From ee862d8bf5347dd2465a6d4fb907a92cb4780788 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 16 Mar 2018 12:28:13 -0400
Subject: [PATCH] replace leading tabs
---
src/BODY/body_nparticle.cpp | 6 +-
src/CORESHELL/pair_born_coul_dsf_cs.cpp | 2 +-
src/CORESHELL/pair_born_coul_wolf_cs.cpp | 6 +-
src/CORESHELL/pair_coul_wolf_cs.cpp | 58 +-
src/CORESHELL/pair_lj_cut_coul_long_cs.cpp | 2 +-
src/DIPOLE/pair_lj_long_dipole_long.cpp | 280 +-
src/GPU/pair_ufm_gpu.cpp | 6 +-
src/KOKKOS/atom_vec_angle_kokkos.cpp | 32 +-
src/KOKKOS/atom_vec_bond_kokkos.cpp | 44 +-
src/KOKKOS/atom_vec_dpd_kokkos.cpp | 6 +-
src/KOKKOS/atom_vec_full_kokkos.cpp | 18 +-
src/KOKKOS/atom_vec_kokkos.cpp | 4 +-
src/KOKKOS/atom_vec_molecular_kokkos.cpp | 26 +-
src/KOKKOS/comm_kokkos.cpp | 4 +-
src/KOKKOS/dihedral_charmm_kokkos.h | 14 +-
src/KOKKOS/pair_coul_debye_kokkos.cpp | 4 +-
..._lj_charmm_coul_charmm_implicit_kokkos.cpp | 4 +-
.../pair_lj_charmm_coul_charmm_kokkos.cpp | 4 +-
.../pair_lj_charmm_coul_long_kokkos.cpp | 4 +-
src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp | 2 +-
.../pair_lj_gromacs_coul_gromacs_kokkos.cpp | 8 +-
src/KOKKOS/pair_lj_gromacs_kokkos.cpp | 8 +-
src/KOKKOS/pair_tersoff_kokkos.cpp | 82 +-
src/KOKKOS/pair_tersoff_kokkos.h | 32 +-
src/KOKKOS/pair_tersoff_mod_kokkos.cpp | 86 +-
src/KOKKOS/pair_tersoff_zbl_kokkos.cpp | 108 +-
src/KOKKOS/sna_kokkos_impl.h | 178 +-
src/KSPACE/pair_buck_long_coul_long.cpp | 2 +-
src/KSPACE/pair_lj_charmmfsw_coul_long.cpp | 2 +-
src/KSPACE/pppm_disp.cpp | 946 ++---
src/KSPACE/pppm_disp.h | 38 +-
src/KSPACE/pppm_disp_tip4p.cpp | 48 +-
src/MANYBODY/pair_comb.cpp | 4 +-
src/MANYBODY/pair_comb3.cpp | 800 ++--
src/MANYBODY/pair_comb3.h | 86 +-
src/MANYBODY/pair_gw.h | 2 +-
src/MANYBODY/pair_nb3b_harmonic.cpp | 78 +-
src/MANYBODY/pair_nb3b_harmonic.h | 2 +-
src/MANYBODY/pair_polymorphic.cpp | 20 +-
src/MANYBODY/pair_polymorphic.h | 8 +-
src/MANYBODY/pair_tersoff.cpp | 4 +-
src/MANYBODY/pair_tersoff_mod.cpp | 46 +-
src/MANYBODY/pair_tersoff_mod.h | 2 +-
src/MANYBODY/pair_tersoff_mod_c.cpp | 10 +-
src/MANYBODY/pair_vashishta.cpp | 12 +-
src/MC/fix_atom_swap.cpp | 42 +-
src/MC/fix_bond_break.cpp | 8 +-
src/MC/fix_bond_create.cpp | 10 +-
src/MC/fix_tfmc.cpp | 10 +-
src/MISC/fix_deposit.cpp | 4 +-
src/MISC/fix_gld.cpp | 94 +-
src/MOLECULE/pair_hbond_dreiding_morse.cpp | 6 +-
.../pair_lj_charmmfsw_coul_charmmfsh.cpp | 104 +-
src/MPIIO/dump_cfg_mpiio.cpp | 40 +-
src/QEQ/fix_qeq_dynamic.cpp | 12 +-
src/QEQ/fix_qeq_fire.cpp | 16 +-
src/QEQ/fix_qeq_point.cpp | 10 +-
src/QEQ/fix_qeq_shielded.cpp | 10 +-
src/QEQ/fix_qeq_slater.cpp | 14 +-
src/RIGID/fix_rigid.cpp | 8 +-
src/RIGID/fix_rigid_small.cpp | 12 +-
src/SNAP/compute_sna_atom.cpp | 50 +-
src/SNAP/compute_snad_atom.cpp | 80 +-
src/SNAP/compute_snav_atom.cpp | 102 +-
src/SNAP/pair_snap.cpp | 142 +-
src/SNAP/sna.cpp | 352 +-
src/SRD/fix_srd.cpp | 28 +-
src/USER-CGDNA/pair_oxdna2_coaxstk.cpp | 22 +-
src/USER-CGDNA/pair_oxdna2_dh.cpp | 84 +-
src/USER-COLVARS/fix_colvars.cpp | 8 +-
src/USER-DIFFRACTION/compute_xrd.cpp | 4 +-
src/USER-H5MD/dump_h5md.cpp | 134 +-
src/USER-INTEL/dihedral_fourier_intel.cpp | 68 +-
src/USER-INTEL/dihedral_fourier_intel.h | 2 +-
src/USER-INTEL/fix_intel.cpp | 8 +-
src/USER-INTEL/intel_buffers.cpp | 10 +-
src/USER-INTEL/intel_intrinsics_airebo.h | 282 +-
src/USER-INTEL/intel_preprocess.h | 22 +-
src/USER-INTEL/nbin_intel.cpp | 4 +-
src/USER-INTEL/npair_full_bin_ghost_intel.cpp | 174 +-
src/USER-INTEL/npair_full_bin_ghost_intel.h | 2 +-
src/USER-INTEL/npair_intel.cpp | 6 +-
src/USER-INTEL/pair_airebo_intel.cpp | 382 +-
src/USER-INTEL/pair_airebo_intel.h | 4 +-
src/USER-INTEL/pair_dpd_intel.cpp | 80 +-
.../pair_lj_charmm_coul_charmm_intel.cpp | 24 +-
src/USER-INTEL/pair_sw_intel.cpp | 8 +-
src/USER-INTEL/pppm_disp_intel.cpp | 60 +-
src/USER-INTEL/pppm_intel.cpp | 32 +-
src/USER-INTEL/pppm_intel.h | 2 +-
src/USER-LB/fix_lb_fluid.cpp | 1756 ++++----
src/USER-LB/fix_lb_momentum.cpp | 250 +-
src/USER-LB/fix_lb_pc.cpp | 304 +-
src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp | 2 +-
src/USER-MISC/angle_dipole.cpp | 2 +-
src/USER-MISC/angle_fourier.cpp | 2 +-
src/USER-MISC/angle_quartic.cpp | 2 +-
src/USER-MISC/bond_harmonic_shift.cpp | 2 +-
src/USER-MISC/bond_harmonic_shift_cut.cpp | 2 +-
src/USER-MISC/compute_ackland_atom.cpp | 24 +-
src/USER-MISC/compute_basal_atom.cpp | 148 +-
src/USER-MISC/compute_pressure_grem.cpp | 2 +-
src/USER-MISC/dihedral_quadratic.cpp | 24 +-
src/USER-MISC/dihedral_spherical.h | 2 +-
src/USER-MISC/fix_filter_corotate.h | 2 +-
src/USER-MISC/fix_flow_gauss.cpp | 6 +-
src/USER-MISC/fix_gle.cpp | 6 +-
src/USER-MISC/fix_ipi.cpp | 2 +-
src/USER-MISC/fix_pimd.cpp | 2 +-
src/USER-MISC/pair_edip_multi.cpp | 72 +-
src/USER-MISC/pair_edip_multi.h | 2 +-
src/USER-MISC/pair_gauss_cut.cpp | 2 +-
src/USER-MISC/pair_lj_sf_dipole_sf.cpp | 10 +-
src/USER-MISC/pair_meam_spline.cpp | 6 +-
src/USER-MISC/pair_meam_spline.h | 16 +-
src/USER-MISC/pair_momb.cpp | 4 +-
src/USER-MISC/temper_npt.cpp | 14 +-
src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp | 2 +-
.../pair_buck6d_coul_gauss_long.cpp | 2 +-
src/USER-OMP/angle_dipole_omp.cpp | 2 +-
src/USER-OMP/fix_omp.cpp | 40 +-
src/USER-OMP/fix_rigid_nh_omp.cpp | 152 +-
src/USER-OMP/fix_rigid_omp.cpp | 150 +-
src/USER-OMP/fix_rigid_small_omp.cpp | 48 +-
src/USER-OMP/improper_fourier_omp.cpp | 44 +-
src/USER-OMP/improper_fourier_omp.h | 8 +-
src/USER-OMP/pair_buck_long_coul_long_omp.cpp | 6 +-
src/USER-OMP/pair_lj_long_coul_long_omp.cpp | 10 +-
src/USER-OMP/pair_morse_smooth_linear_omp.cpp | 2 +-
src/USER-OMP/pair_reaxc_omp.h | 36 +-
src/USER-OMP/pppm_cg_omp.cpp | 92 +-
src/USER-OMP/pppm_cg_omp.h | 2 +-
src/USER-OMP/pppm_disp_omp.cpp | 62 +-
src/USER-OMP/pppm_disp_omp.h | 2 +-
src/USER-OMP/pppm_disp_tip4p_omp.cpp | 62 +-
src/USER-OMP/pppm_disp_tip4p_omp.h | 2 +-
src/USER-OMP/pppm_omp.cpp | 2 +-
src/USER-OMP/pppm_omp.h | 2 +-
src/USER-OMP/pppm_tip4p_omp.cpp | 2 +-
src/USER-OMP/pppm_tip4p_omp.h | 2 +-
src/USER-OMP/reaxc_bond_orders_omp.cpp | 398 +-
src/USER-OMP/reaxc_bond_orders_omp.h | 4 +-
src/USER-OMP/reaxc_bonds_omp.cpp | 78 +-
src/USER-OMP/reaxc_forces_omp.cpp | 288 +-
src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp | 16 +-
src/USER-OMP/reaxc_multi_body_omp.cpp | 26 +-
src/USER-OMP/reaxc_nonbonded_omp.cpp | 392 +-
src/USER-OMP/reaxc_nonbonded_omp.h | 6 +-
src/USER-OMP/reaxc_torsion_angles_omp.cpp | 118 +-
src/USER-OMP/reaxc_torsion_angles_omp.h | 2 +-
src/USER-OMP/reaxc_valence_angles_omp.cpp | 102 +-
src/USER-OMP/respa_omp.cpp | 18 +-
src/USER-QTB/fix_qbmsst.cpp | 126 +-
src/USER-QTB/fix_qtb.cpp | 6 +-
src/USER-REAXC/fix_qeq_reax.cpp | 8 +-
src/USER-REAXC/pair_reaxc.cpp | 22 +-
src/USER-REAXC/reaxc_allocate.cpp | 4 +-
src/USER-REAXC/reaxc_bonds.cpp | 74 +-
src/USER-REAXC/reaxc_forces.cpp | 2 +-
src/USER-REAXC/reaxc_hydrogen_bonds.cpp | 8 +-
src/USER-REAXC/reaxc_multi_body.cpp | 4 +-
src/USER-REAXC/reaxc_torsion_angles.cpp | 10 +-
src/USER-SMD/atom_vec_smd.cpp | 1932 ++++-----
src/USER-SMD/compute_smd_hourglass_error.cpp | 90 +-
src/USER-SMD/compute_smd_rho.cpp | 82 +-
src/USER-SMD/compute_smd_tlsph_defgrad.cpp | 132 +-
src/USER-SMD/compute_smd_tlsph_dt.cpp | 102 +-
src/USER-SMD/compute_smd_tlsph_shape.cpp | 128 +-
src/USER-SMD/compute_smd_tlsph_strain.cpp | 144 +-
.../compute_smd_tlsph_strain_rate.cpp | 90 +-
src/USER-SMD/compute_smd_tlsph_stress.cpp | 116 +-
.../compute_smd_triangle_mesh_vertices.cpp | 4 +-
src/USER-SMD/compute_smd_ulsph_effm.cpp | 102 +-
src/USER-SMD/compute_smd_ulsph_strain.cpp | 94 +-
.../compute_smd_ulsph_strain_rate.cpp | 110 +-
src/USER-SMD/compute_smd_ulsph_stress.cpp | 120 +-
src/USER-SMD/compute_smd_vol.cpp | 114 +-
src/USER-SMD/fix_smd_adjust_dt.cpp | 260 +-
src/USER-SMD/fix_smd_adjust_dt.h | 26 +-
src/USER-SMD/fix_smd_integrate_tlsph.cpp | 340 +-
src/USER-SMD/fix_smd_integrate_tlsph.h | 4 +-
src/USER-SMD/fix_smd_integrate_ulsph.cpp | 448 +-
.../fix_smd_move_triangulated_surface.cpp | 836 ++--
.../fix_smd_move_triangulated_surface.h | 30 +-
src/USER-SMD/fix_smd_setvel.cpp | 540 +--
.../fix_smd_tlsph_reference_configuration.cpp | 798 ++--
.../fix_smd_tlsph_reference_configuration.h | 64 +-
src/USER-SMD/fix_smd_wall_surface.cpp | 790 ++--
src/USER-SMD/fix_smd_wall_surface.h | 26 +-
src/USER-SMD/pair_smd_hertz.cpp | 484 +--
src/USER-SMD/pair_smd_tlsph.cpp | 3772 ++++++++---------
src/USER-SMD/pair_smd_tlsph.h | 304 +-
.../pair_smd_triangulated_surface.cpp | 1176 ++---
src/USER-SMD/pair_smd_ulsph.cpp | 2840 ++++++-------
src/USER-SMD/pair_smd_ulsph.h | 156 +-
src/USER-SMD/smd_kernels.h | 182 +-
src/USER-SMD/smd_material_models.cpp | 444 +-
src/USER-SMD/smd_material_models.h | 18 +-
src/USER-SMD/smd_math.h | 346 +-
src/VORONOI/compute_voronoi_atom.cpp | 64 +-
src/atom.cpp | 20 +-
src/atom_vec_body.cpp | 12 +-
src/comm.cpp | 8 +-
src/compute_chunk_atom.cpp | 16 +-
src/compute_hexorder_atom.cpp | 32 +-
src/compute_msd.cpp | 30 +-
src/compute_orientorder_atom.h | 2 +-
src/compute_pressure.cpp | 4 +-
src/compute_property_chunk.cpp | 8 +-
src/compute_stress_atom.cpp | 92 +-
src/compute_temp_chunk.cpp | 46 +-
src/compute_vacf.cpp | 6 +-
src/domain.cpp | 8 +-
src/dump_cfg.cpp | 10 +-
src/dump_custom.cpp | 160 +-
src/fix_adapt.cpp | 12 +-
src/fix_ave_chunk.cpp | 26 +-
src/fix_group.cpp | 6 +-
src/fix_langevin.cpp | 308 +-
src/fix_langevin.h | 4 +-
src/fix_nh_sphere.cpp | 2 +-
src/fix_nve_sphere.cpp | 2 +-
src/fix_store_state.cpp | 8 +-
src/fix_wall_lj1043.cpp | 6 +-
src/input.cpp | 136 +-
src/kspace.cpp | 6 +-
src/lammps.cpp | 22 +-
src/library.cpp | 8 +-
src/neighbor.cpp | 26 +-
src/pair.h | 2 +-
src/pair_born_coul_dsf.cpp | 2 +-
src/pair_coul_streitz.cpp | 34 +-
src/pair_coul_streitz.h | 4 +-
src/pair_lj_cut_coul_dsf.cpp | 2 +-
src/pair_lj_expand.cpp | 4 +-
src/pair_morse.h | 2 +-
src/pair_zbl.cpp | 34 +-
src/rcb.cpp | 264 +-
src/read_data.cpp | 12 +-
src/region_cylinder.cpp | 8 +-
src/region_union.cpp | 2 +-
src/set.cpp | 26 +-
src/variable.cpp | 96 +-
243 files changed, 14825 insertions(+), 14825 deletions(-)
diff --git a/src/BODY/body_nparticle.cpp b/src/BODY/body_nparticle.cpp
index b2790c19aa..7e3e6f463c 100644
--- a/src/BODY/body_nparticle.cpp
+++ b/src/BODY/body_nparticle.cpp
@@ -196,7 +196,7 @@ void BodyNparticle::data_body(int ibonus, int ninteger, int ndouble,
------------------------------------------------------------------------- */
double BodyNparticle::radius_body(int ninteger, int ndouble,
- int *ifile, double *dfile)
+ int *ifile, double *dfile)
{
int nsub = ifile[0];
if (nsub < 1)
@@ -212,8 +212,8 @@ double BodyNparticle::radius_body(int ninteger, int ndouble,
double onerad;
double maxrad = 0.0;
double delta[3];
-
- int offset = 6;
+
+ int offset = 6;
for (int i = 0; i < nsub; i++) {
delta[0] = dfile[offset];
delta[1] = dfile[offset+1];
diff --git a/src/CORESHELL/pair_born_coul_dsf_cs.cpp b/src/CORESHELL/pair_born_coul_dsf_cs.cpp
index 2cd2f211ff..4a5c9da07e 100644
--- a/src/CORESHELL/pair_born_coul_dsf_cs.cpp
+++ b/src/CORESHELL/pair_born_coul_dsf_cs.cpp
@@ -112,7 +112,7 @@ void PairBornCoulDSFCS::compute(int eflag, int vflag)
if (rsq < cut_coulsq) {
r = sqrt(rsq);
prefactor = qqrd2e*qtmp*q[j] / r;
- arg = alpha * r ;
+ arg = alpha * r ;
erfcd = MathSpecial::expmsq(arg);
erfcc = MathSpecial::my_erfcx(arg) * erfcd;
forcecoul = prefactor * (erfcc/r + 2.0*alpha/MY_PIS * erfcd +
diff --git a/src/CORESHELL/pair_born_coul_wolf_cs.cpp b/src/CORESHELL/pair_born_coul_wolf_cs.cpp
index 3c98f5bf77..f39e2ca816 100644
--- a/src/CORESHELL/pair_born_coul_wolf_cs.cpp
+++ b/src/CORESHELL/pair_born_coul_wolf_cs.cpp
@@ -106,9 +106,9 @@ void PairBornCoulWolfCS::compute(int eflag, int vflag)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- rsq += EPSILON;
- // Add EPISLON for case: r = 0; Interaction must be removed
- // by special bond
+ rsq += EPSILON;
+ // Add EPISLON for case: r = 0; Interaction must be removed
+ // by special bond
r2inv = 1.0/rsq;
if (rsq < cut_coulsq) {
diff --git a/src/CORESHELL/pair_coul_wolf_cs.cpp b/src/CORESHELL/pair_coul_wolf_cs.cpp
index 15de7c6777..5f277dcdd2 100644
--- a/src/CORESHELL/pair_coul_wolf_cs.cpp
+++ b/src/CORESHELL/pair_coul_wolf_cs.cpp
@@ -102,35 +102,35 @@ void PairCoulWolfCS::compute(int eflag, int vflag)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cut_coulsq) {
- rsq += EPSILON;
- // Add EPISLON for case: r = 0; Interaction must be removed
- // by special bond
- r = sqrt(rsq);
- prefactor = qqrd2e*qtmp*q[j]/r;
- erfcc = erfc(alf*r);
- erfcd = exp(-alf*alf*r*r);
- 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;
- fpair = forcecoul / rsq;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (eflag) {
- ecoul = v_sh;
- if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
- } else ecoul = 0.0;
-
- if (evflag) ev_tally(i,j,nlocal,newton_pair,
- 0.0,ecoul,fpair,delx,dely,delz);
+ rsq += EPSILON;
+ // Add EPISLON for case: r = 0; Interaction must be removed
+ // by special bond
+ r = sqrt(rsq);
+ prefactor = qqrd2e*qtmp*q[j]/r;
+ erfcc = erfc(alf*r);
+ erfcd = exp(-alf*alf*r*r);
+ 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;
+ fpair = forcecoul / rsq;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (eflag) {
+ ecoul = v_sh;
+ if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
+ } else ecoul = 0.0;
+
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,
+ 0.0,ecoul,fpair,delx,dely,delz);
}
}
}
diff --git a/src/CORESHELL/pair_lj_cut_coul_long_cs.cpp b/src/CORESHELL/pair_lj_cut_coul_long_cs.cpp
index d418cf20af..c660eee3bc 100644
--- a/src/CORESHELL/pair_lj_cut_coul_long_cs.cpp
+++ b/src/CORESHELL/pair_lj_cut_coul_long_cs.cpp
@@ -458,7 +458,7 @@ void PairLJCutCoulLongCS::compute_outer(int eflag, int vflag)
grij = g_ewald * r;
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
- u = 1. - t;
+ u = 1. - t;
erfc = t * (1.+u*(B0+u*(B1+u*(B2+u*(B3+u*(B4+u*B5)))))) * expm2;
//erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
prefactor = qqrd2e * qtmp*q[j]/r;
diff --git a/src/DIPOLE/pair_lj_long_dipole_long.cpp b/src/DIPOLE/pair_lj_long_dipole_long.cpp
index c9b2b3f4af..262727c5b6 100644
--- a/src/DIPOLE/pair_lj_long_dipole_long.cpp
+++ b/src/DIPOLE/pair_lj_long_dipole_long.cpp
@@ -68,8 +68,8 @@ void PairLJLongDipoleLong::options(char **arg, int order)
for (i=0; option[i]&&strcmp(arg[0], option[i]); ++i);
switch (i) {
default: error->all(FLERR,"Illegal pair_style lj/long/dipole/long command");
- case 0: ewald_order |= 1<<order; break; // set kspace r^-order
- case 2: ewald_off |= 1<<order; // turn r^-order off
+ case 0: ewald_order |= 1<<order; break; // set kspace r^-order
+ case 2: ewald_off |= 1<<order; // turn r^-order off
case 1: break;
}
}
@@ -99,7 +99,7 @@ void PairLJLongDipoleLong::settings(int narg, char **arg)
if (narg == 4) cut_coul = force->numeric(FLERR,*(arg++));
else cut_coul = cut_lj_global;
- if (allocated) { // reset explicit cuts
+ if (allocated) { // reset explicit cuts
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++)
@@ -234,7 +234,7 @@ void PairLJLongDipoleLong::init_style()
if (!atom->q_flag && (ewald_order&(1<<1)))
error->all(FLERR,
- "Invoking coulombic in pair style lj/long/dipole/long requires atom attribute q");
+ "Invoking coulombic in pair style lj/long/dipole/long requires atom attribute q");
if (!atom->mu && (ewald_order&(1<<3)))
error->all(FLERR,"Pair lj/long/dipole/long requires atom attributes mu, torque");
if (!atom->torque && (ewald_order&(1<<3)))
@@ -246,14 +246,14 @@ void PairLJLongDipoleLong::init_style()
// ensure use of KSpace long-range solver, set g_ewald
- if (ewald_order&(1<<3)) { // r^-1 kspace
+ if (ewald_order&(1<<3)) { // r^-1 kspace
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 (ewald_order&(1<<6)) { // r^-6 kspace
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);
@@ -271,7 +271,7 @@ double PairLJLongDipoleLong::init_one(int i, int j)
{
if ((ewald_order&(1<<6))||(setflag[i][j] == 0)) {
epsilon[i][j] = mix_energy(epsilon_read[i][i],epsilon_read[j][j],
- sigma_read[i][i],sigma_read[j][j]);
+ sigma_read[i][i],sigma_read[j][j]);
sigma[i][j] = mix_distance(sigma_read[i][i],sigma_read[j][j]);
if (ewald_order&(1<<6))
cut_lj[i][j] = cut_lj_global;
@@ -436,9 +436,9 @@ void PairLJLongDipoleLong::compute(int eflag, int vflag)
ineighn = (ineigh = list->ilist)+list->inum;
- for (; ineigh<ineighn; ++ineigh) { // loop over all neighs
+ for (; ineigh<ineighn; ++ineigh) { // loop over all neighs
i = *ineigh; fi = f0+3*i; tqi = tq0+3*i;
- qi = q[i]; // initialize constants
+ qi = q[i]; // initialize constants
offseti = offset[typei = type[i]];
lj1i = lj1[typei]; lj2i = lj2[typei]; lj3i = lj3[typei]; lj4i = lj4[typei];
cutsqi = cutsq[typei]; cut_ljsqi = cut_ljsq[typei];
@@ -447,141 +447,141 @@ void PairLJLongDipoleLong::compute(int eflag, int vflag)
jneighn = (jneigh = list->firstneigh[i])+list->numneigh[i];
- for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
+ for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
j = *jneigh;
- ni = sbmask(j); // special index
+ 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];
- d[2] = xi[2] - xj[2]; }
+ 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 (order3 && (rsq < cut_coulsq)) { // dipole
- memcpy(muj, jmu = mu0+(j<<2), sizeof(vector));
- { // series real space
- register double r = sqrt(rsq);
- register double x = g_ewald*r;
- register double f = exp(-x*x)*qqrd2e;
-
- B0 = 1.0/(1.0+EWALD_P*x); // eqn 2.8
- B0 *= ((((A5*B0+A4)*B0+A3)*B0+A2)*B0+A1)*f/r;
- B1 = (B0 + C1 * f) * r2inv;
- B2 = (3.0*B1 + C2 * f) * r2inv;
- B3 = (5.0*B2 + C3 * f) * r2inv;
-
- mudi = mui[0]*d[0]+mui[1]*d[1]+mui[2]*d[2];
- mudj = muj[0]*d[0]+muj[1]*d[1]+muj[2]*d[2];
- muij = mui[0]*muj[0]+mui[1]*muj[1]+mui[2]*muj[2];
- G0 = qi*(qj = q[j]); // eqn 2.10
- 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;
- ti[2] = mudj*d[2]+(qj*d[2]-muj[2])*B1;
-
- if (newton_pair || j < nlocal) {
- tj[0] = mudi*d[0]-(qi*d[0]+mui[0])*B1;
- tj[1] = mudi*d[1]-(qi*d[1]+mui[1])*B1;
- tj[2] = mudi*d[2]-(qi*d[2]+mui[2])*B1;
- }
-
- if (eflag) ecoul = G0*B0+G1*B1+G2*B2;
- if (ni > 0) { // adj part, eqn 2.13
- force_coul -= (f = qqrd2e*(1.0-special_coul[ni])/r)*(
- (3.0*G1+15.0*G2*r2inv)*r2inv+G0)*r2inv;
- if (eflag)
- ecoul -= f*((G1+3.0*G2*r2inv)*r2inv+G0);
- B1 -= f*r2inv;
- }
- B0 = mudj+qj*B1; B3 = -qi*B1+mudi; // position independent
+ if (order3 && (rsq < cut_coulsq)) { // dipole
+ memcpy(muj, jmu = mu0+(j<<2), sizeof(vector));
+ { // series real space
+ register double r = sqrt(rsq);
+ register double x = g_ewald*r;
+ register double f = exp(-x*x)*qqrd2e;
+
+ B0 = 1.0/(1.0+EWALD_P*x); // eqn 2.8
+ B0 *= ((((A5*B0+A4)*B0+A3)*B0+A2)*B0+A1)*f/r;
+ B1 = (B0 + C1 * f) * r2inv;
+ B2 = (3.0*B1 + C2 * f) * r2inv;
+ B3 = (5.0*B2 + C3 * f) * r2inv;
+
+ mudi = mui[0]*d[0]+mui[1]*d[1]+mui[2]*d[2];
+ mudj = muj[0]*d[0]+muj[1]*d[1]+muj[2]*d[2];
+ muij = mui[0]*muj[0]+mui[1]*muj[1]+mui[2]*muj[2];
+ G0 = qi*(qj = q[j]); // eqn 2.10
+ 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;
+ ti[2] = mudj*d[2]+(qj*d[2]-muj[2])*B1;
+
+ if (newton_pair || j < nlocal) {
+ tj[0] = mudi*d[0]-(qi*d[0]+mui[0])*B1;
+ tj[1] = mudi*d[1]-(qi*d[1]+mui[1])*B1;
+ tj[2] = mudi*d[2]-(qi*d[2]+mui[2])*B1;
+ }
+
+ if (eflag) ecoul = G0*B0+G1*B1+G2*B2;
+ if (ni > 0) { // adj part, eqn 2.13
+ force_coul -= (f = qqrd2e*(1.0-special_coul[ni])/r)*(
+ (3.0*G1+15.0*G2*r2inv)*r2inv+G0)*r2inv;
+ if (eflag)
+ ecoul -= f*((G1+3.0*G2*r2inv)*r2inv+G0);
+ B1 -= f*r2inv;
+ }
+ B0 = mudj+qj*B1; B3 = -qi*B1+mudi; // position independent
if (ni > 0) B0 -= f*3.0*mudj*r2inv*r2inv/B2;
if (ni > 0) B3 -= f*3.0*mudi*r2inv*r2inv/B2;
- force_d[0] = B0*mui[0]+B3*muj[0]; // force contribs
- force_d[1] = B0*mui[1]+B3*muj[1];
- force_d[2] = B0*mui[2]+B3*muj[2];
+ force_d[0] = B0*mui[0]+B3*muj[0]; // force contribs
+ force_d[1] = B0*mui[1]+B3*muj[1];
+ force_d[2] = B0*mui[2]+B3*muj[2];
if (ni > 0) {
- ti[0] -= f*(3.0*mudj*r2inv*r2inv*d[0]/B2+(qj*r2inv*d[0]-muj[0]*r2inv));
- ti[1] -= f*(3.0*mudj*r2inv*r2inv*d[1]/B2+(qj*r2inv*d[1]-muj[1]*r2inv));
- ti[2] -= f*(3.0*mudj*r2inv*r2inv*d[2]/B2+(qj*r2inv*d[2]-muj[2]*r2inv));
- if (newton_pair || j < nlocal) {
- tj[0] -= f*(3.0*mudi*r2inv*r2inv*d[0]/B2-(qi*r2inv*d[0]+mui[0]*r2inv));
- tj[1] -= f*(3.0*mudi*r2inv*r2inv*d[1]/B2-(qi*r2inv*d[1]+mui[1]*r2inv));
- tj[2] -= f*(3.0*mudi*r2inv*r2inv*d[2]/B2-(qi*r2inv*d[2]+mui[2]*r2inv));
- }
+ ti[0] -= f*(3.0*mudj*r2inv*r2inv*d[0]/B2+(qj*r2inv*d[0]-muj[0]*r2inv));
+ ti[1] -= f*(3.0*mudj*r2inv*r2inv*d[1]/B2+(qj*r2inv*d[1]-muj[1]*r2inv));
+ ti[2] -= f*(3.0*mudj*r2inv*r2inv*d[2]/B2+(qj*r2inv*d[2]-muj[2]*r2inv));
+ if (newton_pair || j < nlocal) {
+ tj[0] -= f*(3.0*mudi*r2inv*r2inv*d[0]/B2-(qi*r2inv*d[0]+mui[0]*r2inv));
+ tj[1] -= f*(3.0*mudi*r2inv*r2inv*d[1]/B2-(qi*r2inv*d[1]+mui[1]*r2inv));
+ tj[2] -= f*(3.0*mudi*r2inv*r2inv*d[2]/B2-(qi*r2inv*d[2]+mui[2]*r2inv));
+ }
}
- } // table real space
+ } // table real space
} else {
- force_coul = ecoul = 0.0;
- memset(force_d, 0, 3*sizeof(double));
+ force_coul = ecoul = 0.0;
+ memset(force_d, 0, 3*sizeof(double));
}
- if (rsq < cut_ljsqi[typej]) { // lj
- if (order6) { // long-range lj
- register double rn = r2inv*r2inv*r2inv;
- register double x2 = g2*rsq, a2 = 1.0/x2;
- x2 = a2*exp(-x2)*lj4i[typej];
- if (ni < 0) {
- force_lj =
- (rn*=rn)*lj1i[typej]-g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq;
- if (eflag) evdwl = rn*lj3i[typej]-g6*((a2+1.0)*a2+0.5)*x2;
- }
- else { // special case
- 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 =
- f*rn*lj3i[typej]-g6*((a2+1.0)*a2+0.5)*x2+t*lj4i[typej];
- }
- }
- else { // cut lj
- register double rn = r2inv*r2inv*r2inv;
- if (ni < 0) {
- force_lj = rn*(rn*lj1i[typej]-lj2i[typej]);
- if (eflag) evdwl = rn*(rn*lj3i[typej]-lj4i[typej])-offseti[typej];
- }
- else { // special case
- register double f = special_lj[ni];
- force_lj = f*rn*(rn*lj1i[typej]-lj2i[typej]);
- if (eflag) evdwl = f*(
- rn*(rn*lj3i[typej]-lj4i[typej])-offseti[typej]);
- }
- }
- force_lj *= r2inv;
+ if (rsq < cut_ljsqi[typej]) { // lj
+ if (order6) { // long-range lj
+ register double rn = r2inv*r2inv*r2inv;
+ register double x2 = g2*rsq, a2 = 1.0/x2;
+ x2 = a2*exp(-x2)*lj4i[typej];
+ if (ni < 0) {
+ force_lj =
+ (rn*=rn)*lj1i[typej]-g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq;
+ if (eflag) evdwl = rn*lj3i[typej]-g6*((a2+1.0)*a2+0.5)*x2;
+ }
+ else { // special case
+ 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 =
+ f*rn*lj3i[typej]-g6*((a2+1.0)*a2+0.5)*x2+t*lj4i[typej];
+ }
+ }
+ else { // cut lj
+ register double rn = r2inv*r2inv*r2inv;
+ if (ni < 0) {
+ force_lj = rn*(rn*lj1i[typej]-lj2i[typej]);
+ if (eflag) evdwl = rn*(rn*lj3i[typej]-lj4i[typej])-offseti[typej];
+ }
+ else { // special case
+ register double f = special_lj[ni];
+ force_lj = f*rn*(rn*lj1i[typej]-lj2i[typej]);
+ if (eflag) evdwl = f*(
+ rn*(rn*lj3i[typej]-lj4i[typej])-offseti[typej]);
+ }
+ }
+ force_lj *= r2inv;
}
else force_lj = evdwl = 0.0;
- fpair = force_coul+force_lj; // force
+ fpair = force_coul+force_lj; // force
if (newton_pair || j < nlocal) {
- register double *fj = f0+(j+(j<<1));
- fi[0] += fx = d[0]*fpair+force_d[0]; fj[0] -= fx;
- fi[1] += fy = d[1]*fpair+force_d[1]; fj[1] -= fy;
- fi[2] += fz = d[2]*fpair+force_d[2]; fj[2] -= fz;
- tqi[0] += mui[1]*ti[2]-mui[2]*ti[1]; // torque
- tqi[1] += mui[2]*ti[0]-mui[0]*ti[2];
- tqi[2] += mui[0]*ti[1]-mui[1]*ti[0];
- register double *tqj = tq0+(j+(j<<1));
- tqj[0] += muj[1]*tj[2]-muj[2]*tj[1];
- tqj[1] += muj[2]*tj[0]-muj[0]*tj[2];
- tqj[2] += muj[0]*tj[1]-muj[1]*tj[0];
+ register double *fj = f0+(j+(j<<1));
+ fi[0] += fx = d[0]*fpair+force_d[0]; fj[0] -= fx;
+ fi[1] += fy = d[1]*fpair+force_d[1]; fj[1] -= fy;
+ fi[2] += fz = d[2]*fpair+force_d[2]; fj[2] -= fz;
+ tqi[0] += mui[1]*ti[2]-mui[2]*ti[1]; // torque
+ tqi[1] += mui[2]*ti[0]-mui[0]*ti[2];
+ tqi[2] += mui[0]*ti[1]-mui[1]*ti[0];
+ register double *tqj = tq0+(j+(j<<1));
+ tqj[0] += muj[1]*tj[2]-muj[2]*tj[1];
+ tqj[1] += muj[2]*tj[0]-muj[0]*tj[2];
+ tqj[2] += muj[0]*tj[1]-muj[1]*tj[0];
}
else {
- fi[0] += fx = d[0]*fpair+force_d[0]; // force
- fi[1] += fy = d[1]*fpair+force_d[1];
- fi[2] += fz = d[2]*fpair+force_d[2];
- tqi[0] += mui[1]*ti[2]-mui[2]*ti[1]; // torque
- tqi[1] += mui[2]*ti[0]-mui[0]*ti[2];
- tqi[2] += mui[0]*ti[1]-mui[1]*ti[0];
+ fi[0] += fx = d[0]*fpair+force_d[0]; // force
+ fi[1] += fy = d[1]*fpair+force_d[1];
+ fi[2] += fz = d[2]*fpair+force_d[2];
+ tqi[0] += mui[1]*ti[2]-mui[2]*ti[1]; // torque
+ tqi[1] += mui[2]*ti[0]-mui[0]*ti[2];
+ tqi[2] += mui[0]*ti[1]-mui[1]*ti[0];
}
if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,
- evdwl,ecoul,fx,fy,fz,d[0],d[1],d[2]);
+ evdwl,ecoul,fx,fy,fz,d[0],d[1],d[2]);
}
}
@@ -592,8 +592,8 @@ void PairLJLongDipoleLong::compute(int eflag, int vflag)
/*
double PairLJLongDipoleLong::single(int i, int j, int itype, int jtype,
- double rsq, double factor_coul, double factor_lj,
- double &fforce)
+ double rsq, double factor_coul, double factor_lj,
+ double &fforce)
{
double r6inv, force_coul, force_lj;
double g2 = g_ewald*g_ewald, g6 = g2*g2*g2, g8 = g6*g2, *q = atom->q;
@@ -601,18 +601,18 @@ double PairLJLongDipoleLong::single(int i, int j, int itype, int jtype,
double eng = 0.0;
double r2inv = 1.0/rsq;
- if ((ewald_order&(1<<3)) && (rsq < cut_coulsq)) { // coulombic
+ if ((ewald_order&(1<<3)) && (rsq < cut_coulsq)) { // coulombic
double *mui = atom->mu[i], *muj = atom->mu[j];
double *xi = atom->x[i], *xj = atom->x[j];
double qi = q[i], qj = q[j];
double G0, G1, G2, B0, B1, B2, B3, mudi, mudj, muij;
vector d = {xi[0]-xj[0], xi[1]-xj[1], xi[2]-xj[2]};
- { // series real space
+ { // series real space
register double r = sqrt(rsq);
register double x = g_ewald*r;
register double f = exp(-x*x)*qqrd2e;
- B0 = 1.0/(1.0+EWALD_P*x); // eqn 2.8
+ B0 = 1.0/(1.0+EWALD_P*x); // eqn 2.8
B0 *= ((((A5*B0+A4)*B0+A3)*B0+A2)*B0+A1)*f/r;
B1 = (B0 + C1 * f) * r2inv;
B2 = (3.0*B1 + C2 * f) * r2inv;
@@ -621,40 +621,40 @@ double PairLJLongDipoleLong::single(int i, int j, int itype, int jtype,
mudi = mui[0]*d[0]+mui[1]*d[1]+mui[2]*d[2];
mudj = muj[0]*d[0]+muj[1]*d[1]+muj[2]*d[2];
muij = mui[0]*muj[0]+mui[1]*muj[1]+mui[2]*muj[2];
- G0 = qi*(qj = q[j]); // eqn 2.10
+ G0 = qi*(qj = q[j]); // eqn 2.10
G1 = qi*mudj-qj*mudi+muij;
G2 = -mudi*mudj;
force_coul = G0*B1+G1*B2+G2*B3;
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);
- eng -= f*((G1+3.0*G2*r2inv)*r2inv+G0);
- B1 -= f*r2inv;
+ 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);
+ eng -= f*((G1+3.0*G2*r2inv)*r2inv+G0);
+ B1 -= f*r2inv;
}
- B0 = mudj*B2-qj*B1; B3 = qi*B1+mudi*B2; // position independent
- //force_d[0] = B0*mui[0]+B3*muj[0]; // force contributions
+ B0 = mudj*B2-qj*B1; B3 = qi*B1+mudi*B2; // position independent
+ //force_d[0] = B0*mui[0]+B3*muj[0]; // force contributions
//force_d[1] = B0*mui[1]+B3*muj[1];
//force_d[2] = B0*mui[2]+B3*muj[2];
- } // table real space
+ } // table real space
}
else force_coul = 0.0;
- if (rsq < cut_ljsq[itype][jtype]) { // lennard-jones
+ if (rsq < cut_ljsq[itype][jtype]) { // lennard-jones
r6inv = r2inv*r2inv*r2inv;
- if (ewald_order&0x40) { // long-range
+ if (ewald_order&0x40) { // long-range
register double x2 = g2*rsq, a2 = 1.0/x2, t = r6inv*(1.0-factor_lj);
x2 = a2*exp(-x2)*lj4[itype][jtype];
force_lj = factor_lj*(r6inv *= r6inv)*lj1[itype][jtype]-
- g8*(((6.0*a2+6.0)*a2+3.0)*a2+a2)*x2*rsq+t*lj2[itype][jtype];
+ g8*(((6.0*a2+6.0)*a2+3.0)*a2+a2)*x2*rsq+t*lj2[itype][jtype];
eng += factor_lj*r6inv*lj3[itype][jtype]-
- g6*((a2+1.0)*a2+0.5)*x2+t*lj4[itype][jtype];
+ g6*((a2+1.0)*a2+0.5)*x2+t*lj4[itype][jtype];
}
- else { // cut
+ else { // cut
force_lj = factor_lj*r6inv*(lj1[itype][jtype]*r6inv-lj2[itype][jtype]);
eng += factor_lj*(r6inv*(r6inv*lj3[itype][jtype]-
- lj4[itype][jtype])-offset[itype][jtype]);
+ lj4[itype][jtype])-offset[itype][jtype]);
}
}
else force_lj = 0.0;
diff --git a/src/GPU/pair_ufm_gpu.cpp b/src/GPU/pair_ufm_gpu.cpp
index 96af0dc069..88f2c2d3ad 100644
--- a/src/GPU/pair_ufm_gpu.cpp
+++ b/src/GPU/pair_ufm_gpu.cpp
@@ -49,7 +49,7 @@ int ufml_gpu_init(const int ntypes, double **cutsq, double **host_uf1,
int ufml_gpu_reinit(const int ntypes, double **cutsq, double **host_uf1,
double **host_uf2, double **host_uf3, double **host_uf4,
- double **offset);
+ double **offset);
void ufml_gpu_clear();
int ** ufml_gpu_compute_n(const int ago, const int inum,
@@ -222,10 +222,10 @@ void PairUFMGPU::cpu_compute(int start, int inum, int eflag, int vflag,
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
- expuf = exp(- rsq * uf2[itype][jtype]);
+ expuf = exp(- rsq * uf2[itype][jtype]);
fpair = factor_lj * uf1[itype][jtype] * expuf /(1.0 - expuf);
- f[i][0] += delx*fpair;
+ f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
diff --git a/src/KOKKOS/atom_vec_angle_kokkos.cpp b/src/KOKKOS/atom_vec_angle_kokkos.cpp
index a9e55f530a..644ed5280a 100644
--- a/src/KOKKOS/atom_vec_angle_kokkos.cpp
+++ b/src/KOKKOS/atom_vec_angle_kokkos.cpp
@@ -393,22 +393,22 @@ struct AtomVecAngleKokkos_PackCommSelf {
/* ---------------------------------------------------------------------- */
int AtomVecAngleKokkos::pack_comm_self(const int &n, const DAT::tdual_int_2d &list,
- const int & iswap,
- const int nfirst, const int &pbc_flag,
- const int* const pbc) {
+ const int & iswap,
+ const int nfirst, const int &pbc_flag,
+ const int* const pbc) {
if(commKK->forward_comm_on_host) {
sync(Host,X_MASK);
modified(Host,X_MASK);
if(pbc_flag) {
if(domain->triclinic) {
struct AtomVecAngleKokkos_PackCommSelf<LMPHostType,1,1>
- f(atomKK->k_x,nfirst,list,iswap,
+ f(atomKK->k_x,nfirst,list,iswap,
domain->xprd,domain->yprd,domain->zprd,
domain->xy,domain->xz,domain->yz,pbc);
Kokkos::parallel_for(n,f);
} else {
struct AtomVecAngleKokkos_PackCommSelf<LMPHostType,1,0>
- f(atomKK->k_x,nfirst,list,iswap,
+ f(atomKK->k_x,nfirst,list,iswap,
domain->xprd,domain->yprd,domain->zprd,
domain->xy,domain->xz,domain->yz,pbc);
Kokkos::parallel_for(n,f);
@@ -416,13 +416,13 @@ int AtomVecAngleKokkos::pack_comm_self(const int &n, const DAT::tdual_int_2d &li
} else {
if(domain->triclinic) {
struct AtomVecAngleKokkos_PackCommSelf<LMPHostType,0,1>
- f(atomKK->k_x,nfirst,list,iswap,
+ f(atomKK->k_x,nfirst,list,iswap,
domain->xprd,domain->yprd,domain->zprd,
domain->xy,domain->xz,domain->yz,pbc);
Kokkos::parallel_for(n,f);
} else {
struct AtomVecAngleKokkos_PackCommSelf<LMPHostType,0,0>
- f(atomKK->k_x,nfirst,list,iswap,
+ f(atomKK->k_x,nfirst,list,iswap,
domain->xprd,domain->yprd,domain->zprd,
domain->xy,domain->xz,domain->yz,pbc);
Kokkos::parallel_for(n,f);
@@ -434,13 +434,13 @@ int AtomVecAngleKokkos::pack_comm_self(const int &n, const DAT::tdual_int_2d &li
if(pbc_flag) {
if(domain->triclinic) {
struct AtomVecAngleKokkos_PackCommSelf<LMPDeviceType,1,1>
- f(atomKK->k_x,nfirst,list,iswap,
+ f(atomKK->k_x,nfirst,list,iswap,
domain->xprd,domain->yprd,domain->zprd,
domain->xy,domain->xz,domain->yz,pbc);
Kokkos::parallel_for(n,f);
} else {
struct AtomVecAngleKokkos_PackCommSelf<LMPDeviceType,1,0>
- f(atomKK->k_x,nfirst,list,iswap,
+ f(atomKK->k_x,nfirst,list,iswap,
domain->xprd,domain->yprd,domain->zprd,
domain->xy,domain->xz,domain->yz,pbc);
Kokkos::parallel_for(n,f);
@@ -448,20 +448,20 @@ int AtomVecAngleKokkos::pack_comm_self(const int &n, const DAT::tdual_int_2d &li
} else {
if(domain->triclinic) {
struct AtomVecAngleKokkos_PackCommSelf<LMPDeviceType,0,1>
- f(atomKK->k_x,nfirst,list,iswap,
+ f(atomKK->k_x,nfirst,list,iswap,
domain->xprd,domain->yprd,domain->zprd,
domain->xy,domain->xz,domain->yz,pbc);
Kokkos::parallel_for(n,f);
} else {
struct AtomVecAngleKokkos_PackCommSelf<LMPDeviceType,0,0>
- f(atomKK->k_x,nfirst,list,iswap,
+ f(atomKK->k_x,nfirst,list,iswap,
domain->xprd,domain->yprd,domain->zprd,
domain->xy,domain->xz,domain->yz,pbc);
Kokkos::parallel_for(n,f);
}
}
}
- return n*3;
+ return n*3;
}
/* ---------------------------------------------------------------------- */
@@ -1137,7 +1137,7 @@ struct AtomVecAngleKokkos_PackExchangeFunctor {
// 1 to store buffer length
elements = 17+atom->maxspecial+2*atom->bond_per_atom+4*atom->angle_per_atom;
const int maxsendlist = (buf.template view<DeviceType>().dimension_0()*
- buf.template view<DeviceType>().dimension_1())/elements;
+ buf.template view<DeviceType>().dimension_1())/elements;
buffer_view<DeviceType>(_buf,buf,maxsendlist,elements);
}
@@ -1221,7 +1221,7 @@ int AtomVecAngleKokkos::pack_exchange_kokkos(const int &nsend,DAT::tdual_xfloat_
{
const int elements = 17+atom->maxspecial+2*atom->bond_per_atom+4*atom->angle_per_atom;
if(nsend > (int) (k_buf.view<LMPHostType>().dimension_0()*
- k_buf.view<LMPHostType>().dimension_1())/elements) {
+ k_buf.view<LMPHostType>().dimension_1())/elements) {
int newsize = nsend*elements/k_buf.view<LMPHostType>().dimension_1()+1;
k_buf.resize(newsize,k_buf.view<LMPHostType>().dimension_1());
}
@@ -1414,7 +1414,7 @@ int AtomVecAngleKokkos::unpack_exchange(double *buf)
if (nlocal == nmax) grow(0);
modified(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK |
MASK_MASK | IMAGE_MASK | MOLECULE_MASK | BOND_MASK |
- ANGLE_MASK | SPECIAL_MASK);
+ ANGLE_MASK | SPECIAL_MASK);
int k;
int m = 1;
@@ -1705,7 +1705,7 @@ void AtomVecAngleKokkos::write_data(FILE *fp, int n, double **buf)
for (int i = 0; i < n; i++)
fprintf(fp,"%d %d %d %-1.16e %-1.16e %-1.16e %d %d %d\n",
(int) buf[i][0],(int) buf[i][1], (int) buf[i][2],
- buf[i][3],buf[i][4],buf[i][5],
+ buf[i][3],buf[i][4],buf[i][5],
(int) buf[i][6],(int) buf[i][7],(int) buf[i][8]);
}
diff --git a/src/KOKKOS/atom_vec_bond_kokkos.cpp b/src/KOKKOS/atom_vec_bond_kokkos.cpp
index bf682c507f..9441373aa5 100644
--- a/src/KOKKOS/atom_vec_bond_kokkos.cpp
+++ b/src/KOKKOS/atom_vec_bond_kokkos.cpp
@@ -598,24 +598,24 @@ struct AtomVecBondKokkos_PackExchangeFunctor {
_type(atom->k_type.view<DeviceType>()),
_mask(atom->k_mask.view<DeviceType>()),
_image(atom->k_image.view<DeviceType>()),
- _molecule(atom->k_molecule.view<DeviceType>()),
- _nspecial(atom->k_nspecial.view<DeviceType>()),
- _special(atom->k_special.view<DeviceType>()),
- _num_bond(atom->k_num_bond.view<DeviceType>()),
- _bond_type(atom->k_bond_type.view<DeviceType>()),
- _bond_atom(atom->k_bond_atom.view<DeviceType>()),
+ _molecule(atom->k_molecule.view<DeviceType>()),
+ _nspecial(atom->k_nspecial.view<DeviceType>()),
+ _special(atom->k_special.view<DeviceType>()),
+ _num_bond(atom->k_num_bond.view<DeviceType>()),
+ _bond_type(atom->k_bond_type.view<DeviceType>()),
+ _bond_atom(atom->k_bond_atom.view<DeviceType>()),
_xw(atom->k_x.view<DeviceType>()),
_vw(atom->k_v.view<DeviceType>()),
_tagw(atom->k_tag.view<DeviceType>()),
_typew(atom->k_type.view<DeviceType>()),
_maskw(atom->k_mask.view<DeviceType>()),
_imagew(atom->k_image.view<DeviceType>()),
- _moleculew(atom->k_molecule.view<DeviceType>()),
- _nspecialw(atom->k_nspecial.view<DeviceType>()),
- _specialw(atom->k_special.view<DeviceType>()),
- _num_bondw(atom->k_num_bond.view<DeviceType>()),
- _bond_typew(atom->k_bond_type.view<DeviceType>()),
- _bond_atomw(atom->k_bond_atom.view<DeviceType>()),
+ _moleculew(atom->k_molecule.view<DeviceType>()),
+ _nspecialw(atom->k_nspecial.view<DeviceType>()),
+ _specialw(atom->k_special.view<DeviceType>()),
+ _num_bondw(atom->k_num_bond.view<DeviceType>()),
+ _bond_typew(atom->k_bond_type.view<DeviceType>()),
+ _bond_atomw(atom->k_bond_atom.view<DeviceType>()),
_sendlist(sendlist.template view<DeviceType>()),
_copylist(copylist.template view<DeviceType>()),
_nlocal(nlocal),_dim(dim),
@@ -625,7 +625,7 @@ struct AtomVecBondKokkos_PackExchangeFunctor {
// 1 to store buffer lenght
elements = 16+atom->maxspecial+atom->bond_per_atom+atom->bond_per_atom;
const int maxsendlist = (buf.template view<DeviceType>().dimension_0()*
- buf.template view<DeviceType>().dimension_1())/elements;
+ buf.template view<DeviceType>().dimension_1())/elements;
buffer_view<DeviceType>(_buf,buf,maxsendlist,elements);
}
@@ -695,7 +695,7 @@ int AtomVecBondKokkos::pack_exchange_kokkos(const int &nsend,DAT::tdual_xfloat_2
{
const int elements = 16+atomKK->maxspecial+atomKK->bond_per_atom+atomKK->bond_per_atom;
if(nsend > (int) (k_buf.view<LMPHostType>().dimension_0()*
- k_buf.view<LMPHostType>().dimension_1())/elements) {
+ k_buf.view<LMPHostType>().dimension_1())/elements) {
int newsize = nsend*elements/k_buf.view<LMPHostType>().dimension_1()+1;
k_buf.resize(newsize,k_buf.view<LMPHostType>().dimension_1());
}
@@ -785,17 +785,17 @@ struct AtomVecBondKokkos_UnpackExchangeFunctor {
_type(atom->k_type.view<DeviceType>()),
_mask(atom->k_mask.view<DeviceType>()),
_image(atom->k_image.view<DeviceType>()),
- _molecule(atom->k_molecule.view<DeviceType>()),
- _nspecial(atom->k_nspecial.view<DeviceType>()),
- _special(atom->k_special.view<DeviceType>()),
- _num_bond(atom->k_num_bond.view<DeviceType>()),
- _bond_type(atom->k_bond_type.view<DeviceType>()),
- _bond_atom(atom->k_bond_atom.view<DeviceType>()),
+ _molecule(atom->k_molecule.view<DeviceType>()),
+ _nspecial(atom->k_nspecial.view<DeviceType>()),
+ _special(atom->k_special.view<DeviceType>()),
+ _num_bond(atom->k_num_bond.view<DeviceType>()),
+ _bond_type(atom->k_bond_type.view<DeviceType>()),
+ _bond_atom(atom->k_bond_atom.view<DeviceType>()),
_nlocal(nlocal.template view<DeviceType>()),_dim(dim),
_lo(lo),_hi(hi){
elements = 16+atom->maxspecial+atom->bond_per_atom+atom->bond_per_atom;
const int maxsendlist = (buf.template view<DeviceType>().dimension_0()*
- buf.template view<DeviceType>().dimension_1())/elements;
+ buf.template view<DeviceType>().dimension_1())/elements;
buffer_view<DeviceType>(_buf,buf,maxsendlist,elements);
}
@@ -1127,7 +1127,7 @@ void AtomVecBondKokkos::write_data(FILE *fp, int n, double **buf)
for (int i = 0; i < n; i++)
fprintf(fp,"%d %d %d %-1.16e %-1.16e %-1.16e %d %d %d\n",
(int) buf[i][0],(int) buf[i][1], (int) buf[i][2],
- buf[i][3],buf[i][4],buf[i][5],
+ buf[i][3],buf[i][4],buf[i][5],
(int) buf[i][6],(int) buf[i][7],(int) buf[i][8]);
}
diff --git a/src/KOKKOS/atom_vec_dpd_kokkos.cpp b/src/KOKKOS/atom_vec_dpd_kokkos.cpp
index 9c54ffccc5..8f453f1e0d 100644
--- a/src/KOKKOS/atom_vec_dpd_kokkos.cpp
+++ b/src/KOKKOS/atom_vec_dpd_kokkos.cpp
@@ -335,7 +335,7 @@ int AtomVecDPDKokkos::pack_comm_kokkos(const int &n,
}
}
- return n*size_forward;
+ return n*size_forward;
}
/* ---------------------------------------------------------------------- */
@@ -404,7 +404,7 @@ struct AtomVecDPDKokkos_PackCommSelf {
/* ---------------------------------------------------------------------- */
int AtomVecDPDKokkos::pack_comm_self(const int &n, const DAT::tdual_int_2d &list, const int & iswap,
- const int nfirst, const int &pbc_flag, const int* const pbc) {
+ const int nfirst, const int &pbc_flag, const int* const pbc) {
if(commKK->forward_comm_on_host) {
sync(Host,X_MASK|DPDTHETA_MASK|UCOND_MASK|UMECH_MASK|UCHEM_MASK);
modified(Host,X_MASK|DPDTHETA_MASK|UCOND_MASK|UMECH_MASK|UCHEM_MASK);
@@ -478,7 +478,7 @@ int AtomVecDPDKokkos::pack_comm_self(const int &n, const DAT::tdual_int_2d &list
}
}
}
- return n*3;
+ return n*3;
}
/* ---------------------------------------------------------------------- */
diff --git a/src/KOKKOS/atom_vec_full_kokkos.cpp b/src/KOKKOS/atom_vec_full_kokkos.cpp
index 9369d7e844..0560c99037 100644
--- a/src/KOKKOS/atom_vec_full_kokkos.cpp
+++ b/src/KOKKOS/atom_vec_full_kokkos.cpp
@@ -81,22 +81,22 @@ void AtomVecFullKokkos::grow(int n)
memoryKK->grow_kokkos(atomKK->k_nspecial,atomKK->nspecial,nmax,3,"atom:nspecial");
memoryKK->grow_kokkos(atomKK->k_special,atomKK->special,nmax,atomKK->maxspecial,
- "atom:special");
+ "atom:special");
memoryKK->grow_kokkos(atomKK->k_num_bond,atomKK->num_bond,nmax,"atom:num_bond");
memoryKK->grow_kokkos(atomKK->k_bond_type,atomKK->bond_type,nmax,atomKK->bond_per_atom,
- "atom:bond_type");
+ "atom:bond_type");
memoryKK->grow_kokkos(atomKK->k_bond_atom,atomKK->bond_atom,nmax,atomKK->bond_per_atom,
- "atom:bond_atom");
+ "atom:bond_atom");
memoryKK->grow_kokkos(atomKK->k_num_angle,atomKK->num_angle,nmax,"atom:num_angle");
memoryKK->grow_kokkos(atomKK->k_angle_type,atomKK->angle_type,nmax,atomKK->angle_per_atom,
- "atom:angle_type");
+ "atom:angle_type");
memoryKK->grow_kokkos(atomKK->k_angle_atom1,atomKK->angle_atom1,nmax,atomKK->angle_per_atom,
- "atom:angle_atom1");
+ "atom:angle_atom1");
memoryKK->grow_kokkos(atomKK->k_angle_atom2,atomKK->angle_atom2,nmax,atomKK->angle_per_atom,
- "atom:angle_atom2");
+ "atom:angle_atom2");
memoryKK->grow_kokkos(atomKK->k_angle_atom3,atomKK->angle_atom3,nmax,atomKK->angle_per_atom,
- "atom:angle_atom3");
+ "atom:angle_atom3");
memoryKK->grow_kokkos(atomKK->k_num_dihedral,atomKK->num_dihedral,nmax,"atom:num_dihedral");
memoryKK->grow_kokkos(atomKK->k_dihedral_type,atomKK->dihedral_type,nmax,
@@ -956,7 +956,7 @@ int AtomVecFullKokkos::pack_exchange_kokkos(const int &nsend,DAT::tdual_xfloat_2
const int elements = 20+atom->maxspecial+2*atom->bond_per_atom+4*atom->angle_per_atom+
5*atom->dihedral_per_atom + 5*atom->improper_per_atom;
if(nsend > (int) (k_buf.view<LMPHostType>().dimension_0()*
- k_buf.view<LMPHostType>().dimension_1())/elements) {
+ k_buf.view<LMPHostType>().dimension_1())/elements) {
int newsize = nsend*elements/k_buf.view<LMPHostType>().dimension_1()+1;
k_buf.resize(newsize,k_buf.view<LMPHostType>().dimension_1());
}
@@ -1255,7 +1255,7 @@ int AtomVecFullKokkos::unpack_exchange(double *buf)
h_nspecial(nlocal,1) = (int) ubuf(buf[m++]).i;
h_nspecial(nlocal,2) = (int) ubuf(buf[m++]).i;
for (k = 0; k < h_nspecial(nlocal,2); k++)
- h_special(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ h_special(nlocal,k) = (tagint) ubuf(buf[m++]).i;
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
diff --git a/src/KOKKOS/atom_vec_kokkos.cpp b/src/KOKKOS/atom_vec_kokkos.cpp
index 03fb2a4ead..885f190f84 100644
--- a/src/KOKKOS/atom_vec_kokkos.cpp
+++ b/src/KOKKOS/atom_vec_kokkos.cpp
@@ -147,7 +147,7 @@ int AtomVecKokkos::pack_comm_kokkos(const int &n,
}
}
- return n*size_forward;
+ return n*size_forward;
}
/* ---------------------------------------------------------------------- */
@@ -261,7 +261,7 @@ int AtomVecKokkos::pack_comm_self(const int &n, const DAT::tdual_int_2d &list, c
}
}
}
- return n*3;
+ return n*3;
}
/* ---------------------------------------------------------------------- */
diff --git a/src/KOKKOS/atom_vec_molecular_kokkos.cpp b/src/KOKKOS/atom_vec_molecular_kokkos.cpp
index 6f232a319b..380aa0fb7e 100644
--- a/src/KOKKOS/atom_vec_molecular_kokkos.cpp
+++ b/src/KOKKOS/atom_vec_molecular_kokkos.cpp
@@ -79,22 +79,22 @@ void AtomVecMolecularKokkos::grow(int n)
memoryKK->grow_kokkos(atomKK->k_molecule,atomKK->molecule,nmax,"atom:molecule");
memoryKK->grow_kokkos(atomKK->k_nspecial,atomKK->nspecial,nmax,3,"atom:nspecial");
memoryKK->grow_kokkos(atomKK->k_special,atomKK->special,nmax,atomKK->maxspecial,
- "atom:special");
+ "atom:special");
memoryKK->grow_kokkos(atomKK->k_num_bond,atomKK->num_bond,nmax,"atom:num_bond");
memoryKK->grow_kokkos(atomKK->k_bond_type,atomKK->bond_type,nmax,atomKK->bond_per_atom,
- "atom:bond_type");
+ "atom:bond_type");
memoryKK->grow_kokkos(atomKK->k_bond_atom,atomKK->bond_atom,nmax,atomKK->bond_per_atom,
- "atom:bond_atom");
+ "atom:bond_atom");
memoryKK->grow_kokkos(atomKK->k_num_angle,atomKK->num_angle,nmax,"atom:num_angle");
memoryKK->grow_kokkos(atomKK->k_angle_type,atomKK->angle_type,nmax,atomKK->angle_per_atom,
- "atom:angle_type");
+ "atom:angle_type");
memoryKK->grow_kokkos(atomKK->k_angle_atom1,atomKK->angle_atom1,nmax,atomKK->angle_per_atom,
- "atom:angle_atom1");
+ "atom:angle_atom1");
memoryKK->grow_kokkos(atomKK->k_angle_atom2,atomKK->angle_atom2,nmax,atomKK->angle_per_atom,
- "atom:angle_atom2");
+ "atom:angle_atom2");
memoryKK->grow_kokkos(atomKK->k_angle_atom3,atomKK->angle_atom3,nmax,atomKK->angle_per_atom,
- "atom:angle_atom3");
+ "atom:angle_atom3");
memoryKK->grow_kokkos(atomKK->k_num_dihedral,atomKK->num_dihedral,nmax,"atom:num_dihedral");
memoryKK->grow_kokkos(atomKK->k_dihedral_type,atomKK->dihedral_type,nmax,
@@ -320,7 +320,7 @@ struct AtomVecMolecularKokkos_PackComm {
_xprd(xprd),_yprd(yprd),_zprd(zprd),
_xy(xy),_xz(xz),_yz(yz) {
const size_t maxsend = (buf.view<DeviceType>().dimension_0()
- *buf.view<DeviceType>().dimension_1())/3;
+ *buf.view<DeviceType>().dimension_1())/3;
const size_t elements = 3;
buffer_view<DeviceType>(_buf,buf,maxsend,elements);
_pbc[0] = pbc[0]; _pbc[1] = pbc[1]; _pbc[2] = pbc[2];
@@ -416,7 +416,7 @@ int AtomVecMolecularKokkos::pack_comm_kokkos(const int &n,
}
}
- return n*size_forward;
+ return n*size_forward;
}
/* ---------------------------------------------------------------------- */
@@ -533,7 +533,7 @@ int AtomVecMolecularKokkos::pack_comm_self(const int &n, const DAT::tdual_int_2d
}
}
}
- return n*3;
+ return n*3;
}
/* ---------------------------------------------------------------------- */
@@ -1369,7 +1369,7 @@ int AtomVecMolecularKokkos::pack_exchange_kokkos(const int &nsend,DAT::tdual_xfl
const int elements = 19+atom->maxspecial+2*atom->bond_per_atom+4*atom->angle_per_atom+
5*atom->dihedral_per_atom + 5*atom->improper_per_atom;
if(nsend > (int) (k_buf.view<LMPHostType>().dimension_0()*
- k_buf.view<LMPHostType>().dimension_1())/elements) {
+ k_buf.view<LMPHostType>().dimension_1())/elements) {
int newsize = nsend*elements/k_buf.view<LMPHostType>().dimension_1()+1;
k_buf.resize(newsize,k_buf.view<LMPHostType>().dimension_1());
}
@@ -1617,7 +1617,7 @@ int AtomVecMolecularKokkos::unpack_exchange(double *buf)
if (nlocal == nmax) grow(0);
modified(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK |
MASK_MASK | IMAGE_MASK | MOLECULE_MASK | BOND_MASK |
- ANGLE_MASK | DIHEDRAL_MASK | IMPROPER_MASK | SPECIAL_MASK);
+ ANGLE_MASK | DIHEDRAL_MASK | IMPROPER_MASK | SPECIAL_MASK);
int k;
int m = 1;
@@ -1968,7 +1968,7 @@ void AtomVecMolecularKokkos::write_data(FILE *fp, int n, double **buf)
for (int i = 0; i < n; i++)
fprintf(fp,"%d %d %d %-1.16e %-1.16e %-1.16e %d %d %d\n",
(int) buf[i][0],(int) buf[i][1], (int) buf[i][2],
- buf[i][3],buf[i][4],buf[i][5],
+ buf[i][3],buf[i][4],buf[i][5],
(int) buf[i][6],(int) buf[i][7],(int) buf[i][8]);
}
diff --git a/src/KOKKOS/comm_kokkos.cpp b/src/KOKKOS/comm_kokkos.cpp
index de35431eb9..e8eb8b2b82 100644
--- a/src/KOKKOS/comm_kokkos.cpp
+++ b/src/KOKKOS/comm_kokkos.cpp
@@ -736,8 +736,8 @@ void CommKokkos::borders()
template<class DeviceType>
struct BuildBorderListFunctor {
- typedef DeviceType device_type;
- typedef ArrayTypes<DeviceType> AT;
+ typedef DeviceType device_type;
+ typedef ArrayTypes<DeviceType> AT;
X_FLOAT lo,hi;
typename AT::t_x_array x;
int iswap,maxsendlist;
diff --git a/src/KOKKOS/dihedral_charmm_kokkos.h b/src/KOKKOS/dihedral_charmm_kokkos.h
index 2ee596353a..613886d21c 100644
--- a/src/KOKKOS/dihedral_charmm_kokkos.h
+++ b/src/KOKKOS/dihedral_charmm_kokkos.h
@@ -35,13 +35,13 @@ struct s_EVM_FLOAT {
F_FLOAT vp[6];
KOKKOS_INLINE_FUNCTION
s_EVM_FLOAT() {
- evdwl = 0;
- ecoul = 0;
- emol = 0;
- v[0] = 0; v[1] = 0; v[2] = 0;
- v[3] = 0; v[4] = 0; v[5] = 0;
- vp[0] = 0; vp[1] = 0; vp[2] = 0;
- vp[3] = 0; vp[4] = 0; vp[5] = 0;
+ evdwl = 0;
+ ecoul = 0;
+ emol = 0;
+ v[0] = 0; v[1] = 0; v[2] = 0;
+ v[3] = 0; v[4] = 0; v[5] = 0;
+ vp[0] = 0; vp[1] = 0; vp[2] = 0;
+ vp[3] = 0; vp[4] = 0; vp[5] = 0;
}
KOKKOS_INLINE_FUNCTION
diff --git a/src/KOKKOS/pair_coul_debye_kokkos.cpp b/src/KOKKOS/pair_coul_debye_kokkos.cpp
index 4cac18cacf..729b24ff29 100644
--- a/src/KOKKOS/pair_coul_debye_kokkos.cpp
+++ b/src/KOKKOS/pair_coul_debye_kokkos.cpp
@@ -181,7 +181,7 @@ compute_fcoul(const F_FLOAT& rsq, const int& i, const int&j,
F_FLOAT forcecoul;
forcecoul = qqrd2e * qtmp * q(j) * screening * (kappa + rinv) *
- (STACKPARAMS?m_params[itype][jtype].scale:params(itype,jtype).scale);
+ (STACKPARAMS?m_params[itype][jtype].scale:params(itype,jtype).scale);
return factor_coul*forcecoul*r2inv;
@@ -203,7 +203,7 @@ compute_ecoul(const F_FLOAT& rsq, const int& i, const int&j,
const F_FLOAT screening = exp(-kappa*r);
return factor_coul * qqrd2e * qtmp * q(j) * rinv * screening *
- (STACKPARAMS?m_params[itype][jtype].scale:params(itype,jtype).scale);
+ (STACKPARAMS?m_params[itype][jtype].scale:params(itype,jtype).scale);
}
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 7d395cb3b4..70f0c3e00a 100644
--- a/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp
@@ -217,8 +217,8 @@ compute_fpair(const F_FLOAT& rsq, const int& i, const int&j,
(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 -
- (STACKPARAMS?m_params[itype][jtype].lj4:params(itype,jtype).lj4));
+ ((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;
}
diff --git a/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp b/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp
index 2663d71a1f..0316b65aed 100644
--- a/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp
@@ -217,8 +217,8 @@ compute_fpair(const F_FLOAT& rsq, const int& i, const int&j,
(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 -
- (STACKPARAMS?m_params[itype][jtype].lj4:params(itype,jtype).lj4));
+ ((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;
}
diff --git a/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp b/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp
index 81271c7d8a..4d27373824 100644
--- a/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp
@@ -217,8 +217,8 @@ compute_fpair(const F_FLOAT& rsq, const int& i, const int&j,
(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 -
- (STACKPARAMS?m_params[itype][jtype].lj4:params(itype,jtype).lj4));
+ ((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;
}
diff --git a/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp
index 0da5e7f5f5..b64d9fa31a 100644
--- a/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp
@@ -245,7 +245,7 @@ compute_fcoul(const F_FLOAT& rsq, const int& i, const int&j,
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) *
- r2inv;
+ r2inv;
}
/* ----------------------------------------------------------------------
diff --git a/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp b/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp
index bf269288e0..1cc8d9b3e2 100644
--- a/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp
@@ -206,8 +206,8 @@ 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].ljsw2:params(itype,jtype).ljsw2)*tlj);
+ ((STACKPARAMS?m_params[itype][jtype].ljsw1:params(itype,jtype).ljsw1) +
+ (STACKPARAMS?m_params[itype][jtype].ljsw2:params(itype,jtype).ljsw2)*tlj);
forcelj += fswitch;
}
return forcelj*r2inv;
@@ -234,8 +234,8 @@ 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].ljsw4:params(itype,jtype).ljsw4)*tlj);
+ ((STACKPARAMS?m_params[itype][jtype].ljsw3:params(itype,jtype).ljsw3) +
+ (STACKPARAMS?m_params[itype][jtype].ljsw4:params(itype,jtype).ljsw4)*tlj);
englj += eswitch;
}
return englj;
diff --git a/src/KOKKOS/pair_lj_gromacs_kokkos.cpp b/src/KOKKOS/pair_lj_gromacs_kokkos.cpp
index f24ff718c1..f0ad935769 100644
--- a/src/KOKKOS/pair_lj_gromacs_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_gromacs_kokkos.cpp
@@ -193,8 +193,8 @@ 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].ljsw2:params(itype,jtype).ljsw2)*tlj);
+ ((STACKPARAMS?m_params[itype][jtype].ljsw1:params(itype,jtype).ljsw1) +
+ (STACKPARAMS?m_params[itype][jtype].ljsw2:params(itype,jtype).ljsw2)*tlj);
forcelj += fswitch;
}
return forcelj*r2inv;
@@ -221,8 +221,8 @@ 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].ljsw4:params(itype,jtype).ljsw4)*tlj);
+ ((STACKPARAMS?m_params[itype][jtype].ljsw3:params(itype,jtype).ljsw3) +
+ (STACKPARAMS?m_params[itype][jtype].ljsw4:params(itype,jtype).ljsw4)*tlj);
englj += eswitch;
}
return englj;
diff --git a/src/KOKKOS/pair_tersoff_kokkos.cpp b/src/KOKKOS/pair_tersoff_kokkos.cpp
index c585da6029..b64b2f6d43 100644
--- a/src/KOKKOS/pair_tersoff_kokkos.cpp
+++ b/src/KOKKOS/pair_tersoff_kokkos.cpp
@@ -75,7 +75,7 @@ void PairTersoffKokkos<DeviceType>::allocate()
int n = atom->ntypes;
k_params = Kokkos::DualView<params_ters***,Kokkos::LayoutRight,DeviceType>
- ("PairTersoff::paramskk",n+1,n+1,n+1);
+ ("PairTersoff::paramskk",n+1,n+1,n+1);
paramskk = k_params.template view<DeviceType>();
}
@@ -355,7 +355,7 @@ void PairTersoffKokkos<DeviceType>::operator()(TagPairTersoffComputeHalf<NEIGHFL
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 *
- (tmp_fcd - tmp_fce*paramskk(itype,jtype,jtype).lam1) / r;
+ (tmp_fcd - tmp_fce*paramskk(itype,jtype,jtype).lam1) / r;
const F_FLOAT eng = tmp_fce * paramskk(itype,jtype,jtype).biga * tmp_exp;
f_x += delx*frep;
@@ -524,7 +524,7 @@ void PairTersoffKokkos<DeviceType>::operator()(TagPairTersoffComputeFullA<NEIGHF
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 *
- (tmp_fcd - tmp_fce*paramskk(itype,jtype,jtype).lam1) / r;
+ (tmp_fcd - tmp_fce*paramskk(itype,jtype,jtype).lam1) / r;
const F_FLOAT eng = tmp_fce * paramskk(itype,jtype,jtype).biga * tmp_exp;
f_x += delx*frep;
@@ -535,7 +535,7 @@ void PairTersoffKokkos<DeviceType>::operator()(TagPairTersoffComputeFullA<NEIGHF
if (eflag)
ev.evdwl += 0.5*eng;
if (vflag_either || eflag_atom)
- this->template ev_tally<NEIGHFLAG>(ev,i,j,eng,frep,delx,dely,delz);
+ this->template ev_tally<NEIGHFLAG>(ev,i,j,eng,frep,delx,dely,delz);
}
}
@@ -589,7 +589,7 @@ void PairTersoffKokkos<DeviceType>::operator()(TagPairTersoffComputeFullA<NEIGHF
if (EVFLAG) {
if (eflag) ev.evdwl += 0.5*eng;
if (vflag_either || eflag_atom)
- this->template ev_tally<NEIGHFLAG>(ev,i,j,eng,fatt,delx1,dely1,delz1);
+ this->template ev_tally<NEIGHFLAG>(ev,i,j,eng,fatt,delx1,dely1,delz1);
}
// attractive: three-body force
@@ -609,17 +609,17 @@ void PairTersoffKokkos<DeviceType>::operator()(TagPairTersoffComputeFullA<NEIGHF
if (rsq2 > cutsq2) continue;
rik = sqrt(rsq2);
ters_dthb(itype,jtype,ktype,prefactor,rij,delx1,dely1,delz1,
- rik,delx2,dely2,delz2,fi,fj,fk);
+ rik,delx2,dely2,delz2,fi,fj,fk);
f_x += fi[0];
f_y += fi[1];
f_z += fi[2];
if (vflag_atom) {
- F_FLOAT delrij[3], delrik[3];
- delrij[0] = -delx1; delrij[1] = -dely1; delrij[2] = -delz1;
- delrik[0] = -delx2; delrik[1] = -dely2; delrik[2] = -delz2;
- if (vflag_either) this->template v_tally3<NEIGHFLAG>(ev,i,j,k,fj,fk,delrij,delrik);
+ F_FLOAT delrij[3], delrik[3];
+ delrij[0] = -delx1; delrij[1] = -dely1; delrij[2] = -delz1;
+ delrik[0] = -delx2; delrik[1] = -dely2; delrik[2] = -delz2;
+ if (vflag_either) this->template v_tally3<NEIGHFLAG>(ev,i,j,k,fj,fk,delrij,delrik);
}
}
}
@@ -715,7 +715,7 @@ void PairTersoffKokkos<DeviceType>::operator()(TagPairTersoffComputeFullB<NEIGHF
if (eflag)
ev.evdwl += 0.5 * eng;
if (vflag_either || eflag_atom)
- this->template ev_tally<NEIGHFLAG>(ev,i,j,eng,fatt,delx1,dely1,delz1);
+ this->template ev_tally<NEIGHFLAG>(ev,i,j,eng,fatt,delx1,dely1,delz1);
}
// attractive: three-body force
@@ -735,22 +735,22 @@ void PairTersoffKokkos<DeviceType>::operator()(TagPairTersoffComputeFullB<NEIGHF
if (rsq2 > cutsq2) continue;
rik = sqrt(rsq2);
ters_dthbj(jtype,itype,ktype,prefactor,rij,delx1,dely1,delz1,
- rik,delx2,dely2,delz2,fj,fk);
+ rik,delx2,dely2,delz2,fj,fk);
f_x += fj[0];
f_y += fj[1];
f_z += fj[2];
if (vflag_atom) {
- F_FLOAT delrji[3], delrjk[3];
- delrji[0] = -delx1; delrji[1] = -dely1; delrji[2] = -delz1;
- delrjk[0] = -delx2; delrjk[1] = -dely2; delrjk[2] = -delz2;
- if (vflag_either) v_tally3_atom(ev,i,j,k,fj,fk,delrji,delrjk);
+ F_FLOAT delrji[3], delrjk[3];
+ delrji[0] = -delx1; delrji[1] = -dely1; delrji[2] = -delz1;
+ delrjk[0] = -delx2; delrjk[1] = -dely2; delrjk[2] = -delz2;
+ if (vflag_either) v_tally3_atom(ev,i,j,k,fj,fk,delrji,delrjk);
}
const F_FLOAT fa_jk = ters_fa_k(jtype,ktype,itype,rik);
const F_FLOAT prefactor_jk = 0.5*fa_jk * ters_dbij(jtype,ktype,itype,bo_ij);
ters_dthbk(jtype,ktype,itype,prefactor_jk,rik,delx2,dely2,delz2,
- rij,delx1,dely1,delz1,fk);
+ rij,delx1,dely1,delz1,fk);
f_x += fk[0];
f_y += fk[1];
f_z += fk[2];
@@ -774,7 +774,7 @@ 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;
@@ -789,7 +789,7 @@ 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;
@@ -804,8 +804,8 @@ double PairTersoffKokkos<DeviceType>::ters_dfc(const int &i, const int &j,
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 &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
{
F_FLOAT arg, ex_delr;
@@ -827,7 +827,7 @@ double PairTersoffKokkos<DeviceType>::bondorder(const int &i, const int &j, cons
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
double PairTersoffKokkos<DeviceType>::
- ters_gijk(const int &i, const int &j, const int &k, const F_FLOAT &cos) const
+ ters_gijk(const int &i, const int &j, const int &k, const F_FLOAT &cos) const
{
const F_FLOAT ters_c = paramskk(i,j,k).c * paramskk(i,j,k).c;
const F_FLOAT ters_d = paramskk(i,j,k).d * paramskk(i,j,k).d;
@@ -841,7 +841,7 @@ double PairTersoffKokkos<DeviceType>::
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
double PairTersoffKokkos<DeviceType>::
- ters_dgijk(const int &i, const int &j, const int &k, const F_FLOAT &cos) const
+ ters_dgijk(const int &i, const int &j, const int &k, const F_FLOAT &cos) const
{
const F_FLOAT ters_c = paramskk(i,j,k).c * paramskk(i,j,k).c;
const F_FLOAT ters_d = paramskk(i,j,k).d * paramskk(i,j,k).d;
@@ -856,11 +856,11 @@ 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)
- * ters_fc_k(i,j,k,r);
+ * ters_fc_k(i,j,k,r);
}
/* ---------------------------------------------------------------------- */
@@ -868,7 +868,7 @@ 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) *
@@ -880,7 +880,7 @@ 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);
@@ -897,7 +897,7 @@ 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/sqrt(tmp*tmp);//*pow(tmp,-1.5);
@@ -918,10 +918,10 @@ double PairTersoffKokkos<DeviceType>::ters_dbij(const int &i, const int &j,
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void PairTersoffKokkos<DeviceType>::ters_dthb(
- const int &i, const int &j, const int &k, const F_FLOAT &prefactor,
- 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,
- F_FLOAT *fi, F_FLOAT *fj, F_FLOAT *fk) const
+ const int &i, const int &j, const int &k, const F_FLOAT &prefactor,
+ 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,
+ F_FLOAT *fi, F_FLOAT *fj, F_FLOAT *fk) const
{
// from PairTersoff::attractive
F_FLOAT rij_hat[3],rik_hat[3];
@@ -991,10 +991,10 @@ void PairTersoffKokkos<DeviceType>::ters_dthb(
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void PairTersoffKokkos<DeviceType>::ters_dthbj(
- const int &i, const int &j, const int &k, const F_FLOAT &prefactor,
- 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,
- F_FLOAT *fj, F_FLOAT *fk) const
+ const int &i, const int &j, const int &k, const F_FLOAT &prefactor,
+ 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,
+ F_FLOAT *fj, F_FLOAT *fk) const
{
F_FLOAT rij_hat[3],rik_hat[3];
F_FLOAT rijinv,rikinv;
@@ -1053,10 +1053,10 @@ void PairTersoffKokkos<DeviceType>::ters_dthbj(
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void PairTersoffKokkos<DeviceType>::ters_dthbk(
- const int &i, const int &j, const int &k, const F_FLOAT &prefactor,
- 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,
- F_FLOAT *fk) const
+ const int &i, const int &j, const int &k, const F_FLOAT &prefactor,
+ 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,
+ F_FLOAT *fk) const
{
F_FLOAT rij_hat[3],rik_hat[3];
F_FLOAT rijinv,rikinv;
@@ -1179,7 +1179,7 @@ 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,
- F_FLOAT *fj, F_FLOAT *fk, F_FLOAT *drij, F_FLOAT *drik) const
+ F_FLOAT *fj, F_FLOAT *fk, F_FLOAT *drij, F_FLOAT *drik) const
{
// The eatom and vatom arrays are atomic for Half/Thread neighbor style
diff --git a/src/KOKKOS/pair_tersoff_kokkos.h b/src/KOKKOS/pair_tersoff_kokkos.h
index 86427bbc66..f40d28b72b 100644
--- a/src/KOKKOS/pair_tersoff_kokkos.h
+++ b/src/KOKKOS/pair_tersoff_kokkos.h
@@ -102,8 +102,8 @@ class PairTersoffKokkos : public PairTersoff {
KOKKOS_INLINE_FUNCTION
double 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 &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;
KOKKOS_INLINE_FUNCTION
double ters_gijk(const int &i, const int &j, const int &k, const F_FLOAT &cos) const;
@@ -113,21 +113,21 @@ class PairTersoffKokkos : public PairTersoff {
KOKKOS_INLINE_FUNCTION
void ters_dthb(const int &i, const int &j, const int &k, const F_FLOAT &prefactor,
- 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,
- F_FLOAT *fi, F_FLOAT *fj, F_FLOAT *fk) const;
+ 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,
+ F_FLOAT *fi, F_FLOAT *fj, F_FLOAT *fk) const;
KOKKOS_INLINE_FUNCTION
void ters_dthbj(const int &i, const int &j, const int &k, const F_FLOAT &prefactor,
- 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,
- F_FLOAT *fj, F_FLOAT *fk) const;
+ 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,
+ F_FLOAT *fj, F_FLOAT *fk) const;
KOKKOS_INLINE_FUNCTION
void ters_dthbk(const int &i, const int &j, const int &k, const F_FLOAT &prefactor,
- 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,
- F_FLOAT *fk) const;
+ 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,
+ F_FLOAT *fk) const;
KOKKOS_INLINE_FUNCTION
double vec3_dot(const F_FLOAT x[3], const double y[3]) const {
@@ -155,12 +155,12 @@ class PairTersoffKokkos : public PairTersoff {
struct params_ters{
KOKKOS_INLINE_FUNCTION
params_ters(){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;};
+ bigr=0;bigd=0;lam1=0;biga=0;cutsq=0;c1=0;c2=0;c3=0;c4=0;};
KOKKOS_INLINE_FUNCTION
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;};
+ 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,
- bigd, lam1, biga, cutsq, c1, c2, c3, c4;
+ bigd, lam1, biga, cutsq, c1, c2, c3, c4;
};
template<int NEIGHFLAG>
@@ -172,11 +172,11 @@ 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,
- F_FLOAT *fj, F_FLOAT *fk, F_FLOAT *drij, F_FLOAT *drik) const;
+ 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,
- F_FLOAT *fj, F_FLOAT *fk, F_FLOAT *drji, F_FLOAT *drjk) const;
+ F_FLOAT *fj, F_FLOAT *fk, F_FLOAT *drji, F_FLOAT *drjk) const;
void allocate();
void setup_params();
diff --git a/src/KOKKOS/pair_tersoff_mod_kokkos.cpp b/src/KOKKOS/pair_tersoff_mod_kokkos.cpp
index 8e718fbf6f..21c7fbb727 100644
--- a/src/KOKKOS/pair_tersoff_mod_kokkos.cpp
+++ b/src/KOKKOS/pair_tersoff_mod_kokkos.cpp
@@ -75,7 +75,7 @@ void PairTersoffMODKokkos<DeviceType>::allocate()
int n = atom->ntypes;
k_params = Kokkos::DualView<params_ters***,Kokkos::LayoutRight,DeviceType>
- ("PairTersoffMOD::paramskk",n+1,n+1,n+1);
+ ("PairTersoffMOD::paramskk",n+1,n+1,n+1);
paramskk = k_params.template view<DeviceType>();
}
@@ -355,7 +355,7 @@ void PairTersoffMODKokkos<DeviceType>::operator()(TagPairTersoffMODComputeHalf<N
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 *
- (tmp_fcd - tmp_fce*paramskk(itype,jtype,jtype).lam1) / r;
+ (tmp_fcd - tmp_fce*paramskk(itype,jtype,jtype).lam1) / r;
const F_FLOAT eng = tmp_fce * paramskk(itype,jtype,jtype).biga * tmp_exp;
f_x += delx*frep;
@@ -524,7 +524,7 @@ void PairTersoffMODKokkos<DeviceType>::operator()(TagPairTersoffMODComputeFullA<
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 *
- (tmp_fcd - tmp_fce*paramskk(itype,jtype,jtype).lam1) / r;
+ (tmp_fcd - tmp_fce*paramskk(itype,jtype,jtype).lam1) / r;
const F_FLOAT eng = tmp_fce * paramskk(itype,jtype,jtype).biga * tmp_exp;
f_x += delx*frep;
@@ -535,7 +535,7 @@ void PairTersoffMODKokkos<DeviceType>::operator()(TagPairTersoffMODComputeFullA<
if (eflag)
ev.evdwl += 0.5*eng;
if (vflag_either || eflag_atom)
- this->template ev_tally<NEIGHFLAG>(ev,i,j,eng,frep,delx,dely,delz);
+ this->template ev_tally<NEIGHFLAG>(ev,i,j,eng,frep,delx,dely,delz);
}
}
@@ -589,7 +589,7 @@ void PairTersoffMODKokkos<DeviceType>::operator()(TagPairTersoffMODComputeFullA<
if (EVFLAG) {
if (eflag) ev.evdwl += 0.5*eng;
if (vflag_either || eflag_atom)
- this->template ev_tally<NEIGHFLAG>(ev,i,j,eng,fatt,delx1,dely1,delz1);
+ this->template ev_tally<NEIGHFLAG>(ev,i,j,eng,fatt,delx1,dely1,delz1);
}
// attractive: three-body force
@@ -609,17 +609,17 @@ void PairTersoffMODKokkos<DeviceType>::operator()(TagPairTersoffMODComputeFullA<
if (rsq2 > cutsq2) continue;
rik = sqrt(rsq2);
ters_dthb(itype,jtype,ktype,prefactor,rij,delx1,dely1,delz1,
- rik,delx2,dely2,delz2,fi,fj,fk);
+ rik,delx2,dely2,delz2,fi,fj,fk);
f_x += fi[0];
f_y += fi[1];
f_z += fi[2];
if (vflag_atom) {
- F_FLOAT delrij[3], delrik[3];
- delrij[0] = -delx1; delrij[1] = -dely1; delrij[2] = -delz1;
- delrik[0] = -delx2; delrik[1] = -dely2; delrik[2] = -delz2;
- if (vflag_either) this->template v_tally3<NEIGHFLAG>(ev,i,j,k,fj,fk,delrij,delrik);
+ F_FLOAT delrij[3], delrik[3];
+ delrij[0] = -delx1; delrij[1] = -dely1; delrij[2] = -delz1;
+ delrik[0] = -delx2; delrik[1] = -dely2; delrik[2] = -delz2;
+ if (vflag_either) this->template v_tally3<NEIGHFLAG>(ev,i,j,k,fj,fk,delrij,delrik);
}
}
}
@@ -715,7 +715,7 @@ void PairTersoffMODKokkos<DeviceType>::operator()(TagPairTersoffMODComputeFullB<
if (eflag)
ev.evdwl += 0.5 * eng;
if (vflag_either || eflag_atom)
- this->template ev_tally<NEIGHFLAG>(ev,i,j,eng,fatt,delx1,dely1,delz1);
+ this->template ev_tally<NEIGHFLAG>(ev,i,j,eng,fatt,delx1,dely1,delz1);
}
// attractive: three-body force
@@ -735,22 +735,22 @@ void PairTersoffMODKokkos<DeviceType>::operator()(TagPairTersoffMODComputeFullB<
if (rsq2 > cutsq2) continue;
rik = sqrt(rsq2);
ters_dthbj(jtype,itype,ktype,prefactor,rij,delx1,dely1,delz1,
- rik,delx2,dely2,delz2,fj,fk);
+ rik,delx2,dely2,delz2,fj,fk);
f_x += fj[0];
f_y += fj[1];
f_z += fj[2];
if (vflag_atom) {
- F_FLOAT delrji[3], delrjk[3];
- delrji[0] = -delx1; delrji[1] = -dely1; delrji[2] = -delz1;
- delrjk[0] = -delx2; delrjk[1] = -dely2; delrjk[2] = -delz2;
- if (vflag_either) v_tally3_atom(ev,i,j,k,fj,fk,delrji,delrjk);
+ F_FLOAT delrji[3], delrjk[3];
+ delrji[0] = -delx1; delrji[1] = -dely1; delrji[2] = -delz1;
+ delrjk[0] = -delx2; delrjk[1] = -dely2; delrjk[2] = -delz2;
+ if (vflag_either) v_tally3_atom(ev,i,j,k,fj,fk,delrji,delrjk);
}
const F_FLOAT fa_jk = ters_fa_k(jtype,ktype,itype,rik);
const F_FLOAT prefactor_jk = 0.5*fa_jk * ters_dbij(jtype,ktype,itype,bo_ij);
ters_dthbk(jtype,ktype,itype,prefactor_jk,rik,delx2,dely2,delz2,
- rij,delx1,dely1,delz1,fk);
+ rij,delx1,dely1,delz1,fk);
f_x += fk[0];
f_y += fk[1];
f_z += fk[2];
@@ -774,7 +774,7 @@ 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;
@@ -790,7 +790,7 @@ 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;
@@ -806,8 +806,8 @@ double PairTersoffMODKokkos<DeviceType>::ters_dfc(const int &i, const int &j,
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 &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
{
F_FLOAT arg, ex_delr;
@@ -828,7 +828,7 @@ double PairTersoffMODKokkos<DeviceType>::bondorder(const int &i, const int &j, c
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
double PairTersoffMODKokkos<DeviceType>::
- ters_gijk(const int &i, const int &j, const int &k, const F_FLOAT &cos) const
+ ters_gijk(const int &i, const int &j, const int &k, const F_FLOAT &cos) const
{
const F_FLOAT ters_c1 = paramskk(i,j,k).c1;
const F_FLOAT ters_c2 = paramskk(i,j,k).c2;
@@ -847,7 +847,7 @@ double PairTersoffMODKokkos<DeviceType>::
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
double PairTersoffMODKokkos<DeviceType>::
- ters_dgijk(const int &i, const int &j, const int &k, const F_FLOAT &cos) const
+ ters_dgijk(const int &i, const int &j, const int &k, const F_FLOAT &cos) const
{
const F_FLOAT ters_c2 = paramskk(i,j,k).c2;
const F_FLOAT ters_c3 = paramskk(i,j,k).c3;
@@ -866,11 +866,11 @@ 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)
- * ters_fc_k(i,j,k,r);
+ * ters_fc_k(i,j,k,r);
}
/* ---------------------------------------------------------------------- */
@@ -878,7 +878,7 @@ 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) *
@@ -890,7 +890,7 @@ 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)
@@ -905,18 +905,18 @@ 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)
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;
+ pow(tmp,-0.5*(paramskk(i,j,k).powern/paramskk(i,j,k).powern_del)) / bo;
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)*
- pow(1.0+tmp_n, -1.0-(1.0/(2.0*paramskk(i,j,k).powern_del)))*tmp_n / bo;
+ pow(1.0+tmp_n, -1.0-(1.0/(2.0*paramskk(i,j,k).powern_del)))*tmp_n / bo;
}
/* ---------------------------------------------------------------------- */
@@ -924,10 +924,10 @@ double PairTersoffMODKokkos<DeviceType>::ters_dbij(const int &i, const int &j,
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void PairTersoffMODKokkos<DeviceType>::ters_dthb(
- const int &i, const int &j, const int &k, const F_FLOAT &prefactor,
- 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,
- F_FLOAT *fi, F_FLOAT *fj, F_FLOAT *fk) const
+ const int &i, const int &j, const int &k, const F_FLOAT &prefactor,
+ 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,
+ F_FLOAT *fi, F_FLOAT *fj, F_FLOAT *fk) const
{
// from PairTersoffMOD::attractive
F_FLOAT rij_hat[3],rik_hat[3];
@@ -996,10 +996,10 @@ void PairTersoffMODKokkos<DeviceType>::ters_dthb(
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void PairTersoffMODKokkos<DeviceType>::ters_dthbj(
- const int &i, const int &j, const int &k, const F_FLOAT &prefactor,
- 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,
- F_FLOAT *fj, F_FLOAT *fk) const
+ const int &i, const int &j, const int &k, const F_FLOAT &prefactor,
+ 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,
+ F_FLOAT *fj, F_FLOAT *fk) const
{
F_FLOAT rij_hat[3],rik_hat[3];
F_FLOAT rijinv,rikinv;
@@ -1057,10 +1057,10 @@ void PairTersoffMODKokkos<DeviceType>::ters_dthbj(
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void PairTersoffMODKokkos<DeviceType>::ters_dthbk(
- const int &i, const int &j, const int &k, const F_FLOAT &prefactor,
- 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,
- F_FLOAT *fk) const
+ const int &i, const int &j, const int &k, const F_FLOAT &prefactor,
+ 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,
+ F_FLOAT *fk) const
{
F_FLOAT rij_hat[3],rik_hat[3];
F_FLOAT rijinv,rikinv;
@@ -1182,7 +1182,7 @@ 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,
- F_FLOAT *fj, F_FLOAT *fk, F_FLOAT *drij, F_FLOAT *drik) const
+ F_FLOAT *fj, F_FLOAT *fk, F_FLOAT *drij, F_FLOAT *drik) const
{
// The eatom and vatom arrays are atomic for Half/Thread neighbor style
diff --git a/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp b/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp
index 11a5ff1007..8a34dc34ab 100644
--- a/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp
+++ b/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp
@@ -86,7 +86,7 @@ void PairTersoffZBLKokkos<DeviceType>::allocate()
int n = atom->ntypes;
k_params = Kokkos::DualView<params_ters***,Kokkos::LayoutRight,DeviceType>
- ("PairTersoffZBL::paramskk",n+1,n+1,n+1);
+ ("PairTersoffZBL::paramskk",n+1,n+1,n+1);
paramskk = k_params.template view<DeviceType>();
}
@@ -371,19 +371,19 @@ void PairTersoffZBLKokkos<DeviceType>::operator()(TagPairTersoffZBLComputeHalf<N
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 *
- (tmp_fcd - tmp_fce*paramskk(itype,jtype,jtype).lam1);
+ (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) /
- (pow(paramskk(itype,jtype,jtype).Z_i,0.23) + pow(paramskk(itype,jtype,jtype).Z_j,0.23));
+ (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);
+ (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) +
- 0.2802*exp(-0.4029*r_ov_a) + 0.02817*exp(-0.2016*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) -
0.4029*0.2802*exp(-0.4029*r_ov_a) -
@@ -400,7 +400,7 @@ void PairTersoffZBLKokkos<DeviceType>::operator()(TagPairTersoffZBLComputeHalf<N
if (eflag)
eng = (1.0 - fermi_k(itype,jtype,jtype,r)) * eng_z +
- fermi_k(itype,jtype,jtype,r) * eng_t;
+ fermi_k(itype,jtype,jtype,r) * eng_t;
f_x += delx*frep;
f_y += dely*frep;
@@ -570,19 +570,19 @@ void PairTersoffZBLKokkos<DeviceType>::operator()(TagPairTersoffZBLComputeFullA<
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 *
- (tmp_fcd - tmp_fce*paramskk(itype,jtype,jtype).lam1);
+ (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) /
- (pow(paramskk(itype,jtype,jtype).Z_i,0.23) + pow(paramskk(itype,jtype,jtype).Z_j,0.23));
+ (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);
+ (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) +
- 0.2802*exp(-0.4029*r_ov_a) + 0.02817*exp(-0.2016*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) -
0.4029*0.2802*exp(-0.4029*r_ov_a) -
@@ -599,7 +599,7 @@ void PairTersoffZBLKokkos<DeviceType>::operator()(TagPairTersoffZBLComputeFullA<
if (eflag)
eng = (1.0 - fermi_k(itype,jtype,jtype,r)) * eng_z +
- fermi_k(itype,jtype,jtype,r) * eng_t;
+ fermi_k(itype,jtype,jtype,r) * eng_t;
f_x += delx*frep;
f_y += dely*frep;
@@ -609,7 +609,7 @@ void PairTersoffZBLKokkos<DeviceType>::operator()(TagPairTersoffZBLComputeFullA<
if (eflag)
ev.evdwl += 0.5*eng;
if (vflag_either || eflag_atom)
- this->template ev_tally<NEIGHFLAG>(ev,i,j,eng,frep,delx,dely,delz);
+ this->template ev_tally<NEIGHFLAG>(ev,i,j,eng,frep,delx,dely,delz);
}
}
@@ -663,7 +663,7 @@ void PairTersoffZBLKokkos<DeviceType>::operator()(TagPairTersoffZBLComputeFullA<
if (EVFLAG) {
if (eflag) ev.evdwl += 0.5*eng;
if (vflag_either || eflag_atom)
- this->template ev_tally<NEIGHFLAG>(ev,i,j,eng,fatt,delx1,dely1,delz1);
+ this->template ev_tally<NEIGHFLAG>(ev,i,j,eng,fatt,delx1,dely1,delz1);
}
// attractive: three-body force
@@ -683,17 +683,17 @@ void PairTersoffZBLKokkos<DeviceType>::operator()(TagPairTersoffZBLComputeFullA<
if (rsq2 > cutsq2) continue;
rik = sqrt(rsq2);
ters_dthb(itype,jtype,ktype,prefactor,rij,delx1,dely1,delz1,
- rik,delx2,dely2,delz2,fi,fj,fk);
+ rik,delx2,dely2,delz2,fi,fj,fk);
f_x += fi[0];
f_y += fi[1];
f_z += fi[2];
if (vflag_atom) {
- F_FLOAT delrij[3], delrik[3];
- delrij[0] = -delx1; delrij[1] = -dely1; delrij[2] = -delz1;
- delrik[0] = -delx2; delrik[1] = -dely2; delrik[2] = -delz2;
- if (vflag_either) this->template v_tally3<NEIGHFLAG>(ev,i,j,k,fj,fk,delrij,delrik);
+ F_FLOAT delrij[3], delrik[3];
+ delrij[0] = -delx1; delrij[1] = -dely1; delrij[2] = -delz1;
+ delrik[0] = -delx2; delrik[1] = -dely2; delrik[2] = -delz2;
+ if (vflag_either) this->template v_tally3<NEIGHFLAG>(ev,i,j,k,fj,fk,delrij,delrik);
}
}
}
@@ -789,7 +789,7 @@ void PairTersoffZBLKokkos<DeviceType>::operator()(TagPairTersoffZBLComputeFullB<
if (eflag)
ev.evdwl += 0.5 * eng;
if (vflag_either || eflag_atom)
- this->template ev_tally<NEIGHFLAG>(ev,i,j,eng,fatt,delx1,dely1,delz1);
+ this->template ev_tally<NEIGHFLAG>(ev,i,j,eng,fatt,delx1,dely1,delz1);
}
// attractive: three-body force
@@ -809,22 +809,22 @@ void PairTersoffZBLKokkos<DeviceType>::operator()(TagPairTersoffZBLComputeFullB<
if (rsq2 > cutsq2) continue;
rik = sqrt(rsq2);
ters_dthbj(jtype,itype,ktype,prefactor,rij,delx1,dely1,delz1,
- rik,delx2,dely2,delz2,fj,fk);
+ rik,delx2,dely2,delz2,fj,fk);
f_x += fj[0];
f_y += fj[1];
f_z += fj[2];
if (vflag_atom) {
- F_FLOAT delrji[3], delrjk[3];
- delrji[0] = -delx1; delrji[1] = -dely1; delrji[2] = -delz1;
- delrjk[0] = -delx2; delrjk[1] = -dely2; delrjk[2] = -delz2;
- if (vflag_either) v_tally3_atom(ev,i,j,k,fj,fk,delrji,delrjk);
+ F_FLOAT delrji[3], delrjk[3];
+ delrji[0] = -delx1; delrji[1] = -dely1; delrji[2] = -delz1;
+ delrjk[0] = -delx2; delrjk[1] = -dely2; delrjk[2] = -delz2;
+ if (vflag_either) v_tally3_atom(ev,i,j,k,fj,fk,delrji,delrjk);
}
const F_FLOAT fa_jk = ters_fa_k(jtype,ktype,itype,rik);
const F_FLOAT prefactor_jk = 0.5*fa_jk * ters_dbij(jtype,ktype,itype,bo_ij);
ters_dthbk(jtype,ktype,itype,prefactor_jk,rik,delx2,dely2,delz2,
- rij,delx1,dely1,delz1,fk);
+ rij,delx1,dely1,delz1,fk);
f_x += fk[0];
f_y += fk[1];
f_z += fk[2];
@@ -848,7 +848,7 @@ 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;
@@ -863,7 +863,7 @@ 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;
@@ -878,8 +878,8 @@ double PairTersoffZBLKokkos<DeviceType>::ters_dfc(const int &i, const int &j,
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 &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
{
F_FLOAT arg, ex_delr;
@@ -900,7 +900,7 @@ double PairTersoffZBLKokkos<DeviceType>::bondorder(const int &i, const int &j, c
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
double PairTersoffZBLKokkos<DeviceType>::
- ters_gijk(const int &i, const int &j, const int &k, const F_FLOAT &cos) const
+ ters_gijk(const int &i, const int &j, const int &k, const F_FLOAT &cos) const
{
const F_FLOAT ters_c = paramskk(i,j,k).c * paramskk(i,j,k).c;
const F_FLOAT ters_d = paramskk(i,j,k).d * paramskk(i,j,k).d;
@@ -914,7 +914,7 @@ double PairTersoffZBLKokkos<DeviceType>::
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
double PairTersoffZBLKokkos<DeviceType>::
- ters_dgijk(const int &i, const int &j, const int &k, const F_FLOAT &cos) const
+ ters_dgijk(const int &i, const int &j, const int &k, const F_FLOAT &cos) const
{
const F_FLOAT ters_c = paramskk(i,j,k).c * paramskk(i,j,k).c;
@@ -930,11 +930,11 @@ 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)
- * ters_fc_k(i,j,k,r) * fermi_k(i,j,k,r);
+ * ters_fc_k(i,j,k,r) * fermi_k(i,j,k,r);
}
/* ---------------------------------------------------------------------- */
@@ -942,7 +942,7 @@ 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) *
@@ -956,7 +956,7 @@ 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);
@@ -973,7 +973,7 @@ 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);
@@ -994,10 +994,10 @@ double PairTersoffZBLKokkos<DeviceType>::ters_dbij(const int &i, const int &j,
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void PairTersoffZBLKokkos<DeviceType>::ters_dthb(
- const int &i, const int &j, const int &k, const F_FLOAT &prefactor,
- 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,
- F_FLOAT *fi, F_FLOAT *fj, F_FLOAT *fk) const
+ const int &i, const int &j, const int &k, const F_FLOAT &prefactor,
+ 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,
+ F_FLOAT *fi, F_FLOAT *fj, F_FLOAT *fk) const
{
// from PairTersoffZBL::attractive
F_FLOAT rij_hat[3],rik_hat[3];
@@ -1066,10 +1066,10 @@ void PairTersoffZBLKokkos<DeviceType>::ters_dthb(
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void PairTersoffZBLKokkos<DeviceType>::ters_dthbj(
- const int &i, const int &j, const int &k, const F_FLOAT &prefactor,
- 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,
- F_FLOAT *fj, F_FLOAT *fk) const
+ const int &i, const int &j, const int &k, const F_FLOAT &prefactor,
+ 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,
+ F_FLOAT *fj, F_FLOAT *fk) const
{
F_FLOAT rij_hat[3],rik_hat[3];
F_FLOAT rijinv,rikinv;
@@ -1127,10 +1127,10 @@ void PairTersoffZBLKokkos<DeviceType>::ters_dthbj(
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void PairTersoffZBLKokkos<DeviceType>::ters_dthbk(
- const int &i, const int &j, const int &k, const F_FLOAT &prefactor,
- 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,
- F_FLOAT *fk) const
+ const int &i, const int &j, const int &k, const F_FLOAT &prefactor,
+ 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,
+ F_FLOAT *fk) const
{
F_FLOAT rij_hat[3],rik_hat[3];
F_FLOAT rijinv,rikinv;
@@ -1184,10 +1184,10 @@ 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)));
+ (r - paramskk(i,j,k).ZBLcut)));
}
/* ---------------------------------------------------------------------- */
@@ -1195,12 +1195,12 @@ 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 *
- (r - paramskk(i,j,k).ZBLcut)) /
+ (r - paramskk(i,j,k).ZBLcut)) /
pow(1.0 + exp(-paramskk(i,j,k).ZBLexpscale *
- (r - paramskk(i,j,k).ZBLcut)),2.0);
+ (r - paramskk(i,j,k).ZBLcut)),2.0);
}
/* ---------------------------------------------------------------------- */
@@ -1276,7 +1276,7 @@ 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,
- F_FLOAT *fj, F_FLOAT *fk, F_FLOAT *drij, F_FLOAT *drik) const
+ F_FLOAT *fj, F_FLOAT *fk, F_FLOAT *drij, F_FLOAT *drik) const
{
// The eatom and vatom arrays are atomic for Half/Thread neighbor style
diff --git a/src/KOKKOS/sna_kokkos_impl.h b/src/KOKKOS/sna_kokkos_impl.h
index 8454140671..ccc4010f68 100644
--- a/src/KOKKOS/sna_kokkos_impl.h
+++ b/src/KOKKOS/sna_kokkos_impl.h
@@ -249,27 +249,27 @@ void SNAKokkos<DeviceType>::compute_zi(const typename Kokkos::TeamPolicy<DeviceT
const int bound = (j+2)/2;
Kokkos::parallel_for(Kokkos::ThreadVectorRange(team,(j+1)*bound),
[&] (const int mbma ) {
- //for(int mb = 0; 2*mb <= j; mb++)
- //for(int ma = 0; ma <= j; ma++) {
+ //for(int mb = 0; 2*mb <= j; mb++)
+ //for(int ma = 0; ma <= j; ma++) {
const int ma = mbma%(j+1);
const int mb = mbma/(j+1);
- //zarray_r(j1,j2,j,ma,mb) = 0.0;
- //zarray_i(j1,j2,j,ma,mb) = 0.0;
+ //zarray_r(j1,j2,j,ma,mb) = 0.0;
+ //zarray_i(j1,j2,j,ma,mb) = 0.0;
double z_r = 0.0;
double z_i = 0.0;
- for(int ma1 = MAX(0, (2 * ma - j - j2 + j1) / 2);
- ma1 <= MIN(j1, (2 * ma - j + j2 + j1) / 2); ma1++) {
- double sumb1_r = 0.0;
- double sumb1_i = 0.0;
+ for(int ma1 = MAX(0, (2 * ma - j - j2 + j1) / 2);
+ ma1 <= MIN(j1, (2 * ma - j + j2 + j1) / 2); ma1++) {
+ double sumb1_r = 0.0;
+ double sumb1_i = 0.0;
- const int ma2 = (2 * ma - j - (2 * ma1 - j1) + j2) / 2;
+ const int ma2 = (2 * ma - j - (2 * ma1 - j1) + j2) / 2;
- for(int mb1 = MAX( 0, (2 * mb - j - j2 + j1) / 2);
+ for(int mb1 = MAX( 0, (2 * mb - j - j2 + j1) / 2);
mb1 <= MIN(j1, (2 * mb - j + j2 + j1) / 2); mb1++) {
- const int mb2 = (2 * mb - j - (2 * mb1 - j1) + j2) / 2;
+ const int mb2 = (2 * mb - j - (2 * mb1 - j1) + j2) / 2;
const double cga = cgarray(j1,j2,j,mb1,mb2);
const double uat1_r = uarraytot_r(j1,ma1,mb1);
const double uat1_i = uarraytot_i(j1,ma1,mb1);
@@ -277,21 +277,21 @@ void SNAKokkos<DeviceType>::compute_zi(const typename Kokkos::TeamPolicy<DeviceT
const double uat2_i = uarraytot_i(j2,ma2,mb2);
sumb1_r += cga * (uat1_r * uat2_r - uat1_i * uat2_i);
sumb1_i += cga * (uat1_r * uat2_i + uat1_i * uat2_r);
- /*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) *
- (uarraytot_r(j1,ma1,mb1) * uarraytot_i(j2,ma2,mb2) +
- uarraytot_i(j1,ma1,mb1) * uarraytot_r(j2,ma2,mb2));*/
- } // end loop over mb1
+ /*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) *
+ (uarraytot_r(j1,ma1,mb1) * uarraytot_i(j2,ma2,mb2) +
+ uarraytot_i(j1,ma1,mb1) * uarraytot_r(j2,ma2,mb2));*/
+ } // end loop over mb1
const double cga = cgarray(j1,j2,j,ma1,ma2);
- z_r += sumb1_r * cga;//rray(j1,j2,j,ma1,ma2);
- z_i += sumb1_i * cga;//rray(j1,j2,j,ma1,ma2);
- } // end loop over ma1
+ z_r += sumb1_r * cga;//rray(j1,j2,j,ma1,ma2);
+ z_i += sumb1_i * cga;//rray(j1,j2,j,ma1,ma2);
+ } // end loop over ma1
zarray_r(j1,j2,j,mb,ma) = z_r;
- zarray_i(j1,j2,j,mb,ma) = z_i;
- }); // end loop over ma, mb
+ zarray_i(j1,j2,j,mb,ma) = z_i;
+ }); // end loop over ma, mb
// }
//}
});
@@ -675,7 +675,7 @@ void SNAKokkos<DeviceType>::copy_dbi2dbvec(const typename Kokkos::TeamPolicy<Dev
for(j2 = 0; j2 <= j1; j2++)
for(j = abs(j1 - j2);
j <= MIN(twojmax, j1 + j2); j += 2)
- if (j >= j1) {*/
+ if (j >= j1) {*/
Kokkos::parallel_for(Kokkos::ThreadVectorRange(team,idxj_max),
[&] (const int& JJ) {
//for(int JJ = 0; JJ < idxj_max; JJ++) {
@@ -796,25 +796,25 @@ void SNAKokkos<DeviceType>::compute_uarray(const typename Kokkos::TeamPolicy<Dev
uarray_i(j,0,mb) = 0.0;
for (int ma = 0; ma < j; ma++) {
- rootpq = rootpqarray(j - ma,j - mb);
+ rootpq = rootpqarray(j - ma,j - mb);
uarray_r(j,ma,mb) +=
rootpq *
(a_r * uarray_r(j - 1,ma,mb) +
- a_i * uarray_i(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_i * uarray_r(j - 1,ma,mb));
+ a_i * uarray_r(j - 1,ma,mb));
- rootpq = rootpqarray(ma + 1,j - mb);
+ rootpq = rootpqarray(ma + 1,j - mb);
uarray_r(j,ma + 1,mb) =
-rootpq *
(b_r * uarray_r(j - 1,ma,mb) +
- b_i * uarray_i(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_i * uarray_r(j - 1,ma,mb));
+ b_i * uarray_r(j - 1,ma,mb));
}
});
@@ -828,16 +828,16 @@ void SNAKokkos<DeviceType>::compute_uarray(const typename Kokkos::TeamPolicy<Dev
int mbpar = (mb)%2==0?1:-1;
int mapar = -mbpar;
for (int ma = 0; ma <= j; ma++) {
- mapar = -mapar;
- if (mapar == 1) {
- uarray_r(j,j-ma,j-mb) = uarray_r(j,ma,mb);
- uarray_i(j,j-ma,j-mb) = -uarray_i(j,ma,mb);
- } 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);
- }
- //OK
- //printf("%lf %lf %lf %lf %lf %lf %lf SNAP-COMPARE: UARRAY\n",x,y,z,z0,r,uarray_r(j,ma,mb),uarray_i(j,ma,mb));
+ mapar = -mapar;
+ if (mapar == 1) {
+ uarray_r(j,j-ma,j-mb) = uarray_r(j,ma,mb);
+ uarray_i(j,j-ma,j-mb) = -uarray_i(j,ma,mb);
+ } 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);
+ }
+ //OK
+ //printf("%lf %lf %lf %lf %lf %lf %lf SNAP-COMPARE: UARRAY\n",x,y,z,z0,r,uarray_r(j,ma,mb),uarray_i(j,ma,mb));
}
});
}
@@ -854,7 +854,7 @@ KOKKOS_INLINE_FUNCTION
void SNAKokkos<DeviceType>::compute_duarray(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team,
double x, double y, double z,
double z0, double r, double dz0dr,
- double wj, double rcut)
+ double wj, double rcut)
{
double r0inv;
double a_r, a_i, b_r, b_i;
@@ -943,7 +943,7 @@ void SNAKokkos<DeviceType>::compute_duarray(const typename Kokkos::TeamPolicy<De
a_i * duarray_r(j - 1,mb,ma,k));
}
- rootpq = rootpqarray(ma + 1,j - mb);
+ rootpq = rootpqarray(ma + 1,j - mb);
uarray_r(j,ma + 1,mb) =
-rootpq * (b_r * uarray_r(j - 1,ma,mb) +
b_i * uarray_i(j - 1,ma,mb));
@@ -973,22 +973,22 @@ void SNAKokkos<DeviceType>::compute_duarray(const typename Kokkos::TeamPolicy<De
int mbpar = (mb)%2==0?1:-1;
int mapar = -mbpar;
for (int ma = 0; ma <= j; ma++) {
- mapar = -mapar;
- if (mapar == 1) {
- uarray_r(j,j-ma,j-mb) = uarray_r(j,ma,mb);
- uarray_i(j,j-ma,j-mb) = -uarray_i(j,ma,mb);
- for (int k = 0; k < 3; k++) {
- duarray_r(j,j-mb,j-ma,k) = duarray_r(j,mb,ma,k);
- duarray_i(j,j-mb,j-ma,k) = -duarray_i(j,mb,ma,k);
- }
- } 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);
- for (int k = 0; k < 3; k++) {
- duarray_r(j,j-mb,j-ma,k) = -duarray_r(j,mb,ma,k);
- duarray_i(j,j-mb,j-ma,k) = duarray_i(j,mb,ma,k);
- }
- }
+ mapar = -mapar;
+ if (mapar == 1) {
+ uarray_r(j,j-ma,j-mb) = uarray_r(j,ma,mb);
+ uarray_i(j,j-ma,j-mb) = -uarray_i(j,ma,mb);
+ for (int k = 0; k < 3; k++) {
+ duarray_r(j,j-mb,j-ma,k) = duarray_r(j,mb,ma,k);
+ duarray_i(j,j-mb,j-ma,k) = -duarray_i(j,mb,ma,k);
+ }
+ } 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);
+ for (int k = 0; k < 3; k++) {
+ duarray_r(j,j-mb,j-ma,k) = -duarray_r(j,mb,ma,k);
+ duarray_i(j,j-mb,j-ma,k) = duarray_i(j,mb,ma,k);
+ }
+ }
}
});
}
@@ -1149,37 +1149,37 @@ void SNAKokkos<DeviceType>::init_clebsch_gordan()
if(m < 0 || m > j) continue;
- sum = 0.0;
-
- 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));
- z++) {
- ifac = z % 2 ? -1 : 1;
- sum += ifac /
- (factorial(z) *
- factorial((j1 + j2 - j) / 2 - z) *
- factorial((j1 - aa2) / 2 - z) *
- factorial((j2 + bb2) / 2 - z) *
- factorial((j - j2 + aa2) / 2 + z) *
- factorial((j - j1 - bb2) / 2 + z));
- }
-
- cc2 = 2 * m - j;
- dcg = deltacg(j1, j2, j);
- sfaccg = sqrt(factorial((j1 + aa2) / 2) *
- factorial((j1 - aa2) / 2) *
- factorial((j2 + bb2) / 2) *
- factorial((j2 - bb2) / 2) *
- factorial((j + cc2) / 2) *
- factorial((j - cc2) / 2) *
- (j + 1));
-
- h_cgarray(j1,j2,j,m1,m2) = sum * dcg * sfaccg;
- //printf("SNAP-COMPARE: CG: %i %i %i %i %i %e\n",j1,j2,j,m1,m2,cgarray(j1,j2,j,m1,m2));
- }
- }
+ sum = 0.0;
+
+ 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));
+ z++) {
+ ifac = z % 2 ? -1 : 1;
+ sum += ifac /
+ (factorial(z) *
+ factorial((j1 + j2 - j) / 2 - z) *
+ factorial((j1 - aa2) / 2 - z) *
+ factorial((j2 + bb2) / 2 - z) *
+ factorial((j - j2 + aa2) / 2 + z) *
+ factorial((j - j1 - bb2) / 2 + z));
+ }
+
+ cc2 = 2 * m - j;
+ dcg = deltacg(j1, j2, j);
+ sfaccg = sqrt(factorial((j1 + aa2) / 2) *
+ factorial((j1 - aa2) / 2) *
+ factorial((j2 + bb2) / 2) *
+ factorial((j2 - bb2) / 2) *
+ factorial((j + cc2) / 2) *
+ factorial((j - cc2) / 2) *
+ (j + 1));
+
+ h_cgarray(j1,j2,j,m1,m2) = sum * dcg * sfaccg;
+ //printf("SNAP-COMPARE: CG: %i %i %i %i %i %e\n",j1,j2,j,m1,m2,cgarray(j1,j2,j,m1,m2));
+ }
+ }
Kokkos::deep_copy(cgarray,h_cgarray);
}
diff --git a/src/KSPACE/pair_buck_long_coul_long.cpp b/src/KSPACE/pair_buck_long_coul_long.cpp
index 7df8ebac68..7781e24a5e 100644
--- a/src/KSPACE/pair_buck_long_coul_long.cpp
+++ b/src/KSPACE/pair_buck_long_coul_long.cpp
@@ -905,7 +905,7 @@ void PairBuckLongCoulLong::compute_outer(int eflag, int vflag)
force_buck =
r*expr*buck1i[typej]-g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq-respa_buck;
if (eflag) evdwl = expr*buckai[typej]-g6*((a2+1.0)*a2+0.5)*x2;
- }
+ }
else { // correct for special
register double f = special_lj[ni], t = rn*(1.0-f);
force_buck = f*r*expr*buck1i[typej]-
diff --git a/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp b/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp
