag < 1 || itag > static_cast<int>(atom->natoms)) {info = 3; break;}
@@ -602,11 +602,11 @@ void FixPhonon::readmap()
}
fclose(fp);
- if (tag2surf.size() != surf2tag.size() ||
+ if (tag2surf.size() != surf2tag.size() ||
tag2surf.size() != static_cast<std::size_t>(ngroup) )
error->all(FLERR,"The mapping is incomplete!");
if (info) error->all(FLERR,"Error while reading mapping file!");
-
+
// check the correctness of mapping
int *mask = atom->mask;
tagint *tag = atom->tag;
@@ -616,7 +616,7 @@ void FixPhonon::readmap()
if (mask[i] & groupbit){
itag = tag[i];
idx = tag2surf[itag];
- if (itag != surf2tag[idx])
+ if (itag != surf2tag[idx])
error->one(FLERR,"The mapping info read is incorrect!");
}
}
@@ -675,7 +675,7 @@ void FixPhonon::postprocess( )
TempAve += TempSum[idim]*TempFac;
}
TempAve /= sysdim*boltz;
-
+
for (idq = 0; idq < mynq; ++idq){
GaussJordan(fft_dim, Phi_q[idq]);
ndim =0;
@@ -688,7 +688,7 @@ void FixPhonon::postprocess( )
for (int i = 0; i < nprocs; ++i) recvcnts[i] = fft_cnts[i]*fft_dim*2;
for (int i = 1; i < nprocs; ++i) displs[i] = displs[i-1] + recvcnts[i-1];
MPI_Gatherv(Phi_q[0],mynq*fft_dim2*2,MPI_DOUBLE,Phi_all[0],recvcnts,displs,MPI_DOUBLE,0,world);
-
+
// to collect all basis info and averaged it on root
double basis_root[fft_dim];
if (fft_dim > sysdim) MPI_Reduce(&basis[1][0], &basis_root[sysdim], fft_dim-sysdim, MPI_DOUBLE, MPI_SUM, 0, world);
@@ -707,7 +707,7 @@ void FixPhonon::postprocess( )
basevec[7] = hsum[3] * inv_neval / double(nz);
basevec[6] = hsum[4] * inv_neval / double(nz);
basevec[3] = hsum[5] * inv_neval / double(ny);
-
+
// write binary file, in fact, it is the force constants matrix that is written
// Enforcement of ASR and the conversion of dynamical matrix is done in the postprocessing code
char fname[MAXLINE];
@@ -822,7 +822,7 @@ void FixPhonon::GaussJordan(int n, std::complex<double> *Mat)
indxc[i] = icol;
idr = icol*n+icol;
if (Mat[idr] == std::complex<double>(0.,0.)) error->one(FLERR,"Singular matrix in complex GaussJordan!");
-
+
pivinv = 1./ Mat[idr];
Mat[idr] = std::complex<double>(1.,0.);
idr = icol*n;
@@ -881,7 +881,7 @@ void FixPhonon::EnforceASR()
}
}
}
-
+
// symmetrize
for (int k = 0; k < nucell; ++k)
for (int kp = k; kp < nucell; ++kp){
diff --git a/src/USER-PHONON/fix_phonon.h b/src/USER-PHONON/fix_phonon.h
index f1a8af4812..432276eb8a 100644
--- a/src/USER-PHONON/fix_phonon.h
+++ b/src/USER-PHONON/fix_phonon.h
@@ -32,7 +32,7 @@ FixStyle(phonon,FixPhonon)
#define FIX_PHONON_H
#include "lmptype.h"
-#include "mpi.h"
+#include <mpi.h>
#ifdef FFT_SINGLE
typedef float FFT_SCALAR;
@@ -45,9 +45,9 @@ typedef double FFT_SCALAR;
#include <complex>
#include "fix.h"
#include <map>
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
namespace LAMMPS_NS {
@@ -75,7 +75,7 @@ class FixPhonon : public Fix {
int ngroup, nfind; // total number of atoms in group; total number of atoms on this proc
char *prefix, *logfile; // prefix of output file names
FILE *flog;
-
+
double *M_inv_sqrt;
class FFT3d *fft; // to do fft via the fft3d wraper
@@ -84,7 +84,7 @@ class FixPhonon : public Fix {
int *fft_cnts, *fft_disp;
int fft_dim, fft_dim2;
FFT_SCALAR *fft_data;
-
+
tagint itag; // index variables
int idx, idq; // more index variables
std::map<tagint,int> tag2surf; // Mapping info
diff --git a/src/USER-QMMM/fix_qmmm.cpp b/src/USER-QMMM/fix_qmmm.cpp
index 910481a758..08a7ded153 100644
--- a/src/USER-QMMM/fix_qmmm.cpp
+++ b/src/USER-QMMM/fix_qmmm.cpp
@@ -403,7 +403,7 @@ void FixQMMM::exchange_positions()
maxbuf = atom->nmax*size_one;
comm_buf = memory->smalloc(maxbuf,"qmmm:comm_buf");
}
- struct commdata *buf = static_cast<struct commdata *>(comm_buf);
+ struct commdata *buf = static_cast<struct commdata *>(comm_buf);
if (comm->me == 0) {
MPI_Status status;
@@ -498,7 +498,7 @@ void FixQMMM::exchange_forces()
if (qmmm_role == QMMM_ROLE_MASTER) {
MPI_Request req[2];
- struct commdata *buf = static_cast<struct commdata *>(comm_buf);
+ struct commdata *buf = static_cast<struct commdata *>(comm_buf);
if (comm->me == 0) {
// receive QM forces from QE
@@ -605,7 +605,7 @@ void FixQMMM::init()
memory->create(qm_force,3*num_qm,"qmmm:qm_force");
const char fmt[] = "Initializing QM/MM master with %d QM atoms\n";
-
+
if (screen) fprintf(screen,fmt,num_qm);
if (logfile) fprintf(logfile,fmt,num_qm);
@@ -613,7 +613,7 @@ void FixQMMM::init()
const char fm2[] = "Electrostatic coupling with %d atoms\n";
if (screen) fprintf(screen,fm2,num_mm);
if (logfile) fprintf(logfile,fm2,num_mm);
- }
+ }
} else if (qmmm_role == QMMM_ROLE_SLAVE) {
@@ -627,7 +627,7 @@ void FixQMMM::init()
memory->create(qm_force,3*num_qm,"qmmm:qm_force");
const char fmt[] = "Initializing QM/MM slave with %d QM atoms\n";
-
+
if (screen) fprintf(screen,fmt,num_qm);
if (logfile) fprintf(logfile,fmt,num_qm);
@@ -684,7 +684,7 @@ void FixQMMM::init()
qm_remap=taginthash_keys(qm_hash);
if (verbose > 1) {
- const char fmt[] = "qm_remap[%d]=" TAGINT_FORMAT
+ const char fmt[] = "qm_remap[%d]=" TAGINT_FORMAT
" qm_hash[" TAGINT_FORMAT "]=" TAGINT_FORMAT "\n";
// print hashtable and reverse mapping
for (i=0; i < num_qm; ++i) {
@@ -740,7 +740,7 @@ void FixQMMM::post_force(int vflag)
double FixQMMM::memory_usage(void)
{
double bytes;
-
+
bytes = sizeof(FixQMMM);
bytes += maxbuf;
bytes += 6*num_qm*sizeof(double);
diff --git a/src/USER-QTB/fix_qbmsst.cpp b/src/USER-QTB/fix_qbmsst.cpp
index 1e592d9c99..417e7ac87d 100644
--- a/src/USER-QTB/fix_qbmsst.cpp
+++ b/src/USER-QTB/fix_qbmsst.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -16,10 +16,10 @@
Implementation of the Multi-Scale Shock Method with quantum nuclear effects
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "math.h"
-#include "string.h"
-#include "stdlib.h"
+#include <mpi.h>
+#include <math.h>
+#include <string.h>
+#include <stdlib.h>
#include "fix_qbmsst.h"
#include "math_extra.h"
#include "atom.h"
@@ -52,7 +52,7 @@ FixQBMSST::FixQBMSST(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 5) error->all(FLERR,"Illegal fix qbmsst command");
-
+
if ( strcmp(arg[3],"x") == 0 )
direction = 0;
else if ( strcmp(arg[3],"y") == 0 )
@@ -62,10 +62,10 @@ FixQBMSST::FixQBMSST(LAMMPS *lmp, int narg, char **arg) :
else {
error->all(FLERR,"Illegal fix qbmsst command");
}
- velocity = atof(arg[4]);
+ velocity = atof(arg[4]);
if ( velocity < 0 )
error->all(FLERR,"Illegal fix qbmsst command");
-
+
// default parameters
global_freq = 1;
extscalar = 1;
@@ -86,7 +86,7 @@ FixQBMSST::FixQBMSST(LAMMPS *lmp, int narg, char **arg) :
p0_set = 0;
v0_set = 0;
e0_set = 0;
- tscale = 0.01;
+ tscale = 0.01;
t_period = 1.0;
fric_coef = 1/t_period;
seed = 880302;
@@ -160,7 +160,7 @@ FixQBMSST::FixQBMSST(LAMMPS *lmp, int narg, char **arg) :
// check for periodicity in controlled dimensions
if (domain->nonperiodic) error->all(FLERR,"Fix qbmsst requires a periodic box");
-
+
// comments
if (comm->me == 0) {
if (screen) {
@@ -168,18 +168,18 @@ FixQBMSST::FixQBMSST(LAMMPS *lmp, int narg, char **arg) :
if (direction == 0) fprintf(screen," Shock in x direction\n");
else if (direction == 1) fprintf(screen," Shock in y direction\n");
else if (direction == 2) fprintf(screen," Shock in z direction\n");
-
+
fprintf(screen," Cell mass-like parameter qmass (units of mass^2/length^4) = %12.5e\n", qmass);
fprintf(screen," Shock velocity = %12.5e\n", velocity);
fprintf(screen," Artificial viscosity (units of mass/length/time) = %12.5e\n", mu);
-
+
if (p0_set)
fprintf(screen," Initial pressure specified to be %12.5e\n", p0);
else fprintf(screen," Initial pressure calculated on first step\n");
if (v0_set)
fprintf(screen," Initial volume specified to be %12.5e\n", v0);
else fprintf(screen," Initial volume calculated on first step\n");
- if (e0_set)
+ if (e0_set)
fprintf(screen," Initial energy specified to be %12.5e\n", e0);
else fprintf(screen," Initial energy calculated on first step\n");
}
@@ -188,18 +188,18 @@ FixQBMSST::FixQBMSST(LAMMPS *lmp, int narg, char **arg) :
if (direction == 0) fprintf(logfile," Shock in x direction\n");
else if (direction == 1) fprintf(logfile," Shock in y direction\n");
else if (direction == 2) fprintf(logfile," Shock in z direction\n");
-
+
fprintf(logfile," Cell mass-like parameter qmass (units of mass^2/length^4) = %12.5e\n", qmass);
fprintf(logfile," Shock velocity = %12.5e\n", velocity);
fprintf(logfile," Artificial viscosity (units of mass/length/time) = %12.5e\n", mu);
-
- if (p0_set)
+
+ if (p0_set)
fprintf(logfile," Initial pressure specified to be %12.5e\n", p0);
else fprintf(logfile," Initial pressure calculated on first step\n");
- if (v0_set)
+ if (v0_set)
fprintf(logfile," Initial volume specified to be %12.5e\n", v0);
else fprintf(logfile," Initial volume calculated on first step\n");
- if (e0_set)
+ if (e0_set)
fprintf(logfile," Initial energy specified to be %12.5e\n", e0);
else fprintf(logfile," Initial energy calculated on first step\n");
}
@@ -249,7 +249,7 @@ FixQBMSST::FixQBMSST(LAMMPS *lmp, int narg, char **arg) :
modify->add_compute(3,newarg);
delete [] newarg;
peflag = 1;
-
+
// allocate qbmsst
temperature = NULL;
pressure = NULL;
@@ -264,7 +264,7 @@ FixQBMSST::FixQBMSST(LAMMPS *lmp, int narg, char **arg) :
random_array_1 = NULL;
random_array_2 = NULL;
fran = NULL;
-
+
// initialize Marsagxlia RNG with processor-unique seed
random = new RanMars(lmp,seed + comm->me);
@@ -358,13 +358,13 @@ void FixQBMSST::init()
// initiate the counter l and \mu
counter_l=0;
counter_mu=0;
-
+
// initiate qtb temperature
if (!qtb_set) {
t_current = t_init; qtb_set=1;
}
old_eavg = e0;
-
+
//set up the h time step for updating the random force \delta{}h=\frac{\pi}{\Omega_{max}}
if (int(1.0/(2*f_max*dtv)) == 0) {
if (comm->me == 0) printf ("Warning: Either f_max is too high or the time step is too big, setting f_max to be 1/timestep!\n");
@@ -383,8 +383,8 @@ void FixQBMSST::init()
// generate random number array with zero mean and variance equal 1/12.
int nlocal = atom->nlocal;
- for (int i = 0; i < nlocal; i++) {
- for (int m = 0; m < 2*N_f; m++) {
+ for (int i = 0; i < nlocal; i++) {
+ for (int m = 0; m < 2*N_f; m++) {
random_array_0[i][m] = random->uniform()-0.5;
random_array_1[i][m] = random->uniform()-0.5;
random_array_2[i][m] = random->uniform()-0.5;
@@ -422,7 +422,7 @@ void FixQBMSST::init()
}
/* ----------------------------------------------------------------------
- compute T,P before integrator starts
+ compute T,P before integrator starts
------------------------------------------------------------------------- */
void FixQBMSST::setup(int vflag)
{
@@ -440,7 +440,7 @@ void FixQBMSST::setup(int vflag)
if ( screen ) fprintf(screen,"Fix QBMSST v0 = %12.5e\n", v0);
if ( logfile ) fprintf(logfile,"Fix QBMSST v0 = %12.5e\n", v0);
}
- }
+ }
if ( p0_set == 0 ) {
p0 = p_current[direction];
@@ -467,10 +467,10 @@ void FixQBMSST::setup(int vflag)
temperature->compute_vector();
double *ke_tensor = temperature->vector;
double ke_temp = ke_tensor[0]+ke_tensor[1]+ke_tensor[2];
- if (ke_temp > 0.0 && tscale > 0.0 ) {
+ if (ke_temp > 0.0 && tscale > 0.0 ) {
// transfer energy from atom velocities to cell volume motion
- // to bias initial compression
+ // to bias initial compression
double **v = atom->v;
int *mask = atom->mask;
double sqrt_initial_temperature_scaling = sqrt(1.0-tscale);
@@ -497,7 +497,7 @@ void FixQBMSST::setup(int vflag)
}
}
}
- }
+ }
// trigger virial computation on next timestep
pressure->addstep(update->ntimestep+1);
@@ -505,7 +505,7 @@ void FixQBMSST::setup(int vflag)
}
/* ----------------------------------------------------------------------
- 1st half of Verlet update
+ 1st half of Verlet update
------------------------------------------------------------------------- */
void FixQBMSST::initial_integrate(int vflag)
{
@@ -513,7 +513,7 @@ void FixQBMSST::initial_integrate(int vflag)
sd = direction;
double p_qbmsst;// QBMSST driving pressure.
int i, k;
- double vol;
+ double vol;
int nlocal = atom->nlocal;
int *mask = atom->mask;
double **v = atom->v;
@@ -537,10 +537,10 @@ void FixQBMSST::initial_integrate(int vflag)
t_current -= dtv*fric_coef*eta*beta*(old_eavg-e0)/(3*ntotal*boltz);
old_eavg = 0;//clear old energy average
if (t_current < 0.0) t_current=0;
-
+
// load omega_H with calculated spectrum at a specific temperature (corrected spectrum), omega_H is the Fourier transformation of time_H
for (int k = 0; k < 2*N_f; k++) {
- double f_k=(k-N_f)/(2*N_f*h_timestep); //\omega_k=\frac{2\pi}{\delta{}h}\frac{k}{2N_f} for k from -N_f to N_f-1
+ double f_k=(k-N_f)/(2*N_f*h_timestep); //\omega_k=\frac{2\pi}{\delta{}h}\frac{k}{2N_f} for k from -N_f to N_f-1
if(k == N_f) {
omega_H[k]=sqrt(force->boltz * t_current);
} else {
@@ -551,7 +551,7 @@ void FixQBMSST::initial_integrate(int vflag)
}
// construct the signal filter H, filter has the unit of of sqrt(energy) \sqrt{2N_f}^{-1}H\left(t_n\right)
- for (int n = 0; n < 2*N_f; n++) {
+ for (int n = 0; n < 2*N_f; n++) {
time_H[n] = 0;
double t_n=(n-N_f);
for (int k = 0; k < 2*N_f; k++) {
@@ -561,22 +561,22 @@ void FixQBMSST::initial_integrate(int vflag)
time_H[n]/=(2.0*N_f);
}
}
-
+
//update the colored random force every alpha MD steps
if (counter_mu == 0) {
//propagate h_timestep ahead
for (int j = 0; j < nlocal; j++) {
-
+
//update random array
- for (int m = 0; m < 2*N_f-1; m++) {
+ for (int m = 0; m < 2*N_f-1; m++) {
random_array_0[j][m] = random_array_0[j][m+1];
- random_array_1[j][m] = random_array_1[j][m+1];
- random_array_2[j][m] = random_array_2[j][m+1];
+ random_array_1[j][m] = random_array_1[j][m+1];
+ random_array_2[j][m] = random_array_2[j][m+1];
}
- random_array_0[j][2*N_f-1] = random->uniform()-0.5;
+ random_array_0[j][2*N_f-1] = random->uniform()-0.5;
random_array_1[j][2*N_f-1] = random->uniform()-0.5;
random_array_2[j][2*N_f-1] = random->uniform()-0.5;
-
+
//reset random force
fran[j][0] = 0.0;
fran[j][1] = 0.0;
@@ -584,9 +584,9 @@ void FixQBMSST::initial_integrate(int vflag)
if (mask[j] & groupbit) {
double gamma3 = gfactor[type[j]];
- for (int m = 0; m < 2*N_f; m++) {
+ for (int m = 0; m < 2*N_f; m++) {
fran[j][0] += time_H[m] * random_array_0[j][2*N_f-m-1];
- fran[j][1] += time_H[m] * random_array_1[j][2*N_f-m-1];
+ fran[j][1] += time_H[m] * random_array_1[j][2*N_f-m-1];
fran[j][2] += time_H[m] * random_array_2[j][2*N_f-m-1];
}
fran[j][0] = fran[j][0]*gamma3;
@@ -601,11 +601,11 @@ void FixQBMSST::initial_integrate(int vflag)
counter_l = (counter_l + 1) % beta;
counter_mu = (counter_mu + 1) % alpha;
- // propagate the time derivative of
+ // propagate the time derivative of
// the volume 1/2 step at fixed vol, r, rdot.
p_qbmsst = nktv2p * mvv2e * velocity * velocity * total_mass *
( v0 - vol)/( v0 * v0);
- double A = total_mass * ( p_current[sd] - p0 - p_qbmsst ) /
+ double A = total_mass * ( p_current[sd] - p0 - p_qbmsst ) /
(qmass * nktv2p * mvv2e);
double B = total_mass * mu / ( qmass * vol );
@@ -616,21 +616,21 @@ void FixQBMSST::initial_integrate(int vflag)
// use taylor expansion to avoid singularity at B == 0.
if ( B * dthalf > 1.0e-06 ) {
- omega[sd] = ( omega[sd] + A * ( exp(B * dthalf) - 1.0 ) / B )
+ omega[sd] = ( omega[sd] + A * ( exp(B * dthalf) - 1.0 ) / B )
* exp(-B * dthalf);
} else {
omega[sd] = omega[sd] + (A - B * omega[sd]) * dthalf +
0.5 * (B * B * omega[sd] - A * B ) * dthalf * dthalf;
}
- // propagate velocity sum 1/2 step by
+ // propagate velocity sum 1/2 step by
// temporarily propagating the velocities.
velocity_sum = compute_vsum();
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
for ( k = 0; k < 3; k++ ) {
double C = (f[i][k] + fran[i][k])* force->ftm2v / mass[type[i]];// this term now has a random force part
- double D = mu * omega[sd] * omega[sd] /
+ double D = mu * omega[sd] * omega[sd] /
(velocity_sum * mass[type[i]] * vol ) - fric_coef;
old_velocity[i][k] = v[i][k];
if ( k == direction ) {
@@ -663,7 +663,7 @@ void FixQBMSST::initial_integrate(int vflag)
if (mask[i] & groupbit) {
for ( k = 0; k < 3; k++ ) {
double C = (f[i][k] + fran[i][k])* force->ftm2v / mass[type[i]];// this term now has a random force part
- double D = mu * omega[sd] * omega[sd] /
+ double D = mu * omega[sd] * omega[sd] /
(velocity_sum * mass[type[i]] * vol ) - fric_coef;
if ( k == direction ) {
@@ -695,7 +695,7 @@ void FixQBMSST::initial_integrate(int vflag)
x[i][2] += dtv * v[i][2];
}
}
-
+
// propagate the volume 1/2 step.
double vol2 = vol1 + omega[sd] * dthalf;
@@ -707,7 +707,7 @@ void FixQBMSST::initial_integrate(int vflag)
}
/* ----------------------------------------------------------------------
- 2nd half of Verlet update
+ 2nd half of Verlet update
------------------------------------------------------------------------- */
void FixQBMSST::final_integrate()
{
@@ -729,9 +729,9 @@ void FixQBMSST::final_integrate()
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
- for ( int k = 0; k < 3; k++ ) {
+ for ( int k = 0; k < 3; k++ ) {
double C = (f[i][k] + fran[i][k]) * force->ftm2v / mass[type[i]];// this term now has a random force part
- double D = mu * omega[sd] * omega[sd] /
+ double D = mu * omega[sd] * omega[sd] /
(velocity_sum * mass[type[i]] * vol ) - fric_coef;
if ( k == direction ) {
@@ -761,7 +761,7 @@ void FixQBMSST::final_integrate()
p_qbmsst = nktv2p * mvv2e * velocity * velocity * total_mass *
( v0 - vol )/( v0 * v0 );
- double A = total_mass * ( p_current[sd] - p0 - p_qbmsst ) /
+ double A = total_mass * ( p_current[sd] - p0 - p_qbmsst ) /
( qmass * nktv2p * mvv2e );
double B = total_mass * mu / ( qmass * vol );
@@ -774,12 +774,12 @@ void FixQBMSST::final_integrate()
// use taylor expansion to avoid singularity at B == 0.
if ( B * dthalf > 1.0e-06 ) {
- omega[sd] = ( omega[sd] + A *
+ omega[sd] = ( omega[sd] + A *
( exp(B * dthalf) - 1.0 ) / B ) * exp(-B * dthalf);
} else {
omega[sd] = omega[sd] + (A - B * omega[sd]) * dthalf +
0.5 * (B * B * omega[sd] - A * B ) * dthalf * dthalf;
- }
+ }
// calculate Lagrangian position of computational cell
@@ -849,13 +849,13 @@ void FixQBMSST::remap(int flag)
modify->fix[rfix[i]]->deform(1);
for (i = 0; i < n; i++) {
- v[i][direction] = v[i][direction] *
+ v[i][direction] = v[i][direction] *
dilation[direction];
}
}
/* ----------------------------------------------------------------------
- pack entire state of Fix into one write
+ pack entire state of Fix into one write
------------------------------------------------------------------------- */
void FixQBMSST::write_restart(FILE *fp)
{
@@ -874,7 +874,7 @@ void FixQBMSST::write_restart(FILE *fp)
}
/* ----------------------------------------------------------------------
- use state info from restart file to restart the Fix
+ use state info from restart file to restart the Fix
------------------------------------------------------------------------- */
void FixQBMSST::restart(char *buf)
{
@@ -958,7 +958,7 @@ double FixQBMSST::compute_scalar()
i = direction;
energy = qmass * omega[i] * omega[i] / (2.0 * total_mass) * mvv2e;
- energy -= 0.5 * total_mass * velocity * velocity *
+ energy -= 0.5 * total_mass * velocity * velocity *
(1.0 - volume/ v0) *
(1.0 - volume/ v0) * mvv2e;
energy -= p0 * ( v0 - volume ) / nktv2p;
@@ -967,7 +967,7 @@ double FixQBMSST::compute_scalar()
}
/* ----------------------------------------------------------------------
- return a single element from the following vector,
+ return a single element from the following vector,
[dhug,dray,lgr_vel,lgr_pos,T_qm]
------------------------------------------------------------------------- */
double FixQBMSST::compute_vector(int n)
@@ -987,31 +987,31 @@ double FixQBMSST::compute_vector(int n)
}
/* ----------------------------------------------------------------------
- Computes the deviation of the current point
+ Computes the deviation of the current point
from the Hugoniot in Kelvin for the QBMSST.
------------------------------------------------------------------------- */
double FixQBMSST::compute_hugoniot()
{
double v, e, p;
double dhugo;
-
+
e = compute_etotal();
-
+
temperature->compute_vector();
pressure->compute_vector();
p = pressure->vector[direction];
-
+
v = compute_vol();
-
- dhugo = (0.5 * (p + p0 ) * ( v0 - v)) /
+
+ dhugo = (0.5 * (p + p0 ) * ( v0 - v)) /
force->nktv2p + e0 - e;
dhugo /= temperature->dof * force->boltz;
-
+
return dhugo;
}
/* ----------------------------------------------------------------------
- Computes the deviation of the current point from the Rayleigh
+ Computes the deviation of the current point from the Rayleigh
in pressure units for the QBMSST.
------------------------------------------------------------------------- */
double FixQBMSST::compute_rayleigh()
@@ -1033,7 +1033,7 @@ double FixQBMSST::compute_rayleigh()
}
/* ----------------------------------------------------------------------
- Computes the speed of the QBMSST computational cell in the
+ Computes the speed of the QBMSST computational cell in the
unshocked material rest-frame
------------------------------------------------------------------------- */
double FixQBMSST::compute_lagrangian_speed()
@@ -1043,7 +1043,7 @@ double FixQBMSST::compute_lagrangian_speed()
}
/* ----------------------------------------------------------------------
- Computes the distance behind the
+ Computes the distance behind the
shock front of the QBMSST computational cell.
------------------------------------------------------------------------- */
double FixQBMSST::compute_lagrangian_position()
@@ -1052,14 +1052,14 @@ double FixQBMSST::compute_lagrangian_position()
}
/* ----------------------------------------------------------------------
- Computes the atomic kinetic + atomic potential energy. This excludes the QBMSST
- external potential terms in the QBMSST Lagrangian.
+ Computes the atomic kinetic + atomic potential energy. This excludes the QBMSST
+ external potential terms in the QBMSST Lagrangian.
------------------------------------------------------------------------- */
double FixQBMSST::compute_etotal()
{
double epot,ekin,etot;
epot = pe->compute_scalar();
- if (thermo_energy) epot -= compute_scalar();
+ if (thermo_energy) epot -= compute_scalar();
ekin = temperature->compute_scalar();
ekin *= 0.5 * temperature->dof * force->boltz;
etot = epot+ekin;
@@ -1067,13 +1067,13 @@ double FixQBMSST::compute_etotal()
}
/* ----------------------------------------------------------------------
- Computes the atomic kinetic + atomic potential energy + QBMSST external potential.
+ Computes the atomic kinetic + atomic potential energy + QBMSST external potential.
------------------------------------------------------------------------- */
double FixQBMSST::compute_egrand()
{
double epot,ekin,etot;
epot = pe->compute_scalar();
- if (!thermo_energy) epot += compute_scalar();
+ if (!thermo_energy) epot += compute_scalar();
ekin = temperature->compute_scalar();
ekin *= 0.5 * temperature->dof * force->boltz;
etot = epot+ekin;
@@ -1081,8 +1081,8 @@ double FixQBMSST::compute_egrand()
}
/* ----------------------------------------------------------------------
- Computes the atomic kinetic + atomic potential energy. This excludes the QBMSST
- external potential terms in the QBMSST Lagrangian.
+ Computes the atomic kinetic + atomic potential energy. This excludes the QBMSST
+ external potential terms in the QBMSST Lagrangian.
------------------------------------------------------------------------- */
double FixQBMSST::compute_vol()
{
@@ -1106,8 +1106,8 @@ void FixQBMSST::check_alloc(int n)
}
/* ----------------------------------------------------------------------
- Computes the atomic kinetic + atomic potential energy. This excludes the QBMSST
- external potential terms in the QBMSST Lagrangian.
+ Computes the atomic kinetic + atomic potential energy. This excludes the QBMSST
+ external potential terms in the QBMSST Lagrangian.
------------------------------------------------------------------------- */
double FixQBMSST::compute_vsum()
{
@@ -1164,7 +1164,7 @@ void FixQBMSST::copy_arrays(int i, int j, int delflag)
random_array_1[j][m] = random_array_1[i][m];
random_array_2[j][m] = random_array_2[i][m];
}
-
+
for (int m = 0; m < 3; m++)
fran[j][m] = fran[i][m];
}
diff --git a/src/USER-QTB/fix_qbmsst.h b/src/USER-QTB/fix_qbmsst.h
index a170ae96af..0ed210c995 100644
--- a/src/USER-QTB/fix_qbmsst.h
+++ b/src/USER-QTB/fix_qbmsst.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -69,7 +69,7 @@ class FixQBMSST : public Fix {
double dthalf; // half step size
bigint ntotal; // atom->natoms
double boltz,nktv2p, mvv2e; // Boltzmann factor and unit conversions
- class Compute *temperature; // Computes created to evaluate
+ class Compute *temperature; // Computes created to evaluate
class Compute *pressure; // thermodynamic quantities.
class Compute *pe;
double **old_velocity; // Saved velocities.
@@ -81,7 +81,7 @@ class FixQBMSST : public Fix {
int nrigid; // number of rigid fixes
int *rfix; // indices of rigid fixes
double p_current[3]; // pressure
- double velocity_sum; // Sum of the velocities squared.
+ double velocity_sum; // Sum of the velocities squared.
double lagrangian_position; // Lagrangian location of computational cell
// qbmsst parameters
@@ -104,7 +104,7 @@ class FixQBMSST : public Fix {
double **fran; // random forces
double old_eavg; // average previous energies
- // functions
+ // functions
void couple();
void remap(int);
void check_alloc(int n);
diff --git a/src/USER-QTB/fix_qtb.cpp b/src/USER-QTB/fix_qtb.cpp
index 0962bece18..ed9bc75574 100644
--- a/src/USER-QTB/fix_qtb.cpp
+++ b/src/USER-QTB/fix_qtb.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -16,10 +16,10 @@
Implementation of the colored thermostat for quantum nuclear effects
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "math.h"
-#include "string.h"
-#include "stdlib.h"
+#include <mpi.h>
+#include <math.h>
+#include <string.h>
+#include <stdlib.h>
#include "fix_qtb.h"
#include "math_extra.h"
#include "atom.h"
@@ -54,7 +54,7 @@ FixQTB::FixQTB(LAMMPS *lmp, int narg, char **arg) :
global_freq = 1;
extscalar = 1;
nevery = 1;
-
+
t_target = 300.0;
t_period = 1.0;
fric_coef = 1/t_period;
@@ -86,7 +86,7 @@ FixQTB::FixQTB(LAMMPS *lmp, int narg, char **arg) :
N_f = atof(arg[iarg+1]); if (N_f <= 0) error->all(FLERR,"Illegal fix qtb command");
iarg += 2;
} else error->all(FLERR,"Illegal fix qtb command");
- }
+ }
// allocate qtb
gfactor1 = NULL;
@@ -99,7 +99,7 @@ FixQTB::FixQTB(LAMMPS *lmp, int narg, char **arg) :
fran = NULL;
id_temp = NULL;
temperature = NULL;
-
+
// initialize Marsaglia RNG with processor-unique seed
random = new RanMars(lmp,seed + comm->me);
@@ -162,7 +162,7 @@ void FixQTB::init()
//initiate the counter \mu
counter_mu=0;
-
+
//set up the h time step for updating the random force \delta{}h=\frac{\pi}{\Omega_{max}}
if (int(1.0/(2*f_max*dtv)) == 0) {
if (comm->me == 0) printf ("Warning: Either f_max is too high or the time step is too big, setting f_max to be 1/timestep!\n");
@@ -186,8 +186,8 @@ void FixQTB::init()
// generate random number array with zero mean and variance equal 1/12.
int nlocal = atom->nlocal;
- for (int i = 0; i < nlocal; i++) {
- for (int m = 0; m < 2*N_f; m++) {
+ for (int i = 0; i < nlocal; i++) {
+ for (int m = 0; m < 2*N_f; m++) {
random_array_0[i][m] = random->uniform()-0.5;
random_array_1[i][m] = random->uniform()-0.5;
random_array_2[i][m] = random->uniform()-0.5;
@@ -196,7 +196,7 @@ void FixQTB::init()
// load omega_H with calculated spectrum at a specific temperature (corrected spectrum), omega_H is the Fourier transformation of time_H
for (int k = 0; k < 2*N_f; k++) {
- double f_k=(k-N_f)/(2*N_f*h_timestep); //\omega_k=\frac{2\pi}{\delta{}h}\frac{k}{2N_f} for k from -N_f to N_f-1
+ double f_k=(k-N_f)/(2*N_f*h_timestep); //\omega_k=\frac{2\pi}{\delta{}h}\frac{k}{2N_f} for k from -N_f to N_f-1
if(k == N_f) {
omega_H[k]=sqrt(force->boltz * t_target);
} else {
@@ -207,7 +207,7 @@ void FixQTB::init()
}
// construct the signal filter H, filter has the unit of of sqrt(energy) \sqrt{2N_f}^{-1}H\left(t_n\right)
- for (int n = 0; n < 2*N_f; n++) {
+ for (int n = 0; n < 2*N_f; n++) {
time_H[n] = 0;
double t_n=(n-N_f);
for (int k = 0; k < 2*N_f; k++) {
@@ -254,14 +254,14 @@ void FixQTB::post_force(int vflag)
if (counter_mu == alpha) {
//propagate h_timestep ahead
for (int j = 0; j < nlocal; j++) {
-
+
//update random array
- for (int m = 0; m < 2*N_f-1; m++) {
+ for (int m = 0; m < 2*N_f-1; m++) {
random_array_0[j][m] = random_array_0[j][m+1];
- random_array_1[j][m] = random_array_1[j][m+1];
- random_array_2[j][m] = random_array_2[j][m+1];
+ random_array_1[j][m] = random_array_1[j][m+1];
+ random_array_2[j][m] = random_array_2[j][m+1];
}
- random_array_0[j][2*N_f-1] = random->uniform()-0.5;
+ random_array_0[j][2*N_f-1] = random->uniform()-0.5;
random_array_1[j][2*N_f-1] = random->uniform()-0.5;
random_array_2[j][2*N_f-1] = random->uniform()-0.5;
}
@@ -280,9 +280,9 @@ void FixQTB::post_force(int vflag)
if (mask[j] & groupbit) {
gamma3 = gfactor3[type[j]];
- for (int m = 0; m < 2*N_f; m++) {
+ for (int m = 0; m < 2*N_f; m++) {
fran[j][0] += time_H[m] * random_array_0[j][2*N_f-m-1];
- fran[j][1] += time_H[m] * random_array_1[j][2*N_f-m-1];
+ fran[j][1] += time_H[m] * random_array_1[j][2*N_f-m-1];
fran[j][2] += time_H[m] * random_array_2[j][2*N_f-m-1];
}
fran[j][0] = fran[j][0]*gamma3;
@@ -297,27 +297,27 @@ void FixQTB::post_force(int vflag)
fsum[1]=0.0; fsumall[1]=0.0;
fsum[2]=0.0; fsumall[2]=0.0;
- for (int j = 0; j < nlocal; j++) {
+ for (int j = 0; j < nlocal; j++) {
//sum over each atom
if (mask[j] & groupbit) {
gamma1 = gfactor1[type[j]];
-
+
fsum[0]+=fran[j][0]-gamma1*v[j][0];
fsum[1]+=fran[j][1]-gamma1*v[j][1];
fsum[2]+=fran[j][2]-gamma1*v[j][2];
- }
+ }
}
-
+
//compute force sums
MPI_Allreduce(fsum,fsumall,3,MPI_DOUBLE,MPI_SUM,world);
-
+
//implement random forces
for (int j = 0; j < nlocal; j++) {
//make sure there is no net force on the system
f[j][0] -= fsumall[0]/ntotal;
f[j][1] -= fsumall[1]/ntotal;
f[j][2] -= fsumall[2]/ntotal;
-
+
if (mask[j] & groupbit) {
gamma1 = gfactor1[type[j]];
@@ -399,7 +399,7 @@ void FixQTB::copy_arrays(int i, int j, int delflag)
random_array_1[j][m] = random_array_1[i][m];
random_array_2[j][m] = random_array_2[i][m];
}
-
+
for (int m = 0; m < 3; m++)
fran[j][m] = fran[i][m];
}
diff --git a/src/USER-QTB/fix_qtb.h b/src/USER-QTB/fix_qtb.h
index 40fda85f2c..e2b7634537 100644
--- a/src/USER-QTB/fix_qtb.h
+++ b/src/USER-QTB/fix_qtb.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-QUIP/pair_quip.cpp b/src/USER-QUIP/pair_quip.cpp
index d70c3d4708..e8b23c761f 100644
--- a/src/USER-QUIP/pair_quip.cpp
+++ b/src/USER-QUIP/pair_quip.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -16,11 +16,11 @@
Aidan Thompson (Sandia, athomps@sandia.gov)
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <mpi.h>
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_quip.h"
#include "atom.h"
#include "update.h"
@@ -79,7 +79,7 @@ void PairQUIP::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
sum_num_neigh = 0;
quip_num_neigh = new int [inum];
@@ -149,8 +149,8 @@ void PairQUIP::compute(int eflag, int vflag)
if (vflag_global) {
virial[0] = quip_virial[0];
- virial[1] = quip_virial[4];
- virial[2] = quip_virial[8];
+ virial[1] = quip_virial[4];
+ virial[2] = quip_virial[8];
virial[3] = (quip_virial[3] + quip_virial[1])*0.5;
virial[4] = (quip_virial[2] + quip_virial[6])*0.5;
virial[5] = (quip_virial[5] + quip_virial[7])*0.5;
@@ -184,7 +184,7 @@ void PairQUIP::compute(int eflag, int vflag)
}
/* ----------------------------------------------------------------------
- global settings
+ global settings
------------------------------------------------------------------------- */
void PairQUIP::settings(int narg, char **arg)
@@ -218,13 +218,13 @@ void PairQUIP::coeff(int narg, char **arg)
setflag[i][j] = 1;
}
}
-
+
if( narg != (4+n) ) {
char str[1024];
sprintf(str,"Number of arguments %d is not correct, it should be %d", narg, 4+n);
error->all(FLERR,str);
}
-
+
if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0)
error->all(FLERR,"Incorrect args for pair coefficients");
@@ -244,7 +244,7 @@ void PairQUIP::coeff(int narg, char **arg)
error->all(FLERR,str);
}
}
-
+
// Initialise potential
// First call initialises potential via the fortran code in memory, and returns the necessary size
// of quip_potential. This behaviour is invoked by setting n_potential_quip to 0.
diff --git a/src/USER-QUIP/pair_quip.h b/src/USER-QUIP/pair_quip.h
index e7a8c0c0a4..15e143aee7 100644
--- a/src/USER-QUIP/pair_quip.h
+++ b/src/USER-QUIP/pair_quip.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -24,9 +24,9 @@ PairStyle(quip,PairQUIP)
extern "C"
{
- void quip_lammps_wrapper(int*, int*, int*,
- int*, int*, int*,
- int*, int*, double*,
+ void quip_lammps_wrapper(int*, int*, int*,
+ int*, int*, int*,
+ int*, int*, double*,
int*, int*, double*,
double*, double*, double*, double*, double*);
void quip_lammps_potential_initialise(int*, int*, double*, char*, int*, char*, int*);
diff --git a/src/USER-REAXC/compute_spec_atom.cpp b/src/USER-REAXC/compute_spec_atom.cpp
index 0e7cf1ff8d..c719011746 100644
--- a/src/USER-REAXC/compute_spec_atom.cpp
+++ b/src/USER-REAXC/compute_spec_atom.cpp
@@ -5,14 +5,14 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "string.h"
+#include <math.h>
+#include <string.h>
#include "compute_spec_atom.h"
#include "math_extra.h"
#include "atom.h"
@@ -196,7 +196,7 @@ void ComputeSpecAtom::pack_q(int n)
int *mask = atom->mask;
int nlocal = atom->nlocal;
-
+
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = q[i];
@@ -213,7 +213,7 @@ void ComputeSpecAtom::pack_x(int n)
int *mask = atom->mask;
int nlocal = atom->nlocal;
-
+
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = x[i][0];
@@ -230,7 +230,7 @@ void ComputeSpecAtom::pack_y(int n)
int *mask = atom->mask;
int nlocal = atom->nlocal;
-
+
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = x[i][1];
@@ -247,7 +247,7 @@ void ComputeSpecAtom::pack_z(int n)
int *mask = atom->mask;
int nlocal = atom->nlocal;
-
+
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = x[i][2];
@@ -264,7 +264,7 @@ void ComputeSpecAtom::pack_vx(int n)
int *mask = atom->mask;
int nlocal = atom->nlocal;
-
+
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = v[i][0];
@@ -281,7 +281,7 @@ void ComputeSpecAtom::pack_vy(int n)
int *mask = atom->mask;
int nlocal = atom->nlocal;
-
+
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = v[i][1];
@@ -298,7 +298,7 @@ void ComputeSpecAtom::pack_vz(int n)
int *mask = atom->mask;
int nlocal = atom->nlocal;
-
+
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = v[i][2];
diff --git a/src/USER-REAXC/compute_spec_atom.h b/src/USER-REAXC/compute_spec_atom.h
index 908ae3077c..107a2bd39f 100644
--- a/src/USER-REAXC/compute_spec_atom.h
+++ b/src/USER-REAXC/compute_spec_atom.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -39,10 +39,10 @@ class ComputeSpecAtom : public Compute {
double *vector;
double **array;
double *buf;
- double *vbuf;
+ double *vbuf;
typedef void (ComputeSpecAtom::*FnPtrPack)(int);
- FnPtrPack *pack_choice;
+ FnPtrPack *pack_choice;
void pack_q(int);
void pack_x(int);
diff --git a/src/USER-REAXC/fix_qeq_reax.cpp b/src/USER-REAXC/fix_qeq_reax.cpp
index dfcd16316e..794c23da3a 100644
--- a/src/USER-REAXC/fix_qeq_reax.cpp
+++ b/src/USER-REAXC/fix_qeq_reax.cpp
@@ -18,10 +18,10 @@
Hybrid and sub-group capabilities: Ray Shan (Sandia)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "fix_qeq_reax.h"
#include "pair_reax_c.h"
#include "atom.h"
@@ -442,7 +442,7 @@ void FixQEqReax::init_storage()
{
int NN;
- if (reaxc)
+ if (reaxc)
NN = reaxc->list->inum + reaxc->list->gnum;
else
NN = list->inum + list->gnum;
@@ -522,7 +522,7 @@ void FixQEqReax::init_matvec()
for( ii = 0; ii < nn; ++ii ) {
i = ilist[ii];
if (atom->mask[i] & groupbit) {
-
+
/* init pre-conditioner for H and init solution vectors */
Hdia_inv[i] = 1. / eta[ atom->type[i] ];
b_s[i] = -chi[ atom->type[i] ];
@@ -573,7 +573,7 @@ void FixQEqReax::compute_H()
numneigh = list->numneigh;
firstneigh = list->firstneigh;
}
-
+
// fill in the H matrix
m_fill = 0;
r_sqr = 0;
@@ -964,7 +964,7 @@ double FixQEqReax::parallel_dot( double *v1, double *v2, int n)
if (atom->mask[i] & groupbit)
my_dot += v1[i] * v2[i];
}
-
+
MPI_Allreduce( &my_dot, &res, 1, MPI_DOUBLE, MPI_SUM, world );
return res;
diff --git a/src/USER-REAXC/fix_reaxc_bonds.cpp b/src/USER-REAXC/fix_reaxc_bonds.cpp
index ca0219cdf6..0ac32e8fb6 100644
--- a/src/USER-REAXC/fix_reaxc_bonds.cpp
+++ b/src/USER-REAXC/fix_reaxc_bonds.cpp
@@ -15,8 +15,8 @@
Contributing author: Ray Shan (Sandia, tnshan@sandia.gov)
------------------------------------------------------------------------- */
-#include "stdlib.h"
-#include "string.h"
+#include <stdlib.h>
+#include <string.h>
#include "fix_ave_atom.h"
#include "fix_reaxc_bonds.h"
#include "atom.h"
@@ -243,7 +243,7 @@ void FixReaxCBonds::PassBuffer(double *buf, int &nbuf_local)
/* ---------------------------------------------------------------------- */
-void FixReaxCBonds::RecvBuffer(double *buf, int nbuf, int nbuf_local,
+void FixReaxCBonds::RecvBuffer(double *buf, int nbuf, int nbuf_local,
int natoms, int maxnum)
{
int i, j, k, itype;
diff --git a/src/USER-REAXC/fix_reaxc_bonds.h b/src/USER-REAXC/fix_reaxc_bonds.h
index a5f4a6304e..b91085163b 100644
--- a/src/USER-REAXC/fix_reaxc_bonds.h
+++ b/src/USER-REAXC/fix_reaxc_bonds.h
@@ -20,7 +20,7 @@ FixStyle(reax/c/bonds,FixReaxCBonds)
#ifndef LMP_FIX_REAXC_BONDS_H
#define LMP_FIX_REAXC_BONDS_H
-#include "stdio.h"
+#include <stdio.h>
#include "fix.h"
#include "pointers.h"
diff --git a/src/USER-REAXC/fix_reaxc_species.cpp b/src/USER-REAXC/fix_reaxc_species.cpp
index c223859b25..c2a0e2fbb6 100644
--- a/src/USER-REAXC/fix_reaxc_species.cpp
+++ b/src/USER-REAXC/fix_reaxc_species.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -16,10 +16,10 @@
Oleg Sergeev (VNIIA, sergeev@vniia.ru)
------------------------------------------------------------------------- */
-#include "stdlib.h"
-#include "math.h"
+#include <stdlib.h>
+#include <math.h>
#include "atom.h"
-#include "string.h"
+#include <string.h>
#include "fix_ave_atom.h"
#include "fix_reaxc_species.h"
#include "domain.h"
@@ -67,15 +67,15 @@ FixReaxCSpecies::FixReaxCSpecies(LAMMPS *lmp, int narg, char **arg) :
global_freq = nfreq = atoi(arg[5]);
comm_forward = 5;
-
+
if (nevery <= 0 || nrepeat <= 0 || nfreq <= 0)
error->all(FLERR,"Illegal fix reax/c/species command");
if (nfreq % nevery || (nrepeat-1)*nevery >= nfreq)
error->all(FLERR,"Illegal fix reax/c/species command");
-
- // Neighbor lists must stay unchanged during averaging of bonds,
+
+ // Neighbor lists must stay unchanged during averaging of bonds,
// but may be updated when no averaging is performed.
-
+
int rene_flag = 0;
if (nevery * nrepeat != 1 && (nfreq % neighbor->every != 0 || neighbor->every < nevery * nrepeat)) {
int newneighborevery = nevery * nrepeat;
@@ -165,14 +165,14 @@ FixReaxCSpecies::FixReaxCSpecies(LAMMPS *lmp, int narg, char **arg) :
itype = atoi(arg[iarg+1]);
jtype = atoi(arg[iarg+2]);
bo_cut = atof(arg[iarg+3]);
- if (itype > ntypes || jtype > ntypes)
+ if (itype > ntypes || jtype > ntypes)
error->all(FLERR,"Illegal fix reax/c/species command");
- if (itype <= 0 || jtype <= 0)
+ if (itype <= 0 || jtype <= 0)
error->all(FLERR,"Illegal fix reax/c/species command");
if (bo_cut > 1.0 || bo_cut < 0.0)
error->all(FLERR,"Illegal fix reax/c/species command");
- BOCut[itype][jtype] = bo_cut;
+ BOCut[itype][jtype] = bo_cut;
BOCut[jtype][itype] = bo_cut;
iarg += 4;
@@ -377,27 +377,27 @@ void FixReaxCSpecies::create_fix()
args[11] = (char *) "c_SPECATOM[6]"; // vy, 5
args[12] = (char *) "c_SPECATOM[7]"; // vz, 6
args[13] = (char *) "c_SPECATOM[8]"; // abo01, 7
- args[14] = (char *) "c_SPECATOM[9]";
- args[15] = (char *) "c_SPECATOM[10]";
- args[16] = (char *) "c_SPECATOM[11]";
+ args[14] = (char *) "c_SPECATOM[9]";
+ args[15] = (char *) "c_SPECATOM[10]";
+ args[16] = (char *) "c_SPECATOM[11]";
args[17] = (char *) "c_SPECATOM[12]";
args[18] = (char *) "c_SPECATOM[13]";
- args[19] = (char *) "c_SPECATOM[14]";
+ args[19] = (char *) "c_SPECATOM[14]";
args[20] = (char *) "c_SPECATOM[15]";
args[21] = (char *) "c_SPECATOM[16]";
args[22] = (char *) "c_SPECATOM[17]";
args[23] = (char *) "c_SPECATOM[18]";
args[24] = (char *) "c_SPECATOM[19]"; // abo12, 18
- args[25] = (char *) "c_SPECATOM[20]";
- args[26] = (char *) "c_SPECATOM[21]";
+ args[25] = (char *) "c_SPECATOM[20]";
+ args[26] = (char *) "c_SPECATOM[21]";
args[27] = (char *) "c_SPECATOM[22]";
args[28] = (char *) "c_SPECATOM[23]";
- args[29] = (char *) "c_SPECATOM[24]";
+ args[29] = (char *) "c_SPECATOM[24]";
args[30] = (char *) "c_SPECATOM[25]";
args[31] = (char *) "c_SPECATOM[26]";
args[32] = (char *) "c_SPECATOM[27]";
args[33] = (char *) "c_SPECATOM[28]";
- args[34] = (char *) "c_SPECATOM[29]";
+ args[34] = (char *) "c_SPECATOM[29]";
args[35] = (char *) "c_SPECATOM[30]";
args[36] = (char *) "c_SPECATOM[31]";
modify->add_fix(narg,args);
@@ -477,7 +477,7 @@ void FixReaxCSpecies::Output_ReaxC_Bonds(bigint ntimestep, FILE *fp)
AtomCoord chAnchor(AtomCoord in1, AtomCoord in2)
{
- if (in1.x < in2.x)
+ if (in1.x < in2.x)
return in1;
return in2;
}
@@ -528,7 +528,7 @@ void FixReaxCSpecies::FindMolecule ()
if (j < i) continue;
if (!(mask[j] & groupbit)) continue;
- if (clusterID[i] == clusterID[j] && PBCconnected[i] == PBCconnected[j]
+ if (clusterID[i] == clusterID[j] && PBCconnected[i] == PBCconnected[j]
&& x0[i].x == x0[j].x && x0[i].y == x0[j].y && x0[i].z == x0[j].z) continue;
jtype = atom->type[j];
@@ -540,7 +540,7 @@ void FixReaxCSpecies::FindMolecule ()
PBCconnected[i] = PBCconnected[j] = MAX(PBCconnected[i], PBCconnected[j]);
x0[i] = x0[j] = chAnchor(x0[i], x0[j]);
if ((fabs(spec_atom[i][1] - spec_atom[j][1]) > reaxc->control->bond_cut)
- || (fabs(spec_atom[i][2] - spec_atom[j][2]) > reaxc->control->bond_cut)
+ || (fabs(spec_atom[i][2] - spec_atom[j][2]) > reaxc->control->bond_cut)
|| (fabs(spec_atom[i][3] - spec_atom[j][3]) > reaxc->control->bond_cut))
PBCconnected[i] = PBCconnected[j] = 1;
done = 0;
@@ -579,7 +579,7 @@ void FixReaxCSpecies::SortMolecule(int &Nmole)
}
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
- if (flagall && me == 0)
+ if (flagall && me == 0)
error->warning(FLERR,"Atom with cluster ID = 0 included in "
"fix reax/c/species group");
MPI_Allreduce(&lo,&idlo,1,MPI_INT,MPI_MIN,world);
@@ -661,7 +661,7 @@ void FixReaxCSpecies::FindSpecies(int Nmole, int &Nspec)
if (cid == m) {
itype = atom->type[n]-1;
Name[itype] ++;
- flag_mol = 1;
+ flag_mol = 1;
}
}
MPI_Allreduce(&flag_mol,&flag_tmp,1,MPI_INT,MPI_MAX,world);
@@ -674,15 +674,15 @@ void FixReaxCSpecies::FindSpecies(int Nmole, int &Nspec)
flag_identity = 1;
for (k = 0; k < Nspec; k ++) {
flag_spec=0;
- for (l = 0; l < ntypes; l ++)
+ for (l = 0; l < ntypes; l ++)
if (MolName[ntypes*k+l] != Name[l]) flag_spec = 1;
- if (flag_spec == 0) NMol[k] ++;
- flag_identity *= flag_spec;
+ if (flag_spec == 0) NMol[k] ++;
+ flag_identity *= flag_spec;
}
if (Nspec == 0 || flag_identity == 1) {
for (l = 0; l < ntypes; l ++)
MolName[ntypes*Nspec+l] = Name[l];
- Nspec ++;
+ Nspec ++;
}
}
}
@@ -710,7 +710,7 @@ int FixReaxCSpecies::CheckExistence(int id, int ntypes)
molid = MolType[ntypes * i + j];
if (molid != MolName[ntypes * id + j]) flag = 1;
}
- if (flag == 0) return i;
+ if (flag == 0) return i;
}
for (i = 0; i < ntypes; i ++)
MolType[ntypes * Nmoltype + i] = MolName[ntypes *id + i];
@@ -729,7 +729,7 @@ void FixReaxCSpecies::WriteFormulas(int Nmole, int Nspec)
fprintf(fp,"# Timestep No_Moles No_Specs ");
Nmoltype = 0;
-
+
for (i = 0; i < Nspec; i ++)
nd[i] = CheckExistence(i, ntypes);
@@ -765,7 +765,7 @@ void FixReaxCSpecies::OpenPos()
filecurrent = (char*) malloc((strlen(filepos)+16)*sizeof(char));
char *ptr = strchr(filepos,'*');
*ptr = '\0';
- if (padflag == 0)
+ if (padflag == 0)
sprintf(filecurrent,"%s" BIGINT_FORMAT "%s",
filepos,ntimestep,ptr+1);
else {
@@ -797,7 +797,7 @@ void FixReaxCSpecies::WritePos(int Nmole, int Nspec)
double **spec_atom = f_SPECBOND->array_atom;
if (multipos) OpenPos();
-
+
box[0] = domain->boxhi[0] - domain->boxlo[0];
box[1] = domain->boxhi[1] - domain->boxlo[1];
box[2] = domain->boxhi[2] - domain->boxlo[2];
@@ -823,9 +823,9 @@ void FixReaxCSpecies::WritePos(int Nmole, int Nspec)
count = 0;
avq = 0.0;
- for (n = 0; n < 3; n++)
+ for (n = 0; n < 3; n++)
avx[n] = 0.0;
- for (n = 0; n < ntypes; n ++)
+ for (n = 0; n < ntypes; n ++)
Name[n] = 0;
for (i = 0; i < nlocal; i ++) {
@@ -858,7 +858,7 @@ void FixReaxCSpecies::WritePos(int Nmole, int Nspec)
avq_tmp = 0.0;
MPI_Allreduce(&avq,&avq_tmp,1,MPI_DOUBLE,MPI_SUM,world);
avq = avq_tmp;
-
+
for (n = 0; n < 3; n++) {
avx_tmp = 0.0;
MPI_Reduce(&avx[n],&avx_tmp,1,MPI_DOUBLE,MPI_SUM,0,world);
@@ -871,9 +871,9 @@ void FixReaxCSpecies::WritePos(int Nmole, int Nspec)
MPI_Reduce(Name,Nameall,ntypes,MPI_INT,MPI_SUM,0,world);
for (n = 0; n < ntypes; n++) Name[n] = Nameall[n];
- if (me == 0) {
+ if (me == 0) {
fprintf(pos,"%d\t%d\t",m,count);
- for (n = 0; n < ntypes; n++) {
+ for (n = 0; n < ntypes; n++) {
if (Name[n] != 0) {
if (eletype) fprintf(pos,"%s",eletype[n]);
else fprintf(pos,"%c",ele[n]);
@@ -882,7 +882,7 @@ void FixReaxCSpecies::WritePos(int Nmole, int Nspec)
}
if (count > 0) {
avq /= count;
- for (k = 0; k < 3; k++) {
+ for (k = 0; k < 3; k++) {
avx[k] /= count;
if (avx[k] >= domain->boxhi[k])
avx[k] -= box[k];
@@ -906,9 +906,9 @@ void FixReaxCSpecies::WritePos(int Nmole, int Nspec)
double FixReaxCSpecies::compute_vector(int n)
{
- if (n == 0)
+ if (n == 0)
return vector_nmole;
- if (n == 1)
+ if (n == 1)
return vector_nspec;
return 0.0;
@@ -926,7 +926,7 @@ int FixReaxCSpecies::nint(const double &r)
/* ---------------------------------------------------------------------- */
-int FixReaxCSpecies::pack_forward_comm(int n, int *list, double *buf,
+int FixReaxCSpecies::pack_forward_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
diff --git a/src/USER-REAXC/fix_reaxc_species.h b/src/USER-REAXC/fix_reaxc_species.h
index 43d59a0f88..a3a47b29dd 100644
--- a/src/USER-REAXC/fix_reaxc_species.h
+++ b/src/USER-REAXC/fix_reaxc_species.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-REAXC/pair_reax_c.cpp b/src/USER-REAXC/pair_reax_c.cpp
index 0aca805f7d..dc977249fc 100644
--- a/src/USER-REAXC/pair_reax_c.cpp
+++ b/src/USER-REAXC/pair_reax_c.cpp
@@ -15,7 +15,7 @@
Contributing author: Hasan Metin Aktulga, Purdue University
(now at Lawrence Berkeley National Laboratory, hmaktulga@lbl.gov)
Per-atom energy/virial added by Ray Shan (Sandia)
- Fix reax/c/bonds and fix reax/c/species for pair_style reax/c added by
+ Fix reax/c/bonds and fix reax/c/species for pair_style reax/c added by
Ray Shan (Sandia)
Hybrid and hybrid/overlay compatibility added by Ray Shan (Sandia)
------------------------------------------------------------------------- */
@@ -245,14 +245,14 @@ void PairReaxC::settings(int narg, char **arg)
} else if (strcmp(arg[iarg],"safezone") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal pair_style reax/c command");
system->safezone = force->numeric(FLERR,arg[iarg+1]);
- if (system->safezone < 0.0)
+ if (system->safezone < 0.0)
error->all(FLERR,"Illegal pair_style reax/c safezone command");
system->saferzone = system->safezone + 0.2;
iarg += 2;
} else if (strcmp(arg[iarg],"mincap") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal pair_style reax/c command");
system->mincap = force->inumeric(FLERR,arg[iarg+1]);
- if (system->mincap < 0)
+ if (system->mincap < 0)
error->all(FLERR,"Illegal pair_style reax/c mincap command");
iarg += 2;
} else error->all(FLERR,"Illegal pair_style reax/c command");
@@ -282,7 +282,7 @@ void PairReaxC::coeff( int nargs, char **args )
char *file = args[2];
FILE *fp;
fp = force->open_potential(file);
- if (fp != NULL)
+ if (fp != NULL)
Read_Force_Field(fp, &(system->reax_param), control);
else if (comm->me == 0) {
char str[128];
@@ -314,7 +314,7 @@ void PairReaxC::coeff( int nargs, char **args )
}
// error check
- if (itmp != n)
+ if (itmp != n)
error->all(FLERR,"Non-existent ReaxFF type");
for (int i = 1; i <= n; i++)
@@ -573,7 +573,7 @@ void PairReaxC::compute(int eflag, int vflag)
memory->create(tmpid,nmax,MAXSPECBOND,"pair:tmpid");
memory->create(tmpbo,nmax,MAXSPECBOND,"pair:tmpbo");
}
-
+
for (i = 0; i < system->N; i ++)
for (j = 0; j < MAXSPECBOND; j ++) {
tmpbo[i][j] = 0.0;
@@ -770,7 +770,7 @@ void *PairReaxC::extract(const char *str, int &dim)
double PairReaxC::memory_usage()
{
double bytes = 0.0;
-
+
// From pair_reax_c
bytes += 1.0 * system->N * sizeof(int);
bytes += 1.0 * system->N * sizeof(double);
diff --git a/src/USER-REAXC/pair_reax_c.h b/src/USER-REAXC/pair_reax_c.h
index 1f7a5c9f00..679adc34d6 100644
--- a/src/USER-REAXC/pair_reax_c.h
+++ b/src/USER-REAXC/pair_reax_c.h
@@ -95,8 +95,8 @@ class PairReaxC : public Pair {
E: Too many ghost atoms
-Number of ghost atoms has increased too much during simulation and has exceeded
-the size of reax/c arrays. Increase safe_zone and min_cap in pair_style reax/c
+Number of ghost atoms has increased too much during simulation and has exceeded
+the size of reax/c arrays. Increase safe_zone and min_cap in pair_style reax/c
command
*/
diff --git a/src/USER-REAXC/reaxc_bonds.cpp b/src/USER-REAXC/reaxc_bonds.cpp
index 6e3fa75978..e0ef38ba0f 100644
--- a/src/USER-REAXC/reaxc_bonds.cpp
+++ b/src/USER-REAXC/reaxc_bonds.cpp
@@ -66,10 +66,10 @@ void Bonds( reax_system *system, control_params *control,
continue;
if( system->my_atoms[i].orig_id == system->my_atoms[j].orig_id ) {
if (system->my_atoms[j].x[2] < system->my_atoms[i].x[2]) continue;
- if (system->my_atoms[j].x[2] == system->my_atoms[i].x[2] &&
+ if (system->my_atoms[j].x[2] == system->my_atoms[i].x[2] &&
system->my_atoms[j].x[1] < system->my_atoms[i].x[1]) continue;
- if (system->my_atoms[j].x[2] == system->my_atoms[i].x[2] &&
- system->my_atoms[j].x[1] == system->my_atoms[i].x[1] &&
+ if (system->my_atoms[j].x[2] == system->my_atoms[i].x[2] &&
+ system->my_atoms[j].x[1] == system->my_atoms[i].x[1] &&
system->my_atoms[j].x[0] < system->my_atoms[i].x[0]) continue;
}
@@ -80,28 +80,28 @@ void Bonds( reax_system *system, control_params *control,
sbp_j = &( system->reax_param.sbp[type_j] );
twbp = &( system->reax_param.tbp[type_i][type_j] );
bo_ij = &( bonds->select.bond_list[pj].bo_data );
-
+
/* calculate the constants */
pow_BOs_be2 = pow( bo_ij->BO_s, twbp->p_be2 );
exp_be12 = exp( twbp->p_be1 * ( 1.0 - pow_BOs_be2 ) );
CEbo = -twbp->De_s * exp_be12 *
( 1.0 - twbp->p_be1 * twbp->p_be2 * pow_BOs_be2 );
-
+
/* calculate the Bond Energy */
data->my_en.e_bond += ebond =
-twbp->De_s * bo_ij->BO_s * exp_be12
-twbp->De_p * bo_ij->BO_pi
-twbp->De_pp * bo_ij->BO_pi2;
-
+
/* tally into per-atom energy */
if( system->pair_ptr->evflag)
system->pair_ptr->ev_tally(i,j,natoms,1,ebond,0.0,0.0,0.0,0.0,0.0);
-
+
/* calculate derivatives of Bond Orders */
bo_ij->Cdbo += CEbo;
bo_ij->Cdbopi -= (CEbo + twbp->De_p);
bo_ij->Cdbopi2 -= (CEbo + twbp->De_pp);
-
+
/* Stabilisation terminal triple bond */
if( bo_ij->BO >= 1.00 ) {
if( gp37 == 2 ||
@@ -112,21 +112,21 @@ void Bonds( reax_system *system, control_params *control,
exphub1 = exp(-gp3 * (workspace->total_bond_order[j]-bo_ij->BO));
exphuov = exp(gp4 * (workspace->Delta[i] + workspace->Delta[j]));
hulpov = 1.0 / (1.0 + 25.0 * exphuov);
-
+
estriph = gp10 * exphu * hulpov * (exphua1 + exphub1);
data->my_en.e_bond += estriph;
-
+
decobdbo = gp10 * exphu * hulpov * (exphua1 + exphub1) *
( gp3 - 2.0 * gp7 * (bo_ij->BO-2.50) );
decobdboua = -gp10 * exphu * hulpov *
(gp3*exphua1 + 25.0*gp4*exphuov*hulpov*(exphua1+exphub1));
decobdboub = -gp10 * exphu * hulpov *
(gp3*exphub1 + 25.0*gp4*exphuov*hulpov*(exphua1+exphub1));
-
+
/* tally into per-atom energy */
if( system->pair_ptr->evflag)
system->pair_ptr->ev_tally(i,j,natoms,1,estriph,0.0,0.0,0.0,0.0,0.0);
-
+
bo_ij->Cdbo += decobdbo;
workspace->CdDelta[i] += decobdboua;
workspace->CdDelta[j] += decobdboub;
diff --git a/src/USER-REAXC/reaxc_ffield.cpp b/src/USER-REAXC/reaxc_ffield.cpp
index 6007cb7344..912a49daa2 100644
--- a/src/USER-REAXC/reaxc_ffield.cpp
+++ b/src/USER-REAXC/reaxc_ffield.cpp
@@ -443,7 +443,7 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax,
reax->tbp[i][j].lgcij = reax->tbp[j][i].lgcij =
sqrt( reax->sbp[i].lgcij * reax->sbp[j].lgcij );
- reax->tbp[i][j].lgre = reax->tbp[j][i].lgre = 2.0 * reax->gp.l[35] *
+ reax->tbp[i][j].lgre = reax->tbp[j][i].lgre = 2.0 * reax->gp.l[35] *
sqrt( reax->sbp[i].lgre*reax->sbp[j].lgre );
}
diff --git a/src/USER-REAXC/reaxc_torsion_angles.cpp b/src/USER-REAXC/reaxc_torsion_angles.cpp
index bf73fc6ae8..2cfe329765 100644
--- a/src/USER-REAXC/reaxc_torsion_angles.cpp
+++ b/src/USER-REAXC/reaxc_torsion_angles.cpp
@@ -185,10 +185,10 @@ void Torsion_Angles( reax_system *system, control_params *control,
continue;
if( system->my_atoms[j].orig_id == system->my_atoms[k].orig_id ) {
if (system->my_atoms[k].x[2] < system->my_atoms[j].x[2]) continue;
- if (system->my_atoms[k].x[2] == system->my_atoms[j].x[2] &&
+ if (system->my_atoms[k].x[2] == system->my_atoms[j].x[2] &&
system->my_atoms[k].x[1] < system->my_atoms[j].x[1]) continue;
- if (system->my_atoms[k].x[2] == system->my_atoms[j].x[2] &&
- system->my_atoms[k].x[1] == system->my_atoms[j].x[1] &&
+ if (system->my_atoms[k].x[2] == system->my_atoms[j].x[2] &&
+ system->my_atoms[k].x[1] == system->my_atoms[j].x[1] &&
system->my_atoms[k].x[0] < system->my_atoms[j].x[0]) continue;
}
diff --git a/src/USER-REAXC/reaxc_types.h b/src/USER-REAXC/reaxc_types.h
index 5d6d5d8024..0779acaf39 100644
--- a/src/USER-REAXC/reaxc_types.h
+++ b/src/USER-REAXC/reaxc_types.h
@@ -29,14 +29,14 @@
#include "lmptype.h"
-#include "ctype.h"
-#include "math.h"
-#include "mpi.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <ctype.h>
+#include <math.h>
+#include <mpi.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "sys/time.h"
-#include "time.h"
+#include <time.h>
/************* SOME DEFS - crucial for reax_types.h *********/
diff --git a/src/USER-SMD/atom_vec_smd.cpp b/src/USER-SMD/atom_vec_smd.cpp
index 6b61b5c1ef..2a0d65b642 100644
--- a/src/USER-SMD/atom_vec_smd.cpp
+++ b/src/USER-SMD/atom_vec_smd.cpp
@@ -22,9 +22,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "atom_vec_smd.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-SMD/compute_smd_contact_radius.cpp b/src/USER-SMD/compute_smd_contact_radius.cpp
index 865031addb..e641aea5a2 100644
--- a/src/USER-SMD/compute_smd_contact_radius.cpp
+++ b/src/USER-SMD/compute_smd_contact_radius.cpp
@@ -23,7 +23,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "compute_smd_contact_radius.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-SMD/compute_smd_damage.cpp b/src/USER-SMD/compute_smd_damage.cpp
index 95d7bee3be..6630a93735 100644
--- a/src/USER-SMD/compute_smd_damage.cpp
+++ b/src/USER-SMD/compute_smd_damage.cpp
@@ -23,7 +23,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "compute_smd_damage.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-SMD/compute_smd_hourglass_error.cpp b/src/USER-SMD/compute_smd_hourglass_error.cpp
index ae6ffee0e1..99998ed7ee 100644
--- a/src/USER-SMD/compute_smd_hourglass_error.cpp
+++ b/src/USER-SMD/compute_smd_hourglass_error.cpp
@@ -23,7 +23,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "compute_smd_hourglass_error.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-SMD/compute_smd_internal_energy.cpp b/src/USER-SMD/compute_smd_internal_energy.cpp
index 9116df7011..fc869f9f93 100644
--- a/src/USER-SMD/compute_smd_internal_energy.cpp
+++ b/src/USER-SMD/compute_smd_internal_energy.cpp
@@ -23,7 +23,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "compute_smd_internal_energy.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-SMD/compute_smd_plastic_strain.cpp b/src/USER-SMD/compute_smd_plastic_strain.cpp
index 734f40e267..7c0977beb0 100644
--- a/src/USER-SMD/compute_smd_plastic_strain.cpp
+++ b/src/USER-SMD/compute_smd_plastic_strain.cpp
@@ -23,7 +23,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "compute_smd_plastic_strain.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-SMD/compute_smd_plastic_strain_rate.cpp b/src/USER-SMD/compute_smd_plastic_strain_rate.cpp
index 44a890bf82..7df08bd4ac 100644
--- a/src/USER-SMD/compute_smd_plastic_strain_rate.cpp
+++ b/src/USER-SMD/compute_smd_plastic_strain_rate.cpp
@@ -23,7 +23,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "compute_smd_plastic_strain_rate.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-SMD/compute_smd_rho.cpp b/src/USER-SMD/compute_smd_rho.cpp
index 0e9ee9bb27..231165dc0c 100644
--- a/src/USER-SMD/compute_smd_rho.cpp
+++ b/src/USER-SMD/compute_smd_rho.cpp
@@ -22,7 +22,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "compute_smd_rho.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-SMD/compute_smd_tlsph_defgrad.cpp b/src/USER-SMD/compute_smd_tlsph_defgrad.cpp
index 7dcd7faca0..50f849b7f1 100644
--- a/src/USER-SMD/compute_smd_tlsph_defgrad.cpp
+++ b/src/USER-SMD/compute_smd_tlsph_defgrad.cpp
@@ -22,7 +22,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "compute_smd_tlsph_defgrad.h"
#include "atom.h"
#include "update.h"
@@ -34,8 +34,8 @@
#include "pair.h"
#include <iostream>
#include <stdio.h>
-#include "stdlib.h"
-#include "string.h"
+#include <stdlib.h>
+#include <string.h>
#include <Eigen/Eigen>
using namespace Eigen;
using namespace std;
diff --git a/src/USER-SMD/compute_smd_tlsph_defgrad.h b/src/USER-SMD/compute_smd_tlsph_defgrad.h
index c58fc5148d..211b906485 100644
--- a/src/USER-SMD/compute_smd_tlsph_defgrad.h
+++ b/src/USER-SMD/compute_smd_tlsph_defgrad.h
@@ -17,7 +17,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-SMD/compute_smd_tlsph_dt.cpp b/src/USER-SMD/compute_smd_tlsph_dt.cpp
index fdb3c4feeb..d2bcbf246f 100644
--- a/src/USER-SMD/compute_smd_tlsph_dt.cpp
+++ b/src/USER-SMD/compute_smd_tlsph_dt.cpp
@@ -22,7 +22,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "compute_smd_tlsph_dt.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-SMD/compute_smd_tlsph_num_neighs.cpp b/src/USER-SMD/compute_smd_tlsph_num_neighs.cpp
index 7b7b2ce07c..53e7a5c116 100644
--- a/src/USER-SMD/compute_smd_tlsph_num_neighs.cpp
+++ b/src/USER-SMD/compute_smd_tlsph_num_neighs.cpp
@@ -23,7 +23,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "compute_smd_tlsph_num_neighs.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-SMD/compute_smd_tlsph_shape.cpp b/src/USER-SMD/compute_smd_tlsph_shape.cpp
index d4e8c14b37..005fe6e39d 100644
--- a/src/USER-SMD/compute_smd_tlsph_shape.cpp
+++ b/src/USER-SMD/compute_smd_tlsph_shape.cpp
@@ -22,7 +22,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "compute_smd_tlsph_shape.h"
#include "atom.h"
#include "update.h"
@@ -34,8 +34,8 @@
#include "pair.h"
#include <iostream>
#include <stdio.h>
-#include "stdlib.h"
-#include "string.h"
+#include <stdlib.h>
+#include <string.h>
#include <Eigen/Eigen>
#include <Eigen/Geometry>
using namespace Eigen;
diff --git a/src/USER-SMD/compute_smd_tlsph_shape.h b/src/USER-SMD/compute_smd_tlsph_shape.h
index 673080e232..dc5a98618b 100644
--- a/src/USER-SMD/compute_smd_tlsph_shape.h
+++ b/src/USER-SMD/compute_smd_tlsph_shape.h
@@ -17,7 +17,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-SMD/compute_smd_tlsph_strain.cpp b/src/USER-SMD/compute_smd_tlsph_strain.cpp
index f191afeb2c..6b1b9c7231 100644
--- a/src/USER-SMD/compute_smd_tlsph_strain.cpp
+++ b/src/USER-SMD/compute_smd_tlsph_strain.cpp
@@ -23,7 +23,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "compute_smd_tlsph_strain.h"
#include "atom.h"
#include "update.h"
@@ -35,8 +35,8 @@
#include "pair.h"
#include <iostream>
#include <stdio.h>
-#include "stdlib.h"
-#include "string.h"
+#include <stdlib.h>
+#include <string.h>
#include <Eigen/Eigen>
using namespace Eigen;
using namespace std;
diff --git a/src/USER-SMD/compute_smd_tlsph_strain.h b/src/USER-SMD/compute_smd_tlsph_strain.h
index a42fcddde2..0dcd53b9a2 100644
--- a/src/USER-SMD/compute_smd_tlsph_strain.h
+++ b/src/USER-SMD/compute_smd_tlsph_strain.h
@@ -17,7 +17,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-SMD/compute_smd_tlsph_strain_rate.cpp b/src/USER-SMD/compute_smd_tlsph_strain_rate.cpp
index 4298793aef..8ae776da39 100644
--- a/src/USER-SMD/compute_smd_tlsph_strain_rate.cpp
+++ b/src/USER-SMD/compute_smd_tlsph_strain_rate.cpp
@@ -23,7 +23,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "compute_smd_tlsph_strain_rate.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-SMD/compute_smd_tlsph_strain_rate.h b/src/USER-SMD/compute_smd_tlsph_strain_rate.h
index 86da271b45..d3425e6fdc 100644
--- a/src/USER-SMD/compute_smd_tlsph_strain_rate.h
+++ b/src/USER-SMD/compute_smd_tlsph_strain_rate.h
@@ -17,7 +17,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-SMD/compute_smd_tlsph_stress.cpp b/src/USER-SMD/compute_smd_tlsph_stress.cpp
index e5eccd9aeb..541cc39eff 100644
--- a/src/USER-SMD/compute_smd_tlsph_stress.cpp
+++ b/src/USER-SMD/compute_smd_tlsph_stress.cpp
@@ -22,7 +22,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "compute_smd_tlsph_stress.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-SMD/compute_smd_tlsph_stress.h b/src/USER-SMD/compute_smd_tlsph_stress.h
index ed3ce7e7a9..027bfea98a 100644
--- a/src/USER-SMD/compute_smd_tlsph_stress.h
+++ b/src/USER-SMD/compute_smd_tlsph_stress.h
@@ -17,7 +17,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-SMD/compute_smd_triangle_mesh_vertices.cpp b/src/USER-SMD/compute_smd_triangle_mesh_vertices.cpp
index 6e7bac76bc..3e66e34611 100644
--- a/src/USER-SMD/compute_smd_triangle_mesh_vertices.cpp
+++ b/src/USER-SMD/compute_smd_triangle_mesh_vertices.cpp
@@ -23,7 +23,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "compute_smd_triangle_mesh_vertices.h"
#include "atom.h"
#include "update.h"
@@ -35,8 +35,8 @@
#include "pair.h"
#include <iostream>
#include <stdio.h>
-#include "stdlib.h"
-#include "string.h"
+#include <stdlib.h>
+#include <string.h>
#include <Eigen/Eigen>
using namespace Eigen;
using namespace std;
diff --git a/src/USER-SMD/compute_smd_triangle_mesh_vertices.h b/src/USER-SMD/compute_smd_triangle_mesh_vertices.h
index 7514622714..a99330b0eb 100644
--- a/src/USER-SMD/compute_smd_triangle_mesh_vertices.h
+++ b/src/USER-SMD/compute_smd_triangle_mesh_vertices.h
@@ -17,7 +17,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-SMD/compute_smd_ulsph_effm.cpp b/src/USER-SMD/compute_smd_ulsph_effm.cpp
index 313c259632..529ce5bcd6 100644
--- a/src/USER-SMD/compute_smd_ulsph_effm.cpp
+++ b/src/USER-SMD/compute_smd_ulsph_effm.cpp
@@ -22,7 +22,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "compute_smd_ulsph_effm.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-SMD/compute_smd_ulsph_num_neighs.cpp b/src/USER-SMD/compute_smd_ulsph_num_neighs.cpp
index c50db61bb1..169eaa7dfb 100644
--- a/src/USER-SMD/compute_smd_ulsph_num_neighs.cpp
+++ b/src/USER-SMD/compute_smd_ulsph_num_neighs.cpp
@@ -23,7 +23,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "compute_smd_ulsph_num_neighs.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-SMD/compute_smd_ulsph_strain.cpp b/src/USER-SMD/compute_smd_ulsph_strain.cpp
index 5cf4fa53fa..395221d683 100644
--- a/src/USER-SMD/compute_smd_ulsph_strain.cpp
+++ b/src/USER-SMD/compute_smd_ulsph_strain.cpp
@@ -23,7 +23,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "compute_smd_ulsph_strain.h"
#include "atom.h"
#include "update.h"
@@ -35,8 +35,8 @@
#include "pair.h"
#include <iostream>
#include <stdio.h>
-#include "stdlib.h"
-#include "string.h"
+#include <stdlib.h>
+#include <string.h>
#include <Eigen/Eigen>
using namespace Eigen;
using namespace std;
diff --git a/src/USER-SMD/compute_smd_ulsph_strain.h b/src/USER-SMD/compute_smd_ulsph_strain.h
index 820b2450a8..43aaa173bf 100644
--- a/src/USER-SMD/compute_smd_ulsph_strain.h
+++ b/src/USER-SMD/compute_smd_ulsph_strain.h
@@ -17,7 +17,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-SMD/compute_smd_ulsph_strain_rate.cpp b/src/USER-SMD/compute_smd_ulsph_strain_rate.cpp
index b341fdf31a..e35331c64e 100644
--- a/src/USER-SMD/compute_smd_ulsph_strain_rate.cpp
+++ b/src/USER-SMD/compute_smd_ulsph_strain_rate.cpp
@@ -22,7 +22,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "compute_smd_ulsph_strain_rate.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-SMD/compute_smd_ulsph_strain_rate.h b/src/USER-SMD/compute_smd_ulsph_strain_rate.h
index b712ab3c3e..e80d508abd 100644
--- a/src/USER-SMD/compute_smd_ulsph_strain_rate.h
+++ b/src/USER-SMD/compute_smd_ulsph_strain_rate.h
@@ -17,7 +17,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-SMD/compute_smd_ulsph_stress.cpp b/src/USER-SMD/compute_smd_ulsph_stress.cpp
index dc723fc639..9be8646f13 100644
--- a/src/USER-SMD/compute_smd_ulsph_stress.cpp
+++ b/src/USER-SMD/compute_smd_ulsph_stress.cpp
@@ -22,7 +22,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "compute_smd_ulsph_stress.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-SMD/compute_smd_ulsph_stress.h b/src/USER-SMD/compute_smd_ulsph_stress.h
index 4656076e48..04de0a7304 100644
--- a/src/USER-SMD/compute_smd_ulsph_stress.h
+++ b/src/USER-SMD/compute_smd_ulsph_stress.h
@@ -17,7 +17,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-SMD/compute_smd_vol.cpp b/src/USER-SMD/compute_smd_vol.cpp
index 1826e3d976..658ede6439 100644
--- a/src/USER-SMD/compute_smd_vol.cpp
+++ b/src/USER-SMD/compute_smd_vol.cpp
@@ -22,7 +22,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "compute_smd_vol.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-SMD/fix_smd_adjust_dt.cpp b/src/USER-SMD/fix_smd_adjust_dt.cpp
index 48d5835059..4920160a30 100644
--- a/src/USER-SMD/fix_smd_adjust_dt.cpp
+++ b/src/USER-SMD/fix_smd_adjust_dt.cpp
@@ -22,9 +22,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "fix_smd_adjust_dt.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-SMD/fix_smd_integrate_tlsph.cpp b/src/USER-SMD/fix_smd_integrate_tlsph.cpp
index a26ffede0d..b364c4813d 100644
--- a/src/USER-SMD/fix_smd_integrate_tlsph.cpp
+++ b/src/USER-SMD/fix_smd_integrate_tlsph.cpp
@@ -22,9 +22,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "fix_smd_integrate_tlsph.h"
#include "atom.h"
#include "force.h"
@@ -37,7 +37,7 @@
#include "neighbor.h"
#include "comm.h"
#include "modify.h"
-#include "stdio.h"
+#include <stdio.h>
#include <iostream>
using namespace Eigen;
diff --git a/src/USER-SMD/fix_smd_integrate_ulsph.cpp b/src/USER-SMD/fix_smd_integrate_ulsph.cpp
index 91b974b400..3dbf453349 100644
--- a/src/USER-SMD/fix_smd_integrate_ulsph.cpp
+++ b/src/USER-SMD/fix_smd_integrate_ulsph.cpp
@@ -22,12 +22,12 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdio.h"
-#include "string.h"
+#include <stdio.h>
+#include <string.h>
#include "fix_smd_integrate_ulsph.h"
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "atom.h"
#include "comm.h"
#include "force.h"
diff --git a/src/USER-SMD/fix_smd_move_triangulated_surface.cpp b/src/USER-SMD/fix_smd_move_triangulated_surface.cpp
index ab81caeba3..e452923bd4 100644
--- a/src/USER-SMD/fix_smd_move_triangulated_surface.cpp
+++ b/src/USER-SMD/fix_smd_move_triangulated_surface.cpp
@@ -22,12 +22,12 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdio.h"
-#include "string.h"
+#include <stdio.h>
+#include <string.h>
#include "fix_smd_move_triangulated_surface.h"
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "atom.h"
#include "comm.h"
#include "force.h"
diff --git a/src/USER-SMD/fix_smd_setvel.cpp b/src/USER-SMD/fix_smd_setvel.cpp
index dbf21670f9..30ebbeb332 100644
--- a/src/USER-SMD/fix_smd_setvel.cpp
+++ b/src/USER-SMD/fix_smd_setvel.cpp
@@ -23,8 +23,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
-#include "stdlib.h"
+#include <string.h>
+#include <stdlib.h>
#include "fix_smd_setvel.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp b/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp
index 79c22e1056..76fd8021b6 100644
--- a/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp
+++ b/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp
@@ -25,9 +25,9 @@
------------------------------------------------------------------------- */
#include "lattice.h"
-#include "mpi.h"
-#include "string.h"
-#include "stdio.h"
+#include <mpi.h>
+#include <string.h>
+#include <stdio.h>
#include "fix_smd_tlsph_reference_configuration.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-SMD/fix_smd_wall_surface.cpp b/src/USER-SMD/fix_smd_wall_surface.cpp
index 41866b1d3e..0827234265 100644
--- a/src/USER-SMD/fix_smd_wall_surface.cpp
+++ b/src/USER-SMD/fix_smd_wall_surface.cpp
@@ -15,7 +15,7 @@
Contributing authors: Mike Parks (SNL), Ezwanur Rahman, J.T. Foster (UTSA)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "fix_smd_wall_surface.h"
#include "atom.h"
#include "domain.h"
diff --git a/src/USER-SMD/pair_smd_hertz.cpp b/src/USER-SMD/pair_smd_hertz.cpp
index b39ea946c0..0bcf2c8a3e 100644
--- a/src/USER-SMD/pair_smd_hertz.cpp
+++ b/src/USER-SMD/pair_smd_hertz.cpp
@@ -26,10 +26,10 @@
Contributing author: Mike Parks (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "float.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <float.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_smd_hertz.h"
#include "atom.h"
#include "domain.h"
diff --git a/src/USER-SMD/pair_smd_hertz.h b/src/USER-SMD/pair_smd_hertz.h
index 8a207709ad..6b40b6bb5c 100644
--- a/src/USER-SMD/pair_smd_hertz.h
+++ b/src/USER-SMD/pair_smd_hertz.h
@@ -17,7 +17,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-SMD/pair_smd_tlsph.cpp b/src/USER-SMD/pair_smd_tlsph.cpp
index e31d5125c9..aee5eefcc2 100644
--- a/src/USER-SMD/pair_smd_tlsph.cpp
+++ b/src/USER-SMD/pair_smd_tlsph.cpp
@@ -23,10 +23,10 @@
------------------------------------------------------------------------- */
#include "group.h"
-#include "math.h"
-#include "float.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <float.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_smd_tlsph.h"
#include "fix_smd_tlsph_reference_configuration.h"
#include "atom.h"
diff --git a/src/USER-SMD/pair_smd_triangulated_surface.cpp b/src/USER-SMD/pair_smd_triangulated_surface.cpp
index 6d27187260..f5db6acd8e 100644
--- a/src/USER-SMD/pair_smd_triangulated_surface.cpp
+++ b/src/USER-SMD/pair_smd_triangulated_surface.cpp
@@ -26,10 +26,10 @@
Contributing author: Mike Parks (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "float.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <float.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_smd_triangulated_surface.h"
#include "atom.h"
#include "domain.h"
diff --git a/src/USER-SMD/pair_smd_triangulated_surface.h b/src/USER-SMD/pair_smd_triangulated_surface.h
index 9f92e05ca4..6332313646 100644
--- a/src/USER-SMD/pair_smd_triangulated_surface.h
+++ b/src/USER-SMD/pair_smd_triangulated_surface.h
@@ -17,7 +17,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/USER-SMD/pair_smd_ulsph.cpp b/src/USER-SMD/pair_smd_ulsph.cpp
index 37fb48b18c..d048d0b8e7 100644
--- a/src/USER-SMD/pair_smd_ulsph.cpp
+++ b/src/USER-SMD/pair_smd_ulsph.cpp
@@ -22,10 +22,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "float.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <float.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_smd_ulsph.h"
#include "atom.h"
#include "domain.h"
diff --git a/src/USER-SMD/smd_material_models.cpp b/src/USER-SMD/smd_material_models.cpp
index 8660297170..228d1c709a 100644
--- a/src/USER-SMD/smd_material_models.cpp
+++ b/src/USER-SMD/smd_material_models.cpp
@@ -23,7 +23,7 @@
------------------------------------------------------------------------- */
#include <iostream>
#include "math_special.h"
-#include "stdio.h"
+#include <stdio.h>
#include <Eigen/Eigen>
diff --git a/src/USER-SMTBQ/pair_smtbq.cpp b/src/USER-SMTBQ/pair_smtbq.cpp
index 52b431a8c2..0955f7eee2 100644
--- a/src/USER-SMTBQ/pair_smtbq.cpp
+++ b/src/USER-SMTBQ/pair_smtbq.cpp
@@ -10,27 +10,27 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-
+
/* ----------------------------------------------------------------------
The SMTBQ code has been developed with the financial support of CNRS and
of the Regional Council of Burgundy (Convention n¡ 2010-9201AAO037S03129)
-
+
Copyright (2015)
Universite de Bourgogne : Nicolas SALLES, Olivier POLITANO
Universite de Paris-Sud Orsay : R. Tetot
Aalto University (Finland) : E. Maras
-
+
Please cite the related publication:
- N. Salles, O. Politano, E. Amzallag and R. Tetot,
+ N. Salles, O. Politano, E. Amzallag and R. Tetot,
Comput. Mater. Sci., 111 (2016) 181-189
-
+
Contact : lammps@u-bourgogne.fr
-
+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
@@ -38,10 +38,10 @@
<http://www.gnu.org/licenses/>.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_smtbq.h"
#include "atom.h"
#include "comm.h"
@@ -57,7 +57,7 @@
#include "domain.h"
#include <iostream>
-#include <iomanip>
+#include <iomanip>
#include <string>
#include <fstream>
@@ -85,7 +85,7 @@ PairSMTBQ::PairSMTBQ(LAMMPS *lmp) : Pair(lmp)
{
MPI_Comm_rank(world,&me);
MPI_Comm_size(world,&nproc);
-
+
single_enable = 0;
restartinfo = 0;
one_coeff = 1;
@@ -114,13 +114,13 @@ PairSMTBQ::PairSMTBQ(LAMMPS *lmp) : Pair(lmp)
tabsmr = NULL;
dtabsmb = NULL;
dtabsmr = NULL;
-
+
sbcov = NULL;
coord = NULL;
sbmet = NULL;
chimet = NULL;
ecov = NULL;
-
+
potmad = NULL;
potself = NULL;
potcov = NULL;
@@ -137,12 +137,12 @@ PairSMTBQ::PairSMTBQ(LAMMPS *lmp) : Pair(lmp)
nQEqall = NULL;
nteam = 0;
cluster = 0;
-
+
Nevery = 0.0;
Neverypot = 0.0;
-
+
fct = NULL;
-
+
maxpage = 0;
@@ -183,7 +183,7 @@ PairSMTBQ::~PairSMTBQ()
memory->destroy(dfafb);
memory->destroy(potqn);
memory->destroy(dpotqn);
-
+
memory->destroy(ecov);
memory->destroy(sbcov);
memory->destroy(coord);
@@ -192,7 +192,7 @@ PairSMTBQ::~PairSMTBQ()
memory->destroy(tabsmr);
memory->destroy(dtabsmb);
memory->destroy(dtabsmr);
-
+
memory->destroy(potmad);
memory->destroy(potself);
memory->destroy(potcov);
@@ -205,7 +205,7 @@ PairSMTBQ::~PairSMTBQ()
memory->destroy(nQEqall);
memory->destroy(nQEqcall);
memory->destroy(nQEqaall);
-
+
memory->destroy(qf);
memory->destroy(q1);
memory->destroy(q2);
@@ -217,7 +217,7 @@ PairSMTBQ::~PairSMTBQ()
delete [] map;
delete [] esm;
}
-
+
memory->destroy(fct);
}
@@ -301,16 +301,16 @@ void PairSMTBQ::coeff(int narg, char **arg)
if (comm->me == 0 && screen) fprintf(screen,"Pair SMTBQ:\n");
if (comm->me == 0 && screen)
- fprintf(screen," generating Coulomb integral lookup table ...\n");
-
+ fprintf(screen," generating Coulomb integral lookup table ...\n");
+
tabqeq();
-
+
// ------------
if (comm->me == 0 && screen)
fprintf(screen," generating Second Moment integral lookup table ...\n");
-
+
tabsm();
// ------------
@@ -320,7 +320,7 @@ void PairSMTBQ::coeff(int narg, char **arg)
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
-
+
// set setflag i,j for type pairs where both are mapped to elements
@@ -330,7 +330,7 @@ void PairSMTBQ::coeff(int narg, char **arg)
if (map[i] >= 0 && map[j] >= 0) {
setflag[i][j] = 1;
count++;
- }
+ }
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
@@ -369,7 +369,7 @@ double PairSMTBQ::init_one(int i, int j)
return cutmax;
}
-/* ----------------------------------------------------------------------
+/* ----------------------------------------------------------------------
---------------------------------------------------------------------- */
void PairSMTBQ::read_file(char *file)
@@ -384,7 +384,7 @@ void PairSMTBQ::read_file(char *file)
nparams = 0;
maxparam = 0;
maxintparam = 0;
-
+
verbose = 1;
verbose = 0;
@@ -400,7 +400,7 @@ void PairSMTBQ::read_file(char *file)
// store line of params if all 3 element tags are in element list
char *ptr;
-
+
ptr = (char*) malloc(sizeof(char)*MAXLINE);
words = (char**) malloc(sizeof(char*)*MAXTOKENS);
for (i=0; i < MAXTOKENS; i++)
@@ -408,33 +408,33 @@ void PairSMTBQ::read_file(char *file)
/* strip comment, skip line if blank */
-
+
if (verbose) printf ("\n");
fgets(ptr,MAXLINE,fp);
while (strchr(ptr,'#')) {
if (verbose) printf ("%s",ptr);
fgets(ptr,MAXLINE,fp);
- }
-
-
+ }
+
+
// Nombre d'atome different dans la structure
- // ===============================================
+ // ===============================================
c = Tokenize( ptr, &words );
num_atom_types = atoi(words[1]);
if (verbose) printf (" %s %d\n", words[0], num_atom_types);
-
+
memory->create(intype,num_atom_types,num_atom_types,"pair:intype");
-
- m = 0;
+
+ m = 0;
for (i = 0; i < num_atom_types; i++) {
for (j = 0; j < num_atom_types; j++) {
- if (j < i) { intype[i][j] = intype[j][i];}
+ if (j < i) { intype[i][j] = intype[j][i];}
else { intype[i][j] = 0;
- m = m + 1; }
+ m = m + 1; }
if (verbose) printf ("i %d, j %d, intype %d - nb pair %d\n",i,j,intype[i][j],m);
}
- }
-
+ }
+
// load up parameter settings and error check their values
if (nparams == maxparam) {
@@ -445,51 +445,51 @@ void PairSMTBQ::read_file(char *file)
intparams = (Intparam *) memory->srealloc(intparams,(maxintparam+1)*sizeof(Intparam),
"pair:intparams");
}
-
+
for (i=0; i < num_atom_types; i++)
params[i].nom = (char*) malloc(sizeof(char)*3);
-
+
for (i=1; i <= maxintparam; i++)
intparams[i].typepot = (char*) malloc(sizeof(char)*15);
-
+
for (i=1; i <= maxintparam; i++)
intparams[i].mode = (char*) malloc(sizeof(char)*6);
-
+
QEqMode = (char*) malloc(sizeof(char)*18);
Bavard = (char*) malloc(sizeof(char)*5);
QInitMode = (char*) malloc(sizeof(char)*18);
writepot = (char*) malloc(sizeof(char)*5);
writeenerg = (char*) malloc(sizeof(char)*5);
-
-
+
+
// Little loop for ion's parameters
// ================================================
for (i=0; i<num_atom_types; i++) {
-
- fgets(ptr,MAXLINE,fp); if (verbose) printf ("%s",ptr);
+
+ fgets(ptr,MAXLINE,fp); if (verbose) printf ("%s",ptr);
// Line 2 - Al
-
+
fgets( ptr, MAXLINE, fp);
c= Tokenize( ptr, &words );
strcpy(params[i].nom , words[1]);
params[i].sto = atof(words[2]);
if (verbose) printf (" %s %s %f\n", words[0],params[i].nom,params[i].sto);
-
+
//Line 3 - Charges
fgets( ptr, MAXLINE, fp);
- c= Tokenize( ptr, &words );
-
- params[i].qform = atof(words[1]);
+ c= Tokenize( ptr, &words );
+
+ params[i].qform = atof(words[1]);
params[i].masse = atof(words[2]);
if (verbose) printf (" %s %f %f \n", words[0],params[i].qform, params[i].masse);
-
+
// Line 4 - Parametres QEq
-
+
fgets( ptr, MAXLINE, fp);
- c=Tokenize ( ptr, &words );
- params[i].ne = atof(words[1]) ;
+ c=Tokenize ( ptr, &words );
+ params[i].ne = atof(words[1]) ;
params[i].chi = atof(words[2]) ;
params[i].dj = atof(words[3]) ;
@@ -497,17 +497,17 @@ void PairSMTBQ::read_file(char *file)
params[i].R = atof(words[4]) ;
if (verbose) printf(" %s %f %f %f %f\n",words[0],params[i].ne,params[i].chi,
params[i].dj,params[i].R);
- } else {
+ } else {
if (verbose) printf(" %s %f %f %f\n",words[0],params[i].ne,params[i].chi,params[i].dj);
}
-
- // Line 4bis - Coordinance et rayon pour Ox
+
+ // Line 4bis - Coordinance et rayon pour Ox
if(strcmp(params[i].nom,"O")==0){
fgets( ptr, MAXLINE, fp);
- c=Tokenize ( ptr, &words );
-
+ c=Tokenize ( ptr, &words );
+
coordOxBB= atof(words[1]) ;
coordOxBulk= atof(words[2]) ;
coordOxSurf= atof(words[3]) ;
@@ -516,186 +516,186 @@ void PairSMTBQ::read_file(char *file)
ROxSurf = atof(words[6]) ;
if (verbose) printf(" %s %f %f %f %f %f %f\n",words[0],coordOxBB,coordOxBulk,coordOxSurf,ROxBB,params[i].R,ROxSurf);
}
-
+
// Ligne 5 - Nombre d'etats partages
-
+
fgets( ptr, MAXLINE, fp);
c=Tokenize ( ptr, &words );
params[i].n0 = atof(words[1]);
if (verbose) printf(" %s %f\n",words[0],params[i].n0);
-
+
// Parametres de Slater
params[i].dzeta = (2.0*params[i].ne + 1.0)/(4.0*params[i].R);
if (verbose) printf (" Parametre dzeta (Slater) : %f\n",params[i].dzeta);
-
+
} // Fin elements i
- /* =====================================================================
+ /* =====================================================================
reading the interaction's parameters
- ===================================================================== */
-
- m = 0; maxintsm = 0; //
+ ===================================================================== */
+
+ m = 0; maxintsm = 0; //
for (k=0 ; k<=maxintparam ; k++){intparams[k].intsm = 0;}
// ---------------------------------
for (k = 0; k < maxintparam; k++) {
- // ---------------------------------
+ // ---------------------------------
m += 1;
-
- // Ligne 5 - parametre des potentiels
+
+ // Ligne 5 - parametre des potentiels
fgets(ptr,MAXLINE,fp); if (verbose) printf ("%s",ptr);
-
+
// Lecture des protagonistes
fgets( ptr, MAXLINE, fp);
c= Tokenize( ptr, &words );
-
+
test = 0;
- for (i = 0; i <num_atom_types; i++)
+ for (i = 0; i <num_atom_types; i++)
{
if (strcmp(params[i].nom,words[1])==0) break;
- if (i == num_atom_types - 1) test = 1;
+ if (i == num_atom_types - 1) test = 1;
}
// if (test == 0) printf (" on a %s -> %d = %s\n",words[1],i,params[i].nom);
-
- for (j = 0; j <num_atom_types; j++)
+
+ for (j = 0; j <num_atom_types; j++)
{
if (strcmp(params[j].nom,words[2])==0) break;
- if (j == num_atom_types - 1) test = 1;
+ if (j == num_atom_types - 1) test = 1;
}
// if (test == 0) printf (" on a %s -> %d = %s\n",words[2],j,params[j].nom);
-
-
+
+
if ( test == 1 ) {
if (verbose) printf ("========== fin des interaction ==========\n");
break ; }
-
-
+
+
intype[i][j] = m;
intype[j][i] = intype[i][j];
strcpy( intparams[m].typepot , words[3] );
intparams[m].intsm = 0;
if (verbose) printf (" itype %d jtype %d - intype %d\n",i,j,intype[i][j]);
-
- if (strcmp(intparams[m].typepot,"second_moment") !=0 &&
- strcmp(intparams[m].typepot,"buck") != 0 &&
+
+ if (strcmp(intparams[m].typepot,"second_moment") !=0 &&
+ strcmp(intparams[m].typepot,"buck") != 0 &&
strcmp(intparams[m].typepot,"buckPlusAttr") != 0) {
- error->all(FLERR,"the potential other than second_moment or buckingham have not treated here\n");}
-
-
+ error->all(FLERR,"the potential other than second_moment or buckingham have not treated here\n");}
+
+
// On detemrine le type d'interaction
- // -----------------------------------
+ // -----------------------------------
if (strcmp(intparams[m].typepot,"second_moment") == 0) {
- maxintsm += 1;
+ maxintsm += 1;
strcpy( intparams[m].mode , words[4] );
intparams[m].intsm = maxintsm;
-
- if (strcmp(intparams[m].mode,"oxide") != 0 &&
- strcmp(intparams[m].mode,"metal") != 0){
+
+ if (strcmp(intparams[m].mode,"oxide") != 0 &&
+ strcmp(intparams[m].mode,"metal") != 0){
error->all(FLERR,"needs mode to second moment interaction : oxide or metal"); }
// if (strcmp(intparams[m].mode,"oxide") == 0)
// intparams[m].ncov = min((params[i].sto)*(params[i].n0),(params[j].sto)*(params[j].n0));
-
+
if (verbose) printf(" %s %s %s %s %s \n",words[0],words[1],words[2],
- intparams[m].typepot,intparams[m].mode);
+ intparams[m].typepot,intparams[m].mode);
fgets( ptr, MAXLINE, fp);
c= Tokenize( ptr, &words );
-
- intparams[m].a = atof(words[1]) ;
- intparams[m].p = atof(words[2]) ;
- intparams[m].ksi = atof(words[3]) ;
+
+ intparams[m].a = atof(words[1]) ;
+ intparams[m].p = atof(words[2]) ;
+ intparams[m].ksi = atof(words[3]) ;
intparams[m].q = atof(words[4]) ;
if (verbose) printf (" %s %f %f %f %f\n",words[0],
intparams[m].a,intparams[m].p,intparams[m].ksi,intparams[m].q);
-
+
// Ligne 6 - rayon de coupure potentiel SM
-
+
fgets( ptr, MAXLINE, fp);
c= Tokenize( ptr, &words );
-
+
intparams[m].dc1 = atof(words[1]) ;
intparams[m].dc2 = atof(words[2]) ;
intparams[m].r0 = atof(words[3]) ;
-
+
if (strcmp(intparams[m].mode,"metal") == 0) {
if (verbose) printf (" %s %f %f %f\n",words[0],
intparams[m].dc1,intparams[m].dc2,intparams[m].r0);
- } else {
+ } else {
if (verbose) printf (" %s %f %f %f\n",words[0],
intparams[m].dc1,intparams[m].dc2,intparams[m].r0);
}
-
-
+
+
} else if (strcmp(intparams[m].typepot,"buck") == 0) {
-
+
if (verbose) printf(" %s %s %s %s\n",words[0],words[1],words[2],
- intparams[m].typepot);
-
+ intparams[m].typepot);
+
fgets( ptr, MAXLINE, fp);
c= Tokenize( ptr, &words );
-
+
intparams[m].abuck = atof(words[1]) ; intparams[m].rhobuck = atof(words[2]) ;
if (verbose) printf (" %s %f %f\n",words[0],intparams[m].abuck,intparams[m].rhobuck);
-
+
}
else if (strcmp(intparams[m].typepot,"buckPlusAttr") == 0) {
-
+
if (verbose) printf(" %s %s %s %s\n",words[0],words[1],words[2],
- intparams[m].typepot);
-
+ intparams[m].typepot);
+
fgets( ptr, MAXLINE, fp);
c= Tokenize( ptr, &words );
-
+
intparams[m].abuck = atof(words[1]) ; intparams[m].rhobuck = atof(words[2]) ;
if (verbose) printf (" %s %f %f\n",words[0],intparams[m].abuck,intparams[m].rhobuck);
-
+
fgets( ptr, MAXLINE, fp);
c= Tokenize( ptr, &words );
-
+
intparams[m].aOO = atof(words[1]) ; intparams[m].bOO = atof(words[2]) ;
intparams[m].r1OO = atof(words[3]) ;intparams[m].r2OO = atof(words[4]) ;
if (verbose) printf (" %s %f %f %f %f \n",words[0],intparams[m].aOO,
intparams[m].bOO,intparams[m].r1OO,intparams[m].r2OO);
-
+
}
if (verbose) printf (" intsm %d \n",intparams[m].intsm);
-
+
} // for maxintparam
-
-
+
+
/* ====================================================================
tables Parameters
- ==================================================================== */
-
+ ==================================================================== */
+
// Ligne 9 - rayon de coupure Electrostatique
if (test == 0) {
- fgets(ptr,MAXLINE,fp);
+ fgets(ptr,MAXLINE,fp);
if (verbose) printf ("%s\n",ptr);
-
+
fgets( ptr, MAXLINE, fp);
}
- c= Tokenize( ptr, &words );
+ c= Tokenize( ptr, &words );
- for (i=0 ; i<num_atom_types; i++) { params[i].cutsq = atof(words[1]); }
- cutmax = atof(words[1]);
+ for (i=0 ; i<num_atom_types; i++) { params[i].cutsq = atof(words[1]); }
+ cutmax = atof(words[1]);
if (verbose) printf (" %s %f\n",words[0],params[0].cutsq);
-
+
// Ligne 9 - parametre pour les tableaux
-
+
fgets( ptr, MAXLINE, fp);
c= Tokenize( ptr, &words );
-
+
rmin = atof(words[1]) ; dr = atof(words[2]);
if (verbose) printf (" %s %f %f\n",words[0],rmin,dr);
-
+
kmax = int(cutmax*cutmax/(2.0*dr*rmin));
- ds = cutmax*cutmax/double(kmax) ;
- if (verbose) printf (" kmax %d et ds %f\n",kmax,ds);
+ ds = cutmax*cutmax/double(kmax) ;
+ if (verbose) printf (" kmax %d et ds %f\n",kmax,ds);
- /* ======================================================== */
+ /* ======================================================== */
fgets( ptr, MAXLINE, fp);
if (verbose) printf ("%s",ptr);
@@ -710,8 +710,8 @@ void PairSMTBQ::read_file(char *file)
precision = atof(words[2]);
if (verbose) printf (" %s %d %f\n",words[0],loopmax,precision);
- /* Param de coordination ============================================= */
-
+ /* Param de coordination ============================================= */
+
fgets( ptr, MAXLINE, fp);
if (verbose) printf ("%s",ptr);
@@ -721,22 +721,22 @@ void PairSMTBQ::read_file(char *file)
r2Coord = atof(words[2]);
if (verbose) printf (" %s %f %f\n",words[0],r1Coord,r2Coord);
-
- /* Mode for QInit============================================= */
+
+ /* Mode for QInit============================================= */
fgets( ptr, MAXLINE, fp);
if (verbose) printf ("%s",ptr);
fgets( ptr, MAXLINE, fp);
c= Tokenize( ptr, &words );
- strcpy( QInitMode , words[1] );
+ strcpy( QInitMode , words[1] );
if (strcmp(QInitMode,"true") == 0) { QOxInit= atof(words[2]); }
- else { QOxInit = 0.0; }
+ else { QOxInit = 0.0; }
if (verbose) printf (" %s %s %f\n",words[0],QInitMode,QOxInit);
- /* Mode for QEq============================================= */
-
+ /* Mode for QEq============================================= */
+
fgets( ptr, MAXLINE, fp);
if (verbose) printf ("%s",ptr);
@@ -763,12 +763,12 @@ void PairSMTBQ::read_file(char *file)
if (verbose) printf (" %s %f \n",words[0],zlim1QEq);
}
- else if (strcmp(QEqMode,"QEqAll") != 0 &&
+ else if (strcmp(QEqMode,"QEqAll") != 0 &&
strcmp(QEqMode,"QEqAllParallel") != 0 &&
strcmp(QEqMode,"Surface") != 0 )
{ error->all(FLERR,"The QEq Mode is not known. QEq mode should be :\n Possible QEq modes | parameters\n QEqAll | no parameters\n QEqAllParallel | no parameters\n Surface | zlim (QEq only for z>zlim)\n BulkFromSlab | zlim1 zlim2 (QEq only for zlim1<z<zlim2)\n"); }
- /* Bavard============================================= */
+ /* Bavard============================================= */
fgets( ptr, MAXLINE, fp);
if (verbose) printf ("%s",ptr);
@@ -777,7 +777,7 @@ void PairSMTBQ::read_file(char *file)
c= Tokenize( ptr, &words );
strcpy( Bavard , words[1] );
if (verbose) printf (" %s %s\n",words[0],Bavard);
-
+
// ---------------------------------------
// Writing the energy component.
@@ -786,7 +786,7 @@ void PairSMTBQ::read_file(char *file)
strcpy( writeenerg, words[1] );
if (strcmp (writeenerg,"true") == 0) { Nevery = atof(words[2]); }
else { Nevery = 0.0; }
- if (verbose) printf (" %s %s %f\n",words[0],writeenerg,Nevery);
+ if (verbose) printf (" %s %s %f\n",words[0],writeenerg,Nevery);
// ---------------------------------------
// Writing the chimical electronic potential.
@@ -798,8 +798,8 @@ void PairSMTBQ::read_file(char *file)
else { Neverypot = 0.0; }
if (verbose) printf (" %s %s %f\n",words[0],writepot,Neverypot);
-
- /* ======================================================== */
+
+ /* ======================================================== */
/* deallocate helper storage */
for( i = 0; i < MAXTOKENS ; i++ ) free( words[i] );
@@ -807,31 +807,31 @@ void PairSMTBQ::read_file(char *file)
free( ptr );
fclose(fp);
-
+
// === Rayon de coupure premier voisins : 1,2*r0
- for (i=0 ; i<num_atom_types ; i++) {
+ for (i=0 ; i<num_atom_types ; i++) {
for (j=0 ; j<=i ; j++)
{
m = intype[i][j];
if (m == 0) continue;
if (intparams[m].intsm == 0) continue;
-
+
intparams[m].neig_cut = 1.2*intparams[m].r0;
if (strcmp(intparams[m].typepot,"second_moment") == 0 )
- if (verbose) printf (" Rc 1er voisin, typepot %s -> %f Ang\n",
+ if (verbose) printf (" Rc 1er voisin, typepot %s -> %f Ang\n",
intparams[m].typepot,intparams[m].neig_cut);
}
}
-
+
//A adapter au STO
ncov = min((params[0].sto)*(params[0].n0),(params[1].sto)*(params[1].n0));
-
+
if (verbose) printf (" Parametre ncov = %f\n",ncov);
if (verbose) printf (" ********************************************* \n");
-}
+}
/* ----------------------------------------------------------------------
* COMPUTE
@@ -842,17 +842,17 @@ void PairSMTBQ::compute(int eflag, int vflag)
int i,j,ii,jj,inum,jnum,m,gp;
int itag,jtag,itype,jtype;
int *ilist,*jlist,*numneigh,**firstneigh;
-
+
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
double rsq,iq,jq,Eself,natom;
double ecovtot,ErepOO,ErepMO,Eion,Ecoh;
double **tmp,**tmpAll,*nmol;
double dq,dqcov;
-
-
+
+
int bavard;
-
-
+
+
if (atom->nmax > nmax) {
memory->destroy(ecov);
memory->destroy(potmad);
@@ -877,7 +877,7 @@ void PairSMTBQ::compute(int eflag, int vflag)
memory->create(sbcov,nmax,"pair:sbcov");
memory->create(coord,nmax,"pair:coord");
memory->create(sbmet,nmax,"pair:sbmet");
- memory->create(chimet,nmax,"pair:chimet");
+ memory->create(chimet,nmax,"pair:chimet");
memory->create(flag_QEq,nmax,"pair:flag_QEq");
memory->create(qf,nmax,"pair:qf");
memory->create(q1,nmax,"pair:q1");
@@ -888,7 +888,7 @@ void PairSMTBQ::compute(int eflag, int vflag)
evdwl = ecoul = ecovtot = ErepOO = ErepMO = Eion = 0.0;
Eself = 0.0;
-
+
if (eflag || vflag) { ev_setup(eflag,vflag); }
else { evflag = vflag_fdotr = vflag_atom = 0; }
@@ -901,7 +901,7 @@ void PairSMTBQ::compute(int eflag, int vflag)
int nlocal = atom->nlocal;
int step = update->ntimestep;
struct timeval start, end;
-
+
inum = list->inum;
ilist = list->ilist;
@@ -911,11 +911,11 @@ void PairSMTBQ::compute(int eflag, int vflag)
if (step == 0 || (Qstep !=0 && fmod(double(step), double(Qstep)) == 0.0 )) Charge();
// ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
// this is necessary to get sbcov or sbmet table in order to caclulate the covalent or metal bonding
- if (Qstep == 0 || fmod(double(step), double(Qstep)) != 0.0 ) QForce_charge(0);
+ if (Qstep == 0 || fmod(double(step), double(Qstep)) != 0.0 ) QForce_charge(0);
- // Charges Communication
- // ----------------------
+ // Charges Communication
+ // ----------------------
forward(q) ; reverse(q);
memory->create(nmol,nteam+1,"pair:nmol");
@@ -934,21 +934,21 @@ void PairSMTBQ::compute(int eflag, int vflag)
0 -> ionic energy
1 -> coulombian energy
2 -> Electrosatic energy (ionic + Coulombian)
- 3 -> Short int. Ox-Ox
+ 3 -> Short int. Ox-Ox
4 -> Short int. SMTB (repulsion)
5 -> Covalent energy SMTB
6 -> Somme des Q(i)²
------------------------------------------------------------------------- */
-
- // -----------
+
+ // -----------
bavard = 0;
// -----------
/* -------------- N-body forces Calcul --------------- */
-
+
for (ii = 0; ii < inum; ii++) {
// ===============================
- i = ilist[ii];
+ i = ilist[ii];
itag = tag[i];
itype = map[type[i]];
iq = q[i];
@@ -971,23 +971,23 @@ void PairSMTBQ::compute(int eflag, int vflag)
Eself = self(¶ms[itype],iq);
tmp[gp][0] += Eself;
tmp[gp][2] += Eself;
-
+
if (evflag) ev_tally_full (i,0.0,2.0*Eself,0.0,0.0,0.0,0.0);
// N-body energy of i
// ---------------------
dq = fabs(params[itype].qform) - fabs(iq);
- dqcov = dq*(2.0*ncov/params[itype].sto - dq);
+ dqcov = dq*(2.0*ncov/params[itype].sto - dq);
- ecov[i] = - sqrt(sbcov[i]*dqcov + sbmet[i]);
- ecovtot += ecov[i];
+ ecov[i] = - sqrt(sbcov[i]*dqcov + sbmet[i]);
+ ecovtot += ecov[i];
tmp[gp][5] += ecov[i];
- if (evflag) ev_tally_full(i,0.0,2.0*ecov[i],0.0,0.0,0.0,0.0);
+ if (evflag) ev_tally_full(i,0.0,2.0*ecov[i],0.0,0.0,0.0,0.0);
-// Coulombian Interaction
+// Coulombian Interaction
// -----------------------
evdwl = 2.0*Vself*iq*iq ;
tmp[gp][1] += Vself*iq*iq;
@@ -996,7 +996,7 @@ void PairSMTBQ::compute(int eflag, int vflag)
if (evflag) ev_tally_full (i,0.0,evdwl,0.0,0.0,0.0,0.0);
evdwl = 0.0 ;
-
+
jlist = firstneigh[i];
jnum = numneigh[i];
@@ -1019,12 +1019,12 @@ void PairSMTBQ::compute(int eflag, int vflag)
}
// .......................................................................
-
+
// # of interaction
// ----------------
m = intype[itype][jtype];
-
+
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
@@ -1032,41 +1032,41 @@ void PairSMTBQ::compute(int eflag, int vflag)
// ---------------------------------
- if (sqrt(rsq) > cutmax) continue;
+ if (sqrt(rsq) > cutmax) continue;
// ---------------------------------
- // Coulombian Energy
+ // Coulombian Energy
// ------------------
evdwl = 0.0 ; fpair = 0.0;
potqeq(i,j,iq,jq,rsq,fpair,eflag,evdwl);
tmp[gp][1] += evdwl;
tmp[gp][2] += evdwl;
-
-
- // Coulombian Force
+
+
+ // Coulombian Force
// -----------------
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
+ f[i][2] += delz*fpair;
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
-
+
if (evflag)
ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair,delx,dely,delz);
- evdwl = 0.0; fpair = 0.0 ;
+ evdwl = 0.0; fpair = 0.0 ;
-// ---------------------
+// ---------------------
if (m == 0) continue;
// ---------------------
// ----------------------------------------------
- if ( strcmp(intparams[m].typepot,"buck") == 0 ||
+ if ( strcmp(intparams[m].typepot,"buck") == 0 ||
strcmp(intparams[m].typepot,"buckPlusAttr") ==0 ) {
// ----------------------------------------------
@@ -1075,7 +1075,7 @@ void PairSMTBQ::compute(int eflag, int vflag)
ErepOO += evdwl ;
tmp[gp][3] += evdwl;
-
+
// repulsion is pure two-body, sums up pair repulsive forces
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
@@ -1087,7 +1087,7 @@ void PairSMTBQ::compute(int eflag, int vflag)
if (evflag)
ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair,delx,dely,delz);
- evdwl = 0.0; fpair = 0.0 ;
+ evdwl = 0.0; fpair = 0.0 ;
} // ----------------------------------- Rep O-O
@@ -1099,7 +1099,7 @@ void PairSMTBQ::compute(int eflag, int vflag)
ErepOO += evdwl ;
tmp[gp][3] += evdwl;
-
+
// repulsion is pure two-body, sums up pair repulsive forces
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
@@ -1111,7 +1111,7 @@ void PairSMTBQ::compute(int eflag, int vflag)
if (evflag)
ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair,delx,dely,delz);
- evdwl = 0.0; fpair = 0.0 ;
+ evdwl = 0.0; fpair = 0.0 ;
} // ----------------------------------- Attr O-O
@@ -1120,7 +1120,7 @@ void PairSMTBQ::compute(int eflag, int vflag)
if (strcmp(intparams[m].typepot,"second_moment") != 0 ) continue;
// -----------------------------------------------------------------
-
+
if (sqrt(rsq) > intparams[m].dc2) continue;
// -------------------------------------------
@@ -1130,7 +1130,7 @@ void PairSMTBQ::compute(int eflag, int vflag)
repulsive(&intparams[m],rsq,i,j,fpair,eflag,evdwl);
ErepMO += evdwl;
tmp[gp][4] += 2.0*evdwl;
-
+
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
@@ -1138,74 +1138,74 @@ void PairSMTBQ::compute(int eflag, int vflag)
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
-
+
if (evflag)
ev_tally(i,j,nlocal,newton_pair,2.0*evdwl,0.0,fpair,delx,dely,delz);
-
+
evdwl = 0.0 ; fpair = 0.0;
// ----- ----- ----- ----- ----- -----
// Attraction : force
// ------------------
- fpair = 0.0;
+ fpair = 0.0;
f_att(&intparams[m], i, j, rsq, fpair) ;
-
+
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
-
+
if (evflag)
ev_tally(i,j,nlocal,newton_pair,0.0,0.0,fpair,delx,dely,delz);
-
- } // --------------------------------- End j
-
+
+ } // --------------------------------- End j
+
} // ---------------------------------- End i
- if (vflag_fdotr) virial_fdotr_compute();
-
-
- for (i = 0; i < nteam+1; i++) {
- MPI_Allreduce(tmp[i],tmpAll[i],7,MPI_DOUBLE,MPI_SUM,world);
+ if (vflag_fdotr) virial_fdotr_compute();
+
+
+ for (i = 0; i < nteam+1; i++) {
+ MPI_Allreduce(tmp[i],tmpAll[i],7,MPI_DOUBLE,MPI_SUM,world);
}
-
-// ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
+
+// ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
if (me == 0 && fmod(double(step), Nevery) == 0.0 && strcmp(writeenerg,"true") == 0) {
-
+
ofstream fichierE;
-
- if (step == 0) { fichierE.open ("Energy_component.txt", ios::out | ios::trunc) ;}
+
+ if (step == 0) { fichierE.open ("Energy_component.txt", ios::out | ios::trunc) ;}
else { fichierE.open ("Energy_component.txt", ios::out | ios::app) ;}
-
+
if (fichierE) fichierE<< setprecision(9) <<step;
-
+
for (gp = 0; gp < nteam+1; gp++) {
if (nmol[gp] == 0) continue;
if (fichierE) fichierE<< setprecision(9) <<" "<<gp<<" "<<nmol[gp]
<<" "<<tmpAll[gp][2]<<" "<<tmpAll[gp][3]<<" "<<tmpAll[gp][4]+tmpAll[gp][5];
- }
+ }
if (fichierE) fichierE<<endl;
- if (fichierE) fichierE.close();
- }
-// ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
-
+ if (fichierE) fichierE.close();
+ }
+// ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
+
if (me == 0&& strcmp(Bavard,"false") != 0) {
printf ("A la fin de Compute\n");
-
+
printf ("Nemton_pair : %d, evflag %d, tail_flag %d,vflag_fdotr %d\n",
newton_pair,evflag,force->pair->tail_flag,vflag_fdotr);
- printf ("neighbor->includegroup %d\n",neighbor->includegroup);
+ printf ("neighbor->includegroup %d\n",neighbor->includegroup);
for (gp=0; gp<nteam+1; gp++) { // -------------------------- Boucle sur les gp
printf ("Energie de la team %d -- %d atome -------(nteam = %d) \n ",gp,int(nmol[gp]),nteam);
-
+
if (nmol[gp] == 0) {
printf (" ============================================ \n \n");
continue;
@@ -1218,29 +1218,29 @@ void PairSMTBQ::compute(int eflag, int vflag)
printf ("Energie cp pair ox : %f | %f par mol\n",tmpAll[gp][3],tmpAll[gp][3]/nmol[gp]);
printf ("Energie cp pair sm : %f | %f par mol\n",tmpAll[gp][4],tmpAll[gp][4]/nmol[gp]);
printf ("Energie cov sm : %f | %f par mol\n",tmpAll[gp][5],tmpAll[gp][5]/nmol[gp]);
-
+
Ecoh = tmpAll[gp][2] + tmpAll[gp][3] + tmpAll[gp][4] + tmpAll[gp][5];
printf ("Energie totale : %f | %f par mol\n",Ecoh,Ecoh/nmol[gp]);
printf ("================================================= \n");
printf (" \n");
- } // ----------------------------------------------------- Boucle sur les gp
+ } // ----------------------------------------------------- Boucle sur les gp
} // ------------ Call me == 0
- memory->destroy(nmol);
+ memory->destroy(nmol);
memory->destroy(tmp);
- memory->destroy(tmpAll);
+ memory->destroy(tmpAll);
}
/* ----------------------------------------------------------------------
- Partie Electrostatique
+ Partie Electrostatique
----------------------------------------------------------------------*/
-
+
double PairSMTBQ::self(Param *param, double qi)
{
double self_tmp;
@@ -1274,49 +1274,49 @@ void PairSMTBQ::tabqeq()
int nntype;
double rc,s,r;
double alf;
-
+
int ii;
double za,zb,ra,rb,gam,dgam,dza,dzb,
- d2zaa,d2zab,d2zbb,d2zra,d2zrb,d2gamr2,na,nb;
+ d2zaa,d2zab,d2zbb,d2zra,d2zrb,d2gamr2,na,nb;
double aCoeff,bCoeff,rcoupe,nang;
-
+
int n = atom->ntypes;
int nlocal = atom->nlocal;
int nghost = atom->nghost;
nmax = atom->nmax;
-
+
verbose = 1;
verbose = 0;
-
+
nntype = int((n+1)*n/2);
-
+
rc = cutmax ;
alf = 0.3 ;
// alf = 0.2 ;
-
+
if (verbose) printf ("kmax %d, ds %f, nmax %d\n",kmax,ds,nmax);
if (verbose) printf ("nlocal = %d, nghost = %d\n",nlocal,nghost);
if (verbose) printf ("nntypes %d, kmax %d, rc %f, n %d\n",nntype,kmax,rc,n);
-
+
// allocate arrays
-
- memory->create(coultype,n,n,"pair:intype");
+
+ memory->create(coultype,n,n,"pair:intype");
memory->create(potqn,kmax+5,"pair:potqn");
memory->create(dpotqn,kmax+5,"pair:dpotqn");
- memory->create(fafb,kmax+5,nntype,"pair:fafb");
+ memory->create(fafb,kmax+5,nntype,"pair:fafb");
memory->create(dfafb,kmax+5,nntype,"pair:dfafb");
- memory->create(fafbOxOxSurf,kmax+5,"pair:fafbOxOxSurf");
+ memory->create(fafbOxOxSurf,kmax+5,"pair:fafbOxOxSurf");
memory->create(dfafbOxOxSurf,kmax+5,"pair:dfafbOxOxSurf");
- memory->create(fafbTiOxSurf,kmax+5,"pair:fafbTiOxSurf");
+ memory->create(fafbTiOxSurf,kmax+5,"pair:fafbTiOxSurf");
memory->create(dfafbTiOxSurf,kmax+5,"pair:dfafbTiOxSurf");
- memory->create(fafbOxOxBB,kmax+5,"pair:fafbOxOxBB");
+ memory->create(fafbOxOxBB,kmax+5,"pair:fafbOxOxBB");
memory->create(dfafbOxOxBB,kmax+5,"pair:dfafbOxOxBB");
- memory->create(fafbTiOxBB,kmax+5,"pair:fafbTiOxB");
+ memory->create(fafbTiOxBB,kmax+5,"pair:fafbTiOxB");
memory->create(dfafbTiOxBB,kmax+5,"pair:dfafbTiOxBB");
-
+
memory->create(ecov,nmax,"pair:ecov");
memory->create(potmad,nmax,"pair:potmad");
memory->create(potself,nmax,"pair:potself");
@@ -1324,17 +1324,17 @@ void PairSMTBQ::tabqeq()
memory->create(sbcov,nmax,"pair:sbcov");
memory->create(coord,nmax,"pair:coord");
memory->create(sbmet,nmax,"pair:sbmet");
- memory->create(chimet,nmax,"pair:chimet");
+ memory->create(chimet,nmax,"pair:chimet");
// memory->create(nvsm,nmax,"pair:nvsm");
// memory->create(vsm,nmax,nmax,"pair:vsm");
- memory->create(flag_QEq,nmax,"pair:flag_QEq");
+ memory->create(flag_QEq,nmax,"pair:flag_QEq");
memory->create(qf,nmax,"pair:qf");
memory->create(q1,nmax,"pair:q1");
memory->create(q2,nmax,"pair:q2");
memory->create(tab_comm,nmax,"pair:tab_comm");
-
+
memory->create(fct,31,"pair:fct");
// set interaction number: 0-0=0, 1-1=1, 0-1=1-0=2
@@ -1354,36 +1354,36 @@ void PairSMTBQ::tabqeq()
if (verbose) printf ("i %d, j %d, coultype %d\n",i,j,coultype[i][j]);
}
}
-
+
// -------- Tabqn --------
// -------------------
- // Ouverture du fichier
+ // Ouverture du fichier
// ofstream fichier("tabqeq.txt", ios::out | ios::trunc) ;
- // -------------------
+ // -------------------
double pi,mu;
pi = 4.0*atan(1.0);
-
- mu = erfc(alf*rc)/rc ;
-
+
+ mu = erfc(alf*rc)/rc ;
+
//if (fichier) fichier <<" r - potqn " <<endl ;
-
- //-------------------------
- for (k=0; k < kmax+5; k++)
+
+ //-------------------------
+ for (k=0; k < kmax+5; k++)
//-------------------------
{
s = double(k)*ds ; r = sqrt(s);
if (k==0) r=10e-30;
potqn[k] = 14.4*(erfc(alf*r)/r - mu) ;
-
- // $$$ Here is (1/r)*dE/dr
- dpotqn[k] = -14.4*( (erfc(alf*r)/(r*r) + 2.0*alf/sqrt(pi)/r*exp(-alf*alf*r*r))/r ) ;
+
+ // $$$ Here is (1/r)*dE/dr
+ dpotqn[k] = -14.4*( (erfc(alf*r)/(r*r) + 2.0*alf/sqrt(pi)/r*exp(-alf*alf*r*r))/r ) ;
}
-
+
Vself = -14.4*(alf/sqrt(pi) + mu*0.5) ;
-
- // --------------------
+
+ // --------------------
// default arrays to zero
for (i = 0; i < kmax+5; i ++) {
@@ -1405,18 +1405,18 @@ void PairSMTBQ::tabqeq()
// Set Tabqeq
double dij,ddij;
-
+
// -------------------
- // Ouverture du fichier
+ // Ouverture du fichier
//ofstream fichier("dtabqeq.txt", ios::out | ios::trunc) ;
- // -------------------
-
+ // -------------------
+
//if (fichier) fichier <<" k , r , fafb , dfafb , dfafb2 , dgam , d(1/r) , dpotqn" <<endl ;
-
+
rcoupe = cutmax ;
double cang ;
-
+
for (i = 0; i < n ; i++){
for (j = i; j < n ; j++){
@@ -1424,35 +1424,35 @@ void PairSMTBQ::tabqeq()
m = coultype[i][j] ;
na = params[i].ne ;
nb = params[j].ne ;
- za = params[i].dzeta ;
+ za = params[i].dzeta ;
zb = params[j].dzeta ;
ra = params[i].R;
rb = params[j].R;
-
- ii = 0 ; nang =cang= 5.0 ;
- // --------------------------
+
+ ii = 0 ; nang =cang= 5.0 ;
+ // --------------------------
for (k = 0; k < kmax+5; k++)
- // --------------------------
+ // --------------------------
{
- gam = dgam = dza = dzb = d2zaa = d2zab =
+ gam = dgam = dza = dzb = d2zaa = d2zab =
d2zbb = d2zra = d2zrb = d2gamr2 = 0.0 ;
dij = 0.0 ;
-
+
s = double(k)*ds ; r = sqrt(s) ;
if (k==0) r=10e-30;
-
+
gammas(na,nb,za,zb,r,gam,dgam,dza,dzb,
d2zaa,d2zab,d2zbb,d2zra,d2zrb,d2gamr2) ;
- // --- Jij
-
+ // --- Jij
+
dij = 14.4 * (1.0/r - double(gam));
ddij = 14.4 * (-1.0/(r*r) - double(dgam)) ;
// Cutting Fonction
-
-
- if (dij < 0.01 && ii==0)
+
+
+ if (dij < 0.01 && ii==0)
{
ii=2;
if (ii==2) if (verbose) printf ("rc : %f\n",r);
@@ -1464,48 +1464,48 @@ void PairSMTBQ::tabqeq()
if (r > rc) {dij = aCoeff *pow((r- rc-nang),2) *exp(bCoeff*r);
ddij = aCoeff*(r- rc-nang) *(2+bCoeff*(r-rc-nang))*exp(bCoeff*r);
}
-
+
if (r > (rc+nang)) {dij = 0.0 ; ddij = 0.0;}
fafb[k][m] = potqn[k] - dij ;
- if (k == 1) fafb[0][m] = fafb[k][m] ;
-
+ if (k == 1) fafb[0][m] = fafb[k][m] ;
+
dfafb[k][m] = dpotqn[k] - ddij/r ;
}
// Make the table fafbOxOxSurf
rc = cutmax;
- if(strcmp(params[i].nom,"O")==0 || strcmp(params[j].nom,"O")==0){
+ if(strcmp(params[i].nom,"O")==0 || strcmp(params[j].nom,"O")==0){
if(strcmp(params[i].nom,"O")==0) {
- ra = ROxSurf;
+ ra = ROxSurf;
za = (2.0*params[i].ne + 1.0)/(4.0*ra);}
if(strcmp(params[j].nom,"O")==0) {
- rb = ROxSurf;
+ rb = ROxSurf;
zb = (2.0*params[j].ne + 1.0)/(4.0*rb); }
-
-
+
+
ii = 0 ; nang =cang= 5.0 ;
- // --------------------------
+ // --------------------------
for (k = 0; k < kmax+5; k++)
- // --------------------------
+ // --------------------------
{
- gam = dgam = dza = dzb = d2zaa = d2zab =
+ gam = dgam = dza = dzb = d2zaa = d2zab =
d2zbb = d2zra = d2zrb = d2gamr2 = 0.0 ;
dij = 0.0 ;
-
+
s = double(k)*ds ; r = sqrt(s) ;
if (k==0) r=10e-30;
-
+
gammas(na,nb,za,zb,r,gam,dgam,dza,dzb,
d2zaa,d2zab,d2zbb,d2zra,d2zrb,d2gamr2) ;
- // --- Jij
-
+ // --- Jij
+
dij = 14.4 * (1.0/r - double(gam));
ddij = 14.4 * (-1.0/(r*r) - double(dgam)) ;
- if (dij < 0.01 && ii==0)
+ if (dij < 0.01 && ii==0)
{
ii=2;
if (ii==2) if (verbose) printf ("rc : %f\n",r);
@@ -1519,53 +1519,53 @@ void PairSMTBQ::tabqeq()
}
- if (r > (rc+nang)) {dij = 0.0 ; ddij = 0.0;}
-
- if(strcmp(params[i].nom,"O")==0 && strcmp(params[j].nom,"O")==0){
+ if (r > (rc+nang)) {dij = 0.0 ; ddij = 0.0;}
+
+ if(strcmp(params[i].nom,"O")==0 && strcmp(params[j].nom,"O")==0){
fafbOxOxSurf[k] = potqn[k] - dij ;
- if (k == 1) fafbOxOxSurf[0] = fafbOxOxSurf[k] ;
-
+ if (k == 1) fafbOxOxSurf[0] = fafbOxOxSurf[k] ;
+
dfafbOxOxSurf[k] = dpotqn[k] - ddij/r ;
}
else { fafbTiOxSurf[k] = potqn[k] - dij ;
- if (k == 1) fafbTiOxSurf[0] = fafbTiOxSurf[k] ;
-
+ if (k == 1) fafbTiOxSurf[0] = fafbTiOxSurf[k] ;
+
dfafbTiOxSurf[k] = dpotqn[k] - ddij/r ;}
-
+
}
-
+
} //for k
//end of make the table fafbOxOxSurf
// Makes the table fafbOxOxBB
rc = cutmax;
- if(strcmp(params[i].nom,"O")==0 || strcmp(params[j].nom,"O")==0){
+ if(strcmp(params[i].nom,"O")==0 || strcmp(params[j].nom,"O")==0){
if(strcmp(params[i].nom,"O")==0) {
- ra = ROxBB;
+ ra = ROxBB;
za = (2.0*params[i].ne + 1.0)/(4.0*ra);}
if(strcmp(params[j].nom,"O")==0) {
- rb = ROxBB;
+ rb = ROxBB;
zb = (2.0*params[j].ne + 1.0)/(4.0*rb); }
-
-
+
+
ii = 0 ; nang =cang= 5.0 ;
- // --------------------------
+ // --------------------------
for (k = 0; k < kmax+5; k++)
- // --------------------------
+ // --------------------------
{
- gam = dgam = dza = dzb = d2zaa = d2zab =
+ gam = dgam = dza = dzb = d2zaa = d2zab =
d2zbb = d2zra = d2zrb = d2gamr2 = 0.0 ;
dij = 0.0 ;
-
+
s = double(k)*ds ; r = sqrt(s) ;
if (k==0) r=10e-30;
-
+
gammas(na,nb,za,zb,r,gam,dgam,dza,dzb,
d2zaa,d2zab,d2zbb,d2zra,d2zrb,d2gamr2) ;
-
- // --- Jij
-
+
+ // --- Jij
+
dij = 14.4 * (1.0/r - double(gam));
ddij = 14.4 * (-1.0/(r*r) - double(dgam)) ;
@@ -1583,68 +1583,68 @@ void PairSMTBQ::tabqeq()
}
- if (r > (rc+nang)) {dij = 0.0 ; ddij = 0.0;}
-
- if(strcmp(params[i].nom,"O")==0 && strcmp(params[j].nom,"O")==0){
+ if (r > (rc+nang)) {dij = 0.0 ; ddij = 0.0;}
+
+ if(strcmp(params[i].nom,"O")==0 && strcmp(params[j].nom,"O")==0){
fafbOxOxBB[k] = potqn[k] - dij ;
- if (k == 1) fafbOxOxBB[0] = fafbOxOxBB[k] ;
- dfafbOxOxBB[k] = dpotqn[k] - ddij/r ; }
+ if (k == 1) fafbOxOxBB[0] = fafbOxOxBB[k] ;
+ dfafbOxOxBB[k] = dpotqn[k] - ddij/r ; }
else { fafbTiOxBB[k] = potqn[k] - dij ;
- if (k == 1) fafbTiOxBB[0] = fafbTiOxBB[k] ;
- dfafbTiOxBB[k] = dpotqn[k] - ddij/r ;
+ if (k == 1) fafbTiOxBB[0] = fafbTiOxBB[k] ;
+ dfafbTiOxBB[k] = dpotqn[k] - ddij/r ;
}
}
-
-
+
+
} //for k
- //end of make the table fafbOxOxBB
-
-
-
+ //end of make the table fafbOxOxBB
+
+
+
}
} //for i,j
-
+
//if (fichier) fichier.close() ;
}
/* ---------------------------------------------------------------------*/
-void PairSMTBQ::potqeq(int i, int j, double qi, double qj, double rsq,
- double &fforce, int eflag, double &eng)
+void PairSMTBQ::potqeq(int i, int j, double qi, double qj, double rsq,
+ double &fforce, int eflag, double &eng)
{
/* ===================================================================
Coulombian energy calcul between i and j atoms
with fafb table make in sm_table().
fafb[i][j] : i is the table's step (r)
- j is the interaction's # (in intype[itype][jtype])
+ j is the interaction's # (in intype[itype][jtype])
dfafb is derivate energy (force)
==================================================================== */
-
+
int itype,jtype,l,m;
double r,t1,t2,sds,xi,engBulk,engSurf,fforceBulk,fforceSurf,dcoordloc,dcoupureloc;
double engBB,fforceBB, dIntfcoup2loc,iCoord,jCoord,iIntfCoup2,jIntfCoup2;
-
+
int *type = atom->type;
// int n = atom->ntypes;
-
+
itype = map[type[i]];
jtype = map[type[j]];
m = coultype[itype][jtype];
-
+
r = rsq;
sds = r/ds ; l = int(sds) ;
xi = sds - double(l) ;
-
-
+
+
iCoord=coord[i];
jCoord=coord[j];
iIntfCoup2= Intfcoup2(iCoord,coordOxBulk,0.15);
jIntfCoup2= Intfcoup2(jCoord,coordOxBulk,0.15);
-
- // ---- Energies Interpolation
+
+ // ---- Energies Interpolation
t1 = fafb[l][m] + (fafb[l+1][m] - fafb[l][m])*xi;
t2 = fafb[l+1][m] + (fafb[l+2][m] - fafb[l+1][m])*(xi-1.0);
@@ -1652,19 +1652,19 @@ void PairSMTBQ::potqeq(int i, int j, double qi, double qj, double rsq,
engBulk = qi*qj*(t1 + (t2 - t1)*xi/2.0);
eng=engBulk;
-
+
// ---- Forces Interpolation
t1 = dfafb[l][m] + (dfafb[l+1][m] - dfafb[l][m])*xi;
t2 = dfafb[l+1][m] + (dfafb[l+2][m] - dfafb[l+1][m])*(xi-1);
-
-
+
+
fforce = - qi*qj*(t1 + (t2 - t1)*xi/2.0) ;
- if(strcmp(params[itype].nom,"O")==0 || strcmp(params[jtype].nom,"O")==0){
-
- if(strcmp(params[itype].nom,"O")==0 && strcmp(params[jtype].nom,"O")==0){
+ if(strcmp(params[itype].nom,"O")==0 || strcmp(params[jtype].nom,"O")==0){
+
+ if(strcmp(params[itype].nom,"O")==0 && strcmp(params[jtype].nom,"O")==0){
// between two oxygens
t1 = fafbOxOxSurf[l] + (fafbOxOxSurf[l+1] - fafbOxOxSurf[l])*xi;
@@ -1674,14 +1674,14 @@ void PairSMTBQ::potqeq(int i, int j, double qi, double qj, double rsq,
t1 = fafbOxOxBB[l] + (fafbOxOxBB[l+1] - fafbOxOxBB[l])*xi;
t2 = fafbOxOxBB[l+1] + (fafbOxOxBB[l+2] - fafbOxOxBB[l+1])*(xi-1.0);
engBB = qi*qj*(t1 + (t2 - t1)*xi/2.0);
-
+
eng= engBulk + (iCoord+jCoord-2*coordOxBulk)/(2*(coordOxBB-coordOxBulk)) *(engBB-engBulk)
+ (iIntfCoup2+jIntfCoup2)*((engBulk-engSurf)/(2*(coordOxBulk-coordOxSurf))
- (engBB-engBulk)/(2*(coordOxBB-coordOxBulk))) ;
// ---- Interpolation des forces
-
+
fforceBulk=fforce;
t1 = dfafbOxOxSurf[l] + (dfafbOxOxSurf[l+1] - dfafbOxOxSurf[l])*xi;
t2 = dfafbOxOxSurf[l+1] + (dfafbOxOxSurf[l+2] - dfafbOxOxSurf[l+1])*(xi-1);
@@ -1693,28 +1693,28 @@ void PairSMTBQ::potqeq(int i, int j, double qi, double qj, double rsq,
fforce= fforceBulk + (iCoord+jCoord-2*coordOxBulk)/(2*(coordOxBB-coordOxBulk))*(fforceBB-fforceBulk)
+ (iIntfCoup2+jIntfCoup2)*((fforceBulk-fforceSurf)/(2*(coordOxBulk-coordOxSurf))
- - (fforceBB-fforceBulk)/(2*(coordOxBB-coordOxBulk))) ;
+ - (fforceBB-fforceBulk)/(2*(coordOxBB-coordOxBulk))) ;
}
- else{ // between metal and oxygen
-
+ else{ // between metal and oxygen
+
t1 = fafbTiOxSurf[l] + (fafbTiOxSurf[l+1] - fafbTiOxSurf[l])*xi;
t2 = fafbTiOxSurf[l+1] + (fafbTiOxSurf[l+2] - fafbTiOxSurf[l+1])*(xi-1.0);
engSurf = qi*qj*(t1 + (t2 - t1)*xi/2.0);
t1 = fafbTiOxBB[l] + (fafbTiOxBB[l+1] - fafbTiOxBB[l])*xi;
t2 = fafbTiOxBB[l+1] + (fafbTiOxBB[l+2] - fafbTiOxBB[l+1])*(xi-1.0);
engBB = qi*qj*(t1 + (t2 - t1)*xi/2.0);
-
+
if(strcmp(params[jtype].nom,"O")==0) //the atom j is an oxygen
{ iIntfCoup2=jIntfCoup2;
iCoord=jCoord; }
-
+
eng = engBulk + (engBulk-engSurf)/(coordOxBulk-coordOxSurf) * iIntfCoup2
+ (engBB-engBulk)/(coordOxBB-coordOxBulk) * (iCoord-coordOxBulk-iIntfCoup2);
-
+
// ---- Forces Interpolation
-
+
fforceBulk=fforce;
t1 = dfafbTiOxSurf[l] + (dfafbTiOxSurf[l+1] - dfafbTiOxSurf[l])*xi;
t2 = dfafbTiOxSurf[l+1] + (dfafbTiOxSurf[l+2] - dfafbTiOxSurf[l+1])*(xi-1);
@@ -1723,7 +1723,7 @@ void PairSMTBQ::potqeq(int i, int j, double qi, double qj, double rsq,
t1 = dfafbTiOxBB[l] + (dfafbTiOxBB[l+1] - dfafbTiOxBB[l])*xi;
t2 = dfafbTiOxBB[l+1] + (dfafbTiOxBB[l+2] - dfafbTiOxBB[l+1])*(xi-1);
fforceBB = - qi*qj*(t1 + (t2 - t1)*xi/2.0) ;
-
+
dcoordloc = fcoupured(sqrt(r),r1Coord,r2Coord) ;
@@ -1736,11 +1736,11 @@ void PairSMTBQ::potqeq(int i, int j, double qi, double qj, double rsq,
}
-
+
}
-
+
}
@@ -1753,31 +1753,31 @@ void PairSMTBQ::pot_ES (int i, int j, double rsq, double &eng)
Coulombian potentiel energy calcul between i and j atoms
with fafb table make in sm_table().
fafb[i][j] : i is the table's step (r)
- j is the interaction's # (in intype[itype][jtype])
+ j is the interaction's # (in intype[itype][jtype])
dfafb is derivate energy (force)
==================================================================== */
-
+
int itype,jtype,l,m;
double r,t1,t2,sds,xi,engBulk,engSurf,dcoordloc,dcoupureloc;
double engBB, dIntfcoup2loc,iCoord,jCoord,iIntfCoup2,jIntfCoup2;
-
+
int *type = atom->type;
// int n = atom->ntypes;
-
+
itype = map[type[i]];
jtype = map[type[j]];
m = coultype[itype][jtype];
-
+
r = rsq;
sds = r/ds ; l = int(sds) ;
xi = sds - double(l) ;
-
+
iCoord=coord[i];
jCoord=coord[j];
iIntfCoup2= Intfcoup2(iCoord,coordOxBulk,0.15);
jIntfCoup2= Intfcoup2(jCoord,coordOxBulk,0.15);
-
+
// ---- Energies Interpolation
t1 = fafb[l][m] + (fafb[l+1][m] - fafb[l][m])*xi;
@@ -1785,10 +1785,10 @@ void PairSMTBQ::pot_ES (int i, int j, double rsq, double &eng)
eng = (t1 + (t2 - t1)*xi/2.0);
- engBulk=eng;
+ engBulk=eng;
- if(itype==0 || jtype==0){
+ if(itype==0 || jtype==0){
if(itype==0 && jtype==0){ // between two oxygens
@@ -1799,7 +1799,7 @@ void PairSMTBQ::pot_ES (int i, int j, double rsq, double &eng)
t1 = fafbOxOxBB[l] + (fafbOxOxBB[l+1] - fafbOxOxBB[l])*xi;
t2 = fafbOxOxBB[l+1] + (fafbOxOxBB[l+2] - fafbOxOxBB[l+1])*(xi-1.0);
engBB = (t1 + (t2 - t1)*xi/2.0);
-
+
eng= engBulk + (iCoord+jCoord-2*coordOxBulk)/(2*(coordOxBB-coordOxBulk))*(engBB-engBulk)
+ (iIntfCoup2+jIntfCoup2)*((engBulk-engSurf)/(2*(coordOxBulk-coordOxSurf))
- (engBB-engBulk)/(2*(coordOxBB-coordOxBulk))) ;
@@ -1818,17 +1818,17 @@ void PairSMTBQ::pot_ES (int i, int j, double rsq, double &eng)
iIntfCoup2=jIntfCoup2;
iCoord=jCoord;
}
-
- eng = engBulk + (engBulk-engSurf)/(coordOxBulk-coordOxSurf)*iIntfCoup2
+
+ eng = engBulk + (engBulk-engSurf)/(coordOxBulk-coordOxSurf)*iIntfCoup2
+ (engBB-engBulk)/(coordOxBB-coordOxBulk) * (iCoord-coordOxBulk-iIntfCoup2);
}
-
+
}
-
+
}
@@ -1838,32 +1838,32 @@ void PairSMTBQ::pot_ES2 (int i, int j, double rsq, double &pot)
{
int l,m,itype,jtype;
double sds,xi,t1,t2,r;
-
+
int *type = atom->type;
-
-
+
+
if (sqrt(rsq) > cutmax) return ;
-
+
itype = map[type[i]];
jtype = map[type[j]];
m = coultype[itype][jtype];
-
+
r = rsq ;
sds = r/ds ; l = int(sds) ;
xi = sds - double(l) ;
-
- // ---- Energies Interpolation
+
+ // ---- Energies Interpolation
t1 = fafb[l][m] + (fafb[l+1][m] - fafb[l][m])*xi;
t2 = fafb[l+1][m] + (fafb[l+2][m] - fafb[l+1][m])*(xi-1.0);
-
+
pot = (t1 + (t2 - t1)*xi/2.0) ;
-
+
}
/* --------------------------------------------------------------------
- Oxygen-Oxygen Interaction
- -------------------------------------------------------------------- */
+ Oxygen-Oxygen Interaction
+ -------------------------------------------------------------------- */
void PairSMTBQ::rep_OO(Intparam *intparam, double rsq, double &fforce,
int eflag, double &eng)
@@ -1871,13 +1871,13 @@ void PairSMTBQ::rep_OO(Intparam *intparam, double rsq, double &fforce,
double r,tmp_exp,tmp;
double A = intparam->abuck ;
double rho = intparam->rhobuck ;
-
+
r = sqrt(rsq);
tmp = - r/rho ;
tmp_exp = exp( tmp );
-
+
eng = A * tmp_exp ;
-
+
fforce = A/rho * tmp_exp / r ; //( - )
}
@@ -1891,11 +1891,11 @@ void PairSMTBQ::Attr_OO(Intparam *intparam, double rsq, double &fforce,
double bOO = intparam->bOO ;
double r1OO = intparam->r1OO ;
double r2OO = intparam->r2OO ;
-
+
r = sqrt(rsq);
tmp_exp= exp( bOO* r);
- eng = aOO * tmp_exp* fcoupure(r,r1OO,r2OO);
-
+ eng = aOO * tmp_exp* fcoupure(r,r1OO,r2OO);
+
fforce = - (aOO*bOO * tmp_exp * fcoupure(r,r1OO,r2OO)+ aOO*tmp_exp *fcoupured(r,r1OO,r2OO))/ r ; //( - )
}
@@ -1910,17 +1910,17 @@ void PairSMTBQ::tabsm()
{
int k,m;
double s,r,tmpb,tmpr,fcv,fcdv;
-
- memory->create(tabsmb,kmax,maxintsm+1,"pair:tabsmb");
+
+ memory->create(tabsmb,kmax,maxintsm+1,"pair:tabsmb");
memory->create(tabsmr,kmax,maxintsm+1,"pair:tabsmr");
- memory->create(dtabsmb,kmax,maxintsm+1,"pair:dtabsmb");
- memory->create(dtabsmr,kmax,maxintsm+1,"pair:dtabsmr");
-
-
+ memory->create(dtabsmb,kmax,maxintsm+1,"pair:dtabsmb");
+ memory->create(dtabsmr,kmax,maxintsm+1,"pair:dtabsmr");
+
+
for (m = 0; m <= maxintparam; m++) {
-
+
if (intparams[m].intsm == 0) continue;
-
+
double rc1 = intparams[m].dc1;
double rc2 = intparams[m].dc2;
double A = intparams[m].a;
@@ -1928,76 +1928,76 @@ void PairSMTBQ::tabsm()
double Ksi = intparams[m].ksi;
double q = intparams[m].q;
double rzero = intparams[m].r0;
- int sm = intparams[m].intsm;
-
-
- for (k=0; k < kmax; k++)
- {
- s = double(k)*ds ; r = sqrt(s);
- if (k==0) r=10e-30;
+ int sm = intparams[m].intsm;
+
+
+ for (k=0; k < kmax; k++)
+ {
+ s = double(k)*ds ; r = sqrt(s);
+ if (k==0) r=10e-30;
tmpb = exp( -2.0*q*(r/rzero - 1.0));
tmpr = exp( -p*(r/rzero - 1.0));
-
+
if (r <= rc1)
{
-
- // -- Energy
+
+ // -- Energy
tabsmb[k][sm] = Ksi*Ksi * tmpb ;
tabsmr[k][sm] = A * tmpr ;
-
+
// -- Force
- /* dtabsmb ne correspond pas vraiment a une force puisqu'il y a le /r
- (on a donc une unite force/distance). Le programme multiplie ensuite
- (dans le PairSMTBQ::compute ) dtabsmb par la projection du vecteur r
- sur un axe x (ou y ou z) pour determiner la composante de la force selon
- cette direction. Donc tout est ok au final. */
+ /* dtabsmb ne correspond pas vraiment a une force puisqu'il y a le /r
+ (on a donc une unite force/distance). Le programme multiplie ensuite
+ (dans le PairSMTBQ::compute ) dtabsmb par la projection du vecteur r
+ sur un axe x (ou y ou z) pour determiner la composante de la force selon
+ cette direction. Donc tout est ok au final. */
- dtabsmb[k][sm] = - 2.0 *Ksi*Ksi* q/rzero * tmpb /r;
- dtabsmr[k][sm] = - A * p/rzero * tmpr/r ;
+ dtabsmb[k][sm] = - 2.0 *Ksi*Ksi* q/rzero * tmpb /r;
+ dtabsmr[k][sm] = - A * p/rzero * tmpr/r ;
} // if
-
+
else if (r > rc1 && r <= rc2)
{
-
- // -- Energie
+
+ // -- Energie
fcv = fcoupure(r,intparams[sm].dc1,intparams[sm].dc2);
tabsmb[k][sm] = fcv* Ksi*Ksi * tmpb ;
tabsmr[k][sm] = fcv* A * tmpr ;
-
+
// -- Force
- /* dtabsmb ne correspond pas vraiment a une force puisqu'il y a le /r
- (on a donc une unite force/distance). Le programme multiplie ensuite
- (dans le PairSMTBQ::compute ) d tabsmb par la projection du vecteur
- r sur un axe x (ou y ou z) pour determiner la composante de la force
+ /* dtabsmb ne correspond pas vraiment a une force puisqu'il y a le /r
+ (on a donc une unite force/distance). Le programme multiplie ensuite
+ (dans le PairSMTBQ::compute ) d tabsmb par la projection du vecteur
+ r sur un axe x (ou y ou z) pour determiner la composante de la force
selon cette direction. Donc tout est ok au final. */
-
+
fcdv = fcoupured(r,intparams[sm].dc1,intparams[sm].dc2);
dtabsmb[k][sm] = (fcv*( - 2.0 *Ksi*Ksi* q/rzero * tmpb )+fcdv* Ksi*Ksi * tmpb )/r ;
- dtabsmr[k][sm] = (fcv*( - A * p/rzero * tmpr )+fcdv*A * tmpr )/r ;
+ dtabsmr[k][sm] = (fcv*( - A * p/rzero * tmpr )+fcdv*A * tmpr )/r ;
+
+ }
- }
-
- else
+ else
{
-
- // -- Energie
+
+ // -- Energie
tabsmb[k][sm] = 0.0;
tabsmr[k][sm] = 0.0;
-
+
// -- Force
dtabsmb[k][sm] = 0.0;
- dtabsmr[k][sm] = 0.0;
+ dtabsmr[k][sm] = 0.0;
+
+ }
+
- }
-
-
} // for kmax
-
-
+
+
} // for maxintparam
-
+
}
@@ -2013,34 +2013,34 @@ void PairSMTBQ::repulsive(Intparam *intparam, double rsq, int i, int j,
/* ================================================
rsq : square of ij distance
fforce : repulsion force
- eng : repulsion energy
+ eng : repulsion energy
eflag : Si oui ou non on calcule l'energie
=================================================*/
- int l;
+ int l;
double r,sds,xi,t1,t2,dt1,dt2,sweet,iq,jq;
double rrcs = intparam->dc2;
int sm = intparam->intsm;
-
+
// printf ("On rentre dans repulsive\n");
-
+
r = rsq;
if (sqrt(r) > rrcs) return ;
-
+
sds = r/ds ; l = int(sds) ;
xi = sds - double(l) ;
-
+
t1 = tabsmr[l][sm] + (tabsmr[l+1][sm] - tabsmr[l][sm])*xi ;
t2 = tabsmr[l+1][sm] + (tabsmr[l+2][sm] - tabsmr[l+1][sm])*(xi-1.0) ;
-
+
dt1 = dtabsmr[l][sm] + (dtabsmr[l+1][sm] - dtabsmr[l][sm])*xi ;
dt2 = dtabsmr[l+1][sm] + (dtabsmr[l+2][sm] - dtabsmr[l+1][sm])*(xi-1.0) ;
if (strcmp(intparam->mode,"oxide") == 0)
{
- fforce = - 2.0*(dt1 + (dt2 - dt1)*xi/2.0);
+ fforce = - 2.0*(dt1 + (dt2 - dt1)*xi/2.0);
eng = (t1 + (t2 - t1)*xi/2.0) ;
}
else if (strcmp(intparam->mode,"metal") == 0)
@@ -2049,11 +2049,11 @@ void PairSMTBQ::repulsive(Intparam *intparam, double rsq, int i, int j,
fforce = - 2.0*(dt1 + (dt2 - dt1)*xi/2.0) * sweet ;
eng = (t1 + (t2 - t1)*xi/2.0) * sweet ;
}
-
+
}
-/* --------------------------------------------------------------------------------- */
+/* --------------------------------------------------------------------------------- */
void PairSMTBQ::attractive(Intparam *intparam, double rsq,
@@ -2062,45 +2062,45 @@ void PairSMTBQ::attractive(Intparam *intparam, double rsq,
int itype,l;
double r,t1,t2,xi,sds;
double dqcov,sweet,dq,mu;
-
+
double rrcs = intparam->dc2;
int *type = atom->type;
int sm = intparam->intsm;
-
+
itype = map[type[i]];
-
+
r = rsq;
if (sqrt(r) > rrcs) return ;
-
-
+
+
sds = r/ds ; l = int(sds) ;
xi = sds - double(l) ;
-
+
t1 = tabsmb[l][sm] + (tabsmb[l+1][sm] - tabsmb[l][sm])*xi ;
t2 = tabsmb[l+1][sm] + (tabsmb[l+2][sm] - tabsmb[l+1][sm])*(xi-1.0) ;
-
-
-
+
+
+
if (strcmp(intparam->mode,"oxide") == 0) {
mu = 0.5*(sqrt(params[1].sto) + sqrt(params[0].sto));
-
+
// dq = fabs(params[itype].qform) - fabs(iq);
-// dqcov = dq*(2.0*ncov/params[itype].sto - dq);
-
+// dqcov = dq*(2.0*ncov/params[itype].sto - dq);
+
sbcov[i] += (t1 + (t2 - t1)*xi/2.0) *params[itype].sto*mu*mu;
// if (i < 10) printf ("i %d, iq %f sbcov %f \n",i,iq,sbcov[i]);
-
+
if (sqrt(r)<r1Coord) { coord[i] += 1 ; }
else if (sqrt(r)<r2Coord){ coord[i] += fcoupure(sqrt(r),r1Coord,r2Coord) ;}
- }
+ }
else if (strcmp(intparam->mode,"metal") == 0) {
sweet = 1.0;
sbmet[i] += (t1 + (t2 - t1)*xi/2.0) * sweet ;
}
-
+
}
/* ---------------------------------------------------------------------- */
@@ -2109,50 +2109,50 @@ void PairSMTBQ::f_att(Intparam *intparam, int i, int j,double rsq, double &fforc
{
int itype,jtype,l;
int *type = atom->type;
-
+
double r,sds,xi,dt1,dt2,dq,dqcovi,dqcovj;
double fcov_ij,fcov_ji,sweet,iq,jq,mu;
-
+
int sm = intparam->intsm;
double *q = atom->q;
-
+
itype = map[type[i]];
jtype = map[type[j]];
iq = q[i] ; jq = q[j];
-
+
r = rsq;
-
+
sds = r/ds ; l = int(sds) ;
xi = sds - double(l) ;
-
+
dt1 = dtabsmb[l][sm] + (dtabsmb[l+1][sm] - dtabsmb[l][sm])*xi ;
dt2 = dtabsmb[l+1][sm] + (dtabsmb[l+2][sm] - dtabsmb[l+1][sm])*(xi-1.0) ;
-
+
dq = fabs(params[itype].qform) - fabs(iq);
dqcovi = dq*(2.0*ncov/params[itype].sto - dq);
dq = fabs(params[jtype].qform) - fabs(jq);
dqcovj = dq*(2.0*ncov/params[jtype].sto - dq);
-
+
if (strcmp(intparam->mode,"oxide") == 0) {
//------------------------------------------
- mu = 0.5*(sqrt(params[1].sto) + sqrt(params[0].sto));
+ mu = 0.5*(sqrt(params[1].sto) + sqrt(params[0].sto));
fcov_ij = (dt1 + (dt2 - dt1)*xi/2.0) * dqcovi *params[itype].sto*mu*mu;
- fcov_ji = (dt1 + (dt2 - dt1)*xi/2.0) * dqcovj *params[jtype].sto*mu*mu;
-
- fforce = 0.5 * ( fcov_ij/sqrt(sbcov[i]*dqcovi + sbmet[i])
+ fcov_ji = (dt1 + (dt2 - dt1)*xi/2.0) * dqcovj *params[jtype].sto*mu*mu;
+
+ fforce = 0.5 * ( fcov_ij/sqrt(sbcov[i]*dqcovi + sbmet[i])
+ fcov_ji/sqrt(sbcov[j]*dqcovj + sbmet[j]) ) ;
- }
+ }
else if (strcmp(intparam->mode,"metal") == 0) {
//-----------------------------------------------
- sweet = 1.0;
+ sweet = 1.0;
fcov_ij = (dt1 + (dt2 - dt1)*xi/2.0) * sweet ;
-
- fforce = 0.5 * fcov_ij*( 1.0/sqrt(sbcov[i]*dqcovi + sbmet[i])
- + 1.0/sqrt(sbcov[j]*dqcovj + sbmet[j]) ) ;
- }
-
+
+ fforce = 0.5 * fcov_ij*( 1.0/sqrt(sbcov[i]*dqcovi + sbmet[i])
+ + 1.0/sqrt(sbcov[j]*dqcovj + sbmet[j]) ) ;
+ }
+
}
/* ---------------------------------------------------------------------- */
@@ -2164,16 +2164,16 @@ void PairSMTBQ::pot_COV(Param *param, int i, double &qforce)
double *q = atom->q;
double qform = param->qform;
double sto = param->sto;
-
+
sign = qform / fabs(qform);
- iq = q[i];
-
+ iq = q[i];
+
dq = fabs(qform) - fabs(iq);
DQ = dq*(2.0*ncov/sto - dq);
-
- if (fabs(iq) < 1.0e-7 || fabs(sbcov[i]) < 1.0e-7) {
+
+ if (fabs(iq) < 1.0e-7 || fabs(sbcov[i]) < 1.0e-7) {
qforce = 0.0; }
- else {
+ else {
qforce = sign*sbcov[i]/sqrt(sbcov[i]*DQ + sbmet[i])*(ncov/sto - dq) ;
}
@@ -2187,34 +2187,34 @@ double PairSMTBQ::potmet(Intparam *intparam, double rsq,
int l,itype,jtype;
int *type = atom->type;
double chi,sds,xi,t1,t2,r,dsweet,dq,dqcovi,dqcovj;
-
+
int sm = intparam->intsm;
itype = map[type[i]];
jtype = map[type[j]];
-
- r = rsq;
+
+ r = rsq;
sds = r/ds ; l = int(sds) ;
xi = sds - double(l) ;
-
+
t1 = tabsmb[l][sm] + (tabsmb[l+1][sm] - tabsmb[l][sm])*xi ;
t2 = tabsmb[l+1][sm] + (tabsmb[l+2][sm] - tabsmb[l+1][sm])*(xi-1.0) ;
-
+
dq = fabs(params[itype].qform) - fabs(iq);
dqcovi = dq*(2.0*ncov/params[itype].sto - dq);
dq = fabs(params[jtype].qform) - fabs(jq);
dqcovj = dq*(2.0*ncov/params[jtype].sto - dq);
-
+
dsweet = 0.0;
- chi = (t1 + (t2 - t1)*xi/2.0) * dsweet *( 1.0/(2.0*sqrt(sbcov[i]*dqcovi+sbmet[i]))
+ chi = (t1 + (t2 - t1)*xi/2.0) * dsweet *( 1.0/(2.0*sqrt(sbcov[i]*dqcovi+sbmet[i]))
+ 1.0/(2.0*sqrt(sbcov[j]*dqcovj+sbmet[j])) );
return chi;
-}
+}
/* ----------------------------------------------------------------------
- Cutting Function
+ Cutting Function
----------------------------------------------------------------------*/
@@ -2223,7 +2223,7 @@ double PairSMTBQ::potmet(Intparam *intparam, double rsq,
double PairSMTBQ::fcoupure(double r, double rep_dc1, double rep_dc2)
{
double ddc,a3,a4,a5,x;
-
+
if (r<rep_dc1)
{return 1;}
else if (r> rep_dc2)
@@ -2237,7 +2237,7 @@ double PairSMTBQ::fcoupure(double r, double rep_dc1, double rep_dc2)
a3 = -10/(ddc*ddc*ddc);
a4 = -15/(ddc*ddc*ddc*ddc);
a5 = -6/(ddc*ddc*ddc*ddc*ddc);
-
+
return x*x*x*(a3 + x*(a4 + x*a5));}
}
@@ -2250,9 +2250,9 @@ double PairSMTBQ::fcoupure(double r, double rep_dc1, double rep_dc2)
double PairSMTBQ::fcoupured(double r, double rep_dc1, double rep_dc2)
{
-
+
double ddc,a3,a4,a5,x;
-
+
if ( r>rep_dc1 && r<rep_dc2) {
ddc = rep_dc2 - rep_dc1;
x = r - rep_dc2;
@@ -2260,7 +2260,7 @@ double PairSMTBQ::fcoupured(double r, double rep_dc1, double rep_dc2)
a3 = -10/(ddc*ddc*ddc);
a4 = -15/(ddc*ddc*ddc*ddc);
a5 = -6/(ddc*ddc*ddc*ddc*ddc);
-
+
return x*x*(3*a3 + x*(4*a4 + 5*x*a5));}
else {return 0;}
}
@@ -2278,7 +2278,7 @@ double PairSMTBQ::fcoupured(double r, double rep_dc1, double rep_dc2)
double PairSMTBQ::fcoup2(double c, double x, double delta)
{
double dc;
-
+
if (c<x-delta)
{return 1;}
else if (c> x+delta)
@@ -2291,7 +2291,7 @@ double PairSMTBQ::fcoup2(double c, double x, double delta)
}
/* ----------------------------------------------------------------------
- Primitive of cutting function for derive (force)
+ Primitive of cutting function for derive (force)
----------------------------------------------------------------------*/
@@ -2299,8 +2299,8 @@ double PairSMTBQ::fcoup2(double c, double x, double delta)
double PairSMTBQ::Primfcoup2(double c, double x, double delta)
{
-
- return (c*(c*c*c - 4* c*c* x - 4* (x - 2 *delta) * (x+delta)*(x+delta) +
+
+ return (c*(c*c*c - 4* c*c* x - 4* (x - 2 *delta) * (x+delta)*(x+delta) +
6* c *(x*x - delta*delta)))/(16* delta*delta*delta);
}
@@ -2315,7 +2315,7 @@ double PairSMTBQ::Primfcoup2(double c, double x, double delta)
double PairSMTBQ::Intfcoup2(double c, double x, double delta)
{
-
+
if (c<x-delta)
{return c - x + delta + Primfcoup2(x-delta,x,delta) - Primfcoup2(x,x,delta) ;}
else if (c> x+delta)
@@ -2326,8 +2326,8 @@ double PairSMTBQ::Intfcoup2(double c, double x, double delta)
}
-/* ---------------------------------------------------------------------
- Energy derivation respect charge Q
+/* ---------------------------------------------------------------------
+ Energy derivation respect charge Q
--------------------------------------------------------------------- */
void PairSMTBQ::QForce_charge(int loop)
@@ -2345,31 +2345,31 @@ void PairSMTBQ::QForce_charge(int loop)
double *q = atom->q;
int *type = atom->type;
int step = update->ntimestep;
-
+
int inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
int nlocal = atom->nlocal;
-
-
+
+
// loop over full neighbor list of my atoms
fqi = fqj = fqij = fqij2 = fqjj = 0.0;
-
+
// ==================
if (loop == 0) {
// ==================
-
+
for (ii = 0; ii < inum; ii ++) {
//--------------------------------
i = ilist[ii];
itype = map[type[i]];
-
+
gp = flag_QEq[i];
sbcov[i] =coord[i]= sbmet[i] = 0.0;
@@ -2379,9 +2379,9 @@ void PairSMTBQ::QForce_charge(int loop)
ytmp = x[i][1];
ztmp = x[i][2];
iq = q[i];
-
-
-
+
+
+
// two-body interactions
@@ -2406,28 +2406,28 @@ void PairSMTBQ::QForce_charge(int loop)
rsq = vec3_dot(delr,delr);
-// Covalente charge forces - sbcov initialization
+// Covalente charge forces - sbcov initialization
// ------------------------------------------------
if (sqrt(rsq) > intparams[m].dc2) continue;
-
+
attractive (&intparams[m],rsq,eflag,i,iq,j,jq);
} // ---------------------------------------------- for jj
-
-
+
+
} // -------------------------------------------- ii
// ===============================================
- // Communicates the tables *sbcov and *sbmet
+ // Communicates the tables *sbcov and *sbmet
// to calculate the N-body forces
- // ================================================
-
+ // ================================================
+
forward (sbcov) ; reverse (sbcov);
forward (coord) ; reverse (coord);
- forward (sbmet) ; reverse (sbmet);
-
-
+ forward (sbmet) ; reverse (sbmet);
+
+
if (nteam == 0) return; //no oxide
if (Qstep == 0 || fmod(double(step), double(Qstep)) != 0.0) return;
@@ -2436,13 +2436,13 @@ void PairSMTBQ::QForce_charge(int loop)
// =======================
- // ===============================================
+ // ===============================================
- for (ii=0; ii<inum; ii++)
- {
+ for (ii=0; ii<inum; ii++)
+ {
i = ilist[ii]; itype = map[type[i]];
gp = flag_QEq[i]; iq = q[i];
-
+
potmad[i] = potself[i] = potcov[i] = 0.0 ;
if (gp == 0) continue;
@@ -2452,8 +2452,8 @@ void PairSMTBQ::QForce_charge(int loop)
ztmp = x[i][2];
fqi = 0.0 ;
-
- // Madelung potential
+
+ // Madelung potential
// --------------------
potmad[i] += 2.0*Vself*iq ;
@@ -2461,11 +2461,11 @@ void PairSMTBQ::QForce_charge(int loop)
// -----------------------------
fqi = qfo_self(¶ms[itype],iq);
potself[i] = fqi ;
-
+
// Loop on Second moment neighbor
- // -------------------------------
+ // -------------------------------
jlist = firstneigh[i];
jnum = numneigh[i];
@@ -2477,9 +2477,9 @@ void PairSMTBQ::QForce_charge(int loop)
m = intype[itype][jtype];
jq = q[j];
-
+
delr[0] = x[j][0] - xtmp;
- delr[1] = x[j][1] - ytmp;
+ delr[1] = x[j][1] - ytmp;
delr[2] = x[j][2] - ztmp;
rsq = vec3_dot(delr,delr);
@@ -2492,11 +2492,11 @@ void PairSMTBQ::QForce_charge(int loop)
// pot_ES2 (i,j,rsq,fqij2);
pot_ES (i,j,rsq,fqij);
- potmad[i] += jq*fqij ;
+ potmad[i] += jq*fqij ;
} // ------ jj
-
+
fqi = 0.0;
pot_COV (¶ms[itype],i,fqi) ;
potcov[i] = fqi ;
@@ -2515,14 +2515,14 @@ void PairSMTBQ::Charge()
int *ilist;
double heatpq,qmass,dtq,dtq2,qtot,qtotll;
double t_init,t_end,dt;
-
+
double *Transf,*TransfAll;
double *q = atom->q;
double **x = atom->x;
int *type = atom->type;
int step = update->ntimestep;
-
+
int inum = list->inum;
ilist = list->ilist;
@@ -2533,16 +2533,16 @@ void PairSMTBQ::Charge()
// ---------------------------
// Mise en place des groupes
// ---------------------------
-
- if (strcmp(QEqMode,"BulkFromSlab") == 0)
+
+ if (strcmp(QEqMode,"BulkFromSlab") == 0)
groupBulkFromSlab_QEq();
- else if (strcmp(QEqMode,"QEqAll") == 0)
+ else if (strcmp(QEqMode,"QEqAll") == 0)
groupQEqAll_QEq();
- else if (strcmp(QEqMode,"QEqAllParallel") == 0)
+ else if (strcmp(QEqMode,"QEqAllParallel") == 0)
groupQEqAllParallel_QEq();
- else if (strcmp(QEqMode,"Surface") == 0)
+ else if (strcmp(QEqMode,"Surface") == 0)
groupSurface_QEq();
-
+
if (nteam+1 != cluster) {
@@ -2579,24 +2579,24 @@ void PairSMTBQ::Charge()
for (i=0; i<nteam+1; i++) {
- nQEq[i] = nQEqa[i] = nQEqc[i] = 0;
- nQEqall[i] = nQEqcall[i] = nQEqaall[i] = end[i]= 0;
+ nQEq[i] = nQEqa[i] = nQEqc[i] = 0;
+ nQEqall[i] = nQEqcall[i] = nQEqaall[i] = end[i]= 0;
enegchk[i] = enegtot[i] = enegmax[i] = 0.0;
qtota[i] = qtotc[i] = qtotall[i] = qtotcll[i] = 0.0;
- sigmaall[i] = sigmacll[i] = 0.0;
+ sigmaall[i] = sigmacll[i] = 0.0;
}
qtot = qtotll = 0.0 ;
-
- for (ii = 0; ii < inum; ii++) {
+
+ for (ii = 0; ii < inum; ii++) {
i = ilist[ii]; itype = map[type[i]];
gp = flag_QEq[i];
q1[i] = q2[i] = qf[i] = 0.0;
- qtot += q[i] ;
+ qtot += q[i] ;
nQEq[gp] += 1;
if (itype != 0) { qtotc[gp] += q[i]; nQEqc[gp] += 1; }
- if (itype == 0) { qtota[gp] += q[i]; nQEqa[gp] += 1; }
+ if (itype == 0) { qtota[gp] += q[i]; nQEqa[gp] += 1; }
}
MPI_Allreduce(nQEq,nQEqall,nteam+1,MPI_INT,MPI_SUM,world);
@@ -2611,10 +2611,10 @@ void PairSMTBQ::Charge()
// ---------------------------------
// Init_charge(nQEq,nQEqa,nQEqc);
// ---------------------------------
-
+
if (update->ntimestep == 0 && (strcmp(QInitMode,"true") == 0) ) {
//Carefull here it won't be fine if there are more than 2 species!!!