index 859f421763..1fb83db28c 100644
--- a/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp
+++ b/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp
@@ -609,7 +609,7 @@ void PairLJCharmmfswCoulLong::compute_outer(int eflag, int vflag)
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq) {
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
- if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
+ if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
} else {
table = vtable[itable] + fraction*dvtable[itable];
forcecoul = qtmp*q[j] * table;
diff --git a/src/KSPACE/pppm_disp.cpp b/src/KSPACE/pppm_disp.cpp
index 43b2c8236a..821cfd06d5 100644
--- a/src/KSPACE/pppm_disp.cpp
+++ b/src/KSPACE/pppm_disp.cpp
@@ -268,7 +268,7 @@ void PPPMDisp::init()
error->all(FLERR,"Cannot use nonperiodic boundaries with PPPMDisp");
if (slabflag == 1) {
if (domain->xperiodic != 1 || domain->yperiodic != 1 ||
- domain->boundary[2][0] != 1 || domain->boundary[2][1] != 1)
+ domain->boundary[2][0] != 1 || domain->boundary[2][1] != 1)
error->all(FLERR,"Incorrect boundaries with slab PPPMDisp");
}
@@ -306,22 +306,22 @@ void PPPMDisp::init()
int ewald_order = ptr ? *((int *) ptr) : 1<<1;
int ewald_mix = ptr ? *((int *) pair->extract("ewald_mix",tmp)) : GEOMETRIC;
memset(function, 0, EWALD_FUNCS*sizeof(int));
- for (int i=0; i<=EWALD_MAXORDER; ++i) // transcribe order
- if (ewald_order&(1<<i)) { // from pair_style
+ for (int i=0; i<=EWALD_MAXORDER; ++i) // transcribe order
+ if (ewald_order&(1<<i)) { // from pair_style
int k=0;
char str[128];
switch (i) {
- case 1:
- k = 0; break;
- case 6:
- if ((ewald_mix==GEOMETRIC || ewald_mix==SIXTHPOWER ||
+ case 1:
+ k = 0; break;
+ case 6:
+ 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; }
- default:
- sprintf(str, "Unsupported order in kspace_style "
+ else if (ewald_mix==ARITHMETIC && mixflag!=2) { k = 2; break; }
+ else if (mixflag == 2) { k = 3; break; }
+ default:
+ sprintf(str, "Unsupported order in kspace_style "
"pppm/disp, pair_style %s", force->pair_style);
- error->all(FLERR,str);
+ error->all(FLERR,str);
}
function[k] = 1;
}
@@ -377,10 +377,10 @@ 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 ||
- force->angle->setflag[typeA] == 0)
+ force->angle->setflag[typeA] == 0)
error->all(FLERR,"Bad TIP4P angle type for PPPMDisp/TIP4P");
if (typeB < 1 || typeB > atom->nbondtypes ||
- force->bond->setflag[typeB] == 0)
+ force->bond->setflag[typeB] == 0)
error->all(FLERR,"Bad TIP4P bond type for PPPMDisp/TIP4P");
double theta = force->angle->equilibrium_angle(typeA);
double blen = force->bond->equilibrium_distance(typeB);
@@ -486,7 +486,7 @@ void PPPMDisp::init()
acc/two_charge_force);
fprintf(screen," using %s precision FFTs\n",fft_prec);
fprintf(screen," 3d grid and FFT values/proc = %d %d\n",
- ngrid_max, nfft_both_max);
+ ngrid_max, nfft_both_max);
}
if (logfile) {
fprintf(logfile," Coulomb G vector (1/distance) = %g\n",g_ewald);
@@ -499,7 +499,7 @@ void PPPMDisp::init()
acc/two_charge_force);
fprintf(logfile," using %s precision FFTs\n",fft_prec);
fprintf(logfile," 3d grid and FFT values/proc = %d %d\n",
- ngrid_max, nfft_both_max);
+ ngrid_max, nfft_both_max);
}
}
}
@@ -656,7 +656,7 @@ void PPPMDisp::setup()
error->all(FLERR,"Cannot use nonperiodic boundaries with PPPMDisp");
if (slabflag == 1) {
if (domain->xperiodic != 1 || domain->yperiodic != 1 ||
- domain->boundary[2][0] != 1 || domain->boundary[2][1] != 1)
+ domain->boundary[2][0] != 1 || domain->boundary[2][1] != 1)
error->all(FLERR,"Incorrect boundaries with slab PPPMDisp");
}
@@ -723,27 +723,27 @@ void PPPMDisp::setup()
for (k = nzlo_fft; k <= nzhi_fft; k++) {
for (j = nylo_fft; j <= nyhi_fft; j++) {
for (i = nxlo_fft; i <= nxhi_fft; i++) {
- sqk = fkx[i]*fkx[i] + fky[j]*fky[j] + fkz[k]*fkz[k];
- if (sqk == 0.0) {
- vg[n][0] = 0.0;
- vg[n][1] = 0.0;
- vg[n][2] = 0.0;
- vg[n][3] = 0.0;
- vg[n][4] = 0.0;
- vg[n][5] = 0.0;
- } else {
- vterm = -2.0 * (1.0/sqk + 0.25*gew2inv);
- vg[n][0] = 1.0 + vterm*fkx[i]*fkx[i];
- vg[n][1] = 1.0 + vterm*fky[j]*fky[j];
- vg[n][2] = 1.0 + vterm*fkz[k]*fkz[k];
- vg[n][3] = vterm*fkx[i]*fky[j];
- vg[n][4] = vterm*fkx[i]*fkz[k];
- vg[n][5] = vterm*fky[j]*fkz[k];
+ sqk = fkx[i]*fkx[i] + fky[j]*fky[j] + fkz[k]*fkz[k];
+ if (sqk == 0.0) {
+ vg[n][0] = 0.0;
+ vg[n][1] = 0.0;
+ vg[n][2] = 0.0;
+ vg[n][3] = 0.0;
+ vg[n][4] = 0.0;
+ vg[n][5] = 0.0;
+ } else {
+ vterm = -2.0 * (1.0/sqk + 0.25*gew2inv);
+ vg[n][0] = 1.0 + vterm*fkx[i]*fkx[i];
+ vg[n][1] = 1.0 + vterm*fky[j]*fky[j];
+ vg[n][2] = 1.0 + vterm*fkz[k]*fkz[k];
+ vg[n][3] = vterm*fkx[i]*fky[j];
+ vg[n][4] = vterm*fkx[i]*fkz[k];
+ vg[n][5] = vterm*fky[j]*fkz[k];
vg2[n][0] = vterm*0.5*(fkx[i]*fky[j] + fkx2[i]*fky2[j]);
vg2[n][1] = vterm*0.5*(fkx[i]*fkz[k] + fkx2[i]*fkz2[k]);
vg2[n][2] = vterm*0.5*(fky[j]*fkz[k] + fky2[j]*fkz2[k]);
- }
- n++;
+ }
+ n++;
}
}
}
@@ -789,15 +789,15 @@ void PPPMDisp::setup()
for (k = nzlo_fft_6; k <= nzhi_fft_6; k++) {
for (j = nylo_fft_6; j <= nyhi_fft_6; j++) {
for (i = nxlo_fft_6; i <= nxhi_fft_6; i++) {
- sqk = fkx_6[i]*fkx_6[i] + fky_6[j]*fky_6[j] + fkz_6[k]*fkz_6[k];
- if (sqk == 0.0) {
- vg_6[n][0] = 0.0;
- vg_6[n][1] = 0.0;
- vg_6[n][2] = 0.0;
- vg_6[n][3] = 0.0;
- vg_6[n][4] = 0.0;
- vg_6[n][5] = 0.0;
- } else {
+ sqk = fkx_6[i]*fkx_6[i] + fky_6[j]*fky_6[j] + fkz_6[k]*fkz_6[k];
+ if (sqk == 0.0) {
+ vg_6[n][0] = 0.0;
+ vg_6[n][1] = 0.0;
+ vg_6[n][2] = 0.0;
+ vg_6[n][3] = 0.0;
+ vg_6[n][4] = 0.0;
+ vg_6[n][5] = 0.0;
+ } else {
b = 0.5*sqrt(sqk)*gewinv;
bs = b*b;
bt = bs*b;
@@ -807,17 +807,17 @@ void PPPMDisp::setup()
denom = nom + expt;
if (denom == 0) vterm = 3.0/sqk;
else vterm = 3.0*nom/(sqk*denom);
- vg_6[n][0] = 1.0 + vterm*fkx_6[i]*fkx_6[i];
- vg_6[n][1] = 1.0 + vterm*fky_6[j]*fky_6[j];
- vg_6[n][2] = 1.0 + vterm*fkz_6[k]*fkz_6[k];
- vg_6[n][3] = vterm*fkx_6[i]*fky_6[j];
- vg_6[n][4] = vterm*fkx_6[i]*fkz_6[k];
- vg_6[n][5] = vterm*fky_6[j]*fkz_6[k];
+ vg_6[n][0] = 1.0 + vterm*fkx_6[i]*fkx_6[i];
+ vg_6[n][1] = 1.0 + vterm*fky_6[j]*fky_6[j];
+ vg_6[n][2] = 1.0 + vterm*fkz_6[k]*fkz_6[k];
+ vg_6[n][3] = vterm*fkx_6[i]*fky_6[j];
+ vg_6[n][4] = vterm*fkx_6[i]*fkz_6[k];
+ vg_6[n][5] = vterm*fky_6[j]*fkz_6[k];
vg2_6[n][0] = vterm*0.5*(fkx_6[i]*fky_6[j] + fkx2_6[i]*fky2_6[j]);
vg2_6[n][1] = vterm*0.5*(fkx_6[i]*fkz_6[k] + fkx2_6[i]*fkz2_6[k]);
vg2_6[n][2] = vterm*0.5*(fky_6[j]*fkz_6[k] + fky2_6[j]*fkz2_6[k]);
- }
- n++;
+ }
+ n++;
}
}
}
@@ -926,7 +926,7 @@ void PPPMDisp::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;
+ eflag_atom = vflag_atom = 0;
if (evflag_atom && !peratom_allocate_flag) {
allocate_peratom();
@@ -983,7 +983,7 @@ void PPPMDisp::compute(int eflag, int vflag)
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) {
@@ -1007,7 +1007,7 @@ void PPPMDisp::compute(int eflag, int vflag)
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,
- fkx, fky, fkz,fkx2, fky2, fkz2,
+ 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);
@@ -1030,7 +1030,7 @@ void PPPMDisp::compute(int eflag, int vflag)
cg_6->reverse_comm(this, REVERSE_RHO_G);
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);
+ density_brick_g, density_fft_g, work1_6,remap_6);
if (differentiation_flag == 1) {
@@ -1054,7 +1054,7 @@ void PPPMDisp::compute(int eflag, int vflag)
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,
- fkx_6, fky_6, fkz_6,fkx2_6, fky2_6, fkz2_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);
@@ -1110,7 +1110,7 @@ void PPPMDisp::compute(int eflag, int vflag)
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,
- fkx_6, fky_6, fkz_6,fkx2_6, fky2_6, fkz2_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);
poisson_2s_ik(density_fft_a0, density_fft_a6,
@@ -1274,7 +1274,7 @@ void PPPMDisp::compute(int eflag, int vflag)
initialize coefficients needed for the dispersion density on the grids
------------------------------------------------------------------------- */
-void PPPMDisp::init_coeffs() // local pair coeffs
+void PPPMDisp::init_coeffs() // local pair coeffs
{
int tmp;
int n = atom->ntypes;
@@ -1402,13 +1402,13 @@ void PPPMDisp::init_coeffs() // local pair coeffs
memory->destroy(A);
memory->destroy(Q);
}
- if (function[1]) { // geometric 1/r^6
+ if (function[1]) { // geometric 1/r^6
double **b = (double **) force->pair->extract("B",tmp);
B = new double[n+1];
B[0] = 0.0;
for (int i=1; i<=n; ++i) B[i] = sqrt(fabs(b[i][i]));
}
- if (function[2]) { // arithmetic 1/r^6
+ 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);
//cannot use sigma, because this has not been set yet
@@ -1685,10 +1685,10 @@ void PPPMDisp::allocate()
memory->create(vg2,nfft_both,3,"pppm/disp:vg2");
memory->create3d_offset(density_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
- nxlo_out,nxhi_out,"pppm/disp:density_brick");
+ nxlo_out,nxhi_out,"pppm/disp:density_brick");
if ( differentiation_flag == 1) {
memory->create3d_offset(u_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
- nxlo_out,nxhi_out,"pppm/disp:u_brick");
+ nxlo_out,nxhi_out,"pppm/disp:u_brick");
memory->create(sf_precoeff1,nfft_both,"pppm/disp:sf_precoeff1");
memory->create(sf_precoeff2,nfft_both,"pppm/disp:sf_precoeff2");
memory->create(sf_precoeff3,nfft_both,"pppm/disp:sf_precoeff3");
@@ -1698,30 +1698,30 @@ void PPPMDisp::allocate()
} else {
memory->create3d_offset(vdx_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
- nxlo_out,nxhi_out,"pppm/disp:vdx_brick");
+ nxlo_out,nxhi_out,"pppm/disp:vdx_brick");
memory->create3d_offset(vdy_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
- nxlo_out,nxhi_out,"pppm/disp:vdy_brick");
+ nxlo_out,nxhi_out,"pppm/disp:vdy_brick");
memory->create3d_offset(vdz_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
- nxlo_out,nxhi_out,"pppm/disp:vdz_brick");
+ nxlo_out,nxhi_out,"pppm/disp:vdz_brick");
}
memory->create(density_fft,nfft_both,"pppm/disp:density_fft");
int tmp;
fft1 = new FFT3d(lmp,world,nx_pppm,ny_pppm,nz_pppm,
- nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
- nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
- 0,0,&tmp,collective_flag);
+ nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
+ nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
+ 0,0,&tmp,collective_flag);
fft2 = new FFT3d(lmp,world,nx_pppm,ny_pppm,nz_pppm,
- nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
- nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in,
- 0,0,&tmp,collective_flag);
+ nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
+ nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in,
+ 0,0,&tmp,collective_flag);
remap = new Remap(lmp,world,
- nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in,
- nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
- 1,0,0,FFT_PRECISION,collective_flag);
+ nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in,
+ nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
+ 1,0,0,FFT_PRECISION,collective_flag);
// create ghost grid object for rho and electric field communication
@@ -1762,10 +1762,10 @@ void PPPMDisp::allocate()
memory->create(vg2_6,nfft_both_6,3,"pppm/disp:vg2_6");
memory->create3d_offset(density_brick_g,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:density_brick_g");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:density_brick_g");
if ( differentiation_flag == 1) {
memory->create3d_offset(u_brick_g,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:u_brick_g");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:u_brick_g");
memory->create(sf_precoeff1_6,nfft_both_6,"pppm/disp:sf_precoeff1_6");
memory->create(sf_precoeff2_6,nfft_both_6,"pppm/disp:sf_precoeff2_6");
@@ -1776,11 +1776,11 @@ void PPPMDisp::allocate()
} else {
memory->create3d_offset(vdx_brick_g,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:vdx_brick_g");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:vdx_brick_g");
memory->create3d_offset(vdy_brick_g,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:vdy_brick_g");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:vdy_brick_g");
memory->create3d_offset(vdz_brick_g,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:vdz_brick_g");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:vdz_brick_g");
}
memory->create(density_fft_g,nfft_both_6,"pppm/disp:density_fft_g");
@@ -1788,19 +1788,19 @@ void PPPMDisp::allocate()
int tmp;
fft1_6 = new FFT3d(lmp,world,nx_pppm_6,ny_pppm_6,nz_pppm_6,
- nxlo_fft_6,nxhi_fft_6,nylo_fft_6,nyhi_fft_6,nzlo_fft_6,nzhi_fft_6,
- nxlo_fft_6,nxhi_fft_6,nylo_fft_6,nyhi_fft_6,nzlo_fft_6,nzhi_fft_6,
- 0,0,&tmp,collective_flag);
+ nxlo_fft_6,nxhi_fft_6,nylo_fft_6,nyhi_fft_6,nzlo_fft_6,nzhi_fft_6,
+ nxlo_fft_6,nxhi_fft_6,nylo_fft_6,nyhi_fft_6,nzlo_fft_6,nzhi_fft_6,
+ 0,0,&tmp,collective_flag);
fft2_6 = new FFT3d(lmp,world,nx_pppm_6,ny_pppm_6,nz_pppm_6,
- nxlo_fft_6,nxhi_fft_6,nylo_fft_6,nyhi_fft_6,nzlo_fft_6,nzhi_fft_6,
- nxlo_in_6,nxhi_in_6,nylo_in_6,nyhi_in_6,nzlo_in_6,nzhi_in_6,
- 0,0,&tmp,collective_flag);
+ nxlo_fft_6,nxhi_fft_6,nylo_fft_6,nyhi_fft_6,nzlo_fft_6,nzhi_fft_6,
+ nxlo_in_6,nxhi_in_6,nylo_in_6,nyhi_in_6,nzlo_in_6,nzhi_in_6,
+ 0,0,&tmp,collective_flag);
remap_6 = new Remap(lmp,world,
- nxlo_in_6,nxhi_in_6,nylo_in_6,nyhi_in_6,nzlo_in_6,nzhi_in_6,
- nxlo_fft_6,nxhi_fft_6,nylo_fft_6,nyhi_fft_6,nzlo_fft_6,nzhi_fft_6,
- 1,0,0,FFT_PRECISION,collective_flag);
+ nxlo_in_6,nxhi_in_6,nylo_in_6,nyhi_in_6,nzlo_in_6,nzhi_in_6,
+ nxlo_fft_6,nxhi_fft_6,nylo_fft_6,nyhi_fft_6,nzlo_fft_6,nzhi_fft_6,
+ 1,0,0,FFT_PRECISION,collective_flag);
// create ghost grid object for rho and electric field communication
@@ -1841,19 +1841,19 @@ void PPPMDisp::allocate()
memory->create(vg2_6,nfft_both_6,3,"pppm/disp:vg2_6");
memory->create3d_offset(density_brick_a0,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:density_brick_a0");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:density_brick_a0");
memory->create3d_offset(density_brick_a1,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:density_brick_a1");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:density_brick_a1");
memory->create3d_offset(density_brick_a2,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:density_brick_a2");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:density_brick_a2");
memory->create3d_offset(density_brick_a3,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:density_brick_a3");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:density_brick_a3");
memory->create3d_offset(density_brick_a4,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:density_brick_a4");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:density_brick_a4");
memory->create3d_offset(density_brick_a5,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:density_brick_a5");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:density_brick_a5");
memory->create3d_offset(density_brick_a6,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:density_brick_a6");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:density_brick_a6");
memory->create(density_fft_a0,nfft_both_6,"pppm/disp:density_fft_a0");
memory->create(density_fft_a1,nfft_both_6,"pppm/disp:density_fft_a1");
@@ -1866,19 +1866,19 @@ void PPPMDisp::allocate()
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");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:u_brick_a0");
memory->create3d_offset(u_brick_a1,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:u_brick_a1");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:u_brick_a1");
memory->create3d_offset(u_brick_a2,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:u_brick_a2");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:u_brick_a2");
memory->create3d_offset(u_brick_a3,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:u_brick_a3");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:u_brick_a3");
memory->create3d_offset(u_brick_a4,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:u_brick_a4");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:u_brick_a4");
memory->create3d_offset(u_brick_a5,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:u_brick_a5");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:u_brick_a5");
memory->create3d_offset(u_brick_a6,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:u_brick_a6");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:u_brick_a6");
memory->create(sf_precoeff1_6,nfft_both_6,"pppm/disp:sf_precoeff1_6");
memory->create(sf_precoeff2_6,nfft_both_6,"pppm/disp:sf_precoeff2_6");
@@ -1890,53 +1890,53 @@ void PPPMDisp::allocate()
} else {
memory->create3d_offset(vdx_brick_a0,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:vdx_brick_a0");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:vdx_brick_a0");
memory->create3d_offset(vdy_brick_a0,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:vdy_brick_a0");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:vdy_brick_a0");
memory->create3d_offset(vdz_brick_a0,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:vdz_brick_a0");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:vdz_brick_a0");
memory->create3d_offset(vdx_brick_a1,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:vdx_brick_a1");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:vdx_brick_a1");
memory->create3d_offset(vdy_brick_a1,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:vdy_brick_a1");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:vdy_brick_a1");
memory->create3d_offset(vdz_brick_a1,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:vdz_brick_a1");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:vdz_brick_a1");
memory->create3d_offset(vdx_brick_a2,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:vdx_brick_a2");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:vdx_brick_a2");
memory->create3d_offset(vdy_brick_a2,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:vdy_brick_a2");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:vdy_brick_a2");
memory->create3d_offset(vdz_brick_a2,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:vdz_brick_a2");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:vdz_brick_a2");
memory->create3d_offset(vdx_brick_a3,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:vdx_brick_a3");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:vdx_brick_a3");
memory->create3d_offset(vdy_brick_a3,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:vdy_brick_a3");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:vdy_brick_a3");
memory->create3d_offset(vdz_brick_a3,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:vdz_brick_a3");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:vdz_brick_a3");
memory->create3d_offset(vdx_brick_a4,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:vdx_brick_a4");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:vdx_brick_a4");
memory->create3d_offset(vdy_brick_a4,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:vdy_brick_a4");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:vdy_brick_a4");
memory->create3d_offset(vdz_brick_a4,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:vdz_brick_a4");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:vdz_brick_a4");
memory->create3d_offset(vdx_brick_a5,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:vdx_brick_a5");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:vdx_brick_a5");
memory->create3d_offset(vdy_brick_a5,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:vdy_brick_a5");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:vdy_brick_a5");
memory->create3d_offset(vdz_brick_a5,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:vdz_brick_a5");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:vdz_brick_a5");
memory->create3d_offset(vdx_brick_a6,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:vdx_brick_a6");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:vdx_brick_a6");
memory->create3d_offset(vdy_brick_a6,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:vdy_brick_a6");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:vdy_brick_a6");
memory->create3d_offset(vdz_brick_a6,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:vdz_brick_a6");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:vdz_brick_a6");
}
@@ -1944,19 +1944,19 @@ void PPPMDisp::allocate()
int tmp;
fft1_6 = new FFT3d(lmp,world,nx_pppm_6,ny_pppm_6,nz_pppm_6,
- nxlo_fft_6,nxhi_fft_6,nylo_fft_6,nyhi_fft_6,nzlo_fft_6,nzhi_fft_6,
- nxlo_fft_6,nxhi_fft_6,nylo_fft_6,nyhi_fft_6,nzlo_fft_6,nzhi_fft_6,
- 0,0,&tmp,collective_flag);
+ nxlo_fft_6,nxhi_fft_6,nylo_fft_6,nyhi_fft_6,nzlo_fft_6,nzhi_fft_6,
+ nxlo_fft_6,nxhi_fft_6,nylo_fft_6,nyhi_fft_6,nzlo_fft_6,nzhi_fft_6,
+ 0,0,&tmp,collective_flag);
fft2_6 = new FFT3d(lmp,world,nx_pppm_6,ny_pppm_6,nz_pppm_6,
- nxlo_fft_6,nxhi_fft_6,nylo_fft_6,nyhi_fft_6,nzlo_fft_6,nzhi_fft_6,
- nxlo_in_6,nxhi_in_6,nylo_in_6,nyhi_in_6,nzlo_in_6,nzhi_in_6,
- 0,0,&tmp,collective_flag);
+ nxlo_fft_6,nxhi_fft_6,nylo_fft_6,nyhi_fft_6,nzlo_fft_6,nzhi_fft_6,
+ nxlo_in_6,nxhi_in_6,nylo_in_6,nyhi_in_6,nzlo_in_6,nzhi_in_6,
+ 0,0,&tmp,collective_flag);
remap_6 = new Remap(lmp,world,
- nxlo_in_6,nxhi_in_6,nylo_in_6,nyhi_in_6,nzlo_in_6,nzhi_in_6,
- nxlo_fft_6,nxhi_fft_6,nylo_fft_6,nyhi_fft_6,nzlo_fft_6,nzhi_fft_6,
- 1,0,0,FFT_PRECISION,collective_flag);
+ nxlo_in_6,nxhi_in_6,nylo_in_6,nyhi_in_6,nzlo_in_6,nzhi_in_6,
+ nxlo_fft_6,nxhi_fft_6,nylo_fft_6,nyhi_fft_6,nzlo_fft_6,nzhi_fft_6,
+ 1,0,0,FFT_PRECISION,collective_flag);
// create ghost grid object for rho and electric field communication
@@ -1998,10 +1998,10 @@ void PPPMDisp::allocate()
memory->create(vg2_6,nfft_both_6,3,"pppm/disp:vg2_6");
memory->create4d_offset(density_brick_none,nsplit_alloc,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:density_brick_none");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:density_brick_none");
if ( differentiation_flag == 1) {
memory->create4d_offset(u_brick_none,nsplit_alloc,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:u_brick_none");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:u_brick_none");
memory->create(sf_precoeff1_6,nfft_both_6,"pppm/disp:sf_precoeff1_6");
memory->create(sf_precoeff2_6,nfft_both_6,"pppm/disp:sf_precoeff2_6");
@@ -2012,11 +2012,11 @@ void PPPMDisp::allocate()
} else {
memory->create4d_offset(vdx_brick_none,nsplit_alloc,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:vdx_brick_none");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:vdx_brick_none");
memory->create4d_offset(vdy_brick_none,nsplit_alloc,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:vdy_brick_none");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:vdy_brick_none");
memory->create4d_offset(vdz_brick_none,nsplit_alloc,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:vdz_brick_none");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:vdz_brick_none");
}
memory->create(density_fft_none,nsplit_alloc,nfft_both_6,"pppm/disp:density_fft_none");
@@ -2024,19 +2024,19 @@ void PPPMDisp::allocate()
int tmp;
fft1_6 = new FFT3d(lmp,world,nx_pppm_6,ny_pppm_6,nz_pppm_6,
- nxlo_fft_6,nxhi_fft_6,nylo_fft_6,nyhi_fft_6,nzlo_fft_6,nzhi_fft_6,
- nxlo_fft_6,nxhi_fft_6,nylo_fft_6,nyhi_fft_6,nzlo_fft_6,nzhi_fft_6,
- 0,0,&tmp,collective_flag);
+ nxlo_fft_6,nxhi_fft_6,nylo_fft_6,nyhi_fft_6,nzlo_fft_6,nzhi_fft_6,
+ nxlo_fft_6,nxhi_fft_6,nylo_fft_6,nyhi_fft_6,nzlo_fft_6,nzhi_fft_6,
+ 0,0,&tmp,collective_flag);
fft2_6 = new FFT3d(lmp,world,nx_pppm_6,ny_pppm_6,nz_pppm_6,
- nxlo_fft_6,nxhi_fft_6,nylo_fft_6,nyhi_fft_6,nzlo_fft_6,nzhi_fft_6,
- nxlo_in_6,nxhi_in_6,nylo_in_6,nyhi_in_6,nzlo_in_6,nzhi_in_6,
- 0,0,&tmp,collective_flag);
+ nxlo_fft_6,nxhi_fft_6,nylo_fft_6,nyhi_fft_6,nzlo_fft_6,nzhi_fft_6,
+ nxlo_in_6,nxhi_in_6,nylo_in_6,nyhi_in_6,nzlo_in_6,nzhi_in_6,
+ 0,0,&tmp,collective_flag);
remap_6 = new Remap(lmp,world,
- nxlo_in_6,nxhi_in_6,nylo_in_6,nyhi_in_6,nzlo_in_6,nzhi_in_6,
- nxlo_fft_6,nxhi_fft_6,nylo_fft_6,nyhi_fft_6,nzlo_fft_6,nzhi_fft_6,
- 1,0,0,FFT_PRECISION,collective_flag);
+ nxlo_in_6,nxhi_in_6,nylo_in_6,nyhi_in_6,nzlo_in_6,nzhi_in_6,
+ nxlo_fft_6,nxhi_fft_6,nylo_fft_6,nyhi_fft_6,nzlo_fft_6,nzhi_fft_6,
+ 1,0,0,FFT_PRECISION,collective_flag);
// create ghost grid object for rho and electric field communication
@@ -2070,20 +2070,20 @@ void PPPMDisp::allocate_peratom()
if (differentiation_flag != 1)
memory->create3d_offset(u_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
- nxlo_out,nxhi_out,"pppm/disp:u_brick");
+ nxlo_out,nxhi_out,"pppm/disp:u_brick");
memory->create3d_offset(v0_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
- nxlo_out,nxhi_out,"pppm/disp:v0_brick");
+ nxlo_out,nxhi_out,"pppm/disp:v0_brick");
memory->create3d_offset(v1_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
- nxlo_out,nxhi_out,"pppm/disp:v1_brick");
+ nxlo_out,nxhi_out,"pppm/disp:v1_brick");
memory->create3d_offset(v2_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
- nxlo_out,nxhi_out,"pppm/disp:v2_brick");
+ nxlo_out,nxhi_out,"pppm/disp:v2_brick");
memory->create3d_offset(v3_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
- nxlo_out,nxhi_out,"pppm/disp:v3_brick");
+ nxlo_out,nxhi_out,"pppm/disp:v3_brick");
memory->create3d_offset(v4_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
- nxlo_out,nxhi_out,"pppm/disp:v4_brick");
+ nxlo_out,nxhi_out,"pppm/disp:v4_brick");
memory->create3d_offset(v5_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
- nxlo_out,nxhi_out,"pppm/disp:v5_brick");
+ nxlo_out,nxhi_out,"pppm/disp:v5_brick");
// create ghost grid object for rho and electric field communication
@@ -2109,20 +2109,20 @@ void PPPMDisp::allocate_peratom()
if ( differentiation_flag != 1 )
memory->create3d_offset(u_brick_g,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:u_brick_g");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:u_brick_g");
memory->create3d_offset(v0_brick_g,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:v0_brick_g");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:v0_brick_g");
memory->create3d_offset(v1_brick_g,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:v1_brick_g");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:v1_brick_g");
memory->create3d_offset(v2_brick_g,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:v2_brick_g");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:v2_brick_g");
memory->create3d_offset(v3_brick_g,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:v3_brick_g");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:v3_brick_g");
memory->create3d_offset(v4_brick_g,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:v4_brick_g");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:v4_brick_g");
memory->create3d_offset(v5_brick_g,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:v5_brick_g");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:v5_brick_g");
// create ghost grid object for rho and electric field communication
@@ -2147,111 +2147,111 @@ void PPPMDisp::allocate_peratom()
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");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:u_brick_a0");
memory->create3d_offset(u_brick_a1,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:u_brick_a1");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:u_brick_a1");
memory->create3d_offset(u_brick_a2,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:u_brick_a2");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:u_brick_a2");
memory->create3d_offset(u_brick_a3,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:u_brick_a3");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:u_brick_a3");
memory->create3d_offset(u_brick_a4,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:u_brick_a4");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:u_brick_a4");
memory->create3d_offset(u_brick_a5,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:u_brick_a5");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:u_brick_a5");
memory->create3d_offset(u_brick_a6,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:u_brick_a6");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:u_brick_a6");
}
memory->create3d_offset(v0_brick_a0,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:v0_brick_a0");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:v0_brick_a0");
memory->create3d_offset(v1_brick_a0,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:v1_brick_a0");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:v1_brick_a0");
memory->create3d_offset(v2_brick_a0,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:v2_brick_a0");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:v2_brick_a0");
memory->create3d_offset(v3_brick_a0,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:v3_brick_a0");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:v3_brick_a0");
memory->create3d_offset(v4_brick_a0,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:v4_brick_a0");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:v4_brick_a0");
memory->create3d_offset(v5_brick_a0,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:v5_brick_a0");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:v5_brick_a0");
memory->create3d_offset(v0_brick_a1,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:v0_brick_a1");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:v0_brick_a1");
memory->create3d_offset(v1_brick_a1,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:v1_brick_a1");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:v1_brick_a1");
memory->create3d_offset(v2_brick_a1,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:v2_brick_a1");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:v2_brick_a1");
memory->create3d_offset(v3_brick_a1,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:v3_brick_a1");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:v3_brick_a1");
memory->create3d_offset(v4_brick_a1,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:v4_brick_a1");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:v4_brick_a1");
memory->create3d_offset(v5_brick_a1,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:v5_brick_a1");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:v5_brick_a1");
memory->create3d_offset(v0_brick_a2,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:v0_brick_a2");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:v0_brick_a2");
memory->create3d_offset(v1_brick_a2,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:v1_brick_a2");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:v1_brick_a2");
memory->create3d_offset(v2_brick_a2,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:v2_brick_a2");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:v2_brick_a2");
memory->create3d_offset(v3_brick_a2,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:v3_brick_a2");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:v3_brick_a2");
memory->create3d_offset(v4_brick_a2,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:v4_brick_a2");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:v4_brick_a2");
memory->create3d_offset(v5_brick_a2,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:v5_brick_a2");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:v5_brick_a2");
memory->create3d_offset(v0_brick_a3,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:v0_brick_a3");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:v0_brick_a3");
memory->create3d_offset(v1_brick_a3,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:v1_brick_a3");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:v1_brick_a3");
memory->create3d_offset(v2_brick_a3,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:v2_brick_a3");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:v2_brick_a3");
memory->create3d_offset(v3_brick_a3,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:v3_brick_a3");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:v3_brick_a3");
memory->create3d_offset(v4_brick_a3,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:v4_brick_a3");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:v4_brick_a3");
memory->create3d_offset(v5_brick_a3,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:v5_brick_a3");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:v5_brick_a3");
memory->create3d_offset(v0_brick_a4,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:v0_brick_a4");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:v0_brick_a4");
memory->create3d_offset(v1_brick_a4,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:v1_brick_a4");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:v1_brick_a4");
memory->create3d_offset(v2_brick_a4,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:v2_brick_a4");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:v2_brick_a4");
memory->create3d_offset(v3_brick_a4,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:v3_brick_a4");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:v3_brick_a4");
memory->create3d_offset(v4_brick_a4,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:v4_brick_a4");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:v4_brick_a4");
memory->create3d_offset(v5_brick_a4,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:v5_brick_a4");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:v5_brick_a4");
memory->create3d_offset(v0_brick_a5,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:v0_brick_a5");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:v0_brick_a5");
memory->create3d_offset(v1_brick_a5,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:v1_brick_a5");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:v1_brick_a5");
memory->create3d_offset(v2_brick_a5,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:v2_brick_a5");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:v2_brick_a5");
memory->create3d_offset(v3_brick_a5,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:v3_brick_a5");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:v3_brick_a5");
memory->create3d_offset(v4_brick_a5,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:v4_brick_a5");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:v4_brick_a5");
memory->create3d_offset(v5_brick_a5,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:v5_brick_a5");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:v5_brick_a5");
memory->create3d_offset(v0_brick_a6,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:v0_brick_a6");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:v0_brick_a6");
memory->create3d_offset(v1_brick_a6,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:v1_brick_a6");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:v1_brick_a6");
memory->create3d_offset(v2_brick_a6,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:v2_brick_a6");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:v2_brick_a6");
memory->create3d_offset(v3_brick_a6,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:v3_brick_a6");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:v3_brick_a6");
memory->create3d_offset(v4_brick_a6,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:v4_brick_a6");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:v4_brick_a6");
memory->create3d_offset(v5_brick_a6,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:v5_brick_a6");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:v5_brick_a6");
// create ghost grid object for rho and electric field communication
@@ -2276,20 +2276,20 @@ void PPPMDisp::allocate_peratom()
if ( differentiation_flag != 1 )
memory->create4d_offset(u_brick_none,nsplit_alloc,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:u_brick_none");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:u_brick_none");
memory->create4d_offset(v0_brick_none,nsplit_alloc,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:v0_brick_none");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:v0_brick_none");
memory->create4d_offset(v1_brick_none,nsplit_alloc,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:v1_brick_none");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:v1_brick_none");
memory->create4d_offset(v2_brick_none,nsplit_alloc,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:v2_brick_none");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:v2_brick_none");
memory->create4d_offset(v3_brick_none,nsplit_alloc,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:v3_brick_none");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:v3_brick_none");
memory->create4d_offset(v4_brick_none,nsplit_alloc,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:v4_brick_none");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:v4_brick_none");
memory->create4d_offset(v5_brick_none,nsplit_alloc,nzlo_out_6,nzhi_out_6,nylo_out_6,nyhi_out_6,
- nxlo_out_6,nxhi_out_6,"pppm/disp:v5_brick_none");
+ nxlo_out_6,nxhi_out_6,"pppm/disp:v5_brick_none");
// create ghost grid object for rho and electric field communication
@@ -2687,9 +2687,9 @@ void PPPMDisp::set_fft_parameters(int& nx_p,int& ny_p,int& nz_p,
int& nxhi_i,int& nyhi_i,int& nzhi_i,
int& nxlo_o,int& nylo_o,int& nzlo_o,
int& nxhi_o,int& nyhi_o,int& nzhi_o,
- int& nlow, int& nupp,
+ int& nlow, int& nupp,
int& ng, int& nf, int& nfb,
- double& sft,double& sftone, int& ord)
+ double& sft,double& sftone, int& ord)
{
// global indices of PPPM grid range from 0 to N-1
// nlo_in,nhi_in = lower/upper limits of the 3d sub-brick of
@@ -2851,8 +2851,8 @@ int PPPMDisp::factorable(int n)
while (n > 1) {
for (i = 0; i < nfactors; i++) {
if (n % factors[i] == 0) {
- n /= factors[i];
- break;
+ n /= factors[i];
+ break;
}
}
if (i == nfactors) return 0;
@@ -3080,12 +3080,12 @@ double PPPMDisp::compute_qopt_ik()
u2 = pow(wx*wy*wz,2.0);
sum1 += sx*sy*sz*sx*sy*sz/dot2*4.0*4.0*MY_PI*MY_PI;
sum2 += u2*sx*sy*sz*4.0*MY_PI/dot2*dot1;
- sum3 += u2;
+ sum3 += u2;
}
}
}
- sum2 *= sum2;
- sum3 *= sum3*sqk;
+ sum2 *= sum2;
+ sum3 *= sum3*sqk;
qopt += sum1 -sum2/sum3;
}
}
@@ -3255,17 +3255,17 @@ double PPPMDisp::compute_qopt_6_ik()
dot2 = qx*qx+qy*qy+qz*qz;
rtdot2 = sqrt(dot2);
term = (1-2*dot2*inv2ew*inv2ew)*sx*sy*sz +
- 2*dot2*rtdot2*inv2ew*inv2ew*inv2ew*rtpi*erfc(rtdot2*inv2ew);
+ 2*dot2*rtdot2*inv2ew*inv2ew*inv2ew*rtpi*erfc(rtdot2*inv2ew);
term *= g_ewald_6*g_ewald_6*g_ewald_6;
u2 = pow(wx*wy*wz,2.0);
sum1 += term*term*MY_PI*MY_PI*MY_PI/9.0 * dot2;
sum2 += -u2*term*MY_PI*rtpi/3.0*dot1;
- sum3 += u2;
+ sum3 += u2;
}
}
}
- sum2 *= sum2;
- sum3 *= sum3*sqk;
+ sum2 *= sum2;
+ sum3 *= sum3*sqk;
qopt += sum1 -sum2/sum3;
}
}
@@ -3349,7 +3349,7 @@ double PPPMDisp::compute_qopt_6_ad()
dot2 = qx*qx+qy*qy+qz*qz;
rtdot2 = sqrt(dot2);
term = (1-2*dot2*inv2ew*inv2ew)*sx*sy*sz +
- 2*dot2*rtdot2*inv2ew*inv2ew*inv2ew*rtpi*erfc(rtdot2*inv2ew);
+ 2*dot2*rtdot2*inv2ew*inv2ew*inv2ew*rtpi*erfc(rtdot2*inv2ew);
term *= g_ewald_6*g_ewald_6*g_ewald_6;
u2 = pow(wx*wy*wz,2.0);
sum1 += term*term*MY_PI*MY_PI*MY_PI/9.0 * dot2;
@@ -3482,11 +3482,11 @@ void PPPMDisp::calc_csum()
for (i=1; i<=ntypes; i++) {
for (j=1; j<=ntypes; j++) {
for (k=0; k<nsplit; k++) {
- csumi[i] += neach_all[j]*B[k]*B[nsplit*i+k]*B[nsplit*j+k];
- d1 = neach_all[i]*B[nsplit*i+k];
- d2 = neach_all[j]*B[nsplit*j+k];
+ csumi[i] += neach_all[j]*B[k]*B[nsplit*i+k]*B[nsplit*j+k];
+ d1 = neach_all[i]*B[nsplit*i+k];
+ d2 = neach_all[j]*B[nsplit*j+k];
csumij += B[k]*d1*d2;
- }
+ }
}
}
}
@@ -3984,24 +3984,24 @@ void PPPMDisp::compute_gf_6()
wy *= wy;
for (k = nxlo_fft_6; k <= nxhi_fft_6; k++) {
- kper = k - nx_pppm_6*(2*k/nx_pppm_6);
+ kper = k - nx_pppm_6*(2*k/nx_pppm_6);
qx = unitkx*kper;
- snx = sin(0.5*unitkx*kper*xprd/nx_pppm_6);
- snx2 = snx*snx;
+ snx = sin(0.5*unitkx*kper*xprd/nx_pppm_6);
+ snx2 = snx*snx;
sx = exp(-qx*qx*inv2ew*inv2ew);
- wx = 1.0;
- argx = 0.5*qx*xprd/nx_pppm_6;
- if (argx != 0.0) wx = pow(sin(argx)/argx,order_6);
+ wx = 1.0;
+ 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);
+ 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);
- rtsqk = sqrt(sqk);
+ 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);
- greensfn_6[n++] = numerator*term*wx*wy*wz/denominator;
+ greensfn_6[n++] = numerator*term*wx*wy*wz/denominator;
} else greensfn_6[n++] = 0.0;
}
}
@@ -4193,7 +4193,7 @@ void PPPMDisp::brick2fft(int nxlo_i, int nylo_i, int nzlo_i,
for (iz = nzlo_i; iz <= nzhi_i; iz++)
for (iy = nylo_i; iy <= nyhi_i; iy++)
for (ix = nxlo_i; ix <= nxhi_i; ix++)
- dfft[n++] = dbrick[iz][iy][ix];
+ dfft[n++] = dbrick[iz][iy][ix];
rmp->perform(dfft,dfft,work);
}
@@ -4299,8 +4299,8 @@ void PPPMDisp::particle_map(double delx, double dely, double delz,
// check that entire stencil around nx,ny,nz will fit in my 3d brick
if (nx+nlow < nxlo || nx+nup > nxhi ||
- ny+nlow < nylo || ny+nup > nyhi ||
- nz+nlow < nzlo || nz+nup > nzhi)
+ ny+nlow < nylo || ny+nup > nyhi ||
+ nz+nlow < nzlo || nz+nup > nzhi)
flag = 1;
}
@@ -4332,7 +4332,7 @@ void PPPMDisp::make_rho_c()
// clear 3d density array
memset(&(density_brick[nzlo_out][nylo_out][nxlo_out]),0,
- ngrid*sizeof(FFT_SCALAR));
+ ngrid*sizeof(FFT_SCALAR));
// loop over my charges, add their contribution to nearby grid points
// (nx,ny,nz) = global coords of grid pt to "lower left" of charge
@@ -4359,12 +4359,12 @@ void PPPMDisp::make_rho_c()
mz = n+nz;
y0 = z0*rho1d[2][n];
for (m = nlower; m <= nupper; m++) {
- my = m+ny;
- x0 = y0*rho1d[1][m];
- for (l = nlower; l <= nupper; l++) {
- mx = l+nx;
- density_brick[mz][my][mx] += x0*rho1d[0][l];
- }
+ my = m+ny;
+ x0 = y0*rho1d[1][m];
+ for (l = nlower; l <= nupper; l++) {
+ mx = l+nx;
+ density_brick[mz][my][mx] += x0*rho1d[0][l];
+ }
}
}
}
@@ -4385,7 +4385,7 @@ void PPPMDisp::make_rho_g()
// clear 3d density array
memset(&(density_brick_g[nzlo_out_6][nylo_out_6][nxlo_out_6]),0,
- ngrid_6*sizeof(FFT_SCALAR));
+ ngrid_6*sizeof(FFT_SCALAR));
// loop over my charges, add their contribution to nearby grid points
// (nx,ny,nz) = global coords of grid pt to "lower left" of charge
@@ -4411,12 +4411,12 @@ void PPPMDisp::make_rho_g()
mz = n+nz;
y0 = z0*rho1d_6[2][n];
for (m = nlower_6; m <= nupper_6; m++) {
- my = m+ny;
- x0 = y0*rho1d_6[1][m];
- for (l = nlower_6; l <= nupper_6; l++) {
- mx = l+nx;
- density_brick_g[mz][my][mx] += x0*rho1d_6[0][l];
- }
+ my = m+ny;
+ x0 = y0*rho1d_6[1][m];
+ for (l = nlower_6; l <= nupper_6; l++) {
+ mx = l+nx;
+ density_brick_g[mz][my][mx] += x0*rho1d_6[0][l];
+ }
}
}
}
@@ -4438,19 +4438,19 @@ void PPPMDisp::make_rho_a()
// clear 3d density array
memset(&(density_brick_a0[nzlo_out_6][nylo_out_6][nxlo_out_6]),0,
- ngrid_6*sizeof(FFT_SCALAR));
+ ngrid_6*sizeof(FFT_SCALAR));
memset(&(density_brick_a1[nzlo_out_6][nylo_out_6][nxlo_out_6]),0,
- ngrid_6*sizeof(FFT_SCALAR));
+ ngrid_6*sizeof(FFT_SCALAR));
memset(&(density_brick_a2[nzlo_out_6][nylo_out_6][nxlo_out_6]),0,
- ngrid_6*sizeof(FFT_SCALAR));
+ ngrid_6*sizeof(FFT_SCALAR));
memset(&(density_brick_a3[nzlo_out_6][nylo_out_6][nxlo_out_6]),0,
- ngrid_6*sizeof(FFT_SCALAR));
+ ngrid_6*sizeof(FFT_SCALAR));
memset(&(density_brick_a4[nzlo_out_6][nylo_out_6][nxlo_out_6]),0,
- ngrid_6*sizeof(FFT_SCALAR));
+ ngrid_6*sizeof(FFT_SCALAR));
memset(&(density_brick_a5[nzlo_out_6][nylo_out_6][nxlo_out_6]),0,
- ngrid_6*sizeof(FFT_SCALAR));
+ ngrid_6*sizeof(FFT_SCALAR));
memset(&(density_brick_a6[nzlo_out_6][nylo_out_6][nxlo_out_6]),0,
- ngrid_6*sizeof(FFT_SCALAR));
+ ngrid_6*sizeof(FFT_SCALAR));
// loop over my particles, add their contribution to nearby grid points
// (nx,ny,nz) = global coords of grid pt to "lower left" of charge
@@ -4476,19 +4476,19 @@ void PPPMDisp::make_rho_a()
mz = n+nz;
y0 = z0*rho1d_6[2][n];
for (m = nlower_6; m <= nupper_6; m++) {
- my = m+ny;
- x0 = y0*rho1d_6[1][m];
- for (l = nlower_6; l <= nupper_6; l++) {
- mx = l+nx;
+ my = m+ny;
+ x0 = y0*rho1d_6[1][m];
+ for (l = nlower_6; l <= nupper_6; l++) {
+ mx = l+nx;
w = x0*rho1d_6[0][l];
- density_brick_a0[mz][my][mx] += w*B[7*type];
- density_brick_a1[mz][my][mx] += w*B[7*type+1];
- density_brick_a2[mz][my][mx] += w*B[7*type+2];
- density_brick_a3[mz][my][mx] += w*B[7*type+3];
- density_brick_a4[mz][my][mx] += w*B[7*type+4];
- density_brick_a5[mz][my][mx] += w*B[7*type+5];
- density_brick_a6[mz][my][mx] += w*B[7*type+6];
- }
+ density_brick_a0[mz][my][mx] += w*B[7*type];
+ density_brick_a1[mz][my][mx] += w*B[7*type+1];
+ density_brick_a2[mz][my][mx] += w*B[7*type+2];
+ density_brick_a3[mz][my][mx] += w*B[7*type+3];
+ density_brick_a4[mz][my][mx] += w*B[7*type+4];
+ density_brick_a5[mz][my][mx] += w*B[7*type+5];
+ density_brick_a6[mz][my][mx] += w*B[7*type+6];
+ }
}
}
}
@@ -4509,7 +4509,7 @@ void PPPMDisp::make_rho_none()
// clear 3d density array
for (k = 0; k < nsplit_alloc; k++)
memset(&(density_brick_none[k][nzlo_out_6][nylo_out_6][nxlo_out_6]),0,
- ngrid_6*sizeof(FFT_SCALAR));
+ ngrid_6*sizeof(FFT_SCALAR));
// loop over my particles, add their contribution to nearby grid points
@@ -4536,14 +4536,14 @@ void PPPMDisp::make_rho_none()
mz = n+nz;
y0 = z0*rho1d_6[2][n];
for (m = nlower_6; m <= nupper_6; m++) {
- my = m+ny;
- x0 = y0*rho1d_6[1][m];
- for (l = nlower_6; l <= nupper_6; l++) {
- mx = l+nx;
+ my = m+ny;
+ x0 = y0*rho1d_6[1][m];
+ for (l = nlower_6; l <= nupper_6; l++) {
+ mx = l+nx;
w = x0*rho1d_6[0][l];
for (k = 0; k < nsplit; k++)
- density_brick_none[k][mz][my][mx] += w*B[nsplit*type + k];
- }
+ density_brick_none[k][mz][my][mx] += w*B[nsplit*type + k];
+ }
}
}
}
@@ -4592,17 +4592,17 @@ void PPPMDisp::poisson_ik(FFT_SCALAR* wk1, FFT_SCALAR* wk2,
if (vflag_global) {
n = 0;
for (i = 0; i < nft; i++) {
- eng = s2 * gfn[i] * (wk1[n]*wk1[n] + wk1[n+1]*wk1[n+1]);
- for (j = 0; j < 6; j++) vir[j] += eng*vcoeff[i][j];
- if (eflag_global) egy += eng;
- n += 2;
+ eng = s2 * gfn[i] * (wk1[n]*wk1[n] + wk1[n+1]*wk1[n+1]);
+ for (j = 0; j < 6; j++) vir[j] += eng*vcoeff[i][j];
+ if (eflag_global) egy += eng;
+ n += 2;
}
} else {
n = 0;
for (i = 0; i < nft; i++) {
- egy +=
- s2 * gfn[i] * (wk1[n]*wk1[n] + wk1[n+1]*wk1[n+1]);
- n += 2;
+ egy +=
+ s2 * gfn[i] * (wk1[n]*wk1[n] + wk1[n+1]*wk1[n+1]);
+ n += 2;
}
}
}
@@ -4626,9 +4626,9 @@ void PPPMDisp::poisson_ik(FFT_SCALAR* wk1, FFT_SCALAR* wk2,
for (k = nzlo_ft; k <= nzhi_ft; k++)
for (j = nylo_ft; j <= nyhi_ft; j++)
for (i = nxlo_ft; i <= nxhi_ft; i++) {
- wk2[n] = 0.5*(kx[i]-kx2[i])*wk1[n+1] + 0.5*(ky[j]-ky2[j])*wk1[n];
- wk2[n+1] = -0.5*(kx[i]-kx2[i])*wk1[n] + 0.5*(ky[j]-ky2[j])*wk1[n+1];
- n += 2;
+ wk2[n] = 0.5*(kx[i]-kx2[i])*wk1[n+1] + 0.5*(ky[j]-ky2[j])*wk1[n];
+ wk2[n+1] = -0.5*(kx[i]-kx2[i])*wk1[n] + 0.5*(ky[j]-ky2[j])*wk1[n+1];
+ n += 2;
}
ft2->compute(wk2,wk2,-1);
@@ -4637,8 +4637,8 @@ void PPPMDisp::poisson_ik(FFT_SCALAR* wk1, FFT_SCALAR* wk2,
for (k = nzlo_i; k <= nzhi_i; k++)
for (j = nylo_i; j <= nyhi_i; j++)
for (i = nxlo_i; i <= nxhi_i; i++) {
- vx_brick[k][j][i] = wk2[n++];
- vy_brick[k][j][i] = wk2[n++];
+ vx_brick[k][j][i] = wk2[n++];
+ vy_brick[k][j][i] = wk2[n++];
}
if (!eflag_atom) {
@@ -4648,9 +4648,9 @@ void PPPMDisp::poisson_ik(FFT_SCALAR* wk1, FFT_SCALAR* wk2,
for (k = nzlo_ft; k <= nzhi_ft; k++)
for (j = nylo_ft; j <= nyhi_ft; j++)
for (i = nxlo_ft; i <= nxhi_ft; i++) {
- wk2[n] = kz[k]*wk1[n+1];
- wk2[n+1] = -kz[k]*wk1[n];
- n += 2;
+ wk2[n] = kz[k]*wk1[n+1];
+ wk2[n+1] = -kz[k]*wk1[n];
+ n += 2;
}
ft2->compute(wk2,wk2,-1);
@@ -4660,8 +4660,8 @@ void PPPMDisp::poisson_ik(FFT_SCALAR* wk1, FFT_SCALAR* wk2,
for (k = nzlo_i; k <= nzhi_i; k++)
for (j = nylo_i; j <= nyhi_i; j++)
for (i = nxlo_i; i <= nxhi_i; i++) {
- vz_brick[k][j][i] = wk2[n];
- n += 2;
+ vz_brick[k][j][i] = wk2[n];
+ n += 2;
}
}
@@ -4673,9 +4673,9 @@ void PPPMDisp::poisson_ik(FFT_SCALAR* wk1, FFT_SCALAR* wk2,
for (k = nzlo_ft; k <= nzhi_ft; k++)
for (j = nylo_ft; j <= nyhi_ft; j++)
for (i = nxlo_ft; i <= nxhi_ft; i++) {
- wk2[n] = 0.5*(kz[k]-kz2[k])*wk1[n+1] - wk1[n+1];
- wk2[n+1] = -0.5*(kz[k]-kz2[k])*wk1[n] + wk1[n];
- n += 2;
+ wk2[n] = 0.5*(kz[k]-kz2[k])*wk1[n+1] - wk1[n+1];
+ wk2[n+1] = -0.5*(kz[k]-kz2[k])*wk1[n] + wk1[n];
+ n += 2;
}
ft2->compute(wk2,wk2,-1);
@@ -4684,8 +4684,8 @@ void PPPMDisp::poisson_ik(FFT_SCALAR* wk1, FFT_SCALAR* wk2,
for (k = nzlo_i; k <= nzhi_i; k++)
for (j = nylo_i; j <= nyhi_i; j++)
for (i = nxlo_i; i <= nxhi_i; i++) {
- vz_brick[k][j][i] = wk2[n++];
- u_pa[k][j][i] = wk2[n++];;
+ vz_brick[k][j][i] = wk2[n++];
+ u_pa[k][j][i] = wk2[n++];;
}
}
@@ -4733,17 +4733,17 @@ void PPPMDisp::poisson_ad(FFT_SCALAR* wk1, FFT_SCALAR* wk2,
if (vflag_global) {
n = 0;
for (i = 0; i < nft; i++) {
- eng = s2 * gfn[i] * (wk1[n]*wk1[n] + wk1[n+1]*wk1[n+1]);
- for (j = 0; j < 6; j++) vir[j] += eng*vcoeff[i][j];
- if (eflag_global) egy += eng;
- n += 2;
+ eng = s2 * gfn[i] * (wk1[n]*wk1[n] + wk1[n+1]*wk1[n+1]);
+ for (j = 0; j < 6; j++) vir[j] += eng*vcoeff[i][j];
+ if (eflag_global) egy += eng;
+ n += 2;
}
} else {
n = 0;
for (i = 0; i < nft; i++) {
- egy +=
- s2 * gfn[i] * (wk1[n]*wk1[n] + wk1[n+1]*wk1[n+1]);
- n += 2;
+ egy +=
+ s2 * gfn[i] * (wk1[n]*wk1[n] + wk1[n+1]*wk1[n+1]);
+ n += 2;
}
}
}
@@ -4763,8 +4763,8 @@ void PPPMDisp::poisson_ad(FFT_SCALAR* wk1, FFT_SCALAR* wk2,
for (j = nylo_ft; j <= nyhi_ft; j++)
for (i = nxlo_ft; i <= nxhi_ft; i++) {
wk2[n] = wk1[n];
- wk2[n+1] = wk1[n+1];
- n += 2;
+ wk2[n+1] = wk1[n+1];
+ n += 2;
}
ft2->compute(wk2,wk2,-1);
@@ -4774,7 +4774,7 @@ void PPPMDisp::poisson_ad(FFT_SCALAR* wk1, FFT_SCALAR* wk2,
for (k = nzlo_i; k <= nzhi_i; k++)
for (j = nylo_i; j <= nyhi_i; j++)
for (i = nxlo_i; i <= nxhi_i; i++) {
- u_pa[k][j][i] = wk2[n++];
+ u_pa[k][j][i] = wk2[n++];
n++;
}
@@ -4905,17 +4905,17 @@ void PPPMDisp::poisson_2s_ik(FFT_SCALAR* dfft_1, FFT_SCALAR* dfft_2,
if (vflag_global) {
n = 0;
for (i = 0; i < nfft_6; i++) {
- eng = 2 * s2 * greensfn_6[i] * (work1_6[n]*work2_6[n+1] - work1_6[n+1]*work2_6[n]);
- for (j = 0; j < 6; j++) virial_6[j] += eng*vg_6[i][j];
- if (eflag_global)energy_6 += eng;
- n += 2;
+ eng = 2 * s2 * greensfn_6[i] * (work1_6[n]*work2_6[n+1] - work1_6[n+1]*work2_6[n]);
+ for (j = 0; j < 6; j++) virial_6[j] += eng*vg_6[i][j];
+ if (eflag_global)energy_6 += eng;
+ n += 2;
}
} else {
n = 0;
for (i = 0; i < nfft_6; i++) {
- energy_6 +=
- 2 * s2 * greensfn_6[i] * (work1_6[n]*work2_6[n+1] - work1_6[n+1]*work2_6[n]);
- n += 2;
+ energy_6 +=
+ 2 * s2 * greensfn_6[i] * (work1_6[n]*work2_6[n+1] - work1_6[n+1]*work2_6[n]);
+ n += 2;
}
}
// unify the two transformed vectors for efficient calculations later
@@ -4940,9 +4940,9 @@ void PPPMDisp::poisson_2s_ik(FFT_SCALAR* dfft_1, FFT_SCALAR* dfft_2,
for (k = nzlo_fft_6; k <= nzhi_fft_6; k++)
for (j = nylo_fft_6; j <= nyhi_fft_6; j++)
for (i = nxlo_fft_6; i <= nxhi_fft_6; i++) {
- work2_6[n] = 0.5*(fkx_6[i]-fkx2_6[i])*work1_6[n+1];
- work2_6[n+1] = -0.5*(fkx_6[i]-fkx2_6[i])*work1_6[n];
- n += 2;
+ work2_6[n] = 0.5*(fkx_6[i]-fkx2_6[i])*work1_6[n+1];
+ work2_6[n+1] = -0.5*(fkx_6[i]-fkx2_6[i])*work1_6[n];
+ n += 2;
}
fft2_6->compute(work2_6,work2_6,-1);
@@ -4951,7 +4951,7 @@ void PPPMDisp::poisson_2s_ik(FFT_SCALAR* dfft_1, FFT_SCALAR* dfft_2,
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++) {
- vxbrick_1[k][j][i] = work2_6[n++];
+ vxbrick_1[k][j][i] = work2_6[n++];
vxbrick_2[k][j][i] = work2_6[n++];
}
@@ -4961,9 +4961,9 @@ void PPPMDisp::poisson_2s_ik(FFT_SCALAR* dfft_1, FFT_SCALAR* dfft_2,
for (k = nzlo_fft_6; k <= nzhi_fft_6; k++)
for (j = nylo_fft_6; j <= nyhi_fft_6; j++)
for (i = nxlo_fft_6; i <= nxhi_fft_6; i++) {
- work2_6[n] = 0.5*(fky_6[j]-fky2_6[j])*work1_6[n+1];
- work2_6[n+1] = -0.5*(fky_6[j]-fky2_6[j])*work1_6[n];
- n += 2;
+ work2_6[n] = 0.5*(fky_6[j]-fky2_6[j])*work1_6[n+1];
+ work2_6[n+1] = -0.5*(fky_6[j]-fky2_6[j])*work1_6[n];
+ n += 2;
}
fft2_6->compute(work2_6,work2_6,-1);
@@ -4972,7 +4972,7 @@ void PPPMDisp::poisson_2s_ik(FFT_SCALAR* dfft_1, FFT_SCALAR* dfft_2,
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++) {
- vybrick_1[k][j][i] = work2_6[n++];
+ vybrick_1[k][j][i] = work2_6[n++];
vybrick_2[k][j][i] = work2_6[n++];
}
@@ -4982,9 +4982,9 @@ void PPPMDisp::poisson_2s_ik(FFT_SCALAR* dfft_1, FFT_SCALAR* dfft_2,
for (k = nzlo_fft_6; k <= nzhi_fft_6; k++)
for (j = nylo_fft_6; j <= nyhi_fft_6; j++)
for (i = nxlo_fft_6; i <= nxhi_fft_6; i++) {
- work2_6[n] = 0.5*(fkz_6[k]-fkz2_6[k])*work1_6[n+1];
- work2_6[n+1] = -0.5*(fkz_6[k]-fkz2_6[k])*work1_6[n];
- n += 2;
+ work2_6[n] = 0.5*(fkz_6[k]-fkz2_6[k])*work1_6[n+1];
+ work2_6[n+1] = -0.5*(fkz_6[k]-fkz2_6[k])*work1_6[n];
+ n += 2;
}
fft2_6->compute(work2_6,work2_6,-1);
@@ -4993,8 +4993,8 @@ void PPPMDisp::poisson_2s_ik(FFT_SCALAR* dfft_1, FFT_SCALAR* dfft_2,
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++) {
- vzbrick_1[k][j][i] = work2_6[n++];
- vzbrick_2[k][j][i] = work2_6[n++];
+ vzbrick_1[k][j][i] = work2_6[n++];
+ vzbrick_2[k][j][i] = work2_6[n++];
}
//Per-atom energy
@@ -5073,17 +5073,17 @@ void PPPMDisp::poisson_none_ik(int n1, int n2,FFT_SCALAR* dfft_1, FFT_SCALAR* df
if (vflag_global) {
n = 0;
for (i = 0; i < nfft_6; i++) {
- eng = 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]));
- for (j = 0; j < 6; j++) virial_6[j] += eng*vg_6[i][j];
- if (eflag_global)energy_6 += eng;
- n += 2;
+ eng = 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]));
+ for (j = 0; j < 6; j++) virial_6[j] += eng*vg_6[i][j];
+ if (eflag_global)energy_6 += eng;
+ n += 2;
}
} else {
n = 0;
for (i = 0; i < nfft_6; i++) {
- 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;
+ 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;
}
}
// unify the two transformed vectors for efficient calculations later
@@ -5108,9 +5108,9 @@ void PPPMDisp::poisson_none_ik(int n1, int n2,FFT_SCALAR* dfft_1, FFT_SCALAR* df
for (k = nzlo_fft_6; k <= nzhi_fft_6; k++)
for (j = nylo_fft_6; j <= nyhi_fft_6; j++)
for (i = nxlo_fft_6; i <= nxhi_fft_6; i++) {
- work2_6[n] = 0.5*(fkx_6[i]-fkx2_6[i])*work1_6[n+1];
- work2_6[n+1] = -0.5*(fkx_6[i]-fkx2_6[i])*work1_6[n];
- n += 2;
+ work2_6[n] = 0.5*(fkx_6[i]-fkx2_6[i])*work1_6[n+1];
+ work2_6[n+1] = -0.5*(fkx_6[i]-fkx2_6[i])*work1_6[n];
+ n += 2;
}
fft2_6->compute(work2_6,work2_6,-1);
@@ -5119,7 +5119,7 @@ void PPPMDisp::poisson_none_ik(int n1, int n2,FFT_SCALAR* dfft_1, FFT_SCALAR* df
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++) {
- vxbrick_1[k][j][i] = B[n1]*work2_6[n++];
+ vxbrick_1[k][j][i] = B[n1]*work2_6[n++];
vxbrick_2[k][j][i] = B[n2]*work2_6[n++];
}
@@ -5129,9 +5129,9 @@ void PPPMDisp::poisson_none_ik(int n1, int n2,FFT_SCALAR* dfft_1, FFT_SCALAR* df
for (k = nzlo_fft_6; k <= nzhi_fft_6; k++)
for (j = nylo_fft_6; j <= nyhi_fft_6; j++)
for (i = nxlo_fft_6; i <= nxhi_fft_6; i++) {
- work2_6[n] = 0.5*(fky_6[j]-fky2_6[j])*work1_6[n+1];
- work2_6[n+1] = -0.5*(fky_6[j]-fky2_6[j])*work1_6[n];
- n += 2;
+ work2_6[n] = 0.5*(fky_6[j]-fky2_6[j])*work1_6[n+1];
+ work2_6[n+1] = -0.5*(fky_6[j]-fky2_6[j])*work1_6[n];
+ n += 2;
}
fft2_6->compute(work2_6,work2_6,-1);
@@ -5140,7 +5140,7 @@ void PPPMDisp::poisson_none_ik(int n1, int n2,FFT_SCALAR* dfft_1, FFT_SCALAR* df
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++) {
- vybrick_1[k][j][i] = B[n1]*work2_6[n++];
+ vybrick_1[k][j][i] = B[n1]*work2_6[n++];
vybrick_2[k][j][i] = B[n2]*work2_6[n++];
}
@@ -5150,9 +5150,9 @@ void PPPMDisp::poisson_none_ik(int n1, int n2,FFT_SCALAR* dfft_1, FFT_SCALAR* df
for (k = nzlo_fft_6; k <= nzhi_fft_6; k++)
for (j = nylo_fft_6; j <= nyhi_fft_6; j++)
for (i = nxlo_fft_6; i <= nxhi_fft_6; i++) {
- work2_6[n] = 0.5*(fkz_6[k]-fkz2_6[k])*work1_6[n+1];
- work2_6[n+1] = -0.5*(fkz_6[k]-fkz2_6[k])*work1_6[n];
- n += 2;
+ work2_6[n] = 0.5*(fkz_6[k]-fkz2_6[k])*work1_6[n+1];
+ work2_6[n+1] = -0.5*(fkz_6[k]-fkz2_6[k])*work1_6[n];
+ n += 2;
}
fft2_6->compute(work2_6,work2_6,-1);
@@ -5161,8 +5161,8 @@ void PPPMDisp::poisson_none_ik(int n1, int n2,FFT_SCALAR* dfft_1, FFT_SCALAR* df
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++) {
- vzbrick_1[k][j][i] = B[n1]*work2_6[n++];
- vzbrick_2[k][j][i] = B[n2]*work2_6[n++];
+ vzbrick_1[k][j][i] = B[n1]*work2_6[n++];
+ vzbrick_2[k][j][i] = B[n2]*work2_6[n++];
}
//Per-atom energy
@@ -5239,17 +5239,17 @@ void PPPMDisp::poisson_2s_ad(FFT_SCALAR* dfft_1, FFT_SCALAR* dfft_2,
if (vflag_global) {
n = 0;
for (i = 0; i < nfft_6; i++) {
- eng = 2 * s2 * greensfn_6[i] * (work1_6[n]*work2_6[n+1] - work1_6[n+1]*work2_6[n]);
- for (j = 0; j < 6; j++) virial_6[j] += eng*vg_6[i][j];
- if (eflag_global)energy_6 += eng;
- n += 2;
+ eng = 2 * s2 * greensfn_6[i] * (work1_6[n]*work2_6[n+1] - work1_6[n+1]*work2_6[n]);
+ for (j = 0; j < 6; j++) virial_6[j] += eng*vg_6[i][j];
+ if (eflag_global)energy_6 += eng;
+ n += 2;
}
} else {
n = 0;
for (i = 0; i < nfft_6; i++) {
- energy_6 +=
- 2 * s2 * greensfn_6[i] * (work1_6[n]*work2_6[n+1] - work1_6[n+1]*work2_6[n]);
- n += 2;
+ energy_6 +=
+ 2 * s2 * greensfn_6[i] * (work1_6[n]*work2_6[n+1] - work1_6[n+1]*work2_6[n]);
+ n += 2;
}
}
// unify the two transformed vectors for efficient calculations later
@@ -5333,17 +5333,17 @@ void PPPMDisp::poisson_none_ad(int n1, int n2, FFT_SCALAR* dfft_1, FFT_SCALAR* d
if (vflag_global) {
n = 0;
for (i = 0; i < nfft_6; i++) {
- eng = 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]));
- for (j = 0; j < 6; j++) virial_6[j] += eng*vg_6[i][j];
- if (eflag_global)energy_6 += eng;
- n += 2;
+ eng = 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]));
+ for (j = 0; j < 6; j++) virial_6[j] += eng*vg_6[i][j];
+ if (eflag_global)energy_6 += eng;
+ n += 2;
}
} else {
n = 0;
for (i = 0; i < nfft_6; i++) {
- 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;
+ 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;
}
}
// unify the two transformed vectors for efficient calculations later
@@ -5671,15 +5671,15 @@ void PPPMDisp::fieldforce_c_ik()
mz = n+nz;
z0 = rho1d[2][n];
for (m = nlower; m <= nupper; m++) {
- my = m+ny;
- y0 = z0*rho1d[1][m];
- for (l = nlower; l <= nupper; l++) {
- mx = l+nx;
- x0 = y0*rho1d[0][l];
- ekx -= x0*vdx_brick[mz][my][mx];
- eky -= x0*vdy_brick[mz][my][mx];
- ekz -= x0*vdz_brick[mz][my][mx];
- }
+ my = m+ny;
+ y0 = z0*rho1d[1][m];
+ for (l = nlower; l <= nupper; l++) {
+ mx = l+nx;
+ x0 = y0*rho1d[0][l];
+ ekx -= x0*vdx_brick[mz][my][mx];
+ eky -= x0*vdy_brick[mz][my][mx];
+ ekz -= x0*vdz_brick[mz][my][mx];
+ }
}
}
@@ -5817,13 +5817,13 @@ void PPPMDisp::fieldforce_c_peratom()
mz = n+nz;
z0 = rho1d[2][n];
for (m = nlower; m <= nupper; m++) {
- my = m+ny;
- y0 = z0*rho1d[1][m];
- 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 (vflag_atom) {
+ my = m+ny;
+ y0 = z0*rho1d[1][m];
+ 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 (vflag_atom) {
v0 += x0*v0_brick[mz][my][mx];
v1 += x0*v1_brick[mz][my][mx];
v2 += x0*v2_brick[mz][my][mx];
@@ -5831,7 +5831,7 @@ void PPPMDisp::fieldforce_c_peratom()
v4 += x0*v4_brick[mz][my][mx];
v5 += x0*v5_brick[mz][my][mx];
}
- }
+ }
}
}
@@ -5890,15 +5890,15 @@ void PPPMDisp::fieldforce_g_ik()
mz = n+nz;
z0 = rho1d_6[2][n];
for (m = nlower_6; m <= nupper_6; m++) {
- my = m+ny;
- y0 = z0*rho1d_6[1][m];
- for (l = nlower_6; l <= nupper_6; l++) {
- mx = l+nx;
- x0 = y0*rho1d_6[0][l];
- ekx -= x0*vdx_brick_g[mz][my][mx];
- eky -= x0*vdy_brick_g[mz][my][mx];
- ekz -= x0*vdz_brick_g[mz][my][mx];
- }
+ my = m+ny;
+ y0 = z0*rho1d_6[1][m];
+ for (l = nlower_6; l <= nupper_6; l++) {
+ mx = l+nx;
+ x0 = y0*rho1d_6[0][l];
+ ekx -= x0*vdx_brick_g[mz][my][mx];
+ eky -= x0*vdy_brick_g[mz][my][mx];
+ ekz -= x0*vdz_brick_g[mz][my][mx];
+ }
}
}
@@ -6045,13 +6045,13 @@ void PPPMDisp::fieldforce_g_peratom()
mz = n+nz;
z0 = rho1d_6[2][n];
for (m = nlower_6; m <= nupper_6; m++) {
- my = m+ny;
- y0 = z0*rho1d_6[1][m];
- 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 (vflag_atom) {
+ my = m+ny;
+ y0 = z0*rho1d_6[1][m];
+ 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 (vflag_atom) {
v0 += x0*v0_brick_g[mz][my][mx];
v1 += x0*v1_brick_g[mz][my][mx];
v2 += x0*v2_brick_g[mz][my][mx];
@@ -6059,7 +6059,7 @@ void PPPMDisp::fieldforce_g_peratom()
v4 += x0*v4_brick_g[mz][my][mx];
v5 += x0*v5_brick_g[mz][my][mx];
}
- }
+ }
}
}
@@ -6125,33 +6125,33 @@ void PPPMDisp::fieldforce_a_ik()
mz = n+nz;
z0 = rho1d_6[2][n];
for (m = nlower_6; m <= nupper_6; m++) {
- my = m+ny;
- y0 = z0*rho1d_6[1][m];
- for (l = nlower_6; l <= nupper_6; l++) {
- mx = l+nx;
- x0 = y0*rho1d_6[0][l];
- ekx0 -= x0*vdx_brick_a0[mz][my][mx];
- eky0 -= x0*vdy_brick_a0[mz][my][mx];
- ekz0 -= x0*vdz_brick_a0[mz][my][mx];
- ekx1 -= x0*vdx_brick_a1[mz][my][mx];
- eky1 -= x0*vdy_brick_a1[mz][my][mx];
- ekz1 -= x0*vdz_brick_a1[mz][my][mx];
+ my = m+ny;
+ y0 = z0*rho1d_6[1][m];
+ for (l = nlower_6; l <= nupper_6; l++) {
+ mx = l+nx;
+ x0 = y0*rho1d_6[0][l];
+ ekx0 -= x0*vdx_brick_a0[mz][my][mx];
+ eky0 -= x0*vdy_brick_a0[mz][my][mx];
+ ekz0 -= x0*vdz_brick_a0[mz][my][mx];
+ ekx1 -= x0*vdx_brick_a1[mz][my][mx];
+ eky1 -= x0*vdy_brick_a1[mz][my][mx];
+ ekz1 -= x0*vdz_brick_a1[mz][my][mx];
ekx2 -= x0*vdx_brick_a2[mz][my][mx];
- eky2 -= x0*vdy_brick_a2[mz][my][mx];
- ekz2 -= x0*vdz_brick_a2[mz][my][mx];
- ekx3 -= x0*vdx_brick_a3[mz][my][mx];
- eky3 -= x0*vdy_brick_a3[mz][my][mx];
- ekz3 -= x0*vdz_brick_a3[mz][my][mx];
- ekx4 -= x0*vdx_brick_a4[mz][my][mx];
- eky4 -= x0*vdy_brick_a4[mz][my][mx];
- ekz4 -= x0*vdz_brick_a4[mz][my][mx];
+ eky2 -= x0*vdy_brick_a2[mz][my][mx];
+ ekz2 -= x0*vdz_brick_a2[mz][my][mx];
+ ekx3 -= x0*vdx_brick_a3[mz][my][mx];
+ eky3 -= x0*vdy_brick_a3[mz][my][mx];
+ ekz3 -= x0*vdz_brick_a3[mz][my][mx];
+ ekx4 -= x0*vdx_brick_a4[mz][my][mx];
+ eky4 -= x0*vdy_brick_a4[mz][my][mx];
+ ekz4 -= x0*vdz_brick_a4[mz][my][mx];
ekx5 -= x0*vdx_brick_a5[mz][my][mx];
- eky5 -= x0*vdy_brick_a5[mz][my][mx];
- ekz5 -= x0*vdz_brick_a5[mz][my][mx];
+ eky5 -= x0*vdy_brick_a5[mz][my][mx];
+ ekz5 -= x0*vdz_brick_a5[mz][my][mx];
ekx6 -= x0*vdx_brick_a6[mz][my][mx];
- eky6 -= x0*vdy_brick_a6[mz][my][mx];
- ekz6 -= x0*vdz_brick_a6[mz][my][mx];
- }
+ eky6 -= x0*vdy_brick_a6[mz][my][mx];
+ ekz6 -= x0*vdz_brick_a6[mz][my][mx];
+ }
}
}
// convert D-field to force
@@ -6233,9 +6233,9 @@ void PPPMDisp::fieldforce_a_ad()
for (n = nlower_6; n <= nupper_6; n++) {
mz = n+nz;
for (m = nlower_6; m <= nupper_6; m++) {
- my = m+ny;
- for (l = nlower_6; l <= nupper_6; l++) {
- mx = l+nx;
+ my = m+ny;
+ for (l = nlower_6; l <= nupper_6; l++) {
+ mx = l+nx;
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];
@@ -6267,7 +6267,7 @@ void PPPMDisp::fieldforce_a_ad()
ekx6 += x0*u_brick_a6[mz][my][mx];
eky6 += y0*u_brick_a6[mz][my][mx];
ekz6 += z0*u_brick_a6[mz][my][mx];
- }
+ }
}
}
@@ -6380,11 +6380,11 @@ void PPPMDisp::fieldforce_a_peratom()
mz = n+nz;
z0 = rho1d_6[2][n];
for (m = nlower_6; m <= nupper_6; m++) {
- my = m+ny;
- y0 = z0*rho1d_6[1][m];
- for (l = nlower_6; l <= nupper_6; l++) {
- mx = l+nx;
- x0 = y0*rho1d_6[0][l];
+ my = m+ny;
+ y0 = z0*rho1d_6[1][m];
+ for (l = nlower_6; l <= nupper_6; l++) {
+ mx = l+nx;
+ x0 = y0*rho1d_6[0][l];
if (eflag_atom) {
u_pa0 += x0*u_brick_a0[mz][my][mx];
u_pa1 += x0*u_brick_a1[mz][my][mx];
@@ -6393,7 +6393,7 @@ void PPPMDisp::fieldforce_a_peratom()
u_pa4 += x0*u_brick_a4[mz][my][mx];
u_pa5 += x0*u_brick_a5[mz][my][mx];
u_pa6 += x0*u_brick_a6[mz][my][mx];
- }
+ }
if (vflag_atom) {
v00 += x0*v0_brick_a0[mz][my][mx];
v10 += x0*v1_brick_a0[mz][my][mx];
@@ -6438,7 +6438,7 @@ void PPPMDisp::fieldforce_a_peratom()
v46 += x0*v4_brick_a6[mz][my][mx];
v56 += x0*v5_brick_a6[mz][my][mx];
}
- }
+ }
}
}
// convert D-field to force
@@ -6514,17 +6514,17 @@ void PPPMDisp::fieldforce_none_ik()
mz = n+nz;
z0 = rho1d_6[2][n];
for (m = nlower_6; m <= nupper_6; m++) {
- my = m+ny;
- y0 = z0*rho1d_6[1][m];
- for (l = nlower_6; l <= nupper_6; l++) {
- mx = l+nx;
- x0 = y0*rho1d_6[0][l];
+ my = m+ny;
+ y0 = z0*rho1d_6[1][m];
+ for (l = nlower_6; l <= nupper_6; l++) {
+ mx = l+nx;
+ x0 = y0*rho1d_6[0][l];
for (k = 0; k < nsplit; k++) {
- ekx[k] -= x0*vdx_brick_none[k][mz][my][mx];
- eky[k] -= x0*vdy_brick_none[k][mz][my][mx];
- ekz[k] -= x0*vdz_brick_none[k][mz][my][mx];
+ ekx[k] -= x0*vdx_brick_none[k][mz][my][mx];
+ eky[k] -= x0*vdy_brick_none[k][mz][my][mx];
+ ekz[k] -= x0*vdz_brick_none[k][mz][my][mx];
}
- }
+ }
}
}
// convert D-field to force
@@ -6606,9 +6606,9 @@ void PPPMDisp::fieldforce_none_ad()
for (n = nlower_6; n <= nupper_6; n++) {
mz = n+nz;
for (m = nlower_6; m <= nupper_6; m++) {
- my = m+ny;
- for (l = nlower_6; l <= nupper_6; l++) {
- mx = l+nx;
+ my = m+ny;
+ for (l = nlower_6; l <= nupper_6; l++) {
+ mx = l+nx;
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];
@@ -6618,7 +6618,7 @@ void PPPMDisp::fieldforce_none_ad()
eky[k] += y0*u_brick_none[k][mz][my][mx];
ekz[k] += z0*u_brick_none[k][mz][my][mx];
}
- }
+ }
}
}
@@ -6712,15 +6712,15 @@ void PPPMDisp::fieldforce_none_peratom()
mz = n+nz;
z0 = rho1d_6[2][n];
for (m = nlower_6; m <= nupper_6; m++) {
- my = m+ny;
- y0 = z0*rho1d_6[1][m];
- for (l = nlower_6; l <= nupper_6; l++) {
- mx = l+nx;
- x0 = y0*rho1d_6[0][l];
+ my = m+ny;
+ y0 = z0*rho1d_6[1][m];
+ for (l = nlower_6; l <= nupper_6; l++) {
+ mx = l+nx;
+ x0 = y0*rho1d_6[0][l];
if (eflag_atom) {
for (k = 0; k < nsplit; k++)
u_pa[k] += x0*u_brick_none[k][mz][my][mx];
- }
+ }
if (vflag_atom) {
for (k = 0; k < nsplit; k++) {
v0[k] += x0*v0_brick_none[k][mz][my][mx];
@@ -6731,7 +6731,7 @@ void PPPMDisp::fieldforce_none_peratom()
v5[k] += x0*v5_brick_none[k][mz][my][mx];
}
}
- }
+ }
}
}
// convert D-field to force
@@ -7919,12 +7919,12 @@ void PPPMDisp::procs2grid2d(int nprocs, int nx, int ny, int *px, int *py)
if (ny % ipy) boxy++;
surf = boxx + boxy;
if (surf < bestsurf ||
- (surf == bestsurf && boxx*boxy > bestboxx*bestboxy)) {
- bestsurf = surf;
- bestboxx = boxx;
- bestboxy = boxy;
- *px = ipx;
- *py = ipy;
+ (surf == bestsurf && boxx*boxy > bestboxx*bestboxy)) {
+ bestsurf = surf;
+ bestboxx = boxx;
+ bestboxy = boxy;
+ *px = ipx;
+ *py = ipy;
}
}
ipx++;
@@ -7937,7 +7937,7 @@ void PPPMDisp::procs2grid2d(int nprocs, int nx, int ny, int *px, int *py)
------------------------------------------------------------------------- */
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;
@@ -8020,13 +8020,13 @@ void PPPMDisp::compute_rho_coeff(FFT_SCALAR **coeff , FFT_SCALAR **dcoeff,
for (k = -j; k <= j; k += 2) {
s = 0.0;
for (l = 0; l < j; l++) {
- a[l+1][k] = (a[l][k+1]-a[l][k-1]) / (l+1);
+ a[l+1][k] = (a[l][k+1]-a[l][k-1]) / (l+1);
#ifdef FFT_SINGLE
- s += powf(0.5,(float) l+1) *
- (a[l][k-1] + powf(-1.0,(float) l) * a[l][k+1]) / (l+1);
+ 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) *
- (a[l][k-1] + pow(-1.0,(double) l) * a[l][k+1]) / (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
}
a[0][k] = s;
diff --git a/src/KSPACE/pppm_disp.h b/src/KSPACE/pppm_disp.h
index 6993ad6c91..89df3d947e 100644
--- a/src/KSPACE/pppm_disp.h
+++ b/src/KSPACE/pppm_disp.h
@@ -36,8 +36,8 @@ typedef double FFT_SCALAR;
namespace LAMMPS_NS {
-#define EWALD_MAXORDER 6
-#define EWALD_FUNCS 4
+#define EWALD_MAXORDER 6
+#define EWALD_FUNCS 4
class PPPMDisp : public KSpace {
public:
@@ -218,8 +218,8 @@ Variables needed for calculating the 1/r and 1/r^6 potential
int&, int&,int&, int&, int&,int&,
int&, int&,int&, int&, int&,int&,
int&, int&,int&, int&, int&,
- int&, int&, int&,
- double&, double&, int&);
+ int&, int&, int&,
+ double&, double&, int&);
void set_n_pppm_6();
void adjust_gewald();
void adjust_gewald_6();
@@ -266,7 +266,7 @@ Variables needed for calculating the 1/r and 1/r^6 potential
int, int, int,
int, int, int);
virtual void particle_map_c(double, double, double,
- double, int **, int, int,
+ double, int **, int, int,
int, int, int,
int, int, int );
virtual void make_rho_c();
@@ -275,19 +275,19 @@ Variables needed for calculating the 1/r and 1/r^6 potential
virtual void make_rho_none();
virtual void brick2fft(int, int, int, int, int, int,
- FFT_SCALAR ***, FFT_SCALAR *, FFT_SCALAR *,
+ FFT_SCALAR ***, FFT_SCALAR *, FFT_SCALAR *,
LAMMPS_NS::Remap *);
virtual void brick2fft_a();
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, int, int, int,
int, int, int, double&, double *,
double *, double *, double *,
double *, double *, double *,
- FFT_SCALAR ***, FFT_SCALAR ***, FFT_SCALAR ***, double *, double **, double **,
+ FFT_SCALAR ***, FFT_SCALAR ***, FFT_SCALAR ***, double *, double **, double **,
FFT_SCALAR ***, FFT_SCALAR ***, FFT_SCALAR ***, FFT_SCALAR ***,
FFT_SCALAR ***, FFT_SCALAR ***, FFT_SCALAR ***);
@@ -310,31 +310,31 @@ 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 ***, FFT_SCALAR ***, FFT_SCALAR ***, FFT_SCALAR ***,
- FFT_SCALAR ***, FFT_SCALAR ***, FFT_SCALAR ***,
+ FFT_SCALAR ***, 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_2s_ad(FFT_SCALAR *, FFT_SCALAR *,
FFT_SCALAR ***, FFT_SCALAR ***, FFT_SCALAR ***, FFT_SCALAR ***,
- FFT_SCALAR ***, FFT_SCALAR ***, FFT_SCALAR ***,
+ FFT_SCALAR ***, 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_2s_peratom(FFT_SCALAR***, FFT_SCALAR***, FFT_SCALAR***,
- 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_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 ****, FFT_SCALAR ****);
virtual void poisson_none_ik(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 ****,
- FFT_SCALAR ****, FFT_SCALAR ****, FFT_SCALAR ****);
+ FFT_SCALAR ****, FFT_SCALAR ****, FFT_SCALAR ****);
virtual void poisson_none_peratom(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***,
FFT_SCALAR***, FFT_SCALAR***, FFT_SCALAR***);
@@ -353,9 +353,9 @@ Variables needed for calculating the 1/r and 1/r^6 potential
virtual void fieldforce_none_peratom();
void procs2grid2d(int,int,int,int *, int*);
void compute_rho1d(const FFT_SCALAR &, const FFT_SCALAR &,
- const FFT_SCALAR &, int, FFT_SCALAR **, FFT_SCALAR **);
+ const FFT_SCALAR &, int, FFT_SCALAR **, FFT_SCALAR **);
void compute_drho1d(const FFT_SCALAR &, const FFT_SCALAR &,
- const FFT_SCALAR &, int, FFT_SCALAR **, 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 cf3a3943b9..686ed3df8e 100644
--- a/src/KSPACE/pppm_disp_tip4p.cpp
+++ b/src/KSPACE/pppm_disp_tip4p.cpp
@@ -103,8 +103,8 @@ void PPPMDispTIP4P::particle_map_c(double delx, double dely, double delz,
// check that entire stencil around nx,ny,nz will fit in my 3d brick
if (nx+nlow < nxlo || nx+nup > nxhi ||
- ny+nlow < nylo || ny+nup > nyhi ||
- nz+nlow < nzlo || nz+nup > nzhi)
+ ny+nlow < nylo || ny+nup > nyhi ||
+ nz+nlow < nzlo || nz+nup > nzhi)
flag = 1;
}
@@ -159,12 +159,12 @@ void PPPMDispTIP4P::make_rho_c()
mz = n+nz;
y0 = z0*rho1d[2][n];
for (m = nlower; m <= nupper; m++) {
- my = m+ny;
- x0 = y0*rho1d[1][m];
- for (l = nlower; l <= nupper; l++) {
- mx = l+nx;
- density_brick[mz][my][mx] += x0*rho1d[0][l];
- }
+ my = m+ny;
+ x0 = y0*rho1d[1][m];
+ for (l = nlower; l <= nupper; l++) {
+ mx = l+nx;
+ density_brick[mz][my][mx] += x0*rho1d[0][l];
+ }
}
}
}
@@ -217,14 +217,14 @@ void PPPMDispTIP4P::fieldforce_c_ik()
mz = n+nz;
z0 = rho1d[2][n];
for (m = nlower; m <= nupper; m++) {
- my = m+ny;
- y0 = z0*rho1d[1][m];
- for (l = nlower; l <= nupper; l++) {
- mx = l+nx;
- x0 = y0*rho1d[0][l];
- ekx -= x0*vdx_brick[mz][my][mx];
- eky -= x0*vdy_brick[mz][my][mx];
- ekz -= x0*vdz_brick[mz][my][mx];
+ my = m+ny;
+ y0 = z0*rho1d[1][m];
+ for (l = nlower; l <= nupper; l++) {
+ mx = l+nx;
+ x0 = y0*rho1d[0][l];
+ ekx -= x0*vdx_brick[mz][my][mx];
+ eky -= x0*vdy_brick[mz][my][mx];
+ ekz -= x0*vdz_brick[mz][my][mx];
}
}
}
@@ -426,20 +426,20 @@ void PPPMDispTIP4P::fieldforce_c_peratom()
mz = n+nz;
z0 = rho1d[2][n];
for (m = nlower; m <= nupper; m++) {
- my = m+ny;
- y0 = z0*rho1d[1][m];
- 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 (vflag_atom) {
+ my = m+ny;
+ y0 = z0*rho1d[1][m];
+ 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 (vflag_atom) {
v0 += x0*v0_brick[mz][my][mx];
v1 += x0*v1_brick[mz][my][mx];
v2 += x0*v2_brick[mz][my][mx];
v3 += x0*v3_brick[mz][my][mx];
v4 += x0*v4_brick[mz][my][mx];
v5 += x0*v5_brick[mz][my][mx];
- }
+ }
}
}
}
diff --git a/src/MANYBODY/pair_comb.cpp b/src/MANYBODY/pair_comb.cpp
index 00ff865173..5a2b4c2540 100644
--- a/src/MANYBODY/pair_comb.cpp
+++ b/src/MANYBODY/pair_comb.cpp
@@ -1245,8 +1245,8 @@ double PairComb::comb_bij_d(double zeta, Param *param)
if (tmp > param->c1) return param->beta * -0.5*pow(tmp,-1.5);
if (tmp > param->c2)
return param->beta * (-0.5*pow(tmp,-1.5) *
- // error in negligible 2nd term fixed 9/30/2015
- // (1.0 - 0.5*(1.0 + 1.0/(2.0*param->powern)) *
+ // error in negligible 2nd term fixed 9/30/2015
+ // (1.0 - 0.5*(1.0 + 1.0/(2.0*param->powern)) *
(1.0 - (1.0 + 1.0/(2.0*param->powern)) *
pow(tmp,-param->powern)));
if (tmp < param->c4) return 0.0;
diff --git a/src/MANYBODY/pair_comb3.cpp b/src/MANYBODY/pair_comb3.cpp
index 51445cccdd..743511e753 100644
--- a/src/MANYBODY/pair_comb3.cpp
+++ b/src/MANYBODY/pair_comb3.cpp
@@ -166,11 +166,11 @@ void PairComb3::settings(int narg, char **arg)
if (strcmp(arg[0],"polar_on") == 0) {
pol_flag = 1;
if (comm->me == 0 && screen) fprintf(screen,
- " PairComb3: polarization is on \n");
+ " PairComb3: polarization is on \n");
} else if (strcmp(arg[0],"polar_off") == 0) {
pol_flag = 0;
if (comm->me == 0 && screen) fprintf(screen,
- " PairComb3: polarization is off \n");
+ " PairComb3: polarization is off \n");
} else {
error->all(FLERR,"Illegal pair_style command");
}
@@ -209,7 +209,7 @@ void PairComb3::coeff(int narg, char **arg)
for (i = 3; i < narg; i++) {
if ((strcmp(arg[i],"C") == 0) && (cflag == 0)) {
if( comm->me == 0 && screen) fprintf(screen,
- " PairComb3: Found C: reading additional library file\n");
+ " PairComb3: Found C: reading additional library file\n");
read_lib();
cflag = 1;
}
@@ -248,8 +248,8 @@ void PairComb3::coeff(int narg, char **arg)
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
if (map[i] >= 0 && map[j] >= 0) {
- setflag[i][j] = 1;
- count++;
+ setflag[i][j] = 1;
+ count++;
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
@@ -417,7 +417,7 @@ void PairComb3::read_lib()
pcn_gridx[ll][ii][jj][kk] = atof(words[5]);
pcn_gridy[ll][ii][jj][kk] = atof(words[6]);
pcn_gridz[ll][ii][jj][kk] = atof(words[7]);
- }
+ }
for (l=0; l<nsplpcn; l++)
for (i=0; i<maxx; i++)
@@ -439,9 +439,9 @@ void PairComb3::read_lib()
for(m=0; m<32 ; m++) {
mm=iii*32+m;
pcn_cubs[ll][ii][jj][kk][mm] = atof(words[m]);
- }
- }
- }
+ }
+ }
+ }
for (l=0; l<nsplrad; l++)
for (i=0; i<maxxc+1; i++)
@@ -459,7 +459,7 @@ void PairComb3::read_lib()
rad_gridx[ll][ii][jj][kk] = atof(words[5]);
rad_gridy[ll][ii][jj][kk] = atof(words[6]);
rad_gridz[ll][ii][jj][kk] = atof(words[7]);
- }
+ }
for (l=0; l<nsplrad; l++)
for (i=0; i<maxxc; i++)
@@ -481,9 +481,9 @@ void PairComb3::read_lib()
for(m=0; m<32 ; m++){
mm=iii*32+m;
rad_spl[ll][ii][jj][kk][mm] = atof(words[m]);
- }
- }
- }
+ }
+ }
+ }
for (l=0; l<nspltor; l++)
for (i=0; i<maxxc+1; i++)
@@ -501,7 +501,7 @@ void PairComb3::read_lib()
tor_gridx[ll][ii][jj][kk] = atof(words[5]);
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++)
@@ -523,9 +523,9 @@ void PairComb3::read_lib()
for (m=0; m<32 ; m++){
mm=iii*32+m;
tor_spl[ll][ii][jj][kk][mm] = atof(words[m]);
- }
- }
- }
+ }
+ }
+ }
fclose(fp);
}
@@ -623,8 +623,8 @@ void PairComb3::read_file(char *file)
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fp);
if (ptr == NULL) {
- eof = 1;
- fclose(fp);
+ eof = 1;
+ fclose(fp);
} else n = strlen(line) + 1;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
@@ -647,8 +647,8 @@ void PairComb3::read_file(char *file)
if (comm->me == 0) {
ptr = fgets(&line[n],MAXLINE-n,fp);
if (ptr == NULL) {
- eof = 1;
- fclose(fp);
+ eof = 1;
+ fclose(fp);
} else n = strlen(line) + 1;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
@@ -689,7 +689,7 @@ void PairComb3::read_file(char *file)
if (nparams == maxparam) {
maxparam += DELTA;
params = (Param *) memory->srealloc(params,maxparam*sizeof(Param),
- "pair:params");
+ "pair:params");
}
params[nparams].ielement = ielement;
@@ -771,20 +771,20 @@ 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 ||
- 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].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].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].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
+ )
error->all(FLERR,"Illegal COMB3 parameter");
nparams++;
@@ -809,16 +809,16 @@ void PairComb3::setup_params()
for (i = 0; i < nelements; i++)
for (j = 0; j < nelements; j++)
for (k = 0; k < nelements; k++) {
- n = -1;
- for (m = 0; m < nparams; m++) {
- 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;
- }
- }
- if (n < 0) error->all(FLERR,"Potential file is missing an entry");
- elem2param[i][j][k] = n;
+ n = -1;
+ for (m = 0; m < nparams; m++) {
+ 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;
+ }
+ }
+ if (n < 0) error->all(FLERR,"Potential file is missing an entry");
+ elem2param[i][j][k] = n;
}
// compute parameter values derived from inputs
@@ -837,9 +837,9 @@ void PairComb3::setup_params()
(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));
+ 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].QU-params[m].QL);
params[m].lcut = params[m].coulcut;
params[m].lcutsq = params[m].lcut*params[m].lcut;
@@ -873,7 +873,7 @@ void PairComb3::Short_neigh()
memory->sfree(sht_first);
nmax = atom->nmax;
sht_first = (int **) memory->smalloc(nmax*sizeof(int *),
- "pair:sht_first");
+ "pair:sht_first");
memory->grow(dpl,nmax,3,"pair:dpl");
memory->grow(xcctmp,nmax,"pair:xcctmp");
memory->grow(xchtmp,nmax,"pair:xchtmp");
@@ -929,9 +929,9 @@ void PairComb3::Short_neigh()
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;
+ 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;
}
@@ -1125,20 +1125,20 @@ void PairComb3::compute(int eflag, int vflag)
f[j][2] -= delz*fpair;
if (evflag)
- ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair,delx,dely,delz);
+ 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,
- fac11, fac11e, eng_tmp, fvionij, i, j);
+ mr1, mr2, mr3, rsq, sr1, sr2, sr3, iq, jq,
+ fac11, fac11e, eng_tmp, fvionij, i, j);
vionij = eng_tmp;
// field correction to self energy
field(¶ms[iparam_ij], ¶ms[iparam_ji],rsq,iq,jq,
- eng_tmp,fvionij);
+ eng_tmp,fvionij);
vionij += eng_tmp;
// sums up long range Q-dependent forces (excluding dipole)
@@ -1151,18 +1151,18 @@ void PairComb3::compute(int eflag, int vflag)
// sums up long range Q-dependent energies (excluding dipole)
if (evflag)
- ev_tally(i,j,nlocal,newton_pair,0.0,vionij,fvionij,delx,dely,delz);
+ ev_tally(i,j,nlocal,newton_pair,0.0,vionij,fvionij,delx,dely,delz);
// polarization field
if (pol_flag) {
dipole_calc(¶ms[iparam_ij], ¶ms[iparam_ji],fac11,
- delx,dely,delz,rsq,mr1,mr2,mr3,
- sr1,sr2,sr3,iq,jq,i,j,eng_tmp,fvionij,ddprx);
- vionij = eng_tmp;
+ delx,dely,delz,rsq,mr1,mr2,mr3,
+ sr1,sr2,sr3,iq,jq,i,j,eng_tmp,fvionij,ddprx);
+ vionij = eng_tmp;
// sums up dipole energies
if (evflag)
- ev_tally(i,j,nlocal,newton_pair,0.0,vionij,fvionij,delx,dely,delz);
+ ev_tally(i,j,nlocal,newton_pair,0.0,vionij,fvionij,delx,dely,delz);
// sums up dipole forces
f[i][0] += (ddprx[0] + delx*fvionij);
@@ -1176,7 +1176,7 @@ void PairComb3::compute(int eflag, int vflag)
if (rsq > params[iparam_ij].cutsq) continue;
repulsive(¶ms[iparam_ij], ¶ms[iparam_ji], rsq,
- fpair, eflag, eng_tmp, iq, jq);
+ fpair, eflag, eng_tmp, iq, jq);
evdwl = eng_tmp;
@@ -1189,7 +1189,7 @@ void PairComb3::compute(int eflag, int vflag)
f[j][2] -= delz*fpair;
if (evflag)
- ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair,delx,dely,delz);
+ ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair,delx,dely,delz);
}
// many-body interactions: start of short-range
@@ -1222,27 +1222,27 @@ void PairComb3::compute(int eflag, int vflag)
bbtor = 0.0;
kconjug = 0.0;
- for (kk = 0; kk < sht_jnum; kk++) { // kk is neighbor of ii
- k = sht_jlist[kk];
- if (j == k) continue;
+ for (kk = 0; kk < sht_jnum; kk++) { // kk is neighbor of ii
+ k = sht_jlist[kk];
+ if (j == k) continue;
- ktype = map[type[k]];
- iparam_ijk = elem2param[itype][jtype][ktype];
- iparam_ikj = elem2param[itype][ktype][jtype];
- iparam_jik = elem2param[jtype][itype][ktype];
- iparam_ik = elem2param[itype][ktype][ktype];
- delrk[0] = x[k][0] - xtmp;
- delrk[1] = x[k][1] - ytmp;
- delrk[2] = x[k][2] - ztmp;
- rsq2 = vec3_dot(delrk,delrk);
+ ktype = map[type[k]];
+ iparam_ijk = elem2param[itype][jtype][ktype];
+ iparam_ikj = elem2param[itype][ktype][jtype];
+ iparam_jik = elem2param[jtype][itype][ktype];
+ iparam_ik = elem2param[itype][ktype][ktype];
+ delrk[0] = x[k][0] - xtmp;
+ delrk[1] = x[k][1] - ytmp;
+ delrk[2] = x[k][2] - ztmp;
+ rsq2 = vec3_dot(delrk,delrk);
- if (rsq2 > params[iparam_ik].cutsq) continue;
+ if (rsq2 > params[iparam_ik].cutsq) continue;
- // 3-body zeta in bond order
- zeta_ij += zeta(¶ms[iparam_ijk], ¶ms[iparam_ik],
- rsq1, rsq2, delrj, delrk, i, xcn);
+ // 3-body zeta in bond order
+ zeta_ij += zeta(¶ms[iparam_ijk], ¶ms[iparam_ik],
+ rsq1, rsq2, delrj, delrk, i, xcn);
- // radical initialization: apply only to CC,CO,OC bonds
+ // radical initialization: apply only to CC,CO,OC bonds
if (params[iparam_ij].rad_flag > 0 &&
params[iparam_ik].ielementgp == 1 &&
params[iparam_ik].jelementgp == 1) {
@@ -1252,68 +1252,68 @@ void PairComb3::compute(int eflag, int vflag)
}
- // torsion: i-j-k-l: apply to all C-C bonds
+ // torsion: i-j-k-l: apply to all C-C bonds
- if( params[iparam_ij].tor_flag != 0 ) {
- srmu = vec3_dot(delrj,delrk)/(sqrt(rsq1*rsq2));
- srmu = sqrt(1.0-srmu*srmu);
+ if( params[iparam_ij].tor_flag != 0 ) {
+ srmu = vec3_dot(delrj,delrk)/(sqrt(rsq1*rsq2));
+ srmu = sqrt(1.0-srmu*srmu);
- if(srmu > 0.1) {
- for (ll = 0; ll < sht_lnum; ll++) { // ll is neighbor of jj
- l = sht_llist[ll];
+ 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;
+ if(l==i || l==j || l==k) continue;
- ltype = map[type[l]];
+ ltype = map[type[l]];
- 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];
+ 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;
+ 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],
+ bbtor += bbtor1(torindx, ¶ms[iparam_ikl],¶ms[iparam_jl],
rsq1,rsq2,rsq3,delrj,delrk,delrl,srmu);
- }
- }
- }
+ }
+ }
+ }
}
zeta_ji = 0.0;
lconjug = 0.0;
for (ll = 0; ll < sht_lnum; ll++) {
- l = sht_llist[ll];
- if (l == i) continue;
+ l = sht_llist[ll];
+ if (l == i) continue;
- ltype = map[type[l]];
- iparam_jil = elem2param[jtype][itype][ltype];
- iparam_ijl = elem2param[itype][jtype][ltype];
- iparam_jl = elem2param[jtype][ltype][ltype];
- iparam_lj = elem2param[ltype][jtype][jtype];
+ ltype = map[type[l]];
+ iparam_jil = elem2param[jtype][itype][ltype];
+ iparam_ijl = elem2param[itype][jtype][ltype];
+ iparam_jl = elem2param[jtype][ltype][ltype];
+ iparam_lj = elem2param[ltype][jtype][jtype];
- delrk[0] = x[l][0] - x[j][0];
- delrk[1] = x[l][1] - x[j][1];
- delrk[2] = x[l][2] - x[j][2];
- rsq2 = vec3_dot(delrk,delrk);
+ delrk[0] = x[l][0] - x[j][0];
+ delrk[1] = x[l][1] - x[j][1];
+ delrk[2] = x[l][2] - x[j][2];
+ rsq2 = vec3_dot(delrk,delrk);
- delrl[0] = x[l][0] - x[j][0];
- delrl[1] = x[l][1] - x[j][1];
- delrl[2] = x[l][2] - x[j][2];
- rsq2 = vec3_dot(delrl,delrl);
+ delrl[0] = x[l][0] - x[j][0];
+ delrl[1] = x[l][1] - x[j][1];
+ delrl[2] = x[l][2] - x[j][2];
+ rsq2 = vec3_dot(delrl,delrl);
- if (rsq2 > params[iparam_jl].cutsq) continue;
+ if (rsq2 > params[iparam_jl].cutsq) continue;
- vec3_scale(-1,delrj,delrl); // ji_hat is -(ij_hat)
+ vec3_scale(-1,delrj,delrl); // ji_hat is -(ij_hat)
- zeta_ji += zeta(¶ms[iparam_jil], ¶ms[iparam_jl]
- , rsq1, rsq2, delrl, delrk, j, ycn);
+ zeta_ji += zeta(¶ms[iparam_jil], ¶ms[iparam_jl]
+ , rsq1, rsq2, delrl, delrk, j, ycn);
- // radical initialization: apply only to CC,CO,OC bonds
+ // radical initialization: apply only to CC,CO,OC bonds
if(params[iparam_ji].rad_flag > 0
&& params[iparam_jl].ielementgp == 1
&& params[iparam_jl].jelementgp == 1) {
@@ -1324,10 +1324,10 @@ void PairComb3::compute(int eflag, int vflag)
}
force_zeta(¶ms[iparam_ij], ¶ms[iparam_ji],
- rsq1, xcn, ycn, zeta_ij, zeta_ji, fpair,
- prefac_ij1, prefac_ij2, prefac_ij3, prefac_ij4, prefac_ij5,
- prefac_ji1, prefac_ji2, prefac_ji3, prefac_ji4, prefac_ji5,
- eflag, eng_tmp, iq, jq, i, j, nj, bbtor, kconjug, lconjug);
+ rsq1, xcn, ycn, zeta_ij, zeta_ji, fpair,
+ prefac_ij1, prefac_ij2, prefac_ij3, prefac_ij4, prefac_ij5,
+ prefac_ji1, prefac_ji2, prefac_ji3, prefac_ji4, prefac_ji5,
+ eflag, eng_tmp, iq, jq, i, j, nj, bbtor, kconjug, lconjug);
evdwl = eng_tmp;
selfp6p(¶ms[iparam_ij],¶ms[iparam_ji],rsq1,eng_tmp,fpair);
@@ -1347,77 +1347,77 @@ void PairComb3::compute(int eflag, int vflag)
zet_addj=0;
for (kk = 0; kk < sht_jnum; kk++) {
- k = sht_jlist[kk];
- if (j == k) continue;
+ k = sht_jlist[kk];
+ if (j == k) continue;
sht_mlist = sht_first[k];
sht_mnum = sht_num[k];
- ktype = map[type[k]];
- iparam_ijk = elem2param[itype][jtype][ktype];
- iparam_ikj = elem2param[itype][ktype][jtype];
- iparam_jik = elem2param[jtype][itype][ktype];
- iparam_ik = elem2param[itype][ktype][ktype];
- delrk[0] = x[k][0] - xtmp;
- delrk[1] = x[k][1] - ytmp;
- 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);
-
- // Sums up i-j-k forces: LP contribution
- for (im = 0; im < 3; im++) {
- fi[im] += fip6p[im];
- fj[im] += fjp6p[im];
- fk[im] += fkp6p[im];
- }
-
- // Sums up i-j-k forces: Tallies into global force vector
- for (im = 0; im < 3; im++) {
- f[i][im] += fi[im];
- f[j][im] += fj[im];
- f[k][im] += fk[im];
- }
-
- // torsion and radical: apply to all C-C bonds
- if( params[iparam_ijk].tor_flag != 0 && fabs(ptorr)>1.0e-8) {
- srmu = vec3_dot(delrj,delrk)/(sqrt(rsq1*rsq2));
- srmu = sqrt(1.0-srmu*srmu);
-
- 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;
-
- ltype = map[type[l]];
-
- 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];
+ ktype = map[type[k]];
+ iparam_ijk = elem2param[itype][jtype][ktype];
+ iparam_ikj = elem2param[itype][ktype][jtype];
+ iparam_jik = elem2param[jtype][itype][ktype];
+ iparam_ik = elem2param[itype][ktype][ktype];
+ delrk[0] = x[k][0] - xtmp;
+ delrk[1] = x[k][1] - ytmp;
+ 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);
+
+ // Sums up i-j-k forces: LP contribution
+ for (im = 0; im < 3; im++) {
+ fi[im] += fip6p[im];
+ fj[im] += fjp6p[im];
+ fk[im] += fkp6p[im];
+ }
+
+ // Sums up i-j-k forces: Tallies into global force vector
+ for (im = 0; im < 3; im++) {
+ f[i][im] += fi[im];
+ f[j][im] += fj[im];
+ f[k][im] += fk[im];
+ }
+
+ // torsion and radical: apply to all C-C bonds
+ if( params[iparam_ijk].tor_flag != 0 && fabs(ptorr)>1.0e-8) {
+ srmu = vec3_dot(delrj,delrk)/(sqrt(rsq1*rsq2));
+ srmu = sqrt(1.0-srmu*srmu);
+
+ 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;
+
+ ltype = map[type[l]];
+
+ 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];
torindx = params[iparam_ij].tor_flag;
- tor_force(torindx, ¶ms[iparam_ikl], ¶ms[iparam_jl],srmu,
+ tor_force(torindx, ¶ms[iparam_ikl], ¶ms[iparam_jl],srmu,
rsq1,rsq2,rsq3,delrj,delrk,delrl);
- for (im = 0; im < 3; im++) {
- f[i][im] += fi_tor[im];
- f[j][im] += fj_tor[im];
- f[k][im] += fk_tor[im];
- f[l][im] += fl_tor[im];
- }
- }
- }
- }
+ for (im = 0; im < 3; im++) {
+ f[i][im] += fi_tor[im];
+ f[j][im] += fj_tor[im];
+ f[k][im] += fk_tor[im];
+ f[l][im] += fl_tor[im];
+ }
+ }
+ }
+ }
if( params[iparam_ijk].rad_flag>=1 &&
params[iparam_ijk].ielementgp==1 &&
@@ -1427,95 +1427,95 @@ void PairComb3::compute(int eflag, int vflag)
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);
+ rad_forceik(¶ms[iparam_ki],rsq2,delrk,kconjug,kradtot);
- for (im = 0; im < 3; im++) {
- f[i][im] += fi_rad[im];
- f[k][im] += fk_rad[im];
- }
+ for (im = 0; im < 3; im++) {
+ f[i][im] += fi_rad[im];
+ f[k][im] += fk_rad[im];
+ }
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;
+ for (mm = 0; mm < sht_mnum; mm++) { // mm is neighbor of kk
+ m = sht_mlist[mm];
+ if (m == k) continue;
mtype = map[type[m]];
- 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);
+ 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);
- iparam_km = elem2param[ktype][mtype][mtype];
- iparam_ki = elem2param[ktype][itype][itype];
+ iparam_km = elem2param[ktype][mtype][mtype];
+ iparam_ki = elem2param[ktype][itype][itype];
- if (rsq3 > params[iparam_km].cutsq) continue;
+ if (rsq3 > params[iparam_km].cutsq) continue;
- rad_force(¶ms[iparam_km],rsq3,delrm,radtmp);
+ rad_force(¶ms[iparam_km],rsq3,delrm,radtmp);
- for (im = 0; im < 3; im++) {
- f[k][im] += fj_rad[im];
- f[m][im] += fk_rad[im];
- }
- }
- }
- }
+ for (im = 0; im < 3; im++) {
+ f[k][im] += fj_rad[im];
+ f[m][im] += fk_rad[im];
+ }
+ }
+ }
+ }
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);
+ 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);
- } // k-loop
+ } // k-loop
// attractive term via loop over l (3-body forces: j-i-l)
for (ll = 0; ll < sht_lnum; ll++) {
- l = sht_llist[ll];
- if (l == i) continue;
+ l = sht_llist[ll];
+ if (l == i) continue;
sht_plist = sht_first[l];
sht_pnum = sht_num[l];
- ltype = map[type[l]];