- QOxInit=max(QOxInit, -0.98* params[1].qform *nQEqcall[gp]/nQEqaall[gp]) ;
+ QOxInit=max(QOxInit, -0.98* params[1].qform *nQEqcall[gp]/nQEqaall[gp]) ;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii]; itype = map[type[i]];
@@ -2623,8 +2623,8 @@ void PairSMTBQ::Charge()
// if (gp == 0) continue;
if (itype == 0) q[i] = QOxInit ;
- if (itype > 0) q[i] = -QOxInit * nQEqaall[gp]/nQEqcall[gp];
- }
+ if (itype > 0) q[i] = -QOxInit * nQEqaall[gp]/nQEqcall[gp];
+ }
}
if (nteam == 0 || Qstep == 0) return;
@@ -2638,12 +2638,12 @@ void PairSMTBQ::Charge()
if (me == 0 && strcmp(Bavard,"false") != 0) {
for (gp = 0; gp < nteam+1; gp++) {
- printf (" ++++ Groupe %d - Nox %d Ncat %d\n",gp,nQEqaall[gp],nQEqcall[gp]);
+ printf (" ++++ Groupe %d - Nox %d Ncat %d\n",gp,nQEqaall[gp],nQEqcall[gp]);
if (nQEqcall[gp] !=0 && nQEqaall[gp] !=0 )
- printf (" neutralite des charges %f\n qtotc %f qtota %f\n",
- qtotll,qtotcll[gp]/nQEqcall[gp],qtotall[gp]/nQEqaall[gp]);
+ printf (" neutralite des charges %f\n qtotc %f qtota %f\n",
+ qtotll,qtotcll[gp]/nQEqcall[gp],qtotall[gp]/nQEqaall[gp]);
printf (" ---------------------------- \n");}
- }
+ }
// ======================= Tab transfert ==================
// Transf[gp] = enegtot[gp]
@@ -2651,7 +2651,7 @@ void PairSMTBQ::Charge()
// Transf[gp+2cluster] = Qtota[gp]
// Transf[3cluster] = Qtot
// -------------------------------------------------------
- memory->create(Transf,3*cluster+1,"pair:Tranf");
+ memory->create(Transf,3*cluster+1,"pair:Tranf");
memory->create(TransfAll,3*cluster+1,"pair:TranfAll");
// ========================================================
@@ -2664,11 +2664,11 @@ void PairSMTBQ::Charge()
for (gp=0; gp<nteam+1; gp++) {
Transf[gp] = Transf[gp+cluster] = Transf[gp+2*cluster] = 0.0;
TransfAll[gp] = TransfAll[gp+cluster] = TransfAll[gp+2*cluster] = 0.0;
- enegtot[gp] = enegtotall[gp] = enegchkall[gp] = enegmaxall[gp] = 0.0 ;
+ enegtot[gp] = enegtotall[gp] = enegchkall[gp] = enegmaxall[gp] = 0.0 ;
}
for (ii = 0; ii < inum; ii++) {
- i = ilist[ii];
+ i = ilist[ii];
q1[i] += qf[i]*dtq2 - heatpq*q1[i];
q[i] += q1[i];
@@ -2678,24 +2678,24 @@ void PairSMTBQ::Charge()
if (itype == 0) Transf[gp+2*cluster] += q[i];
if (itype != 0) Transf[gp+cluster] += q[i];
}
-
+
// Communication des charges
- // ---------------------------
+ // ---------------------------
forward(q) ; reverse(q);
// Calcul des potentiel
// ----------------------
- QForce_charge(iloop);
+ QForce_charge(iloop);
// exit(1);
- for (ii = 0; ii < inum; ii++)
+ for (ii = 0; ii < inum; ii++)
{
i = ilist[ii]; itype = map[type[i]];
gp = flag_QEq[i];
- qf[i] = 0.0;
+ qf[i] = 0.0;
qf[i] = potself[i]+potmad[i]+potcov[i]+chimet[i] ;
Transf[gp] += qf[i];
}
@@ -2704,21 +2704,21 @@ void PairSMTBQ::Charge()
for (i = 0; i < nteam+1; i++) {
- if (nQEqall[i] !=0) TransfAll[i] /= double(nQEqall[i]);
+ if (nQEqall[i] !=0) TransfAll[i] /= double(nQEqall[i]);
enegchk[i] = enegmax[i] = 0.0;
}
-
+
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
itype = map[type[i]];
gp = flag_QEq[i];
-
+
if (gp == 0) continue;
-
+
q2[i] = TransfAll[gp] - qf[i];
enegmax[gp] = MAX(enegmax[gp],fabs(q2[i]));
- enegchk[gp] += fabs(q2[i]);
+ enegchk[gp] += fabs(q2[i]);
qf[i] = q2[i];
} // Boucle local
@@ -2727,15 +2727,15 @@ void PairSMTBQ::Charge()
MPI_Allreduce(enegmax,enegmaxall,nteam+1,MPI_DOUBLE,MPI_MAX,world);
- for (gp = 0; gp < nteam+1; gp++) {
- if(nQEqall[gp] !=0) {
- enegchk[gp] = enegchkall[gp]/double(nQEqall[gp]);
+ for (gp = 0; gp < nteam+1; gp++) {
+ if(nQEqall[gp] !=0) {
+ enegchk[gp] = enegchkall[gp]/double(nQEqall[gp]);
enegmax[gp] = enegmaxall[gp];
}
- }
+ }
// -----------------------------------------------------
- // Convergence Test
+ // Convergence Test
// -----------------------------------------------------
m = 0;
@@ -2744,62 +2744,62 @@ void PairSMTBQ::Charge()
}
for (gp = 1; gp < nteam+1; gp++) { m += end[gp] ; }
- if (m == nteam) { break; }
- // -----------------------------------------------------
+ if (m == nteam) { break; }
+ // -----------------------------------------------------
// -----------------------------------------------------
- for (ii = 0; ii < inum; ii++) {
+ for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
- q1[i] += qf[i]*dtq2 - heatpq*q1[i];
+ q1[i] += qf[i]*dtq2 - heatpq*q1[i];
}
// --------------------------------------------
} // -------------------------------- iloop
// --------------------------------------------
-
+
// =======================================
// Charge Communication.
- // =======================================
+ // =======================================
forward(q); reverse(q);
-
+
//:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
// ==========================================
// Ecriture des potentiels dans un fichier
// ==========================================
- if (strcmp(writepot,"true") == 0 && fmod(double(step), Neverypot) == 0.0) {
-
+ if (strcmp(writepot,"true") == 0 && fmod(double(step), Neverypot) == 0.0) {
+
ofstream fichierpot("Electroneg_component.txt", ios::out | ios::trunc) ;
-
+
for (ii = 0; ii < inum; ii++) {
- i = ilist[ii];
+ i = ilist[ii];
itype = map[type[i]];
gp = flag_QEq[i];
-
-
+
+
if (fichierpot) fichierpot<< setprecision(9) <<i <<" "<<itype<<" "<<x[i][0]<<" "<<x[i][1]
<<" "<<x[i][2]<<" "<<q[i]<<" "<<potself[i] + potmad[i]<<" "<<potcov[i]
<<" "<<sbcov[i]<<" "<<TransfAll[gp]<<endl;
-
+
}
if (fichierpot) fichierpot.close() ;
- }
-
+ }
+
//:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
-
-
+
+
// Statistique (ecart type)
// ------------------------
for (i=0; i<nteam+1; i++) {
if(nQEqcall[i] !=0)
{ TransfAll[i+cluster] /= double(nQEqcall[i]) ;
TransfAll[i+2*cluster] /= double(nQEqaall[i]) ;}
- sigmaa[i] = sigmac[i] = 0.0;
+ sigmaa[i] = sigmac[i] = 0.0;
}
-
+
qtot = 0.0 ;
- for (ii = 0; ii < inum; ii++)
+ for (ii = 0; ii < inum; ii++)
{
i = ilist[ii];
itype = map[type[i]];
@@ -2810,37 +2810,37 @@ void PairSMTBQ::Charge()
if (itype == 0) sigmaa[gp] += (q[i]-TransfAll[gp+2*cluster])*(q[i]-TransfAll[gp+2*cluster]);
if (itype == 1) sigmac[gp] += (q[i]-TransfAll[gp+cluster])*(q[i]-TransfAll[gp+cluster]);
- }
+ }
MPI_Allreduce(sigmaa,sigmaall,nteam+1,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(sigmac,sigmacll,nteam+1,MPI_DOUBLE,MPI_SUM,world);
for (gp = 1; gp < nteam+1; gp++) {
sigmaall[gp] = sqrt(sigmaall[gp]/double(nQEqaall[gp])) ;
- sigmacll[gp] = sqrt(sigmacll[gp]/double(nQEqcall[gp])) ;
+ sigmacll[gp] = sqrt(sigmacll[gp]/double(nQEqcall[gp])) ;
}
-
-
+
+
if (me == 0 && strcmp(Bavard,"false") != 0){
for (gp = 0; gp < nteam+1; gp++) {
printf (" -------------- Groupe %d -----------------\n",gp);
printf (" qtotc %f(+- %f) qtota %f(+- %f)\n",
TransfAll[gp+cluster],sigmacll[gp],TransfAll[gp+2*cluster],sigmaall[gp]);
printf (" Potentiel elec total : %f\n iloop %d, qtot %f\n",TransfAll[gp],iloop,TransfAll[3*cluster]);
- printf (" convergence : %f - %f\n",enegchk[gp],enegmax[gp]);
+ printf (" convergence : %f - %f\n",enegchk[gp],enegmax[gp]);
}
-
+
t_end = MPI_Wtime();
dt = t_end - t_init;
printf (" temps dans charges : %f seconde. \n",dt);
printf (" ======================================================== \n");
- }
+ }
// ============== Destroy Tab
memory->destroy(Transf);
memory->destroy(TransfAll);
-
+
}
/* ---------------------------------------------------------------------- */
@@ -2857,15 +2857,15 @@ void PairSMTBQ::groupBulkFromSlab_QEq()
{
i = ilist[ii];
ztmp = x[i][2];
- if (ztmp>zlim1QEq && ztmp< zlim2QEq)
+ if (ztmp>zlim1QEq && ztmp< zlim2QEq)
flag_QEq[i]=1;
else
flag_QEq[i]=0;
nteam=1;
-
+
}
-
+
}
// ----------------------------------------------
@@ -2875,7 +2875,7 @@ void PairSMTBQ::groupQEqAll_QEq()
int *ilist;
int inum = list->inum;
ilist = list->ilist;
-
+
nteam=1;
for (ii = 0; ii < inum; ii++)
@@ -2883,7 +2883,7 @@ void PairSMTBQ::groupQEqAll_QEq()
i= ilist[ii];
flag_QEq[i]=1;
}
-
+
}
// ----------------------------------------------
@@ -2895,20 +2895,20 @@ void PairSMTBQ::groupSurface_QEq()
double ztmp;
int inum = list->inum;
ilist = list->ilist;
-
+
for (ii = 0; ii < inum; ii++)
{
i = ilist[ii];
ztmp = x[i][2];
- if (ztmp>zlim1QEq)
+ if (ztmp>zlim1QEq)
flag_QEq[i]=1;
else
flag_QEq[i]=0;
nteam=1;
-
+
}
-
+
}
@@ -2920,7 +2920,7 @@ void PairSMTBQ::groupQEqAllParallel_QEq()
double delr[3],xtmp,ytmp,ztmp,rsq;
int **flag_gp, *nelt, **tab_gp;
int QEq,QEqall[nproc];
-
+
double **x = atom->x;
int *type = atom->type;
int inum = list->inum;
@@ -2937,7 +2937,7 @@ void PairSMTBQ::groupQEqAllParallel_QEq()
nboite = nlocal + nghost;
int **tabtemp,**Alltabtemp, *gptmp, *Allgptmp;
-
+
memory->create(tabtemp,10*nproc+10,nproc,"pair:tabtemp");
memory->create(Alltabtemp,10*nproc+10,nproc,"pair:Alltabtemp");
memory->create(gptmp,10*nproc+10,"pair:gptmp");
@@ -2949,23 +2949,23 @@ void PairSMTBQ::groupQEqAllParallel_QEq()
for (i = 0; i < nlocal+nghost ; i++) { flag_QEq[i] = 0; }
- for (i = 0; i < 10*nproc; i++) {
+ for (i = 0; i < 10*nproc; i++) {
gptmp[i] = 0; Allgptmp[i] = 0;
- for (j=0;j<nproc;j++) { tabtemp[i][j] = 0;
- Alltabtemp[i][j] = 0;}
+ for (j=0;j<nproc;j++) { tabtemp[i][j] = 0;
+ Alltabtemp[i][j] = 0;}
}
- for (i = 0; i < 10; i++) {
- for (k = 0; k < nboite; k++) { tab_gp[i][k] = 0;
- if (i == 0) nelt[k] = 0;
+ for (i = 0; i < 10; i++) {
+ for (k = 0; k < nboite; k++) { tab_gp[i][k] = 0;
+ if (i == 0) nelt[k] = 0;
}
for (j = 0; j < nproc; j++) {
team_elt[i][j] = 0;
- for (k = 0; k < 5; k++) { team_QEq[i][j][k] = 0; }
- }
+ for (k = 0; k < 5; k++) { team_QEq[i][j][k] = 0; }
+ }
}
QEq = 0;
-
+
// printf ("groupeQEq me %d - nloc %d nghost %d boite %d\n",
// me,nlocal,nghost,nboite);
@@ -2985,7 +2985,7 @@ void PairSMTBQ::groupQEqAllParallel_QEq()
jlist = firstneigh[i];
jnum = numneigh[i];
- for (jj = 0; jj < jnum; jj++ )
+ for (jj = 0; jj < jnum; jj++ )
{
j = jlist[jj] ; jtype = map[type[j]];
if (jtype == itype) continue;
@@ -2996,12 +2996,12 @@ void PairSMTBQ::groupQEqAllParallel_QEq()
delr[2] = x[j][2] - ztmp;
rsq = vec3_dot(delr,delr);
- if (sqrt(rsq) <= intparams[m].dc2) {
- flag_QEq[i] = 1; flag_QEq[j] = 1;
+ if (sqrt(rsq) <= intparams[m].dc2) {
+ flag_QEq[i] = 1; flag_QEq[j] = 1;
}
}
if (flag_QEq[i] == 1) {
- QEq = 1;
+ QEq = 1;
}
}
@@ -3041,7 +3041,7 @@ void PairSMTBQ::groupQEqAllParallel_QEq()
for (ii = 0; ii < inum; ii++) {
i = ilist[ii] ; itype = map[type[i]];
- if (itype != 0 || flag_QEq[i] == 0) continue;
+ if (itype != 0 || flag_QEq[i] == 0) continue;
m = 0;
@@ -3049,7 +3049,7 @@ void PairSMTBQ::groupQEqAllParallel_QEq()
// Grouping Initialisation
- // -----------------------------
+ // -----------------------------
if (flag_gp[me][i] == 0) {
ngp += 1; nelt[ngp] = 0;
tab_gp[ngp][nelt[ngp]] = i;
@@ -3067,16 +3067,16 @@ void PairSMTBQ::groupQEqAllParallel_QEq()
ktype = map[type[k]];
// printf ("[me %d] kk - gp %d elemt %d : atom %d(%d)\n",me,ngp,kk,k,ktype);
if (k >= nlocal) continue;
-
+
xtmp = x[k][0];
ytmp = x[k][1];
ztmp = x[k][2];
// Loop on the oxygen's neighbor of the group
- // ---------------------------------------------
+ // ---------------------------------------------
jlist = firstneigh[k];
jnum = numneigh[k];
- for (j = 0; j < nboite; j++ )
+ for (j = 0; j < nboite; j++ )
{
jtype = map[type[j]];
if (jtype == ktype) continue;
@@ -3085,7 +3085,7 @@ void PairSMTBQ::groupQEqAllParallel_QEq()
if (jtype == 0 && flag_QEq[j] == 0) continue;
- if (flag_gp[me][j] == ngp) continue;
+ if (flag_gp[me][j] == ngp) continue;
delr[0] = x[j][0] - xtmp;
delr[1] = x[j][1] - ytmp;
@@ -3101,7 +3101,7 @@ void PairSMTBQ::groupQEqAllParallel_QEq()
if (flag_gp[me][j] != 0 && flag_gp[me][j] != ngp && nelt[flag_gp[me][j]] != 0) {
printf("[me %d] (atom %d) %d [elt %d] rencontre un nouveau groupe %d [elt %d] (atom %d)\n",
- me,k,ngp,nelt[ngp],flag_gp[me][j],nelt[flag_gp[me][j]],j);
+ me,k,ngp,nelt[ngp],flag_gp[me][j],nelt[flag_gp[me][j]],j);
// On met a jours les tableaux
// -----------------------------
@@ -3109,15 +3109,15 @@ void PairSMTBQ::groupQEqAllParallel_QEq()
z = min(igp,ngp);
if (z == igp) { igp = z; }
- else if (z == ngp) {
+ else if (z == ngp) {
ngp = igp ; igp = z;
- flag_gp[me][j] = ngp;
+ flag_gp[me][j] = ngp;
}
for (zz = 0; zz < nelt[ngp]; zz++) {
z = tab_gp[ngp][zz];
tab_gp[igp][nelt[igp]] = z;
- nelt[igp] += 1;
+ nelt[igp] += 1;
flag_gp[me][z] = igp;
tab_gp[ngp][zz] = 0;
}
@@ -3127,38 +3127,38 @@ void PairSMTBQ::groupQEqAllParallel_QEq()
if (flag_gp[me][z] == ngp) flag_gp[me][z] = igp;
}
- m = 1; kk = 0;
+ m = 1; kk = 0;
ngp = igp;
break;
}
// ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
- flag_gp[me][j] = ngp;
- if (j < nlocal)
+ flag_gp[me][j] = ngp;
+ if (j < nlocal)
{
tab_gp[ngp][nelt[ngp]] = j;
- nelt[ngp] += 1;
- }
- }
- } // for j
- } // for k
+ nelt[ngp] += 1;
+ }
+ }
+ } // for j
+ } // for k
} // for ii
// OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
- // Groups communication
+ // Groups communication
// OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
for (i = 0; i < nproc; i++) {
forward_int(flag_gp[i]); reverse_int(flag_gp[i]);
}
- // ---
+ // ---
- // =======================================================
+ // =======================================================
// Loop on the cation to make them joined in the oxygen's
// group which it interacts
// =======================================================
igp = 0;
- for (ii = 0; ii < inum; ii++)
+ for (ii = 0; ii < inum; ii++)
{
i = ilist[ii] ; itype = map[type[i]];
if (itype == 0) continue;
@@ -3169,16 +3169,16 @@ void PairSMTBQ::groupQEqAllParallel_QEq()
jlist = firstneigh[i];
jnum = numneigh[i];
- for (jj = 0; jj < jnum; jj++ )
+ for (jj = 0; jj < jnum; jj++ )
{
j = jlist[jj] ; jtype = map[type[j]];
if (jtype != 0) continue;
- m = 0;
+ m = 0;
for (iproc = 0; iproc < nproc; iproc++) {
- if (flag_gp[iproc][j] != 0) m = flag_gp[iproc][j];
+ if (flag_gp[iproc][j] != 0) m = flag_gp[iproc][j];
}
- if (m == 0) continue;
+ if (m == 0) continue;
delr[0] = x[j][0] - xtmp;
delr[1] = x[j][1] - ytmp;
@@ -3190,7 +3190,7 @@ void PairSMTBQ::groupQEqAllParallel_QEq()
// if (sqrt(rsq) <= intparams[m].dc2) {
// ----------------------------------------
- flag_QEq[i] = 1; igp = flag_gp[me][j];
+ flag_QEq[i] = 1; igp = flag_gp[me][j];
if (flag_gp[me][i] == 0) flag_gp[me][i] = igp;
@@ -3201,11 +3201,11 @@ void PairSMTBQ::groupQEqAllParallel_QEq()
igp = min(flag_gp[me][i],flag_gp[me][j]);
if (igp == flag_gp[me][i]) { kgp = flag_gp[me][j]; }
else { kgp = flag_gp[me][i]; }
-
+
for (k = 0; k < nelt[kgp]; k++) {
z = tab_gp[kgp][k];
tab_gp[igp][nelt[igp]] = z;
- nelt[igp] += 1;
+ nelt[igp] += 1;
flag_gp[me][z] = igp;
tab_gp[kgp][k] = 0;
}
@@ -3242,17 +3242,17 @@ void PairSMTBQ::groupQEqAllParallel_QEq()
// =============== End of COMM =================
- for (i = 0; i < nboite; i++) {
+ for (i = 0; i < nboite; i++) {
m = 10*me + flag_gp[me][i];
if (m == 10*me) continue; // Pas de groupe zero
gptmp[m] = 1;
- for (k = 0; k < nproc; k++) {
+ for (k = 0; k < nproc; k++) {
if (k == me) continue;
if (tabtemp[m][k] != 0) continue;
- if (flag_gp[k][i] != 0) {
+ if (flag_gp[k][i] != 0) {
tabtemp[m][k] = 10*k + flag_gp[k][i];
}
}
@@ -3261,7 +3261,7 @@ void PairSMTBQ::groupQEqAllParallel_QEq()
for (k = 0; k < 10*nproc; k++) {
MPI_Allreduce(tabtemp[k],Alltabtemp[k],nproc,MPI_INT,MPI_SUM,world); }
- MPI_Allreduce(gptmp,Allgptmp,10*nproc,MPI_INT,MPI_SUM,world);
+ MPI_Allreduce(gptmp,Allgptmp,10*nproc,MPI_INT,MPI_SUM,world);
nteam = 0; iproc = 0;
for (igp = 0; igp < 10*nproc; igp++) {
@@ -3273,22 +3273,22 @@ void PairSMTBQ::groupQEqAllParallel_QEq()
nteam += 1;
team_elt[nteam][iproc] = 0;
team_QEq[nteam][iproc][team_elt[nteam][iproc]] = ngp;
- team_elt[nteam][iproc] += 1;
- } else {
+ team_elt[nteam][iproc] += 1;
+ } else {
m = 0;
for (i = 1; i < nteam+1; i++) {
for (k = 0; k < team_elt[i][iproc]; k++) {
if (ngp == team_QEq[i][iproc][k]) m = 1;
- } }
- if (m == 1) continue;
+ } }
+ if (m == 1) continue;
// create a new team!!
// ---------------------------
if (m == 0) {
nteam += 1;
team_elt[nteam][iproc] = 0;
team_QEq[nteam][iproc][team_elt[nteam][iproc]] = ngp;
- team_elt[nteam][iproc] += 1;
- }
+ team_elt[nteam][iproc] += 1;
+ }
}
// -------
// On a mis une graine dans le groupe et nous allons
@@ -3314,7 +3314,7 @@ void PairSMTBQ::groupQEqAllParallel_QEq()
m = 0;
for (j = 0; j < team_elt[nteam][i]; j++) {
if (team_QEq[nteam][i][j] == ngp) m = 1;
- }
+ }
if (m == 0) {
iproc = i; k = 0;
@@ -3324,7 +3324,7 @@ void PairSMTBQ::groupQEqAllParallel_QEq()
} // regard sur les autre proc
} // On rempli de proche en proche
- } // boucle kk sur les proc
+ } // boucle kk sur les proc
}
// Finalement on met le numero de la team en indice du flag_QEq, c mieu!
@@ -3340,7 +3340,7 @@ void PairSMTBQ::groupQEqAllParallel_QEq()
for (k = 0; k < team_elt[j][me]; k++) {
if (gp == team_QEq[j][me][k]) {
flag_QEq[i] = j; m = 1;
- break;
+ break;
}
}
if (m == 1) break;
@@ -3377,8 +3377,8 @@ void PairSMTBQ::Init_charge(int *nQEq, int *nQEqa, int *nQEqc)
test[gp] = 0; init[gp] = 0;
}
-
- // On fait un test sur les charges pour voir sont
+
+ // On fait un test sur les charges pour voir sont
// elles sont dans le domaine delimiter par DeltaQ
// -------------------------------------------------
for (ii = 0; ii < inum; ii++) {
@@ -3392,7 +3392,7 @@ void PairSMTBQ::Init_charge(int *nQEq, int *nQEqa, int *nQEqc)
}
}
- MPI_Allreduce(test,init,nteam+1,MPI_INT,MPI_SUM,world);
+ MPI_Allreduce(test,init,nteam+1,MPI_INT,MPI_SUM,world);
// On fait que sur les atomes hybrides!!!
// ----------------------------------------
@@ -3402,7 +3402,7 @@ void PairSMTBQ::Init_charge(int *nQEq, int *nQEqa, int *nQEqc)
i = ilist[ii]; itype = map[type[i]];
gp = flag_QEq[i];
- if (gp != 0 && init[gp] != 0) {
+ if (gp != 0 && init[gp] != 0) {
if (itype == 0) q[i] = -1.96;
if (itype != 0) q[i] = 1.96 * double(nQEqaall[gp]) / double(nQEqcall[gp]);
}
@@ -3477,15 +3477,15 @@ void PairSMTBQ::unpack_reverse_comm(int n, int *list, double *buf)
void PairSMTBQ::forward(double *tab)
{
- int i;
+ int i;
int nlocal = atom->nlocal;
int nghost = atom->nghost;
-
+
for (i=0; i<nlocal+nghost; i++) tab_comm[i] = tab[i];
-
+
comm->forward_comm_pair(this);
-
- for (i=0; i<nlocal+nghost; i++) tab[i] = tab_comm[i];
+
+ for (i=0; i<nlocal+nghost; i++) tab[i] = tab_comm[i];
}
/* ---------------------------------------------------------------------- */
@@ -3497,24 +3497,24 @@ void PairSMTBQ::reverse(double *tab)
int nghost = atom->nghost;
for (i=0; i<nlocal+nghost; i++) tab_comm[i] = tab[i];
-
+
comm->reverse_comm_pair(this);
-
- for (i=0; i<nlocal+nghost; i++) tab[i] = tab_comm[i];
+
+ for (i=0; i<nlocal+nghost; i++) tab[i] = tab_comm[i];
}
/* ---------------------------------------------------------------------- */
void PairSMTBQ::forward_int(int *tab)
{
- int i;
+ int i;
int nlocal = atom->nlocal;
int nghost = atom->nghost;
-
+
for (i=0; i<nlocal+nghost; i++) { tab_comm[i] = double(tab[i]);}
-
+
comm->forward_comm_pair(this);
-
+
for (i=0; i<nlocal+nghost; i++) {
if (fabs(tab_comm[i]) > 0.1) tab[i] = int(tab_comm[i]) ; }
}
@@ -3528,9 +3528,9 @@ void PairSMTBQ::reverse_int(int *tab)
int nghost = atom->nghost;
for (i=0; i<nlocal+nghost; i++) { tab_comm[i] = double(tab[i]);}
-
+
comm->reverse_comm_pair(this);
-
+
for (i=0; i<nlocal+nghost; i++) {
if (fabs(tab_comm[i]) > 0.1) tab[i] = int(tab_comm[i]); }
}
@@ -3538,7 +3538,7 @@ void PairSMTBQ::reverse_int(int *tab)
/* ---------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
-double PairSMTBQ::memory_usage()
+double PairSMTBQ::memory_usage()
{
double bytes = maxeatom * sizeof(double);
bytes += maxvatom*6 * sizeof(double);
@@ -3570,7 +3570,7 @@ int PairSMTBQ::Tokenize( char* s, char*** tok )
char *mot;
int count=0;
mot = NULL;
-
+
strncpy( test, s, MAXLINE );
@@ -3591,9 +3591,9 @@ void PairSMTBQ::CheckEnergyVSForce()
int itype,jtype,l,m;
double r,t1,t2,sds,xi,engSurf,fforceSurf;
double eng,fforce,engBB,fforceBB;
-
+
double za,zb,gam,dgam,dza,dzb,
- d2zaa,d2zab,d2zbb,d2zra,d2zrb,d2gamr2,na,nb;
+ d2zaa,d2zab,d2zbb,d2zra,d2zrb,d2gamr2,na,nb;
int *type = atom->type;
char *NameFile;
@@ -3603,7 +3603,7 @@ void PairSMTBQ::CheckEnergyVSForce()
map[type[i]]=0; //ox
itype=map[type[i]];
iq=-1;
-
+
map[type[j]]=0; //ox
jtype=map[type[j]];
@@ -3615,11 +3615,11 @@ void PairSMTBQ::CheckEnergyVSForce()
na = params[itype].ne ;
nb = params[jtype].ne ;
- za = params[itype].dzeta ;
+ za = params[itype].dzeta ;
zb = params[jtype].dzeta ;
-
- // Ouverture du fichier
+
+ // Ouverture du fichier
for (iCoord=1;iCoord<5; iCoord++)
{
@@ -3656,24 +3656,24 @@ void PairSMTBQ::CheckEnergyVSForce()
evdwlCoul = 0.0 ; fpairCoul = 0.0;
potqeq(i,j,iq,jq,rsq,fpairCoul,eflag,evdwlCoul);
fpairCoul=fpairCoul*r;
-
+
rep_OO (&intparams[m],rsq,fpair,eflag,evdwl);
ErepR = evdwl;
frepR= fpair*r;
- gam = dgam = dza = dzb = d2zaa = d2zab =
+ gam = dgam = dza = dzb = d2zaa = d2zab =
d2zbb = d2zra = d2zrb = d2gamr2 = 0.0 ;
-
+
// gammas_(na,nb,za,zb,r,gam,dgam,dza,dzb,
// d2zaa,d2zab,d2zbb,d2zra,d2zrb,d2gamr2) ;
gammas(na,nb,za,zb,r,gam,dgam,dza,dzb,
d2zaa,d2zab,d2zbb,d2zra,d2zrb,d2gamr2) ;
-
+
sds = rsq/ds ; l = int(sds) ;
xi = sds - double(l) ;
-
+
t1 = fafb[l][m] + (fafb[l+1][m] - fafb[l][m])*xi;
t2 = fafb[l+1][m] + (fafb[l+2][m] - fafb[l+1][m])*(xi-1.0);
@@ -3701,7 +3701,7 @@ void PairSMTBQ::CheckEnergyVSForce()
fforceBB = - iq*jq*(t1 + (t2 - t1)*xi/2.0)*r ;
if (fichierOxOx) { fichierOxOx<< setprecision (9) <<r <<" "<<evdwlCoul <<" " <<fpairCoul <<" "<<eng <<" " <<fforce <<" "<<engSurf <<" " <<fforceSurf <<" "<<engBB <<" " <<fforceBB <<" "<<ErepR<<" "<<frepR<<" "<<gam<<" "<<dgam<<endl ;}
-
+
}
@@ -3720,11 +3720,11 @@ void PairSMTBQ::CheckEnergyVSForce()
na = params[itype].ne ;
nb = params[jtype].ne ;
- za = params[itype].dzeta ;
+ za = params[itype].dzeta ;
zb = params[jtype].dzeta ;
-
- // Ouverture du fichier
+
+ // Ouverture du fichier
for (iCoord=1;iCoord<4; iCoord++)
{
@@ -3756,15 +3756,15 @@ void PairSMTBQ::CheckEnergyVSForce()
evdwlCoul = 0.0 ; fpairCoul = 0.0;
potqeq(i,j,iq,jq,rsq,fpairCoul,eflag,evdwlCoul);
fpairCoul=fpairCoul*r;
-
+
rep_OO (&intparams[m],rsq,fpair,eflag,evdwl);
ErepR = evdwl;
frepR= fpair*r;
- gam = dgam = dza = dzb = d2zaa = d2zab =
+ gam = dgam = dza = dzb = d2zaa = d2zab =
d2zbb = d2zra = d2zrb = d2gamr2 = 0.0 ;
-
+
// gammas_(na,nb,za,zb,r,gam,dgam,dza,dzb,
// d2zaa,d2zab,d2zbb,d2zra,d2zrb,d2gamr2) ;
gammas(na,nb,za,zb,r,gam,dgam,dza,dzb,
@@ -3772,7 +3772,7 @@ void PairSMTBQ::CheckEnergyVSForce()
if (fichierOxTi) { fichierOxTi<< setprecision (9) <<r <<" "<<evdwlCoul <<" " <<fpairCoul <<" "<<ErepR<<" "<<frepR<<" "<<gam<<" "<<dgam<<endl ;}
-
+
}
@@ -3785,11 +3785,11 @@ void PairSMTBQ::CheckEnergyVSForce()
/* :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
GAMMAS FUNCTION (GALE)
::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: */
-
+
void PairSMTBQ::gammas(double &na, double &nb, double &za, double &zb, double &r, double &gam,
double &dgam, double &dza, double &dzb, double &d2zaa, double &d2zab, double &d2zbb,
double &d2zra, double &d2zrb, double &d2gamr2)
-{
+{
/* ---------------------------------------------------------------
Subroutine calculates the integral over two s orbtials
for Slater functions
@@ -3817,7 +3817,7 @@ void PairSMTBQ::gammas(double &na, double &nb, double &za, double &zb, double &r
Julian Gale, Imperial College, December 1997
---------------------------------------------------------------- */
-
+
int i;
double z2ra,z2rb,na2,nb2,halfr,d2rtm,drtrm,rtrm,ss,deriv,
dzeta1,dzeta2,d2zeta11,d2zeta12,d2zeta22,d2zeta1r,
@@ -3857,11 +3857,11 @@ void PairSMTBQ::gammas(double &na, double &nb, double &za, double &zb, double &r
// First term
- css(ss,na2-1,0,z2ra,0.0,r,deriv,dzeta1,dzeta2,
- d2zeta11,d2zeta12,d2zeta22,d2zeta1r,d2zeta2r,
+ css(ss,na2-1,0,z2ra,0.0,r,deriv,dzeta1,dzeta2,
+ d2zeta11,d2zeta12,d2zeta22,d2zeta1r,d2zeta2r,
deriv2) ;
- gam=rtrm*ss;
+ gam=rtrm*ss;
dgam=rtrm*deriv+float(na)*drtrm*ss;
dza=rtrm*dzeta1;
d2zaa=rtrm*d2zeta11;
@@ -3873,19 +3873,19 @@ void PairSMTBQ::gammas(double &na, double &nb, double &za, double &zb, double &r
rtrm=drtrm;
drtrm=d2rtrm;
ztrm=0.5/(zb*float(nb2));
-
+
for (i = nb2; i >= 1; i--) {
rtrm=rtrm*halfr;
drtrm=drtrm*halfr;
ztrm=ztrm*2.0*zb;
ctrm=ztrm/factorial(nb2-i);
-
- css(ss,na2-1,nb2-i,z2ra,z2rb,r,deriv,dzeta1,dzeta2,
+
+ css(ss,na2-1,nb2-i,z2ra,z2rb,r,deriv,dzeta1,dzeta2,
d2zeta11,d2zeta12,d2zeta22,d2zeta1r,d2zeta2r,deriv2);
-
+
trm1=float(i)*ctrm;
trm2=trm1*rtrm;
- gam=gam-trm2*ss;
+ gam=gam-trm2*ss;
trm3=trm1*float(na2+nb2-i)*drtrm;
dgam=dgam-trm2*deriv-0.5*trm3*ss;
d2gamr2=d2gamr2-trm2*deriv2-trm3*deriv-0.5*trm3*float(na2+nb2-i-1)*ss/r;
@@ -3893,17 +3893,17 @@ void PairSMTBQ::gammas(double &na, double &nb, double &za, double &zb, double &r
dzb=dzb-(trm2/zb)*((float(nb2-i))*ss+zb*dzeta2);
d2zaa=d2zaa-trm2*d2zeta11;
d2zab=d2zab-(trm2/zb)*((float(nb2-i))*dzeta1+zb*d2zeta12);
- d2zbb=d2zbb-(trm2/zb)*(2.0*(float(nb2-i))*dzeta2+zb*d2zeta22 +
+ d2zbb=d2zbb-(trm2/zb)*(2.0*(float(nb2-i))*dzeta2+zb*d2zeta22 +
(float((nb2-i-1)*(nb2-i))*ss/zb));
d2zra=d2zra-trm2*d2zeta1r-0.5*trm3*dzeta1;
- d2zrb=d2zrb-(trm2/zb)*((float(nb2-i))*deriv+zb*d2zeta2r) -
+ d2zrb=d2zrb-(trm2/zb)*((float(nb2-i))*deriv+zb*d2zeta2r) -
0.5*(trm3/zb)*((float(nb2-i))*ss+zb*dzeta2);
}
// Multiply by coefficients
trm3=pow(2.0*za,na2+1)/factorial(na2);
- gam=gam*trm3;
+ gam=gam*trm3;
dgam=dgam*trm3;
rfct1=((float(na2+1))/za);
rgam1=rfct1*gam;
@@ -3927,7 +3927,7 @@ void PairSMTBQ::gammas(double &na, double &nb, double &za, double &zb, double &r
void PairSMTBQ::css(double &s, double nn1, double nn2, double alpha, double beta, double r,
double &deriv, double &dzeta1, double &dzeta2, double &d2zeta11, double &d2zeta12,
double &d2zeta22, double &d2zeta1r, double &d2zeta2r, double &deriv2)
-{
+{
// implicit real (a-h,o-z)
// common /fctrl/ fct(30) // A RAJOUTER DANS Pair_SMTBQ.h
/* ------------------------------------------------------------------
@@ -3954,7 +3954,7 @@ void PairSMTBQ::css(double &s, double nn1, double nn2, double alpha, double beta
double *a,*b;
memory->create(a,31,"pair:a");
memory->create(b,31,"pair:a");
-
+
// Set up factorials - stored as factorial(n) in location(n+1)
@@ -4058,17 +4058,17 @@ void PairSMTBQ::css(double &s, double nn1, double nn2, double alpha, double beta
x=x+coff*a[i1]*b[nni1];
dzeta1=dzeta1+coff*(da1[i1]*b[nni1]+a[i1]*db1[nni1]);
dzeta2=dzeta2+coff*(da2[i1]*b[nni1]+a[i1]*db2[nni1]);
- d2zeta11=d2zeta11+coff*(d2a11[i1]*b[nni1]+a[i1]*d2b11[nni1]+
+ d2zeta11=d2zeta11+coff*(d2a11[i1]*b[nni1]+a[i1]*d2b11[nni1]+
2.0*da1[i1]*db1[nni1]);
- d2zeta12=d2zeta12+coff*(d2a12[i1]*b[nni1]+a[i1]*d2b12[nni1]+
+ d2zeta12=d2zeta12+coff*(d2a12[i1]*b[nni1]+a[i1]*d2b12[nni1]+
da1[i1]*db2[nni1]+da2[i1]*db1[nni1]);
- d2zeta22=d2zeta22+coff*(d2a22[i1]*b[nni1]+a[i1]*d2b22[nni1]+
+ d2zeta22=d2zeta22+coff*(d2a22[i1]*b[nni1]+a[i1]*d2b22[nni1]+
2.0*da2[i1]*db2[nni1]);
- d2zeta1r=d2zeta1r+coff*(d2a1r[i1]*b[nni1]+dar[i1]*db1[nni1]+
+ d2zeta1r=d2zeta1r+coff*(d2a1r[i1]*b[nni1]+dar[i1]*db1[nni1]+
da1[i1]*dbr[nni1]+a[i1]*d2b1r[nni1]);
- d2zeta2r=d2zeta2r+coff*(d2a2r[i1]*b[nni1]+dar[i1]*db2[nni1]+
+ d2zeta2r=d2zeta2r+coff*(d2a2r[i1]*b[nni1]+dar[i1]*db2[nni1]+
da2[i1]*dbr[nni1]+a[i1]*d2b2r[nni1]);
- deriv2=deriv2+coff*(d2ar2[i1]*b[nni1]+a[i1]*d2br2[nni1]+
+ deriv2=deriv2+coff*(d2ar2[i1]*b[nni1]+a[i1]*d2br2[nni1]+
2.0*dar[i1]*dbr[nni1]);
}
s=x*0.5;
@@ -4086,7 +4086,7 @@ void PairSMTBQ::css(double &s, double nn1, double nn2, double alpha, double beta
memory->destroy(b);
return;
-}
+}
/* -------------------------------------------------------------------------------
coeffs
------------------------------------------------------------------------------- */
@@ -4094,10 +4094,10 @@ void PairSMTBQ::css(double &s, double nn1, double nn2, double alpha, double beta
{
// implicit real (a-h,o-z)
// common /fctrl/ fct(30)
-
+
int il,lie,je,ia,i,j,ie,l;
double coeffs;
-
+
// Statement function
// binm(n,i)=fct(n+1)/(fct(n-i+1)*fct(i+1));
@@ -4113,13 +4113,13 @@ void PairSMTBQ::css(double &s, double nn1, double nn2, double alpha, double beta
}
return coeffs;
}
-
-// ============================================
+
+// ============================================
double PairSMTBQ::binm(int n, int i)
{
return fct[n+1]/(fct[n-i+1]*fct[i+1]);
-}
+}
/* ---------------------------------------------------------------------------------
Caintgs
@@ -4138,9 +4138,9 @@ double PairSMTBQ::binm(int n, int i)
a[i+1]=(a[i]*float(i)+cste)*rx;
}
return;
- }
+ }
/* -----------------------------------------------------------------------------------
- Cbintgs
+ Cbintgs
----------------------------------------------------------------------------------- */
void PairSMTBQ::cbintgs( double x, int k, double *b)
{
@@ -4192,7 +4192,7 @@ void PairSMTBQ::cbintgs( double x, int k, double *b)
b[i+1]=(float(i)*b[i]+ pow(-1.0,i)*expx-expmx)*rx;
}
goto g190;
-//
+//
// Series to calculate b(i)
//
g140: for (i = i0; i <= k ; i++) {
@@ -4212,16 +4212,16 @@ void PairSMTBQ::cbintgs( double x, int k, double *b)
}
g190:
return;
- }
+ }
/* ------------------------------------------------------------------------------------
- Factorial
+ Factorial
------------------------------------------------------------------------------------ */
-double PairSMTBQ::factorial(double n)
+double PairSMTBQ::factorial(double n)
{
// implicit real(a-h,o-z)
double rn,factorial;
int i;
-
+
//
// Calculates the factorial of an integer n
//
diff --git a/src/USER-SPH/atom_vec_meso.cpp b/src/USER-SPH/atom_vec_meso.cpp
index 947139e791..daa7c10740 100644
--- a/src/USER-SPH/atom_vec_meso.cpp
+++ b/src/USER-SPH/atom_vec_meso.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
-#include "stdlib.h"
+#include <string.h>
+#include <stdlib.h>
#include "atom_vec_meso.h"
#include "atom.h"
#include "comm.h"
@@ -929,7 +929,7 @@ int AtomVecMeso::pack_data_hybrid(int i, double *buf)
void AtomVecMeso::write_data(FILE *fp, int n, double **buf)
{
for (int i = 0; i < n; i++)
- fprintf(fp,TAGINT_FORMAT
+ fprintf(fp,TAGINT_FORMAT
" %d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e "
"%d %d %d\n",
(tagint) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).i,
@@ -969,7 +969,7 @@ int AtomVecMeso::property_atom(char *name)
index maps to data specific to this atom style
------------------------------------------------------------------------- */
-void AtomVecMeso::pack_property_atom(int index, double *buf,
+void AtomVecMeso::pack_property_atom(int index, double *buf,
int nvalues, int groupbit)
{
int *mask = atom->mask;
diff --git a/src/USER-SPH/compute_meso_e_atom.cpp b/src/USER-SPH/compute_meso_e_atom.cpp
index 0446d948c4..5db9dbbedf 100644
--- a/src/USER-SPH/compute_meso_e_atom.cpp
+++ b/src/USER-SPH/compute_meso_e_atom.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "compute_meso_e_atom.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-SPH/compute_meso_rho_atom.cpp b/src/USER-SPH/compute_meso_rho_atom.cpp
index e1db218544..fa286d7e05 100644
--- a/src/USER-SPH/compute_meso_rho_atom.cpp
+++ b/src/USER-SPH/compute_meso_rho_atom.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "compute_meso_rho_atom.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-SPH/compute_meso_t_atom.cpp b/src/USER-SPH/compute_meso_t_atom.cpp
index 98b0c88f55..ce594cdff2 100644
--- a/src/USER-SPH/compute_meso_t_atom.cpp
+++ b/src/USER-SPH/compute_meso_t_atom.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "compute_meso_t_atom.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-SPH/fix_meso.cpp b/src/USER-SPH/fix_meso.cpp
index 3e827ace81..665c9e0f3f 100644
--- a/src/USER-SPH/fix_meso.cpp
+++ b/src/USER-SPH/fix_meso.cpp
@@ -11,12 +11,12 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdio.h"
-#include "string.h"
+#include <stdio.h>
+#include <string.h>
#include "fix_meso.h"
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "atom.h"
#include "comm.h"
#include "force.h"
@@ -67,7 +67,7 @@ void FixMeso::init() {
void FixMeso::setup_pre_force(int vflag)
{
- // set vest equal to v
+ // set vest equal to v
double **v = atom->v;
double **vest = atom->vest;
int *mask = atom->mask;
diff --git a/src/USER-SPH/fix_meso_stationary.cpp b/src/USER-SPH/fix_meso_stationary.cpp
index d61edcfc20..0607f2f3d0 100644
--- a/src/USER-SPH/fix_meso_stationary.cpp
+++ b/src/USER-SPH/fix_meso_stationary.cpp
@@ -11,12 +11,12 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdio.h"
-#include "string.h"
+#include <stdio.h>
+#include <string.h>
#include "fix_meso_stationary.h"
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "atom.h"
#include "comm.h"
#include "force.h"
diff --git a/src/USER-SPH/pair_sph_heatconduction.cpp b/src/USER-SPH/pair_sph_heatconduction.cpp
index 6590a0afde..0b3716658c 100644
--- a/src/USER-SPH/pair_sph_heatconduction.cpp
+++ b/src/USER-SPH/pair_sph_heatconduction.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdlib.h>
#include "pair_sph_heatconduction.h"
#include "atom.h"
#include "force.h"
diff --git a/src/USER-SPH/pair_sph_idealgas.cpp b/src/USER-SPH/pair_sph_idealgas.cpp
index 0336aa8025..caea8eb3e4 100644
--- a/src/USER-SPH/pair_sph_idealgas.cpp
+++ b/src/USER-SPH/pair_sph_idealgas.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdlib.h>
#include "pair_sph_idealgas.h"
#include "atom.h"
#include "force.h"
diff --git a/src/USER-SPH/pair_sph_lj.cpp b/src/USER-SPH/pair_sph_lj.cpp
index c934f2b5de..f0f3e3df33 100644
--- a/src/USER-SPH/pair_sph_lj.cpp
+++ b/src/USER-SPH/pair_sph_lj.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdlib.h>
#include "pair_sph_lj.h"
#include "atom.h"
#include "force.h"
diff --git a/src/USER-SPH/pair_sph_rhosum.cpp b/src/USER-SPH/pair_sph_rhosum.cpp
index db0749b2a2..4b7b028ad2 100644
--- a/src/USER-SPH/pair_sph_rhosum.cpp
+++ b/src/USER-SPH/pair_sph_rhosum.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdlib.h>
#include "pair_sph_rhosum.h"
#include "atom.h"
#include "force.h"
@@ -287,7 +287,7 @@ double PairSPHRhoSum::single(int i, int j, int itype, int jtype, double rsq,
/* ---------------------------------------------------------------------- */
-int PairSPHRhoSum::pack_forward_comm(int n, int *list, double *buf,
+int PairSPHRhoSum::pack_forward_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc) {
int i, j, m;
double *rho = atom->rho;
diff --git a/src/USER-SPH/pair_sph_taitwater.cpp b/src/USER-SPH/pair_sph_taitwater.cpp
index f9c9bbc2b0..846ec11893 100644
--- a/src/USER-SPH/pair_sph_taitwater.cpp
+++ b/src/USER-SPH/pair_sph_taitwater.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdlib.h>
#include "pair_sph_taitwater.h"
#include "atom.h"
#include "force.h"
diff --git a/src/USER-SPH/pair_sph_taitwater_morris.cpp b/src/USER-SPH/pair_sph_taitwater_morris.cpp
index a6b89893f3..d6a94f51cd 100644
--- a/src/USER-SPH/pair_sph_taitwater_morris.cpp
+++ b/src/USER-SPH/pair_sph_taitwater_morris.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdlib.h>
#include "pair_sph_taitwater_morris.h"
#include "atom.h"
#include "force.h"
diff --git a/src/USER-TALLY/compute_force_tally.cpp b/src/USER-TALLY/compute_force_tally.cpp
index b9281a2d59..90464d7949 100644
--- a/src/USER-TALLY/compute_force_tally.cpp
+++ b/src/USER-TALLY/compute_force_tally.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "compute_force_tally.h"
#include "atom.h"
#include "group.h"
@@ -91,7 +91,7 @@ void ComputeForceTally::pair_tally_callback(int i, int j, int nlocal, int newton
if (did_compute != update->ntimestep) {
did_compute = update->ntimestep;
-
+
// grow local force array if necessary
// needs to be atom->nmax in length
diff --git a/src/USER-TALLY/compute_force_tally.h b/src/USER-TALLY/compute_force_tally.h
index fce6b0fdd5..0f7bc35a6d 100644
--- a/src/USER-TALLY/compute_force_tally.h
+++ b/src/USER-TALLY/compute_force_tally.h
@@ -25,13 +25,13 @@ ComputeStyle(force/tally,ComputeForceTally)
namespace LAMMPS_NS {
class ComputeForceTally : public Compute {
-
+
public:
ComputeForceTally(class LAMMPS *, int, char **);
virtual ~ComputeForceTally();
void init();
-
+
double compute_scalar();
void compute_peratom();
diff --git a/src/USER-TALLY/compute_heat_flux_tally.cpp b/src/USER-TALLY/compute_heat_flux_tally.cpp
index 890a3ffd6d..214311cb3d 100644
--- a/src/USER-TALLY/compute_heat_flux_tally.cpp
+++ b/src/USER-TALLY/compute_heat_flux_tally.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "compute_heat_flux_tally.h"
#include "atom.h"
#include "group.h"
@@ -91,7 +91,7 @@ void ComputeHeatFluxTally::pair_tally_callback(int i, int j, int nlocal, int new
if (did_compute != update->ntimestep) {
did_compute = update->ntimestep;
-
+
// grow local stress and eatom arrays if necessary
// needs to be atom->nmax in length
@@ -233,7 +233,7 @@ void ComputeHeatFluxTally::compute_vector()
// compute heat currents
// heat flux vector = jc[3] + jv[3]
// jc[3] = convective portion of heat flux = sum_i (ke_i + pe_i) v_i[3]
- // jv[3] = virial portion of heat flux = sum_i (stress_tensor_i . v_i[3])
+ // jv[3] = virial portion of heat flux = sum_i (stress_tensor_i . v_i[3])
// normalization by volume is not included
// J = sum_i( (0.5*m*v_i^2 + 0.5*(evdwl_i+ecoul_i))*v_i +
// + (F_ij . v_i)*dR_ij/2 )
diff --git a/src/USER-TALLY/compute_heat_flux_tally.h b/src/USER-TALLY/compute_heat_flux_tally.h
index 7480052104..8c6671cf1e 100644
--- a/src/USER-TALLY/compute_heat_flux_tally.h
+++ b/src/USER-TALLY/compute_heat_flux_tally.h
@@ -25,7 +25,7 @@ ComputeStyle(heat/flux/tally,ComputeHeatFluxTally)
namespace LAMMPS_NS {
class ComputeHeatFluxTally : public Compute {
-
+
public:
ComputeHeatFluxTally(class LAMMPS *, int, char **);
virtual ~ComputeHeatFluxTally();
diff --git a/src/USER-TALLY/compute_pe_tally.cpp b/src/USER-TALLY/compute_pe_tally.cpp
index da9549f70a..f18a58e44e 100644
--- a/src/USER-TALLY/compute_pe_tally.cpp
+++ b/src/USER-TALLY/compute_pe_tally.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "compute_pe_tally.h"
#include "atom.h"
#include "group.h"
@@ -90,7 +90,7 @@ void ComputePETally::pair_tally_callback(int i, int j, int nlocal, int newton,
if (did_compute != update->ntimestep) {
did_compute = update->ntimestep;
-
+
// grow local eatom array if necessary
// needs to be atom->nmax in length
@@ -189,7 +189,7 @@ void ComputePETally::compute_peratom()
const int nall = atom->nlocal + atom->nghost;
for (int i = atom->nlocal; i < nall; ++i)
eatom[i][0] = eatom[i][1] = 0.0;
- }
+ }
}
/* ----------------------------------------------------------------------
diff --git a/src/USER-TALLY/compute_pe_tally.h b/src/USER-TALLY/compute_pe_tally.h
index d502570dbc..2335bbecee 100644
--- a/src/USER-TALLY/compute_pe_tally.h
+++ b/src/USER-TALLY/compute_pe_tally.h
@@ -25,7 +25,7 @@ ComputeStyle(pe/tally,ComputePETally)
namespace LAMMPS_NS {
class ComputePETally : public Compute {
-
+
public:
ComputePETally(class LAMMPS *, int, char **);
virtual ~ComputePETally();
diff --git a/src/USER-TALLY/compute_stress_tally.cpp b/src/USER-TALLY/compute_stress_tally.cpp
index 89bcb408eb..2a5f522636 100644
--- a/src/USER-TALLY/compute_stress_tally.cpp
+++ b/src/USER-TALLY/compute_stress_tally.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "compute_stress_tally.h"
#include "atom.h"
#include "group.h"
@@ -91,7 +91,7 @@ void ComputeStressTally::pair_tally_callback(int i, int j, int nlocal, int newto
if (did_compute != update->ntimestep) {
did_compute = update->ntimestep;
-
+
// grow local stress array if necessary
// needs to be atom->nmax in length
@@ -128,7 +128,7 @@ void ComputeStressTally::pair_tally_callback(int i, int j, int nlocal, int newto
const double v3 = dx*dy*fpair;
const double v4 = dx*dz*fpair;
const double v5 = dy*dz*fpair;
-
+
if (newton || i < nlocal) {
virial[0] += v0; stress[i][0] += v0;
virial[1] += v1; stress[i][1] += v1;
@@ -197,7 +197,7 @@ double ComputeStressTally::compute_scalar()
MPI_Allreduce(virial,vector,size_peratom_cols,MPI_DOUBLE,MPI_SUM,world);
- if (domain->dimension == 3)
+ if (domain->dimension == 3)
scalar = (vector[0]+vector[1]+vector[2])/3.0;
else
scalar = (vector[0]+vector[1])/2.0;
diff --git a/src/USER-TALLY/compute_stress_tally.h b/src/USER-TALLY/compute_stress_tally.h
index 4ce2466bd3..a677d2eef6 100644
--- a/src/USER-TALLY/compute_stress_tally.h
+++ b/src/USER-TALLY/compute_stress_tally.h
@@ -25,7 +25,7 @@ ComputeStyle(stress/tally,ComputeStressTally)
namespace LAMMPS_NS {
class ComputeStressTally : public Compute {
-
+
public:
ComputeStressTally(class LAMMPS *, int, char **);
virtual ~ComputeStressTally();
diff --git a/src/VORONOI/compute_voronoi_atom.cpp b/src/VORONOI/compute_voronoi_atom.cpp
index adf7b7846e..eccce4f5b1 100644
--- a/src/VORONOI/compute_voronoi_atom.cpp
+++ b/src/VORONOI/compute_voronoi_atom.cpp
@@ -15,10 +15,10 @@
Contributing author: Daniel Schwen
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "math.h"
-#include "string.h"
-#include "stdlib.h"
+#include <mpi.h>
+#include <math.h>
+#include <string.h>
+#include <stdlib.h>
#include "compute_voronoi_atom.h"
#include "atom.h"
#include "group.h"
@@ -71,7 +71,7 @@ ComputeVoronoi::ComputeVoronoi(LAMMPS *lmp, int narg, char **arg) :
iarg++;
}
else if (strcmp(arg[iarg], "radius") == 0) {
- if (iarg + 2 > narg || strstr(arg[iarg+1],"v_") != arg[iarg+1] )
+ if (iarg + 2 > narg || strstr(arg[iarg+1],"v_") != arg[iarg+1] )
error->all(FLERR,"Illegal compute voronoi/atom command");
int n = strlen(&arg[iarg+1][2]) + 1;
radstr = new char[n];
diff --git a/src/XTC/dump_xtc.cpp b/src/XTC/dump_xtc.cpp
index 7b8afbd3a9..e2eec30bd0 100644
--- a/src/XTC/dump_xtc.cpp
+++ b/src/XTC/dump_xtc.cpp
@@ -22,11 +22,11 @@
support for groups
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
-#include "limits.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <limits.h>
#include "dump_xtc.h"
#include "domain.h"
#include "atom.h"
@@ -86,7 +86,7 @@ DumpXTC::DumpXTC(LAMMPS *lmp, int narg, char **arg) : Dump(lmp, narg, arg)
// in reduced units we do not scale anything
if (strcmp(update->unit_style,"lj") == 0) {
sfactor = tfactor = 1.0;
- if (comm->me == 0)
+ if (comm->me == 0)
error->warning(FLERR,"No automatic unit conversion to XTC file "
"format conventions possible for units lj");
}
diff --git a/src/XTC/dump_xtc.h b/src/XTC/dump_xtc.h
index 4112c65a41..44c444d120 100644
--- a/src/XTC/dump_xtc.h
+++ b/src/XTC/dump_xtc.h
@@ -42,7 +42,7 @@ class DumpXTC : public Dump {
int unwrap_flag; // 1 if atom coords are unwrapped, 0 if no
float precision; // user-adjustable precision setting
float *coords;
- double sfactor,tfactor; // scaling factors for positions and time unit
+ double sfactor,tfactor; // scaling factors for positions and time unit
XDR xd;
void init_style();
diff --git a/src/angle.cpp b/src/angle.cpp
index 3913db685a..e8488b0b1a 100644
--- a/src/angle.cpp
+++ b/src/angle.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "angle.h"
#include "atom.h"
#include "comm.h"
@@ -66,7 +66,7 @@ Angle::~Angle()
void Angle::init()
{
- if (!allocated && atom->nangletypes)
+ if (!allocated && atom->nangletypes)
error->all(FLERR,"Angle coeffs are not set");
for (int i = 1; i <= atom->nangletypes; i++)
if (setflag[i] == 0) error->all(FLERR,"All angle coeffs are not set");
diff --git a/src/angle.h b/src/angle.h
index 535fe2b229..31d73176ac 100644
--- a/src/angle.h
+++ b/src/angle.h
@@ -14,7 +14,7 @@
#ifndef LMP_ANGLE_H
#define LMP_ANGLE_H
-#include "stdio.h"
+#include <stdio.h>
#include "pointers.h"
namespace LAMMPS_NS {
diff --git a/src/angle_hybrid.cpp b/src/angle_hybrid.cpp
index 8b638286fa..42b6860b6c 100644
--- a/src/angle_hybrid.cpp
+++ b/src/angle_hybrid.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "string.h"
-#include "ctype.h"
+#include <math.h>
+#include <string.h>
+#include <ctype.h>
#include "angle_hybrid.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/angle_hybrid.h b/src/angle_hybrid.h
index 8cefe7d1bd..4ae34c176f 100644
--- a/src/angle_hybrid.h
+++ b/src/angle_hybrid.h
@@ -20,7 +20,7 @@ AngleStyle(hybrid,AngleHybrid)
#ifndef LMP_ANGLE_HYBRID_H
#define LMP_ANGLE_HYBRID_H
-#include "stdio.h"
+#include <stdio.h>
#include "angle.h"
namespace LAMMPS_NS {
diff --git a/src/atom.cpp b/src/atom.cpp
index 6d7bb5b4ed..5b091a26bd 100644
--- a/src/atom.cpp
+++ b/src/atom.cpp
@@ -11,12 +11,12 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
-#include "limits.h"
+#include <mpi.h>
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <limits.h>
#include "atom.h"
#include "style_atom.h"
#include "atom_vec.h"
@@ -611,11 +611,11 @@ void Atom::tag_check()
if (minall < 0) error->all(FLERR,"One or more Atom IDs is negative");
if (maxall >= MAXTAGINT) error->all(FLERR,"One or more atom IDs is too big");
- if (maxall > 0 && minall == 0)
+ if (maxall > 0 && minall == 0)
error->all(FLERR,"One or more atom IDs is zero");
if (maxall > 0 && tag_enable == 0)
error->all(FLERR,"Non-zero atom IDs with atom_modify id = no");
- if (maxall == 0 && natoms && tag_enable)
+ if (maxall == 0 && natoms && tag_enable)
error->all(FLERR,"All atom IDs = 0 but atom_modify id = yes");
if (tag_enable && maxall < natoms)
error->all(FLERR,"Duplicate atom IDs exist");
@@ -735,23 +735,23 @@ void Atom::deallocate_topology()
memory->destroy(atom->angle_atom3);
atom->angle_type = NULL;
atom->angle_atom1 = atom->angle_atom2 = atom->angle_atom3 = NULL;
-
+
memory->destroy(atom->dihedral_type);
memory->destroy(atom->dihedral_atom1);
memory->destroy(atom->dihedral_atom2);
memory->destroy(atom->dihedral_atom3);
memory->destroy(atom->dihedral_atom4);
atom->dihedral_type = NULL;
- atom->dihedral_atom1 = atom->dihedral_atom2 =
+ atom->dihedral_atom1 = atom->dihedral_atom2 =
atom->dihedral_atom3 = atom->dihedral_atom4 = NULL;
-
+
memory->destroy(atom->improper_type);
memory->destroy(atom->improper_atom1);
memory->destroy(atom->improper_atom2);
memory->destroy(atom->improper_atom3);
memory->destroy(atom->improper_atom4);
atom->improper_type = NULL;
- atom->improper_atom1 = atom->improper_atom2 =
+ atom->improper_atom1 = atom->improper_atom2 =
atom->improper_atom3 = atom->improper_atom4 = NULL;
}
@@ -760,7 +760,7 @@ void Atom::deallocate_topology()
call style-specific routine to parse line
------------------------------------------------------------------------- */
-void Atom::data_atoms(int n, char *buf, tagint id_offset, int type_offset,
+void Atom::data_atoms(int n, char *buf, tagint id_offset, int type_offset,
int shiftflag, double *shift)
{
int m,xptr,iptr;
@@ -865,7 +865,7 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, int type_offset,
(((imageint) (atoi(values[iptr+2]) + IMGMAX) & IMGMASK) << IMG2BITS);
else imagedata = ((imageint) IMGMAX << IMG2BITS) |
((imageint) IMGMAX << IMGBITS) | IMGMAX;
-
+
xdata[0] = atof(values[xptr]);
xdata[1] = atof(values[xptr+1]);
xdata[2] = atof(values[xptr+2]);
@@ -951,7 +951,7 @@ void Atom::data_vels(int n, char *buf, tagint id_offset)
------------------------------------------------------------------------- */
void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset,
- int type_offset)
+ int type_offset)
{
int m,tmp,itype;
tagint atom1,atom2;
@@ -1004,7 +1004,7 @@ void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset,
------------------------------------------------------------------------- */
void Atom::data_angles(int n, char *buf, int *count, tagint id_offset,
- int type_offset)
+ int type_offset)
{
int m,tmp,itype;
tagint atom1,atom2,atom3;
@@ -1083,7 +1083,7 @@ void Atom::data_dihedrals(int n, char *buf, int *count, tagint id_offset,
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
*next = '\0';
- sscanf(buf,"%d %d "
+ sscanf(buf,"%d %d "
TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT,
&tmp,&itype,&atom1,&atom2,&atom3,&atom4);
if (id_offset) {
@@ -1170,7 +1170,7 @@ void Atom::data_impropers(int n, char *buf, int *count, tagint id_offset,
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
*next = '\0';
- sscanf(buf,"%d %d "
+ sscanf(buf,"%d %d "
TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT,
&tmp,&itype,&atom1,&atom2,&atom3,&atom4);
if (id_offset) {
@@ -1292,7 +1292,7 @@ void Atom::data_bonus(int n, char *buf, AtomVec *avec_bonus, tagint id_offset)
call style-specific routine to parse line
------------------------------------------------------------------------- */
-void Atom::data_bodies(int n, char *buf, AtomVecBody *avec_body,
+void Atom::data_bodies(int n, char *buf, AtomVecBody *avec_body,
tagint id_offset)
{
int j,m,tagdata,ninteger,ndouble;
@@ -1501,7 +1501,7 @@ void Atom::add_molecule(int narg, char **arg)
{
if (narg < 1) error->all(FLERR,"Illegal molecule command");
- if (find_molecule(arg[0]) >= 0)
+ if (find_molecule(arg[0]) >= 0)
error->all(FLERR,"Reuse of molecule template ID");
// 1st molecule in set stores nset = # of mols, others store nset = 0
@@ -1548,7 +1548,7 @@ void Atom::add_molecule_atom(Molecule *onemol, int iatom,
if (onemol->qflag && q_flag) q[ilocal] = onemol->q[iatom];
if (onemol->radiusflag && radius_flag) radius[ilocal] = onemol->radius[iatom];
if (onemol->rmassflag && rmass_flag) rmass[ilocal] = onemol->rmass[iatom];
- else if (rmass_flag)
+ else if (rmass_flag)
rmass[ilocal] = 4.0*MY_PI/3.0 *
radius[ilocal]*radius[ilocal]*radius[ilocal];
@@ -2050,9 +2050,9 @@ void *Atom::extract(char *name)
if (strcmp(name, "contact_radius") == 0) return (void *) contact_radius;
if (strcmp(name, "smd_data_9") == 0) return (void *) smd_data_9;
if (strcmp(name, "smd_stress") == 0) return (void *) smd_stress;
- if (strcmp(name, "eff_plastic_strain") == 0)
+ if (strcmp(name, "eff_plastic_strain") == 0)
return (void *) eff_plastic_strain;
- if (strcmp(name, "eff_plastic_strain_rate") == 0)
+ if (strcmp(name, "eff_plastic_strain_rate") == 0)
return (void *) eff_plastic_strain_rate;
if (strcmp(name, "damage") == 0) return (void *) damage;
diff --git a/src/atom.h b/src/atom.h
index dd0d9821a1..96a42320e7 100644
--- a/src/atom.h
+++ b/src/atom.h
@@ -245,7 +245,7 @@ class Atom : protected Pointers {
int find_custom(char *, int &);
int add_custom(char *, int);
void remove_custom(int, int);
-
+
virtual void sync_modify(ExecutionSpace, unsigned int, unsigned int) {}
void *extract(char *);
diff --git a/src/atom_map.cpp b/src/atom_map.cpp
index 3613b59fca..bbfe014dec 100644
--- a/src/atom_map.cpp
+++ b/src/atom_map.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "atom.h"
#include "comm.h"
#include "memory.h"
@@ -47,7 +47,7 @@ void Atom::map_init(int check)
// if not recreating:
// for array, initialize current map_tag_max values
- // for hash, set all buckets to empty, put all entries in free list
+ // for hash, set all buckets to empty, put all entries in free list
if (!recreate) {
if (map_style == 1) {
@@ -69,7 +69,7 @@ void Atom::map_init(int check)
map_maxarray = map_tag_max;
memory->create(map_array,map_maxarray+1,"atom:map_array");
for (int i = 0; i <= map_tag_max; i++) map_array[i] = -1;
-
+
} else {
// map_nhash = max # of atoms that can be hashed on this proc
@@ -91,7 +91,7 @@ void Atom::map_init(int check)
// set all buckets to empty
// set hash to map_nhash in length
// put all hash entries in free list and point them to each other
-
+
map_bucket = new int[map_nbucket];
for (int i = 0; i < map_nbucket; i++) map_bucket[i] = -1;
@@ -301,7 +301,7 @@ int Atom::map_style_set()
// if user-selected, use that setting
// else if map_tag_max > 1M, use hash
// else use array
-
+
int map_style_old = map_style;
if (map_user) map_style = map_user;
else if (map_tag_max > 1000000) map_style = 2;
diff --git a/src/atom_vec.cpp b/src/atom_vec.cpp
index 157e9c0969..c6f54ec19e 100644
--- a/src/atom_vec.cpp
+++ b/src/atom_vec.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
-#include "stdlib.h"
+#include <string.h>
+#include <stdlib.h>
#include "atom_vec.h"
#include "atom.h"
#include "force.h"
@@ -265,7 +265,7 @@ int AtomVec::pack_angle(tagint **buf)
void AtomVec::write_angle(FILE *fp, int n, tagint **buf, int index)
{
for (int i = 0; i < n; i++) {
- fprintf(fp,"%d " TAGINT_FORMAT " " TAGINT_FORMAT " "
+ fprintf(fp,"%d " TAGINT_FORMAT " " TAGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT "\n",
index,buf[i][0],buf[i][1],buf[i][2],buf[i][3]);
index++;
@@ -321,7 +321,7 @@ void AtomVec::pack_dihedral(tagint **buf)
void AtomVec::write_dihedral(FILE *fp, int n, tagint **buf, int index)
{
for (int i = 0; i < n; i++) {
- fprintf(fp,"%d " TAGINT_FORMAT " " TAGINT_FORMAT " "
+ fprintf(fp,"%d " TAGINT_FORMAT " " TAGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT "\n",
index,buf[i][0],buf[i][1],buf[i][2],buf[i][3],buf[i][4]);
index++;
@@ -377,7 +377,7 @@ void AtomVec::pack_improper(tagint **buf)
void AtomVec::write_improper(FILE *fp, int n, tagint **buf, int index)
{
for (int i = 0; i < n; i++) {
- fprintf(fp,"%d " TAGINT_FORMAT " " TAGINT_FORMAT " "
+ fprintf(fp,"%d " TAGINT_FORMAT " " TAGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT "\n",
index,buf[i][0],buf[i][1],buf[i][2],buf[i][3],buf[i][4]);
index++;
diff --git a/src/atom_vec.h b/src/atom_vec.h
index baa27dfaa6..66bfd14608 100644
--- a/src/atom_vec.h
+++ b/src/atom_vec.h
@@ -14,7 +14,7 @@
#ifndef LMP_ATOM_VEC_H
#define LMP_ATOM_VEC_H
-#include "stdio.h"
+#include <stdio.h>
#include "pointers.h"
namespace LAMMPS_NS {
@@ -113,7 +113,7 @@ class AtomVec : protected Pointers {
void write_dihedral(FILE *, int, tagint **, int);
void pack_improper(tagint **);
void write_improper(FILE *, int, tagint **, int);
-
+
virtual int property_atom(char *) {return -1;}
virtual void pack_property_atom(int, double *, int, int) {}
diff --git a/src/atom_vec_atomic.cpp b/src/atom_vec_atomic.cpp
index 24d6f3d92c..c29e04ea87 100644
--- a/src/atom_vec_atomic.cpp
+++ b/src/atom_vec_atomic.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdlib.h"
+#include <stdlib.h>
#include "atom_vec_atomic.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/atom_vec_body.cpp b/src/atom_vec_body.cpp
index b4b1d3f210..2f6c4e48b3 100644
--- a/src/atom_vec_body.cpp
+++ b/src/atom_vec_body.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "atom_vec_body.h"
#include "style_body.h"
#include "body.h"
@@ -1301,7 +1301,7 @@ int AtomVecBody::data_atom_hybrid(int nlocal, char **values)
unpack one body from Bodies section of data file
------------------------------------------------------------------------- */
-void AtomVecBody::data_body(int m, int ninteger, int ndouble,
+void AtomVecBody::data_body(int m, int ninteger, int ndouble,
char **ivalues, char **dvalues)
{
if (body[m]) error->one(FLERR,"Assigning body parameters to non-body atom");
@@ -1466,7 +1466,7 @@ bigint AtomVecBody::memory_usage()
if (atom->memcheck("rmass")) bytes += memory->usage(rmass,nmax);
if (atom->memcheck("angmom")) bytes += memory->usage(angmom,nmax,3);
- if (atom->memcheck("torque")) bytes +=
+ if (atom->memcheck("torque")) bytes +=
memory->usage(torque,nmax*comm->nthreads,3);
if (atom->memcheck("body")) bytes += memory->usage(body,nmax);
@@ -1496,8 +1496,8 @@ void AtomVecBody::check(int flag)
}
}
for (int i = atom->nlocal; i < atom->nlocal+atom->nghost; i++) {
- if (atom->body[i] >= 0 &&
- (atom->body[i] < nlocal_bonus ||
+ if (atom->body[i] >= 0 &&
+ (atom->body[i] < nlocal_bonus ||
atom->body[i] >= nlocal_bonus+nghost_bonus)) {
printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag);
errorx->one(FLERR,"BAD BBB");
@@ -1516,7 +1516,7 @@ void AtomVecBody::check(int flag)
}
}
for (int i = nlocal_bonus; i < nlocal_bonus+nghost_bonus; i++) {
- if (bonus[i].ilocal < atom->nlocal ||
+ if (bonus[i].ilocal < atom->nlocal ||
bonus[i].ilocal >= atom->nlocal+atom->nghost) {
printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag);
errorx->one(FLERR,"BAD EEE");
diff --git a/src/atom_vec_charge.cpp b/src/atom_vec_charge.cpp
index 0cdea95e1a..08c3186a45 100644
--- a/src/atom_vec_charge.cpp
+++ b/src/atom_vec_charge.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdlib.h"
+#include <stdlib.h>
#include "atom_vec_charge.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/atom_vec_ellipsoid.cpp b/src/atom_vec_ellipsoid.cpp
index 889636963a..4d1dc01c07 100755
--- a/src/atom_vec_ellipsoid.cpp
+++ b/src/atom_vec_ellipsoid.cpp
@@ -15,7 +15,7 @@
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
-#include "stdlib.h"
+#include <stdlib.h>
#include "atom_vec_ellipsoid.h"
#include "math_extra.h"
#include "atom.h"
@@ -1134,7 +1134,7 @@ void AtomVecEllipsoid::create_atom(int itype, double *coord)
initialize other atom quantities
------------------------------------------------------------------------- */
-void AtomVecEllipsoid::data_atom(double *coord, imageint imagetmp,
+void AtomVecEllipsoid::data_atom(double *coord, imageint imagetmp,
char **values)
{
int nlocal = atom->nlocal;
@@ -1301,7 +1301,7 @@ int AtomVecEllipsoid::pack_data_hybrid(int i, double *buf)
void AtomVecEllipsoid::write_data(FILE *fp, int n, double **buf)
{
for (int i = 0; i < n; i++)
- fprintf(fp,TAGINT_FORMAT
+ fprintf(fp,TAGINT_FORMAT
" %d %d %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d\n",
(tagint) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).i,
(int) ubuf(buf[i][2]).i,
@@ -1357,7 +1357,7 @@ int AtomVecEllipsoid::pack_vel_hybrid(int i, double *buf)
void AtomVecEllipsoid::write_vel(FILE *fp, int n, double **buf)
{
for (int i = 0; i < n; i++)
- fprintf(fp,TAGINT_FORMAT
+ fprintf(fp,TAGINT_FORMAT
" %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e\n",
(tagint) ubuf(buf[i][0]).i,buf[i][1],buf[i][2],buf[i][3],
buf[i][4],buf[i][5],buf[i][6]);
@@ -1391,7 +1391,7 @@ bigint AtomVecEllipsoid::memory_usage()
if (atom->memcheck("rmass")) bytes += memory->usage(rmass,nmax);
if (atom->memcheck("angmom")) bytes += memory->usage(angmom,nmax,3);
- if (atom->memcheck("torque"))
+ if (atom->memcheck("torque"))
bytes += memory->usage(torque,nmax*comm->nthreads,3);
if (atom->memcheck("ellipsoid")) bytes += memory->usage(ellipsoid,nmax);
diff --git a/src/atom_vec_hybrid.cpp b/src/atom_vec_hybrid.cpp
index fb0dd9da7a..7d34931b44 100644
--- a/src/atom_vec_hybrid.cpp
+++ b/src/atom_vec_hybrid.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdlib.h"
-#include "string.h"
+#include <stdlib.h>
+#include <string.h>
#include "atom_vec_hybrid.h"
#include "atom.h"
#include "domain.h"
@@ -207,7 +207,7 @@ void AtomVecHybrid::clear_bonus()
void AtomVecHybrid::force_clear(int n, size_t nbytes)
{
- for (int k = 0; k < nstyles; k++)
+ for (int k = 0; k < nstyles; k++)
if (styles[k]->forceclearflag) styles[k]->force_clear(n,nbytes);
}
@@ -1024,7 +1024,7 @@ int AtomVecHybrid::property_atom(char *name)
index maps to data specific to this atom style
------------------------------------------------------------------------- */
-void AtomVecHybrid::pack_property_atom(int multiindex, double *buf,
+void AtomVecHybrid::pack_property_atom(int multiindex, double *buf,
int nvalues, int groupbit)
{
int k = multiindex % nstyles;
diff --git a/src/atom_vec_hybrid.h b/src/atom_vec_hybrid.h
index 7524066c1b..fd8a3e433c 100644
--- a/src/atom_vec_hybrid.h
+++ b/src/atom_vec_hybrid.h
@@ -20,7 +20,7 @@ AtomStyle(hybrid,AtomVecHybrid)
#ifndef LMP_ATOM_VEC_HYBRID_H
#define LMP_ATOM_VEC_HYBRID_H
-#include "stdio.h"
+#include <stdio.h>
#include "atom_vec.h"
namespace LAMMPS_NS {
diff --git a/src/atom_vec_line.cpp b/src/atom_vec_line.cpp
index ccbed481d0..3c2272cc60 100644
--- a/src/atom_vec_line.cpp
+++ b/src/atom_vec_line.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "atom_vec_line.h"
#include "atom.h"
#include "comm.h"
@@ -1221,7 +1221,7 @@ int AtomVecLine::pack_vel_hybrid(int i, double *buf)
void AtomVecLine::write_vel(FILE *fp, int n, double **buf)
{
for (int i = 0; i < n; i++)
- fprintf(fp,TAGINT_FORMAT
+ fprintf(fp,TAGINT_FORMAT
" %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e\n",
(tagint) ubuf(buf[i][0]).i,buf[i][1],buf[i][2],buf[i][3],
buf[i][4],buf[i][5],buf[i][6]);
@@ -1256,7 +1256,7 @@ bigint AtomVecLine::memory_usage()
if (atom->memcheck("molecule")) bytes += memory->usage(molecule,nmax);
if (atom->memcheck("rmass")) bytes += memory->usage(rmass,nmax);
if (atom->memcheck("omega")) bytes += memory->usage(omega,nmax,3);
- if (atom->memcheck("torque"))
+ if (atom->memcheck("torque"))
bytes += memory->usage(torque,nmax*comm->nthreads,3);
if (atom->memcheck("line")) bytes += memory->usage(line,nmax);
diff --git a/src/atom_vec_sphere.cpp b/src/atom_vec_sphere.cpp
index f67435a10f..7bf4d40825 100644
--- a/src/atom_vec_sphere.cpp
+++ b/src/atom_vec_sphere.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "atom_vec_sphere.h"
#include "atom.h"
#include "comm.h"
@@ -1060,7 +1060,7 @@ void AtomVecSphere::pack_data(double **buf)
buf[i][1] = ubuf(type[i]).d;
buf[i][2] = 2.0*radius[i];
if (radius[i] == 0.0) buf[i][3] = rmass[i];
- else
+ else
buf[i][3] = rmass[i] / (4.0*MY_PI/3.0 * radius[i]*radius[i]*radius[i]);
buf[i][4] = x[i][0];
buf[i][5] = x[i][1];
@@ -1090,7 +1090,7 @@ int AtomVecSphere::pack_data_hybrid(int i, double *buf)
void AtomVecSphere::write_data(FILE *fp, int n, double **buf)
{
for (int i = 0; i < n; i++)
- fprintf(fp,TAGINT_FORMAT
+ fprintf(fp,TAGINT_FORMAT
" %d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d\n",
(tagint) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).i,
buf[i][2],buf[i][3],
@@ -1146,7 +1146,7 @@ int AtomVecSphere::pack_vel_hybrid(int i, double *buf)
void AtomVecSphere::write_vel(FILE *fp, int n, double **buf)
{
for (int i = 0; i < n; i++)
- fprintf(fp,TAGINT_FORMAT
+ fprintf(fp,TAGINT_FORMAT
" %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e\n",
(tagint) ubuf(buf[i][0]).i,buf[i][1],buf[i][2],buf[i][3],
buf[i][4],buf[i][5],buf[i][6]);
@@ -1181,7 +1181,7 @@ bigint AtomVecSphere::memory_usage()
if (atom->memcheck("radius")) bytes += memory->usage(radius,nmax);
if (atom->memcheck("rmass")) bytes += memory->usage(rmass,nmax);
if (atom->memcheck("omega")) bytes += memory->usage(omega,nmax,3);
- if (atom->memcheck("torque"))
+ if (atom->memcheck("torque"))
bytes += memory->usage(torque,nmax*comm->nthreads,3);
return bytes;
diff --git a/src/atom_vec_tri.cpp b/src/atom_vec_tri.cpp
index 9a120522cb..f95255ee3f 100644
--- a/src/atom_vec_tri.cpp
+++ b/src/atom_vec_tri.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "atom_vec_tri.h"
#include "math_extra.h"
#include "atom.h"
@@ -1669,7 +1669,7 @@ int AtomVecTri::pack_vel_hybrid(int i, double *buf)
void AtomVecTri::write_vel(FILE *fp, int n, double **buf)
{
for (int i = 0; i < n; i++)
- fprintf(fp,TAGINT_FORMAT
+ fprintf(fp,TAGINT_FORMAT
" %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e\n",
(tagint) ubuf(buf[i][0]).i,buf[i][1],buf[i][2],buf[i][3],
buf[i][4],buf[i][5],buf[i][6]);
@@ -1704,7 +1704,7 @@ bigint AtomVecTri::memory_usage()
if (atom->memcheck("molecule")) bytes += memory->usage(molecule,nmax);
if (atom->memcheck("rmass")) bytes += memory->usage(rmass,nmax);
if (atom->memcheck("angmom")) bytes += memory->usage(angmom,nmax,3);
- if (atom->memcheck("torque")) bytes +=
+ if (atom->memcheck("torque")) bytes +=
memory->usage(torque,nmax*comm->nthreads,3);
if (atom->memcheck("tri")) bytes += memory->usage(tri,nmax);
diff --git a/src/balance.cpp b/src/balance.cpp
index 88ca0a62fa..c615db6112 100644
--- a/src/balance.cpp
+++ b/src/balance.cpp
@@ -13,10 +13,10 @@
//#define BALANCE_DEBUG 1
-#include "mpi.h"
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <mpi.h>
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "balance.h"
#include "atom.h"
#include "comm.h"
@@ -107,7 +107,7 @@ void Balance::command(int narg, char **arg)
int iarg = 1;
while (iarg < narg) {
if (strcmp(arg[iarg],"x") == 0) {
- if (style != -1 && style != XYZ)
+ if (style != -1 && style != XYZ)
error->all(FLERR,"Illegal balance command");
style = XYZ;
if (strcmp(arg[iarg+1],"uniform") == 0) {
@@ -127,7 +127,7 @@ void Balance::command(int narg, char **arg)
user_xsplit[procgrid[0]] = 1.0;
}
} else if (strcmp(arg[iarg],"y") == 0) {
- if (style != -1 && style != XYZ)
+ if (style != -1 && style != XYZ)
error->all(FLERR,"Illegal balance command");
style = XYZ;
if (strcmp(arg[iarg+1],"uniform") == 0) {
@@ -147,7 +147,7 @@ void Balance::command(int narg, char **arg)
user_ysplit[procgrid[1]] = 1.0;
}
} else if (strcmp(arg[iarg],"z") == 0) {
- if (style != -1 && style != XYZ)
+ if (style != -1 && style != XYZ)
error->all(FLERR,"Illegal balance command");
style = XYZ;
if (strcmp(arg[iarg+1],"uniform") == 0) {
@@ -237,7 +237,7 @@ void Balance::command(int narg, char **arg)
}
}
- if (style == BISECTION && comm->style == 0)
+ if (style == BISECTION && comm->style == 0)
error->all(FLERR,"Balance rcb cannot be used with comm_style brick");
// insure atoms are in current box & update box via shrink-wrap
@@ -510,14 +510,14 @@ int *Balance::bisection(int sortflag)
double *shrinkhi = &shrinkall[3];
// invoke RCB
- // then invert() to create list of proc assignements for my atoms
+ // then invert() to create list of proc assignements for my atoms
//rcb->compute(dim,atom->nlocal,atom->x,NULL,boxlo,boxhi);
rcb->compute(dim,atom->nlocal,atom->x,NULL,shrinklo,shrinkhi);
rcb->invert(sortflag);
// reset RCB lo/hi bounding box to full simulation box as needed
-
+
double *lo = rcb->lo;
double *hi = rcb->hi;
@@ -529,7 +529,7 @@ int *Balance::bisection(int sortflag)
if (hi[2] == shrinkhi[2]) hi[2] = boxhi[2];
// store RCB cut, dim, lo/hi box in CommTiled
- // cut and lo/hi need to be in fractional form so can
+ // cut and lo/hi need to be in fractional form so can
// OK if changes by epsilon from what RCB used since particles
// will subsequently migrate to new owning procs by exchange() anyway
// ditto for particles exactly on lo/hi RCB box boundaries due to ties
@@ -546,11 +546,11 @@ int *Balance::bisection(int sortflag)
mysplit[0][0] = (lo[0] - boxlo[0]) / prd[0];
if (hi[0] == boxhi[0]) mysplit[0][1] = 1.0;
else mysplit[0][1] = (hi[0] - boxlo[0]) / prd[0];
-
+
mysplit[1][0] = (lo[1] - boxlo[1]) / prd[1];
if (hi[1] == boxhi[1]) mysplit[1][1] = 1.0;
else mysplit[1][1] = (hi[1] - boxlo[1]) / prd[1];
-
+
mysplit[2][0] = (lo[2] - boxlo[2]) / prd[2];
if (hi[2] == boxhi[2]) mysplit[2][1] = 1.0;
else mysplit[2][1] = (hi[2] - boxlo[2]) / prd[2];
@@ -941,7 +941,7 @@ void Balance::dumpout(bigint tstep, FILE *fp)
double **boxall;
memory->create(boxall,nprocs,6,"balance:dumpout");
MPI_Allgather(box,6,MPI_DOUBLE,&boxall[0][0],6,MPI_DOUBLE,world);
-
+
if (me) {