- iparam_jil = elem2param[jtype][itype][ltype];
- 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[1] = x[l][1] - x[j][1];
- delrk[2] = x[l][2] - x[j][2];
+ ltype = map[type[l]];
+ iparam_jil = elem2param[jtype][itype][ltype];
+ 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[1] = x[l][1] - x[j][1];
+ delrk[2] = x[l][2] - x[j][2];
- rsq2 = vec3_dot(delrk,delrk);
- if (rsq2 > params[iparam_jl].cutsq) continue;
- vec3_scale(-1,delrj,delrl);
+ rsq2 = vec3_dot(delrk,delrk);
+ if (rsq2 > params[iparam_jl].cutsq) continue;
+ vec3_scale(-1,delrj,delrl);
- attractive(¶ms[iparam_jil],¶ms[iparam_ijl],¶ms[iparam_jli],
- prefac_ji1,prefac_ji2,prefac_ji3,prefac_ji4,prefac_ji5,
- rsq1,rsq2,delrl,delrk,fj,fi,fl,j,ycn);
+ attractive(¶ms[iparam_jil],¶ms[iparam_ijl],¶ms[iparam_jli],
+ prefac_ji1,prefac_ji2,prefac_ji3,prefac_ji4,prefac_ji5,
+ rsq1,rsq2,delrl,delrk,fj,fi,fl,j,ycn);
- // 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);
+ // 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);
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
- for (im = 0; im < 3; im++) {
- fj[im] += fjp6p[im];
- fi[im] += fip6p[im];
- fl[im] += flp6p[im];
- }
-
- // Sums up j-i-l forces: Tallies into global force vector
- for (im = 0; im < 3; im++) {
- f[j][im] += fj[im];
- 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 &&
+ 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
+ for (im = 0; im < 3; im++) {
+ fj[im] += fjp6p[im];
+ fi[im] += fip6p[im];
+ fl[im] += flp6p[im];
+ }
+
+ // Sums up j-i-l forces: Tallies into global force vector
+ for (im = 0; im < 3; im++) {
+ f[j][im] += fj[im];
+ 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 &&
params[iparam_jil].ielementgp == 1 &&
params[iparam_jil].kelementgp == 1 ) {
iparam_lj = elem2param[ltype][jtype][jtype];
@@ -1525,39 +1525,39 @@ void PairComb3::compute(int eflag, int vflag)
rad_forceik(¶ms[iparam_lj],rsq2,delrk,lconjug,lradtot);
- for (im = 0; im < 3; im++) {
- f[j][im] += fi_rad[im];
- f[l][im] += fk_rad[im];
- }
+ for (im = 0; im < 3; im++) {
+ f[j][im] += fi_rad[im];
+ f[l][im] += fk_rad[im];
+ }
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;
- ptype = map[type[p]];
-
- 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);
-
- iparam_lp = elem2param[ltype][ptype][ptype];
-
- if (rsq3 > params[iparam_lp].cutsq) continue;
-
- vec3_scale(-1,delrj,delrj);
- rad_force(¶ms[iparam_lp],rsq3,delrp,radtmp);
- vec3_scale(-1,delrj,delrj);
- for (im = 0; im < 3; im++) {
- f[l][im] += fj_rad[im];
- f[p][im] += fk_rad[im];
- }
- }
- }
- }
-
- if (vflag_atom)
- v_tally3(j,i,l,fi,fl,delrl,delrk);
+ for (pp = 0; pp < sht_pnum; pp++) { // pp is neighbor of ll
+ p = sht_plist[pp];
+ if (p == l) continue;
+ ptype = map[type[p]];
+
+ 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);
+
+ iparam_lp = elem2param[ltype][ptype][ptype];
+
+ if (rsq3 > params[iparam_lp].cutsq) continue;
+
+ vec3_scale(-1,delrj,delrj);
+ rad_force(¶ms[iparam_lp],rsq3,delrp,radtmp);
+ vec3_scale(-1,delrj,delrj);
+ for (im = 0; im < 3; im++) {
+ f[l][im] += fj_rad[im];
+ f[p][im] += fk_rad[im];
+ }
+ }
+ }
+ }
+
+ if (vflag_atom)
+ v_tally3(j,i,l,fi,fl,delrl,delrk);
}
}
}
@@ -1569,7 +1569,7 @@ void PairComb3::compute(int eflag, int vflag)
/* ---------------------------------------------------------------------- */
void PairComb3::repulsive(Param *parami, Param *paramj, double rsq,
- double &fforce,int eflag, double &eng, double iq, double jq)
+ double &fforce,int eflag, double &eng, double iq, double jq)
{
double r,tmp_fc,tmp_fc_d,Di,Dj;
double caj,vrcs,fvrcs;
@@ -1614,7 +1614,7 @@ void PairComb3::repulsive(Param *parami, Param *paramj, double rsq,
/* ---------------------------------------------------------------------- */
double PairComb3::zeta(Param *parami, Param *paramj, double rsqij,
- double rsqik, double *delrij, double *delrik, int i, double xcn)
+ double rsqik, double *delrij, double *delrik, int i, double xcn)
{
double rij,rik,costheta,arg,ex_delr,rlm3;
@@ -1635,7 +1635,7 @@ double PairComb3::zeta(Param *parami, Param *paramj, double rsqij,
/* ---------------------------------------------------------------------- */
void PairComb3::selfp6p(Param *parami, Param *paramj, double rsq,
- double &eng, double &force)
+ double &eng, double &force)
{
double r,comtti,comttj,fcj,fcj_d;
@@ -1661,7 +1661,7 @@ void PairComb3::selfp6p(Param *parami, Param *paramj, double rsq,
/* ---------------------------------------------------------------------- */
double PairComb3::ep6p(Param *paramj, Param *paramk, double rsqij, double rsqik,
- double *delrij, double *delrik , double &zet_add)
+ double *delrij, double *delrik , double &zet_add)
{
double comtt;
double pplp0 = paramj->p6p0;
@@ -1693,8 +1693,8 @@ 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 *drjlp, double *drklp)
+ double *delrij, double *delrik, double *drilp,
+ double *drjlp, double *drklp)
{
double pplp0 = paramij->p6p0;
double pplp1 = paramij->p6p1, pplp2 = paramij->p6p2, pplp3 = paramij->p6p3;
@@ -1760,13 +1760,13 @@ void PairComb3::fp6p(Param *paramij,Param *paramik, double rsqij, double rsqik,
/* ---------------------------------------------------------------------- */
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 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_ji4, double &prefac_ji5,
int eflag, double &eng, double iq, double jq,
- int i, int j, int nj, double bbtor, double kconjug, double lconjug)
+ int i, int j, int nj, double bbtor, double kconjug, double lconjug)
{
double r,att_eng,att_force,bij; // att_eng is -cbj
double boij, dbij1, dbij2, dbij3, dbij4, dbij5;
@@ -1803,17 +1803,17 @@ void PairComb3::force_zeta(Param *parami, Param *paramj, double rsq,
fforce = 1.0*bij*att_force/r; // divide by r will done compute
bbij[i][nj] = bij;
- prefac_ij1 = -0.5*att_eng*dbij1; // prefac_ij1 = -pfij
- prefac_ij2 = -0.5*att_eng*dbij2; // prefac_ij2 = -pfij1
- prefac_ij3 = -0.5*att_eng*dbij3; // prefac_ij3 = -pfij2
- prefac_ij4 = -0.5*att_eng*dbij4; // prefac_ij4 = -pfij3
- prefac_ij5 = -0.5*att_eng*dbij5; // prefac_ij5 = -pfij4
+ prefac_ij1 = -0.5*att_eng*dbij1; // prefac_ij1 = -pfij
+ prefac_ij2 = -0.5*att_eng*dbij2; // prefac_ij2 = -pfij1
+ prefac_ij3 = -0.5*att_eng*dbij3; // prefac_ij3 = -pfij2
+ prefac_ij4 = -0.5*att_eng*dbij4; // prefac_ij4 = -pfij3
+ prefac_ij5 = -0.5*att_eng*dbij5; // prefac_ij5 = -pfij4
- prefac_ji1 = -0.5*att_eng*dbji1; // prefac_ji1 = -pfji
- prefac_ji2 = -0.5*att_eng*dbji2; // prefac_ji2 = -pfji1
- prefac_ji3 = -0.5*att_eng*dbji3; // prefac_ji3 = -pfji2
- prefac_ji4 = -0.5*att_eng*dbji4; // prefac_ji4 = -pfji3
- prefac_ji5 = -0.5*att_eng*dbji5; // prefac_ji5 = -pfji4
+ prefac_ji1 = -0.5*att_eng*dbji1; // prefac_ji1 = -pfji
+ prefac_ji2 = -0.5*att_eng*dbji2; // prefac_ji2 = -pfji1
+ prefac_ji3 = -0.5*att_eng*dbji3; // prefac_ji3 = -pfji2
+ prefac_ji4 = -0.5*att_eng*dbji4; // prefac_ji4 = -pfji3
+ prefac_ji5 = -0.5*att_eng*dbji5; // prefac_ji5 = -pfji4
// combines com6 & com7 below
if ( parami->rad_flag>0 || parami->tor_flag!=0 ) {
@@ -1954,7 +1954,7 @@ double PairComb3::self(Param *param, double qi)
/* ---------------------------------------------------------------------- */
void PairComb3::comb_fa(double r, Param *parami, Param *paramj, double iq,
- double jq, double &att_eng, double &att_force)
+ double jq, double &att_eng, double &att_force)
{
double Bsi;
double qi,qj,Di,Dj;
@@ -1977,12 +1977,12 @@ void PairComb3::comb_fa(double r, Param *parami, Param *paramj, double iq,
if (YYBn*YYBj > 0.0 ) {
AlfDiAlfDj = exp(0.5*(parami->alfi*Di+paramj->alfi*Dj));
Bsi = (pbij1*exp(-alfij1*r)+pbij2*exp(-alfij2*r)+pbij3*exp(-alfij3*r))*
- sqrt(YYBn*YYBj)*AlfDiAlfDj; // Bsi is cbj
+ sqrt(YYBn*YYBj)*AlfDiAlfDj; // Bsi is cbj
att_eng = -Bsi * comb_fc(r,parami);
att_force = -(Bsi*comb_fc_d(r,parami)-comb_fc(r,parami)*sqrt(YYBn*YYBj)*
- AlfDiAlfDj*(alfij1*pbij1*exp(-alfij1*r)+
- alfij2*pbij2*exp(-alfij2*r)+alfij3*pbij3*exp(-alfij3*r)));
+ AlfDiAlfDj*(alfij1*pbij1*exp(-alfij1*r)+
+ alfij2*pbij2*exp(-alfij2*r)+alfij3*pbij3*exp(-alfij3*r)));
} else {
att_eng = 0.0;
@@ -1994,15 +1994,15 @@ 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,
- double &tbij3, double &tbij4, double &tbij5, double xcn)
+ double &tbij, double &tbij1, double &tbij2,
+ double &tbij3, double &tbij4, double &tbij5, double xcn)
{
double pcorn,dpcorn,dxccij,dxchij,dxcoij;
double zeta = zet;
double zetang,tmp_tbij, pow_n;
pcorn = dpcorn = dxccij = dxchij = dxcoij = 0.0;
- coord(param,r,i,pcorn,dpcorn,dxccij,dxchij,dxcoij,xcn); // coordination term
+ coord(param,r,i,pcorn,dpcorn,dxccij,dxchij,dxcoij,xcn); // coordination term
zetang=zeta;
pow_n=param->powern;
@@ -2042,8 +2042,8 @@ 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 &dxchij, double &dxcoij, double xcn)
+ double &pcorn, double &dpcorn, double &dxccij,
+ double &dxchij, double &dxcoij, double xcn)
{
int ixmin,iymin,izmin;
double xcntot,xcccn,xchcn,xcocn;
@@ -2109,7 +2109,7 @@ 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,
- double &dvalx, double &dvaly, double &dvalz, Param *param)
+ double &dvalx, double &dvaly, double &dvalz, Param *param)
{
double x;
vval = 0.0; dvalx = 0.0; dvaly = 0.0; dvalz = 0.0;
@@ -2183,7 +2183,7 @@ 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 &gijk_d, double &com3jk)
{
double rmu1 = costheta;
double rmu2 = rmu1*rmu1;
@@ -2252,9 +2252,9 @@ 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,
- double *delrik, double *fi, double *fj,double *fk, int i, double xcn)
+ 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];
double rij,rijinv,rik,rikinv;
@@ -2268,16 +2268,16 @@ void PairComb3::attractive(Param *parami, Param *paramj , Param *paramk, double
vec3_scale(rikinv,delrik,rik_hat);
comb_zetaterm_d(prefac_ij1, prefac_ij2, prefac_ij3, prefac_ij4, prefac_ij5,
- rij_hat, rij,rik_hat, rik, fi, fj, fk, parami, paramj, paramk,xcn);
+ rij_hat, rij,rik_hat, rik, fi, fj, fk, parami, paramj, paramk,xcn);
}
/* ---------------------------------------------------------------------- */
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 *drj, double *drk, Param *parami, Param *paramj, Param *paramk, double xcn)
+ double prefac_ij3, double prefac_ij4, double prefac_ij5,
+ 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;
double dcosdri[3],dcosdrj[3],dcosdrk[3],dfc_i,dfc_k;
@@ -2325,32 +2325,32 @@ void PairComb3::comb_zetaterm_d(double prefac_ij1, double prefac_ij2,
}
ex_delr_d = mint*pow(rlm3,mint)*pow((rij-rik),(mint-1))*ex_delr; // com3
- vec3_scale(-dfc_k*gijk*ex_delr,rik_hat,dri); // com1
- vec3_scaleadd(fc_k*gijk_d*ex_delr,dcosdri,dri,dri); // com2
- vec3_scaleadd(fc_k*gijk*ex_delr_d,rik_hat,dri,dri); // com3 cont'd
- vec3_scaleadd(-fc_k*gijk*ex_delr_d,rij_hat,dri,dri); // com3 sums j
- vec3_scaleadd(-com3k,rik_hat,dri,dri); // com3k
- vec3_scaleadd(-com3j,rij_hat,dri,dri); // com3j
+ vec3_scale(-dfc_k*gijk*ex_delr,rik_hat,dri); // com1
+ vec3_scaleadd(fc_k*gijk_d*ex_delr,dcosdri,dri,dri); // com2
+ vec3_scaleadd(fc_k*gijk*ex_delr_d,rik_hat,dri,dri); // com3 cont'd
+ vec3_scaleadd(-fc_k*gijk*ex_delr_d,rij_hat,dri,dri); // com3 sums j
+ vec3_scaleadd(-com3k,rik_hat,dri,dri); // com3k
+ vec3_scaleadd(-com3j,rij_hat,dri,dri); // com3j
vec3_scale(prefac_ij1,dri,dri);
- vec3_scaleadd(-com6,rik_hat,dri,dri); // com6
+ vec3_scaleadd(-com6,rik_hat,dri,dri); // com6
- vec3_scale(fc_k*gijk_d*ex_delr,dcosdrj,drj); // com2
- 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(fc_k*gijk_d*ex_delr,dcosdrj,drj); // com2
+ 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_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_scale(prefac_ij1,drk,drk);
- vec3_scaleadd(com6,rik_hat,drk,drk); // com6
+ vec3_scaleadd(com6,rik_hat,drk,drk); // com6
}
/* ---------------------------------------------------------------------- */
void PairComb3::costheta_d(double *rij_hat, double rij, double *rik_hat,
- double rik, double *dri, double *drj, double *drk)
+ double rik, double *dri, double *drj, double *drk)
{
double cos_theta = vec3_dot(rij_hat,rik_hat);
@@ -2641,11 +2641,11 @@ void PairComb3::tables()
drf13= 12.0*(1.0/vrc[12]-1.0/r13);
vvdw[k][inty] = vepst*(vsigt*vsigt*rf12-vsigt*rf6);
vdvdw[k][inty] = vepst*(vsigt*vsigt*drf13-vsigt*drf7);
- }
- } else {
+ }
+ } else {
vvdw[k][inty]=0.0;
vdvdw[k][inty]=0.0;
- }
+ }
r += dra;
}
}
@@ -2673,7 +2673,7 @@ void PairComb3::potal_calc(double &calc1, double &calc2, double &calc3)
esucon = force->qqr2e;
calc2 = (erfc(rcoul*alf)/rcoul/rcoul+2.0*alf/MY_PIS*
- exp(-alf*alf*rcoul*rcoul)/rcoul)*esucon/rcoul;
+ exp(-alf*alf*rcoul*rcoul)/rcoul)*esucon/rcoul;
calc3 = (erfc(rcoul*alf)/rcoul)*esucon;
calc1 = -(alf/MY_PIS*esucon+calc3*0.5);
}
@@ -2681,7 +2681,7 @@ void PairComb3::potal_calc(double &calc1, double &calc2, double &calc3)
/* ---------------------------------------------------------------------- */
void PairComb3::tri_point(double rsq, int &mr1, int &mr2,
- int &mr3, double &sr1, double &sr2, double &sr3)
+ int &mr3, double &sr1, double &sr2, double &sr3)
{
double r, rin, dr, dd, rr1, rridr, rridr2;
@@ -2710,8 +2710,8 @@ 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 &eng, double &fforce)
+ double sr1, double sr2, double sr3,
+ double &eng, double &fforce)
{
double r = sqrt(rsq);
@@ -2722,9 +2722,9 @@ 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,
- double &pot_tmp, double &for_tmp, int i, int j)
+ 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;
double r3,erfcd,dfafbnl,smf2,dvdrr,alf,alfdpi;
@@ -2814,7 +2814,7 @@ void PairComb3::direct(Param *parami, Param *paramj, int mr1,
/* ---------------------------------------------------------------------- */
void PairComb3::field(Param *parami, Param *paramj, double rsq, double iq,
- double jq, double &eng_tmp,double &for_tmp)
+ double jq, double &eng_tmp,double &for_tmp)
{
double r,r3,r4,r5,rc,rc2,rc3,rc4,rc5;
double cmi1,cmi2,cmj1,cmj2,pcmi1,pcmi2;
@@ -2868,7 +2868,7 @@ void PairComb3::field(Param *parami, Param *paramj, double rsq, double iq,
/* ---------------------------------------------------------------------- */
double PairComb3::rad_init(double rsq2,Param *param,int i,
- double &radtot, double cnconj)
+ double &radtot, double cnconj)
{
double r, fc1k, radcut;
@@ -2882,7 +2882,7 @@ double PairComb3::rad_init(double rsq2,Param *param,int i,
/* ---------------------------------------------------------------------- */
void PairComb3::rad_calc(double r, Param *parami, Param *paramj,
- double kconjug, double lconjug, int i, int j, double xcn, double ycn)
+ double kconjug, double lconjug, int i, int j, double xcn, double ycn)
{
int ixmin, iymin, izmin;
int radindx;
@@ -2907,7 +2907,7 @@ void PairComb3::rad_calc(double r, Param *parami, Param *paramj,
fabs(float(iymin)-yrad)>1.0e-8 ||
fabs(float(izmin)-zcon)>1.0e-8) {
rad_int(radindx,xrad,yrad,zcon,ixmin,iymin,izmin,
- vrad,pradx,prady,pradz);
+ vrad,pradx,prady,pradz);
} else {
vrad = rad_grid[radindx][ixmin][iymin][izmin-1];
pradx = rad_gridx[radindx][ixmin][iymin][izmin-1];
@@ -2924,8 +2924,8 @@ 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,
- double &pradz)
+ int m, int n, double &vrad, double &pradx, double &prady,
+ double &pradz)
{
int j;
double x;
@@ -2936,7 +2936,7 @@ void PairComb3::rad_int(int radindx,double xrad, double yrad, double zcon, int l
for (j=0; j<64; j++) {
x = rad_spl[radindx][l][m][n-1][j] * pow(xrad,iin3[j][0])
- * pow(yrad,iin3[j][1]) * pow(zcon,iin3[j][2]);
+ * pow(yrad,iin3[j][1]) * pow(zcon,iin3[j][2]);
vrad += x;
if(xrad > 1.0e-8) pradx += x*iin3[j][0]/xrad;
if(yrad > 1.0e-8) prady += x*iin3[j][1]/yrad;
@@ -2983,7 +2983,7 @@ void PairComb3::rad_forceik(Param *paramk, double rsq2, double *delrk,
/* ---------------------------------------------------------------------- */
void PairComb3::rad_force(Param *paramm, double rsq3,
- double *delrm, double dpradk)
+ double *delrm, double dpradk)
{
int nm;
double rkm, fcp1m;
@@ -3061,7 +3061,7 @@ double PairComb3::bbtor1(int torindx, Param *paramk, Param *paraml,
/* ---------------------------------------------------------------------- */
void PairComb3::tor_calc(double r, Param *parami, Param *paramj,
- double kconjug, double lconjug, int i, int j, double xcn, double ycn)
+ double kconjug, double lconjug, int i, int j, double xcn, double ycn)
{
int ixmin, iymin, izmin;
double vtor, dtorx, dtory, dtorz;
@@ -3115,7 +3115,7 @@ void PairComb3::tor_calc(double r, Param *parami, Param *paramj,
/* ---------------------------------------------------------------------- */
void PairComb3::tor_int(int torindx,double xtor, double ytor, double zcon, int l,
- int m, int n, double &vtor, double &dtorx, double &dtory, double &dtorz)
+ int m, int n, double &vtor, double &dtorx, double &dtory, double &dtorz)
{
int j;
double x;
@@ -3127,7 +3127,7 @@ void PairComb3::tor_int(int torindx,double xtor, double ytor, double zcon, int l
for (j=0; j<64; j++) {
x = tor_spl[torindx][l][m][n-1][j] * pow(xtor,iin3[j][0])
- * pow(ytor,iin3[j][1]) * pow(zcon,iin3[j][2]);
+ * pow(ytor,iin3[j][1]) * pow(zcon,iin3[j][2]);
vtor += x;
if(xtor > 1.0e-8 ) dtorx += x*iin3[j][0]/xtor;
@@ -3191,11 +3191,11 @@ void PairComb3::tor_force(int torindx, Param *paramk, Param *paraml,
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]
- + delrk[1]*torl[2] - delrl[1]*tork[2];
+ + delrk[1]*torl[2] - delrl[1]*tork[2];
dt2dij[1] = -delrk[0]*torl[2] + delrl[0]*tork[2]
- + delrk[2]*torl[0] - delrl[2]*tork[0];
+ + delrk[2]*torl[0] - delrl[2]*tork[0];
dt2dij[2] = -delrk[1]*torl[0] + delrl[1]*tork[0]
- + delrk[0]*torl[1] - delrl[0]*tork[1];
+ + delrk[0]*torl[1] - delrl[0]*tork[1];
rmut = TT2/TT1;
@@ -3217,10 +3217,10 @@ void PairComb3::tor_force(int torindx, Param *paramk, Param *paraml,
tfij[3] = AA2/rij/rij - dt1djl*AA2*rmul/rij/rij;
tfik[0] = tfij[0];
tfik[1] = (AA2/rik - btt*ptorr*fc1l*fcp1k)/rik -
- dt1dik*AA2*rmu/rik/rik;
+ dt1dik*AA2*rmu/rik/rik;
tfjl[0] = tfij[2];
tfjl[1] = (AA2/rjl - btt*ptorr*fc1k*fcp1l)/rjl -
- dt1djl*AA2*rmul/rjl/rjl;
+ dt1djl*AA2*rmul/rjl/rjl;
tjx[0] = tfij[0]*delrk[0] - tfij[1]*delrj[0];
tjy[0] = tfij[0]*delrk[1] - tfij[1]*delrj[1];
@@ -3338,7 +3338,7 @@ double PairComb3::combqeq(double *qf_fix, int &igroup)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj] & NEIGHMASK;
- jtag = tag[j];
+ jtag = tag[j];
if (itag >= jtag) continue;
jtype = map[type[j]];
@@ -3362,30 +3362,30 @@ double PairComb3::combqeq(double *qf_fix, int &igroup)
// 1/r charge forces
qfo_direct(¶ms[iparam_ij],¶ms[iparam_ji],
- mr1,mr2,mr3,rsq1,sr1,sr2,sr3,fac11e,fqij,fqji,
- iq,jq,i,j);
+ 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
qfo_field(¶ms[iparam_ij],¶ms[iparam_ji],rsq1,
- iq,jq,fqij,fqji);
+ iq,jq,fqij,fqji);
fqi += fqij; qf[j] += fqji;
// polarization field charge force
- if (pol_flag) {
- qfo_dipole(fac11,mr1,mr2,mr3,inty,rsq1,delrj,sr1,sr2,sr3,
- fqij,fqji,i,j);
+ if (pol_flag) {
+ qfo_dipole(fac11,mr1,mr2,mr3,inty,rsq1,delrj,sr1,sr2,sr3,
+ fqij,fqji,i,j);
fqi += fqij; qf[j] += fqji;
- }
+ }
}
for (jj = 0; jj < sht_jnum; jj++) {
j = sht_jlist[jj];
- jtag = tag[j];
+ jtag = tag[j];
if (itag >= jtag) continue;
jtype = map[type[j]];
@@ -3401,11 +3401,11 @@ double PairComb3::combqeq(double *qf_fix, int &igroup)
iparam_ji = elem2param[jtype][itype][itype];
if (rsq1 >= params[iparam_ij].cutsq) continue;
- nj ++;
+ nj ++;
// charge force in Aij and Bij
qfo_short(¶ms[iparam_ij],¶ms[iparam_ji],
- rsq1,iq,jq,fqij,fqji,i,j,nj);
+ rsq1,iq,jq,fqij,fqji,i,j,nj);
fqi += fqij; qf[j] += fqji;
}
@@ -3422,7 +3422,7 @@ double PairComb3::combqeq(double *qf_fix, int &igroup)
i = ilist[ii];
if (mask[i] & groupbit){
eneg += qf[i];
- itag=tag[i];
+ itag=tag[i];
}
}
@@ -3458,9 +3458,9 @@ 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,
- double sr3, double fac11e, double &fqij, double &fqji,
- double iq, double jq, int i, int j)
+ 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)
{
double r, erfcc, fafbnl, vm, vmfafb, esucon;
double afbn, afbj, sme1n, sme1j;
@@ -3519,7 +3519,7 @@ void PairComb3::qfo_direct(Param *parami, Param *paramj, int mr1,
/* ---------------------------------------------------------------------- */
void PairComb3::qfo_field(Param *parami, Param *paramj, double rsq,
- double iq,double jq, double &fqij, double &fqji)
+ double iq,double jq, double &fqij, double &fqji)
{
double r,r3,r5,rc,rc2,rc3,rc4,rc5;
double cmi1,cmi2,cmj1,cmj2,pcmi1,pcmi2;
@@ -3561,8 +3561,8 @@ 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,
- double sr3, double &fqij, double &fqji, int i, int j)
+ 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;
double r, r3, alfdpi, esucon;
@@ -3588,8 +3588,8 @@ void PairComb3::qfo_dipole(double fac11, int mr1, int mr2, int mr3,
/* ---------------------------------------------------------------------- */
void PairComb3::qfo_short(Param *parami, Param *paramj, double rsq,
- double iq, double jq, double &fqij, double &fqji,
- int i, int j, int nj)
+ double iq, double jq, double &fqij, double &fqji,
+ int i, int j, int nj)
{
double r, tmp_fc;
double Di, Dj, dDi, dDj, Bsi, Bsj, dBsi, dBsj;
@@ -3623,10 +3623,10 @@ void PairComb3::qfo_short(Param *parami, Param *paramj, double rsq,
Di = parami->DU;
dDi = Bsi = dBsi = 0.0;
} else {
- Di = parami->DU + pow(QUchi,parami->nD); // YYDin
- dDi = -parami->nD * parami->bD * pow(QUchi,(parami->nD-1.0)); // YYDiqp
- Bsi = parami->aB - pow(QOchi,10); // YYBsin
- dBsi = -parami->bB * 10.0 * pow(QOchi,9.0); // YYBsiqp
+ Di = parami->DU + pow(QUchi,parami->nD); // YYDin
+ dDi = -parami->nD * parami->bD * pow(QUchi,(parami->nD-1.0)); // YYDiqp
+ Bsi = parami->aB - pow(QOchi,10); // YYBsin
+ dBsi = -parami->bB * 10.0 * pow(QOchi,9.0); // YYBsiqp
}
if (jq < paramj->QL-0.2) {
@@ -3638,10 +3638,10 @@ void PairComb3::qfo_short(Param *parami, Param *paramj, double rsq,
Dj = paramj->DU;
dDj = Bsj = dBsj = 0.0;
} else {
- Dj = paramj->DU + pow(QUchj,paramj->nD); // YYDij
- dDj = -paramj->nD * paramj->bD * pow(QUchj,(paramj->nD-1.0)); // YYDiqpj
- Bsj = paramj->aB - pow(QOchj,10); // YYBsij
- dBsj = -paramj->bB * 10.0 * pow(QOchj,9.0); // YYBsiqpj
+ Dj = paramj->DU + pow(QUchj,paramj->nD); // YYDij
+ dDj = -paramj->nD * paramj->bD * pow(QUchj,(paramj->nD-1.0)); // YYDiqpj
+ 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);
@@ -3668,8 +3668,8 @@ 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 sr2, double sr3, double iq, double jq, int i, int j)
+ 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;
double r, r3, alfdpi, esucon;
@@ -3730,10 +3730,10 @@ double PairComb3::dipole_self(Param *parami, int i)
/* ---------------------------------------------------------------------- */
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,
- double &fvionij, double *ddprx)
+ 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,
+ double &fvionij, double *ddprx)
{
double erfcc, erfcd, dvdrr, dfafbnl, ef, phinn, phinj, efn, efj;
double r, r3, alf, alfdpi, esucon, dphinn, dphinj, ddfafbnl;
@@ -3803,7 +3803,7 @@ void PairComb3::dipole_calc(Param *parami, Param *paramj, double fac11,
for (nm = 0; nm < 3; nm ++) {
ddprx[nm] = dcoef * (ddpr*delr1[nm] - tmurn*dpl[j][nm] - tmurj*dpl[i][nm])
- + demuTmu * delr1[nm];
+ + demuTmu * delr1[nm];
}
// dipole - charge force
@@ -3847,7 +3847,7 @@ double PairComb3::switching(double rr)
if (rr <= 0.0) return 1.0;
else if (rr >= 1.0) return 0.0;
else return heaviside(-rr)+heaviside(rr)*heaviside(1.0-rr)
- * (1.0-(3.0-2.0*rr)*rr*rr);
+ * (1.0-(3.0-2.0*rr)*rr*rr);
}
/* ---------------------------------------------------------------------- */
@@ -3857,7 +3857,7 @@ double PairComb3::switching_d(double rr)
if (rr <= 0.0) return 0.0;
else if (rr >= 1.0) return 0.0;
else return heaviside(rr)*heaviside(1.0-rr)
- * 6.0*rr*(rr-1.0);
+ * 6.0*rr*(rr-1.0);
}
/* ---------------------------------------------------------------------- */
diff --git a/src/MANYBODY/pair_comb3.h b/src/MANYBODY/pair_comb3.h
index bc21120e8e..5d7e5d6beb 100644
--- a/src/MANYBODY/pair_comb3.h
+++ b/src/MANYBODY/pair_comb3.h
@@ -42,8 +42,8 @@ class PairComb3 : public Pair {
protected:
struct Param {
int ielement,jelement,kelement,powermint;
- int ielementgp,jelementgp,kelementgp; //element group
- int ang_flag,pcn_flag,rad_flag,tor_flag; //angle, coordination,radical, torsion flag
+ int ielementgp,jelementgp,kelementgp; //element group
+ int ang_flag,pcn_flag,rad_flag,tor_flag; //angle, coordination,radical, torsion flag
double lami,lambda,alfi,alpha1,alpha2,alpha3,beta;
double pcos6,pcos5,pcos4,pcos3,pcos2,pcos1,pcos0;
double gamma,powerm,powern,bigA,bigB1,bigB2,bigB3;
@@ -60,18 +60,18 @@ class PairComb3 : public Pair {
};
// general setups
- int nelements; // # of unique elements
- int ***elem2param; // mapping from element triplets to parameters
- int *map; // mapping from atom types to elements
- int nparams; // # of stored parameter sets
- int maxparam; // max # of parameter sets
- double PI,PI2,PI4,PIsq; // PIs
- double cutmin; // min cutoff for all elements
- double cutmax; // max cutoff for all elements
- double precision; // tolerance for QEq convergence
- char **elements; // names of unique elements
- Param *params; // parameter set for an I-J-K interaction
- int debug_eng1, debug_eng2, debug_fq; // logic controlling debugging outputs
+ int nelements; // # of unique elements
+ int ***elem2param; // mapping from element triplets to parameters
+ int *map; // mapping from atom types to elements
+ int nparams; // # of stored parameter sets
+ int maxparam; // max # of parameter sets
+ double PI,PI2,PI4,PIsq; // PIs
+ double cutmin; // min cutoff for all elements
+ double cutmax; // max cutoff for all elements
+ double precision; // tolerance for QEq convergence
+ char **elements; // names of unique elements
+ Param *params; // parameter set for an I-J-K interaction
+ int debug_eng1, debug_eng2, debug_fq; // logic controlling debugging outputs
int pack_flag;
// Short range neighbor list
@@ -105,8 +105,8 @@ class PairComb3 : public Pair {
double ccutoff[6],ch_a[7];
//COMB3-v18 arrays for CHO
- // We wanna dynamic arrays
- // C angle arrays, size = ntab+1
+ // We wanna dynamic arrays
+ // C angle arrays, size = ntab+1
double pang[20001];
double dpang[20001];
double ddpang[20001];
@@ -153,12 +153,12 @@ class PairComb3 : public Pair {
// short range terms
void attractive(Param *, Param *, Param *, double, double, double, double,
- double, double, double, double *, double *, double *,
- double *, double *, int, double);
+ double, double, double, double *, double *, double *,
+ double *, double *, int, double);
virtual void comb_fa(double, Param *, Param *, double, double,
- double &, double &);
+ double &, double &);
virtual void repulsive(Param *, Param *,double, double &, int,
- double &, double, double);
+ double &, double, double);
// bond order terms
double comb_bij(double, Param *, double, int, double);
@@ -166,19 +166,19 @@ class PairComb3 : public Pair {
void comb_gijk_d(double, Param *, double, double &, double &);
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);
+ double &, double &, double &, double &, double &, double);
void coord(Param *, double, int, 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);
+ double *, double, double *, double, double *, double *,
+ double *, Param *, Param *, Param *, double);
void costheta_d(double *, double, double *, 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,
- 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 *);
@@ -186,18 +186,18 @@ class PairComb3 : public Pair {
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 *,
- 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 &,
- double &);
+ double &);
void vdwaals(int,int,int,int,double,double,double,double,
- double &, double &);
+ double &, double &);
void direct(Param *, Param *, int,int,int,double,double,
- double,double,double,double, double,double,double &,double &,
+ double,double,double,double, double,double,double &,double &,
int, int);
void field(Param *, Param *,double,double,double,double &,double &);
int heaviside(double);
@@ -208,9 +208,9 @@ class PairComb3 : public Pair {
// radical terms
double rad_init(double, Param *, int, double &, double);
void rad_calc(double, Param *, Param *, double, double, int,
- int, double, double);
+ int, double, double);
void rad_int(int , double, double, double, int, int, int,
- double &, double &, double &, double &);
+ double &, double &, double &, double &);
void rad_forceik(Param *, double, double *, double, double);
void rad_force(Param *, double, double *, double);
@@ -218,7 +218,7 @@ class PairComb3 : public Pair {
double bbtor1(int, Param *, Param *, double, double, double,
double *, double *, double *, double); //modified by TAO
void tor_calc(double, Param *, Param *, double, double, int,
- int, double, double);
+ 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,
@@ -227,22 +227,22 @@ class PairComb3 : public Pair {
// charge force terms
double qfo_self(Param *, double);
void qfo_short(Param *, Param *, double, double, double,
- double &, double &, int, int, int);
+ double &, double &, int, int, int);
void qfo_direct(Param *, Param *, int, int, int, double,
- double, double, double, double, double &, double &,
- double, double, int, int);
+ 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,
- double, double, double &, double &, int, int);
+ 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,
- int, int, int, double, double, double, double, double, int , int);
+ int, int, int, double, double, double, double, double, int , int);
void dipole_calc(Param *, Param *, double, double, double, double, double,
- int, int, int, double, double, double, double, double, int , int,
- double &, double &, double *);
+ int, int, int, double, double, double, double, double, int , int,
+ double &, double &, double *);
// communication functions
int pack_reverse_comm(int, int, double *);
diff --git a/src/MANYBODY/pair_gw.h b/src/MANYBODY/pair_gw.h
index eedc2a1f9f..00cbaa2beb 100644
--- a/src/MANYBODY/pair_gw.h
+++ b/src/MANYBODY/pair_gw.h
@@ -101,7 +101,7 @@ class PairGW : public Pair {
const double gw_d = param->d * param->d;
const double hcth = param->h - costheta;
- //printf("gw_gijk: gw_c=%f gw_d=%f hcth=%f=%f-%f\n", gw_c, gw_d, hcth, param->h, costheta);
+ //printf("gw_gijk: gw_c=%f gw_d=%f hcth=%f=%f-%f\n", gw_c, gw_d, hcth, param->h, costheta);
return param->gamma*(1.0 + gw_c/gw_d - gw_c / (gw_d + hcth*hcth));
}
diff --git a/src/MANYBODY/pair_nb3b_harmonic.cpp b/src/MANYBODY/pair_nb3b_harmonic.cpp
index d1d5880839..0b930c7360 100644
--- a/src/MANYBODY/pair_nb3b_harmonic.cpp
+++ b/src/MANYBODY/pair_nb3b_harmonic.cpp
@@ -124,32 +124,32 @@ void PairNb3bHarmonic::compute(int eflag, int vflag)
if (rsq1 > params[ijparam].cutsq) continue;
for (kk = jj+1; kk < jnum; kk++) {
- k = jlist[kk];
- k &= NEIGHMASK;
- ktype = map[type[k]];
- ikparam = elem2param[itype][ktype][ktype];
- ijkparam = elem2param[itype][jtype][ktype];
-
- delr2[0] = x[k][0] - xtmp;
- delr2[1] = x[k][1] - ytmp;
- delr2[2] = x[k][2] - ztmp;
- rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
- if (rsq2 > params[ikparam].cutsq) continue;
+ k = jlist[kk];
+ k &= NEIGHMASK;
+ ktype = map[type[k]];
+ ikparam = elem2param[itype][ktype][ktype];
+ ijkparam = elem2param[itype][jtype][ktype];
+
+ delr2[0] = x[k][0] - xtmp;
+ delr2[1] = x[k][1] - ytmp;
+ delr2[2] = x[k][2] - ztmp;
+ rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
+ if (rsq2 > params[ikparam].cutsq) continue;
threebody(¶ms[ijparam],¶ms[ikparam],¶ms[ijkparam],
rsq1,rsq2,delr1,delr2,fj,fk,eflag,evdwl);
- f[i][0] -= fj[0] + fk[0];
- f[i][1] -= fj[1] + fk[1];
- f[i][2] -= fj[2] + fk[2];
- f[j][0] += fj[0];
- f[j][1] += fj[1];
- f[j][2] += fj[2];
- f[k][0] += fk[0];
- f[k][1] += fk[1];
- f[k][2] += fk[2];
-
- if (evflag) ev_tally3(i,j,k,evdwl,0.0,fj,fk,delr1,delr2);
+ f[i][0] -= fj[0] + fk[0];
+ f[i][1] -= fj[1] + fk[1];
+ f[i][2] -= fj[2] + fk[2];
+ f[j][0] += fj[0];
+ f[j][1] += fj[1];
+ f[j][2] += fj[2];
+ f[k][0] += fk[0];
+ f[k][1] += fk[1];
+ f[k][2] += fk[2];
+
+ if (evflag) ev_tally3(i,j,k,evdwl,0.0,fj,fk,delr1,delr2);
}
}
}
@@ -244,8 +244,8 @@ void PairNb3bHarmonic::coeff(int narg, char **arg)
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
if (map[i] >= 0 && map[j] >= 0) {
- setflag[i][j] = 1;
- count++;
+ setflag[i][j] = 1;
+ count++;
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
@@ -316,8 +316,8 @@ void PairNb3bHarmonic::read_file(char *file)
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fp);
if (ptr == NULL) {
- eof = 1;
- fclose(fp);
+ eof = 1;
+ fclose(fp);
} else n = strlen(line) + 1;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
@@ -338,8 +338,8 @@ void PairNb3bHarmonic::read_file(char *file)
if (comm->me == 0) {
ptr = fgets(&line[n],MAXLINE-n,fp);
if (ptr == NULL) {
- eof = 1;
- fclose(fp);
+ eof = 1;
+ fclose(fp);
} else n = strlen(line) + 1;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
@@ -378,7 +378,7 @@ void PairNb3bHarmonic::read_file(char *file)
if (nparams == maxparam) {
maxparam += DELTA;
params = (Param *) memory->srealloc(params,maxparam*sizeof(Param),
- "pair:params");
+ "pair:params");
}
params[nparams].ielement = ielement;
@@ -415,16 +415,16 @@ void PairNb3bHarmonic::setup_params()
for (i = 0; i < nelements; i++)
for (j = 0; j < nelements; j++)
for (k = 0; k < nelements; k++) {
- n = -1;
- for (m = 0; m < nparams; m++) {
- 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;
- }
- }
- if (n < 0) error->all(FLERR,"Potential file is missing an entry");
- elem2param[i][j][k] = n;
+ n = -1;
+ for (m = 0; m < nparams; m++) {
+ 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;
+ }
+ }
+ if (n < 0) error->all(FLERR,"Potential file is missing an entry");
+ elem2param[i][j][k] = n;
}
// compute parameter values derived from inputs
diff --git a/src/MANYBODY/pair_nb3b_harmonic.h b/src/MANYBODY/pair_nb3b_harmonic.h
index 8445a98970..75a378e35b 100644
--- a/src/MANYBODY/pair_nb3b_harmonic.h
+++ b/src/MANYBODY/pair_nb3b_harmonic.h
@@ -55,7 +55,7 @@ class PairNb3bHarmonic : public Pair {
void setup_params();
void twobody(Param *, double, double &, int, double &);
void threebody(Param *, Param *, Param *, double, double, double *, double *,
- double *, double *, int, double &);
+ double *, double *, int, double &);
};
}
diff --git a/src/MANYBODY/pair_polymorphic.cpp b/src/MANYBODY/pair_polymorphic.cpp
index 02075ed5b4..110fc0a44d 100644
--- a/src/MANYBODY/pair_polymorphic.cpp
+++ b/src/MANYBODY/pair_polymorphic.cpp
@@ -234,13 +234,13 @@ void PairPolymorphic::compute(int eflag, int vflag)
jtag = tag[j];
if (itag > jtag) {
- if ((itag+jtag) % 2 == 0) continue;
+ if ((itag+jtag) % 2 == 0) continue;
} else if (itag < jtag) {
- if ((itag+jtag) % 2 == 1) continue;
+ if ((itag+jtag) % 2 == 1) continue;
} else {
- 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;
+ 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;
}
if (rsq >= (p.U)->get_xmaxsq() || (p.U)->get_vmax() <= epsilon) continue;
@@ -255,7 +255,7 @@ void PairPolymorphic::compute(int eflag, int vflag)
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,delx,dely,delz);
}
if (eta) {
@@ -524,8 +524,8 @@ void PairPolymorphic::coeff(int narg, char **arg)
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
if (map[i] >= 0 && map[j] >= 0) {
- setflag[i][j] = 1;
- count++;
+ setflag[i][j] = 1;
+ count++;
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
@@ -851,8 +851,8 @@ void PairPolymorphic::ters_zetaterm_d(double prefactor,
/* ---------------------------------------------------------------------- */
void PairPolymorphic::costheta_d(double *rij_hat, double rij,
- double *rik_hat, double rik,
- double *dri, double *drj, double *drk)
+ double *rik_hat, double rik,
+ double *dri, double *drj, double *drk)
{
// first element is devative wrt Ri, second wrt Rj, third wrt Rk
diff --git a/src/MANYBODY/pair_polymorphic.h b/src/MANYBODY/pair_polymorphic.h
index 1ce7600f10..8855ce7c25 100644
--- a/src/MANYBODY/pair_polymorphic.h
+++ b/src/MANYBODY/pair_polymorphic.h
@@ -288,7 +288,7 @@ class PairPolymorphic : public Pair {
void ters_zetaterm_d(double, double *, double, double *, double, double *,
double *, double *, PairParameters *, TripletParameters *);
void costheta_d(double *, double, double *, double,
- double *, double *, double *);
+ double *, double *, double *);
// inlined functions for efficiency
@@ -297,17 +297,17 @@ class PairPolymorphic : public Pair {
}
inline void vec3_add(const double x[3], const double y[3],
- double * const z) const {
+ double * const z) const {
z[0] = x[0]+y[0]; z[1] = x[1]+y[1]; z[2] = x[2]+y[2];
}
inline void vec3_scale(const double k, const double x[3],
- double y[3]) const {
+ double y[3]) const {
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],
- const double y[3], double * const z) const {
+ 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];
diff --git a/src/MANYBODY/pair_tersoff.cpp b/src/MANYBODY/pair_tersoff.cpp
index 9f976281c8..047c59fc87 100644
--- a/src/MANYBODY/pair_tersoff.cpp
+++ b/src/MANYBODY/pair_tersoff.cpp
@@ -720,8 +720,8 @@ double PairTersoff::ters_bij_d(double zeta, Param *param)
if (tmp > param->c1) return param->beta * -0.5*pow(tmp,-1.5);
if (tmp > param->c2)
return param->beta * (-0.5*pow(tmp,-1.5) *
- // error in negligible 2nd term fixed 9/30/2015
- // (1.0 - 0.5*(1.0 + 1.0/(2.0*param->powern)) *
+ // error in negligible 2nd term fixed 9/30/2015
+ // (1.0 - 0.5*(1.0 + 1.0/(2.0*param->powern)) *
(1.0 - (1.0 + 1.0/(2.0*param->powern)) *
pow(tmp,-param->powern)));
if (tmp < param->c4) return 0.0;
diff --git a/src/MANYBODY/pair_tersoff_mod.cpp b/src/MANYBODY/pair_tersoff_mod.cpp
index e810130dba..a90cf3bb77 100644
--- a/src/MANYBODY/pair_tersoff_mod.cpp
+++ b/src/MANYBODY/pair_tersoff_mod.cpp
@@ -76,8 +76,8 @@ void PairTersoffMOD::read_file(char *file)
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fp);
if (ptr == NULL) {
- eof = 1;
- fclose(fp);
+ eof = 1;
+ fclose(fp);
} else n = strlen(line) + 1;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
@@ -98,8 +98,8 @@ void PairTersoffMOD::read_file(char *file)
if (comm->me == 0) {
ptr = fgets(&line[n],MAXLINE-n,fp);
if (ptr == NULL) {
- eof = 1;
- fclose(fp);
+ eof = 1;
+ fclose(fp);
} else n = strlen(line) + 1;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
@@ -138,7 +138,7 @@ void PairTersoffMOD::read_file(char *file)
if (nparams == maxparam) {
maxparam += DELTA;
params = (Param *) memory->srealloc(params,maxparam*sizeof(Param),
- "pair:params");
+ "pair:params");
}
params[nparams].ielement = ielement;
@@ -203,16 +203,16 @@ void PairTersoffMOD::setup_params()
for (i = 0; i < nelements; i++)
for (j = 0; j < nelements; j++)
for (k = 0; k < nelements; k++) {
- n = -1;
- for (m = 0; m < nparams; m++) {
- 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;
- }
- }
- if (n < 0) error->all(FLERR,"Potential file is missing an entry");
- elem2param[i][j][k] = n;
+ n = -1;
+ for (m = 0; m < nparams; m++) {
+ 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;
+ }
+ }
+ if (n < 0) error->all(FLERR,"Potential file is missing an entry");
+ elem2param[i][j][k] = n;
}
@@ -236,14 +236,14 @@ void PairTersoffMOD::setup_params()
/* ---------------------------------------------------------------------- */
double PairTersoffMOD::zeta(Param *param, double rsqij, double rsqik,
- double *delrij, double *delrik)
+ double *delrij, double *delrik)
{
double rij,rik,costheta,arg,ex_delr;
rij = sqrt(rsqij);
rik = sqrt(rsqik);
costheta = (delrij[0]*delrik[0] + delrij[1]*delrik[1] +
- delrij[2]*delrik[2]) / (rij*rik);
+ delrij[2]*delrik[2]) / (rij*rik);
if (param->powermint == 3) arg = pow(param->lam3 * (rij-rik),3.0);
else arg = param->lam3 * (rij-rik);
@@ -297,21 +297,21 @@ double PairTersoffMOD::ters_bij_d(double zeta, Param *param)
{
double tmp = param->beta * zeta;
if (tmp > param->ca1) return -0.5*(param->powern/param->powern_del)*
- pow(tmp,-0.5*(param->powern/param->powern_del)) / zeta;
+ 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)*
- pow(1.0+tmp_n, -1.0-(1.0/(2.0*param->powern_del)))*tmp_n / zeta;
+ pow(1.0+tmp_n, -1.0-(1.0/(2.0*param->powern_del)))*tmp_n / zeta;
}
/* ---------------------------------------------------------------------- */
void PairTersoffMOD::ters_zetaterm_d(double prefactor,
- double *rij_hat, double rij,
- double *rik_hat, double rik,
- double *dri, double *drj, double *drk,
- Param *param)
+ double *rij_hat, double rij,
+ double *rik_hat, double rik,
+ double *dri, double *drj, double *drk,
+ Param *param)
{
double gijk,gijk_d,ex_delr,ex_delr_d,fc,dfc,cos_theta,tmp;
double dcosdri[3],dcosdrj[3],dcosdrk[3];
diff --git a/src/MANYBODY/pair_tersoff_mod.h b/src/MANYBODY/pair_tersoff_mod.h
index fea3919be3..42a3a2b26c 100644
--- a/src/MANYBODY/pair_tersoff_mod.h
+++ b/src/MANYBODY/pair_tersoff_mod.h
@@ -40,7 +40,7 @@ class PairTersoffMOD : public PairTersoff {
double ters_bij(double, Param *);
double ters_bij_d(double, Param *);
void ters_zetaterm_d(double, double *, double, double *, double,
- double *, double *, double *, Param *);
+ double *, double *, double *, Param *);
// inlined functions for efficiency
// these replace but do not override versions in PairTersoff
diff --git a/src/MANYBODY/pair_tersoff_mod_c.cpp b/src/MANYBODY/pair_tersoff_mod_c.cpp
index 0edf2ddef9..c0d6cb164a 100644
--- a/src/MANYBODY/pair_tersoff_mod_c.cpp
+++ b/src/MANYBODY/pair_tersoff_mod_c.cpp
@@ -71,8 +71,8 @@ void PairTersoffMODC::read_file(char *file)
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fp);
if (ptr == NULL) {
- eof = 1;
- fclose(fp);
+ eof = 1;
+ fclose(fp);
} else n = strlen(line) + 1;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
@@ -93,8 +93,8 @@ void PairTersoffMODC::read_file(char *file)
if (comm->me == 0) {
ptr = fgets(&line[n],MAXLINE-n,fp);
if (ptr == NULL) {
- eof = 1;
- fclose(fp);
+ eof = 1;
+ fclose(fp);
} else n = strlen(line) + 1;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
@@ -133,7 +133,7 @@ void PairTersoffMODC::read_file(char *file)
if (nparams == maxparam) {
maxparam += DELTA;
params = (Param *) memory->srealloc(params,maxparam*sizeof(Param),
- "pair:params");
+ "pair:params");
}
params[nparams].ielement = ielement;
diff --git a/src/MANYBODY/pair_vashishta.cpp b/src/MANYBODY/pair_vashishta.cpp
index 2b867bc046..9f2ed03945 100644
--- a/src/MANYBODY/pair_vashishta.cpp
+++ b/src/MANYBODY/pair_vashishta.cpp
@@ -170,7 +170,7 @@ void PairVashishta::compute(int eflag, int vflag)
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,delx,dely,delz);
}
jnumm1 = numshort - 1;
@@ -585,12 +585,12 @@ void PairVashishta::twobody(Param *param, double rsq, double &fforce,
vc3 = param->mbigd * r4inv*exp(-lam4r);
fforce = (param->dvrc*r
- - (4.0*vc3 + lam4r*vc3+param->big6w*r6inv
- - param->heta*reta - vc2 - lam1r*vc2)
- ) * rinvsq;
+ - (4.0*vc3 + lam4r*vc3+param->big6w*r6inv
+ - param->heta*reta - vc2 - lam1r*vc2)
+ ) * rinvsq;
if (eflag) eng = param->bigh*reta
- + vc2 - vc3 - param->bigw*r6inv
- - r*param->dvrc + param->c0;
+ + 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 6500707bf3..669afb5d48 100644
--- a/src/MC/fix_atom_swap.cpp
+++ b/src/MC/fix_atom_swap.cpp
@@ -167,9 +167,9 @@ void FixAtomSwap::options(int narg, char **arg)
iarg++;
while (iarg < narg) {
if (isalpha(arg[iarg][0])) break;
- if (nswaptypes >= atom->ntypes) error->all(FLERR,"Illegal fix atom/swap command");
+ if (nswaptypes >= atom->ntypes) error->all(FLERR,"Illegal fix atom/swap command");
type_list[nswaptypes] = force->numeric(FLERR,arg[iarg]);
- nswaptypes++;
+ nswaptypes++;
iarg++;
}
} else if (strcmp(arg[iarg],"mu") == 0) {
@@ -178,7 +178,7 @@ void FixAtomSwap::options(int narg, char **arg)
while (iarg < narg) {
if (isalpha(arg[iarg][0])) break;
nmutypes++;
- if (nmutypes > atom->ntypes) error->all(FLERR,"Illegal fix atom/swap command");
+ if (nmutypes > atom->ntypes) error->all(FLERR,"Illegal fix atom/swap command");
mu[nmutypes] = force->numeric(FLERR,arg[iarg]);
iarg++;
}
@@ -246,14 +246,14 @@ void FixAtomSwap::init()
first = 1;
for (int i = 0; i < atom->nlocal; i++) {
if (atom->mask[i] & groupbit) {
- if (type[i] == type_list[iswaptype]) {
- if (first) {
- qtype[iswaptype] = atom->q[i];
- first = 0;
- } else if (qtype[iswaptype] != atom->q[i])
- error->one(FLERR,"All atoms of a swapped type must have the same charge.");
- }
- }
+ if (type[i] == type_list[iswaptype]) {
+ if (first) {
+ qtype[iswaptype] = atom->q[i];
+ first = 0;
+ } else if (qtype[iswaptype] != atom->q[i])
+ error->one(FLERR,"All atoms of a swapped type must have the same charge.");
+ }
+ }
}
MPI_Allreduce(&first,&firstall,1,MPI_INT,MPI_MIN,world);
if (firstall) error->all(FLERR,"At least one atom of each swapped type must be present to define charges.");
@@ -600,11 +600,11 @@ void FixAtomSwap::update_semi_grand_atoms_list()
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) {
- int itype = atom->type[i];
- int iswaptype;
- for (iswaptype = 0; iswaptype < nswaptypes; iswaptype++)
- if (itype == type_list[iswaptype]) break;
- if (iswaptype == nswaptypes) continue;
+ int itype = atom->type[i];
+ int iswaptype;
+ for (iswaptype = 0; iswaptype < nswaptypes; iswaptype++)
+ if (itype == type_list[iswaptype]) break;
+ if (iswaptype == nswaptypes) continue;
local_swap_atom_list[nswap_local] = i;
nswap_local++;
}
@@ -614,11 +614,11 @@ void FixAtomSwap::update_semi_grand_atoms_list()
} else {
for (int i = 0; i < nlocal; i++) {
if (atom->mask[i] & groupbit) {
- int itype = atom->type[i];
- int iswaptype;
- for (iswaptype = 0; iswaptype < nswaptypes; iswaptype++)
- if (itype == type_list[iswaptype]) break;
- if (iswaptype == nswaptypes) continue;
+ int itype = atom->type[i];
+ int iswaptype;
+ for (iswaptype = 0; iswaptype < nswaptypes; iswaptype++)
+ if (itype == type_list[iswaptype]) break;
+ if (iswaptype == nswaptypes) continue;
local_swap_atom_list[nswap_local] = i;
nswap_local++;
}
diff --git a/src/MC/fix_bond_break.cpp b/src/MC/fix_bond_break.cpp
index afb18cc1c2..711f764282 100644
--- a/src/MC/fix_bond_break.cpp
+++ b/src/MC/fix_bond_break.cpp
@@ -806,18 +806,18 @@ void FixBondBreak::print_bb()
printf("TAG " TAGINT_FORMAT ": %d nangles: ",atom->tag[i],atom->num_angle[i]);
for (int j = 0; j < atom->num_angle[i]; j++) {
printf(" %d %d %d,",atom->angle_atom1[i][j],
- atom->angle_atom2[i][j],atom->angle_atom3[i][j]);
+ atom->angle_atom2[i][j],atom->angle_atom3[i][j]);
}
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(" %d %d %d %d,",atom->dihedral_atom1[i][j],
- atom->dihedral_atom2[i][j],atom->dihedral_atom3[i][j],
- atom->dihedral_atom4[i][j]);
+ atom->dihedral_atom2[i][j],atom->dihedral_atom3[i][j],
+ atom->dihedral_atom4[i][j]);
}
printf("\n");
printf("TAG " TAGINT_FORMAT ": %d %d %d nspecial: ",atom->tag[i],
- atom->nspecial[i][0],atom->nspecial[i][1],atom->nspecial[i][2]);
+ atom->nspecial[i][0],atom->nspecial[i][1],atom->nspecial[i][2]);
for (int j = 0; j < atom->nspecial[i][2]; j++) {
printf(" %d",atom->special[i][j]);
}
diff --git a/src/MC/fix_bond_create.cpp b/src/MC/fix_bond_create.cpp
index 14270e7c77..789f1794f1 100644
--- a/src/MC/fix_bond_create.cpp
+++ b/src/MC/fix_bond_create.cpp
@@ -1414,20 +1414,20 @@ void FixBondCreate::print_bb()
for (int j = 0; j < atom->num_dihedral[i]; j++) {
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]);
+ atom->dihedral_atom2[i][j],atom->dihedral_atom3[i][j],
+ atom->dihedral_atom4[i][j]);
}
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 " "
TAGINT_FORMAT ",",atom->improper_atom1[i][j],
- atom->improper_atom2[i][j],atom->improper_atom3[i][j],
- atom->improper_atom4[i][j]);
+ atom->improper_atom2[i][j],atom->improper_atom3[i][j],
+ atom->improper_atom4[i][j]);
}
printf("\n");
printf("TAG " TAGINT_FORMAT ": %d %d %d nspecial: ",atom->tag[i],
- atom->nspecial[i][0],atom->nspecial[i][1],atom->nspecial[i][2]);
+ atom->nspecial[i][0],atom->nspecial[i][1],atom->nspecial[i][2]);
for (int j = 0; j < atom->nspecial[i][2]; j++) {
printf(" " TAGINT_FORMAT,atom->special[i][j]);
}
diff --git a/src/MC/fix_tfmc.cpp b/src/MC/fix_tfmc.cpp
index 01bb7456e0..46a93914a7 100644
--- a/src/MC/fix_tfmc.cpp
+++ b/src/MC/fix_tfmc.cpp
@@ -255,11 +255,11 @@ void FixTFMC::initial_integrate(int vflag)
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
- // "velocities" by a displacement vector and proceed from there.
- // this of course requires "forking" group->angmom(), which is
- // what we do here.
+ // 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
+ // what we do here.
double p[3];
p[0] = p[1] = p[2] = 0.0;
diff --git a/src/MISC/fix_deposit.cpp b/src/MISC/fix_deposit.cpp
index 9c1082f816..023ec797df 100644
--- a/src/MISC/fix_deposit.cpp
+++ b/src/MISC/fix_deposit.cpp
@@ -543,9 +543,9 @@ void FixDeposit::pre_exchange()
atom->v[n][1] = vnew[1];
atom->v[n][2] = vnew[2];
if (mode == MOLECULE) {
- onemols[imol]->quat_external = quat;
+ onemols[imol]->quat_external = quat;
atom->add_molecule_atom(onemols[imol],m,n,maxtag_all);
- }
+ }
modify->create_attribute(n);
}
}
diff --git a/src/MISC/fix_gld.cpp b/src/MISC/fix_gld.cpp
index 945ddb531b..a515ade91f 100644
--- a/src/MISC/fix_gld.cpp
+++ b/src/MISC/fix_gld.cpp
@@ -71,7 +71,7 @@ FixGLD::FixGLD(LAMMPS *lmp, int narg, char **arg) :
// 7 = series type
if(strcmp(arg[7],"pprony") == 0) {
- series_type = 1; // series type 1 is 'positive Prony series'
+ series_type = 1; // series type 1 is 'positive Prony series'
} else {
error->all(FLERR,"Fix gld series type must be pprony for now");
}
@@ -131,13 +131,13 @@ 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");
+ error->all(FLERR, "Illegal fix gld command");
}
if (strcmp(arg[iarg+1],"no") == 0) {
} else if (strcmp(arg[iarg+1],"yes") == 0) {
- zeroflag = 1;
+ zeroflag = 1;
} else {
- error->all(FLERR,"Illegal fix gld command");
+ error->all(FLERR,"Illegal fix gld command");
}
iarg += 2;
}
@@ -248,28 +248,28 @@ void FixGLD::initial_integrate(int vflag)
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
dtfm = dtf / rmass[i];
- // Advance V by dt/2
+ // Advance V by dt/2
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
for (int k = 0; k < 3*prony_terms; k=k+3) {
- v[i][0] += dtfm * s_gld[i][k];
- v[i][1] += dtfm * s_gld[i][k+1];
- v[i][2] += dtfm * s_gld[i][k+2];
- }
+ v[i][0] += dtfm * s_gld[i][k];
+ v[i][1] += dtfm * s_gld[i][k+1];
+ v[i][2] += dtfm * s_gld[i][k+2];
+ }
- // Advance X by dt
+ // Advance X by dt
x[i][0] += dtv * v[i][0];
x[i][1] += dtv * v[i][1];
x[i][2] += dtv * v[i][2];
- // Advance S by dt
- icoeff = 0;
- for (int k = 0; k < 3*prony_terms; k=k+3) {
- double theta = exp(-dtv/prony_tau[icoeff]);
+ // Advance S by dt
+ icoeff = 0;
+ for (int k = 0; k < 3*prony_terms; k=k+3) {
+ double theta = exp(-dtv/prony_tau[icoeff]);
double ck = prony_c[icoeff];
double vmult = (theta-1.)*ck/ftm2v;
- double rmult = sqrt(2.0*kT*ck/dtv)*(1.-theta)/ftm2v;
+ double rmult = sqrt(2.0*kT*ck/dtv)*(1.-theta)/ftm2v;
// random force
#ifdef GLD_GAUSSIAN_DISTRO
@@ -286,9 +286,9 @@ void FixGLD::initial_integrate(int vflag)
#endif
// sum of random forces
- fsum[0] += fran[0];
- fsum[1] += fran[1];
- fsum[2] += fran[2];
+ fsum[0] += fran[0];
+ fsum[1] += fran[1];
+ fsum[2] += fran[2];
s_gld[i][k] *= theta;
s_gld[i][k+1] *= theta;
@@ -300,36 +300,36 @@ void FixGLD::initial_integrate(int vflag)
s_gld[i][k+1] += fran[1];
s_gld[i][k+2] += fran[2];
- icoeff += 1;
- }
+ icoeff += 1;
+ }
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
dtfm = dtf / mass[type[i]];
- // Advance V by dt/2
+ // Advance V by dt/2
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
for (int k = 0; k < 3*prony_terms; k=k+3) {
- v[i][0] += dtfm * s_gld[i][k];
- v[i][1] += dtfm * s_gld[i][k+1];
- v[i][2] += dtfm * s_gld[i][k+2];
- }
+ v[i][0] += dtfm * s_gld[i][k];
+ v[i][1] += dtfm * s_gld[i][k+1];
+ v[i][2] += dtfm * s_gld[i][k+2];
+ }
- // Advance X by dt
+ // Advance X by dt
x[i][0] += dtv * v[i][0];
x[i][1] += dtv * v[i][1];
x[i][2] += dtv * v[i][2];
- // Advance S by dt
- icoeff = 0;
- for (int k = 0; k < 3*prony_terms; k=k+3) {
- double theta = exp(-dtv/prony_tau[icoeff]);
+ // Advance S by dt
+ icoeff = 0;
+ for (int k = 0; k < 3*prony_terms; k=k+3) {
+ double theta = exp(-dtv/prony_tau[icoeff]);
double ck = prony_c[icoeff];
double vmult = (theta-1.)*ck/ftm2v;
- double rmult = sqrt(2.0*kT*ck/dtv)*(1.-theta)/ftm2v;
+ double rmult = sqrt(2.0*kT*ck/dtv)*(1.-theta)/ftm2v;
// random force
#ifdef GLD_GAUSSIAN_DISTRO
@@ -339,16 +339,16 @@ void FixGLD::initial_integrate(int vflag)
#endif
#ifdef GLD_UNIFORM_DISTRO
- rmult *= sqrt(12.0); // correct variance of uniform distribution
+ 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];
- fsum[2] += fran[2];
+ fsum[0] += fran[0];
+ fsum[1] += fran[1];
+ fsum[2] += fran[2];
s_gld[i][k] *= theta;
s_gld[i][k+1] *= theta;
@@ -360,9 +360,9 @@ void FixGLD::initial_integrate(int vflag)
s_gld[i][k+1] += fran[1];
s_gld[i][k+2] += fran[2];
- icoeff += 1;
+ icoeff += 1;
- }
+ }
}
}
@@ -377,11 +377,11 @@ void FixGLD::initial_integrate(int vflag)
fsumall[2] /= (count*prony_terms);
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
- for (int k = 0; k < 3*prony_terms; k=k+3) {
+ for (int k = 0; k < 3*prony_terms; k=k+3) {
s_gld[i][k] -= fsumall[0];
s_gld[i][k+1] -= fsumall[1];
s_gld[i][k+2] -= fsumall[2];
- }
+ }
}
}
}
@@ -415,10 +415,10 @@ void FixGLD::final_integrate()
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
for (int k = 0; k < 3*prony_terms; k=k+3) {
- v[i][0] += dtfm * s_gld[i][k];
- v[i][1] += dtfm * s_gld[i][k+1];
- v[i][2] += dtfm * s_gld[i][k+2];
- }
+ v[i][0] += dtfm * s_gld[i][k];
+ v[i][1] += dtfm * s_gld[i][k+1];
+ v[i][2] += dtfm * s_gld[i][k+2];
+ }
}
} else {
@@ -429,10 +429,10 @@ void FixGLD::final_integrate()
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
for (int k = 0; k < 3*prony_terms; k=k+3) {
- v[i][0] += dtfm * s_gld[i][k];
- v[i][1] += dtfm * s_gld[i][k+1];
- v[i][2] += dtfm * s_gld[i][k+2];
- }
+ v[i][0] += dtfm * s_gld[i][k];
+ v[i][1] += dtfm * s_gld[i][k+1];
+ v[i][2] += dtfm * s_gld[i][k+2];
+ }
}
}
diff --git a/src/MOLECULE/pair_hbond_dreiding_morse.cpp b/src/MOLECULE/pair_hbond_dreiding_morse.cpp
index 5c61ea4a45..83b03f9a2f 100644
--- a/src/MOLECULE/pair_hbond_dreiding_morse.cpp
+++ b/src/MOLECULE/pair_hbond_dreiding_morse.cpp
@@ -162,7 +162,7 @@ void PairHbondDreidingMorse::compute(int eflag, int vflag)
eng_morse = pm.d0 * (dexp*dexp - 2.0*dexp);
force_kernel = pm.morse1*(dexp*dexp - dexp)/r * powint(c,pm.ap);
force_angle = pm.ap * eng_morse * powint(c,pm.ap-1)*s;
- force_switch = 0.0;
+ force_switch = 0.0;
if (rsq > pm.cut_innersq) {
switch1 = (pm.cut_outersq-rsq) * (pm.cut_outersq-rsq) *
@@ -172,8 +172,8 @@ void PairHbondDreidingMorse::compute(int eflag, int vflag)
(rsq-pm.cut_innersq) / pm.denom_vdw;
force_kernel *= switch1;
- force_angle *= switch1;
- force_switch = eng_morse*switch2/rsq;
+ force_angle *= switch1;
+ force_switch = eng_morse*switch2/rsq;
eng_morse *= switch1;
}
diff --git a/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp b/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp
index 0d2159b671..7d69995fed 100644
--- a/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp
+++ b/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp
@@ -145,43 +145,43 @@ void PairLJCharmmfswCoulCharmmfsh::compute(int eflag, int vflag)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cut_bothsq) {
- r2inv = 1.0/rsq;
- r = sqrt(rsq);
+ r2inv = 1.0/rsq;
+ r = sqrt(rsq);
- if (rsq < cut_coulsq) {
- forcecoul = qqrd2e * qtmp*q[j]*
+ if (rsq < cut_coulsq) {
+ forcecoul = qqrd2e * qtmp*q[j]*
(sqrt(r2inv) - r*cut_coulinv*cut_coulinv);
- } else forcecoul = 0.0;
-
- if (rsq < cut_ljsq) {
- r6inv = r2inv*r2inv*r2inv;
- jtype = type[j];
- forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
- if (rsq > cut_lj_innersq) {
- switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
- (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
- forcelj = forcelj*switch1;
- }
- } else forcelj = 0.0;
-
- fpair = (factor_coul*forcecoul + factor_lj*forcelj) * r2inv;
-
- f[i][0] += delx*fpair;
- f[i][1] += dely*fpair;
- f[i][2] += delz*fpair;
- if (newton_pair || j < nlocal) {
- f[j][0] -= delx*fpair;
- f[j][1] -= dely*fpair;
- f[j][2] -= delz*fpair;
- }
-
- if (eflag) {
- if (rsq < cut_coulsq) {
- ecoul = qqrd2e * qtmp*q[j]*
+ } else forcecoul = 0.0;
+
+ if (rsq < cut_ljsq) {
+ r6inv = r2inv*r2inv*r2inv;
+ jtype = type[j];
+ forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
+ if (rsq > cut_lj_innersq) {
+ switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
+ (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
+ forcelj = forcelj*switch1;
+ }
+ } else forcelj = 0.0;
+
+ fpair = (factor_coul*forcecoul + factor_lj*forcelj) * r2inv;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (eflag) {
+ if (rsq < cut_coulsq) {
+ ecoul = qqrd2e * qtmp*q[j]*
(sqrt(r2inv) + cut_coulinv*cut_coulinv*r - 2.0*cut_coulinv);
- ecoul *= factor_coul;
- } else ecoul = 0.0;
- if (rsq < cut_ljsq) {
+ ecoul *= factor_coul;
+ } else ecoul = 0.0;
+ if (rsq < cut_ljsq) {
if (rsq > cut_lj_innersq) {
rinv = 1.0/r;
r3inv = rinv*rinv*rinv;
@@ -197,12 +197,12 @@ void PairLJCharmmfswCoulCharmmfsh::compute(int eflag, int vflag)
lj4[itype][jtype]*cut_lj_inner3inv*cut_lj3inv;
evdwl = evdwl12 + evdwl6;
}
- evdwl *= factor_lj;
- } else evdwl = 0.0;
- }
+ evdwl *= factor_lj;
+ } else evdwl = 0.0;
+ }
- if (evflag) ev_tally(i,j,nlocal,newton_pair,
- evdwl,ecoul,fpair,delx,dely,delz);
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,
+ evdwl,ecoul,fpair,delx,dely,delz);
}
}
}
@@ -345,10 +345,10 @@ double PairLJCharmmfswCoulCharmmfsh::init_one(int i, int j)
{
if (setflag[i][j] == 0) {
epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j],
- sigma[i][i],sigma[j][j]);
+ sigma[i][i],sigma[j][j]);
sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]);
eps14[i][j] = mix_energy(eps14[i][i],eps14[j][j],
- sigma14[i][i],sigma14[j][j]);
+ sigma14[i][i],sigma14[j][j]);
sigma14[i][j] = mix_distance(sigma14[i][i],sigma14[j][j]);
}
@@ -437,16 +437,16 @@ void PairLJCharmmfswCoulCharmmfsh::read_restart(FILE *fp)
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
- if (me == 0) {
- fread(&epsilon[i][j],sizeof(double),1,fp);
- fread(&sigma[i][j],sizeof(double),1,fp);
- fread(&eps14[i][j],sizeof(double),1,fp);
- fread(&sigma14[i][j],sizeof(double),1,fp);
- }
- MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&eps14[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&sigma14[i][j],1,MPI_DOUBLE,0,world);
+ if (me == 0) {
+ fread(&epsilon[i][j],sizeof(double),1,fp);
+ fread(&sigma[i][j],sizeof(double),1,fp);
+ fread(&eps14[i][j],sizeof(double),1,fp);
+ fread(&sigma14[i][j],sizeof(double),1,fp);
+ }
+ MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&eps14[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&sigma14[i][j],1,MPI_DOUBLE,0,world);
}
}
}
@@ -508,7 +508,7 @@ single(int i, int j, int itype, int jtype,
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
- (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
+ (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
forcelj = forcelj*switch1;
}
} else forcelj = 0.0;
diff --git a/src/MPIIO/dump_cfg_mpiio.cpp b/src/MPIIO/dump_cfg_mpiio.cpp
index 50683ecf64..1cca047bb2 100644
--- a/src/MPIIO/dump_cfg_mpiio.cpp
+++ b/src/MPIIO/dump_cfg_mpiio.cpp
@@ -137,10 +137,10 @@ void DumpCFGMPIIO::write()
{
#ifdef LMP_USER_IO_TIMER
- long startTimeBase, endTimeBase;
- MPI_Barrier(world); // timestamp barrier
- if (me == 0)
- startTimeBase = GetTimeBase();
+ long startTimeBase, endTimeBase;
+ MPI_Barrier(world); // timestamp barrier
+ if (me == 0)
+ startTimeBase = GetTimeBase();
#endif
if (domain->triclinic == 0) {
@@ -211,23 +211,23 @@ void DumpCFGMPIIO::write()
MPI_Bcast(&sumFileSize, 1, MPI_LMP_BIGINT, (nprocs-1), world);
#ifdef LMP_USER_IO_TIMER
- MPI_Barrier(world); // timestamp barrier
- dumpCFGTimestamps[0] = GetTimeBase();
+ MPI_Barrier(world); // timestamp barrier
+ dumpCFGTimestamps[0] = GetTimeBase();
#endif
openfile();
#ifdef LMP_USER_IO_TIMER
- MPI_Barrier(world); // timestamp barrier
- dumpCFGTimestamps[1] = GetTimeBase();
+ MPI_Barrier(world); // timestamp barrier
+ dumpCFGTimestamps[1] = GetTimeBase();
#endif
performEstimate = 0;
write_header(nheader); // mpifo now points to end of header info
#ifdef LMP_USER_IO_TIMER
- MPI_Barrier(world); // timestamp barrier
- dumpCFGTimestamps[2] = GetTimeBase();
+ MPI_Barrier(world); // timestamp barrier
+ dumpCFGTimestamps[2] = GetTimeBase();
#endif
// now actually write the data
@@ -235,20 +235,20 @@ void DumpCFGMPIIO::write()
write_data(nme,buf);
#ifdef LMP_USER_IO_TIMER
- MPI_Barrier(world); // timestamp barrier
- dumpCFGTimestamps[3] = GetTimeBase();
+ MPI_Barrier(world); // timestamp barrier
+ dumpCFGTimestamps[3] = GetTimeBase();
#endif
if (multifile) MPI_File_close(&mpifh);
if (multifile) delete [] filecurrent;
#ifdef LMP_USER_IO_TIMER
- MPI_Barrier(world); // timestamp barrier
- dumpCFGTimestamps[4] = GetTimeBase();
- if (me == 0) {
- endTimeBase = GetTimeBase();
- printf("total dump cycles: %ld - estimates and setup: %ld openfile: %ld write header: %ld write data: %ld close file: %ld\n",(long) (endTimeBase-startTimeBase),(long) (dumpCFGTimestamps[0]-startTimeBase),(long) (dumpCFGTimestamps[1]-dumpCFGTimestamps[0]),(long) (dumpCFGTimestamps[2]-dumpCFGTimestamps[1]),(long) (dumpCFGTimestamps[3]-dumpCFGTimestamps[2]),(long) (dumpCFGTimestamps[4]-dumpCFGTimestamps[3]));
- }
+ MPI_Barrier(world); // timestamp barrier
+ dumpCFGTimestamps[4] = GetTimeBase();
+ if (me == 0) {
+ endTimeBase = GetTimeBase();
+ printf("total dump cycles: %ld - estimates and setup: %ld openfile: %ld write header: %ld write data: %ld close file: %ld\n",(long) (endTimeBase-startTimeBase),(long) (dumpCFGTimestamps[0]-startTimeBase),(long) (dumpCFGTimestamps[1]-dumpCFGTimestamps[0]),(long) (dumpCFGTimestamps[2]-dumpCFGTimestamps[1]),(long) (dumpCFGTimestamps[3]-dumpCFGTimestamps[2]),(long) (dumpCFGTimestamps[4]-dumpCFGTimestamps[3]));
+ }
#endif
}
@@ -401,10 +401,10 @@ int DumpCFGMPIIO::convert_string_omp(int n, double *mybuf)
for (int j = 0; j < size_one; j++) {
double unwrap_coord;
if (j == 0) {
- //offset += sprintf(&sbuf[offset],"%f \n",mybuf[m]);
+ //offset += sprintf(&sbuf[offset],"%f \n",mybuf[m]);
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),"%f \n",mybuf[bufOffset[tid]+m]);
} else if (j == 1) {
- // offset += sprintf(&sbuf[offset],"%s \n",typenames[(int) mybuf[m]]);
+ // offset += sprintf(&sbuf[offset],"%s \n",typenames[(int) mybuf[m]]);
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),"%s \n",typenames[(int) mybuf[bufOffset[tid]+m]]);
} else if (j >= 2 && j <= 4) {
unwrap_coord = (mybuf[bufOffset[tid]+m] - 0.5)/UNWRAPEXPAND + 0.5;
diff --git a/src/QEQ/fix_qeq_dynamic.cpp b/src/QEQ/fix_qeq_dynamic.cpp
index 5408db650b..43e9a9c874 100644
--- a/src/QEQ/fix_qeq_dynamic.cpp
+++ b/src/QEQ/fix_qeq_dynamic.cpp
@@ -79,7 +79,7 @@ void FixQEqDynamic::init()
if (tolerance < 1e-4)
if (comm->me == 0)
error->warning(FLERR,"Fix qeq/dynamic tolerance may be too small"
- " for damped dynamics");
+ " for damped dynamics");
if (strstr(update->integrate_style,"respa"))
nlevels_respa = ((Respa *) update->integrate)->nlevels;
@@ -161,7 +161,7 @@ void FixQEqDynamic::pre_force(int vflag)
if (iloop == maxiter) {
char str[128];
sprintf(str,"Charges did not converge at step " BIGINT_FORMAT
- ": %lg",update->ntimestep,enegchk);
+ ": %lg",update->ntimestep,enegchk);
error->warning(FLERR,str);
}
}
@@ -211,7 +211,7 @@ double FixQEqDynamic::compute_eneg()
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
- j &= NEIGHMASK;
+ j &= NEIGHMASK;
delr[0] = x[i][0] - x[j][0];
delr[1] = x[i][1] - x[j][1];
@@ -221,9 +221,9 @@ double FixQEqDynamic::compute_eneg()
if (rsq > cutoff_sq) continue;
r = sqrt(rsq);
- rinv = 1.0/r;
- qf[i] += q[j] * rinv;
- qf[j] += q[i] * rinv;
+ rinv = 1.0/r;
+ qf[i] += q[j] * rinv;
+ qf[j] += q[i] * rinv;
}
}
}
diff --git a/src/QEQ/fix_qeq_fire.cpp b/src/QEQ/fix_qeq_fire.cpp
index 2404ae536d..763a39e82e 100644
--- a/src/QEQ/fix_qeq_fire.cpp
+++ b/src/QEQ/fix_qeq_fire.cpp
@@ -92,7 +92,7 @@ void FixQEqFire::init()
if (tolerance < 1e-4)
if (comm->me == 0)
error->warning(FLERR,"Fix qeq/fire tolerance may be too small"
- " for damped fires");
+ " for damped fires");
if (strstr(update->integrate_style,"respa"))
nlevels_respa = ((Respa *) update->integrate)->nlevels;
@@ -152,7 +152,7 @@ void FixQEqFire::pre_force(int vflag)
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
- qf[i] -= enegtot; // Enforce adiabatic
+ qf[i] -= enegtot; // Enforce adiabatic
}
// FIRE minimization algorithm
@@ -192,7 +192,7 @@ void FixQEqFire::pre_force(int vflag)
alpha = ALPHA0;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
- qv[i] = 0.0;
+ qv[i] = 0.0;
}
}
@@ -225,7 +225,7 @@ void FixQEqFire::pre_force(int vflag)
if (iloop == maxiter) {
char str[128];
sprintf(str,"Charges did not converge at step " BIGINT_FORMAT
- ": %lg",update->ntimestep,enegchk);
+ ": %lg",update->ntimestep,enegchk);
error->warning(FLERR,str);
}
}
@@ -275,7 +275,7 @@ double FixQEqFire::compute_eneg()
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
- j &= NEIGHMASK;
+ j &= NEIGHMASK;
delr[0] = x[i][0] - x[j][0];
delr[1] = x[i][1] - x[j][1];
@@ -285,9 +285,9 @@ double FixQEqFire::compute_eneg()
if (rsq > cutoff_sq) continue;
r = sqrt(rsq);
- rinv = 1.0/r;
- qf[i] += q[j] * rinv;
- qf[j] += q[i] * rinv;
+ rinv = 1.0/r;
+ qf[i] += q[j] * rinv;
+ qf[j] += q[i] * rinv;
}
}
}
diff --git a/src/QEQ/fix_qeq_point.cpp b/src/QEQ/fix_qeq_point.cpp
index 63d20ad911..906f737991 100644
--- a/src/QEQ/fix_qeq_point.cpp
+++ b/src/QEQ/fix_qeq_point.cpp
@@ -79,8 +79,8 @@ void FixQEqPoint::pre_force(int vflag)
reallocate_matrix();
init_matvec();
- matvecs = CG(b_s, s); // CG on s - parallel
- matvecs += CG(b_t, t); // CG on t - parallel
+ matvecs = CG(b_s, s); // CG on s - parallel
+ matvecs += CG(b_t, t); // CG on t - parallel
calculate_Q();
if (force->kspace) force->kspace->qsum_qsq();
@@ -143,16 +143,16 @@ void FixQEqPoint::compute_H()
for( jj = 0; jj < jnum; jj++ ) {
j = jlist[jj];
- j &= NEIGHMASK;
+ j &= NEIGHMASK;
dx = x[j][0] - x[i][0];
dy = x[j][1] - x[i][1];
dz = x[j][2] - x[i][2];
r_sqr = dx*dx + dy*dy + dz*dz;
- if (r_sqr <= cutoff_sq) {
+ if (r_sqr <= cutoff_sq) {
H.jlist[m_fill] = j;
- r = sqrt(r_sqr);
+ r = sqrt(r_sqr);
H.val[m_fill] = 0.5/r;
m_fill++;
}
diff --git a/src/QEQ/fix_qeq_shielded.cpp b/src/QEQ/fix_qeq_shielded.cpp
index a5e0324d69..e23384b1c9 100644
--- a/src/QEQ/fix_qeq_shielded.cpp
+++ b/src/QEQ/fix_qeq_shielded.cpp
@@ -123,8 +123,8 @@ void FixQEqShielded::pre_force(int vflag)
reallocate_matrix();
init_matvec();
- matvecs = CG(b_s, s); // CG on s - parallel
- matvecs += CG(b_t, t); // CG on t - parallel
+ matvecs = CG(b_s, s); // CG on s - parallel
+ matvecs += CG(b_t, t); // CG on t - parallel
calculate_Q();
if (force->kspace) force->kspace->qsum_qsq();
@@ -189,16 +189,16 @@ void FixQEqShielded::compute_H()
for( jj = 0; jj < jnum; jj++ ) {
j = jlist[jj];
- j &= NEIGHMASK;
+ j &= NEIGHMASK;
dx = x[j][0] - x[i][0];
dy = x[j][1] - x[i][1];
dz = x[j][2] - x[i][2];
r_sqr = dx*dx + dy*dy + dz*dz;
- if (r_sqr <= cutoff_sq) {
+ if (r_sqr <= cutoff_sq) {
H.jlist[m_fill] = j;
- r = sqrt(r_sqr);
+ r = sqrt(r_sqr);
H.val[m_fill] = 0.5 * calculate_H( r, shld[type[i]][type[j]] );
m_fill++;
}
diff --git a/src/QEQ/fix_qeq_slater.cpp b/src/QEQ/fix_qeq_slater.cpp
index 44e1a0750b..544b9f037a 100644
--- a/src/QEQ/fix_qeq_slater.cpp
+++ b/src/QEQ/fix_qeq_slater.cpp
@@ -101,7 +101,7 @@ void FixQEqSlater::extract_streitz()
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");
+ "Fix qeq/slater could not extract params from pair coul/streitz");
}
@@ -120,8 +120,8 @@ void FixQEqSlater::pre_force(int vflag)
reallocate_matrix();
init_matvec();
- matvecs = CG(b_s, s); // CG on s - parallel
- matvecs += CG(b_t, t); // CG on t - parallel
+ matvecs = CG(b_s, s); // CG on s - parallel
+ matvecs += CG(b_t, t); // CG on t - parallel
calculate_Q();
if (force->kspace) force->kspace->qsum_qsq();
@@ -223,7 +223,7 @@ void FixQEqSlater::compute_H()
/* ---------------------------------------------------------------------- */
double FixQEqSlater::calculate_H(double zei, double zej, double zj,
- double r, double &zjtmp)
+ double r, double &zjtmp)
{
double rinv = 1.0/r;
@@ -276,7 +276,7 @@ double FixQEqSlater::calculate_H(double zei, double zej, double zj,
/* ---------------------------------------------------------------------- */
double FixQEqSlater::calculate_H_wolf(double zei, double zej, double zj,
- double r, double &zjtmp)
+ double r, double &zjtmp)
{
double rinv = 1.0/r;
@@ -321,7 +321,7 @@ double FixQEqSlater::calculate_H_wolf(double zei, double zej, double zj,
if (zei == zej) {
eshift = -exp2zirsh*(rcinv + zei*(sm1 + sm2*zei*rc + sm3*zei2*rc*rc));
ci_fifj = -exp2zir*(rinv + zei*(sm1 + sm2*zei*r + sm3*zei2*r*r))
- - eshift - (r-rc)*fshift;
+ - eshift - (r-rc)*fshift;
} else {
e1 = zei*zej4/((zei+zej)*(zei+zej)*(zei-zej)*(zei-zej));
e2 = zej*zei4/((zei+zej)*(zei+zej)*(zej-zei)*(zej-zei));
@@ -332,7 +332,7 @@ double FixQEqSlater::calculate_H_wolf(double zei, double zej, double zj,
eshift = -exp2zirsh*(e1+e3/rc) - exp2zjrsh*(e2+e4/rc);
ci_fifj = -exp2zir*(e1+e3/r) - exp2zjr*(e2+e4/r)
- - eshift - (r-rc)*fshift;
+ - eshift - (r-rc)*fshift;
}
etmp1 = erfcr/r - erfcrc/rc;
diff --git a/src/RIGID/fix_rigid.cpp b/src/RIGID/fix_rigid.cpp
index 33a4b441fd..630c89fe93 100644
--- a/src/RIGID/fix_rigid.cpp
+++ b/src/RIGID/fix_rigid.cpp
@@ -440,8 +440,8 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
force->numeric(FLERR,arg[iarg+3]);
p_flag[0] = p_flag[1] = p_flag[2] = 1;
if (dimension == 2) {
- p_start[2] = p_stop[2] = p_period[2] = 0.0;
- p_flag[2] = 0;
+ p_start[2] = p_stop[2] = p_period[2] = 0.0;
+ p_flag[2] = 0;
}
iarg += 4;
@@ -457,8 +457,8 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
force->numeric(FLERR,arg[iarg+3]);
p_flag[0] = p_flag[1] = p_flag[2] = 1;
if (dimension == 2) {
- p_start[2] = p_stop[2] = p_period[2] = 0.0;
- p_flag[2] = 0;
+ p_start[2] = p_stop[2] = p_period[2] = 0.0;
+ p_flag[2] = 0;
}
iarg += 4;
diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp
index e6083f6493..6eb2a2cc23 100644
--- a/src/RIGID/fix_rigid_small.cpp
+++ b/src/RIGID/fix_rigid_small.cpp
@@ -267,7 +267,7 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
if (iarg+4 > narg) error->all(FLERR,"Illegal fix rigid/small command");
if (strcmp(style,"rigid/npt/small") != 0 &&
strcmp(style,"rigid/nph/small") != 0)
- error->all(FLERR,"Illegal fix rigid/small command");
+ 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]);
@@ -275,8 +275,8 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
force->numeric(FLERR,arg[iarg+3]);
p_flag[0] = p_flag[1] = p_flag[2] = 1;
if (domain->dimension == 2) {
- p_start[2] = p_stop[2] = p_period[2] = 0.0;
- p_flag[2] = 0;
+ p_start[2] = p_stop[2] = p_period[2] = 0.0;
+ p_flag[2] = 0;
}
iarg += 4;
@@ -284,15 +284,15 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
if (iarg+4 > narg) error->all(FLERR,"Illegal fix rigid/small command");
if (strcmp(style,"rigid/npt/small") != 0 &&
strcmp(style,"rigid/nph/small") != 0)
- error->all(FLERR,"Illegal fix rigid/small command");
+ 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] =
force->numeric(FLERR,arg[iarg+3]);
p_flag[0] = p_flag[1] = p_flag[2] = 1;
if (domain->dimension == 2) {
- p_start[2] = p_stop[2] = p_period[2] = 0.0;
- p_flag[2] = 0;
+ p_start[2] = p_stop[2] = p_period[2] = 0.0;
+ p_flag[2] = 0;
}
iarg += 4;
diff --git a/src/SNAP/compute_sna_atom.cpp b/src/SNAP/compute_sna_atom.cpp
index 5341d16efa..75b08f08bf 100644
--- a/src/SNAP/compute_sna_atom.cpp
+++ b/src/SNAP/compute_sna_atom.cpp
@@ -87,29 +87,29 @@ ComputeSNAAtom::ComputeSNAAtom(LAMMPS *lmp, int narg, char **arg) :
while (iarg < narg) {
if (strcmp(arg[iarg],"diagonal") == 0) {
if (iarg+2 > narg)
- error->all(FLERR,"Illegal compute sna/atom command");
+ 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");
+ error->all(FLERR,"Illegal compute sna/atom command");
iarg += 2;
} else if (strcmp(arg[iarg],"rmin0") == 0) {
if (iarg+2 > narg)
- error->all(FLERR,"Illegal compute sna/atom command");
+ 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)
- error->all(FLERR,"Illegal compute sna/atom command");
+ error->all(FLERR,"Illegal compute sna/atom command");
switchflag = atoi(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"bzeroflag") == 0) {
if (iarg+2 > narg)
- error->all(FLERR,"Illegal compute sna/atom command");
+ error->all(FLERR,"Illegal compute sna/atom command");
bzeroflag = atoi(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"quadraticflag") == 0) {
if (iarg+2 > narg)
- error->all(FLERR,"Illegal compute sna/atom command");
+ error->all(FLERR,"Illegal compute sna/atom command");
quadraticflag = atoi(arg[iarg+1]);
iarg += 2;
} else error->all(FLERR,"Illegal compute sna/atom command");
@@ -246,23 +246,23 @@ void ComputeSNAAtom::compute_peratom()
int ninside = 0;
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];
- const double rsq = delx*delx + dely*dely + delz*delz;
- int jtype = type[j];
- if (rsq < cutsq[itype][jtype] && rsq>1e-20) {
- snaptr[tid]->rij[ninside][0] = delx;
- snaptr[tid]->rij[ninside][1] = dely;
- snaptr[tid]->rij[ninside][2] = delz;
- snaptr[tid]->inside[ninside] = j;
- snaptr[tid]->wj[ninside] = wjelem[jtype];
- snaptr[tid]->rcutij[ninside] = (radi+radelem[jtype])*rcutfac;
- ninside++;
- }
+ 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];
+ const double rsq = delx*delx + dely*dely + delz*delz;
+ int jtype = type[j];
+ if (rsq < cutsq[itype][jtype] && rsq>1e-20) {
+ snaptr[tid]->rij[ninside][0] = delx;
+ snaptr[tid]->rij[ninside][1] = dely;
+ snaptr[tid]->rij[ninside][2] = delz;
+ snaptr[tid]->inside[ninside] = j;
+ snaptr[tid]->wj[ninside] = wjelem[jtype];
+ snaptr[tid]->rcutij[ninside] = (radi+radelem[jtype])*rcutfac;
+ ninside++;
+ }
}
snaptr[tid]->compute_ui(ninside);
@@ -270,7 +270,7 @@ void ComputeSNAAtom::compute_peratom()
snaptr[tid]->compute_bi();
snaptr[tid]->copy_bi2bvec();
for (int icoeff = 0; icoeff < ncoeff; icoeff++)
- sna[i][icoeff] = snaptr[tid]->bvec[icoeff];
+ sna[i][icoeff] = snaptr[tid]->bvec[icoeff];
if (quadraticflag) {
int ncount = ncoeff;
for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
@@ -284,7 +284,7 @@ void ComputeSNAAtom::compute_peratom()
}
} else {
for (int icoeff = 0; icoeff < size_peratom_cols; icoeff++)
- sna[i][icoeff] = 0.0;
+ sna[i][icoeff] = 0.0;
}
}
}
diff --git a/src/SNAP/compute_snad_atom.cpp b/src/SNAP/compute_snad_atom.cpp
index c2ac5f5afd..0f522edf82 100644
--- a/src/SNAP/compute_snad_atom.cpp
+++ b/src/SNAP/compute_snad_atom.cpp
@@ -85,10 +85,10 @@ ComputeSNADAtom::ComputeSNADAtom(LAMMPS *lmp, int narg, char **arg) :
while (iarg < narg) {
if (strcmp(arg[iarg],"diagonal") == 0) {
if (iarg+2 > narg)
- error->all(FLERR,"Illegal compute snad/atom command");
+ error->all(FLERR,"Illegal compute snad/atom command");
diagonalstyle = atof(arg[iarg+1]);
if (diagonalstyle < 0 || diagonalstyle > 3)
- error->all(FLERR,"Illegal compute snad/atom command");
+ error->all(FLERR,"Illegal compute snad/atom command");
iarg += 2;
} else if (strcmp(arg[iarg],"rmin0") == 0) {
if (iarg+2 > narg)
@@ -97,12 +97,12 @@ ComputeSNADAtom::ComputeSNADAtom(LAMMPS *lmp, int narg, char **arg) :
iarg += 2;
} else if (strcmp(arg[iarg],"switchflag") == 0) {
if (iarg+2 > narg)
- error->all(FLERR,"Illegal compute snad/atom command");
+ error->all(FLERR,"Illegal compute snad/atom command");
switchflag = atoi(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"quadraticflag") == 0) {
if (iarg+2 > narg)
- error->all(FLERR,"Illegal compute snad/atom command");
+ error->all(FLERR,"Illegal compute snad/atom command");
quadraticflag = atoi(arg[iarg+1]);
iarg += 2;
} else error->all(FLERR,"Illegal compute snad/atom command");
@@ -205,7 +205,7 @@ void ComputeSNADAtom::compute_peratom()
memory->destroy(snad);
nmax = atom->nmax;
memory->create(snad,nmax,size_peratom_cols,
- "snad/atom:snad");
+ "snad/atom:snad");
array_atom = snad;
}
@@ -263,23 +263,23 @@ void ComputeSNADAtom::compute_peratom()
int ninside = 0;
for (int jj = 0; jj < jnum; jj++) {
- int j = jlist[jj];
- j &= NEIGHMASK;
+ 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;
+ 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];
- if (rsq < cutsq[itype][jtype]&&rsq>1e-20) {
- snaptr[tid]->rij[ninside][0] = delx;
- snaptr[tid]->rij[ninside][1] = dely;
- snaptr[tid]->rij[ninside][2] = delz;
- snaptr[tid]->inside[ninside] = j;
- snaptr[tid]->wj[ninside] = wjelem[jtype];
- snaptr[tid]->rcutij[ninside] = (radi+radelem[jtype])*rcutfac;
- ninside++;
- }
+ if (rsq < cutsq[itype][jtype]&&rsq>1e-20) {
+ snaptr[tid]->rij[ninside][0] = delx;
+ snaptr[tid]->rij[ninside][1] = dely;
+ snaptr[tid]->rij[ninside][2] = delz;
+ snaptr[tid]->inside[ninside] = j;
+ snaptr[tid]->wj[ninside] = wjelem[jtype];
+ snaptr[tid]->rcutij[ninside] = (radi+radelem[jtype])*rcutfac;
+ ninside++;
+ }
}
snaptr[tid]->compute_ui(ninside);
@@ -290,26 +290,26 @@ void ComputeSNADAtom::compute_peratom()
}
for (int jj = 0; jj < ninside; jj++) {
- const int j = snaptr[tid]->inside[jj];
- snaptr[tid]->compute_duidrj(snaptr[tid]->rij[jj],
- snaptr[tid]->wj[jj],
- snaptr[tid]->rcutij[jj]);
- snaptr[tid]->compute_dbidrj();
- snaptr[tid]->copy_dbi2dbvec();
-
- // Accumulate -dBi/dRi, -dBi/dRj
-
- double *snadi = snad[i]+typeoffset;
- double *snadj = snad[j]+typeoffset;
-
- for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
- snadi[icoeff] += snaptr[tid]->dbvec[icoeff][0];
- snadi[icoeff+ncoeff] += snaptr[tid]->dbvec[icoeff][1];
- snadi[icoeff+twoncoeff] += snaptr[tid]->dbvec[icoeff][2];
- snadj[icoeff] -= snaptr[tid]->dbvec[icoeff][0];
- snadj[icoeff+ncoeff] -= snaptr[tid]->dbvec[icoeff][1];
- snadj[icoeff+twoncoeff] -= snaptr[tid]->dbvec[icoeff][2];
- }
+ const int j = snaptr[tid]->inside[jj];
+ snaptr[tid]->compute_duidrj(snaptr[tid]->rij[jj],
+ snaptr[tid]->wj[jj],
+ snaptr[tid]->rcutij[jj]);
+ snaptr[tid]->compute_dbidrj();
+ snaptr[tid]->copy_dbi2dbvec();
+
+ // Accumulate -dBi/dRi, -dBi/dRj
+
+ double *snadi = snad[i]+typeoffset;
+ double *snadj = snad[j]+typeoffset;
+
+ for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
+ snadi[icoeff] += snaptr[tid]->dbvec[icoeff][0];
+ snadi[icoeff+ncoeff] += snaptr[tid]->dbvec[icoeff][1];
+ snadi[icoeff+twoncoeff] += snaptr[tid]->dbvec[icoeff][2];
+ snadj[icoeff] -= snaptr[tid]->dbvec[icoeff][0];
+ snadj[icoeff+ncoeff] -= snaptr[tid]->dbvec[icoeff][1];
+ snadj[icoeff+twoncoeff] -= snaptr[tid]->dbvec[icoeff][2];
+ }
if (quadraticflag) {
double *snadi = snad[i]+quadraticoffset;
diff --git a/src/SNAP/compute_snav_atom.cpp b/src/SNAP/compute_snav_atom.cpp
index 3b5383ddf4..f284ddab0b 100644
--- a/src/SNAP/compute_snav_atom.cpp
+++ b/src/SNAP/compute_snav_atom.cpp
@@ -81,24 +81,24 @@ ComputeSNAVAtom::ComputeSNAVAtom(LAMMPS *lmp, int narg, char **arg) :
while (iarg < narg) {
if (strcmp(arg[iarg],"diagonal") == 0) {
if (iarg+2 > narg)
- error->all(FLERR,"Illegal compute snav/atom command");
+ 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");
+ error->all(FLERR,"Illegal compute snav/atom command");
iarg += 2;
} else if (strcmp(arg[iarg],"rmin0") == 0) {
if (iarg+2 > narg)
- error->all(FLERR,"Illegal compute snav/atom command");
+ 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)
- error->all(FLERR,"Illegal compute snav/atom command");
+ error->all(FLERR,"Illegal compute snav/atom command");
switchflag = atoi(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"quadraticflag") == 0) {
if (iarg+2 > narg)
- error->all(FLERR,"Illegal compute snav/atom command");
+ error->all(FLERR,"Illegal compute snav/atom command");
quadraticflag = atoi(arg[iarg+1]);
iarg += 2;
} else error->all(FLERR,"Illegal compute snav/atom command");
@@ -208,7 +208,7 @@ void ComputeSNAVAtom::compute_peratom()
memory->destroy(snav);
nmax = atom->nmax;
memory->create(snav,nmax,size_peratom_cols,
- "snav/atom:snav");
+ "snav/atom:snav");
array_atom = snav;
}
@@ -257,7 +257,7 @@ void ComputeSNAVAtom::compute_peratom()
// insure rij, inside, and typej are of size jnum
- snaptr[tid]->grow_rij(jnum);
+ snaptr[tid]->grow_rij(jnum);
// rij[][3] = displacements between atom I and those neighbors
// inside = indices of neighbors of I within cutoff
@@ -266,23 +266,23 @@ void ComputeSNAVAtom::compute_peratom()
int ninside = 0;
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];
- if (rsq < cutsq[itype][jtype]&&rsq>1e-20) {
- snaptr[tid]->rij[ninside][0] = delx;
- snaptr[tid]->rij[ninside][1] = dely;
- snaptr[tid]->rij[ninside][2] = delz;
- snaptr[tid]->inside[ninside] = j;
- snaptr[tid]->wj[ninside] = wjelem[jtype];
- snaptr[tid]->rcutij[ninside] = (radi+radelem[jtype])*rcutfac;
- ninside++;
- }
+ 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];
+ if (rsq < cutsq[itype][jtype]&&rsq>1e-20) {
+ snaptr[tid]->rij[ninside][0] = delx;
+ snaptr[tid]->rij[ninside][1] = dely;
+ snaptr[tid]->rij[ninside][2] = delz;
+ snaptr[tid]->inside[ninside] = j;
+ snaptr[tid]->wj[ninside] = wjelem[jtype];
+ snaptr[tid]->rcutij[ninside] = (radi+radelem[jtype])*rcutfac;
+ ninside++;
+ }
}
snaptr[tid]->compute_ui(ninside);
@@ -293,33 +293,33 @@ void ComputeSNAVAtom::compute_peratom()
}
for (int jj = 0; jj < ninside; jj++) {
- const int j = snaptr[tid]->inside[jj];
-
- snaptr[tid]->compute_duidrj(snaptr[tid]->rij[jj],
- snaptr[tid]->wj[jj],
- snaptr[tid]->rcutij[jj]);
- snaptr[tid]->compute_dbidrj();
- snaptr[tid]->copy_dbi2dbvec();
-
- // Accumulate -dBi/dRi*Ri, -dBi/dRj*Rj
-
- 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;
- snavi[icoeff+twoncoeff] += snaptr[tid]->dbvec[icoeff][2]*ztmp;
- snavi[icoeff+threencoeff] += snaptr[tid]->dbvec[icoeff][1]*ztmp;
- snavi[icoeff+fourncoeff] += snaptr[tid]->dbvec[icoeff][0]*ztmp;
- snavi[icoeff+fivencoeff] += snaptr[tid]->dbvec[icoeff][0]*ytmp;
- snavj[icoeff] -= snaptr[tid]->dbvec[icoeff][0]*x[j][0];
- snavj[icoeff+ncoeff] -= snaptr[tid]->dbvec[icoeff][1]*x[j][1];
- snavj[icoeff+twoncoeff] -= snaptr[tid]->dbvec[icoeff][2]*x[j][2];
- snavj[icoeff+threencoeff] -= snaptr[tid]->dbvec[icoeff][1]*x[j][2];
- snavj[icoeff+fourncoeff] -= snaptr[tid]->dbvec[icoeff][0]*x[j][2];
- snavj[icoeff+fivencoeff] -= snaptr[tid]->dbvec[icoeff][0]*x[j][1];
- }
+ const int j = snaptr[tid]->inside[jj];
+
+ snaptr[tid]->compute_duidrj(snaptr[tid]->rij[jj],
+ snaptr[tid]->wj[jj],
+ snaptr[tid]->rcutij[jj]);
+ snaptr[tid]->compute_dbidrj();
+ snaptr[tid]->copy_dbi2dbvec();
+
+ // Accumulate -dBi/dRi*Ri, -dBi/dRj*Rj
+
+ 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;
+ snavi[icoeff+twoncoeff] += snaptr[tid]->dbvec[icoeff][2]*ztmp;
+ snavi[icoeff+threencoeff] += snaptr[tid]->dbvec[icoeff][1]*ztmp;
+ snavi[icoeff+fourncoeff] += snaptr[tid]->dbvec[icoeff][0]*ztmp;
+ snavi[icoeff+fivencoeff] += snaptr[tid]->dbvec[icoeff][0]*ytmp;
+ snavj[icoeff] -= snaptr[tid]->dbvec[icoeff][0]*x[j][0];
+ snavj[icoeff+ncoeff] -= snaptr[tid]->dbvec[icoeff][1]*x[j][1];
+ snavj[icoeff+twoncoeff] -= snaptr[tid]->dbvec[icoeff][2]*x[j][2];
+ snavj[icoeff+threencoeff] -= snaptr[tid]->dbvec[icoeff][1]*x[j][2];
+ snavj[icoeff+fourncoeff] -= snaptr[tid]->dbvec[icoeff][0]*x[j][2];
+ snavj[icoeff+fivencoeff] -= snaptr[tid]->dbvec[icoeff][0]*x[j][1];
+ }
if (quadraticflag) {
double *snavi = snav[i]+quadraticoffset;
diff --git a/src/SNAP/pair_snap.cpp b/src/SNAP/pair_snap.cpp
index e8e57a72a2..3de5d0c6c8 100644
--- a/src/SNAP/pair_snap.cpp
+++ b/src/SNAP/pair_snap.cpp
@@ -132,9 +132,9 @@ PairSNAP::~PairSNAP()
time[i] = 0;
timeave[i] = 0;
for (int tid = 0; tid<nthreads; tid++) {
- if (sna[tid]->timers[i]>time[i])
- time[i] = sna[tid]->timers[i];
- timeave[i] += sna[tid]->timers[i];
+ if (sna[tid]->timers[i]>time[i])
+ time[i] = sna[tid]->timers[i];
+ timeave[i] += sna[tid]->timers[i];
}
timeave[i] /= nthreads;
}
@@ -224,13 +224,13 @@ void PairSNAP::compute_regular(int eflag, int vflag)
int jelem = map[jtype];
if (rsq < cutsq[itype][jtype]&&rsq>1e-20) {
- snaptr->rij[ninside][0] = delx;
- snaptr->rij[ninside][1] = dely;
- snaptr->rij[ninside][2] = delz;
- snaptr->inside[ninside] = j;
- snaptr->wj[ninside] = wjelem[jelem];
- snaptr->rcutij[ninside] = (radi + radelem[jelem])*rcutfac;
- ninside++;
+ snaptr->rij[ninside][0] = delx;
+ snaptr->rij[ninside][1] = dely;
+ snaptr->rij[ninside][2] = delz;
+ snaptr->inside[ninside] = j;
+ snaptr->wj[ninside] = wjelem[jelem];
+ snaptr->rcutij[ninside] = (radi + radelem[jelem])*rcutfac;
+ ninside++;
}
}
@@ -252,7 +252,7 @@ void PairSNAP::compute_regular(int eflag, int vflag)
for (int jj = 0; jj < ninside; jj++) {
int j = snaptr->inside[jj];
snaptr->compute_duidrj(snaptr->rij[jj],
- snaptr->wj[jj],snaptr->rcutij[jj]);
+ snaptr->wj[jj],snaptr->rcutij[jj]);
snaptr->compute_dbidrj();
snaptr->copy_dbi2dbvec();
@@ -264,10 +264,10 @@ void PairSNAP::compute_regular(int eflag, int vflag)
// linear contributions
for (int k = 1; k <= ncoeff; k++) {
- double bgb = coeffi[k];
- fij[0] += bgb*snaptr->dbvec[k-1][0];
- fij[1] += bgb*snaptr->dbvec[k-1][1];
- fij[2] += bgb*snaptr->dbvec[k-1][2];
+ double bgb = coeffi[k];
+ fij[0] += bgb*snaptr->dbvec[k-1][0];
+ fij[1] += bgb*snaptr->dbvec[k-1][1];
+ fij[2] += bgb*snaptr->dbvec[k-1][2];
}
// quadratic contributions
@@ -305,9 +305,9 @@ void PairSNAP::compute_regular(int eflag, int vflag)
if (vflag)
ev_tally_xyz(i,j,nlocal,newton_pair,0.0,0.0,
- fij[0],fij[1],fij[2],
- -snaptr->rij[jj][0],-snaptr->rij[jj][1],
- -snaptr->rij[jj][2]);
+ fij[0],fij[1],fij[2],
+ -snaptr->rij[jj][0],-snaptr->rij[jj][1],
+ -snaptr->rij[jj][2]);
}
// tally energy contribution
@@ -532,8 +532,8 @@ void PairSNAP::compute_optimized(int eflag, int vflag)
i = i_pairs[iijj][0];
if (iold != i) {
set_sna_to_shared(tid,i_pairs[iijj][3]);
- ielem = map[type[i]];
- }
+ ielem = map[type[i]];
+ }
iold = i;
} else {
i = pairs[iijj][0];
@@ -543,8 +543,8 @@ void PairSNAP::compute_optimized(int eflag, int vflag)
const double ytmp = x[i][1];
const double ztmp = x[i][2];
const int itype = type[i];
- ielem = map[itype];
- const double radi = radelem[ielem];
+ ielem = map[itype];
+ const double radi = radelem[ielem];
if (i < nlocal) {
jlist = firstneigh[i];
@@ -573,7 +573,7 @@ void PairSNAP::compute_optimized(int eflag, int vflag)
delz = x[j][2] - ztmp;
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
- int jelem = map[jtype];
+ int jelem = map[jtype];
if (rsq < cutsq[itype][jtype]&&rsq>1e-20) { //unitialised
sna[tid]->rij[ninside][0] = delx;
@@ -582,7 +582,7 @@ void PairSNAP::compute_optimized(int eflag, int vflag)
sna[tid]->inside[ninside] = j;
sna[tid]->wj[ninside] = wjelem[jelem];
sna[tid]->rcutij[ninside] = (radi + radelem[jelem])*rcutfac;
- ninside++;
+ ninside++;
// update index list with inside index
pairs[iijj + (jj - pairs[iijj][1])][2] =
@@ -613,7 +613,7 @@ void PairSNAP::compute_optimized(int eflag, int vflag)
jj = pairs[iijj][2];
int j = sna[tid]->inside[jj];
sna[tid]->compute_duidrj(sna[tid]->rij[jj],
- sna[tid]->wj[jj],sna[tid]->rcutij[jj]);
+ sna[tid]->wj[jj],sna[tid]->rcutij[jj]);
sna[tid]->compute_dbidrj();
sna[tid]->copy_dbi2dbvec();
@@ -625,10 +625,10 @@ void PairSNAP::compute_optimized(int eflag, int vflag)
// linear contributions
for (k = 1; k <= ncoeff; k++) {
- double bgb = coeffi[k];
- fij[0] += bgb*sna[tid]->dbvec[k-1][0];
- fij[1] += bgb*sna[tid]->dbvec[k-1][1];
- fij[2] += bgb*sna[tid]->dbvec[k-1][2];
+ double bgb = coeffi[k];
+ fij[0] += bgb*sna[tid]->dbvec[k-1][0];
+ fij[1] += bgb*sna[tid]->dbvec[k-1][1];
+ fij[2] += bgb*sna[tid]->dbvec[k-1][2];
}
// quadratic contributions
@@ -681,7 +681,7 @@ void PairSNAP::compute_optimized(int eflag, int vflag)
// if atom has no pairs, eatom=0, which is wrong
if (eflag&&pairs[iijj][1] == 0) {
- evdwl = coeffi[0];
+ evdwl = coeffi[0];
if (!quadraticflag) {
sna[tid]->compute_bi();
@@ -1184,7 +1184,7 @@ void PairSNAP::build_per_atom_arrays()
const double delz = atom->x[j][2] - ztmp;
const double rsq = delx*delx + dely*dely + delz*delz;
int jtype = atom->type[j];
- int jelem = map[jtype];
+ int jelem = map[jtype];
i_pairs[i_numpairs][0] = i;
i_pairs[i_numpairs][1] = jj;
@@ -1350,40 +1350,40 @@ void PairSNAP::settings(int narg, char **arg)
if (strcmp(arg[i],"loadbalance")==0) {
do_load_balance = force->inumeric(FLERR,arg[++i]);
if (do_load_balance) {
- double mincutoff = extra_cutoff() +
- rcutmax + neighbor->skin;
- if (comm->cutghostuser < mincutoff) {
- char buffer[255];
+ double mincutoff = extra_cutoff() +
+ rcutmax + neighbor->skin;
+ if (comm->cutghostuser < mincutoff) {
+ char buffer[255];
- //apparently mincutoff is 0 after sprintf command ?????