memory->destroy(boxall);
return;
@@ -949,7 +949,7 @@ void Balance::dumpout(bigint tstep, FILE *fp)
// proc 0 writes out nodal coords
// some will be duplicates
-
+
double *boxlo = domain->boxlo;
double *boxhi = domain->boxhi;
@@ -1036,7 +1036,7 @@ void Balance::dumpout(bigint tstep, FILE *fp)
fprintf(fp,"%d\n",nprocs);
if (dimension == 2) fprintf(fp,"ITEM: SQUARES\n");
else fprintf(fp,"ITEM: CUBES\n");
-
+
if (dimension == 2) {
int m = 0;
for (int i = 0; i < nprocs; i++) {
diff --git a/src/balance.h b/src/balance.h
index f00566881a..c4168cabbb 100644
--- a/src/balance.h
+++ b/src/balance.h
@@ -20,7 +20,7 @@ CommandStyle(balance,Balance)
#ifndef LMP_BALANCE_H
#define LMP_BALANCE_H
-#include "stdio.h"
+#include <stdio.h>
#include "pointers.h"
namespace LAMMPS_NS {
diff --git a/src/body.cpp b/src/body.cpp
index 20b4416376..144ee13c92 100644
--- a/src/body.cpp
+++ b/src/body.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "body.h"
#include "error.h"
diff --git a/src/body.h b/src/body.h
index 8b4dce4517..87e9f59be1 100644
--- a/src/body.h
+++ b/src/body.h
@@ -38,7 +38,7 @@ class Body : protected Pointers {
virtual int pack_comm_body(struct AtomVecBody::Bonus *, double *) {return 0;}
virtual int unpack_comm_body(struct AtomVecBody::Bonus *, double *) {return 0;}
virtual int pack_border_body(struct AtomVecBody::Bonus *, double *) {return 0;}
- virtual int unpack_border_body(struct AtomVecBody::Bonus *,
+ virtual int unpack_border_body(struct AtomVecBody::Bonus *,
double *) {return 0;}
virtual void data_body(int, int, int, char **, char **) = 0;
diff --git a/src/bond.cpp b/src/bond.cpp
index 3ce0e26f81..443816418f 100644
--- a/src/bond.cpp
+++ b/src/bond.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "bond.h"
#include "atom.h"
#include "comm.h"
@@ -67,7 +67,7 @@ Bond::~Bond()
void Bond::init()
{
- if (!allocated && atom->nbondtypes)
+ if (!allocated && atom->nbondtypes)
error->all(FLERR,"Bond coeffs are not set");
for (int i = 1; i <= atom->nbondtypes; i++)
if (setflag[i] == 0) error->all(FLERR,"All bond coeffs are not set");
diff --git a/src/bond.h b/src/bond.h
index a38fc97f13..6841e9362d 100644
--- a/src/bond.h
+++ b/src/bond.h
@@ -14,7 +14,7 @@
#ifndef LMP_BOND_H
#define LMP_BOND_H
-#include "stdio.h"
+#include <stdio.h>
#include "pointers.h"
namespace LAMMPS_NS {
diff --git a/src/bond_hybrid.cpp b/src/bond_hybrid.cpp
index 1137035ea8..519a1a3008 100644
--- a/src/bond_hybrid.cpp
+++ b/src/bond_hybrid.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "string.h"
-#include "ctype.h"
+#include <math.h>
+#include <string.h>
+#include <ctype.h>
#include "bond_hybrid.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/bond_hybrid.h b/src/bond_hybrid.h
index a99fd790cc..e1d567c886 100644
--- a/src/bond_hybrid.h
+++ b/src/bond_hybrid.h
@@ -20,7 +20,7 @@ BondStyle(hybrid,BondHybrid)
#ifndef LMP_BOND_HYBRID_H
#define LMP_BOND_HYBRID_H
-#include "stdio.h"
+#include <stdio.h>
#include "bond.h"
namespace LAMMPS_NS {
diff --git a/src/change_box.cpp b/src/change_box.cpp
index a969bc7465..add1fe1d0a 100644
--- a/src/change_box.cpp
+++ b/src/change_box.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <mpi.h>
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "change_box.h"
#include "atom.h"
#include "modify.h"
diff --git a/src/citeme.cpp b/src/citeme.cpp
index 66c6eb9dc9..d021722671 100644
--- a/src/citeme.cpp
+++ b/src/citeme.cpp
@@ -18,7 +18,7 @@
using namespace LAMMPS_NS;
-static const char cite_header[] =
+static const char cite_header[] =
"This LAMMPS simulation made specific use of work described in the\n"
"following references. See http://lammps.sandia.gov/cite.html\n"
"for details.\n\n";
@@ -34,7 +34,7 @@ CiteMe::CiteMe(LAMMPS *lmp) : Pointers(lmp)
cs = new citeset();
}
-/* ----------------------------------------------------------------------
+/* ----------------------------------------------------------------------
write out nag-line at the end of the regular output and clean up
------------------------------------------------------------------------- */
diff --git a/src/citeme.h b/src/citeme.h
index b834015332..80b642ab6d 100644
--- a/src/citeme.h
+++ b/src/citeme.h
@@ -15,7 +15,7 @@
#define LMP_CITEME_H
#include "pointers.h"
-#include "stdio.h"
+#include <stdio.h>
#include <set>
namespace LAMMPS_NS {
diff --git a/src/comm.cpp b/src/comm.cpp
index dfeb707490..073166d229 100644
--- a/src/comm.cpp
+++ b/src/comm.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "stdlib.h"
-#include "string.h"
+#include <mpi.h>
+#include <stdlib.h>
+#include <string.h>
#include "comm.h"
#include "universe.h"
#include "atom.h"
@@ -33,7 +33,7 @@
#include "error.h"
#ifdef _OPENMP
-#include "omp.h"
+#include <omp.h>
#endif
using namespace LAMMPS_NS;
@@ -134,7 +134,7 @@ void Comm::copy_arrays(Comm *oldcomm)
"comm:grid2proc");
memcpy(&grid2proc[0][0][0],&oldcomm->grid2proc[0][0][0],
(procgrid[0]*procgrid[1]*procgrid[2])*sizeof(int));
-
+
memory->create(xsplit,procgrid[0]+1,"comm:xsplit");
memory->create(ysplit,procgrid[1]+1,"comm:ysplit");
memory->create(zsplit,procgrid[2]+1,"comm:zsplit");
@@ -195,14 +195,14 @@ void Comm::init()
for (int i = 0; i < modify->nfix; i++)
size_border += modify->fix[i]->comm_border;
-
+
// per-atom limits for communication
// maxexchange = max # of datums in exchange comm, set in exchange()
// maxforward = # of datums in largest forward comm
// maxreverse = # of datums in largest reverse comm
// query pair,fix,compute,dump for their requirements
// pair style can force reverse comm even if newton off
-
+
maxforward = MAX(size_forward,size_border);
maxreverse = size_reverse;
diff --git a/src/comm.h b/src/comm.h
index f3d941f96d..6861a034fc 100644
--- a/src/comm.h
+++ b/src/comm.h
@@ -89,7 +89,7 @@ class Comm : protected Pointers {
// exchange of info on neigh stencil
// set processor mapping options
- virtual void forward_comm_array(int, double **) = 0;
+ virtual void forward_comm_array(int, double **) = 0;
virtual int exchange_variable(int, double *, double *&) = 0;
int binary(double, int, double *);
@@ -106,8 +106,8 @@ class Comm : protected Pointers {
void ring(int, int, void *, int, void (*)(int, char *),
void *, int self = 1);
- int read_lines_from_file(FILE *, int, int, char *);
- int read_lines_from_file_universe(FILE *, int, int, char *);
+ int read_lines_from_file(FILE *, int, int, char *);
+ int read_lines_from_file_universe(FILE *, int, int, char *);
protected:
int bordergroup; // only communicate this group in borders
@@ -121,7 +121,7 @@ class Comm : protected Pointers {
int size_border; // # of datums in forward border comm
int maxforward,maxreverse; // max # of datums in forward/reverse comm
- int maxexchange; // max # of datums/atom in exchange comm
+ int maxexchange; // max # of datums/atom in exchange comm
int gridflag; // option for creating 3d grid
int mapflag; // option for mapping procs to 3d grid
diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp
index 761dfcb37b..4ccd936c3f 100644
--- a/src/comm_brick.cpp
+++ b/src/comm_brick.cpp
@@ -15,11 +15,11 @@
Contributing author (triclinic) : Pieter in 't Veld (SNL)
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "math.h"
-#include "string.h"
-#include "stdio.h"
-#include "stdlib.h"
+#include <mpi.h>
+#include <math.h>
+#include <string.h>
+#include <stdio.h>
+#include <stdlib.h>
#include "comm_brick.h"
#include "comm_tiled.h"
#include "universe.h"
@@ -1027,7 +1027,7 @@ void CommBrick::reverse_comm_fix(Fix *fix, int size)
if (sendnum[iswap]) MPI_Wait(&request,MPI_STATUS_IGNORE);
buf = buf_recv;
} else buf = buf_send;
-
+
// unpack buffer
fix->unpack_reverse_comm(sendnum[iswap],sendlist[iswap],buf);
@@ -1258,7 +1258,7 @@ int CommBrick::exchange_variable(int n, double *inbuf, double *&outbuf)
// loop over dimensions
for (int dim = 0; dim < 3; dim++) {
-
+
// no exchange if only one proc in a dimension
if (procgrid[dim] == 1) continue;
@@ -1278,12 +1278,12 @@ int CommBrick::exchange_variable(int n, double *inbuf, double *&outbuf)
} else nrecv2 = 0;
if (nrecv > maxrecv) grow_recv(nrecv);
-
+
MPI_Irecv(&buf_recv[nsend],nrecv1,MPI_DOUBLE,procneigh[dim][1],0,
world,&request);
MPI_Send(buf_recv,nsend,MPI_DOUBLE,procneigh[dim][0],0,world);
MPI_Wait(&request,MPI_STATUS_IGNORE);
-
+
if (procgrid[dim] > 2) {
MPI_Irecv(&buf_recv[nsend+nrecv1],nrecv2,MPI_DOUBLE,procneigh[dim][0],0,
world,&request);
diff --git a/src/comm_brick.h b/src/comm_brick.h
index e264408ab6..ddcf8e6fbd 100644
--- a/src/comm_brick.h
+++ b/src/comm_brick.h
@@ -33,7 +33,7 @@ class CommBrick : public Comm {
virtual void forward_comm_pair(class Pair *); // forward comm from a Pair
virtual void reverse_comm_pair(class Pair *); // reverse comm from a Pair
- virtual void forward_comm_fix(class Fix *, int size=0);
+ virtual void forward_comm_fix(class Fix *, int size=0);
// forward comm from a Fix
virtual void reverse_comm_fix(class Fix *, int size=0);
// reverse comm from a Fix
diff --git a/src/comm_tiled.cpp b/src/comm_tiled.cpp
index a54a6b0c9e..98f406b293 100644
--- a/src/comm_tiled.cpp
+++ b/src/comm_tiled.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "comm_tiled.h"
#include "comm_brick.h"
#include "atom.h"
@@ -123,7 +123,7 @@ void CommTiled::init()
// temporary restrictions
- if (triclinic)
+ if (triclinic)
error->all(FLERR,"Cannot yet use comm_style tiled with triclinic box");
if (mode == MULTI)
error->all(FLERR,"Cannot yet use comm_style tiled with multi-mode comm");
@@ -222,7 +222,7 @@ void CommTiled::setup()
lo1[idim] = subhi[idim];
hi1[idim] = subhi[idim] + cut;
}
-
+
two = 0;
if (idir == 0 && periodicity[idim] && lo1[idim] < boxlo[idim]) two = 1;
if (idir == 1 && periodicity[idim] && hi1[idim] > boxhi[idim]) two = 1;
@@ -305,16 +305,16 @@ void CommTiled::setup()
// = obox in other 2 dims
// if sbox touches other proc's sub-box boundaries in lower dims,
// extend sbox in those lower dims to include ghost atoms
-
+
double oboxlo[3],oboxhi[3],sbox[6];
for (i = 0; i < noverlap; i++) {
pbc_flag[iswap][i] = 0;
pbc[iswap][i][0] = pbc[iswap][i][1] = pbc[iswap][i][2] =
pbc[iswap][i][3] = pbc[iswap][i][4] = pbc[iswap][i][5] = 0;
-
+
(this->*box_other)(idim,idir,overlap[i],oboxlo,oboxhi);
-
+
if (i < noverlap1) {
sbox[0] = MAX(oboxlo[0],lo1[0]);
sbox[1] = MAX(oboxlo[1],lo1[1]);
@@ -352,7 +352,7 @@ void CommTiled::setup()
if (sbox[1] == oboxlo[1]) sbox[1] -= cut;
if (sbox[4] == oboxhi[1]) sbox[4] += cut;
}
-
+
memcpy(sendbox[iswap][i],sbox,6*sizeof(double));
}
@@ -412,7 +412,7 @@ void CommTiled::setup()
MPI_Barrier(world);
// reallocate exchproc and exchnum if needed based on noverlap
-
+
if (noverlap > nexchprocmax[idim]) {
while (nexchprocmax[idim] < noverlap) nexchprocmax[idim] += DELTA_PROCS;
delete [] exchproc[idim];
@@ -429,7 +429,7 @@ void CommTiled::setup()
if (cutzero) {
for (i = 0; i < nswap; i++) {
- nsendproc[i] = nrecvproc[i] =
+ nsendproc[i] = nrecvproc[i] =
sendother[i] = recvother[i] = sendself[i] = 0;
}
}
@@ -596,7 +596,7 @@ void CommTiled::reverse_comm()
reverse_recv_offset[iswap][irecv]]);
}
}
-
+
} else {
if (sendother[iswap]) {
for (i = 0; i < nsend; i++)
@@ -709,7 +709,7 @@ void CommTiled::exchange()
int flag = 0;
for (int k = 0; k < nexchproc[dim]; k++)
if (proc == exchproc[k]) flag = 1;
- if (!flag)
+ if (!flag)
printf("Losing exchange atom: dim %d me %d %proc %d: %g %g %g\n",
dim,me,proc,x[i][0],x[i][1],x[i][2]);
*/
@@ -814,7 +814,7 @@ void CommTiled::borders()
x = atom->x;
if (iswap % 2 == 0) nlast = atom->nlocal + atom->nghost;
-
+
ncountall = 0;
for (m = 0; m < nsendproc[iswap]; m++) {
bbox = sendbox[iswap][m];
@@ -879,7 +879,7 @@ void CommTiled::borders()
for (m = 0; m < nsendproc[iswap]; m++) {
size_reverse_recv[iswap][m] = sendnum[iswap][m]*size_reverse;
if (m == 0) reverse_recv_offset[iswap][0] = 0;
- else reverse_recv_offset[iswap][m] =
+ else reverse_recv_offset[iswap][m] =
reverse_recv_offset[iswap][m-1] + sendnum[iswap][m-1];
}
@@ -896,7 +896,7 @@ void CommTiled::borders()
forward_recv_offset[iswap][0] = 0;
} else {
firstrecv[iswap][m] = firstrecv[iswap][m-1] + recvnum[iswap][m-1];
- forward_recv_offset[iswap][m] =
+ forward_recv_offset[iswap][m] =
forward_recv_offset[iswap][m-1] + recvnum[iswap][m-1];
}
}
@@ -972,7 +972,7 @@ void CommTiled::borders()
// increment ghost atoms
n = nrecvproc[iswap];
- if (n)
+ if (n)
atom->nghost += forward_recv_offset[iswap][n-1] + recvnum[iswap][n-1];
}
@@ -1375,7 +1375,7 @@ void CommTiled::reverse_comm_dump(Dump *dump)
------------------------------------------------------------------------- */
void CommTiled::forward_comm_array(int nsize, double **array)
-{
+{
int i,j,k,m,iatom,last,irecv,nsend,nrecv;
// insure send/recv bufs are big enough for nsize
@@ -1491,12 +1491,12 @@ void CommTiled::box_drop_brick(int idim, double *lo, double *hi, int &indexme)
split = zsplit;
}
- if (index < 0 || index > procgrid[idim])
+ if (index < 0 || index > procgrid[idim])
error->one(FLERR,"Comm tiled invalid index in box drop brick");
while (1) {
lower = boxlo[idim] + prd[idim]*split[index];
- if (index < procgrid[idim]-1)
+ if (index < procgrid[idim]-1)
upper = boxlo[idim] + prd[idim]*split[index+1];
else upper = boxhi[idim];
if (lower >= hi[idim] || upper <= lo[idim]) break;
@@ -1529,7 +1529,7 @@ void CommTiled::box_drop_tiled(int idim, double *lo, double *hi, int &indexme)
box_drop_tiled_recurse(lo,hi,0,nprocs-1,indexme);
}
-void CommTiled::box_drop_tiled_recurse(double *lo, double *hi,
+void CommTiled::box_drop_tiled_recurse(double *lo, double *hi,
int proclower, int procupper,
int &indexme)
{
@@ -1557,8 +1557,8 @@ void CommTiled::box_drop_tiled_recurse(double *lo, double *hi,
int procmid = proclower + (procupper - proclower) / 2 + 1;
int idim = rcbinfo[procmid].dim;
double cut = boxlo[idim] + prd[idim]*rcbinfo[procmid].cutfrac;
-
- if (lo[idim] < cut)
+
+ if (lo[idim] < cut)
box_drop_tiled_recurse(lo,hi,proclower,procmid-1,indexme);
if (hi[idim] > cut)
box_drop_tiled_recurse(lo,hi,procmid,procupper,indexme);
@@ -1571,8 +1571,8 @@ void CommTiled::box_drop_tiled_recurse(double *lo, double *hi,
void CommTiled::box_other_brick(int idim, int idir,
int proc, double *lo, double *hi)
{
- lo[0] = sublo[0]; lo[1] = sublo[1]; lo[2] = sublo[2];
- hi[0] = subhi[0]; hi[1] = subhi[1]; hi[2] = subhi[2];
+ lo[0] = sublo[0]; lo[1] = sublo[1]; lo[2] = sublo[2];
+ hi[0] = subhi[0]; hi[1] = subhi[1]; hi[2] = subhi[2];
int other1,other2,oproc;
double *split;
@@ -1604,7 +1604,7 @@ void CommTiled::box_other_brick(int idim, int idir,
if (proc == oproc) {
lo[idim] = boxlo[idim] + prd[idim]*split[index];
- if (split[index+1] < 1.0)
+ if (split[index+1] < 1.0)
hi[idim] = boxlo[idim] + prd[idim]*split[index+1];
else hi[idim] = boxhi[idim];
return;
@@ -1657,7 +1657,7 @@ int CommTiled::box_touch_tiled(int proc, int idim, int idir)
if (idir == 0) {
if (rcbinfo[proc].mysplit[idim][1] == rcbinfo[me].mysplit[idim][0])
return 1;
- else if (rcbinfo[proc].mysplit[idim][1] == 1.0 &&
+ else if (rcbinfo[proc].mysplit[idim][1] == 1.0 &&
rcbinfo[me].mysplit[idim][0] == 0.0)
return 1;
@@ -1667,7 +1667,7 @@ int CommTiled::box_touch_tiled(int proc, int idim, int idir)
} else {
if (rcbinfo[proc].mysplit[idim][0] == rcbinfo[me].mysplit[idim][1])
return 1;
- else if (rcbinfo[proc].mysplit[idim][0] == 0.0 &&
+ else if (rcbinfo[proc].mysplit[idim][0] == 0.0 &&
rcbinfo[me].mysplit[idim][1] == 1.0)
return 1;
}
@@ -1749,14 +1749,14 @@ int CommTiled::point_drop_tiled(int idim, double *x)
recursive point drop thru RCB tree
------------------------------------------------------------------------- */
-int CommTiled::point_drop_tiled_recurse(double *x,
+int CommTiled::point_drop_tiled_recurse(double *x,
int proclower, int procupper)
{
// end recursion when partition is a single proc
// return proc
if (proclower == procupper) return proclower;
-
+
// drop point on side of cut it is on
// use < criterion so point is not on high edge of proc sub-domain
// procmid = 1st processor in upper half of partition
@@ -1800,8 +1800,8 @@ void CommTiled::coord2proc_setup()
{
if (!rcbnew) return;
- if (!rcbinfo)
- rcbinfo = (RCBinfo *)
+ if (!rcbinfo)
+ rcbinfo = (RCBinfo *)
memory->smalloc(nprocs*sizeof(RCBinfo),"comm:rcbinfo");
rcbnew = 0;
RCBinfo rcbone;
@@ -1831,7 +1831,7 @@ int CommTiled::coord2proc(double *x, int &igx, int &igy, int &igz)
if flag = 1, realloc
if flag = 0, don't need to realloc with copy, just free/malloc
------------------------------------------------------------------------- */
-
+
void CommTiled::grow_send(int n, int flag)
{
maxsend = static_cast<int> (BUFFACTOR * n);
diff --git a/src/comm_tiled.h b/src/comm_tiled.h
index 7443e1019d..dd86ecfdba 100644
--- a/src/comm_tiled.h
+++ b/src/comm_tiled.h
@@ -33,7 +33,7 @@ class CommTiled : public Comm {
void forward_comm_pair(class Pair *); // forward comm from a Pair
void reverse_comm_pair(class Pair *); // reverse comm from a Pair
- virtual void forward_comm_fix(class Fix *, int size=0);
+ virtual void forward_comm_fix(class Fix *, int size=0);
// forward comm from a Fix
virtual void reverse_comm_fix(class Fix *, int size=0);
// reverse comm from a Fix
diff --git a/src/compute.cpp b/src/compute.cpp
index 4c5da8bc94..44eb851887 100644
--- a/src/compute.cpp
+++ b/src/compute.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "stdlib.h"
-#include "string.h"
-#include "ctype.h"
+#include <mpi.h>
+#include <stdlib.h>
+#include <string.h>
+#include <ctype.h>
#include "compute.h"
#include "atom.h"
#include "domain.h"
@@ -163,7 +163,7 @@ void Compute::adjust_dof_fix()
fix_dof = 0;
for (int i = 0; i < nfix; i++)
- if (fix[i]->dof_flag)
+ if (fix[i]->dof_flag)
fix_dof += fix[i]->dof(igroup);
}
diff --git a/src/compute_angle_local.cpp b/src/compute_angle_local.cpp
index e1dad85769..031d4856b5 100644
--- a/src/compute_angle_local.cpp
+++ b/src/compute_angle_local.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "string.h"
+#include <math.h>
+#include <string.h>
#include "compute_angle_local.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/compute_angmom_chunk.cpp b/src/compute_angmom_chunk.cpp
index 78c7190865..93a843ac31 100644
--- a/src/compute_angmom_chunk.cpp
+++ b/src/compute_angmom_chunk.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "compute_angmom_chunk.h"
#include "atom.h"
#include "update.h"
@@ -25,7 +25,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-ComputeAngmomChunk::ComputeAngmomChunk(LAMMPS *lmp, int narg, char **arg) :
+ComputeAngmomChunk::ComputeAngmomChunk(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 4) error->all(FLERR,"Illegal compute angmom/chunk command");
diff --git a/src/compute_bond_local.cpp b/src/compute_bond_local.cpp
index 152bfd5d78..9cea55de58 100644
--- a/src/compute_bond_local.cpp
+++ b/src/compute_bond_local.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "string.h"
+#include <math.h>
+#include <string.h>
#include "compute_bond_local.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/compute_centro_atom.cpp b/src/compute_centro_atom.cpp
index 0676ad0a4a..a6561f3136 100644
--- a/src/compute_centro_atom.cpp
+++ b/src/compute_centro_atom.cpp
@@ -15,8 +15,8 @@
Contributing author: Michel Perez (U Lyon) for non-fcc lattices
------------------------------------------------------------------------- */
-#include "string.h"
-#include "stdlib.h"
+#include <string.h>
+#include <stdlib.h>
#include "compute_centro_atom.h"
#include "atom.h"
#include "update.h"
diff --git a/src/compute_chunk_atom.cpp b/src/compute_chunk_atom.cpp
index 487bd43de2..ffd827608f 100644
--- a/src/compute_chunk_atom.cpp
+++ b/src/compute_chunk_atom.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "string.h"
-#include "stdlib.h"
+#include <mpi.h>
+#include <string.h>
+#include <stdlib.h>
#include "compute_chunk_atom.h"
#include "atom.h"
#include "update.h"
@@ -99,8 +99,8 @@ ComputeChunkAtom::ComputeChunkAtom(LAMMPS *lmp, int narg, char **arg) :
which = MOLECULE;
iarg = 4;
- } else if (strstr(arg[3],"c_") == arg[3] ||
- strstr(arg[3],"f_") == arg[3] ||
+ } else if (strstr(arg[3],"c_") == arg[3] ||
+ strstr(arg[3],"f_") == arg[3] ||
strstr(arg[3],"v_") == arg[3]) {
if (arg[3][0] == 'c') which = COMPUTE;
else if (arg[3][0] == 'f') which = FIX;
@@ -118,7 +118,7 @@ ComputeChunkAtom::ComputeChunkAtom(LAMMPS *lmp, int narg, char **arg) :
argindex = atoi(ptr+1);
*ptr = '\0';
} else argindex = 0;
-
+
n = strlen(suffix) + 1;
cfvid = new char[n];
strcpy(cfvid,suffix);
@@ -172,7 +172,7 @@ ComputeChunkAtom::ComputeChunkAtom(LAMMPS *lmp, int narg, char **arg) :
if (limit && !compress) limitfirst = 1;
iarg += 2;
if (limit) {
- if (iarg+1 > narg)
+ if (iarg+1 > narg)
error->all(FLERR,"Illegal compute chunk/atom command");
if (strcmp(arg[iarg+1],"max") == 0) limitstyle = LIMITMAX;
else if (strcmp(arg[iarg+1],"exact") == 0) limitstyle = LIMITEXACT;
@@ -209,11 +209,11 @@ ComputeChunkAtom::ComputeChunkAtom(LAMMPS *lmp, int narg, char **arg) :
else error->all(FLERR,"Illegal compute chunk/atom command");
if (strcmp(arg[iarg+2],"lower") == 0) minflag[idim] = LOWER;
else minflag[idim] = COORD;
- if (minflag[idim] == COORD)
+ if (minflag[idim] == COORD)
minvalue[idim] = force->numeric(FLERR,arg[iarg+2]);
if (strcmp(arg[iarg+3],"upper") == 0) maxflag[idim] = UPPER;
else maxflag[idim] = COORD;
- if (maxflag[idim] == COORD)
+ if (maxflag[idim] == COORD)
maxvalue[idim] = force->numeric(FLERR,arg[iarg+3]);
else error->all(FLERR,"Illegal compute chunk/atom command");
iarg += 4;
@@ -251,17 +251,17 @@ ComputeChunkAtom::ComputeChunkAtom(LAMMPS *lmp, int narg, char **arg) :
// error checks
- if (which == MOLECULE && !atom->molecule_flag)
+ if (which == MOLECULE && !atom->molecule_flag)
error->all(FLERR,"Compute chunk/atom molecule for non-molecular system");
if (!binflag && discard == MIXED)
error->all(FLERR,"Compute chunk/atom without bins "
"cannot use discard mixed");
- if (which == BIN1D && delta[0] <= 0.0)
+ if (which == BIN1D && delta[0] <= 0.0)
error->all(FLERR,"Illegal compute chunk/atom command");
if (which == BIN2D && (delta[0] <= 0.0 || delta[1] <= 0.0))
error->all(FLERR,"Illegal compute chunk/atom command");
- if (which == BIN3D &&
+ if (which == BIN3D &&
(delta[0] <= 0.0 || delta[1] <= 0.0 || delta[2] <= 0.0))
error->all(FLERR,"Illegal compute chunk/atom command");
@@ -452,7 +452,7 @@ void ComputeChunkAtom::init()
if (molecule[i] > maxone) maxone = molecule[i];
tagint maxall;
MPI_Allreduce(&maxone,&maxall,1,MPI_LMP_TAGINT,MPI_MAX,world);
- if (maxall > MAXSMALLINT)
+ if (maxall > MAXSMALLINT)
error->all(FLERR,"Molecule IDs too large for compute chunk/atom");
}
@@ -486,7 +486,7 @@ void ComputeChunkAtom::init()
id_fix = new char[n];
strcpy(id_fix,id);
strcat(id_fix,"_COMPUTE_STORE");
-
+
char **newarg = new char*[5];
newarg[0] = id_fix;
newarg[1] = group->names[igroup];
@@ -535,7 +535,7 @@ void ComputeChunkAtom::compute_peratom()
memory->create(chunk,nmax,"chunk/atom:chunk");
vector_atom = chunk;
}
-
+
setup_chunks();
compute_ichunk();
@@ -672,13 +672,13 @@ void ComputeChunkAtom::compute_ichunk()
// if newly calculated IDs need to persist, store them in fixstore
// yes if idsflag = ONCE or idsflag = NFREQ and lock is in place
- if (idsflag == ONCE || (idsflag == NFREQ && lockfix)) {
+ if (idsflag == ONCE || (idsflag == NFREQ && lockfix)) {
double *vstore = fixstore->vstore;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) vstore[i] = ichunk[i];
}
- // one-time check if which = MOLECULE and
+ // one-time check if which = MOLECULE and
// any chunks do not contain all atoms in the molecule
if (molcheck) {
@@ -740,14 +740,14 @@ int ComputeChunkAtom::setup_chunks()
if (which == TYPE) nchunk = atom->ntypes;
else if (!binflag) {
-
+
int nlocal = atom->nlocal;
int hi = -1;
for (int i = 0; i < nlocal; i++) {
if (exclude[i]) continue;
if (ichunk[i] > hi) hi = ichunk[i];
}
-
+
MPI_Allreduce(&hi,&nchunk,1,MPI_INT,MPI_MAX,world);
if (nchunk <= 0) nchunk = 1;
}
@@ -810,7 +810,7 @@ void ComputeChunkAtom::assign_chunk_ids()
if (regionflag) {
for (i = 0; i < nlocal; i++) {
- if (mask[i] & groupbit &&
+ if (mask[i] & groupbit &&
region->match(x[i][0],x[i][1],x[i][2])) exclude[i] = 0;
else exclude[i] = 1;
}
@@ -932,7 +932,7 @@ void ComputeChunkAtom::compress_chunk_ids()
bigint nbone = n;
bigint nball;
MPI_Allreduce(&nbone,&nball,1,MPI_LMP_BIGINT,MPI_SUM,world);
-
+
// create my list of populated IDs
int *list = NULL;
@@ -963,9 +963,9 @@ void ComputeChunkAtom::compress_chunk_ids()
displs[0] = 0;
for (int iproc = 1; iproc < nprocs; iproc++)
displs[iproc] = displs[iproc-1] + recvcounts[iproc-1];
-
+
// allgatherv acquires list of populated IDs from all procs
-
+
MPI_Allgatherv(list,n,MPI_INT,listall,recvcounts,displs,MPI_INT,world);
// add all unique IDs in listall to my hash
@@ -1039,7 +1039,7 @@ void ComputeChunkAtom::check_molecules()
if (!compress) {
for (int i = 0; i < nlocal; i++) {
- if (molecule[i] > 0 && molecule[i] <= nchunk &&
+ if (molecule[i] > 0 && molecule[i] <= nchunk &&
ichunk[i] == 0) flag = 1;
}
} else {
@@ -1049,7 +1049,7 @@ void ComputeChunkAtom::check_molecules()
if (hash->find(molid) != hash->end() && ichunk[i] == 0) flag = 1;
}
}
-
+
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
if (flagall && comm->me == 0)
@@ -1238,10 +1238,10 @@ void ComputeChunkAtom::atom2bin1d()
if (xremap < boxlo[idim]) xremap += prd[idim];
if (xremap >= boxhi[idim]) xremap -= prd[idim];
}
-
+
ibin = static_cast<int> ((xremap - offset[0]) * invdelta[0]);
if (xremap < offset[0]) ibin--;
-
+
if (discard == MIXED) {
if (!minflag[idim]) ibin = MAX(ibin,0);
else if (ibin < 0) {
@@ -1260,7 +1260,7 @@ void ComputeChunkAtom::atom2bin1d()
exclude[i] = 1;
continue;
}
-
+
ichunk[i] = ibin+1;
}
@@ -1312,10 +1312,10 @@ void ComputeChunkAtom::atom2bin2d()
if (xremap < boxlo[idim]) xremap += prd[idim];
if (xremap >= boxhi[idim]) xremap -= prd[idim];
}
-
+
i1bin = static_cast<int> ((xremap - offset[0]) * invdelta[0]);
if (xremap < offset[0]) i1bin--;
-
+
if (discard == MIXED) {
if (!minflag[idim]) i1bin = MAX(i1bin,0);
else if (i1bin < 0) {
@@ -1420,7 +1420,7 @@ void ComputeChunkAtom::atom2bin3d()
i1bin = static_cast<int> ((xremap - offset[0]) * invdelta[0]);
if (xremap < offset[0]) i1bin--;
-
+
if (discard == MIXED) {
if (!minflag[idim]) i1bin = MAX(i1bin,0);
else if (i1bin < 0) {
@@ -1439,7 +1439,7 @@ void ComputeChunkAtom::atom2bin3d()
exclude[i] = 1;
continue;
}
-
+
yremap = x[i][jdim];
if (periodicity[jdim]) {
if (yremap < boxlo[jdim]) yremap += prd[jdim];
@@ -1495,7 +1495,7 @@ void ComputeChunkAtom::atom2bin3d()
exclude[i] = 1;
continue;
}
-
+
ibin = i1bin*nlayers[1]*nlayers[2] + i2bin*nlayers[2] + i3bin;
ichunk[i] = ibin+1;
}
@@ -1521,9 +1521,9 @@ void ComputeChunkAtom::readdim(int narg, char **arg, int iarg, int idim)
else if (strcmp(arg[iarg+1],"center") == 0) originflag[idim] = CENTER;
else if (strcmp(arg[iarg+1],"upper") == 0) originflag[idim] = UPPER;
else originflag[idim] = COORD;
- if (originflag[idim] == COORD)
+ if (originflag[idim] == COORD)
origin[idim] = force->numeric(FLERR,arg[iarg+1]);
-
+
delta[idim] = force->numeric(FLERR,arg[iarg+2]);
}
diff --git a/src/compute_cluster_atom.cpp b/src/compute_cluster_atom.cpp
index 343a0dd1bd..ade4ce5d87 100644
--- a/src/compute_cluster_atom.cpp
+++ b/src/compute_cluster_atom.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "string.h"
-#include "stdlib.h"
+#include <math.h>
+#include <string.h>
+#include <stdlib.h>
#include "compute_cluster_atom.h"
#include "atom.h"
#include "update.h"
diff --git a/src/compute_cna_atom.cpp b/src/compute_cna_atom.cpp
index 69425457e8..4e0d7e907b 100644
--- a/src/compute_cna_atom.cpp
+++ b/src/compute_cna_atom.cpp
@@ -15,8 +15,8 @@
Contributing author: Wan Liang (Chinese Academy of Sciences)
------------------------------------------------------------------------- */
-#include "string.h"
-#include "stdlib.h"
+#include <string.h>
+#include <stdlib.h>
#include "compute_cna_atom.h"
#include "atom.h"
#include "update.h"
@@ -29,7 +29,7 @@
#include "comm.h"
#include "memory.h"
#include "error.h"
-#include "math.h"
+#include <math.h>
using namespace LAMMPS_NS;
diff --git a/src/compute_com_chunk.cpp b/src/compute_com_chunk.cpp
index 0af54d9b77..ebf2b30f6e 100644
--- a/src/compute_com_chunk.cpp
+++ b/src/compute_com_chunk.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "compute_com_chunk.h"
#include "atom.h"
#include "update.h"
diff --git a/src/compute_contact_atom.cpp b/src/compute_contact_atom.cpp
index 8db5c3e4bd..99c4766b6b 100644
--- a/src/compute_contact_atom.cpp
+++ b/src/compute_contact_atom.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "string.h"
-#include "stdlib.h"
+#include <math.h>
+#include <string.h>
+#include <stdlib.h>
#include "compute_contact_atom.h"
#include "atom.h"
#include "update.h"
diff --git a/src/compute_coord_atom.cpp b/src/compute_coord_atom.cpp
index beb03812b0..2769edc12d 100644
--- a/src/compute_coord_atom.cpp
+++ b/src/compute_coord_atom.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "string.h"
-#include "stdlib.h"
+#include <math.h>
+#include <string.h>
+#include <stdlib.h>
#include "compute_coord_atom.h"
#include "atom.h"
#include "update.h"
@@ -169,7 +169,7 @@ void ComputeCoordAtom::compute_peratom()
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
-
+
jtype = type[j];
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
@@ -177,7 +177,7 @@ void ComputeCoordAtom::compute_peratom()
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cutsq && jtype >= typelo[0] && jtype <= typehi[0]) n++;
}
-
+
cvec[i] = n;
} else cvec[i] = 0.0;
}
@@ -199,7 +199,7 @@ void ComputeCoordAtom::compute_peratom()
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
-
+
jtype = type[j];
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
diff --git a/src/compute_dihedral_local.cpp b/src/compute_dihedral_local.cpp
index 8316df01b0..66523d00a1 100644
--- a/src/compute_dihedral_local.cpp
+++ b/src/compute_dihedral_local.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "string.h"
+#include <math.h>
+#include <string.h>
#include "compute_dihedral_local.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/compute_displace_atom.cpp b/src/compute_displace_atom.cpp
index df3bde77c6..a95a645632 100644
--- a/src/compute_displace_atom.cpp
+++ b/src/compute_displace_atom.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "string.h"
+#include <math.h>
+#include <string.h>
#include "compute_displace_atom.h"
#include "atom.h"
#include "update.h"
diff --git a/src/compute_erotate_sphere.cpp b/src/compute_erotate_sphere.cpp
index 0ae3cfd604..31ed0aaba5 100644
--- a/src/compute_erotate_sphere.cpp
+++ b/src/compute_erotate_sphere.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
+#include <mpi.h>
#include "compute_erotate_sphere.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/compute_erotate_sphere_atom.cpp b/src/compute_erotate_sphere_atom.cpp
index c058a5eb58..9c2d4d9caf 100644
--- a/src/compute_erotate_sphere_atom.cpp
+++ b/src/compute_erotate_sphere_atom.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "compute_erotate_sphere_atom.h"
#include "atom.h"
#include "update.h"
@@ -31,7 +31,7 @@ ComputeErotateSphereAtom::
ComputeErotateSphereAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
- if (narg != 3)
+ if (narg != 3)
error->all(FLERR,"Illegal compute erotate/sphere//atom command");
peratom_flag = 1;
diff --git a/src/compute_group_group.cpp b/src/compute_group_group.cpp
index 900af68528..741d4a667b 100644
--- a/src/compute_group_group.cpp
+++ b/src/compute_group_group.cpp
@@ -16,8 +16,8 @@
K-space terms added by Stan Moore (BYU)
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "string.h"
+#include <mpi.h>
+#include <string.h>
#include "compute_group_group.h"
#include "atom.h"
#include "update.h"
@@ -29,7 +29,7 @@
#include "group.h"
#include "kspace.h"
#include "error.h"
-#include "math.h"
+#include <math.h>
#include "comm.h"
#include "domain.h"
#include "math_const.h"
@@ -227,7 +227,7 @@ void ComputeGroupGroup::pair_contribution()
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
// skip if atom I is not in either group
- if (!(mask[i] & groupbit || mask[i] & jgroupbit)) continue;
+ if (!(mask[i] & groupbit || mask[i] & jgroupbit)) continue;
xtmp = x[i][0];
ytmp = x[i][1];
diff --git a/src/compute_gyration.cpp b/src/compute_gyration.cpp
index 1025b8fc2a..fab413e670 100644
--- a/src/compute_gyration.cpp
+++ b/src/compute_gyration.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "compute_gyration.h"
#include "update.h"
#include "atom.h"
diff --git a/src/compute_gyration_chunk.cpp b/src/compute_gyration_chunk.cpp
index a14fb6f205..e006a82299 100644
--- a/src/compute_gyration_chunk.cpp
+++ b/src/compute_gyration_chunk.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "string.h"
+#include <math.h>
+#include <string.h>
#include "compute_gyration_chunk.h"
#include "atom.h"
#include "update.h"
diff --git a/src/compute_heat_flux.cpp b/src/compute_heat_flux.cpp
index 335304ef9d..33e7f7a449 100644
--- a/src/compute_heat_flux.cpp
+++ b/src/compute_heat_flux.cpp
@@ -16,8 +16,8 @@
Mario Pinto (Computational Research Lab, Pune, India)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "string.h"
+#include <math.h>
+#include <string.h>
#include "compute_heat_flux.h"
#include "atom.h"
#include "update.h"
diff --git a/src/compute_improper_local.cpp b/src/compute_improper_local.cpp
index 439a2bd3b2..3c0af24a10 100644
--- a/src/compute_improper_local.cpp
+++ b/src/compute_improper_local.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "string.h"
+#include <math.h>
+#include <string.h>
#include "compute_improper_local.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/compute_inertia_chunk.cpp b/src/compute_inertia_chunk.cpp
index 5d47fee583..33660b839f 100644
--- a/src/compute_inertia_chunk.cpp
+++ b/src/compute_inertia_chunk.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "compute_inertia_chunk.h"
#include "atom.h"
#include "update.h"
@@ -25,7 +25,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-ComputeInertiaChunk::ComputeInertiaChunk(LAMMPS *lmp, int narg, char **arg) :
+ComputeInertiaChunk::ComputeInertiaChunk(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 4) error->all(FLERR,"Illegal compute inertia/chunk command");
@@ -136,7 +136,7 @@ void ComputeInertiaChunk::compute_array()
MPI_Allreduce(&com[0][0],&comall[0][0],3*nchunk,MPI_DOUBLE,MPI_SUM,world);
for (int i = 0; i < nchunk; i++) {
- comall[i][0] /= masstotal[i];
+ comall[i][0] /= masstotal[i];
comall[i][1] /= masstotal[i];
comall[i][2] /= masstotal[i];
}
diff --git a/src/compute_ke.cpp b/src/compute_ke.cpp
index 3efd698325..fb3c5a9695 100644
--- a/src/compute_ke.cpp
+++ b/src/compute_ke.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
+#include <mpi.h>
#include "compute_ke.h"
#include "atom.h"
#include "update.h"
diff --git a/src/compute_ke_atom.cpp b/src/compute_ke_atom.cpp
index 5709c42837..5cc6f7a939 100644
--- a/src/compute_ke_atom.cpp
+++ b/src/compute_ke_atom.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "compute_ke_atom.h"
#include "atom.h"
#include "update.h"
diff --git a/src/compute_msd.cpp b/src/compute_msd.cpp
index 91e758ef6d..0d35a88620 100644
--- a/src/compute_msd.cpp
+++ b/src/compute_msd.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "compute_msd.h"
#include "atom.h"
#include "update.h"
@@ -85,7 +85,7 @@ ComputeMSD::ComputeMSD(LAMMPS *lmp, int narg, char **arg) :
else xoriginal[i][0] = xoriginal[i][1] = xoriginal[i][2] = 0.0;
// adjust for COM if requested
-
+
if (comflag) {
double cm[3];
masstotal = group->mass(igroup);
diff --git a/src/compute_msd_chunk.cpp b/src/compute_msd_chunk.cpp
index 317b601bc3..81603f2e44 100644
--- a/src/compute_msd_chunk.cpp
+++ b/src/compute_msd_chunk.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "compute_msd_chunk.h"
#include "atom.h"
#include "update.h"
@@ -120,7 +120,7 @@ void ComputeMSDChunk::compute_array()
nchunk = n;
allocate();
size_array_rows = nchunk;
- } else if (n != nchunk)
+ } else if (n != nchunk)
error->all(FLERR,"Compute msd/chunk nchunk is not static");
// zero local per-chunk values
diff --git a/src/compute_omega_chunk.cpp b/src/compute_omega_chunk.cpp
index 4e3f08d774..c437dd66b3 100644
--- a/src/compute_omega_chunk.cpp
+++ b/src/compute_omega_chunk.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "compute_omega_chunk.h"
#include "atom.h"
#include "update.h"
@@ -25,7 +25,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-ComputeOmegaChunk::ComputeOmegaChunk(LAMMPS *lmp, int narg, char **arg) :
+ComputeOmegaChunk::ComputeOmegaChunk(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 4) error->all(FLERR,"Illegal compute omega/chunk command");
@@ -219,12 +219,12 @@ void ComputeOmegaChunk::compute_array()
ione[0][1]*ione[1][2]*ione[2][0] + ione[0][2]*ione[1][0]*ione[2][1] -
ione[0][0]*ione[1][2]*ione[2][1] - ione[0][1]*ione[1][0]*ione[2][2] -
ione[2][0]*ione[1][1]*ione[0][2];
-
+
if (determinant > 0.0)
for (int i = 0; i < 3; i++)
for (int j = 0; j < 3; j++)
inverse[i][j] /= determinant;
-
+
omega[i][0] = inverse[0][0]*angmom[i][0] + inverse[0][1]*angmom[i][1] +
inverse[0][2]*angmom[i][2];
omega[i][1] = inverse[1][0]*angmom[i][0] + inverse[1][1]*angmom[i][1] +
diff --git a/src/compute_pair.cpp b/src/compute_pair.cpp
index 8c7fa0cef3..b411794f61 100644
--- a/src/compute_pair.cpp
+++ b/src/compute_pair.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "string.h"
+#include <mpi.h>
+#include <string.h>
#include "compute_pair.h"
#include "update.h"
#include "force.h"
diff --git a/src/compute_pair_local.cpp b/src/compute_pair_local.cpp
index 1cbd72dc58..ad404b3f5e 100644
--- a/src/compute_pair_local.cpp
+++ b/src/compute_pair_local.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "string.h"
-#include "stdlib.h"
+#include <math.h>
+#include <string.h>
+#include <stdlib.h>
#include "compute_pair_local.h"
#include "atom.h"
#include "update.h"
diff --git a/src/compute_pe.cpp b/src/compute_pe.cpp
index aaa87d8204..1055ab4eb1 100644
--- a/src/compute_pe.cpp
+++ b/src/compute_pe.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "string.h"
+#include <mpi.h>
+#include <string.h>
#include "compute_pe.h"
#include "atom.h"
#include "update.h"
diff --git a/src/compute_pe_atom.cpp b/src/compute_pe_atom.cpp
index b1892e42f4..e157bf29fd 100755
--- a/src/compute_pe_atom.cpp
+++ b/src/compute_pe_atom.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "compute_pe_atom.h"
#include "atom.h"
#include "update.h"
diff --git a/src/compute_pressure.cpp b/src/compute_pressure.cpp
index d4a3109ea9..ca493e46fd 100644
--- a/src/compute_pressure.cpp
+++ b/src/compute_pressure.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "string.h"
-#include "stdlib.h"
+#include <mpi.h>
+#include <string.h>
+#include <stdlib.h>
#include "compute_pressure.h"
#include "atom.h"
#include "update.h"
@@ -96,7 +96,7 @@ ComputePressure::ComputePressure(LAMMPS *lmp, int narg, char **arg) :
// error check
- if (keflag && id_temp == NULL)
+ if (keflag && id_temp == NULL)
error->all(FLERR,"Compute pressure requires temperature ID "
"to include kinetic energy");
diff --git a/src/compute_property_atom.cpp b/src/compute_property_atom.cpp
index 336fbed5b0..54fcb9d722 100644
--- a/src/compute_property_atom.cpp
+++ b/src/compute_property_atom.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "string.h"
+#include <math.h>
+#include <string.h>
#include "compute_property_atom.h"
#include "math_extra.h"
#include "atom.h"
@@ -201,28 +201,28 @@ ComputePropertyAtom::ComputePropertyAtom(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"quatw") == 0) {
avec_ellipsoid = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
avec_body = (AtomVecBody *) atom->style_match("body");
- if (!avec_ellipsoid && !avec_body)
+ if (!avec_ellipsoid && !avec_body)
error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_quatw;
} else if (strcmp(arg[iarg],"quati") == 0) {
avec_ellipsoid = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
avec_body = (AtomVecBody *) atom->style_match("body");
- if (!avec_ellipsoid && !avec_body)
+ if (!avec_ellipsoid && !avec_body)
error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_quati;
} else if (strcmp(arg[iarg],"quatj") == 0) {
avec_ellipsoid = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
avec_body = (AtomVecBody *) atom->style_match("body");
- if (!avec_ellipsoid && !avec_body)
+ if (!avec_ellipsoid && !avec_body)
error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_quatj;
} else if (strcmp(arg[iarg],"quatk") == 0) {
avec_ellipsoid = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
avec_body = (AtomVecBody *) atom->style_match("body");
- if (!avec_ellipsoid && !avec_body)
+ if (!avec_ellipsoid && !avec_body)
error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_quatk;
diff --git a/src/compute_property_chunk.cpp b/src/compute_property_chunk.cpp
index 0fc67118f1..9567748918 100644
--- a/src/compute_property_chunk.cpp
+++ b/src/compute_property_chunk.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "compute_property_chunk.h"
#include "atom.h"
#include "update.h"
@@ -51,7 +51,7 @@ ComputePropertyChunk::ComputePropertyChunk(LAMMPS *lmp, int narg, char **arg) :
pack_choice[i] = &ComputePropertyChunk::pack_count;
countflag = 1;
} else if (strcmp(arg[iarg],"id") == 0) {
- if (!cchunk->compress)
+ if (!cchunk->compress)
error->all(FLERR,"Compute chunk/atom stores no IDs for "
"compute property/chunk");
pack_choice[i] = &ComputePropertyChunk::pack_id;
diff --git a/src/compute_property_local.cpp b/src/compute_property_local.cpp
index c08d723cb2..864efa4646 100644
--- a/src/compute_property_local.cpp
+++ b/src/compute_property_local.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "compute_property_local.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/compute_rdf.cpp b/src/compute_rdf.cpp
index 65bd4eabe2..14a12bb5c6 100644
--- a/src/compute_rdf.cpp
+++ b/src/compute_rdf.cpp
@@ -15,9 +15,9 @@
Contributing authors: Paul Crozier (SNL), Jeff Greathouse (SNL)
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "math.h"
-#include "stdlib.h"
+#include <mpi.h>
+#include <math.h>
+#include <stdlib.h>
#include "compute_rdf.h"
#include "atom.h"
#include "update.h"
diff --git a/src/compute_rdf.h b/src/compute_rdf.h
index 9d0956212b..3f9fde7cad 100644
--- a/src/compute_rdf.h
+++ b/src/compute_rdf.h
@@ -20,7 +20,7 @@ ComputeStyle(rdf,ComputeRDF)
#ifndef LMP_COMPUTE_RDF_H
#define LMP_COMPUTE_RDF_H
-#include "stdio.h"
+#include <stdio.h>
#include "compute.h"
namespace LAMMPS_NS {
diff --git a/src/compute_reduce.cpp b/src/compute_reduce.cpp
index 6f77436522..f6305f4806 100644
--- a/src/compute_reduce.cpp
+++ b/src/compute_reduce.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
-#include "stdlib.h"
+#include <string.h>
+#include <stdlib.h>
#include "compute_reduce.h"
#include "atom.h"
#include "update.h"
diff --git a/src/compute_reduce_region.cpp b/src/compute_reduce_region.cpp
index fe33fc3c79..420a85c91f 100644
--- a/src/compute_reduce_region.cpp
+++ b/src/compute_reduce_region.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
-#include "stdlib.h"
+#include <string.h>
+#include <stdlib.h>
#include "compute_reduce_region.h"
#include "atom.h"
#include "update.h"
diff --git a/src/compute_slice.cpp b/src/compute_slice.cpp
index e28e9d5bce..700b2545c9 100644
--- a/src/compute_slice.cpp
+++ b/src/compute_slice.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdlib.h"
-#include "string.h"
+#include <stdlib.h>
+#include <string.h>
#include "compute_slice.h"
#include "update.h"
#include "modify.h"
diff --git a/src/compute_stress_atom.cpp b/src/compute_stress_atom.cpp
index 45d8e20d9c..3455d9eb08 100644
--- a/src/compute_stress_atom.cpp
+++ b/src/compute_stress_atom.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdlib.h"
-#include "string.h"
+#include <stdlib.h>
+#include <string.h>
#include "compute_stress_atom.h"
#include "atom.h"
#include "update.h"
@@ -308,7 +308,7 @@ void ComputeStressAtom::compute_peratom()
stress[i][5] += onemass*v[i][1]*v[i][2];
temperature->restore_bias(i,v[i]);
}
-
+
} else {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
diff --git a/src/compute_temp.cpp b/src/compute_temp.cpp
index 6748bea4ef..1fbab924b8 100644
--- a/src/compute_temp.cpp
+++ b/src/compute_temp.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "string.h"
+#include <mpi.h>
+#include <string.h>
#include "compute_temp.h"
#include "atom.h"
#include "update.h"
@@ -97,7 +97,7 @@ double ComputeTemp::compute_scalar()
MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
if (dynamic) dof_compute();
- if (dof < 0.0 && natoms_temp > 0.0)
+ if (dof < 0.0 && natoms_temp > 0.0)
error->all(FLERR,"Temperature compute degrees of freedom < 0");
scalar *= tfactor;
return scalar;
diff --git a/src/compute_temp_chunk.cpp b/src/compute_temp_chunk.cpp
index 3c0cdff80d..5a5853514f 100644
--- a/src/compute_temp_chunk.cpp
+++ b/src/compute_temp_chunk.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "compute_temp_chunk.h"
#include "atom.h"
#include "update.h"
@@ -236,7 +236,7 @@ double ComputeTempChunk::compute_scalar()
if (mask[i] & groupbit) {
index = ichunk[i]-1;
if (index < 0) continue;
- t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
+ t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
rmass[i];
mycount++;
}
@@ -509,7 +509,7 @@ void ComputeTempChunk::temperature(int icol)
if (mask[i] & groupbit) {
index = ichunk[i]-1;
if (index < 0) continue;
- sum[index] += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
+ sum[index] += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
rmass[i];
count[index]++;
}
diff --git a/src/compute_temp_com.cpp b/src/compute_temp_com.cpp
index 9e734299af..7e05dcb776 100644
--- a/src/compute_temp_com.cpp
+++ b/src/compute_temp_com.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "stdlib.h"
-#include "string.h"
+#include <mpi.h>
+#include <stdlib.h>
+#include <string.h>
#include "compute_temp_com.h"
#include "atom.h"
#include "update.h"
@@ -111,7 +111,7 @@ double ComputeTempCOM::compute_scalar()
MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
if (dynamic) dof_compute();
- if (dof < 0.0 && natoms_temp > 0.0)
+ if (dof < 0.0 && natoms_temp > 0.0)
error->all(FLERR,"Temperature compute degrees of freedom < 0");
scalar *= tfactor;
return scalar;
diff --git a/src/compute_temp_deform.cpp b/src/compute_temp_deform.cpp
index 0035cbf4df..8c1d2d85fc 100644
--- a/src/compute_temp_deform.cpp
+++ b/src/compute_temp_deform.cpp
@@ -15,8 +15,8 @@
Contributing author: Pieter in 't Veld (SNL)
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "string.h"
+#include <mpi.h>
+#include <string.h>
#include "compute_temp_deform.h"
#include "domain.h"
#include "atom.h"
@@ -148,7 +148,7 @@ double ComputeTempDeform::compute_scalar()
MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
if (dynamic) dof_compute();
- if (dof < 0.0 && natoms_temp > 0.0)
+ if (dof < 0.0 && natoms_temp > 0.0)
error->all(FLERR,"Temperature compute degrees of freedom < 0");
scalar *= tfactor;
return scalar;
diff --git a/src/compute_temp_partial.cpp b/src/compute_temp_partial.cpp
index f00a44f942..c4e8e7cd88 100644
--- a/src/compute_temp_partial.cpp
+++ b/src/compute_temp_partial.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "stdlib.h"
+#include <mpi.h>
+#include <stdlib.h>
#include "compute_temp_partial.h"
#include "atom.h"
#include "update.h"
@@ -119,7 +119,7 @@ double ComputeTempPartial::compute_scalar()
MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
if (dynamic) dof_compute();
- if (dof < 0.0 && natoms_temp > 0.0)
+ if (dof < 0.0 && natoms_temp > 0.0)
error->all(FLERR,"Temperature compute degrees of freedom < 0");
scalar *= tfactor;
return scalar;
diff --git a/src/compute_temp_profile.cpp b/src/compute_temp_profile.cpp
index 4cc9a3e896..b800047175 100644
--- a/src/compute_temp_profile.cpp
+++ b/src/compute_temp_profile.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "stdlib.h"
-#include "string.h"
+#include <mpi.h>
+#include <stdlib.h>
+#include <string.h>
#include "compute_temp_profile.h"
#include "atom.h"
#include "update.h"
@@ -102,7 +102,7 @@ ComputeTempProfile::ComputeTempProfile(LAMMPS *lmp, int narg, char **arg) :
// optional keywords
outflag = TENSOR;
-
+
while (iarg < narg) {
if (strcmp(arg[iarg],"out") == 0) {
if (iarg+2 > narg)
@@ -244,7 +244,7 @@ double ComputeTempProfile::compute_scalar()
MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
if (dynamic) dof_compute();
- if (dof < 0.0 && natoms_temp > 0.0)
+ if (dof < 0.0 && natoms_temp > 0.0)
error->all(FLERR,"Temperature compute degrees of freedom < 0");
scalar *= tfactor;
return scalar;
diff --git a/src/compute_temp_ramp.cpp b/src/compute_temp_ramp.cpp
index a922cded8c..ba5ed8ca68 100644
--- a/src/compute_temp_ramp.cpp
+++ b/src/compute_temp_ramp.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "stdlib.h"
-#include "string.h"
+#include <mpi.h>
+#include <stdlib.h>
+#include <string.h>
#include "compute_temp_ramp.h"
#include "atom.h"
#include "update.h"
@@ -170,7 +170,7 @@ double ComputeTempRamp::compute_scalar()
MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
if (dynamic) dof_compute();
- if (dof < 0.0 && natoms_temp > 0.0)
+ if (dof < 0.0 && natoms_temp > 0.0)
error->all(FLERR,"Temperature compute degrees of freedom < 0");
scalar *= tfactor;
return scalar;
diff --git a/src/compute_temp_region.cpp b/src/compute_temp_region.cpp
index e746ea1fc1..158c93b2fb 100644
--- a/src/compute_temp_region.cpp
+++ b/src/compute_temp_region.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "string.h"
+#include <mpi.h>
+#include <string.h>
#include "compute_temp_region.h"
#include "atom.h"
#include "update.h"
@@ -136,7 +136,7 @@ double ComputeTempRegion::compute_scalar()
tarray[1] = t;
MPI_Allreduce(tarray,tarray_all,2,MPI_DOUBLE,MPI_SUM,world);
dof = domain->dimension * tarray_all[0] - extra_dof;
- if (dof < 0.0 && tarray_all[0] > 0.0)
+ if (dof < 0.0 && tarray_all[0] > 0.0)
error->all(FLERR,"Temperature compute degrees of freedom < 0");
if (dof > 0) scalar = force->mvv2e * tarray_all[1] / (dof * force->boltz);
else scalar = 0.0;
diff --git a/src/compute_temp_sphere.cpp b/src/compute_temp_sphere.cpp
index 001a7c2de4..64b23308e2 100644
--- a/src/compute_temp_sphere.cpp
+++ b/src/compute_temp_sphere.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "string.h"
+#include <mpi.h>
+#include <string.h>
#include "compute_temp_sphere.h"
#include "atom.h"
#include "atom_vec.h"
@@ -250,7 +250,7 @@ double ComputeTempSphere::compute_scalar()
MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
if (dynamic || tempbias == 2) dof_compute();
- if (dof < 0.0 && natoms_temp > 0.0)
+ if (dof < 0.0 && natoms_temp > 0.0)
error->all(FLERR,"Temperature compute degrees of freedom < 0");
scalar *= tfactor;
return scalar;
diff --git a/src/compute_torque_chunk.cpp b/src/compute_torque_chunk.cpp
index 0cd69721a4..41ae0c628c 100644
--- a/src/compute_torque_chunk.cpp
+++ b/src/compute_torque_chunk.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "compute_torque_chunk.h"
#include "atom.h"
#include "update.h"
@@ -25,7 +25,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-ComputeTorqueChunk::ComputeTorqueChunk(LAMMPS *lmp, int narg, char **arg) :
+ComputeTorqueChunk::ComputeTorqueChunk(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 4) error->all(FLERR,"Illegal compute torque/chunk command");
diff --git a/src/compute_vacf.cpp b/src/compute_vacf.cpp
index bbfd2651e9..bc3ffbd21a 100755
--- a/src/compute_vacf.cpp
+++ b/src/compute_vacf.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "compute_vacf.h"
#include "atom.h"
#include "update.h"
diff --git a/src/compute_vcm_chunk.cpp b/src/compute_vcm_chunk.cpp
index dd2c075653..a3751fa13a 100644
--- a/src/compute_vcm_chunk.cpp
+++ b/src/compute_vcm_chunk.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "compute_vcm_chunk.h"
#include "atom.h"
#include "update.h"
@@ -117,7 +117,7 @@ void ComputeVCMChunk::compute_array()
for (int i = 0; i < nchunk; i++)
vcm[i][0] = vcm[i][1] = vcm[i][2] = 0.0;
- if (massneed)
+ if (massneed)
for (int i = 0; i < nchunk; i++) massproc[i] = 0.0;
// compute VCM for each chunk
@@ -142,7 +142,7 @@ void ComputeVCMChunk::compute_array()
}
MPI_Allreduce(&vcm[0][0],&vcmall[0][0],3*nchunk,MPI_DOUBLE,MPI_SUM,world);
- if (massneed)
+ if (massneed)
MPI_Allreduce(massproc,masstotal,nchunk,MPI_DOUBLE,MPI_SUM,world);
for (int i = 0; i < nchunk; i++) {
diff --git a/src/create_atoms.cpp b/src/create_atoms.cpp
index a192dbb6f4..22d58bdc64 100644
--- a/src/create_atoms.cpp
+++ b/src/create_atoms.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "create_atoms.h"
#include "atom.h"
#include "atom_vec.h"
@@ -225,7 +225,7 @@ void CreateAtoms::command(int narg, char **arg)
onemol->compute_center();
// molecule random number generator, different for each proc
-
+
ranmol = new RanMars(lmp,molseed+comm->me);
}
@@ -422,8 +422,8 @@ void CreateAtoms::command(int narg, char **arg)
int molcreate = (atom->nlocal - nlocal_previous) / onemol->natoms;
- // increment total bonds,angles,etc
-
+ // increment total bonds,angles,etc
+
bigint nmolme = molcreate;
bigint nmoltotal;
MPI_Allreduce(&nmolme,&nmoltotal,1,MPI_LMP_BIGINT,MPI_SUM,world);
@@ -509,7 +509,7 @@ void CreateAtoms::command(int narg, char **arg)
improper_atom4[ilocal][j] += offset;
}
if (onemol->specialflag)
- for (int j = 0; j < nspecial[ilocal][2]; j++)
+ for (int j = 0; j < nspecial[ilocal][2]; j++)
special[ilocal][j] += offset;
}
ilocal++;
diff --git a/src/create_bonds.cpp b/src/create_bonds.cpp
index a471285724..309faa7167 100644
--- a/src/create_bonds.cpp
+++ b/src/create_bonds.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdlib.h"
-#include "string.h"
+#include <stdlib.h>
+#include <string.h>
#include "create_bonds.h"
#include "atom.h"
#include "domain.h"
@@ -39,7 +39,7 @@ void CreateBonds::command(int narg, char **arg)
error->all(FLERR,"Create_bonds command before simulation box is defined");
if (atom->tag_enable == 0)
error->all(FLERR,"Cannot use create_bonds unless atoms have IDs");
- if (atom->molecular != 1)
+ if (atom->molecular != 1)
error->all(FLERR,"Cannot use create_bonds with non-molecular system");
if (narg != 5) error->all(FLERR,"Illegal create_bonds command");
@@ -57,7 +57,7 @@ void CreateBonds::command(int narg, char **arg)
double rmin = force->numeric(FLERR,arg[3]);
double rmax = force->numeric(FLERR,arg[4]);
- if (btype <= 0 || btype > atom->nbondtypes)
+ if (btype <= 0 || btype > atom->nbondtypes)
error->all(FLERR,"Invalid bond type in create_bonds command");
if (rmin > rmax) error->all(FLERR,"Illegal create_bonds command");
@@ -136,7 +136,7 @@ void CreateBonds::command(int narg, char **arg)
tagint **bond_atom = atom->bond_atom;
double newton_bond = force->newton_bond;
int nlocal = atom->nlocal;
-
+
int i,j,ii,jj,inum,jnum,flag;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *ilist,*jlist,*numneigh,**firstneigh;
@@ -161,7 +161,7 @@ void CreateBonds::command(int narg, char **arg)
// only consider bond creation if I,J distance between 2 cutoffs
// compute rsq identically on both I,J loop iterations
// if I,J tags equal, do not bond atom to itself
-
+
if (tag[i] < tag[j]) {
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
diff --git a/src/create_box.cpp b/src/create_box.cpp
index 21e20aab56..94a11c1af8 100644
--- a/src/create_box.cpp
+++ b/src/create_box.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdlib.h"
-#include "string.h"
+#include <stdlib.h>
+#include <string.h>
#include "create_box.h"
#include "atom.h"
#include "atom_vec.h"
@@ -110,49 +110,49 @@ void CreateBox::command(int narg, char **arg)
while (iarg < narg) {
if (strcmp(arg[iarg],"bond/types") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal create_box command");
- if (!atom->avec->bonds_allow)
+ if (!atom->avec->bonds_allow)
error->all(FLERR,"No bonds allowed with this atom style");
atom->nbondtypes = force->inumeric(FLERR,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"angle/types") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal create_box command");
- if (!atom->avec->angles_allow)
+ if (!atom->avec->angles_allow)
error->all(FLERR,"No angles allowed with this atom style");
atom->nangletypes = force->inumeric(FLERR,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"dihedral/types") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal create_box command");
- if (!atom->avec->dihedrals_allow)
+ if (!atom->avec->dihedrals_allow)
error->all(FLERR,"No dihedrals allowed with this atom style");
atom->ndihedraltypes = force->inumeric(FLERR,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"improper/types") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal create_box command");
- if (!atom->avec->impropers_allow)
+ if (!atom->avec->impropers_allow)
error->all(FLERR,"No impropers allowed with this atom style");
atom->nimpropertypes = force->inumeric(FLERR,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"extra/bond/per/atom") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal create_box command");
- if (!atom->avec->bonds_allow)
+ if (!atom->avec->bonds_allow)
error->all(FLERR,"No bonds allowed with this atom style");
atom->bond_per_atom = force->inumeric(FLERR,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"extra/angle/per/atom") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal create_box command");
- if (!atom->avec->angles_allow)
+ if (!atom->avec->angles_allow)
error->all(FLERR,"No angles allowed with this atom style");
atom->angle_per_atom = force->inumeric(FLERR,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"extra/dihedral/per/atom") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal create_box command");
- if (!atom->avec->dihedrals_allow)
+ if (!atom->avec->dihedrals_allow)
error->all(FLERR,"No dihedrals allowed with this atom style");
atom->dihedral_per_atom = force->inumeric(FLERR,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"extra/improper/per/atom") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal create_box command");
- if (!atom->avec->impropers_allow)
+ if (!atom->avec->impropers_allow)
error->all(FLERR,"No impropers allowed with this atom style");
atom->improper_per_atom = force->inumeric(FLERR,arg[iarg+1]);
iarg += 2;
diff --git a/src/delete_atoms.cpp b/src/delete_atoms.cpp
index eca1cbd752..5777ed19fb 100644
--- a/src/delete_atoms.cpp
+++ b/src/delete_atoms.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdlib.h"
-#include "string.h"
+#include <stdlib.h>
+#include <string.h>
#include "delete_atoms.h"
#include "atom.h"
#include "atom_vec.h"
@@ -128,19 +128,19 @@ void DeleteAtoms::command(int narg, char **arg)
" atoms, new total = " BIGINT_FORMAT "\n",
ndelete,atom->natoms);
if (bond_flag || mol_flag) {
- if (nbonds_previous)
+ if (nbonds_previous)
fprintf(screen,"Deleted " BIGINT_FORMAT
" bonds, new total = " BIGINT_FORMAT "\n",
ndelete_bonds,atom->nbonds);
- if (nangles_previous)
+ if (nangles_previous)
fprintf(screen,"Deleted " BIGINT_FORMAT
" angles, new total = " BIGINT_FORMAT "\n",
ndelete_angles,atom->nangles);
- if (ndihedrals_previous)
+ if (ndihedrals_previous)
fprintf(screen,"Deleted " BIGINT_FORMAT
" dihedrals, new total = " BIGINT_FORMAT "\n",
ndelete_dihedrals,atom->ndihedrals);
- if (nimpropers_previous)
+ if (nimpropers_previous)
fprintf(screen,"Deleted " BIGINT_FORMAT
" impropers, new total = " BIGINT_FORMAT "\n",
ndelete_impropers,atom->nimpropers);
@@ -152,19 +152,19 @@ void DeleteAtoms::command(int narg, char **arg)
" atoms, new total = " BIGINT_FORMAT "\n",
ndelete,atom->natoms);
if (bond_flag || mol_flag) {
- if (nbonds_previous)
+ if (nbonds_previous)
fprintf(logfile,"Deleted " BIGINT_FORMAT
" bonds, new total = " BIGINT_FORMAT "\n",
ndelete_bonds,atom->nbonds);
- if (nangles_previous)
+ if (nangles_previous)
fprintf(logfile,"Deleted " BIGINT_FORMAT
" angles, new total = " BIGINT_FORMAT "\n",
ndelete_angles,atom->nangles);
- if (ndihedrals_previous)
+ if (ndihedrals_previous)
fprintf(logfile,"Deleted " BIGINT_FORMAT
" dihedrals, new total = " BIGINT_FORMAT "\n",
ndelete_dihedrals,atom->ndihedrals);
- if (nimpropers_previous)
+ if (nimpropers_previous)
fprintf(logfile,"Deleted " BIGINT_FORMAT
" impropers, new total = " BIGINT_FORMAT "\n",
ndelete_impropers,atom->nimpropers);
@@ -712,10 +712,10 @@ void DeleteAtoms::options(int narg, char **arg)
iarg += 2;
} else if (strcmp(arg[iarg],"bond") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal delete_atoms command");
- if (atom->molecular == 0)
+ if (atom->molecular == 0)
error->all(FLERR,"Cannot delete_atoms bond yes for "
"non-molecular systems");
- if (atom->molecular == 2)
+ if (atom->molecular == 2)
error->all(FLERR,"Cannot use delete_atoms bond yes with "
"atom_style template");
if (strcmp(arg[iarg+1],"yes") == 0) bond_flag = 1;
@@ -724,7 +724,7 @@ void DeleteAtoms::options(int narg, char **arg)
iarg += 2;
} else if (strcmp(arg[iarg],"mol") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal delete_atoms command");
- if (atom->molecule_flag == 0)
+ if (atom->molecule_flag == 0)
error->all(FLERR,"Delete_atoms mol yes requires "
"atom attribute molecule");
if (strcmp(arg[iarg+1],"yes") == 0) mol_flag = 1;
diff --git a/src/delete_bonds.cpp b/src/delete_bonds.cpp
index c4823cc01b..3871641e0e 100644
--- a/src/delete_bonds.cpp
+++ b/src/delete_bonds.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "stdlib.h"
-#include "string.h"
+#include <mpi.h>
+#include <stdlib.h>
+#include <string.h>
#include "delete_bonds.h"
#include "atom.h"
#include "atom_vec.h"
@@ -146,7 +146,7 @@ void DeleteBonds::command(int narg, char **arg)
int i,m,n,consider,flag,itype;
int atom1,atom2,atom3,atom4;
- if (atom->avec->bonds_allow &&
+ if (atom->avec->bonds_allow &&
(style == BOND || style == MULTI || style == ATOM)) {
int *num_bond = atom->num_bond;
int **bond_type = atom->bond_type;
@@ -299,7 +299,7 @@ void DeleteBonds::command(int narg, char **arg)
}
delete [] tlist;
-
+
// induce turn off of angles, dihedral, impropers due to turned off bonds
// induce turn off of dihedrals due to turned off angles
// all atoms or any atom in interaction must be in group, based on any_flag
diff --git a/src/dihedral.cpp b/src/dihedral.cpp
index 8cd66bee1f..3cd4a33ce9 100644
--- a/src/dihedral.cpp
+++ b/src/dihedral.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "dihedral.h"
#include "atom.h"
#include "comm.h"
@@ -67,7 +67,7 @@ Dihedral::~Dihedral()
void Dihedral::init()
{
- if (!allocated && atom->ndihedraltypes)
+ if (!allocated && atom->ndihedraltypes)
error->all(FLERR,"Dihedral coeffs are not set");
for (int i = 1; i <= atom->ndihedraltypes; i++)
if (setflag[i] == 0) error->all(FLERR,"All dihedral coeffs are not set");
diff --git a/src/dihedral.h b/src/dihedral.h
index e16c26a629..3e3ec0a4f2 100644
--- a/src/dihedral.h
+++ b/src/dihedral.h
@@ -14,7 +14,7 @@
#ifndef LMP_DIHEDRAL_H
#define LMP_DIHEDRAL_H
-#include "stdio.h"
+#include <stdio.h>
#include "pointers.h"
namespace LAMMPS_NS {
diff --git a/src/dihedral_hybrid.cpp b/src/dihedral_hybrid.cpp
index 72c0c0510a..ed73351b3a 100644
--- a/src/dihedral_hybrid.cpp
+++ b/src/dihedral_hybrid.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "string.h"
-#include "ctype.h"
+#include <math.h>
+#include <string.h>
+#include <ctype.h>
#include "dihedral_hybrid.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/dihedral_hybrid.h b/src/dihedral_hybrid.h
index bb6bf56211..6e30d3d693 100644
--- a/src/dihedral_hybrid.h
+++ b/src/dihedral_hybrid.h
@@ -20,7 +20,7 @@ DihedralStyle(hybrid,DihedralHybrid)
#ifndef LMP_DIHEDRAL_HYBRID_H
#define LMP_DIHEDRAL_HYBRID_H
-#include "stdio.h"
+#include <stdio.h>
#include "dihedral.h"
namespace LAMMPS_NS {
diff --git a/src/displace_atoms.cpp b/src/displace_atoms.cpp
index 2a72958bc9..32cfc74cc8 100644
--- a/src/displace_atoms.cpp
+++ b/src/displace_atoms.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "stdlib.h"
-#include "string.h"
+#include <mpi.h>
+#include <stdlib.h>
+#include <string.h>
#include "displace_atoms.h"
#include "atom.h"
#include "modify.h"
@@ -44,7 +44,7 @@ DisplaceAtoms::DisplaceAtoms(LAMMPS *lmp) : Pointers(lmp)
/* ---------------------------------------------------------------------- */
-DisplaceAtoms::~DisplaceAtoms()
+DisplaceAtoms::~DisplaceAtoms()
{
memory->destroy(mvec);
}
@@ -190,7 +190,7 @@ void DisplaceAtoms::command(int narg, char **arg)
delete random;
}
-
+
// rotate atoms by right-hand rule by theta around R
// P = point = vector = point of rotation
// R = vector = axis of rotation
@@ -205,7 +205,7 @@ void DisplaceAtoms::command(int narg, char **arg)
if (style == ROTATE) {
double axis[3],point[3];
double a[3],b[3],c[3],d[3],disp[3],runit[3];
-
+
int dim = domain->dimension;
point[0] = xscale*force->numeric(FLERR,arg[2]);
point[1] = yscale*force->numeric(FLERR,arg[3]);
diff --git a/src/domain.cpp b/src/domain.cpp
index b19a7c5084..5bf75bc8cb 100644
--- a/src/domain.cpp
+++ b/src/domain.cpp
@@ -15,11 +15,11 @@
Contributing author (triclinic) : Pieter in 't Veld (SNL)
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "stdlib.h"
-#include "string.h"
-#include "stdio.h"
-#include "math.h"
+#include <mpi.h>
+#include <stdlib.h>
+#include <string.h>
+#include <stdio.h>
+#include <math.h>
#include "domain.h"
#include "style_region.h"
#include "atom.h"
@@ -176,7 +176,7 @@ void Domain::set_initial_box(int expandflag)
// error check or warning on triclinic tilt factors
if (triclinic) {
- if ((fabs(xy/(boxhi[0]-boxlo[0])) > 0.5 && xperiodic) ||
+ if ((fabs(xy/(boxhi[0]-boxlo[0])) > 0.5 && xperiodic) ||
(fabs(xz/(boxhi[0]-boxlo[0])) > 0.5 && xperiodic) ||
(fabs(yz/(boxhi[1]-boxlo[1])) > 0.5 && yperiodic)) {
if (tiltsmall)
@@ -300,7 +300,7 @@ void Domain::set_lamda_box()
void Domain::set_local_box()
{
if (triclinic) return;
-
+
if (comm->layout != LAYOUT_TILED) {
int *myloc = comm->myloc;
int *procgrid = comm->procgrid;
@@ -461,7 +461,7 @@ void Domain::reset_box()
// if shrink-wrapped & kspace is defined (i.e. using MSM), call setup()
// also call init() (to test for compatibility) ?
-
+
if (nonperiodic == 2 && force->kspace) {
//force->kspace->init();
force->kspace->setup();
@@ -634,7 +634,7 @@ int Domain::inside_nonperiodic(double* x)
double delta[3];
if (xperiodic && yperiodic && zperiodic) return 1;
-
+
if (triclinic == 0) {
lo = boxlo;
hi = boxhi;
@@ -719,7 +719,7 @@ void Domain::image_check()
iatom = molatom[i];
n = onemols[imol]->num_bond[iatom];
}
-
+
for (j = 0; j < n; j++) {
if (molecular == 1) {
if (bond_type[i][j] <= 0) continue;
@@ -740,7 +740,7 @@ void Domain::image_check()
delx = unwrap[i][0] - unwrap[k][0];
dely = unwrap[i][1] - unwrap[k][1];
delz = unwrap[i][2] - unwrap[k][2];
-
+
if (xperiodic && delx > xprd_half) flag = 1;
if (xperiodic && dely > yprd_half) flag = 1;
if (dimension == 3 && zperiodic && delz > zprd_half) flag = 1;
@@ -752,13 +752,13 @@ void Domain::image_check()
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_MAX,world);
- if (flagall && comm->me == 0)
+ if (flagall && comm->me == 0)
error->warning(FLERR,"Inconsistent image flags");
if (lostbond == WARN) {
int all;
MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
- if (all && comm->me == 0)
+ if (all && comm->me == 0)
error->warning(FLERR,"Bond atom missing in image check");
}
@@ -848,7 +848,7 @@ void Domain::box_too_small_check()
if (lostbond == WARN) {
int all;
MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
- if (all && comm->me == 0)
+ if (all && comm->me == 0)
error->warning(FLERR,"Bond atom missing in box size check");
}
@@ -903,7 +903,7 @@ void Domain::subbox_too_small_check(double thresh)
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
- if (flagall && comm->me == 0)
+ if (flagall && comm->me == 0)
error->warning(FLERR,"Proc sub-domain size < neighbor skin, "
"could lead to lost atoms");
}
@@ -1461,8 +1461,8 @@ void Domain::image_flip(int m, int n, int p)
ybox -= p*zbox;
xbox -= m*ybox + n*zbox;
- image[i] = ((imageint) (xbox + IMGMAX) & IMGMASK) |
- (((imageint) (ybox + IMGMAX) & IMGMASK) << IMGBITS) |
+ image[i] = ((imageint) (xbox + IMGMAX) & IMGMASK) |
+ (((imageint) (ybox + IMGMAX) & IMGMASK) << IMGBITS) |
(((imageint) (zbox + IMGMAX) & IMGMASK) << IMG2BITS);
}
}
diff --git a/src/domain.h b/src/domain.h
index 65681a5133..8654b59168 100644
--- a/src/domain.h
+++ b/src/domain.h
@@ -14,7 +14,7 @@
#ifndef LMP_DOMAIN_H
#define LMP_DOMAIN_H
-#include "math.h"
+#include <math.h>
#include "pointers.h"
namespace LAMMPS_NS {
@@ -138,10 +138,10 @@ class Domain : protected Pointers {
// minimum image convention check
// return 1 if any distance > 1/2 of box size
- // indicates a special neighbor is actually not in a bond,
+ // indicates a special neighbor is actually not in a bond,
// but is a far-away image that should be treated as an unbonded neighbor
// inline since called from neighbor build inner loop
- //
+ //
inline int minimum_image_check(double dx, double dy, double dz) {
if (xperiodic && fabs(dx) > xprd_half) return 1;
if (yperiodic && fabs(dy) > yprd_half) return 1;
diff --git a/src/dump.cpp b/src/dump.cpp
index 73c805df5e..622badb236 100644
--- a/src/dump.cpp
+++ b/src/dump.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "stdlib.h"
-#include "string.h"
-#include "stdio.h"
+#include <mpi.h>
+#include <stdlib.h>
+#include <string.h>
+#include <stdio.h>
#include "dump.h"
#include "atom.h"
#include "irregular.h"
@@ -186,7 +186,7 @@ void Dump::init()
}
if (sort_flag) {
- if (multiproc > 1)
+ if (multiproc > 1)
error->all(FLERR,
"Cannot dump sort when multiple dump files are written");
if (sortcol == 0 && atom->tag_enable == 0)
@@ -339,7 +339,7 @@ void Dump::write()
if (sort_flag && sortcol == 0) pack(ids);
else pack(NULL);
if (sort_flag) sort();
-
+
// if buffering, convert doubles into strings
// insure sbuf is sized for communicating
// cannot buffer if output is to binary file
@@ -349,7 +349,7 @@ void Dump::write()
int nsmin,nsmax;
MPI_Allreduce(&nsme,&nsmin,1,MPI_INT,MPI_MIN,world);
if (nsmin < 0) error->all(FLERR,"Too much buffered per-proc info for dump");
- if (multiproc != nprocs)
+ if (multiproc != nprocs)
MPI_Allreduce(&nsme,&nsmax,1,MPI_INT,MPI_MAX,world);
else nsmax = nsme;
if (nsmax > maxsbuf) {
@@ -378,11 +378,11 @@ void Dump::write()
MPI_Get_count(&status,MPI_DOUBLE,&nlines);
nlines /= size_one;
} else nlines = nme;
-
+
write_data(nlines,buf);
}
if (flush_flag && fp) fflush(fp);
-
+
} else {
MPI_Recv(&tmp,0,MPI_INT,fileproc,0,world,MPI_STATUS_IGNORE);
MPI_Rsend(buf,nme*size_one,MPI_DOUBLE,fileproc,0,world);
@@ -399,11 +399,11 @@ void Dump::write()
MPI_Wait(&request,&status);
MPI_Get_count(&status,MPI_CHAR,&nchars);
} else nchars = nsme;
-
+
write_data(nchars,(double *) sbuf);
}
if (flush_flag && fp) fflush(fp);
-
+
} else {
MPI_Recv(&tmp,0,MPI_INT,fileproc,0,world,MPI_STATUS_IGNORE);
MPI_Rsend(sbuf,nsme,MPI_CHAR,fileproc,0,world);
@@ -760,7 +760,7 @@ void Dump::modify_params(int narg, char **arg)
"without % in dump file name");
int nper = force->inumeric(FLERR,arg[iarg+1]);
if (nper <= 0) error->all(FLERR,"Illegal dump_modify command");
-
+
multiproc = nprocs/nper;
if (nprocs % nper) multiproc++;
fileproc = me/nper * nper;
@@ -820,7 +820,7 @@ void Dump::modify_params(int narg, char **arg)
fileproc = static_cast<int> ((bigint) icluster * nprocs/nfile);
int fcluster = static_cast<int> ((bigint) fileproc * nfile/nprocs);
if (fcluster < icluster) fileproc++;
- int fileprocnext =
+ int fileprocnext =
static_cast<int> ((bigint) (icluster+1) * nprocs/nfile);
fcluster = static_cast<int> ((bigint) fileprocnext * nfile/nprocs);
if (fcluster < icluster+1) fileprocnext++;
diff --git a/src/dump.h b/src/dump.h
index 3a035672cc..940dc828f4 100644
--- a/src/dump.h
+++ b/src/dump.h
@@ -14,8 +14,8 @@
#ifndef LMP_DUMP_H
#define LMP_DUMP_H
-#include "mpi.h"
-#include "stdio.h"
+#include <mpi.h>
+#include <stdio.h>
#include "pointers.h"
namespace LAMMPS_NS {
diff --git a/src/dump_atom.cpp b/src/dump_atom.cpp
index 068c4e3dff..8b90cf76d7 100644
--- a/src/dump_atom.cpp
+++ b/src/dump_atom.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "dump_atom.h"
#include "domain.h"
#include "atom.h"
@@ -422,9 +422,9 @@ int DumpAtom::convert_image(int n, double *mybuf)
}
offset += sprintf(&sbuf[offset],format,
- static_cast<tagint> (mybuf[m]),
+ static_cast<tagint> (mybuf[m]),
static_cast<int> (mybuf[m+1]),
- mybuf[m+2],mybuf[m+3],mybuf[m+4],
+ mybuf[m+2],mybuf[m+3],mybuf[m+4],
static_cast<int> (mybuf[m+5]),
static_cast<int> (mybuf[m+6]),
static_cast<int> (mybuf[m+7]));
diff --git a/src/dump_cfg.cpp b/src/dump_cfg.cpp
index b1acae791b..9005c3924a 100755
--- a/src/dump_cfg.cpp
+++ b/src/dump_cfg.cpp
@@ -16,9 +16,9 @@
Memory efficiency improved by Ray Shan (Sandia)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "dump_cfg.h"
#include "atom.h"
#include "domain.h"
@@ -188,16 +188,16 @@ int DumpCFG::convert_string(int n, double *mybuf)
} else if (j == 1) {
offset += sprintf(&sbuf[offset],"%s \n",typenames[(int) mybuf[m]]);
} else if (j >= 2) {
- if (vtype[j] == INT)
- offset +=
+ if (vtype[j] == INT)
+ offset +=
sprintf(&sbuf[offset],vformat[j],static_cast<int> (mybuf[m]));
- else if (vtype[j] == DOUBLE)
+ else if (vtype[j] == DOUBLE)
offset += sprintf(&sbuf[offset],vformat[j],mybuf[m]);
- else if (vtype[j] == STRING)
- offset +=
+ else if (vtype[j] == STRING)
+ offset +=
sprintf(&sbuf[offset],vformat[j],typenames[(int) mybuf[m]]);
- else if (vtype[j] == BIGINT)
- offset +=
+ else if (vtype[j] == BIGINT)
+ offset +=
sprintf(&sbuf[offset],vformat[j],static_cast<bigint> (mybuf[m]));
}
m++;
@@ -223,16 +223,16 @@ int DumpCFG::convert_string(int n, double *mybuf)
unwrap_coord = (mybuf[m] - 0.5)/UNWRAPEXPAND + 0.5;
offset += sprintf(&sbuf[offset],vformat[j],unwrap_coord);
} else if (j >= 5 ) {
- if (vtype[j] == INT)
- offset +=
+ if (vtype[j] == INT)
+ offset +=
sprintf(&sbuf[offset],vformat[j],static_cast<int> (mybuf[m]));
- else if (vtype[j] == DOUBLE)
+ else if (vtype[j] == DOUBLE)
offset += sprintf(&sbuf[offset],vformat[j],mybuf[m]);
- else if (vtype[j] == STRING)
- offset +=
+ else if (vtype[j] == STRING)
+ offset +=
sprintf(&sbuf[offset],vformat[j],typenames[(int) mybuf[m]]);
- else if (vtype[j] == BIGINT)
- offset +=
+ else if (vtype[j] == BIGINT)
+ offset +=
sprintf(&sbuf[offset],vformat[j],static_cast<bigint> (mybuf[m]));
}
m++;
@@ -273,13 +273,13 @@ void DumpCFG::write_lines(int n, double *mybuf)
} else if (j == 1) {
fprintf(fp,"%s \n",typenames[(int) mybuf[m]]);
} else if (j >= 2) {
- if (vtype[j] == INT)
+ if (vtype[j] == INT)
fprintf(fp,vformat[j],static_cast<int> (mybuf[m]));
- else if (vtype[j] == DOUBLE)
+ else if (vtype[j] == DOUBLE)
fprintf(fp,vformat[j],mybuf[m]);
- else if (vtype[j] == STRING)
+ else if (vtype[j] == STRING)
fprintf(fp,vformat[j],typenames[(int) mybuf[m]]);
- else if (vtype[j] == BIGINT)
+ else if (vtype[j] == BIGINT)
fprintf(fp,vformat[j],static_cast<bigint> (mybuf[m]));
}
m++;
@@ -299,13 +299,13 @@ void DumpCFG::write_lines(int n, double *mybuf)
unwrap_coord = (mybuf[m] - 0.5)/UNWRAPEXPAND + 0.5;
fprintf(fp,vformat[j],unwrap_coord);
} else if (j >= 5 ) {
- if (vtype[j] == INT)
+ if (vtype[j] == INT)
fprintf(fp,vformat[j],static_cast<int> (mybuf[m]));
- else if (vtype[j] == DOUBLE)
+ else if (vtype[j] == DOUBLE)
fprintf(fp,vformat[j],mybuf[m]);
- else if (vtype[j] == STRING)
+ else if (vtype[j] == STRING)
fprintf(fp,vformat[j],typenames[(int) mybuf[m]]);
- else if (vtype[j] == BIGINT)
+ else if (vtype[j] == BIGINT)
fprintf(fp,vformat[j],static_cast<bigint> (mybuf[m]));
}
m++;
diff --git a/src/dump_custom.cpp b/src/dump_custom.cpp
index 725f7ec8a1..dbb1c3cd9e 100644
--- a/src/dump_custom.cpp
+++ b/src/dump_custom.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "dump_custom.h"
#include "atom.h"
#include "force.h"
@@ -104,7 +104,7 @@ DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) :
ioptional = parse_fields(narg,arg);
- if (ioptional < narg &&
+ if (ioptional < narg &&
strcmp(style,"image") != 0 && strcmp(style,"movie") != 0)
error->all(FLERR,"Invalid attribute in dump custom command");
size_one = nfield = ioptional - 5;
@@ -581,7 +581,7 @@ int DumpCustom::count()
imageint *image = atom->image;
double yprd = domain->yprd;
for (i = 0; i < nlocal; i++)
- dchoose[i] = x[i][1] +
+ dchoose[i] = x[i][1] +
((image[i] >> IMGBITS & IMGMASK) - IMGMAX) * yprd;
ptr = dchoose;
nstride = 1;
@@ -637,7 +637,7 @@ int DumpCustom::count()
double boxxlo = domain->boxlo[0];
double invxprd = 1.0/domain->xprd;
for (i = 0; i < nlocal; i++)
- dchoose[i] = (x[i][0] - boxxlo) * invxprd +
+ dchoose[i] = (x[i][0] - boxxlo) * invxprd +
(image[i] & IMGMASK) - IMGMAX;
ptr = dchoose;
nstride = 1;
@@ -649,7 +649,7 @@ int DumpCustom::count()
double invyprd = 1.0/domain->yprd;
for (i = 0; i < nlocal; i++)
dchoose[i] =
- (x[i][1] - boxylo) * invyprd +
+ (x[i][1] - boxylo) * invyprd +
(image[i] >> IMGBITS & IMGMASK) - IMGMAX;
ptr = dchoose;
nstride = 1;
@@ -660,7 +660,7 @@ int DumpCustom::count()
double boxzlo = domain->boxlo[2];
double invzprd = 1.0/domain->zprd;
for (i = 0; i < nlocal; i++)
- dchoose[i] = (x[i][2] - boxzlo) * invzprd +
+ dchoose[i] = (x[i][2] - boxzlo) * invzprd +
(image[i] >> IMG2BITS) - IMGMAX;
ptr = dchoose;
nstride = 1;
@@ -949,13 +949,13 @@ int DumpCustom::convert_string(int n, double *mybuf)
}
for (j = 0; j < size_one; j++) {
- if (vtype[j] == INT)
+ if (vtype[j] == INT)
offset += sprintf(&sbuf[offset],vformat[j],static_cast<int> (mybuf[m]));
- else if (vtype[j] == DOUBLE)
+ else if (vtype[j] == DOUBLE)
offset += sprintf(&sbuf[offset],vformat[j],mybuf[m]);
else if (vtype[j] == STRING)
offset += sprintf(&sbuf[offset],vformat[j],typenames[(int) mybuf[m]]);
- else if (vtype[j] == BIGINT)
+ else if (vtype[j] == BIGINT)
offset += sprintf(&sbuf[offset],vformat[j],
static_cast<bigint> (mybuf[m]));
m++;
@@ -1002,7 +1002,7 @@ void DumpCustom::write_lines(int n, double *mybuf)
else if (vtype[j] == DOUBLE) fprintf(fp,vformat[j],mybuf[m]);
else if (vtype[j] == STRING)
fprintf(fp,vformat[j],typenames[(int) mybuf[m]]);
- else if (vtype[j] == BIGINT)
+ else if (vtype[j] == BIGINT)
fprintf(fp,vformat[j],static_cast<bigint> (mybuf[m]));
m++;
}
@@ -1306,7 +1306,7 @@ int DumpCustom::parse_fields(int narg, char **arg)
n = atom->find_custom(suffix,tmp);
if (n < 0)
error->all(FLERR,"Could not find custom per-atom property ID");
-
+
if (tmp != 1)
error->all(FLERR,"Custom per-atom property ID is not floating point");
@@ -1328,7 +1328,7 @@ int DumpCustom::parse_fields(int narg, char **arg)
n = atom->find_custom(suffix,tmp);
if (n < 0)
error->all(FLERR,"Could not find custom per-atom property ID");
-
+
if (tmp != 0)
error->all(FLERR,"Custom per-atom property ID is not integer");
@@ -1438,7 +1438,7 @@ int DumpCustom::add_custom(char *id, int flag)
memory->srealloc(id_custom,(ncustom+1)*sizeof(char *),"dump:id_custom");
flag_custom = (int *)
memory->srealloc(flag_custom,(ncustom+1)*sizeof(int),"dump:flag_custom");
-
+
int n = strlen(id) + 1;
id_custom[ncustom] = new char[n];
strcpy(id_custom[ncustom],id);
@@ -1703,7 +1703,7 @@ int DumpCustom::modify_param(int narg, char **arg)
int tmp = -1;
n = atom->find_custom(suffix,tmp);
- if ((n < 0) || (tmp != 1))
+ if ((n < 0) || (tmp != 1))
error->all(FLERR,"Could not find dump modify "
"custom atom floating point property ID");
@@ -1724,7 +1724,7 @@ int DumpCustom::modify_param(int narg, char **arg)
int tmp = -1;
n = atom->find_custom(suffix,tmp);
- if ((n < 0) || (tmp != 0))
+ if ((n < 0) || (tmp != 0))
error->all(FLERR,"Could not find dump modify "
"custom atom integer property ID");
@@ -1830,7 +1830,7 @@ void DumpCustom::pack_variable(int n)
void DumpCustom::pack_custom(int n)
{
-
+
int index = field2index[n];
if (flag_custom[index] == 0) { // integer
diff --git a/src/dump_dcd.cpp b/src/dump_dcd.cpp
index c679df62b9..7414d7cc2b 100644
--- a/src/dump_dcd.cpp
+++ b/src/dump_dcd.cpp
@@ -16,11 +16,11 @@
Axel Kohlmeyer (Temple U), support for groups
------------------------------------------------------------------------- */
-#include "math.h"
-#include "inttypes.h"
-#include "stdio.h"
-#include "time.h"
-#include "string.h"
+#include <math.h>
+#include <inttypes.h>
+#include <stdio.h>
+#include <time.h>
+#include <string.h>
#include "dump_dcd.h"
#include "domain.h"
#include "atom.h"
diff --git a/src/dump_image.cpp b/src/dump_image.cpp
index 05074e609c..3d36f1a797 100644
--- a/src/dump_image.cpp
+++ b/src/dump_image.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "ctype.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <ctype.h>
+#include <stdlib.h>
+#include <string.h>
#include "dump_image.h"
#include "image.h"
#include "atom.h"
@@ -952,7 +952,7 @@ void DumpImage::create_image()
/* ---------------------------------------------------------------------- */
-int DumpImage::pack_forward_comm(int n, int *list, double *buf,
+int DumpImage::pack_forward_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
diff --git a/src/dump_local.cpp b/src/dump_local.cpp
index 53094dd5e4..eb08a912fc 100644
--- a/src/dump_local.cpp
+++ b/src/dump_local.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "string.h"
-#include "stdlib.h"
+#include <mpi.h>
+#include <string.h>
+#include <stdlib.h>
#include "dump_local.h"
#include "atom.h"
#include "modify.h"
@@ -298,9 +298,9 @@ int DumpLocal::convert_string(int n, double *mybuf)
}
for (j = 0; j < size_one; j++) {
- if (vtype[j] == INT)
+ if (vtype[j] == INT)
offset += sprintf(&sbuf[offset],vformat[j],static_cast<int> (mybuf[m]));
- else
+ else
offset += sprintf(&sbuf[offset],vformat[j],mybuf[m]);
m++;
}
diff --git a/src/dump_movie.cpp b/src/dump_movie.cpp
index 6e08b5474e..cb8982cabe 100644
--- a/src/dump_movie.cpp
+++ b/src/dump_movie.cpp
@@ -15,9 +15,9 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "dump_movie.h"
#include "comm.h"
#include "force.h"
diff --git a/src/dump_xyz.cpp b/src/dump_xyz.cpp
index 273ec06e44..4153c8224c 100644
--- a/src/dump_xyz.cpp
+++ b/src/dump_xyz.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "dump_xyz.h"
#include "atom.h"
#include "group.h"
diff --git a/src/error.cpp b/src/error.cpp
index 46f098328f..6989e00034 100644
--- a/src/error.cpp
+++ b/src/error.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "stdlib.h"
+#include <mpi.h>
+#include <stdlib.h>
#include "error.h"
#include "universe.h"
#include "output.h"
diff --git a/src/finish.cpp b/src/finish.cpp
index b2ca44945a..d622dedb1a 100644
--- a/src/finish.cpp
+++ b/src/finish.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "math.h"
-#include "string.h"
-#include "stdio.h"
+#include <mpi.h>
+#include <math.h>
+#include <string.h>
+#include <stdio.h>
#include "finish.h"
#include "timer.h"
#include "universe.h"
@@ -105,7 +105,7 @@ void Finish::end(int flag)
// loop stats
if (timer->has_loop()) {
-
+
// overall loop time
time_loop = timer->get_wall(Timer::TOTAL);
@@ -115,7 +115,7 @@ void Finish::end(int flag)
MPI_Allreduce(&cpu_loop,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
cpu_loop = tmp/nprocs;
if (time_loop > 0.0) cpu_loop = cpu_loop/time_loop*100.0;
-
+
if (me == 0) {
int ntasks = nprocs * nthreads;
const char fmt1[] = "Loop time of %g on %d procs "
@@ -147,7 +147,7 @@ void Finish::end(int flag)
} else {
double hrs_ns = t_step / update->dt * 1000000.0 * one_fs / 3600.0;
double ns_day = 24.0*3600.0 / t_step * update->dt / one_fs/1000000.0;
- const char perf[] =
+ const char perf[] =
"Performance: %.3f ns/day, %.3f hours/ns, %.3f timesteps/s\n";
if (screen) fprintf(screen,perf,ns_day,hrs_ns,step_t);
if (logfile) fprintf(logfile,perf,ns_day,hrs_ns,step_t);
@@ -157,7 +157,7 @@ void Finish::end(int flag)
// CPU use on MPI tasks and OpenMP threads
#ifdef LMP_USER_OMP
- const char fmt2[] =
+ const char fmt2[] =
"%.1f%% CPU use with %d MPI tasks x %d OpenMP threads\n";
if (screen) fprintf(screen,fmt2,cpu_loop,nprocs,nthreads);
if (logfile) fprintf(logfile,fmt2,cpu_loop,nprocs,nthreads);
@@ -180,7 +180,7 @@ void Finish::end(int flag)
if (timer->has_normal())
time_other = timer->get_wall(Timer::TOTAL) - timer->get_wall(Timer::ALL);
-
+
// minimization stats
if (minflag) {
@@ -430,7 +430,7 @@ void Finish::end(int flag)
if (atom->molecular)
mpi_timings("Bond",timer,Timer::BOND,world,nprocs,
nthreads,me,time_loop,screen,logfile);
-
+
if (force->kspace)
mpi_timings("Kspace",timer,Timer::KSPACE,world,nprocs,
nthreads,me,time_loop,screen,logfile);
@@ -464,7 +464,7 @@ void Finish::end(int flag)
}
#ifdef LMP_USER_OMP
- const char thr_hdr_fmt[] =
+ const char thr_hdr_fmt[] =
"\nThread timing breakdown (MPI rank %d):\nTotal threaded time %.4g / %.1f%%\n";
const char thr_header[] =
"Section | min time | avg time | max time |%varavg| %total\n"
@@ -540,7 +540,7 @@ void Finish::end(int flag)
nsample *= 2;
nfft = force->kspace->timing_1d(nsample,time1d);
}
-
+
time1d = nsteps * time1d / nsample;
MPI_Allreduce(&time1d,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time1d = tmp/nprocs;
@@ -833,7 +833,7 @@ void mpi_timings(const char *label, Timer *t, enum Timer::ttype tt,
{
double tmp, time_max, time_min, time_sq;
double time = t->get_wall(tt);
-
+
double time_cpu = t->get_cpu(tt);
if (time/time_loop < 0.001) // insufficient timer resolution!
time_cpu = 1.0;
diff --git a/src/fix.cpp b/src/fix.cpp
index ac7e014393..ccb5996456 100644
--- a/src/fix.cpp
+++ b/src/fix.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
-#include "ctype.h"
+#include <string.h>
+#include <ctype.h>
#include "fix.h"
#include "atom.h"
#include "group.h"
diff --git a/src/fix_adapt.cpp b/src/fix_adapt.cpp
index d5ae80c070..1d6e890613 100644
--- a/src/fix_adapt.cpp
+++ b/src/fix_adapt.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "string.h"
-#include "stdlib.h"
+#include <math.h>
+#include <string.h>
+#include <stdlib.h>
#include "fix_adapt.h"
#include "atom.h"
#include "update.h"
@@ -118,8 +118,8 @@ FixAdapt::FixAdapt(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
adapt[nadapt].aparam = DIAMETER;
diamflag = 1;
} else if (strcmp(arg[iarg+1],"charge") == 0) {
- adapt[nadapt].aparam = CHARGE;
- chgflag = 1;
+ adapt[nadapt].aparam = CHARGE;
+ chgflag = 1;
} else error->all(FLERR,"Illegal fix adapt command");
if (strstr(arg[iarg+2],"v_") == arg[iarg+2]) {
int n = strlen(&arg[iarg+2][2]) + 1;
@@ -275,9 +275,9 @@ void FixAdapt::init()
if (group->dynamic[igroup])
for (int i = 0; i < nadapt; i++)
- if (adapt[i].which == ATOM)
+ if (adapt[i].which == ATOM)
error->all(FLERR,"Cannot use dynamic group with fix adapt atom");
-
+
// setup and error checks
anypair = 0;
@@ -322,7 +322,7 @@ void FixAdapt::init()
if (pair == NULL) pair = force->pair_match(pstyle,1,nsub);
if (pair == NULL) error->all(FLERR,"Fix adapt pair style does not exist");
void *ptr = pair->extract(ad->pparam,ad->pdim);
- if (ptr == NULL)
+ if (ptr == NULL)
error->all(FLERR,"Fix adapt pair style param not supported");
ad->pdim = 2;
@@ -372,7 +372,7 @@ void FixAdapt::init()
}
// fixes that store initial per-atom values
-
+
if (id_fix_diam) {
int ifix = modify->find_fix(id_fix_diam);
if (ifix < 0) error->all(FLERR,"Could not find fix adapt storage fix ID");
@@ -498,13 +498,13 @@ void FixAdapt::change_settings()
}
}
} else if (ad->aparam == CHARGE) {
- double *q = atom->q;
+ double *q = atom->q;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
for (i = 0; i < nall; i++)
- if (mask[i] & groupbit) q[i] = value;
+ if (mask[i] & groupbit) q[i] = value;
}
}
}
diff --git a/src/fix_adapt.h b/src/fix_adapt.h
index bb465daad7..7ae659df45 100644
--- a/src/fix_adapt.h
+++ b/src/fix_adapt.h
@@ -27,7 +27,7 @@ namespace LAMMPS_NS {
class FixAdapt : public Fix {
public:
int diamflag; // 1 if atom diameters will vary, for AtomVecGranular
- int chgflag;
+ int chgflag;
FixAdapt(class LAMMPS *, int, char **);
~FixAdapt();
diff --git a/src/fix_addforce.cpp b/src/fix_addforce.cpp
index 0f65873265..0ffa7751cd 100644
--- a/src/fix_addforce.cpp
+++ b/src/fix_addforce.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
-#include "stdlib.h"
+#include <string.h>
+#include <stdlib.h>
#include "fix_addforce.h"
#include "atom.h"
#include "atom_masks.h"
diff --git a/src/fix_ave_atom.cpp b/src/fix_ave_atom.cpp
index 68e370d60b..b43c505b51 100644
--- a/src/fix_ave_atom.cpp
+++ b/src/fix_ave_atom.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdlib.h"
-#include "string.h"
+#include <stdlib.h>
+#include <string.h>
#include "fix_ave_atom.h"
#include "atom.h"
#include "domain.h"
@@ -283,7 +283,7 @@ void FixAveAtom::end_of_step()
// error check if timestep was reset in an invalid manner
bigint ntimestep = update->ntimestep;
- if (ntimestep < nvalid_last || ntimestep > nvalid)
+ if (ntimestep < nvalid_last || ntimestep > nvalid)
error->all(FLERR,"Invalid timestep reset for fix ave/atom");
if (ntimestep != nvalid) return;
nvalid_last = nvalid;
diff --git a/src/fix_ave_atom.h b/src/fix_ave_atom.h
index c8a0b8e139..c2f5067309 100644
--- a/src/fix_ave_atom.h
+++ b/src/fix_ave_atom.h
@@ -20,7 +20,7 @@ FixStyle(ave/atom,FixAveAtom)
#ifndef LMP_FIX_AVE_ATOM_H
#define LMP_FIX_AVE_ATOM_H
-#include "stdio.h"
+#include <stdio.h>
#include "fix.h"
namespace LAMMPS_NS {
diff --git a/src/fix_ave_chunk.cpp b/src/fix_ave_chunk.cpp
index 07e858e592..b210fc40b4 100644
--- a/src/fix_ave_chunk.cpp
+++ b/src/fix_ave_chunk.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdlib.h"
-#include "string.h"
-#include "unistd.h"
+#include <stdlib.h>
+#include <string.h>
+#include <unistd.h>
#include "fix_ave_chunk.h"
#include "atom.h"
#include "update.h"
@@ -310,7 +310,7 @@ FixAveChunk::FixAveChunk(LAMMPS *lmp, int narg, char **arg) :
// increment lock counter in compute chunk/atom
// only if nrepeat > 1 or ave = RUNNING/WINDOW,
- // so that locking spans multiple timesteps
+ // so that locking spans multiple timesteps
int icompute = modify->find_compute(idchunk);
if (icompute < 0)
@@ -339,13 +339,13 @@ FixAveChunk::FixAveChunk(LAMMPS *lmp, int narg, char **arg) :
if (ncoord == 0) fprintf(fp,"# Chunk Ncount");
else if (ncoord == 1) fprintf(fp,"# Chunk Coord1 Ncount");
else if (ncoord == 2) fprintf(fp,"# Chunk Coord1 Coord2 Ncount");
- else if (ncoord == 3)
+ else if (ncoord == 3)
fprintf(fp,"# Chunk Coord1 Coord2 Coord3 Ncount");
} else {
if (ncoord == 0) fprintf(fp,"# Chunk OrigID Ncount");
else if (ncoord == 1) fprintf(fp,"# Chunk OrigID Coord1 Ncount");
else if (ncoord == 2) fprintf(fp,"# Chunk OrigID Coord1 Coord2 Ncount");
- else if (ncoord == 3)
+ else if (ncoord == 3)
fprintf(fp,"# Chunk OrigID Coord1 Coord2 Coord3 Ncount");
}
for (int i = 0; i < nvalues; i++) fprintf(fp," %s",arg[7+i]);
@@ -526,7 +526,7 @@ void FixAveChunk::end_of_step()
// error check if timestep was reset in an invalid manner
bigint ntimestep = update->ntimestep;
- if (ntimestep < nvalid_last || ntimestep > nvalid)
+ if (ntimestep < nvalid_last || ntimestep > nvalid)
error->all(FLERR,"Invalid timestep reset for fix ave/chunk");
if (ntimestep != nvalid) return;
nvalid_last = nvalid;
@@ -541,8 +541,8 @@ void FixAveChunk::end_of_step()
// if ave = RUNNING/WINDOW and not yet locked:
// set forever, will be unlocked in fix destructor
// wrap setup_chunks in clearstep/addstep b/c it may invoke computes
- // both nevery and nfreq are future steps,
- // since call below to cchunk->ichunk()
+ // both nevery and nfreq are future steps,
+ // since call below to cchunk->ichunk()
// does not re-invoke internal cchunk compute on this same step
if (irepeat == 0) {
@@ -666,15 +666,15 @@ void FixAveChunk::end_of_step()
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit && ichunk[i] > 0) {
index = ichunk[i]-1;
- values_one[index][m] +=
+ values_one[index][m] +=
(v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) * rmass[i];
}
} else {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit && ichunk[i] > 0) {
index = ichunk[i]-1;
- values_one[index][m] +=
- (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
+ values_one[index][m] +=
+ (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
mass[type[i]];
}
}
@@ -760,7 +760,7 @@ void FixAveChunk::end_of_step()
if (count_many[m] > 0.0)
for (j = 0; j < nvalues; j++) {
if (which[j] == TEMPERATURE)
- values_many[m][j] += mvv2e*values_one[m][j] /
+ values_many[m][j] += mvv2e*values_one[m][j] /
((cdof + adof*count_many[m]) * boltz);
else if (which[j] == DENSITY_NUMBER || which[j] == DENSITY_MASS ||
scaleflag == NOSCALE)
diff --git a/src/fix_ave_chunk.h b/src/fix_ave_chunk.h
index a7aa9c2c9c..1a6771fc67 100644
--- a/src/fix_ave_chunk.h
+++ b/src/fix_ave_chunk.h
@@ -20,7 +20,7 @@ FixStyle(ave/chunk,FixAveChunk)
#ifndef LMP_FIX_AVE_CHUNK_H
#define LMP_FIX_AVE_CHUNK_H
-#include "stdio.h"
+#include <stdio.h>
#include "fix.h"
namespace LAMMPS_NS {
diff --git a/src/fix_ave_correlate.cpp b/src/fix_ave_correlate.cpp
index a3e20cb2db..336723943c 100644
--- a/src/fix_ave_correlate.cpp
+++ b/src/fix_ave_correlate.cpp
@@ -17,9 +17,9 @@
Reese Jones (Sandia)
------------------------------------------------------------------------- */
-#include "stdlib.h"
-#include "string.h"
-#include "unistd.h"
+#include <stdlib.h>
+#include <string.h>
+#include <unistd.h>
#include "fix_ave_correlate.h"
#include "update.h"
#include "modify.h"
@@ -398,7 +398,7 @@ void FixAveCorrelate::end_of_step()
// error check if timestep was reset in an invalid manner
bigint ntimestep = update->ntimestep;
- if (ntimestep < nvalid_last || ntimestep > nvalid)
+ if (ntimestep < nvalid_last || ntimestep > nvalid)
error->all(FLERR,"Invalid timestep reset for fix ave/correlate");
if (ntimestep != nvalid) return;
nvalid_last = nvalid;
diff --git a/src/fix_ave_correlate.h b/src/fix_ave_correlate.h
index cf0bad68b7..7647492ba3 100644
--- a/src/fix_ave_correlate.h
+++ b/src/fix_ave_correlate.h
@@ -20,7 +20,7 @@ FixStyle(ave/correlate,FixAveCorrelate)
#ifndef LMP_FIX_AVE_CORRELATE_H
#define LMP_FIX_AVE_CORRELATE_H
-#include "stdio.h"
+#include <stdio.h>
#include "fix.h"
namespace LAMMPS_NS {
diff --git a/src/fix_ave_histo.cpp b/src/fix_ave_histo.cpp
index 921d6aacf8..db0eb205f4 100644
--- a/src/fix_ave_histo.cpp
+++ b/src/fix_ave_histo.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdlib.h"
-#include "string.h"
-#include "unistd.h"
+#include <stdlib.h>
+#include <string.h>
+#include <unistd.h>
#include "fix_ave_histo.h"
#include "atom.h"
#include "update.h"
@@ -597,7 +597,7 @@ void FixAveHisto::end_of_step()
// error check if timestep was reset in an invalid manner
bigint ntimestep = update->ntimestep;
- if (ntimestep < nvalid_last || ntimestep > nvalid)
+ if (ntimestep < nvalid_last || ntimestep > nvalid)
error->all(FLERR,"Invalid timestep reset for fix ave/histo");
if (ntimestep != nvalid) return;
nvalid_last = nvalid;
diff --git a/src/fix_ave_histo.h b/src/fix_ave_histo.h
index 89a214efa6..dc095cd42d 100644
--- a/src/fix_ave_histo.h
+++ b/src/fix_ave_histo.h
@@ -20,7 +20,7 @@ FixStyle(ave/histo,FixAveHisto)
#ifndef LMP_FIX_AVE_HISTO_H
#define LMP_FIX_AVE_HISTO_H
-#include "stdio.h"
+#include <stdio.h>
#include "fix.h"
namespace LAMMPS_NS {
diff --git a/src/fix_ave_histo_weight.cpp b/src/fix_ave_histo_weight.cpp
index 55a55fd5f9..47901a5164 100644
--- a/src/fix_ave_histo_weight.cpp
+++ b/src/fix_ave_histo_weight.cpp
@@ -15,9 +15,9 @@
Contributing author: Shawn Coleman (ARL)
------------------------------------------------------------------------- */
-#include "stdlib.h"
-#include "string.h"
-#include "unistd.h"
+#include <stdlib.h>
+#include <string.h>
+#include <unistd.h>
#include "fix_ave_histo_weight.h"
#include "atom.h"
#include "update.h"
@@ -61,7 +61,7 @@ FixAveHistoWeight::FixAveHistoWeight(LAMMPS *lmp, int narg, char **arg) :
int size[2];
- for (int i = 0; i < nvalues; i++) {
+ for (int i = 0; i < nvalues; i++) {
if (which[i] == X || which[i] == V || which[i] == F) {
size[i] = atom->nlocal;
} else if (which[i] == COMPUTE && kind == GLOBAL && mode == SCALAR) {
@@ -73,13 +73,13 @@ FixAveHistoWeight::FixAveHistoWeight(LAMMPS *lmp, int narg, char **arg) :
} else if (which[i] == COMPUTE && kind == PERATOM) {
size[i] = atom->nlocal;
} else if (which[i] == COMPUTE && kind == LOCAL) {
- int icompute = modify->find_compute(ids[i]);
+ int icompute = modify->find_compute(ids[i]);
size[i] = modify->compute[icompute]->size_local_rows;
} else if (which[i] == FIX && kind == GLOBAL && mode == SCALAR) {
- int ifix = modify->find_fix(ids[i]);
+ int ifix = modify->find_fix(ids[i]);
size[i] = modify->fix[ifix]->size_vector;
} else if (which[i] == FIX && kind == GLOBAL && mode == VECTOR) {
- int ifix = modify->find_fix(ids[i]);
+ int ifix = modify->find_fix(ids[i]);
size[i]= modify->fix[ifix]->size_array_rows;
} else if (which[i] == FIX && kind == PERATOM) {
size[i] = atom->nlocal;
@@ -89,9 +89,9 @@ FixAveHistoWeight::FixAveHistoWeight(LAMMPS *lmp, int narg, char **arg) :
} else if (which[i] == VARIABLE && kind == PERATOM) {
size[i] = atom->nlocal;
}
- }
-
- if (size[0] != size[1])
+ }
+
+ if (size[0] != size[1])
error->all(FLERR,"Fix ave/histo/weight value and weight vector "
"lengths do not match");
}
@@ -106,7 +106,7 @@ void FixAveHistoWeight::end_of_step()
// error check if timestep was reset in an invalid manner
bigint ntimestep = update->ntimestep;
- if (ntimestep < nvalid_last || ntimestep > nvalid)
+ if (ntimestep < nvalid_last || ntimestep > nvalid)
error->all(FLERR,"Invalid timestep reset for fix ave/histo");
if (ntimestep != nvalid) return;
nvalid_last = nvalid;
@@ -127,7 +127,7 @@ void FixAveHistoWeight::end_of_step()
modify->clearstep_compute();
// calcualte weight factors which are 2nd value (i = 1)
-
+
double weight = 0.0;
double *weights = NULL;
int stride = 0;
@@ -137,7 +137,7 @@ void FixAveHistoWeight::end_of_step()
j = argindex[i];
// atom attributes
-
+
if (which[i] == X) {
weights = &atom->x[0][j];
stride = 3;
@@ -151,7 +151,7 @@ void FixAveHistoWeight::end_of_step()
}
// invoke compute if not previously invoked
-
+
if (which[i] == COMPUTE) {
Compute *compute = modify->compute[m];
if (kind == GLOBAL && mode == SCALAR) {
@@ -194,7 +194,7 @@ void FixAveHistoWeight::end_of_step()
stride = 1;
} else if (compute->array_atom) {
weights = &compute->array_atom[0][j-1];
- stride = compute->size_peratom_cols;
+ stride = compute->size_peratom_cols;
}
} else if (kind == LOCAL) {
if (!(compute->invoked_flag & INVOKED_LOCAL)) {
@@ -213,17 +213,17 @@ void FixAveHistoWeight::end_of_step()
// access fix fields, guaranteed to be ready
} else if (which[i] == FIX) {
-
+
Fix *fix = modify->fix[m];
-
+
if (kind == GLOBAL && mode == SCALAR) {
if (j == 0) weight = fix->compute_scalar();
else weight = fix->compute_vector(j-1);
-
+
} else if (kind == GLOBAL && mode == VECTOR) {
-
+
error->all(FLERR,"Illegal fix ave/spatial command");
-
+
if (j == 0) {
int n = fix->size_vector;
for (i = 0; i < n; i++) weights[n] = fix->compute_vector(i);
@@ -231,7 +231,7 @@ void FixAveHistoWeight::end_of_step()
int n = fix->size_vector;
for (i = 0; i < n; i++) weights[n] = fix->compute_array(i,j-1);
}
-
+
} else if (kind == PERATOM) {
if (j == 0) {
weights = fix->vector_atom;
@@ -247,14 +247,14 @@ void FixAveHistoWeight::end_of_step()
} else if (fix->array_local) {
weights = &fix->array_local[0][j-1];
stride = fix->size_local_cols;
- }
+ }
}
// evaluate equal-style variable
-
+
} else if (which[i] == VARIABLE && kind == GLOBAL) {
weight = input->variable->compute_equal(m);
-
+
} else if (which[i] == VARIABLE && kind == PERATOM) {
if (atom->nlocal > maxatom) {
memory->destroy(vector);
@@ -265,10 +265,10 @@ void FixAveHistoWeight::end_of_step()
weights = vector;
stride = 1;
}
-
+
// bin values using weights, values are 1st value (i = 0)
-
- i = 0;
+
+ i = 0;
m = value2index[i];
j = argindex[i];
@@ -280,9 +280,9 @@ void FixAveHistoWeight::end_of_step()
bin_atoms_weights(&atom->v[0][j],3,weights,stride);
else if (which[i] == F && weights != NULL)
bin_atoms_weights(&atom->f[0][j],3,weights,stride);
-
+
// invoke compute if not previously invoked
-
+
if (which[i] == COMPUTE) {
Compute *compute = modify->compute[m];
if (kind == GLOBAL && mode == SCALAR) {
@@ -316,18 +316,18 @@ void FixAveHistoWeight::end_of_step()
bin_vector_weights(compute->size_array_rows,&compute->array[0][j-1],
compute->size_array_cols,weights,stride);
}
-
+
} else if (kind == PERATOM) {
if (!(compute->invoked_flag & INVOKED_PERATOM)) {
compute->compute_peratom();
compute->invoked_flag |= INVOKED_PERATOM;
}
- if (j == 0)
+ if (j == 0)
bin_atoms_weights(compute->vector_atom,1,weights, stride);
else if (compute->array_atom)
bin_atoms_weights(&compute->array_atom[0][j-1],
compute->size_peratom_cols,weights,stride);
-
+
} else if (kind == LOCAL) {
if (!(compute->invoked_flag & INVOKED_LOCAL)) {
compute->compute_local();
@@ -341,36 +341,36 @@ void FixAveHistoWeight::end_of_step()
&compute->array_local[0][j-1],
compute->size_local_cols,weights,stride);
}
-
+
// access fix fields, guaranteed to be ready
-
+
} else if (which[i] == FIX) {
-
+
Fix *fix = modify->fix[m];
-
+
if (kind == GLOBAL && mode == SCALAR) {
if (j == 0) bin_one_weights(fix->compute_scalar(),weight);
else bin_one_weights(fix->compute_vector(j-1),weight);
-
+
} else if (kind == GLOBAL && mode == VECTOR) {
if (j == 0) {
int n = fix->size_vector;
- for (i = 0; i < n; i++)
+ for (i = 0; i < n; i++)
bin_one_weights(fix->compute_vector(i),weights[i*stride]);
} else {
int n = fix->size_vector;
- for (i = 0; i < n; i++)
+ for (i = 0; i < n; i++)
bin_one_weights(fix->compute_array(i,j-1),weights[i*stride]);
}
-
+
} else if (kind == PERATOM) {
- if (j == 0)
+ if (j == 0)
bin_atoms_weights(fix->vector_atom,1,weights,stride);
else if (fix->array_atom)
bin_atoms_weights(fix->array_atom[j-1],fix->size_peratom_cols,
weights,stride);
-
-
+
+
} else if (kind == LOCAL) {
if (j == 0) bin_vector_weights(fix->size_local_rows,fix->vector_local,1,
weights,stride);
@@ -378,12 +378,12 @@ void FixAveHistoWeight::end_of_step()
bin_vector_weights(fix->size_local_rows,&fix->array_local[0][j-1],
fix->size_local_cols,weights,stride);
}
-
+
// evaluate equal-style variable
-
+
} else if (which[i] == VARIABLE && kind == GLOBAL) {
bin_one_weights(input->variable->compute_equal(m),weight);
-
+
} else if (which[i] == VARIABLE && kind == PERATOM) {
if (atom->nlocal > maxatom) {
memory->destroy(vector);
@@ -392,7 +392,7 @@ void FixAveHistoWeight::end_of_step()
}
input->variable->compute_atom(m,igroup,vector,1,0);
bin_atoms_weights(vector,1,weights,stride);
- }
+ }
// code beyond this point is identical to FixAveHisto
@@ -536,8 +536,8 @@ void FixAveHistoWeight::bin_one_weights(double value, double weight)
values and weights each have a stride
------------------------------------------------------------------------- */
-void FixAveHistoWeight::bin_vector_weights(int n, double *values,
- int stride, double *weights,
+void FixAveHistoWeight::bin_vector_weights(int n, double *values,
+ int stride, double *weights,
int stridewt)
{
int m = 0;
diff --git a/src/fix_ave_histo_weight.h b/src/fix_ave_histo_weight.h
index 99db7333d8..e29f199710 100644
--- a/src/fix_ave_histo_weight.h
+++ b/src/fix_ave_histo_weight.h
@@ -20,7 +20,7 @@ FixStyle(ave/histo/weight,FixAveHistoWeight)
#ifndef LMP_FIX_AVE_HISTO_WEIGHT_H
#define LMP_FIX_AVE_HISTO_WEIGHT_H
-#include "stdio.h"
+#include <stdio.h>
#include "fix_ave_histo.h"
namespace LAMMPS_NS {
@@ -34,7 +34,7 @@ class FixAveHistoWeight : public FixAveHisto {
private:
void bin_one_weights(double, double);
void bin_vector_weights(int, double *, int, double *, int);
- void bin_atoms_weights(double *, int, double *, int);
+ void bin_atoms_weights(double *, int, double *, int);
};
}
diff --git a/src/fix_ave_spatial.cpp b/src/fix_ave_spatial.cpp
index 62b7f057af..866b76f878 100644
--- a/src/fix_ave_spatial.cpp
+++ b/src/fix_ave_spatial.cpp
@@ -15,9 +15,9 @@
Contributing author: Pieter in 't Veld (SNL)
------------------------------------------------------------------------- */
-#include "stdlib.h"
-#include "string.h"
-#include "unistd.h"
+#include <stdlib.h>
+#include <string.h>
+#include <unistd.h>
#include "fix_ave_spatial.h"
#include "atom.h"
#include "update.h"
@@ -83,7 +83,7 @@ FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
else if (strcmp(arg[iarg+1],"center") == 0) originflag[ndim] = CENTER;
else if (strcmp(arg[iarg+1],"upper") == 0) originflag[ndim] = UPPER;
else originflag[ndim] = COORD;
- if (originflag[ndim] == COORD)
+ if (originflag[ndim] == COORD)
origin[ndim] = force->numeric(FLERR,arg[iarg+1]);
delta[ndim] = force->numeric(FLERR,arg[iarg+2]);
@@ -208,11 +208,11 @@ FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
else error->all(FLERR,"Illegal fix ave/spatial command");
if (strcmp(arg[iarg+2],"lower") == 0) minflag[idim] = LOWER;
else minflag[idim] = COORD;
- if (minflag[idim] == COORD)
+ if (minflag[idim] == COORD)
minvalue[idim] = force->numeric(FLERR,arg[iarg+2]);
if (strcmp(arg[iarg+3],"upper") == 0) maxflag[idim] = UPPER;
else maxflag[idim] = COORD;
- if (maxflag[idim] == COORD)
+ if (maxflag[idim] == COORD)
maxvalue[idim] = force->numeric(FLERR,arg[iarg+3]);
else error->all(FLERR,"Illegal fix ave/spatial command");
iarg += 4;
@@ -552,7 +552,7 @@ void FixAveSpatial::end_of_step()
// error check if timestep was reset in an invalid manner
bigint ntimestep = update->ntimestep;
- if (ntimestep < nvalid_last || ntimestep > nvalid)
+ if (ntimestep < nvalid_last || ntimestep > nvalid)
error->all(FLERR,"Invalid timestep reset for fix ave/spatial");
if (ntimestep != nvalid) return;
nvalid_last = nvalid;
@@ -619,7 +619,7 @@ void FixAveSpatial::end_of_step()
values_one[bin[i]][m] += attribute[i][j];
} else {
for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]) &&
+ if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]) &&
bin[i] >= 0)
values_one[bin[i]][m] += attribute[i][j];
}
@@ -634,7 +634,7 @@ void FixAveSpatial::end_of_step()
values_one[bin[i]][m] += 1.0;
} else {
for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]) &&
+ if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]) &&
bin[i] >= 0)
values_one[bin[i]][m] += 1.0;
}
@@ -654,7 +654,7 @@ void FixAveSpatial::end_of_step()
}
} else {
for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]) &&
+ if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]) &&
bin[i] >= 0) {
if (rmass) values_one[bin[i]][m] += rmass[i];
else values_one[bin[i]][m] += mass[type[i]];
@@ -682,7 +682,7 @@ void FixAveSpatial::end_of_step()
}
} else {
for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]) &&
+ if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]) &&
bin[i] >= 0) {
if (j == 0) values_one[bin[i]][m] += vector[i];
else values_one[bin[i]][m] += array[i][jm1];
@@ -705,7 +705,7 @@ void FixAveSpatial::end_of_step()
}
} else {
for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]) &&
+ if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]) &&
bin[i] >= 0) {
if (j == 0) values_one[bin[i]][m] += vector[i];
else values_one[bin[i]][m] += array[i][jm1];
@@ -730,7 +730,7 @@ void FixAveSpatial::end_of_step()
values_one[bin[i]][m] += varatom[i];
} else {
for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]) &&
+ if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]) &&
bin[i] >= 0)
values_one[bin[i]][m] += varatom[i];
}
diff --git a/src/fix_ave_spatial.h b/src/fix_ave_spatial.h
index 7d6a9f031a..1df4c363b2 100644
--- a/src/fix_ave_spatial.h
+++ b/src/fix_ave_spatial.h
@@ -20,7 +20,7 @@ FixStyle(ave/spatial,FixAveSpatial)
#ifndef LMP_FIX_AVE_SPATIAL_H
#define LMP_FIX_AVE_SPATIAL_H
-#include "stdio.h"
+#include <stdio.h>
#include "fix.h"
namespace LAMMPS_NS {
diff --git a/src/fix_ave_time.cpp b/src/fix_ave_time.cpp
index d502f6a963..2db0fbec64 100644
--- a/src/fix_ave_time.cpp
+++ b/src/fix_ave_time.cpp
@@ -15,9 +15,9 @@
Contributing author: Pieter in 't Veld (SNL)
------------------------------------------------------------------------- */
-#include "stdlib.h"
-#include "string.h"
-#include "unistd.h"
+#include <stdlib.h>
+#include <string.h>
+#include <unistd.h>
#include "fix_ave_time.h"
#include "update.h"
#include "force.h"
@@ -192,7 +192,7 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
modify->compute[icompute]->size_vector_variable == 0)
error->all(FLERR,
"Fix ave/time compute vector is accessed out-of-range");
- if (argindex[i] && modify->compute[icompute]->size_vector_variable)
+ if (argindex[i] && modify->compute[icompute]->size_vector_variable)
varlen[i] = 1;
} else if (which[i] == COMPUTE && mode == VECTOR) {
@@ -235,7 +235,7 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,"Fix ave/time fix does not calculate a vector");
if (argindex[i] && modify->fix[ifix]->array_flag == 0)
error->all(FLERR,"Fix ave/time fix does not calculate an array");
- if (argindex[i] && modify->fix[ifix]->size_array_rows_variable)
+ if (argindex[i] && modify->fix[ifix]->size_array_rows_variable)
error->all(FLERR,"Fix ave/time fix array cannot be variable length");
if (argindex[i] && argindex[i] > modify->fix[ifix]->size_array_cols)
error->all(FLERR,"Fix ave/time fix array is accessed out-of-range");
@@ -274,12 +274,12 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
else nrows = 1;
memory->create(column,nrows,"ave/time:column");
}
-
+
// enable locking of row count by this fix for computes of variable length
// only if nrepeat > 1 or ave = RUNNING/WINDOW,
- // so that locking spans multiple timesteps
+ // so that locking spans multiple timesteps
- if (any_variable_length &&
+ if (any_variable_length &&
(nrepeat > 1 || ave == RUNNING || ave == WINDOW)) {
for (int i = 0; i < nvalues; i++)
if (varlen[i]) {
@@ -288,7 +288,7 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
}
lockforever = 0;
}
-
+
// print file comment lines
// for mode = VECTOR, cannot use arg to print
// since array args may have been expanded to multiple vectors
@@ -461,13 +461,13 @@ FixAveTime::~FixAveTime()
{
// decrement lock counter in compute chunk/atom, it if still exists
- if (any_variable_length &&
+ if (any_variable_length &&
(nrepeat > 1 || ave == RUNNING || ave == WINDOW)) {
for (int i = 0; i < nvalues; i++)
if (varlen[i]) {
int icompute = modify->find_compute(ids[i]);
if (icompute >= 0) {
- if (ave == RUNNING || ave == WINDOW)
+ if (ave == RUNNING || ave == WINDOW)
modify->compute[icompute]->unlock(this);
modify->compute[icompute]->lock_disable();
}
@@ -559,7 +559,7 @@ void FixAveTime::end_of_step()
// error check if timestep was reset in an invalid manner
bigint ntimestep = update->ntimestep;
- if (ntimestep < nvalid_last || ntimestep > nvalid)
+ if (ntimestep < nvalid_last || ntimestep > nvalid)
error->all(FLERR,"Invalid timestep reset for fix ave/time");
if (ntimestep != nvalid) return;
nvalid_last = nvalid;
@@ -729,8 +729,8 @@ void FixAveTime::invoke_vector(bigint ntimestep)
// if ave = RUNNING/WINDOW and not yet locked:
// set forever, will be unlocked in fix destructor
// wrap setup_chunks in clearstep/addstep b/c it may invoke computes
- // both nevery and nfreq are future steps,
- // since call below to cchunk->ichunk()
+ // both nevery and nfreq are future steps,
+ // since call below to cchunk->ichunk()
// does not re-invoke internal cchunk compute on this same step
if (irepeat == 0) {
@@ -786,7 +786,7 @@ void FixAveTime::invoke_vector(bigint ntimestep)
compute->invoked_flag |= INVOKED_VECTOR;
}
double *cvector = compute->vector;
- for (i = 0; i < nrows; i++)
+ for (i = 0; i < nrows; i++)
column[i] = cvector[i];
} else {
@@ -928,7 +928,7 @@ int FixAveTime::column_length(int dynamic)
if (varlen[i]) continue;
if (which[i] == COMPUTE) {
int icompute = modify->find_compute(ids[i]);
- if (argindex[i] == 0)
+ if (argindex[i] == 0)
lengthone = modify->compute[icompute]->size_vector;
else lengthone = modify->compute[icompute]->size_array_rows;
} else if (which[i] == FIX) {
@@ -960,7 +960,7 @@ int FixAveTime::column_length(int dynamic)
else if (lengthone != length)
error->all(FLERR,"Fix ave/time columns are inconsistent lengths");
} else {
- if (lengthone != nrows)
+ if (lengthone != nrows)
error->all(FLERR,"Fix ave/time columns are inconsistent lengths");
}
}
diff --git a/src/fix_ave_time.h b/src/fix_ave_time.h
index 98e9ad5e47..8671e28219 100644
--- a/src/fix_ave_time.h
+++ b/src/fix_ave_time.h
@@ -20,7 +20,7 @@ FixStyle(ave/time,FixAveTime)
#ifndef LMP_FIX_AVE_TIME_H
#define LMP_FIX_AVE_TIME_H
-#include "stdio.h"
+#include <stdio.h>
#include "fix.h"
namespace LAMMPS_NS {
diff --git a/src/fix_aveforce.cpp b/src/fix_aveforce.cpp
index 9b9380130e..443ae6ea57 100644
--- a/src/fix_aveforce.cpp
+++ b/src/fix_aveforce.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "string.h"
-#include "stdlib.h"
+#include <mpi.h>
+#include <string.h>
+#include <stdlib.h>
#include "fix_aveforce.h"
#include "atom.h"
#include "update.h"
diff --git a/src/fix_balance.cpp b/src/fix_balance.cpp
index 5eb4fde54b..b27fc13632 100644
--- a/src/fix_balance.cpp
+++ b/src/fix_balance.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
-#include "stdlib.h"
+#include <string.h>
+#include <stdlib.h>
#include "fix_balance.h"
#include "balance.h"
#include "update.h"
@@ -103,7 +103,7 @@ FixBalance::FixBalance(LAMMPS *lmp, int narg, char **arg) :
}
}
- if (lbstyle == BISECTION && comm->style == 0)
+ if (lbstyle == BISECTION && comm->style == 0)
error->all(FLERR,"Fix balance rcb cannot be used with comm_style brick");
// create instance of Balance class
diff --git a/src/fix_balance.h b/src/fix_balance.h
index 9ea1fe45ba..3b4299a39e 100644
--- a/src/fix_balance.h
+++ b/src/fix_balance.h
@@ -20,7 +20,7 @@ FixStyle(balance,FixBalance)
#ifndef LMP_FIX_BALANCE_H
#define LMP_FIX_BALANCE_H
-#include "stdio.h"
+#include <stdio.h>
#include "fix.h"
namespace LAMMPS_NS {
diff --git a/src/fix_box_relax.cpp b/src/fix_box_relax.cpp
index 0842ea01de..8dd0b3344d 100644
--- a/src/fix_box_relax.cpp
+++ b/src/fix_box_relax.cpp
@@ -15,9 +15,9 @@
Contributing author: Aidan Thompson (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "string.h"
-#include "stdlib.h"
+#include <math.h>
+#include <string.h>
+#include <stdlib.h>
#include "fix_box_relax.h"
#include "atom.h"
#include "domain.h"
diff --git a/src/fix_deform.cpp b/src/fix_deform.cpp
index 3d350c569a..7003b4d396 100644
--- a/src/fix_deform.cpp
+++ b/src/fix_deform.cpp
@@ -15,9 +15,9 @@
Contributing author: Pieter in 't Veld (SNL)
------------------------------------------------------------------------- */
-#include "string.h"
-#include "stdlib.h"
-#include "math.h"
+#include <string.h>
+#include <stdlib.h>
+#include <math.h>
#include "fix_deform.h"
#include "atom.h"
#include "update.h"
diff --git a/src/fix_drag.cpp b/src/fix_drag.cpp
index 1771be42c8..6a28e89806 100644
--- a/src/fix_drag.cpp
+++ b/src/fix_drag.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "fix_drag.h"
#include "atom.h"
#include "update.h"
diff --git a/src/fix_dt_reset.cpp b/src/fix_dt_reset.cpp
index 5e0338ed0e..0a8ecd7626 100644
--- a/src/fix_dt_reset.cpp
+++ b/src/fix_dt_reset.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "fix_dt_reset.h"
#include "atom.h"
#include "update.h"
diff --git a/src/fix_enforce2d.cpp b/src/fix_enforce2d.cpp
index ed169d36e5..66c9c4c292 100644
--- a/src/fix_enforce2d.cpp
+++ b/src/fix_enforce2d.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "fix_enforce2d.h"
#include "atom.h"
#include "update.h"
diff --git a/src/fix_external.cpp b/src/fix_external.cpp
index a09dd62ffd..16494662f7 100644
--- a/src/fix_external.cpp
+++ b/src/fix_external.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdio.h"
-#include "string.h"
-#include "stdlib.h"
+#include <stdio.h>
+#include <string.h>
+#include <stdlib.h>
#include "fix_external.h"
#include "atom.h"
#include "update.h"
@@ -42,7 +42,7 @@ FixExternal::FixExternal(LAMMPS *lmp, int narg, char **arg) :
mode = PF_CALLBACK;
ncall = force->inumeric(FLERR,arg[4]);
napply = force->inumeric(FLERR,arg[5]);
- if (ncall <= 0 || napply <= 0)
+ if (ncall <= 0 || napply <= 0)
error->all(FLERR,"Illegal fix external command");
} else if (strcmp(arg[3],"pf/array") == 0) {
if (narg != 5) error->all(FLERR,"Illegal fix external command");
diff --git a/src/fix_gravity.cpp b/src/fix_gravity.cpp
index 2e9d6e40f4..a08213e3d0 100644
--- a/src/fix_gravity.cpp
+++ b/src/fix_gravity.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "fix_gravity.h"
#include "atom.h"
#include "update.h"
diff --git a/src/fix_group.cpp b/src/fix_group.cpp
index 690d42c150..ac4a84d63f 100644
--- a/src/fix_group.cpp
+++ b/src/fix_group.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "fix_group.h"
#include "group.h"
#include "update.h"
@@ -50,7 +50,7 @@ FixGroup::FixGroup(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
varflag = 0;
idvar = NULL;
nevery = 1;
-
+
int iarg = 3;
while (iarg < narg) {
if (strcmp(arg[iarg],"region") == 0) {
@@ -145,7 +145,7 @@ void FixGroup::init()
}
}
- if (warn && comm->me == 0)
+ if (warn && comm->me == 0)
error->warning(FLERR,"One or more dynamic groups may not be "
"updated at correct point in timestep");
}
@@ -184,7 +184,7 @@ void FixGroup::set_group()
input->variable->compute_atom(ivar,igroup,var,1,0);
modify->addstep_compute(update->ntimestep + nevery);
}
-
+
// update region in case it has a variable dependence or is dynamic
if (regionflag) region->prematch();
diff --git a/src/fix_heat.cpp b/src/fix_heat.cpp
index de23927fe9..65dc960f42 100644
--- a/src/fix_heat.cpp
+++ b/src/fix_heat.cpp
@@ -15,9 +15,9 @@
Contributing author: Paul Crozier (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "fix_heat.h"
#include "atom.h"
#include "domain.h"
@@ -121,7 +121,7 @@ void FixHeat::init()
if (hstr) {
hvar = input->variable->find(hstr);
- if (hvar < 0)
+ if (hvar < 0)
error->all(FLERR,"Variable name for fix heat does not exist");
if (input->variable->equalstyle(hvar)) hstyle = EQUAL;
else if (input->variable->atomstyle(hvar)) hstyle = ATOM;
@@ -196,7 +196,7 @@ void FixHeat::end_of_step()
if (hstyle != ATOM) {
heat = heat_input*nevery*update->dt*force->ftm2v;
- double escale =
+ double escale =
(ke + heat - 0.5*vcmsq*masstotal)/(ke - 0.5*vcmsq*masstotal);
if (escale < 0.0) error->all(FLERR,"Fix heat kinetic energy went negative");
scale = sqrt(escale);
@@ -231,9 +231,9 @@ void FixHeat::end_of_step()
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
heat = vheat[i]*nevery*update->dt*force->ftm2v;
- vscale[i] =
+ vscale[i] =
(ke + heat - 0.5*vcmsq*masstotal)/(ke - 0.5*vcmsq*masstotal);
- if (vscale[i] < 0.0)
+ if (vscale[i] < 0.0)
error->all(FLERR,
"Fix heat kinetic energy of an atom went negative");
scale = sqrt(vscale[i]);
@@ -261,9 +261,9 @@ void FixHeat::end_of_step()
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
heat = vheat[i]*nevery*update->dt*force->ftm2v;
- vscale[i] =
+ vscale[i] =
(ke + heat - 0.5*vcmsq*masstotal)/(ke - 0.5*vcmsq*masstotal);
- if (vscale[i] < 0.0)
+ if (vscale[i] < 0.0)
error->all(FLERR,
"Fix heat kinetic energy of an atom went negative");
scale = sqrt(vscale[i]);
@@ -295,7 +295,7 @@ void FixHeat::end_of_step()
double FixHeat::compute_scalar()
{
double average_scale = scale;
- if (hstyle == ATOM) {
+ if (hstyle == ATOM) {
double scale_sum = 0.0;
int ncount = 0;
int *mask = atom->mask;
diff --git a/src/fix_indent.cpp b/src/fix_indent.cpp
index 9e214de763..4b85dd2788 100644
--- a/src/fix_indent.cpp
+++ b/src/fix_indent.cpp
@@ -15,9 +15,9 @@
Contributing author: Ravi Agrawal (Northwestern U)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "string.h"
-#include "stdlib.h"
+#include <math.h>
+#include <string.h>
+#include <stdlib.h>
#include "fix_indent.h"
#include "atom.h"
#include "input.h"
diff --git a/src/fix_langevin.cpp b/src/fix_langevin.cpp
index e8f3290be9..c71ffbc3fd 100644
--- a/src/fix_langevin.cpp
+++ b/src/fix_langevin.cpp
@@ -16,10 +16,10 @@
Aidan Thompson (SNL) GJF formulation
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "math.h"
-#include "string.h"
-#include "stdlib.h"
+#include <mpi.h>
+#include <math.h>
+#include <string.h>
+#include <stdlib.h>
#include "fix_langevin.h"
#include "math_extra.h"
#include "atom.h"
@@ -300,7 +300,7 @@ void FixLangevin::post_force(int vflag)
double *rmass = atom->rmass;
// enumerate all 2^6 possibilities for template parameters
- // this avoids testing them inside inner loop:
+ // this avoids testing them inside inner loop:
// TSTYLEATOM, GJF, TALLY, BIAS, RMASS, ZERO
#ifdef TEMPLATED_FIX_LANGEVIN
@@ -431,7 +431,7 @@ void FixLangevin::post_force(int vflag)
if (zeroflag) post_force_templated<0,0,0,0,0,1>();
else post_force_templated<0,0,0,0,0,0>();
#else
- post_force_untemplated(int(tstyle==ATOM), gjfflag, tallyflag,
+ post_force_untemplated(int(tstyle==ATOM), gjfflag, tallyflag,
int(tbiasflag==BIAS), int(rmass!=NULL), zeroflag);
#endif
}
@@ -448,12 +448,12 @@ void FixLangevin::post_force_respa(int vflag, int ilevel, int iloop)
------------------------------------------------------------------------- */
#ifdef TEMPLATED_FIX_LANGEVIN
-template < int Tp_TSTYLEATOM, int Tp_GJF, int Tp_TALLY,
+template < int Tp_TSTYLEATOM, int Tp_GJF, int Tp_TALLY,
int Tp_BIAS, int Tp_RMASS, int Tp_ZERO >
void FixLangevin::post_force_templated()
#else
void FixLangevin::post_force_untemplated
- (int Tp_TSTYLEATOM, int Tp_GJF, int Tp_TALLY,
+ (int Tp_TSTYLEATOM, int Tp_GJF, int Tp_TALLY,
int Tp_BIAS, int Tp_RMASS, int Tp_ZERO)
#endif
{
@@ -681,7 +681,7 @@ void FixLangevin::omega_thermostat()
double tendivthree = 10.0/3.0;
double tran[3];
double inertiaone;
-
+
for (int i = 0; i < nlocal; i++) {
if ((mask[i] & groupbit) && (radius[i] > 0.0)) {
inertiaone = SINERTIA*radius[i]*radius[i]*rmass[i];
@@ -880,7 +880,7 @@ double FixLangevin::memory_usage()
}
/* ----------------------------------------------------------------------
- allocate atom-based array for franprev
+ allocate atom-based array for franprev
------------------------------------------------------------------------- */
void FixLangevin::grow_arrays(int nmax)
diff --git a/src/fix_langevin.h b/src/fix_langevin.h
index b736000107..1e084c9e98 100644
--- a/src/fix_langevin.h
+++ b/src/fix_langevin.h
@@ -74,11 +74,11 @@ class FixLangevin : public Fix {
// comment next line to turn off templating
#define TEMPLATED_FIX_LANGEVIN
#ifdef TEMPLATED_FIX_LANGEVIN
- template < int Tp_TSTYLEATOM, int Tp_GJF, int Tp_TALLY,
- int Tp_BIAS, int Tp_RMASS, int Tp_ZERO >
+ template < int Tp_TSTYLEATOM, int Tp_GJF, int Tp_TALLY,
+ int Tp_BIAS, int Tp_RMASS, int Tp_ZERO >
void post_force_templated();
#else
- void post_force_untemplated(int, int, int,
+ void post_force_untemplated(int, int, int,
int, int, int);
#endif
void omega_thermostat();
diff --git a/src/fix_lineforce.cpp b/src/fix_lineforce.cpp
index 7128d24572..f82ed957f7 100644
--- a/src/fix_lineforce.cpp
+++ b/src/fix_lineforce.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "string.h"
-#include "stdlib.h"
+#include <math.h>
+#include <string.h>
+#include <stdlib.h>
#include "fix_lineforce.h"
#include "atom.h"
#include "update.h"
diff --git a/src/fix_minimize.cpp b/src/fix_minimize.cpp
index 3b63cc948a..1cd8456f57 100644
--- a/src/fix_minimize.cpp
+++ b/src/fix_minimize.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdlib.h"
+#include <stdlib.h>
#include "fix_minimize.h"
#include "atom.h"
#include "domain.h"
diff --git a/src/fix_momentum.cpp b/src/fix_momentum.cpp
index abdeca2495..b8ca3c2c01 100644
--- a/src/fix_momentum.cpp
+++ b/src/fix_momentum.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdlib.h"
-#include "string.h"
+#include <stdlib.h>
+#include <string.h>
#include "fix_momentum.h"
#include "atom.h"
#include "domain.h"
@@ -61,7 +61,7 @@ FixMomentum::FixMomentum(LAMMPS *lmp, int narg, char **arg) :
if (linear)
if (xflag < 0 || xflag > 1 || yflag < 0 || yflag > 1 ||
- zflag < 0 || zflag > 1)
+ zflag < 0 || zflag > 1)
error->all(FLERR,"Illegal fix momentum command");
// cannot have 0 atoms in group
diff --git a/src/fix_move.cpp b/src/fix_move.cpp
index c2e7131395..e1f522177b 100644
--- a/src/fix_move.cpp
+++ b/src/fix_move.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
-#include "stdlib.h"
-#include "math.h"
+#include <string.h>
+#include <stdlib.h>
+#include <math.h>
#include "fix_move.h"
#include "atom.h"
#include "group.h"
diff --git a/src/fix_move.h b/src/fix_move.h
index 9a40a9a52f..bcd8775708 100644
--- a/src/fix_move.h
+++ b/src/fix_move.h
@@ -20,7 +20,7 @@ FixStyle(move,FixMove)
#ifndef LMP_FIX_MOVE_H
#define LMP_FIX_MOVE_H
-#include "stdio.h"
+#include <stdio.h>
#include "fix.h"
namespace LAMMPS_NS {
diff --git a/src/fix_nh.cpp b/src/fix_nh.cpp
index 92da3e33cd..ec18dffb91 100644
--- a/src/fix_nh.cpp
+++ b/src/fix_nh.cpp
@@ -15,9 +15,9 @@
Contributing authors: Mark Stevens (SNL), Aidan Thompson (SNL)
------------------------------------------------------------------------- */
-#include "string.h"
-#include "stdlib.h"
-#include "math.h"
+#include <string.h>
+#include <stdlib.h>
+#include <math.h>
#include "fix_nh.h"
#include "math_extra.h"
#include "atom.h"
@@ -131,7 +131,7 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
pcouple = XYZ;
p_start[0] = p_start[1] = p_start[2] = force->numeric(FLERR,arg[iarg+1]);
p_stop[0] = p_stop[1] = p_stop[2] = force->numeric(FLERR,arg[iarg+2]);
- p_period[0] = p_period[1] = p_period[2] =
+ p_period[0] = p_period[1] = p_period[2] =
force->numeric(FLERR,arg[iarg+3]);
p_flag[0] = p_flag[1] = p_flag[2] = 1;
if (dimension == 2) {
@@ -144,7 +144,7 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
pcouple = NONE;
p_start[0] = p_start[1] = p_start[2] = force->numeric(FLERR,arg[iarg+1]);
p_stop[0] = p_stop[1] = p_stop[2] = force->numeric(FLERR,arg[iarg+2]);
- p_period[0] = p_period[1] = p_period[2] =
+ p_period[0] = p_period[1] = p_period[2] =
force->numeric(FLERR,arg[iarg+3]);
p_flag[0] = p_flag[1] = p_flag[2] = 1;
if (dimension == 2) {
@@ -158,12 +158,12 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
scalexy = scalexz = scaleyz = 0;
p_start[0] = p_start[1] = p_start[2] = force->numeric(FLERR,arg[iarg+1]);
p_stop[0] = p_stop[1] = p_stop[2] = force->numeric(FLERR,arg[iarg+2]);
- p_period[0] = p_period[1] = p_period[2] =
+ p_period[0] = p_period[1] = p_period[2] =
force->numeric(FLERR,arg[iarg+3]);
p_flag[0] = p_flag[1] = p_flag[2] = 1;
p_start[3] = p_start[4] = p_start[5] = 0.0;
p_stop[3] = p_stop[4] = p_stop[5] = 0.0;
- p_period[3] = p_period[4] = p_period[5] =
+ p_period[3] = p_period[4] = p_period[5] =
force->numeric(FLERR,arg[iarg+3]);
p_flag[3] = p_flag[4] = p_flag[5] = 1;
if (dimension == 2) {
@@ -844,11 +844,11 @@ void FixNH::final_integrate()
// re-compute temp before nh_v_press()
// only needed for temperature computes with BIAS on reneighboring steps:
- // b/c some biases store per-atom values (e.g. temp/profile)
+ // b/c some biases store per-atom values (e.g. temp/profile)
// per-atom values are invalid if reneigh/comm occurred
// since temp->compute() in initial_integrate()
- if (which == BIAS && neighbor->ago == 0)
+ if (which == BIAS && neighbor->ago == 0)
t_current = temperature->compute_scalar();
if (pstat_flag) nh_v_press();
diff --git a/src/fix_nh_sphere.cpp b/src/fix_nh_sphere.cpp
index c6a09f2954..9db1e34e39 100644
--- a/src/fix_nh_sphere.cpp
+++ b/src/fix_nh_sphere.cpp
@@ -15,7 +15,7 @@
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "fix_nh_sphere.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/fix_nph.cpp b/src/fix_nph.cpp
index 419a6980a0..6f3678ed3a 100644
--- a/src/fix_nph.cpp
+++ b/src/fix_nph.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "fix_nph.h"
#include "modify.h"
#include "error.h"
diff --git a/src/fix_nph_sphere.cpp b/src/fix_nph_sphere.cpp
index 2c87e6b34f..93d9bf8af2 100644
--- a/src/fix_nph_sphere.cpp
+++ b/src/fix_nph_sphere.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "fix_nph_sphere.h"
#include "modify.h"
#include "error.h"
diff --git a/src/fix_npt.cpp b/src/fix_npt.cpp
index cf83ded491..0326c06c77 100644
--- a/src/fix_npt.cpp
+++ b/src/fix_npt.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "fix_npt.h"
#include "modify.h"
#include "error.h"
diff --git a/src/fix_npt_sphere.cpp b/src/fix_npt_sphere.cpp
index 81c0e3c799..6e7c074d5e 100644
--- a/src/fix_npt_sphere.cpp
+++ b/src/fix_npt_sphere.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "fix_npt_sphere.h"
#include "modify.h"
#include "error.h"
diff --git a/src/fix_nve.cpp b/src/fix_nve.cpp
index 8914a18f4c..64ec3373f1 100644
--- a/src/fix_nve.cpp
+++ b/src/fix_nve.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdio.h"
-#include "string.h"
+#include <stdio.h>
+#include <string.h>
#include "fix_nve.h"
#include "atom.h"
#include "force.h"
diff --git a/src/fix_nve_limit.cpp b/src/fix_nve_limit.cpp
index 42ea5a676f..966fcfbb09 100644
--- a/src/fix_nve_limit.cpp
+++ b/src/fix_nve_limit.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "fix_nve_limit.h"
#include "atom.h"
#include "force.h"
diff --git a/src/fix_nve_noforce.cpp b/src/fix_nve_noforce.cpp
index e373e00b19..aa24c26e03 100644
--- a/src/fix_nve_noforce.cpp
+++ b/src/fix_nve_noforce.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdio.h"
-#include "string.h"
+#include <stdio.h>
+#include <string.h>
#include "fix_nve_noforce.h"
#include "atom.h"
#include "update.h"
diff --git a/src/fix_nve_sphere.cpp b/src/fix_nve_sphere.cpp
index 0ad787a27f..c72797b8ce 100644
--- a/src/fix_nve_sphere.cpp
+++ b/src/fix_nve_sphere.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <string.h>
#include "fix_nve_sphere.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/fix_nvt.cpp b/src/fix_nvt.cpp
index 839b7ce0a3..a86f46c3b5 100644
--- a/src/fix_nvt.cpp
+++ b/src/fix_nvt.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "fix_nvt.h"
#include "group.h"
#include "modify.h"
diff --git a/src/fix_nvt_sllod.cpp b/src/fix_nvt_sllod.cpp
index 460ba7a393..8257afae05 100644
--- a/src/fix_nvt_sllod.cpp
+++ b/src/fix_nvt_sllod.cpp
@@ -15,8 +15,8 @@
Contributing author: Pieter in 't Veld (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "string.h"
+#include <math.h>
+#include <string.h>
#include "fix_nvt_sllod.h"
#include "math_extra.h"
#include "atom.h"
diff --git a/src/fix_nvt_sphere.cpp b/src/fix_nvt_sphere.cpp
index 58dbbb782c..c886935f12 100644
--- a/src/fix_nvt_sphere.cpp
+++ b/src/fix_nvt_sphere.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "fix_nvt_sphere.h"
#include "group.h"
#include "modify.h"
diff --git a/src/fix_planeforce.cpp b/src/fix_planeforce.cpp
index 217aec9c36..872bd98716 100644
--- a/src/fix_planeforce.cpp
+++ b/src/fix_planeforce.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "string.h"
-#include "stdlib.h"
+#include <math.h>
+#include <string.h>
+#include <stdlib.h>
#include "fix_planeforce.h"
#include "atom.h"
#include "update.h"
diff --git a/src/fix_press_berendsen.cpp b/src/fix_press_berendsen.cpp
index 25e0f9a44c..58dd0dae92 100644
--- a/src/fix_press_berendsen.cpp
+++ b/src/fix_press_berendsen.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
-#include "stdlib.h"
-#include "math.h"
+#include <string.h>
+#include <stdlib.h>
+#include <math.h>
#include "fix_press_berendsen.h"
#include "atom.h"
#include "force.h"
diff --git a/src/fix_print.cpp b/src/fix_print.cpp
index f93356c043..3c54772a73 100644
--- a/src/fix_print.cpp
+++ b/src/fix_print.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdlib.h"
-#include "string.h"
+#include <stdlib.h>
+#include <string.h>
#include "fix_print.h"
#include "update.h"
#include "input.h"
diff --git a/src/fix_print.h b/src/fix_print.h
index b6eb05dc43..c3897b815f 100644