+ //apparently mincutoff is 0 after sprintf command ?????
- double tmp = mincutoff + 0.1;
- sprintf(buffer, "Communication cutoff is too small "
- "for SNAP micro load balancing, increased to %lf",
- mincutoff+0.1);
- if (comm->me==0)
- error->warning(FLERR,buffer);
+ double tmp = mincutoff + 0.1;
+ sprintf(buffer, "Communication cutoff is too small "
+ "for SNAP micro load balancing, increased to %lf",
+ mincutoff+0.1);
+ if (comm->me==0)
+ error->warning(FLERR,buffer);
- comm->cutghostuser = tmp;
+ comm->cutghostuser = tmp;
- }
+ }
}
continue;
}
if (strcmp(arg[i],"schedule")==0) {
i++;
if (strcmp(arg[i],"static")==0)
- schedule_user = 1;
+ schedule_user = 1;
if (strcmp(arg[i],"dynamic")==0)
- schedule_user = 2;
+ schedule_user = 2;
if (strcmp(arg[i],"guided")==0)
- schedule_user = 3;
+ schedule_user = 3;
if (strcmp(arg[i],"auto")==0)
- schedule_user = 4;
+ schedule_user = 4;
if (strcmp(arg[i],"determine")==0)
- schedule_user = 5;
+ schedule_user = 5;
if (schedule_user == 0)
- error->all(FLERR,"Illegal pair_style command");
+ error->all(FLERR,"Illegal pair_style command");
continue;
}
error->all(FLERR,"Illegal pair_style command");
@@ -1403,9 +1403,9 @@ void PairSNAP::settings(int narg, char **arg)
if (!use_optimized)
if (nthreads > 1 ||
- use_shared_arrays ||
- do_load_balance ||
- schedule_user)
+ use_shared_arrays ||
+ do_load_balance ||
+ schedule_user)
error->all(FLERR,"Illegal pair_style command");
}
@@ -1484,7 +1484,7 @@ void PairSNAP::coeff(int narg, char **arg)
int jelem;
for (jelem = 0; jelem < nelements; jelem++)
if (strcmp(elemname,elements[jelem]) == 0)
- break;
+ break;
if (jelem < nelements)
map[i] = jelem;
@@ -1523,7 +1523,7 @@ void PairSNAP::coeff(int narg, char **arg)
int tid = omp_get_thread_num();
sna[tid] = new SNA(lmp,rfac0,twojmax,
diagonalstyle,use_shared_arrays,
- rmin0,switchflag,bzeroflag);
+ rmin0,switchflag,bzeroflag);
if (!use_shared_arrays)
sna[tid]->grow_rij(nmax);
}
@@ -1575,7 +1575,7 @@ 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]] +
- radelem[map[j]])*rcutfac;
+ radelem[map[j]])*rcutfac;
}
/* ---------------------------------------------------------------------- */
@@ -1650,8 +1650,8 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename)
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fpcoeff);
if (ptr == NULL) {
- eof = 1;
- fclose(fpcoeff);
+ eof = 1;
+ fclose(fpcoeff);
} else n = strlen(line) + 1;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
@@ -1682,8 +1682,8 @@ 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 < ncoeffall; icoeff++)
- ptr = fgets(line,MAXLINE,fpcoeff);
+ for (int icoeff = 0; icoeff < ncoeffall; icoeff++)
+ ptr = fgets(line,MAXLINE,fpcoeff);
continue;
}
@@ -1691,8 +1691,8 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename)
if (found[ielem]) {
if (comm->me == 0)
- for (int icoeff = 0; icoeff < ncoeffall; icoeff++)
- ptr = fgets(line,MAXLINE,fpcoeff);
+ for (int icoeff = 0; icoeff < ncoeffall; icoeff++)
+ ptr = fgets(line,MAXLINE,fpcoeff);
continue;
}
@@ -1703,29 +1703,29 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename)
if (comm->me == 0) {
if (screen) fprintf(screen,"SNAP Element = %s, Radius %g, Weight %g \n",
- elements[ielem], radelem[ielem], wjelem[ielem]);
+ elements[ielem], radelem[ielem], wjelem[ielem]);
if (logfile) fprintf(logfile,"SNAP Element = %s, Radius %g, Weight %g \n",
- elements[ielem], radelem[ielem], wjelem[ielem]);
+ elements[ielem], radelem[ielem], wjelem[ielem]);
}
for (int icoeff = 0; icoeff < ncoeffall; icoeff++) {
if (comm->me == 0) {
- ptr = fgets(line,MAXLINE,fpcoeff);
- if (ptr == NULL) {
- eof = 1;
- fclose(fpcoeff);
- } else n = strlen(line) + 1;
+ ptr = fgets(line,MAXLINE,fpcoeff);
+ if (ptr == NULL) {
+ eof = 1;
+ fclose(fpcoeff);
+ } else n = strlen(line) + 1;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
if (eof)
- error->all(FLERR,"Incorrect format in SNAP coefficient file");
+ 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)
- error->all(FLERR,"Incorrect format in SNAP coefficient file");
+ error->all(FLERR,"Incorrect format in SNAP coefficient file");
iword = 0;
words[iword] = strtok(line,"' \t\n\r\f");
diff --git a/src/SNAP/sna.cpp b/src/SNAP/sna.cpp
index 2c20e78b71..21470876d4 100644
--- a/src/SNAP/sna.cpp
+++ b/src/SNAP/sna.cpp
@@ -268,12 +268,12 @@ void SNA::build_indexlist()
for(int j1 = 0; j1 <= twojmax; j1++)
for(int j2 = 0; j2 <= j1; j2++)
for(int j = abs(j1 - j2); j <= MIN(twojmax, j1 + j2); j += 2)
- if (j >= j1) {
- idxj[idxj_count].j1 = j1;
- idxj[idxj_count].j2 = j2;
- idxj[idxj_count].j = j;
- idxj_count++;
- }
+ if (j >= j1) {
+ idxj[idxj_count].j1 = j1;
+ idxj[idxj_count].j2 = j2;
+ idxj[idxj_count].j = j;
+ idxj_count++;
+ }
}
}
@@ -414,38 +414,38 @@ void SNA::compute_zi()
for(int j1 = 0; j1 <= twojmax; j1++)
for(int j2 = 0; j2 <= j1; j2++) {
for(int j = j1 - j2; j <= MIN(twojmax, j1 + j2); j += 2) {
- double sumb1_r, sumb1_i;
- int ma2, mb2;
- for(int mb = 0; 2*mb <= j; mb++)
- 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;
+ double sumb1_r, sumb1_i;
+ int ma2, mb2;
+ for(int mb = 0; 2*mb <= j; mb++)
+ 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;
- sumb1_i = 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;
+ sumb1_i = 0.0;
- ma2 = (2 * ma - j - (2 * ma1 - j1) + j2) / 2;
+ ma2 = (2 * ma - j - (2 * ma1 - j1) + j2) / 2;
- for(int mb1 = MAX(0, (2 * mb - j - j2 + j1) / 2);
+ for(int mb1 = MAX(0, (2 * mb - j - j2 + j1) / 2);
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] *
- (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] *
- (uarraytot_r[j1][ma1][mb1] * uarraytot_i[j2][ma2][mb2] +
- uarraytot_i[j1][ma1][mb1] * uarraytot_r[j2][ma2][mb2]);
- } // end loop over mb1
-
- zarray_r[j1][j2][j][ma][mb] +=
- sumb1_r * cgarray[j1][j2][j][ma1][ma2];
- zarray_i[j1][j2][j][ma][mb] +=
- sumb1_i * cgarray[j1][j2][j][ma1][ma2];
- } // end loop over ma1
- } // end loop over ma, mb
+ mb2 = (2 * mb - j - (2 * mb1 - j1) + j2) / 2;
+ 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] *
+ (uarraytot_r[j1][ma1][mb1] * uarraytot_i[j2][ma2][mb2] +
+ uarraytot_i[j1][ma1][mb1] * uarraytot_r[j2][ma2][mb2]);
+ } // end loop over mb1
+
+ zarray_r[j1][j2][j][ma][mb] +=
+ sumb1_r * cgarray[j1][j2][j][ma1][ma2];
+ zarray_i[j1][j2][j][ma][mb] +=
+ sumb1_i * cgarray[j1][j2][j][ma1][ma2];
+ } // end loop over ma1
+ } // end loop over ma, mb
} // end loop over j
} // end loop over j1, j2
@@ -506,11 +506,11 @@ void SNA::compute_zi_omp(int sub_threads)
mb2 = (2 * mb - j - (2 * mb1 - j1) + j2) / 2;
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]);
+ (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] *
- (uarraytot_r[j1][ma1][mb1] * uarraytot_i[j2][ma2][mb2] +
- uarraytot_i[j1][ma1][mb1] * uarraytot_r[j2][ma2][mb2]);
+ (uarraytot_r[j1][ma1][mb1] * uarraytot_i[j2][ma2][mb2] +
+ uarraytot_i[j1][ma1][mb1] * uarraytot_r[j2][ma2][mb2]);
}
zarray_r[j1][j2][j][ma][mb] +=
@@ -547,29 +547,29 @@ void SNA::compute_bi()
j <= MIN(twojmax, j1 + j2); j += 2) {
barray[j1][j2][j] = 0.0;
- for(int mb = 0; 2*mb < j; mb++)
- for(int ma = 0; ma <= j; ma++)
+ for(int mb = 0; 2*mb < j; mb++)
+ for(int ma = 0; ma <= j; ma++)
barray[j1][j2][j] +=
uarraytot_r[j][ma][mb] * zarray_r[j1][j2][j][ma][mb] +
- uarraytot_i[j][ma][mb] * zarray_i[j1][j2][j][ma][mb];
-
- // For j even, special treatment for middle column
-
- if (j%2 == 0) {
- int mb = j/2;
- for(int ma = 0; ma < mb; ma++)
- barray[j1][j2][j] +=
- uarraytot_r[j][ma][mb] * zarray_r[j1][j2][j][ma][mb] +
- uarraytot_i[j][ma][mb] * zarray_i[j1][j2][j][ma][mb];
- int ma = mb;
- barray[j1][j2][j] +=
- (uarraytot_r[j][ma][mb] * zarray_r[j1][j2][j][ma][mb] +
- uarraytot_i[j][ma][mb] * zarray_i[j1][j2][j][ma][mb])*0.5;
- }
+ uarraytot_i[j][ma][mb] * zarray_i[j1][j2][j][ma][mb];
+
+ // For j even, special treatment for middle column
+
+ if (j%2 == 0) {
+ int mb = j/2;
+ for(int ma = 0; ma < mb; ma++)
+ barray[j1][j2][j] +=
+ uarraytot_r[j][ma][mb] * zarray_r[j1][j2][j][ma][mb] +
+ uarraytot_i[j][ma][mb] * zarray_i[j1][j2][j][ma][mb];
+ int ma = mb;
+ barray[j1][j2][j] +=
+ (uarraytot_r[j][ma][mb] * zarray_r[j1][j2][j][ma][mb] +
+ uarraytot_i[j][ma][mb] * zarray_i[j1][j2][j][ma][mb])*0.5;
+ }
barray[j1][j2][j] *= 2.0;
- if (bzero_flag)
- barray[j1][j2][j] -= bzero[j];
+ if (bzero_flag)
+ barray[j1][j2][j] -= bzero[j];
}
}
@@ -614,10 +614,10 @@ void SNA::copy_bi2bvec()
for(j2 = 0; j2 <= j1; j2++)
for(j = abs(j1 - j2);
j <= MIN(twojmax, j1 + j2); j += 2)
- if (j >= j1) {
- bvec[ncount] = barray[j1][j2][j];
- ncount++;
- }
+ if (j >= j1) {
+ bvec[ncount] = barray[j1][j2][j];
+ ncount++;
+ }
}
}
@@ -874,12 +874,12 @@ void SNA::compute_dbidrj()
dudr_r = duarray_r[j][ma][mb];
dudr_i = duarray_i[j][ma][mb];
- jjjmambzarray_r = jjjzarray_r[ma][mb];
- jjjmambzarray_i = jjjzarray_i[ma][mb];
+ jjjmambzarray_r = jjjzarray_r[ma][mb];
+ jjjmambzarray_i = jjjzarray_i[ma][mb];
for(int k = 0; k < 3; k++)
sumzdu_r[k] +=
dudr_r[k] * jjjmambzarray_r +
- dudr_i[k] * jjjmambzarray_i;
+ dudr_i[k] * jjjmambzarray_i;
} //end loop over ma mb
@@ -889,13 +889,13 @@ void SNA::compute_dbidrj()
int mb = j/2;
for(int ma = 0; ma < mb; ma++) {
dudr_r = duarray_r[j][ma][mb];
- dudr_i = duarray_i[j][ma][mb];
- jjjmambzarray_r = jjjzarray_r[ma][mb];
- jjjmambzarray_i = jjjzarray_i[ma][mb];
+ dudr_i = duarray_i[j][ma][mb];
+ jjjmambzarray_r = jjjzarray_r[ma][mb];
+ jjjmambzarray_i = jjjzarray_i[ma][mb];
for(int k = 0; k < 3; k++)
sumzdu_r[k] +=
dudr_r[k] * jjjmambzarray_r +
- dudr_i[k] * jjjmambzarray_i;
+ dudr_i[k] * jjjmambzarray_i;
}
int ma = mb;
dudr_r = duarray_r[j][ma][mb];
@@ -903,9 +903,9 @@ void SNA::compute_dbidrj()
jjjmambzarray_r = jjjzarray_r[ma][mb];
jjjmambzarray_i = jjjzarray_i[ma][mb];
for(int k = 0; k < 3; k++)
- sumzdu_r[k] +=
- (dudr_r[k] * jjjmambzarray_r +
- dudr_i[k] * jjjmambzarray_i)*0.5;
+ sumzdu_r[k] +=
+ (dudr_r[k] * jjjmambzarray_r +
+ dudr_i[k] * jjjmambzarray_i)*0.5;
} // end if jeven
for(int k = 0; k < 3; k++)
@@ -933,12 +933,12 @@ void SNA::compute_dbidrj()
dudr_r = duarray_r[j1][ma1][mb1];
dudr_i = duarray_i[j1][ma1][mb1];
- jjjmambzarray_r = jjjzarray_r[ma1][mb1];
- jjjmambzarray_i = jjjzarray_i[ma1][mb1];
+ jjjmambzarray_r = jjjzarray_r[ma1][mb1];
+ jjjmambzarray_i = jjjzarray_i[ma1][mb1];
for(int k = 0; k < 3; k++)
sumzdu_r[k] +=
dudr_r[k] * jjjmambzarray_r +
- dudr_i[k] * jjjmambzarray_i;
+ dudr_i[k] * jjjmambzarray_i;
} //end loop over ma1 mb1
@@ -948,13 +948,13 @@ void SNA::compute_dbidrj()
int mb1 = j1/2;
for(int ma1 = 0; ma1 < mb1; ma1++) {
dudr_r = duarray_r[j1][ma1][mb1];
- dudr_i = duarray_i[j1][ma1][mb1];
- jjjmambzarray_r = jjjzarray_r[ma1][mb1];
- jjjmambzarray_i = jjjzarray_i[ma1][mb1];
+ dudr_i = duarray_i[j1][ma1][mb1];
+ jjjmambzarray_r = jjjzarray_r[ma1][mb1];
+ jjjmambzarray_i = jjjzarray_i[ma1][mb1];
for(int k = 0; k < 3; k++)
sumzdu_r[k] +=
dudr_r[k] * jjjmambzarray_r +
- dudr_i[k] * jjjmambzarray_i;
+ dudr_i[k] * jjjmambzarray_i;
}
int ma1 = mb1;
dudr_r = duarray_r[j1][ma1][mb1];
@@ -962,9 +962,9 @@ void SNA::compute_dbidrj()
jjjmambzarray_r = jjjzarray_r[ma1][mb1];
jjjmambzarray_i = jjjzarray_i[ma1][mb1];
for(int k = 0; k < 3; k++)
- sumzdu_r[k] +=
- (dudr_r[k] * jjjmambzarray_r +
- dudr_i[k] * jjjmambzarray_i)*0.5;
+ sumzdu_r[k] +=
+ (dudr_r[k] * jjjmambzarray_r +
+ dudr_i[k] * jjjmambzarray_i)*0.5;
} // end if j1even
for(int k = 0; k < 3; k++)
@@ -992,12 +992,12 @@ void SNA::compute_dbidrj()
dudr_r = duarray_r[j2][ma2][mb2];
dudr_i = duarray_i[j2][ma2][mb2];
- jjjmambzarray_r = jjjzarray_r[ma2][mb2];
- jjjmambzarray_i = jjjzarray_i[ma2][mb2];
+ jjjmambzarray_r = jjjzarray_r[ma2][mb2];
+ jjjmambzarray_i = jjjzarray_i[ma2][mb2];
for(int k = 0; k < 3; k++)
sumzdu_r[k] +=
dudr_r[k] * jjjmambzarray_r +
- dudr_i[k] * jjjmambzarray_i;
+ dudr_i[k] * jjjmambzarray_i;
} //end loop over ma2 mb2
@@ -1007,13 +1007,13 @@ void SNA::compute_dbidrj()
int mb2 = j2/2;
for(int ma2 = 0; ma2 < mb2; ma2++) {
dudr_r = duarray_r[j2][ma2][mb2];
- dudr_i = duarray_i[j2][ma2][mb2];
- jjjmambzarray_r = jjjzarray_r[ma2][mb2];
- jjjmambzarray_i = jjjzarray_i[ma2][mb2];
+ dudr_i = duarray_i[j2][ma2][mb2];
+ jjjmambzarray_r = jjjzarray_r[ma2][mb2];
+ jjjmambzarray_i = jjjzarray_i[ma2][mb2];
for(int k = 0; k < 3; k++)
sumzdu_r[k] +=
dudr_r[k] * jjjmambzarray_r +
- dudr_i[k] * jjjmambzarray_i;
+ dudr_i[k] * jjjmambzarray_i;
}
int ma2 = mb2;
dudr_r = duarray_r[j2][ma2][mb2];
@@ -1021,9 +1021,9 @@ void SNA::compute_dbidrj()
jjjmambzarray_r = jjjzarray_r[ma2][mb2];
jjjmambzarray_i = jjjzarray_i[ma2][mb2];
for(int k = 0; k < 3; k++)
- sumzdu_r[k] +=
- (dudr_r[k] * jjjmambzarray_r +
- dudr_i[k] * jjjmambzarray_i)*0.5;
+ sumzdu_r[k] +=
+ (dudr_r[k] * jjjmambzarray_r +
+ dudr_i[k] * jjjmambzarray_i)*0.5;
} // end if j2even
for(int k = 0; k < 3; k++)
@@ -1078,12 +1078,12 @@ void SNA::copy_dbi2dbvec()
for(j2 = 0; j2 <= j1; j2++)
for(j = abs(j1 - j2);
j <= MIN(twojmax, j1 + j2); j += 2)
- if (j >= j1) {
- dbvec[ncount][0] = dbarray[j1][j2][j][0];
- dbvec[ncount][1] = dbarray[j1][j2][j][1];
- dbvec[ncount][2] = dbarray[j1][j2][j][2];
- ncount++;
- }
+ if (j >= j1) {
+ dbvec[ncount][0] = dbarray[j1][j2][j][0];
+ dbvec[ncount][1] = dbarray[j1][j2][j][1];
+ dbvec[ncount][2] = dbarray[j1][j2][j][2];
+ ncount++;
+ }
}
}
}
@@ -1187,25 +1187,25 @@ void SNA::compute_uarray(double x, double y, double z,
uarray_i[j][0][mb] = 0.0;
for (int ma = 0; ma < j; ma++) {
- rootpq = rootpqarray[j - ma][j - mb];
+ rootpq = rootpqarray[j - ma][j - mb];
uarray_r[j][ma][mb] +=
rootpq *
(a_r * uarray_r[j - 1][ma][mb] +
- a_i * uarray_i[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_i * uarray_r[j - 1][ma][mb]);
+ a_i * uarray_r[j - 1][ma][mb]);
- rootpq = rootpqarray[ma + 1][j - mb];
+ rootpq = rootpqarray[ma + 1][j - mb];
uarray_r[j][ma + 1][mb] =
-rootpq *
(b_r * uarray_r[j - 1][ma][mb] +
- b_i * uarray_i[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_i * uarray_r[j - 1][ma][mb]);
+ b_i * uarray_r[j - 1][ma][mb]);
}
}
@@ -1217,14 +1217,14 @@ void SNA::compute_uarray(double x, double y, double z,
mbpar = -mbpar;
int mapar = -mbpar;
for (int ma = 0; ma <= j; ma++) {
- mapar = -mapar;
- if (mapar == 1) {
- uarray_r[j][j-ma][j-mb] = uarray_r[j][ma][mb];
- uarray_i[j][j-ma][j-mb] = -uarray_i[j][ma][mb];
- } 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];
- }
+ mapar = -mapar;
+ if (mapar == 1) {
+ uarray_r[j][j-ma][j-mb] = uarray_r[j][ma][mb];
+ uarray_i[j][j-ma][j-mb] = -uarray_i[j][ma][mb];
+ } 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];
+ }
}
}
}
@@ -1259,25 +1259,25 @@ void SNA::compute_uarray_omp(double x, double y, double z,
uarray_i[j][0][mb] = 0.0;
for (int ma = 0; ma < j; ma++) {
- rootpq = rootpqarray[j - ma][j - mb];
+ rootpq = rootpqarray[j - ma][j - mb];
uarray_r[j][ma][mb] +=
- rootpq *
+ rootpq *
(a_r * uarray_r[j - 1][ma][mb] +
- a_i * uarray_i[j - 1][ma][mb]);
+ a_i * uarray_i[j - 1][ma][mb]);
uarray_i[j][ma][mb] +=
- rootpq *
+ rootpq *
(a_r * uarray_i[j - 1][ma][mb] -
- a_i * uarray_r[j - 1][ma][mb]);
+ a_i * uarray_r[j - 1][ma][mb]);
- rootpq = rootpqarray[ma + 1][j - mb];
+ rootpq = rootpqarray[ma + 1][j - mb];
uarray_r[j][ma + 1][mb] =
- -rootpq *
+ -rootpq *
(b_r * uarray_r[j - 1][ma][mb] +
- b_i * uarray_i[j - 1][ma][mb]);
+ b_i * uarray_i[j - 1][ma][mb]);
uarray_i[j][ma + 1][mb] =
- -rootpq *
+ -rootpq *
(b_r * uarray_i[j - 1][ma][mb] -
- b_i * uarray_r[j - 1][ma][mb]);
+ b_i * uarray_r[j - 1][ma][mb]);
}
}
@@ -1291,23 +1291,23 @@ void SNA::compute_uarray_omp(double x, double y, double z,
for (int ma = 0; ma < j; ma++) {
rootpq = rootpqarray[j - ma][mb];
uarray_r[j][ma][mb] +=
- rootpq *
+ rootpq *
(b_r * uarray_r[j - 1][ma][mb - 1] -
- b_i * uarray_i[j - 1][ma][mb - 1]);
+ b_i * uarray_i[j - 1][ma][mb - 1]);
uarray_i[j][ma][mb] +=
- rootpq *
+ rootpq *
(b_r * uarray_i[j - 1][ma][mb - 1] +
- b_i * uarray_r[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 *
+ rootpq *
(a_r * uarray_r[j - 1][ma][mb - 1] -
- a_i * uarray_i[j - 1][ma][mb - 1]);
+ a_i * uarray_i[j - 1][ma][mb - 1]);
uarray_i[j][ma + 1][mb] =
- rootpq *
+ rootpq *
(a_r * uarray_i[j - 1][ma][mb - 1] +
- a_i * uarray_r[j - 1][ma][mb - 1]);
+ a_i * uarray_r[j - 1][ma][mb - 1]);
}
}
}
@@ -1319,7 +1319,7 @@ void SNA::compute_uarray_omp(double x, double y, double z,
void SNA::compute_duarray(double x, double y, double z,
double z0, double r, double dz0dr,
- double wj, double rcut)
+ double wj, double rcut)
{
double r0inv;
double a_r, a_i, b_r, b_i;
@@ -1405,7 +1405,7 @@ void SNA::compute_duarray(double x, double y, double z,
a_i * duarray_r[j - 1][ma][mb][k]);
}
- rootpq = rootpqarray[ma + 1][j - mb];
+ rootpq = rootpqarray[ma + 1][j - mb];
uarray_r[j][ma + 1][mb] =
-rootpq * (b_r * uarray_r[j - 1][ma][mb] +
b_i * uarray_i[j - 1][ma][mb]);
@@ -1433,22 +1433,22 @@ void SNA::compute_duarray(double x, double y, double z,
mbpar = -mbpar;
int mapar = -mbpar;
for (int ma = 0; ma <= j; ma++) {
- mapar = -mapar;
- if (mapar == 1) {
- uarray_r[j][j-ma][j-mb] = uarray_r[j][ma][mb];
- uarray_i[j][j-ma][j-mb] = -uarray_i[j][ma][mb];
- for (int k = 0; k < 3; k++) {
- duarray_r[j][j-ma][j-mb][k] = duarray_r[j][ma][mb][k];
- duarray_i[j][j-ma][j-mb][k] = -duarray_i[j][ma][mb][k];
- }
- } 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];
- for (int k = 0; k < 3; k++) {
- duarray_r[j][j-ma][j-mb][k] = -duarray_r[j][ma][mb][k];
- duarray_i[j][j-ma][j-mb][k] = duarray_i[j][ma][mb][k];
- }
- }
+ mapar = -mapar;
+ if (mapar == 1) {
+ uarray_r[j][j-ma][j-mb] = uarray_r[j][ma][mb];
+ uarray_i[j][j-ma][j-mb] = -uarray_i[j][ma][mb];
+ for (int k = 0; k < 3; k++) {
+ duarray_r[j][j-ma][j-mb][k] = duarray_r[j][ma][mb][k];
+ duarray_i[j][j-ma][j-mb][k] = -duarray_i[j][ma][mb][k];
+ }
+ } 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];
+ for (int k = 0; k < 3; k++) {
+ duarray_r[j][j-ma][j-mb][k] = -duarray_r[j][ma][mb][k];
+ duarray_i[j][j-ma][j-mb][k] = duarray_i[j][ma][mb][k];
+ }
+ }
}
}
}
@@ -1794,36 +1794,36 @@ void SNA::init_clebsch_gordan()
if(m < 0 || m > j) continue;
- sum = 0.0;
-
- 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));
- z++) {
- ifac = z % 2 ? -1 : 1;
- sum += ifac /
- (factorial(z) *
- factorial((j1 + j2 - j) / 2 - z) *
- factorial((j1 - aa2) / 2 - z) *
- factorial((j2 + bb2) / 2 - z) *
- factorial((j - j2 + aa2) / 2 + z) *
- factorial((j - j1 - bb2) / 2 + z));
- }
-
- cc2 = 2 * m - j;
- dcg = deltacg(j1, j2, j);
- sfaccg = sqrt(factorial((j1 + aa2) / 2) *
- factorial((j1 - aa2) / 2) *
- factorial((j2 + bb2) / 2) *
- factorial((j2 - bb2) / 2) *
- factorial((j + cc2) / 2) *
- factorial((j - cc2) / 2) *
- (j + 1));
-
- cgarray[j1][j2][j][m1][m2] = sum * dcg * sfaccg;
- }
- }
+ sum = 0.0;
+
+ 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));
+ z++) {
+ ifac = z % 2 ? -1 : 1;
+ sum += ifac /
+ (factorial(z) *
+ factorial((j1 + j2 - j) / 2 - z) *
+ factorial((j1 - aa2) / 2 - z) *
+ factorial((j2 + bb2) / 2 - z) *
+ factorial((j - j2 + aa2) / 2 + z) *
+ factorial((j - j1 - bb2) / 2 + z));
+ }
+
+ cc2 = 2 * m - j;
+ dcg = deltacg(j1, j2, j);
+ sfaccg = sqrt(factorial((j1 + aa2) / 2) *
+ factorial((j1 - aa2) / 2) *
+ factorial((j2 + bb2) / 2) *
+ factorial((j2 - bb2) / 2) *
+ factorial((j + cc2) / 2) *
+ factorial((j - cc2) / 2) *
+ (j + 1));
+
+ cgarray[j1][j2][j][m1][m2] = sum * dcg * sfaccg;
+ }
+ }
}
/* ----------------------------------------------------------------------
diff --git a/src/SRD/fix_srd.cpp b/src/SRD/fix_srd.cpp
index 7e43901dc9..c1c83ce59a 100644
--- a/src/SRD/fix_srd.cpp
+++ b/src/SRD/fix_srd.cpp
@@ -1037,8 +1037,8 @@ void FixSRD::reset_velocities()
for (i = 0; i < nbins; i++){
if (vbin[i].owner) {
if (vbin[i].n > 1) {
- srd_bin_temp += vbin[i].value[0]/(vbin[i].n-dof_temp);
- srd_bin_count++;
+ srd_bin_temp += vbin[i].value[0]/(vbin[i].n-dof_temp);
+ srd_bin_count++;
}
}
}
@@ -1348,16 +1348,16 @@ void FixSRD::collisions_single()
"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);
- error->warning(FLERR,str);
- } else{
+ if (insideflag == INSIDE_ERROR) error->one(FLERR,str);
+ error->warning(FLERR,str);
+ } else{
sprintf(str,
"SRD particle " TAGINT_FORMAT " started "
"inside wall %d on step " BIGINT_FORMAT " bounce %d",
atom->tag[i],j,update->ntimestep,ibounce+1);
- if (insideflag == INSIDE_ERROR) error->one(FLERR,str);
- error->warning(FLERR,str);
- }
+ if (insideflag == INSIDE_ERROR) error->one(FLERR,str);
+ error->warning(FLERR,str);
+ }
}
break;
}
@@ -1507,16 +1507,16 @@ void FixSRD::collisions_multi()
"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);
- error->warning(FLERR,str);
- } else{
+ if (insideflag == INSIDE_ERROR) error->one(FLERR,str);
+ error->warning(FLERR,str);
+ } else{
sprintf(str,
"SRD particle " TAGINT_FORMAT " started "
"inside wall %d on step " BIGINT_FORMAT " bounce %d",
atom->tag[i],j,update->ntimestep,ibounce+1);
- if (insideflag == INSIDE_ERROR) error->one(FLERR,str);
- error->warning(FLERR,str);
- }
+ if (insideflag == INSIDE_ERROR) error->one(FLERR,str);
+ error->warning(FLERR,str);
+ }
}
t_first = 0.0;
break;
diff --git a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp b/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp
index c0ed980023..9d10fe1614 100644
--- a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp
+++ b/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp
@@ -234,8 +234,8 @@ void PairOxdna2Coaxstk::compute(int eflag, int vflag)
theta1p = 2 * MY_PI - theta1;
f4f6t1 = F4(theta1, a_cxst1[atype][btype], theta_cxst1_0[atype][btype], dtheta_cxst1_ast[atype][btype],
- b_cxst1[atype][btype], dtheta_cxst1_c[atype][btype]) +
- F6(theta1, AA_cxst1[atype][btype], BB_cxst1[atype][btype]);
+ b_cxst1[atype][btype], dtheta_cxst1_c[atype][btype]) +
+ F6(theta1, AA_cxst1[atype][btype], BB_cxst1[atype][btype]);
// early rejection criterium
if (f4f6t1) {
@@ -296,8 +296,8 @@ void PairOxdna2Coaxstk::compute(int eflag, int vflag)
rsint = 1.0/sin(theta1);
df4f6t1 = DF4(theta1, a_cxst1[atype][btype], theta_cxst1_0[atype][btype], dtheta_cxst1_ast[atype][btype],
- b_cxst1[atype][btype], dtheta_cxst1_c[atype][btype])*rsint +
- DF6(theta1, AA_cxst1[atype][btype], BB_cxst1[atype][btype])*rsint;
+ b_cxst1[atype][btype], dtheta_cxst1_c[atype][btype])*rsint +
+ DF6(theta1, AA_cxst1[atype][btype], BB_cxst1[atype][btype])*rsint;
df4t4 = DF4(theta4, a_cxst4[atype][btype], theta_cxst4_0[atype][btype], dtheta_cxst4_ast[atype][btype],
b_cxst4[atype][btype], dtheta_cxst4_c[atype][btype])/sin(theta4);
@@ -874,8 +874,8 @@ void PairOxdna2Coaxstk::read_restart(FILE *fp)
fread(&b_cxst6[i][j],sizeof(double),1,fp);
fread(&dtheta_cxst6_c[i][j],sizeof(double),1,fp);
- fread(&AA_cxst1[i][j],sizeof(double),1,fp);
- fread(&BB_cxst1[i][j],sizeof(double),1,fp);
+ fread(&AA_cxst1[i][j],sizeof(double),1,fp);
+ fread(&BB_cxst1[i][j],sizeof(double),1,fp);
}
@@ -895,7 +895,7 @@ void PairOxdna2Coaxstk::read_restart(FILE *fp)
MPI_Bcast(&b_cxst1[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&dtheta_cxst1_c[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&a_cxst4[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&a_cxst4[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&theta_cxst4_0[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&dtheta_cxst4_ast[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&b_cxst4[i][j],1,MPI_DOUBLE,0,world);
@@ -962,7 +962,7 @@ void PairOxdna2Coaxstk::write_data(FILE *fp)
%g %g %g %g %g\
%g %g %g %g %g\
%g %g %g %g %g\
- %g %g\
+ %g %g\
\n",i,
k_cxst[i][i],cut_cxst_0[i][i],cut_cxst_c[i][i],cut_cxst_lo[i][i],cut_cxst_hi[i][i],
cut_cxst_lc[i][i],cut_cxst_hc[i][i],b_cxst_lo[i][i],b_cxst_hi[i][i],
@@ -970,7 +970,7 @@ void PairOxdna2Coaxstk::write_data(FILE *fp)
a_cxst4[i][i],theta_cxst4_0[i][i],dtheta_cxst4_ast[i][i],b_cxst4[i][i],dtheta_cxst4_c[i][i],
a_cxst5[i][i],theta_cxst5_0[i][i],dtheta_cxst5_ast[i][i],b_cxst5[i][i],dtheta_cxst5_c[i][i],
a_cxst6[i][i],theta_cxst6_0[i][i],dtheta_cxst6_ast[i][i],b_cxst6[i][i],dtheta_cxst6_c[i][i],
- AA_cxst1[i][i],BB_cxst1[i][i]);
+ AA_cxst1[i][i],BB_cxst1[i][i]);
}
/* ----------------------------------------------------------------------
@@ -988,7 +988,7 @@ void PairOxdna2Coaxstk::write_data_all(FILE *fp)
%g %g %g %g %g\
%g %g %g %g %g\
%g %g %g %g %g\
- %g %g\
+ %g %g\
\n",i,j,
k_cxst[i][j],cut_cxst_0[i][j],cut_cxst_c[i][j],cut_cxst_lo[i][j],cut_cxst_hi[i][j],
cut_cxst_lc[i][j],cut_cxst_hc[i][j],b_cxst_lo[i][j],b_cxst_hi[i][j],
@@ -996,7 +996,7 @@ void PairOxdna2Coaxstk::write_data_all(FILE *fp)
a_cxst4[i][j],theta_cxst4_0[i][j],dtheta_cxst4_ast[i][j],b_cxst4[i][j],dtheta_cxst4_c[i][j],
a_cxst5[i][j],theta_cxst5_0[i][j],dtheta_cxst5_ast[i][j],b_cxst5[i][j],dtheta_cxst5_c[i][j],
a_cxst6[i][j],theta_cxst6_0[i][j],dtheta_cxst6_ast[i][j],b_cxst6[i][j],dtheta_cxst6_c[i][j],
- AA_cxst1[i][j],BB_cxst1[i][j]);
+ AA_cxst1[i][j],BB_cxst1[i][j]);
}
diff --git a/src/USER-CGDNA/pair_oxdna2_dh.cpp b/src/USER-CGDNA/pair_oxdna2_dh.cpp
index ea91dad0a0..73072f4c0e 100644
--- a/src/USER-CGDNA/pair_oxdna2_dh.cpp
+++ b/src/USER-CGDNA/pair_oxdna2_dh.cpp
@@ -163,20 +163,20 @@ void PairOxdna2Dh::compute(int eflag, int vflag)
if (rsq <= cutsq_dh_c[atype][btype]) {
- r = sqrt(rsq);
- rinv = 1.0/r;
+ r = sqrt(rsq);
+ rinv = 1.0/r;
- if (r <= cut_dh_ast[atype][btype]) {
+ if (r <= cut_dh_ast[atype][btype]) {
- fpair = qeff_dh_pf[atype][btype] * exp(-kappa_dh[atype][btype] * r) *
- (kappa_dh[atype][btype] + rinv) * rinv * rinv;
+ fpair = qeff_dh_pf[atype][btype] * exp(-kappa_dh[atype][btype] * r) *
+ (kappa_dh[atype][btype] + rinv) * rinv * rinv;
- if (eflag) {
- evdwl = qeff_dh_pf[atype][btype] * exp(-kappa_dh[atype][btype]*r) * rinv;
- }
+ if (eflag) {
+ evdwl = qeff_dh_pf[atype][btype] * exp(-kappa_dh[atype][btype]*r) * rinv;
+ }
- }
- else {
+ }
+ else {
fpair = 2.0 * b_dh[atype][btype] * (cut_dh_c[atype][btype] - r) * rinv;
@@ -184,50 +184,50 @@ void PairOxdna2Dh::compute(int eflag, int vflag)
evdwl = b_dh[atype][btype] * (r - cut_dh_c[atype][btype]) * (r - cut_dh_c[atype][btype]);
}
- }
+ }
// knock out nearest-neighbour interaction between adjacent backbone sites
fpair *= factor_lj;
evdwl *= factor_lj;
- delf[0] = delr[0] * fpair;
- delf[1] = delr[1] * fpair;
- delf[2] = delr[2] * fpair;
+ delf[0] = delr[0] * fpair;
+ delf[1] = delr[1] * fpair;
+ delf[2] = delr[2] * fpair;
- // apply force and torque to each of 2 atoms
+ // apply force and torque to each of 2 atoms
- if (newton_pair || a < nlocal) {
+ if (newton_pair || a < nlocal) {
- f[a][0] += delf[0];
- f[a][1] += delf[1];
- f[a][2] += delf[2];
+ f[a][0] += delf[0];
+ f[a][1] += delf[1];
+ f[a][2] += delf[2];
- MathExtra::cross3(ra_cs,delf,delta);
+ MathExtra::cross3(ra_cs,delf,delta);
- torque[a][0] += delta[0];
- torque[a][1] += delta[1];
- torque[a][2] += delta[2];
+ torque[a][0] += delta[0];
+ torque[a][1] += delta[1];
+ torque[a][2] += delta[2];
- }
+ }
- if (newton_pair || b < nlocal) {
+ if (newton_pair || b < nlocal) {
- f[b][0] -= delf[0];
- f[b][1] -= delf[1];
- f[b][2] -= delf[2];
+ f[b][0] -= delf[0];
+ f[b][1] -= delf[1];
+ f[b][2] -= delf[2];
- MathExtra::cross3(rb_cs,delf,deltb);
+ MathExtra::cross3(rb_cs,delf,deltb);
- torque[b][0] -= deltb[0];
- torque[b][1] -= deltb[1];
- torque[b][2] -= deltb[2];
+ torque[b][0] -= deltb[0];
+ torque[b][1] -= deltb[1];
+ torque[b][2] -= deltb[2];
- }
+ }
- // increment energy and virial
+ // increment energy and virial
- if (evflag) ev_tally(a,b,nlocal,newton_pair,
- evdwl,0.0,fpair,delr[0],delr[1],delr[2]);
+ if (evflag) ev_tally(a,b,nlocal,newton_pair,
+ evdwl,0.0,fpair,delr[0],delr[1],delr[2]);
}
}
@@ -302,7 +302,7 @@ void PairOxdna2Dh::coeff(int narg, char **arg)
The numerical factor is the Debye length in s.u.
lambda(T = 300 K = 0.1) =
sqrt(eps_0 * eps_r * k_B * T/(2 * N_A * e^2 * 1000 mol/m^3))
- * 1/oxDNA_energy_unit
+ * 1/oxDNA_energy_unit
(see B. Snodin et al., J. Chem. Phys. 142, 234901 (2015).)
We use
@@ -324,7 +324,7 @@ void PairOxdna2Dh::coeff(int narg, char **arg)
NOTE:
The numerical factor is
qeff_dh_pf = e^2/(4 * pi * eps_0 * eps_r)
- * 1/(oxDNA_energy_unit * oxDNA_length_unit)
+ * 1/(oxDNA_energy_unit * oxDNA_length_unit)
(see B. Snodin et al., J. Chem. Phys. 142, 234901 (2015).)
In addition to the above units we use
@@ -515,10 +515,10 @@ void PairOxdna2Dh::write_data(FILE *fp)
for (int i = 1; i <= atom->ntypes; i++)
fprintf(fp,"%d\
%g %g\
- %g %g %g\
+ %g %g %g\
\n",i,
kappa_dh[i][i],qeff_dh_pf[i][i],
- b_dh[i][i],cut_dh_ast[i][i],cut_dh_c[i][i]);
+ b_dh[i][i],cut_dh_ast[i][i],cut_dh_c[i][i]);
}
/* ----------------------------------------------------------------------
@@ -531,10 +531,10 @@ void PairOxdna2Dh::write_data_all(FILE *fp)
for (int j = i; j <= atom->ntypes; j++)
fprintf(fp,"%d %d\
%g %g\
- %g %g %g\
+ %g %g %g\
\n",i,j,
kappa_dh[i][j],qeff_dh_pf[i][j],
- b_dh[i][j],cut_dh_ast[i][j],cut_dh_c[i][j]);
+ b_dh[i][j],cut_dh_ast[i][j],cut_dh_c[i][j]);
}
/* ---------------------------------------------------------------------- */
diff --git a/src/USER-COLVARS/fix_colvars.cpp b/src/USER-COLVARS/fix_colvars.cpp
index 956ba6498a..84b3ee07d6 100644
--- a/src/USER-COLVARS/fix_colvars.cpp
+++ b/src/USER-COLVARS/fix_colvars.cpp
@@ -549,9 +549,9 @@ void FixColvars::setup(int vflag)
} else {
m[i] = atom->mass[type[k]];
}
- if (atom->q_flag) {
- q[i] = atom->q[k];
- }
+ if (atom->q_flag) {
+ q[i] = atom->q[k];
+ }
}
}
@@ -616,7 +616,7 @@ void FixColvars::setup(int vflag)
comm_buf[nme].m = atom->mass[type[k]];
}
- if (atom->q_flag) {
+ if (atom->q_flag) {
comm_buf[nme].q = atom->q[k];
}
diff --git a/src/USER-DIFFRACTION/compute_xrd.cpp b/src/USER-DIFFRACTION/compute_xrd.cpp
index f56409f57c..380629ffb9 100644
--- a/src/USER-DIFFRACTION/compute_xrd.cpp
+++ b/src/USER-DIFFRACTION/compute_xrd.cpp
@@ -216,10 +216,10 @@ ComputeXRD::ComputeXRD(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 (4 >= dinv2 * lambda * lambda ) {
- ang = asin(lambda * sqrt(dinv2) * 0.5);
+ ang = asin(lambda * sqrt(dinv2) * 0.5);
if ((ang <= Max2Theta) && (ang >= Min2Theta)) {
nRows++;
- }
+ }
}
}
}
diff --git a/src/USER-H5MD/dump_h5md.cpp b/src/USER-H5MD/dump_h5md.cpp
index 7456d6fa44..4e85b5c8b6 100644
--- a/src/USER-H5MD/dump_h5md.cpp
+++ b/src/USER-H5MD/dump_h5md.cpp
@@ -125,7 +125,7 @@ DumpH5MD::DumpH5MD(LAMMPS *lmp, int narg, char **arg) : Dump(lmp, narg, arg)
size_one+=1;
} else if (strcmp(arg[iarg], "charge")==0) {
if (!atom->q_flag)
- error->all(FLERR, "Requesting non-allocated quantity q in dump_h5md");
+ error->all(FLERR, "Requesting non-allocated quantity q in dump_h5md");
every_charge = default_every;
iarg+=1;
n_parsed = element_args(narg-iarg, &arg[iarg], &every_charge);
@@ -137,10 +137,10 @@ DumpH5MD::DumpH5MD(LAMMPS *lmp, int narg, char **arg) : Dump(lmp, narg, arg)
error->all(FLERR, "Invalid number of arguments in dump h5md");
}
if (box_is_set||create_group_is_set)
- error->all(FLERR, "Cannot set file_from in dump h5md after box or create_group");
+ error->all(FLERR, "Cannot set file_from in dump h5md after box or create_group");
int idump;
for (idump = 0; idump < output->ndump; idump++)
- if (strcmp(arg[iarg+1],output->dump[idump]->id) == 0) break;
+ if (strcmp(arg[iarg+1],output->dump[idump]->id) == 0) break;
if (idump == output->ndump) error->all(FLERR,"Cound not find dump_modify ID");
datafile_from_dump = idump;
do_box=false;
@@ -152,11 +152,11 @@ DumpH5MD::DumpH5MD(LAMMPS *lmp, int narg, char **arg) : Dump(lmp, narg, arg)
}
box_is_set = true;
if (strcmp(arg[iarg+1], "yes")==0)
- do_box=true;
+ do_box=true;
else if (strcmp(arg[iarg+1], "no")==0)
- do_box=false;
+ do_box=false;
else
- error->all(FLERR, "Illegal dump h5md command");
+ error->all(FLERR, "Illegal dump h5md command");
iarg+=2;
} else if (strcmp(arg[iarg], "create_group")==0) {
if (iarg+1>=narg) {
@@ -164,22 +164,22 @@ DumpH5MD::DumpH5MD(LAMMPS *lmp, int narg, char **arg) : Dump(lmp, narg, arg)
}
create_group_is_set = true;
if (strcmp(arg[iarg+1], "yes")==0)
- create_group=true;
+ create_group=true;
else if (strcmp(arg[iarg+1], "no")==0) {
- create_group=false;
+ create_group=false;
}
else
- error->all(FLERR, "Illegal dump h5md command");
+ error->all(FLERR, "Illegal dump h5md command");
iarg+=2;
} else if (strcmp(arg[iarg], "author")==0) {
if (iarg+1>=narg) {
error->all(FLERR, "Invalid number of arguments in dump h5md");
}
if (author_name==NULL) {
- author_name = new char[strlen(arg[iarg])+1];
- strcpy(author_name, arg[iarg+1]);
+ author_name = new char[strlen(arg[iarg])+1];
+ strcpy(author_name, arg[iarg+1]);
} else {
- error->all(FLERR, "Illegal dump h5md command: author argument repeated");
+ error->all(FLERR, "Illegal dump h5md command: author argument repeated");
}
iarg+=2;
} else {
@@ -218,7 +218,7 @@ DumpH5MD::~DumpH5MD()
if (me==0) {
h5md_close_element(particles_data.position);
if (do_box)
- h5md_close_element(particles_data.box_edges);
+ h5md_close_element(particles_data.box_edges);
}
}
if (every_image>=0) {
@@ -272,36 +272,36 @@ void DumpH5MD::openfile()
if (me == 0) {
if (datafile_from_dump<0) {
if (author_name==NULL) {
- datafile = h5md_create_file(filename, "N/A", NULL, "lammps", LAMMPS_VERSION);
+ datafile = h5md_create_file(filename, "N/A", NULL, "lammps", LAMMPS_VERSION);
} else {
- datafile = h5md_create_file(filename, author_name, NULL, "lammps", LAMMPS_VERSION);
+ datafile = h5md_create_file(filename, author_name, NULL, "lammps", LAMMPS_VERSION);
}
group_name_length = strlen(group->names[igroup])+1;
group_name = new char[group_name_length];
strcpy(group_name, group->names[igroup]);
if (create_group) {
- particles_data = h5md_create_particles_group(datafile, group_name);
+ particles_data = h5md_create_particles_group(datafile, group_name);
} else {
- particles_data.group = h5md_open_particles_group(datafile.particles, group_name);
+ particles_data.group = h5md_open_particles_group(datafile.particles, group_name);
}
delete [] group_name;
dims[0] = natoms;
dims[1] = domain->dimension;
if (every_position>0) {
- particles_data.position = h5md_create_time_data(particles_data.group, "position", 2, dims, H5T_NATIVE_DOUBLE, NULL);
- h5md_create_box(&particles_data, dims[1], boundary, true, NULL, &particles_data.position);
+ particles_data.position = h5md_create_time_data(particles_data.group, "position", 2, dims, H5T_NATIVE_DOUBLE, NULL);
+ h5md_create_box(&particles_data, dims[1], boundary, true, NULL, &particles_data.position);
}
if (every_image>0)
- particles_data.image = h5md_create_time_data(particles_data.group, "image", 2, dims, H5T_NATIVE_INT, &particles_data.position);
+ particles_data.image = h5md_create_time_data(particles_data.group, "image", 2, dims, H5T_NATIVE_INT, &particles_data.position);
if (every_velocity>0)
- particles_data.velocity = h5md_create_time_data(particles_data.group, "velocity", 2, dims, H5T_NATIVE_DOUBLE, NULL);
+ particles_data.velocity = h5md_create_time_data(particles_data.group, "velocity", 2, dims, H5T_NATIVE_DOUBLE, NULL);
if (every_force>0)
- particles_data.force = h5md_create_time_data(particles_data.group, "force", 2, dims, H5T_NATIVE_DOUBLE, NULL);
+ particles_data.force = h5md_create_time_data(particles_data.group, "force", 2, dims, H5T_NATIVE_DOUBLE, NULL);
if (every_species>0)
- particles_data.species = h5md_create_time_data(particles_data.group, "species", 1, dims, H5T_NATIVE_INT, NULL);
+ particles_data.species = h5md_create_time_data(particles_data.group, "species", 1, dims, H5T_NATIVE_INT, NULL);
if (every_charge>0) {
- particles_data.charge = h5md_create_time_data(particles_data.group, "charge", 1, dims, H5T_NATIVE_DOUBLE, NULL);
- h5md_write_string_attribute(particles_data.group, "charge", "type", "effective");
+ particles_data.charge = h5md_create_time_data(particles_data.group, "charge", 1, dims, H5T_NATIVE_DOUBLE, NULL);
+ h5md_write_string_attribute(particles_data.group, "charge", "type", "effective");
}
} else {
DumpH5MD* other_dump;
@@ -311,27 +311,27 @@ void DumpH5MD::openfile()
group_name = new char[group_name_length];
strcpy(group_name, group->names[igroup]);
if (create_group) {
- particles_data = h5md_create_particles_group(datafile, group_name);
+ particles_data = h5md_create_particles_group(datafile, group_name);
} else {
- particles_data = other_dump->particles_data;
+ particles_data = other_dump->particles_data;
}
dims[0] = natoms;
dims[1] = domain->dimension;
if (every_position>0) {
- particles_data.position = h5md_create_time_data(particles_data.group, "position", 2, dims, H5T_NATIVE_DOUBLE, NULL);
- h5md_create_box(&particles_data, dims[1], boundary, true, NULL, &particles_data.position);
+ particles_data.position = h5md_create_time_data(particles_data.group, "position", 2, dims, H5T_NATIVE_DOUBLE, NULL);
+ h5md_create_box(&particles_data, dims[1], boundary, true, NULL, &particles_data.position);
}
if (every_image>0)
- particles_data.image = h5md_create_time_data(particles_data.group, "image", 2, dims, H5T_NATIVE_INT, &particles_data.position);
+ particles_data.image = h5md_create_time_data(particles_data.group, "image", 2, dims, H5T_NATIVE_INT, &particles_data.position);
if (every_velocity>0)
- particles_data.velocity = h5md_create_time_data(particles_data.group, "velocity", 2, dims, H5T_NATIVE_DOUBLE, NULL);
+ particles_data.velocity = h5md_create_time_data(particles_data.group, "velocity", 2, dims, H5T_NATIVE_DOUBLE, NULL);
if (every_force>0)
- particles_data.force = h5md_create_time_data(particles_data.group, "force", 2, dims, H5T_NATIVE_DOUBLE, NULL);
+ particles_data.force = h5md_create_time_data(particles_data.group, "force", 2, dims, H5T_NATIVE_DOUBLE, NULL);
if (every_species>0)
- particles_data.species = h5md_create_time_data(particles_data.group, "species", 1, dims, H5T_NATIVE_INT, NULL);
+ particles_data.species = h5md_create_time_data(particles_data.group, "species", 1, dims, H5T_NATIVE_INT, NULL);
if (every_charge>0) {
- particles_data.charge = h5md_create_time_data(particles_data.group, "charge", 1, dims, H5T_NATIVE_DOUBLE, NULL);
- h5md_write_string_attribute(particles_data.group, "charge", "type", "effective");
+ particles_data.charge = h5md_create_time_data(particles_data.group, "charge", 1, dims, H5T_NATIVE_DOUBLE, NULL);
+ h5md_write_string_attribute(particles_data.group, "charge", "type", "effective");
}
}
@@ -376,38 +376,38 @@ void DumpH5MD::pack(tagint *ids)
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (every_position>=0) {
- int ix = (image[i] & IMGMASK) - IMGMAX;
- int iy = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
- int iz = (image[i] >> IMG2BITS) - IMGMAX;
- if (unwrap_flag == 1) {
- buf[m++] = (x[i][0] + ix * xprd);
- buf[m++] = (x[i][1] + iy * yprd);
- if (dim>2) buf[m++] = (x[i][2] + iz * zprd);
- } else {
- buf[m++] = x[i][0];
- buf[m++] = x[i][1];
- if (dim>2) buf[m++] = x[i][2];
- }
- if (every_image>=0) {
- buf[m++] = ix;
- buf[m++] = iy;
- if (dim>2) buf[m++] = iz;
- }
+ int ix = (image[i] & IMGMASK) - IMGMAX;
+ int iy = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
+ int iz = (image[i] >> IMG2BITS) - IMGMAX;
+ if (unwrap_flag == 1) {
+ buf[m++] = (x[i][0] + ix * xprd);
+ buf[m++] = (x[i][1] + iy * yprd);
+ if (dim>2) buf[m++] = (x[i][2] + iz * zprd);
+ } else {
+ buf[m++] = x[i][0];
+ buf[m++] = x[i][1];
+ if (dim>2) buf[m++] = x[i][2];
+ }
+ if (every_image>=0) {
+ buf[m++] = ix;
+ buf[m++] = iy;
+ if (dim>2) buf[m++] = iz;
+ }
}
if (every_velocity>=0) {
- buf[m++] = v[i][0];
- buf[m++] = v[i][1];
- if (dim>2) buf[m++] = v[i][2];
+ buf[m++] = v[i][0];
+ buf[m++] = v[i][1];
+ if (dim>2) buf[m++] = v[i][2];
}
if (every_force>=0) {
- buf[m++] = f[i][0];
- buf[m++] = f[i][1];
- if (dim>2) buf[m++] = f[i][2];
+ buf[m++] = f[i][0];
+ buf[m++] = f[i][1];
+ if (dim>2) buf[m++] = f[i][2];
}
if (every_species>=0)
- buf[m++] = species[i];
+ buf[m++] = species[i];
if (every_charge>=0)
- buf[m++] = q[i];
+ buf[m++] = q[i];
ids[n++] = tag[i];
}
}
@@ -429,20 +429,20 @@ void DumpH5MD::write_data(int n, double *mybuf)
for (int i = 0; i < n; i++) {
if (every_position>=0) {
for (int j=0; j<dim; j++) {
- dump_position[k++] = mybuf[m++];
+ dump_position[k++] = mybuf[m++];
}
if (every_image>=0)
- for (int j=0; j<dim; j++) {
- dump_image[k_image++] = mybuf[m++];
- }
+ for (int j=0; j<dim; j++) {
+ dump_image[k_image++] = mybuf[m++];
+ }
}
if (every_velocity>=0)
for (int j=0; j<dim; j++) {
- dump_velocity[k_velocity++] = mybuf[m++];
+ dump_velocity[k_velocity++] = mybuf[m++];
}
if (every_force>=0)
for (int j=0; j<dim; j++) {
- dump_force[k_force++] = mybuf[m++];
+ dump_force[k_force++] = mybuf[m++];
}
if (every_species>=0)
dump_species[k_species++] = mybuf[m++];
@@ -494,7 +494,7 @@ void DumpH5MD::write_frame()
h5md_append(particles_data.position, dump_position, local_step, local_time);
h5md_append(particles_data.box_edges, edges, local_step, local_time);
if (every_image>0)
- h5md_append(particles_data.image, dump_image, local_step, local_time);
+ h5md_append(particles_data.image, dump_image, local_step, local_time);
}
} else {
if (do_box) h5md_append(particles_data.box_edges, edges, local_step, local_time);
diff --git a/src/USER-INTEL/dihedral_fourier_intel.cpp b/src/USER-INTEL/dihedral_fourier_intel.cpp
index 772ea5b02f..17a33b6f65 100644
--- a/src/USER-INTEL/dihedral_fourier_intel.cpp
+++ b/src/USER-INTEL/dihedral_fourier_intel.cpp
@@ -70,8 +70,8 @@ void DihedralFourierIntel::compute(int eflag, int vflag)
template <class flt_t, class acc_t>
void DihedralFourierIntel::compute(int eflag, int vflag,
- IntelBuffers<flt_t,acc_t> *buffers,
- const ForceConst<flt_t> &fc)
+ IntelBuffers<flt_t,acc_t> *buffers,
+ const ForceConst<flt_t> &fc)
{
if (eflag || vflag) {
ev_setup(eflag,vflag);
@@ -99,8 +99,8 @@ void DihedralFourierIntel::compute(int eflag, int vflag,
template <int EFLAG, int VFLAG, int NEWTON_BOND, class flt_t, class acc_t>
void DihedralFourierIntel::eval(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 inum = neighbor->ndihedrallist;
@@ -238,30 +238,30 @@ void DihedralFourierIntel::eval(const int vflag,
if (EFLAG) deng = (flt_t)0.0;
for (int j = 0; j < nterms[type]; j++) {
- const flt_t tcos_shift = fc.bp[j][type].cos_shift;
- const flt_t tsin_shift = fc.bp[j][type].sin_shift;
- const flt_t tk = fc.bp[j][type].k;
- const int m = fc.bp[j][type].multiplicity;
-
- flt_t p = (flt_t)1.0;
- flt_t ddf1, df1;
- ddf1 = df1 = (flt_t)0.0;
-
- for (int i = 0; i < m; i++) {
- ddf1 = p*c - df1*s;
- df1 = p*s + df1*c;
- p = ddf1;
- }
-
- p = p*tcos_shift + df1*tsin_shift;
- df1 = df1*tcos_shift - ddf1*tsin_shift;
- df1 *= -m;
- p += (flt_t)1.0;
-
- if (m == 0) {
- p = (flt_t)1.0 + tcos_shift;
- df1 = (flt_t)0.0;
- }
+ const flt_t tcos_shift = fc.bp[j][type].cos_shift;
+ const flt_t tsin_shift = fc.bp[j][type].sin_shift;
+ const flt_t tk = fc.bp[j][type].k;
+ const int m = fc.bp[j][type].multiplicity;
+
+ flt_t p = (flt_t)1.0;
+ flt_t ddf1, df1;
+ ddf1 = df1 = (flt_t)0.0;
+
+ for (int i = 0; i < m; i++) {
+ ddf1 = p*c - df1*s;
+ df1 = p*s + df1*c;
+ p = ddf1;
+ }
+
+ p = p*tcos_shift + df1*tsin_shift;
+ df1 = df1*tcos_shift - ddf1*tsin_shift;
+ df1 *= -m;
+ p += (flt_t)1.0;
+
+ if (m == 0) {
+ p = (flt_t)1.0 + tcos_shift;
+ df1 = (flt_t)0.0;
+ }
if (EFLAG) deng += tk * p;
df -= tk * df1;
@@ -401,7 +401,7 @@ void DihedralFourierIntel::init_style()
template <class flt_t, class acc_t>
void DihedralFourierIntel::pack_force_const(ForceConst<flt_t> &fc,
- IntelBuffers<flt_t,acc_t> *buffers)
+ IntelBuffers<flt_t,acc_t> *buffers)
{
const int bp1 = atom->ndihedraltypes + 1;
fc.set_ntypes(bp1, setflag, nterms, memory);
@@ -410,9 +410,9 @@ void DihedralFourierIntel::pack_force_const(ForceConst<flt_t> &fc,
if (setflag[i]) {
for (int j = 0; j < nterms[i]; j++) {
fc.bp[j][i].cos_shift = cos_shift[i][j];
- fc.bp[j][i].sin_shift = sin_shift[i][j];
- fc.bp[j][i].k = k[i][j];
- fc.bp[j][i].multiplicity = multiplicity[i][j];
+ fc.bp[j][i].sin_shift = sin_shift[i][j];
+ fc.bp[j][i].k = k[i][j];
+ fc.bp[j][i].multiplicity = multiplicity[i][j];
}
}
}
@@ -423,8 +423,8 @@ void DihedralFourierIntel::pack_force_const(ForceConst<flt_t> &fc,
template <class flt_t>
void DihedralFourierIntel::ForceConst<flt_t>::set_ntypes(const int nbondtypes,
int *setflag,
- int *nterms,
- Memory *memory) {
+ int *nterms,
+ Memory *memory) {
if (nbondtypes != _nbondtypes) {
if (_nbondtypes > 0)
_memory->destroy(bp);
diff --git a/src/USER-INTEL/dihedral_fourier_intel.h b/src/USER-INTEL/dihedral_fourier_intel.h
index cb83b8167c..26007f4118 100644
--- a/src/USER-INTEL/dihedral_fourier_intel.h
+++ b/src/USER-INTEL/dihedral_fourier_intel.h
@@ -66,7 +66,7 @@ class DihedralFourierIntel : public DihedralFourier {
~ForceConst() { set_ntypes(0, NULL, NULL, NULL); }
void set_ntypes(const int nbondtypes, int *setflag, int *nterms,
- Memory *memory);
+ Memory *memory);
private:
int _nbondtypes, _maxnterms;
diff --git a/src/USER-INTEL/fix_intel.cpp b/src/USER-INTEL/fix_intel.cpp
index cac5e0b49c..d05e059578 100644
--- a/src/USER-INTEL/fix_intel.cpp
+++ b/src/USER-INTEL/fix_intel.cpp
@@ -755,7 +755,7 @@ void FixIntel::add_oresults(const ft * _noalias const f_in,
double * _noalias const lmp_eatom = force->pair->eatom + out_offset;
#if defined(LMP_SIMD_COMPILER)
#pragma vector aligned
- #pragma ivdep
+ #pragma ivdep
#endif
for (int i = ifrom; i < ito; i++) {
f[i].x += f_in[ii].x;
@@ -770,7 +770,7 @@ void FixIntel::add_oresults(const ft * _noalias const f_in,
} else {
#if defined(LMP_SIMD_COMPILER)
#pragma vector aligned
- #pragma ivdep
+ #pragma ivdep
#endif
for (int i = ifrom; i < ito; i++) {
f[i].x += f_in[ii].x;
@@ -787,7 +787,7 @@ void FixIntel::add_oresults(const ft * _noalias const f_in,
double * _noalias const lmp_eatom = force->pair->eatom + out_offset;
#if defined(LMP_SIMD_COMPILER)
#pragma vector aligned
- #pragma ivdep
+ #pragma ivdep
#endif
for (int i = ifrom; i < ito; i++) {
f[i].x += f_in[i].x;
@@ -798,7 +798,7 @@ void FixIntel::add_oresults(const ft * _noalias const f_in,
} else {
#if defined(LMP_SIMD_COMPILER)
#pragma vector aligned
- #pragma ivdep
+ #pragma ivdep
#endif
for (int i = ifrom; i < ito; i++) {
f[i].x += f_in[i].x;
diff --git a/src/USER-INTEL/intel_buffers.cpp b/src/USER-INTEL/intel_buffers.cpp
index ac208f5a0c..1ef078821e 100644
--- a/src/USER-INTEL/intel_buffers.cpp
+++ b/src/USER-INTEL/intel_buffers.cpp
@@ -532,7 +532,7 @@ void IntelBuffers<flt_t, acc_t>::grow_ncache(const int off_flag,
lmp->memory->create(_ncachetag, tsize, "_ncachetag");
}
int *ncachetag = _ncachetag;
- #pragma offload_transfer target(mic:_cop) \
+ #pragma offload_transfer target(mic:_cop) \
nocopy(ncachetag:length(tsize) alloc_if(1) free_if(0))
_off_ncache = 1;
}
@@ -570,7 +570,7 @@ void IntelBuffers<flt_t, acc_t>::fdotr_reduce(const int nall,
template <class flt_t, class acc_t>
void IntelBuffers<flt_t, acc_t>::set_ntypes(const int ntypes,
- const int use_ghost_cut)
+ const int use_ghost_cut)
{
if (ntypes != _ntypes) {
if (_ntypes > 0) {
@@ -582,7 +582,7 @@ void IntelBuffers<flt_t, acc_t>::set_ntypes(const int ntypes,
}
flt_t * cutneighghostsqo;
if (_cutneighghostsq && _off_threads > 0 && cutneighghostsqo != 0) {
- cutneighghostsqo = _cutneighghostsq[0];
+ cutneighghostsqo = _cutneighghostsq[0];
#pragma offload_transfer target(mic:_cop) \
nocopy(cutneighghostsqo:alloc_if(0) free_if(1))
}
@@ -593,8 +593,8 @@ void IntelBuffers<flt_t, acc_t>::set_ntypes(const int ntypes,
if (ntypes > 0) {
lmp->memory->create(_cutneighsq, ntypes, ntypes, "_cutneighsq");
if (use_ghost_cut)
- lmp->memory->create(_cutneighghostsq, ntypes, ntypes,
- "_cutneighghostsq");
+ lmp->memory->create(_cutneighghostsq, ntypes, ntypes,
+ "_cutneighghostsq");
#ifdef _LMP_INTEL_OFFLOAD
flt_t * cutneighsqo = _cutneighsq[0];
const int ntypes2 = ntypes * ntypes;
diff --git a/src/USER-INTEL/intel_intrinsics_airebo.h b/src/USER-INTEL/intel_intrinsics_airebo.h
index 35c5cb7a43..f17fd69856 100644
--- a/src/USER-INTEL/intel_intrinsics_airebo.h
+++ b/src/USER-INTEL/intel_intrinsics_airebo.h
@@ -61,59 +61,59 @@ namespace mm512 {
#ifndef FVEC_FIRST_PASS
VEC_INLINE static inline __m512i _mm512_mask_expand_epi32(__m512i src,
- __mmask16 k,
- __m512i a) {
+ __mmask16 k,
+ __m512i a) {
int buf[16] __attribute__((aligned(64)));
_mm512_store_epi32(buf, a);
return _mm512_mask_loadunpacklo_epi32(src, k, buf);
}
VEC_INLINE static inline __m512i _mm512_maskz_expand_epi32(__mmask16 k,
- __m512i a) {
+ __m512i a) {
int buf[16] __attribute__((aligned(64)));
_mm512_store_epi32(buf, a);
return _mm512_mask_loadunpacklo_epi32(_mm512_setzero_epi32(), k, buf);
}
VEC_INLINE static inline __m512i _mm512_mask_compress_epi32(__m512i src,
- __mmask16 k,
- __m512i a) {
+ __mmask16 k,
+ __m512i a) {
int buf[16] __attribute__((aligned(64)));
_mm512_store_epi32(buf, src);
_mm512_mask_packstorelo_epi32(buf, k, a);
return _mm512_load_epi32(buf);
}
VEC_INLINE static inline __m512i _mm512_maskz_compress_epi32(__mmask16 k,
- __m512i a) {
+ __m512i a) {
int buf[16] __attribute__((aligned(64))) = {0};
_mm512_mask_packstorelo_epi32(buf, k, a);
return _mm512_load_epi32(buf);
}
VEC_INLINE static inline void _mm512_mask_compressstoreu_epi32(int * dest,
- __mmask16 mask,
- __m512i src) {
+ __mmask16 mask,
+ __m512i src) {
_mm512_mask_packstorelo_epi32(dest, mask, src);
_mm512_mask_packstorehi_epi32(dest + 16, mask, src);
}
VEC_INLINE static inline __m512i _mm512_mask_loadu_epi32(__m512i src,
- __mmask16 k,
- const int * mem_addr) {
+ __mmask16 k,
+ const int * mem_addr) {
assert((k & (k + 1)) == 0);
__m512i ret = _mm512_mask_loadunpacklo_epi32(src, k, mem_addr);
ret = _mm512_mask_loadunpackhi_epi32(ret, k, mem_addr + 16);
return ret;
}
VEC_INLINE static inline __m512i _mm512_maskz_loadu_epi32(__mmask16 k,
- const int * mem_addr) {
+ const int * mem_addr) {
assert((k & (k + 1)) == 0);
__m512i ret = _mm512_mask_loadunpacklo_epi32(_mm512_setzero_epi32(), k,
- mem_addr);
+ mem_addr);
ret = _mm512_mask_loadunpackhi_epi32(ret, k, mem_addr + 16);
return ret;
}
VEC_INLINE static inline void _mm512_mask_storeu_epi32(int * dest,
- __mmask16 mask,
- __m512i src) {
+ __mmask16 mask,
+ __m512i src) {
assert((mask & (mask + 1)) == 0);
_mm512_mask_packstorelo_epi32(dest, mask, src);
_mm512_mask_packstorehi_epi32(dest + 16, mask, src);
@@ -131,7 +131,7 @@ VEC_INLINE static inline FVEC_VEC_T FVEC_SUFFIX(_mm512_maskz_expand_)
FVEC_SCAL_T buf[FVEC_LEN] __attribute__((aligned(64)));
FVEC_SUFFIX(_mm512_store_)(buf, a);
return FVEC_SUFFIX(_mm512_mask_loadunpacklo_)(FVEC_SUFFIX(_mm512_setzero_)(),
- k, buf);
+ k, buf);
}
VEC_INLINE static inline FVEC_VEC_T FVEC_SUFFIX(_mm512_mask_compress_)
(FVEC_VEC_T src, __mmask16 k, FVEC_VEC_T a) {
@@ -182,24 +182,24 @@ public:
return _mm512_kortestz(a.val_, b.val_);
}
VEC_INLINE static BVEC_NAME masku_compress(const BVEC_NAME &mask,
- const BVEC_NAME &a) {
+ const BVEC_NAME &a) {
const __m512i c_i1 = _mm512_set1_epi32(1);
__m512i a_int_vec = _mm512_mask_blend_epi32(a.val_, _mm512_setzero_epi32(),
- c_i1);
+ c_i1);
__m512i compressed = _mm512_mask_compress_epi32(_mm512_undefined_epi32(),
- mask.val_, a_int_vec);
+ mask.val_, a_int_vec);
return _mm512_cmpeq_epi32_mask(compressed, c_i1);
}
VEC_INLINE static BVEC_NAME mask_expand(const BVEC_NAME &src,
- const BVEC_NAME &mask,
- const BVEC_NAME &a) {
+ const BVEC_NAME &mask,
+ const BVEC_NAME &a) {
const __m512i c_i1 = _mm512_set1_epi32(1);
__m512i a_int_vec = _mm512_mask_blend_epi32(a.val_, _mm512_setzero_epi32(),
- c_i1);
+ c_i1);
__m512i src_int_vec = _mm512_mask_blend_epi32(src.val_,
- _mm512_setzero_epi32(), c_i1);
+ _mm512_setzero_epi32(), c_i1);
__m512i compressed = _mm512_mask_expand_epi32(src_int_vec, mask.val_,
- a_int_vec);
+ a_int_vec);
return _mm512_cmpeq_epi32_mask(compressed, c_i1);
}
VEC_INLINE static BVEC_NAME full() {
@@ -254,29 +254,29 @@ public:
VEC_INLINE IVEC_NAME() {}
#define IVEC_MASK_BINFN_B(the_name) \
- VEC_INLINE static BVEC_NAME the_name(const IVEC_NAME &a, \
- const IVEC_NAME &b) { \
+ VEC_INLINE static BVEC_NAME the_name(const IVEC_NAME &a, \
+ const IVEC_NAME &b) { \
return _mm512_##the_name##_epi32_mask(a.val_, b.val_); \
- } \
- VEC_INLINE static BVEC_NAME mask_##the_name( \
- const BVEC_NAME &mask, \
- const IVEC_NAME &a, \
- const IVEC_NAME &b \
- ) { \
- return _mm512_mask_##the_name##_epi32_mask( \
- mask.val_, a.val_, b.val_); \
+ } \
+ VEC_INLINE static BVEC_NAME mask_##the_name( \
+ const BVEC_NAME &mask, \
+ const IVEC_NAME &a, \
+ const IVEC_NAME &b \
+ ) { \
+ return _mm512_mask_##the_name##_epi32_mask( \
+ mask.val_, a.val_, b.val_); \
}
IVEC_MASK_BINFN_B(cmpeq)
IVEC_MASK_BINFN_B(cmplt)
IVEC_MASK_BINFN_B(cmpneq)
IVEC_MASK_BINFN_B(cmpgt)
- #define IVEC_MASK_BINFN_I(the_name) \
- VEC_INLINE static IVEC_NAME mask_##the_name( \
+ #define IVEC_MASK_BINFN_I(the_name) \
+ VEC_INLINE static IVEC_NAME mask_##the_name( \
const IVEC_NAME &src, const BVEC_NAME &mask, \
const IVEC_NAME &a, const IVEC_NAME &b \
) { \
- return _mm512_mask_##the_name##_epi32( \
+ return _mm512_mask_##the_name##_epi32( \
src.val_, mask.val_, a.val_, b.val_); \
}
IVEC_MASK_BINFN_I(add)
@@ -287,8 +287,8 @@ public:
}
#define IVEC_BINFN_I(the_name) \
- VEC_INLINE static IVEC_NAME the_name(const IVEC_NAME &a, \
- const IVEC_NAME &b) { \
+ VEC_INLINE static IVEC_NAME the_name(const IVEC_NAME &a, \
+ const IVEC_NAME &b) { \
return _mm512_##the_name##_epi32(a.val_, b.val_); \
}
IVEC_BINFN_I(mullo)
@@ -407,7 +407,7 @@ public:
#define FVEC_MASK_BINFN_B(the_name) \
VEC_INLINE static BVEC_NAME the_name(const FVEC_NAME &a, \
- const FVEC_NAME &b) { \
+ const FVEC_NAME &b) { \
return FVEC_SUFFIX_MASK(_mm512_##the_name##_)(a.val_, b.val_); \
} \
VEC_INLINE static BVEC_NAME mask_##the_name( \
@@ -481,7 +481,7 @@ public:
const BVEC_NAME &a, const FVEC_NAME &b
) {
return FVEC_SUFFIX(_mm512_mask_compress_)(FVEC_SUFFIX(_mm512_undefined_)(),
- a.val_, b.val_);
+ a.val_, b.val_);
}
VEC_INLINE static FVEC_NAME set1(const FVEC_SCAL_T &a) {
@@ -498,7 +498,7 @@ public:
return FVEC_SUFFIX(_mm512_load_)(mem);
}
VEC_INLINE static void mask_storeu(const BVEC_NAME &mask, FVEC_SCAL_T * dest,
- const FVEC_NAME &a) {
+ const FVEC_NAME &a) {
FVEC_SUFFIX(_mm512_mask_storeu_)(dest, mask.val_, a.val_);
}
VEC_INLINE static void store(FVEC_SCAL_T * dest, const FVEC_NAME &a) {
@@ -506,8 +506,8 @@ public:
}
VEC_INLINE static FVEC_NAME gather(const IVEC_NAME &idx,
- const FVEC_SCAL_T * mem,
- const int scale) {
+ const FVEC_SCAL_T * mem,
+ const int scale) {
assert(scale == sizeof(FVEC_SCAL_T));
# if FVEC_LEN==8
return FVEC_SUFFIX(_mm512_i32logather_)(idx.val_, mem, sizeof(FVEC_SCAL_T));
@@ -530,22 +530,22 @@ public:
}
VEC_INLINE static void gather_3_adjacent(const IVEC_NAME &idx,
- const FVEC_SCAL_T * mem,
- const int scale,
- FVEC_NAME * out_0,
- FVEC_NAME * out_1,
- FVEC_NAME * out_2) {
+ const FVEC_SCAL_T * mem,
+ const int scale,
+ FVEC_NAME * out_0,
+ FVEC_NAME * out_1,
+ FVEC_NAME * out_2) {
assert(scale == sizeof(FVEC_SCAL_T));
*out_0 = FVEC_NAME::gather(idx, mem + 0, scale);
*out_1 = FVEC_NAME::gather(idx, mem + 1, scale);
*out_2 = FVEC_NAME::gather(idx, mem + 2, scale);
}
VEC_INLINE static void gather_4_adjacent(const IVEC_NAME &idx,
- const FVEC_SCAL_T * mem,
- const int scale, FVEC_NAME * out_0,
- FVEC_NAME * out_1,
- FVEC_NAME * out_2,
- FVEC_NAME * out_3) {
+ const FVEC_SCAL_T * mem,
+ const int scale, FVEC_NAME * out_0,
+ FVEC_NAME * out_1,
+ FVEC_NAME * out_2,
+ FVEC_NAME * out_3) {
assert(scale == sizeof(FVEC_SCAL_T));
*out_0 = FVEC_NAME::gather(idx, mem + 0, scale);
*out_1 = FVEC_NAME::gather(idx, mem + 1, scale);
@@ -554,7 +554,7 @@ public:
}
VEC_INLINE static FVEC_SCAL_T mask_reduce_add(const BVEC_NAME &mask,
- const FVEC_NAME &a) {
+ const FVEC_NAME &a) {
return FVEC_SUFFIX(_mm512_mask_reduce_add_)(mask.val_, a.val_);
}
VEC_INLINE static FVEC_SCAL_T reduce_add(const FVEC_NAME &a) {
@@ -609,7 +609,7 @@ public:
assert(scale == sizeof(FVEC_SCAL_T));
# if FVEC_LEN==8
return FVEC_SUFFIX(_mm512_mask_i32logather_)(src.val_, mask.val_, idx.val_,
- mem, sizeof(FVEC_SCAL_T));
+ mem, sizeof(FVEC_SCAL_T));
# else
return FVEC_SUFFIX(_mm512_mask_i32gather_)(src.val_, mask.val_, idx.val_,
mem, sizeof(FVEC_SCAL_T));
@@ -622,10 +622,10 @@ public:
assert(scale == sizeof(FVEC_SCAL_T));
# if FVEC_LEN==8
FVEC_SUFFIX(_mm512_mask_i32loscatter_)(mem, mask.val_, idx.val_, a.val_,
- sizeof(FVEC_SCAL_T));
+ sizeof(FVEC_SCAL_T));
# else
FVEC_SUFFIX(_mm512_mask_i32scatter_)(mem, mask.val_, idx.val_, a.val_,
- sizeof(FVEC_SCAL_T));
+ sizeof(FVEC_SCAL_T));
# endif
}
@@ -637,7 +637,7 @@ public:
VEC_INLINE static void gather_prefetch0(const IVEC_NAME &a, void * mem) {
_mm512_mask_prefetch_i32gather_ps(a.val_, BVEC_NAME::full().val_, mem,
- sizeof(FVEC_SCAL_T), _MM_HINT_T0);
+ sizeof(FVEC_SCAL_T), _MM_HINT_T0);
}
};
@@ -666,10 +666,10 @@ public:
) {
assert(scale == sizeof(double));
__m512d lo = _mm512_mask_i32logather_pd(src.lo_, mask.val_, idx.val_, mem,
- sizeof(double));
+ sizeof(double));
__m512d hi = _mm512_mask_i32logather_pd(src.hi_, get_bvec_hi(mask.val_),
- get_ivec_hi(idx.val_), mem,
- sizeof(double));
+ get_ivec_hi(idx.val_), mem,
+ sizeof(double));
return avec16pd(lo, hi);
}
VEC_INLINE static void mask_i32loscatter(
@@ -678,9 +678,9 @@ public:
) {
assert(scale == sizeof(double));
_mm512_mask_i32loscatter_pd(mem, mask.val_, idx.val_, a.lo_,
- sizeof(double));
+ sizeof(double));
_mm512_mask_i32loscatter_pd(mem, get_bvec_hi(mask.val_),
- get_ivec_hi(idx.val_), a.hi_, sizeof(double));
+ get_ivec_hi(idx.val_), a.hi_, sizeof(double));
}
#define AVEC2_BINOP(the_sym, the_name) \
@@ -693,7 +693,7 @@ public:
VEC_INLINE static void gather_prefetch0(const IVEC_NAME &a, void * mem) {
_mm512_mask_prefetch_i32gather_ps(a.val_, BVEC_NAME::full().val_, mem,
- sizeof(double), _MM_HINT_T0);
+ sizeof(double), _MM_HINT_T0);
}
};
#endif
@@ -809,17 +809,17 @@ VEC_INLINE inline __m256i _cm256_and_si256(const __m256i &a, const __m256i &b) {
}
VEC_INLINE inline __m256i _cm256_andnot_si256(const __m256i &a,
- const __m256i &b) {
+ const __m256i &b) {
IVEC_EM_BIN(_mm_andnot_si128)
}
VEC_INLINE inline __m256i _cm256_cmpeq_epi32(const __m256i &a,
- const __m256i &b) {
+ const __m256i &b) {
IVEC_EM_BIN(_mm_cmpeq_epi32)
}
VEC_INLINE inline __m256i _cm256_cmpgt_epi32(const __m256i &a,
- const __m256i &b) {
+ const __m256i &b) {
IVEC_EM_BIN(_mm_cmpgt_epi32)
}
@@ -838,13 +838,13 @@ VEC_INLINE inline __m256i _cm256_cvtepu8_epi32(const __m128i &a) {
int dest[8] __attribute__((aligned(32))); \
_mm256_store_si256((__m256i*)buf_a, a); \
_mm256_store_si256((__m256i*)buf_b, b); \
- for (int i = 0; i < 8; i++) { \
- dest[i] = op; \
- } \
+ for (int i = 0; i < 8; i++) { \
+ dest[i] = op; \
+ } \
return _mm256_load_si256((__m256i*) dest);
VEC_INLINE inline __m256i _cm256_permutevar8x32_epi32(const __m256i &a,
- const __m256i &b) {
+ const __m256i &b) {
IVEC_EM_SCAL(buf_a[buf_b[i]])
}
@@ -858,9 +858,9 @@ VEC_INLINE inline __m256i _cm256_srlv_epi32(__m256i a, __m256i b) {
VEC_INLINE inline __m256 _cm256_permutevar8x32_ps(const __m256 &a,
- const __m256i &b) {
+ const __m256i &b) {
return _mm256_castsi256_ps(_cm256_permutevar8x32_epi32(_mm256_castps_si256(a),
- b));
+ b));
}
VEC_INLINE inline __m128i _cm_maskload_epi32(int const * mem, __m128i mask) {
@@ -878,10 +878,10 @@ VEC_INLINE inline __m256i _cm256_maskload_epi32(int const * mem, __m256i mask) {
VEC_INLINE inline __m256i _cm256_mask_i32gather_epi32(__m256i src,
- int const * base_addr,
- __m256i index,
- __m256i mask,
- const int scale) {
+ int const * base_addr,
+ __m256i index,
+ __m256i mask,
+ const int scale) {
assert(scale == sizeof(int));
int buf_index[8] __attribute__((aligned(32)));
int buf_mask[8] __attribute__((aligned(32)));
@@ -896,18 +896,18 @@ VEC_INLINE inline __m256i _cm256_mask_i32gather_epi32(__m256i src,
}
VEC_INLINE inline __m256 _cm256_mask_i32gather_ps(__m256 src,
- float const * base_addr,
- __m256i index, __m256 mask,
- const int scale) {
+ float const * base_addr,
+ __m256i index, __m256 mask,
+ const int scale) {
return _mm256_castsi256_ps(_cm256_mask_i32gather_epi32(
_mm256_castps_si256(src), (const int *) base_addr, index,
_mm256_castps_si256(mask), scale));
}
VEC_INLINE inline __m256d _cm256_mask_i32gather_pd(__m256d src,
- double const * base_addr,
- __m128i index, __m256d mask,
- const int scale) {
+ double const * base_addr,
+ __m128i index, __m256d mask,
+ const int scale) {
assert(scale == sizeof(double));
int buf_index[4] __attribute__((aligned(32)));
int buf_mask[8] __attribute__((aligned(32)));
@@ -922,8 +922,8 @@ VEC_INLINE inline __m256d _cm256_mask_i32gather_pd(__m256d src,
}
VEC_INLINE inline __m256i _cm256_i32gather_epi32(int const * base_addr,
- __m256i index,
- const int scale) {
+ __m256i index,
+ const int scale) {
assert(scale == sizeof(int));
int buf_index[8] __attribute__((aligned(32)));
int dest[8] __attribute__((aligned(32)));
@@ -935,13 +935,13 @@ VEC_INLINE inline __m256i _cm256_i32gather_epi32(int const * base_addr,
}
VEC_INLINE inline __m256 _cm256_i32gather_ps(float const * base_addr,
- __m256i index, const int scale) {
+ __m256i index, const int scale) {
return _mm256_castsi256_ps(_cm256_i32gather_epi32((const int *) base_addr,
- index, scale));
+ index, scale));
}
VEC_INLINE inline __m256d _cm256_i32gather_pd(double const * base_addr,
- __m128i index, const int scale) {
+ __m128i index, const int scale) {
assert(scale == sizeof(double));
int buf_index[4] __attribute__((aligned(32)));
double dest[4] __attribute__((aligned(32)));
@@ -1008,7 +1008,7 @@ VEC_INLINE inline uint64_t _cext_u64(uint64_t tmp, uint64_t mask) {
VEC_INLINE inline __m256 _mm256_compress_ps(__m256 mask, __m256 a) {
# ifdef __AVX2__
uint64_t expanded_mask = _pdep_u64(_mm256_movemask_ps(mask),
- 0x0101010101010101);
+ 0x0101010101010101);
// unpack each bit to a byte
expanded_mask *= 0xFF; // mask |= mask<<1 | mask<<2 | ... | mask<<7;
// the identity shuffle for vpermps, packed to one index per byte
@@ -1037,7 +1037,7 @@ VEC_INLINE inline __m256 _mm256_compress_ps(__m256 mask, __m256 a) {
VEC_INLINE inline __m256 _mm256_expand_ps(__m256 mask, __m256 a) {
# ifdef __AVX2__
uint64_t expanded_mask = _pdep_u64(_mm256_movemask_ps(mask),
- 0x0101010101010101);
+ 0x0101010101010101);
expanded_mask *= 0xFF;
const uint64_t identity_indices = 0x0706050403020100;
uint64_t wanted_indices = _pdep_u64(identity_indices, expanded_mask);
@@ -1062,7 +1062,7 @@ VEC_INLINE inline __m256 _mm256_expand_ps(__m256 mask, __m256 a) {
VEC_INLINE inline __m256d _mm256_compress_pd(__m256d mask, __m256d a) {
return _mm256_castps_pd(_mm256_compress_ps(_mm256_castpd_ps(mask),
- _mm256_castpd_ps(a)));
+ _mm256_castpd_ps(a)));
}
VEC_INLINE inline __m256d _mm256_expand_pd(__m256d mask, __m256d a) {
return _mm256_castps_pd(_mm256_expand_ps(_mm256_castpd_ps(mask),
@@ -1084,7 +1084,7 @@ class BVEC_NAME {
FVEC_MASK_T val_;
VEC_INLINE BVEC_NAME(const FVEC_MASK_T &v) : val_(v) {}
VEC_INLINE BVEC_NAME(const __m256i &v) : val_(FVEC_SUFFIX(_mm256_castsi256_)
- (v)) {}
+ (v)) {}
public:
VEC_INLINE BVEC_NAME() {}
VEC_INLINE static BVEC_NAME kand(const BVEC_NAME &a, const BVEC_NAME &b) {
@@ -1094,16 +1094,16 @@ public:
return FVEC_SUFFIX(_mm256_andnot_)(a.val_, b.val_);
}
VEC_INLINE static BVEC_NAME masku_compress(const BVEC_NAME &mask,
- const BVEC_NAME &a) {
+ const BVEC_NAME &a) {
return FVEC_SUFFIX(_mm256_compress_)(mask.val_, a.val_);
}
VEC_INLINE static BVEC_NAME mask_expand(const BVEC_NAME &src,
- const BVEC_NAME &mask,
- const BVEC_NAME &a) {
+ const BVEC_NAME &mask,
+ const BVEC_NAME &a) {
FVEC_MASK_T ret = FVEC_SUFFIX(_mm256_expand_)(mask.val_, a.val_);
ret = FVEC_SUFFIX(_mm256_and_)(mask.val_, ret);
ret = FVEC_SUFFIX(_mm256_or_)(ret, FVEC_SUFFIX(_mm256_andnot_)
- (mask.val_, src.val_));
+ (mask.val_, src.val_));
return ret;
}
VEC_INLINE static BVEC_NAME full() {
@@ -1210,7 +1210,7 @@ public:
#define IVEC_MASK_BINFN_B(the_name) \
VEC_INLINE static BVEC_NAME the_name(const IVEC_NAME &a, \
- const IVEC_NAME &b) { \
+ const IVEC_NAME &b) { \
return _mm256_##the_name##_epi32(a.val_, b.val_); \
} \
VEC_INLINE static BVEC_NAME mask_##the_name( \
@@ -1253,15 +1253,15 @@ public:
const IVEC_NAME &a, const IVEC_NAME &b \
) { \
IVEC_NAME ret = _mm256_##the_name##_epi32( \
- a.val_, b.val_); \
- return mask_blend(mask, src, ret); \
+ a.val_, b.val_); \
+ return mask_blend(mask, src, ret); \
}
IVEC_MASK_BINFN_I(add)
#undef IVEC_MASK_BINFN_I
#define IVEC_BINFN_I(the_name) \
VEC_INLINE static IVEC_NAME the_name(const IVEC_NAME &a, \
- const IVEC_NAME &b) { \
+ const IVEC_NAME &b) { \
return _mm256_##the_name##_epi32(a.val_, b.val_); \
}
IVEC_BINFN_I(mullo)
@@ -1272,7 +1272,7 @@ public:
}
VEC_INLINE static IVEC_NAME masku_compress(const BVEC_NAME &mask,
- const IVEC_NAME &b) {
+ const IVEC_NAME &b) {
return to(FVEC_SUFFIX(_mm256_compress_)(mask.val_, from(b.val_)));
}
VEC_INLINE static IVEC_NAME mask_expand(
@@ -1281,7 +1281,7 @@ public:
FVEC_VEC_T ret = FVEC_SUFFIX(_mm256_expand_)(mask.val_, from(b.val_));
ret = FVEC_SUFFIX(_mm256_and_)(mask.val_, ret);
ret = FVEC_SUFFIX(_mm256_or_)(ret, FVEC_SUFFIX(_mm256_andnot_)
- (mask.val_, from(src.val_)));
+ (mask.val_, from(src.val_)));
return to(ret);
}
@@ -1311,7 +1311,7 @@ public:
}
VEC_INLINE static IVEC_NAME maskz_loadu(const BVEC_NAME &mask,
- const int * src) {
+ const int * src) {
FVEC_VEC_T mask_val = mask.val_;
# if FVEC_LEN==4
# ifdef __AVX2__
@@ -1349,11 +1349,11 @@ public:
) {
assert(scale == sizeof(int));
return _mm256_mask_i32gather_epi32(src.val_, mem, idx.val_, to(mask.val_),
- sizeof(int));
+ sizeof(int));
}
VEC_INLINE static void mask_compressstore(const BVEC_NAME &mask, int * dest,
- const IVEC_NAME &src) {
+ const IVEC_NAME &src) {
int buf[8] __attribute__((aligned(64)));
const int stride = FVEC_LEN==4 ? 2 : 1;
_mm256_store_si256((__m256i*)buf, src.val_);
@@ -1403,18 +1403,18 @@ public:
return data[i];
}
- #define FVEC_MASK_BINFN_B(the_name, the_imm) \
- VEC_INLINE static BVEC_NAME the_name(const FVEC_NAME &a, \
- const FVEC_NAME &b) { \
+ #define FVEC_MASK_BINFN_B(the_name, the_imm) \
+ VEC_INLINE static BVEC_NAME the_name(const FVEC_NAME &a, \
+ const FVEC_NAME &b) { \
return FVEC_SUFFIX(_mm256_cmp_)(a.val_, b.val_, the_imm); \
- } \
+ } \
VEC_INLINE static BVEC_NAME mask_##the_name( \
const BVEC_NAME &mask, \
const FVEC_NAME &a, const FVEC_NAME &b \
) { \
BVEC_NAME ret = FVEC_SUFFIX(_mm256_cmp_)( \
a.val_, b.val_, the_imm); \
- return mask & ret; \
+ return mask & ret; \
}
FVEC_MASK_BINFN_B(cmple, _CMP_LE_OS)
FVEC_MASK_BINFN_B(cmplt, _CMP_LT_OS)
@@ -1434,15 +1434,15 @@ public:
const unsigned long long abs_mask = 0x7FFFFFFFFFFFFFFF;
const unsigned long long abs_full[8] =
{abs_mask, abs_mask, abs_mask, abs_mask, abs_mask, abs_mask, abs_mask,
- abs_mask};
+ abs_mask};
return _mm256_and_pd(_mm256_load_pd((double*)abs_full), a);
}
VEC_INLINE static __m256 _mm256_abs_ps(__m256 a) {
const unsigned long long abs_mask = 0x7FFFFFFF;
const unsigned long long abs_full[16] =
{abs_mask, abs_mask, abs_mask, abs_mask, abs_mask, abs_mask, abs_mask,
- abs_mask, abs_mask, abs_mask, abs_mask, abs_mask, abs_mask,
- abs_mask, abs_mask, abs_mask};
+ abs_mask, abs_mask, abs_mask, abs_mask, abs_mask, abs_mask,
+ abs_mask, abs_mask, abs_mask};
return _mm256_and_ps(_mm256_load_ps((float*)abs_full), a);
}
@@ -1468,8 +1468,8 @@ public:
const FVEC_NAME &a \
) { \
FVEC_NAME ret = FVEC_SUFFIX(_mm256_##the_name##_)( \
- a.val_); \
- return mask_blend(mask, src, ret); \
+ a.val_); \
+ return mask_blend(mask, src, ret); \
}
FVEC_MASK_UNFN_F(cos)
FVEC_MASK_UNFN_F(recip)
@@ -1478,15 +1478,15 @@ public:
#define FVEC_BINFN_F(the_name) \
VEC_INLINE static FVEC_NAME the_name(const FVEC_NAME &a, \
- const FVEC_NAME &b) { \
- return FVEC_SUFFIX(_mm256_##the_name##_)(a.val_, b.val_); \
+ const FVEC_NAME &b) { \
+ return FVEC_SUFFIX(_mm256_##the_name##_)(a.val_, b.val_); \
}
FVEC_BINFN_F(max)
FVEC_BINFN_F(min)
#undef FVEC_BINFN_F
#define FVEC_MASK_BINFN_F(the_name) \
- VEC_INLINE static FVEC_NAME mask_##the_name( \
+ VEC_INLINE static FVEC_NAME mask_##the_name( \
const FVEC_NAME &src, const BVEC_NAME &mask, \
const FVEC_NAME &a, const FVEC_NAME &b \
) { \
@@ -1633,11 +1633,11 @@ public:
# endif
}
VEC_INLINE static void gather_3_adjacent(const IVEC_NAME &idx,
- const FVEC_SCAL_T * mem,
- const int scale,
- FVEC_NAME * out_0,
- FVEC_NAME * out_1,
- FVEC_NAME * out_2) {
+ const FVEC_SCAL_T * mem,
+ const int scale,
+ FVEC_NAME * out_0,
+ FVEC_NAME * out_1,
+ FVEC_NAME * out_2) {
assert(scale == sizeof(FVEC_SCAL_T));
FVEC_NAME tmp_3;
gather_4_adjacent(idx, mem, scale, out_0, out_1, out_2, &tmp_3);
@@ -1663,7 +1663,7 @@ public:
return FVEC_SUFFIX(_mm256_reduce_add_)(a.val_);
}
VEC_INLINE static FVEC_SCAL_T mask_reduce_add(const BVEC_NAME &mask,
- const FVEC_NAME &a) {
+ const FVEC_NAME &a) {
return reduce_add(FVEC_SUFFIX(_mm256_and_)(mask.val_, a.val_));
}
@@ -1800,9 +1800,9 @@ public:
__m256d hi_mask = _mm256_castps_pd(_mm256_permutevar8x32_ps(mask.val_,
_mm256_load_si256((__m256i*) hi_shuffle)));
__m256d lo = _mm256_mask_i32gather_pd(src.lo_, mem, get_si_lo(idx.val_),
- lo_mask, sizeof(double));
+ lo_mask, sizeof(double));
__m256d hi = _mm256_mask_i32gather_pd(src.hi_, mem, get_si_hi(idx.val_),
- hi_mask, sizeof(double));
+ hi_mask, sizeof(double));
# endif
return avec8pd(lo, hi);
}
@@ -1912,7 +1912,7 @@ public:
return mask.val_ ? a.val_ : false;
}
VEC_INLINE static bvec mask_expand(const bvec &src, const bvec &mask,