--- a/src/fix_print.h
+++ b/src/fix_print.h
@@ -20,7 +20,7 @@ FixStyle(print,FixPrint)
#ifndef LMP_FIX_PRINT_H
#define LMP_FIX_PRINT_H
-#include "stdio.h"
+#include <stdio.h>
#include "fix.h"
namespace LAMMPS_NS {
diff --git a/src/fix_property_atom.cpp b/src/fix_property_atom.cpp
index 05e9c11dde..10f73aa53b 100644
--- a/src/fix_property_atom.cpp
+++ b/src/fix_property_atom.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdlib.h"
-#include "string.h"
+#include <stdlib.h>
+#include <string.h>
#include "fix_property_atom.h"
#include "atom.h"
#include "comm.h"
@@ -50,7 +50,7 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) :
if (atom->molecule_flag)
error->all(FLERR,"Fix property/atom mol when atom_style "
"already has molecule attribute");
- if (molecule_flag)
+ if (molecule_flag)
error->all(FLERR,"Fix property/atom cannot specify mol twice");
style[nvalue] = MOLECULE;
atom->molecule_flag = molecule_flag = 1;
@@ -59,7 +59,7 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) :
if (atom->q_flag)
error->all(FLERR,"Fix property/atom q when atom_style "
"already has charge attribute");
- if (q_flag)
+ if (q_flag)
error->all(FLERR,"Fix property/atom cannot specify q twice");
style[nvalue] = CHARGE;
atom->q_flag = q_flag = 1;
@@ -68,7 +68,7 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) :
style[nvalue] = INTEGER;
int tmp;
index[nvalue] = atom->find_custom(&arg[iarg][2],tmp);
- if (index[nvalue] >= 0)
+ if (index[nvalue] >= 0)
error->all(FLERR,"Fix property/atom vector name already exists");
index[nvalue] = atom->add_custom(&arg[iarg][2],0);
nvalue++;
@@ -76,7 +76,7 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) :
style[nvalue] = DOUBLE;
int tmp;
index[nvalue] = atom->find_custom(&arg[iarg][2],tmp);
- if (index[nvalue] >= 0)
+ if (index[nvalue] >= 0)
error->all(FLERR,"Fix property/atom vector name already exists");
index[nvalue] = atom->add_custom(&arg[iarg][2],1);
nvalue++;
@@ -106,7 +106,7 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) :
int flag = 0;
for (int i = 0; i < nvalue; i++)
if (style[i] == MOLECULE || style[i] == CHARGE) flag = 1;
- if (flag && comm->me == 0)
+ if (flag && comm->me == 0)
error->warning(FLERR,"Fix property/atom mol or charge w/out "
"ghost communication");
}
@@ -240,7 +240,7 @@ void FixPropertyAtom::read_data_section(char *keyword, int n, char *buf,
else if (style[j] == CHARGE) atom->q[m] = atof(values[j+1]);
else if (style[j] == INTEGER)
atom->ivector[index[j]][m] = atoi(values[j+1]);
- else if (style[j] == DOUBLE)
+ else if (style[j] == DOUBLE)
atom->dvector[index[j]][m] = atof(values[j+1]);
}
}
@@ -333,7 +333,7 @@ void FixPropertyAtom::write_data_section_keyword(int mth, FILE *fp)
only called by proc 0
------------------------------------------------------------------------- */
-void FixPropertyAtom::write_data_section(int mth, FILE *fp,
+void FixPropertyAtom::write_data_section(int mth, FILE *fp,
int n, double **buf, int index)
{
int m;
@@ -370,7 +370,7 @@ double FixPropertyAtom::memory_usage()
/* ----------------------------------------------------------------------
allocate atom-based arrays
initialize new values to 0,
- since AtomVec class won't do it as atoms are added,
+ since AtomVec class won't do it as atoms are added,
e.g. in create_atom() or data_atom()
------------------------------------------------------------------------- */
@@ -515,11 +515,11 @@ int FixPropertyAtom::pack_exchange(int i, double *buf)
int FixPropertyAtom::unpack_exchange(int nlocal, double *buf)
{
for (int m = 0; m < nvalue; m++) {
- if (style[m] == MOLECULE)
+ if (style[m] == MOLECULE)
atom->molecule[nlocal] = (tagint) ubuf(buf[m]).i;
else if (style[m] == CHARGE)
atom->q[nlocal] = buf[m];
- else if (style[m] == INTEGER)
+ else if (style[m] == INTEGER)
atom->ivector[index[m]][nlocal] = (int) ubuf(buf[m]).i;
else if (style[m] == DOUBLE)
atom->dvector[index[m]][nlocal] = buf[m];
@@ -561,11 +561,11 @@ void FixPropertyAtom::unpack_restart(int nlocal, int nth)
m++;
for (int i = 0; i < nvalue; i++) {
- if (style[i] == MOLECULE)
+ if (style[i] == MOLECULE)
atom->molecule[nlocal] = (tagint) ubuf(extra[nlocal][m++]).i;
else if (style[i] == CHARGE)
atom->q[nlocal] = extra[nlocal][m++];
- else if (style[i] == INTEGER)
+ else if (style[i] == INTEGER)
atom->ivector[index[i]][nlocal] = (int) ubuf(extra[nlocal][m++]).i;
else if (style[i] == DOUBLE)
atom->dvector[index[i]][nlocal] = extra[nlocal][m++];
diff --git a/src/fix_read_restart.cpp b/src/fix_read_restart.cpp
index a1d1b7c655..3d49db7196 100644
--- a/src/fix_read_restart.cpp
+++ b/src/fix_read_restart.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdlib.h"
+#include <stdlib.h>
#include "fix_read_restart.h"
#include "atom.h"
#include "memory.h"
diff --git a/src/fix_recenter.cpp b/src/fix_recenter.cpp
index 4cbf0248ca..7d30c2f865 100644
--- a/src/fix_recenter.cpp
+++ b/src/fix_recenter.cpp
@@ -15,8 +15,8 @@
Contributing author: Naveen Michaud-Agrawal (Johns Hopkins U)
------------------------------------------------------------------------- */
-#include "stdlib.h"
-#include "string.h"
+#include <stdlib.h>
+#include <string.h>
#include "fix_recenter.h"
#include "atom.h"
#include "group.h"
diff --git a/src/fix_respa.cpp b/src/fix_respa.cpp
index 6d3a948a95..2902ae8a11 100644
--- a/src/fix_respa.cpp
+++ b/src/fix_respa.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdlib.h"
-#include "string.h"
+#include <stdlib.h>
+#include <string.h>
#include "fix_respa.h"
#include "atom.h"
#include "force.h"
diff --git a/src/fix_restrain.cpp b/src/fix_restrain.cpp
index 70b0d72d02..97e898494e 100644
--- a/src/fix_restrain.cpp
+++ b/src/fix_restrain.cpp
@@ -16,9 +16,9 @@
support for bond and angle restraints by Andres Jaramillo-Botero (Caltech)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "string.h"
-#include "stdlib.h"
+#include <math.h>
+#include <string.h>
+#include <stdlib.h>
#include "fix_restrain.h"
#include "atom.h"
#include "force.h"
@@ -512,8 +512,8 @@ void FixRestrain::restrain_dihedral(int m)
MPI_Comm_rank(world,&me);
if (screen) {
char str[128];
- sprintf(str,"Restrain problem: %d " BIGINT_FORMAT " "
- TAGINT_FORMAT " " TAGINT_FORMAT " "
+ sprintf(str,"Restrain problem: %d " BIGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT,
me,update->ntimestep,
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
diff --git a/src/fix_setforce.cpp b/src/fix_setforce.cpp
index 6ba34ce822..0fe56e7548 100644
--- a/src/fix_setforce.cpp
+++ b/src/fix_setforce.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
-#include "stdlib.h"
+#include <string.h>
+#include <stdlib.h>
#include "fix_setforce.h"
#include "atom.h"
#include "update.h"
diff --git a/src/fix_shear_history.cpp b/src/fix_shear_history.cpp
index ddfe2224d9..da69a95603 100644
--- a/src/fix_shear_history.cpp
+++ b/src/fix_shear_history.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "string.h"
-#include "stdio.h"
+#include <mpi.h>
+#include <string.h>
+#include <stdio.h>
#include "fix_shear_history.h"
#include "atom.h"
#include "comm.h"
@@ -293,7 +293,7 @@ void FixShearHistory::grow_arrays(int nmax)
partner = (tagint **) memory->srealloc(partner,nmax*sizeof(tagint *),
"shear_history:partner");
typedef double (*sptype)[3];
- shearpartner = (sptype *)
+ shearpartner = (sptype *)
memory->srealloc(shearpartner,nmax*sizeof(sptype),
"shear_history:shearpartner");
}
diff --git a/src/fix_spring.cpp b/src/fix_spring.cpp
index d80d2cb170..ddc161e50d 100644
--- a/src/fix_spring.cpp
+++ b/src/fix_spring.cpp
@@ -15,9 +15,9 @@
Contributing author: Paul Crozier (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "fix_spring.h"
#include "atom.h"
#include "update.h"
diff --git a/src/fix_spring_rg.cpp b/src/fix_spring_rg.cpp
index 765edac8b9..5e267340c1 100644
--- a/src/fix_spring_rg.cpp
+++ b/src/fix_spring_rg.cpp
@@ -16,9 +16,9 @@
Paul Crozier (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "fix_spring_rg.h"
#include "atom.h"
#include "update.h"
diff --git a/src/fix_spring_self.cpp b/src/fix_spring_self.cpp
index c14a4b5731..830af42162 100644
--- a/src/fix_spring_self.cpp
+++ b/src/fix_spring_self.cpp
@@ -15,8 +15,8 @@
Contributing author: Naveen Michaud-Agrawal (Johns Hopkins University)
------------------------------------------------------------------------- */
-#include "stdlib.h"
-#include "string.h"
+#include <stdlib.h>
+#include <string.h>
#include "fix_spring_self.h"
#include "atom.h"
#include "update.h"
diff --git a/src/fix_store.cpp b/src/fix_store.cpp
index 45eeaaa502..4e3d612cce 100644
--- a/src/fix_store.cpp
+++ b/src/fix_store.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdlib.h"
-#include "string.h"
+#include <stdlib.h>
+#include <string.h>
#include "fix_store.h"
#include "atom.h"
#include "memory.h"
@@ -53,7 +53,7 @@ FixStore::FixStore(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
if (vecflag)
for (int i = 0; i < nlocal; i++)
vstore[i] = 0.0;
- else
+ else
for (int i = 0; i < nlocal; i++)
for (int j = 0; j < nvalues; j++)
astore[i][j] = 0.0;
@@ -132,7 +132,7 @@ int FixStore::pack_exchange(int i, double *buf)
int FixStore::unpack_exchange(int nlocal, double *buf)
{
if (vecflag) vstore[nlocal] = buf[0];
- else
+ else
for (int m = 0; m < nvalues; m++)
astore[nlocal][m] = buf[m];
return nvalues;
@@ -168,7 +168,7 @@ void FixStore::unpack_restart(int nlocal, int nth)
if (vecflag) vstore[nlocal] = extra[nlocal][m];
else
- for (int i = 0; i < nvalues; i++)
+ for (int i = 0; i < nvalues; i++)
astore[nlocal][i] = extra[nlocal][m++];
}
diff --git a/src/fix_store_force.cpp b/src/fix_store_force.cpp
index 3f132be8f2..521e456891 100644
--- a/src/fix_store_force.cpp
+++ b/src/fix_store_force.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "fix_store_force.h"
#include "atom.h"
#include "update.h"
diff --git a/src/fix_store_state.cpp b/src/fix_store_state.cpp
index 4a567cbcab..efcc73f032 100644
--- a/src/fix_store_state.cpp
+++ b/src/fix_store_state.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdlib.h"
-#include "string.h"
+#include <stdlib.h>
+#include <string.h>
#include "fix_store_state.h"
#include "atom.h"
#include "domain.h"
diff --git a/src/fix_temp_berendsen.cpp b/src/fix_temp_berendsen.cpp
index e4b2452455..bb86eb4866 100644
--- a/src/fix_temp_berendsen.cpp
+++ b/src/fix_temp_berendsen.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
-#include "stdlib.h"
-#include "math.h"
+#include <string.h>
+#include <stdlib.h>
+#include <math.h>
#include "fix_temp_berendsen.h"
#include "atom.h"
#include "force.h"
diff --git a/src/fix_temp_csld.cpp b/src/fix_temp_csld.cpp
index 28235b00fc..e89f26ec69 100644
--- a/src/fix_temp_csld.cpp
+++ b/src/fix_temp_csld.cpp
@@ -15,9 +15,9 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "string.h"
-#include "stdlib.h"
-#include "math.h"
+#include <string.h>
+#include <stdlib.h>
+#include <math.h>
#include "fix_temp_csld.h"
#include "atom.h"
#include "force.h"
@@ -138,7 +138,7 @@ void FixTempCSLD::init()
if (has_shake > 0)
error->all(FLERR,"Fix temp/csld is not compatible with fix rattle or fix shake");
-
+
// check variable
if (tstr) {
@@ -222,7 +222,7 @@ void FixTempCSLD::end_of_step()
v[i][2] = vz;
}
}
-
+
// mixing factors
const double c1 = exp(-update->dt/t_period);
const double c2 = sqrt((1.0-c1*c1)*t_target/temperature->compute_scalar());
diff --git a/src/fix_temp_csvr.cpp b/src/fix_temp_csvr.cpp
index 6171e688c0..81f87d4caa 100644
--- a/src/fix_temp_csvr.cpp
+++ b/src/fix_temp_csvr.cpp
@@ -16,9 +16,9 @@
Based on code by Paolo Raiteri (Curtin U) and Giovanni Bussi (SISSA)
------------------------------------------------------------------------- */
-#include "string.h"
-#include "stdlib.h"
-#include "math.h"
+#include <string.h>
+#include <stdlib.h>
+#include <math.h>
#include "fix_temp_csvr.h"
#include "atom.h"
#include "force.h"
diff --git a/src/fix_temp_rescale.cpp b/src/fix_temp_rescale.cpp
index b84bab20c7..5e6036214b 100644
--- a/src/fix_temp_rescale.cpp
+++ b/src/fix_temp_rescale.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
-#include "stdlib.h"
-#include "math.h"
+#include <string.h>
+#include <stdlib.h>
+#include <math.h>
#include "fix_temp_rescale.h"
#include "atom.h"
#include "force.h"
diff --git a/src/fix_tmd.cpp b/src/fix_tmd.cpp
index 5820ffb5ed..4be97a816e 100644
--- a/src/fix_tmd.cpp
+++ b/src/fix_tmd.cpp
@@ -16,10 +16,10 @@
Christian Burisch (Bochum Univeristy, Germany)
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <mpi.h>
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "fix_tmd.h"
#include "atom.h"
#include "update.h"
diff --git a/src/fix_tmd.h b/src/fix_tmd.h
index d00bb303ec..dc994936df 100644
--- a/src/fix_tmd.h
+++ b/src/fix_tmd.h
@@ -20,7 +20,7 @@ FixStyle(tmd,FixTMD)
#ifndef LMP_FIX_TMD_H
#define LMP_FIX_TMD_H
-#include "stdio.h"
+#include <stdio.h>
#include "fix.h"
namespace LAMMPS_NS {
diff --git a/src/fix_vector.cpp b/src/fix_vector.cpp
index 8cdf58564c..7abb2f6454 100644
--- a/src/fix_vector.cpp
+++ b/src/fix_vector.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "fix_vector.h"
#include "update.h"
#include "force.h"
@@ -68,7 +68,7 @@ FixVector::FixVector(LAMMPS *lmp, int narg, char **arg) :
argindex[nvalues] = atoi(ptr+1);
*ptr = '\0';
} else argindex[nvalues] = 0;
-
+
n = strlen(suffix) + 1;
ids[nvalues] = new char[n];
strcpy(ids[nvalues],suffix);
@@ -223,7 +223,7 @@ void FixVector::init()
// reallocate vector or array for accumulated size at end of run
// use endstep to allow for subsequent runs with "pre no"
- // nsize = # of entries from initialstep to finalstep
+ // nsize = # of entries from initialstep to finalstep
bigint finalstep = update->endstep/nevery * nevery;
if (finalstep > update->endstep) finalstep -= nevery;
@@ -248,7 +248,7 @@ void FixVector::end_of_step()
// skip if not step which requires doing something
if (update->ntimestep != nextstep) return;
- if (ncount == ncountmax)
+ if (ncount == ncountmax)
error->all(FLERR,"Overflow of allocated fix vector storage");
// accumulate results of computes,fixes,variables to local copy
@@ -259,7 +259,7 @@ void FixVector::end_of_step()
else result = array[ncount];
modify->clearstep_compute();
-
+
for (int i = 0; i < nvalues; i++) {
int m = value2index[i];
diff --git a/src/fix_viscous.cpp b/src/fix_viscous.cpp
index f1ad471404..bc5059ae69 100644
--- a/src/fix_viscous.cpp
+++ b/src/fix_viscous.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "fix_viscous.h"
#include "atom.h"
#include "update.h"
diff --git a/src/fix_wall.cpp b/src/fix_wall.cpp
index d3c88d7533..fcebd77a9a 100644
--- a/src/fix_wall.cpp
+++ b/src/fix_wall.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "fix_wall.h"
#include "atom.h"
#include "input.h"
@@ -319,7 +319,7 @@ void FixWall::post_force(int vflag)
}
if (sstyle[m] == VARIABLE) {
sigma[m] = input->variable->compute_equal(sindex[m]);
- if (sigma[m] < 0.0)
+ if (sigma[m] < 0.0)
error->all(FLERR,"Variable evaluation in fix wall gave bad value");
}
precompute(m);
diff --git a/src/fix_wall_harmonic.cpp b/src/fix_wall_harmonic.cpp
index 1766fa63c9..41d630b7fe 100644
--- a/src/fix_wall_harmonic.cpp
+++ b/src/fix_wall_harmonic.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "fix_wall_harmonic.h"
#include "atom.h"
#include "error.h"
diff --git a/src/fix_wall_lj1043.cpp b/src/fix_wall_lj1043.cpp
index 0ef78ec0cd..72d71fbb3c 100644
--- a/src/fix_wall_lj1043.cpp
+++ b/src/fix_wall_lj1043.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -15,7 +15,7 @@
Contributing author: Jonathan Lee (Sandia)
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "fix_wall_lj1043.h"
#include "atom.h"
#include "math_const.h"
@@ -25,7 +25,7 @@ using namespace MathConst;
/* ---------------------------------------------------------------------- */
-FixWallLJ1043::FixWallLJ1043(LAMMPS *lmp, int narg, char **arg) :
+FixWallLJ1043::FixWallLJ1043(LAMMPS *lmp, int narg, char **arg) :
FixWall(lmp, narg, arg) {}
/* ---------------------------------------------------------------------- */
@@ -43,7 +43,7 @@ void FixWallLJ1043::precompute(int m)
double rinv = 1.0/cutoff[m];
double r2inv = rinv*rinv;
double r4inv = r2inv*r2inv;
- offset[m] = coeff1[m]*r4inv*r4inv*r2inv - coeff2[m]*r4inv -
+ offset[m] = coeff1[m]*r4inv*r4inv*r2inv - coeff2[m]*r4inv -
coeff3[m]*pow(cutoff[m]+coeff4[m],-3.0);
}
@@ -73,10 +73,10 @@ void FixWallLJ1043::wall_particle(int m, int which, double coord)
r4inv = r2inv*r2inv;
r10inv = r4inv*r4inv*r2inv;
- fwall = side * (coeff5[m]*r10inv*rinv - coeff6[m]*r4inv*rinv -
+ fwall = side * (coeff5[m]*r10inv*rinv - coeff6[m]*r4inv*rinv -
coeff7[m]*pow(delta+coeff4[m],-4.0));
f[i][dim] -= fwall;
- ewall[0] += coeff1[m]*r10inv - coeff2[m]*r4inv -
+ ewall[0] += coeff1[m]*r10inv - coeff2[m]*r4inv -
coeff3[m]*pow(delta+coeff4[m],-3.0) - offset[m];
ewall[m+1] += fwall;
}
diff --git a/src/fix_wall_lj1043.h b/src/fix_wall_lj1043.h
index 8b9ad178f8..a7fdf5ae18 100644
--- a/src/fix_wall_lj1043.h
+++ b/src/fix_wall_lj1043.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
diff --git a/src/fix_wall_lj126.cpp b/src/fix_wall_lj126.cpp
index c942a34acd..f6d8654eea 100644
--- a/src/fix_wall_lj126.cpp
+++ b/src/fix_wall_lj126.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "fix_wall_lj126.h"
#include "atom.h"
#include "error.h"
diff --git a/src/fix_wall_lj93.cpp b/src/fix_wall_lj93.cpp
index a4cd6b6516..f7a3aaf14c 100644
--- a/src/fix_wall_lj93.cpp
+++ b/src/fix_wall_lj93.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "fix_wall_lj93.h"
#include "atom.h"
#include "error.h"
diff --git a/src/fix_wall_reflect.cpp b/src/fix_wall_reflect.cpp
index 5f14fa23c6..b5c70037b2 100644
--- a/src/fix_wall_reflect.cpp
+++ b/src/fix_wall_reflect.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdlib.h"
-#include "string.h"
+#include <stdlib.h>
+#include <string.h>
#include "fix_wall_reflect.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/fix_wall_region.cpp b/src/fix_wall_region.cpp
index 08aa7c9f93..ca17304f36 100644
--- a/src/fix_wall_region.cpp
+++ b/src/fix_wall_region.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "fix_wall_region.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/force.cpp b/src/force.cpp
index f51b0c1818..b31b8eda4e 100644
--- a/src/force.cpp
+++ b/src/force.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdlib.h"
-#include "string.h"
-#include "ctype.h"
+#include <stdlib.h>
+#include <string.h>
+#include <ctype.h>
#include "force.h"
#include "style_bond.h"
#include "style_angle.h"
@@ -262,7 +262,7 @@ Bond *Force::new_bond(const char *style, int trysuffix, int &sflag)
sflag = 1;
char estyle[256];
sprintf(estyle,"%s/%s",style,lmp->suffix);
-
+
if (0) return NULL;
#define BOND_CLASS
@@ -277,7 +277,7 @@ Bond *Force::new_bond(const char *style, int trysuffix, int &sflag)
sflag = 2;
char estyle[256];
sprintf(estyle,"%s/%s",style,lmp->suffix2);
-
+
if (0) return NULL;
#define BOND_CLASS
@@ -342,7 +342,7 @@ Angle *Force::new_angle(const char *style, int trysuffix, int &sflag)
sflag = 1;
char estyle[256];
sprintf(estyle,"%s/%s",style,lmp->suffix);
-
+
if (0) return NULL;
#define ANGLE_CLASS
@@ -357,7 +357,7 @@ Angle *Force::new_angle(const char *style, int trysuffix, int &sflag)
sflag = 2;
char estyle[256];
sprintf(estyle,"%s/%s",style,lmp->suffix);
-
+
if (0) return NULL;
#define ANGLE_CLASS
@@ -759,7 +759,7 @@ void Force::bounds(char *str, int nmax, int &nlo, int &nhi, int nmin)
nhi = atoi(ptr+1);
}
- if (nlo < nmin || nhi > nmax || nlo > nhi)
+ if (nlo < nmin || nhi > nmax || nlo > nhi)
error->all(FLERR,"Numeric index is out of bounds");
}
@@ -772,7 +772,7 @@ void Force::bounds(char *str, int nmax, int &nlo, int &nhi, int nmin)
return nlo,nhi
------------------------------------------------------------------------- */
-void Force::boundsbig(char *str, bigint nmax, bigint &nlo, bigint &nhi,
+void Force::boundsbig(char *str, bigint nmax, bigint &nlo, bigint &nhi,
bigint nmin)
{
char *ptr = strchr(str,'*');
@@ -793,7 +793,7 @@ void Force::boundsbig(char *str, bigint nmax, bigint &nlo, bigint &nhi,
nhi = ATOBIGINT(ptr+1);
}
- if (nlo < nmin || nhi > nmax || nlo > nhi)
+ if (nlo < nmin || nhi > nmax || nlo > nhi)
error->all(FLERR,"Numeric index is out of bounds");
}
@@ -832,11 +832,11 @@ double Force::numeric(const char *file, int line, char *str)
int Force::inumeric(const char *file, int line, char *str)
{
- if (!str)
+ if (!str)
error->all(file,line,
"Expected integer parameter in input script or data file");
int n = strlen(str);
- if (n == 0)
+ if (n == 0)
error->all(file,line,
"Expected integer parameter in input script or data file");
@@ -857,11 +857,11 @@ int Force::inumeric(const char *file, int line, char *str)
bigint Force::bnumeric(const char *file, int line, char *str)
{
- if (!str)
+ if (!str)
error->all(file,line,
"Expected integer parameter in input script or data file");
int n = strlen(str);
- if (n == 0)
+ if (n == 0)
error->all(file,line,
"Expected integer parameter in input script or data file");
@@ -882,11 +882,11 @@ bigint Force::bnumeric(const char *file, int line, char *str)
tagint Force::tnumeric(const char *file, int line, char *str)
{
- if (!str)
+ if (!str)
error->all(file,line,
"Expected integer parameter in input script or data file");
int n = strlen(str);
- if (n == 0)
+ if (n == 0)
error->all(file,line,
"Expected integer parameter in input script or data file");
@@ -964,7 +964,7 @@ const char *Force::potential_name(const char *path)
#if defined(_WIN32)
// skip over the disk drive part of windows pathnames
- if (isalpha(path[0]) && path[1] == ':')
+ if (isalpha(path[0]) && path[1] == ':')
path += 2;
#endif
diff --git a/src/force.h b/src/force.h
index 54b6612689..7ff668f81a 100644
--- a/src/force.h
+++ b/src/force.h
@@ -15,7 +15,7 @@
#define LMP_FORCE_H
#include "pointers.h"
-#include "stdio.h"
+#include <stdio.h>
#include <map>
#include <string>
diff --git a/src/group.cpp b/src/group.cpp
index 0b5d6974ea..5b572b2070 100644
--- a/src/group.cpp
+++ b/src/group.cpp
@@ -11,11 +11,11 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "math.h"
-#include "stdio.h"
-#include "string.h"
-#include "stdlib.h"
+#include <mpi.h>
+#include <math.h>
+#include <stdio.h>
+#include <string.h>
+#include <stdlib.h>
#include "group.h"
#include "domain.h"
#include "atom.h"
@@ -204,7 +204,7 @@ void Group::assign(int narg, char **arg)
else if (strcmp(arg[1],"id") == 0) category = ID;
// args = logical condition
-
+
if (narg > 3 &&
(strcmp(arg[2],"<") == 0 || strcmp(arg[2],">") == 0 ||
strcmp(arg[2],"<=") == 0 || strcmp(arg[2],">=") == 0 ||
@@ -220,7 +220,7 @@ void Group::assign(int narg, char **arg)
else if (strcmp(arg[2],"!=") == 0) condition = NEQ;
else if (strcmp(arg[2],"<>") == 0) condition = BETWEEN;
else error->all(FLERR,"Illegal group command");
-
+
tagint bound1,bound2;
bound1 = force->tnumeric(FLERR,arg[3]);
bound2 = -1;
@@ -240,22 +240,22 @@ void Group::assign(int narg, char **arg)
if (attribute) {
if (condition == LT) {
- for (i = 0; i < nlocal; i++)
+ for (i = 0; i < nlocal; i++)
if (attribute[i] < bound1) mask[i] |= bit;
} else if (condition == LE) {
- for (i = 0; i < nlocal; i++)
+ for (i = 0; i < nlocal; i++)
if (attribute[i] <= bound1) mask[i] |= bit;
} else if (condition == GT) {
- for (i = 0; i < nlocal; i++)
+ for (i = 0; i < nlocal; i++)
if (attribute[i] > bound1) mask[i] |= bit;
} else if (condition == GE) {
- for (i = 0; i < nlocal; i++)
+ for (i = 0; i < nlocal; i++)
if (attribute[i] >= bound1) mask[i] |= bit;
} else if (condition == EQ) {
- for (i = 0; i < nlocal; i++)
+ for (i = 0; i < nlocal; i++)
if (attribute[i] == bound1) mask[i] |= bit;
} else if (condition == NEQ) {
- for (i = 0; i < nlocal; i++)
+ for (i = 0; i < nlocal; i++)
if (attribute[i] != bound1) mask[i] |= bit;
} else if (condition == BETWEEN) {
for (i = 0; i < nlocal; i++)
@@ -264,22 +264,22 @@ void Group::assign(int narg, char **arg)
}
} else {
if (condition == LT) {
- for (i = 0; i < nlocal; i++)
+ for (i = 0; i < nlocal; i++)
if (tattribute[i] < bound1) mask[i] |= bit;
} else if (condition == LE) {
- for (i = 0; i < nlocal; i++)
+ for (i = 0; i < nlocal; i++)
if (tattribute[i] <= bound1) mask[i] |= bit;
} else if (condition == GT) {
- for (i = 0; i < nlocal; i++)
+ for (i = 0; i < nlocal; i++)
if (tattribute[i] > bound1) mask[i] |= bit;
} else if (condition == GE) {
- for (i = 0; i < nlocal; i++)
+ for (i = 0; i < nlocal; i++)
if (tattribute[i] >= bound1) mask[i] |= bit;
} else if (condition == EQ) {
- for (i = 0; i < nlocal; i++)
+ for (i = 0; i < nlocal; i++)
if (tattribute[i] == bound1) mask[i] |= bit;
} else if (condition == NEQ) {
- for (i = 0; i < nlocal; i++)
+ for (i = 0; i < nlocal; i++)
if (tattribute[i] != bound1) mask[i] |= bit;
} else if (condition == BETWEEN) {
for (i = 0; i < nlocal; i++)
@@ -289,24 +289,24 @@ void Group::assign(int narg, char **arg)
}
// args = list of values
-
+
} else {
int *attribute = NULL;
tagint *tattribute = NULL;
if (category == TYPE) attribute = atom->type;
else if (category == MOLECULE) tattribute = atom->molecule;
else if (category == ID) tattribute = atom->tag;
-
+
char *ptr;
tagint start,stop,delta;
for (int iarg = 2; iarg < narg; iarg++) {
delta = 1;
if (strchr(arg[iarg],':')) {
- ptr = strtok(arg[iarg],":");
- start = force->tnumeric(FLERR,ptr);
- ptr = strtok(NULL,":");
- stop = force->tnumeric(FLERR,ptr);
+ ptr = strtok(arg[iarg],":");
+ start = force->tnumeric(FLERR,ptr);
+ ptr = strtok(NULL,":");
+ stop = force->tnumeric(FLERR,ptr);
ptr = strtok(NULL,":");
if (ptr) delta = force->tnumeric(FLERR,ptr);
} else {
@@ -316,7 +316,7 @@ void Group::assign(int narg, char **arg)
error->all(FLERR,"Illegal range increment value");
// add to group if attribute matches value or sequence
-
+
if (attribute) {
for (i = 0; i < nlocal; i++)
if (attribute[i] >= start && attribute[i] <= stop &&
@@ -340,7 +340,7 @@ void Group::assign(int narg, char **arg)
error->all(FLERR,"Variable for group is invalid style");
double *aflag;
-
+
// aflag = evaluation of per-atom variable
memory->create(aflag,nlocal,"group:aflag");
@@ -358,7 +358,7 @@ void Group::assign(int narg, char **arg)
} else if (strcmp(arg[1],"include") == 0) {
if (narg != 3) error->all(FLERR,"Illegal group command");
- if (strcmp(arg[2],"molecule") != 0)
+ if (strcmp(arg[2],"molecule") != 0)
error->all(FLERR,"Illegal group command");
add_molecules(igroup,bit);
@@ -376,7 +376,7 @@ void Group::assign(int narg, char **arg)
for (int iarg = 2; iarg < narg; iarg++) {
jgroup = find(arg[iarg]);
if (jgroup == -1) error->all(FLERR,"Group ID does not exist");
- if (dynamic[jgroup])
+ if (dynamic[jgroup])
error->all(FLERR,"Cannot subtract groups using a dynamic group");
list[iarg-2] = jgroup;
}
@@ -414,7 +414,7 @@ void Group::assign(int narg, char **arg)
for (int iarg = 2; iarg < narg; iarg++) {
jgroup = find(arg[iarg]);
if (jgroup == -1) error->all(FLERR,"Group ID does not exist");
- if (dynamic[jgroup])
+ if (dynamic[jgroup])
error->all(FLERR,"Cannot union groups using a dynamic group");
list[iarg-2] = jgroup;
}
@@ -444,7 +444,7 @@ void Group::assign(int narg, char **arg)
for (int iarg = 2; iarg < narg; iarg++) {
jgroup = find(arg[iarg]);
if (jgroup == -1) error->all(FLERR,"Group ID does not exist");
- if (dynamic[jgroup])
+ if (dynamic[jgroup])
error->all(FLERR,"Cannot intersect groups using a dynamic group");
list[iarg-2] = jgroup;
}
@@ -470,9 +470,9 @@ void Group::assign(int narg, char **arg)
} else if (strcmp(arg[1],"dynamic") == 0) {
if (narg < 4) error->all(FLERR,"Illegal group command");
- if (strcmp(arg[0],arg[2]) == 0)
+ if (strcmp(arg[0],arg[2]) == 0)
error->all(FLERR,"Group dynamic cannot reference itself");
- if (find(arg[2]) < 0)
+ if (find(arg[2]) < 0)
error->all(FLERR,"Group dynamic parent group does not exist");
if (igroup == 0) error->all(FLERR,"Group all cannot be made dynamic");
@@ -537,7 +537,7 @@ void Group::assign(int narg, char **arg)
if (screen) fprintf(screen,"dynamic group %s defined\n",names[igroup]);
if (logfile) fprintf(logfile,"dynamic group %s defined\n",names[igroup]);
} else {
- if (screen)
+ if (screen)
fprintf(screen,"%.15g atoms in group %s\n",all,names[igroup]);
if (logfile)
fprintf(logfile,"%.15g atoms in group %s\n",all,names[igroup]);
diff --git a/src/group.h b/src/group.h
index cef184102e..4fbdb0cc6e 100644
--- a/src/group.h
+++ b/src/group.h
@@ -14,7 +14,7 @@
#ifndef LMP_GROUP_H
#define LMP_GROUP_H
-#include "stdio.h"
+#include <stdio.h>
#include "pointers.h"
#include <map>
diff --git a/src/image.cpp b/src/image.cpp
index ab6824d7fb..033bcfb669 100644
--- a/src/image.cpp
+++ b/src/image.cpp
@@ -15,11 +15,11 @@
Contributing author: Nathan Fabian (Sandia)
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "math.h"
-#include "ctype.h"
-#include "stdlib.h"
-#include "string.h"
+#include <mpi.h>
+#include <math.h>
+#include <ctype.h>
+#include <stdlib.h>
+#include <string.h>
#include "image.h"
#include "math_extra.h"
#include "random_mars.h"
@@ -1816,7 +1816,7 @@ int ColorMap::reset(int narg, char **arg)
}
/* ----------------------------------------------------------------------
- set explicit values for all min/max settings in color map
+ set explicit values for all min/max settings in color map
from min/max dynamic values
set lo/hi current and lvalue/hvalue entries that are MIN/MAX VALUE
called only once if mlo/mhi != MIN/MAX VALUE, else called repeatedly
@@ -1838,7 +1838,7 @@ int ColorMap::minmax(double mindynamic, double maxdynamic)
if (mrange == ABSOLUTE) mentry[nentry-1].svalue = hicurrent;
else mentry[nentry-1].svalue = 1.0;
- // error in ABSOLUTE mode if new lo/hi current cause
+ // error in ABSOLUTE mode if new lo/hi current cause
// first/last entry to become lo > hi with adjacent entry
if (mrange == ABSOLUTE) {
diff --git a/src/image.h b/src/image.h
index 6895750ea7..58050ada32 100644
--- a/src/image.h
+++ b/src/image.h
@@ -14,8 +14,8 @@
#ifndef LMP_IMAGE_H
#define LMP_IMAGE_H
-#include "math.h"
-#include "stdio.h"
+#include <math.h>
+#include <stdio.h>
#include "pointers.h"
namespace LAMMPS_NS {
diff --git a/src/improper.cpp b/src/improper.cpp
index 643e7a63ff..3b5453de59 100644
--- a/src/improper.cpp
+++ b/src/improper.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "improper.h"
#include "atom.h"
#include "comm.h"
@@ -51,7 +51,7 @@ Improper::Improper(LAMMPS *lmp) : Pointers(lmp)
/* ---------------------------------------------------------------------- */
Improper::~Improper()
-{
+{
if (copymode) return;
memory->destroy(eatom);
@@ -64,7 +64,7 @@ Improper::~Improper()
void Improper::init()
{
- if (!allocated && atom->nimpropertypes)
+ if (!allocated && atom->nimpropertypes)
error->all(FLERR,"Improper coeffs are not set");
for (int i = 1; i <= atom->nimpropertypes; i++)
if (setflag[i] == 0) error->all(FLERR,"All improper coeffs are not set");
diff --git a/src/improper.h b/src/improper.h
index 039da0ab84..5e0b525b6d 100644
--- a/src/improper.h
+++ b/src/improper.h
@@ -14,7 +14,7 @@
#ifndef LMP_IMPROPER_H
#define LMP_IMPROPER_H
-#include "stdio.h"
+#include <stdio.h>
#include "pointers.h"
namespace LAMMPS_NS {
diff --git a/src/improper_hybrid.cpp b/src/improper_hybrid.cpp
index 140bd2e9dc..1a2a0bdc50 100644
--- a/src/improper_hybrid.cpp
+++ b/src/improper_hybrid.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "string.h"
-#include "ctype.h"
+#include <math.h>
+#include <string.h>
+#include <ctype.h>
#include "improper_hybrid.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/improper_hybrid.h b/src/improper_hybrid.h
index 4429ce9c6e..cab5184891 100644
--- a/src/improper_hybrid.h
+++ b/src/improper_hybrid.h
@@ -20,7 +20,7 @@ ImproperStyle(hybrid,ImproperHybrid)
#ifndef LMP_IMPROPER_HYBRID_H
#define LMP_IMPROPER_HYBRID_H
-#include "stdio.h"
+#include <stdio.h>
#include "improper.h"
namespace LAMMPS_NS {
diff --git a/src/info.cpp b/src/info.cpp
index 1eba5a8b92..e2f3eab992 100644
--- a/src/info.cpp
+++ b/src/info.cpp
@@ -15,7 +15,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "info.h"
#include "accelerator_cuda.h"
#include "accelerator_kokkos.h"
@@ -243,7 +243,7 @@ void Info::command(int narg, char **arg)
fprintf(out,"\nCommunication information:\n");
fprintf(out,"MPI library level: MPI v%d.%d\n",major,minor);
fprintf(out,"Comm style = %s, Comm layout = %s\n",
- commstyles[comm->style], commlayout[comm->layout]);
+ commstyles[comm->style], commlayout[comm->layout]);
fprintf(out,"Communicate velocities for ghost atoms = %s\n",
comm->ghost_velocity ? "yes" : "no");
diff --git a/src/input.cpp b/src/input.cpp
index b048389c3c..a38e91b2d4 100644
--- a/src/input.cpp
+++ b/src/input.cpp
@@ -11,13 +11,13 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
-#include "errno.h"
-#include "ctype.h"
-#include "unistd.h"
+#include <mpi.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <errno.h>
+#include <ctype.h>
+#include <unistd.h>
#include "sys/stat.h"
#include "input.h"
#include "style_command.h"
@@ -52,7 +52,7 @@
#include "memory.h"
#ifdef _OPENMP
-#include "omp.h"
+#include <omp.h>
#endif
#ifdef _WIN32
@@ -151,13 +151,13 @@ Input::~Input()
void Input::file()
{
int m,n;
-
+
while (1) {
-
+
// read a line from input script
// n = length of line including str terminator, 0 if end of file
// if line ends in continuation char '&', concatenate next line
-
+
if (me == 0) {
m = 0;
while (1) {
@@ -165,7 +165,7 @@ void Input::file()
// end of file reached, so break
// n == 0 if nothing read, else n = line with str terminator
-
+
if (fgets(&line[m],maxline-m,infile) == NULL) {
if (m) n = strlen(line) + 1;
else n = 0;
@@ -195,13 +195,13 @@ void Input::file()
}
}
}
-
+
// bcast the line
// if n = 0, end-of-file
// error if label_active is set, since label wasn't encountered
// if original input file, code is done
// else go back to previous input file
-
+
MPI_Bcast(&n,1,MPI_INT,0,world);
if (n == 0) {
if (label_active) error->all(FLERR,"Label wasn't found in input script");
@@ -217,29 +217,29 @@ void Input::file()
if (me == 0) infile = infiles[nfile-1];
continue;
}
-
+
if (n > maxline) reallocate(line,maxline,n);
MPI_Bcast(line,n,MPI_CHAR,0,world);
-
+
// echo the command unless scanning for label
-
+
if (me == 0 && label_active == 0) {
if (echo_screen && screen) fprintf(screen,"%s\n",line);
if (echo_log && logfile) fprintf(logfile,"%s\n",line);
}
-
+
// parse the line
// if no command, skip to next line in input script
-
+
parse();
if (command == NULL) continue;
-
+
// if scanning for label, skip command unless it's a label command
-
+
if (label_active && strcmp(command,"label") != 0) continue;
-
+
// execute the command
-
+
if (execute_command()) {
char *str = new char[maxline+32];
sprintf(str,"Unknown command: %s",line);
@@ -263,7 +263,7 @@ void Input::file(const char *filename)
if (nfile > 1)
error->one(FLERR,"Invalid use of library file() function");
- if (infile && infile != stdin) fclose(infile);
+ if (infile && infile != stdin) fclose(infile);
infile = fopen(filename,"r");
if (infile == NULL) {
char str[128];
@@ -273,7 +273,7 @@ void Input::file(const char *filename)
infiles[0] = infile;
nfile = 1;
}
-
+
file();
}
@@ -287,32 +287,32 @@ char *Input::one(const char *single)
int n = strlen(single) + 1;
if (n > maxline) reallocate(line,maxline,n);
strcpy(line,single);
-
+
// echo the command unless scanning for label
-
+
if (me == 0 && label_active == 0) {
if (echo_screen && screen) fprintf(screen,"%s\n",line);
if (echo_log && logfile) fprintf(logfile,"%s\n",line);
}
-
+
// parse the line
// if no command, just return NULL
-
+
parse();
if (command == NULL) return NULL;
-
+
// if scanning for label, skip command unless it's a label command
-
+
if (label_active && strcmp(command,"label") != 0) return NULL;
-
+
// execute the command and return its name
-
+
if (execute_command()) {
char *str = new char[maxline+32];
sprintf(str,"Unknown command: %s",line);
error->all(FLERR,str);
}
-
+
return command;
}
@@ -329,11 +329,11 @@ char *Input::one(const char *single)
void Input::parse()
{
// duplicate line into copy string to break into words
-
+
int n = strlen(line) + 1;
if (n > maxcopy) reallocate(copy,maxcopy,n);
strcpy(copy,line);
-
+
// strip any # comment by replacing it with 0
// do not strip from a # inside single/double/triple quotes
// quoteflag = 1,2,3 when encounter first single/double,triple quote
@@ -363,22 +363,22 @@ void Input::parse()
}
ptr++;
}
-
+
// perform $ variable substitution (print changes)
// except if searching for a label since earlier variable may not be defined
-
+
if (!label_active) substitute(copy,work,maxcopy,maxwork,1);
-
+
// command = 1st arg in copy string
-
+
char *next;
command = nextword(copy,&next);
if (command == NULL) return;
-
+
// point arg[] at each subsequent arg in copy string
// nextword() inserts string terminators into copy string to delimit args
// nextword() treats text between single/double/triple quotes as one arg
-
+
narg = 0;
ptr = next;
while (ptr) {
@@ -407,12 +407,12 @@ void Input::parse()
char *Input::nextword(char *str, char **next)
{
char *start,*stop;
-
+
// start = first non-whitespace char
start = &str[strspn(str," \t\n\v\f\r")];
if (*start == '\0') return NULL;
-
+
// if start is single/double/triple quote:
// start = first char beyond quote
// stop = first char of matching quote
@@ -464,45 +464,45 @@ void Input::substitute(char *&str, char *&str2, int &max, int &max2, int flag)
// if $ is followed by '{', trailing '}' becomes NULL
// else $x becomes x followed by NULL
// beyond = points to text following variable
-
+
int i,n,paren_count;
char immediate[256];
char *var,*value,*beyond;
int quoteflag = 0;
char *ptr = str;
-
+
n = strlen(str) + 1;
if (n > max2) reallocate(str2,max2,n);
*str2 = '\0';
char *ptr2 = str2;
-
+
while (*ptr) {
// variable substitution
-
+
if (*ptr == '$' && !quoteflag) {
// value = ptr to expanded variable
// variable name between curly braces, e.g. ${a}
-
+
if (*(ptr+1) == '{') {
var = ptr+2;
i = 0;
-
+
while (var[i] != '\0' && var[i] != '}') i++;
-
+
if (var[i] == '\0') error->one(FLERR,"Invalid variable name");
var[i] = '\0';
beyond = ptr + strlen(var) + 3;
value = variable->retrieve(var);
-
+
// immediate variable between parenthesis, e.g. $(1/2)
-
+
} else if (*(ptr+1) == '(') {
var = ptr+2;
paren_count = 0;
i = 0;
-
+
while (var[i] != '\0' && !(var[i] == ')' && paren_count == 0)) {
switch (var[i]) {
case '(': paren_count++; break;
@@ -511,15 +511,15 @@ void Input::substitute(char *&str, char *&str2, int &max, int &max2, int flag)
}
i++;
}
-
+
if (var[i] == '\0') error->one(FLERR,"Invalid immediate variable");
var[i] = '\0';
beyond = ptr + strlen(var) + 3;
sprintf(immediate,"%.20g",variable->compute_equal(var));
value = immediate;
-
+
// single character variable name, e.g. $a
-
+
} else {
var = ptr;
var[0] = var[1];
@@ -527,25 +527,25 @@ void Input::substitute(char *&str, char *&str2, int &max, int &max2, int flag)
beyond = ptr + 2;
value = variable->retrieve(var);
}
-
+
if (value == NULL) error->one(FLERR,"Substitution for illegal variable");
-
+
// check if storage in str2 needs to be expanded
// re-initialize ptr and ptr2 to the point beyond the variable.
-
+
n = strlen(str2) + strlen(value) + strlen(beyond) + 1;
if (n > max2) reallocate(str2,max2,n);
strcat(str2,value);
ptr2 = str2 + strlen(str2);
ptr = beyond;
-
+
// output substitution progress if requested
-
+
if (flag && me == 0 && label_active == 0) {
if (echo_screen && screen) fprintf(screen,"%s%s\n",str2,beyond);
if (echo_log && logfile) fprintf(logfile,"%s%s\n",str2,beyond);
}
-
+
continue;
}
@@ -558,7 +558,7 @@ void Input::substitute(char *&str, char *&str2, int &max, int &max2, int flag)
quoteflag = 3;
*ptr2++ = *ptr++;
*ptr2++ = *ptr++;
- }
+ }
else if (*ptr == '"') quoteflag = 2;
else if (*ptr == '\'') quoteflag = 1;
} else {
@@ -572,14 +572,14 @@ void Input::substitute(char *&str, char *&str2, int &max, int &max2, int flag)
}
// copy current character into str2
-
+
*ptr2++ = *ptr++;
*ptr2 = '\0';
}
-
+
// set length of input str to length of work str2
// copy work string back to input str
-
+
if (max2 > max) reallocate(str,max,max2);
strcpy(str,str2);
}
@@ -610,7 +610,7 @@ void Input::reallocate(char *&str, int &max, int n)
if (n) {
while (n > max) max += DELTALINE;
} else max += DELTALINE;
-
+
str = (char *) memory->srealloc(str,max*sizeof(char),"input:str");
}
@@ -622,7 +622,7 @@ void Input::reallocate(char *&str, int &max, int n)
int Input::execute_command()
{
int flag = 1;
-
+
if (!strcmp(command,"clear")) clear();
else if (!strcmp(command,"echo")) echo();
else if (!strcmp(command,"if")) ifthenelse();
@@ -637,7 +637,7 @@ int Input::execute_command()
else if (!strcmp(command,"quit")) quit();
else if (!strcmp(command,"shell")) shell();
else if (!strcmp(command,"variable")) variable_command();
-
+
else if (!strcmp(command,"angle_coeff")) angle_coeff();
else if (!strcmp(command,"angle_style")) angle_style();
else if (!strcmp(command,"atom_modify")) atom_modify();
@@ -692,23 +692,23 @@ int Input::execute_command()
else if (!strcmp(command,"undump")) undump();
else if (!strcmp(command,"unfix")) unfix();
else if (!strcmp(command,"units")) units();
-
+
else flag = 0;
-
+
// return if command was listed above
-
+
if (flag) return 0;
-
+
// invoke commands added via style_command.h
-
+
if (command_map->find(command) != command_map->end()) {
CommandCreator command_creator = (*command_map)[command];
command_creator(lmp,narg,arg);
return 0;
}
-
+
// unrecognized command
-
+
return -1;
}
@@ -885,7 +885,7 @@ void Input::include()
// NOTE: this check will fail if a 2nd if command was inside the if command
// and came before the include
- if (ifthenelse_flag)
+ if (ifthenelse_flag)
error->all(FLERR,"Cannot use include command within an if command");
if (me == 0) {
@@ -1165,7 +1165,7 @@ void Input::shell()
for (int i = 1; i < narg; i++) {
char *ptr = strdup(arg[i]);
rv = 0;
-#ifdef _WIN32
+#ifdef _WIN32
if (ptr != NULL) rv = _putenv(ptr);
#else
if (ptr != NULL) rv = putenv(ptr);
diff --git a/src/input.h b/src/input.h
index f03655657c..37a6cf2409 100644
--- a/src/input.h
+++ b/src/input.h
@@ -14,7 +14,7 @@
#ifndef LMP_INPUT_H
#define LMP_INPUT_H
-#include "stdio.h"
+#include <stdio.h>
#include "pointers.h"
#include <map>
#include <string>
@@ -33,7 +33,7 @@ class Input : protected Pointers {
void file(); // process all input
void file(const char *); // process an input script
char *one(const char *); // process a single command
- void substitute(char *&, char *&, int &, int &, int);
+ void substitute(char *&, char *&, int &, int &, int);
// substitute for variables in a string
private:
diff --git a/src/integrate.cpp b/src/integrate.cpp
index 429659b6e1..b825a19784 100644
--- a/src/integrate.cpp
+++ b/src/integrate.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdlib.h"
+#include <stdlib.h>
#include "integrate.h"
#include "update.h"
#include "force.h"
diff --git a/src/irregular.cpp b/src/irregular.cpp
index d90df8f122..3947001541 100644
--- a/src/irregular.cpp
+++ b/src/irregular.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "stdlib.h"
-#include "string.h"
+#include <mpi.h>
+#include <stdlib.h>
+#include <string.h>
#include "irregular.h"
#include "atom.h"
#include "atom_vec.h"
@@ -313,7 +313,7 @@ int Irregular::create_atom(int n, int *sizes, int *proclist, int sortflag)
#ifdef LAMMPS_RS_ALLREDUCE_INPLACE
MPI_Allreduce(MPI_IN_PLACE,work1,nprocs,MPI_INT,MPI_SUM,world);
nrecv_proc = work1[me];
-#else
+#else
#ifdef LAMMPS_RS_ALLREDUCE
MPI_Allreduce(work1,work2,nprocs,MPI_INT,MPI_SUM,world);
nrecv_proc = work2[me];
@@ -559,7 +559,7 @@ int Irregular::create_data(int n, int *proclist, int sortflag)
#ifdef LAMMPS_RS_ALLREDUCE_INPLACE
MPI_Allreduce(MPI_IN_PLACE,work1,nprocs,MPI_INT,MPI_SUM,world);
nrecv_proc = work1[me];
-#else
+#else
#ifdef LAMMPS_RS_ALLREDUCE
MPI_Allreduce(work1,work2,nprocs,MPI_INT,MPI_SUM,world);
nrecv_proc = work2[me];
diff --git a/src/irregular.h b/src/irregular.h
index fe5b80a04b..ea0fee2eb8 100644
--- a/src/irregular.h
+++ b/src/irregular.h
@@ -72,7 +72,7 @@ class Irregular : protected Pointers {
int *length_recv; // # of doubles to recv from each proc
int *offset_send; // where each atom starts in send buffer
- // extra plan params plan for irregular communication of datums
+ // extra plan params plan for irregular communication of datums
// 2 self params refer to data copied to self
int *num_recv; // # of datums to recv from each proc
diff --git a/src/kspace.cpp b/src/kspace.cpp
index 16ed8be14b..8724ca2559 100644
--- a/src/kspace.cpp
+++ b/src/kspace.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdlib.h"
-#include "string.h"
+#include <stdlib.h>
+#include <string.h>
#include "kspace.h"
#include "atom.h"
#include "comm.h"
@@ -394,7 +394,7 @@ void KSpace::lamda2xvector(double *lamda, double *v)
/* ----------------------------------------------------------------------
convert a sphere in box coords to an ellipsoid in lamda (0-1)
- coords and return the tight (axis-aligned) bounding box, does not
+ coords and return the tight (axis-aligned) bounding box, does not
preserve vector magnitude
see http://www.loria.fr/~shornus/ellipsoid-bbox.html and
http://yiningkarlli.blogspot.com/2013/02/
@@ -412,7 +412,7 @@ void KSpace::kspacebbox(double r, double *b)
xz = h[4];
xy = h[5];
- b[0] = r*sqrt(ly*ly*lz*lz + ly*ly*xz*xz - 2.0*ly*xy*xz*yz + lz*lz*xy*xy +
+ b[0] = r*sqrt(ly*ly*lz*lz + ly*ly*xz*xz - 2.0*ly*xy*xz*yz + lz*lz*xy*xy +
xy*xy*yz*yz)/(lx*ly*lz);
b[1] = r*sqrt(lz*lz + yz*yz)/(ly*lz);
b[2] = r/lz;
@@ -551,7 +551,7 @@ void KSpace::modify_params(int narg, char **arg)
} else if (strcmp(arg[iarg],"eigtol") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal kspace_modify command");
splittol = atof(arg[iarg+1]);
- if (splittol >= 1.0)
+ if (splittol >= 1.0)
error->all(FLERR,"Kspace_modify eigtol must be smaller than one");
iarg += 2;
} else if (strcmp(arg[iarg],"pressure/scalar") == 0) {
diff --git a/src/kspace.h b/src/kspace.h
index fe46ae2d4b..5519a8c56f 100644
--- a/src/kspace.h
+++ b/src/kspace.h
@@ -45,9 +45,9 @@ class KSpace : protected Pointers {
int tip4pflag; // 1 if a TIP4P solver
int dipoleflag; // 1 if a dipole solver
int differentiation_flag;
- int neighrequest_flag; // used to avoid obsolete construction
+ int neighrequest_flag; // used to avoid obsolete construction
// of neighbor lists
- int mixflag; // 1 if geometric mixing rules are enforced
+ int mixflag; // 1 if geometric mixing rules are enforced
// for LJ coefficients
int slabflag;
int scalar_pressure_flag; // 1 if using MSM fast scalar pressure
@@ -64,9 +64,9 @@ class KSpace : protected Pointers {
double accuracy_absolute; // user-specifed accuracy in force units
double accuracy_relative; // user-specified dimensionless accuracy
// accurary = acc_rel * two_charge_force
- double accuracy_real_6; // real space accuracy for
+ double accuracy_real_6; // real space accuracy for
// dispersion solver (force units)
- double accuracy_kspace_6; // reciprocal space accuracy for
+ double accuracy_kspace_6; // reciprocal space accuracy for
// dispersion solver (force units)
int auto_disp_flag; // use automatic paramter generation for pppm/disp
double two_charge_force; // force in user units of two point
@@ -134,7 +134,7 @@ class KSpace : protected Pointers {
see Eq 4 from Parallel Computing 35 (2009) 164–177
------------------------------------------------------------------------- */
- double gamma(const double &rho) const
+ double gamma(const double &rho) const
{
if (rho <= 1.0) {
const int split_order = order/2;
@@ -154,7 +154,7 @@ class KSpace : protected Pointers {
see Eq 4 from Parallel Computing 35 (2009) 164-177
------------------------------------------------------------------------- */
- double dgamma(const double &rho) const
+ double dgamma(const double &rho) const
{
if (rho <= 1.0) {
const int split_order = order/2;
@@ -168,7 +168,7 @@ class KSpace : protected Pointers {
return dg;
} else return (-1.0/rho/rho);
}
-
+
double **get_gcons() { return gcons; }
double **get_dgcons() { return dgcons; }
diff --git a/src/lammps.cpp b/src/lammps.cpp
index 95d925b6cb..bb1f0e507c 100644
--- a/src/lammps.cpp
+++ b/src/lammps.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "string.h"
-#include "ctype.h"
+#include <mpi.h>
+#include <string.h>
+#include <ctype.h>
#include "lammps.h"
#include "style_angle.h"
#include "style_atom.h"
@@ -455,24 +455,24 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
"lmptype.h are not compatible");
#ifdef LAMMPS_SMALLBIG
- if (sizeof(smallint) != 4 || sizeof(imageint) != 4 ||
+ if (sizeof(smallint) != 4 || sizeof(imageint) != 4 ||
sizeof(tagint) != 4 || sizeof(bigint) != 8)
error->all(FLERR,"Small to big integers are not sized correctly");
#endif
#ifdef LAMMPS_BIGBIG
- if (sizeof(smallint) != 4 || sizeof(imageint) != 8 ||
+ if (sizeof(smallint) != 4 || sizeof(imageint) != 8 ||
sizeof(tagint) != 8 || sizeof(bigint) != 8)
error->all(FLERR,"Small to big integers are not sized correctly");
#endif
#ifdef LAMMPS_SMALLSMALL
- if (sizeof(smallint) != 4 || sizeof(imageint) != 4 ||
+ if (sizeof(smallint) != 4 || sizeof(imageint) != 4 ||
sizeof(tagint) != 4 || sizeof(bigint) != 4)
error->all(FLERR,"Small to big integers are not sized correctly");
#endif
// error check on accelerator packages
- if (cudaflag == 1 && kokkosflag == 1)
+ if (cudaflag == 1 && kokkosflag == 1)
error->all(FLERR,"Cannot use -cuda on and -kokkos on together");
// create Cuda class if USER-CUDA installed, unless explicitly switched off
@@ -696,7 +696,7 @@ void LAMMPS::post_create()
error->all(FLERR,"Using suffix gpu without GPU package installed");
if (strcmp(suffix,"intel") == 0 && !modify->check_package("INTEL"))
error->all(FLERR,"Using suffix intel without USER-INTEL package installed");
- if (strcmp(suffix,"kk") == 0 &&
+ if (strcmp(suffix,"kk") == 0 &&
(kokkos == NULL || kokkos->kokkos_exists == 0))
error->all(FLERR,"Using suffix kk without KOKKOS package enabled");
if (strcmp(suffix,"omp") == 0 && !modify->check_package("OMP"))
@@ -810,12 +810,12 @@ void LAMMPS::help()
"-partition size1 size2 ... : assign partition sizes (-p)\n"
"-plog basename : basename for partition logs (-pl)\n"
"-pscreen basename : basename for partition screens (-ps)\n"
- "-restart rfile dfile ... : convert restart to data file (-r)\n"
+ "-restart rfile dfile ... : convert restart to data file (-r)\n"
"-reorder topology-specs : processor reordering (-r)\n"
"-screen none/filename : where to send screen output (-sc)\n"
"-suffix cuda/gpu/opt/omp : style suffix to apply (-sf)\n"
"-var varname value : set index style variable (-v)\n\n");
-
+
fprintf(screen,"Style options compiled with this executable\n\n");
int pos = 80;
@@ -941,7 +941,7 @@ void LAMMPS::print_style(const char *str, int &pos)
if (isupper(str[0])) return;
int len = strlen(str);
- if (pos+len > 80) {
+ if (pos+len > 80) {
fprintf(screen,"\n");
pos = 0;
}
diff --git a/src/lammps.h b/src/lammps.h
index 53848b1010..88449a4d88 100644
--- a/src/lammps.h
+++ b/src/lammps.h
@@ -14,7 +14,7 @@
#ifndef LMP_LAMMPS_H
#define LMP_LAMMPS_H
-#include "stdio.h"
+#include <stdio.h>
namespace LAMMPS_NS {
diff --git a/src/lattice.cpp b/src/lattice.cpp
index e5081d75f7..e851760792 100644
--- a/src/lattice.cpp
+++ b/src/lattice.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "string.h"
-#include "stdlib.h"
+#include <math.h>
+#include <string.h>
+#include <stdlib.h>
#include "lattice.h"
#include "update.h"
#include "domain.h"
diff --git a/src/library.cpp b/src/library.cpp
index ea3c66398a..f6d9b621d1 100644
--- a/src/library.cpp
+++ b/src/library.cpp
@@ -14,9 +14,9 @@
// C or Fortran style library interface to LAMMPS
// customize by adding new LAMMPS-specific functions
-#include "mpi.h"
-#include "string.h"
-#include "stdlib.h"
+#include <mpi.h>
+#include <string.h>
+#include <stdlib.h>
#include "library.h"
#include "lammps.h"
#include "universe.h"
@@ -405,7 +405,7 @@ int lammps_get_natoms(void *ptr)
data must be pre-allocated by caller to correct length
------------------------------------------------------------------------- */
-void lammps_gather_atoms(void *ptr, char *name,
+void lammps_gather_atoms(void *ptr, char *name,
int type, int count, void *data)
{
LAMMPS *lmp = (LAMMPS *) ptr;
diff --git a/src/library.h b/src/library.h
index a01d593b21..3bdeddbac4 100644
--- a/src/library.h
+++ b/src/library.h
@@ -16,7 +16,7 @@
new LAMMPS-specific functions can be added
*/
-#include "mpi.h"
+#include <mpi.h>
/* ifdefs allow this file to be included in a C program */
diff --git a/src/lmptype.h b/src/lmptype.h
index 87b7da51ed..7a63ee4e53 100644
--- a/src/lmptype.h
+++ b/src/lmptype.h
@@ -36,9 +36,9 @@
#define __STDC_FORMAT_MACROS
#endif
-#include "limits.h"
-#include "stdint.h"
-#include "inttypes.h"
+#include <limits.h>
+#include <stdint.h>
+#include <inttypes.h>
// grrr - IBM Power6 does not provide this def in their system header files
diff --git a/src/lmpwindows.h b/src/lmpwindows.h
index 419aa9aff5..d20d0f87ba 100644
--- a/src/lmpwindows.h
+++ b/src/lmpwindows.h
@@ -2,8 +2,8 @@
#if !defined(__MINGW32__)
#include "erf.h"
#endif
-#include "direct.h"
-#include "math.h"
+#include <direct.h>
+#include <math.h>
// LAMMPS uses usleep with 100 ms arguments, no microsecond precision needed
#if !defined(__MINGW32__)
#include "sleep.h"
diff --git a/src/main.cpp b/src/main.cpp
index d85a79d831..fdf7a791d0 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
+#include <mpi.h>
#include "lammps.h"
#include "input.h"
-#include "stdio.h"
+#include <stdio.h>
using namespace LAMMPS_NS;
diff --git a/src/math_extra.cpp b/src/math_extra.cpp
index eb2afcea2c..0b33fc59c1 100644
--- a/src/math_extra.cpp
+++ b/src/math_extra.cpp
@@ -15,8 +15,8 @@
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
-#include "stdio.h"
-#include "string.h"
+#include <stdio.h>
+#include <string.h>
#include "math_extra.h"
#define MAXJACOBI 50
@@ -230,7 +230,7 @@ void richardson(double *q, double *m, double *w, double *moments, double dtq)
apply evolution operators to quat, quat momentum
Miller et al., J Chem Phys. 116, 8649-8659 (2002)
------------------------------------------------------------------------- */
-void no_squish_rotate(int k, double *p, double *q, double *inertia,
+void no_squish_rotate(int k, double *p, double *q, double *inertia,
double dt)
{
double phi,c_phi,s_phi,kp[4],kq[4];
diff --git a/src/math_extra.h b/src/math_extra.h
index f676cee2ba..f768715ca0 100755
--- a/src/math_extra.h
+++ b/src/math_extra.h
@@ -18,9 +18,9 @@
#ifndef LMP_MATH_EXTRA_H
#define LMP_MATH_EXTRA_H
-#include "math.h"
-#include "stdio.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <string.h>
#include "error.h"
namespace MathExtra {
diff --git a/src/math_vector.h b/src/math_vector.h
index 000c2fc07f..9304cf0804 100644
--- a/src/math_vector.h
+++ b/src/math_vector.h
@@ -18,8 +18,8 @@
#ifndef LMP_MATH_VECTOR_H
#define LMP_MATH_VECTOR_H
-#include "math.h"
-#include "string.h"
+#include <math.h>
+#include <string.h>
#define VECTOR_NULL {0, 0, 0}
#define SHAPE_NULL {0, 0, 0, 0, 0, 0}
diff --git a/src/memory.cpp b/src/memory.cpp
index b8f71016e0..c3ec21565b 100644
--- a/src/memory.cpp
+++ b/src/memory.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "memory.h"
#include "error.h"
diff --git a/src/memory.h b/src/memory.h
index b5dcd610b0..b83482e4c2 100644
--- a/src/memory.h
+++ b/src/memory.h
@@ -44,7 +44,7 @@ class Memory : protected Pointers {
/* ----------------------------------------------------------------------
create/grow/destroy vecs and multidim arrays with contiguous memory blocks
only use with primitive data types, e.g. 1d vec of ints, 2d array of doubles
- fail() prevents use with pointers,
+ fail() prevents use with pointers,
e.g. 1d vec of int*, due to mismatched destroy
avoid use with non-primitive data types to avoid code bloat
for these other cases, use smalloc/srealloc/sfree directly
@@ -63,7 +63,7 @@ class Memory : protected Pointers {
}
template <typename TYPE>
- TYPE **create(TYPE **&array, int n, const char *name)
+ TYPE **create(TYPE **&array, int n, const char *name)
{fail(name); return NULL;}
/* ----------------------------------------------------------------------
@@ -134,7 +134,7 @@ class Memory : protected Pointers {
TYPE *data = (TYPE *) smalloc(nbytes,name);
nbytes = ((bigint) sizeof(TYPE *)) * n1;
array = (TYPE **) smalloc(nbytes,name);
-
+
bigint n = 0;
for (int i = 0; i < n1; i++) {
array[i] = &data[n];
@@ -156,12 +156,12 @@ class Memory : protected Pointers {
TYPE **grow(TYPE **&array, int n1, int n2, const char *name)
{
if (array == NULL) return create(array,n1,n2,name);
-
+
bigint nbytes = ((bigint) sizeof(TYPE)) * n1*n2;
TYPE *data = (TYPE *) srealloc(array[0],nbytes,name);
nbytes = ((bigint) sizeof(TYPE *)) * n1;
array = (TYPE **) srealloc(array,nbytes,name);
-
+
bigint n = 0;
for (int i = 0; i < n1; i++) {
array[i] = &data[n];
@@ -169,11 +169,11 @@ class Memory : protected Pointers {
}
return array;
}
-
+
template <typename TYPE>
TYPE ***grow(TYPE ***&array, int n1, int n2, const char *name)
{fail(name); return NULL;}
-
+
/* ----------------------------------------------------------------------
destroy a 2d array
------------------------------------------------------------------------- */
@@ -196,12 +196,12 @@ class Memory : protected Pointers {
{
bigint n2sum = 0;
for (int i = 0; i < n1; i++) n2sum += n2[i];
-
+
bigint nbytes = ((bigint) sizeof(TYPE)) * n2sum;
TYPE *data = (TYPE *) smalloc(nbytes,name);
nbytes = ((bigint) sizeof(TYPE *)) * n1;
array = (TYPE **) smalloc(nbytes,name);
-
+
bigint n = 0;
for (int i = 0; i < n1; i++) {
array[i] = &data[n];
@@ -209,11 +209,11 @@ class Memory : protected Pointers {
}
return array;
}
-
+
template <typename TYPE>
TYPE ***create_ragged(TYPE ***&array, int n1, int *n2, const char *name)
{fail(name); return NULL;}
-
+
/* ----------------------------------------------------------------------
create a 2d array with 2nd index from n2lo to n2hi inclusive
cannot grow it
@@ -228,15 +228,15 @@ class Memory : protected Pointers {
for (int i = 0; i < n1; i++) array[i] -= n2lo;
return array;
}
-
+
template <typename TYPE>
TYPE ***create2d_offset(TYPE ***&array, int n1, int n2lo, int n2hi,
const char *name) {fail(name); return NULL;}
-
+
/* ----------------------------------------------------------------------
destroy a 2d array with 2nd index offset
------------------------------------------------------------------------- */
-
+
template <typename TYPE>
void destroy2d_offset(TYPE **&array, int offset)
{
@@ -245,7 +245,7 @@ class Memory : protected Pointers {
sfree(array);
array = NULL;
}
-
+
/* ----------------------------------------------------------------------
create a 3d array
------------------------------------------------------------------------- */
@@ -259,7 +259,7 @@ class Memory : protected Pointers {
TYPE **plane = (TYPE **) smalloc(nbytes,name);
nbytes = ((bigint) sizeof(TYPE **)) * n1;
array = (TYPE ***) smalloc(nbytes,name);
-
+
int i,j;
bigint m;
bigint n = 0;
@@ -287,14 +287,14 @@ class Memory : protected Pointers {
TYPE ***grow(TYPE ***&array, int n1, int n2, int n3, const char *name)
{
if (array == NULL) return create(array,n1,n2,n3,name);
-
+
bigint nbytes = ((bigint) sizeof(TYPE)) * n1*n2*n3;
TYPE *data = (TYPE *) srealloc(array[0][0],nbytes,name);
nbytes = ((bigint) sizeof(TYPE *)) * n1*n2;
TYPE **plane = (TYPE **) srealloc(array[0],nbytes,name);
nbytes = ((bigint) sizeof(TYPE **)) * n1;
array = (TYPE ***) srealloc(array,nbytes,name);
-
+
int i,j;
bigint m;
bigint n = 0;
@@ -308,7 +308,7 @@ class Memory : protected Pointers {
}
return array;
}
-
+
template <typename TYPE>
TYPE ****grow(TYPE ****&array, int n1, int n2, int n3, const char *name)
{fail(name); return NULL;}
@@ -341,7 +341,7 @@ class Memory : protected Pointers {
array -= n1lo;
return array;
}
-
+
template <typename TYPE>
TYPE ****create3d_offset(TYPE ****&array, int n1lo, int n1hi,
int n2, int n3, const char *name)
@@ -378,14 +378,14 @@ class Memory : protected Pointers {
int n2 = n2hi - n2lo + 1;
int n3 = n3hi - n3lo + 1;
create(array,n1,n2,n3,name);
-
+
bigint m = ((bigint) n1) * n2;
for (bigint i = 0; i < m; i++) array[0][i] -= n3lo;
for (int i = 0; i < n1; i++) array[i] -= n2lo;
array -= n1lo;
return array;
}
-
+
template <typename TYPE>
TYPE ****create3d_offset(TYPE ****&array, int n1lo, int n1hi,
int n2lo, int n2hi, int n3lo, int n3hi,
@@ -406,7 +406,7 @@ class Memory : protected Pointers {
sfree(&array[n1_offset]);
array = NULL;
}
-
+
/* ----------------------------------------------------------------------
create a 4d array
------------------------------------------------------------------------- */
@@ -443,7 +443,7 @@ class Memory : protected Pointers {
}
return array;
}
-
+
template <typename TYPE>
TYPE *****create(TYPE *****&array, int n1, int n2, int n3, int n4,
const char *name)
@@ -481,7 +481,7 @@ class Memory : protected Pointers {
int n3 = n3hi - n3lo + 1;
int n4 = n4hi - n4lo + 1;
create(array,n1,n2,n3,n4,name);
-
+
bigint m = ((bigint) n1) * n2 * n3;
for (bigint i = 0; i < m; i++) array[0][0][i] -= n4lo;
m = ((bigint) n1) * n2;
@@ -489,19 +489,19 @@ class Memory : protected Pointers {
for (int i = 0; i < n1; i++) array[i] -= n2lo;
return array;
}
-
+
template <typename TYPE>
TYPE ****create4d_offset(TYPE *****&array, int n1, int n2lo, int n2hi,
int n3lo, int n3hi, int n4lo, int n4hi,
const char *name)
{fail(name); return NULL;}
-
+
/* ----------------------------------------------------------------------
free a 4d array with indices 2,3, and 4 offset
------------------------------------------------------------------------- */
template <typename TYPE>
- void destroy4d_offset(TYPE ****&array,
+ void destroy4d_offset(TYPE ****&array,
int n2_offset, int n3_offset, int n4_offset)
{
if (array == NULL) return;
@@ -530,7 +530,7 @@ class Memory : protected Pointers {
TYPE ****level2 = (TYPE ****) smalloc(nbytes,name);
nbytes = ((bigint) sizeof(TYPE ****)) * n1;
array = (TYPE *****) smalloc(nbytes,name);
-
+
int i,j,k,l;
bigint m1,m2;
bigint n = 0;
@@ -557,7 +557,7 @@ class Memory : protected Pointers {
}
return array;
}
-
+
template <typename TYPE>
TYPE ******create(TYPE ******&array, int n1, int n2, int n3, int n4,
int n5, const char *name)
@@ -578,7 +578,7 @@ class Memory : protected Pointers {
sfree(array);
array = NULL;
}
-
+
/* ----------------------------------------------------------------------
memory usage of arrays, including pointers
------------------------------------------------------------------------- */
@@ -590,7 +590,7 @@ class Memory : protected Pointers {
bigint bytes = ((bigint) sizeof(TYPE)) * n;
return bytes;
}
-
+
template <typename TYPE>
bigint usage(TYPE **array, int n1, int n2)
{
@@ -599,7 +599,7 @@ class Memory : protected Pointers {
bytes += ((bigint) sizeof(TYPE *)) * n1;
return bytes;
}
-
+
template <typename TYPE>
bigint usage(TYPE ***array, int n1, int n2, int n3)
{
@@ -609,7 +609,7 @@ class Memory : protected Pointers {
bytes += ((bigint) sizeof(TYPE **)) * n1;
return bytes;
}
-
+
template <typename TYPE>
bigint usage(TYPE ****array, int n1, int n2, int n3, int n4)
{
diff --git a/src/min.cpp b/src/min.cpp
index 7588211a8c..f447cf3429 100644
--- a/src/min.cpp
+++ b/src/min.cpp
@@ -19,9 +19,9 @@
JR Shewchuk, http://www-2.cs.cmu.edu/~jrs/jrspapers.html#cg
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "min.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/min_cg.cpp b/src/min_cg.cpp
index af3ef5b7a4..9bf41d1687 100644
--- a/src/min_cg.cpp
+++ b/src/min_cg.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "math.h"
-#include "string.h"
+#include <mpi.h>
+#include <math.h>
+#include <string.h>
#include "min_cg.h"
#include "atom.h"
#include "update.h"
diff --git a/src/min_fire.cpp b/src/min_fire.cpp
index 115e91e63c..186c8232a8 100644
--- a/src/min_fire.cpp
+++ b/src/min_fire.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "min_fire.h"
#include "universe.h"
#include "atom.h"
diff --git a/src/min_hftn.cpp b/src/min_hftn.cpp
index cdd9bcda3b..78dbe2836b 100644
--- a/src/min_hftn.cpp
+++ b/src/min_hftn.cpp
@@ -17,8 +17,8 @@
"Parallel Unconstrained Min", Plantenga, SAND98-8201
------------------------------------------------------------------------- */
-#include "math.h"
-#include "string.h"
+#include <math.h>
+#include <string.h>
#include "atom.h"
#include "fix_minimize.h"
#include "min_hftn.h"
diff --git a/src/min_linesearch.cpp b/src/min_linesearch.cpp
index 1becb224fe..3b5566e897 100644
--- a/src/min_linesearch.cpp
+++ b/src/min_linesearch.cpp
@@ -21,7 +21,7 @@
JR Shewchuk, http://www-2.cs.cmu.edu/~jrs/jrspapers.html#cg
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "min_linesearch.h"
#include "atom.h"
#include "update.h"
diff --git a/src/min_quickmin.cpp b/src/min_quickmin.cpp
index 84abf5487f..48aee919e3 100644
--- a/src/min_quickmin.cpp
+++ b/src/min_quickmin.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "math.h"
+#include <mpi.h>
+#include <math.h>
#include "min_quickmin.h"
#include "universe.h"
#include "atom.h"
diff --git a/src/min_sd.cpp b/src/min_sd.cpp
index 1394f379fa..5f97a117e3 100644
--- a/src/min_sd.cpp
+++ b/src/min_sd.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "mpi.h"
+#include <math.h>
+#include <mpi.h>
#include "min_sd.h"
#include "atom.h"
#include "update.h"