- const bvec &a) {
+ const bvec &a) {
return mask.val_ ? a.val_ : src.val_;
}
VEC_INLINE static bvec full() {
@@ -2038,14 +2038,14 @@ public:
VEC_INLINE static ivec mask_gather(
const ivec &src, const bvec &mask, const ivec &idx, const int * mem,
- const int scale
+ const int scale
) {
return mask.val_ ? *reinterpret_cast<const int *>
(reinterpret_cast<const char*>(mem) + scale * idx.val_) : src.val_;
}
VEC_INLINE static void mask_i32scatter(
int * mem, const bvec &mask, const ivec &idx, const ivec &a,
- const int scale
+ const int scale
) {
if (mask.val_) *reinterpret_cast<int *>(reinterpret_cast<char*>(mem) +
scale * idx.val_) = a.val_;
@@ -2176,7 +2176,7 @@ public:
return *mem;
}
VEC_INLINE static void mask_storeu(const bvec &mask, flt_t * dest,
- const fvec &a) {
+ const fvec &a) {
if (mask.val_) *dest = a.val_;
}
VEC_INLINE static void store(flt_t * dest, const fvec &a) {
@@ -2184,7 +2184,7 @@ public:
}
VEC_INLINE static fvec gather(const ivec &idx, const flt_t * mem,
- const int scale) {
+ const int scale) {
return *reinterpret_cast<const flt_t*>(reinterpret_cast<const char*>(mem) +
scale * idx.val_);
}
@@ -2197,17 +2197,17 @@ public:
}
VEC_INLINE static void gather_3_adjacent(const ivec &idx, const flt_t * mem,
- const int scale, fvec * out_0,
- fvec * out_1, fvec * out_2) {
+ const int scale, fvec * out_0,
+ fvec * out_1, fvec * out_2) {
assert(scale == sizeof(flt_t));
*out_0 = gather(idx, mem + 0, scale);
*out_1 = gather(idx, mem + 1, scale);
*out_2 = gather(idx, mem + 2, scale);
}
VEC_INLINE static void gather_4_adjacent(const ivec &idx, const flt_t * mem,
- const int scale, fvec * out_0,
- fvec * out_1, fvec * out_2,
- fvec * out_3) {
+ const int scale, fvec * out_0,
+ fvec * out_1, fvec * out_2,
+ fvec * out_3) {
assert(scale == sizeof(flt_t));
*out_0 = gather(idx, mem + 0, scale);
*out_1 = gather(idx, mem + 1, scale);
@@ -2255,16 +2255,16 @@ public:
return 1337.1337;
}
VEC_INLINE static avec mask_gather(const avec &src, const bvec &mask,
- const ivec &idx, const acc_t * mem,
- const int scale) {
+ const ivec &idx, const acc_t * mem,
+ const int scale) {
return mask.val_ ? *reinterpret_cast<const acc_t*>
(reinterpret_cast<const char*>(mem) + scale * idx.val_) : src.val_;
}
VEC_INLINE static void mask_i32loscatter(acc_t * mem, const bvec &mask,
- const ivec &idx, const avec &a,
- const int scale) {
+ const ivec &idx, const avec &a,
+ const int scale) {
if (mask.val_) *reinterpret_cast<acc_t*>(reinterpret_cast<char*>(mem) +
- idx.val_ * scale) = a.val_;
+ idx.val_ * scale) = a.val_;
}
#define AVEC_BINOP(the_sym, the_name) \
diff --git a/src/USER-INTEL/intel_preprocess.h b/src/USER-INTEL/intel_preprocess.h
index 068f61023e..29cc45f755 100644
--- a/src/USER-INTEL/intel_preprocess.h
+++ b/src/USER-INTEL/intel_preprocess.h
@@ -211,8 +211,8 @@ enum {TIME_PACK, TIME_HOST_NEIGHBOR, TIME_HOST_PAIR, TIME_OFFLOAD_NEIGHBOR,
datasize); \
}
-#define IP_PRE_omp_range_vec(ifrom, ito, tid, inum, nthreads, \
- vecsize) \
+#define IP_PRE_omp_range_vec(ifrom, ito, tid, inum, nthreads, \
+ vecsize) \
{ \
int idelta = static_cast<int>(ceil(static_cast<float>(inum) \
/vecsize/nthreads)); \
@@ -226,8 +226,8 @@ enum {TIME_PACK, TIME_HOST_NEIGHBOR, TIME_HOST_PAIR, TIME_OFFLOAD_NEIGHBOR,
nthreads, vecsize) \
{ \
tid = omp_get_thread_num(); \
- IP_PRE_omp_range_vec(ifrom, ito, tid, inum, nthreads, \
- vecsize); \
+ IP_PRE_omp_range_vec(ifrom, ito, tid, inum, nthreads, \
+ vecsize); \
}
#define IP_PRE_omp_stride_id_vec(ifrom, ip, ito, tid, inum, \
@@ -242,12 +242,12 @@ enum {TIME_PACK, TIME_HOST_NEIGHBOR, TIME_HOST_PAIR, TIME_OFFLOAD_NEIGHBOR,
int nd = nthr / INTEL_HTHREADS; \
int td = tid / INTEL_HTHREADS; \
int tm = tid % INTEL_HTHREADS; \
- IP_PRE_omp_range_vec(ifrom, ito, td, inum, nd, vecsize); \
+ IP_PRE_omp_range_vec(ifrom, ito, td, inum, nd, vecsize); \
ifrom += tm * vecsize; \
ip = INTEL_HTHREADS * vecsize; \
} else { \
- IP_PRE_omp_range_vec(ifrom, ito, tid, inum, nthr, \
- vecsize); \
+ IP_PRE_omp_range_vec(ifrom, ito, tid, inum, nthr, \
+ vecsize); \
ip = vecsize; \
} \
}
@@ -301,10 +301,10 @@ enum {TIME_PACK, TIME_HOST_NEIGHBOR, TIME_HOST_PAIR, TIME_OFFLOAD_NEIGHBOR,
#define IP_PRE_omp_stride_id_vec(ifrom, ip, ito, tid, inum, \
nthr, vecsize) \
{ \
- tid = 0; \
- ifrom = 0; \
- ip = 1; \
- ito = inum; \
+ tid = 0; \
+ ifrom = 0; \
+ ip = 1; \
+ ito = inum; \
}
#endif
diff --git a/src/USER-INTEL/nbin_intel.cpp b/src/USER-INTEL/nbin_intel.cpp
index 9a1dae36ca..e071b141fe 100644
--- a/src/USER-INTEL/nbin_intel.cpp
+++ b/src/USER-INTEL/nbin_intel.cpp
@@ -212,8 +212,8 @@ void NBinIntel::bin_atoms(IntelBuffers<flt_t,acc_t> * buffers) {
for (i = nall-1; i >= nlocal; i--) {
if (mask[i] & bitmask) {
ibin = coord2bin(atom->x[i]);
- // Only necessary to store when neighboring ghost
- atombin[i] = ibin;
+ // Only necessary to store when neighboring ghost
+ atombin[i] = ibin;
bins[i] = binhead[ibin];
binhead[ibin] = i;
}
diff --git a/src/USER-INTEL/npair_full_bin_ghost_intel.cpp b/src/USER-INTEL/npair_full_bin_ghost_intel.cpp
index a814891f25..574855e468 100644
--- a/src/USER-INTEL/npair_full_bin_ghost_intel.cpp
+++ b/src/USER-INTEL/npair_full_bin_ghost_intel.cpp
@@ -68,7 +68,7 @@ void NPairFullBinGhostIntel::build(NeighList *list)
template<class flt_t, class acc_t>
void NPairFullBinGhostIntel::fbi(NeighList * list,
- IntelBuffers<flt_t,acc_t> * buffers)
+ IntelBuffers<flt_t,acc_t> * buffers)
{
const int nlocal = atom->nlocal;
const int nall = atom->nlocal + atom->nghost;
@@ -87,12 +87,12 @@ void NPairFullBinGhostIntel::fbi(NeighList * list,
// only uses offload_end_neighbor to check whether we are doing offloading
// at all, no need to correct this later
buffers->grow_list(list, nall, comm->nthreads, off_end,
- _fix->nbor_pack_width());
+ _fix->nbor_pack_width());
int need_ic = 0;
if (atom->molecular)
dminimum_image_check(need_ic, neighbor->cutneighmax, neighbor->cutneighmax,
- neighbor->cutneighmax);
+ neighbor->cutneighmax);
if (need_ic) {
fbi<flt_t,acc_t,1>(1, list, buffers, 0, off_end);
@@ -107,8 +107,8 @@ void NPairFullBinGhostIntel::fbi(NeighList * list,
template<class flt_t, class acc_t, int need_ic>
void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list,
- IntelBuffers<flt_t,acc_t> * buffers,
- const int pstart, const int pend) {
+ IntelBuffers<flt_t,acc_t> * buffers,
+ const int pstart, const int pend) {
if (pend-pstart == 0) return;
const int nall = atom->nlocal + atom->nghost;
@@ -164,7 +164,7 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list,
else moltemplate = 0;
if (moltemplate)
error->all(FLERR,
- "Can't use moltemplate with npair style full/bin/ghost/intel.");
+ "Can't use moltemplate with npair style full/bin/ghost/intel.");
int tnum;
int *overflow;
@@ -316,38 +316,38 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list,
if (ibin != oldbin) {
oldbin = ibin;
ncount = 0;
- if (i < nlocal) {
- for (int k = 0; k < nstencilp; k++) {
- const int bstart = binhead[ibin + binstart[k]];
- const int bend = binhead[ibin + binend[k]];
+ if (i < nlocal) {
+ for (int k = 0; k < nstencilp; k++) {
+ const int bstart = binhead[ibin + binstart[k]];
+ const int bend = binhead[ibin + binend[k]];
#if defined(LMP_SIMD_COMPILER)
#pragma simd
#endif
for (int jj = bstart; jj < bend; jj++)
tj[ncount++] = binpacked[jj];
- }
- } else {
- const int zbin = ibin / mbinyx;
- const int zrem = ibin % mbinyx;
- const int ybin = zrem / mbinx;
- const int xbin = zrem % mbinx;
- for (int k = 0; k < nstencil; k++) {
- const int xbin2 = xbin + stencilxyz[3 * k + 0];
- const int ybin2 = ybin + stencilxyz[3 * k + 1];
- const int zbin2 = zbin + stencilxyz[3 * k + 2];
- if (xbin2 < 0 || xbin2 >= mbinx ||
+ }
+ } else {
+ const int zbin = ibin / mbinyx;
+ const int zrem = ibin % mbinyx;
+ const int ybin = zrem / mbinx;
+ const int xbin = zrem % mbinx;
+ for (int k = 0; k < nstencil; k++) {
+ const int xbin2 = xbin + stencilxyz[3 * k + 0];
+ const int ybin2 = ybin + stencilxyz[3 * k + 1];
+ const int zbin2 = zbin + stencilxyz[3 * k + 2];
+ if (xbin2 < 0 || xbin2 >= mbinx ||
ybin2 < 0 || ybin2 >= mbiny ||
zbin2 < 0 || zbin2 >= mbinz) continue;
- const int bstart = binhead[ibin + stencil[k]];
- const int bend = binhead[ibin + stencil[k] + 1];
+ const int bstart = binhead[ibin + stencil[k]];
+ const int bend = binhead[ibin + stencil[k] + 1];
#if defined(LMP_SIMD_COMPILER)
#pragma simd
#endif
for (int jj = bstart; jj < bend; jj++)
tj[ncount++] = binpacked[jj];
- }
- } // if i < nlocal
+ }
+ } // if i < nlocal
#if defined(LMP_SIMD_COMPILER)
#pragma vector aligned
#pragma simd
@@ -358,20 +358,20 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list,
ty[u] = x[j].y;
tz[u] = x[j].z;
tjtype[u] = x[j].w;
- ttag[u] = tag[j];
+ ttag[u] = tag[j];
}
- } // if ibin != oldbin
+ } // if ibin != oldbin
// ---------------------- Loop over other bins
int n = maxnbors;
int n2 = n * 2;
- int *neighptr2 = neighptr;
- const flt_t * _noalias cutsq;
- if (i < nlocal) cutsq = cutneighsq;
- else cutsq = cutneighghostsq;
+ int *neighptr2 = neighptr;
+ const flt_t * _noalias cutsq;
+ if (i < nlocal) cutsq = cutneighsq;
+ else cutsq = cutneighghostsq;
- const int icp = i;
+ const int icp = i;
#if defined(LMP_SIMD_COMPILER)
#pragma vector aligned
@@ -381,41 +381,41 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list,
int addme = 1;
int j = tj[u];
- if (i == j) addme = 0;
+ if (i == j) addme = 0;
// Cutoff Check
const flt_t delx = xtmp - tx[u];
const flt_t dely = ytmp - ty[u];
const flt_t delz = ztmp - tz[u];
const int jtype = tjtype[u];
- const int jtag = ttag[u];
+ const int jtag = ttag[u];
const flt_t rsq = delx * delx + dely * dely + delz * delz;
if (rsq > cutsq[ioffset + jtype]) addme = 0;
if (need_ic && icp < nlocal) {
int no_special;
- ominimum_image_check(no_special, delx, dely, delz);
+ ominimum_image_check(no_special, delx, dely, delz);
if (no_special)
j = -j - 1;
}
- int flist = 0;
- if (itag > jtag) {
- if (((itag+jtag) & 1) == 0) flist = 1;
- } else if (itag < jtag) {
- if (((itag+jtag) & 1) == 1) flist = 1;
- } else {
- if (tz[u] < ztmp) flist = 1;
- else if (tz[u] == ztmp && ty[u] < ytmp) flist = 1;
- else if (tz[u] == ztmp && ty[u] == ytmp && tx[u] < xtmp)
- flist = 1;
- }
- if (addme) {
- if (flist)
- neighptr2[n2++] = j;
- else
- neighptr[n++] = j;
- }
+ int flist = 0;
+ if (itag > jtag) {
+ if (((itag+jtag) & 1) == 0) flist = 1;
+ } else if (itag < jtag) {
+ if (((itag+jtag) & 1) == 1) flist = 1;
+ } else {
+ if (tz[u] < ztmp) flist = 1;
+ else if (tz[u] == ztmp && ty[u] < ytmp) flist = 1;
+ else if (tz[u] == ztmp && ty[u] == ytmp && tx[u] < xtmp)
+ flist = 1;
+ }
+ if (addme) {
+ if (flist)
+ neighptr2[n2++] = j;
+ else
+ neighptr[n++] = j;
+ }
} // for u
#ifndef _LMP_INTEL_OFFLOAD
@@ -431,45 +431,45 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list,
if (exclusion(i,pj,itype,jtype,mask,molecule)) continue;
neighptr[n++] = j;
}
- alln = n2;
- n2 = maxnbors * 2;
- for (int u = n2; u < alln; u++) {
- const int j = neighptr[u];
- int pj = j;
- if (need_ic)
- if (pj < 0) pj = -j - 1;
- const int jtype = x[pj].w;
- if (exclusion(i,pj,itype,jtype,mask,molecule)) continue;
- neighptr[n2++] = j;
- }
+ alln = n2;
+ n2 = maxnbors * 2;
+ for (int u = n2; u < alln; u++) {
+ const int j = neighptr[u];
+ int pj = j;
+ if (need_ic)
+ if (pj < 0) pj = -j - 1;
+ const int jtype = x[pj].w;
+ if (exclusion(i,pj,itype,jtype,mask,molecule)) continue;
+ neighptr[n2++] = j;
+ }
}
#endif
int ns = n - maxnbors;
- int alln = n;
- atombin[i] = ns;
- n = 0;
- for (int u = maxnbors; u < alln; u++)
+ int alln = n;
+ atombin[i] = ns;
+ n = 0;
+ for (int u = maxnbors; u < alln; u++)
neighptr[n++] = neighptr[u];
- ns += n2 - maxnbors * 2;
- for (int u = maxnbors * 2; u < n2; u++)
+ ns += n2 - maxnbors * 2;
+ for (int u = maxnbors * 2; u < n2; u++)
neighptr[n++] = neighptr[u];
- if (ns > maxnbors) *overflow = 1;
+ if (ns > maxnbors) *overflow = 1;
ilist[i] = i;
cnumneigh[i] = ct;
numneigh[i] = ns;
- ct += ns;
- const int alignb = (INTEL_DATA_ALIGN / sizeof(int));
- const int edge = ct & (alignb - 1);
- if (edge) ct += alignb - edge;
- neighptr = firstneigh + ct;
- if (ct + obound > list_size) {
- if (i < ito - 1) {
- *overflow = 1;
- ct = (ifrom + tid * 2) * maxnbors;
- }
- }
+ ct += ns;
+ const int alignb = (INTEL_DATA_ALIGN / sizeof(int));
+ const int edge = ct & (alignb - 1);
+ if (edge) ct += alignb - edge;
+ neighptr = firstneigh + ct;
+ if (ct + obound > list_size) {
+ if (i < ito - 1) {
+ *overflow = 1;
+ ct = (ifrom + tid * 2) * maxnbors;
+ }
+ }
}
if (*overflow == 1)
@@ -492,10 +492,10 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list,
}
}
- overflow[LMP_LOCAL_MIN] = 0;
- overflow[LMP_LOCAL_MAX] = nlocal - 1;
- overflow[LMP_GHOST_MIN] = nlocal;
- overflow[LMP_GHOST_MAX] = e_nall - 1;
+ overflow[LMP_LOCAL_MIN] = 0;
+ overflow[LMP_LOCAL_MAX] = nlocal - 1;
+ overflow[LMP_GHOST_MIN] = nlocal;
+ overflow[LMP_GHOST_MAX] = e_nall - 1;
int nghost = overflow[LMP_GHOST_MAX] + 1 - overflow[LMP_GHOST_MIN];
if (nghost < 0) nghost = 0;
@@ -510,8 +510,8 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list,
#endif
if (molecular) {
- int ito_m = ito;
- if (ito >= nlocal) ito_m = nlocal;
+ int ito_m = ito;
+ if (ito >= nlocal) ito_m = nlocal;
for (int i = ifrom; i < ito_m; ++i) {
int * _noalias jlist = firstneigh + cnumneigh[i];
const int jnum = numneigh[i];
diff --git a/src/USER-INTEL/npair_full_bin_ghost_intel.h b/src/USER-INTEL/npair_full_bin_ghost_intel.h
index 1571539505..94e6fc3928 100644
--- a/src/USER-INTEL/npair_full_bin_ghost_intel.h
+++ b/src/USER-INTEL/npair_full_bin_ghost_intel.h
@@ -41,7 +41,7 @@ class NPairFullBinGhostIntel : public NPairIntel {
void fbi(NeighList * list, IntelBuffers<flt_t,acc_t> * buffers);
template<class flt_t, class acc_t, int need_ic>
void fbi(const int offload, NeighList * list,
- IntelBuffers<flt_t,acc_t> * buffers,
+ IntelBuffers<flt_t,acc_t> * buffers,
const int astart, const int aend);
};
diff --git a/src/USER-INTEL/npair_intel.cpp b/src/USER-INTEL/npair_intel.cpp
index 234557c941..d3d2745aee 100644
--- a/src/USER-INTEL/npair_intel.cpp
+++ b/src/USER-INTEL/npair_intel.cpp
@@ -292,7 +292,7 @@ void NPairIntel::bin_newton(const int offload, NeighList *list,
ty[u] = x[j].y;
tz[u] = x[j].z;
tjtype[u] = x[j].w;
- if (THREE) ttag[u] = tag[j];
+ if (THREE) ttag[u] = tag[j];
}
if (FULL == 0 || TRI == 1) {
@@ -440,9 +440,9 @@ void NPairIntel::bin_newton(const int offload, NeighList *list,
const int jtag = ttag[u];
int flist = 0;
if (itag > jtag) {
- if (((itag+jtag) & 1) == 0) flist = 1;
+ if (((itag+jtag) & 1) == 0) flist = 1;
} else if (itag < jtag) {
- if (((itag+jtag) & 1) == 1) flist = 1;
+ if (((itag+jtag) & 1) == 1) flist = 1;
} else {
if (tz[u] < ztmp) flist = 1;
else if (tz[u] == ztmp && ty[u] < ytmp) flist = 1;
diff --git a/src/USER-INTEL/pair_airebo_intel.cpp b/src/USER-INTEL/pair_airebo_intel.cpp
index b35d0210a7..0499d2ad62 100644
--- a/src/USER-INTEL/pair_airebo_intel.cpp
+++ b/src/USER-INTEL/pair_airebo_intel.cpp
@@ -233,18 +233,18 @@ PairAIREBOIntelParam<flt_t,acc_t> PairAIREBOIntel::get_param()
#define A(a) \
for (int i = 0; i < sizeof(this->a)/sizeof(double); i++) { \
- reinterpret_cast<flt_t*>(&fc.a)[i] = \
- reinterpret_cast<double*>(&this->a)[i]; \
+ reinterpret_cast<flt_t*>(&fc.a)[i] = \
+ reinterpret_cast<double*>(&this->a)[i]; \
}
-#define A0(a) \
- for (int i = 0; i < sizeof(fc.a)/sizeof(flt_t); i++) { \
- reinterpret_cast<flt_t*>(&fc.a)[i] = \
- reinterpret_cast<double*>(this->a[0])[i]; \
+#define A0(a) \
+ for (int i = 0; i < sizeof(fc.a)/sizeof(flt_t); i++) { \
+ reinterpret_cast<flt_t*>(&fc.a)[i] = \
+ reinterpret_cast<double*>(this->a[0])[i]; \
}
-#define B(a) \
- for (int i = 0; i < sizeof(this->a)/sizeof(double); i++) { \
- reinterpret_cast<acc_t*>(&fc.a)[i] = \
- reinterpret_cast<double*>(&this->a)[i]; \
+#define B(a) \
+ for (int i = 0; i < sizeof(this->a)/sizeof(double); i++) { \
+ reinterpret_cast<acc_t*>(&fc.a)[i] = \
+ reinterpret_cast<double*>(&this->a)[i]; \
}
A(cutlj) A(cutljrebosq) A(cut3rebo) A(sigmin);
@@ -265,11 +265,11 @@ PairAIREBOIntelParam<flt_t,acc_t> PairAIREBOIntel::get_param()
for (int i = 0; i < 5; i++) fc.gDom[i] = fc.gCdom[i];
for (int i = 0; i < 4; i++) fc.gDom[5+i] = fc.gHdom[i];
for (int i = 0; i < 4; i++) for (int j = 0; j < 6; j++)
- fc.gVal[6*i+j] = fc.gC1[i][j];
+ fc.gVal[6*i+j] = fc.gC1[i][j];
for (int i = 0; i < 4; i++) for (int j = 0; j < 6; j++)
- fc.gVal[4*6+6*i+j] = fc.gC2[i][j];
+ fc.gVal[4*6+6*i+j] = fc.gC2[i][j];
for (int i = 0; i < 3; i++) for (int j = 0; j < 6; j++)
- fc.gVal[8*6+6*i+j] = fc.gH[i][j];
+ fc.gVal[8*6+6*i+j] = fc.gH[i][j];
return fc;
}
@@ -408,8 +408,8 @@ void PairAIREBOIntel::eval(
int x_size, q_size, f_stride, ev_size, separate_flag;
IP_PRE_get_transfern(ago, 1 /*NEWTON_PAIR*/, EFLAG, vflag,
- buffers, offload, fix, separate_flag,
- x_size, q_size, ev_size, f_stride);
+ buffers, offload, fix, separate_flag,
+ x_size, q_size, ev_size, f_stride);
int tc;
FORCE_T * _noalias f_start;
@@ -469,7 +469,7 @@ void PairAIREBOIntel::eval(
#endif
IP_PRE_repack_for_offload(1 /*NEWTON_PAIR*/, separate_flag, nlocal, nall,
- f_stride, x, 0/*q*/);
+ f_stride, x, 0/*q*/);
acc_t oevdwl, oecoul, ov0, ov1, ov2, ov3, ov4, ov5;
if (EVFLAG) {
@@ -480,7 +480,7 @@ void PairAIREBOIntel::eval(
// loop over neighbors of my atoms
#if defined(_OPENMP)
#pragma omp parallel \
- shared(f_start,f_stride,nlocal,nall,minlocal) \
+ shared(f_start,f_stride,nlocal,nall,minlocal) \
reduction(+:oevdwl,oecoul,ov0,ov1,ov2,ov3,ov4,ov5)
#endif
{
@@ -740,7 +740,7 @@ inline flt_t gSpline(KernelArgsAIREBOT<flt_t,acc_t> * ka, int itype, flt_t cos,
template<typename flt_t>
inline flt_t eval_poly_bi(int n, flt_t * coeffs, flt_t x, flt_t y,
- flt_t * deriv) {
+ flt_t * deriv) {
flt_t dy;
flt_t vy = eval_poly_lin(n, &coeffs[n * (n - 1)], y, &dy);
flt_t result = vy;
@@ -759,7 +759,7 @@ inline flt_t eval_poly_bi(int n, flt_t * coeffs, flt_t x, flt_t y,
template<typename flt_t>
inline flt_t eval_poly_tri(int n, flt_t * coeffs, flt_t x, flt_t y, flt_t z,
- flt_t * deriv) {
+ flt_t * deriv) {
flt_t dyz[2];
flt_t vyz = eval_poly_bi(n, &coeffs[n * n * (n - 1)], y, z, &dyz[0]);
flt_t result = vyz;
@@ -781,7 +781,7 @@ inline flt_t eval_poly_tri(int n, flt_t * coeffs, flt_t x, flt_t y, flt_t z,
template<typename flt_t, typename acc_t>
inline flt_t PijSpline(KernelArgsAIREBOT<flt_t,acc_t> * ka, int itype,
- int jtype, flt_t NC, flt_t NH, flt_t * dN) {
+ int jtype, flt_t NC, flt_t NH, flt_t * dN) {
dN[0] = 0.0;
dN[1] = 0.0;
if (itype == HYDROGEN) return 0;
@@ -814,7 +814,7 @@ inline flt_t TijSpline(KernelArgsAIREBOT<flt_t,acc_t> * ka, flt_t Nij,
int nji = floor(Nji);
int nijconj = floor(Nijconj);
if (fabs(Nij - nij) < TOL && fabs(Nji - nji) <
- TOL && fabs(Nijconj - nijconj) < TOL) {
+ TOL && fabs(Nijconj - nijconj) < TOL) {
dN3[0] = ka->params.Tdfdx[nij][nji][nijconj];
dN3[1] = ka->params.Tdfdy[nij][nji][nijconj];
dN3[2] = ka->params.Tdfdz[nij][nji][nijconj];
@@ -835,11 +835,11 @@ inline flt_t piRCSpline(KernelArgsAIREBOT<flt_t,acc_t> * ka, int itype,
/* const int CC = 0; */
int select = itype + jtype;
#define piRCSelect(a, b, c) (select == HH ? ka->params.a : select == CH ? \
- ka->params.b : ka->params.c)
+ ka->params.b : ka->params.c)
flt_t * piIJdom = &piRCSelect(piHHdom, piCHdom, piCCdom)[0][0];
if (select == HH) {
if (Nij < piIJdom[0] || Nij > piIJdom[1] || Nji < piIJdom[2] ||
- Nji > piIJdom[3] || Nijconj < piIJdom[4] || Nijconj > piIJdom[5]) {
+ Nji > piIJdom[3] || Nijconj < piIJdom[4] || Nijconj > piIJdom[5]) {
Nij = 0;
Nji = 0;
Nijconj = 0;
@@ -852,7 +852,7 @@ inline flt_t piRCSpline(KernelArgsAIREBOT<flt_t,acc_t> * ka, int itype,
int nji = floor(Nji);
int nijconj = floor(Nijconj);
if (fabs(Nij - nij) < TOL && fabs(Nji - nji) <
- TOL && fabs(Nijconj - nijconj) < TOL) {
+ TOL && fabs(Nijconj - nijconj) < TOL) {
dN3[0] = piRCSelect(piHHdfdx, piCHdfdx, piCCdfdx)[nij][nji][nijconj];
dN3[1] = piRCSelect(piHHdfdy, piCHdfdy, piCCdfdy)[nij][nji][nijconj];
dN3[2] = piRCSelect(piHHdfdz, piCHdfdz, piCCdfdz)[nij][nji][nijconj];
@@ -922,7 +922,7 @@ inline flt_t frebo_pij(KernelArgsAIREBOT<flt_t,acc_t> * ka, int i, int j,
flt_t wik = Sp(rikmag, rcminik, rcmaxik, &dwik);
flt_t Nki = nC[k] + nH[k] - wik;
flt_t cosjik = (rijx * rikx + rijy * riky + rijz * rikz) /
- (rijmag * rikmag);
+ (rijmag * rikmag);
cosjik = fmin_nonan<flt_t>(1, fmax_nonan<flt_t>(-1, cosjik));
flt_t dgdc, dgdN;
flt_t g = gSpline(ka, itype, cosjik, Nij, &dgdc, &dgdN);
@@ -1132,7 +1132,7 @@ inline flt_t frebo_sum_omega(KernelArgsAIREBOT<flt_t,acc_t> * ka, int i, int j,
flt_t r34z = x[a3].z - x[a4].z;
flt_t r34mag = overloaded::sqrt(r34x * r34x + r34y * r34y + r34z * r34z);
flt_t cos234 = (r32x * r34x + r32y * r34y + r32z * r34z) /
- (r23mag * r34mag);
+ (r23mag * r34mag);
cos234 = fmin_nonan<flt_t>(1, fmax_nonan<flt_t>(-1, cos234));
flt_t sin234 = overloaded::sqrt(1 - cos234 * cos234);
if (sin234 == 0) continue;
@@ -2128,9 +2128,9 @@ void ref_lennard_jones_single_interaction(KernelArgsAIREBOT<flt_t,acc_t> * ka,
flt_t r6inv = r2inv * r2inv * r2inv;
vdw = r6inv * (ka->params.lj3[itype][jtype]*r6inv -
- ka->params.lj4[itype][jtype]);
+ ka->params.lj4[itype][jtype]);
dvdw = -r6inv * (ka->params.lj1[itype][jtype]*r6inv -
- ka->params.lj2[itype][jtype]) / rij;
+ ka->params.lj2[itype][jtype]) / rij;
}
flt_t VLJ = vdw * slw;
@@ -2165,7 +2165,7 @@ void ref_lennard_jones_single_interaction(KernelArgsAIREBOT<flt_t,acc_t> * ka,
template<typename flt_t, typename acc_t>
void ref_lennard_jones_single_atom(KernelArgsAIREBOT<flt_t,acc_t> * ka, int i,
- int morseflag) {
+ int morseflag) {
AtomAIREBOT<flt_t> * x = ka->x;
int jj;
int * neighs = ka->neigh_lmp.entries + ka->neigh_lmp.offset[i];
@@ -2320,10 +2320,10 @@ static void aut_rebo_neigh(KernelArgsAIREBOT<flt_t,acc_t> * ka) {
fvec rcmin1 = fvec::set1(ka->params.rcmin[itype][1]);
fvec rcmaxskinsq0 = fvec::set1(
(ka->params.rcmax[itype][0] + ka->skin) * (ka->params.rcmax[itype][0] +
- ka->skin));
+ ka->skin));
fvec rcmaxskinsq1 = fvec::set1(
(ka->params.rcmax[itype][1] + ka->skin) * (ka->params.rcmax[itype][1] +
- ka->skin));
+ ka->skin));
fvec nC = fvec::setzero();
fvec nH = fvec::setzero();
@@ -2356,7 +2356,7 @@ static void aut_rebo_neigh(KernelArgsAIREBOT<flt_t,acc_t> * ka) {
fvec rsq = delx * delx + dely * dely + delz * delz;
if (ka->rebuild_flag) {
fvec rcmaxskinsq = fvec::mask_blend(jtype_mask, rcmaxskinsq0,
- rcmaxskinsq1);
+ rcmaxskinsq1);
bvec c_mask = fvec::mask_cmplt(j_mask, rsq, rcmaxskinsq);
ivec::mask_compressstore(c_mask, &skin_target[n_skin], ji);
n_skin += bvec::popcnt(c_mask);
@@ -2393,7 +2393,7 @@ static void aut_rebo_neigh(KernelArgsAIREBOT<flt_t,acc_t> * ka) {
static fvec aut_eval_poly_lin_pd_2(int n, flt_t * vals, ivec idx, fvec x,
- fvec * deriv) {
+ fvec * deriv) {
fvec c_1 = fvec::set1(1);
fvec x_i = c_1;
fvec x_im1 = fvec::setzero();
@@ -2413,8 +2413,8 @@ static fvec aut_eval_poly_lin_pd_2(int n, flt_t * vals, ivec idx, fvec x,
}
static fvec aut_mask_gSpline_pd_2(KernelArgsAIREBOT<flt_t,acc_t> * ka,
- bvec active_mask, int itype, fvec cosjik,
- fvec Nij, fvec *dgdc, fvec *dgdN) {
+ bvec active_mask, int itype, fvec cosjik,
+ fvec Nij, fvec *dgdc, fvec *dgdN) {
int i;
flt_t * gDom = NULL;
int nDom = 0;
@@ -2431,7 +2431,7 @@ static fvec aut_mask_gSpline_pd_2(KernelArgsAIREBOT<flt_t,acc_t> * ka,
offs = ivec::set1(8 * 6);
}
cosjik = fvec::max(fvec::set1(gDom[0]), fvec::min(fvec::set1(gDom[nDom]),
- cosjik));
+ cosjik));
ivec index6 = ivec::setzero();
for (i = 0; i < nDom; i++) {
bvec cosge = fvec::cmpnlt(cosjik, fvec::set1(gDom[i])); //ge
@@ -2439,7 +2439,7 @@ static fvec aut_mask_gSpline_pd_2(KernelArgsAIREBOT<flt_t,acc_t> * ka,
index6 = ivec::mask_blend(cosge & cosle, index6, ivec::set1(6*i));
}
fvec g = aut_eval_poly_lin_pd_2(6, &ka->params.gVal[0], offs + index6,
- cosjik, dgdc);
+ cosjik, dgdc);
*dgdN = fvec::setzero();
if (itype == 0) {
fvec NCmax = fvec::set1(ka->params.NCmax);
@@ -2448,7 +2448,7 @@ static fvec aut_mask_gSpline_pd_2(KernelArgsAIREBOT<flt_t,acc_t> * ka,
if (bvec::test_any_set(Nmask)) {
fvec dg1;
fvec g1 = aut_eval_poly_lin_pd_2(6, &ka->params.gVal[0], index6, cosjik,
- &dg1);
+ &dg1);
fvec dS;
fvec cut = aut_Sp_deriv(Nij, NCmin, NCmax, &dS);
*dgdN = fvec::mask_mul(*dgdN, Nmask, dS, g1 - g);
@@ -2460,7 +2460,7 @@ static fvec aut_mask_gSpline_pd_2(KernelArgsAIREBOT<flt_t,acc_t> * ka,
}
static fvec aut_PijSpline(KernelArgsAIREBOT<flt_t,acc_t> * ka, int itype,
- int jtype, fvec NijC, fvec NijH, fvec *dN2) {
+ int jtype, fvec NijC, fvec NijH, fvec *dN2) {
flt_t ret[fvec::VL] __attribute__((aligned(64)));
flt_t dN20[fvec::VL] __attribute__((aligned(64)));
flt_t dN21[fvec::VL] __attribute__((aligned(64)));
@@ -2580,10 +2580,10 @@ static fvec aut_frebo_pij_pd_2(
fvec sum_dpij_dN = fvec::setzero();
fvec dN2[2];
ivec offseti = ivec::mask_gather(ivec::setzero(), bvec::full(), vi,
- ka->neigh_rebo.offset, sizeof(int));
+ ka->neigh_rebo.offset, sizeof(int));
int buf_len = 0;
ivec knum = ivec::mask_gather(ivec::setzero(), bvec::full(), vi,
- ka->neigh_rebo.num, sizeof(int));
+ ka->neigh_rebo.num, sizeof(int));
ivec kk = ivec::setzero();
bvec active_mask = ivec::cmplt(kk, knum);
ivec c_i1 = ivec::set1(1);
@@ -2613,7 +2613,7 @@ static fvec aut_frebo_pij_pd_2(
{
while (bvec::test_any_set(active_mask)) {
ivec k = ivec::mask_gather(ivec::setzero(), active_mask, kk + offseti,
- ka->neigh_rebo.entries, sizeof(int));
+ ka->neigh_rebo.entries, sizeof(int));
bvec excluded_mask = ivec::cmpeq(k, vj) & active_mask;
if (bvec::test_any_set(excluded_mask)) {
kk = ivec::mask_add(kk, excluded_mask, kk, c_i1);
@@ -2623,35 +2623,35 @@ static fvec aut_frebo_pij_pd_2(
fvec x_k, y_k, z_k;
bvec ktype_mask;
aut_loadatoms_vec(x, k, &x_k, &y_k, &z_k, &ktype_mask, ka->map, map_i,
- c_i1);
+ c_i1);
fvec rikx = x_i - x_k;
fvec riky = y_i - y_k;
fvec rikz = z_i - z_k;
fvec rikmag = fvec::sqrt(rikx * rikx + riky * riky + rikz * rikz);
fvec rho_k = fvec::mask_blend(ktype_mask, rho_k0, rho_k1);
fvec lamdajik = c_4 * factor_itype * ( rho_k - rikmag - ( rho_j -
- rijmag));
+ rijmag));
fvec ex_lam = fvec::exp(lamdajik);
fvec rcmax = fvec::mask_blend(ktype_mask, rcmax0, rcmax1);
fvec rcmin = fvec::mask_blend(ktype_mask, rcmin0, rcmin1);
fvec dwik;
fvec wik = aut_Sp_deriv(rikmag, rcmin, rcmax, &dwik);
fvec Nki = fvec::gather(k, nC, sizeof(flt_t)) +
- fvec::gather(k, nH, sizeof(flt_t)) - wik;
+ fvec::gather(k, nH, sizeof(flt_t)) - wik;
fvec cosjik = (rijx * rikx + rijy * riky + rijz * rikz) /
- ( rijmag * rikmag);
+ ( rijmag * rikmag);
cosjik = fvec::min(c_1, fvec::max(c_m1, cosjik));
fvec dgdc, dgdN;
fvec g = aut_mask_gSpline_pd_2(ka, active_mask, itype, cosjik, Nij,
- &dgdc, &dgdN);
+ &dgdc, &dgdN);
sum_pij = fvec::mask_add(sum_pij, active_mask, sum_pij, wik * g * ex_lam);
sum_dpij_dN = fvec::mask_add(sum_dpij_dN, active_mask, sum_dpij_dN,
- wik * ex_lam * dgdN);
+ wik * ex_lam * dgdN);
fvec dcutN;
fvec cutN = aut_Sp_deriv(Nki, Nmin, Nmax, &dcutN);
*sum_N = fvec::mask_add(*sum_N, active_mask, *sum_N,
- fvec::mask_blend(ktype_mask, c_1,
- fvec::setzero()) * wik * cutN);
+ fvec::mask_blend(ktype_mask, c_1,
+ fvec::setzero()) * wik * cutN);
if (buf_len == BUF_CAP) goto exceed_buffer;
data->rikx_buf[buf_len] = rikx;
data->riky_buf[buf_len] = riky;
@@ -2956,15 +2956,15 @@ static void aut_frebo_N_spline_force(
}
static fvec aut_frebo_pi_rc_pd(KernelArgsAIREBOT<flt_t,acc_t> * ka, int itype,
- int jtype, fvec Nij, fvec Nji, fvec Nijconj,
- fvec * dN3) {
+ int jtype, fvec Nij, fvec Nji, fvec Nijconj,
+ fvec * dN3) {
flt_t ret[fvec::VL] __attribute__((aligned(64)));
flt_t dN3ret[3][fvec::VL] __attribute__((aligned(64)));
int i;
for (i = 0; i < fvec::VL; i++) {
flt_t dN3tmp[3];
ret[i] = frebo_pi_rc(ka, itype, jtype, fvec::at(Nij, i), fvec::at(Nji, i),
- fvec::at(Nijconj, i), &dN3tmp[0]);
+ fvec::at(Nijconj, i), &dN3tmp[0]);
dN3ret[0][i] = dN3tmp[0];
dN3ret[1][i] = dN3tmp[1];
dN3ret[2][i] = dN3tmp[2];
@@ -2976,15 +2976,15 @@ static fvec aut_frebo_pi_rc_pd(KernelArgsAIREBOT<flt_t,acc_t> * ka, int itype,
}
static fvec aut_frebo_Tij(KernelArgsAIREBOT<flt_t,acc_t> * ka, int itype,
- int jtype, fvec Nij, fvec Nji, fvec Nijconj,
- fvec * dN3) {
+ int jtype, fvec Nij, fvec Nji, fvec Nijconj,
+ fvec * dN3) {
flt_t ret[fvec::VL] __attribute__((aligned(64)));
flt_t dN3ret[3][fvec::VL] __attribute__((aligned(64)));
int i;
for (i = 0; i < fvec::VL; i++) {
flt_t dN3tmp[3];
ret[i] = frebo_Tij(ka, itype, jtype, fvec::at(Nij, i), fvec::at(Nji, i),
- fvec::at(Nijconj, i), &dN3tmp[0]);
+ fvec::at(Nijconj, i), &dN3tmp[0]);
dN3ret[0][i] = dN3tmp[0];
dN3ret[1][i] = dN3tmp[1];
dN3ret[2][i] = dN3tmp[2];
@@ -3031,9 +3031,9 @@ static fvec aut_frebo_sum_omega(
bvec mask_outer = fvec::cmpneq(fvec::setzero(), sin321) & mask_start;
// add "continue"
fvec sink2i = fvec::mask_recip(fvec::undefined(), mask_outer,
- sin321 * sin321);
+ sin321 * sin321);
fvec rik2i = fvec::mask_recip(fvec::undefined(), mask_outer,
- r21mag * r21mag);
+ r21mag * r21mag);
fvec rr = r23mag * r23mag - r21mag * r21mag;
fvec r31x = r21x - r23x;
fvec r31y = r21y - r23y;
@@ -3042,9 +3042,9 @@ static fvec aut_frebo_sum_omega(
fvec rijrik = c_2 * r23mag * r21mag;
fvec r21mag2 = r21mag * r21mag;
fvec dctik = fvec::mask_div(fvec::undefined(), mask_outer, r31mag2 - rr,
- rijrik * r21mag2);
+ rijrik * r21mag2);
fvec dctij = fvec::mask_div(fvec::undefined(), mask_outer, r31mag2 + rr,
- rijrik * r23mag * r23mag);
+ rijrik * r23mag * r23mag);
fvec dctjk = fvec::mask_div(fvec::undefined(), mask_outer, c_m2, rijrik);
fvec dw21 = i_data->dwik_buf[buf_idx_i];
fvec w21 = i_data->wik_buf[buf_idx_i];
@@ -3057,25 +3057,25 @@ static fvec aut_frebo_sum_omega(
// l == a4 == buf_idx_j
ivec l = j_data->k_buf[buf_idx_j];
bvec mask_inner_0 = ivec::mask_cmpneq(mask_outer, k, l) &
- j_data->mask_buf[buf_idx_j];
+ j_data->mask_buf[buf_idx_j];
// add "continue"
fvec r34x = j_data->rikx_buf[buf_idx_j];
fvec r34y = j_data->riky_buf[buf_idx_j];
fvec r34z = j_data->rikz_buf[buf_idx_j];
fvec r34mag = j_data->rikmag_buf[buf_idx_j];
fvec cos234 = fvec::mask_div(fvec::undefined(), mask_inner_0,
- r32x * r34x + r32y * r34y + r32z * r34z,
- r23mag * r34mag);
+ r32x * r34x + r32y * r34y + r32z * r34z,
+ r23mag * r34mag);
cos234 = fvec::min(c_1, fvec::max(c_m1, cos234));
fvec sin234 = fvec::mask_sqrt(fvec::undefined(), mask_inner_0,
- c_1 - cos234 * cos234);
+ c_1 - cos234 * cos234);
bvec mask_inner_1 = fvec::mask_cmpneq(mask_inner_0, sin234,
- fvec::setzero());
+ fvec::setzero());
// add "continue"
fvec sinl2i = fvec::mask_recip(fvec::undefined(), mask_inner_1,
- sin234 * sin234);
+ sin234 * sin234);
fvec rjl2i = fvec::mask_recip(fvec::undefined(), mask_inner_1,
- r34mag * r34mag);
+ r34mag * r34mag);
fvec dw34 = j_data->dwik_buf[buf_idx_j];
fvec w34 = j_data->wik_buf[buf_idx_j];
fvec rr = r23mag * r23mag - r34mag * r34mag;
@@ -3086,11 +3086,11 @@ static fvec aut_frebo_sum_omega(
fvec rijrjl = c_2 * r23mag * r34mag;
fvec rjl2 = r34mag * r34mag;
fvec dctjl = fvec::mask_div(fvec::undefined(), mask_inner_1, r242 - rr,
- rijrjl * rjl2);
+ rijrjl * rjl2);
fvec dctji = fvec::mask_div(fvec::undefined(), mask_inner_1, r242 + rr,
- rijrjl * r23mag * r23mag);
+ rijrjl * r23mag * r23mag);
fvec dctil = fvec::mask_div(fvec::undefined(), mask_inner_1, c_m2,
- rijrjl);
+ rijrjl);
fvec dtsijl;
fvec tspijl = aut_Sp2_deriv(cos234, thmin, thmax, &dtsijl);
dtsijl = fvec::setzero() - dtsijl;
@@ -3104,22 +3104,22 @@ static fvec aut_frebo_sum_omega(
fvec cross234z = r23x * r34y - r23y * r34x;
fvec cwnum = cross321x * cross234x + cross321y * cross234y + cross321z *
- cross234z;
+ cross234z;
fvec cwnom = r21mag * r34mag * r23mag * r23mag * sin321 * sin234;
fvec om1234 = fvec::mask_div(fvec::undefined(), mask_inner_1, cwnum,
- cwnom);
+ cwnom);
fvec cw = om1234;
fvec sum_omega_contrib = (c_1 - om1234 * om1234) * w21 * w34 *
- (c_1 - tspjik) * ( c_1 - tspijl);
+ (c_1 - tspjik) * ( c_1 - tspijl);
sum_omega = fvec::mask_add(sum_omega, mask_inner_1, sum_omega,
- sum_omega_contrib);
+ sum_omega_contrib);
fvec dt1dik = rik2i - dctik * sink2i * cos321;
fvec dt1djk = fvec::setzero() - dctjk * sink2i * cos321;
fvec dt1djl = rjl2i - dctjl * sinl2i * cos234;
fvec dt1dil = fvec::setzero() - dctil * sinl2i * cos234;
fvec dt1dij = fvec::mask_div(fvec::undefined(), mask_inner_1, c_2,
- r23mag * r23mag) -
- dctij * sink2i * cos321 - dctji * sinl2i * cos234;
+ r23mag * r23mag) -
+ dctij * sink2i * cos321 - dctji * sinl2i * cos234;
fvec dt2dikx = r23y * cross234z - r23z * cross234y;
fvec dt2diky = r23z * cross234x - r23x * cross234z;
@@ -3130,23 +3130,23 @@ static fvec aut_frebo_sum_omega(
fvec dt2djlz = r23y * cross321x - r23x * cross321y;
fvec dt2dijx = r21z * cross234y + r34y * cross321z -
- ( r34z * cross321y + r21y * cross234z);
+ ( r34z * cross321y + r21y * cross234z);
fvec dt2dijy = r21x * cross234z + r34z * cross321x -
- ( r34x * cross321z + r21z * cross234x);
+ ( r34x * cross321z + r21z * cross234x);
fvec dt2dijz = r21y * cross234x + r34x * cross321y -
- ( r34y * cross321x + r21x * cross234y);
+ ( r34y * cross321x + r21x * cross234y);
fvec aa = prefactor * c_2 * fvec::mask_div(fvec::undefined(),
- mask_inner_1, cw, cwnom) *
- w21 * w34 * (c_1 - tspjik) * ( c_1 - tspijl);
+ mask_inner_1, cw, cwnom) *
+ w21 * w34 * (c_1 - tspjik) * ( c_1 - tspijl);
fvec aaa1 = (fvec::setzero() - prefactor) * (c_1 - om1234 * om1234) *
- (c_1 - tspjik) * (c_1 - tspijl);
+ (c_1 - tspjik) * (c_1 - tspijl);
fvec aaa2 = (fvec::setzero() - prefactor) * (c_1 - om1234 * om1234) *
- w21 * w34;
+ w21 * w34;
fvec at2 = aa * cwnum;
fvec fcijpc = aaa2 * dtsjik * dctij * (c_1 - tspijl) + aaa2 * dtsijl *
- dctji * (c_1 - tspjik) - dt1dij * at2;
+ dctji * (c_1 - tspjik) - dt1dij * at2;
fvec fcikpc = aaa2 * dtsjik * dctik * (c_1 - tspijl) - dt1dik * at2;
fvec fcjlpc = aaa2 * dtsijl * dctjl * (c_1 - tspjik) - dt1djl * at2;
fvec fcjkpc = aaa2 * dtsjik * dctjk * (c_1 - tspijl) - dt1djk * at2;
@@ -3193,8 +3193,8 @@ static fvec aut_frebo_sum_omega(
F23z + F24z - F31z);
fvec tmp20 = VA * (c_1 - om1234 * om1234) * (c_1 - tspjik) *
- (c_1 - tspijl) * dw21 * w34 * fvec::mask_recip(fvec::undefined(),
- mask_inner_1, r21mag);
+ (c_1 - tspijl) * dw21 * w34 * fvec::mask_recip(fvec::undefined(),
+ mask_inner_1, r21mag);
f2x = f2x - tmp20 * r21x;
f2y = f2y - tmp20 * r21y;
f2z = f2z - tmp20 * r21z;
@@ -3203,8 +3203,8 @@ static fvec aut_frebo_sum_omega(
f1z = f1z + tmp20 * r21z;
fvec tmp21 = VA * (c_1 - om1234 * om1234) * (c_1 - tspjik) *
- (c_1 - tspijl) * w21 * dw34 * fvec::mask_recip(fvec::undefined(),
- mask_inner_1, r34mag);
+ (c_1 - tspijl) * w21 * dw34 * fvec::mask_recip(fvec::undefined(),
+ mask_inner_1, r34mag);
f3x = f3x - tmp21 * r34x;
f3y = f3y - tmp21 * r34y;
f3z = f3z - tmp21 * r34z;
@@ -3214,35 +3214,35 @@ static fvec aut_frebo_sum_omega(
// 1 == buf_idx_i, 2 == i, 3 == j, 4 == buf_idx_j
i_data->force_k_x_buf[buf_idx_i] =
- fvec::mask_add(i_data->force_k_x_buf[buf_idx_i],
- mask_inner_1, i_data->force_k_x_buf[buf_idx_i], f1x);
+ fvec::mask_add(i_data->force_k_x_buf[buf_idx_i],
+ mask_inner_1, i_data->force_k_x_buf[buf_idx_i], f1x);
i_data->force_k_y_buf[buf_idx_i] =
- fvec::mask_add(i_data->force_k_y_buf[buf_idx_i], mask_inner_1,
- i_data->force_k_y_buf[buf_idx_i], f1y);
+ fvec::mask_add(i_data->force_k_y_buf[buf_idx_i], mask_inner_1,
+ i_data->force_k_y_buf[buf_idx_i], f1y);
i_data->force_k_z_buf[buf_idx_i] =
- fvec::mask_add(i_data->force_k_z_buf[buf_idx_i], mask_inner_1,
- i_data->force_k_z_buf[buf_idx_i], f1z);
+ fvec::mask_add(i_data->force_k_z_buf[buf_idx_i], mask_inner_1,
+ i_data->force_k_z_buf[buf_idx_i], f1z);
i_data->force_i_x =
- fvec::mask_add(i_data->force_i_x, mask_inner_1, i_data->force_i_x, f2x);
+ fvec::mask_add(i_data->force_i_x, mask_inner_1, i_data->force_i_x, f2x);
i_data->force_i_y =
- fvec::mask_add(i_data->force_i_y, mask_inner_1, i_data->force_i_y, f2y);
+ fvec::mask_add(i_data->force_i_y, mask_inner_1, i_data->force_i_y, f2y);
i_data->force_i_z =
- fvec::mask_add(i_data->force_i_z, mask_inner_1, i_data->force_i_z, f2z);
+ fvec::mask_add(i_data->force_i_z, mask_inner_1, i_data->force_i_z, f2z);
j_data->force_i_x =
- fvec::mask_add(j_data->force_i_x, mask_inner_1, j_data->force_i_x, f3x);
+ fvec::mask_add(j_data->force_i_x, mask_inner_1, j_data->force_i_x, f3x);
j_data->force_i_y =
- fvec::mask_add(j_data->force_i_y, mask_inner_1, j_data->force_i_y, f3y);
+ fvec::mask_add(j_data->force_i_y, mask_inner_1, j_data->force_i_y, f3y);
j_data->force_i_z =
- fvec::mask_add(j_data->force_i_z, mask_inner_1, j_data->force_i_z, f3z);
+ fvec::mask_add(j_data->force_i_z, mask_inner_1, j_data->force_i_z, f3z);
j_data->force_k_x_buf[buf_idx_j] =
- fvec::mask_add(j_data->force_k_x_buf[buf_idx_j], mask_inner_1,
- j_data->force_k_x_buf[buf_idx_j], f4x);
+ fvec::mask_add(j_data->force_k_x_buf[buf_idx_j], mask_inner_1,
+ j_data->force_k_x_buf[buf_idx_j], f4x);
j_data->force_k_y_buf[buf_idx_j] =
- fvec::mask_add(j_data->force_k_y_buf[buf_idx_j], mask_inner_1,
- j_data->force_k_y_buf[buf_idx_j], f4y);
+ fvec::mask_add(j_data->force_k_y_buf[buf_idx_j], mask_inner_1,
+ j_data->force_k_y_buf[buf_idx_j], f4y);
j_data->force_k_z_buf[buf_idx_j] =
- fvec::mask_add(j_data->force_k_z_buf[buf_idx_j], mask_inner_1,
- j_data->force_k_z_buf[buf_idx_j], f4z);
+ fvec::mask_add(j_data->force_k_z_buf[buf_idx_j], mask_inner_1,
+ j_data->force_k_z_buf[buf_idx_j], f4z);
}
}
return sum_omega;
@@ -3269,9 +3269,9 @@ static fvec aut_frebo_pi_dh(
r23x, r23y, r23z, r23mag, VA * Tij, fij);
sum_omega = fvec::mask_blend(TijgtTOLmask, fvec::setzero(), sum_omega);
aut_frebo_N_spline_force(ka, i_data, itype, jtype, vi, vj, VA * sum_omega,
- dN3[0], dN3[2], NconjtmpI);
+ dN3[0], dN3[2], NconjtmpI);
aut_frebo_N_spline_force(ka, j_data, jtype, itype, vj, vi, VA * sum_omega,
- dN3[1], dN3[2], NconjtmpJ);
+ dN3[1], dN3[2], NconjtmpJ);
}
return Tij * sum_omega;
}
@@ -3351,7 +3351,7 @@ static void aut_torsion_vec(
for (int buf_idx_j = 0; buf_idx_j < j_data->buf_len; buf_idx_j++) {
ivec l = j_data->k_buf[buf_idx_j];
bvec mask_inner_0 = ivec::mask_cmpneq(mask_start, k, l) &
- j_data->mask_buf[buf_idx_j];
+ j_data->mask_buf[buf_idx_j];
if (! bvec::test_any_set(mask_inner_0)) continue;
fvec del34x = j_data->rikx_buf[buf_idx_j];
fvec del34y = j_data->riky_buf[buf_idx_j];
@@ -3380,16 +3380,16 @@ static void aut_torsion_vec(
fvec cross321y = del32z * del21x - del32x * del21z;
fvec cross321z = del32x * del21y - del32y * del21x;
fvec cross321mag = fvec::sqrt(cross321x * cross321x +
- cross321y * cross321y +
- cross321z * cross321z);
+ cross321y * cross321y +
+ cross321z * cross321z);
fvec cross234x = del23y * del34z - del23z * del34y;
fvec cross234y = del23z * del34x - del23x * del34z;
fvec cross234z = del23x * del34y - del23y * del34x;
fvec cross234mag = fvec::sqrt(cross234x * cross234x +
- cross234y * cross234y +
- cross234z * cross234z);
+ cross234y * cross234y +
+ cross234z * cross234z);
fvec cwnum = cross321x * cross234x + cross321y * cross234y +
- cross321z * cross234z;
+ cross321z * cross234z;
fvec cwnom = r21 * r34 * r32 * r32 * sin321 * sin234;
fvec cw = cwnum / cwnom;
@@ -3459,7 +3459,7 @@ static void aut_torsion_vec(
fvec dcwdn = fvec::recip(cwnom);
fvec cw2_4 = cw2 * cw2 * cw2 * cw2;
fvec dvpdcw = c_2_5 * Ec * cw2_4 * w23 * w21 * w34 * (c_1_0 - tspjik) *
- (c_1_0 - tspijl);
+ (c_1_0 - tspijl);
fvec Ftmpx = dvpdcw * (dcwdn * dndijx + dcwddn * ddndij * del23x / r23);
fvec Ftmpy = dvpdcw * (dcwdn * dndijy + dcwddn * ddndij * del23y / r23);
@@ -3514,7 +3514,7 @@ static void aut_torsion_vec(
// coordination forces
fvec fpair = Vtors * dw21 * w23 * w34 * (c_1_0 - tspjik) *
- (c_1_0 - tspijl) / r21;
+ (c_1_0 - tspijl) / r21;
fix = fix - del21x * fpair;
fiy = fiy - del21y * fpair;
fiz = fiz - del21z * fpair;
@@ -3523,7 +3523,7 @@ static void aut_torsion_vec(
fkz = fkz + del21z * fpair;
fpair = Vtors * w21 * dw23 * w34 * (c_1_0 - tspjik) * (c_1_0 - tspijl) /
- r23;
+ r23;
fix = fix - del23x * fpair;
fiy = fiy - del23y * fpair;
fiz = fiz - del23z * fpair;
@@ -3532,7 +3532,7 @@ static void aut_torsion_vec(
fjz = fjz + del23z * fpair;
fpair = Vtors * w21 * w23 * dw34 * (c_1_0 - tspjik) * (c_1_0 - tspijl) /
- r34;
+ r34;
fjx = fjx - del34x * fpair;
fjy = fjy - del34y * fpair;
fjz = fjz - del34z * fpair;
@@ -3543,7 +3543,7 @@ static void aut_torsion_vec(
// additional cut off function forces
fvec fcpc = fvec::setzero() - Vtors * w21 * w23 * w34 * dtsjik * (c_1_0 -
- tspijl);
+ tspijl);
fpair = fcpc * dcidij / rij;
fix = fix + fpair * del23x;
fiy = fiy + fpair * del23y;
@@ -3569,7 +3569,7 @@ static void aut_torsion_vec(
fkz = fkz - fpair * deljkz;
fcpc = fvec::setzero() - Vtors * w21 * w23 * w34 * (c_1_0 - tspjik) *
- dtsijl;
+ dtsijl;
fpair = fcpc * dcjdji / rij;
fix = fix + fpair * del23x;
fiy = fiy + fpair * del23y;
@@ -3597,35 +3597,35 @@ static void aut_torsion_vec(
// sum per-atom forces into atom force array
i_data->force_i_x = fvec::mask_add(i_data->force_i_x, mask_inner_0,
- i_data->force_i_x, fix);
+ i_data->force_i_x, fix);
i_data->force_i_y = fvec::mask_add(i_data->force_i_y, mask_inner_0,
- i_data->force_i_y, fiy);
+ i_data->force_i_y, fiy);
i_data->force_i_z = fvec::mask_add(i_data->force_i_z, mask_inner_0,
- i_data->force_i_z, fiz);
+ i_data->force_i_z, fiz);
i_data->force_j_x = fvec::mask_add(i_data->force_j_x, mask_inner_0,
- i_data->force_j_x, fjx);
+ i_data->force_j_x, fjx);
i_data->force_j_y = fvec::mask_add(i_data->force_j_y, mask_inner_0,
- i_data->force_j_y, fjy);
+ i_data->force_j_y, fjy);
i_data->force_j_z = fvec::mask_add(i_data->force_j_z, mask_inner_0,
- i_data->force_j_z, fjz);
+ i_data->force_j_z, fjz);
i_data->force_k_x_buf[buf_idx_i] =
- fvec::mask_add(i_data->force_k_x_buf[buf_idx_i], mask_inner_0,
- i_data->force_k_x_buf[buf_idx_i], fkx);
+ fvec::mask_add(i_data->force_k_x_buf[buf_idx_i], mask_inner_0,
+ i_data->force_k_x_buf[buf_idx_i], fkx);
i_data->force_k_y_buf[buf_idx_i] =
- fvec::mask_add(i_data->force_k_y_buf[buf_idx_i], mask_inner_0,
- i_data->force_k_y_buf[buf_idx_i], fky);
+ fvec::mask_add(i_data->force_k_y_buf[buf_idx_i], mask_inner_0,
+ i_data->force_k_y_buf[buf_idx_i], fky);
i_data->force_k_z_buf[buf_idx_i] =
- fvec::mask_add(i_data->force_k_z_buf[buf_idx_i], mask_inner_0,
- i_data->force_k_z_buf[buf_idx_i], fkz);
+ fvec::mask_add(i_data->force_k_z_buf[buf_idx_i], mask_inner_0,
+ i_data->force_k_z_buf[buf_idx_i], fkz);
j_data->force_k_x_buf[buf_idx_j] =
- fvec::mask_add(j_data->force_k_x_buf[buf_idx_j], mask_inner_0,
- j_data->force_k_x_buf[buf_idx_j], flx);
+ fvec::mask_add(j_data->force_k_x_buf[buf_idx_j], mask_inner_0,
+ j_data->force_k_x_buf[buf_idx_j], flx);
j_data->force_k_y_buf[buf_idx_j] =
- fvec::mask_add(j_data->force_k_y_buf[buf_idx_j], mask_inner_0,
- j_data->force_k_y_buf[buf_idx_j], fly);
+ fvec::mask_add(j_data->force_k_y_buf[buf_idx_j], mask_inner_0,
+ j_data->force_k_y_buf[buf_idx_j], fly);
j_data->force_k_z_buf[buf_idx_j] =
- fvec::mask_add(j_data->force_k_z_buf[buf_idx_j], mask_inner_0,
- j_data->force_k_z_buf[buf_idx_j], flz);
+ fvec::mask_add(j_data->force_k_z_buf[buf_idx_j], mask_inner_0,
+ j_data->force_k_z_buf[buf_idx_j], flz);
}
}
}
@@ -3636,8 +3636,8 @@ static void aut_torsion_vec(
* torsion calculaltion.
*/
static void aut_frebo_batch_of_kind(KernelArgsAIREBOT<flt_t,acc_t> * ka,
- int torflag, int itype, int jtype,
- int * i_buf, int * j_buf) {
+ int torflag, int itype, int jtype,
+ int * i_buf, int * j_buf) {
{ // jump-scope for exceed_limits
AtomAIREBOT<flt_t> * x = ka->x;
int * map = ka->map;
@@ -3758,12 +3758,12 @@ static void aut_frebo_batch_of_kind(KernelArgsAIREBOT<flt_t,acc_t> * ka,
fvec dN3[3];
fvec pi_rc = aut_frebo_pi_rc_pd(ka, itype, jtype, Nij, Nji, Nijconj, dN3);
aut_frebo_N_spline_force(ka, &i_data, itype, jtype, vi, vj, VA, dN3[0],
- dN3[2], NconjtmpI);
+ dN3[2], NconjtmpI);
aut_frebo_N_spline_force(ka, &j_data, jtype, itype, vj, vi, VA, dN3[1],
- dN3[2], NconjtmpJ);
+ dN3[2], NconjtmpJ);
fvec pi_dh = aut_frebo_pi_dh(ka, &i_data, &j_data, itype, jtype, vi, vj,
- delx, dely, delz, rij, VA, Nij, Nji, Nijconj,
- NconjtmpI, NconjtmpJ, fij);
+ delx, dely, delz, rij, VA, Nij, Nji, Nijconj,
+ NconjtmpI, NconjtmpJ, fij);
fvec bij = c_0_5 * ( pij + pji) + pi_rc + pi_dh;
fvec dVAdi = bij * dVA;
@@ -3895,7 +3895,7 @@ static void aut_frebo(KernelArgsAIREBOT<flt_t,acc_t> * ka, int torflag) {
int j = j_buf[itype][jtype][l];
ref_frebo_single_interaction(ka, i, j);
if (torflag && itype == 0 && jtype == 0)
- ref_torsion_single_interaction(ka, i, j);
+ ref_torsion_single_interaction(ka, i, j);
}
}
}
@@ -3983,7 +3983,7 @@ static bool aut_airebo_lj_test_all_paths(KernelArgsAIREBOT<flt_t,acc_t> * ka,
int start_hash_slot = aut_lj_tap_hash_fn(j, attempt);
int hash_slot = start_hash_slot;
while (result->i[hash_slot] == i && result->j[hash_slot] != j &&
- attempt < OPT_TEST_PATH_SIZE) {
+ attempt < OPT_TEST_PATH_SIZE) {
hash_slot = aut_lj_tap_hash_fn(j, ++attempt);
}
if (attempt >= OPT_TEST_PATH_SIZE) goto exceed_limits;
@@ -3996,7 +3996,7 @@ static bool aut_airebo_lj_test_all_paths(KernelArgsAIREBOT<flt_t,acc_t> * ka,
if (path_insert_pos >= OPT_TEST_PATH_ITEMS) goto exceed_limits;
result->testpath_idx[hash_slot] = path_insert_pos;
LennardJonesPathAIREBOT<flt_t> *path =
- &result->testpath[path_insert_pos++];
+ &result->testpath[path_insert_pos++];
path->num = 2;
path->del[0].x = dijx;
path->del[0].y = dijy;
@@ -4028,7 +4028,7 @@ static bool aut_airebo_lj_test_all_paths(KernelArgsAIREBOT<flt_t,acc_t> * ka,
int start_hash_slot = aut_lj_tap_hash_fn(k, attempt);
int hash_slot = start_hash_slot;
while (result->i[hash_slot] == i && result->j[hash_slot] != k &&
- attempt < OPT_TEST_PATH_SIZE) {
+ attempt < OPT_TEST_PATH_SIZE) {
hash_slot = aut_lj_tap_hash_fn(k, ++attempt);
}
if (attempt >= OPT_TEST_PATH_SIZE) goto exceed_limits;
@@ -4041,7 +4041,7 @@ static bool aut_airebo_lj_test_all_paths(KernelArgsAIREBOT<flt_t,acc_t> * ka,
if (path_insert_pos >= OPT_TEST_PATH_ITEMS) goto exceed_limits;
result->testpath_idx[hash_slot] = path_insert_pos;
LennardJonesPathAIREBOT<flt_t> *path =
- &result->testpath[path_insert_pos++];
+ &result->testpath[path_insert_pos++];
path->num = 3;
path->del[0].x = dijx;
path->del[0].y = dijy;
@@ -4081,7 +4081,7 @@ static bool aut_airebo_lj_test_all_paths(KernelArgsAIREBOT<flt_t,acc_t> * ka,
int start_hash_slot = aut_lj_tap_hash_fn(l, attempt);
int hash_slot = start_hash_slot;
while (result->i[hash_slot] == i && result->j[hash_slot] != l &&
- attempt < OPT_TEST_PATH_SIZE) {
+ attempt < OPT_TEST_PATH_SIZE) {
hash_slot = aut_lj_tap_hash_fn(l, ++attempt);
}
if (attempt >= OPT_TEST_PATH_SIZE) goto exceed_limits;
@@ -4094,7 +4094,7 @@ static bool aut_airebo_lj_test_all_paths(KernelArgsAIREBOT<flt_t,acc_t> * ka,
if (path_insert_pos >= OPT_TEST_PATH_ITEMS) goto exceed_limits;
result->testpath_idx[hash_slot] = path_insert_pos;
LennardJonesPathAIREBOT<flt_t> *path =
- &result->testpath[path_insert_pos++];
+ &result->testpath[path_insert_pos++];
path->num = 4;
path->del[0].x = dijx;
path->del[0].y = dijy;
@@ -4174,7 +4174,7 @@ static fvec aut_airebo_lj_tap_test_path(KernelArgsAIREBOT<flt_t,acc_t> * ka,
another_attempt = correct_i & ~ found_items;
}
cij = fvec::mask_gather(cij, found_items, hash_slot,
- &test_path_result->cij[0], sizeof(flt_t));
+ &test_path_result->cij[0], sizeof(flt_t));
bvec need_testpath = fvec::mask_cmplt(found_items, fvec::setzero(), cij);
if (bvec::test_any_set(need_testpath)) {
for (int i = 0; i < fvec::VL; i++) {
@@ -4304,8 +4304,8 @@ static void aut_lj_with_bo(
fvec NconjtmpI;
fvec pij = aut_frebo_pij_pd_2(ka, &i_data, itype, jtype, vi, vj,
- delx * scale, dely * scale, delz * scale,
- the_r, wij, VA, &NconjtmpI, fij);
+ delx * scale, dely * scale, delz * scale,
+ the_r, wij, VA, &NconjtmpI, fij);
if (i_data.buf_len < 0) goto exceed_limits;
@@ -4314,8 +4314,8 @@ static void aut_lj_with_bo(
fvec rjiy = fvec::setzero() - dely;
fvec rjiz = fvec::setzero() - delz;
fvec pji = aut_frebo_pij_pd_2(ka, &j_data, jtype, itype, vj, vi,
- rjix * scale, rjiy * scale, rjiz * scale,
- the_r, wij, VA, &NconjtmpJ, fji);
+ rjix * scale, rjiy * scale, rjiz * scale,
+ the_r, wij, VA, &NconjtmpJ, fji);
fij[0] = fij[0] - fji[0];
fij[1] = fij[1] - fji[1];
fij[2] = fij[2] - fji[2];
@@ -4376,23 +4376,23 @@ static void aut_lj_with_bo(
fijc[1] = dStb * fij[1];
fijc[2] = dStb * fij[2];
fij[0] = scale * (fijc[0] - (delx * delx * fijc[0] + dely * delx *
- fijc[1] + delz * delx * fijc[2]) / rsq);
+ fijc[1] + delz * delx * fijc[2]) / rsq);
fij[1] = scale * (fijc[1] - (delx * dely * fijc[0] + dely * dely *
- fijc[1] + delz * dely * fijc[2]) / rsq);
+ fijc[1] + delz * dely * fijc[2]) / rsq);
fij[2] = scale * (fijc[2] - (delx * delz * fijc[0] + dely * delz *
- fijc[1] + delz * delz * fijc[2]) / rsq);
+ fijc[1] + delz * delz * fijc[2]) / rsq);
aut_frebo_N_spline_force(ka, &i_data, itype, jtype, vi, vj, dStb * VA,
- dN3[0], dN3[2], NconjtmpI);
+ dN3[0], dN3[2], NconjtmpI);
aut_frebo_N_spline_force(ka, &j_data, jtype, itype, vj, vi, dStb * VA,
- dN3[1], dN3[2], NconjtmpJ);
+ dN3[1], dN3[2], NconjtmpJ);
if (bvec::test_any_set(TijgtTOLmask)) {
aut_frebo_N_spline_force(ka, &i_data, itype, jtype, vi, vj,
- dStb * VA * sum_omega, dN3_dh[0], dN3_dh[2],
- NconjtmpI);
+ dStb * VA * sum_omega, dN3_dh[0], dN3_dh[2],
+ NconjtmpI);
aut_frebo_N_spline_force(ka, &j_data, jtype, itype, vj, vi,
- dStb * VA * sum_omega, dN3_dh[1], dN3_dh[2],
- NconjtmpJ);
+ dStb * VA * sum_omega, dN3_dh[1], dN3_dh[2],
+ NconjtmpJ);
}
aut_frebo_data_writeback(ka, &i_data);
@@ -4475,7 +4475,7 @@ static void aut_lj_with_bo(
exceed_limits:
for (int l = 0; l < fvec::VL; l++) {
ref_lennard_jones_single_interaction(ka, ivec::at(i, l), ivec::at(j, l),
- MORSEFLAG);
+ MORSEFLAG);
}
return;
}
@@ -4584,14 +4584,14 @@ static void aut_lennard_jones(KernelArgsAIREBOT<flt_t,acc_t> * ka) {
ivec j;
if (rest_j) {
bvec mask_0 = bvec::full();
- //0xFF >> (8 - (jnum - jj));
+ //0xFF >> (8 - (jnum - jj));
if (jj + (fvec::VL - 1) >= jnum) mask_0 = bvec::only(jnum - jj);
j = ivec::maskz_loadu(mask_0, &neighs[jj]);
fvec x_j, y_j, z_j;
aut_loadatoms_vec(x, j, &x_j, &y_j, &z_j, &jtype_mask, map, map_i,
- c_i1);
+ c_i1);
fvec::gather_prefetch0(ivec::mullo(c_i4,
- ivec::maskz_loadu(bvec::full(), &neighs[jj + fvec::VL])), x);
+ ivec::maskz_loadu(bvec::full(), &neighs[jj + fvec::VL])), x);
_mm_prefetch((const char*)&neighs[jj + 2 * fvec::VL], _MM_HINT_T0);
delx = x_i - x_j;
dely = y_i - y_j;
@@ -4624,7 +4624,7 @@ static void aut_lennard_jones(KernelArgsAIREBOT<flt_t,acc_t> * ka) {
}
num_2 -= fvec::VL;
- //(0xFF >> (8 - num_2)) << (_cc_popcnt(within_cutoff) - num_2);
+ //(0xFF >> (8 - num_2)) << (_cc_popcnt(within_cutoff) - num_2);
mask_2 = bvec::onlyafter(num_2, bvec::popcnt(within_cutoff) - num_2);
{
ivec tmp_j = j_2;
@@ -4676,7 +4676,7 @@ static void aut_lennard_jones(KernelArgsAIREBOT<flt_t,acc_t> * ka) {
fvec p_rcmax = fvec::mask_blend(jtype_mask, p_rcmax0, p_rcmax1);
#pragma noinline
cij = aut_airebo_lj_tap_test_path(ka, &test_path_result, need_search,
- i_bc, j, testpath);
+ i_bc, j, testpath);
}
current_mask = fvec::mask_cmplt(current_mask, c_0_0, cij);
if (bvec::test_all_unset(current_mask)) {
@@ -4735,13 +4735,13 @@ static void aut_lennard_jones(KernelArgsAIREBOT<flt_t,acc_t> * ka) {
fvec cijtmp = fvec::masku_compress(need_bo_with_jtype, cij);
bvec insert_mask = bvec::after(num_bo[itype][jtype]);
i_bo[itype][jtype] = ivec::mask_expand(i_bo[itype][jtype],
- insert_mask, itmp);
+ insert_mask, itmp);
j_bo[itype][jtype] = ivec::mask_expand(j_bo[itype][jtype],
- insert_mask, jtmp);
+ insert_mask, jtmp);
cij_bo[itype][jtype] = fvec::mask_expand(cij_bo[itype][jtype],
- insert_mask, cijtmp);
+ insert_mask, cijtmp);
bvec need_path_force_with_jtype = need_bo_with_jtype &
- need_path_force;
+ need_path_force;
int testpath_end = fvec::VL;
if (bvec::test_any_set(need_path_force_with_jtype)) {
int pos = num_bo[itype][jtype];
@@ -4759,16 +4759,16 @@ static void aut_lennard_jones(KernelArgsAIREBOT<flt_t,acc_t> * ka) {
}
}
num_bo[itype][jtype] = num_bo[itype][jtype] +
- bvec::popcnt(need_bo_with_jtype);
+ bvec::popcnt(need_bo_with_jtype);
if (num_bo[itype][jtype] >= fvec::VL) {
#pragma noinline
aut_lj_with_bo<MORSEFLAG>(ka, itype, jtype, i_bo[itype][jtype],
- j_bo[itype][jtype], cij_bo[itype][jtype],
- testpath_bo[itype][jtype]);
+ j_bo[itype][jtype], cij_bo[itype][jtype],
+ testpath_bo[itype][jtype]);
num_bo[itype][jtype] -= fvec::VL;
insert_mask = bvec::onlyafter(num_bo[itype][jtype],
- bvec::popcnt(need_bo_with_jtype) -
- num_bo[itype][jtype]);
+ bvec::popcnt(need_bo_with_jtype) -
+ num_bo[itype][jtype]);
i_bo[itype][jtype] = ivec::masku_compress(insert_mask, itmp);
j_bo[itype][jtype] = ivec::masku_compress(insert_mask, jtmp);
cij_bo[itype][jtype] = fvec::masku_compress(insert_mask, cijtmp);
@@ -4798,30 +4798,30 @@ static void aut_lennard_jones(KernelArgsAIREBOT<flt_t,acc_t> * ka) {
fvec fiy = fpair * dely + fij[1];
fvec fiz = fpair * delz + fij[2];
result_f_i_x = fvec::mask_add(result_f_i_x, current_mask, result_f_i_x,
- fix);
+ fix);
result_f_i_y = fvec::mask_add(result_f_i_y, current_mask, result_f_i_y,
- fiy);
+ fiy);
result_f_i_z = fvec::mask_add(result_f_i_z, current_mask, result_f_i_z,
- fiz);
+ fiz);
result_eng = fvec::mask_add(result_eng, current_mask, result_eng, evdwl);
ivec j_dbl_idx = ivec::mullo(j, c_i4);
avec fjx = avec::mask_gather(avec::undefined(), current_mask, j_dbl_idx,
- &ka->result_f[0].x, sizeof(acc_t));
+ &ka->result_f[0].x, sizeof(acc_t));
avec fjy = avec::mask_gather(avec::undefined(), current_mask, j_dbl_idx,
- &ka->result_f[0].y, sizeof(acc_t));
+ &ka->result_f[0].y, sizeof(acc_t));
avec fjz = avec::mask_gather(avec::undefined(), current_mask, j_dbl_idx,
- &ka->result_f[0].z, sizeof(acc_t));
+ &ka->result_f[0].z, sizeof(acc_t));
fjx = fjx - fix;
fjy = fjy - fiy;
fjz = fjz - fiz;
avec::mask_i32loscatter(&ka->result_f[0].x, current_mask, j_dbl_idx, fjx,
- sizeof(acc_t));
+ sizeof(acc_t));
avec::mask_i32loscatter(&ka->result_f[0].y, current_mask, j_dbl_idx, fjy,
- sizeof(acc_t));
+ sizeof(acc_t));
avec::mask_i32loscatter(&ka->result_f[0].z, current_mask, j_dbl_idx, fjz,
- sizeof(acc_t));
+ sizeof(acc_t));
if (bvec::test_any_set(need_path_force)) {
fvec dC = VLJ * ( Str * Stb + c_1_0 - Str);
@@ -4839,8 +4839,8 @@ static void aut_lennard_jones(KernelArgsAIREBOT<flt_t,acc_t> * ka) {
for (int jtype = 0; jtype < 2; jtype++) {
for (int l = 0; l < num_bo[itype][jtype]; l++) {
ref_lennard_jones_single_interaction(ka,ivec::at(i_bo[itype][jtype],l),
- ivec::at(j_bo[itype][jtype], l),
- MORSEFLAG);
+ ivec::at(j_bo[itype][jtype], l),
+ MORSEFLAG);
}
}
}
diff --git a/src/USER-INTEL/pair_airebo_intel.h b/src/USER-INTEL/pair_airebo_intel.h
index d3179c09f1..2d32925f68 100644
--- a/src/USER-INTEL/pair_airebo_intel.h
+++ b/src/USER-INTEL/pair_airebo_intel.h
@@ -47,8 +47,8 @@ class PairAIREBOIntel : public PairAIREBO {
template <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 int astart, const int aend);
+ IntelBuffers<flt_t,acc_t> * buffers,
+ const int astart, const int aend);
template <class flt_t, class acc_t>
void pack_force_const(IntelBuffers<flt_t,acc_t> * buffers);
diff --git a/src/USER-INTEL/pair_dpd_intel.cpp b/src/USER-INTEL/pair_dpd_intel.cpp
index 09f27504a1..889e1a1da2 100644
--- a/src/USER-INTEL/pair_dpd_intel.cpp
+++ b/src/USER-INTEL/pair_dpd_intel.cpp
@@ -255,33 +255,33 @@ void PairDPDIntel::eval(const int offload, const int vflag,
const flt_t xtmp = x[i].x;
const flt_t ytmp = x[i].y;
const flt_t ztmp = x[i].z;
- const flt_t vxtmp = v[i].x;
- const flt_t vytmp = v[i].y;
- const flt_t vztmp = v[i].z;
+ const flt_t vxtmp = v[i].x;
+ const flt_t vytmp = v[i].y;
+ const flt_t vztmp = v[i].z;
fxtmp = fytmp = fztmp = (acc_t)0;
if (EFLAG) fwtmp = sevdwl = (acc_t)0;
if (NEWTON_PAIR == 0)
if (vflag==1) sv0 = sv1 = sv2 = sv3 = sv4 = sv5 = (acc_t)0;
- if (rngi + jnum > rng_size) {
+ if (rngi + jnum > rng_size) {
#ifdef LMP_USE_MKL_RNG
- if (sizeof(flt_t) == sizeof(float))
- vsRngGaussian(VSL_RNG_METHOD_GAUSSIAN_ICDF, *my_random, rngi,
- (float*)my_rand_buffer, (float)0.0, (float)1.0 );
- else
- vdRngGaussian(VSL_RNG_METHOD_GAUSSIAN_ICDF, *my_random, rngi,
- (double*)my_rand_buffer, 0.0, 1.0 );
+ if (sizeof(flt_t) == sizeof(float))
+ vsRngGaussian(VSL_RNG_METHOD_GAUSSIAN_ICDF, *my_random, rngi,
+ (float*)my_rand_buffer, (float)0.0, (float)1.0 );
+ else
+ vdRngGaussian(VSL_RNG_METHOD_GAUSSIAN_ICDF, *my_random, rngi,
+ (double*)my_rand_buffer, 0.0, 1.0 );
#else
for (int jj = 0; jj < rngi; jj++)
my_rand_buffer[jj] = my_random->gaussian();
#endif
- rngi = 0;
- }
+ rngi = 0;
+ }
#if defined(LMP_SIMD_COMPILER)
- #pragma vector aligned
- #pragma simd reduction(+:fxtmp, fytmp, fztmp, fwtmp, sevdwl, \
- sv0, sv1, sv2, sv3, sv4, sv5)
+ #pragma vector aligned
+ #pragma simd reduction(+:fxtmp, fytmp, fztmp, fwtmp, sevdwl, \
+ sv0, sv1, sv2, sv3, sv4, sv5)
#endif
for (int jj = 0; jj < jnum; jj++) {
flt_t forcelj, evdwl;
@@ -302,29 +302,29 @@ void PairDPDIntel::eval(const int offload, const int vflag,
icut = parami[jtype].icut;
}
const flt_t rsq = delx * delx + dely * dely + delz * delz;
- const flt_t rinv = (flt_t)1.0/sqrt(rsq);
+ const flt_t rinv = (flt_t)1.0/sqrt(rsq);
if (rinv > icut) {
flt_t factor_dpd;
if (!ONETYPE) factor_dpd = special_lj[sbindex];
- flt_t delvx = vxtmp - v[j].x;
- flt_t delvy = vytmp - v[j].y;
- flt_t delvz = vztmp - v[j].z;
- flt_t dot = delx*delvx + dely*delvy + delz*delvz;
- flt_t randnum = my_rand_buffer[jj];
+ flt_t delvx = vxtmp - v[j].x;
+ flt_t delvy = vytmp - v[j].y;
+ flt_t delvz = vztmp - v[j].z;
+ flt_t dot = delx*delvx + dely*delvy + delz*delvz;
+ flt_t randnum = my_rand_buffer[jj];
- flt_t iwd = rinv - icut;
- if (rinv > (flt_t)IEPSILON) iwd = (flt_t)0.0;
+ flt_t iwd = rinv - icut;
+ if (rinv > (flt_t)IEPSILON) iwd = (flt_t)0.0;
- if (!ONETYPE) {
- a0 = parami[jtype].a0;
- gamma = parami[jtype].gamma;
- sigma = parami[jtype].sigma;
- }
- flt_t fpair = a0 - iwd * gamma * dot + sigma * randnum * dtinvsqrt;
- if (!ONETYPE) fpair *= factor_dpd;
- fpair *= iwd;
+ if (!ONETYPE) {
+ a0 = parami[jtype].a0;
+ gamma = parami[jtype].gamma;
+ sigma = parami[jtype].sigma;
+ }
+ flt_t fpair = a0 - iwd * gamma * dot + sigma * randnum * dtinvsqrt;
+ if (!ONETYPE) fpair *= factor_dpd;
+ fpair *= iwd;
const flt_t fpx = fpair * delx;
fxtmp += fpx;
@@ -337,10 +337,10 @@ void PairDPDIntel::eval(const int offload, const int vflag,
if (NEWTON_PAIR) f[j].z -= fpz;
if (EFLAG) {
- flt_t cut = (flt_t)1.0/icut;
- flt_t r = (flt_t)1.0/rinv;
- evdwl = (flt_t)0.5 * a0 * (cut - (flt_t)2.0*r + rsq * icut);
- if (!ONETYPE) evdwl *= factor_dpd;
+ flt_t cut = (flt_t)1.0/icut;
+ flt_t r = (flt_t)1.0/rinv;
+ evdwl = (flt_t)0.5 * a0 * (cut - (flt_t)2.0*r + rsq * icut);
+ if (!ONETYPE) evdwl *= factor_dpd;
sevdwl += evdwl;
if (eatom) {
fwtmp += (flt_t)0.5 * evdwl;
@@ -364,7 +364,7 @@ void PairDPDIntel::eval(const int offload, const int vflag,
}
IP_PRE_ev_tally_atom(NEWTON_PAIR, EFLAG, vflag, f, fwtmp);
- rngi += jnum;
+ rngi += jnum;
} // for ii
IP_PRE_fdotr_reduce_omp(NEWTON_PAIR, nall, minlocal, nthreads, f_start,
@@ -441,7 +441,7 @@ void PairDPDIntel::settings(int narg, char **arg) {
{
int tid = omp_get_thread_num();
vslNewStream(&random_thread[tid], LMP_MKL_RNG,
- seed + comm->me + comm->nprocs * tid );
+ seed + comm->me + comm->nprocs * tid );
}
#endif
@@ -545,7 +545,7 @@ void PairDPDIntel::pack_force_const(ForceConst<flt_t> &fc,
template <class flt_t>
void PairDPDIntel::ForceConst<flt_t>::set_ntypes(const int ntypes,
const int nthreads,
- const int max_nbors,
+ const int max_nbors,
Memory *memory,
const int cop) {
if (ntypes != _ntypes) {
@@ -558,7 +558,7 @@ void PairDPDIntel::ForceConst<flt_t>::set_ntypes(const int ntypes,
_cop = cop;
memory->create(param,ntypes,ntypes,"fc.param");
memory->create(rand_buffer_thread, nthreads, max_nbors,
- "fc.rand_buffer_thread");
+ "fc.rand_buffer_thread");
memory->create(rngi,nthreads,"fc.param");
for (int i = 0; i < nthreads; i++) rngi[i] = max_nbors;
}
@@ -596,7 +596,7 @@ void PairDPDIntel::read_restart_settings(FILE *fp)
{
int tid = omp_get_thread_num();
vslNewStream(&random_thread[tid], LMP_MKL_RNG,
- seed + comm->me + comm->nprocs * tid );
+ seed + comm->me + comm->nprocs * tid );
}
#endif
diff --git a/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp b/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp
index e3afcd64a6..05ffa2d50e 100644
--- a/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp
+++ b/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp
@@ -297,11 +297,11 @@ void PairLJCharmmCoulCharmmIntel::eval(const int offload, const int vflag,
const int sbindex = tj[jj] >> SBBITS & 3;
const flt_t rsq = trsq[jj];
const flt_t r2inv = (flt_t)1.0 / rsq;
- const flt_t r_inv = (flt_t)1.0 / sqrt(rsq);
- forcecoul = qqrd2e * qtmp * q[j] * r_inv;
- if (rsq > cut_coul_innersq) {
- const flt_t ccr = cut_coulsq - rsq;
- const flt_t switch1 = ccr * ccr * inv_denom_coul *
+ const flt_t r_inv = (flt_t)1.0 / sqrt(rsq);
+ forcecoul = qqrd2e * qtmp * q[j] * r_inv;
+ if (rsq > cut_coul_innersq) {
+ const flt_t ccr = cut_coulsq - rsq;
+ const flt_t switch1 = ccr * ccr * inv_denom_coul *
(cut_coulsq + (flt_t)2.0 * rsq - (flt_t)3.0 * cut_coul_innersq);
forcecoul *= switch1;
}
@@ -309,7 +309,7 @@ void PairLJCharmmCoulCharmmIntel::eval(const int offload, const int vflag,
#ifdef INTEL_VMASK
if (rsq < cut_ljsq) {
#endif
- const int jtype = tjtype[jj];
+ const int jtype = tjtype[jj];
flt_t r6inv = r2inv * r2inv * r2inv;
forcelj = r6inv * (lji[jtype].x * r6inv - lji[jtype].y);
if (EFLAG) evdwl = r6inv*(lji[jtype].z * r6inv - lji[jtype].w);
@@ -348,12 +348,12 @@ void PairLJCharmmCoulCharmmIntel::eval(const int offload, const int vflag,
#else
if (rsq > cut_ljsq) { forcelj = (flt_t)0.0; evdwl = (flt_t)0.0; }
#endif
- if (sbindex) {
- const flt_t factor_coul = special_coul[sbindex];
- forcecoul *= factor_coul;
- const flt_t factor_lj = special_lj[sbindex];
- forcelj *= factor_lj;
- if (EFLAG) evdwl *= factor_lj;
+ if (sbindex) {
+ const flt_t factor_coul = special_coul[sbindex];
+ forcecoul *= factor_coul;
+ const flt_t factor_lj = special_lj[sbindex];
+ forcelj *= factor_lj;
+ if (EFLAG) evdwl *= factor_lj;
}
const flt_t fpair = (forcecoul + forcelj) * r2inv;
diff --git a/src/USER-INTEL/pair_sw_intel.cpp b/src/USER-INTEL/pair_sw_intel.cpp
index fff104f39b..2c28fcfd94 100644
--- a/src/USER-INTEL/pair_sw_intel.cpp
+++ b/src/USER-INTEL/pair_sw_intel.cpp
@@ -346,10 +346,10 @@ void PairSWIntel::eval(const int offload, const int vflag,
}
}
- int ejrem = ejnum & (pad_width - 1);
- if (ejrem) ejrem = pad_width - ejrem;
- const int ejnum_pad = ejnum + ejrem;
- for (int jj = ejnum; jj < ejnum_pad; jj++) {
+ int ejrem = ejnum & (pad_width - 1);
+ if (ejrem) ejrem = pad_width - ejrem;
+ const int ejnum_pad = ejnum + ejrem;
+ for (int jj = ejnum; jj < ejnum_pad; jj++) {
tdelx[jj] = (flt_t)0.0;
tdely[jj] = (flt_t)0.0;
tdelz[jj] = (flt_t)0.0;
diff --git a/src/USER-INTEL/pppm_disp_intel.cpp b/src/USER-INTEL/pppm_disp_intel.cpp
index bd41f8b531..52e418c713 100644
--- a/src/USER-INTEL/pppm_disp_intel.cpp
+++ b/src/USER-INTEL/pppm_disp_intel.cpp
@@ -1500,8 +1500,8 @@ void PPPMDispIntel::fieldforce_c_ik(IntelBuffers<flt_t,acc_t> *buffers)
for (int l = 0; l < order; l++) {
ekx += ekx_arr[l];
- eky += eky_arr[l];
- ekz += ekz_arr[l];
+ eky += eky_arr[l];
+ ekz += ekz_arr[l];
}
// convert E-field to force
@@ -1848,8 +1848,8 @@ void PPPMDispIntel::fieldforce_g_ik(IntelBuffers<flt_t,acc_t> *buffers)
for (int l = 0; l < order; l++) {
ekx += ekx_arr[l];
- eky += eky_arr[l];
- ekz += ekz_arr[l];
+ eky += eky_arr[l];
+ ekz += ekz_arr[l];
}
// convert E-field to force
@@ -2232,27 +2232,27 @@ void PPPMDispIntel::fieldforce_a_ik(IntelBuffers<flt_t,acc_t> *buffers)
ekx6 = eky6 = ekz6 = ZEROF;
for (int l = 0; l < order; l++) {
- ekx0 += ekx0_arr[l];
- eky0 += eky0_arr[l];
- ekz0 += ekz0_arr[l];
- ekx1 += ekx1_arr[l];
- eky1 += eky1_arr[l];
- ekz1 += ekz1_arr[l];
- ekx2 += ekx2_arr[l];
- eky2 += eky2_arr[l];
- ekz2 += ekz2_arr[l];
- ekx3 += ekx3_arr[l];
- eky3 += eky3_arr[l];
- ekz3 += ekz3_arr[l];
- ekx4 += ekx4_arr[l];
- eky4 += eky4_arr[l];
- ekz4 += ekz4_arr[l];
- ekx5 += ekx5_arr[l];
- eky5 += eky5_arr[l];
- ekz5 += ekz5_arr[l];
- ekx6 += ekx6_arr[l];
- eky6 += eky6_arr[l];
- ekz6 += ekz6_arr[l];
+ ekx0 += ekx0_arr[l];
+ eky0 += eky0_arr[l];
+ ekz0 += ekz0_arr[l];
+ ekx1 += ekx1_arr[l];
+ eky1 += eky1_arr[l];
+ ekz1 += ekz1_arr[l];
+ ekx2 += ekx2_arr[l];
+ eky2 += eky2_arr[l];
+ ekz2 += ekz2_arr[l];
+ ekx3 += ekx3_arr[l];
+ eky3 += eky3_arr[l];
+ ekz3 += ekz3_arr[l];
+ ekx4 += ekx4_arr[l];
+ eky4 += eky4_arr[l];
+ ekz4 += ekz4_arr[l];
+ ekx5 += ekx5_arr[l];
+ eky5 += eky5_arr[l];
+ ekz5 += ekz5_arr[l];
+ ekx6 += ekx6_arr[l];
+ eky6 += eky6_arr[l];
+ ekz6 += ekz6_arr[l];
}
// convert D-field to force
@@ -2729,11 +2729,11 @@ void PPPMDispIntel::fieldforce_none_ik(IntelBuffers<flt_t,acc_t> *buffers)
}
for (int l = 0; l < order; l++) {
- for (int k = 0; k < nsplit; k++) {
- ekx[k] += ekx_arr[k*INTEL_P3M_ALIGNED_MAXORDER + l];
- eky[k] += eky_arr[k*INTEL_P3M_ALIGNED_MAXORDER + l];
- ekz[k] += ekz_arr[k*INTEL_P3M_ALIGNED_MAXORDER + l];
- }
+ for (int k = 0; k < nsplit; k++) {
+ ekx[k] += ekx_arr[k*INTEL_P3M_ALIGNED_MAXORDER + l];
+ eky[k] += eky_arr[k*INTEL_P3M_ALIGNED_MAXORDER + l];
+ ekz[k] += ekz_arr[k*INTEL_P3M_ALIGNED_MAXORDER + l];
+ }
}
// convert E-field to force
diff --git a/src/USER-INTEL/pppm_intel.cpp b/src/USER-INTEL/pppm_intel.cpp
index 30f8f4c5c0..e187216b62 100644
--- a/src/USER-INTEL/pppm_intel.cpp
+++ b/src/USER-INTEL/pppm_intel.cpp
@@ -626,7 +626,7 @@ void PPPMIntel::fieldforce_ik(IntelBuffers<flt_t,acc_t> *buffers)
#pragma simd
#endif
for (int k = 0; k < INTEL_P3M_ALIGNED_MAXORDER; k++) {
- rho0[k] = rho_lookup[idx][k];
+ rho0[k] = rho_lookup[idx][k];
rho1[k] = rho_lookup[idy][k];
rho2[k] = rho_lookup[idz][k];
}
@@ -643,7 +643,7 @@ void PPPMIntel::fieldforce_ik(IntelBuffers<flt_t,acc_t> *buffers)
r2 = rho_coeff[l][k] + r2*dy;
r3 = rho_coeff[l][k] + r3*dz;
}
- rho0[k-nlower] = r1;
+ rho0[k-nlower] = r1;
rho1[k-nlower] = r2;
rho2[k-nlower] = r3;
}
@@ -673,9 +673,9 @@ void PPPMIntel::fieldforce_ik(IntelBuffers<flt_t,acc_t> *buffers)
for (int l = 0; l < INTEL_P3M_ALIGNED_MAXORDER; l++) {
int mx = l+nxsum;
FFT_SCALAR x0 = y0*rho0[l];
- ekx_arr[l] -= x0*vdx_brick[mz][my][mx];
- eky_arr[l] -= x0*vdy_brick[mz][my][mx];
- ekz_arr[l] -= x0*vdz_brick[mz][my][mx];
+ ekx_arr[l] -= x0*vdx_brick[mz][my][mx];
+ eky_arr[l] -= x0*vdy_brick[mz][my][mx];
+ ekz_arr[l] -= x0*vdz_brick[mz][my][mx];
}
}
}
@@ -684,9 +684,9 @@ void PPPMIntel::fieldforce_ik(IntelBuffers<flt_t,acc_t> *buffers)
ekx = eky = ekz = ZEROF;
for (int l = 0; l < order; l++) {
- ekx += ekx_arr[l];
- eky += eky_arr[l];
- ekz += ekz_arr[l];
+ ekx += ekx_arr[l];
+ eky += eky_arr[l];
+ ekz += ekz_arr[l];
}
// convert E-field to force
@@ -1004,22 +1004,22 @@ void PPPMIntel::allocate()
PPPM::allocate();
memory->destroy3d_offset(density_brick,nzlo_out,nylo_out,nxlo_out);
create3d_offset(density_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
- nxlo_out,nxhi_out,"pppm:density_brick");
+ nxlo_out,nxhi_out,"pppm:density_brick");
if (differentiation_flag == 1) {
memory->destroy3d_offset(u_brick,nzlo_out,nylo_out,nxlo_out);
create3d_offset(u_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
- nxlo_out,nxhi_out,"pppm:u_brick");
+ nxlo_out,nxhi_out,"pppm:u_brick");
} else {
memory->destroy3d_offset(vdx_brick,nzlo_out,nylo_out,nxlo_out);
memory->destroy3d_offset(vdy_brick,nzlo_out,nylo_out,nxlo_out);
memory->destroy3d_offset(vdz_brick,nzlo_out,nylo_out,nxlo_out);
create3d_offset(vdx_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
- nxlo_out,nxhi_out,"pppm:vdx_brick");
+ nxlo_out,nxhi_out,"pppm:vdx_brick");
create3d_offset(vdy_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
- nxlo_out,nxhi_out,"pppm:vdy_brick");
+ nxlo_out,nxhi_out,"pppm:vdy_brick");
create3d_offset(vdz_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
- nxlo_out,nxhi_out,"pppm:vdz_brick");
+ nxlo_out,nxhi_out,"pppm:vdz_brick");
}
}
@@ -1028,9 +1028,9 @@ void PPPMIntel::allocate()
------------------------------------------------------------------------- */
FFT_SCALAR *** PPPMIntel::create3d_offset(FFT_SCALAR ***&array, int n1lo,
- int n1hi, int n2lo, int n2hi,
- int n3lo, int n3hi,
- const char *name)
+ int n1hi, int n2lo, int n2hi,
+ int n3lo, int n3hi,
+ const char *name)
{
int n1 = n1hi - n1lo + 1;
int n2 = n2hi - n2lo + 1;
diff --git a/src/USER-INTEL/pppm_intel.h b/src/USER-INTEL/pppm_intel.h
index 2a57372558..87f0bc9de8 100644
--- a/src/USER-INTEL/pppm_intel.h
+++ b/src/USER-INTEL/pppm_intel.h
@@ -105,7 +105,7 @@ class PPPMIntel : public PPPM {
}
}
FFT_SCALAR ***create3d_offset(FFT_SCALAR ***&, int, int, int,
- int, int, int, const char *name);
+ int, int, int, const char *name);
};
}
diff --git a/src/USER-LB/fix_lb_fluid.cpp b/src/USER-LB/fix_lb_fluid.cpp
index d6c3e23ab4..638901d6b3 100644
--- a/src/USER-LB/fix_lb_fluid.cpp
+++ b/src/USER-LB/fix_lb_fluid.cpp
@@ -48,7 +48,7 @@ FixLbFluid::FixLbFluid(LAMMPS *lmp, int narg, char **arg) :
// fix # group lb/fluid nevery typeLB viscosity densityinit_real
//
// where: nevery: call this fix every nevery timesteps.
- // (keep this set to 1 for now).
+ // (keep this set to 1 for now).
// typeLB: there are two different integrators
// in the code labeled "1" and "2".
// viscosity: the viscosity of the fluid.
@@ -124,37 +124,37 @@ FixLbFluid::FixLbFluid(LAMMPS *lmp, int narg, char **arg) :
while (iarg < narg){
if(strcmp(arg[iarg],"setArea")==0){
if(setGamma == 1)
- error->all(FLERR,"Illegal fix lb/fluid command: cannot use a combination of default and user-specified gamma values");
+ error->all(FLERR,"Illegal fix lb/fluid command: cannot use a combination of default and user-specified gamma values");
setArea = 1;
int itype = atoi(arg[iarg+1]);
double areafactor = atof(arg[iarg+2]);
if(itype <= 0 || itype > atom->ntypes || areafactor < 0.0)
- error->all(FLERR,"Illegal fix lb/fluid command: setArea");
+ error->all(FLERR,"Illegal fix lb/fluid command: setArea");
if(NodeArea == NULL){
- NodeArea = new double[atom->ntypes+1];
- for(int i=0; i<=atom->ntypes; i++) NodeArea[i] = -1.0;
+ NodeArea = new double[atom->ntypes+1];
+ for(int i=0; i<=atom->ntypes; i++) NodeArea[i] = -1.0;
}
NodeArea[itype] = areafactor;
iarg += 3;
}
else if(strcmp(arg[iarg],"setGamma")==0){
if(setArea == 1)
- error->all(FLERR,"Illegal fix lb/fluid command: cannot use a combination of default and user-specified gamma values");
+ error->all(FLERR,"Illegal fix lb/fluid command: cannot use a combination of default and user-specified gamma values");
setGamma = 1;
double Gammaone;
Gammaone = atof(arg[iarg+1]);
if(Gamma == NULL)
- Gamma = new double[atom->ntypes+1];
+ Gamma = new double[atom->ntypes+1];
for(int i=0; i<=atom->ntypes; i++) Gamma[i] = Gammaone;
iarg += 2;
}
else if(strcmp(arg[iarg],"scaleGamma")==0){
if(setGamma == 0)
- error->all(FLERR,"Illegal fix lb/fluid command: must set a value for Gamma before scaling it");
+ error->all(FLERR,"Illegal fix lb/fluid command: must set a value for Gamma before scaling it");
int itype = atoi(arg[iarg+1]);
double scalefactor = atof(arg[iarg+2]);
if(itype <= 0 || itype > atom->ntypes || scalefactor < 0.0)
- error->all(FLERR,"Illegal fix lb/fluid command: scaleGamma");
+ error->all(FLERR,"Illegal fix lb/fluid command: scaleGamma");
Gamma[itype] *= scalefactor;
iarg += 3;
}
@@ -295,7 +295,7 @@ a z wall velocity without implementing fixed BCs in z");
if(setGamma == 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");
+ 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");
}
NodeArea = new double[atom->ntypes+1];
for(int i=0; i<=atom->ntypes; i++) NodeArea[i] = -1.0;
@@ -637,10 +637,10 @@ void FixLbFluid::init(void)
int *mask = atom->mask;
int nlocal = atom->nlocal;
for(j=0; j<nlocal; j++){
- if((mask[j] & groupbit) && (mask[j] & groupbit_viscouslb) && (mask[j] & groupbit_pc))
- error->one(FLERR,"should not use the lb/viscous command when integrating with the lb/pc fix");
- if((mask[j] & groupbit) && (mask[j] & groupbit_viscouslb) && (mask[j] & groupbit_rigid_pc_sphere))
- error->one(FLERR,"should not use the lb/viscous command when integrating with the lb/rigid/pc/sphere fix");
+ if((mask[j] & groupbit) && (mask[j] & groupbit_viscouslb) && (mask[j] & groupbit_pc))
+ error->one(FLERR,"should not use the lb/viscous command when integrating with the lb/pc fix");
+ if((mask[j] & groupbit) && (mask[j] & groupbit_viscouslb) && (mask[j] & groupbit_rigid_pc_sphere))
+ error->one(FLERR,"should not use the lb/viscous command when integrating with the lb/rigid/pc/sphere fix");
}
}
@@ -817,15 +817,15 @@ void FixLbFluid::calc_fluidforce(void)
for(i=0; i<nlocal; i++){
if(mask[i] & group->bitmask[igroupforce]){
- domain->unmap(x[i],image[i],unwrap);
+ domain->unmap(x[i],image[i],unwrap);
- if(rmass) massone = rmass[i];
- else massone = mass[type[i]];
+ 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;
- sum[3] += massone;
+ sum[0] += unwrap[0]*massone;
+ sum[1] += unwrap[1]*massone;
+ sum[2] += unwrap[2]*massone;
+ sum[3] += massone;
}
}
MPI_Allreduce(&sum[0],&xcm[0],4,MPI_DOUBLE,MPI_SUM,world);
@@ -840,26 +840,26 @@ void FixLbFluid::calc_fluidforce(void)
for(i=0; i<nlocal; i++){
if(mask[i] & groupbit){
if(trilinear_stencil==1) {
- trilinear_interpolation(i);
+ trilinear_interpolation(i);
}else{
- peskin_interpolation(i);
+ 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];
- }
+ 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];
+ }
}
}
}
@@ -885,11 +885,11 @@ void FixLbFluid::calc_fluidforce(void)
for(j=0; j<subNby+3; j++){
for(k=0; k<subNbz+3; k++){
for(m=0; m<3; m++){
- Ff[subNbx-2][j][k][m] += Fftempx[0][j][k][m];
- Ff[subNbx-3][j][k][m] += Fftempx[1][j][k][m];
- Ff[1][j][k][m] += Fftempx[2][j][k][m];
- Ff[2][j][k][m] += Fftempx[3][j][k][m];
- Ff[3][j][k][m] += Fftempx[4][j][k][m];
+ Ff[subNbx-2][j][k][m] += Fftempx[0][j][k][m];
+ Ff[subNbx-3][j][k][m] += Fftempx[1][j][k][m];
+ Ff[1][j][k][m] += Fftempx[2][j][k][m];
+ Ff[2][j][k][m] += Fftempx[3][j][k][m];
+ Ff[3][j][k][m] += Fftempx[4][j][k][m];
}
}
}
@@ -911,11 +911,11 @@ void FixLbFluid::calc_fluidforce(void)
for(i=0; i<subNbx+3; i++){
for(k=0; k<subNbz+3; k++){
for(m=0; m<3; m++){
- Ff[i][subNby-2][k][m] += Fftempy[i][0][k][m];
- Ff[i][subNby-3][k][m] += Fftempy[i][1][k][m];
- Ff[i][1][k][m] += Fftempy[i][2][k][m];
- Ff[i][2][k][m] += Fftempy[i][3][k][m];
- Ff[i][3][k][m] += Fftempy[i][4][k][m];
+ Ff[i][subNby-2][k][m] += Fftempy[i][0][k][m];
+ Ff[i][subNby-3][k][m] += Fftempy[i][1][k][m];
+ Ff[i][1][k][m] += Fftempy[i][2][k][m];
+ Ff[i][2][k][m] += Fftempy[i][3][k][m];
+ Ff[i][3][k][m] += Fftempy[i][4][k][m];
}
}
}
@@ -937,11 +937,11 @@ void FixLbFluid::calc_fluidforce(void)
for(i=0; i<subNbx+3; i++){
for(j=0; j<subNby+3; j++){
for(m=0; m<3; m++){
- Ff[i][j][subNbz-2][m] += Fftempz[i][j][0][m];
- Ff[i][j][subNbz-3][m] += Fftempz[i][j][1][m];
- Ff[i][j][1][m] += Fftempz[i][j][2][m];
- Ff[i][j][2][m] += Fftempz[i][j][3][m];
- Ff[i][j][3][m] += Fftempz[i][j][4][m];
+ Ff[i][j][subNbz-2][m] += Fftempz[i][j][0][m];
+ Ff[i][j][subNbz-3][m] += Fftempz[i][j][1][m];
+ Ff[i][j][1][m] += Fftempz[i][j][2][m];
+ Ff[i][j][2][m] += Fftempz[i][j][3][m];
+ Ff[i][j][3][m] += Fftempz[i][j][4][m];
}
}
}
@@ -955,7 +955,7 @@ void FixLbFluid::calc_fluidforce(void)
if(me==0){
printf("%E %E %E %E %E %E\n",force[0],force[1],force[2],
- torque[0],torque[1],torque[2]);
+ torque[0],torque[1],torque[2]);
}
}
@@ -1022,63 +1022,63 @@ void FixLbFluid::peskin_interpolation(int i)
else{
r=sqrt(rsq);
if(rsq>1){
- weightx=(5.0-2.0*r-sqrt(-7.0+12.0*r-4.0*rsq))/8.;
+ weightx=(5.0-2.0*r-sqrt(-7.0+12.0*r-4.0*rsq))/8.;
} else{
- weightx=(3.0-2.0*r+sqrt(1.0+4.0*r-4.0*rsq))/8.;
+ weightx=(3.0-2.0*r+sqrt(1.0+4.0*r-4.0*rsq))/8.;
}
}
for(jj=-1; jj<3; jj++){
rsq=(-dy1+jj)*(-dy1+jj);
if(rsq>=4)
- weighty=0.0;
+ weighty=0.0;
else{
- r=sqrt(rsq);
- if(rsq>1){
- weighty=(5.0-2.0*r-sqrt(-7.0+12.0*r-4.0*rsq))/8.;
- } else{
- weighty=(3.0-2.0*r+sqrt(1.0+4.0*r-4.0*rsq))/8.;
- }
+ r=sqrt(rsq);
+ if(rsq>1){
+ weighty=(5.0-2.0*r-sqrt(-7.0+12.0*r-4.0*rsq))/8.;
+ } else{
+ weighty=(3.0-2.0*r+sqrt(1.0+4.0*r-4.0*rsq))/8.;
+ }
}
for(kk=-1; kk<3; kk++){
- rsq=(-dz1+kk)*(-dz1+kk);
- if(rsq>=4)
- weightz=0.0;
- else{
- r=sqrt(rsq);
- if(rsq>1){
- weightz=(5.0-2.0*r-sqrt(-7.0+12.0*r-4.0*rsq))/8.;
- } else{
- weightz=(3.0-2.0*r+sqrt(1.0+4.0*r-4.0*rsq))/8.;
- }
- }
- ixp = ix+ii;
- iyp = iy+jj;
- izp = iz+kk;
-
- //The atom is allowed to be within one lattice grid point outside the
- //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 \
+ rsq=(-dz1+kk)*(-dz1+kk);
+ if(rsq>=4)
+ weightz=0.0;
+ else{
+ r=sqrt(rsq);
+ if(rsq>1){
+ weightz=(5.0-2.0*r-sqrt(-7.0+12.0*r-4.0*rsq))/8.;
+ } else{
+ weightz=(3.0-2.0*r+sqrt(1.0+4.0*r-4.0*rsq))/8.;
+ }
+ }
+ ixp = ix+ii;
+ iyp = iy+jj;
+ izp = iz+kk;
+
+ //The atom is allowed to be within one lattice grid point outside the
+ //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");
- if(domain->periodicity[2] == 0 && comm->myloc[2] == 0 && 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) ))
- error->warning(FLERR,"Atom too close to upper z wall. Unphysical results may occur");
+ if(domain->periodicity[2] == 0 && comm->myloc[2] == 0 && 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) ))
+ 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;
+ 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++){
- unode[k] += u_lb[ixp][iyp][izp][k]*FfP[isten];
- }
- if(setGamma==0)
- mnode += density_lb[ixp][iyp][izp]*FfP[isten];
+ FfP[isten] = weightx*weighty*weightz;
+ // interpolated velocity based on delta function.
+ for(k=0; k<3; k++){
+ unode[k] += u_lb[ixp][iyp][izp][k]*FfP[isten];
+ }
+ if(setGamma==0)
+ mnode += density_lb[ixp][iyp][izp]*FfP[isten];
- isten++;
+ isten++;
}
}
}
@@ -1099,20 +1099,20 @@ require more frequent neighborlist rebuilds");
for(ii=-1; ii<3; ii++)
for(jj=-1; jj<3; jj++)
for(kk=-1; kk<3; kk++){
- 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;
- // Compute the force on the fluid. Need to convert the velocity from
- // LAMMPS units to LB units.
- for(k=0; k<3; k++){
- Ff[ixp][iyp][izp][k] += gammavalue*((v[i][k]*dt_lb/dx_lb)-unode[k])*FfP[isten];
- }
-
- isten++;
+ 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;
+ // Compute the force on the fluid. Need to convert the velocity from
+ // LAMMPS units to LB units.
+ 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++)
hydroF[i][k] = -1.0*gammavalue*((v[i][k]*dt_lb/dx_lb)-unode[k])*dm_lb*dx_lb/dt_lb/dt_lb;
@@ -1191,7 +1191,7 @@ require more frequent neighborlist rebuilds");
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
+ 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]
+ u_lb[ix][iyp][iz][k]*FfP[2]
@@ -1397,7 +1397,7 @@ satisfy the Courant condition.\n");
Dcoeff=(1.0-(1.0-expminusdtovertau)*tau);
namp = 2.0*kB*T/3.;
noisefactor=sqrt((1.0-expminusdtovertau*expminusdtovertau)/
- (2.0))/(1.0-expminusdtovertau);
+ (2.0))/(1.0-expminusdtovertau);
K_0 = 4.5*(1.0/3.0-a_0);
dtoverdtcollision = dt_lb*3.0*viscosity/densityinit_real/dx_lb/dx_lb;
}
@@ -1558,16 +1558,16 @@ void FixLbFluid::initializeLB15(void)
for(i=0; i<subNbx+3; i++)
for(j=0; j<subNby+3; j++)
for(k=0; k<subNbz+3; k++){
- u_lb[i][j][k][0]=0.0;
- u_lb[i][j][k][1]=0.0;
- u_lb[i][j][k][2]=0.0;
- density_lb[i][j][k] = densityinit;
+ u_lb[i][j][k][0]=0.0;
+ u_lb[i][j][k][1]=0.0;
+ u_lb[i][j][k][2]=0.0;
+ density_lb[i][j][k] = densityinit;
}
for(i=0; i<subNbx; i++)
for(j=0; j<subNby; j++)
for(k=0; k<subNbz; k++)
- for(m=0; m<15; m++)
- f_lb[i][j][k][m] = density_lb[i][j][k]/15.0;
+ for(m=0; m<15; m++)
+ f_lb[i][j][k][m] = density_lb[i][j][k]/15.0;
}
@@ -1795,16 +1795,16 @@ void FixLbFluid::initializeLB19(void)
for(i=0; i<subNbx+3; i++)
for(j=0; j<subNby+3; j++)
for(k=0; k<subNbz+3; k++){
- u_lb[i][j][k][0]=0.0;
- u_lb[i][j][k][1]=0.0;
- u_lb[i][j][k][2]=0.0;
- density_lb[i][j][k] = densityinit;
+ u_lb[i][j][k][0]=0.0;
+ u_lb[i][j][k][1]=0.0;
+ u_lb[i][j][k][2]=0.0;
+ density_lb[i][j][k] = densityinit;
}
for(i=0; i<subNbx; i++)
for(j=0; j<subNby; j++)
for(k=0; k<subNbz; k++)
- for(m=0; m<19; m++)
- f_lb[i][j][k][m] = density_lb[i][j][k]/19.0;
+ for(m=0; m<19; m++)
+ f_lb[i][j][k][m] = density_lb[i][j][k]/19.0;
}
@@ -1881,12 +1881,12 @@ void FixLbFluid::initialize_feq(void)
//Save feqold.
if(typeLB == 2){
for(i=0; i<subNbx; i++)
- for(j=0; j<subNby; j++)
- for(k=0; k<subNbz; k++)
- for(p=0; p<numvel; p++){
- feqold[i][j][k][p] = feq[i][j][k][p];
- feqoldn[i][j][k][p] = feqn[i][j][k][p];
- }
+ for(j=0; j<subNby; j++)
+ for(k=0; k<subNbz; k++)
+ for(p=0; p<numvel; p++){
+ feqold[i][j][k][p] = feq[i][j][k][p];
+ feqoldn[i][j][k][p] = feqn[i][j][k][p];
+ }
}
}else{
step = 1;
@@ -1895,7 +1895,7 @@ void FixLbFluid::initialize_feq(void)
if(typeLB == 2){
for(i=0; i<8; i++)
- requests[i]=MPI_REQUEST_NULL;
+ requests[i]=MPI_REQUEST_NULL;
MPI_Isend(&feqold[1][1][1][0],1,passxf,comm->procneigh[0][0],15,world,&requests[0]);
MPI_Irecv(&feqold[0][1][1][0],1,passxf,comm->procneigh[0][0],25,world,&requests[1]);
MPI_Isend(&feqold[subNbx-2][1][1][0],1,passxf,comm->procneigh[0][1],25,world,&requests[2]);
@@ -1907,7 +1907,7 @@ void FixLbFluid::initialize_feq(void)
MPI_Waitall(8,requests,MPI_STATUS_IGNORE);
for(i=0; i<8; i++)
- requests[i]=MPI_REQUEST_NULL;
+ 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_Isend(&feqold[0][subNby-2][1][0],1,passyf,comm->procneigh[1][1],25,world,&requests[2]);
@@ -1919,7 +1919,7 @@ void FixLbFluid::initialize_feq(void)
MPI_Waitall(8,requests,MPI_STATUS_IGNORE);
for(i=0; i<8; i++)
- requests[i]=MPI_REQUEST_NULL;
+ 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]);
@@ -1963,151 +1963,151 @@ void FixLbFluid::equilibriumdist15(int xstart, int xend, int ystart, int yend, i
jup=j+1;
jdwn=j-1;
for (k=zstart; k<zend; k++) {
- kup=k+1;
- kdwn=k-1;
-
- rho=density_lb[i][j][k];
- total_density += rho;
-
- // 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] +
- 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] +
- 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] +
- 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] -
- density_lb[i][j][k+2])/2.0;
- 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] -
- density_lb[i][j][k-2])/2.0;
- 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;
-
- p0 = rho*a_0-kappa_lb*rho*(drhoxx + drhoyy + drhozz);
+ kup=k+1;
+ kdwn=k-1;
+
+ rho=density_lb[i][j][k];
+ total_density += rho;
+
+ // 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] +
+ 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] +
+ 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] +
+ 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] -
+ density_lb[i][j][k+2])/2.0;
+ 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] -
+ density_lb[i][j][k-2])/2.0;
+ 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;
+
+ p0 = rho*a_0-kappa_lb*rho*(drhoxx + drhoyy + drhozz);
// kappa_lb is the square gradient coeff in the pressure tensor
- dPdrho = a_0; //assuming here that kappa_lb = 0.
-
-
- if(typeLB==1){
- Pxx = p0 + kappa_lb*(drhox*drhox - 0.5*grs)+(tau-0.5)*(1.0/3.0-dPdrho)*
- (3.0*u_lb[i][j][k][0]*drhox+u_lb[i][j][k][1]*drhoy+u_lb[i][j][k][2]*drhoz);
- Pyy = p0 + kappa_lb*(drhoy*drhoy - 0.5*grs)+(tau-0.5)*(1.0/3.0-dPdrho)*
- (u_lb[i][j][k][0]*drhox+3.0*u_lb[i][j][k][1]*drhoy+u_lb[i][j][k][2]*drhoz);
- Pzz = p0 + kappa_lb*(drhoz*drhoz - 0.5*grs)+(tau-0.5)*(1.0/3.0-dPdrho)*
- (u_lb[i][j][k][0]*drhox+u_lb[i][j][k][1]*drhoy+3.0*u_lb[i][j][k][2]*drhoz);
- Pxy = kappa_lb*drhox*drhoy+(tau-0.5)*(1.0/3.0-dPdrho)*
- (u_lb[i][j][k][0]*drhoy+u_lb[i][j][k][1]*drhox);
- Pxz = kappa_lb*drhox*drhoz+(tau-0.5)*(1.0/3.0-dPdrho)*
- (u_lb[i][j][k][0]*drhoz+u_lb[i][j][k][2]*drhox);
- Pyz = kappa_lb*drhoy*drhoz+(tau-0.5)*(1.0/3.0-dPdrho)*
- (u_lb[i][j][k][1]*drhoz+u_lb[i][j][k][2]*drhoy);
- }else if(typeLB==2){
- Pxx = p0 + kappa_lb*(drhox*drhox - 0.5*grs)+tau*(1.0/3.0-dPdrho)*
- (3.0*u_lb[i][j][k][0]*drhox+u_lb[i][j][k][1]*drhoy+u_lb[i][j][k][2]*drhoz);
- Pyy = p0 + kappa_lb*(drhoy*drhoy - 0.5*grs)+tau*(1.0/3.0-dPdrho)*
- (u_lb[i][j][k][0]*drhox+3.0*u_lb[i][j][k][1]*drhoy+u_lb[i][j][k][2]*drhoz);
- Pzz = p0 + kappa_lb*(drhoz*drhoz - 0.5*grs)+tau*(1.0/3.0-dPdrho)*
- (u_lb[i][j][k][0]*drhox+u_lb[i][j][k][1]*drhoy+3.0*u_lb[i][j][k][2]*drhoz);
- Pxy = kappa_lb*drhox*drhoy+tau*(1.0/3.0-dPdrho)*
- (u_lb[i][j][k][0]*drhoy+u_lb[i][j][k][1]*drhox);
- Pxz = kappa_lb*drhox*drhoz+tau*(1.0/3.0-dPdrho)*
- (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];
- Fz_w = Ff[i][j][k][2];
-
- etacov[0] = rho;
- etacov[1] = rho*u_lb[i][j][k][0] + Fx_w*tau + rho*bodyforcex*tau;
- 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. +
- 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. +
- 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. +
- 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] +
- 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] +
- 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] +
- 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[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++)
- feq[i][j][k][l] += w_lb[l]*mg_lb[ii][l]*etacov[ii]*Ng_lb[ii];
-
- if(typeLB == 2){
- feqn[i][j][k][l] = feq[i][j][k][l];
- }
- }
-
- if(noisestress==1){
- std = sqrt(namp*rho);
-
- for(jj=0; jj<3; jj++)
- S[0][jj] = std*random->gaussian();
- for(jj=0; jj<3; jj++)
- 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)+
- sqrt((8.0-12.0*a_0)/(3.0-3.0*a_0))*S[0][1]);
- etacov[6] = ((1.0-3.0*a_0)*S[0][0]/sqrt(3.0-3.0*a_0)+
- (2.0-6.0*a_0)*S[0][1]/sqrt((8.0-12.0*a_0)*(3.0-3.0*a_0))+
- sqrt((5.0-9.0*a_0)/(2.0-3.0*a_0))*S[0][2]);
- etacov[7] = S[1][0];
- etacov[8] = S[1][1];
- etacov[9] = S[1][2];
-
- for (l=10; l<15; l++) {
- etacov[l] = sqrt(9.0*namp*rho/Ng_lb[l])*random->gaussian();
- }
- etacov[14] += -K_0*(etacov[4]+etacov[5]+etacov[6]); //correction from noise to TrP
-
- 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[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;
- }
- }
+ dPdrho = a_0; //assuming here that kappa_lb = 0.
+
+
+ if(typeLB==1){
+ Pxx = p0 + kappa_lb*(drhox*drhox - 0.5*grs)+(tau-0.5)*(1.0/3.0-dPdrho)*
+ (3.0*u_lb[i][j][k][0]*drhox+u_lb[i][j][k][1]*drhoy+u_lb[i][j][k][2]*drhoz);
+ Pyy = p0 + kappa_lb*(drhoy*drhoy - 0.5*grs)+(tau-0.5)*(1.0/3.0-dPdrho)*
+ (u_lb[i][j][k][0]*drhox+3.0*u_lb[i][j][k][1]*drhoy+u_lb[i][j][k][2]*drhoz);
+ Pzz = p0 + kappa_lb*(drhoz*drhoz - 0.5*grs)+(tau-0.5)*(1.0/3.0-dPdrho)*
+ (u_lb[i][j][k][0]*drhox+u_lb[i][j][k][1]*drhoy+3.0*u_lb[i][j][k][2]*drhoz);
+ Pxy = kappa_lb*drhox*drhoy+(tau-0.5)*(1.0/3.0-dPdrho)*
+ (u_lb[i][j][k][0]*drhoy+u_lb[i][j][k][1]*drhox);
+ Pxz = kappa_lb*drhox*drhoz+(tau-0.5)*(1.0/3.0-dPdrho)*
+ (u_lb[i][j][k][0]*drhoz+u_lb[i][j][k][2]*drhox);
+ Pyz = kappa_lb*drhoy*drhoz+(tau-0.5)*(1.0/3.0-dPdrho)*
+ (u_lb[i][j][k][1]*drhoz+u_lb[i][j][k][2]*drhoy);
+ }else if(typeLB==2){
+ Pxx = p0 + kappa_lb*(drhox*drhox - 0.5*grs)+tau*(1.0/3.0-dPdrho)*
+ (3.0*u_lb[i][j][k][0]*drhox+u_lb[i][j][k][1]*drhoy+u_lb[i][j][k][2]*drhoz);
+ Pyy = p0 + kappa_lb*(drhoy*drhoy - 0.5*grs)+tau*(1.0/3.0-dPdrho)*
+ (u_lb[i][j][k][0]*drhox+3.0*u_lb[i][j][k][1]*drhoy+u_lb[i][j][k][2]*drhoz);
+ Pzz = p0 + kappa_lb*(drhoz*drhoz - 0.5*grs)+tau*(1.0/3.0-dPdrho)*
+ (u_lb[i][j][k][0]*drhox+u_lb[i][j][k][1]*drhoy+3.0*u_lb[i][j][k][2]*drhoz);
+ Pxy = kappa_lb*drhox*drhoy+tau*(1.0/3.0-dPdrho)*
+ (u_lb[i][j][k][0]*drhoy+u_lb[i][j][k][1]*drhox);
+ Pxz = kappa_lb*drhox*drhoz+tau*(1.0/3.0-dPdrho)*
+ (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];
+ Fz_w = Ff[i][j][k][2];
+
+ etacov[0] = rho;
+ etacov[1] = rho*u_lb[i][j][k][0] + Fx_w*tau + rho*bodyforcex*tau;
+ 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. +
+ 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. +
+ 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. +
+ 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] +
+ 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] +
+ 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] +
+ 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[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++)
+ feq[i][j][k][l] += w_lb[l]*mg_lb[ii][l]*etacov[ii]*Ng_lb[ii];
+
+ if(typeLB == 2){
+ feqn[i][j][k][l] = feq[i][j][k][l];
+ }
+ }
+
+ if(noisestress==1){
+ std = sqrt(namp*rho);
+
+ for(jj=0; jj<3; jj++)
+ S[0][jj] = std*random->gaussian();
+ for(jj=0; jj<3; jj++)
+ 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)+
+ sqrt((8.0-12.0*a_0)/(3.0-3.0*a_0))*S[0][1]);
+ etacov[6] = ((1.0-3.0*a_0)*S[0][0]/sqrt(3.0-3.0*a_0)+
+ (2.0-6.0*a_0)*S[0][1]/sqrt((8.0-12.0*a_0)*(3.0-3.0*a_0))+
+ sqrt((5.0-9.0*a_0)/(2.0-3.0*a_0))*S[0][2]);
+ etacov[7] = S[1][0];
+ etacov[8] = S[1][1];
+ etacov[9] = S[1][2];
+
+ for (l=10; l<15; l++) {
+ etacov[l] = sqrt(9.0*namp*rho/Ng_lb[l])*random->gaussian();
+ }
+ etacov[14] += -K_0*(etacov[4]+etacov[5]+etacov[6]); //correction from noise to TrP
+
+ 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[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;
+ }
+ }
}
}
}
@@ -2141,155 +2141,155 @@ void FixLbFluid::equilibriumdist19(int xstart, int xend, int ystart, int yend, i
jup=j+1;
jdwn=j-1;
for (k=zstart; k<zend; k++) {
- kup=k+1;
- kdwn=k-1;
-
- rho=density_lb[i][j][k];
- total_density += rho;
-
- // 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] +
- 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] +
- 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] +
- 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] -
- density_lb[i][j][k+2])/2.0;
- 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] -
- density_lb[i][j][k-2])/2.0;
- 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;
-
- p0 = rho*a_0-kappa_lb*rho*(drhoxx + drhoyy + drhozz);
+ kup=k+1;
+ kdwn=k-1;
+
+ rho=density_lb[i][j][k];
+ total_density += rho;
+
+ // 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] +
+ 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] +
+ 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] +
+ 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] -
+ density_lb[i][j][k+2])/2.0;
+ 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] -
+ density_lb[i][j][k-2])/2.0;
+ 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;
+
+ p0 = rho*a_0-kappa_lb*rho*(drhoxx + drhoyy + drhozz);
// kappa_lb is the square gradient coeff in the pressure tensor
- dPdrho = a_0; //assuming here that kappa_lb = 0.
-
-
- if(typeLB==1){
- Pxx = p0 + kappa_lb*(drhox*drhox - 0.5*grs)+(tau-0.5)*(1.0/3.0-dPdrho)*
- (3.0*u_lb[i][j][k][0]*drhox+u_lb[i][j][k][1]*drhoy+u_lb[i][j][k][2]*drhoz);
- Pyy = p0 + kappa_lb*(drhoy*drhoy - 0.5*grs)+(tau-0.5)*(1.0/3.0-dPdrho)*
- (u_lb[i][j][k][0]*drhox+3.0*u_lb[i][j][k][1]*drhoy+u_lb[i][j][k][2]*drhoz);
- Pzz = p0 + kappa_lb*(drhoz*drhoz - 0.5*grs)+(tau-0.5)*(1.0/3.0-dPdrho)*
- (u_lb[i][j][k][0]*drhox+u_lb[i][j][k][1]*drhoy+3.0*u_lb[i][j][k][2]*drhoz);
- Pxy = kappa_lb*drhox*drhoy+(tau-0.5)*(1.0/3.0-dPdrho)*
- (u_lb[i][j][k][0]*drhoy+u_lb[i][j][k][1]*drhox);
- Pxz = kappa_lb*drhox*drhoz+(tau-0.5)*(1.0/3.0-dPdrho)*
- (u_lb[i][j][k][0]*drhoz+u_lb[i][j][k][2]*drhox);
- Pyz = kappa_lb*drhoy*drhoz+(tau-0.5)*(1.0/3.0-dPdrho)*
- (u_lb[i][j][k][1]*drhoz+u_lb[i][j][k][2]*drhoy);
- }else if(typeLB==2){
- Pxx = p0 + kappa_lb*(drhox*drhox - 0.5*grs)+tau*(1.0/3.0-dPdrho)*
- (3.0*u_lb[i][j][k][0]*drhox+u_lb[i][j][k][1]*drhoy+u_lb[i][j][k][2]*drhoz);
- Pyy = p0 + kappa_lb*(drhoy*drhoy - 0.5*grs)+tau*(1.0/3.0-dPdrho)*
- (u_lb[i][j][k][0]*drhox+3.0*u_lb[i][j][k][1]*drhoy+u_lb[i][j][k][2]*drhoz);
- Pzz = p0 + kappa_lb*(drhoz*drhoz - 0.5*grs)+tau*(1.0/3.0-dPdrho)*
- (u_lb[i][j][k][0]*drhox+u_lb[i][j][k][1]*drhoy+3.0*u_lb[i][j][k][2]*drhoz);
- Pxy = kappa_lb*drhox*drhoy+tau*(1.0/3.0-dPdrho)*
- (u_lb[i][j][k][0]*drhoy+u_lb[i][j][k][1]*drhox);
- Pxz = kappa_lb*drhox*drhoz+tau*(1.0/3.0-dPdrho)*
- (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];
- Fz_w = Ff[i][j][k][2];
-
- etacov[0] = rho;
- etacov[1] = rho*u_lb[i][j][k][0] + Fx_w*tau + rho*bodyforcex*tau;
- 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. +
- 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. +
- 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. +
- 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] +
- 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] +
- 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] +
- 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[12] = 0.0;
- etacov[13] = 0.0;
- etacov[14] = 0.0;
- etacov[15] = 0.0;
- 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++)
- feq[i][j][k][l] += w_lb[l]*mg_lb[ii][l]*etacov[ii]*Ng_lb[ii];
-
- if(typeLB == 2){
- feqn[i][j][k][l] = feq[i][j][k][l];
- }
- }
-
- if(noisestress==1){
- std = sqrt(namp*rho);
-
- for(jj=0; jj<3; jj++)
- S[0][jj] = std*random->gaussian();
- for(jj=0; jj<3; jj++)
- 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)+
- sqrt((8.0-12.0*a_0)/(3.0-3.0*a_0))*S[0][1]);
- etacov[6] = ((1.0-3.0*a_0)*S[0][0]/sqrt(3.0-3.0*a_0)+
- (2.0-6.0*a_0)*S[0][1]/sqrt((8.0-12.0*a_0)*(3.0-3.0*a_0))+
- sqrt((5.0-9.0*a_0)/(2.0-3.0*a_0))*S[0][2]);
- etacov[7] = S[1][0];
- etacov[8] = S[1][1];
- etacov[9] = S[1][2];
-
- 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[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]
- + mg_lb[16][l]*etacov[16]*Ng_lb[16] + mg_lb[17][l]*etacov[17]*Ng_lb[17]
- + mg_lb[18][l]*etacov[18]*Ng_lb[18]);
- feq[i][j][k][l] += ghostnoise*noisefactor;
- }
- }
+ dPdrho = a_0; //assuming here that kappa_lb = 0.
+
+
+ if(typeLB==1){
+ Pxx = p0 + kappa_lb*(drhox*drhox - 0.5*grs)+(tau-0.5)*(1.0/3.0-dPdrho)*
+ (3.0*u_lb[i][j][k][0]*drhox+u_lb[i][j][k][1]*drhoy+u_lb[i][j][k][2]*drhoz);
+ Pyy = p0 + kappa_lb*(drhoy*drhoy - 0.5*grs)+(tau-0.5)*(1.0/3.0-dPdrho)*
+ (u_lb[i][j][k][0]*drhox+3.0*u_lb[i][j][k][1]*drhoy+u_lb[i][j][k][2]*drhoz);
+ Pzz = p0 + kappa_lb*(drhoz*drhoz - 0.5*grs)+(tau-0.5)*(1.0/3.0-dPdrho)*
+ (u_lb[i][j][k][0]*drhox+u_lb[i][j][k][1]*drhoy+3.0*u_lb[i][j][k][2]*drhoz);
+ Pxy = kappa_lb*drhox*drhoy+(tau-0.5)*(1.0/3.0-dPdrho)*
+ (u_lb[i][j][k][0]*drhoy+u_lb[i][j][k][1]*drhox);
+ Pxz = kappa_lb*drhox*drhoz+(tau-0.5)*(1.0/3.0-dPdrho)*
+ (u_lb[i][j][k][0]*drhoz+u_lb[i][j][k][2]*drhox);
+ Pyz = kappa_lb*drhoy*drhoz+(tau-0.5)*(1.0/3.0-dPdrho)*
+ (u_lb[i][j][k][1]*drhoz+u_lb[i][j][k][2]*drhoy);
+ }else if(typeLB==2){
+ Pxx = p0 + kappa_lb*(drhox*drhox - 0.5*grs)+tau*(1.0/3.0-dPdrho)*
+ (3.0*u_lb[i][j][k][0]*drhox+u_lb[i][j][k][1]*drhoy+u_lb[i][j][k][2]*drhoz);
+ Pyy = p0 + kappa_lb*(drhoy*drhoy - 0.5*grs)+tau*(1.0/3.0-dPdrho)*
+ (u_lb[i][j][k][0]*drhox+3.0*u_lb[i][j][k][1]*drhoy+u_lb[i][j][k][2]*drhoz);
+ Pzz = p0 + kappa_lb*(drhoz*drhoz - 0.5*grs)+tau*(1.0/3.0-dPdrho)*
+ (u_lb[i][j][k][0]*drhox+u_lb[i][j][k][1]*drhoy+3.0*u_lb[i][j][k][2]*drhoz);
+ Pxy = kappa_lb*drhox*drhoy+tau*(1.0/3.0-dPdrho)*
+ (u_lb[i][j][k][0]*drhoy+u_lb[i][j][k][1]*drhox);
+ Pxz = kappa_lb*drhox*drhoz+tau*(1.0/3.0-dPdrho)*
+ (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];
+ Fz_w = Ff[i][j][k][2];
+
+ etacov[0] = rho;
+ etacov[1] = rho*u_lb[i][j][k][0] + Fx_w*tau + rho*bodyforcex*tau;
+ 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. +
+ 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. +
+ 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. +
+ 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] +
+ 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] +
+ 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] +
+ 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[12] = 0.0;
+ etacov[13] = 0.0;
+ etacov[14] = 0.0;
+ etacov[15] = 0.0;
+ 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++)
+ feq[i][j][k][l] += w_lb[l]*mg_lb[ii][l]*etacov[ii]*Ng_lb[ii];
+
+ if(typeLB == 2){
+ feqn[i][j][k][l] = feq[i][j][k][l];
+ }
+ }
+
+ if(noisestress==1){
+ std = sqrt(namp*rho);
+
+ for(jj=0; jj<3; jj++)
+ S[0][jj] = std*random->gaussian();
+ for(jj=0; jj<3; jj++)
+ 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)+
+ sqrt((8.0-12.0*a_0)/(3.0-3.0*a_0))*S[0][1]);
+ etacov[6] = ((1.0-3.0*a_0)*S[0][0]/sqrt(3.0-3.0*a_0)+
+ (2.0-6.0*a_0)*S[0][1]/sqrt((8.0-12.0*a_0)*(3.0-3.0*a_0))+
+ sqrt((5.0-9.0*a_0)/(2.0-3.0*a_0))*S[0][2]);
+ etacov[7] = S[1][0];
+ etacov[8] = S[1][1];
+ etacov[9] = S[1][2];
+
+ 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[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]
+ + mg_lb[16][l]*etacov[16]*Ng_lb[16] + mg_lb[17][l]*etacov[17]*Ng_lb[17]
+ + mg_lb[18][l]*etacov[18]*Ng_lb[18]);
+ feq[i][j][k][l] += ghostnoise*noisefactor;
+ }
+ }
}
}
@@ -2430,38 +2430,38 @@ void FixLbFluid::parametercalc_part(int xstart, int xend, int ystart, int yend,
for(j=ystart; j<yend; j++){
for(k=zstart; k<zend; k++){
- density_lb[i][j][k]=0.0;
- u_lb[i][j][k][0]=0.0;
- 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){
- if(k==1){
- u_lb[i][j][k][2]=0.0;
- }
- }
- if(comm->myloc[2]==comm->procgrid[2]-1){
- if(k==subNbz-2){
- 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];
+ density_lb[i][j][k]=0.0;
+ u_lb[i][j][k][0]=0.0;
+ 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){
+ if(k==1){
+ u_lb[i][j][k][2]=0.0;
+ }
+ }
+ if(comm->myloc[2]==comm->procgrid[2]-1){
+ if(k==subNbz-2){
+ 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];
}
}
}
@@ -2481,37 +2481,37 @@ void FixLbFluid::update_periodic(int xstart, int xend, int ystart, int yend, int
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];
- jmod = j-e[m][1];
- 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];
- jmod = j-e[m][1];
- kmod = k-e[m][2];
- 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]);
-
- }
- }
+ if(typeLB==1){
+ 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] = 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];
+ jmod = j-e[m][1];
+ kmod = k-e[m][2];
+ 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]);
+
+ }
+ }
}
}
@@ -2536,10 +2536,10 @@ void FixLbFluid::streamout(void)
// for(i=1; i<subNbx-1; i++){
// for(j=1; j<subNby-1; j++){
// for(k=1; k<subNbz-1; k++){
- // massloc += density_lb[i][j][k];
- // momentumloc[0] += density_lb[i][j][k]*u_lb[i][j][k][0];
- // momentumloc[1] += density_lb[i][j][k]*u_lb[i][j][k][1];
- // momentumloc[2] += density_lb[i][j][k]*u_lb[i][j][k][2];
+ // massloc += density_lb[i][j][k];
+ // momentumloc[0] += density_lb[i][j][k]*u_lb[i][j][k][0];
+ // momentumloc[1] += density_lb[i][j][k]*u_lb[i][j][k][1];
+ // momentumloc[2] += density_lb[i][j][k]*u_lb[i][j][k][2];
// }
// }
// }
@@ -2557,45 +2557,45 @@ void FixLbFluid::streamout(void)
if(me==0){
for(iproc=0; iproc < comm->nprocs; iproc++){
if(iproc){
- MPI_Irecv(&buf[0][0][0][0],size,MPI_DOUBLE,iproc,0,world,&request_recv);
- MPI_Wait(&request_recv,&status);
-
- istart=static_cast<int> (buf[0][0][0][0]);
- jstart=static_cast<int> (buf[0][0][0][1]);
- kstart=static_cast<int> (buf[0][0][0][2]);
- iend=static_cast<int> (buf[0][0][1][0]);
- jend=static_cast<int> (buf[0][0][1][1]);
- kend=static_cast<int> (buf[0][0][1][2]);
-
- for(i=istart; i<iend; i++){
- for(j=jstart; j<jend; j++){
- for(k=kstart; k<kend; k++){
- for(w=0; w<4; w++){
- altogether[i][j][k][w]=buf[i-istart+1][j-jstart+1][k-kstart+1][w];
- }
- }
- }
- }
+ MPI_Irecv(&buf[0][0][0][0],size,MPI_DOUBLE,iproc,0,world,&request_recv);
+ MPI_Wait(&request_recv,&status);
+
+ istart=static_cast<int> (buf[0][0][0][0]);
+ jstart=static_cast<int> (buf[0][0][0][1]);
+ kstart=static_cast<int> (buf[0][0][0][2]);
+ iend=static_cast<int> (buf[0][0][1][0]);
+ jend=static_cast<int> (buf[0][0][1][1]);
+ kend=static_cast<int> (buf[0][0][1][2]);
+
+ for(i=istart; i<iend; i++){
+ for(j=jstart; j<jend; j++){
+ for(k=kstart; k<kend; k++){
+ for(w=0; w<4; w++){
+ altogether[i][j][k][w]=buf[i-istart+1][j-jstart+1][k-kstart+1][w];
+ }
+ }
+ }
+ }
}else{
- for(i=1; i<subNbx-1; i++){
- for(j=1; j<subNby-1; j++){
- for(k=1; k<subNbz-1; k++){
- altogether[i-1][j-1][k-1][0]=density_lb[i][j][k];
- altogether[i-1][j-1][k-1][1]=u_lb[i][j][k][0];
- altogether[i-1][j-1][k-1][2]=u_lb[i][j][k][1];
- altogether[i-1][j-1][k-1][3]=u_lb[i][j][k][2];
- }
- }
- }
+ for(i=1; i<subNbx-1; i++){
+ for(j=1; j<subNby-1; j++){
+ for(k=1; k<subNbz-1; k++){
+ altogether[i-1][j-1][k-1][0]=density_lb[i][j][k];
+ altogether[i-1][j-1][k-1][1]=u_lb[i][j][k][0];
+ altogether[i-1][j-1][k-1][2]=u_lb[i][j][k][1];
+ altogether[i-1][j-1][k-1][3]=u_lb[i][j][k][2];
+ }
+ }
+ }
}
}
//i = Nbx/2;
//j = Nby/2;
for(i=0; i<Nbx; i++)
for(j=0; j<Nby; j++)
- 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);
- }
+ 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 {
@@ -2603,9 +2603,9 @@ void FixLbFluid::streamout(void)
jstart=comm->myloc[1]*(subNby-2);
if(domain->periodicity[2]==0){
if(comm->myloc[2]==comm->procgrid[2]-1){
- kstart=comm->myloc[2]*(subNbz-3);
+ kstart=comm->myloc[2]*(subNbz-3);
}else{
- kstart=comm->myloc[2]*(subNbz-2);
+ kstart=comm->myloc[2]*(subNbz-2);
}
}else{
kstart=comm->myloc[2]*(subNbz-2);
@@ -2615,12 +2615,12 @@ void FixLbFluid::streamout(void)
kend=kstart+subNbz-2;
for(i=0; i<subNbx; i++){
for(j=0; j<subNby; j++){
- for(k=0; k<subNbz; k++){
- buf[i][j][k][0]=density_lb[i][j][k];
- buf[i][j][k][1]=u_lb[i][j][k][0];
- buf[i][j][k][2]=u_lb[i][j][k][1];
- buf[i][j][k][3]=u_lb[i][j][k][2];
- }
+ for(k=0; k<subNbz; k++){
+ buf[i][j][k][0]=density_lb[i][j][k];
+ buf[i][j][k][1]=u_lb[i][j][k][0];
+ buf[i][j][k][2]=u_lb[i][j][k][1];
+ buf[i][j][k][3]=u_lb[i][j][k][2];
+ }
}
}
buf[0][0][0][0]=istart;
@@ -2721,124 +2721,124 @@ void FixLbFluid::update_full15(void)
update_periodic(1,subNbx-1,1,subNby-1,subNbz-2,subNbz-1);
}else if(typeLB==2){
if(comm->myloc[2]==0){
- for(i=1; i<subNbx-1; i++){
- for(j=1;j<subNby-1;j++){
- k=1;
- for(m=0; m<15; 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;
- }
-
- for(m=0; m<15; m++){
- imod = i-e[m][0];
- jmod = j-e[m][1];
- kmod = k-e[m][2];
- 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]) +
- (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]) +
- (0.5-Dcoeff*(tau+0.5))*(feqoldn[imod][jmod][kmod][m] - feqoldn[imod][jmod][kmod][11] - feqn[imod][jmod][kmod][11]);
- else if(m==8)
- fnew[i][j][k][m] += Dcoeff*(feq[imod][jmod][kmod][12] - feqold[imod][jmod][kmod][m]) +
- (0.5-Dcoeff*(tau+0.5))*(feqoldn[imod][jmod][kmod][m] - feqoldn[imod][jmod][kmod][12] - feqn[imod][jmod][kmod][12]);
- else if(m==9)
- 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==10)
- fnew[i][j][k][m] += Dcoeff*(feq[imod][jmod][kmod][14] - feqold[imod][jmod][kmod][m]) +
- (0.5-Dcoeff*(tau+0.5))*(feqoldn[imod][jmod][kmod][m] - feqoldn[imod][jmod][kmod][14] - feqn[imod][jmod][kmod][14]);
- else if(m==6)
- 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][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]);
- 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]);
- 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]);
- 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]);
- 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]);
-
- }
- }
- }
+ for(i=1; i<subNbx-1; i++){
+ for(j=1;j<subNby-1;j++){
+ k=1;
+ for(m=0; m<15; 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;
+ }
+
+ for(m=0; m<15; m++){
+ imod = i-e[m][0];
+ jmod = j-e[m][1];
+ kmod = k-e[m][2];
+ 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]) +
+ (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]) +
+ (0.5-Dcoeff*(tau+0.5))*(feqoldn[imod][jmod][kmod][m] - feqoldn[imod][jmod][kmod][11] - feqn[imod][jmod][kmod][11]);
+ else if(m==8)
+ fnew[i][j][k][m] += Dcoeff*(feq[imod][jmod][kmod][12] - feqold[imod][jmod][kmod][m]) +
+ (0.5-Dcoeff*(tau+0.5))*(feqoldn[imod][jmod][kmod][m] - feqoldn[imod][jmod][kmod][12] - feqn[imod][jmod][kmod][12]);
+ else if(m==9)
+ 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==10)
+ fnew[i][j][k][m] += Dcoeff*(feq[imod][jmod][kmod][14] - feqold[imod][jmod][kmod][m]) +
+ (0.5-Dcoeff*(tau+0.5))*(feqoldn[imod][jmod][kmod][m] - feqoldn[imod][jmod][kmod][14] - feqn[imod][jmod][kmod][14]);
+ else if(m==6)
+ 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][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]);
+ 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]);
+ 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]);
+ 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]);
+ 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]);
+
+ }
+ }
+ }
}else{
- update_periodic(1,subNbx-1,1,subNby-1,1,2);
+ update_periodic(1,subNbx-1,1,subNby-1,1,2);
}
if(comm->myloc[2]==comm->procgrid[2]-1){
- for(i=1;i<subNbx-1;i++){
- for(j=1;j<subNby-1;j++){
- k=subNbz-2;
- for(m=0; m<15; 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;
- }
- for(m=0; m<15; m++){
- imod = i-e[m][0];
- jmod = j-e[m][1];
- kmod = k-e[m][2];
- 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]) +
- (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]) +
- (0.5-Dcoeff*(tau+0.5))*(feqoldn[imod][jmod][kmod][m] - feqoldn[imod][jmod][kmod][7] - feqn[imod][jmod][kmod][7]);
- else if(m==12)
- fnew[i][j][k][m] += Dcoeff*(feq[imod][jmod][kmod][8] - feqold[imod][jmod][kmod][m]) +
- (0.5-Dcoeff*(tau+0.5))*(feqoldn[imod][jmod][kmod][m] - feqoldn[imod][jmod][kmod][8] - feqn[imod][jmod][kmod][8]);
- else if(m==13)
- fnew[i][j][k][m] += Dcoeff*(feq[imod][jmod][kmod][9] - feqold[imod][jmod][kmod][m]) +
- (0.5-Dcoeff*(tau+0.5))*(feqoldn[imod][jmod][kmod][m] - feqoldn[imod][jmod][kmod][9] - feqn[imod][jmod][kmod][9]);
- else if(m==14)
- fnew[i][j][k][m] += Dcoeff*(feq[imod][jmod][kmod][10] - feqold[imod][jmod][kmod][m]) +
- (0.5-Dcoeff*(tau+0.5))*(feqoldn[imod][jmod][kmod][m] - feqoldn[imod][jmod][kmod][10] - feqn[imod][jmod][kmod][10]);
- 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]);
- 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]);
- 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]);
- 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]);
- 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]);
- 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]);
-
- }
- }
- }
+ for(i=1;i<subNbx-1;i++){
+ for(j=1;j<subNby-1;j++){
+ k=subNbz-2;
+ for(m=0; m<15; 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;
+ }
+ for(m=0; m<15; m++){
+ imod = i-e[m][0];
+ jmod = j-e[m][1];
+ kmod = k-e[m][2];
+ 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]) +
+ (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]) +
+ (0.5-Dcoeff*(tau+0.5))*(feqoldn[imod][jmod][kmod][m] - feqoldn[imod][jmod][kmod][7] - feqn[imod][jmod][kmod][7]);
+ else if(m==12)
+ fnew[i][j][k][m] += Dcoeff*(feq[imod][jmod][kmod][8] - feqold[imod][jmod][kmod][m]) +
+ (0.5-Dcoeff*(tau+0.5))*(feqoldn[imod][jmod][kmod][m] - feqoldn[imod][jmod][kmod][8] - feqn[imod][jmod][kmod][8]);
+ else if(m==13)
+ fnew[i][j][k][m] += Dcoeff*(feq[imod][jmod][kmod][9] - feqold[imod][jmod][kmod][m]) +
+ (0.5-Dcoeff*(tau+0.5))*(feqoldn[imod][jmod][kmod][m] - feqoldn[imod][jmod][kmod][9] - feqn[imod][jmod][kmod][9]);
+ else if(m==14)
+ fnew[i][j][k][m] += Dcoeff*(feq[imod][jmod][kmod][10] - feqold[imod][jmod][kmod][m]) +
+ (0.5-Dcoeff*(tau+0.5))*(feqoldn[imod][jmod][kmod][m] - feqoldn[imod][jmod][kmod][10] - feqn[imod][jmod][kmod][10]);
+ 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]);
+ 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]);
+ 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]);
+ 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]);
+ 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]);
+ 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]);
+
+ }
+ }
+ }
}
else{
- update_periodic(1,subNbx-1,1,subNby-1,subNbz-2,subNbz-1);
+ update_periodic(1,subNbx-1,1,subNby-1,subNbz-2,subNbz-1);
}
}
@@ -2861,39 +2861,39 @@ void FixLbFluid::update_full15(void)
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];
- }
- 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] +
- feqn[i+1][j+1][k+1][9] + feqn[i-1][j+1][k+1][10]);
- }
-
- fnew[i][j][k][7]=-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][11]-2.0*fnew[i][j][k][13]-tmp1);
- fnew[i][j][k][8]=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][14]-2.0*fnew[i][j][k][12]+tmp1);
- fnew[i][j][k][9]=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][11]-2.0*fnew[i][j][k][13]+tmp1);
- fnew[i][j][k][10]=-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][14]-2.0*fnew[i][j][k][12]-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]+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;
- fnew[i][j][k][10] += -0.25*rb*vwbt;
- }
+ 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];
+ }
+ 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] +
+ feqn[i+1][j+1][k+1][9] + feqn[i-1][j+1][k+1][10]);
+ }
+
+ fnew[i][j][k][7]=-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][11]-2.0*fnew[i][j][k][13]-tmp1);
+ fnew[i][j][k][8]=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][14]-2.0*fnew[i][j][k][12]+tmp1);
+ fnew[i][j][k][9]=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][11]-2.0*fnew[i][j][k][13]+tmp1);
+ fnew[i][j][k][10]=-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][14]-2.0*fnew[i][j][k][12]-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]+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;
+ fnew[i][j][k][10] += -0.25*rb*vwbt;
+ }
}
}
@@ -2902,39 +2902,39 @@ void FixLbFluid::update_full15(void)
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] +
- 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]+
- fnew[i][j][k][4]-2.0*fnew[i][j][k][8]+2.0*fnew[i][j][k][10]+tmp1);
- fnew[i][j][k][13]=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][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;
- }
+ 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] +
+ 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]+
+ fnew[i][j][k][4]-2.0*fnew[i][j][k][8]+2.0*fnew[i][j][k][10]+tmp1);
+ fnew[i][j][k][13]=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][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;
+ }
}
}
@@ -3080,122 +3080,122 @@ void FixLbFluid::update_full19(void)
update_periodic(1,subNbx-1,1,subNby-1,subNbz-2,subNbz-1);
}else if(typeLB==2){
if(comm->myloc[2]==0){
- for(i=1; i<subNbx-1; i++){
- for(j=1;j<subNby-1;j++){
- k=1;
- for(m=0; m<19; 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;
- }
-
- for(m=0; m<19; m++){
- imod = i-e[m][0];
- jmod = j-e[m][1];
- kmod = k-e[m][2];
- 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]) +
- (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]) +
- (0.5-Dcoeff*(tau+0.5))*(feqoldn[imod][jmod][kmod][m] - feqoldn[imod][jmod][kmod][12] - feqn[imod][jmod][kmod][12]);
- else if(m==13)
- fnew[i][j][k][m] += Dcoeff*(feq[imod][jmod][kmod][14] - feqold[imod][jmod][kmod][m]) +
- (0.5-Dcoeff*(tau+0.5))*(feqoldn[imod][jmod][kmod][m] - feqoldn[imod][jmod][kmod][14] - feqn[imod][jmod][kmod][14]);
- else if(m==15)
- fnew[i][j][k][m] += Dcoeff*(feq[imod][jmod][kmod][16] - feqold[imod][jmod][kmod][m]) +
- (0.5-Dcoeff*(tau+0.5))*(feqoldn[imod][jmod][kmod][m] - feqoldn[imod][jmod][kmod][16] - feqn[imod][jmod][kmod][16]);
- else if(m==17)
- fnew[i][j][k][m] += Dcoeff*(feq[imod][jmod][kmod][18] - feqold[imod][jmod][kmod][m]) +
- (0.5-Dcoeff*(tau+0.5))*(feqoldn[imod][jmod][kmod][m] - feqoldn[imod][jmod][kmod][18] - feqn[imod][jmod][kmod][18]);
- else if(m==6)
- 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][5] - 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][11] - 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][13] - feqoldn[i][j][k][m] - feqn[i][j][k][m] + feqoldn[imod][jmod][kmod][m]);
- else if(m==16)
- 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][15] - feqoldn[i][j][k][m] - feqn[i][j][k][m] + feqoldn[imod][jmod][kmod][m]);
- else if(m==18)
- 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]) +
- (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]);
- }
- }
- }
+ for(i=1; i<subNbx-1; i++){
+ for(j=1;j<subNby-1;j++){
+ k=1;
+ for(m=0; m<19; 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;
+ }
+
+ for(m=0; m<19; m++){
+ imod = i-e[m][0];
+ jmod = j-e[m][1];
+ kmod = k-e[m][2];
+ 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]) +
+ (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]) +
+ (0.5-Dcoeff*(tau+0.5))*(feqoldn[imod][jmod][kmod][m] - feqoldn[imod][jmod][kmod][12] - feqn[imod][jmod][kmod][12]);
+ else if(m==13)
+ fnew[i][j][k][m] += Dcoeff*(feq[imod][jmod][kmod][14] - feqold[imod][jmod][kmod][m]) +
+ (0.5-Dcoeff*(tau+0.5))*(feqoldn[imod][jmod][kmod][m] - feqoldn[imod][jmod][kmod][14] - feqn[imod][jmod][kmod][14]);
+ else if(m==15)
+ fnew[i][j][k][m] += Dcoeff*(feq[imod][jmod][kmod][16] - feqold[imod][jmod][kmod][m]) +
+ (0.5-Dcoeff*(tau+0.5))*(feqoldn[imod][jmod][kmod][m] - feqoldn[imod][jmod][kmod][16] - feqn[imod][jmod][kmod][16]);
+ else if(m==17)
+ fnew[i][j][k][m] += Dcoeff*(feq[imod][jmod][kmod][18] - feqold[imod][jmod][kmod][m]) +
+ (0.5-Dcoeff*(tau+0.5))*(feqoldn[imod][jmod][kmod][m] - feqoldn[imod][jmod][kmod][18] - feqn[imod][jmod][kmod][18]);
+ else if(m==6)
+ 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][5] - 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][11] - 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][13] - feqoldn[i][j][k][m] - feqn[i][j][k][m] + feqoldn[imod][jmod][kmod][m]);
+ else if(m==16)
+ 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][15] - feqoldn[i][j][k][m] - feqn[i][j][k][m] + feqoldn[imod][jmod][kmod][m]);
+ else if(m==18)
+ 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]) +
+ (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);
+ update_periodic(1,subNbx-1,1,subNby-1,1,2);
}
if(comm->myloc[2]==comm->procgrid[2]-1){
- for(i=1;i<subNbx-1;i++){
- for(j=1;j<subNby-1;j++){
- k=subNbz-2;
- for(m=0; m<19; 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;
- }
- for(m=0; m<19; m++){
- imod = i-e[m][0];
- jmod = j-e[m][1];
- kmod = k-e[m][2];
- 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]) +
- (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]) +
- (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]) +
- (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]) +
- (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]) +
- (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]);
- 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]);
- 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]);
- 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]);
- 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]);
- }
- }
- }
+ for(i=1;i<subNbx-1;i++){
+ for(j=1;j<subNby-1;j++){
+ k=subNbz-2;
+ for(m=0; m<19; 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;
+ }
+ for(m=0; m<19; m++){
+ imod = i-e[m][0];
+ jmod = j-e[m][1];
+ kmod = k-e[m][2];
+ 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]) +
+ (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]) +
+ (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]) +
+ (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]) +
+ (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]) +
+ (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]);
+ 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]);
+ 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]);
+ 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]);
+ 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]);
+ }
+ }
+ }
}
else{
- update_periodic(1,subNbx-1,1,subNby-1,subNbz-2,subNbz-1);
+ update_periodic(1,subNbx-1,1,subNby-1,subNbz-2,subNbz-1);
}
}
@@ -3218,35 +3218,35 @@ void FixLbFluid::update_full19(void)
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];
- }
- 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]);
- }
-
- 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);
- }
+ 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];
+ }
+ 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]);
+ }
+
+ 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);
+ }
}
}
@@ -3255,35 +3255,35 @@ void FixLbFluid::update_full19(void)
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];
- }
- 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] +
- 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);
- }
+ 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];
+ }
+ 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] +
+ 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);
+ }
}
}
diff --git a/src/USER-LB/fix_lb_momentum.cpp b/src/USER-LB/fix_lb_momentum.cpp
index 18d98edda8..d604d8fed4 100644
--- a/src/USER-LB/fix_lb_momentum.cpp
+++ b/src/USER-LB/fix_lb_momentum.cpp
@@ -64,7 +64,7 @@ FixLbMomentum::FixLbMomentum(LAMMPS *lmp, int narg, char **arg) :
if (linear)
if (xflag < 0 || xflag > 1 || yflag < 0 || yflag > 1 ||
- zflag < 0 || zflag > 1) error->all(FLERR,"Illegal fix lb/momentum command");
+ zflag < 0 || zflag > 1) error->all(FLERR,"Illegal fix lb/momentum command");
// cannot have 0 atoms in group
@@ -138,12 +138,12 @@ void FixLbMomentum::end_of_step()
for(int i = 1; i<subNbx-1; i++)
for(int j = 1; j<subNby-1; j++)
- for(int k = 1; k<subNbz-1; k++){
- masslbloc += density_lb[i][j][k];
- momentumlbloc[0] += density_lb[i][j][k]*u_lb[i][j][k][0];
- momentumlbloc[1] += density_lb[i][j][k]*u_lb[i][j][k][1];
- momentumlbloc[2] += density_lb[i][j][k]*u_lb[i][j][k][2];
- }
+ for(int k = 1; k<subNbz-1; k++){
+ masslbloc += density_lb[i][j][k];
+ momentumlbloc[0] += density_lb[i][j][k]*u_lb[i][j][k][0];
+ momentumlbloc[1] += density_lb[i][j][k]*u_lb[i][j][k][1];
+ momentumlbloc[2] += density_lb[i][j][k]*u_lb[i][j][k][2];
+ }
MPI_Allreduce(&masslbloc,&masslb,1,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(&momentumlbloc[0],&momentumlb[0],3,MPI_DOUBLE,MPI_SUM,world);
@@ -160,9 +160,9 @@ void FixLbMomentum::end_of_step()
//Subtract vcm from the particles.
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- if (xflag) v[i][0] -= vcmtotal[0];
- if (yflag) v[i][1] -= vcmtotal[1];
- if (zflag) v[i][2] -= vcmtotal[2];
+ if (xflag) v[i][0] -= vcmtotal[0];
+ if (yflag) v[i][1] -= vcmtotal[1];
+ if (zflag) v[i][2] -= vcmtotal[2];
}
vcmtotal[0] *= dt_lb/dx_lb;
@@ -177,121 +177,121 @@ void FixLbMomentum::end_of_step()
//Subtract vcm from the fluid.
for(int i=0; i<subNbx; i++)
for(int j=0; j<subNby; j++)
- for(int k=0; k<subNbz; k++){
- rho = density_lb[i][j][k];
- if(xflag) ucmx = vcmtotal[0];
- if(yflag) ucmy = vcmtotal[1];
- if(zflag) ucmz = vcmtotal[2];
- if(numvel==15){
- etacov[0]=0.0;
- etacov[1]=rho*ucmx;
- etacov[2]=rho*ucmy;
- etacov[3]=rho*ucmz;
- etacov[4]=rho*(2.*u_lb[i][j][k][0]*ucmx-ucmx*ucmx);
- etacov[5]=rho*(2.*u_lb[i][j][k][1]*ucmy-ucmy*ucmy);
- etacov[6]=rho*(2.*u_lb[i][j][k][2]*ucmz-ucmz*ucmz);
- 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][1]*ucmz+u_lb[i][j][k][2]*ucmy-ucmy*ucmz);
- etacov[9]=rho*(u_lb[i][j][k][0]*ucmz+u_lb[i][j][k][2]*ucmx-ucmx*ucmz);
- 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]*ucmz+u_lb[i][j][k][0]*ucmy*u_lb[i][j][k][2]-
- 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;
- }else{
- etacov[0] = 0.0;
- etacov[1] = rho*ucmx;
- etacov[2] = rho*ucmy;
- etacov[3] = rho*ucmz;
- etacov[4]=rho*(2.*u_lb[i][j][k][0]*ucmx-ucmx*ucmx);
- etacov[5]=rho*(2.*u_lb[i][j][k][1]*ucmy-ucmy*ucmy);
- etacov[6]=rho*(2.*u_lb[i][j][k][2]*ucmz-ucmz*ucmz);
- 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[12] = 0.0;
- etacov[13] = 0.0;
- etacov[14] = 0.0;
- etacov[15] = 0.0;
- 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;
- double ****feqoldn = fix_lb_fluid->feqoldn;
- density_old = 0.0;
- u_old[0] = u_old[1] = u_old[2] = 0.0;
- for(int l=0; l<numvel; l++){
- density_old += feqold[i][j][k][l];
- u_old[0] += feqold[i][j][k][l]*e[l][0];
- u_old[1] += feqold[i][j][k][l]*e[l][1];
- u_old[2] += feqold[i][j][k][l]*e[l][2];
- }
- 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;
- etacov[2]=density_old*ucmy;
- etacov[3]=density_old*ucmz;
- etacov[4]=density_old*(2.*u_old[0]*ucmx-ucmx*ucmx);
- etacov[5]=density_old*(2.*u_old[1]*ucmy-ucmy*ucmy);
- etacov[6]=density_old*(2.*u_old[2]*ucmz-ucmz*ucmz);
- etacov[7]=density_old*(u_old[0]*ucmy+u_old[1]*ucmx-ucmx*ucmy);
- etacov[8]=density_old*(u_old[1]*ucmz+u_old[2]*ucmy-ucmy*ucmz);
- etacov[9]=density_old*(u_old[0]*ucmz+u_old[2]*ucmx-ucmx*ucmz);
- etacov[10]=0.0;
- etacov[11]=0.0;
- etacov[12]=0.0;
- etacov[13]=density_old*(u_old[0]*u_old[1]*ucmz+u_old[0]*ucmy*u_old[2]-
- 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;
- }else{
- etacov[0] = 0.0;
- etacov[1] = density_old*ucmx;
- etacov[2] = density_old*ucmy;
- etacov[3] = density_old*ucmz;
- etacov[4] = density_old*(2.*u_lb[i][j][k][0]*ucmx-ucmx*ucmx);
- etacov[5] = density_old*(2.*u_lb[i][j][k][1]*ucmy-ucmy*ucmy);
- etacov[6] = density_old*(2.*u_lb[i][j][k][2]*ucmz-ucmz*ucmz);
- 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[12] = 0.0;
- etacov[13] = 0.0;
- etacov[14] = 0.0;
- etacov[15] = 0.0;
- 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++){
- 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];
- }
- }
- }
+ for(int k=0; k<subNbz; k++){
+ rho = density_lb[i][j][k];
+ if(xflag) ucmx = vcmtotal[0];
+ if(yflag) ucmy = vcmtotal[1];
+ if(zflag) ucmz = vcmtotal[2];
+ if(numvel==15){
+ etacov[0]=0.0;
+ etacov[1]=rho*ucmx;
+ etacov[2]=rho*ucmy;
+ etacov[3]=rho*ucmz;
+ etacov[4]=rho*(2.*u_lb[i][j][k][0]*ucmx-ucmx*ucmx);
+ etacov[5]=rho*(2.*u_lb[i][j][k][1]*ucmy-ucmy*ucmy);
+ etacov[6]=rho*(2.*u_lb[i][j][k][2]*ucmz-ucmz*ucmz);
+ 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][1]*ucmz+u_lb[i][j][k][2]*ucmy-ucmy*ucmz);
+ etacov[9]=rho*(u_lb[i][j][k][0]*ucmz+u_lb[i][j][k][2]*ucmx-ucmx*ucmz);
+ 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]*ucmz+u_lb[i][j][k][0]*ucmy*u_lb[i][j][k][2]-
+ 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;
+ }else{
+ etacov[0] = 0.0;
+ etacov[1] = rho*ucmx;
+ etacov[2] = rho*ucmy;
+ etacov[3] = rho*ucmz;
+ etacov[4]=rho*(2.*u_lb[i][j][k][0]*ucmx-ucmx*ucmx);
+ etacov[5]=rho*(2.*u_lb[i][j][k][1]*ucmy-ucmy*ucmy);
+ etacov[6]=rho*(2.*u_lb[i][j][k][2]*ucmz-ucmz*ucmz);
+ 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[12] = 0.0;
+ etacov[13] = 0.0;
+ etacov[14] = 0.0;
+ etacov[15] = 0.0;
+ 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;
+ double ****feqoldn = fix_lb_fluid->feqoldn;
+ density_old = 0.0;
+ u_old[0] = u_old[1] = u_old[2] = 0.0;
+ for(int l=0; l<numvel; l++){
+ density_old += feqold[i][j][k][l];
+ u_old[0] += feqold[i][j][k][l]*e[l][0];
+ u_old[1] += feqold[i][j][k][l]*e[l][1];
+ u_old[2] += feqold[i][j][k][l]*e[l][2];
+ }
+ 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;
+ etacov[2]=density_old*ucmy;
+ etacov[3]=density_old*ucmz;
+ etacov[4]=density_old*(2.*u_old[0]*ucmx-ucmx*ucmx);
+ etacov[5]=density_old*(2.*u_old[1]*ucmy-ucmy*ucmy);
+ etacov[6]=density_old*(2.*u_old[2]*ucmz-ucmz*ucmz);
+ etacov[7]=density_old*(u_old[0]*ucmy+u_old[1]*ucmx-ucmx*ucmy);
+ etacov[8]=density_old*(u_old[1]*ucmz+u_old[2]*ucmy-ucmy*ucmz);
+ etacov[9]=density_old*(u_old[0]*ucmz+u_old[2]*ucmx-ucmx*ucmz);
+ etacov[10]=0.0;
+ etacov[11]=0.0;
+ etacov[12]=0.0;
+ etacov[13]=density_old*(u_old[0]*u_old[1]*ucmz+u_old[0]*ucmy*u_old[2]-
+ 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;
+ }else{
+ etacov[0] = 0.0;
+ etacov[1] = density_old*ucmx;
+ etacov[2] = density_old*ucmy;
+ etacov[3] = density_old*ucmz;
+ etacov[4] = density_old*(2.*u_lb[i][j][k][0]*ucmx-ucmx*ucmx);
+ etacov[5] = density_old*(2.*u_lb[i][j][k][1]*ucmy-ucmy*ucmy);
+ etacov[6] = density_old*(2.*u_lb[i][j][k][2]*ucmz-ucmz*ucmz);
+ 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[12] = 0.0;
+ etacov[13] = 0.0;
+ etacov[14] = 0.0;
+ etacov[15] = 0.0;
+ 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++){
+ 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];
+ }
+ }
+ }
}
fix_lb_fluid->parametercalc_full();
diff --git a/src/USER-LB/fix_lb_pc.cpp b/src/USER-LB/fix_lb_pc.cpp
index 9ea1afc2ea..c4d7cf70d3 100644
--- a/src/USER-LB/fix_lb_pc.cpp
+++ b/src/USER-LB/fix_lb_pc.cpp
@@ -148,30 +148,30 @@ void FixLbPC::initial_integrate(int vflag) {
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]);
-
- 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];
-
- 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 +
- 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 +
- 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 +
- f[i][2]*force->ftm2v/Gamma_MD[type[i]] + up[i][2];
- }
+ dtfm = dtf/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];
+
+ 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 +
+ 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 +
+ 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 +
+ f[i][2]*force->ftm2v/Gamma_MD[type[i]] + up[i][2];
+ }
}
}
@@ -179,30 +179,30 @@ void FixLbPC::initial_integrate(int vflag) {
// this does NOT take varying masses into account
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]]);
-
- 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]];
- 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/mass[type[i]];
-
- 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 +
- 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 +
- 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 +
- f[i][2]*force->ftm2v/Gamma_MD[type[i]] + up[i][2];
- }
+ dtfm = dtf/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]];
+ 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/mass[type[i]];
+
+ 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 +
+ 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 +
+ 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 +
+ f[i][2]*force->ftm2v/Gamma_MD[type[i]] + up[i][2];
+ }
}
}
}
@@ -226,19 +226,19 @@ void FixLbPC::final_integrate()
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]]);
+ 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;
- v[i][2] += 0.5*(f[i][2] - force_old[i][2])*dtfm;
- }else{
- 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;
- }
+ 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;
+ v[i][2] += 0.5*(f[i][2] - force_old[i][2])*dtfm;
+ }else{
+ 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;
+ }
}
@@ -247,19 +247,19 @@ void FixLbPC::final_integrate()
// this does NOT take varying masses into account
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]]);
- 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;
- v[i][2] += 0.5*(f[i][2] - force_old[i][2])*dtfm;
- }else{
- 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;
- }
+ 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;
+ v[i][2] += 0.5*(f[i][2] - force_old[i][2])*dtfm;
+ }else{
+ 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;
+ }
}
}
@@ -383,88 +383,88 @@ int FixLbPC::unpack_exchange(int nlocal, double *buf)
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{
- r=sqrt(rsq);
- if(rsq>1){
- weightx=(5.0-2.0*r-sqrt(-7.0+12.0*r-4.0*rsq))/8.;
- } else{
- weightx=(3.0-2.0*r+sqrt(1.0+4.0*r-4.0*rsq))/8.;
- }
- }
- for(jj=-1; jj<3; jj++){
- rsq=(-dy1+jj)*(-dy1+jj);
- if(rsq>=4)
- weighty=0.0;
- else{
- r=sqrt(rsq);
- if(rsq>1){
- weighty=(5.0-2.0*r-sqrt(-7.0+12.0*r-4.0*rsq))/8.;
- } else{
- weighty=(3.0-2.0*r+sqrt(1.0+4.0*r-4.0*rsq))/8.;
- }
- }
- for(kk=-1; kk<3; kk++){
- rsq=(-dz1+kk)*(-dz1+kk);
- if(rsq>=4)
- weightz=0.0;
- else{
- r=sqrt(rsq);
- if(rsq>1){
- weightz=(5.0-2.0*r-sqrt(-7.0+12.0*r-4.0*rsq))/8.;
- } else{
- weightz=(3.0-2.0*r+sqrt(1.0+4.0*r-4.0*rsq))/8.;
- }
- }
- 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++){
- up[i][k] += u_lb[ixp][iyp][izp][k]*FfP[isten];
- }
- }
- }
- }
+ isten=0;
+ for(ii=-1; ii<3; ii++){
+ rsq=(-dx1+ii)*(-dx1+ii);
+
+ if(rsq>=4)
+ weightx=0.0;
+ else{
+ r=sqrt(rsq);
+ if(rsq>1){
+ weightx=(5.0-2.0*r-sqrt(-7.0+12.0*r-4.0*rsq))/8.;
+ } else{
+ weightx=(3.0-2.0*r+sqrt(1.0+4.0*r-4.0*rsq))/8.;
+ }
+ }
+ for(jj=-1; jj<3; jj++){
+ rsq=(-dy1+jj)*(-dy1+jj);
+ if(rsq>=4)
+ weighty=0.0;
+ else{
+ r=sqrt(rsq);
+ if(rsq>1){
+ weighty=(5.0-2.0*r-sqrt(-7.0+12.0*r-4.0*rsq))/8.;
+ } else{
+ weighty=(3.0-2.0*r+sqrt(1.0+4.0*r-4.0*rsq))/8.;
+ }
+ }
+ for(kk=-1; kk<3; kk++){
+ rsq=(-dz1+kk)*(-dz1+kk);
+ if(rsq>=4)
+ weightz=0.0;
+ else{
+ r=sqrt(rsq);
+ if(rsq>1){
+ weightz=(5.0-2.0*r-sqrt(-7.0+12.0*r-4.0*rsq))/8.;
+ } else{
+ weightz=(3.0-2.0*r+sqrt(1.0+4.0*r-4.0*rsq))/8.;
+ }
+ }
+ 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++){
+ up[i][k] += u_lb[ixp][iyp][izp][k]*FfP[isten];
+ }
+ }
+ }
+ }
}else{
- FfP[0] = (1.-dx1)*(1.-dy1)*(1.-dz1);
- FfP[1] = (1.-dx1)*(1.-dy1)*dz1;
- FfP[2] = (1.-dx1)*dy1*(1.-dz1);
- FfP[3] = (1.-dx1)*dy1*dz1;
- FfP[4] = dx1*(1.-dy1)*(1.-dz1);
- 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]
- + u_lb[ix][iyp][iz][k]*FfP[2]
- + u_lb[ix][iyp][izp][k]*FfP[3]
- + 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];
- }
+ FfP[0] = (1.-dx1)*(1.-dy1)*(1.-dz1);
+ FfP[1] = (1.-dx1)*(1.-dy1)*dz1;
+ FfP[2] = (1.-dx1)*dy1*(1.-dz1);
+ FfP[3] = (1.-dx1)*dy1*dz1;
+ FfP[4] = dx1*(1.-dy1)*(1.-dz1);
+ 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]
+ + u_lb[ix][iyp][iz][k]*FfP[2]
+ + u_lb[ix][iyp][izp][k]*FfP[3]
+ + 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];
+ }
}
for(k=0; k<3; k++)
- up[i][k] = up[i][k]*dx_lb/dt_lb;
+ up[i][k] = up[i][k]*dx_lb/dt_lb;
}
}
diff --git a/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp b/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp
index 67f298d8df..5d32ef777d 100644
--- a/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp
+++ b/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp
@@ -156,7 +156,7 @@ FixNVEManifoldRattle::FixNVEManifoldRattle( LAMMPS *lmp, int &narg, char **arg,
next_output = update->ntimestep + nevery;
if( comm->me == 0 ){
fprintf(screen,"Outputing every %d steps, next is %d\n",
- nevery, next_output);
+ nevery, next_output);
}
argi += 2;
}else if( error_on_unknown_keyword ){
diff --git a/src/USER-MISC/angle_dipole.cpp b/src/USER-MISC/angle_dipole.cpp
index 990096ae7f..e393b3717b 100644
--- a/src/USER-MISC/angle_dipole.cpp
+++ b/src/USER-MISC/angle_dipole.cpp
@@ -101,7 +101,7 @@ void AngleDipole::compute(int eflag, int vflag)
torque[iDip][0] += delTx;
torque[iDip][1] += delTy;
torque[iDip][2] += delTz;
-
+
// Force couple that counterbalances dipolar torque
fx = dely*delTz - delz*delTy; // direction (fi): - r x (-T)
fy = delz*delTx - delx*delTz;
diff --git a/src/USER-MISC/angle_fourier.cpp b/src/USER-MISC/angle_fourier.cpp
index c4dbf3f08b..689caeaa5f 100644
--- a/src/USER-MISC/angle_fourier.cpp
+++ b/src/USER-MISC/angle_fourier.cpp
@@ -143,7 +143,7 @@ void AngleFourier::compute(int eflag, int vflag)
}
if (evflag) ev_tally(i1,i2,i3,nlocal,newton_bond,eangle,f1,f3,
- delx1,dely1,delz1,delx2,dely2,delz2);
+ delx1,dely1,delz1,delx2,dely2,delz2);
}
}
diff --git a/src/USER-MISC/angle_quartic.cpp b/src/USER-MISC/angle_quartic.cpp
index f9801edb0e..5d990003a8 100644
--- a/src/USER-MISC/angle_quartic.cpp
+++ b/src/USER-MISC/angle_quartic.cpp
@@ -153,7 +153,7 @@ void AngleQuartic::compute(int eflag, int vflag)
}
if (evflag) ev_tally(i1,i2,i3,nlocal,newton_bond,eangle,f1,f3,
- delx1,dely1,delz1,delx2,dely2,delz2);
+ delx1,dely1,delz1,delx2,dely2,delz2);
}
}
diff --git a/src/USER-MISC/bond_harmonic_shift.cpp b/src/USER-MISC/bond_harmonic_shift.cpp
index c4ee00cb27..70db2cc2bd 100644
--- a/src/USER-MISC/bond_harmonic_shift.cpp
+++ b/src/USER-MISC/bond_harmonic_shift.cpp
@@ -204,7 +204,7 @@ void BondHarmonicShift::write_data(FILE *fp)
/* ---------------------------------------------------------------------- */
double BondHarmonicShift::single(int type, double rsq, int i, int j,
- double &fforce)
+ double &fforce)
{
double r = sqrt(rsq);
double dr = r - r0[type];
diff --git a/src/USER-MISC/bond_harmonic_shift_cut.cpp b/src/USER-MISC/bond_harmonic_shift_cut.cpp
index 26fd32c1b5..aa0091019d 100644
--- a/src/USER-MISC/bond_harmonic_shift_cut.cpp
+++ b/src/USER-MISC/bond_harmonic_shift_cut.cpp
@@ -206,7 +206,7 @@ void BondHarmonicShiftCut::write_data(FILE *fp)
/* ---------------------------------------------------------------------- */
double BondHarmonicShiftCut::single(int type, double rsq, int i, int j,
- double &fforce)
+ double &fforce)
{
fforce = 0.0;
double r = sqrt(rsq);
diff --git a/src/USER-MISC/compute_ackland_atom.cpp b/src/USER-MISC/compute_ackland_atom.cpp
index ac48d75bc6..285f64a5e9 100644
--- a/src/USER-MISC/compute_ackland_atom.cpp
+++ b/src/USER-MISC/compute_ackland_atom.cpp
@@ -256,25 +256,25 @@ void ComputeAcklandAtom::compute_peratom()
+(double)chi[1]+(double)chi[2]+(double)chi[3]
-9.0))/12.0;
- // Identification of the local structure according to the reference
+ // Identification of the local structure according to the reference
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
+ // not part of Ackland-Jones 2006; included for backward compatibility
if (chi[4] < 3. && n1 == 12) structure[i] = ICO;
else {
- if (delta_bcc <= delta_cp && n1 > 10 && n1 < 13) structure[i] = BCC;
- else {
- if (n0 > 12) structure[i] = UNKNOWN;
- else {
- if (delta_fcc < delta_hcp) structure[i] = FCC;
- else
- structure[i] = HCP;
- }
- }
- }
+ if (delta_bcc <= delta_cp && n1 > 10 && n1 < 13) structure[i] = BCC;
+ else {
+ if (n0 > 12) structure[i] = UNKNOWN;
+ else {
+ if (delta_fcc < delta_hcp) structure[i] = FCC;
+ else
+ structure[i] = HCP;
+ }
+ }
+ }
}
} else structure[i] = 0.0;
}
diff --git a/src/USER-MISC/compute_basal_atom.cpp b/src/USER-MISC/compute_basal_atom.cpp
index 881b253131..cd393eb2ac 100644
--- a/src/USER-MISC/compute_basal_atom.cpp
+++ b/src/USER-MISC/compute_basal_atom.cpp
@@ -144,15 +144,15 @@ void ComputeBasalAtom::compute_peratom()
// ensure distsq and nearest arrays are long enough
if (jnum > maxneigh) {
- memory->destroy(distsq);
- memory->destroy(nearest);
- memory->destroy(nearest_n0);
- memory->destroy(nearest_n1);
- maxneigh = jnum;
- memory->create(distsq,maxneigh,"compute/basal/atom:distsq");
- memory->create(nearest,maxneigh,"compute/basal/atom:nearest");
- memory->create(nearest_n0,maxneigh,"compute/basal/atom:nearest_n0");
- memory->create(nearest_n1,maxneigh,"compute/basal/atom:nearest_n1");
+ memory->destroy(distsq);
+ memory->destroy(nearest);
+ memory->destroy(nearest_n0);
+ memory->destroy(nearest_n1);
+ maxneigh = jnum;
+ memory->create(distsq,maxneigh,"compute/basal/atom:distsq");
+ memory->create(nearest,maxneigh,"compute/basal/atom:nearest");
+ memory->create(nearest_n0,maxneigh,"compute/basal/atom:nearest_n0");
+ memory->create(nearest_n1,maxneigh,"compute/basal/atom:nearest_n1");
}
// neighbor selection is identical to ackland/atom algorithm
@@ -162,17 +162,17 @@ void ComputeBasalAtom::compute_peratom()
n = 0;
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];
- rsq = delx*delx + dely*dely + delz*delz;
- if (rsq < cutsq) {
- distsq[n] = rsq;
- nearest[n++] = j;
- }
+ j = jlist[jj];
+ j &= NEIGHMASK;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+ if (rsq < cutsq) {
+ distsq[n] = rsq;
+ nearest[n++] = j;
+ }
}
// Select 6 nearest neighbors
@@ -189,7 +189,7 @@ void ComputeBasalAtom::compute_peratom()
// n1 near neighbors with: distsq<1.55*r0_sq
double n0_dist_sq = 1.45*r0_sq,
- n1_dist_sq = 1.55*r0_sq;
+ n1_dist_sq = 1.55*r0_sq;
int n0 = 0, n1 = 0;
for (j = 0; j < n; j++) {
if (distsq[j] < n1_dist_sq) {
@@ -207,31 +207,31 @@ void ComputeBasalAtom::compute_peratom()
double x_ij, y_ij, z_ij, x_ik, y_ik, z_ik,x3[n0],y3[n0],z3[n0],
xmean5, ymean5, zmean5, xmean6, ymean6, zmean6, xmean7, ymean7, zmean7;
for (j = 0; j < n0; j++) {
- x_ij = x[i][0]-x[nearest_n0[j]][0];
- y_ij = x[i][1]-x[nearest_n0[j]][1];
- z_ij = x[i][2]-x[nearest_n0[j]][2];
- norm_j = sqrt (x_ij*x_ij + y_ij*y_ij + z_ij*z_ij);
- if (norm_j <= 0.) {continue;}
- for (k = j+1; k < n0; k++) {
- x_ik = x[i][0]-x[nearest_n0[k]][0];
- y_ik = x[i][1]-x[nearest_n0[k]][1];
- z_ik = x[i][2]-x[nearest_n0[k]][2];
- norm_k = sqrt (x_ik*x_ik + y_ik*y_ik + z_ik*z_ik);
- 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) {
- x3[chi[0]] = x_ik - x_ij;
- y3[chi[0]] = y_ik - y_ij;
- z3[chi[0]] = z_ik - z_ij;
+ x_ij = x[i][0]-x[nearest_n0[j]][0];
+ y_ij = x[i][1]-x[nearest_n0[j]][1];
+ z_ij = x[i][2]-x[nearest_n0[j]][2];
+ norm_j = sqrt (x_ij*x_ij + y_ij*y_ij + z_ij*z_ij);
+ if (norm_j <= 0.) {continue;}
+ for (k = j+1; k < n0; k++) {
+ x_ik = x[i][0]-x[nearest_n0[k]][0];
+ y_ik = x[i][1]-x[nearest_n0[k]][1];
+ z_ik = x[i][2]-x[nearest_n0[k]][2];
+ norm_k = sqrt (x_ik*x_ik + y_ik*y_ik + z_ik*z_ik);
+ 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) {
+ x3[chi[0]] = x_ik - x_ij;
+ y3[chi[0]] = y_ik - y_ij;
+ z3[chi[0]] = z_ik - z_ij;
chi[0]++;
- }
- }
+ }
+ }
}
// for atoms that have 2 or 3 ~180 bond angles:
if (2 == chi[0] || 3 == chi[0]) {
count = value = 0;
- if (chi[0] == 2) {
+ if (chi[0] == 2) {
k2[0] = 0;
j1[0] = 1;
}
@@ -244,13 +244,13 @@ void ComputeBasalAtom::compute_peratom()
j1[2]=2;
}
xmean5 = ymean5 = zmean5 = xmean6 = ymean6 = zmean6 = xmean7 = ymean7 = zmean7 = 0.0;
- for (j = 0; j < chi[0]; j++) {
+ for (j = 0; j < chi[0]; j++) {
for (k = j+1; k < chi[0]; k++) {
- //get cross products
+ //get cross products
x4[count] = y3[j1[count]]*z3[k2[count]]-y3[k2[count]]*z3[j1[count]];
y4[count] = z3[j1[count]]*x3[k2[count]]-z3[k2[count]]*x3[j1[count]];
z4[count] = x3[j1[count]]*y3[k2[count]]-x3[k2[count]]*y3[j1[count]];
- //get all sign combinations of cross products
+ //get all sign combinations of cross products
x5[count] = x4[count]*copysign(1.0,x4[count]);
y5[count] = y4[count]*copysign(1.0,x4[count]);
z5[count] = z4[count]*copysign(1.0,x4[count]);
@@ -260,7 +260,7 @@ void ComputeBasalAtom::compute_peratom()
x7[count] = x4[count]*copysign(1.0,z4[count]);
y7[count] = y4[count]*copysign(1.0,z4[count]);
z7[count] = z4[count]*copysign(1.0,z4[count]);
- //get average cross products
+ //get average cross products
xmean5 += x5[count];
ymean5 += y5[count];
zmean5 += z5[count];
@@ -285,7 +285,7 @@ void ComputeBasalAtom::compute_peratom()
zmean7 /= count;
}
var5 = var6 = var7 = 0.0;
- //find standard deviations
+ //find standard deviations
for (j=0;j<count;j++){
var5 = var5 + x5[j]*x5[j]-2*x5[j]*xmean5+xmean5*xmean5+y5[j]*y5[j]-2*y5[j]*ymean5+ymean5*ymean5+z5[j]*z5[j]-2*z5[j]*zmean5+zmean5*zmean5;
var6 = var6 + x6[j]*x6[j]-2*x6[j]*xmean6+xmean6*xmean6+y6[j]*y6[j]-2*y6[j]*ymean6+ymean6*ymean6+z6[j]*z6[j]-2*z6[j]*zmean6+zmean6*zmean6;
@@ -298,7 +298,7 @@ void ComputeBasalAtom::compute_peratom()
}
else if (var6 < var7) {value = 1;}
else {value = 2;}
- //BPV is average of cross products of all neighbor vectors which are part of 180 degree angles
+ //BPV is average of cross products of all neighbor vectors which are part of 180 degree angles
BPV[i][0] = 0;
BPV[i][1] = 0;
BPV[i][2] = 0;
@@ -332,12 +332,12 @@ void ComputeBasalAtom::compute_peratom()
j1[0]=1;
j1[1]=2;
j1[2]=2;
- //algorithm is as above, but now all combinations of three 180 degree angles are compared, and the combination with minimum standard deviation is chosen
+ //algorithm is as above, but now all combinations of three 180 degree angles are compared, and the combination with minimum standard deviation is chosen
for (j=0; j<chi[0]; j++) {
for (k=j+1; k<chi[0]; k++) {
for (l=k+1; l<chi[0]; l++) {
if (k >= chi[0] || l >= chi[0]) continue;
- //get unique combination of three neighbor vectors
+ //get unique combination of three neighbor vectors
x4[0] = x3[j];
x4[1] = x3[k];
x4[2] = x3[l];
@@ -349,7 +349,7 @@ void ComputeBasalAtom::compute_peratom()
z4[2] = z3[l];
xmean5 = ymean5 = zmean5 = xmean6 = ymean6 = zmean6 = xmean7 = ymean7 = zmean7 = 0;
for (m=0;m<3;m++) {
- //get cross products
+ //get cross products
x44[m] = y4[j1[m]]*z4[k2[m]]-y4[k2[m]]*z4[j1[m]];
y44[m] = z4[j1[m]]*x4[k2[m]]-z4[k2[m]]*x4[j1[m]];
z44[m] = x4[j1[m]]*y4[k2[m]]-x4[k2[m]]*y4[j1[m]];
@@ -362,7 +362,7 @@ void ComputeBasalAtom::compute_peratom()
x7[m] = x44[m]*copysign(1.0,z44[m]);
y7[m] = y44[m]*copysign(1.0,z44[m]);
z7[m] = z44[m]*copysign(1.0,z44[m]);
- //get average cross products
+ //get average cross products
xmean5 = xmean5 + x5[m];
ymean5 = ymean5 + y5[m];
zmean5 = zmean5 + z5[m];
@@ -383,13 +383,13 @@ void ComputeBasalAtom::compute_peratom()
zmean6 = zmean6/3;
zmean7 = zmean7/3;
var5 = var6 = var7 = 0;
- //get standard deviations
+ //get standard deviations
for (m=0;m<3;m++){
var5 = var5 + x5[m]*x5[m]-2*x5[m]*xmean5+xmean5*xmean5+y5[m]*y5[m]-2*y5[m]*ymean5+ymean5*ymean5+z5[m]*z5[m]-2*z5[m]*zmean5+zmean5*zmean5;
var6 = var6 + x6[m]*x6[m]-2*x6[m]*xmean6+xmean6*xmean6+y6[m]*y6[m]-2*y6[m]*ymean6+ymean6*ymean6+z6[m]*z6[m]-2*z6[m]*zmean6+zmean6*zmean6;
var7 = var7 + x7[m]*x7[m]-2*x7[m]*xmean7+xmean7*xmean7+y7[m]*y7[m]-2*y7[m]*ymean7+ymean7*ymean7+z7[m]*z7[m]-2*z7[m]*zmean7+zmean7*zmean7;
}
- //choose minimum standard deviation
+ //choose minimum standard deviation
if (var5 < S0) {
S0 = var5;
BPV[i][0] = (x5[0]+x5[1]+x5[2])/3;
@@ -446,29 +446,29 @@ void ComputeBasalAtom::select(int k, int n, double *arr)
for (;;) {
if (ir <= l+1) {
if (ir == l+1 && arr[ir] < arr[l]) {
- SWAP(arr[l],arr[ir])
+ SWAP(arr[l],arr[ir])
}
return;
} else {
mid=(l+ir) >> 1;
SWAP(arr[mid],arr[l+1])
if (arr[l] > arr[ir]) {
- SWAP(arr[l],arr[ir])
+ SWAP(arr[l],arr[ir])
}
if (arr[l+1] > arr[ir]) {
- SWAP(arr[l+1],arr[ir])
+ SWAP(arr[l+1],arr[ir])
}
if (arr[l] > arr[l+1]) {
- SWAP(arr[l],arr[l+1])
+ SWAP(arr[l],arr[l+1])
}
i = l+1;
j = ir;
a = arr[l+1];
for (;;) {
- do i++; while (arr[i] < a);
- do j--; while (arr[j] > a);
- if (j < i) break;
- SWAP(arr[i],arr[j])
+ do i++; while (arr[i] < a);
+ do j--; while (arr[j] > a);
+ if (j < i) break;
+ SWAP(arr[i],arr[j])
}
arr[l+1] = arr[j];
arr[j] = a;
@@ -492,8 +492,8 @@ void ComputeBasalAtom::select2(int k, int n, double *arr, int *iarr)
for (;;) {
if (ir <= l+1) {
if (ir == l+1 && arr[ir] < arr[l]) {
- SWAP(arr[l],arr[ir])
- ISWAP(iarr[l],iarr[ir])
+ SWAP(arr[l],arr[ir])
+ ISWAP(iarr[l],iarr[ir])
}
return;
} else {
@@ -501,27 +501,27 @@ void ComputeBasalAtom::select2(int k, int n, double *arr, int *iarr)
SWAP(arr[mid],arr[l+1])
ISWAP(iarr[mid],iarr[l+1])
if (arr[l] > arr[ir]) {
- SWAP(arr[l],arr[ir])
- ISWAP(iarr[l],iarr[ir])
+ SWAP(arr[l],arr[ir])
+ ISWAP(iarr[l],iarr[ir])
}
if (arr[l+1] > arr[ir]) {
- SWAP(arr[l+1],arr[ir])
- ISWAP(iarr[l+1],iarr[ir])
+ SWAP(arr[l+1],arr[ir])
+ ISWAP(iarr[l+1],iarr[ir])
}
if (arr[l] > arr[l+1]) {
- SWAP(arr[l],arr[l+1])
- ISWAP(iarr[l],iarr[l+1])
+ SWAP(arr[l],arr[l+1])
+ ISWAP(iarr[l],iarr[l+1])
}
i = l+1;
j = ir;
a = arr[l+1];
ia = iarr[l+1];
for (;;) {
- do i++; while (arr[i] < a);
- do j--; while (arr[j] > a);
- if (j < i) break;
- SWAP(arr[i],arr[j])
- ISWAP(iarr[i],iarr[j])
+ do i++; while (arr[i] < a);
+ do j--; while (arr[j] > a);
+ if (j < i) break;
+ SWAP(arr[i],arr[j])
+ ISWAP(iarr[i],iarr[j])
}
arr[l+1] = arr[j];
arr[j] = a;
diff --git a/src/USER-MISC/compute_pressure_grem.cpp b/src/USER-MISC/compute_pressure_grem.cpp
index 984ac9894e..ae9179cc43 100644
--- a/src/USER-MISC/compute_pressure_grem.cpp
+++ b/src/USER-MISC/compute_pressure_grem.cpp
@@ -116,7 +116,7 @@ void ComputePressureGrem::compute_vector()
if (force->kspace && kspace_virial && force->kspace->scalar_pressure_flag)
error->all(FLERR,"Must use 'kspace_modify pressure/scalar no' for "
- "tensor components with kspace_style msm");
+ "tensor components with kspace_style msm");
// invoke temperature if it hasn't been already
diff --git a/src/USER-MISC/dihedral_quadratic.cpp b/src/USER-MISC/dihedral_quadratic.cpp
index ac261153b4..6841492b2f 100644
--- a/src/USER-MISC/dihedral_quadratic.cpp
+++ b/src/USER-MISC/dihedral_quadratic.cpp
@@ -161,21 +161,21 @@ void DihedralQuadratic::compute(int eflag, int vflag)
int me;
MPI_Comm_rank(world,&me);
if (screen) {
- char str[128];
+ char str[128];
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]);
- error->warning(FLERR,str,0);
- fprintf(screen," 1st atom: %d %g %g %g\n",
- me,x[i1][0],x[i1][1],x[i1][2]);
- fprintf(screen," 2nd atom: %d %g %g %g\n",
- me,x[i2][0],x[i2][1],x[i2][2]);
- fprintf(screen," 3rd atom: %d %g %g %g\n",
- me,x[i3][0],x[i3][1],x[i3][2]);
- fprintf(screen," 4th atom: %d %g %g %g\n",
- me,x[i4][0],x[i4][1],x[i4][2]);
+ atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
+ error->warning(FLERR,str,0);
+ fprintf(screen," 1st atom: %d %g %g %g\n",
+ me,x[i1][0],x[i1][1],x[i1][2]);
+ fprintf(screen," 2nd atom: %d %g %g %g\n",
+ me,x[i2][0],x[i2][1],x[i2][2]);
+ fprintf(screen," 3rd atom: %d %g %g %g\n",
+ me,x[i3][0],x[i3][1],x[i3][2]);
+ fprintf(screen," 4th atom: %d %g %g %g\n",
+ me,x[i4][0],x[i4][1],x[i4][2]);
}
}
@@ -257,7 +257,7 @@ void DihedralQuadratic::compute(int eflag, int vflag)
if (evflag)
ev_tally(i1,i2,i3,i4,nlocal,newton_bond,edihedral,f1,f3,f4,
- vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
+ vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
}
}
diff --git a/src/USER-MISC/dihedral_spherical.h b/src/USER-MISC/dihedral_spherical.h
index a21c322083..0067e5eca8 100644
--- a/src/USER-MISC/dihedral_spherical.h
+++ b/src/USER-MISC/dihedral_spherical.h
@@ -31,7 +31,7 @@ class DihedralSpherical : public Dihedral {
virtual ~DihedralSpherical();
virtual void compute(int, int);
double CalcGeneralizedForces(int, double, double, double,
- double*, double*, double*);
+ double*, double*, double*);
void coeff(int, char **);
void write_restart(FILE *);
void read_restart(FILE *);
diff --git a/src/USER-MISC/fix_filter_corotate.h b/src/USER-MISC/fix_filter_corotate.h
index 67e3fb4f01..7693feb94c 100644
--- a/src/USER-MISC/fix_filter_corotate.h
+++ b/src/USER-MISC/fix_filter_corotate.h
@@ -36,7 +36,7 @@ namespace LAMMPS_NS
FixFilterCorotate(class LAMMPS *, int, char **);
~FixFilterCorotate();
- void setup(int);
+ void setup(int);
void setup_pre_neighbor();
void pre_neighbor();
void setup_pre_force_respa(int,int);
diff --git a/src/USER-MISC/fix_flow_gauss.cpp b/src/USER-MISC/fix_flow_gauss.cpp
index 6817170013..435e3972c8 100644
--- a/src/USER-MISC/fix_flow_gauss.cpp
+++ b/src/USER-MISC/fix_flow_gauss.cpp
@@ -179,8 +179,8 @@ void FixFlowGauss::post_force(int vflag)
for(ii=0; ii<nlocal; ii++)
if (mask[ii] & groupbit)
for (jj=0; jj<3; jj++)
- if (flow[jj])
- f_thisProc[jj] += f[ii][jj];
+ if (flow[jj])
+ f_thisProc[jj] += f[ii][jj];
//add the processor sums together
MPI_Allreduce(f_thisProc, f_tot, 3, MPI_DOUBLE, MPI_SUM, world);
@@ -210,7 +210,7 @@ void FixFlowGauss::post_force(int vflag)
//calculate added energy, since more costly, only do this if requested
if (workflag)
- peAdded += f_app[0]*v[ii][0] + f_app[1]*v[ii][1] + f_app[2]*v[ii][2];
+ peAdded += f_app[0]*v[ii][0] + f_app[1]*v[ii][1] + f_app[2]*v[ii][2];
}
//finish calculation of work done, sum over all procs
diff --git a/src/USER-MISC/fix_gle.cpp b/src/USER-MISC/fix_gle.cpp
index 40d1047648..ecb3390e5e 100644
--- a/src/USER-MISC/fix_gle.cpp
+++ b/src/USER-MISC/fix_gle.cpp
@@ -85,10 +85,10 @@ void StabCholesky(int n, const double* MMt, double* M)
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]);
+ 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.);
- }
+ D[i]=(D[i]>0.?sqrt(D[i]):0.);
+ }
for(i=0; i<n; ++i) for (j=0; j<n; j++) M[midx(n,i,j)]=L[midx(n,i,j)]*D[j];
}
diff --git a/src/USER-MISC/fix_ipi.cpp b/src/USER-MISC/fix_ipi.cpp
index 2715746139..8326ef6667 100644
--- a/src/USER-MISC/fix_ipi.cpp
+++ b/src/USER-MISC/fix_ipi.cpp
@@ -252,7 +252,7 @@ void FixIPI::init()
{
//only opens socket on master process
if (master) {
- if (!socketflag) open_socket(ipisock, inet, port, host, error);
+ if (!socketflag) open_socket(ipisock, inet, port, host, error);
} else ipisock=0;
//! should check for success in socket opening -- but the current open_socket routine dies brutally if unsuccessful
// tell lammps we have assigned a socket
diff --git a/src/USER-MISC/fix_pimd.cpp b/src/USER-MISC/fix_pimd.cpp
index bba6b2e2be..2c89ddda57 100644
--- a/src/USER-MISC/fix_pimd.cpp
+++ b/src/USER-MISC/fix_pimd.cpp
@@ -397,7 +397,7 @@ void FixPIMD::nhc_update_v()
expfac = exp(-dt8 * eta_dot[ichain+1]);
eta_dot[ichain] *= expfac;
eta_dotdot[ichain] = (nhc_eta_mass[i][ichain-1] * eta_dot[ichain-1] * eta_dot[ichain-1]
- - KT) / nhc_eta_mass[i][ichain];
+ - KT) / nhc_eta_mass[i][ichain];
eta_dot[ichain] += eta_dotdot[ichain] * dt4;
eta_dot[ichain] *= expfac;
}
diff --git a/src/USER-MISC/pair_edip_multi.cpp b/src/USER-MISC/pair_edip_multi.cpp
index 3345549ae3..bcef1b013b 100644
--- a/src/USER-MISC/pair_edip_multi.cpp
+++ b/src/USER-MISC/pair_edip_multi.cpp
@@ -168,12 +168,12 @@ void PairEDIPMulti::compute(int eflag, int vflag)
r_ij = sqrt(r_ij);
- // zeta and its derivative dZ/dr
+ // zeta and its derivative dZ/dr
if (r_ij < params[ijparam].cutoffC) zeta_i += 1.0;
else {
- double f, fdr;
- edip_fc(r_ij, ¶ms[ijparam], f, fdr);
+ double f, fdr;
+ edip_fc(r_ij, ¶ms[ijparam], f, fdr);
zeta_i += f;
dzetair = -fdr / r_ij;
@@ -248,24 +248,24 @@ void PairEDIPMulti::compute(int eflag, int vflag)
r_ik = sqrt(r_ik);
- costheta=vec3_dot(dr_ij, dr_ik) / r_ij / r_ik;
+ costheta=vec3_dot(dr_ij, dr_ik) / r_ij / r_ik;
- double v1, v2, v3, v4, v5, v6, v7;
+ double v1, v2, v3, v4, v5, v6, v7;
- edip_fcut3(r_ij, ¶ms[ijparam], v1, v2);
- edip_fcut3(r_ik, ¶ms[ikparam], v3, v4);
- edip_h(costheta, zeta_i, ¶ms[ijkparam], v5, v6, v7);
+ edip_fcut3(r_ij, ¶ms[ijparam], v1, v2);
+ edip_fcut3(r_ik, ¶ms[ikparam], v3, v4);
+ edip_h(costheta, zeta_i, ¶ms[ijkparam], v5, v6, v7);
- // potential energy and forces
- evdwl = v1 * v3 * v5;
- dtripleZ += v1 * v3 * v7;
+ // potential energy and forces
+ evdwl = v1 * v3 * v5;
+ dtripleZ += v1 * v3 * v7;
- double dri[3], drj[3], drk[3];
+ double dri[3], drj[3], drk[3];
double dhl, dfr;
dhl = v1 * v3 * v6;
- costheta_d(dr_ij, r_ij, dr_ik, r_ik, dri, drj, drk);
+ costheta_d(dr_ij, r_ij, dr_ik, r_ik, dri, drj, drk);
f_ij[0] = -dhl * drj[0];
f_ij[1] = -dhl * drj[1];
@@ -315,7 +315,7 @@ void PairEDIPMulti::compute(int eflag, int vflag)
delz = preForceCoord[preForceCoord_counter+3];
j = static_cast<int> (preForceCoord[preForceCoord_counter+4]);
- dzetair *= (dpairZ + dtripleZ);
+ dzetair *= (dpairZ + dtripleZ);
f[j][0] += dzetair * delx;
f[j][1] += dzetair * dely;
@@ -586,8 +586,8 @@ void PairEDIPMulti::coeff(int narg, char **arg)
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
if (map[i] >= 0 && map[j] >= 0) {
- setflag[i][j] = 1;
- count++;
+ setflag[i][j] = 1;
+ count++;
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
@@ -661,8 +661,8 @@ void PairEDIPMulti::read_file(char *file)
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fp);
if (ptr == NULL) {
- eof = 1;
- fclose(fp);
+ eof = 1;
+ fclose(fp);
} else n = strlen(line) + 1;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
@@ -683,8 +683,8 @@ void PairEDIPMulti::read_file(char *file)
if (comm->me == 0) {
ptr = fgets(&line[n],MAXLINE-n,fp);
if (ptr == NULL) {
- eof = 1;
- fclose(fp);
+ eof = 1;
+ fclose(fp);
} else n = strlen(line) + 1;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
@@ -723,7 +723,7 @@ void PairEDIPMulti::read_file(char *file)
if (nparams == maxparam) {
maxparam += DELTA;
params = (Param *) memory->srealloc(params,maxparam*sizeof(Param),
- "pair:params");
+ "pair:params");
}
params[nparams].ielement = ielement;
@@ -748,11 +748,11 @@ void PairEDIPMulti::read_file(char *file)
params[nparams].u4 = atof(words[19]);
if (params[nparams].A < 0.0 || params[nparams].B < 0.0 ||
- params[nparams].cutoffA < 0.0 || params[nparams].cutoffC < 0.0 ||
- params[nparams].alpha < 0.0 || params[nparams].beta < 0.0 ||
- params[nparams].eta < 0.0 || params[nparams].gamma < 0.0 ||
- params[nparams].lambda < 0.0 || params[nparams].mu < 0.0 ||
- params[nparams].rho < 0.0 || params[nparams].sigma < 0.0)
+ params[nparams].cutoffA < 0.0 || params[nparams].cutoffC < 0.0 ||
+ params[nparams].alpha < 0.0 || params[nparams].beta < 0.0 ||
+ params[nparams].eta < 0.0 || params[nparams].gamma < 0.0 ||
+ params[nparams].lambda < 0.0 || params[nparams].mu < 0.0 ||
+ params[nparams].rho < 0.0 || params[nparams].sigma < 0.0)
error->all(FLERR,"Illegal EDIP parameter");
nparams++;
@@ -778,16 +778,16 @@ void PairEDIPMulti::setup()
for (i = 0; i < nelements; i++)
for (j = 0; j < nelements; j++)
for (k = 0; k < nelements; k++) {
- n = -1;
- for (m = 0; m < nparams; m++) {
- 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;
- }
- }
- if (n < 0) error->all(FLERR,"Potential file is missing an entry");
- elem2param[i][j][k] = n;
+ n = -1;
+ for (m = 0; m < nparams; m++) {
+ 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;
+ }
+ }
+ if (n < 0) error->all(FLERR,"Potential file is missing an entry");
+ elem2param[i][j][k] = n;
}
// set cutoff square
diff --git a/src/USER-MISC/pair_edip_multi.h b/src/USER-MISC/pair_edip_multi.h
index fd94594d93..26433a66fa 100644
--- a/src/USER-MISC/pair_edip_multi.h
+++ b/src/USER-MISC/pair_edip_multi.h
@@ -95,7 +95,7 @@ class PairEDIPMulti : public Pair {
//dr_ij=r_j - r_i
//dr_ik=r_k - r_i
void costheta_d(double *dr_ij, double r_ij, double *dr_ik, double r_ik,
- double *dri, double *drj, double *drk)
+ double *dri, double *drj, double *drk)
{
double costheta;
diff --git a/src/USER-MISC/pair_gauss_cut.cpp b/src/USER-MISC/pair_gauss_cut.cpp
index 4408545c34..c1daf9c923 100644
--- a/src/USER-MISC/pair_gauss_cut.cpp
+++ b/src/USER-MISC/pair_gauss_cut.cpp
@@ -226,7 +226,7 @@ double PairGaussCut::init_one(int i, int j)
{
if (setflag[i][j] == 0) {
hgauss[i][j] = mix_energy(fabs(hgauss[i][i]), fabs(hgauss[j][j]),
- fabs(sigmah[i][i]), fabs(sigmah[j][j]));
+ fabs(sigmah[i][i]), fabs(sigmah[j][j]));
// If either of the particles is repulsive (ie, if hgauss > 0),
// then the interaction between both is repulsive.