diff --git a/src/minimize.cpp b/src/minimize.cpp
index 6483e100bf..d8ac95926c 100644
--- a/src/minimize.cpp
+++ b/src/minimize.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdlib.h"
+#include <stdlib.h>
#include "minimize.h"
#include "domain.h"
#include "update.h"
diff --git a/src/modify.cpp b/src/modify.cpp
index 9ca992738a..ab4275e17d 100644
--- a/src/modify.cpp
+++ b/src/modify.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdio.h"
-#include "string.h"
+#include <stdio.h>
+#include <string.h>
#include "modify.h"
#include "style_compute.h"
#include "style_fix.h"
@@ -231,7 +231,7 @@ void Modify::init()
}
for (i = 0; i < ncompute; i++)
- if (!compute[i]->dynamic_group_allow &&
+ if (!compute[i]->dynamic_group_allow &&
group->dynamic[compute[i]->igroup]) {
char str[128];
sprintf(str,"Compute %s does not allow use of dynamic group",fix[i]->id);
@@ -696,7 +696,7 @@ void Modify::add_fix(int narg, char **arg, int trysuffix)
// since some fixes access domain settings in their constructor
// MUST change NEXCEPT above when add new fix to this list
- const char *exceptions[NEXCEPT] =
+ const char *exceptions[NEXCEPT] =
{"GPU","OMP","INTEL","property/atom","cmap"};
if (domain->box_exist == 0) {
@@ -731,7 +731,7 @@ void Modify::add_fix(int narg, char **arg, int trysuffix)
if (ifix < nfix) {
newflag = 0;
-
+
int match = 0;
if (strcmp(arg[2],fix[ifix]->style) == 0) match = 1;
if (!match && trysuffix && lmp->suffix_enable) {
@@ -955,7 +955,7 @@ void Modify::add_compute(int narg, char **arg, int trysuffix)
}
}
- if (compute[ncompute] == NULL &&
+ if (compute[ncompute] == NULL &&
compute_map->find(arg[2]) != compute_map->end()) {
ComputeCreator compute_creator = (*compute_map)[arg[2]];
compute[ncompute] = compute_creator(lmp,narg,arg);
@@ -989,7 +989,7 @@ void Modify::modify_compute(int narg, char **arg)
int icompute;
for (icompute = 0; icompute < ncompute; icompute++)
if (strcmp(arg[0],compute[icompute]->id) == 0) break;
- if (icompute == ncompute)
+ if (icompute == ncompute)
error->all(FLERR,"Could not find compute_modify ID");
compute[icompute]->modify_params(narg-1,&arg[1]);
diff --git a/src/modify.h b/src/modify.h
index 12a475cf0b..0367761037 100644
--- a/src/modify.h
+++ b/src/modify.h
@@ -14,7 +14,7 @@
#ifndef LMP_MODIFY_H
#define LMP_MODIFY_H
-#include "stdio.h"
+#include <stdio.h>
#include "pointers.h"
#include <map>
#include <string>
diff --git a/src/molecule.cpp b/src/molecule.cpp
index 83157200eb..36239352a3 100644
--- a/src/molecule.cpp
+++ b/src/molecule.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdlib.h"
-#include "string.h"
+#include <stdlib.h>
+#include <string.h>
#include "molecule.h"
#include "atom.h"
#include "atom_vec.h"
@@ -35,7 +35,7 @@ using namespace MathConst;
/* ---------------------------------------------------------------------- */
-Molecule::Molecule(LAMMPS *lmp, int narg, char **arg, int &index) :
+Molecule::Molecule(LAMMPS *lmp, int narg, char **arg, int &index) :
Pointers(lmp)
{
me = comm->me;
@@ -68,8 +68,8 @@ Molecule::Molecule(LAMMPS *lmp, int narg, char **arg, int &index) :
aoffset = force->inumeric(FLERR,arg[iarg+3]);
doffset = force->inumeric(FLERR,arg[iarg+4]);
ioffset = force->inumeric(FLERR,arg[iarg+5]);
- if (toffset < 0 || boffset < 0 || aoffset < 0 ||
- doffset < 0 || ioffset < 0)
+ if (toffset < 0 || boffset < 0 || aoffset < 0 ||
+ doffset < 0 || ioffset < 0)
error->all(FLERR,"Illegal molecule command");
iarg += 6;
} else if (strcmp(arg[iarg],"toff") == 0) {
@@ -129,7 +129,7 @@ Molecule::Molecule(LAMMPS *lmp, int narg, char **arg, int &index) :
if (me == 0) fclose(fp);
// stats
-
+
if (me == 0) {
if (screen)
fprintf(screen,"Read molecule %s:\n"
@@ -336,10 +336,10 @@ void Molecule::compute_inertia()
tensor[1][2] = tensor[2][1] = itensor[3];
tensor[0][2] = tensor[2][0] = itensor[4];
tensor[0][1] = tensor[1][0] = itensor[5];
-
+
if (MathExtra::jacobi(tensor,inertia,evectors))
error->all(FLERR,"Insufficient Jacobi rotations for rigid molecule");
-
+
ex[0] = evectors[0][0];
ex[1] = evectors[1][0];
ex[2] = evectors[2][0];
@@ -351,23 +351,23 @@ void Molecule::compute_inertia()
ez[2] = evectors[2][2];
// if any principal moment < scaled EPSILON, set to 0.0
-
+
double max;
max = MAX(inertia[0],inertia[1]);
max = MAX(max,inertia[2]);
-
+
if (inertia[0] < EPSILON*max) inertia[0] = 0.0;
if (inertia[1] < EPSILON*max) inertia[1] = 0.0;
if (inertia[2] < EPSILON*max) inertia[2] = 0.0;
-
+
// enforce 3 evectors as a right-handed coordinate system
// flip 3rd vector if needed
-
+
MathExtra::cross3(ex,ey,cross);
if (MathExtra::dot3(cross,ez) < 0.0) MathExtra::negate3(ez);
-
+
// create quaternion
-
+
MathExtra::exyz_to_q(ex,ey,ez,quat);
// compute displacements in body frame defined by quat
@@ -454,16 +454,16 @@ void Molecule::read(int flag)
if (natoms < 1) error->all(FLERR,"No or invalid atom count in molecule file");
if (nbonds < 0) error->all(FLERR,"Invalid bond count in molecule file");
if (nangles < 0) error->all(FLERR,"Invalid angle count in molecule file");
- if (ndihedrals < 0)
+ if (ndihedrals < 0)
error->all(FLERR,"Invalid dihedral count in molecule file");
- if (nimpropers < 0)
+ if (nimpropers < 0)
error->all(FLERR,"Invalid improper count in molecule file");
// count = vector for tallying bonds,angles,etc per atom
if (flag == 0) memory->create(count,natoms,"molecule:count");
else count = NULL;
-
+
// grab keyword and skip next line
parse_keyword(0,line,keyword);
@@ -499,7 +499,7 @@ void Molecule::read(int flag)
bondflag = tag_require = 1;
bonds(flag,line);
} else if (strcmp(keyword,"Angles") == 0) {
- if (nangles == 0)
+ if (nangles == 0)
error->all(FLERR,"Molecule file has angles but no nangles setting");
angleflag = tag_require = 1;
angles(flag,line);
@@ -529,20 +529,20 @@ void Molecule::read(int flag)
} else if (strcmp(keyword,"Shake Atoms") == 0) {
shakeatomflag = tag_require = 1;
if (shaketypeflag) shakeflag = 1;
- if (!shakeflagflag)
+ if (!shakeflagflag)
error->all(FLERR,"Molecule file shake flags not before shake atoms");
if (flag) shakeatom_read(line);
else skip_lines(natoms,line);
} else if (strcmp(keyword,"Shake Bond Types") == 0) {
shaketypeflag = 1;
if (shakeatomflag) shakeflag = 1;
- if (!shakeflagflag)
+ if (!shakeflagflag)
error->all(FLERR,"Molecule file shake flags not before shake bonds");
if (flag) shaketype_read(line);
else skip_lines(natoms,line);
} else error->one(FLERR,"Unknown section in molecule file");
-
+
parse_keyword(1,line,keyword);
}
@@ -555,7 +555,7 @@ void Molecule::read(int flag)
if (flag == 0) {
if ((nspecialflag && !specialflag) || (!nspecialflag && specialflag))
error->all(FLERR,"Molecule file needs both Special Bond sections");
- if (specialflag && !bondflag)
+ if (specialflag && !bondflag)
error->all(FLERR,"Molecule file has special flags but no bonds");
if ((shakeflagflag || shakeatomflag || shaketypeflag) && !shakeflag)
error->all(FLERR,"Molecule file shake info is incomplete");
@@ -582,7 +582,7 @@ void Molecule::coords(char *line)
readline(line);
if (i == 0) {
int nwords = atom->count_words(line);
- if (nwords != 4)
+ if (nwords != 4)
error->all(FLERR,"Invalid Coords section in molecule file");
}
sscanf(line,"%d %lg %lg %lg",&tmp,&x[i][0],&x[i][1],&x[i][2]);
@@ -593,7 +593,7 @@ void Molecule::coords(char *line)
if (domain->dimension == 2) {
for (int i = 0; i < natoms; i++)
- if (x[i][2] != 0.0)
+ if (x[i][2] != 0.0)
error->all(FLERR,"Molecule file z coord must be 0.0 for 2d");
}
}
@@ -610,7 +610,7 @@ void Molecule::types(char *line)
readline(line);
if (i == 0) {
int nwords = atom->count_words(line);
- if (nwords != 2)
+ if (nwords != 2)
error->all(FLERR,"Invalid Types section in molecule file");
}
sscanf(line,"%d %d",&tmp,&type[i]);
@@ -636,7 +636,7 @@ void Molecule::charges(char *line)
readline(line);
if (i == 0) {
int nwords = atom->count_words(line);
- if (nwords != 2)
+ if (nwords != 2)
error->all(FLERR,"Invalid Charges section in molecule file");
}
sscanf(line,"%d %lg",&tmp,&q[i]);
@@ -655,7 +655,7 @@ void Molecule::diameters(char *line)
readline(line);
if (i == 0) {
int nwords = atom->count_words(line);
- if (nwords != 2)
+ if (nwords != 2)
error->all(FLERR,"Invalid Diameters section in molecule file");
}
sscanf(line,"%d %lg",&tmp,&radius[i]);
@@ -665,7 +665,7 @@ void Molecule::diameters(char *line)
}
for (int i = 0; i < natoms; i++)
- if (radius[i] < 0.0)
+ if (radius[i] < 0.0)
error->all(FLERR,"Invalid atom diameter in molecule file");
}
@@ -680,7 +680,7 @@ void Molecule::masses(char *line)
readline(line);
if (i == 0) {
int nwords = atom->count_words(line);
- if (nwords != 2)
+ if (nwords != 2)
error->all(FLERR,"Invalid Masses section in molecule file");
}
sscanf(line,"%d %lg",&tmp,&rmass[i]);
@@ -714,7 +714,7 @@ void Molecule::bonds(int flag, char *line)
readline(line);
if (i == 0) {
int nwords = atom->count_words(line);
- if (nwords != 4)
+ if (nwords != 4)
error->all(FLERR,"Invalid Bonds section in molecule file");
}
sscanf(line,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT,
@@ -776,7 +776,7 @@ void Molecule::angles(int flag, char *line)
readline(line);
if (i == 0) {
int nwords = atom->count_words(line);
- if (nwords != 5)
+ if (nwords != 5)
error->all(FLERR,"Invalid Angles section in molecule file");
}
sscanf(line,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT,
@@ -852,10 +852,10 @@ void Molecule::dihedrals(int flag, char *line)
readline(line);
if (i == 0) {
int nwords = atom->count_words(line);
- if (nwords != 6)
+ if (nwords != 6)
error->all(FLERR,"Invalid Dihedrals section in molecule file");
}
- sscanf(line,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT " "
+ sscanf(line,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT " ",
&tmp,&itype,&atom1,&atom2,&atom3,&atom4);
itype += doffset;
@@ -943,10 +943,10 @@ void Molecule::impropers(int flag, char *line)
readline(line);
if (i == 0) {
int nwords = atom->count_words(line);
- if (nwords != 6)
+ if (nwords != 6)
error->all(FLERR,"Invalid Impropers section in molecule file");
}
- sscanf(line,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT " "
+ sscanf(line,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT " ",
&tmp,&itype,&atom1,&atom2,&atom3,&atom4);
itype += ioffset;
@@ -1028,7 +1028,7 @@ void Molecule::nspecial_read(int flag, char *line)
readline(line);
if (i == 0) {
int nwords = atom->count_words(line);
- if (nwords != 4)
+ if (nwords != 4)
error->all(FLERR,"Invalid Special Bond Counts section in "
"molecule file");
}
@@ -1094,8 +1094,8 @@ void Molecule::special_generate()
error->one(FLERR,"Molecule auto special bond generation overflow");
special[i][count[i]++] = atom2 + 1;
special[atom2][count[atom2]++] = i + 1;
- }
- }
+ }
+ }
} else {
for (int i = 0; i < natoms; i++) {
nspecial[i][0] = num_bond[i];
@@ -1104,7 +1104,7 @@ void Molecule::special_generate()
atom2 = bond_atom[i][j];
if (count[atom1] >= maxspecial)
error->one(FLERR,"");
- special[i][count[atom1]++] = atom2;
+ special[i][count[atom1]++] = atom2;
}
}
}
@@ -1129,15 +1129,15 @@ void Molecule::special_generate()
error->one(FLERR,"");
special[i][count[i]++] = special[special[i][m]-1][j];
nspecial[i][1]++;
- }
+ }
}
- }
+ }
}
// 1-4 neighbors with no duplicates
for (int i = 0; i < natoms; i++) nspecial[i][2] = nspecial[i][1];
-
+
for (int i = 0; i < natoms; i++) {
for (int m = nspecial[i][0]; m < nspecial[i][1]; m++) {
for (int j = 0; j < nspecial[special[i][m]-1][0]; j++) {
@@ -1153,9 +1153,9 @@ void Molecule::special_generate()
error->one(FLERR,"");
special[i][count[i]++] = special[special[i][m]-1][j];
nspecial[i][2]++;
- }
+ }
}
- }
+ }
}
}
@@ -1172,7 +1172,7 @@ void Molecule::shakeflag_read(char *line)
}
for (int i = 0; i < natoms; i++)
- if (shake_flag[i] < 0 || shake_flag[i] > 4)
+ if (shake_flag[i] < 0 || shake_flag[i] > 4)
error->all(FLERR,"Invalid shake flag in molecule file");
}
@@ -1195,7 +1195,7 @@ void Molecule::shakeatom_read(char *line)
sscanf(line,"%d " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT,
&tmp,&shake_atom[i][0],&shake_atom[i][1],&shake_atom[i][2]);
else if (shake_flag[i] == 4)
- sscanf(line,"%d " TAGINT_FORMAT " " TAGINT_FORMAT " "
+ sscanf(line,"%d " TAGINT_FORMAT " " TAGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT,
&tmp,&shake_atom[i][0],&shake_atom[i][1],
&shake_atom[i][2],&shake_atom[i][3]);
@@ -1257,7 +1257,7 @@ void Molecule::check_attributes(int flag)
for (int i = imol; i < imol+n; i++) {
Molecule *onemol = atom->molecules[imol];
-
+
// check per-atom attributes of molecule
// warn if not a match
@@ -1266,7 +1266,7 @@ void Molecule::check_attributes(int flag)
if (onemol->radiusflag && !atom->radius_flag) mismatch = 1;
if (onemol->rmassflag && !atom->rmass_flag) mismatch = 1;
- if (mismatch && me == 0)
+ if (mismatch && me == 0)
error->warning(FLERR,
"Molecule attributes do not match system attributes");
@@ -1278,7 +1278,7 @@ void Molecule::check_attributes(int flag)
if (atom->ndihedraltypes < onemol->ndihedraltypes) mismatch = 1;
if (atom->nimpropertypes < onemol->nimpropertypes) mismatch = 1;
- if (mismatch)
+ if (mismatch)
error->all(FLERR,"Molecule topology type exceeds system topology type");
// for molecular atom styles, check bond_per_atom,etc + maxspecial
@@ -1295,13 +1295,13 @@ void Molecule::check_attributes(int flag)
atom->improper_per_atom < onemol->improper_per_atom) mismatch = 1;
if (atom->maxspecial < onemol->maxspecial) mismatch = 1;
- if (mismatch)
+ if (mismatch)
error->all(FLERR,"Molecule toplogy/atom exceeds system topology/atom");
}
// warn if molecule topology defined but no special settings
- if (onemol->bondflag && !onemol->specialflag)
+ if (onemol->bondflag && !onemol->specialflag)
if (me == 0) error->warning(FLERR,"Molecule has bond topology "
"but no special bond settings");
}
@@ -1457,24 +1457,24 @@ void Molecule::deallocate()
memory->destroy(q);
memory->destroy(radius);
memory->destroy(rmass);
-
+
memory->destroy(num_bond);
memory->destroy(bond_type);
memory->destroy(bond_atom);
-
+
memory->destroy(num_angle);
memory->destroy(angle_type);
memory->destroy(angle_atom1);
memory->destroy(angle_atom2);
memory->destroy(angle_atom3);
-
+
memory->destroy(num_dihedral);
memory->destroy(dihedral_type);
memory->destroy(dihedral_atom1);
memory->destroy(dihedral_atom2);
memory->destroy(dihedral_atom3);
memory->destroy(dihedral_atom4);
-
+
memory->destroy(num_improper);
memory->destroy(improper_type);
memory->destroy(improper_atom1);
@@ -1642,7 +1642,7 @@ void Molecule::print()
for (int i = 0; i < natoms; i++)
printf(" %d %g\n",i+1,rmass[i]);
}
-
+
if (bondflag) {
printf( "Bonds:\n");
for (int i = 0; i < natoms; i++) {
diff --git a/src/molecule.h b/src/molecule.h
index 9ecb86b202..35b25edf88 100644
--- a/src/molecule.h
+++ b/src/molecule.h
@@ -63,15 +63,15 @@ class Molecule : protected Pointers {
int *num_bond; // bonds, angles, dihedrals, impropers for each atom
int **bond_type;
tagint **bond_atom;
-
+
int *num_angle;
int **angle_type;
tagint **angle_atom1,**angle_atom2,**angle_atom3;
-
+
int *num_dihedral;
int **dihedral_type;
tagint **dihedral_atom1,**dihedral_atom2,**dihedral_atom3,**dihedral_atom4;
-
+
int *num_improper;
int **improper_type;
tagint **improper_atom1,**improper_atom2,**improper_atom3,**improper_atom4;
@@ -93,7 +93,7 @@ class Molecule : protected Pointers {
double maxradius; // max radius of any atom in molecule
double molradius; // radius of molecule from geometric center
- // including finite-size particle radii
+ // including finite-size particle radii
int comatom; // index (1-Natom) of atom closest to COM
double maxextent; // furthest any atom in molecule is from comatom
diff --git a/src/my_page.h b/src/my_page.h
index 8add279494..9df08dc31c 100644
--- a/src/my_page.h
+++ b/src/my_page.h
@@ -48,7 +48,7 @@ methods:
#ifndef LAMMPS_MY_PAGE_H
#define LAMMPS_MY_PAGE_H
-#include "stdlib.h"
+#include <stdlib.h>
namespace LAMMPS_NS {
template<class T>
@@ -67,7 +67,7 @@ class MyPage {
// (re)initialize allocation params
// also allocate first page(s)
- int init(int user_maxchunk = 1, int user_pagesize = 1024,
+ int init(int user_maxchunk = 1, int user_pagesize = 1024,
int user_pagedelta = 1) {
maxchunk = user_maxchunk;
pagesize = user_pagesize;
@@ -146,7 +146,7 @@ class MyPage {
// get ptr to location that can store maxchunk datums
// will return same ptr as previous call if vgot() not called
// return NULL if run out of memory
-
+
T *vget() {
if (index+maxchunk <= pagesize) return &page[index];
ipage++;
@@ -196,7 +196,7 @@ class MyPage {
int npage; // # of allocated pages
int ipage; // index of current page
int index; // current index on current page
-
+
int maxchunk; // max # of datums in one requested chunk
int pagesize; // # of datums in one page, default = 1024
int pagedelta; // # of pages to allocate at once, default = 1
diff --git a/src/my_pool_chunk.h b/src/my_pool_chunk.h
index 9ae98cee34..e3a1775c13 100644
--- a/src/my_pool_chunk.h
+++ b/src/my_pool_chunk.h
@@ -43,7 +43,7 @@ public varaibles:
#ifndef LAMMPS_MY_POOL_CHUNK_H
#define LAMMPS_MY_POOL_CHUNK_H
-#include "stdlib.h"
+#include <stdlib.h>
namespace LAMMPS_NS {
diff --git a/src/neigh_bond.cpp b/src/neigh_bond.cpp
index b3dcc22665..c85407c45b 100644
--- a/src/neigh_bond.cpp
+++ b/src/neigh_bond.cpp
@@ -59,7 +59,7 @@ void Neighbor::bond_all()
nmissing++;
if (lostbond == ERROR) {
char str[128];
- sprintf(str,"Bond atoms " TAGINT_FORMAT " " TAGINT_FORMAT
+ sprintf(str,"Bond atoms " TAGINT_FORMAT " " TAGINT_FORMAT
" missing on proc %d at step " BIGINT_FORMAT,
tag[i],bond_atom[i][m],me,update->ntimestep);
error->one(FLERR,str);
@@ -131,7 +131,7 @@ void Neighbor::bond_template()
nmissing++;
if (lostbond == ERROR) {
char str[128];
- sprintf(str,"Bond atoms " TAGINT_FORMAT " " TAGINT_FORMAT
+ sprintf(str,"Bond atoms " TAGINT_FORMAT " " TAGINT_FORMAT
" missing on proc %d at step " BIGINT_FORMAT,
tag[i],bond_atom[iatom][m]+tagprev,me,update->ntimestep);
error->one(FLERR,str);
@@ -190,7 +190,7 @@ void Neighbor::bond_partial()
nmissing++;
if (lostbond == ERROR) {
char str[128];
- sprintf(str,"Bond atoms " TAGINT_FORMAT " " TAGINT_FORMAT
+ sprintf(str,"Bond atoms " TAGINT_FORMAT " " TAGINT_FORMAT
" missing on proc %d at step " BIGINT_FORMAT,
tag[i],bond_atom[i][m],me,update->ntimestep);
error->one(FLERR,str);
@@ -229,7 +229,7 @@ void Neighbor::bond_check()
{
int i,j;
double dx,dy,dz,dxstart,dystart,dzstart;
-
+
double **x = atom->x;
int flag = 0;
@@ -276,7 +276,7 @@ void Neighbor::angle_all()
if (lostbond == ERROR) {
char str[128];
sprintf(str,"Angle atoms "
- TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT
+ TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT
" missing on proc %d at step " BIGINT_FORMAT,
angle_atom1[i][m],angle_atom2[i][m],angle_atom3[i][m],
me,update->ntimestep);
@@ -357,7 +357,7 @@ void Neighbor::angle_template()
if (lostbond == ERROR) {
char str[128];
sprintf(str,"Angle atoms "
- TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT
+ TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT
" missing on proc %d at step " BIGINT_FORMAT,
angle_atom1[iatom][m]+tagprev,angle_atom2[iatom][m]+tagprev,
angle_atom3[iatom][m]+tagprev,
@@ -425,7 +425,7 @@ void Neighbor::angle_partial()
if (lostbond == ERROR) {
char str[128];
sprintf(str,"Angle atoms "
- TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT
+ TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT
" missing on proc %d at step " BIGINT_FORMAT,
angle_atom1[i][m],angle_atom2[i][m],angle_atom3[i][m],
me,update->ntimestep);
@@ -468,7 +468,7 @@ void Neighbor::angle_check()
{
int i,j,k;
double dx,dy,dz,dxstart,dystart,dzstart;
-
+
double **x = atom->x;
int flag = 0;
@@ -531,8 +531,8 @@ void Neighbor::dihedral_all()
if (lostbond == ERROR) {
char str[128];
sprintf(str,"Dihedral atoms "
- TAGINT_FORMAT " " TAGINT_FORMAT " "
- TAGINT_FORMAT " " TAGINT_FORMAT
+ TAGINT_FORMAT " " TAGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT
" missing on proc %d at step " BIGINT_FORMAT,
dihedral_atom1[i][m],dihedral_atom2[i][m],
dihedral_atom3[i][m],dihedral_atom4[i][m],
@@ -618,8 +618,8 @@ void Neighbor::dihedral_template()
if (lostbond == ERROR) {
char str[128];
sprintf(str,"Dihedral atoms "
- TAGINT_FORMAT " " TAGINT_FORMAT " "
- TAGINT_FORMAT " " TAGINT_FORMAT
+ TAGINT_FORMAT " " TAGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT
" missing on proc %d at step " BIGINT_FORMAT,
dihedral_atom1[iatom][m]+tagprev,
dihedral_atom2[iatom][m]+tagprev,
@@ -694,8 +694,8 @@ void Neighbor::dihedral_partial()
if (lostbond == ERROR) {
char str[128];
sprintf(str,"Dihedral atoms "
- TAGINT_FORMAT " " TAGINT_FORMAT " "
- TAGINT_FORMAT " " TAGINT_FORMAT
+ TAGINT_FORMAT " " TAGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT
" missing on proc %d at step " BIGINT_FORMAT,
dihedral_atom1[i][m],dihedral_atom2[i][m],
dihedral_atom3[i][m],dihedral_atom4[i][m],
@@ -742,7 +742,7 @@ void Neighbor::dihedral_check(int nlist, int **list)
{
int i,j,k,l;
double dx,dy,dz,dxstart,dystart,dzstart;
-
+
double **x = atom->x;
int flag = 0;
@@ -788,7 +788,7 @@ void Neighbor::dihedral_check(int nlist, int **list)
int flag_all;
MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_SUM,world);
- if (flag_all)
+ if (flag_all)
error->all(FLERR,"Dihedral/improper extent > half of periodic box length");
}
@@ -822,8 +822,8 @@ void Neighbor::improper_all()
if (lostbond == ERROR) {
char str[128];
sprintf(str,"Improper atoms "
- TAGINT_FORMAT " " TAGINT_FORMAT " "
- TAGINT_FORMAT " " TAGINT_FORMAT
+ TAGINT_FORMAT " " TAGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT
" missing on proc %d at step " BIGINT_FORMAT,
improper_atom1[i][m],improper_atom2[i][m],
improper_atom3[i][m],improper_atom4[i][m],
@@ -909,8 +909,8 @@ void Neighbor::improper_template()
if (lostbond == ERROR) {
char str[128];
sprintf(str,"Improper atoms "
- TAGINT_FORMAT " " TAGINT_FORMAT " "
- TAGINT_FORMAT " " TAGINT_FORMAT
+ TAGINT_FORMAT " " TAGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT
" missing on proc %d at step " BIGINT_FORMAT,
improper_atom1[iatom][m]+tagprev,
improper_atom2[iatom][m]+tagprev,
@@ -985,8 +985,8 @@ void Neighbor::improper_partial()
if (lostbond == ERROR) {
char str[128];
sprintf(str,"Improper atoms "
- TAGINT_FORMAT " " TAGINT_FORMAT " "
- TAGINT_FORMAT " " TAGINT_FORMAT
+ TAGINT_FORMAT " " TAGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT
" missing on proc %d at step " BIGINT_FORMAT,
improper_atom1[i][m],improper_atom2[i][m],
improper_atom3[i][m],improper_atom4[i][m],
diff --git a/src/neigh_list.cpp b/src/neigh_list.cpp
index 56577ed63c..e4015e6bb1 100644
--- a/src/neigh_list.cpp
+++ b/src/neigh_list.cpp
@@ -103,7 +103,7 @@ NeighList::~NeighList()
/* ---------------------------------------------------------------------- */
-void NeighList::setup_pages(int pgsize_caller, int oneatom_caller,
+void NeighList::setup_pages(int pgsize_caller, int oneatom_caller,
int dnum_caller)
{
pgsize = pgsize_caller;
diff --git a/src/neigh_request.cpp b/src/neigh_request.cpp
index 5f47bf5da4..7c9cd448c7 100644
--- a/src/neigh_request.cpp
+++ b/src/neigh_request.cpp
@@ -104,7 +104,7 @@ int NeighRequest::identical(NeighRequest *other)
// prevents an old fix from being unfix/refix in same memory location
// and appearing to be old, when it is really new
// only needed for classes with persistent neigh lists: Fix, Compute, Pair
-
+
if (other->unprocessed) same = 0;
if (requestor != other->requestor) same = 0;
diff --git a/src/neigh_request.h b/src/neigh_request.h
index 53ca2b797c..e835230638 100644
--- a/src/neigh_request.h
+++ b/src/neigh_request.h
@@ -41,7 +41,7 @@ class NeighRequest : protected Pointers {
int full; // 1 if full neigh list
int full_cluster; // only used by Kokkos pair styles
- int gran; // 1 if granular list
+ int gran; // 1 if granular list
int granhistory; // 1 if granular history list
int respainner; // 1 if a rRESPA inner list
@@ -89,7 +89,7 @@ class NeighRequest : protected Pointers {
int kokkos_host;
int kokkos_device;
-
+
// set by neighbor and pair_hybrid after all requests are made
// these settings do not change kind value
diff --git a/src/neighbor.cpp b/src/neighbor.cpp
index 4e93ae9cd9..9844226a52 100644
--- a/src/neighbor.cpp
+++ b/src/neighbor.cpp
@@ -15,10 +15,10 @@
Contributing author (triclinic and multi-neigh) : Pieter in 't Veld (SNL)
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <mpi.h>
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
@@ -170,24 +170,24 @@ Neighbor::~Neighbor()
delete [] cuttype;
delete [] cuttypesq;
delete [] fixchecklist;
-
+
memory->destroy(xhold);
-
+
memory->destroy(binhead);
memory->destroy(bins);
-
+
memory->destroy(ex1_type);
memory->destroy(ex2_type);
memory->destroy(ex_type);
-
+
memory->destroy(ex1_group);
memory->destroy(ex2_group);
delete [] ex1_bit;
delete [] ex2_bit;
-
+
memory->destroy(ex_mol_group);
delete [] ex_mol_bit;
-
+
for (int i = 0; i < nlist; i++) delete lists[i];
delete [] lists;
delete [] pair_build;
@@ -195,12 +195,12 @@ Neighbor::~Neighbor()
delete [] blist;
delete [] glist;
delete [] slist;
-
+
for (int i = 0; i < nrequest; i++) delete requests[i];
memory->sfree(requests);
for (int i = 0; i < old_nrequest; i++) delete old_requests[i];
memory->sfree(old_requests);
-
+
memory->destroy(bondlist);
memory->destroy(anglelist);
memory->destroy(dihedrallist);
@@ -449,7 +449,7 @@ void Neighbor::init()
// no need to re-create if:
// neigh style, triclinic, pgsize, oneatom have not changed
// current requests = old requests
- // first archive request params for current requests
+ // first archive request params for current requests
// before Neighbor possibly changes them below
for (i = 0; i < nrequest; i++) requests[i]->archive();
@@ -594,7 +594,7 @@ void Neighbor::init()
requests[i]->half_from_full = 1;
lists[i]->listfull = lists[j];
}
-
+
// fix/compute requests:
// whether request is occasional or not doesn't matter
// if request = half and non-skip pair half/respaouter exists,
@@ -792,7 +792,7 @@ void Neighbor::init()
// output neighbor list info, only first time or when info changes
- if (!same || every != old_every || delay != old_delay ||
+ if (!same || every != old_every || delay != old_delay ||
old_check != dist_check || old_cutoff != cutneighmax) {
if (me == 0) {
const double cutghost = MAX(cutneighmax,comm->cutghostuser);
@@ -817,7 +817,7 @@ void Neighbor::init()
fprintf(logfile," ghost atom cutoff = %g\n",cutghost);
if (style != NSQ)
fprintf(logfile," binsize = %g -> bins = %g %g %g\n",binsize,
- ceil(bbox[0]/binsize), ceil(bbox[1]/binsize),
+ ceil(bbox[0]/binsize), ceil(bbox[1]/binsize),
ceil(bbox[2]/binsize));
}
if (screen) {
@@ -1069,7 +1069,7 @@ void Neighbor::choose_build(int index, NeighRequest *rq)
else pb = &Neighbor::half_bin_no_newton_ghost;
} else if (triclinic == 0) {
pb = &Neighbor::half_bin_newton;
- } else if (triclinic == 1)
+ } else if (triclinic == 1)
pb = &Neighbor::half_bin_newton_tri;
} else if (rq->newton == 1) {
if (triclinic == 0) pb = &Neighbor::half_bin_newton;
@@ -2140,7 +2140,7 @@ bigint Neighbor::memory_usage()
bytes += memory->usage(binhead,maxhead);
}
- for (int i = 0; i < nrequest; i++)
+ for (int i = 0; i < nrequest; i++)
if (lists[i]) bytes += lists[i]->memory_usage();
bytes += memory->usage(bondlist,maxbond,3);
diff --git a/src/output.cpp b/src/output.cpp
index 44892f5bd8..db667e8694 100644
--- a/src/output.cpp
+++ b/src/output.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "output.h"
#include "style_dump.h"
#include "atom.h"
@@ -552,7 +552,7 @@ void Output::add_dump(int narg, char **arg)
error->all(FLERR,"Reuse of dump ID");
int igroup = group->find(arg[1]);
if (igroup == -1) error->all(FLERR,"Could not find dump group ID");
- if (force->inumeric(FLERR,arg[3]) <= 0)
+ if (force->inumeric(FLERR,arg[3]) <= 0)
error->all(FLERR,"Invalid dump frequency");
// extend Dump list if necessary
@@ -771,7 +771,7 @@ void Output::create_restart(int narg, char **arg)
if (strchr(arg[1],'%')) multiproc = comm->nprocs;
else multiproc = 0;
if (nfile == 2) {
- if (multiproc && !strchr(arg[2],'%'))
+ if (multiproc && !strchr(arg[2],'%'))
error->all(FLERR,"Both restart files must use % or neither");
if (!multiproc && strchr(arg[2],'%'))
error->all(FLERR,"Both restart files must use % or neither");
@@ -781,7 +781,7 @@ void Output::create_restart(int narg, char **arg)
if (strstr(arg[1],".mpi")) mpiioflag = 1;
else mpiioflag = 0;
if (nfile == 2) {
- if (mpiioflag && !strstr(arg[2],".mpi"))
+ if (mpiioflag && !strstr(arg[2],".mpi"))
error->all(FLERR,"Both restart files must use MPI-IO or neither");
if (!mpiioflag && strstr(arg[2],".mpi"))
error->all(FLERR,"Both restart files must use MPI-IO or neither");
diff --git a/src/pair.cpp b/src/pair.cpp
index 665615edd0..ffeabde416 100644
--- a/src/pair.cpp
+++ b/src/pair.cpp
@@ -15,14 +15,14 @@
Contributing author: Paul Crozier (SNL)
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "ctype.h"
-#include "float.h"
-#include "limits.h"
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <mpi.h>
+#include <ctype.h>
+#include <float.h>
+#include <limits.h>
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair.h"
#include "atom.h"
#include "neighbor.h"
@@ -210,11 +210,11 @@ void Pair::init()
if (manybody_flag && atom->molecular) {
int flag = 0;
- if (atom->nbonds > 0 && force->special_lj[1] == 0.0 &&
+ if (atom->nbonds > 0 && force->special_lj[1] == 0.0 &&
force->special_coul[1] == 0.0) flag = 1;
- if (atom->nangles > 0 && force->special_lj[2] == 0.0 &&
+ if (atom->nangles > 0 && force->special_lj[2] == 0.0 &&
force->special_coul[2] == 0.0) flag = 1;
- if (atom->ndihedrals > 0 && force->special_lj[3] == 0.0 &&
+ if (atom->ndihedrals > 0 && force->special_lj[3] == 0.0 &&
force->special_coul[3] == 0.0) flag = 1;
if (flag && comm->me == 0)
error->warning(FLERR,"Using a manybody potential with "
@@ -321,9 +321,9 @@ void Pair::init_tables(double cut_coul, double *cut_respa)
if (force->kspace == NULL)
error->all(FLERR,"Pair style requires a KSpace style");
double g_ewald = force->kspace->g_ewald;
-
+
double cut_coulsq = cut_coul * cut_coul;
-
+
tabinnersq = tabinner*tabinner;
init_bitmap(tabinner,cut_coul,ncoultablebits,
masklo,maskhi,ncoulmask,ncoulshiftbits);
@@ -530,33 +530,33 @@ void Pair::init_tables_disp(double cut_lj_global)
double rsq;
double g_ewald_6 = force->kspace->g_ewald_6;
double g2 = g_ewald_6*g_ewald_6, g6 = g2*g2*g2, g8 = g6*g2;
-
+
tabinnerdispsq = tabinner_disp*tabinner_disp;
init_bitmap(tabinner_disp,cut_lj_global,ndisptablebits,
masklo,maskhi,ndispmask,ndispshiftbits);
-
+
int ntable = 1;
for (int i = 0; i < ndisptablebits; i++) ntable *= 2;
-
+
// linear lookup tables of length N = 2^ndisptablebits
// stored value = value at lower edge of bin
// d values = delta from lower edge to upper edge of bin
-
+
if (fdisptable) free_disp_tables();
-
+
memory->create(rdisptable,ntable,"pair:rdisptable");
memory->create(fdisptable,ntable,"pair:fdisptable");
memory->create(edisptable,ntable,"pair:edisptable");
memory->create(drdisptable,ntable,"pair:drdisptable");
memory->create(dfdisptable,ntable,"pair:dfdisptable");
memory->create(dedisptable,ntable,"pair:dedisptable");
-
+
union_int_float_t rsq_lookup;
union_int_float_t minrsq_lookup;
int itablemin;
minrsq_lookup.i = 0 << ndispshiftbits;
minrsq_lookup.i |= maskhi;
-
+
for (int i = 0; i < ntable; i++) {
rsq_lookup.i = i << ndispshiftbits;
rsq_lookup.i |= masklo;
@@ -567,38 +567,38 @@ void Pair::init_tables_disp(double cut_lj_global)
rsq = rsq_lookup.f;
register double x2 = g2*rsq, a2 = 1.0/x2;
x2 = a2*exp(-x2);
-
+
rdisptable[i] = rsq_lookup.f;
fdisptable[i] = g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq;
edisptable[i] = g6*((a2+1.0)*a2+0.5)*x2;
-
+
minrsq_lookup.f = MIN(minrsq_lookup.f,rsq_lookup.f);
}
-
+
tabinnerdispsq = minrsq_lookup.f;
-
+
int ntablem1 = ntable - 1;
-
+
for (int i = 0; i < ntablem1; i++) {
drdisptable[i] = 1.0/(rdisptable[i+1] - rdisptable[i]);
dfdisptable[i] = fdisptable[i+1] - fdisptable[i];
dedisptable[i] = edisptable[i+1] - edisptable[i];
}
-
+
// get the delta values for the last table entries
// tables are connected periodically between 0 and ntablem1
-
+
drdisptable[ntablem1] = 1.0/(rdisptable[0] - rdisptable[ntablem1]);
dfdisptable[ntablem1] = fdisptable[0] - fdisptable[ntablem1];
dedisptable[ntablem1] = edisptable[0] - edisptable[ntablem1];
-
+
// get the correct delta values at itablemax
// smallest r is in bin itablemin
// largest r is in bin itablemax, which is itablemin-1,
// or ntablem1 if itablemin=0
// deltas at itablemax only needed if corresponding rsq < cut*cut
// if so, compute deltas between rsq and cut*cut
-
+
double f_tmp,e_tmp;
double cut_lj_globalsq;
itablemin = minrsq_lookup.i & ndispmask;
@@ -607,15 +607,15 @@ void Pair::init_tables_disp(double cut_lj_global)
if (itablemin == 0) itablemax = ntablem1;
rsq_lookup.i = itablemax << ndispshiftbits;
rsq_lookup.i |= maskhi;
-
+
if (rsq_lookup.f < (cut_lj_globalsq = cut_lj_global * cut_lj_global)) {
rsq_lookup.f = cut_lj_globalsq;
-
+
register double x2 = g2*rsq, a2 = 1.0/x2;
x2 = a2*exp(-x2);
f_tmp = g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq;
e_tmp = g6*((a2+1.0)*a2+0.5)*x2;
-
+
drdisptable[itablemax] = 1.0/(rsq_lookup.f - rdisptable[itablemax]);
dfdisptable[itablemax] = f_tmp - fdisptable[itablemax];
dedisptable[itablemax] = e_tmp - edisptable[itablemax];
@@ -931,7 +931,7 @@ void Pair::ev_tally(int i, int j, int nlocal, int newton_pair,
}
}
}
-
+
/* ----------------------------------------------------------------------
tally eng_vdwl and virial into global and per-atom accumulators
can use this version with full neighbor lists
@@ -1519,7 +1519,7 @@ void Pair::virial_fdotr_compute()
virial[5] += f[i][2]*x[i][1];
}
}
-
+
// prevent multiple calls to update the virial
// when a hybrid pair style uses both a gpu and non-gpu pair style
// or when respa is used with gpu pair styles
diff --git a/src/pair.h b/src/pair.h
index bc4db091f3..a03f4c378d 100644
--- a/src/pair.h
+++ b/src/pair.h
@@ -142,7 +142,7 @@ class Pair : protected Pointers {
virtual void compute_outer(int, int) {}
virtual double single(int, int, int, int,
- double, double, double,
+ double, double, double,
double& fforce) {
fforce = 0.0;
return 0.0;
diff --git a/src/pair_beck.cpp b/src/pair_beck.cpp
index 986a6c74ff..0e05afb43b 100644
--- a/src/pair_beck.cpp
+++ b/src/pair_beck.cpp
@@ -15,9 +15,9 @@
Contributing author: Jonathan Zimmerman (Sandia)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
#include "pair_beck.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/pair_born.cpp b/src/pair_born.cpp
index 623452f643..d925af1030 100644
--- a/src/pair_born.cpp
+++ b/src/pair_born.cpp
@@ -15,10 +15,10 @@
Contributing Author: Sai Jayaraman (Sandia)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_born.h"
#include "atom.h"
#include "comm.h"
@@ -33,7 +33,7 @@ using namespace MathConst;
/* ---------------------------------------------------------------------- */
-PairBorn::PairBorn(LAMMPS *lmp) : Pair(lmp)
+PairBorn::PairBorn(LAMMPS *lmp) : Pair(lmp)
{
writedata = 1;
}
diff --git a/src/pair_born_coul_wolf.cpp b/src/pair_born_coul_wolf.cpp
index 3eb5973b08..48066fc43e 100644
--- a/src/pair_born_coul_wolf.cpp
+++ b/src/pair_born_coul_wolf.cpp
@@ -15,10 +15,10 @@
Contributing author: Yongfeng Zhang (INL), yongfeng.zhang@inl.gov
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_born_coul_wolf.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/pair_buck.cpp b/src/pair_buck.cpp
index 24b930af1e..baaea7ccdd 100644
--- a/src/pair_buck.cpp
+++ b/src/pair_buck.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_buck.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/pair_buck_coul_cut.cpp b/src/pair_buck_coul_cut.cpp
index 1021bd1e4d..06aeea3083 100644
--- a/src/pair_buck_coul_cut.cpp
+++ b/src/pair_buck_coul_cut.cpp
@@ -15,9 +15,9 @@
Contributing author: Eduardo Bringa (LLNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
#include "pair_buck_coul_cut.h"
#include "atom.h"
#include "comm.h"
@@ -219,7 +219,7 @@ void PairBuckCoulCut::settings(int narg, char **arg)
void PairBuckCoulCut::coeff(int narg, char **arg)
{
- if (narg < 5 || narg > 7)
+ if (narg < 5 || narg > 7)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
diff --git a/src/pair_coul_cut.cpp b/src/pair_coul_cut.cpp
index 4a54f2f2a8..4f21ba5ac1 100644
--- a/src/pair_coul_cut.cpp
+++ b/src/pair_coul_cut.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_coul_cut.h"
#include "atom.h"
#include "comm.h"
@@ -166,7 +166,7 @@ void PairCoulCut::settings(int narg, char **arg)
void PairCoulCut::coeff(int narg, char **arg)
{
- if (narg < 2 || narg > 3)
+ if (narg < 2 || narg > 3)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
diff --git a/src/pair_coul_debye.cpp b/src/pair_coul_debye.cpp
index c772961ec0..dcb84d7e2d 100644
--- a/src/pair_coul_debye.cpp
+++ b/src/pair_coul_debye.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_coul_debye.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/pair_coul_dsf.cpp b/src/pair_coul_dsf.cpp
index 2fa7b69fc9..264ba7648b 100644
--- a/src/pair_coul_dsf.cpp
+++ b/src/pair_coul_dsf.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -16,10 +16,10 @@
References: Fennell and Gezelter, JCP 124, 234104 (2006)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_coul_dsf.h"
#include "atom.h"
#include "comm.h"
@@ -69,11 +69,11 @@ void PairCoulDSF::compute(int eflag, int vflag)
double r,rsq,r2inv,forcecoul,factor_coul;
double prefactor,erfcc,erfcd,t;
int *ilist,*jlist,*numneigh,**firstneigh;
-
+
ecoul = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
-
+
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
@@ -86,7 +86,7 @@ void PairCoulDSF::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@@ -97,7 +97,7 @@ void PairCoulDSF::compute(int eflag, int vflag)
ztmp = x[i][2];
jlist = firstneigh[i];
jnum = numneigh[i];
-
+
if (eflag) {
double e_self = -(e_shift/2.0 + alpha/MY_PIS) * qtmp*qtmp*qqrd2e;
ev_tally(i,i,nlocal,0,0.0,e_self,0.0,0.0,0.0,0.0);
@@ -121,7 +121,7 @@ void PairCoulDSF::compute(int eflag, int vflag)
erfcd = exp(-alpha*alpha*rsq);
t = 1.0 / (1.0 + EWALD_P*alpha*r);
erfcc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * erfcd;
- forcecoul = prefactor * (erfcc/r + 2.0*alpha/MY_PIS * erfcd +
+ forcecoul = prefactor * (erfcc/r + 2.0*alpha/MY_PIS * erfcd +
r*f_shift) * r;
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
fpair = forcecoul * r2inv;
@@ -190,7 +190,7 @@ void PairCoulDSF::coeff(int narg, char **arg)
int ilo,ihi,jlo,jhi;
force->bounds(arg[0],atom->ntypes,ilo,ihi);
force->bounds(arg[1],atom->ntypes,jlo,jhi);
-
+
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
@@ -214,10 +214,10 @@ void PairCoulDSF::init_style()
neighbor->request(this,instance_me);
cut_coulsq = cut_coul * cut_coul;
- double erfcc = erfc(alpha*cut_coul);
+ double erfcc = erfc(alpha*cut_coul);
double erfcd = exp(-alpha*alpha*cut_coul*cut_coul);
- f_shift = -(erfcc/cut_coulsq + 2.0/MY_PIS*alpha*erfcd/cut_coul);
- e_shift = erfcc/cut_coul - f_shift*cut_coul;
+ f_shift = -(erfcc/cut_coulsq + 2.0/MY_PIS*alpha*erfcd/cut_coul);
+ e_shift = erfcc/cut_coul - f_shift*cut_coul;
}
/* ----------------------------------------------------------------------
@@ -300,7 +300,7 @@ double PairCoulDSF::single(int i, int j, int itype, int jtype, double rsq,
{
double r2inv,r,erfcc,erfcd,prefactor,t;
double forcecoul,phicoul;
-
+
r2inv = 1.0/rsq;
double eng = 0.0;
@@ -310,16 +310,16 @@ double PairCoulDSF::single(int i, int j, int itype, int jtype, double rsq,
erfcd = exp(-alpha*alpha*rsq);
t = 1.0 / (1.0 + EWALD_P*alpha*r);
erfcc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * erfcd;
-
- forcecoul = prefactor * (erfcc/r + 2.0*alpha/MY_PIS*erfcd +
+
+ forcecoul = prefactor * (erfcc/r + 2.0*alpha/MY_PIS*erfcd +
r*f_shift) * r;
phicoul = prefactor * (erfcc - r*e_shift - rsq*f_shift);
eng += phicoul;
} else forcecoul = 0.0;
-
+
fforce = forcecoul * r2inv;
-
+
return eng;
}
diff --git a/src/pair_coul_dsf.h b/src/pair_coul_dsf.h
index 7a6f74edf5..c74c88ee16 100644
--- a/src/pair_coul_dsf.h
+++ b/src/pair_coul_dsf.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -44,7 +44,7 @@ class PairCoulDSF : public Pair {
double cut_coul,cut_coulsq;
double alpha;
double f_shift,e_shift;
-
+
void allocate();
};
diff --git a/src/pair_coul_streitz.cpp b/src/pair_coul_streitz.cpp
index 31aa7adabd..97b9b551a6 100644
--- a/src/pair_coul_streitz.cpp
+++ b/src/pair_coul_streitz.cpp
@@ -15,10 +15,10 @@
Contributing author: Ray Shan (Sandia)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_coul_streitz.h"
#include "atom.h"
#include "comm.h"
@@ -340,8 +340,8 @@ void PairCoulStreitz::read_file(char *file)
params[nparams].zcore = atof(words[5]);
// parameter sanity check
-
- if (params[nparams].eta < 0.0 || params[nparams].zeta < 0.0 ||
+
+ if (params[nparams].eta < 0.0 || params[nparams].zeta < 0.0 ||
params[nparams].zcore < 0.0 || params[nparams].gamma != 0.0 )
error->all(FLERR,"Illegal coul/streitz parameter");
@@ -357,7 +357,7 @@ void PairCoulStreitz::setup()
{
int i,m,n;
- // set elem2param
+ // set elem2param
memory->destroy(elem2param);
memory->create(elem2param,nelements,"pair:elem2param");
@@ -400,7 +400,7 @@ void PairCoulStreitz::compute(int eflag, int vflag)
double xtmp, ytmp, ztmp, ecoul, fpair;
double qi, qj, selfion, r, rsq, delr[3];
- double zei, zej, zj, ci_jfi, dci_jfi, ci_fifj, dci_fifj;
+ double zei, zej, zj, ci_jfi, dci_jfi, ci_fifj, dci_fifj;
double forcecoul, factor_coul;
double **x = atom->x;
@@ -422,7 +422,7 @@ void PairCoulStreitz::compute(int eflag, int vflag)
firstneigh = list->firstneigh;
// Wolf sum
-
+
if (kspacetype == 1) {
for (ii = 0; ii < inum; ii++) {
@@ -472,9 +472,9 @@ void PairCoulStreitz::compute(int eflag, int vflag)
// Wolf Sum
- wolf_sum(qi, qj, zj, r, ci_jfi, dci_jfi, ci_fifj, dci_fifj,
+ wolf_sum(qi, qj, zj, r, ci_jfi, dci_jfi, ci_fifj, dci_fifj,
ecoul, forcecoul);
-
+
// Forces
fpair = -forcecoul / r;
@@ -495,7 +495,7 @@ void PairCoulStreitz::compute(int eflag, int vflag)
}
// Ewald Sum
-
+
} else if (kspacetype == 2) {
for (ii = 0; ii < inum; ii++) {
@@ -543,8 +543,8 @@ void PairCoulStreitz::compute(int eflag, int vflag)
coulomb_integral_ewald(zei, zej, r, ci_jfi, dci_jfi, ci_fifj, dci_fifj);
// Ewald: real-space
-
- ewald_sum(qi, qj, zj, r, ci_jfi, dci_jfi, ci_fifj, dci_fifj,
+
+ ewald_sum(qi, qj, zj, r, ci_jfi, dci_jfi, ci_fifj, dci_fifj,
ecoul, forcecoul, factor_coul);
// Forces
@@ -577,7 +577,7 @@ double PairCoulStreitz::self(Param *param, double qi)
double qqrd2e = force->qqrd2e;
if (kspacetype == 1) return 1.0*qi*(s1+qi*(0.50*s2 - qqrd2e*woself));
-
+
if (kspacetype == 2) return 1.0*qi*(s1+qi*(0.50*s2));
return 0.0;
@@ -586,7 +586,7 @@ double PairCoulStreitz::self(Param *param, double qi)
/* ---------------------------------------------------------------------- */
void PairCoulStreitz::coulomb_integral_wolf(double zei, double zej, double r,
- double &ci_jfi, double &dci_jfi, double &ci_fifj,
+ double &ci_jfi, double &dci_jfi, double &ci_fifj,
double &dci_fifj)
{
double rinv = 1.0/r;
@@ -646,17 +646,17 @@ void PairCoulStreitz::coulomb_integral_wolf(double zei, double zej, double r,
fshift = (exp2zirsh*(2.0*zei*(e1+e3/rc) + e3*rcinv2)
+ exp2zjrsh*(2.0*zej*(e2+e4/rc) + e4*rcinv2));
- ci_fifj = -exp2zir*(e1+e3/r) - exp2zjr*(e2+e4/r)
+ ci_fifj = -exp2zir*(e1+e3/r) - exp2zjr*(e2+e4/r)
- eshift - (r-rc)*fshift;
- dci_fifj = (exp2zir*(2.0*zei*(e1+e3/r) + e3*rinv2) +
+ dci_fifj = (exp2zir*(2.0*zei*(e1+e3/r) + e3*rinv2) +
exp2zjr*(2.0*zej*(e2+e4/r) + e4*rinv2)) - fshift;
}
}
/* ---------------------------------------------------------------------- */
-void PairCoulStreitz::wolf_sum(double qi, double qj, double zj, double r,
- double ci_jfi, double dci_jfi, double ci_fifj,
+void PairCoulStreitz::wolf_sum(double qi, double qj, double zj, double r,
+ double ci_jfi, double dci_jfi, double ci_fifj,
double dci_fifj, double &etmp, double &ftmp)
{
double a = g_wolf;
@@ -676,7 +676,7 @@ void PairCoulStreitz::wolf_sum(double qi, double qj, double zj, double r,
etmp1 = erfcr/r - erfcrc/rc;
etmp2 = qi * zj * (ci_jfi - ci_fifj);
etmp3 = qi * qj * 0.50 * (etmp1 + ci_fifj);
-
+
ftmp1 = -erfcr/r/r - 2.0*a/MY_PIS*derfcr/r - dwoself;
ftmp2 = qi * zj * (dci_jfi - dci_fifj);
ftmp3 = qi * qj * 0.50 * (ftmp1 + dci_fifj);
@@ -689,7 +689,7 @@ void PairCoulStreitz::wolf_sum(double qi, double qj, double zj, double r,
/* ---------------------------------------------------------------------- */
void PairCoulStreitz::coulomb_integral_ewald(double zei, double zej, double r,
- double &ci_jfi, double &dci_jfi, double &ci_fifj,
+ double &ci_jfi, double &dci_jfi, double &ci_fifj,
double &dci_fifj)
{
double rinv = 1.0/r;
@@ -718,7 +718,7 @@ void PairCoulStreitz::coulomb_integral_ewald(double zei, double zej, double r,
if (zei == zej) {
ci_fifj = -exp2zir*(rinv + zei*(sm1 + sm2*zei*r + sm3*zei2*r*r));
- dci_fifj = exp2zir*(rinv2 + 2.0*zei*rinv +
+ dci_fifj = exp2zir*(rinv2 + 2.0*zei*rinv +
zei2*(2.0 + 7.0/6.0*zei*r + 1.0/3.0*zei2*r*r));
} else {
@@ -739,8 +739,8 @@ void PairCoulStreitz::coulomb_integral_ewald(double zei, double zej, double r,
/* ---------------------------------------------------------------------- */
-void PairCoulStreitz::ewald_sum(double qi, double qj, double zj, double r,
- double ci_jfi, double dci_jfi, double ci_fifj,
+void PairCoulStreitz::ewald_sum(double qi, double qj, double zj, double r,
+ double ci_jfi, double dci_jfi, double ci_fifj,
double dci_fifj, double &etmp, double &ftmp, double fac)
{
double etmp1, etmp2, etmp3, etmp4;
@@ -760,7 +760,7 @@ void PairCoulStreitz::ewald_sum(double qi, double qj, double zj, double r,
etmp2 = qi * qj * 0.50 * ci_fifj;
etmp3 = qqrd2e * (etmp1 + etmp2);
etmp4 = qqrd2e * 0.50*qi*qj/r;
-
+
ftmp1 = qi * zj * (dci_jfi - dci_fifj);
ftmp2 = qi * qj * 0.50 * dci_fifj;
ftmp3 = qqrd2e * (ftmp1 + ftmp2);
diff --git a/src/pair_coul_streitz.h b/src/pair_coul_streitz.h
index 87ced6ed78..5c14fa4c38 100644
--- a/src/pair_coul_streitz.h
+++ b/src/pair_coul_streitz.h
@@ -57,10 +57,10 @@ class PairCoulStreitz : public Pair {
double cut_coul, cut_coulsq;
double *cut_respa;
double **scale;
-
+
// Wolf
double g_wolf, woself, dwoself;
-
+
// Ewald
double g_ewald;
@@ -73,11 +73,11 @@ class PairCoulStreitz : public Pair {
double self(Param *, double);
void coulomb_integral_wolf(double, double, double, double &, double &,
double &, double &);
- void wolf_sum(double, double, double, double, double, double, double,
+ void wolf_sum(double, double, double, double, double, double, double,
double, double &, double &);
void coulomb_integral_ewald(double, double, double, double &, double &,
double &, double &);
- void ewald_sum(double, double, double, double, double, double, double,
+ void ewald_sum(double, double, double, double, double, double, double,
double, double &, double &, double);
};
diff --git a/src/pair_coul_wolf.cpp b/src/pair_coul_wolf.cpp
index 170f458346..8b9e3fc07d 100644
--- a/src/pair_coul_wolf.cpp
+++ b/src/pair_coul_wolf.cpp
@@ -15,10 +15,10 @@
Contributing author: Yongfeng Zhang (INL), yongfeng.zhang@inl.gov
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_coul_wolf.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/pair_dpd.cpp b/src/pair_dpd.cpp
index 87af68d7fa..9dc16cab4b 100644
--- a/src/pair_dpd.cpp
+++ b/src/pair_dpd.cpp
@@ -15,9 +15,9 @@
Contributing author: Kurt Smith (U Pittsburgh)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
#include "pair_dpd.h"
#include "atom.h"
#include "atom_vec.h"
@@ -214,7 +214,7 @@ void PairDPD::settings(int narg, char **arg)
void PairDPD::coeff(int narg, char **arg)
{
- if (narg < 4 || narg > 5)
+ if (narg < 4 || narg > 5)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
diff --git a/src/pair_dpd_tstat.cpp b/src/pair_dpd_tstat.cpp
index 8d039a2bd5..2c51bb8d85 100644
--- a/src/pair_dpd_tstat.cpp
+++ b/src/pair_dpd_tstat.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
+#include <math.h>
#include "pair_dpd_tstat.h"
#include "atom.h"
#include "update.h"
@@ -170,7 +170,7 @@ void PairDPDTstat::settings(int narg, char **arg)
void PairDPDTstat::coeff(int narg, char **arg)
{
- if (narg < 3 || narg > 4)
+ if (narg < 3 || narg > 4)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
diff --git a/src/pair_gauss.cpp b/src/pair_gauss.cpp
index 80b3d3a79c..58373021e2 100644
--- a/src/pair_gauss.cpp
+++ b/src/pair_gauss.cpp
@@ -15,10 +15,10 @@
Contributing author: Sai Jayaraman (Sandia)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_gauss.h"
#include "atom.h"
#include "comm.h"
@@ -183,7 +183,7 @@ void PairGauss::settings(int narg, char **arg)
void PairGauss::coeff(int narg, char **arg)
{
- if (narg < 4 || narg > 5)
+ if (narg < 4 || narg > 5)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
@@ -217,7 +217,7 @@ void PairGauss::coeff(int narg, char **arg)
double PairGauss::init_one(int i, int j)
{
-
+
// This error is triggered when ti is performed on lj/cut tail
// in presence of extra atom type for tether sites
// "i = 2 j = 1 ERROR: All pair coeffs are not set (pair_gauss.cpp:223)"
@@ -315,7 +315,7 @@ double PairGauss::single(int i, int j, int itype, int jtype, double rsq,
double factor_coul, double factor_lj,
double &fforce)
{
- double philj =
+ double philj =
-(a[itype][jtype]*exp(-b[itype][jtype]*rsq) - offset[itype][jtype]);
fforce = -2.0*a[itype][jtype]*b[itype][jtype] * exp(-b[itype][jtype]*rsq);
return philj;
diff --git a/src/pair_hybrid.cpp b/src/pair_hybrid.cpp
index 7ca6c0fb80..1493a8e165 100644
--- a/src/pair_hybrid.cpp
+++ b/src/pair_hybrid.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
-#include "ctype.h"
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
+#include <ctype.h>
#include "pair_hybrid.h"
#include "atom.h"
#include "force.h"
@@ -130,7 +130,7 @@ void PairHybrid::compute(int eflag, int vflag)
// outerflag is set and sub-style has a compute_outer() method
if (styles[m]->compute_flag == 0) continue;
- if (outerflag && styles[m]->respa_enable)
+ if (outerflag && styles[m]->respa_enable)
styles[m]->compute_outer(eflag,vflag_substyle);
else styles[m]->compute(eflag,vflag_substyle);
}
@@ -813,7 +813,7 @@ void PairHybrid::modify_params(int narg, char **arg)
int multiflag = force->inumeric(FLERR,arg[2]);
for (m = 0; m < nstyles; m++)
if (strcmp(arg[1],keywords[m]) == 0 && multiflag == multiple[m]) break;
- if (m == nstyles)
+ if (m == nstyles)
error->all(FLERR,"Unknown pair_modify hybrid sub-style");
iarg = 3;
}
diff --git a/src/pair_hybrid.h b/src/pair_hybrid.h
index 27eaf47208..1be07d1efe 100644
--- a/src/pair_hybrid.h
+++ b/src/pair_hybrid.h
@@ -20,7 +20,7 @@ PairStyle(hybrid,PairHybrid)
#ifndef LMP_PAIR_HYBRID_H
#define LMP_PAIR_HYBRID_H
-#include "stdio.h"
+#include <stdio.h>
#include "pair.h"
namespace LAMMPS_NS {
diff --git a/src/pair_hybrid_overlay.cpp b/src/pair_hybrid_overlay.cpp
index cf48dc14a0..30c1d7d54e 100644
--- a/src/pair_hybrid_overlay.cpp
+++ b/src/pair_hybrid_overlay.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdlib.h"
-#include "string.h"
-#include "ctype.h"
+#include <stdlib.h>
+#include <string.h>
+#include <ctype.h>
#include "pair_hybrid_overlay.h"
#include "atom.h"
#include "force.h"
diff --git a/src/pair_lj96_cut.cpp b/src/pair_lj96_cut.cpp
index d5e24be739..cba6fdbdb4 100644
--- a/src/pair_lj96_cut.cpp
+++ b/src/pair_lj96_cut.cpp
@@ -15,10 +15,10 @@
Contributing author: Chuanfu Luo (luochuanfu@gmail.com)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_lj96_cut.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/pair_lj_cubic.cpp b/src/pair_lj_cubic.cpp
index 87c774c690..68b664fe21 100644
--- a/src/pair_lj_cubic.cpp
+++ b/src/pair_lj_cubic.cpp
@@ -16,10 +16,10 @@
Contributing author: Aidan Thompson (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_lj_cubic.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/pair_lj_cut.cpp b/src/pair_lj_cut.cpp
index 8426862e04..ab1710b2fc 100644
--- a/src/pair_lj_cut.cpp
+++ b/src/pair_lj_cut.cpp
@@ -15,10 +15,10 @@
Contributing author: Paul Crozier (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_lj_cut.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/pair_lj_cut_coul_cut.cpp b/src/pair_lj_cut_coul_cut.cpp
index 65e7aef5e2..79d3fa12a8 100644
--- a/src/pair_lj_cut_coul_cut.cpp
+++ b/src/pair_lj_cut_coul_cut.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_lj_cut_coul_cut.h"
#include "atom.h"
#include "comm.h"
@@ -212,7 +212,7 @@ void PairLJCutCoulCut::settings(int narg, char **arg)
void PairLJCutCoulCut::coeff(int narg, char **arg)
{
- if (narg < 4 || narg > 6)
+ if (narg < 4 || narg > 6)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
diff --git a/src/pair_lj_cut_coul_debye.cpp b/src/pair_lj_cut_coul_debye.cpp
index 44f2b395b2..8f5e8e7a17 100644
--- a/src/pair_lj_cut_coul_debye.cpp
+++ b/src/pair_lj_cut_coul_debye.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdlib.h>
#include "pair_lj_cut_coul_debye.h"
#include "atom.h"
#include "neigh_list.h"
diff --git a/src/pair_lj_cut_coul_dsf.cpp b/src/pair_lj_cut_coul_dsf.cpp
index af8064a131..d80c7e74c0 100644
--- a/src/pair_lj_cut_coul_dsf.cpp
+++ b/src/pair_lj_cut_coul_dsf.cpp
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -16,10 +16,10 @@
References: Fennell and Gezelter, JCP 124, 234104 (2006)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_lj_cut_coul_dsf.h"
#include "atom.h"
#include "comm.h"
@@ -79,11 +79,11 @@ void PairLJCutCoulDSF::compute(int eflag, int vflag)
double r,rsq,r2inv,r6inv,forcecoul,forcelj,factor_coul,factor_lj;
double prefactor,erfcc,erfcd,t;
int *ilist,*jlist,*numneigh,**firstneigh;
-
+
evdwl = ecoul = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
-
+
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
@@ -98,7 +98,7 @@ void PairLJCutCoulDSF::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
-
+
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@@ -110,7 +110,7 @@ void PairLJCutCoulDSF::compute(int eflag, int vflag)
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
-
+
if (eflag) {
double e_self = -(e_shift/2.0 + alpha/MY_PIS) * qtmp*qtmp*qqrd2e;
ev_tally(i,i,nlocal,0,0.0,e_self,0.0,0.0,0.0,0.0);
@@ -142,7 +142,7 @@ void PairLJCutCoulDSF::compute(int eflag, int vflag)
erfcd = exp(-alpha*alpha*r*r);
t = 1.0 / (1.0 + EWALD_P*alpha*r);
erfcc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * erfcd;
- forcecoul = prefactor * (erfcc/r + 2.0*alpha/MY_PIS * erfcd +
+ forcecoul = prefactor * (erfcc/r + 2.0*alpha/MY_PIS * erfcd +
r*f_shift) * r;
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
} else forcecoul = 0.0;
@@ -218,7 +218,7 @@ void PairLJCutCoulDSF::settings(int narg, char **arg)
cut_lj_global = force->numeric(FLERR,arg[1]);
if (narg == 2) cut_coul = cut_lj_global;
else cut_coul = force->numeric(FLERR,arg[2]);
-
+
// reset cutoffs that have been explicitly set
if (allocated) {
@@ -236,20 +236,20 @@ void PairLJCutCoulDSF::settings(int narg, char **arg)
void PairLJCutCoulDSF::coeff(int narg, char **arg)
{
- if (narg < 4 || narg > 5)
+ if (narg < 4 || narg > 5)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
int ilo,ihi,jlo,jhi;
force->bounds(arg[0],atom->ntypes,ilo,ihi);
force->bounds(arg[1],atom->ntypes,jlo,jhi);
-
+
double epsilon_one = force->numeric(FLERR,arg[2]);
double sigma_one = force->numeric(FLERR,arg[3]);
double cut_lj_one = cut_lj_global;
if (narg == 5) cut_lj_one = force->numeric(FLERR,arg[4]);
-
+
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
@@ -276,10 +276,10 @@ void PairLJCutCoulDSF::init_style()
neighbor->request(this,instance_me);
cut_coulsq = cut_coul * cut_coul;
- double erfcc = erfc(alpha*cut_coul);
+ double erfcc = erfc(alpha*cut_coul);
double erfcd = exp(-alpha*alpha*cut_coul*cut_coul);
- f_shift = -(erfcc/cut_coulsq + 2.0/MY_PIS*alpha*erfcd/cut_coul);
- e_shift = erfcc/cut_coul - f_shift*cut_coul;
+ f_shift = -(erfcc/cut_coulsq + 2.0/MY_PIS*alpha*erfcd/cut_coul);
+ e_shift = erfcc/cut_coul - f_shift*cut_coul;
}
/* ----------------------------------------------------------------------
@@ -297,17 +297,17 @@ double PairLJCutCoulDSF::init_one(int i, int j)
double cut = MAX(cut_lj[i][j],cut_coul);
cut_ljsq[i][j] = cut_lj[i][j] * cut_lj[i][j];
-
+
lj1[i][j] = 48.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
lj2[i][j] = 24.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
lj3[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
lj4[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
-
+
if (offset_flag) {
double ratio = sigma[i][j] / cut_lj[i][j];
offset[i][j] = 4.0 * epsilon[i][j] * (pow(ratio,12.0) - pow(ratio,6.0));
} else offset[i][j] = 0.0;
-
+
cut_ljsq[j][i] = cut_ljsq[i][j];
lj1[j][i] = lj1[i][j];
lj2[j][i] = lj2[i][j];
@@ -329,17 +329,17 @@ double PairLJCutCoulDSF::init_one(int i, int j)
if (type[k] == j) count[1] += 1.0;
}
MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world);
-
+
double sig2 = sigma[i][j]*sigma[i][j];
double sig6 = sig2*sig2*sig2;
double rc3 = cut_lj[i][j]*cut_lj[i][j]*cut_lj[i][j];
double rc6 = rc3*rc3;
double rc9 = rc3*rc6;
- etail_ij = 8.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
- sig6 * (sig6 - 3.0*rc6) / (9.0*rc9);
- ptail_ij = 16.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
- sig6 * (2.0*sig6 - 3.0*rc6) / (9.0*rc9);
- }
+ etail_ij = 8.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
+ sig6 * (sig6 - 3.0*rc6) / (9.0*rc9);
+ ptail_ij = 16.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
+ sig6 * (2.0*sig6 - 3.0*rc6) / (9.0*rc9);
+ }
return cut;
}
@@ -436,7 +436,7 @@ double PairLJCutCoulDSF::single(int i, int j, int itype, int jtype, double rsq,
{
double r2inv,r6inv,r,erfcc,erfcd,prefactor;
double forcecoul,forcelj,phicoul,philj;
-
+
r2inv = 1.0/rsq;
if (rsq < cut_ljsq[itype][jtype]) {
r6inv = r2inv*r2inv*r2inv;
@@ -446,14 +446,14 @@ double PairLJCutCoulDSF::single(int i, int j, int itype, int jtype, double rsq,
if (rsq < cut_coulsq) {
r = sqrt(rsq);
prefactor = factor_coul * force->qqrd2e * atom->q[i]*atom->q[j]/r;
- erfcc = erfc(alpha*r);
+ erfcc = erfc(alpha*r);
erfcd = exp(-alpha*alpha*r*r);
- forcecoul = prefactor * (erfcc/r + 2.0*alpha/MY_PIS * erfcd +
+ forcecoul = prefactor * (erfcc/r + 2.0*alpha/MY_PIS * erfcd +
r*f_shift) * r;
} else forcecoul = 0.0;
-
+
fforce = (forcecoul + factor_lj*forcelj) * r2inv;
-
+
double eng = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
philj = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
@@ -461,11 +461,11 @@ double PairLJCutCoulDSF::single(int i, int j, int itype, int jtype, double rsq,
eng += factor_lj*philj;
}
- if (rsq < cut_coulsq) {
+ if (rsq < cut_coulsq) {
phicoul = prefactor * (erfcc - r*e_shift - rsq*f_shift);
eng += phicoul;
- }
-
+ }
+
return eng;
}
diff --git a/src/pair_lj_cut_coul_dsf.h b/src/pair_lj_cut_coul_dsf.h
index 5a0a6b553d..3dfe272777 100644
--- a/src/pair_lj_cut_coul_dsf.h
+++ b/src/pair_lj_cut_coul_dsf.h
@@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
+ certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@@ -45,11 +45,11 @@ class PairLJCutCoulDSF : public Pair {
double **cut_lj,**cut_ljsq;
double **epsilon,**sigma;
double **lj1,**lj2,**lj3,**lj4,**offset;
-
+
double cut_coul,cut_coulsq;
double alpha;
double f_shift,e_shift;
-
+
virtual void allocate();
};
diff --git a/src/pair_lj_expand.cpp b/src/pair_lj_expand.cpp
index dc78373b4f..237ee91cce 100644
--- a/src/pair_lj_expand.cpp
+++ b/src/pair_lj_expand.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_lj_expand.h"
#include "atom.h"
#include "comm.h"
@@ -277,13 +277,13 @@ double PairLJExpand::init_one(int i, int j)
double shift2 = shift1*shift1;
double shift3 = shift2*shift1;
- etail_ij = 8.0*MY_PI*all[0]*all[1]*epsilon[i][j] * sig6 *
+ etail_ij = 8.0*MY_PI*all[0]*all[1]*epsilon[i][j] * sig6 *
((1.0/9.0 + 2.0*shift1/(10.0*rc1) + shift2/(11.0*rc2))*sig6/rc9 -
(1.0/3.0 + 2.0*shift1/(4.0*rc1) + shift2/(5.0*rc2))/rc3);
- ptail_ij = 16.0*MY_PI*all[0]*all[1]*epsilon[i][j] * sig6 *
- ((1.0/9.0 + 3.0*shift1/(10.0*rc1) +
+ ptail_ij = 16.0*MY_PI*all[0]*all[1]*epsilon[i][j] * sig6 *
+ ((1.0/9.0 + 3.0*shift1/(10.0*rc1) +
3.0*shift2/(11.0*rc2) + shift3/(12.0*rc3))*2.0*sig6/rc9 -
- (1.0/3.0 + 3.0*shift1/(4.0*rc1) +
+ (1.0/3.0 + 3.0*shift1/(4.0*rc1) +
3.0*shift2/(5.0*rc2) + shift3/(6.0*rc3))/rc3);
}
diff --git a/src/pair_lj_gromacs.cpp b/src/pair_lj_gromacs.cpp
index d81be7e83d..d5b24b733e 100644
--- a/src/pair_lj_gromacs.cpp
+++ b/src/pair_lj_gromacs.cpp
@@ -15,10 +15,10 @@
Contributing author: Mark Stevens (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_lj_gromacs.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/pair_lj_gromacs_coul_gromacs.cpp b/src/pair_lj_gromacs_coul_gromacs.cpp
index bd9bb56c7e..b68a557dcb 100644
--- a/src/pair_lj_gromacs_coul_gromacs.cpp
+++ b/src/pair_lj_gromacs_coul_gromacs.cpp
@@ -15,10 +15,10 @@
Contributing author: Mark Stevens (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_lj_gromacs_coul_gromacs.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/pair_lj_smooth.cpp b/src/pair_lj_smooth.cpp
index 0e532ee1ed..b73545f57b 100644
--- a/src/pair_lj_smooth.cpp
+++ b/src/pair_lj_smooth.cpp
@@ -15,9 +15,9 @@
Contributing author: Craig Maloney (UCSB)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
#include "pair_lj_smooth.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/pair_lj_smooth_linear.cpp b/src/pair_lj_smooth_linear.cpp
index a2cf43e50f..fa41bcae4b 100644
--- a/src/pair_lj_smooth_linear.cpp
+++ b/src/pair_lj_smooth_linear.cpp
@@ -15,9 +15,9 @@
Contributing author: Jonathan Zimmerman (Sandia)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
#include "pair_lj_smooth_linear.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/pair_mie_cut.cpp b/src/pair_mie_cut.cpp
index 0f7cb5eabe..7cb67b9437 100644
--- a/src/pair_mie_cut.cpp
+++ b/src/pair_mie_cut.cpp
@@ -15,10 +15,10 @@
Contributing author: Cassiano Aimoli (aimoli@gmail.com)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_mie_cut.h"
#include "atom.h"
#include "comm.h"
@@ -380,7 +380,7 @@ void PairMIECut::compute_outer(int eflag, int vflag)
r2inv = 1.0/rsq;
rgamA = pow(r2inv,(gamA[itype][jtype]/2.0));
rgamR = pow(r2inv,(gamR[itype][jtype]/2.0));
- evdwl = (mie3[itype][jtype]*rgamR - mie4[itype][jtype]*rgamA) -
+ evdwl = (mie3[itype][jtype]*rgamR - mie4[itype][jtype]*rgamA) -
offset[itype][jtype];
evdwl *= factor_mie;
}
@@ -567,22 +567,22 @@ double PairMIECut::init_one(int i, int j)
gamA[i][j] = mix_distance(gamA[i][i],gamA[j][j]);
cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
}
-
+
gamA[j][i] = gamA[i][j];
gamR[j][i] = gamR[i][j];
- Cmie[i][j] = (gamR[i][j]/(gamR[i][j]-gamA[i][j]) *
+ Cmie[i][j] = (gamR[i][j]/(gamR[i][j]-gamA[i][j]) *
pow((gamR[i][j]/gamA[i][j]),
(gamA[i][j]/(gamR[i][j]-gamA[i][j]))));
- mie1[i][j] = Cmie[i][j] * gamR[i][j]* epsilon[i][j] *
+ mie1[i][j] = Cmie[i][j] * gamR[i][j]* epsilon[i][j] *
pow(sigma[i][j],gamR[i][j]);
- mie2[i][j] = Cmie[i][j] * gamA[i][j] * epsilon[i][j] *
+ mie2[i][j] = Cmie[i][j] * gamA[i][j] * epsilon[i][j] *
pow(sigma[i][j],gamA[i][j]);
mie3[i][j] = Cmie[i][j] * epsilon[i][j] * pow(sigma[i][j],gamR[i][j]);
mie4[i][j] = Cmie[i][j] * epsilon[i][j] * pow(sigma[i][j],gamA[i][j]);
if (offset_flag) {
double ratio = sigma[i][j] / cut[i][j];
- offset[i][j] = Cmie[i][j] * epsilon[i][j] *
+ offset[i][j] = Cmie[i][j] * epsilon[i][j] *
(pow(ratio,gamR[i][j]) - pow(ratio,gamA[i][j]));
} else offset[i][j] = 0.0;
diff --git a/src/pair_morse.cpp b/src/pair_morse.cpp
index 1122ed78ff..4e2d47be5c 100644
--- a/src/pair_morse.cpp
+++ b/src/pair_morse.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_morse.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/pair_soft.cpp b/src/pair_soft.cpp
index 3b94997881..d9b9bb819b 100644
--- a/src/pair_soft.cpp
+++ b/src/pair_soft.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_soft.h"
#include "atom.h"
#include "comm.h"
@@ -169,7 +169,7 @@ void PairSoft::settings(int narg, char **arg)
void PairSoft::coeff(int narg, char **arg)
{
- if (narg < 3 || narg > 4)
+ if (narg < 3 || narg > 4)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
diff --git a/src/pair_table.cpp b/src/pair_table.cpp
index 4c637b2d1f..9bce67b529 100644
--- a/src/pair_table.cpp
+++ b/src/pair_table.cpp
@@ -15,10 +15,10 @@
Contributing author: Paul Crozier (SNL)
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <mpi.h>
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_table.h"
#include "atom.h"
#include "force.h"
diff --git a/src/pair_yukawa.cpp b/src/pair_yukawa.cpp
index 69ca737bc1..2cc309d949 100644
--- a/src/pair_yukawa.cpp
+++ b/src/pair_yukawa.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
+#include <math.h>
+#include <stdlib.h>
#include "pair_yukawa.h"
#include "atom.h"
#include "force.h"
diff --git a/src/pair_zbl.cpp b/src/pair_zbl.cpp
index 57278c7a3a..6962200982 100644
--- a/src/pair_zbl.cpp
+++ b/src/pair_zbl.cpp
@@ -15,10 +15,10 @@
Contributing authors: Stephen Foiles, Aidan Thompson (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "pair_zbl.h"
#include "atom.h"
#include "comm.h"
@@ -33,7 +33,7 @@
#include "memory.h"
#include "error.h"
-// From J.F. Zeigler, J. P. Biersack and U. Littmark,
+// From J.F. Zeigler, J. P. Biersack and U. Littmark,
// "The Stopping and Range of Ions in Matter" volume 1, Pergamon, 1985.