diff --git a/src/USER-MISC/pair_lj_sf_dipole_sf.cpp b/src/USER-MISC/pair_lj_sf_dipole_sf.cpp
index fb63638b52..ab342fd055 100644
--- a/src/USER-MISC/pair_lj_sf_dipole_sf.cpp
+++ b/src/USER-MISC/pair_lj_sf_dipole_sf.cpp
@@ -535,8 +535,8 @@ void PairLJSFDipoleSF::read_restart_settings(FILE *fp)
// PairLJSFDipoleSF: calculation of force is missing (to be implemented)
double PairLJSFDipoleSF::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
- double &fforce)
+ double factor_coul, double factor_lj,
+ double &fforce)
{
double r2inv,r6inv;
double pdotp,pidotr,pjdotr,pre1,delx,dely,delz;
@@ -580,7 +580,7 @@ double PairLJSFDipoleSF::single(int i, int j, int itype, int jtype, double rsq,
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;
bfac = 1.0 - 4.0*rsq*sqrt(rsq)*rcutcoul2inv*sqrt(rcutcoul2inv) +
- 3.0*rsq*rsq*rcutcoul2inv*rcutcoul2inv;
+ 3.0*rsq*rsq*rcutcoul2inv*rcutcoul2inv;
}
if (mu[i][3] > 0.0 && q[j] != 0.0) {
r3inv = r2inv*rinv;
@@ -588,7 +588,7 @@ double PairLJSFDipoleSF::single(int i, int j, int itype, int jtype, double rsq,
pidotr = mu[i][0]*delx + mu[i][1]*dely + mu[i][2]*delz;
rcutcoul2inv=1.0/cut_coulsq[itype][jtype];
pqfac = 1.0 - 3.0*rsq*rcutcoul2inv +
- 2.0*rsq*sqrt(rsq)*rcutcoul2inv*sqrt(rcutcoul2inv);
+ 2.0*rsq*sqrt(rsq)*rcutcoul2inv*sqrt(rcutcoul2inv);
}
if (mu[j][3] > 0.0 && qtmp != 0.0) {
r3inv = r2inv*rinv;
@@ -596,7 +596,7 @@ double PairLJSFDipoleSF::single(int i, int j, int itype, int jtype, double rsq,
pjdotr = mu[j][0]*delx + mu[j][1]*dely + mu[j][2]*delz;
rcutcoul2inv=1.0/cut_coulsq[itype][jtype];
qpfac = 1.0 - 3.0*rsq*rcutcoul2inv +
- 2.0*rsq*sqrt(rsq)*rcutcoul2inv*sqrt(rcutcoul2inv);
+ 2.0*rsq*sqrt(rsq)*rcutcoul2inv*sqrt(rcutcoul2inv);
}
}
if (rsq < cut_ljsq[itype][jtype]) {
diff --git a/src/USER-MISC/pair_meam_spline.cpp b/src/USER-MISC/pair_meam_spline.cpp
index 0148ed51cb..10659e8654 100644
--- a/src/USER-MISC/pair_meam_spline.cpp
+++ b/src/USER-MISC/pair_meam_spline.cpp
@@ -600,7 +600,7 @@ double PairMEAMSpline::init_one(int i, int j)
/* ---------------------------------------------------------------------- */
int PairMEAMSpline::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int pbc_flag, int *pbc)
{
int* list_iter = list;
int* list_iter_end = list + n;
@@ -640,7 +640,7 @@ double PairMEAMSpline::memory_usage()
/// Parses the spline knots from a text file.
void PairMEAMSpline::SplineFunction::parse(FILE* fp, Error* error,
- bool isNewFormat)
+ bool isNewFormat)
{
char line[MAXLINE];
@@ -756,7 +756,7 @@ void PairMEAMSpline::SplineFunction::communicate(MPI_Comm& world, int me)
///
/// This function is for debugging only!
void PairMEAMSpline::SplineFunction::writeGnuplot(const char* filename,
- const char* title) const
+ const char* title) const
{
FILE* fp = fopen(filename, "w");
fprintf(fp, "#!/usr/bin/env gnuplot\n");
diff --git a/src/USER-MISC/pair_meam_spline.h b/src/USER-MISC/pair_meam_spline.h
index d3554f056e..7b5ff3bf6d 100644
--- a/src/USER-MISC/pair_meam_spline.h
+++ b/src/USER-MISC/pair_meam_spline.h
@@ -139,7 +139,7 @@ protected:
double a = (Xs[khi] - x)/h;
double b = 1.0 - a; // = (x - X[klo])/h
return a * Y[klo] + b * Y[khi] +
- ((a*a*a - a) * Y2[klo] + (b*b*b - b) * Y2[khi])*(h*h)/6.0;
+ ((a*a*a - a) * Y2[klo] + (b*b*b - b) * Y2[khi])*(h*h)/6.0;
#else
// For a spline with regular grid, we directly calculate the interval X is in.
int klo = (int)(x / h);
@@ -147,7 +147,7 @@ protected:
double a = Xs[khi] - x;
double b = h - a;
return Y[khi] - a * Ydelta[klo] +
- ((a*a - hsq) * a * Y2[klo] + (b*b - hsq) * b * Y2[khi]);
+ ((a*a - hsq) * a * Y2[klo] + (b*b - hsq) * b * Y2[khi]);
#endif
}
}
@@ -179,11 +179,11 @@ protected:
double a = (Xs[khi] - x)/h;
double b = 1.0 - a; // = (x - X[klo])/h
deriv = (Y[khi] - Y[klo]) / h +
- ((3.0*b*b - 1.0) * Y2[khi] -
- (3.0*a*a - 1.0) * Y2[klo]) * h / 6.0;
+ ((3.0*b*b - 1.0) * Y2[khi] -
+ (3.0*a*a - 1.0) * Y2[klo]) * h / 6.0;
return a * Y[klo] + b * Y[khi] +
- ((a*a*a - a) * Y2[klo] +
- (b*b*b - b) * Y2[khi]) * (h*h) / 6.0;
+ ((a*a*a - a) * Y2[klo] +
+ (b*b*b - b) * Y2[khi]) * (h*h) / 6.0;
#else
// For a spline with regular grid, we directly calculate the interval X is in.
int klo = (int)(x / h);
@@ -191,9 +191,9 @@ protected:
double a = Xs[khi] - x;
double b = h - a;
deriv = Ydelta[klo] + ((3.0*b*b - hsq) * Y2[khi]
- - (3.0*a*a - hsq) * Y2[klo]);
+ - (3.0*a*a - hsq) * Y2[klo]);
return Y[khi] - a * Ydelta[klo] +
- ((a*a - hsq) * a * Y2[klo] + (b*b - hsq) * b * Y2[khi]);
+ ((a*a - hsq) * a * Y2[klo] + (b*b - hsq) * b * Y2[khi]);
#endif
}
}
diff --git a/src/USER-MISC/pair_momb.cpp b/src/USER-MISC/pair_momb.cpp
index 0d8d2e060e..98339bf60a 100644
--- a/src/USER-MISC/pair_momb.cpp
+++ b/src/USER-MISC/pair_momb.cpp
@@ -366,8 +366,8 @@ void PairMomb::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
double PairMomb::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
- double &fforce)
+ double factor_coul, double factor_lj,
+ double &fforce)
{
double r,dr,dexp,phi,r2inv,r6inv,ddexp,invexp;
diff --git a/src/USER-MISC/temper_npt.cpp b/src/USER-MISC/temper_npt.cpp
index 60f9313fdd..66ab92a43b 100644
--- a/src/USER-MISC/temper_npt.cpp
+++ b/src/USER-MISC/temper_npt.cpp
@@ -264,16 +264,16 @@ void TemperNPT::command(int narg, char **arg)
if (partner != -1) {
if (me_universe > partner) {
MPI_Send(&pe,1,MPI_DOUBLE,partner,0,universe->uworld);
- }
+ }
else {
- MPI_Recv(&pe_partner,1,MPI_DOUBLE,partner,0,universe->uworld,MPI_STATUS_IGNORE);
- }
+ MPI_Recv(&pe_partner,1,MPI_DOUBLE,partner,0,universe->uworld,MPI_STATUS_IGNORE);
+ }
if (me_universe > partner) {
- MPI_Send(&vol,1, MPI_DOUBLE,partner,0,universe->uworld);
- }
+ MPI_Send(&vol,1, MPI_DOUBLE,partner,0,universe->uworld);
+ }
else {
- MPI_Recv(&vol_partner,1,MPI_DOUBLE,partner,0,universe->uworld,MPI_STATUS_IGNORE);
- }
+ MPI_Recv(&vol_partner,1,MPI_DOUBLE,partner,0,universe->uworld,MPI_STATUS_IGNORE);
+ }
// Acceptance criteria changed for NPT ensemble
if (me_universe < partner) {
press_units = press_set/nktv2p;
diff --git a/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp b/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp
index 415348cbec..baa42a4bc0 100644
--- a/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp
+++ b/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp
@@ -400,7 +400,7 @@ void PairBuck6dCoulGaussDSF::write_restart(FILE *fp)
fwrite(&buck6d4[i][j],sizeof(double),1,fp);
fwrite(&alpha_ij[i][j],sizeof(double),1,fp);
fwrite(&cut_lj[i][j],sizeof(double),1,fp);
- }
+ }
}
}
diff --git a/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp b/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp
index 46ef91f0b1..36018613a2 100644
--- a/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp
+++ b/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp
@@ -433,7 +433,7 @@ void PairBuck6dCoulGaussLong::write_restart(FILE *fp)
fwrite(&buck6d4[i][j],sizeof(double),1,fp);
fwrite(&alpha_ij[i][j],sizeof(double),1,fp);
fwrite(&cut_lj[i][j],sizeof(double),1,fp);
- }
+ }
}
}
diff --git a/src/USER-OMP/angle_dipole_omp.cpp b/src/USER-OMP/angle_dipole_omp.cpp
index f582ce4c41..2fa6fff0ef 100644
--- a/src/USER-OMP/angle_dipole_omp.cpp
+++ b/src/USER-OMP/angle_dipole_omp.cpp
@@ -126,7 +126,7 @@ void AngleDipoleOMP::eval(int nfrom, int nto, ThrData * const thr)
torque[iDip][0] += delTx;
torque[iDip][1] += delTy;
torque[iDip][2] += delTz;
-
+
// Force couple that counterbalances dipolar torque
fx = dely*delTz - delz*delTy; // direction (fi): - r x (-T)
fy = delz*delTx - delx*delTz;
diff --git a/src/USER-OMP/fix_omp.cpp b/src/USER-OMP/fix_omp.cpp
index b3fe2c29e8..2a3717da0d 100644
--- a/src/USER-OMP/fix_omp.cpp
+++ b/src/USER-OMP/fix_omp.cpp
@@ -110,13 +110,13 @@ FixOMP::FixOMP(LAMMPS *lmp, int narg, char **arg)
if (screen) {
if (reset_thr)
- fprintf(screen,"set %d OpenMP thread(s) per MPI task\n", nthreads);
+ fprintf(screen,"set %d OpenMP thread(s) per MPI task\n", nthreads);
fprintf(screen,"using %s neighbor list subroutines\n", nmode);
}
if (logfile) {
if (reset_thr)
- fprintf(logfile,"set %d OpenMP thread(s) per MPI task\n", nthreads);
+ fprintf(logfile,"set %d OpenMP thread(s) per MPI task\n", nthreads);
fprintf(logfile,"using %s neighbor list subroutines\n", nmode);
}
#else
@@ -226,29 +226,29 @@ void FixOMP::init()
// determine which is the last force style with OpenMP
// support as this is the one that has to reduce the forces
-#define CheckStyleForOMP(name) \
- check_hybrid = 0; \
- if (force->name) { \
- if ( (strcmp(force->name ## _style,"hybrid") == 0) || \
- (strcmp(force->name ## _style,"hybrid/overlay") == 0) ) \
- check_hybrid=1; \
- if (force->name->suffix_flag & Suffix::OMP) { \
- last_force_name = (const char *) #name; \
- last_omp_name = force->name ## _style; \
- last_omp_style = (void *) force->name; \
- } \
+#define CheckStyleForOMP(name) \
+ check_hybrid = 0; \
+ if (force->name) { \
+ if ( (strcmp(force->name ## _style,"hybrid") == 0) || \
+ (strcmp(force->name ## _style,"hybrid/overlay") == 0) ) \
+ check_hybrid=1; \
+ if (force->name->suffix_flag & Suffix::OMP) { \
+ last_force_name = (const char *) #name; \
+ last_omp_name = force->name ## _style; \
+ last_omp_style = (void *) force->name; \
+ } \
}
#define CheckHybridForOMP(name,Class) \
- if (check_hybrid) { \
+ if (check_hybrid) { \
Class ## Hybrid *style = (Class ## Hybrid *) force->name; \
- for (int i=0; i < style->nstyles; i++) { \
+ for (int i=0; i < style->nstyles; i++) { \
if (style->styles[i]->suffix_flag & Suffix::OMP) { \
- last_force_name = (const char *) #name; \
- last_omp_name = style->keywords[i]; \
- last_omp_style = style->styles[i]; \
- } \
- } \
+ last_force_name = (const char *) #name; \
+ last_omp_name = style->keywords[i]; \
+ last_omp_style = style->styles[i]; \
+ } \
+ } \
}
if (kspace_split <= 0) {
diff --git a/src/USER-OMP/fix_rigid_nh_omp.cpp b/src/USER-OMP/fix_rigid_nh_omp.cpp
index f2d6d8513b..9341f83079 100644
--- a/src/USER-OMP/fix_rigid_nh_omp.cpp
+++ b/src/USER-OMP/fix_rigid_nh_omp.cpp
@@ -42,8 +42,8 @@ using namespace LAMMPS_NS;
using namespace FixConst;
using namespace MathConst;
-enum{SINGLE,MOLECULE,GROUP}; // same as in FixRigid
-enum{ISO,ANISO,TRICLINIC}; // same as in FixRigid
+enum{SINGLE,MOLECULE,GROUP}; // same as in FixRigid
+enum{ISO,ANISO,TRICLINIC}; // same as in FixRigid
#define EINERTIA 0.4 // moment of inertia prefactor for ellipsoid
@@ -294,9 +294,9 @@ void FixRigidNHOMP::final_integrate()
s5 += dx*f[i].y - dy*f[i].x;
if (extended && (eflags[i] & TORQUE)) {
- s3 += torque_one[i][0];
- s4 += torque_one[i][1];
- s5 += torque_one[i][2];
+ s3 += torque_one[i][0];
+ s4 += torque_one[i][1];
+ s5 += torque_one[i][2];
}
}
sum[0][0]=s0; sum[0][1]=s1; sum[0][2]=s2;
@@ -315,28 +315,28 @@ void FixRigidNHOMP::final_integrate()
#pragma omp parallel for default(none) private(i) shared(ib) reduction(+:s0,s1,s2,s3,s4,s5)
#endif
for (i = 0; i < nlocal; i++) {
- const int ibody = body[i];
- if (ibody != ib) continue;
-
- s0 += f[i].x;
- s1 += f[i].y;
- s2 += f[i].z;
-
- double unwrap[3];
- domain->unmap(x[i],xcmimage[i],unwrap);
- const double dx = unwrap[0] - xcm[ibody][0];
- const double dy = unwrap[1] - xcm[ibody][1];
- const double dz = unwrap[2] - xcm[ibody][2];
-
- s3 += dy*f[i].z - dz*f[i].y;
- s4 += dz*f[i].x - dx*f[i].z;
- s5 += dx*f[i].y - dy*f[i].x;
-
- if (extended && (eflags[i] & TORQUE)) {
- s3 += torque_one[i][0];
- s4 += torque_one[i][1];
- s5 += torque_one[i][2];
- }
+ const int ibody = body[i];
+ if (ibody != ib) continue;
+
+ s0 += f[i].x;
+ s1 += f[i].y;
+ s2 += f[i].z;
+
+ double unwrap[3];
+ domain->unmap(x[i],xcmimage[i],unwrap);
+ const double dx = unwrap[0] - xcm[ibody][0];
+ const double dy = unwrap[1] - xcm[ibody][1];
+ const double dz = unwrap[2] - xcm[ibody][2];
+
+ s3 += dy*f[i].z - dz*f[i].y;
+ s4 += dz*f[i].x - dx*f[i].z;
+ s5 += dx*f[i].y - dy*f[i].x;
+
+ if (extended && (eflags[i] & TORQUE)) {
+ s3 += torque_one[i][0];
+ s4 += torque_one[i][1];
+ s5 += torque_one[i][2];
+ }
}
sum[ib][0]=s0; sum[ib][1]=s1; sum[ib][2]=s2;
@@ -363,31 +363,31 @@ void FixRigidNHOMP::final_integrate()
#endif
for (int i = 0; i < nlocal; i++) {
- const int ibody = body[i];
- if ((ibody < 0) || (ibody % nthreads != tid)) continue;
-
- double unwrap[3];
- domain->unmap(x[i],xcmimage[i],unwrap);
- const double dx = unwrap[0] - xcm[ibody][0];
- const double dy = unwrap[1] - xcm[ibody][1];
- const double dz = unwrap[2] - xcm[ibody][2];
-
- const double s0 = f[i].x;
- const double s1 = f[i].y;
- const double s2 = f[i].z;
-
- double s3 = dy*s2 - dz*s1;
- double s4 = dz*s0 - dx*s2;
- double s5 = dx*s1 - dy*s0;
-
- if (extended && (eflags[i] & TORQUE)) {
- s3 += torque_one[i][0];
- s4 += torque_one[i][1];
- s5 += torque_one[i][2];
- }
-
- sum[ibody][0] += s0; sum[ibody][1] += s1; sum[ibody][2] += s2;
- sum[ibody][3] += s3; sum[ibody][4] += s4; sum[ibody][5] += s5;
+ const int ibody = body[i];
+ if ((ibody < 0) || (ibody % nthreads != tid)) continue;
+
+ double unwrap[3];
+ domain->unmap(x[i],xcmimage[i],unwrap);
+ const double dx = unwrap[0] - xcm[ibody][0];
+ const double dy = unwrap[1] - xcm[ibody][1];
+ const double dz = unwrap[2] - xcm[ibody][2];
+
+ const double s0 = f[i].x;
+ const double s1 = f[i].y;
+ const double s2 = f[i].z;
+
+ double s3 = dy*s2 - dz*s1;
+ double s4 = dz*s0 - dx*s2;
+ double s5 = dx*s1 - dy*s0;
+
+ if (extended && (eflags[i] & TORQUE)) {
+ s3 += torque_one[i][0];
+ s4 += torque_one[i][1];
+ s5 += torque_one[i][2];
+ }
+
+ sum[ibody][0] += s0; sum[ibody][1] += s1; sum[ibody][2] += s2;
+ sum[ibody][3] += s3; sum[ibody][4] += s4; sum[ibody][5] += s5;
}
}
} else
@@ -678,22 +678,22 @@ void FixRigidNHOMP::set_xv_thr()
// Fix::v_tally() is not thread safe, so we do this manually here
// accumulate global virial into thread-local variables for reduction
if (vflag_global) {
- v0 += vr[0];
- v1 += vr[1];
- v2 += vr[2];
- v3 += vr[3];
- v4 += vr[4];
- v5 += vr[5];
+ v0 += vr[0];
+ v1 += vr[1];
+ v2 += vr[2];
+ v3 += vr[3];
+ v4 += vr[4];
+ v5 += vr[5];
}
// accumulate per atom virial directly since we parallelize over atoms.
if (vflag_atom) {
- vatom[i][0] += vr[0];
- vatom[i][1] += vr[1];
- vatom[i][2] += vr[2];
- vatom[i][3] += vr[3];
- vatom[i][4] += vr[4];
- vatom[i][5] += vr[5];
+ vatom[i][0] += vr[0];
+ vatom[i][1] += vr[1];
+ vatom[i][2] += vr[2];
+ vatom[i][3] += vr[3];
+ vatom[i][4] += vr[4];
+ vatom[i][5] += vr[5];
}
}
}
@@ -868,22 +868,22 @@ void FixRigidNHOMP::set_v_thr()
// Fix::v_tally() is not thread safe, so we do this manually here
// accumulate global virial into thread-local variables and reduce them later
if (vflag_global) {
- v0 += vr[0];
- v1 += vr[1];
- v2 += vr[2];
- v3 += vr[3];
- v4 += vr[4];
- v5 += vr[5];
+ v0 += vr[0];
+ v1 += vr[1];
+ v2 += vr[2];
+ v3 += vr[3];
+ v4 += vr[4];
+ v5 += vr[5];
}
// accumulate per atom virial directly since we parallelize over atoms.
if (vflag_atom) {
- vatom[i][0] += vr[0];
- vatom[i][1] += vr[1];
- vatom[i][2] += vr[2];
- vatom[i][3] += vr[3];
- vatom[i][4] += vr[4];
- vatom[i][5] += vr[5];
+ vatom[i][0] += vr[0];
+ vatom[i][1] += vr[1];
+ vatom[i][2] += vr[2];
+ vatom[i][3] += vr[3];
+ vatom[i][4] += vr[4];
+ vatom[i][5] += vr[5];
}
}
} // end of parallel for
diff --git a/src/USER-OMP/fix_rigid_omp.cpp b/src/USER-OMP/fix_rigid_omp.cpp
index f3ef1d2985..6f084c628c 100644
--- a/src/USER-OMP/fix_rigid_omp.cpp
+++ b/src/USER-OMP/fix_rigid_omp.cpp
@@ -37,7 +37,7 @@ using namespace LAMMPS_NS;
using namespace FixConst;
using namespace MathConst;
-enum{SINGLE,MOLECULE,GROUP}; // same as in FixRigid
+enum{SINGLE,MOLECULE,GROUP}; // same as in FixRigid
#define EINERTIA 0.2 // moment of inertia prefactor for ellipsoid
@@ -145,9 +145,9 @@ void FixRigidOMP::final_integrate()
s5 += dx*f[i].y - dy*f[i].x;
if (extended && (eflags[i] & TORQUE)) {
- s3 += torque_one[i][0];
- s4 += torque_one[i][1];
- s5 += torque_one[i][2];
+ s3 += torque_one[i][0];
+ s4 += torque_one[i][1];
+ s5 += torque_one[i][2];
}
}
sum[0][0]=s0; sum[0][1]=s1; sum[0][2]=s2;
@@ -166,28 +166,28 @@ void FixRigidOMP::final_integrate()
#pragma omp parallel for default(none) private(i) shared(ib) reduction(+:s0,s1,s2,s3,s4,s5)
#endif
for (i = 0; i < nlocal; i++) {
- const int ibody = body[i];
- if (ibody != ib) continue;
-
- s0 += f[i].x;
- s1 += f[i].y;
- s2 += f[i].z;
-
- double unwrap[3];
- domain->unmap(x[i],xcmimage[i],unwrap);
- const double dx = unwrap[0] - xcm[ibody][0];
- const double dy = unwrap[1] - xcm[ibody][1];
- const double dz = unwrap[2] - xcm[ibody][2];
-
- s3 += dy*f[i].z - dz*f[i].y;
- s4 += dz*f[i].x - dx*f[i].z;
- s5 += dx*f[i].y - dy*f[i].x;
-
- if (extended && (eflags[i] & TORQUE)) {
- s3 += torque_one[i][0];
- s4 += torque_one[i][1];
- s5 += torque_one[i][2];
- }
+ const int ibody = body[i];
+ if (ibody != ib) continue;
+
+ s0 += f[i].x;
+ s1 += f[i].y;
+ s2 += f[i].z;
+
+ double unwrap[3];
+ domain->unmap(x[i],xcmimage[i],unwrap);
+ const double dx = unwrap[0] - xcm[ibody][0];
+ const double dy = unwrap[1] - xcm[ibody][1];
+ const double dz = unwrap[2] - xcm[ibody][2];
+
+ s3 += dy*f[i].z - dz*f[i].y;
+ s4 += dz*f[i].x - dx*f[i].z;
+ s5 += dx*f[i].y - dy*f[i].x;
+
+ if (extended && (eflags[i] & TORQUE)) {
+ s3 += torque_one[i][0];
+ s4 += torque_one[i][1];
+ s5 += torque_one[i][2];
+ }
}
sum[ib][0]=s0; sum[ib][1]=s1; sum[ib][2]=s2;
@@ -214,31 +214,31 @@ void FixRigidOMP::final_integrate()
#endif
for (int i = 0; i < nlocal; i++) {
- const int ibody = body[i];
- if ((ibody < 0) || (ibody % nthreads != tid)) continue;
-
- double unwrap[3];
- domain->unmap(x[i],xcmimage[i],unwrap);
- const double dx = unwrap[0] - xcm[ibody][0];
- const double dy = unwrap[1] - xcm[ibody][1];
- const double dz = unwrap[2] - xcm[ibody][2];
-
- const double s0 = f[i].x;
- const double s1 = f[i].y;
- const double s2 = f[i].z;
-
- double s3 = dy*s2 - dz*s1;
- double s4 = dz*s0 - dx*s2;
- double s5 = dx*s1 - dy*s0;
-
- if (extended && (eflags[i] & TORQUE)) {
- s3 += torque_one[i][0];
- s4 += torque_one[i][1];
- s5 += torque_one[i][2];
- }
-
- sum[ibody][0] += s0; sum[ibody][1] += s1; sum[ibody][2] += s2;
- sum[ibody][3] += s3; sum[ibody][4] += s4; sum[ibody][5] += s5;
+ const int ibody = body[i];
+ if ((ibody < 0) || (ibody % nthreads != tid)) continue;
+
+ double unwrap[3];
+ domain->unmap(x[i],xcmimage[i],unwrap);
+ const double dx = unwrap[0] - xcm[ibody][0];
+ const double dy = unwrap[1] - xcm[ibody][1];
+ const double dz = unwrap[2] - xcm[ibody][2];
+
+ const double s0 = f[i].x;
+ const double s1 = f[i].y;
+ const double s2 = f[i].z;
+
+ double s3 = dy*s2 - dz*s1;
+ double s4 = dz*s0 - dx*s2;
+ double s5 = dx*s1 - dy*s0;
+
+ if (extended && (eflags[i] & TORQUE)) {
+ s3 += torque_one[i][0];
+ s4 += torque_one[i][1];
+ s5 += torque_one[i][2];
+ }
+
+ sum[ibody][0] += s0; sum[ibody][1] += s1; sum[ibody][2] += s2;
+ sum[ibody][3] += s3; sum[ibody][4] += s4; sum[ibody][5] += s5;
}
}
} else
@@ -393,22 +393,22 @@ void FixRigidOMP::set_xv_thr()
// Fix::v_tally() is not thread safe, so we do this manually here
// accumulate global virial into thread-local variables for reduction
if (vflag_global) {
- v0 += vr[0];
- v1 += vr[1];
- v2 += vr[2];
- v3 += vr[3];
- v4 += vr[4];
- v5 += vr[5];
+ v0 += vr[0];
+ v1 += vr[1];
+ v2 += vr[2];
+ v3 += vr[3];
+ v4 += vr[4];
+ v5 += vr[5];
}
// accumulate per atom virial directly since we parallelize over atoms.
if (vflag_atom) {
- vatom[i][0] += vr[0];
- vatom[i][1] += vr[1];
- vatom[i][2] += vr[2];
- vatom[i][3] += vr[3];
- vatom[i][4] += vr[4];
- vatom[i][5] += vr[5];
+ vatom[i][0] += vr[0];
+ vatom[i][1] += vr[1];
+ vatom[i][2] += vr[2];
+ vatom[i][3] += vr[3];
+ vatom[i][4] += vr[4];
+ vatom[i][5] += vr[5];
}
}
}
@@ -583,22 +583,22 @@ void FixRigidOMP::set_v_thr()
// Fix::v_tally() is not thread safe, so we do this manually here
// accumulate global virial into thread-local variables and reduce them later
if (vflag_global) {
- v0 += vr[0];
- v1 += vr[1];
- v2 += vr[2];
- v3 += vr[3];
- v4 += vr[4];
- v5 += vr[5];
+ v0 += vr[0];
+ v1 += vr[1];
+ v2 += vr[2];
+ v3 += vr[3];
+ v4 += vr[4];
+ v5 += vr[5];
}
// accumulate per atom virial directly since we parallelize over atoms.
if (vflag_atom) {
- vatom[i][0] += vr[0];
- vatom[i][1] += vr[1];
- vatom[i][2] += vr[2];
- vatom[i][3] += vr[3];
- vatom[i][4] += vr[4];
- vatom[i][5] += vr[5];
+ vatom[i][0] += vr[0];
+ vatom[i][1] += vr[1];
+ vatom[i][2] += vr[2];
+ vatom[i][3] += vr[3];
+ vatom[i][4] += vr[4];
+ vatom[i][5] += vr[5];
}
}
} // end of parallel for
diff --git a/src/USER-OMP/fix_rigid_small_omp.cpp b/src/USER-OMP/fix_rigid_small_omp.cpp
index e3939a829d..156ef8a2d7 100644
--- a/src/USER-OMP/fix_rigid_small_omp.cpp
+++ b/src/USER-OMP/fix_rigid_small_omp.cpp
@@ -343,22 +343,22 @@ void FixRigidSmallOMP::set_xv_thr()
// Fix::v_tally() is not thread safe, so we do this manually here
// accumulate global virial into thread-local variables for reduction
if (vflag_global) {
- v0 += vr[0];
- v1 += vr[1];
- v2 += vr[2];
- v3 += vr[3];
- v4 += vr[4];
- v5 += vr[5];
+ v0 += vr[0];
+ v1 += vr[1];
+ v2 += vr[2];
+ v3 += vr[3];
+ v4 += vr[4];
+ v5 += vr[5];
}
// accumulate per atom virial directly since we parallelize over atoms.
if (vflag_atom) {
- vatom[i][0] += vr[0];
- vatom[i][1] += vr[1];
- vatom[i][2] += vr[2];
- vatom[i][3] += vr[3];
- vatom[i][4] += vr[4];
- vatom[i][5] += vr[5];
+ vatom[i][0] += vr[0];
+ vatom[i][1] += vr[1];
+ vatom[i][2] += vr[2];
+ vatom[i][3] += vr[3];
+ vatom[i][4] += vr[4];
+ vatom[i][5] += vr[5];
}
}
}
@@ -529,22 +529,22 @@ void FixRigidSmallOMP::set_v_thr()
// Fix::v_tally() is not thread safe, so we do this manually here
// accumulate global virial into thread-local variables and reduce them later
if (vflag_global) {
- v0 += vr[0];
- v1 += vr[1];
- v2 += vr[2];
- v3 += vr[3];
- v4 += vr[4];
- v5 += vr[5];
+ v0 += vr[0];
+ v1 += vr[1];
+ v2 += vr[2];
+ v3 += vr[3];
+ v4 += vr[4];
+ v5 += vr[5];
}
// accumulate per atom virial directly since we parallelize over atoms.
if (vflag_atom) {
- vatom[i][0] += vr[0];
- vatom[i][1] += vr[1];
- vatom[i][2] += vr[2];
- vatom[i][3] += vr[3];
- vatom[i][4] += vr[4];
- vatom[i][5] += vr[5];
+ vatom[i][0] += vr[0];
+ vatom[i][1] += vr[1];
+ vatom[i][2] += vr[2];
+ vatom[i][3] += vr[3];
+ vatom[i][4] += vr[4];
+ vatom[i][5] += vr[5];
}
}
} // end of parallel for
diff --git a/src/USER-OMP/improper_fourier_omp.cpp b/src/USER-OMP/improper_fourier_omp.cpp
index 9e7912e335..c1699baf02 100644
--- a/src/USER-OMP/improper_fourier_omp.cpp
+++ b/src/USER-OMP/improper_fourier_omp.cpp
@@ -117,36 +117,36 @@ void ImproperFourierOMP::eval(int nfrom, int nto, ThrData * const thr)
vb3z = x[i4][2] - x[i1][2];
add1_thr<EVFLAG,EFLAG,NEWTON_BOND>(i1,i2,i3,i4,type,
- vb1x,vb1y,vb1z,
- vb2x,vb2y,vb2z,
- vb3x,vb3y,vb3z,thr);
+ vb1x,vb1y,vb1z,
+ vb2x,vb2y,vb2z,
+ vb3x,vb3y,vb3z,thr);
if ( all[type] ) {
add1_thr<EVFLAG,EFLAG,NEWTON_BOND>(i1,i4,i2,i3,type,
- vb3x,vb3y,vb3z,
- vb1x,vb1y,vb1z,
- vb2x,vb2y,vb2z,thr);
+ vb3x,vb3y,vb3z,
+ vb1x,vb1y,vb1z,
+ vb2x,vb2y,vb2z,thr);
add1_thr<EVFLAG,EFLAG,NEWTON_BOND>(i1,i3,i4,i2,type,
- vb2x,vb2y,vb2z,
- vb3x,vb3y,vb3z,
- vb1x,vb1y,vb1z,thr);
+ vb2x,vb2y,vb2z,
+ vb3x,vb3y,vb3z,
+ vb1x,vb1y,vb1z,thr);
}
}
}
template <int EVFLAG, int EFLAG, int NEWTON_BOND>
void ImproperFourierOMP::add1_thr(const int i1,const int i2,
- const int i3,const int i4,
- const int type,
- const double &vb1x,
- const double &vb1y,
- const double &vb1z,
- const double &vb2x,
- const double &vb2y,
- const double &vb2z,
- const double &vb3x,
- const double &vb3y,
- const double &vb3z,
- ThrData * const thr)
+ const int i3,const int i4,
+ const int type,
+ const double &vb1x,
+ const double &vb1y,
+ const double &vb1z,
+ const double &vb2x,
+ const double &vb2y,
+ const double &vb2z,
+ const double &vb3x,
+ const double &vb3y,
+ const double &vb3z,
+ ThrData * const thr)
{
double eimproper,f1[3],f2[3],f3[3],f4[3];
double c,c2,a,s,projhfg,dhax,dhay,dhaz,dahx,dahy,dahz,cotphi;
@@ -283,5 +283,5 @@ void ImproperFourierOMP::add1_thr(const int i1,const int i2,
if (EVFLAG)
ev_tally_thr(this,i1,i2,i3,i4,nlocal,NEWTON_BOND,eimproper,f1,f3,f4,
- vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,thr);
+ vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,thr);
}
diff --git a/src/USER-OMP/improper_fourier_omp.h b/src/USER-OMP/improper_fourier_omp.h
index 765554bcaf..8bd99cf4ca 100644
--- a/src/USER-OMP/improper_fourier_omp.h
+++ b/src/USER-OMP/improper_fourier_omp.h
@@ -41,10 +41,10 @@ class ImproperFourierOMP : public ImproperFourier, public ThrOMP {
template <int EVFLAG, int EFLAG, int NEWTON_BOND>
void add1_thr(const int,const int,const int,const int,const int,
- const double &, const double &, const double &,
- const double &, const double &, const double &,
- const double &, const double &, const double &,
- ThrData * const thr);
+ const double &, const double &, const double &,
+ const double &, const double &, const double &,
+ const double &, const double &, const double &,
+ ThrData * const thr);
};
}
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 f996372409..dbcef106d2 100644
--- a/src/USER-OMP/pair_buck_long_coul_long_omp.cpp
+++ b/src/USER-OMP/pair_buck_long_coul_long_omp.cpp
@@ -788,7 +788,7 @@ void PairBuckLongCoulLongOMP::eval(int iifrom, int iito, ThrData * const thr)
}
if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,
- evdwl,ecoul,fpair,d[0],d[1],d[2],thr);
+ evdwl,ecoul,fpair,d[0],d[1],d[2],thr);
}
}
}
@@ -1116,7 +1116,7 @@ void PairBuckLongCoulLongOMP::eval_outer(int iiform, int iito, ThrData * const t
force_buck =
r*expr*buck1i[typej]-g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq-respa_buck;
if (EFLAG) evdwl = expr*buckai[typej]-g6*((a2+1.0)*a2+0.5)*x2;
- }
+ }
else { // correct for special
register double f = special_lj[ni], t = rn*(1.0-f);
force_buck = f*r*expr*buck1i[typej]-
@@ -1175,7 +1175,7 @@ void PairBuckLongCoulLongOMP::eval_outer(int iiform, int iito, ThrData * const t
if (EVFLAG) {
fvirial = (force_coul + force_buck + respa_coul + respa_buck)*r2inv;
ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,
- evdwl,ecoul,fvirial,d[0],d[1],d[2],thr);
+ evdwl,ecoul,fvirial,d[0],d[1],d[2],thr);
}
}
}
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 c0c87e7481..8cc4c95fc2 100644
--- a/src/USER-OMP/pair_lj_long_coul_long_omp.cpp
+++ b/src/USER-OMP/pair_lj_long_coul_long_omp.cpp
@@ -733,7 +733,7 @@ void PairLJLongCoulLongOMP::eval(int iifrom, int iito, ThrData * const thr)
if (EFLAG)
evdwl = f*rn*lj3i[typej]-g6*((a2+1.0)*a2+0.5)*x2+t*lj4i[typej];
}
- }
+ }
else { // table real space
register union_int_float_t disp_t;
disp_t.f = rsq;
@@ -744,7 +744,7 @@ void PairLJLongCoulLongOMP::eval(int iifrom, int iito, ThrData * const thr)
force_lj = (rn*=rn)*lj1i[typej]-(fdisptable[disp_k]+f_disp*dfdisptable[disp_k])*lj4i[typej];
if (EFLAG) evdwl = rn*lj3i[typej]-(edisptable[disp_k]+f_disp*dedisptable[disp_k])*lj4i[typej];
}
- else { // special case
+ else { // special case
register double f = special_lj[ni], t = rn*(1.0-f);
force_lj = f*(rn *= rn)*lj1i[typej]-(fdisptable[disp_k]+f_disp*dfdisptable[disp_k])*lj4i[typej]+t*lj2i[typej];
if (EFLAG) evdwl = f*rn*lj3i[typej]-(edisptable[disp_k]+f_disp*dedisptable[disp_k])*lj4i[typej]+t*lj4i[typej];
@@ -1116,7 +1116,7 @@ void PairLJLongCoulLongOMP::eval_outer(int iiform, int iito, ThrData * const thr
evdwl = f*rn*lj3i[typej]-g6*((a2+1.0)*a2+0.5)*x2+t*lj4i[typej];
}
}
- else { // table real space
+ else { // table real space
register union_int_float_t disp_t;
disp_t.f = rsq;
register const int disp_k = (disp_t.i & ndispmask)>>ndispshiftbits;
@@ -1126,7 +1126,7 @@ void PairLJLongCoulLongOMP::eval_outer(int iiform, int iito, ThrData * const thr
force_lj = (rn*=rn)*lj1i[typej]-(fdisptable[disp_k]+f_disp*dfdisptable[disp_k])*lj4i[typej]-respa_lj;
if (EFLAG) evdwl = rn*lj3i[typej]-(edisptable[disp_k]+f_disp*dedisptable[disp_k])*lj4i[typej];
}
- else { // special case
+ else { // special case
register double f = special_lj[ni], t = rn*(1.0-f);
force_lj = f*(rn *= rn)*lj1i[typej]-(fdisptable[disp_k]+f_disp*dfdisptable[disp_k])*lj4i[typej]+t*lj2i[typej]-respa_lj;
if (EFLAG) evdwl = f*rn*lj3i[typej]-(edisptable[disp_k]+f_disp*dedisptable[disp_k])*lj4i[typej]+t*lj4i[typej];
@@ -1165,7 +1165,7 @@ void PairLJLongCoulLongOMP::eval_outer(int iiform, int iito, ThrData * const thr
if (EVFLAG) {
fvirial = (force_coul + force_lj + respa_coul + respa_lj)*r2inv;
ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,
- evdwl,ecoul,fvirial,d[0],d[1],d[2],thr);
+ evdwl,ecoul,fvirial,d[0],d[1],d[2],thr);
}
}
}
diff --git a/src/USER-OMP/pair_morse_smooth_linear_omp.cpp b/src/USER-OMP/pair_morse_smooth_linear_omp.cpp
index d207f58fa6..113f6f2a02 100644
--- a/src/USER-OMP/pair_morse_smooth_linear_omp.cpp
+++ b/src/USER-OMP/pair_morse_smooth_linear_omp.cpp
@@ -143,7 +143,7 @@ void PairMorseSmoothLinearOMP::eval(int iifrom, int iito, ThrData * const thr)
if (EFLAG) {
evdwl = d0[itype][jtype] * (dexp*dexp - 2.0*dexp) -
- offset[itype][jtype];
+ offset[itype][jtype];
evdwl += ( r - cut[itype][jtype] ) * der_at_cutoff[itype][jtype];
evdwl *= factor_lj;
}
diff --git a/src/USER-OMP/pair_reaxc_omp.h b/src/USER-OMP/pair_reaxc_omp.h
index d0dedf7e3c..ad8c368aaf 100644
--- a/src/USER-OMP/pair_reaxc_omp.h
+++ b/src/USER-OMP/pair_reaxc_omp.h
@@ -34,44 +34,44 @@ class PairReaxCOMP : public PairReaxC, public ThrOMP {
virtual void init_style();
inline FixOMP *getFixOMP() {
- return fix;
+ return fix;
};
inline void ev_setup_thr_proxy(int eflagparm, int vflagparm, int nallparm,
- double *eatomparm, double **vatomparm, ThrData *thrparm) {
+ double *eatomparm, double **vatomparm, ThrData *thrparm) {
ev_setup_thr(eflagparm, vflagparm, nallparm, eatomparm, vatomparm, thrparm);
};
// reduce per thread data as needed
inline void reduce_thr_proxy(void * const styleparm, const int eflagparm,
- const int vflagparm, ThrData * const thrparm) {
+ const int vflagparm, ThrData * const thrparm) {
reduce_thr(styleparm, eflagparm, vflagparm, thrparm);
}
inline void ev_tally_thr_proxy(Pair * const pairparm, const int iparm, const int jparm,
- const int nlocalparm, const int newton_pairparm,
- const double evdwlparm, const double ecoulparm,
- const double fpairparm, const double delxparm,
- const double delyparm, const double delzparm,
- ThrData * const thrparm) {
+ const int nlocalparm, const int newton_pairparm,
+ const double evdwlparm, const double ecoulparm,
+ const double fpairparm, const double delxparm,
+ const double delyparm, const double delzparm,
+ ThrData * const thrparm) {
ev_tally_thr(pairparm, iparm, jparm, nlocalparm, newton_pairparm,
- evdwlparm, ecoulparm, fpairparm, delxparm, delyparm, delzparm, thrparm);
+ evdwlparm, ecoulparm, fpairparm, delxparm, delyparm, delzparm, thrparm);
}
inline void ev_tally_xyz_thr_proxy(Pair * const pairparm, const int iparm, const int jparm,
- const int nlocalparm, const int newton_pairparm,
- const double evdwlparm, const double ecoulparm,
- const double fxparm, const double fyparm, const double fzparm,
- const double delxparm, const double delyparm,
- const double delzparm, ThrData * const thrparm) {
+ const int nlocalparm, const int newton_pairparm,
+ const double evdwlparm, const double ecoulparm,
+ const double fxparm, const double fyparm, const double fzparm,
+ const double delxparm, const double delyparm,
+ const double delzparm, ThrData * const thrparm) {
ev_tally_xyz_thr(pairparm, iparm, jparm, nlocalparm, newton_pairparm,
- evdwlparm, ecoulparm, fxparm, fyparm, fzparm,
- delxparm, delyparm, delzparm, thrparm);
+ evdwlparm, ecoulparm, fxparm, fyparm, fzparm,
+ delxparm, delyparm, delzparm, thrparm);
}
inline void ev_tally3_thr_proxy(Pair * const pairparm,int i, int j, int k,
- double evdwl, double ecoul, double *fj, double *fk,
- double *drji, double *drki, ThrData * const thrparm) {
+ double evdwl, double ecoul, double *fj, double *fk,
+ double *drji, double *drki, ThrData * const thrparm) {
ev_tally3_thr(pairparm, i, j, k, evdwl, ecoul, fj, fk, drji, drki, thrparm);
}
diff --git a/src/USER-OMP/pppm_cg_omp.cpp b/src/USER-OMP/pppm_cg_omp.cpp
index df0e632f78..eb230a3bb4 100644
--- a/src/USER-OMP/pppm_cg_omp.cpp
+++ b/src/USER-OMP/pppm_cg_omp.cpp
@@ -159,35 +159,35 @@ void PPPMCGOMP::compute_gf_ik()
sqk = square(unitkx*kper) + square(unitky*lper) + square(unitkz*mper);
if (sqk != 0.0) {
- numerator = 12.5663706/sqk;
- denominator = gf_denom(snx,sny,snz);
- sum1 = 0.0;
-
- for (nx = -nbx; nx <= nbx; nx++) {
- qx = unitkx*(kper+nx_pppm*nx);
- sx = exp(-0.25*square(qx/g_ewald));
- argx = 0.5*qx*xprd/nx_pppm;
- wx = powsinxx(argx,twoorder);
-
- for (ny = -nby; ny <= nby; ny++) {
- qy = unitky*(lper+ny_pppm*ny);
- sy = exp(-0.25*square(qy/g_ewald));
- argy = 0.5*qy*yprd/ny_pppm;
- wy = powsinxx(argy,twoorder);
-
- for (nz = -nbz; nz <= nbz; nz++) {
- qz = unitkz*(mper+nz_pppm*nz);
- sz = exp(-0.25*square(qz/g_ewald));
- argz = 0.5*qz*zprd_slab/nz_pppm;
- wz = powsinxx(argz,twoorder);
-
- dot1 = unitkx*kper*qx + unitky*lper*qy + unitkz*mper*qz;
- dot2 = qx*qx+qy*qy+qz*qz;
- sum1 += (dot1/dot2) * sx*sy*sz * wx*wy*wz;
- }
- }
- }
- greensfn[n] = numerator*sum1/denominator;
+ numerator = 12.5663706/sqk;
+ denominator = gf_denom(snx,sny,snz);
+ sum1 = 0.0;
+
+ for (nx = -nbx; nx <= nbx; nx++) {
+ qx = unitkx*(kper+nx_pppm*nx);
+ sx = exp(-0.25*square(qx/g_ewald));
+ argx = 0.5*qx*xprd/nx_pppm;
+ wx = powsinxx(argx,twoorder);
+
+ for (ny = -nby; ny <= nby; ny++) {
+ qy = unitky*(lper+ny_pppm*ny);
+ sy = exp(-0.25*square(qy/g_ewald));
+ argy = 0.5*qy*yprd/ny_pppm;
+ wy = powsinxx(argy,twoorder);
+
+ for (nz = -nbz; nz <= nbz; nz++) {
+ qz = unitkz*(mper+nz_pppm*nz);
+ sz = exp(-0.25*square(qz/g_ewald));
+ argz = 0.5*qz*zprd_slab/nz_pppm;
+ wz = powsinxx(argz,twoorder);
+
+ dot1 = unitkx*kper*qx + unitky*lper*qy + unitkz*mper*qz;
+ dot2 = qx*qx+qy*qy+qz*qz;
+ sum1 += (dot1/dot2) * sx*sy*sz * wx*wy*wz;
+ }
+ }
+ }
+ greensfn[n] = numerator*sum1/denominator;
} else greensfn[n] = 0.0;
}
thr->timer(Timer::KSPACE);
@@ -263,23 +263,23 @@ void PPPMCGOMP::compute_gf_ad()
sqk = qx*qx + qy*qy + qz*qz;
if (sqk != 0.0) {
- numerator = MY_4PI/sqk;
- denominator = gf_denom(snx,sny,snz);
- greensfn[n] = numerator*sx*sy*sz*wx*wy*wz/denominator;
- sf0 += sf_precoeff1[n]*greensfn[n];
- sf1 += sf_precoeff2[n]*greensfn[n];
- sf2 += sf_precoeff3[n]*greensfn[n];
- sf3 += sf_precoeff4[n]*greensfn[n];
- sf4 += sf_precoeff5[n]*greensfn[n];
- sf5 += sf_precoeff6[n]*greensfn[n];
+ numerator = MY_4PI/sqk;
+ denominator = gf_denom(snx,sny,snz);
+ greensfn[n] = numerator*sx*sy*sz*wx*wy*wz/denominator;
+ sf0 += sf_precoeff1[n]*greensfn[n];
+ sf1 += sf_precoeff2[n]*greensfn[n];
+ sf2 += sf_precoeff3[n]*greensfn[n];
+ sf3 += sf_precoeff4[n]*greensfn[n];
+ sf4 += sf_precoeff5[n]*greensfn[n];
+ sf5 += sf_precoeff6[n]*greensfn[n];
} else {
- greensfn[n] = 0.0;
- sf0 += sf_precoeff1[n]*greensfn[n];
- sf1 += sf_precoeff2[n]*greensfn[n];
- sf2 += sf_precoeff3[n]*greensfn[n];
- sf3 += sf_precoeff4[n]*greensfn[n];
- sf4 += sf_precoeff5[n]*greensfn[n];
- sf5 += sf_precoeff6[n]*greensfn[n];
+ greensfn[n] = 0.0;
+ sf0 += sf_precoeff1[n]*greensfn[n];
+ sf1 += sf_precoeff2[n]*greensfn[n];
+ sf2 += sf_precoeff3[n]*greensfn[n];
+ sf3 += sf_precoeff4[n]*greensfn[n];
+ sf4 += sf_precoeff5[n]*greensfn[n];
+ sf5 += sf_precoeff6[n]*greensfn[n];
}
}
thr->timer(Timer::KSPACE);
@@ -713,7 +713,7 @@ void PPPMCGOMP::compute_rho1d_thr(FFT_SCALAR * const * const r1d, const FFT_SCAL
------------------------------------------------------------------------- */
void PPPMCGOMP::compute_drho1d_thr(FFT_SCALAR * const * const d1d, const FFT_SCALAR &dx,
- const FFT_SCALAR &dy, const FFT_SCALAR &dz)
+ const FFT_SCALAR &dy, const FFT_SCALAR &dz)
{
int k,l;
FFT_SCALAR r1,r2,r3;
diff --git a/src/USER-OMP/pppm_cg_omp.h b/src/USER-OMP/pppm_cg_omp.h
index 07763eba38..057f86099d 100644
--- a/src/USER-OMP/pppm_cg_omp.h
+++ b/src/USER-OMP/pppm_cg_omp.h
@@ -46,7 +46,7 @@ class PPPMCGOMP : public PPPMCG, public ThrOMP {
void compute_rho1d_thr(FFT_SCALAR * const * const, const FFT_SCALAR &,
const FFT_SCALAR &, const FFT_SCALAR &);
void compute_drho1d_thr(FFT_SCALAR * const * const, const FFT_SCALAR &,
- const FFT_SCALAR &, const FFT_SCALAR &);
+ const FFT_SCALAR &, const FFT_SCALAR &);
};
}
diff --git a/src/USER-OMP/pppm_disp_omp.cpp b/src/USER-OMP/pppm_disp_omp.cpp
index 6cf2983761..74881c9a8a 100644
--- a/src/USER-OMP/pppm_disp_omp.cpp
+++ b/src/USER-OMP/pppm_disp_omp.cpp
@@ -272,24 +272,24 @@ void PPPMDispOMP::compute_gf_6()
nn = k-nxlo_fft_6 + nnx*(l-nylo_fft_6 + nny*(m-nzlo_fft_6));
if ((nn < nnfrom) || (nn >=nnto)) continue;
- kper = k - nx_pppm_6*(2*k/nx_pppm_6);
+ kper = k - nx_pppm_6*(2*k/nx_pppm_6);
qx = unitkx*kper;
- snx = sin(0.5*unitkx*kper*xprd/nx_pppm_6);
- snx2 = snx*snx;
+ snx = sin(0.5*unitkx*kper*xprd/nx_pppm_6);
+ snx2 = snx*snx;
sx = exp(-qx*qx*inv2ew*inv2ew);
- wx = 1.0;
- argx = 0.5*qx*xprd/nx_pppm_6;
- if (argx != 0.0) wx = pow(sin(argx)/argx,order_6);
+ wx = 1.0;
+ 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);
+ 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);
- rtsqk = sqrt(sqk);
+ 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);
- greensfn_6[nn] = numerator*term*wx*wy*wz/denominator;
+ greensfn_6[nn] = numerator*term*wx*wy*wz/denominator;
} else greensfn_6[nn] = 0.0;
}
}
@@ -1404,27 +1404,27 @@ void PPPMDispOMP::fieldforce_a_ik()
for (l = nlower_6; l <= nupper_6; l++) {
mx = l+nx;
x0 = y0*r1d[0][l];
- ekx0 -= x0*vdx_brick_a0[mz][my][mx];
- eky0 -= x0*vdy_brick_a0[mz][my][mx];
- ekz0 -= x0*vdz_brick_a0[mz][my][mx];
- ekx1 -= x0*vdx_brick_a1[mz][my][mx];
- eky1 -= x0*vdy_brick_a1[mz][my][mx];
- ekz1 -= x0*vdz_brick_a1[mz][my][mx];
+ ekx0 -= x0*vdx_brick_a0[mz][my][mx];
+ eky0 -= x0*vdy_brick_a0[mz][my][mx];
+ ekz0 -= x0*vdz_brick_a0[mz][my][mx];
+ ekx1 -= x0*vdx_brick_a1[mz][my][mx];
+ eky1 -= x0*vdy_brick_a1[mz][my][mx];
+ ekz1 -= x0*vdz_brick_a1[mz][my][mx];
ekx2 -= x0*vdx_brick_a2[mz][my][mx];
- eky2 -= x0*vdy_brick_a2[mz][my][mx];
- ekz2 -= x0*vdz_brick_a2[mz][my][mx];
- ekx3 -= x0*vdx_brick_a3[mz][my][mx];
- eky3 -= x0*vdy_brick_a3[mz][my][mx];
- ekz3 -= x0*vdz_brick_a3[mz][my][mx];
- ekx4 -= x0*vdx_brick_a4[mz][my][mx];
- eky4 -= x0*vdy_brick_a4[mz][my][mx];
- ekz4 -= x0*vdz_brick_a4[mz][my][mx];
+ eky2 -= x0*vdy_brick_a2[mz][my][mx];
+ ekz2 -= x0*vdz_brick_a2[mz][my][mx];
+ ekx3 -= x0*vdx_brick_a3[mz][my][mx];
+ eky3 -= x0*vdy_brick_a3[mz][my][mx];
+ ekz3 -= x0*vdz_brick_a3[mz][my][mx];
+ ekx4 -= x0*vdx_brick_a4[mz][my][mx];
+ eky4 -= x0*vdy_brick_a4[mz][my][mx];
+ ekz4 -= x0*vdz_brick_a4[mz][my][mx];
ekx5 -= x0*vdx_brick_a5[mz][my][mx];
- eky5 -= x0*vdy_brick_a5[mz][my][mx];
- ekz5 -= x0*vdz_brick_a5[mz][my][mx];
+ eky5 -= x0*vdy_brick_a5[mz][my][mx];
+ ekz5 -= x0*vdz_brick_a5[mz][my][mx];
ekx6 -= x0*vdx_brick_a6[mz][my][mx];
- eky6 -= x0*vdy_brick_a6[mz][my][mx];
- ekz6 -= x0*vdz_brick_a6[mz][my][mx];
+ eky6 -= x0*vdy_brick_a6[mz][my][mx];
+ ekz6 -= x0*vdz_brick_a6[mz][my][mx];
}
}
}
@@ -1728,7 +1728,7 @@ void PPPMDispOMP::fieldforce_a_peratom()
u4 += x0*u_brick_a4[mz][my][mx];
u5 += x0*u_brick_a5[mz][my][mx];
u6 += x0*u_brick_a6[mz][my][mx];
- }
+ }
if (vflag_atom) {
v00 += x0*v0_brick_a0[mz][my][mx];
v10 += x0*v1_brick_a0[mz][my][mx];
@@ -1815,7 +1815,7 @@ void PPPMDispOMP::fieldforce_a_peratom()
dx,dy,dz = distance of particle from "lower left" grid point
------------------------------------------------------------------------- */
void PPPMDispOMP::compute_rho1d_thr(FFT_SCALAR * const * const r1d, const FFT_SCALAR &dx,
- const FFT_SCALAR &dy, const FFT_SCALAR &dz,
+ const FFT_SCALAR &dy, const FFT_SCALAR &dz,
const int ord, FFT_SCALAR * const * const rho_c)
{
int k,l;
@@ -1841,7 +1841,7 @@ void PPPMDispOMP::compute_rho1d_thr(FFT_SCALAR * const * const r1d, const FFT_SC
------------------------------------------------------------------------- */
void PPPMDispOMP::compute_drho1d_thr(FFT_SCALAR * const * const dr1d, const FFT_SCALAR &dx,
- const FFT_SCALAR &dy, const FFT_SCALAR &dz,
+ const FFT_SCALAR &dy, const FFT_SCALAR &dz,
const int ord, FFT_SCALAR * const * const drho_c)
{
int k,l;
diff --git a/src/USER-OMP/pppm_disp_omp.h b/src/USER-OMP/pppm_disp_omp.h
index b1ec2856bb..ac4a54c9f8 100644
--- a/src/USER-OMP/pppm_disp_omp.h
+++ b/src/USER-OMP/pppm_disp_omp.h
@@ -60,7 +60,7 @@ namespace LAMMPS_NS {
const FFT_SCALAR &, const FFT_SCALAR &,
const int, FFT_SCALAR * const * const);
void compute_drho1d_thr(FFT_SCALAR * const * const, const FFT_SCALAR &,
- const FFT_SCALAR &, const FFT_SCALAR &,
+ const FFT_SCALAR &, const FFT_SCALAR &,
const int, FFT_SCALAR * const * const);
// void compute_rho_coeff();
// void slabcorr(int);
diff --git a/src/USER-OMP/pppm_disp_tip4p_omp.cpp b/src/USER-OMP/pppm_disp_tip4p_omp.cpp
index 29aeeb79dc..49e3681f6e 100644
--- a/src/USER-OMP/pppm_disp_tip4p_omp.cpp
+++ b/src/USER-OMP/pppm_disp_tip4p_omp.cpp
@@ -269,23 +269,23 @@ void PPPMDispTIP4POMP::compute_gf_6()
nn = k-nxlo_fft_6 + nnx*(l-nylo_fft_6 + nny*(m-nzlo_fft_6));
if ((nn < nnfrom) || (nn >=nnto)) continue;
- kper = k - nx_pppm_6*(2*k/nx_pppm_6);
+ kper = k - nx_pppm_6*(2*k/nx_pppm_6);
qx = unitkx*kper;
- snx = sin(0.5*unitkx*kper*xprd/nx_pppm_6);
- snx2 = snx*snx;
+ snx = sin(0.5*unitkx*kper*xprd/nx_pppm_6);
+ snx2 = snx*snx;
sx = exp(-qx*qx*inv2ew*inv2ew);
- wx = 1.0;
- argx = 0.5*qx*xprd/nx_pppm_6;
- if (argx != 0.0) wx = pow(sin(argx)/argx,order_6);
+ wx = 1.0;
+ 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);
+ sqk = pow(qx,2.0) + pow(qy,2.0) + pow(qz,2.0);
- denominator = gf_denom(snx2,sny2,snz2, gf_b_6, order_6);
- rtsqk = sqrt(sqk);
+ 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);
- greensfn_6[nn] = numerator*term*wx*wy*wz/denominator;
+ greensfn_6[nn] = numerator*term*wx*wy*wz/denominator;
}
}
}
@@ -1383,27 +1383,27 @@ void PPPMDispTIP4POMP::fieldforce_a_ik()
for (l = nlower_6; l <= nupper_6; l++) {
mx = l+nx;
x0 = y0*r1d[0][l];
- ekx0 -= x0*vdx_brick_a0[mz][my][mx];
- eky0 -= x0*vdy_brick_a0[mz][my][mx];
- ekz0 -= x0*vdz_brick_a0[mz][my][mx];
- ekx1 -= x0*vdx_brick_a1[mz][my][mx];
- eky1 -= x0*vdy_brick_a1[mz][my][mx];
- ekz1 -= x0*vdz_brick_a1[mz][my][mx];
+ ekx0 -= x0*vdx_brick_a0[mz][my][mx];
+ eky0 -= x0*vdy_brick_a0[mz][my][mx];
+ ekz0 -= x0*vdz_brick_a0[mz][my][mx];
+ ekx1 -= x0*vdx_brick_a1[mz][my][mx];
+ eky1 -= x0*vdy_brick_a1[mz][my][mx];
+ ekz1 -= x0*vdz_brick_a1[mz][my][mx];
ekx2 -= x0*vdx_brick_a2[mz][my][mx];
- eky2 -= x0*vdy_brick_a2[mz][my][mx];
- ekz2 -= x0*vdz_brick_a2[mz][my][mx];
- ekx3 -= x0*vdx_brick_a3[mz][my][mx];
- eky3 -= x0*vdy_brick_a3[mz][my][mx];
- ekz3 -= x0*vdz_brick_a3[mz][my][mx];
- ekx4 -= x0*vdx_brick_a4[mz][my][mx];
- eky4 -= x0*vdy_brick_a4[mz][my][mx];
- ekz4 -= x0*vdz_brick_a4[mz][my][mx];
+ eky2 -= x0*vdy_brick_a2[mz][my][mx];
+ ekz2 -= x0*vdz_brick_a2[mz][my][mx];
+ ekx3 -= x0*vdx_brick_a3[mz][my][mx];
+ eky3 -= x0*vdy_brick_a3[mz][my][mx];
+ ekz3 -= x0*vdz_brick_a3[mz][my][mx];
+ ekx4 -= x0*vdx_brick_a4[mz][my][mx];
+ eky4 -= x0*vdy_brick_a4[mz][my][mx];
+ ekz4 -= x0*vdz_brick_a4[mz][my][mx];
ekx5 -= x0*vdx_brick_a5[mz][my][mx];
- eky5 -= x0*vdy_brick_a5[mz][my][mx];
- ekz5 -= x0*vdz_brick_a5[mz][my][mx];
+ eky5 -= x0*vdy_brick_a5[mz][my][mx];
+ ekz5 -= x0*vdz_brick_a5[mz][my][mx];
ekx6 -= x0*vdx_brick_a6[mz][my][mx];
- eky6 -= x0*vdy_brick_a6[mz][my][mx];
- ekz6 -= x0*vdz_brick_a6[mz][my][mx];
+ eky6 -= x0*vdy_brick_a6[mz][my][mx];
+ ekz6 -= x0*vdz_brick_a6[mz][my][mx];
}
}
}
@@ -1701,7 +1701,7 @@ void PPPMDispTIP4POMP::fieldforce_a_peratom()
u4 += x0*u_brick_a4[mz][my][mx];
u5 += x0*u_brick_a5[mz][my][mx];
u6 += x0*u_brick_a6[mz][my][mx];
- }
+ }
if (vflag_atom) {
v00 += x0*v0_brick_a0[mz][my][mx];
v10 += x0*v1_brick_a0[mz][my][mx];
@@ -1787,7 +1787,7 @@ void PPPMDispTIP4POMP::fieldforce_a_peratom()
dx,dy,dz = distance of particle from "lower left" grid point
------------------------------------------------------------------------- */
void PPPMDispTIP4POMP::compute_rho1d_thr(FFT_SCALAR * const * const r1d, const FFT_SCALAR &dx,
- const FFT_SCALAR &dy, const FFT_SCALAR &dz,
+ const FFT_SCALAR &dy, const FFT_SCALAR &dz,
const int ord, FFT_SCALAR * const * const rho_c)
{
int k,l;
@@ -1813,7 +1813,7 @@ void PPPMDispTIP4POMP::compute_rho1d_thr(FFT_SCALAR * const * const r1d, const F
------------------------------------------------------------------------- */
void PPPMDispTIP4POMP::compute_drho1d_thr(FFT_SCALAR * const * const dr1d, const FFT_SCALAR &dx,
- const FFT_SCALAR &dy, const FFT_SCALAR &dz,
+ const FFT_SCALAR &dy, const FFT_SCALAR &dz,
const int ord, FFT_SCALAR * const * const drho_c)
{
int k,l;
diff --git a/src/USER-OMP/pppm_disp_tip4p_omp.h b/src/USER-OMP/pppm_disp_tip4p_omp.h
index 296444366b..8f499e2964 100644
--- a/src/USER-OMP/pppm_disp_tip4p_omp.h
+++ b/src/USER-OMP/pppm_disp_tip4p_omp.h
@@ -63,7 +63,7 @@ namespace LAMMPS_NS {
const FFT_SCALAR &, const FFT_SCALAR &,
const int, FFT_SCALAR * const * const);
void compute_drho1d_thr(FFT_SCALAR * const * const, const FFT_SCALAR &,
- const FFT_SCALAR &, const FFT_SCALAR &,
+ const FFT_SCALAR &, const FFT_SCALAR &,
const int, FFT_SCALAR * const * const);
virtual void find_M_thr(int, int &, int &, dbl3_t &);
diff --git a/src/USER-OMP/pppm_omp.cpp b/src/USER-OMP/pppm_omp.cpp
index 48b91e3a7b..ef03ef1bba 100644
--- a/src/USER-OMP/pppm_omp.cpp
+++ b/src/USER-OMP/pppm_omp.cpp
@@ -718,7 +718,7 @@ void PPPMOMP::compute_rho1d_thr(FFT_SCALAR * const * const r1d, const FFT_SCALAR
------------------------------------------------------------------------- */
void PPPMOMP::compute_drho1d_thr(FFT_SCALAR * const * const d1d, const FFT_SCALAR &dx,
- const FFT_SCALAR &dy, const FFT_SCALAR &dz)
+ const FFT_SCALAR &dy, const FFT_SCALAR &dz)
{
int k,l;
FFT_SCALAR r1,r2,r3;
diff --git a/src/USER-OMP/pppm_omp.h b/src/USER-OMP/pppm_omp.h
index bf8a9e0c21..c447003605 100644
--- a/src/USER-OMP/pppm_omp.h
+++ b/src/USER-OMP/pppm_omp.h
@@ -46,7 +46,7 @@ class PPPMOMP : public PPPM, public ThrOMP {
void compute_rho1d_thr(FFT_SCALAR * const * const, const FFT_SCALAR &,
const FFT_SCALAR &, const FFT_SCALAR &);
void compute_drho1d_thr(FFT_SCALAR * const * const, const FFT_SCALAR &,
- const FFT_SCALAR &, const FFT_SCALAR &);
+ const FFT_SCALAR &, const FFT_SCALAR &);
// void slabcorr(int);
};
diff --git a/src/USER-OMP/pppm_tip4p_omp.cpp b/src/USER-OMP/pppm_tip4p_omp.cpp
index 1eab140cec..f9733ed95b 100644
--- a/src/USER-OMP/pppm_tip4p_omp.cpp
+++ b/src/USER-OMP/pppm_tip4p_omp.cpp
@@ -871,7 +871,7 @@ void PPPMTIP4POMP::compute_rho1d_thr(FFT_SCALAR * const * const r1d, const FFT_S
------------------------------------------------------------------------- */
void PPPMTIP4POMP::compute_drho1d_thr(FFT_SCALAR * const * const d1d, const FFT_SCALAR &dx,
- const FFT_SCALAR &dy, const FFT_SCALAR &dz)
+ const FFT_SCALAR &dy, const FFT_SCALAR &dz)
{
int k,l;
FFT_SCALAR r1,r2,r3;
diff --git a/src/USER-OMP/pppm_tip4p_omp.h b/src/USER-OMP/pppm_tip4p_omp.h
index 59559cd587..1060f73c07 100644
--- a/src/USER-OMP/pppm_tip4p_omp.h
+++ b/src/USER-OMP/pppm_tip4p_omp.h
@@ -48,7 +48,7 @@ class PPPMTIP4POMP : public PPPMTIP4P, public ThrOMP {
void compute_rho1d_thr(FFT_SCALAR * const * const, const FFT_SCALAR &,
const FFT_SCALAR &, const FFT_SCALAR &);
void compute_drho1d_thr(FFT_SCALAR * const * const, const FFT_SCALAR &,
- const FFT_SCALAR &, const FFT_SCALAR &);
+ const FFT_SCALAR &, const FFT_SCALAR &);
void find_M_thr(const int, int &, int &, dbl3_t &);
diff --git a/src/USER-OMP/reaxc_bond_orders_omp.cpp b/src/USER-OMP/reaxc_bond_orders_omp.cpp
index e0bd5e9f94..e0b08fa49e 100644
--- a/src/USER-OMP/reaxc_bond_orders_omp.cpp
+++ b/src/USER-OMP/reaxc_bond_orders_omp.cpp
@@ -118,8 +118,8 @@ void Add_dBond_to_ForcesOMP( reax_system *system, int i, int pj,
rvec_ScaledSum( delij, 1., system->my_atoms[i].x,-1., system->my_atoms[j].x );
pair_reax_ptr->ev_tally_xyz_thr_proxy(system->pair_ptr,i,j,system->N,0,0,0,
- fi_tmp[0],fi_tmp[1],fi_tmp[2],
- delij[0],delij[1],delij[2],thr);
+ fi_tmp[0],fi_tmp[1],fi_tmp[2],
+ delij[0],delij[1],delij[2],thr);
}
// forces on j
@@ -152,8 +152,8 @@ void Add_dBond_to_ForcesOMP( reax_system *system, int i, int pj,
rvec_ScaledSum( delji, 1., system->my_atoms[j].x,-1., system->my_atoms[i].x );
pair_reax_ptr->ev_tally_xyz_thr_proxy(system->pair_ptr,j,i,system->N,0,0,0,
- fj_tmp[0],fj_tmp[1],fj_tmp[2],
- delji[0],delji[1],delji[2],thr);
+ fj_tmp[0],fj_tmp[1],fj_tmp[2],
+ delji[0],delji[1],delji[2],thr);
}
// forces on k: i neighbor
@@ -176,13 +176,13 @@ void Add_dBond_to_ForcesOMP( reax_system *system, int i, int pj,
rvec_ScaledSum(delki,1.,system->my_atoms[k].x,-1.,system->my_atoms[i].x);
pair_reax_ptr->ev_tally_xyz_thr_proxy(system->pair_ptr,k,i,system->N,0,0,0,
- fk_tmp[0],fk_tmp[1],fk_tmp[2],
- delki[0],delki[1],delki[2],thr);
+ fk_tmp[0],fk_tmp[1],fk_tmp[2],
+ delki[0],delki[1],delki[2],thr);
rvec_ScaledSum(delkj,1.,system->my_atoms[k].x,-1.,system->my_atoms[j].x);
pair_reax_ptr->ev_tally_xyz_thr_proxy(system->pair_ptr,k,j,system->N,0,0,0,
- fk_tmp[0],fk_tmp[1],fk_tmp[2],
- delkj[0],delkj[1],delkj[2],thr);
+ fk_tmp[0],fk_tmp[1],fk_tmp[2],
+ delkj[0],delkj[1],delkj[2],thr);
}
}
@@ -206,14 +206,14 @@ void Add_dBond_to_ForcesOMP( reax_system *system, int i, int pj,
rvec_ScaledSum(delki,1.,system->my_atoms[k].x,-1.,system->my_atoms[i].x);
pair_reax_ptr->ev_tally_xyz_thr_proxy(system->pair_ptr,k,i,system->N,0,0,0,
- fk_tmp[0],fk_tmp[1],fk_tmp[2],
- delki[0],delki[1],delki[2],thr);
+ fk_tmp[0],fk_tmp[1],fk_tmp[2],
+ delki[0],delki[1],delki[2],thr);
rvec_ScaledSum(delkj,1.,system->my_atoms[k].x,-1.,system->my_atoms[j].x);
pair_reax_ptr->ev_tally_xyz_thr_proxy(system->pair_ptr,k,j,system->N,0,0,0,
- fk_tmp[0],fk_tmp[1],fk_tmp[2],
- delkj[0],delkj[1],delkj[2],thr);
+ fk_tmp[0],fk_tmp[1],fk_tmp[2],
+ delkj[0],delkj[1],delkj[2],thr);
}
}
}
@@ -221,7 +221,7 @@ void Add_dBond_to_ForcesOMP( reax_system *system, int i, int pj,
/* ---------------------------------------------------------------------- */
void Add_dBond_to_Forces_NPTOMP( reax_system *system, int i, int pj, simulation_data *data,
- storage *workspace, reax_list **lists ) {
+ storage *workspace, reax_list **lists ) {
reax_list *bonds = (*lists) + BONDS;
bond_data *nbr_j, *nbr_k;
bond_order_data *bo_ij, *bo_ji;
@@ -344,10 +344,10 @@ void Add_dBond_to_Forces_NPTOMP( reax_system *system, int i, int pj, simulation_
/* ---------------------------------------------------------------------- */
int BOp_OMP( storage *workspace, reax_list *bonds, double bo_cut,
- int i, int btop_i, far_neighbor_data *nbr_pj,
- single_body_parameters *sbp_i, single_body_parameters *sbp_j,
- two_body_parameters *twbp,
- int btop_j, double C12, double C34, double C56, double BO, double BO_s, double BO_pi, double BO_pi2) {
+ int i, int btop_i, far_neighbor_data *nbr_pj,
+ single_body_parameters *sbp_i, single_body_parameters *sbp_j,
+ two_body_parameters *twbp,
+ int btop_j, double C12, double C34, double C56, double BO, double BO_s, double BO_pi, double BO_pi2) {
int j;
double rr2;
double Cln_BOp_s, Cln_BOp_pi, Cln_BOp_pi2;
@@ -395,15 +395,15 @@ int BOp_OMP( storage *workspace, reax_list *bonds, double bo_cut,
rvec_Scale(bo_ij->dln_BOp_s,-bo_ij->BO_s*Cln_BOp_s,ibond->dvec);
rvec_Scale(bo_ij->dln_BOp_pi,-bo_ij->BO_pi*Cln_BOp_pi,ibond->dvec);
rvec_Scale(bo_ij->dln_BOp_pi2,
- -bo_ij->BO_pi2*Cln_BOp_pi2,ibond->dvec);
+ -bo_ij->BO_pi2*Cln_BOp_pi2,ibond->dvec);
rvec_Scale(bo_ji->dln_BOp_s, -1., bo_ij->dln_BOp_s);
rvec_Scale(bo_ji->dln_BOp_pi, -1., bo_ij->dln_BOp_pi );
rvec_Scale(bo_ji->dln_BOp_pi2, -1., bo_ij->dln_BOp_pi2 );
rvec_Scale( bo_ij->dBOp,
- -(bo_ij->BO_s * Cln_BOp_s +
- bo_ij->BO_pi * Cln_BOp_pi +
- bo_ij->BO_pi2 * Cln_BOp_pi2), ibond->dvec );
+ -(bo_ij->BO_s * Cln_BOp_s +
+ bo_ij->BO_pi * Cln_BOp_pi +
+ bo_ij->BO_pi2 * Cln_BOp_pi2), ibond->dvec );
rvec_Scale( bo_ji->dBOp, -1., bo_ij->dBOp );
bo_ij->BO_s -= bo_cut;
@@ -420,7 +420,7 @@ int BOp_OMP( storage *workspace, reax_list *bonds, double bo_cut,
/* ---------------------------------------------------------------------- */
void BOOMP( reax_system *system, control_params *control, simulation_data *data,
- storage *workspace, reax_list **lists, output_controls *out_control )
+ storage *workspace, reax_list **lists, output_controls *out_control )
{
#ifdef OMP_TIMING
double endTimeBase, startTimeBase;
@@ -459,7 +459,7 @@ void BOOMP( reax_system *system, control_params *control, simulation_data *data,
sbp_i = &(system->reax_param.sbp[type_i]);
workspace->Deltap[i] = workspace->total_bond_order[i] - sbp_i->valency;
workspace->Deltap_boc[i] =
- workspace->total_bond_order[i] - sbp_i->valency_val;
+ workspace->total_bond_order[i] - sbp_i->valency_val;
workspace->total_bond_order[i] = 0;
}
@@ -484,151 +484,151 @@ void BOOMP( reax_system *system, control_params *control, simulation_data *data,
end_i = End_Index(i, bonds);
for (pj = start_i; pj < end_i; ++pj) {
- j = bonds->select.bond_list[pj].nbr;
- type_j = system->my_atoms[j].type;
- if(type_j < 0) continue;
- bo_ij = &( bonds->select.bond_list[pj].bo_data );
-
- if( i < j || workspace->bond_mark[j] > 3) {
- twbp = &( system->reax_param.tbp[type_i][type_j] );
-
- if( twbp->ovc < 0.001 && twbp->v13cor < 0.001 ) {
- bo_ij->C1dbo = 1.000000;
- bo_ij->C2dbo = 0.000000;
- bo_ij->C3dbo = 0.000000;
-
- bo_ij->C1dbopi = 1.000000;
- bo_ij->C2dbopi = 0.000000;
- bo_ij->C3dbopi = 0.000000;
- bo_ij->C4dbopi = 0.000000;
-
- bo_ij->C1dbopi2 = 1.000000;
- bo_ij->C2dbopi2 = 0.000000;
- bo_ij->C3dbopi2 = 0.000000;
- bo_ij->C4dbopi2 = 0.000000;
-
- }
- else {
- val_j = system->reax_param.sbp[type_j].valency;
- Deltap_j = workspace->Deltap[j];
- Deltap_boc_j = workspace->Deltap_boc[j];
-
- /* on page 1 */
- if( twbp->ovc >= 0.001 ) {
- /* Correction for overcoordination */
- exp_p1i = exp( -p_boc1 * Deltap_i );
- exp_p2i = exp( -p_boc2 * Deltap_i );
- exp_p1j = exp( -p_boc1 * Deltap_j );
- exp_p2j = exp( -p_boc2 * Deltap_j );
-
- f2 = exp_p1i + exp_p1j;
- f3 = -1.0 / p_boc2 * log( 0.5 * ( exp_p2i + exp_p2j ) );
- f1 = 0.5 * ( ( val_i + f2 )/( val_i + f2 + f3 ) +
- ( val_j + f2 )/( val_j + f2 + f3 ) );
-
- /* Now come the derivates */
- /* Bond Order pages 5-7, derivative of f1 */
- temp = f2 + f3;
- u1_ij = val_i + temp;
- u1_ji = val_j + temp;
- Cf1A_ij = 0.5 * f3 * (1.0 / SQR( u1_ij ) +
- 1.0 / SQR( u1_ji ));
- Cf1B_ij = -0.5 * (( u1_ij - f3 ) / SQR( u1_ij ) +
- ( u1_ji - f3 ) / SQR( u1_ji ));
-
- Cf1_ij = 0.50 * ( -p_boc1 * exp_p1i / u1_ij -
- ((val_i+f2) / SQR(u1_ij)) *
- ( -p_boc1 * exp_p1i +
- exp_p2i / ( exp_p2i + exp_p2j ) ) +
- -p_boc1 * exp_p1i / u1_ji -
- ((val_j+f2) / SQR(u1_ji)) *
- ( -p_boc1 * exp_p1i +
- exp_p2i / ( exp_p2i + exp_p2j ) ));
-
-
- Cf1_ji = -Cf1A_ij * p_boc1 * exp_p1j +
- Cf1B_ij * exp_p2j / ( exp_p2i + exp_p2j );
- }
- else {
- /* No overcoordination correction! */
- f1 = 1.0;
- Cf1_ij = Cf1_ji = 0.0;
- }
-
- if( twbp->v13cor >= 0.001 ) {
- /* Correction for 1-3 bond orders */
- exp_f4 =exp(-(twbp->p_boc4 * SQR( bo_ij->BO ) -
- Deltap_boc_i) * twbp->p_boc3 + twbp->p_boc5);
- exp_f5 =exp(-(twbp->p_boc4 * SQR( bo_ij->BO ) -
- Deltap_boc_j) * twbp->p_boc3 + twbp->p_boc5);
-
- f4 = 1. / (1. + exp_f4);
- f5 = 1. / (1. + exp_f5);
- f4f5 = f4 * f5;
-
- /* Bond Order pages 8-9, derivative of f4 and f5 */
- Cf45_ij = -f4 * exp_f4;
- Cf45_ji = -f5 * exp_f5;
- }
- else {
- f4 = f5 = f4f5 = 1.0;
- Cf45_ij = Cf45_ji = 0.0;
- }
-
- /* Bond Order page 10, derivative of total bond order */
- A0_ij = f1 * f4f5;
- A1_ij = -2 * twbp->p_boc3 * twbp->p_boc4 * bo_ij->BO *
- (Cf45_ij + Cf45_ji);
- A2_ij = Cf1_ij / f1 + twbp->p_boc3 * Cf45_ij;
- A2_ji = Cf1_ji / f1 + twbp->p_boc3 * Cf45_ji;
- A3_ij = A2_ij + Cf1_ij / f1;
- A3_ji = A2_ji + Cf1_ji / f1;
-
- /* find corrected bond orders and their derivative coef */
- bo_ij->BO = bo_ij->BO * A0_ij;
- bo_ij->BO_pi = bo_ij->BO_pi * A0_ij *f1;
- bo_ij->BO_pi2= bo_ij->BO_pi2* A0_ij *f1;
- bo_ij->BO_s = bo_ij->BO - ( bo_ij->BO_pi + bo_ij->BO_pi2 );
-
- bo_ij->C1dbo = A0_ij + bo_ij->BO * A1_ij;
- bo_ij->C2dbo = bo_ij->BO * A2_ij;
- bo_ij->C3dbo = bo_ij->BO * A2_ji;
-
- bo_ij->C1dbopi = f1*f1*f4*f5;
- bo_ij->C2dbopi = bo_ij->BO_pi * A1_ij;
- bo_ij->C3dbopi = bo_ij->BO_pi * A3_ij;
- bo_ij->C4dbopi = bo_ij->BO_pi * A3_ji;
-
- bo_ij->C1dbopi2 = f1*f1*f4*f5;
- bo_ij->C2dbopi2 = bo_ij->BO_pi2 * A1_ij;
- bo_ij->C3dbopi2 = bo_ij->BO_pi2 * A3_ij;
- bo_ij->C4dbopi2 = bo_ij->BO_pi2 * A3_ji;
- }
-
- /* neglect bonds that are < 1e-10 */
- if( bo_ij->BO < 1e-10 )
- bo_ij->BO = 0.0;
- if( bo_ij->BO_s < 1e-10 )
- bo_ij->BO_s = 0.0;
- if( bo_ij->BO_pi < 1e-10 )
- bo_ij->BO_pi = 0.0;
- if( bo_ij->BO_pi2 < 1e-10 )
- bo_ij->BO_pi2 = 0.0;
-
- workspace->total_bond_order[i] += bo_ij->BO; //now keeps total_BO
- }
- // else {
- // /* We only need to update bond orders from bo_ji
- // everything else is set in uncorrected_bo calculations */
- // sym_index = bonds->select.bond_list[pj].sym_index;
- // bo_ji = &(bonds->select.bond_list[ sym_index ].bo_data);
- // bo_ij->BO = bo_ji->BO;
- // bo_ij->BO_s = bo_ji->BO_s;
- // bo_ij->BO_pi = bo_ji->BO_pi;
- // bo_ij->BO_pi2 = bo_ji->BO_pi2;
-
- // workspace->total_bond_order[i] += bo_ij->BO;// now keeps total_BO
- // }
+ j = bonds->select.bond_list[pj].nbr;
+ type_j = system->my_atoms[j].type;
+ if(type_j < 0) continue;
+ bo_ij = &( bonds->select.bond_list[pj].bo_data );
+
+ if( i < j || workspace->bond_mark[j] > 3) {
+ twbp = &( system->reax_param.tbp[type_i][type_j] );
+
+ if( twbp->ovc < 0.001 && twbp->v13cor < 0.001 ) {
+ bo_ij->C1dbo = 1.000000;
+ bo_ij->C2dbo = 0.000000;
+ bo_ij->C3dbo = 0.000000;
+
+ bo_ij->C1dbopi = 1.000000;
+ bo_ij->C2dbopi = 0.000000;
+ bo_ij->C3dbopi = 0.000000;
+ bo_ij->C4dbopi = 0.000000;
+
+ bo_ij->C1dbopi2 = 1.000000;
+ bo_ij->C2dbopi2 = 0.000000;
+ bo_ij->C3dbopi2 = 0.000000;
+ bo_ij->C4dbopi2 = 0.000000;
+
+ }
+ else {
+ val_j = system->reax_param.sbp[type_j].valency;
+ Deltap_j = workspace->Deltap[j];
+ Deltap_boc_j = workspace->Deltap_boc[j];
+
+ /* on page 1 */
+ if( twbp->ovc >= 0.001 ) {
+ /* Correction for overcoordination */
+ exp_p1i = exp( -p_boc1 * Deltap_i );
+ exp_p2i = exp( -p_boc2 * Deltap_i );
+ exp_p1j = exp( -p_boc1 * Deltap_j );
+ exp_p2j = exp( -p_boc2 * Deltap_j );
+
+ f2 = exp_p1i + exp_p1j;
+ f3 = -1.0 / p_boc2 * log( 0.5 * ( exp_p2i + exp_p2j ) );
+ f1 = 0.5 * ( ( val_i + f2 )/( val_i + f2 + f3 ) +
+ ( val_j + f2 )/( val_j + f2 + f3 ) );
+
+ /* Now come the derivates */
+ /* Bond Order pages 5-7, derivative of f1 */
+ temp = f2 + f3;
+ u1_ij = val_i + temp;
+ u1_ji = val_j + temp;
+ Cf1A_ij = 0.5 * f3 * (1.0 / SQR( u1_ij ) +
+ 1.0 / SQR( u1_ji ));
+ Cf1B_ij = -0.5 * (( u1_ij - f3 ) / SQR( u1_ij ) +
+ ( u1_ji - f3 ) / SQR( u1_ji ));
+
+ Cf1_ij = 0.50 * ( -p_boc1 * exp_p1i / u1_ij -
+ ((val_i+f2) / SQR(u1_ij)) *
+ ( -p_boc1 * exp_p1i +
+ exp_p2i / ( exp_p2i + exp_p2j ) ) +
+ -p_boc1 * exp_p1i / u1_ji -
+ ((val_j+f2) / SQR(u1_ji)) *
+ ( -p_boc1 * exp_p1i +
+ exp_p2i / ( exp_p2i + exp_p2j ) ));
+
+
+ Cf1_ji = -Cf1A_ij * p_boc1 * exp_p1j +
+ Cf1B_ij * exp_p2j / ( exp_p2i + exp_p2j );
+ }
+ else {
+ /* No overcoordination correction! */
+ f1 = 1.0;
+ Cf1_ij = Cf1_ji = 0.0;
+ }
+
+ if( twbp->v13cor >= 0.001 ) {
+ /* Correction for 1-3 bond orders */
+ exp_f4 =exp(-(twbp->p_boc4 * SQR( bo_ij->BO ) -
+ Deltap_boc_i) * twbp->p_boc3 + twbp->p_boc5);
+ exp_f5 =exp(-(twbp->p_boc4 * SQR( bo_ij->BO ) -
+ Deltap_boc_j) * twbp->p_boc3 + twbp->p_boc5);
+
+ f4 = 1. / (1. + exp_f4);
+ f5 = 1. / (1. + exp_f5);
+ f4f5 = f4 * f5;
+
+ /* Bond Order pages 8-9, derivative of f4 and f5 */
+ Cf45_ij = -f4 * exp_f4;
+ Cf45_ji = -f5 * exp_f5;
+ }
+ else {
+ f4 = f5 = f4f5 = 1.0;
+ Cf45_ij = Cf45_ji = 0.0;
+ }
+
+ /* Bond Order page 10, derivative of total bond order */
+ A0_ij = f1 * f4f5;
+ A1_ij = -2 * twbp->p_boc3 * twbp->p_boc4 * bo_ij->BO *
+ (Cf45_ij + Cf45_ji);
+ A2_ij = Cf1_ij / f1 + twbp->p_boc3 * Cf45_ij;
+ A2_ji = Cf1_ji / f1 + twbp->p_boc3 * Cf45_ji;
+ A3_ij = A2_ij + Cf1_ij / f1;
+ A3_ji = A2_ji + Cf1_ji / f1;
+
+ /* find corrected bond orders and their derivative coef */
+ bo_ij->BO = bo_ij->BO * A0_ij;
+ bo_ij->BO_pi = bo_ij->BO_pi * A0_ij *f1;
+ bo_ij->BO_pi2= bo_ij->BO_pi2* A0_ij *f1;
+ bo_ij->BO_s = bo_ij->BO - ( bo_ij->BO_pi + bo_ij->BO_pi2 );
+
+ bo_ij->C1dbo = A0_ij + bo_ij->BO * A1_ij;
+ bo_ij->C2dbo = bo_ij->BO * A2_ij;
+ bo_ij->C3dbo = bo_ij->BO * A2_ji;
+
+ bo_ij->C1dbopi = f1*f1*f4*f5;
+ bo_ij->C2dbopi = bo_ij->BO_pi * A1_ij;
+ bo_ij->C3dbopi = bo_ij->BO_pi * A3_ij;
+ bo_ij->C4dbopi = bo_ij->BO_pi * A3_ji;
+
+ bo_ij->C1dbopi2 = f1*f1*f4*f5;
+ bo_ij->C2dbopi2 = bo_ij->BO_pi2 * A1_ij;
+ bo_ij->C3dbopi2 = bo_ij->BO_pi2 * A3_ij;
+ bo_ij->C4dbopi2 = bo_ij->BO_pi2 * A3_ji;
+ }
+
+ /* neglect bonds that are < 1e-10 */
+ if( bo_ij->BO < 1e-10 )
+ bo_ij->BO = 0.0;
+ if( bo_ij->BO_s < 1e-10 )
+ bo_ij->BO_s = 0.0;
+ if( bo_ij->BO_pi < 1e-10 )
+ bo_ij->BO_pi = 0.0;
+ if( bo_ij->BO_pi2 < 1e-10 )
+ bo_ij->BO_pi2 = 0.0;
+
+ workspace->total_bond_order[i] += bo_ij->BO; //now keeps total_BO
+ }
+ // else {
+ // /* We only need to update bond orders from bo_ji
+ // everything else is set in uncorrected_bo calculations */
+ // sym_index = bonds->select.bond_list[pj].sym_index;
+ // bo_ji = &(bonds->select.bond_list[ sym_index ].bo_data);
+ // bo_ij->BO = bo_ji->BO;
+ // bo_ij->BO_s = bo_ji->BO_s;
+ // bo_ij->BO_pi = bo_ji->BO_pi;
+ // bo_ij->BO_pi2 = bo_ji->BO_pi2;
+
+ // workspace->total_bond_order[i] += bo_ij->BO;// now keeps total_BO
+ // }
}
}
@@ -649,26 +649,26 @@ void BOOMP( reax_system *system, control_params *control, simulation_data *data,
end_i = End_Index(i, bonds);
for (pj = start_i; pj < end_i; ++pj) {
- j = bonds->select.bond_list[pj].nbr;
- type_j = system->my_atoms[j].type;
- if(type_j < 0) continue;
-
- if( i < j || workspace->bond_mark[j] > 3) {
- // Computed in previous for-loop
- } else {
- /* We only need to update bond orders from bo_ji
- everything else is set in uncorrected_bo calculations */
- sym_index = bonds->select.bond_list[pj].sym_index;
-
- bo_ij = &( bonds->select.bond_list[pj].bo_data );
- bo_ji = &(bonds->select.bond_list[ sym_index ].bo_data);
- bo_ij->BO = bo_ji->BO;
- bo_ij->BO_s = bo_ji->BO_s;
- bo_ij->BO_pi = bo_ji->BO_pi;
- bo_ij->BO_pi2 = bo_ji->BO_pi2;
-
- workspace->total_bond_order[i] += bo_ij->BO;// now keeps total_BO
- }
+ j = bonds->select.bond_list[pj].nbr;
+ type_j = system->my_atoms[j].type;
+ if(type_j < 0) continue;
+
+ if( i < j || workspace->bond_mark[j] > 3) {
+ // Computed in previous for-loop
+ } else {
+ /* We only need to update bond orders from bo_ji
+ everything else is set in uncorrected_bo calculations */
+ sym_index = bonds->select.bond_list[pj].sym_index;
+
+ bo_ij = &( bonds->select.bond_list[pj].bo_data );
+ bo_ji = &(bonds->select.bond_list[ sym_index ].bo_data);
+ bo_ij->BO = bo_ji->BO;
+ bo_ij->BO_s = bo_ji->BO_s;
+ bo_ij->BO_pi = bo_ji->BO_pi;
+ bo_ij->BO_pi2 = bo_ji->BO_pi2;
+
+ workspace->total_bond_order[i] += bo_ij->BO;// now keeps total_BO
+ }
}
}
@@ -692,12 +692,12 @@ void BOOMP( reax_system *system, control_params *control, simulation_data *data,
workspace->Delta[j] = workspace->total_bond_order[j] - sbp_j->valency;
workspace->Delta_e[j] = workspace->total_bond_order[j] - sbp_j->valency_e;
workspace->Delta_boc[j] = workspace->total_bond_order[j] -
- sbp_j->valency_boc;
+ sbp_j->valency_boc;
workspace->Delta_val[j] = workspace->total_bond_order[j] -
- sbp_j->valency_val;
+ sbp_j->valency_val;
workspace->vlpex[j] = workspace->Delta_e[j] -
- 2.0 * (int)(workspace->Delta_e[j]/2.0);
+ 2.0 * (int)(workspace->Delta_e[j]/2.0);
explp1 = exp(-p_lp1 * SQR(2.0 + workspace->vlpex[j]));
workspace->nlp[j] = explp1 - (int)(workspace->Delta_e[j] / 2.0);
workspace->Delta_lp[j] = sbp_j->nlp_opt - workspace->nlp[j];
@@ -705,22 +705,22 @@ void BOOMP( reax_system *system, control_params *control, simulation_data *data,
workspace->dDelta_lp[j] = workspace->Clp[j];
if( sbp_j->mass > 21.0 ) {
- workspace->nlp_temp[j] = 0.5 * (sbp_j->valency_e - sbp_j->valency);
- workspace->Delta_lp_temp[j] = sbp_j->nlp_opt - workspace->nlp_temp[j];
- workspace->dDelta_lp_temp[j] = 0.;
+ workspace->nlp_temp[j] = 0.5 * (sbp_j->valency_e - sbp_j->valency);
+ workspace->Delta_lp_temp[j] = sbp_j->nlp_opt - workspace->nlp_temp[j];
+ workspace->dDelta_lp_temp[j] = 0.;
}
else {
- workspace->nlp_temp[j] = workspace->nlp[j];
- workspace->Delta_lp_temp[j] = sbp_j->nlp_opt - workspace->nlp_temp[j];
- workspace->dDelta_lp_temp[j] = workspace->Clp[j];
+ workspace->nlp_temp[j] = workspace->nlp[j];
+ workspace->Delta_lp_temp[j] = sbp_j->nlp_opt - workspace->nlp_temp[j];
+ workspace->dDelta_lp_temp[j] = workspace->Clp[j];
}
}
} // parallel region
#ifdef OMP_TIMING
- endTimeBase = MPI_Wtime();
- ompTimingData[COMPUTEBOINDEX] += (endTimeBase-startTimeBase);
+ endTimeBase = MPI_Wtime();
+ ompTimingData[COMPUTEBOINDEX] += (endTimeBase-startTimeBase);
#endif
}
diff --git a/src/USER-OMP/reaxc_bond_orders_omp.h b/src/USER-OMP/reaxc_bond_orders_omp.h
index cea31539a9..36be3337ad 100644
--- a/src/USER-OMP/reaxc_bond_orders_omp.h
+++ b/src/USER-OMP/reaxc_bond_orders_omp.h
@@ -37,8 +37,8 @@ void Add_dBond_to_Forces_NPTOMP( reax_system *system, int, int,
simulation_data*, storage*, reax_list** );
int BOp_OMP(storage*, reax_list*, double, int, int, far_neighbor_data*,
- single_body_parameters*, single_body_parameters*, two_body_parameters*,
- int, double, double, double, double, double, double, double);
+ single_body_parameters*, single_body_parameters*, two_body_parameters*,
+ int, double, double, double, double, double, double, double);
void BOOMP( reax_system*, control_params*, simulation_data*,
storage*, reax_list**, output_controls* );
diff --git a/src/USER-OMP/reaxc_bonds_omp.cpp b/src/USER-OMP/reaxc_bonds_omp.cpp
index 7522df2f60..bc038e2aa1 100644
--- a/src/USER-OMP/reaxc_bonds_omp.cpp
+++ b/src/USER-OMP/reaxc_bonds_omp.cpp
@@ -86,8 +86,8 @@ void BondsOMP( reax_system *system, control_params *control,
class ThrData *thr = pair_reax_ptr->getFixOMP()->get_thr(tid);
pair_reax_ptr->ev_setup_thr_proxy(system->pair_ptr->eflag_either,
- system->pair_ptr->vflag_either, system->N,
- system->pair_ptr->eatom, system->pair_ptr->vatom, thr);
+ system->pair_ptr->vflag_either, system->N,
+ system->pair_ptr->eatom, system->pair_ptr->vatom, thr);
#if defined(_OPENMP)
#pragma omp for schedule(guided)
@@ -103,11 +103,11 @@ void BondsOMP( reax_system *system, control_params *control,
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] &&
- 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] &&
- system->my_atoms[j].x[0] < system->my_atoms[i].x[0]) continue;
+ 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] &&
+ system->my_atoms[j].x[0] < system->my_atoms[i].x[0]) continue;
}
/* set the pointers */
@@ -123,18 +123,18 @@ void BondsOMP( reax_system *system, control_params *control,
else 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 );
+ ( 1.0 - twbp->p_be1 * twbp->p_be2 * pow_BOs_be2 );
/* calculate the Bond Energy */
total_Ebond += ebond =
- -twbp->De_s * bo_ij->BO_s * exp_be12
- -twbp->De_p * bo_ij->BO_pi
- -twbp->De_pp * bo_ij->BO_pi2;
+ -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)
- pair_reax_ptr->ev_tally_thr_proxy(system->pair_ptr, i, j, natoms, 1,
- ebond, 0.0, 0.0, 0.0, 0.0, 0.0, thr);
+ pair_reax_ptr->ev_tally_thr_proxy(system->pair_ptr, i, j, natoms, 1,
+ ebond, 0.0, 0.0, 0.0, 0.0, 0.0, thr);
/* calculate derivatives of Bond Orders */
bo_ij->Cdbo += CEbo;
@@ -143,33 +143,33 @@ void BondsOMP( reax_system *system, control_params *control,
/* Stabilisation terminal triple bond */
if (bo_ij->BO >= 1.00) {
- if (gp37 == 2 ||
- (sbp_i->mass == 12.0000 && sbp_j->mass == 15.9990) ||
- (sbp_j->mass == 12.0000 && sbp_i->mass == 15.9990)) {
- exphu = exp( -gp7 * SQR(bo_ij->BO - 2.50) );
- exphua1 = exp(-gp3 * (workspace->total_bond_order[i]-bo_ij->BO));
- 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);
- total_Ebond += 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)
- pair_reax_ptr->ev_tally_thr_proxy(system->pair_ptr, i, j, natoms, 1,
- estriph, 0.0, 0.0, 0.0, 0.0, 0.0, thr);
-
- bo_ij->Cdbo += decobdbo;
- workspace->CdDelta[i] += decobdboua;
- workspace->CdDeltaReduction[reductionOffset+j] += decobdboub;
+ if (gp37 == 2 ||
+ (sbp_i->mass == 12.0000 && sbp_j->mass == 15.9990) ||
+ (sbp_j->mass == 12.0000 && sbp_i->mass == 15.9990)) {
+ exphu = exp( -gp7 * SQR(bo_ij->BO - 2.50) );
+ exphua1 = exp(-gp3 * (workspace->total_bond_order[i]-bo_ij->BO));
+ 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);
+ total_Ebond += 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)
+ pair_reax_ptr->ev_tally_thr_proxy(system->pair_ptr, i, j, natoms, 1,
+ estriph, 0.0, 0.0, 0.0, 0.0, 0.0, thr);
+
+ bo_ij->Cdbo += decobdbo;
+ workspace->CdDelta[i] += decobdboua;
+ workspace->CdDeltaReduction[reductionOffset+j] += decobdboub;
}
}
}
diff --git a/src/USER-OMP/reaxc_forces_omp.cpp b/src/USER-OMP/reaxc_forces_omp.cpp
index 321d104b00..f02c527d9f 100644
--- a/src/USER-OMP/reaxc_forces_omp.cpp
+++ b/src/USER-OMP/reaxc_forces_omp.cpp
@@ -115,10 +115,10 @@ void Compute_NonBonded_ForcesOMP( reax_system *system, control_params *control,
if( control->tabulate == 0 )
vdW_Coulomb_Energy_OMP( system, control, data, workspace,
- lists, out_control );
+ lists, out_control );
else
Tabulated_vdW_Coulomb_Energy_OMP( system, control, data, workspace,
- lists, out_control );
+ lists, out_control );
#ifdef OMP_TIMING
endTimeBase = MPI_Wtime();
@@ -162,14 +162,14 @@ void Compute_Total_ForceOMP( reax_system *system, control_params *control,
class ThrData *thr = pair_reax_ptr->getFixOMP()->get_thr(tid);
pair_reax_ptr->ev_setup_thr_proxy(0, 1, natoms, system->pair_ptr->eatom,
- system->pair_ptr->vatom, thr);
+ system->pair_ptr->vatom, thr);
#if defined(_OPENMP)
#pragma omp for schedule(guided)
#endif
for (i = 0; i < system->N; ++i) {
for (j = 0; j < nthreads; ++j)
- workspace->CdDelta[i] += workspace->CdDeltaReduction[system->N*j+i];
+ workspace->CdDelta[i] += workspace->CdDeltaReduction[system->N*j+i];
}
#if defined(_OPENMP)
@@ -180,21 +180,21 @@ void Compute_Total_ForceOMP( reax_system *system, control_params *control,
end_j = End_Index(j, bonds);
for (pk = start_j; pk < end_j; ++pk) {
- bo_jk = &( bonds->select.bond_list[pk].bo_data );
- for (k = 0; k < nthreads; ++k)
- bo_jk->Cdbo += bo_jk->CdboReduction[k];
+ bo_jk = &( bonds->select.bond_list[pk].bo_data );
+ for (k = 0; k < nthreads; ++k)
+ bo_jk->Cdbo += bo_jk->CdboReduction[k];
}
}
// #pragma omp for schedule(guided) //(dynamic,50)
// for (i = 0; i < system->N; ++i)
// for (pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj)
-// if (i < bonds->select.bond_list[pj].nbr) {
-// if (control->virial == 0)
-// Add_dBond_to_ForcesOMP( system, i, pj, workspace, lists );
-// else
-// Add_dBond_to_Forces_NPTOMP(system, i, pj, data, workspace, lists );
-// }
+// if (i < bonds->select.bond_list[pj].nbr) {
+// if (control->virial == 0)
+// Add_dBond_to_ForcesOMP( system, i, pj, workspace, lists );
+// else
+// Add_dBond_to_Forces_NPTOMP(system, i, pj, data, workspace, lists );
+// }
if(control->virial == 0) {
@@ -202,11 +202,11 @@ void Compute_Total_ForceOMP( reax_system *system, control_params *control,
#pragma omp for schedule(dynamic,50)
#endif
for (i = 0; i < system->N; ++i) {
- const int startj = Start_Index(i, bonds);
- const int endj = End_Index(i, bonds);
- for (pj = startj; pj < endj; ++pj)
- if (i < bonds->select.bond_list[pj].nbr)
- Add_dBond_to_ForcesOMP( system, i, pj, workspace, lists );
+ const int startj = Start_Index(i, bonds);
+ const int endj = End_Index(i, bonds);
+ for (pj = startj; pj < endj; ++pj)
+ if (i < bonds->select.bond_list[pj].nbr)
+ Add_dBond_to_ForcesOMP( system, i, pj, workspace, lists );
}
} else {
@@ -215,11 +215,11 @@ void Compute_Total_ForceOMP( reax_system *system, control_params *control,
#pragma omp for schedule(dynamic,50)
#endif
for (i = 0; i < system->N; ++i) {
- const int startj = Start_Index(i, bonds);
- const int endj = End_Index(i, bonds);
- for (pj = startj; pj < endj; ++pj)
- if (i < bonds->select.bond_list[pj].nbr)
- Add_dBond_to_Forces_NPTOMP(system, i, pj, data, workspace, lists );
+ const int startj = Start_Index(i, bonds);
+ const int endj = End_Index(i, bonds);
+ for (pj = startj; pj < endj; ++pj)
+ if (i < bonds->select.bond_list[pj].nbr)
+ Add_dBond_to_Forces_NPTOMP(system, i, pj, data, workspace, lists );
}
} // if(virial == 0)
@@ -231,7 +231,7 @@ void Compute_Total_ForceOMP( reax_system *system, control_params *control,
#endif
for (i = 0; i < system->N; ++i) {
for (j = 0; j < nthreads; ++j)
- rvec_Add( workspace->f[i], workspace->forceReduction[system->N*j+i] );
+ rvec_Add( workspace->f[i], workspace->forceReduction[system->N*j+i] );
}
@@ -328,9 +328,9 @@ void Validate_ListsOMP( reax_system *system, storage *workspace, reax_list **lis
void Init_Forces_noQEq_OMP( reax_system *system, control_params *control,
- simulation_data *data, storage *workspace,
- reax_list **lists, output_controls *out_control,
- MPI_Comm comm ) {
+ simulation_data *data, storage *workspace,
+ reax_list **lists, output_controls *out_control,
+ MPI_Comm comm ) {
#ifdef OMP_TIMING
double startTimeBase, endTimeBase;
startTimeBase = MPI_Wtime();
@@ -393,88 +393,88 @@ void Init_Forces_noQEq_OMP( reax_system *system, control_params *control,
for( pj = start_i; pj < end_i; ++pj ) {
nbr_pj = &( far_nbrs->select.far_nbr_list[pj] );
if (nbr_pj->d <= cutoff) {
- j = nbr_pj->nbr;
- atom_j = &(system->my_atoms[j]);
- type_j = atom_j->type;
- sbp_j = &(system->reax_param.sbp[type_j]);
- twbp = &(system->reax_param.tbp[type_i][type_j]);
+ j = nbr_pj->nbr;
+ atom_j = &(system->my_atoms[j]);
+ type_j = atom_j->type;
+ sbp_j = &(system->reax_param.sbp[type_j]);
+ twbp = &(system->reax_param.tbp[type_i][type_j]);
// #pragma omp critical
-// {
-// btop_i = End_Index(i, bonds);
-// if( BOp(workspace, bonds, control->bo_cut, i, btop_i, nbr_pj, sbp_i, sbp_j, twbp) ) {
+// {
+// btop_i = End_Index(i, bonds);
+// if( BOp(workspace, bonds, control->bo_cut, i, btop_i, nbr_pj, sbp_i, sbp_j, twbp) ) {
// num_bonds++;
// btop_i++;
// Set_End_Index(i, btop_i, bonds);
-// }
-
-// }
-
- // Trying to minimize time spent in critical section by moving initial part of BOp()
- // outside of critical section.