using namespace LAMMPS_NS;
@@ -117,7 +117,7 @@ void PairZBL::compute(int eflag, int vflag)
if (rsq > cut_innersq) {
t = r - cut_inner;
- fswitch = t*t *
+ fswitch = t*t *
(sw1[itype][jtype] + sw2[itype][jtype]*t);
fpair += fswitch;
}
@@ -136,7 +136,7 @@ void PairZBL::compute(int eflag, int vflag)
evdwl = e_zbl(r, itype, jtype);
evdwl += sw5[itype][jtype];
if (rsq > cut_innersq) {
- eswitch = t*t*t *
+ eswitch = t*t*t *
(sw3[itype][jtype] + sw4[itype][jtype]*t);
evdwl += eswitch;
}
@@ -275,7 +275,7 @@ double PairZBL::single(int i, int j, int itype, int jtype, double rsq,
fforce = dzbldr(r, itype, jtype);
if (rsq > cut_innersq) {
t = r - cut_inner;
- fswitch = t*t *
+ fswitch = t*t *
(sw1[itype][jtype] + sw2[itype][jtype]*t);
fforce += fswitch;
}
@@ -284,7 +284,7 @@ double PairZBL::single(int i, int j, int itype, int jtype, double rsq,
phi = e_zbl(r, itype, jtype);
phi += sw5[itype][jtype];
if (rsq > cut_innersq) {
- eswitch = t*t*t *
+ eswitch = t*t*t *
(sw3[itype][jtype] + sw4[itype][jtype]*t);
phi += eswitch;
}
@@ -297,7 +297,7 @@ double PairZBL::single(int i, int j, int itype, int jtype, double rsq,
------------------------------------------------------------------------- */
double PairZBL::e_zbl(double r, int i, int j) {
-
+
double d1aij = d1a[i][j];
double d2aij = d2a[i][j];
double d3aij = d3a[i][j];
@@ -343,9 +343,9 @@ double PairZBL::dzbldr(double r, int i, int j) {
sum_p -= c2*d2aij*e2;
sum_p -= c3*d3aij*e3;
sum_p -= c4*d4aij*e4;
-
+
double result = zzeij*(sum_p - sum*rinv)*rinv;
-
+
return result;
}
@@ -381,15 +381,15 @@ double PairZBL::d2zbldr2(double r, int i, int j) {
sum_pp += c2*e2*d2aij*d2aij;
sum_pp += c3*e3*d3aij*d3aij;
sum_pp += c4*e4*d4aij*d4aij;
-
- double result = zzeij*(sum_pp + 2.0*sum_p*rinv +
+
+ double result = zzeij*(sum_pp + 2.0*sum_p*rinv +
2.0*sum*rinv*rinv)*rinv;
-
+
return result;
}
/* ----------------------------------------------------------------------
- calculate the i,j entries in the various coeff arrays
+ calculate the i,j entries in the various coeff arrays
------------------------------------------------------------------------- */
void PairZBL::set_coeff(int i, int j, double zi, double zj)
@@ -400,51 +400,51 @@ void PairZBL::set_coeff(int i, int j, double zi, double zj)
d3a[i][j] = d3*ainv;
d4a[i][j] = d4*ainv;
zze[i][j] = zi*zj*force->qqr2e*force->qelectron*force->qelectron;
-
+
d1a[j][i] = d1a[i][j];
d2a[j][i] = d2a[i][j];
d3a[j][i] = d3a[i][j];
d4a[j][i] = d4a[i][j];
zze[j][i] = zze[i][j];
-
- // e = t^3 (sw3 + sw4*t) + sw5
+
+ // e = t^3 (sw3 + sw4*t) + sw5
// = A/3*t^3 + B/4*t^4 + C
- // sw3 = A/3
- // sw4 = B/4
+ // sw3 = A/3
+ // sw4 = B/4
// sw5 = C
-
- // dedr = t^2 (sw1 + sw2*t)
+
+ // dedr = t^2 (sw1 + sw2*t)
// = A*t^2 + B*t^3
- // sw1 = A
- // sw2 = B
-
+ // sw1 = A
+ // sw2 = B
+
// de2dr2 = 2*A*t + 3*B*t^2
-
+
// Require that at t = tc:
// e = -Fc
// dedr = -Fc'
- // d2edr2 = -Fc''
-
+ // d2edr2 = -Fc''
+
// Hence:
// A = (-3Fc' + tc*Fc'')/tc^2
// B = ( 2Fc' - tc*Fc'')/tc^3
// C = -Fc + tc/2*Fc' - tc^2/12*Fc''
-
+
double tc = cut_global - cut_inner;
double fc = e_zbl(cut_global, i, j);
double fcp = dzbldr(cut_global, i, j);
double fcpp = d2zbldr2(cut_global, i, j);
-
+
double swa = (-3.0*fcp + tc*fcpp)/(tc*tc);
double swb = ( 2.0*fcp - tc*fcpp)/(tc*tc*tc);
- double swc = -fc + (tc/2.0)*fcp - (tc*tc/12.0)*fcpp;
-
+ double swc = -fc + (tc/2.0)*fcp - (tc*tc/12.0)*fcpp;
+
sw1[i][j] = swa;
sw2[i][j] = swb;
sw3[i][j] = swa/3.0;
sw4[i][j] = swb/4.0;
sw5[i][j] = swc;
-
+
sw1[j][i] = sw1[i][j];
sw2[j][i] = sw2[i][j];
sw3[j][i] = sw3[i][j];
diff --git a/src/pointers.h b/src/pointers.h
index faca833130..dd528c3a74 100644
--- a/src/pointers.h
+++ b/src/pointers.h
@@ -22,7 +22,7 @@
#define LMP_POINTERS_H
#include "lmptype.h"
-#include "mpi.h"
+#include <mpi.h>
#include "lammps.h"
namespace LAMMPS_NS {
diff --git a/src/random_mars.cpp b/src/random_mars.cpp
index fb5725b8c3..96398b170c 100644
--- a/src/random_mars.cpp
+++ b/src/random_mars.cpp
@@ -14,7 +14,7 @@
// Marsaglia random number generator
// see RANMAR in F James, Comp Phys Comm, 60, 329 (1990)
-#include "math.h"
+#include <math.h>
#include "random_mars.h"
#include "error.h"
diff --git a/src/random_park.cpp b/src/random_park.cpp
index 89e89fc4b9..28580c5cf5 100644
--- a/src/random_park.cpp
+++ b/src/random_park.cpp
@@ -13,7 +13,7 @@
// Park/Miller RNG
-#include "math.h"
+#include <math.h>
#include "random_park.h"
#include "error.h"
diff --git a/src/rcb.cpp b/src/rcb.cpp
index 94cdb155ac..7223e4616a 100644
--- a/src/rcb.cpp
+++ b/src/rcb.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "string.h"
+#include <mpi.h>
+#include <string.h>
#include "rcb.h"
#include "irregular.h"
#include "memory.h"
@@ -142,7 +142,7 @@ void RCB::compute(int dimension, int n, double **x, double *wt,
// initial bounding box = simulation box
// includes periodic or shrink-wrapped boundaries
-
+
lo = bbox.lo;
hi = bbox.hi;
@@ -193,7 +193,7 @@ void RCB::compute(int dimension, int n, double **x, double *wt,
procpartner = me + (procmid - proclower);
else
procpartner = me - (procmid - proclower);
-
+
int readnumber = 1;
if (procpartner > procupper) {
readnumber = 0;
@@ -203,7 +203,7 @@ void RCB::compute(int dimension, int n, double **x, double *wt,
readnumber = 2;
procpartner2 = procpartner + 1;
}
-
+
// wttot = summed weight of entire partition
// search tolerance = largest single weight (plus epsilon)
// targetlo = desired weight in lower half of partition
@@ -276,14 +276,14 @@ void RCB::compute(int dimension, int n, double **x, double *wt,
// choose bisector value
// use old value on 1st iteration if old cut dimension is the same
- // on 2nd option: could push valuehalf towards geometric center
+ // on 2nd option: could push valuehalf towards geometric center
// with "1.0-factor" to force overshoot
if (first_iteration && reuse && dim == tree[procmid].dim) {
counters[5]++;
valuehalf = tree[procmid].cut;
if (valuehalf < valuemin || valuehalf > valuemax)
- valuehalf = 0.5 * (valuemin + valuemax);
+ valuehalf = 0.5 * (valuemin + valuemax);
} else if (wt)
valuehalf = valuemin + (targetlo - wtlo) /
(wttot - wtlo - wthi) * (valuemax - valuemin);
@@ -291,7 +291,7 @@ void RCB::compute(int dimension, int n, double **x, double *wt,
valuehalf = 0.5 * (valuemin + valuemax);
first_iteration = 0;
-
+
// initialize local median data structure
medme.totallo = medme.totalhi = 0.0;
@@ -361,7 +361,7 @@ void RCB::compute(int dimension, int n, double **x, double *wt,
else { // multiple dots to move
breakflag = 0;
wtok = 0.0;
- if (medme.valuehi == med.valuehi) wtok = medme.wthi;
+ if (medme.valuehi == med.valuehi) wtok = medme.wthi;
if (wtlo + med.wthi >= targetlo) { // all done
MPI_Scan(&wtok,&wtupto,1,MPI_DOUBLE,MPI_SUM,comm);
wtmax = targetlo - wtlo;
@@ -404,7 +404,7 @@ void RCB::compute(int dimension, int n, double **x, double *wt,
else { // multiple dots to move
breakflag = 0;
wtok = 0.0;
- if (medme.valuelo == med.valuelo) wtok = medme.wtlo;
+ if (medme.valuelo == med.valuelo) wtok = medme.wtlo;
if (wthi + med.wtlo >= targethi) { // all done
MPI_Scan(&wtok,&wtupto,1,MPI_DOUBLE,MPI_SUM,comm);
wtmax = targethi - wthi;
@@ -414,7 +414,7 @@ void RCB::compute(int dimension, int n, double **x, double *wt,
for (j = 0, wtsum = 0.0; j < nlist && wtsum < wtok; j++) {
i = dotlist[j];
if (dots[i].x[dim] == med.valuelo) { // only move if better
- if (wtsum + dots[i].wt - wtok < wtok - wtsum)
+ if (wtsum + dots[i].wt - wtok < wtok - wtsum)
dotmark[i] = 1;
wtsum += dots[i].wt;
}
@@ -433,7 +433,7 @@ void RCB::compute(int dimension, int n, double **x, double *wt,
break;
// shrink the active list
-
+
k = 0;
for (j = 0; j < nlist; j++) {
i = dotlist[j];
@@ -463,7 +463,7 @@ void RCB::compute(int dimension, int n, double **x, double *wt,
if (dotmark[i] == markactive) outgoing++;
else if (i < nkeep) keep++;
nkeep = keep;
-
+
// alert partner how many dots I'll send, read how many I'll recv
MPI_Send(&outgoing,1,MPI_INT,procpartner,0,world);
@@ -489,7 +489,7 @@ void RCB::compute(int dimension, int n, double **x, double *wt,
counters[2] += incoming;
if (ndotnew > counters[3]) counters[3] = ndotnew;
if (maxdot > counters[4]) counters[4] = maxdot;
-
+
// malloc comm send buffer
if (outgoing > maxbuf) {
@@ -500,7 +500,7 @@ void RCB::compute(int dimension, int n, double **x, double *wt,
// fill buffer with dots that are marked for sending
// pack down the unmarked ones
-
+
keep = outgoing = 0;
for (i = 0; i < ndot; i++) {
if (dotmark[i] == markactive)
@@ -520,9 +520,9 @@ void RCB::compute(int dimension, int n, double **x, double *wt,
procpartner2,1,world,&request2);
}
}
-
+
// handshake before sending dots to insure recvs have been posted
-
+
if (readnumber > 0) {
MPI_Send(NULL,0,MPI_INT,procpartner,0,world);
if (readnumber == 2) MPI_Send(NULL,0,MPI_INT,procpartner2,0,world);
@@ -532,7 +532,7 @@ void RCB::compute(int dimension, int n, double **x, double *wt,
// send dots to partner
MPI_Rsend(buf,outgoing*sizeof(Dot),MPI_CHAR,procpartner,1,world);
-
+
// wait until all dots are received
if (readnumber > 0) {
@@ -620,7 +620,7 @@ void median_merge(void *in, void *inout, int *len, MPI_Datatype *dptr)
{
RCB::Median *med1 = (RCB::Median *) in;
RCB::Median *med2 = (RCB::Median *) inout;
-
+
med2->totallo += med1->totallo;
if (med1->valuelo > med2->valuelo) {
med2->valuelo = med1->valuelo;
@@ -668,7 +668,7 @@ void RCB::invert(int sortflag)
int *proclist;
memory->create(proclist,nsend,"RCB:proclist");
- Invert *sinvert =
+ Invert *sinvert =
(Invert *) memory->smalloc(nsend*sizeof(Invert),"RCB:sinvert");
int m = 0;
@@ -679,12 +679,12 @@ void RCB::invert(int sortflag)
sinvert[m].sindex = i;
m++;
}
-
+
// perform inversion via irregular comm
// nrecv = # of my dots to send to other procs
int nrecv = irregular->create_data(nsend,proclist,sortflag);
- Invert *rinvert =
+ Invert *rinvert =
(Invert *) memory->smalloc(nrecv*sizeof(Invert),"RCB:rinvert");
irregular->exchange_data((char *) sinvert,sizeof(Invert),(char *) rinvert);
irregular->destroy_data();
@@ -744,11 +744,11 @@ void RCB::check()
MPI_Allreduce(&ndotorig,&total1,1,MPI_INT,MPI_SUM,world);
MPI_Allreduce(&ndot,&total2,1,MPI_INT,MPI_SUM,world);
if (total1 != total2) {
- if (me == 0)
+ if (me == 0)
printf("ERROR: Points before RCB = %d, Points after RCB = %d\n",
total1,total2);
}
-
+
// check that result is load-balanced within log2(P)*max-wt
weight = wtone = 0.0;
@@ -768,17 +768,17 @@ void RCB::check()
tolerance = tolerance * i * (1.0 + TINY);
if (wtmax - wtmin > tolerance) {
- if (me == 0)
+ if (me == 0)
printf("ERROR: Load-imbalance > tolerance of %g\n",tolerance);
MPI_Barrier(world);
if (weight == wtmin) printf(" Proc %d has weight = %g\n",me,weight);
if (weight == wtmax) printf(" Proc %d has weight = %g\n",me,weight);
}
-
+
MPI_Barrier(world);
-
+
// check that final set of points is inside RCB box of each proc
-
+
iflag = 0;
for (i = 0; i < ndot; i++) {
if (dots[i].x[0] < lo[0] || dots[i].x[0] > hi[0] ||
@@ -786,7 +786,7 @@ void RCB::check()
dots[i].x[2] < lo[2] || dots[i].x[2] > hi[2])
iflag++;
}
- if (iflag > 0)
+ if (iflag > 0)
printf("ERROR: %d points are out-of-box on proc %d\n",iflag,me);
}
@@ -801,7 +801,7 @@ void RCB::stats(int flag)
if (me == 0) printf("RCB Statistics:\n");
// distribution info
-
+
for (i = 0, weight = 0.0; i < ndot; i++) weight += dots[i].wt;
MPI_Allreduce(&weight,&wttot,1,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(&weight,&wtmin,1,MPI_DOUBLE,MPI_MIN,world);
@@ -817,10 +817,10 @@ void RCB::stats(int flag)
printf(" Proc %d has weight = %g\n",me,weight);
}
- for (i = 0, weight = 0.0; i < ndot; i++)
+ for (i = 0, weight = 0.0; i < ndot; i++)
if (dots[i].wt > weight) weight = dots[i].wt;
MPI_Allreduce(&weight,&wtmax,1,MPI_DOUBLE,MPI_MAX,world);
-
+
if (me == 0) printf(" Maximum weight of single dot = %g\n",wtmax);
if (flag) {
MPI_Barrier(world);
@@ -833,7 +833,7 @@ void RCB::stats(int flag)
MPI_Allreduce(&counters[0],&min,1,MPI_INT,MPI_MIN,world);
MPI_Allreduce(&counters[0],&max,1,MPI_INT,MPI_MAX,world);
ave = ((double) sum)/nprocs;
- if (me == 0)
+ if (me == 0)
printf(" Median iter: ave = %g, min = %d, max = %d\n",ave,min,max);
if (flag) {
MPI_Barrier(world);
@@ -844,7 +844,7 @@ void RCB::stats(int flag)
MPI_Allreduce(&counters[1],&min,1,MPI_INT,MPI_MIN,world);
MPI_Allreduce(&counters[1],&max,1,MPI_INT,MPI_MAX,world);
ave = ((double) sum)/nprocs;
- if (me == 0)
+ if (me == 0)
printf(" Send count: ave = %g, min = %d, max = %d\n",ave,min,max);
if (flag) {
MPI_Barrier(world);
@@ -855,7 +855,7 @@ void RCB::stats(int flag)
MPI_Allreduce(&counters[2],&min,1,MPI_INT,MPI_MIN,world);
MPI_Allreduce(&counters[2],&max,1,MPI_INT,MPI_MAX,world);
ave = ((double) sum)/nprocs;
- if (me == 0)
+ if (me == 0)
printf(" Recv count: ave = %g, min = %d, max = %d\n",ave,min,max);
if (flag) {
MPI_Barrier(world);
@@ -866,7 +866,7 @@ void RCB::stats(int flag)
MPI_Allreduce(&counters[3],&min,1,MPI_INT,MPI_MIN,world);
MPI_Allreduce(&counters[3],&max,1,MPI_INT,MPI_MAX,world);
ave = ((double) sum)/nprocs;
- if (me == 0)
+ if (me == 0)
printf(" Max dots: ave = %g, min = %d, max = %d\n",ave,min,max);
if (flag) {
MPI_Barrier(world);
@@ -877,7 +877,7 @@ void RCB::stats(int flag)
MPI_Allreduce(&counters[4],&min,1,MPI_INT,MPI_MIN,world);
MPI_Allreduce(&counters[4],&max,1,MPI_INT,MPI_MAX,world);
ave = ((double) sum)/nprocs;
- if (me == 0)
+ if (me == 0)
printf(" Max memory: ave = %g, min = %d, max = %d\n",ave,min,max);
if (flag) {
MPI_Barrier(world);
@@ -889,19 +889,19 @@ void RCB::stats(int flag)
MPI_Allreduce(&counters[5],&min,1,MPI_INT,MPI_MIN,world);
MPI_Allreduce(&counters[5],&max,1,MPI_INT,MPI_MAX,world);
ave = ((double) sum)/nprocs;
- if (me == 0)
+ if (me == 0)
printf(" # of Reuse: ave = %g, min = %d, max = %d\n",ave,min,max);
if (flag) {
MPI_Barrier(world);
printf(" Proc %d # of Reuse = %d\n",me,counters[5]);
}
}
-
+
MPI_Allreduce(&counters[6],&sum,1,MPI_INT,MPI_SUM,world);
MPI_Allreduce(&counters[6],&min,1,MPI_INT,MPI_MIN,world);
MPI_Allreduce(&counters[6],&max,1,MPI_INT,MPI_MAX,world);
ave = ((double) sum)/nprocs;
- if (me == 0)
+ if (me == 0)
printf(" # of OverAlloc: ave = %g, min = %d, max = %d\n",ave,min,max);
if (flag) {
MPI_Barrier(world);
@@ -909,7 +909,7 @@ void RCB::stats(int flag)
}
// RCB boxes for each proc
-
+
if (flag) {
if (me == 0) printf(" RCB sub-domain boxes:\n");
for (i = 0; i < 3; i++) {
diff --git a/src/rcb.h b/src/rcb.h
index 345e0c6bb9..7a82d42f93 100644
--- a/src/rcb.h
+++ b/src/rcb.h
@@ -14,7 +14,7 @@
#ifndef LAMMPS_RCB_H
#define LAMMPS_RCB_H
-#include "mpi.h"
+#include <mpi.h>
#include "pointers.h"
namespace LAMMPS_NS {
@@ -50,7 +50,7 @@ class RCB : protected Pointers {
//void stats(int);
// RCB cut info
-
+
struct Median {
double totallo,totalhi; // weight in each half of active partition
double valuelo,valuehi; // position of dot(s) nearest to cut
@@ -62,7 +62,7 @@ class RCB : protected Pointers {
struct BBox {
double lo[3],hi[3]; // corner points of a bounding box
};
-
+
private:
int me,nprocs;
@@ -81,7 +81,7 @@ class RCB : protected Pointers {
double cut; // position of cut
int dim; // dimension = 0/1/2 of cut
};
-
+
// inversion message
struct Invert {
@@ -114,7 +114,7 @@ class RCB : protected Pointers {
int reuse; // 1/0 to use/not use previous cuts
int dottop; // dots >= this index are new
double bboxlo[3]; // bounding box of final RCB sub-domain
- double bboxhi[3];
+ double bboxhi[3];
Tree *tree; // tree of RCB cuts, used by reuse()
int counters[7]; // diagnostic counts
// 0 = # of median iterations
diff --git a/src/read_data.cpp b/src/read_data.cpp
index 7e4b70484b..dfafa8a24b 100644
--- a/src/read_data.cpp
+++ b/src/read_data.cpp
@@ -15,12 +15,12 @@
// due to OpenMPI bug which sets INT64_MAX via its mpi.h
// before lmptype.h can set flags to insure it is done correctly
-#include "lmptype.h"
-#include "mpi.h"
-#include "math.h"
-#include "string.h"
-#include "stdlib.h"
-#include "ctype.h"
+#include "lmptype.h"
+#include <mpi.h>
+#include <math.h>
+#include <string.h>
+#include <stdlib.h>
+#include <ctype.h>
#include "read_data.h"
#include "atom.h"
#include "atom_vec.h"
@@ -125,7 +125,7 @@ void ReadData::command(int narg, char **arg)
offsetflag = shiftflag = 0;
toffset = boffset = aoffset = doffset = ioffset = 0;
shift[0] = shift[1] = shift[2] = 0.0;
- extra_atom_types = extra_bond_types = extra_angle_types =
+ extra_atom_types = extra_bond_types = extra_angle_types =
extra_dihedral_types = extra_improper_types = 0;
groupbit = 0;
@@ -144,7 +144,7 @@ void ReadData::command(int narg, char **arg)
else {
addflag = VALUE;
bigint offset = force->bnumeric(FLERR,arg[iarg+1]);
- if (offset > MAXTAGINT)
+ if (offset > MAXTAGINT)
error->all(FLERR,"Read data add offset is too big");
id_offset = offset;
}
@@ -157,8 +157,8 @@ void ReadData::command(int narg, char **arg)
aoffset = force->inumeric(FLERR,arg[iarg+3]);
doffset = force->inumeric(FLERR,arg[iarg+4]);
ioffset = force->inumeric(FLERR,arg[iarg+5]);
- if (toffset < 0 || boffset < 0 || aoffset < 0 ||
- doffset < 0 || ioffset < 0)
+ if (toffset < 0 || boffset < 0 || aoffset < 0 ||
+ doffset < 0 || ioffset < 0)
error->all(FLERR,"Illegal read_data command");
iarg += 6;
} else if (strcmp(arg[iarg],"shift") == 0) {
@@ -178,32 +178,32 @@ void ReadData::command(int narg, char **arg)
iarg += 2;
} else if (strcmp(arg[iarg],"extra/bond/types") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal read_data command");
- if (!atom->avec->bonds_allow)
+ if (!atom->avec->bonds_allow)
error->all(FLERR,"No bonds allowed with this atom style");
extra_bond_types = force->inumeric(FLERR,arg[iarg+1]);
if (extra_bond_types < 0) error->all(FLERR,"Illegal read_data command");
iarg += 2;
} else if (strcmp(arg[iarg],"extra/angle/types") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal read_data command");
- if (!atom->avec->angles_allow)
+ if (!atom->avec->angles_allow)
error->all(FLERR,"No angles allowed with this atom style");
extra_angle_types = force->inumeric(FLERR,arg[iarg+1]);
if (extra_angle_types < 0) error->all(FLERR,"Illegal read_data command");
iarg += 2;
} else if (strcmp(arg[iarg],"extra/dihedral/types") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal read_data command");
- if (!atom->avec->dihedrals_allow)
+ if (!atom->avec->dihedrals_allow)
error->all(FLERR,"No dihedrals allowed with this atom style");
extra_dihedral_types = force->inumeric(FLERR,arg[iarg+1]);
- if (extra_dihedral_types < 0)
+ if (extra_dihedral_types < 0)
error->all(FLERR,"Illegal read_data command");
iarg += 2;
} else if (strcmp(arg[iarg],"extra/improper/types") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal read_data command");
- if (!atom->avec->impropers_allow)
+ if (!atom->avec->impropers_allow)
error->all(FLERR,"No impropers allowed with this atom style");
extra_improper_types = force->inumeric(FLERR,arg[iarg+1]);
- if (extra_improper_types < 0)
+ if (extra_improper_types < 0)
error->all(FLERR,"Illegal read_data command");
iarg += 2;
@@ -255,8 +255,8 @@ void ReadData::command(int narg, char **arg)
error->all(FLERR,"Cannot use read_data offset without add flag");
if (shiftflag && addflag == NONE)
error->all(FLERR,"Cannot use read_data shift without add flag");
- if (addflag != NONE &&
- (extra_atom_types || extra_bond_types || extra_angle_types ||
+ if (addflag != NONE &&
+ (extra_atom_types || extra_bond_types || extra_angle_types ||
extra_dihedral_types || extra_improper_types))
error->all(FLERR,"Cannot use read_data extra with add flag");
@@ -312,9 +312,9 @@ void ReadData::command(int narg, char **arg)
if (firstpass && screen) fprintf(screen,"Reading data file ...\n");
open(arg[0]);
} else fp = NULL;
-
+
// read header info
-
+
header(firstpass);
// problem setup using info from header
@@ -405,7 +405,7 @@ void ReadData::command(int narg, char **arg)
atoms();
} else skip_lines(natoms);
} else if (strcmp(keyword,"Velocities") == 0) {
- if (atomflag == 0)
+ if (atomflag == 0)
error->all(FLERR,"Must read Atoms before Velocities");
if (firstpass) velocities();
else skip_lines(natoms);
@@ -434,14 +434,14 @@ void ReadData::command(int narg, char **arg)
error->all(FLERR,"Invalid data file section: Impropers");
if (atomflag == 0) error->all(FLERR,"Must read Atoms before Impropers");
impropers(firstpass);
-
+
} else if (strcmp(keyword,"Ellipsoids") == 0) {
ellipsoidflag = 1;
if (!avec_ellipsoid)
error->all(FLERR,"Invalid data file section: Ellipsoids");
- if (atomflag == 0)
+ if (atomflag == 0)
error->all(FLERR,"Must read Atoms before Ellipsoids");
- if (firstpass)
+ if (firstpass)
bonus(nellipsoids,(AtomVec *) avec_ellipsoid,"ellipsoids");
else skip_lines(nellipsoids);
} else if (strcmp(keyword,"Lines") == 0) {
@@ -590,7 +590,7 @@ void ReadData::command(int narg, char **arg)
"Must define dihedral_style before BondBond13 Coeffs");
if (firstpass) dihedralcoeffs(5);
else skip_lines(ndihedraltypes);
-
+
} else if (strcmp(keyword,"AngleAngle Coeffs") == 0) {
if (atom->avec->impropers_allow == 0)
error->all(FLERR,"Invalid data file section: AngleAngle Coeffs");
@@ -605,7 +605,7 @@ void ReadData::command(int narg, char **arg)
sprintf(str,"Unknown identifier in data file: %s",keyword);
error->all(FLERR,str);
}
-
+
parse_keyword(0);
}
@@ -613,9 +613,9 @@ void ReadData::command(int narg, char **arg)
if (natoms > 0 && atomflag == 0)
error->all(FLERR,"No atoms in data file");
-
+
// close file
-
+
if (me == 0) {
if (compressed) pclose(fp);
else fclose(fp);
@@ -639,7 +639,7 @@ void ReadData::command(int narg, char **arg)
// break out of loop if no molecular topology in file
// else make 2nd pass
-
+
if (!topoflag) break;
firstpass = 0;
@@ -668,7 +668,7 @@ void ReadData::command(int narg, char **arg)
special.build();
}
- // for atom style template systems, count total bonds,angles,etc
+ // for atom style template systems, count total bonds,angles,etc
if (atom->molecular == 2) {
Molecule **onemols = atom->avec->onemols;
@@ -894,7 +894,7 @@ void ReadData::header(int firstpass)
sscanf(line,BIGINT_FORMAT,&nimpropers);
if (addflag == NONE) atom->nimpropers = nimpropers;
else atom->nimpropers += nimpropers;
-
+
// Atom class type settings are only set by first data file
} else if (strstr(line,"atom types")) {
@@ -908,11 +908,11 @@ void ReadData::header(int firstpass)
if (addflag == NONE) atom->nangletypes = nangletypes + extra_angle_types;
} else if (strstr(line,"dihedral types")) {
sscanf(line,"%d",&ndihedraltypes);
- if (addflag == NONE)
+ if (addflag == NONE)
atom->ndihedraltypes = ndihedraltypes + extra_dihedral_types;
} else if (strstr(line,"improper types")) {
sscanf(line,"%d",&nimpropertypes);
- if (addflag == NONE)
+ if (addflag == NONE)
atom->nimpropertypes = nimpropertypes + extra_improper_types;
// these settings only used by first data file
@@ -979,7 +979,7 @@ void ReadData::header(int firstpass)
if ((atom->nimpropers || atom->nimpropertypes) &&
atom->avec->impropers_allow == 0)
error->all(FLERR,"No impropers allowed with this atom style");
-
+
if (atom->nbonds > 0 && atom->nbondtypes <= 0)
error->all(FLERR,"Bonds defined but no bond types");
if (atom->nangles > 0 && atom->nangletypes <= 0)
@@ -1032,7 +1032,7 @@ void ReadData::atoms()
if (sum != atom->natoms)
error->all(FLERR,"Did not assign all atoms correctly");
-
+
// check that atom IDs are valid
atom->tag_check();
@@ -1143,7 +1143,7 @@ void ReadData::bonds(int firstpass)
}
if (addflag != NONE) {
- if (maxall > atom->bond_per_atom)
+ if (maxall > atom->bond_per_atom)
error->all(FLERR,"Subsequent read data induced "
"too many bonds per atom");
} else atom->bond_per_atom = maxall;
@@ -1226,7 +1226,7 @@ void ReadData::angles(int firstpass)
}
if (addflag != NONE) {
- if (maxall > atom->angle_per_atom)
+ if (maxall > atom->angle_per_atom)
error->all(FLERR,"Subsequent read data induced "
"too many angles per atom");
} else atom->angle_per_atom = maxall;
@@ -1309,7 +1309,7 @@ void ReadData::dihedrals(int firstpass)
}
if (addflag != NONE) {
- if (maxall > atom->dihedral_per_atom)
+ if (maxall > atom->dihedral_per_atom)
error->all(FLERR,"Subsequent read data induced "
"too many dihedrals per atom");
} else atom->dihedral_per_atom = maxall;
@@ -1393,7 +1393,7 @@ void ReadData::impropers(int firstpass)
}
if (addflag != NONE) {
- if (maxall > atom->improper_per_atom)
+ if (maxall > atom->improper_per_atom)
error->all(FLERR,"Subsequent read data induced "
"too many impropers per atom");
} else atom->improper_per_atom = maxall;
@@ -1586,7 +1586,7 @@ void ReadData::pairIJcoeffs()
{
int i,j;
char *next;
-
+
int nsq = ntypes * (ntypes+1) / 2;
char *buf = new char[nsq * MAXLINE];
diff --git a/src/read_data.h b/src/read_data.h
index 925ec1f07e..7a03692086 100644
--- a/src/read_data.h
+++ b/src/read_data.h
@@ -20,7 +20,7 @@ CommandStyle(read_data,ReadData)
#ifndef LMP_READ_DATA_H
#define LMP_READ_DATA_H
-#include "stdio.h"
+#include <stdio.h>
#include "pointers.h"
namespace LAMMPS_NS {
@@ -72,7 +72,7 @@ class ReadData : protected Pointers {
int extra_dihedral_types,extra_improper_types;
int groupbit;
- int nfix;
+ int nfix;
int *fix_index;
char **fix_header;
char **fix_section;
diff --git a/src/read_dump.cpp b/src/read_dump.cpp
index 1aa121da57..47888c5ed8 100644
--- a/src/read_dump.cpp
+++ b/src/read_dump.cpp
@@ -19,10 +19,10 @@
// due to OpenMPI bug which sets INT64_MAX via its mpi.h
// before lmptype.h can set flags to insure it is done correctly
-#include "lmptype.h"
-#include "mpi.h"
-#include "string.h"
-#include "stdlib.h"
+#include "lmptype.h"
+#include <mpi.h>
+#include <string.h>
+#include <stdlib.h>
#include "read_dump.h"
#include "reader.h"
#include "style_reader.h"
@@ -810,8 +810,8 @@ void ReadDump::process_atoms(int n)
if (!wrapped) xbox = ybox = zbox = 0;
- image[m] = ((imageint) (xbox + IMGMAX) & IMGMASK) |
- (((imageint) (ybox + IMGMAX) & IMGMASK) << IMGBITS) |
+ image[m] = ((imageint) (xbox + IMGMAX) & IMGMASK) |
+ (((imageint) (ybox + IMGMAX) & IMGMASK) << IMGBITS) |
(((imageint) (zbox + IMGMAX) & IMGMASK) << IMG2BITS);
}
}
@@ -899,8 +899,8 @@ void ReadDump::process_atoms(int n)
// replace image flag in case changed by ix,iy,iz fields
- image[m] = ((imageint) (xbox + IMGMAX) & IMGMASK) |
- (((imageint) (ybox + IMGMAX) & IMGMASK) << IMGBITS) |
+ image[m] = ((imageint) (xbox + IMGMAX) & IMGMASK) |
+ (((imageint) (ybox + IMGMAX) & IMGMASK) << IMGBITS) |
(((imageint) (zbox + IMGMAX) & IMGMASK) << IMG2BITS);
}
}
diff --git a/src/read_dump.h b/src/read_dump.h
index 8301c8a5d0..8322ac0157 100644
--- a/src/read_dump.h
+++ b/src/read_dump.h
@@ -22,7 +22,7 @@ CommandStyle(read_dump,ReadDump)
#ifndef LMP_READ_DUMP_H
#define LMP_READ_DUMP_H
-#include "stdio.h"
+#include <stdio.h>
#include "pointers.h"
namespace LAMMPS_NS {
diff --git a/src/read_restart.cpp b/src/read_restart.cpp
index 743c88ba2c..b53b102c91 100644
--- a/src/read_restart.cpp
+++ b/src/read_restart.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "string.h"
-#include "stdlib.h"
-#include "dirent.h"
+#include <mpi.h>
+#include <string.h>
+#include <stdlib.h>
+#include <dirent.h>
#include "read_restart.h"
#include "atom.h"
#include "atom_vec.h"
@@ -110,13 +110,13 @@ void ReadRestart::command(int narg, char **arg)
if (strstr(arg[0],".mpiio")) mpiioflag = 1;
else mpiioflag = 0;
- if (multiproc && mpiioflag)
+ if (multiproc && mpiioflag)
error->all(FLERR,
"Read restart MPI-IO input not allowed with % in filename");
if (mpiioflag) {
mpiio = new RestartMPIIO(lmp);
- if (!mpiio->mpiio_exists)
+ if (!mpiio->mpiio_exists)
error->all(FLERR,"Reading from MPI-IO filename when "
"MPIIO package is not installed");
}
@@ -234,7 +234,7 @@ void ReadRestart::command(int narg, char **arg)
}
for (int iproc = 0; iproc < nprocs_file; iproc++) {
- if (read_int() != PERPROC)
+ if (read_int() != PERPROC)
error->all(FLERR,"Invalid flag in peratom section of restart file");
n = read_int();
@@ -294,16 +294,16 @@ void ReadRestart::command(int narg, char **arg)
}
fread(&flag,sizeof(int),1,fp);
- if (flag != PROCSPERFILE)
+ if (flag != PROCSPERFILE)
error->one(FLERR,"Invalid flag in peratom section of restart file");
int procsperfile;
fread(&procsperfile,sizeof(int),1,fp);
for (int i = 0; i < procsperfile; i++) {
fread(&flag,sizeof(int),1,fp);
- if (flag != PERPROC)
+ if (flag != PERPROC)
error->one(FLERR,"Invalid flag in peratom section of restart file");
-
+
fread(&n,sizeof(int),1,fp);
if (n > maxbuf) {
maxbuf = n;
@@ -342,7 +342,7 @@ void ReadRestart::command(int narg, char **arg)
int fileproc = static_cast<int> ((bigint) icluster * nprocs/nfile);
int fcluster = static_cast<int> ((bigint) fileproc * nfile/nprocs);
if (fcluster < icluster) fileproc++;
- int fileprocnext =
+ int fileprocnext =
static_cast<int> ((bigint) (icluster+1) * nprocs/nfile);
fcluster = static_cast<int> ((bigint) fileprocnext * nfile/nprocs);
if (fcluster < icluster+1) fileprocnext++;
@@ -371,7 +371,7 @@ void ReadRestart::command(int narg, char **arg)
if (filereader) {
fread(&flag,sizeof(int),1,fp);
- if (flag != PROCSPERFILE)
+ if (flag != PROCSPERFILE)
error->one(FLERR,"Invalid flag in peratom section of restart file");
fread(&procsperfile,sizeof(int),1,fp);
}
@@ -383,7 +383,7 @@ void ReadRestart::command(int narg, char **arg)
for (int i = 0; i < procsperfile; i++) {
if (filereader) {
fread(&flag,sizeof(int),1,fp);
- if (flag != PERPROC)
+ if (flag != PERPROC)
error->one(FLERR,"Invalid flag in peratom section of restart file");
fread(&n,sizeof(int),1,fp);
@@ -666,7 +666,7 @@ void ReadRestart::header(int incompatible)
if (screen) fprintf(screen," restart file = %s, LAMMPS = %s\n",
version,universe->version);
}
- if (incompatible)
+ if (incompatible)
error->all(FLERR,"Restart file incompatible with current version");
delete [] version;
@@ -729,7 +729,7 @@ void ReadRestart::header(int incompatible)
procgrid[1] != comm->user_procgrid[1]) flag = 1;
if (comm->user_procgrid[2] != 0 &&
procgrid[2] != comm->user_procgrid[2]) flag = 1;
- if (flag && me == 0)
+ if (flag && me == 0)
error->warning(FLERR,"Restart file used different 3d processor grid");
// don't set newton_pair, leave input script value unchanged
@@ -894,7 +894,7 @@ void ReadRestart::header(int incompatible)
atom->sortfreq = read_int();
} else if (flag == ATOM_SORTBIN) {
atom->userbinsize = read_double();
-
+
} else if (flag == COMM_MODE) {
comm->mode = read_int();
} else if (flag == COMM_CUTOFF) {
@@ -996,7 +996,7 @@ void ReadRestart::file_layout()
if (mpiioflag && mpiioflag_file == 0)
error->all(FLERR,"Restart file is not a MPI-IO file");
- if (mpiioflag) {
+ if (mpiioflag) {
bigint *nproc_chunk_offsets;
memory->create(nproc_chunk_offsets,nprocs,
"write_restart:nproc_chunk_offsets");
@@ -1016,45 +1016,45 @@ void ReadRestart::file_layout()
int *nproc_chunk_number;
memory->create(nproc_chunk_number,nprocs,
"write_restart:nproc_chunk_number");
-
+
fread(all_written_send_sizes,sizeof(int),nprocs_file,fp);
-
+
int init_chunk_number = nprocs_file/nprocs;
int num_extra_chunks = nprocs_file - (nprocs*init_chunk_number);
-
+
for (int i = 0; i < nprocs; i++) {
if (i < num_extra_chunks)
nproc_chunk_number[i] = init_chunk_number+1;
else
nproc_chunk_number[i] = init_chunk_number;
}
-
+
int all_written_send_sizes_index = 0;
bigint current_offset = 0;
for (int i=0;i<nprocs;i++) {
nproc_chunk_offsets[i] = current_offset;
nproc_chunk_sizes[i] = 0;
for (int j=0;j<nproc_chunk_number[i];j++) {
- nproc_chunk_sizes[i] +=
+ nproc_chunk_sizes[i] +=
all_written_send_sizes[all_written_send_sizes_index];
- current_offset +=
- (all_written_send_sizes[all_written_send_sizes_index] *
+ current_offset +=
+ (all_written_send_sizes[all_written_send_sizes_index] *
sizeof(double));
all_written_send_sizes_index++;
}
-
+
}
memory->destroy(all_written_send_sizes);
memory->destroy(nproc_chunk_number);
}
// scatter chunk sizes and offsets to all procs
-
+
MPI_Scatter(nproc_chunk_sizes, 1, MPI_LMP_BIGINT,
&assignedChunkSize , 1, MPI_LMP_BIGINT, 0,world);
MPI_Scatter(nproc_chunk_offsets, 1, MPI_LMP_BIGINT,
&assignedChunkOffset , 1, MPI_LMP_BIGINT, 0,world);
-
+
memory->destroy(nproc_chunk_sizes);
memory->destroy(nproc_chunk_offsets);
}
@@ -1089,10 +1089,10 @@ void ReadRestart::magic_string()
int count;
if (me == 0) count = fread(str,sizeof(char),n,fp);
MPI_Bcast(&count,1,MPI_INT,0,world);
- if (count < n)
+ if (count < n)
error->all(FLERR,"Invalid LAMMPS restart file");
MPI_Bcast(str,n,MPI_CHAR,0,world);
- if (strcmp(str,MAGIC_STRING) != 0)
+ if (strcmp(str,MAGIC_STRING) != 0)
error->all(FLERR,"Invalid LAMMPS restart file");
delete [] str;
}
diff --git a/src/read_restart.h b/src/read_restart.h
index 586a13c210..e21c9dcbf3 100644
--- a/src/read_restart.h
+++ b/src/read_restart.h
@@ -20,7 +20,7 @@ CommandStyle(read_restart,ReadRestart)
#ifndef LMP_READ_RESTART_H
#define LMP_READ_RESTART_H
-#include "stdio.h"
+#include <stdio.h>
#include "pointers.h"
namespace LAMMPS_NS {
diff --git a/src/reader.cpp b/src/reader.cpp
index 588b21062c..b8914d1b10 100644
--- a/src/reader.cpp
+++ b/src/reader.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdio.h"
-#include "string.h"
+#include <stdio.h>
+#include <string.h>
#include "reader.h"
#include "error.h"
diff --git a/src/reader_native.cpp b/src/reader_native.cpp
index 769a651739..0a876d0728 100644
--- a/src/reader_native.cpp
+++ b/src/reader_native.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
-#include "stdlib.h"
+#include <string.h>
+#include <stdlib.h>
#include "reader_native.h"
#include "atom.h"
#include "memory.h"
diff --git a/src/reader_xyz.cpp b/src/reader_xyz.cpp
index b95d917bd0..a56b503f5e 100644
--- a/src/reader_xyz.cpp
+++ b/src/reader_xyz.cpp
@@ -15,8 +15,8 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "string.h"
-#include "stdlib.h"
+#include <string.h>
+#include <stdlib.h>
#include "reader_xyz.h"
#include "atom.h"
#include "memory.h"
diff --git a/src/region.cpp b/src/region.cpp
index 9c0897ecb1..b8489401f2 100644
--- a/src/region.cpp
+++ b/src/region.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "region.h"
#include "update.h"
#include "domain.h"
diff --git a/src/region_block.cpp b/src/region_block.cpp
index 0325ae4b1c..c06eeda544 100644
--- a/src/region_block.cpp
+++ b/src/region_block.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdlib.h"
-#include "string.h"
+#include <stdlib.h>
+#include <string.h>
#include "region_block.h"
#include "domain.h"
#include "error.h"
diff --git a/src/region_cone.cpp b/src/region_cone.cpp
index 09408c8d93..deb8d04841 100644
--- a/src/region_cone.cpp
+++ b/src/region_cone.cpp
@@ -15,9 +15,9 @@
Contributing author: Pim Schravendijk
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "region_cone.h"
#include "domain.h"
#include "error.h"
diff --git a/src/region_cylinder.cpp b/src/region_cylinder.cpp
index 2e46f5523d..b77ff2a881 100644
--- a/src/region_cylinder.cpp
+++ b/src/region_cylinder.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "region_cylinder.h"
#include "update.h"
#include "domain.h"
diff --git a/src/region_intersect.cpp b/src/region_intersect.cpp
index 96c2e59a7c..bfbe579367 100644
--- a/src/region_intersect.cpp
+++ b/src/region_intersect.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdlib.h"
-#include "string.h"
+#include <stdlib.h>
+#include <string.h>
#include "region_intersect.h"
#include "domain.h"
#include "error.h"
@@ -43,7 +43,7 @@ RegIntersect::RegIntersect(LAMMPS *lmp, int narg, char **arg) :
idsub[nregion] = new char[m];
strcpy(idsub[nregion],arg[iarg+3]);
iregion = domain->find_region(idsub[nregion]);
- if (iregion == -1)
+ if (iregion == -1)
error->all(FLERR,"Region intersect region ID does not exist");
list[nregion++] = iregion;
}
@@ -117,7 +117,7 @@ void RegIntersect::init()
int iregion;
for (int ilist = 0; ilist < nregion; ilist++) {
iregion = domain->find_region(idsub[ilist]);
- if (iregion == -1)
+ if (iregion == -1)
error->all(FLERR,"Region union region ID does not exist");
list[ilist] = iregion;
}
diff --git a/src/region_plane.cpp b/src/region_plane.cpp
index 9a0d47c1fe..38d5b92bcb 100644
--- a/src/region_plane.cpp
+++ b/src/region_plane.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "region_plane.h"
#include "error.h"
#include "force.h"
diff --git a/src/region_prism.cpp b/src/region_prism.cpp
index 01e6f60c8a..1efd3d964b 100644
--- a/src/region_prism.cpp
+++ b/src/region_prism.cpp
@@ -15,9 +15,9 @@
Contributing author: Pieter in 't Veld (SNL)
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "region_prism.h"
#include "domain.h"
#include "force.h"
diff --git a/src/region_sphere.cpp b/src/region_sphere.cpp
index 709080866d..409a497f11 100644
--- a/src/region_sphere.cpp
+++ b/src/region_sphere.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "region_sphere.h"
#include "update.h"
#include "input.h"
diff --git a/src/region_union.cpp b/src/region_union.cpp
index 30a33bf48a..2772d7b4d5 100644
--- a/src/region_union.cpp
+++ b/src/region_union.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdlib.h"
-#include "string.h"
+#include <stdlib.h>
+#include <string.h>
#include "region_union.h"
#include "domain.h"
#include "error.h"
@@ -44,7 +44,7 @@ RegUnion::RegUnion(LAMMPS *lmp, int narg, char **arg) : Region(lmp, narg, arg)
idsub[nregion] = new char[m];
strcpy(idsub[nregion],arg[iarg+3]);
iregion = domain->find_region(idsub[nregion]);
- if (iregion == -1)
+ if (iregion == -1)
error->all(FLERR,"Region union region ID does not exist");
list[nregion++] = iregion;
}
@@ -109,7 +109,7 @@ void RegUnion::init()
int iregion;
for (int ilist = 0; ilist < nregion; ilist++) {
iregion = domain->find_region(idsub[ilist]);
- if (iregion == -1)
+ if (iregion == -1)
error->all(FLERR,"Region union region ID does not exist");
list[ilist] = iregion;
}
diff --git a/src/replicate.cpp b/src/replicate.cpp
index d94940d5e4..941ec32492 100644
--- a/src/replicate.cpp
+++ b/src/replicate.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdlib.h"
-#include "string.h"
+#include <stdlib.h>
+#include <string.h>
#include "replicate.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/rerun.cpp b/src/rerun.cpp
index bb98f23dfa..2f357c2102 100644
--- a/src/rerun.cpp
+++ b/src/rerun.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdlib.h"
-#include "string.h"
+#include <stdlib.h>
+#include <string.h>
#include "rerun.h"
#include "read_dump.h"
#include "domain.h"
diff --git a/src/respa.cpp b/src/respa.cpp
index dbd3effb63..e4afa2bd13 100644
--- a/src/respa.cpp
+++ b/src/respa.cpp
@@ -15,8 +15,8 @@
Contributing authors: Mark Stevens (SNL), Paul Crozier (SNL)
------------------------------------------------------------------------- */
-#include "stdlib.h"
-#include "string.h"
+#include <stdlib.h>
+#include <string.h>
#include "respa.h"
#include "neighbor.h"
#include "atom.h"
@@ -269,7 +269,7 @@ Respa::Respa(LAMMPS *lmp, int narg, char **arg) : Integrate(lmp, narg, arg)
cutoff[3] = cutoff[1];
}
- // ensure that pair->compute() is run properly when the "hybrid" keyword is not used.
+ // ensure that pair->compute() is run properly when the "hybrid" keyword is not used.
if (nhybrid_styles < 1) {
pair_compute = 1;
tally_global = 1;
@@ -628,7 +628,7 @@ void Respa::recurse(int ilevel)
}
timer->stamp();
comm->exchange();
- if (atom->sortfreq > 0 &&
+ if (atom->sortfreq > 0 &&
update->ntimestep >= atom->nextsort) atom->sort();
comm->borders();
if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
diff --git a/src/run.cpp b/src/run.cpp
index d321f921f8..b120d2a14c 100644
--- a/src/run.cpp
+++ b/src/run.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "stdlib.h"
-#include "string.h"
+#include <stdlib.h>
+#include <string.h>
#include "run.h"
#include "domain.h"
#include "update.h"
diff --git a/src/set.cpp b/src/set.cpp
index 9919518294..33f6b77dc7 100644
--- a/src/set.cpp
+++ b/src/set.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include <mpi.h>
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "set.h"
#include "atom.h"
#include "atom_vec.h"
@@ -565,7 +565,7 @@ void Set::set(int keyword)
// overwrite dvalue, ivalue, xyzw value if variables defined
// else the input script scalar value remains in place
-
+
if (varflag) {
if (varflag1) {
dvalue = xvalue = vec1[i];
@@ -583,7 +583,7 @@ void Set::set(int keyword)
if (ivalue <= 0 || ivalue > atom->ntypes)
error->one(FLERR,"Invalid value in set command");
atom->type[i] = ivalue;
- }
+ }
else if (keyword == MOLECULE) atom->molecule[i] = ivalue;
else if (keyword == X) atom->x[i][0] = dvalue;
else if (keyword == Y) atom->x[i][1] = dvalue;
@@ -592,7 +592,7 @@ void Set::set(int keyword)
else if (keyword == MASS) {
if (dvalue <= 0.0) error->one(FLERR,"Invalid mass in set command");
atom->rmass[i] = dvalue;
- }
+ }
else if (keyword == DIAMETER) {
if (dvalue < 0.0) error->one(FLERR,"Invalid diameter in set command");
atom->radius[i] = 0.5 * dvalue;
@@ -730,8 +730,8 @@ void Set::set(int keyword)
if (ximageflag) xbox = ximage;
if (yimageflag) ybox = yimage;
if (zimageflag) zbox = zimage;
- atom->image[i] = ((imageint) (xbox + IMGMAX) & IMGMASK) |
- (((imageint) (ybox + IMGMAX) & IMGMASK) << IMGBITS) |
+ atom->image[i] = ((imageint) (xbox + IMGMAX) & IMGMASK) |
+ (((imageint) (ybox + IMGMAX) & IMGMASK) << IMGBITS) |
(((imageint) (zbox + IMGMAX) & IMGMASK) << IMG2BITS);
}
diff --git a/src/special.cpp b/src/special.cpp
index ebabbff281..ae566ec4f5 100644
--- a/src/special.cpp
+++ b/src/special.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "stdio.h"
+#include <mpi.h>
+#include <stdio.h>
#include "special.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/thermo.cpp b/src/thermo.cpp
index 34ccfce9f4..b96be64bf6 100644
--- a/src/thermo.cpp
+++ b/src/thermo.cpp
@@ -15,11 +15,11 @@
// due to OpenMPI bug which sets INT64_MAX via its mpi.h
// before lmptype.h can set flags to insure it is done correctly
-#include "lmptype.h"
-#include "mpi.h"
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
+#include "lmptype.h"
+#include <mpi.h>
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
#include "thermo.h"
#include "atom.h"
#include "update.h"
@@ -842,11 +842,11 @@ void Thermo::parse_fields(char *str)
if (ptr == NULL) argindex1[nfield] = 0;
else {
*ptr = '\0';
- argindex1[nfield] =
+ argindex1[nfield] =
(int) input->variable->int_between_brackets(ptr,0);
ptr++;
if (*ptr == '[') {
- argindex2[nfield] =
+ argindex2[nfield] =
(int) input->variable->int_between_brackets(ptr,0);
ptr++;
} else argindex2[nfield] = 0;
@@ -890,7 +890,7 @@ void Thermo::parse_fields(char *str)
if (argindex1[nfield] > 0 && argindex2[nfield] == 0) {
if (modify->fix[n]->vector_flag == 0)
error->all(FLERR,"Thermo fix does not compute vector");
- if (argindex1[nfield] > modify->fix[n]->size_vector &&
+ if (argindex1[nfield] > modify->fix[n]->size_vector &&
modify->fix[n]->size_vector_variable == 0)
error->all(FLERR,"Thermo fix vector is accessed out-of-range");
}
@@ -909,7 +909,7 @@ void Thermo::parse_fields(char *str)
} else if (word[0] == 'v') {
n = input->variable->find(id);
- if (n < 0)
+ if (n < 0)
error->all(FLERR,"Could not find thermo custom variable name");
if (input->variable->equalstyle(n) == 0)
error->all(FLERR,
@@ -1431,7 +1431,7 @@ void Thermo::compute_compute()
dvalue = compute->scalar;
if (normflag && compute->extscalar) dvalue /= natoms;
} else if (compute_which[m] == VECTOR) {
- if (compute->size_vector_variable && argindex1[ifield] >
+ if (compute->size_vector_variable && argindex1[ifield] >
compute->size_vector) dvalue = 0.0;
else dvalue = compute->vector[argindex1[ifield]-1];
if (normflag) {
@@ -1440,7 +1440,7 @@ void Thermo::compute_compute()
else if (compute->extlist[argindex1[ifield]-1]) dvalue /= natoms;
}
} else {
- if (compute->size_array_rows_variable && argindex1[ifield] >
+ if (compute->size_array_rows_variable && argindex1[ifield] >
compute->size_array_rows) dvalue = 0.0;
else dvalue = compute->array[argindex1[ifield]-1][argindex2[ifield]-1];
if (normflag && compute->extarray) dvalue /= natoms;
@@ -1575,7 +1575,7 @@ void Thermo::compute_spcpu()
void Thermo::compute_cpuremain()
{
if (firststep == 0) dvalue = 0.0;
- else dvalue = timer->elapsed(Timer::TOTAL) *
+ else dvalue = timer->elapsed(Timer::TOTAL) *
(update->laststep - update->ntimestep) /
(update->ntimestep - update->firststep);
}
diff --git a/src/timer.cpp b/src/timer.cpp
index 2fb8453684..a075ff3dec 100644
--- a/src/timer.cpp
+++ b/src/timer.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "string.h"
+#include <mpi.h>
+#include <string.h>
#include "timer.h"
#include "comm.h"
#include "error.h"
@@ -88,7 +88,7 @@ void Timer::_stamp(enum ttype which)
if ((which > TOTAL) && (which < NUM_TIMER)) {
const double delta_cpu = current_cpu - previous_cpu;
const double delta_wall = current_wall - previous_wall;
-
+
cpu_array[which] += delta_cpu;
wall_array[which] += delta_wall;
cpu_array[ALL] += delta_cpu;
@@ -200,7 +200,7 @@ void Timer::modify_params(int narg, char **arg)
} else if (strcmp(arg[iarg],timer_mode[NORMAL]) == 0) {
_sync = NORMAL;
} else error->all(FLERR,"Illegal timers command");
- ++iarg;
+ ++iarg;
}
if (comm->me == 0) {
diff --git a/src/timer.h b/src/timer.h
index adf554f468..5737b52834 100644
--- a/src/timer.h
+++ b/src/timer.h
@@ -36,7 +36,7 @@ class Timer : protected Pointers {
void stamp(enum ttype which=START) {
if (_level > LOOP) _stamp(which);
}
-
+
void barrier_start();
void barrier_stop();
diff --git a/src/universe.cpp b/src/universe.cpp
index 35415bffa9..a856555de4 100644
--- a/src/universe.cpp
+++ b/src/universe.cpp
@@ -11,11 +11,11 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "ctype.h"
-#include "stdlib.h"
-#include "string.h"
-#include "stdio.h"
+#include <mpi.h>
+#include <ctype.h>
+#include <stdlib.h>
+#include <string.h>
+#include <stdio.h>
#include "universe.h"
#include "version.h"
#include "error.h"
diff --git a/src/universe.h b/src/universe.h
index 897b6c9681..017f869f5e 100644
--- a/src/universe.h
+++ b/src/universe.h
@@ -14,7 +14,7 @@
#ifndef LMP_UNIVERSE_H
#define LMP_UNIVERSE_H
-#include "stdio.h"
+#include <stdio.h>
#include "pointers.h"
namespace LAMMPS_NS {
diff --git a/src/update.cpp b/src/update.cpp
index 78f4fe73a3..f53acbed3a 100644
--- a/src/update.cpp
+++ b/src/update.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
-#include "stdlib.h"
+#include <string.h>
+#include <stdlib.h>
#include "update.h"
#include "integrate.h"
#include "min.h"
@@ -261,8 +261,8 @@ void Update::set_units(const char *style)
dt = 2.0;
neighbor->skin = 0.1;
-
- } else if (strcmp(style,"nano") == 0) {
+
+ } else if (strcmp(style,"nano") == 0) {
force->boltz = 0.013806504;
force->hplanck = 6.62606896e-4;
force->mvv2e = 1.0;
@@ -279,7 +279,7 @@ void Update::set_units(const char *style)
force->angstrom = 1.0e-1;
force->femtosecond = 1.0e-6;
force->qelectron = 1.0;
-
+
dt = 0.00045;
neighbor->skin = 0.1;
@@ -339,11 +339,11 @@ void Update::new_integrate(char *style, int narg, char **arg,
#include "style_integrate.h"
#undef IntegrateStyle
#undef INTEGRATE_CLASS
-
+
else success = 0;
if (success) return;
}
-
+
if (lmp->suffix2) {
sflag = 2;
char estyle[256];
@@ -358,7 +358,7 @@ void Update::new_integrate(char *style, int narg, char **arg,
#include "style_integrate.h"
#undef IntegrateStyle
#undef INTEGRATE_CLASS
-
+
else success = 0;
if (success) return;
}
diff --git a/src/variable.cpp b/src/variable.cpp
index 2e88da4fd3..ddaff7d991 100644
--- a/src/variable.cpp
+++ b/src/variable.cpp
@@ -11,11 +11,11 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
-#include "ctype.h"
-#include "unistd.h"
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
+#include <ctype.h>
+#include <unistd.h>
#include "variable.h"
#include "universe.h"
#include "atom.h"
@@ -533,8 +533,8 @@ int Variable::next(int narg, char **arg)
// invalid styles: STRING, EQUAL, WORLD, ATOM, GETENV, FORMAT, PYTHON
int istyle = style[find(arg[0])];
- if (istyle == STRING || istyle == EQUAL || istyle == WORLD ||
- istyle == GETENV || istyle == ATOM || istyle == FORMAT ||
+ if (istyle == STRING || istyle == EQUAL || istyle == WORLD ||
+ istyle == GETENV || istyle == ATOM || istyle == FORMAT ||
istyle == PYTHON)
error->all(FLERR,"Invalid variable style with next command");
@@ -546,7 +546,7 @@ int Variable::next(int narg, char **arg)
int iarg = 0;
for (iarg = 0; iarg < narg; iarg++)
if (strcmp(arg[iarg],names[i]) == 0) break;
- if (iarg == narg)
+ if (iarg == narg)
error->universe_one(FLERR,"Next command must list all "
"universe and uloop variables");
}
@@ -730,7 +730,7 @@ char *Variable::pythonstyle(char *name, char *funcname)
/* ----------------------------------------------------------------------
return ptr to the data text associated with a variable
- if INDEX or WORLD or UNIVERSE or STRING or SCALARFILE,
+ if INDEX or WORLD or UNIVERSE or STRING or SCALARFILE,
return ptr to stored string
if LOOP or ULOOP, write int to data[0] and return ptr to string
if EQUAL, evaluate variable and put result in str
@@ -748,13 +748,13 @@ char *Variable::retrieve(char *name)
if (ivar < 0) return NULL;
if (which[ivar] >= num[ivar]) return NULL;
- if (eval_in_progress[ivar])
+ if (eval_in_progress[ivar])
error->all(FLERR,"Variable has circular dependency");
eval_in_progress[ivar] = 1;
char *str = NULL;
if (style[ivar] == INDEX || style[ivar] == WORLD ||
- style[ivar] == UNIVERSE || style[ivar] == STRING ||
+ style[ivar] == UNIVERSE || style[ivar] == STRING ||
style[ivar] == SCALARFILE) {
str = data[ivar][which[ivar]];
} else if (style[ivar] == LOOP || style[ivar] == ULOOP) {
@@ -793,7 +793,7 @@ char *Variable::retrieve(char *name)
str = data[ivar][1];
} else if (style[ivar] == PYTHON) {
int ifunc = python->variable_match(data[ivar][0],names[ivar],0);
- if (ifunc < 0)
+ if (ifunc < 0)
error->all(FLERR,"Python variable does not match Python function");
python->invoke_function(ifunc,data[ivar][1]);
str = data[ivar][1];
@@ -813,7 +813,7 @@ char *Variable::retrieve(char *name)
double Variable::compute_equal(int ivar)
{
- if (eval_in_progress[ivar])
+ if (eval_in_progress[ivar])
error->all(FLERR,"Variable has circular dependency");
eval_in_progress[ivar] = 1;
@@ -853,8 +853,8 @@ void Variable::compute_atom(int ivar, int igroup,
{
Tree *tree;
double *vstore;
-
- if (eval_in_progress[ivar])
+
+ if (eval_in_progress[ivar])
error->all(FLERR,"Variable has circular dependency");
eval_in_progress[ivar] = 1;
@@ -867,7 +867,7 @@ void Variable::compute_atom(int ivar, int igroup,
eval_in_progress[ivar] = 0;
return;
}
-
+
int groupbit = group->bitmask[igroup];
int *mask = atom->mask;
int nlocal = atom->nlocal;
@@ -991,7 +991,7 @@ void Variable::grow()
memory->grow(which,maxvar,"var:which");
memory->grow(pad,maxvar,"var:pad");
- reader = (VarReader **)
+ reader = (VarReader **)
memory->srealloc(reader,maxvar*sizeof(VarReader *),"var:reader");
for (int i = old; i < maxvar; i++) reader[i] = NULL;
@@ -1151,7 +1151,7 @@ double Variable::evaluate(char *str, Tree **tree)
"Variable evaluation before simulation box is defined");
int icompute = modify->find_compute(word+2);
- if (icompute < 0)
+ if (icompute < 0)
error->all(FLERR,"Invalid compute ID in variable formula");
Compute *compute = modify->compute[icompute];
@@ -1216,7 +1216,7 @@ double Variable::evaluate(char *str, Tree **tree)
compute->invoked_flag |= INVOKED_VECTOR;
}
- if (compute->size_vector_variable &&
+ if (compute->size_vector_variable &&
index1 > compute->size_vector) value1 = 0.0;
else value1 = compute->vector[index1-1];
if (tree) {
@@ -1248,7 +1248,7 @@ double Variable::evaluate(char *str, Tree **tree)
compute->invoked_flag |= INVOKED_ARRAY;
}
- if (compute->size_array_rows_variable &&
+ if (compute->size_array_rows_variable &&
index1 > compute->size_array_rows) value1 = 0.0;
else value1 = compute->array[index1-1][index2-1];
if (tree) {
@@ -1424,7 +1424,7 @@ double Variable::evaluate(char *str, Tree **tree)
"accessed out-of-range");
if (update->whichflag > 0 && update->ntimestep % fix->global_freq)
error->all(FLERR,"Fix in variable not computed at compatible time");
-
+
value1 = fix->compute_vector(index1-1);
if (tree) {
Tree *newtree = new Tree();
@@ -1891,7 +1891,7 @@ double Variable::evaluate(char *str, Tree **tree)
/* ----------------------------------------------------------------------
one-time collapse of an atom-style variable parse tree
tree was created by one-time parsing of formula string via evaluate()
- only keep tree nodes that depend on
+ only keep tree nodes that depend on
ATOMARRAY, TYPEARRAY, INTARRAY, BIGINTARRAY
remainder is converted to single VALUE
this enables optimal eval_tree loop over atoms
@@ -2321,8 +2321,8 @@ double Variable::collapse_tree(Tree *tree)
int ivalue5 = static_cast<int> (collapse_tree(tree->extra[2]));
int ivalue6 = static_cast<int> (collapse_tree(tree->extra[3]));
if (tree->first->type != VALUE || tree->second->type != VALUE ||
- tree->extra[0]->type != VALUE || tree->extra[1]->type != VALUE ||
- tree->extra[2]->type != VALUE || tree->extra[3]->type != VALUE)
+ tree->extra[0]->type != VALUE || tree->extra[1]->type != VALUE ||
+ tree->extra[2]->type != VALUE || tree->extra[3]->type != VALUE)
return 0.0;
tree->type = VALUE;
if (ivalue1 < 0 || ivalue2 < 0 || ivalue3 <= 0 || ivalue1 > ivalue2)
@@ -2337,7 +2337,7 @@ double Variable::collapse_tree(Tree *tree)
if (update->ntimestep < ivalue4 || update->ntimestep > ivalue5) {
int offset = update->ntimestep - ivalue1;
istep = ivalue1 + (offset/ivalue3)*ivalue3 + ivalue3;
- if (update->ntimestep < ivalue2 && istep > ivalue4)
+ if (update->ntimestep < ivalue2 && istep > ivalue4)
tree->value = ivalue4;
} else {
int offset = update->ntimestep - ivalue4;
@@ -2657,7 +2657,7 @@ double Variable::eval_tree(Tree *tree, int i)
if (update->ntimestep < ivalue4 || update->ntimestep > ivalue5) {
int offset = update->ntimestep - ivalue1;
istep = ivalue1 + (offset/ivalue3)*ivalue3 + ivalue3;
- if (update->ntimestep < ivalue2 && istep > ivalue4)
+ if (update->ntimestep < ivalue2 && istep > ivalue4)
tree->value = ivalue4;
} else {
int offset = update->ntimestep - ivalue4;
@@ -2859,7 +2859,7 @@ int Variable::math_function(char *word, char *contents, Tree **tree,
if (strcmp(word,"sqrt") && strcmp(word,"exp") &&
strcmp(word,"ln") && strcmp(word,"log") &&
- strcmp(word,"abs") &&
+ strcmp(word,"abs") &&
strcmp(word,"sin") && strcmp(word,"cos") &&
strcmp(word,"tan") && strcmp(word,"asin") &&
strcmp(word,"acos") && strcmp(word,"atan") &&
@@ -2867,15 +2867,15 @@ int Variable::math_function(char *word, char *contents, Tree **tree,
strcmp(word,"normal") && strcmp(word,"ceil") &&
strcmp(word,"floor") && strcmp(word,"round") &&
strcmp(word,"ramp") && strcmp(word,"stagger") &&
- strcmp(word,"logfreq") && strcmp(word,"logfreq2") &&
- strcmp(word,"stride") && strcmp(word,"stride2") &&
- strcmp(word,"vdisplace") && strcmp(word,"swiggle") &&
+ strcmp(word,"logfreq") && strcmp(word,"logfreq2") &&
+ strcmp(word,"stride") && strcmp(word,"stride2") &&
+ strcmp(word,"vdisplace") && strcmp(word,"swiggle") &&
strcmp(word,"cwiggle"))
return 0;
// parse contents for comma-separated args
// narg = number of args, args = strings between commas
-
+
char *args[MAXFUNCARG];
int narg = parse_args(contents,args);
@@ -2909,7 +2909,7 @@ int Variable::math_function(char *word, char *contents, Tree **tree,
if (narg > 1) {
value2 = evaluate(args[1],NULL);
if (narg > 2) {
- for (int i = 2; i < narg; i++)
+ for (int i = 2; i < narg; i++)
values[i-2] = evaluate(args[i],NULL);
}
}
@@ -3264,7 +3264,7 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
// parse contents for comma-separated args
// narg = number of args, args = strings between commas
-
+
char *args[MAXFUNCARG];
int narg = parse_args(contents,args);
@@ -3501,7 +3501,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
if (strcmp(word,"sum") && strcmp(word,"min") && strcmp(word,"max") &&
strcmp(word,"ave") && strcmp(word,"trap") && strcmp(word,"slope") &&
- strcmp(word,"gmask") && strcmp(word,"rmask") &&
+ strcmp(word,"gmask") && strcmp(word,"rmask") &&
strcmp(word,"grmask") && strcmp(word,"next") &&
strcmp(word,"is_active") && strcmp(word,"is_defined") &&
strcmp(word,"is_available"))
@@ -3509,7 +3509,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
// parse contents for comma-separated args
// narg = number of args, args = strings between commas
-
+
char *args[MAXFUNCARG];
int narg = parse_args(contents,args);
@@ -3527,7 +3527,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
else if (strcmp(word,"trap") == 0) method = TRAP;
else if (strcmp(word,"slope") == 0) method = SLOPE;
- if (narg != 1)
+ if (narg != 1)
error->all(FLERR,"Invalid special function in variable formula");
Compute *compute = NULL;
@@ -3544,7 +3544,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
} else index = 0;
int icompute = modify->find_compute(&args[0][2]);
- if (icompute < 0)
+ if (icompute < 0)
error->all(FLERR,"Invalid compute ID in variable formula");
compute = modify->compute[icompute];
if (index == 0 && compute->vector_flag) {
@@ -3654,9 +3654,9 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
}
}
if (method == TRAP) {
- if (index) value -= 0.5*fix->compute_array(0,index-1) +
+ if (index) value -= 0.5*fix->compute_array(0,index-1) +
0.5*fix->compute_array(nvec-1,index-1);
- else value -= 0.5*fix->compute_vector(0) +
+ else value -= 0.5*fix->compute_vector(0) +
0.5*fix->compute_vector(nvec-1);
}
}
@@ -3686,7 +3686,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
} else if (strcmp(word,"gmask") == 0) {
if (tree == NULL)
error->all(FLERR,"Gmask function in equal-style variable formula");
- if (narg != 1)
+ if (narg != 1)
error->all(FLERR,"Invalid special function in variable formula");
int igroup = group->find(args[0]);
@@ -3703,7 +3703,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
} else if (strcmp(word,"rmask") == 0) {
if (tree == NULL)
error->all(FLERR,"Rmask function in equal-style variable formula");
- if (narg != 1)
+ if (narg != 1)
error->all(FLERR,"Invalid special function in variable formula");
int iregion = region_function(args[0]);
@@ -3719,7 +3719,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
} else if (strcmp(word,"grmask") == 0) {
if (tree == NULL)
error->all(FLERR,"Grmask function in equal-style variable formula");
- if (narg != 2)
+ if (narg != 2)
error->all(FLERR,"Invalid special function in variable formula");
int igroup = group->find(args[0]);
@@ -3739,7 +3739,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
// special function for file-style or atomfile-style variables
} else if (strcmp(word,"next") == 0) {
- if (narg != 1)
+ if (narg != 1)
error->all(FLERR,"Invalid special function in variable formula");
int ivar = find(args[0]);
@@ -3768,7 +3768,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
// set selfalloc = 1 so result will be deleted by free_tree() after eval
} else if (style[ivar] == ATOMFILE) {
- if (tree == NULL)
+ if (tree == NULL)
error->all(FLERR,"Atomfile variable in equal-style variable formula");
double *result;
@@ -3790,7 +3790,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
} else error->all(FLERR,"Invalid variable style in special function next");
} else if (strcmp(word,"is_active") == 0) {
- if (narg != 2)
+ if (narg != 2)
error->all(FLERR,"Invalid is_active() function in variable formula");
Info info(lmp);
@@ -3808,7 +3808,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
} else argstack[nargstack++] = value;
} else if (strcmp(word,"is_available") == 0) {
- if (narg != 2)
+ if (narg != 2)
error->all(FLERR,"Invalid is_available() function in variable formula");
Info info(lmp);
@@ -3826,7 +3826,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
} else argstack[nargstack++] = value;
} else if (strcmp(word,"is_defined") == 0) {
- if (narg != 2)
+ if (narg != 2)
error->all(FLERR,"Invalid is_defined() function in variable formula");
Info info(lmp);
@@ -3892,7 +3892,7 @@ void Variable::peratom2global(int flag, char *word,
}
else if (strcmp(word,"type") == 0) mine = atom->type[index];
else if (strcmp(word,"mol") == 0) {
- if (!atom->molecule_flag)
+ if (!atom->molecule_flag)
error->one(FLERR,"Variable uses atom property that isn't allocated");
mine = atom->molecule[index];
}
@@ -3906,7 +3906,7 @@ void Variable::peratom2global(int flag, char *word,
else if (strcmp(word,"fy") == 0) mine = atom->f[index][1];
else if (strcmp(word,"fz") == 0) mine = atom->f[index][2];
else if (strcmp(word,"q") == 0) {
- if (!atom->q_flag)
+ if (!atom->q_flag)
error->one(FLERR,"Variable uses atom property that isn't allocated");
mine = atom->q[index];
}
@@ -4002,7 +4002,7 @@ void Variable::atom_vector(char *word, Tree **tree,
newtree->iarray = atom->type;
} else if (strcmp(word,"mol") == 0) {
- if (!atom->molecule_flag)
+ if (!atom->molecule_flag)
error->one(FLERR,"Variable uses atom property that isn't allocated");
if (sizeof(tagint) == sizeof(smallint)) {
newtree->type = INTARRAY;
@@ -4169,7 +4169,7 @@ double Variable::evaluate_boolean(char *str)
// ----------------
else if (onechar == '(') {
- if (expect == OP)
+ if (expect == OP)
error->all(FLERR,"Invalid Boolean syntax in if command");
expect = OP;
@@ -4190,7 +4190,7 @@ double Variable::evaluate_boolean(char *str)
// ----------------
} else if (isdigit(onechar) || onechar == '.' || onechar == '-') {
- if (expect == OP)
+ if (expect == OP)
error->all(FLERR,"Invalid Boolean syntax in if command");
expect = OP;
@@ -4216,7 +4216,7 @@ double Variable::evaluate_boolean(char *str)
// ----------------
} else if (isalpha(onechar)) {
- if (expect == OP)
+ if (expect == OP)
error->all(FLERR,"Invalid Boolean syntax in if command");
expect = OP;
@@ -4280,7 +4280,7 @@ double Variable::evaluate_boolean(char *str)
continue;
}
- if (expect == ARG)
+ if (expect == ARG)
error->all(FLERR,"Invalid Boolean syntax in if command");
expect = ARG;
@@ -4411,7 +4411,7 @@ unsigned int Variable::data_mask(char *str)
"Variable evaluation before simulation box is defined");
int icompute = modify->find_compute(word+2);
- if (icompute < 0)
+ if (icompute < 0)
error->all(FLERR,"Invalid compute ID in variable formula");
datamask &= modify->compute[icompute]->data_mask();
@@ -4421,13 +4421,13 @@ unsigned int Variable::data_mask(char *str)
if (domain->box_exist == 0)
error->all(FLERR,
"Variable evaluation before simulation box is defined");
-
+
int ifix = modify->find_fix(word+2);
if (ifix < 0) error->all(FLERR,"Invalid fix ID in variable formula");
-
+
datamask &= modify->fix[ifix]->data_mask();
}
-
+
if ((strncmp(word,"v_",2) == 0) && (i>0) && (!isalnum(str[i-1]))) {
int ivar = find(word+2);
if (ivar < 0) error->all(FLERR,"Invalid variable name in variable formula");
@@ -4446,7 +4446,7 @@ unsigned int Variable::data_mask(char *str)
for flag = ATOMFILE, reads set of one value per atom
------------------------------------------------------------------------- */
-VarReader::VarReader(LAMMPS *lmp, char *name, char *file, int flag) :
+VarReader::VarReader(LAMMPS *lmp, char *name, char *file, int flag) :
Pointers(lmp)
{
me = comm->me;
diff --git a/src/variable.h b/src/variable.h
index ee554ad781..e9bf29d4af 100644
--- a/src/variable.h
+++ b/src/variable.h
@@ -14,7 +14,7 @@
#ifndef LMP_VARIABLE_H
#define LMP_VARIABLE_H
-#include "stdlib.h"
+#include <stdlib.h>
#include "pointers.h"
namespace LAMMPS_NS {
@@ -74,7 +74,7 @@ class Variable : protected Pointers {
class Python *python; // ptr to embedded Python interpreter
struct Tree { // parse tree for atom-style variables
- double value; // single scalar
+ double value; // single scalar
double *array; // per-atom or per-type list of doubles
int *iarray; // per-atom list of ints
bigint *barray; // per-atom list of bigints
diff --git a/src/velocity.cpp b/src/velocity.cpp
index 37785af5c3..e5eb19c81d 100644
--- a/src/velocity.cpp
+++ b/src/velocity.cpp
@@ -11,11 +11,11 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <mpi.h>
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
#include "velocity.h"
#include "atom.h"
#include "update.h"
@@ -104,7 +104,7 @@ void Velocity::command(int narg, char **arg)
// b/c methods invoked in the compute/fix perform forward/reverse comm
int initcomm = 0;
- if (style == ZERO && rfix >= 0 &&
+ if (style == ZERO && rfix >= 0 &&
strcmp(modify->fix[rfix]->style,"rigid/small") == 0) initcomm = 1;
if ((style == CREATE || style == SET) && temperature &&
strcmp(temperature->style,"temp/cs") == 0) initcomm = 1;
diff --git a/src/verlet.cpp b/src/verlet.cpp
index e5a067777e..de9a9034d0 100644
--- a/src/verlet.cpp
+++ b/src/verlet.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "verlet.h"
#include "neighbor.h"
#include "domain.h"
diff --git a/src/write_data.cpp b/src/write_data.cpp
index 2bf1ad84f8..5a67c1081e 100644
--- a/src/write_data.cpp
+++ b/src/write_data.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "string.h"
+#include <mpi.h>
+#include <string.h>
#include "write_data.h"
#include "atom.h"
#include "atom_vec.h"
@@ -198,7 +198,7 @@ void WriteData::write(char *file)
// extra sections managed by fixes
for (int i = 0; i < modify->nfix; i++)
- if (modify->fix[i]->wd_section)
+ if (modify->fix[i]->wd_section)
for (int m = 0; m < modify->fix[i]->wd_section; m++) fix(i,m);
// close data file
@@ -243,10 +243,10 @@ void WriteData::header()
}
for (int i = 0; i < modify->nfix; i++)
- if (modify->fix[i]->wd_header)
- for (int m = 0; m < modify->fix[i]->wd_header; m++)
+ if (modify->fix[i]->wd_header)
+ for (int m = 0; m < modify->fix[i]->wd_header; m++)
modify->fix[i]->write_data_header(fp,m);
-
+
fprintf(fp,"\n");
fprintf(fp,"%-1.16e %-1.16e xlo xhi\n",domain->boxlo[0],domain->boxhi[0]);
@@ -349,7 +349,7 @@ void WriteData::atoms()
atom->avec->write_data(fp,recvrow,buf);
}
-
+
} else {
MPI_Recv(&tmp,0,MPI_INT,0,0,world,MPI_STATUS_IGNORE);
MPI_Rsend(&buf[0][0],sendrow*ncol,MPI_DOUBLE,0,0,world);
@@ -400,10 +400,10 @@ void WriteData::velocities()
MPI_Get_count(&status,MPI_DOUBLE,&recvrow);
recvrow /= ncol;
} else recvrow = sendrow;
-
+
atom->avec->write_vel(fp,recvrow,buf);
}
-
+
} else {
MPI_Recv(&tmp,0,MPI_INT,0,0,world,MPI_STATUS_IGNORE);
MPI_Rsend(&buf[0][0],sendrow*ncol,MPI_DOUBLE,0,0,world);
@@ -457,7 +457,7 @@ void WriteData::bonds()
atom->avec->write_bond(fp,recvrow,buf,index);
index += recvrow;
}
-
+
} else {
MPI_Recv(&tmp,0,MPI_INT,0,0,world,MPI_STATUS_IGNORE);
MPI_Rsend(&buf[0][0],sendrow*ncol,MPI_LMP_TAGINT,0,0,world);
@@ -507,11 +507,11 @@ void WriteData::angles()
MPI_Get_count(&status,MPI_LMP_TAGINT,&recvrow);
recvrow /= ncol;
} else recvrow = sendrow;
-
+
atom->avec->write_angle(fp,recvrow,buf,index);
index += recvrow;
}
-
+
} else {
MPI_Recv(&tmp,0,MPI_INT,0,0,world,MPI_STATUS_IGNORE);
MPI_Rsend(&buf[0][0],sendrow*ncol,MPI_LMP_TAGINT,0,0,world);
@@ -579,11 +579,11 @@ void WriteData::dihedrals()
MPI_Get_count(&status,MPI_LMP_TAGINT,&recvrow);
recvrow /= ncol;
} else recvrow = sendrow;
-
+
atom->avec->write_dihedral(fp,recvrow,buf,index);
index += recvrow;
}
-
+
} else {
MPI_Recv(&tmp,0,MPI_INT,0,0,world,MPI_STATUS_IGNORE);
MPI_Rsend(&buf[0][0],sendrow*ncol,MPI_LMP_TAGINT,0,0,world);
@@ -651,11 +651,11 @@ void WriteData::impropers()
MPI_Get_count(&status,MPI_LMP_TAGINT,&recvrow);
recvrow /= ncol;
} else recvrow = sendrow;
-
+
atom->avec->write_improper(fp,recvrow,buf,index);
index += recvrow;
}
-
+
} else {
MPI_Recv(&tmp,0,MPI_INT,0,0,world,MPI_STATUS_IGNORE);
MPI_Rsend(&buf[0][0],sendrow*ncol,MPI_LMP_TAGINT,0,0,world);
@@ -709,7 +709,7 @@ void WriteData::fix(int ifix, int mth)
modify->fix[ifix]->write_data_section(mth,fp,recvrow,buf,index);
index += recvrow;
}
-
+
} else {
MPI_Recv(&tmp,0,MPI_INT,0,0,world,MPI_STATUS_IGNORE);
MPI_Rsend(&buf[0][0],sendrow*ncol,MPI_DOUBLE,0,0,world);
diff --git a/src/write_data.h b/src/write_data.h
index 8a4fdfac4c..8c19635602 100644
--- a/src/write_data.h
+++ b/src/write_data.h
@@ -20,7 +20,7 @@ CommandStyle(write_data,WriteData)
#ifndef LMP_WRITE_DATA_H
#define LMP_WRITE_DATA_H
-#include "stdio.h"
+#include <stdio.h>
#include "pointers.h"
namespace LAMMPS_NS {
diff --git a/src/write_dump.cpp b/src/write_dump.cpp
index e906e23007..f56faa0fcd 100644
--- a/src/write_dump.cpp
+++ b/src/write_dump.cpp
@@ -15,7 +15,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include "string.h"
+#include <string.h>
#include "write_dump.h"
#include "style_dump.h"
#include "dump.h"
@@ -71,7 +71,7 @@ void WriteDump::command(int narg, char **arg)
// write out one frame and then delete the dump again
// set multifile_override for DumpImage so that filename needs no "*"
- if (strcmp(arg[1],"image") == 0)
+ if (strcmp(arg[1],"image") == 0)
((DumpImage *) dump)->multifile_override = 1;
if (strcmp(arg[1],"cfg") == 0)
diff --git a/src/write_restart.cpp b/src/write_restart.cpp
index c2824eff99..9305c34ba6 100644
--- a/src/write_restart.cpp
+++ b/src/write_restart.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "mpi.h"
-#include "string.h"
+#include <mpi.h>
+#include <string.h>
#include "write_restart.h"
#include "atom.h"
#include "atom_vec.h"
@@ -150,13 +150,13 @@ void WriteRestart::multiproc_options(int multiproc_caller, int mpiioflag_caller,
// error checks
- if (multiproc && mpiioflag)
+ if (multiproc && mpiioflag)
error->all(FLERR,
"Restart file MPI-IO output not allowed with % in filename");
if (mpiioflag) {
mpiio = new RestartMPIIO(lmp);
- if (!mpiio->mpiio_exists)
+ if (!mpiio->mpiio_exists)
error->all(FLERR,"Writing to MPI-IO filename when "
"MPIIO package is not installed");
}
@@ -186,7 +186,7 @@ void WriteRestart::multiproc_options(int multiproc_caller, int mpiioflag_caller,
"without % in restart file name");
int nper = force->inumeric(FLERR,arg[iarg+1]);
if (nper <= 0) error->all(FLERR,"Illegal write_restart command");
-
+
multiproc = nprocs/nper;
if (nprocs % nper) multiproc++;
fileproc = me/nper * nper;
@@ -211,7 +211,7 @@ void WriteRestart::multiproc_options(int multiproc_caller, int mpiioflag_caller,
fileproc = static_cast<int> ((bigint) icluster * nprocs/nfile);
int fcluster = static_cast<int> ((bigint) fileproc * nfile/nprocs);
if (fcluster < icluster) fileproc++;
- int fileprocnext =
+ int fileprocnext =
static_cast<int> ((bigint) (icluster+1) * nprocs/nfile);
fcluster = static_cast<int> ((bigint) fileprocnext * nfile/nprocs);
if (fcluster < icluster+1) fileprocnext++;
@@ -418,7 +418,7 @@ void WriteRestart::write(char *file)
MPI_Wait(&request,&status);
MPI_Get_count(&status,MPI_DOUBLE,&recv_size);
} else recv_size = send_size;
-
+
write_double_vec(PERPROC,recv_size,buf);
}
fclose(fp);
@@ -515,7 +515,7 @@ void WriteRestart::header()
write_int(ATOM_SORTFREQ,atom->sortfreq);
write_double(ATOM_SORTBIN,atom->userbinsize);
- write_int(COMM_MODE,comm->mode);
+ write_int(COMM_MODE,comm->mode);
write_double(COMM_CUTOFF,comm->cutghostuser);
write_int(COMM_VEL,comm->ghost_velocity);
diff --git a/src/write_restart.h b/src/write_restart.h
index a27da32e3d..df710759ab 100644
--- a/src/write_restart.h
+++ b/src/write_restart.h
@@ -20,7 +20,7 @@ CommandStyle(write_restart,WriteRestart)
#ifndef LMP_WRITE_RESTART_H
#define LMP_WRITE_RESTART_H
-#include "stdio.h"
+#include <stdio.h>
#include "pointers.h"
namespace LAMMPS_NS {
--
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