-
- // Start top portion of BOp()
- double C12, C34, C56;
- double BO, BO_s, BO_pi, BO_pi2;
- double bo_cut = control->bo_cut;
-
- if( sbp_i->r_s > 0.0 && sbp_j->r_s > 0.0 ) {
- C12 = twbp->p_bo1 * pow( nbr_pj->d / twbp->r_s, twbp->p_bo2 );
- BO_s = (1.0 + bo_cut) * exp( C12 );
- }
- else BO_s = C12 = 0.0;
-
- if( sbp_i->r_pi > 0.0 && sbp_j->r_pi > 0.0 ) {
- C34 = twbp->p_bo3 * pow( nbr_pj->d / twbp->r_p, twbp->p_bo4 );
- BO_pi = exp( C34 );
- }
- else BO_pi = C34 = 0.0;
-
- if( sbp_i->r_pi_pi > 0.0 && sbp_j->r_pi_pi > 0.0 ) {
- C56 = twbp->p_bo5 * pow( nbr_pj->d / twbp->r_pp, twbp->p_bo6 );
- BO_pi2= exp( C56 );
- }
- else BO_pi2 = C56 = 0.0;
-
- /* Initially BO values are the uncorrected ones, page 1 */
- BO = BO_s + BO_pi + BO_pi2;
- // End top portion of BOp()
-
- if(BO >= bo_cut) {
- int btop_j;
-
- // Update indices in critical section
+// }
+
+// }
+
+ // Trying to minimize time spent in critical section by moving initial part of BOp()
+ // outside of critical section.
+
+ // Start top portion of BOp()
+ double C12, C34, C56;
+ double BO, BO_s, BO_pi, BO_pi2;
+ double bo_cut = control->bo_cut;
+
+ if( sbp_i->r_s > 0.0 && sbp_j->r_s > 0.0 ) {
+ C12 = twbp->p_bo1 * pow( nbr_pj->d / twbp->r_s, twbp->p_bo2 );
+ BO_s = (1.0 + bo_cut) * exp( C12 );
+ }
+ else BO_s = C12 = 0.0;
+
+ if( sbp_i->r_pi > 0.0 && sbp_j->r_pi > 0.0 ) {
+ C34 = twbp->p_bo3 * pow( nbr_pj->d / twbp->r_p, twbp->p_bo4 );
+ BO_pi = exp( C34 );
+ }
+ else BO_pi = C34 = 0.0;
+
+ if( sbp_i->r_pi_pi > 0.0 && sbp_j->r_pi_pi > 0.0 ) {
+ C56 = twbp->p_bo5 * pow( nbr_pj->d / twbp->r_pp, twbp->p_bo6 );
+ BO_pi2= exp( C56 );
+ }
+ else BO_pi2 = C56 = 0.0;
+
+ /* Initially BO values are the uncorrected ones, page 1 */
+ BO = BO_s + BO_pi + BO_pi2;
+ // End top portion of BOp()
+
+ if(BO >= bo_cut) {
+ int btop_j;
+
+ // Update indices in critical section
#if defined(_OPENMP)
#pragma omp critical
#endif
- {
- btop_i = End_Index( i, bonds );
- btop_j = End_Index( j, bonds );
- Set_End_Index( j, btop_j+1, bonds );
- Set_End_Index( i, btop_i+1, bonds );
- } // omp critical
-
- // Finish remaining BOp() work
- BOp_OMP(workspace, bonds, bo_cut,
- i , btop_i, nbr_pj, sbp_i, sbp_j, twbp, btop_j,
- C12, C34, C56, BO, BO_s, BO_pi, BO_pi2);
-
- bond_data * ibond = &(bonds->select.bond_list[btop_i]);
- bond_order_data * bo_ij = &(ibond->bo_data);
-
- bond_data * jbond = &(bonds->select.bond_list[btop_j]);
- bond_order_data * bo_ji = &(jbond->bo_data);
-
- workspace->total_bond_order[i] += bo_ij->BO;
- tmp_bond_order[reductionOffset + j] += bo_ji->BO;
-
- rvec_Add(workspace->dDeltap_self[i], bo_ij->dBOp);
- rvec_Add(tmp_ddelta[reductionOffset + j], bo_ji->dBOp);
-
- btop_i++;
- num_bonds++;
- } // if(BO>=bo_cut)
-
+ {
+ btop_i = End_Index( i, bonds );
+ btop_j = End_Index( j, bonds );
+ Set_End_Index( j, btop_j+1, bonds );
+ Set_End_Index( i, btop_i+1, bonds );
+ } // omp critical
+
+ // Finish remaining BOp() work
+ BOp_OMP(workspace, bonds, bo_cut,
+ i , btop_i, nbr_pj, sbp_i, sbp_j, twbp, btop_j,
+ C12, C34, C56, BO, BO_s, BO_pi, BO_pi2);
+
+ bond_data * ibond = &(bonds->select.bond_list[btop_i]);
+ bond_order_data * bo_ij = &(ibond->bo_data);
+
+ bond_data * jbond = &(bonds->select.bond_list[btop_j]);
+ bond_order_data * bo_ji = &(jbond->bo_data);
+
+ workspace->total_bond_order[i] += bo_ij->BO;
+ tmp_bond_order[reductionOffset + j] += bo_ji->BO;
+
+ rvec_Add(workspace->dDeltap_self[i], bo_ij->dBOp);
+ rvec_Add(tmp_ddelta[reductionOffset + j], bo_ji->dBOp);
+
+ btop_i++;
+ num_bonds++;
+ } // if(BO>=bo_cut)
+
} // if(cutoff)
} // for(pj)
@@ -516,49 +516,49 @@ void Init_Forces_noQEq_OMP( reax_system *system, control_params *control,
{
if (ihb == 1 || ihb == 2) {
- start_i = Start_Index(i, far_nbrs);
- end_i = End_Index(i, far_nbrs);
-
- for (pj = start_i; pj < end_i; ++pj) {
- nbr_pj = &( far_nbrs->select.far_nbr_list[pj] );
- j = nbr_pj->nbr;
- atom_j = &(system->my_atoms[j]);
- type_j = atom_j->type;
- if(type_j < 0) continue;
- sbp_j = &(system->reax_param.sbp[type_j]);
- jhb = sbp_j->p_hbond;
-
- if (nbr_pj->d <= control->hbond_cut) {
- int iflag = 0;
- int jflag = 0;
-
- if(ihb==1 && jhb==2) iflag = 1;
- else if(j<system->n && ihb == 2 && jhb == 1) jflag = 1;
-
- if(iflag || jflag) {
- if(iflag) {
- ihb_top = End_Index(atom_i->Hindex, hbonds);
- Set_End_Index(atom_i->Hindex, ihb_top+1, hbonds);
- } else if(jflag) {
- jhb_top = End_Index(atom_j->Hindex, hbonds);
- Set_End_Index(atom_j->Hindex, jhb_top+1, hbonds);
- }
-
- if(iflag) {
- hbonds->select.hbond_list[ihb_top].nbr = j;
- hbonds->select.hbond_list[ihb_top].scl = 1;
- hbonds->select.hbond_list[ihb_top].ptr = nbr_pj;
- } else if(jflag) {
- hbonds->select.hbond_list[jhb_top].nbr = i;
- hbonds->select.hbond_list[jhb_top].scl = -1;
- hbonds->select.hbond_list[jhb_top].ptr = nbr_pj;
- }
-
- num_hbonds++;
- } // if(iflag || jflag)
-
- }
- }
+ start_i = Start_Index(i, far_nbrs);
+ end_i = End_Index(i, far_nbrs);
+
+ for (pj = start_i; pj < end_i; ++pj) {
+ nbr_pj = &( far_nbrs->select.far_nbr_list[pj] );
+ j = nbr_pj->nbr;
+ atom_j = &(system->my_atoms[j]);
+ type_j = atom_j->type;
+ if(type_j < 0) continue;
+ sbp_j = &(system->reax_param.sbp[type_j]);
+ jhb = sbp_j->p_hbond;
+
+ if (nbr_pj->d <= control->hbond_cut) {
+ int iflag = 0;
+ int jflag = 0;
+
+ if(ihb==1 && jhb==2) iflag = 1;
+ else if(j<system->n && ihb == 2 && jhb == 1) jflag = 1;
+
+ if(iflag || jflag) {
+ if(iflag) {
+ ihb_top = End_Index(atom_i->Hindex, hbonds);
+ Set_End_Index(atom_i->Hindex, ihb_top+1, hbonds);
+ } else if(jflag) {
+ jhb_top = End_Index(atom_j->Hindex, hbonds);
+ Set_End_Index(atom_j->Hindex, jhb_top+1, hbonds);
+ }
+
+ if(iflag) {
+ hbonds->select.hbond_list[ihb_top].nbr = j;
+ hbonds->select.hbond_list[ihb_top].scl = 1;
+ hbonds->select.hbond_list[ihb_top].ptr = nbr_pj;
+ } else if(jflag) {
+ hbonds->select.hbond_list[jhb_top].nbr = i;
+ hbonds->select.hbond_list[jhb_top].scl = -1;
+ hbonds->select.hbond_list[jhb_top].ptr = nbr_pj;
+ }
+
+ num_hbonds++;
+ } // if(iflag || jflag)
+
+ }
+ }
}
} // omp critical
diff --git a/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp b/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp
index c6486ae8e6..062436a703 100644
--- a/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp
+++ b/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp
@@ -124,7 +124,7 @@ void Hydrogen_BondsOMP( reax_system *system, control_params *control,
pbond_ij = &( bond_list[pi] );
i = pbond_ij->nbr;
type_i = system->my_atoms[i].type;
- if(type_i < 0) continue;
+ if(type_i < 0) continue;
bo_ij = &(pbond_ij->bo_data);
if( system->reax_param.sbp[type_i].p_hbond == 2 &&
@@ -136,7 +136,7 @@ void Hydrogen_BondsOMP( reax_system *system, control_params *control,
/* set k's varibles */
k = hbond_list[pk].nbr;
type_k = system->my_atoms[k].type;
- if(type_k < 0) continue;
+ if(type_k < 0) continue;
nbr_jk = hbond_list[pk].ptr;
r_jk = nbr_jk->d;
rvec_Scale( dvec_jk, hbond_list[pk].scl, nbr_jk->dvec );
@@ -149,7 +149,7 @@ void Hydrogen_BondsOMP( reax_system *system, control_params *control,
if( system->my_atoms[i].orig_id != system->my_atoms[k].orig_id ) {
bo_ij = &(pbond_ij->bo_data);
type_i = system->my_atoms[i].type;
- if(type_i < 0) continue;
+ if(type_i < 0) continue;
hbp = &(system->reax_param.hbp[ type_i ][ type_j ][ type_k ]);
++num_hb_intrs;
@@ -157,8 +157,8 @@ void Hydrogen_BondsOMP( reax_system *system, control_params *control,
&theta, &cos_theta );
/* the derivative of cos(theta) */
Calculate_dCos_ThetaOMP( pbond_ij->dvec, pbond_ij->d, dvec_jk, r_jk,
- &dcos_theta_di, &dcos_theta_dj,
- &dcos_theta_dk );
+ &dcos_theta_di, &dcos_theta_dj,
+ &dcos_theta_dk );
/* hydrogen bond energy*/
sin_theta2 = sin( theta/2.0 );
@@ -180,7 +180,7 @@ void Hydrogen_BondsOMP( reax_system *system, control_params *control,
bo_ij->Cdbo += CEhb1; // dbo term
if( control->virial == 0 ) {
- // dcos terms
+ // dcos terms
rvec_ScaledAdd(workspace->forceReduction[reductionOffset+i], +CEhb2, dcos_theta_di );
rvec_ScaledAdd(workspace->forceReduction[reductionOffset+j], +CEhb2, dcos_theta_dj );
rvec_ScaledAdd(workspace->forceReduction[reductionOffset+k], +CEhb2, dcos_theta_dk );
@@ -192,7 +192,7 @@ void Hydrogen_BondsOMP( reax_system *system, control_params *control,
/* for pressure coupling, terms that are not related to bond order
derivatives are added directly into pressure vector/tensor */
rvec_Scale( force, +CEhb2, dcos_theta_di ); // dcos terms
- rvec_Add(workspace->forceReduction[reductionOffset+i], force );
+ rvec_Add(workspace->forceReduction[reductionOffset+i], force );
rvec_iMultiply( ext_press, pbond_ij->rel_box, force );
rvec_ScaledAdd( workspace->my_ext_pressReduction[tid],1.0, ext_press );
@@ -224,7 +224,7 @@ void Hydrogen_BondsOMP( reax_system *system, control_params *control,
rvec_ScaledAdd(fk_tmp, CEhb3/r_jk, dvec_jk);
pair_reax_ptr->ev_tally3_thr_proxy(system->pair_ptr,i,j,k,e_hb,0.0,fi_tmp,fk_tmp,delij,delkj,thr);
- }
+ }
}
}
}
diff --git a/src/USER-OMP/reaxc_multi_body_omp.cpp b/src/USER-OMP/reaxc_multi_body_omp.cpp
index 27779f8e85..4653ada714 100644
--- a/src/USER-OMP/reaxc_multi_body_omp.cpp
+++ b/src/USER-OMP/reaxc_multi_body_omp.cpp
@@ -119,7 +119,7 @@ void Atom_EnergyOMP( reax_system *system, control_params *control,
/* calculate the energy */
if(numbonds > 0)
total_Elp += e_lp =
- p_lp2 * workspace->Delta_lp[i] * inv_expvd2;
+ p_lp2 * workspace->Delta_lp[i] * inv_expvd2;
dElp = p_lp2 * inv_expvd2 +
75 * p_lp2 * workspace->Delta_lp[i] * expvd2 * SQR(inv_expvd2);
@@ -130,34 +130,34 @@ void Atom_EnergyOMP( reax_system *system, control_params *control,
/* tally into per-atom energy */
if( system->pair_ptr->evflag)
pair_reax_ptr->ev_tally_thr_proxy(system->pair_ptr, i, i, system->n, 1,
- e_lp, 0.0, 0.0, 0.0, 0.0, 0.0, thr);
+ e_lp, 0.0, 0.0, 0.0, 0.0, 0.0, thr);
/* correction for C2 */
if( p_lp3 > 0.001 && !strcmp(system->reax_param.sbp[type_i].name, "C") )
for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj ) {
j = bonds->select.bond_list[pj].nbr;
type_j = system->my_atoms[j].type;
- if(type_j < 0) continue;
+ if(type_j < 0) continue;
if( !strcmp( system->reax_param.sbp[type_j].name, "C" ) ) {
twbp = &( system->reax_param.tbp[type_i][type_j]);
bo_ij = &( bonds->select.bond_list[pj].bo_data );
Di = workspace->Delta[i];
vov3 = bo_ij->BO - Di - 0.040*pow(Di, 4.);
-
+
if( vov3 > 3. ) {
- total_Elp += e_lph = p_lp3 * SQR(vov3-3.0);
+ total_Elp += e_lph = p_lp3 * SQR(vov3-3.0);
deahu2dbo = 2.*p_lp3*(vov3 - 3.);
deahu2dsbo = 2.*p_lp3*(vov3 - 3.)*(-1. - 0.16*pow(Di, 3.));
-
+
bo_ij->Cdbo += deahu2dbo;
workspace->CdDelta[i] += deahu2dsbo;
-
+
/* tally into per-atom energy */
if( system->pair_ptr->evflag)
pair_reax_ptr->ev_tally_thr_proxy(system->pair_ptr, i, j, system->n, 1,
- e_lph, 0.0, 0.0, 0.0, 0.0, 0.0, thr);
+ e_lph, 0.0, 0.0, 0.0, 0.0, 0.0, thr);
}
}
}
@@ -187,7 +187,7 @@ void Atom_EnergyOMP( reax_system *system, control_params *control,
sum_ovun1 += twbp->p_ovun1 * twbp->De_s * bo_ij->BO;
sum_ovun2 += (workspace->Delta[j] - dfvl*workspace->Delta_lp_temp[j])*
- ( bo_ij->BO_pi + bo_ij->BO_pi2 );
+ ( bo_ij->BO_pi + bo_ij->BO_pi2 );
}
exp_ovun1 = p_ovun3 * exp( p_ovun4 * sum_ovun2 );
@@ -228,7 +228,7 @@ void Atom_EnergyOMP( reax_system *system, control_params *control,
numbonds ++;
if(numbonds > 0) total_Eun += e_un =
- -p_ovun5 * (1.0 - exp_ovun6) * inv_exp_ovun2n * inv_exp_ovun8;
+ -p_ovun5 * (1.0 - exp_ovun6) * inv_exp_ovun2n * inv_exp_ovun8;
CEunder1 = inv_exp_ovun2n *
( p_ovun5 * p_ovun6 * exp_ovun6 * inv_exp_ovun8 +
@@ -243,7 +243,7 @@ void Atom_EnergyOMP( reax_system *system, control_params *control,
eng_tmp = e_ov;
if(numbonds > 0) eng_tmp+= e_un;
pair_reax_ptr->ev_tally_thr_proxy(system->pair_ptr, i, i, system->n, 1,
- eng_tmp, 0.0, 0.0, 0.0, 0.0, 0.0, thr);
+ eng_tmp, 0.0, 0.0, 0.0, 0.0, 0.0, thr);
}
/* forces */
@@ -259,7 +259,7 @@ void Atom_EnergyOMP( reax_system *system, control_params *control,
bo_ij->Cdbo += CEover1 * twbp->p_ovun1 * twbp->De_s; // OvCoor-1st
workspace->CdDeltaReduction[reductionOffset+j] +=
- CEover4 * (1.0 - dfvl*workspace->dDelta_lp[j]) * (bo_ij->BO_pi + bo_ij->BO_pi2); // OvCoor-3a
+ CEover4 * (1.0 - dfvl*workspace->dDelta_lp[j]) * (bo_ij->BO_pi + bo_ij->BO_pi2); // OvCoor-3a
bo_ij->Cdbopi += CEover4 *
(workspace->Delta[j] - dfvl*workspace->Delta_lp_temp[j]); // OvCoor-3b
@@ -267,7 +267,7 @@ void Atom_EnergyOMP( reax_system *system, control_params *control,
(workspace->Delta[j] - dfvl*workspace->Delta_lp_temp[j]); // OvCoor-3b
workspace->CdDeltaReduction[reductionOffset+j] +=
- CEunder4 * (1.0 - dfvl*workspace->dDelta_lp[j]) * (bo_ij->BO_pi + bo_ij->BO_pi2); // UnCoor - 2a
+ CEunder4 * (1.0 - dfvl*workspace->dDelta_lp[j]) * (bo_ij->BO_pi + bo_ij->BO_pi2); // UnCoor - 2a
bo_ij->Cdbopi += CEunder4 *
(workspace->Delta[j] - dfvl*workspace->Delta_lp_temp[j]); // UnCoor-2b
diff --git a/src/USER-OMP/reaxc_nonbonded_omp.cpp b/src/USER-OMP/reaxc_nonbonded_omp.cpp
index d131195ca0..504dfbe685 100644
--- a/src/USER-OMP/reaxc_nonbonded_omp.cpp
+++ b/src/USER-OMP/reaxc_nonbonded_omp.cpp
@@ -46,8 +46,8 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
void vdW_Coulomb_Energy_OMP( reax_system *system, control_params *control,
- simulation_data *data, storage *workspace,
- reax_list **lists, output_controls *out_control ) {
+ simulation_data *data, storage *workspace,
+ reax_list **lists, output_controls *out_control ) {
int natoms = system->n;
reax_list *far_nbrs = (*lists) + FAR_NBRS;
@@ -108,139 +108,139 @@ void vdW_Coulomb_Energy_OMP( reax_system *system, control_params *control,
flag = 0;
if(nbr_pj->d <= control->nonb_cut) {
- if(j < natoms) flag = 1;
- else if (orig_i < orig_j) flag = 1;
- else if (orig_i == orig_j) {
- if (nbr_pj->dvec[2] > SMALL) flag = 1;
- else if (fabs(nbr_pj->dvec[2]) < SMALL) {
- if (nbr_pj->dvec[1] > SMALL) flag = 1;
- else if (fabs(nbr_pj->dvec[1]) < SMALL && nbr_pj->dvec[0] > SMALL)
- flag = 1;
- }
- }
+ if(j < natoms) flag = 1;
+ else if (orig_i < orig_j) flag = 1;
+ else if (orig_i == orig_j) {
+ if (nbr_pj->dvec[2] > SMALL) flag = 1;
+ else if (fabs(nbr_pj->dvec[2]) < SMALL) {
+ if (nbr_pj->dvec[1] > SMALL) flag = 1;
+ else if (fabs(nbr_pj->dvec[1]) < SMALL && nbr_pj->dvec[0] > SMALL)
+ flag = 1;
+ }
+ }
}
if (flag) {
-
- r_ij = nbr_pj->d;
- twbp = &(system->reax_param.tbp[ system->my_atoms[i].type ]
- [ system->my_atoms[j].type ]);
-
- /* Calculate Taper and its derivative */
- // Tap = nbr_pj->Tap; -- precomputed during compte_H
- Tap = workspace->Tap[7] * r_ij + workspace->Tap[6];
- Tap = Tap * r_ij + workspace->Tap[5];
- Tap = Tap * r_ij + workspace->Tap[4];
- Tap = Tap * r_ij + workspace->Tap[3];
- Tap = Tap * r_ij + workspace->Tap[2];
- Tap = Tap * r_ij + workspace->Tap[1];
- Tap = Tap * r_ij + workspace->Tap[0];
-
- dTap = 7*workspace->Tap[7] * r_ij + 6*workspace->Tap[6];
- dTap = dTap * r_ij + 5*workspace->Tap[5];
- dTap = dTap * r_ij + 4*workspace->Tap[4];
- dTap = dTap * r_ij + 3*workspace->Tap[3];
- dTap = dTap * r_ij + 2*workspace->Tap[2];
- dTap += workspace->Tap[1]/r_ij;
-
- /*vdWaals Calculations*/
- if(system->reax_param.gp.vdw_type==1 || system->reax_param.gp.vdw_type==3)
- { // shielding
- powr_vdW1 = pow(r_ij, p_vdW1);
- powgi_vdW1 = pow( 1.0 / twbp->gamma_w, p_vdW1);
-
- fn13 = pow( powr_vdW1 + powgi_vdW1, p_vdW1i );
- exp1 = exp( twbp->alpha * (1.0 - fn13 / twbp->r_vdW) );
- exp2 = exp( 0.5 * twbp->alpha * (1.0 - fn13 / twbp->r_vdW) );
-
- e_vdW = twbp->D * (exp1 - 2.0 * exp2);
- total_EvdW += Tap * e_vdW;
-
- dfn13 = pow( powr_vdW1 + powgi_vdW1, p_vdW1i - 1.0) *
- pow(r_ij, p_vdW1 - 2.0);
-
- CEvd = dTap * e_vdW -
- Tap * twbp->D * (twbp->alpha / twbp->r_vdW) * (exp1 - exp2) * dfn13;
- }
- else{ // no shielding
- exp1 = exp( twbp->alpha * (1.0 - r_ij / twbp->r_vdW) );
- exp2 = exp( 0.5 * twbp->alpha * (1.0 - r_ij / twbp->r_vdW) );
-
- e_vdW = twbp->D * (exp1 - 2.0 * exp2);
- total_EvdW += Tap * e_vdW;
-
- CEvd = dTap * e_vdW -
- Tap * twbp->D * (twbp->alpha / twbp->r_vdW) * (exp1 - exp2) / r_ij;
- }
-
- if(system->reax_param.gp.vdw_type==2 || system->reax_param.gp.vdw_type==3)
- { // innner wall
- e_core = twbp->ecore * exp(twbp->acore * (1.0-(r_ij/twbp->rcore)));
- total_EvdW += Tap * e_core;
-
- de_core = -(twbp->acore/twbp->rcore) * e_core;
- CEvd += dTap * e_core + Tap * de_core / r_ij;
-
- // lg correction, only if lgvdw is yes
- if (control->lgflag) {
- r_ij5 = pow( r_ij, 5.0 );
- r_ij6 = pow( r_ij, 6.0 );
- re6 = pow( twbp->lgre, 6.0 );
-
- e_lg = -(twbp->lgcij/( r_ij6 + re6 ));
- total_EvdW += Tap * e_lg;
-
- de_lg = -6.0 * e_lg * r_ij5 / ( r_ij6 + re6 ) ;
- CEvd += dTap * e_lg + Tap * de_lg / r_ij;
- }
-
- }
-
- /*Coulomb Calculations*/
- dr3gamij_1 = ( r_ij * r_ij * r_ij + twbp->gamma );
- dr3gamij_3 = pow( dr3gamij_1 , 0.33333333333333 );
-
- tmp = Tap / dr3gamij_3;
- total_Eele += e_ele =
- C_ele * system->my_atoms[i].q * system->my_atoms[j].q * tmp;
-
- CEclmb = C_ele * system->my_atoms[i].q * system->my_atoms[j].q *
- ( dTap - Tap * r_ij / dr3gamij_1 ) / dr3gamij_3;
-
- /* tally into per-atom energy */
- if( system->pair_ptr->evflag || system->pair_ptr->vflag_atom) {
- pe_vdw = Tap * (e_vdW + e_core + e_lg);
- rvec_ScaledSum( delij, 1., system->my_atoms[i].x,
- -1., system->my_atoms[j].x );
- f_tmp = -(CEvd + CEclmb);
- pair_reax_ptr->ev_tally_thr_proxy( system->pair_ptr, i, j, natoms,
- 1, pe_vdw, e_ele, f_tmp,
- delij[0], delij[1], delij[2], thr);
- }
-
- if( control->virial == 0 ) {
- rvec_ScaledAdd( workspace->f[i], -(CEvd + CEclmb), nbr_pj->dvec );
- rvec_ScaledAdd( workspace->forceReduction[reductionOffset+j],
- +(CEvd + CEclmb), nbr_pj->dvec );
- }
- else { /* NPT, iNPT or sNPT */
- /* for pressure coupling, terms not related to bond order
- derivatives are added directly into pressure vector/tensor */
-
- rvec_Scale( temp, CEvd + CEclmb, nbr_pj->dvec );
- rvec_ScaledAdd( workspace->f[reductionOffset+i], -1., temp );
- rvec_Add( workspace->forceReduction[reductionOffset+j], temp);
-
- rvec_iMultiply( ext_press, nbr_pj->rel_box, temp );
-
- rvec_Add( workspace->my_ext_pressReduction[tid], ext_press );
- }
- }
+
+ r_ij = nbr_pj->d;
+ twbp = &(system->reax_param.tbp[ system->my_atoms[i].type ]
+ [ system->my_atoms[j].type ]);
+
+ /* Calculate Taper and its derivative */
+ // Tap = nbr_pj->Tap; -- precomputed during compte_H
+ Tap = workspace->Tap[7] * r_ij + workspace->Tap[6];
+ Tap = Tap * r_ij + workspace->Tap[5];
+ Tap = Tap * r_ij + workspace->Tap[4];
+ Tap = Tap * r_ij + workspace->Tap[3];
+ Tap = Tap * r_ij + workspace->Tap[2];
+ Tap = Tap * r_ij + workspace->Tap[1];
+ Tap = Tap * r_ij + workspace->Tap[0];
+
+ dTap = 7*workspace->Tap[7] * r_ij + 6*workspace->Tap[6];
+ dTap = dTap * r_ij + 5*workspace->Tap[5];
+ dTap = dTap * r_ij + 4*workspace->Tap[4];
+ dTap = dTap * r_ij + 3*workspace->Tap[3];
+ dTap = dTap * r_ij + 2*workspace->Tap[2];
+ dTap += workspace->Tap[1]/r_ij;
+
+ /*vdWaals Calculations*/
+ if(system->reax_param.gp.vdw_type==1 || system->reax_param.gp.vdw_type==3)
+ { // shielding
+ powr_vdW1 = pow(r_ij, p_vdW1);
+ powgi_vdW1 = pow( 1.0 / twbp->gamma_w, p_vdW1);
+
+ fn13 = pow( powr_vdW1 + powgi_vdW1, p_vdW1i );
+ exp1 = exp( twbp->alpha * (1.0 - fn13 / twbp->r_vdW) );
+ exp2 = exp( 0.5 * twbp->alpha * (1.0 - fn13 / twbp->r_vdW) );
+
+ e_vdW = twbp->D * (exp1 - 2.0 * exp2);
+ total_EvdW += Tap * e_vdW;
+
+ dfn13 = pow( powr_vdW1 + powgi_vdW1, p_vdW1i - 1.0) *
+ pow(r_ij, p_vdW1 - 2.0);
+
+ CEvd = dTap * e_vdW -
+ Tap * twbp->D * (twbp->alpha / twbp->r_vdW) * (exp1 - exp2) * dfn13;
+ }
+ else{ // no shielding
+ exp1 = exp( twbp->alpha * (1.0 - r_ij / twbp->r_vdW) );
+ exp2 = exp( 0.5 * twbp->alpha * (1.0 - r_ij / twbp->r_vdW) );
+
+ e_vdW = twbp->D * (exp1 - 2.0 * exp2);
+ total_EvdW += Tap * e_vdW;
+
+ CEvd = dTap * e_vdW -
+ Tap * twbp->D * (twbp->alpha / twbp->r_vdW) * (exp1 - exp2) / r_ij;
+ }
+
+ if(system->reax_param.gp.vdw_type==2 || system->reax_param.gp.vdw_type==3)
+ { // innner wall
+ e_core = twbp->ecore * exp(twbp->acore * (1.0-(r_ij/twbp->rcore)));
+ total_EvdW += Tap * e_core;
+
+ de_core = -(twbp->acore/twbp->rcore) * e_core;
+ CEvd += dTap * e_core + Tap * de_core / r_ij;
+
+ // lg correction, only if lgvdw is yes
+ if (control->lgflag) {
+ r_ij5 = pow( r_ij, 5.0 );
+ r_ij6 = pow( r_ij, 6.0 );
+ re6 = pow( twbp->lgre, 6.0 );
+
+ e_lg = -(twbp->lgcij/( r_ij6 + re6 ));
+ total_EvdW += Tap * e_lg;
+
+ de_lg = -6.0 * e_lg * r_ij5 / ( r_ij6 + re6 ) ;
+ CEvd += dTap * e_lg + Tap * de_lg / r_ij;
+ }
+
+ }
+
+ /*Coulomb Calculations*/
+ dr3gamij_1 = ( r_ij * r_ij * r_ij + twbp->gamma );
+ dr3gamij_3 = pow( dr3gamij_1 , 0.33333333333333 );
+
+ tmp = Tap / dr3gamij_3;
+ total_Eele += e_ele =
+ C_ele * system->my_atoms[i].q * system->my_atoms[j].q * tmp;
+
+ CEclmb = C_ele * system->my_atoms[i].q * system->my_atoms[j].q *
+ ( dTap - Tap * r_ij / dr3gamij_1 ) / dr3gamij_3;
+
+ /* tally into per-atom energy */
+ if( system->pair_ptr->evflag || system->pair_ptr->vflag_atom) {
+ pe_vdw = Tap * (e_vdW + e_core + e_lg);
+ rvec_ScaledSum( delij, 1., system->my_atoms[i].x,
+ -1., system->my_atoms[j].x );
+ f_tmp = -(CEvd + CEclmb);
+ pair_reax_ptr->ev_tally_thr_proxy( system->pair_ptr, i, j, natoms,
+ 1, pe_vdw, e_ele, f_tmp,
+ delij[0], delij[1], delij[2], thr);
+ }
+
+ if( control->virial == 0 ) {
+ rvec_ScaledAdd( workspace->f[i], -(CEvd + CEclmb), nbr_pj->dvec );
+ rvec_ScaledAdd( workspace->forceReduction[reductionOffset+j],
+ +(CEvd + CEclmb), nbr_pj->dvec );
+ }
+ else { /* NPT, iNPT or sNPT */
+ /* for pressure coupling, terms not related to bond order
+ derivatives are added directly into pressure vector/tensor */
+
+ rvec_Scale( temp, CEvd + CEclmb, nbr_pj->dvec );
+ rvec_ScaledAdd( workspace->f[reductionOffset+i], -1., temp );
+ rvec_Add( workspace->forceReduction[reductionOffset+j], temp);
+
+ rvec_iMultiply( ext_press, nbr_pj->rel_box, temp );
+
+ rvec_Add( workspace->my_ext_pressReduction[tid], ext_press );
+ }
+ }
}
}
pair_reax_ptr->reduce_thr_proxy(system->pair_ptr, system->pair_ptr->eflag_either,
- system->pair_ptr->vflag_either, thr);
+ system->pair_ptr->vflag_either, thr);
} // parallel region
data->my_en.e_vdW = total_EvdW;
@@ -252,9 +252,9 @@ void vdW_Coulomb_Energy_OMP( reax_system *system, control_params *control,
/* ---------------------------------------------------------------------- */
void Tabulated_vdW_Coulomb_Energy_OMP(reax_system *system,control_params *control,
- simulation_data *data, storage *workspace,
- reax_list **lists,
- output_controls *out_control ) {
+ simulation_data *data, storage *workspace,
+ reax_list **lists,
+ output_controls *out_control ) {
double SMALL = 0.0001;
int natoms = system->n;
@@ -306,80 +306,80 @@ void Tabulated_vdW_Coulomb_Energy_OMP(reax_system *system,control_params *contro
flag = 0;
if(nbr_pj->d <= control->nonb_cut) {
- if(j < natoms) flag = 1;
- else if (orig_i < orig_j) flag = 1;
- else if (orig_i == orig_j) {
- if (nbr_pj->dvec[2] > SMALL) flag = 1;
- else if (fabs(nbr_pj->dvec[2]) < SMALL) {
- if (nbr_pj->dvec[1] > SMALL) flag = 1;
- else if (fabs(nbr_pj->dvec[1]) < SMALL && nbr_pj->dvec[0] > SMALL)
- flag = 1;
- }
- }
+ if(j < natoms) flag = 1;
+ else if (orig_i < orig_j) flag = 1;
+ else if (orig_i == orig_j) {
+ if (nbr_pj->dvec[2] > SMALL) flag = 1;
+ else if (fabs(nbr_pj->dvec[2]) < SMALL) {
+ if (nbr_pj->dvec[1] > SMALL) flag = 1;
+ else if (fabs(nbr_pj->dvec[1]) < SMALL && nbr_pj->dvec[0] > SMALL)
+ flag = 1;
+ }
+ }
}
if (flag) {
-
- r_ij = nbr_pj->d;
- tmin = MIN( type_i, type_j );
- tmax = MAX( type_i, type_j );
- t = &( LR[tmin][tmax] );
-
- /* Cubic Spline Interpolation */
- r = (int)(r_ij * t->inv_dx);
- if( r == 0 ) ++r;
- base = (double)(r+1) * t->dx;
- dif = r_ij - base;
-
- e_vdW = ((t->vdW[r].d*dif + t->vdW[r].c)*dif + t->vdW[r].b)*dif +
- t->vdW[r].a;
-
- e_ele = ((t->ele[r].d*dif + t->ele[r].c)*dif + t->ele[r].b)*dif +
- t->ele[r].a;
- e_ele *= system->my_atoms[i].q * system->my_atoms[j].q;
-
- total_EvdW += e_vdW;
- total_Eele += e_ele;
-
- CEvd = ((t->CEvd[r].d*dif + t->CEvd[r].c)*dif + t->CEvd[r].b)*dif +
- t->CEvd[r].a;
-
- CEclmb = ((t->CEclmb[r].d*dif+t->CEclmb[r].c)*dif+t->CEclmb[r].b)*dif +
- t->CEclmb[r].a;
- CEclmb *= system->my_atoms[i].q * system->my_atoms[j].q;
-
- /* tally into per-atom energy */
- if( system->pair_ptr->evflag || system->pair_ptr->vflag_atom) {
- rvec_ScaledSum( delij, 1., system->my_atoms[i].x,
- -1., system->my_atoms[j].x );
- f_tmp = -(CEvd + CEclmb);
- pair_reax_ptr->ev_tally_thr_proxy(system->pair_ptr, i, j, natoms, 1, e_vdW, e_ele,
- f_tmp, delij[0], delij[1], delij[2], thr);
- }
-
- if( control->virial == 0 ) {
- rvec_ScaledAdd( workspace->f[i], -(CEvd + CEclmb), nbr_pj->dvec );
- rvec_ScaledAdd( workspace->forceReduction[froffset+j],
- +(CEvd + CEclmb), nbr_pj->dvec );
- }
- else { // NPT, iNPT or sNPT
- /* for pressure coupling, terms not related to bond order derivatives
- are added directly into pressure vector/tensor */
- rvec_Scale( temp, CEvd + CEclmb, nbr_pj->dvec );
-
- rvec_ScaledAdd( workspace->f[i], -1., temp );
- rvec_Add( workspace->forceReduction[froffset+j], temp );
-
- rvec_iMultiply( ext_press, nbr_pj->rel_box, temp );
- rvec_Add( workspace->my_ext_pressReduction[tid], ext_press );
- }
+
+ r_ij = nbr_pj->d;
+ tmin = MIN( type_i, type_j );
+ tmax = MAX( type_i, type_j );
+ t = &( LR[tmin][tmax] );
+
+ /* Cubic Spline Interpolation */
+ r = (int)(r_ij * t->inv_dx);
+ if( r == 0 ) ++r;
+ base = (double)(r+1) * t->dx;
+ dif = r_ij - base;
+
+ e_vdW = ((t->vdW[r].d*dif + t->vdW[r].c)*dif + t->vdW[r].b)*dif +
+ t->vdW[r].a;
+
+ e_ele = ((t->ele[r].d*dif + t->ele[r].c)*dif + t->ele[r].b)*dif +
+ t->ele[r].a;
+ e_ele *= system->my_atoms[i].q * system->my_atoms[j].q;
+
+ total_EvdW += e_vdW;
+ total_Eele += e_ele;
+
+ CEvd = ((t->CEvd[r].d*dif + t->CEvd[r].c)*dif + t->CEvd[r].b)*dif +
+ t->CEvd[r].a;
+
+ CEclmb = ((t->CEclmb[r].d*dif+t->CEclmb[r].c)*dif+t->CEclmb[r].b)*dif +
+ t->CEclmb[r].a;
+ CEclmb *= system->my_atoms[i].q * system->my_atoms[j].q;
+
+ /* tally into per-atom energy */
+ if( system->pair_ptr->evflag || system->pair_ptr->vflag_atom) {
+ rvec_ScaledSum( delij, 1., system->my_atoms[i].x,
+ -1., system->my_atoms[j].x );
+ f_tmp = -(CEvd + CEclmb);
+ pair_reax_ptr->ev_tally_thr_proxy(system->pair_ptr, i, j, natoms, 1, e_vdW, e_ele,
+ f_tmp, delij[0], delij[1], delij[2], thr);
+ }
+
+ if( control->virial == 0 ) {
+ rvec_ScaledAdd( workspace->f[i], -(CEvd + CEclmb), nbr_pj->dvec );
+ rvec_ScaledAdd( workspace->forceReduction[froffset+j],
+ +(CEvd + CEclmb), nbr_pj->dvec );
+ }
+ else { // NPT, iNPT or sNPT
+ /* for pressure coupling, terms not related to bond order derivatives
+ are added directly into pressure vector/tensor */
+ rvec_Scale( temp, CEvd + CEclmb, nbr_pj->dvec );
+
+ rvec_ScaledAdd( workspace->f[i], -1., temp );
+ rvec_Add( workspace->forceReduction[froffset+j], temp );
+
+ rvec_iMultiply( ext_press, nbr_pj->rel_box, temp );
+ rvec_Add( workspace->my_ext_pressReduction[tid], ext_press );
+ }
}
}
}
pair_reax_ptr->reduce_thr_proxy(system->pair_ptr, system->pair_ptr->eflag_either,
- system->pair_ptr->vflag_either, thr);
+ system->pair_ptr->vflag_either, thr);
} // end omp parallel
data->my_en.e_vdW = total_EvdW;
diff --git a/src/USER-OMP/reaxc_nonbonded_omp.h b/src/USER-OMP/reaxc_nonbonded_omp.h
index f64e1abe48..a5d895533a 100644
--- a/src/USER-OMP/reaxc_nonbonded_omp.h
+++ b/src/USER-OMP/reaxc_nonbonded_omp.h
@@ -32,9 +32,9 @@
#include "reaxc_types.h"
void vdW_Coulomb_Energy_OMP( reax_system*, control_params*, simulation_data*,
- storage*, reax_list**, output_controls* );
+ storage*, reax_list**, output_controls* );
void Tabulated_vdW_Coulomb_Energy_OMP( reax_system*, control_params*,
- simulation_data*, storage*,
- reax_list**, output_controls* );
+ simulation_data*, storage*,
+ reax_list**, output_controls* );
#endif
diff --git a/src/USER-OMP/reaxc_torsion_angles_omp.cpp b/src/USER-OMP/reaxc_torsion_angles_omp.cpp
index 4227f62763..ed9ae6c21e 100644
--- a/src/USER-OMP/reaxc_torsion_angles_omp.cpp
+++ b/src/USER-OMP/reaxc_torsion_angles_omp.cpp
@@ -46,8 +46,8 @@ using namespace LAMMPS_NS;
// Functions defined in reaxc_torsion_angles.cpp
extern double Calculate_Omega(rvec, double, rvec, double, rvec, double, rvec, double,
- three_body_interaction_data*, three_body_interaction_data*,
- rvec, rvec, rvec, rvec, output_controls*);
+ three_body_interaction_data*, three_body_interaction_data*,
+ rvec, rvec, rvec, rvec, output_controls*);
/* ---------------------------------------------------------------------- */
@@ -134,7 +134,7 @@ void Torsion_AnglesOMP( reax_system *system, control_params *control,
for (pk = start_j; pk < end_j; ++pk) {
bo_jk = &( bonds->select.bond_list[pk].bo_data );
for (k = 0; k < nthreads; ++k)
- bo_jk->CdboReduction[k] = 0.;
+ bo_jk->CdboReduction[k] = 0.;
}
}
@@ -159,7 +159,7 @@ void Torsion_AnglesOMP( reax_system *system, control_params *control,
if (system->my_atoms[j].orig_id < system->my_atoms[k].orig_id &&
bo_jk->BO > control->thb_cut/*0*/ && Num_Entries(pk, thb_intrs)) {
pj = pbond_jk->sym_index; // pj points to j on k's list
-
+
/* do the same check as above:
are there any 3-body interactions involving k&j
where k is the central atom */
@@ -167,28 +167,28 @@ void Torsion_AnglesOMP( reax_system *system, control_params *control,
type_k = system->my_atoms[k].type;
Delta_k = workspace->Delta_boc[k];
r_jk = pbond_jk->d;
-
+
start_pk = Start_Index(pk, thb_intrs );
end_pk = End_Index(pk, thb_intrs );
start_pj = Start_Index(pj, thb_intrs );
end_pj = End_Index(pj, thb_intrs );
-
+
exp_tor2_jk = exp( -p_tor2 * BOA_jk );
exp_cot2_jk = exp( -p_cot2 * SQR(BOA_jk - 1.5) );
exp_tor3_DjDk = exp( -p_tor3 * (Delta_j + Delta_k) );
exp_tor4_DjDk = exp( p_tor4 * (Delta_j + Delta_k) );
exp_tor34_inv = 1.0 / (1.0 + exp_tor3_DjDk + exp_tor4_DjDk);
f11_DjDk = (2.0 + exp_tor3_DjDk) * exp_tor34_inv;
-
-
+
+
/* pick i up from j-k interaction where j is the central atom */
for (pi = start_pk; pi < end_pk; ++pi) {
p_ijk = &( thb_intrs->select.three_body_list[pi] );
- pij = p_ijk->pthb; // pij is pointer to i on j's bond_list
+ pij = p_ijk->pthb; // pij is pointer to i on j's bond_list
pbond_ij = &( bonds->select.bond_list[pij] );
bo_ij = &( pbond_ij->bo_data );
-
- if (bo_ij->BO > control->thb_cut/*0*/) {
+
+ if (bo_ij->BO > control->thb_cut/*0*/) {
i = p_ijk->thb;
type_i = system->my_atoms[i].type;
r_ij = pbond_ij->d;
@@ -221,18 +221,18 @@ void Torsion_AnglesOMP( reax_system *system, control_params *control,
fbp = &(system->reax_param.fbp[type_i][type_j]
[type_k][type_l].prm[0]);
- if (i != l && fbh->cnt &&
+ if (i != l && fbh->cnt &&
bo_kl->BO > control->thb_cut/*0*/ &&
bo_ij->BO * bo_jk->BO * bo_kl->BO > control->thb_cut/*0*/) {
++num_frb_intrs;
//fprintf(stderr,
- // "%5d: %6d %6d %6d %6d\n", num_frb_intrs,
- // system->my_atoms[i].orig_id,system->my_atoms[j].orig_id,
- // system->my_atoms[k].orig_id,system->my_atoms[l].orig_id);
+ // "%5d: %6d %6d %6d %6d\n", num_frb_intrs,
+ // system->my_atoms[i].orig_id,system->my_atoms[j].orig_id,
+ // system->my_atoms[k].orig_id,system->my_atoms[l].orig_id);
r_kl = pbond_kl->d;
BOA_kl = bo_kl->BO - control->thb_cut;
-
+
theta_jkl = p_jkl->theta;
sin_jkl = sin( theta_jkl );
cos_jkl = cos( theta_jkl );
@@ -242,12 +242,12 @@ void Torsion_AnglesOMP( reax_system *system, control_params *control,
else if( sin_jkl <= 0 && sin_jkl >= -MIN_SINE )
tan_jkl_i = cos_jkl / -MIN_SINE;
else tan_jkl_i = cos_jkl /sin_jkl;
-
+
rvec_ScaledSum( dvec_li, 1., system->my_atoms[i].x,
-1., system->my_atoms[l].x );
r_li = rvec_Norm( dvec_li );
-
-
+
+
/* omega and its derivative */
omega = Calculate_Omega( pbond_ij->dvec, r_ij,
pbond_jk->dvec, r_jk,
@@ -262,7 +262,7 @@ void Torsion_AnglesOMP( reax_system *system, control_params *control,
cos2omega = cos( 2. * omega );
cos3omega = cos( 3. * omega );
/* end omega calculations */
-
+
/* torsion energy */
exp_tor1 = exp( fbp->p_tor1 *
SQR(2.0 - bo_jk->BO_pi - f11_DjDk) );
@@ -275,7 +275,7 @@ void Torsion_AnglesOMP( reax_system *system, control_params *control,
fbp->V2 * exp_tor1 * (1.0 - cos2omega) +
fbp->V3 * (1.0 + cos3omega) );
- total_Etor += e_tor = fn10 * sin_ijk * sin_jkl * CV;
+ total_Etor += e_tor = fn10 * sin_ijk * sin_jkl * CV;
dfn11 = (-p_tor3 * exp_tor3_DjDk +
(p_tor3 * exp_tor3_DjDk - p_tor4 * exp_tor4_DjDk) *
@@ -309,7 +309,7 @@ void Torsion_AnglesOMP( reax_system *system, control_params *control,
/* 4-body conjugation energy */
fn12 = exp_cot2_ij * exp_cot2_jk * exp_cot2_kl;
//data->my_en.e_con += e_con =
- total_Econ += e_con =
+ total_Econ += e_con =
fbp->p_cot1 * fn12 *
(1.0 + (SQR(cos_omega) - 1.0) * sin_ijk * sin_jkl);
@@ -331,18 +331,18 @@ void Torsion_AnglesOMP( reax_system *system, control_params *control,
/* FORCES */
bo_jk->Cdbopi += CEtors2;
workspace->CdDelta[j] += CEtors3;
- //workspace->CdDelta[k] += CEtors3;
+ //workspace->CdDelta[k] += CEtors3;
workspace->CdDeltaReduction[reductionOffset+k] += CEtors3;
bo_ij->Cdbo += (CEtors4 + CEconj1);
bo_jk->Cdbo += (CEtors5 + CEconj2);
//bo_kl->Cdbo += (CEtors6 + CEconj3);
- bo_kl->CdboReduction[tid] += (CEtors6 + CEconj3);
+ bo_kl->CdboReduction[tid] += (CEtors6 + CEconj3);
if( control->virial == 0 ) {
/* dcos_theta_ijk */
rvec_ScaledAdd( workspace->f[j],
CEtors7 + CEconj4, p_ijk->dcos_dj );
- rvec_ScaledAdd( workspace->forceReduction[reductionOffset+i],
+ rvec_ScaledAdd( workspace->forceReduction[reductionOffset+i],
CEtors7 + CEconj4, p_ijk->dcos_dk );
rvec_ScaledAdd( workspace->forceReduction[reductionOffset+k],
CEtors7 + CEconj4, p_ijk->dcos_di );
@@ -350,7 +350,7 @@ void Torsion_AnglesOMP( reax_system *system, control_params *control,
/* dcos_theta_jkl */
rvec_ScaledAdd( workspace->f[j],
CEtors8 + CEconj5, p_jkl->dcos_di );
- rvec_ScaledAdd( workspace->forceReduction[reductionOffset+k],
+ rvec_ScaledAdd( workspace->forceReduction[reductionOffset+k],
CEtors8 + CEconj5, p_jkl->dcos_dj );
rvec_ScaledAdd( workspace->forceReduction[reductionOffset+l],
CEtors8 + CEconj5, p_jkl->dcos_dk );
@@ -358,7 +358,7 @@ void Torsion_AnglesOMP( reax_system *system, control_params *control,
/* dcos_omega */
rvec_ScaledAdd( workspace->f[j],
CEtors9 + CEconj6, dcos_omega_dj );
- rvec_ScaledAdd( workspace->forceReduction[reductionOffset+i],
+ rvec_ScaledAdd( workspace->forceReduction[reductionOffset+i],
CEtors9 + CEconj6, dcos_omega_di );
rvec_ScaledAdd( workspace->forceReduction[reductionOffset+k],
CEtors9 + CEconj6, dcos_omega_dk );
@@ -367,58 +367,58 @@ void Torsion_AnglesOMP( reax_system *system, control_params *control,
}
else {
ivec_Sum(rel_box_jl, pbond_jk->rel_box, pbond_kl->rel_box);
-
+
/* dcos_theta_ijk */
rvec_Scale( force, CEtors7 + CEconj4, p_ijk->dcos_dk );
- rvec_Add( workspace->forceReduction[reductionOffset+i], force );
+ rvec_Add( workspace->forceReduction[reductionOffset+i], force );
rvec_iMultiply( ext_press, pbond_ij->rel_box, force );
- rvec_Add( workspace->my_ext_pressReduction[tid], ext_press );
-
+ rvec_Add( workspace->my_ext_pressReduction[tid], ext_press );
+
rvec_ScaledAdd( workspace->f[j],
CEtors7 + CEconj4, p_ijk->dcos_dj );
-
+
rvec_Scale( force, CEtors7 + CEconj4, p_ijk->dcos_di );
- rvec_Add( workspace->forceReduction[reductionOffset+k], force );
+ rvec_Add( workspace->forceReduction[reductionOffset+k], force );
rvec_iMultiply( ext_press, pbond_jk->rel_box, force );
- rvec_Add( workspace->my_ext_pressReduction[tid], ext_press );
-
+ rvec_Add( workspace->my_ext_pressReduction[tid], ext_press );
+
/* dcos_theta_jkl */
rvec_ScaledAdd( workspace->f[j],
CEtors8 + CEconj5, p_jkl->dcos_di );
-
+
rvec_Scale( force, CEtors8 + CEconj5, p_jkl->dcos_dj );
- rvec_Add( workspace->forceReduction[reductionOffset+k], force );
+ rvec_Add( workspace->forceReduction[reductionOffset+k], force );
rvec_iMultiply( ext_press, pbond_jk->rel_box, force );
- rvec_Add( workspace->my_ext_pressReduction[tid], ext_press );
-
+ rvec_Add( workspace->my_ext_pressReduction[tid], ext_press );
+
rvec_Scale( force, CEtors8 + CEconj5, p_jkl->dcos_dk );
- rvec_Add( workspace->forceReduction[reductionOffset+l], force );
+ rvec_Add( workspace->forceReduction[reductionOffset+l], force );
rvec_iMultiply( ext_press, rel_box_jl, force );
- rvec_Add( workspace->my_ext_pressReduction[tid], ext_press );
-
+ rvec_Add( workspace->my_ext_pressReduction[tid], ext_press );
+
/* dcos_omega */
rvec_Scale( force, CEtors9 + CEconj6, dcos_omega_di );
- rvec_Add( workspace->forceReduction[reductionOffset+i], force );
+ rvec_Add( workspace->forceReduction[reductionOffset+i], force );
rvec_iMultiply( ext_press, pbond_ij->rel_box, force );
- rvec_Add( workspace->my_ext_pressReduction[tid], ext_press );
+ rvec_Add( workspace->my_ext_pressReduction[tid], ext_press );
rvec_ScaledAdd( workspace->f[j],
CEtors9 + CEconj6, dcos_omega_dj );
rvec_Scale( force, CEtors9 + CEconj6, dcos_omega_dk );
- rvec_Add( workspace->forceReduction[reductionOffset+k], force );
+ rvec_Add( workspace->forceReduction[reductionOffset+k], force );
rvec_iMultiply( ext_press, pbond_jk->rel_box, force );
- rvec_Add( workspace->my_ext_pressReduction[tid], ext_press );
+ rvec_Add( workspace->my_ext_pressReduction[tid], ext_press );
rvec_Scale( force, CEtors9 + CEconj6, dcos_omega_dl );
- rvec_Add( workspace->forceReduction[reductionOffset+i], force );
+ rvec_Add( workspace->forceReduction[reductionOffset+i], force );
rvec_iMultiply( ext_press, rel_box_jl, force );
- rvec_Add( workspace->my_ext_pressReduction[tid], ext_press );
+ rvec_Add( workspace->my_ext_pressReduction[tid], ext_press );
}
/* tally into per-atom virials */
if( system->pair_ptr->vflag_atom || system->pair_ptr->evflag) {
-
+
// acquire vectors
rvec_ScaledSum( delil, 1., system->my_atoms[l].x,
-1., system->my_atoms[i].x );
@@ -430,29 +430,29 @@ void Torsion_AnglesOMP( reax_system *system, control_params *control,
rvec_Scale( fi_tmp, CEtors7 + CEconj4, p_ijk->dcos_dk );
rvec_Scale( fj_tmp, CEtors7 + CEconj4, p_ijk->dcos_dj );
rvec_Scale( fk_tmp, CEtors7 + CEconj4, p_ijk->dcos_di );
-
+
// dcos_theta_jkl
rvec_ScaledAdd( fj_tmp, CEtors8 + CEconj5, p_jkl->dcos_di );
rvec_ScaledAdd( fk_tmp, CEtors8 + CEconj5, p_jkl->dcos_dj );
-
+
// dcos_omega
rvec_ScaledAdd( fi_tmp, CEtors9 + CEconj6, dcos_omega_di );
rvec_ScaledAdd( fj_tmp, CEtors9 + CEconj6, dcos_omega_dj );
rvec_ScaledAdd( fk_tmp, CEtors9 + CEconj6, dcos_omega_dk );
-
+
// tally
eng_tmp = e_tor + e_con;
-
+
if (system->pair_ptr->evflag)
- pair_reax_ptr->ev_tally_thr_proxy(system->pair_ptr, j, k, system->n, 1,
- eng_tmp, 0.0, 0.0, 0.0, 0.0, 0.0, thr);
+ pair_reax_ptr->ev_tally_thr_proxy(system->pair_ptr, j, k, system->n, 1,
+ eng_tmp, 0.0, 0.0, 0.0, 0.0, 0.0, thr);
- // NEED TO MAKE AN OMP VERSION OF THIS CALL!
+ // NEED TO MAKE AN OMP VERSION OF THIS CALL!
if (system->pair_ptr->vflag_atom)
- system->pair_ptr->v_tally4(i, j, k, l, fi_tmp, fj_tmp, fk_tmp,
- delil, deljl, delkl );
+ system->pair_ptr->v_tally4(i, j, k, l, fi_tmp, fj_tmp, fk_tmp,
+ delil, deljl, delkl );
}
-
+
} // pl check ends
} // pl loop ends
} // pi check ends
diff --git a/src/USER-OMP/reaxc_torsion_angles_omp.h b/src/USER-OMP/reaxc_torsion_angles_omp.h
index 39f8691877..62cb760f41 100644
--- a/src/USER-OMP/reaxc_torsion_angles_omp.h
+++ b/src/USER-OMP/reaxc_torsion_angles_omp.h
@@ -33,6 +33,6 @@
#include "reaxc_torsion_angles.h"
void Torsion_AnglesOMP( reax_system*, control_params*, simulation_data*,
- storage*, reax_list**, output_controls* );
+ storage*, reax_list**, output_controls* );
#endif
diff --git a/src/USER-OMP/reaxc_valence_angles_omp.cpp b/src/USER-OMP/reaxc_valence_angles_omp.cpp
index 6c15a529d3..5366a84878 100644
--- a/src/USER-OMP/reaxc_valence_angles_omp.cpp
+++ b/src/USER-OMP/reaxc_valence_angles_omp.cpp
@@ -45,9 +45,9 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
void Calculate_dCos_ThetaOMP( rvec dvec_ji, double d_ji, rvec dvec_jk, double d_jk,
- rvec* dcos_theta_di,
- rvec* dcos_theta_dj,
- rvec* dcos_theta_dk )
+ rvec* dcos_theta_di,
+ rvec* dcos_theta_dj,
+ rvec* dcos_theta_dk )
{
double sqr_d_ji = SQR(d_ji);
double sqr_d_jk = SQR(d_jk);
@@ -198,21 +198,21 @@ void Valence_AnglesOMP( reax_system *system, control_params *control,
BOA_ij = bo_ij->BO - control->thb_cut;
if (BOA_ij > 0.0) {
- i = pbond_ij->nbr;
-
+ i = pbond_ij->nbr;
+
/* first copy 3-body intrs from previously computed ones where i>k.
in the second for-loop below,
we compute only new 3-body intrs where i < k */
for (pk = start_j; pk < pi; ++pk) {
start_pk = Start_Index( pk, thb_intrs );
end_pk = End_Index( pk, thb_intrs );
-
+
for (t = start_pk; t < end_pk; ++t)
if (thb_intrs->select.three_body_list[t].thb == i) {
p_ijk = &(thb_intrs->select.three_body_list[my_offset] );
p_ijk->thb = bonds->select.bond_list[pk].nbr;
-
+
++my_offset;
break;
}
@@ -227,7 +227,7 @@ void Valence_AnglesOMP( reax_system *system, control_params *control,
p_ijk = &( thb_intrs->select.three_body_list[my_offset] );
p_ijk->thb = k;
-
+
++my_offset; // add this to the list of 3-body interactions
} // for(pk)
} // if()
@@ -345,34 +345,34 @@ void Valence_AnglesOMP( reax_system *system, control_params *control,
if (BOA_ij > 0.0) {
i = pbond_ij->nbr;
type_i = system->my_atoms[i].type;
-
-
+
+
/* first copy 3-body intrs from previously computed ones where i>k.
in the second for-loop below,
we compute only new 3-body intrs where i < k */
for (pk = start_j; pk < pi; ++pk) {
start_pk = Start_Index( pk, thb_intrs );
end_pk = End_Index( pk, thb_intrs );
-
+
for (t = start_pk; t < end_pk; ++t)
if (thb_intrs->select.three_body_list[t].thb == i) {
p_ijk = &(thb_intrs->select.three_body_list[my_offset] );
p_kji = &(thb_intrs->select.three_body_list[t]);
-
+
p_ijk->thb = bonds->select.bond_list[pk].nbr;
p_ijk->pthb = pk;
p_ijk->theta = p_kji->theta;
rvec_Copy( p_ijk->dcos_di, p_kji->dcos_dk );
rvec_Copy( p_ijk->dcos_dj, p_kji->dcos_dj );
rvec_Copy( p_ijk->dcos_dk, p_kji->dcos_di );
-
+
++my_offset;
++num_thb_intrs;
break;
}
} // for(pk)
-
-
+
+
/* and this is the second for loop mentioned above */
for (pk = pi+1; pk < end_j; ++pk) {
pbond_jk = &(bonds->select.bond_list[pk]);
@@ -381,15 +381,15 @@ void Valence_AnglesOMP( reax_system *system, control_params *control,
k = pbond_jk->nbr;
type_k = system->my_atoms[k].type;
p_ijk = &( thb_intrs->select.three_body_list[my_offset] );
-
+
// Fix by Sudhir
// if (BOA_jk <= 0) continue;
if (j >= system->n && i >= system->n && k >= system->n) continue;
-
+
Calculate_Theta( pbond_ij->dvec, pbond_ij->d,
pbond_jk->dvec, pbond_jk->d,
&theta, &cos_theta );
-
+
Calculate_dCos_ThetaOMP( pbond_ij->dvec, pbond_ij->d,
pbond_jk->dvec, pbond_jk->d,
&(p_ijk->dcos_di), &(p_ijk->dcos_dj),
@@ -397,66 +397,66 @@ void Valence_AnglesOMP( reax_system *system, control_params *control,
p_ijk->thb = k;
p_ijk->pthb = pk;
p_ijk->theta = theta;
-
+
sin_theta = sin( theta );
if( sin_theta < 1.0e-5 )
sin_theta = 1.0e-5;
-
+
++my_offset; // add this to the list of 3-body interactions
++num_thb_intrs;
-
+
if ((j < system->n) && (BOA_jk > 0.0) &&
(bo_ij->BO > control->thb_cut) &&
(bo_jk->BO > control->thb_cut) &&
(bo_ij->BO * bo_jk->BO > control->thb_cutsq)) {
thbh = &( system->reax_param.thbp[ type_i ][ type_j ][ type_k ] );
-
+
for (cnt = 0; cnt < thbh->cnt; ++cnt) {
-
+
if( fabs(thbh->prm[cnt].p_val1) > 0.001 ) {
thbp = &( thbh->prm[cnt] );
-
+
/* ANGLE ENERGY */
p_val1 = thbp->p_val1;
p_val2 = thbp->p_val2;
p_val4 = thbp->p_val4;
p_val7 = thbp->p_val7;
theta_00 = thbp->theta_00;
-
+
exp3ij = exp( -p_val3 * pow( BOA_ij, p_val4 ) );
f7_ij = 1.0 - exp3ij;
Cf7ij = p_val3 * p_val4 * pow( BOA_ij, p_val4 - 1.0 ) * exp3ij;
-
+
exp3jk = exp( -p_val3 * pow( BOA_jk, p_val4 ) );
f7_jk = 1.0 - exp3jk;
Cf7jk = p_val3 * p_val4 * pow( BOA_jk, p_val4 - 1.0 ) * exp3jk;
-
+
expval7 = exp( -p_val7 * workspace->Delta_boc[j] );
trm8 = 1.0 + expval6 + expval7;
f8_Dj = p_val5 - ( (p_val5 - 1.0) * (2.0 + expval6) / trm8 );
Cf8j = ( (1.0 - p_val5) / SQR(trm8) ) *
( p_val6 * expval6 * trm8 -
(2.0 + expval6) * ( p_val6*expval6 - p_val7*expval7 ) );
-
+
theta_0 = 180.0 - theta_00 * (1.0 -
exp(-p_val10 * (2.0 - SBO2)));
theta_0 = DEG2RAD( theta_0 );
-
+
expval2theta = exp( -p_val2 * SQR(theta_0 - theta) );
if (p_val1 >= 0)
expval12theta = p_val1 * (1.0 - expval2theta);
else // To avoid linear Me-H-Me angles (6/6/06)
expval12theta = p_val1 * -expval2theta;
-
+
CEval1 = Cf7ij * f7_jk * f8_Dj * expval12theta;
CEval2 = Cf7jk * f7_ij * f8_Dj * expval12theta;
CEval3 = Cf8j * f7_ij * f7_jk * expval12theta;
CEval4 = -2.0 * p_val1 * p_val2 * f7_ij * f7_jk * f8_Dj *
expval2theta * (theta_0 - theta);
-
+
Ctheta_0 = p_val10 * DEG2RAD(theta_00) *
exp( -p_val10 * (2.0 - SBO2) );
-
+
CEval5 = -CEval4 * Ctheta_0 * CSBO2;
CEval6 = CEval5 * dSBO1;
CEval7 = CEval5 * dSBO2;
@@ -465,8 +465,8 @@ void Valence_AnglesOMP( reax_system *system, control_params *control,
total_Eang += e_ang =
f7_ij * f7_jk * f8_Dj * expval12theta;
/* END ANGLE ENERGY*/
-
-
+
+
/* PENALTY ENERGY */
p_pen1 = thbp->p_pen1;
p_pen2 = system->reax_param.gp.l[19];
@@ -486,20 +486,20 @@ void Valence_AnglesOMP( reax_system *system, control_params *control,
total_Epen += e_pen =
p_pen1 * f9_Dj * exp_pen2ij * exp_pen2jk;
-
+
CEpen1 = e_pen * Cf9j / f9_Dj;
temp = -2.0 * p_pen2 * e_pen;
CEpen2 = temp * (BOA_ij - 2.0);
CEpen3 = temp * (BOA_jk - 2.0);
/* END PENALTY ENERGY */
-
-
+
+
/* COALITION ENERGY */
p_coa1 = thbp->p_coa1;
p_coa2 = system->reax_param.gp.l[2];
p_coa3 = system->reax_param.gp.l[38];
p_coa4 = system->reax_param.gp.l[30];
-
+
exp_coa2 = exp( p_coa2 * workspace->Delta_val[j] );
total_Ecoa += e_coa =
p_coa1 / (1. + exp_coa2) *
@@ -507,7 +507,7 @@ void Valence_AnglesOMP( reax_system *system, control_params *control,
exp( -p_coa3 * SQR(workspace->total_bond_order[k]-BOA_jk) ) *
exp( -p_coa4 * SQR(BOA_ij - 1.5) ) *
exp( -p_coa4 * SQR(BOA_jk - 1.5) );
-
+
CEcoa1 = -2 * p_coa4 * (BOA_ij - 1.5) * e_coa;
CEcoa2 = -2 * p_coa4 * (BOA_jk - 1.5) * e_coa;
CEcoa3 = -p_coa2 * exp_coa2 * e_coa / (1 + exp_coa2);
@@ -516,15 +516,15 @@ void Valence_AnglesOMP( reax_system *system, control_params *control,
CEcoa5 = -2 * p_coa3 *
(workspace->total_bond_order[k]-BOA_jk) * e_coa;
/* END COALITION ENERGY */
-
-
+
+
/* FORCES */
bo_ij->Cdbo += (CEval1 + CEpen2 + (CEcoa1 - CEcoa4));
bo_jk->Cdbo += (CEval2 + CEpen3 + (CEcoa2 - CEcoa5));
workspace->CdDelta[j] += ((CEval3 + CEval7) + CEpen1 + CEcoa3);
workspace->CdDeltaReduction[reductionOffset+i] += CEcoa4;
workspace->CdDeltaReduction[reductionOffset+k] += CEcoa5;
-
+
for (t = start_j; t < end_j; ++t) {
pbond_jt = &( bonds->select.bond_list[t] );
bo_jt = &(pbond_jt->bo_data);
@@ -536,7 +536,7 @@ void Valence_AnglesOMP( reax_system *system, control_params *control,
bo_jt->Cdbopi += CEval5;
bo_jt->Cdbopi2 += CEval5;
}
-
+
if( control->virial == 0 ) {
rvec_ScaledAdd( workspace->f[j], CEval8, p_ijk->dcos_dj );
rvec_ScaledAdd( workspace->forceReduction[reductionOffset+i],
@@ -549,34 +549,34 @@ void Valence_AnglesOMP( reax_system *system, control_params *control,
added directly into forces and pressure vector/tensor */
rvec_Scale( force, CEval8, p_ijk->dcos_di );
rvec_Add( workspace->forceReduction[reductionOffset+i], force );
-
+
rvec_iMultiply( ext_press, pbond_ij->rel_box, force );
rvec_Add( workspace->my_ext_pressReduction[tid], ext_press );
-
+
rvec_ScaledAdd( workspace->f[j], CEval8, p_ijk->dcos_dj );
-
+
rvec_Scale( force, CEval8, p_ijk->dcos_dk );
rvec_Add( workspace->forceReduction[reductionOffset+k], force );
rvec_iMultiply( ext_press, pbond_jk->rel_box, force );
rvec_Add( workspace->my_ext_pressReduction[tid], ext_press );
}
-
+
/* tally into per-atom virials */
if( system->pair_ptr->vflag_atom || system->pair_ptr->evflag) {
-
+
/* Acquire vectors */
rvec_ScaledSum( delij, 1., system->my_atoms[i].x,
-1., system->my_atoms[j].x );
rvec_ScaledSum( delkj, 1., system->my_atoms[k].x,
-1., system->my_atoms[j].x );
-
+
rvec_Scale( fi_tmp, -CEval8, p_ijk->dcos_di );
rvec_Scale( fj_tmp, -CEval8, p_ijk->dcos_dj );
rvec_Scale( fk_tmp, -CEval8, p_ijk->dcos_dk );
-
+
eng_tmp = e_ang + e_pen + e_coa;
-
+
if( system->pair_ptr->evflag)
pair_reax_ptr->ev_tally_thr_proxy(system->pair_ptr, j, j, system->N, 1,
eng_tmp, 0.0, 0.0, 0.0, 0.0, 0.0, thr);
diff --git a/src/USER-OMP/respa_omp.cpp b/src/USER-OMP/respa_omp.cpp
index e596caab81..d4fa529b1c 100644
--- a/src/USER-OMP/respa_omp.cpp
+++ b/src/USER-OMP/respa_omp.cpp
@@ -155,11 +155,11 @@ void RespaOMP::setup(int flag)
#endif
{
#if defined(_OPENMP)
- int tid = omp_get_thread_num();
+ int tid = omp_get_thread_num();
#else
- int tid = 0;
+ int tid = 0;
#endif
- data_reduce_thr(atom->f[0], nall, nthreads, 3, tid);
+ data_reduce_thr(atom->f[0], nall, nthreads, 3, tid);
}
fix->did_reduce();
}
@@ -250,11 +250,11 @@ void RespaOMP::setup_minimal(int flag)
#endif
{
#if defined(_OPENMP)
- int tid = omp_get_thread_num();
+ int tid = omp_get_thread_num();
#else
- int tid = 0;
+ int tid = 0;
#endif
- data_reduce_thr(atom->f[0], nall, nthreads, 3, tid);
+ data_reduce_thr(atom->f[0], nall, nthreads, 3, tid);
}
fix->did_reduce();
}
@@ -403,11 +403,11 @@ void RespaOMP::recurse(int ilevel)
#endif
{
#if defined(_OPENMP)
- int tid = omp_get_thread_num();
+ int tid = omp_get_thread_num();
#else
- int tid = 0;
+ int tid = 0;
#endif
- data_reduce_thr(atom->f[0], nall, nthreads, 3, tid);
+ data_reduce_thr(atom->f[0], nall, nthreads, 3, tid);
}
fix->did_reduce();
}
diff --git a/src/USER-QTB/fix_qbmsst.cpp b/src/USER-QTB/fix_qbmsst.cpp
index 417e7ac87d..21ae464e10 100644
--- a/src/USER-QTB/fix_qbmsst.cpp
+++ b/src/USER-QTB/fix_qbmsst.cpp
@@ -174,13 +174,13 @@ FixQBMSST::FixQBMSST(LAMMPS *lmp, int narg, char **arg) :
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);
+ 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);
+ fprintf(screen," Initial volume specified to be %12.5e\n", v0);
else fprintf(screen," Initial volume calculated on first step\n");
if (e0_set)
- fprintf(screen," Initial energy specified to be %12.5e\n", e0);
+ fprintf(screen," Initial energy specified to be %12.5e\n", e0);
else fprintf(screen," Initial energy calculated on first step\n");
}
if (logfile) {
@@ -194,13 +194,13 @@ FixQBMSST::FixQBMSST(LAMMPS *lmp, int narg, char **arg) :
fprintf(logfile," Artificial viscosity (units of mass/length/time) = %12.5e\n", mu);
if (p0_set)
- fprintf(logfile," Initial pressure specified to be %12.5e\n", p0);
+ fprintf(logfile," Initial pressure specified to be %12.5e\n", p0);
else fprintf(logfile," Initial pressure calculated on first step\n");
if (v0_set)
- fprintf(logfile," Initial volume specified to be %12.5e\n", v0);
+ fprintf(logfile," Initial volume specified to be %12.5e\n", v0);
else fprintf(logfile," Initial volume calculated on first step\n");
if (e0_set)
- fprintf(logfile," Initial energy specified to be %12.5e\n", e0);
+ fprintf(logfile," Initial energy specified to be %12.5e\n", e0);
else fprintf(logfile," Initial energy calculated on first step\n");
}
}
@@ -361,7 +361,7 @@ void FixQBMSST::init()
// initiate qtb temperature
if (!qtb_set) {
- t_current = t_init; qtb_set=1;
+ t_current = t_init; qtb_set=1;
}
old_eavg = e0;
@@ -411,13 +411,13 @@ void FixQBMSST::init()
nrigid = 0;
for (int i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"rigid") == 0 ||
- strcmp(modify->fix[i]->style,"poems") == 0) nrigid++;
+ strcmp(modify->fix[i]->style,"poems") == 0) nrigid++;
if (nrigid) {
rfix = new int[nrigid];
nrigid = 0;
for (int i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"rigid") == 0 ||
- strcmp(modify->fix[i]->style,"poems") == 0) rfix[nrigid++] = i;
+ strcmp(modify->fix[i]->style,"poems") == 0) rfix[nrigid++] = i;
}
}
@@ -482,19 +482,19 @@ void FixQBMSST::setup(int vflag)
if ( comm->me == 0 && tscale != 1.0) {
if ( screen )
- fprintf(screen,"Fix QBMSST initial strain rate of %12.5e established "
- "by reducing temperature by factor of %12.5e\n",
- fac2,tscale);
+ fprintf(screen,"Fix QBMSST initial strain rate of %12.5e established "
+ "by reducing temperature by factor of %12.5e\n",
+ fac2,tscale);
if ( logfile )
- fprintf(logfile,"Fix QBMSST initial strain rate of %12.5e established "
- "by reducing temperature by factor of %12.5e\n",
- fac2,tscale);
+ fprintf(logfile,"Fix QBMSST initial strain rate of %12.5e established "
+ "by reducing temperature by factor of %12.5e\n",
+ fac2,tscale);
}
for (int i = 0; i < atom->nlocal; i++) {
if (mask[i] & groupbit) {
for (int k = 0; k < 3; k++ ) {
v[i][k]*=sqrt_initial_temperature_scaling;
- }
+ }
}
}
}
@@ -569,9 +569,9 @@ void FixQBMSST::initial_integrate(int vflag)
//update random array
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_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_0[j][2*N_f-1] = random->uniform()-0.5;
random_array_1[j][2*N_f-1] = random->uniform()-0.5;
@@ -629,20 +629,20 @@ void FixQBMSST::initial_integrate(int vflag)
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] /
- (velocity_sum * mass[type[i]] * vol ) - fric_coef;
- old_velocity[i][k] = v[i][k];
- if ( k == direction ) {
- D = D - 2.0 * omega[sd] / vol;
- }
- if ( fabs(dthalf * D) > 1.0e-06 ) {
- double expd = exp(D * dthalf);
- v[i][k] = expd * ( C + D * v[i][k] - C / expd ) / D;
- } else {
- v[i][k] = v[i][k] + ( C + D * v[i][k] ) * dthalf +
- 0.5 * (D * D * v[i][k] + C * D ) * dthalf * dthalf;
- }
+ 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] /
+ (velocity_sum * mass[type[i]] * vol ) - fric_coef;
+ old_velocity[i][k] = v[i][k];
+ if ( k == direction ) {
+ D = D - 2.0 * omega[sd] / vol;
+ }
+ if ( fabs(dthalf * D) > 1.0e-06 ) {
+ double expd = exp(D * dthalf);
+ v[i][k] = expd * ( C + D * v[i][k] - C / expd ) / D;
+ } else {
+ v[i][k] = v[i][k] + ( C + D * v[i][k] ) * dthalf +
+ 0.5 * (D * D * v[i][k] + C * D ) * dthalf * dthalf;
+ }
}
}
}
@@ -653,7 +653,7 @@ void FixQBMSST::initial_integrate(int vflag)
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
for ( k = 0; k < 3; k++ ) {
- v[i][k] = old_velocity[i][k];
+ v[i][k] = old_velocity[i][k];
}
}
}
@@ -662,20 +662,20 @@ void FixQBMSST::initial_integrate(int vflag)
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] /
- (velocity_sum * mass[type[i]] * vol ) - fric_coef;
-
- if ( k == direction ) {
- D = D - 2.0 * omega[sd] / vol;
- }
- if ( fabs(dthalf * D) > 1.0e-06 ) {
- double expd = exp(D * dthalf);
- v[i][k] = expd * ( C + D * v[i][k] - C / expd ) / D;
- } else {
- v[i][k] = v[i][k] + ( C + D * v[i][k] ) * dthalf +
- 0.5 * (D * D * v[i][k] + C * D ) * dthalf * dthalf;
- }
+ 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] /
+ (velocity_sum * mass[type[i]] * vol ) - fric_coef;
+
+ if ( k == direction ) {
+ D = D - 2.0 * omega[sd] / vol;
+ }
+ if ( fabs(dthalf * D) > 1.0e-06 ) {
+ double expd = exp(D * dthalf);
+ v[i][k] = expd * ( C + D * v[i][k] - C / expd ) / D;
+ } else {
+ v[i][k] = v[i][k] + ( C + D * v[i][k] ) * dthalf +
+ 0.5 * (D * D * v[i][k] + C * D ) * dthalf * dthalf;
+ }
}
}
}
@@ -730,20 +730,20 @@ void FixQBMSST::final_integrate()
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
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] /
- (velocity_sum * mass[type[i]] * vol ) - fric_coef;
-
- if ( k == direction ) {
- D = D - 2.0 * omega[sd] / vol;
- }
- if ( fabs(dthalf * D) > 1.0e-06 ) {
- double expd = exp(D * dthalf);
- v[i][k] = expd * ( C + D * v[i][k] - C / expd ) / D;
- } else {
- v[i][k] = v[i][k] + ( C + D * v[i][k] ) * dthalf +
- 0.5 * (D * D * v[i][k] + C * D ) * dthalf * dthalf;
- }
+ 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] /
+ (velocity_sum * mass[type[i]] * vol ) - fric_coef;
+
+ if ( k == direction ) {
+ D = D - 2.0 * omega[sd] / vol;
+ }
+ if ( fabs(dthalf * D) > 1.0e-06 ) {
+ double expd = exp(D * dthalf);
+ v[i][k] = expd * ( C + D * v[i][k] - C / expd ) / D;
+ } else {
+ v[i][k] = v[i][k] + ( C + D * v[i][k] ) * dthalf +
+ 0.5 * (D * D * v[i][k] + C * D ) * dthalf * dthalf;
+ }
}
}
}
@@ -775,7 +775,7 @@ void FixQBMSST::final_integrate()
if ( B * dthalf > 1.0e-06 ) {
omega[sd] = ( omega[sd] + A *
- ( exp(B * dthalf) - 1.0 ) / B ) * exp(-B * dthalf);
+ ( 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;
diff --git a/src/USER-QTB/fix_qtb.cpp b/src/USER-QTB/fix_qtb.cpp
index ed9bc75574..98dd498088 100644
--- a/src/USER-QTB/fix_qtb.cpp
+++ b/src/USER-QTB/fix_qtb.cpp
@@ -257,9 +257,9 @@ void FixQTB::post_force(int vflag)
//update random array
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_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_0[j][2*N_f-1] = random->uniform()-0.5;
random_array_1[j][2*N_f-1] = random->uniform()-0.5;
diff --git a/src/USER-REAXC/fix_qeq_reax.cpp b/src/USER-REAXC/fix_qeq_reax.cpp
index a79c5edd07..326af7505a 100644
--- a/src/USER-REAXC/fix_qeq_reax.cpp
+++ b/src/USER-REAXC/fix_qeq_reax.cpp
@@ -504,7 +504,7 @@ void FixQEqReax::pre_force(int vflag)
init_matvec();
- matvecs_s = CG(b_s, s); // CG on s - parallel
+ matvecs_s = CG(b_s, s); // CG on s - parallel
matvecs_t = CG(b_t, t); // CG on t - parallel
matvecs = matvecs_s + matvecs_t;
@@ -631,9 +631,9 @@ void FixQEqReax::compute_H()
if (dy > SMALL) flag = 1;
else if (fabs(dy) < SMALL && dx > SMALL)
flag = 1;
- }
- }
- }
+ }
+ }
+ }
if (flag) {
H.jlist[m_fill] = j;
diff --git a/src/USER-REAXC/pair_reaxc.cpp b/src/USER-REAXC/pair_reaxc.cpp
index 626e965667..6081563e18 100644
--- a/src/USER-REAXC/pair_reaxc.cpp
+++ b/src/USER-REAXC/pair_reaxc.cpp
@@ -16,7 +16,7 @@
(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
- Ray Shan (Sandia)
+ Ray Shan (Sandia)
Hybrid and hybrid/overlay compatibility added by Ray Shan (Sandia)
------------------------------------------------------------------------- */
@@ -261,14 +261,14 @@ void PairReaxC::settings(int narg, char **arg)
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)
- error->all(FLERR,"Illegal pair_style reax/c safezone command");
+ error->all(FLERR,"Illegal pair_style reax/c safezone command");
system->saferzone = system->safezone*1.2 + 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)
- error->all(FLERR,"Illegal pair_style reax/c mincap command");
+ error->all(FLERR,"Illegal pair_style reax/c mincap command");
iarg += 2;
} else error->all(FLERR,"Illegal pair_style reax/c command");
}
@@ -325,7 +325,7 @@ void PairReaxC::coeff( int nargs, char **args )
for (int j = 0; j < nreax_types; j++)
if (strcasecmp(args[i],system->reax_param.sbp[j].name) == 0) {
map[i-2] = j;
- itmp ++;
+ itmp ++;
}
// error check
@@ -390,8 +390,8 @@ void PairReaxC::init_style( )
cutmax = MAX3(control->nonb_cut, control->hbond_cut, control->bond_cut);
if ((cutmax < 2.0*control->bond_cut) && (comm->me == 0))
error->warning(FLERR,"Total cutoff < 2*bond cutoff. May need to use an "
- "increased neighbor list skin.");
-
+ "increased neighbor list skin.");
+
for( int i = 0; i < LIST_N; ++i )
lists[i].allocated = 0;
@@ -597,7 +597,7 @@ void PairReaxC::compute(int eflag, int vflag)
for (i = 0; i < system->N; i ++)
for (j = 0; j < MAXSPECBOND; j ++) {
tmpbo[i][j] = 0.0;
- tmpid[i][j] = 0;
+ tmpid[i][j] = 0;
}
FindBond();
}
@@ -841,10 +841,10 @@ void PairReaxC::FindBond()
bo_tmp = bo_ij->bo_data.BO;
if (bo_tmp >= bo_cut ) {
- tmpid[i][nj] = j;
- tmpbo[i][nj] = bo_tmp;
- nj ++;
- if (nj > MAXSPECBOND) error->all(FLERR,"Increase MAXSPECBOND in reaxc_defs.h");
+ tmpid[i][nj] = j;
+ tmpbo[i][nj] = bo_tmp;
+ nj ++;
+ if (nj > MAXSPECBOND) error->all(FLERR,"Increase MAXSPECBOND in reaxc_defs.h");
}
}
}
diff --git a/src/USER-REAXC/reaxc_allocate.cpp b/src/USER-REAXC/reaxc_allocate.cpp
index e46fe8ba9f..a07f090f92 100644
--- a/src/USER-REAXC/reaxc_allocate.cpp
+++ b/src/USER-REAXC/reaxc_allocate.cpp
@@ -300,10 +300,10 @@ int Allocate_Workspace( reax_system *system, control_params *control,
// storage for reductions with multiple threads
#ifdef LMP_USER_OMP
workspace->CdDeltaReduction = (double *) scalloc(sizeof(double), total_cap*control->nthreads,
- "cddelta_reduce", comm);
+ "cddelta_reduce", comm);
workspace->forceReduction = (rvec *) scalloc(sizeof(rvec), total_cap*control->nthreads,
- "forceReduction", comm);
+ "forceReduction", comm);
workspace->valence_angle_atom_myoffset = (int *) scalloc(sizeof(int), total_cap, "valence_angle_atom_myoffset", comm);
workspace->my_ext_pressReduction = (rvec *) calloc(sizeof(rvec), control->nthreads);
diff --git a/src/USER-REAXC/reaxc_bonds.cpp b/src/USER-REAXC/reaxc_bonds.cpp
index cf536fe606..9678addd6b 100644
--- a/src/USER-REAXC/reaxc_bonds.cpp
+++ b/src/USER-REAXC/reaxc_bonds.cpp
@@ -63,14 +63,14 @@ void Bonds( reax_system *system, control_params *control,
j = bonds->select.bond_list[pj].nbr;
if( system->my_atoms[i].orig_id > system->my_atoms[j].orig_id )
- continue;
+ 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] &&
- 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] &&
- system->my_atoms[j].x[0] < system->my_atoms[i].x[0]) continue;
+ 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] &&
+ system->my_atoms[j].x[0] < system->my_atoms[i].x[0]) continue;
}
/* set the pointers */
@@ -86,17 +86,17 @@ void Bonds( reax_system *system, control_params *control,
else 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 );
+ ( 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;
+ -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);
+ 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;
@@ -105,33 +105,33 @@ void Bonds( reax_system *system, control_params *control,
/* Stabilisation terminal triple bond */
if( bo_ij->BO >= 1.00 ) {
- if( gp37 == 2 ||
- (sbp_i->mass == 12.0000 && sbp_j->mass == 15.9990) ||
- (sbp_j->mass == 12.0000 && sbp_i->mass == 15.9990) ) {
- exphu = exp( -gp7 * SQR(bo_ij->BO - 2.50) );
- exphua1 = exp(-gp3 * (workspace->total_bond_order[i]-bo_ij->BO));
- 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;
- }
+ if( gp37 == 2 ||
+ (sbp_i->mass == 12.0000 && sbp_j->mass == 15.9990) ||
+ (sbp_j->mass == 12.0000 && sbp_i->mass == 15.9990) ) {
+ exphu = exp( -gp7 * SQR(bo_ij->BO - 2.50) );
+ exphua1 = exp(-gp3 * (workspace->total_bond_order[i]-bo_ij->BO));
+ 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_forces.cpp b/src/USER-REAXC/reaxc_forces.cpp
index fe3cc07a70..00b29824ea 100644
--- a/src/USER-REAXC/reaxc_forces.cpp
+++ b/src/USER-REAXC/reaxc_forces.cpp
@@ -257,7 +257,7 @@ void Init_Forces_noQEq( reax_system *system, control_params *control,
if( flag ) {
type_j = atom_j->type;
- if (type_j < 0) continue;
+ if (type_j < 0) continue;
sbp_j = &(system->reax_param.sbp[type_j]);
twbp = &(system->reax_param.tbp[type_i][type_j]);
diff --git a/src/USER-REAXC/reaxc_hydrogen_bonds.cpp b/src/USER-REAXC/reaxc_hydrogen_bonds.cpp
index ff771ad65b..cb516b24f7 100644
--- a/src/USER-REAXC/reaxc_hydrogen_bonds.cpp
+++ b/src/USER-REAXC/reaxc_hydrogen_bonds.cpp
@@ -76,7 +76,7 @@ void Hydrogen_Bonds( reax_system *system, control_params *control,
pbond_ij = &( bond_list[pi] );
i = pbond_ij->nbr;
type_i = system->my_atoms[i].type;
- if (type_i < 0) continue;
+ if (type_i < 0) continue;
bo_ij = &(pbond_ij->bo_data);
if( system->reax_param.sbp[type_i].p_hbond == 2 &&
@@ -88,7 +88,7 @@ void Hydrogen_Bonds( reax_system *system, control_params *control,
/* set k's varibles */
k = hbond_list[pk].nbr;
type_k = system->my_atoms[k].type;
- if (type_k < 0) continue;
+ if (type_k < 0) continue;
nbr_jk = hbond_list[pk].ptr;
r_jk = nbr_jk->d;
rvec_Scale( dvec_jk, hbond_list[pk].scl, nbr_jk->dvec );
@@ -101,9 +101,9 @@ void Hydrogen_Bonds( reax_system *system, control_params *control,
if( system->my_atoms[i].orig_id != system->my_atoms[k].orig_id ) {
bo_ij = &(pbond_ij->bo_data);
type_i = system->my_atoms[i].type;
- if (type_i < 0) continue;
+ if (type_i < 0) continue;
hbp = &(system->reax_param.hbp[ type_i ][ type_j ][ type_k ]);
- if (hbp->r0_hb <= 0.0) continue;
+ if (hbp->r0_hb <= 0.0) continue;
++num_hb_intrs;
Calculate_Theta( pbond_ij->dvec, pbond_ij->d, dvec_jk, r_jk,
diff --git a/src/USER-REAXC/reaxc_multi_body.cpp b/src/USER-REAXC/reaxc_multi_body.cpp
index ecfd3ad04d..ce5b966529 100644
--- a/src/USER-REAXC/reaxc_multi_body.cpp
+++ b/src/USER-REAXC/reaxc_multi_body.cpp
@@ -99,7 +99,7 @@ void Atom_Energy( reax_system *system, control_params *control,
for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj ) {
j = bonds->select.bond_list[pj].nbr;
type_j = system->my_atoms[j].type;
- if (type_j < 0) continue;
+ if (type_j < 0) continue;
if( !strcmp( system->reax_param.sbp[type_j].name, "C" ) ) {
twbp = &( system->reax_param.tbp[type_i][type_j]);
@@ -141,7 +141,7 @@ void Atom_Energy( reax_system *system, control_params *control,
for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj ) {
j = bonds->select.bond_list[pj].nbr;
type_j = system->my_atoms[j].type;
- if (type_j < 0) continue;
+ if (type_j < 0) continue;
bo_ij = &(bonds->select.bond_list[pj].bo_data);
twbp = &(system->reax_param.tbp[ type_i ][ type_j ]);
diff --git a/src/USER-REAXC/reaxc_torsion_angles.cpp b/src/USER-REAXC/reaxc_torsion_angles.cpp
index 74d5b04f20..c5a7f23b30 100644
--- a/src/USER-REAXC/reaxc_torsion_angles.cpp
+++ b/src/USER-REAXC/reaxc_torsion_angles.cpp
@@ -182,14 +182,14 @@ void Torsion_Angles( reax_system *system, control_params *control,
BOA_jk = bo_jk->BO - control->thb_cut;
if( system->my_atoms[j].orig_id > system->my_atoms[k].orig_id )
- continue;
+ 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] &&
- 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] &&
- system->my_atoms[k].x[0] < system->my_atoms[j].x[0]) continue;
+ 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] &&
+ system->my_atoms[k].x[0] < system->my_atoms[j].x[0]) continue;
}
if( bo_jk->BO > control->thb_cut/*0*/ && Num_Entries(pk, thb_intrs) ) {
diff --git a/src/USER-SMD/atom_vec_smd.cpp b/src/USER-SMD/atom_vec_smd.cpp
index d2d72a855a..84fbfd93ef 100644
--- a/src/USER-SMD/atom_vec_smd.cpp
+++ b/src/USER-SMD/atom_vec_smd.cpp
@@ -45,44 +45,44 @@ using namespace MathConst;
/* ---------------------------------------------------------------------- */
AtomVecSMD::AtomVecSMD(LAMMPS *lmp) :
- AtomVec(lmp) {
- molecular = 0;
-
- comm_x_only = 0;
- comm_f_only = 0;
- size_forward = 6; // variables that are changed by time integration
- size_reverse = 4; // f[3] + de
- size_border = 31;
- size_velocity = 6; // v + vest
- size_data_atom = 13; // 7 + 3 x0 + 3 x
- size_data_vel = 4;
- xcol_data = 11;
-
- atom->radius_flag = 1;
- atom->rmass_flag = 1;
- atom->vfrac_flag = 1;
- atom->contact_radius_flag = 1;
- atom->molecule_flag = 1;
- atom->smd_data_9_flag = 1;
- atom->e_flag = 1;
- atom->vest_flag = 1;
- atom->smd_stress_flag = 1;
- atom->eff_plastic_strain_flag = 1;
- atom->x0_flag = 1;
- atom->damage_flag = 1;
- atom->eff_plastic_strain_rate_flag = 1;
-
- forceclearflag = 1;
-
- atom->smd_flag = 1;
+ AtomVec(lmp) {
+ molecular = 0;
+
+ comm_x_only = 0;
+ comm_f_only = 0;
+ size_forward = 6; // variables that are changed by time integration
+ size_reverse = 4; // f[3] + de
+ size_border = 31;
+ size_velocity = 6; // v + vest
+ size_data_atom = 13; // 7 + 3 x0 + 3 x
+ size_data_vel = 4;
+ xcol_data = 11;
+
+ atom->radius_flag = 1;
+ atom->rmass_flag = 1;
+ atom->vfrac_flag = 1;
+ atom->contact_radius_flag = 1;
+ atom->molecule_flag = 1;
+ atom->smd_data_9_flag = 1;
+ atom->e_flag = 1;
+ atom->vest_flag = 1;
+ atom->smd_stress_flag = 1;
+ atom->eff_plastic_strain_flag = 1;
+ atom->x0_flag = 1;
+ atom->damage_flag = 1;
+ atom->eff_plastic_strain_rate_flag = 1;
+
+ forceclearflag = 1;
+
+ atom->smd_flag = 1;
}
/* ---------------------------------------------------------------------- */
void AtomVecSMD::init() {
- AtomVec::init();
+ AtomVec::init();
- // do nothing here
+ // do nothing here
}
/* ----------------------------------------------------------------------
@@ -92,43 +92,43 @@ void AtomVecSMD::init() {
------------------------------------------------------------------------- */
void AtomVecSMD::grow(int n) {
- if (n == 0)
- grow_nmax();
- else
- nmax = n;
- atom->nmax = nmax;
- if (nmax < 0 || nmax > MAXSMALLINT)
- error->one(FLERR, "Per-processor system is too big");
-
- //printf("in grow, nmax is now %d\n", nmax);
-
- tag = memory->grow(atom->tag, nmax, "atom:tag");
- type = memory->grow(atom->type, nmax, "atom:type");
- mask = memory->grow(atom->mask, nmax, "atom:mask");
- image = memory->grow(atom->image, nmax, "atom:image");
- x = memory->grow(atom->x, nmax, 3, "atom:x");
- v = memory->grow(atom->v, nmax, 3, "atom:v");
-
- f = memory->grow(atom->f, nmax * comm->nthreads, 3, "atom:f");
- de = memory->grow(atom->de, nmax * comm->nthreads, "atom:de");
-
- vfrac = memory->grow(atom->vfrac, nmax, "atom:vfrac");
- rmass = memory->grow(atom->rmass, nmax, "atom:rmass");
- x0 = memory->grow(atom->x0, nmax, 3, "atom:x0");
- radius = memory->grow(atom->radius, nmax, "atom:radius");
- contact_radius = memory->grow(atom->contact_radius, nmax, "atom:contact_radius");
- molecule = memory->grow(atom->molecule, nmax, "atom:molecule");
- smd_data_9 = memory->grow(atom->smd_data_9, nmax, NMAT_FULL, "atom:defgrad_old");
- e = memory->grow(atom->e, nmax, "atom:e");
- vest = memory->grow(atom->vest, nmax, 3, "atom:vest");
- tlsph_stress = memory->grow(atom->smd_stress, nmax, NMAT_SYMM, "atom:tlsph_stress");
- eff_plastic_strain = memory->grow(atom->eff_plastic_strain, nmax, "atom:eff_plastic_strain");
- eff_plastic_strain_rate = memory->grow(atom->eff_plastic_strain_rate, nmax, "atom:eff_plastic_strain_rate");
- damage = memory->grow(atom->damage, nmax, "atom:damage");
-
- if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
- modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
+ if (n == 0)
+ grow_nmax();
+ else
+ nmax = n;
+ atom->nmax = nmax;
+ if (nmax < 0 || nmax > MAXSMALLINT)
+ error->one(FLERR, "Per-processor system is too big");
+
+ //printf("in grow, nmax is now %d\n", nmax);
+
+ tag = memory->grow(atom->tag, nmax, "atom:tag");
+ type = memory->grow(atom->type, nmax, "atom:type");
+ mask = memory->grow(atom->mask, nmax, "atom:mask");
+ image = memory->grow(atom->image, nmax, "atom:image");
+ x = memory->grow(atom->x, nmax, 3, "atom:x");
+ v = memory->grow(atom->v, nmax, 3, "atom:v");
+
+ f = memory->grow(atom->f, nmax * comm->nthreads, 3, "atom:f");
+ de = memory->grow(atom->de, nmax * comm->nthreads, "atom:de");
+
+ vfrac = memory->grow(atom->vfrac, nmax, "atom:vfrac");
+ rmass = memory->grow(atom->rmass, nmax, "atom:rmass");
+ x0 = memory->grow(atom->x0, nmax, 3, "atom:x0");
+ radius = memory->grow(atom->radius, nmax, "atom:radius");
+ contact_radius = memory->grow(atom->contact_radius, nmax, "atom:contact_radius");
+ molecule = memory->grow(atom->molecule, nmax, "atom:molecule");
+ smd_data_9 = memory->grow(atom->smd_data_9, nmax, NMAT_FULL, "atom:defgrad_old");
+ e = memory->grow(atom->e, nmax, "atom:e");
+ vest = memory->grow(atom->vest, nmax, 3, "atom:vest");
+ tlsph_stress = memory->grow(atom->smd_stress, nmax, NMAT_SYMM, "atom:tlsph_stress");
+ eff_plastic_strain = memory->grow(atom->eff_plastic_strain, nmax, "atom:eff_plastic_strain");
+ eff_plastic_strain_rate = memory->grow(atom->eff_plastic_strain_rate, nmax, "atom:eff_plastic_strain_rate");
+ damage = memory->grow(atom->damage, nmax, "atom:damage");
+
+ if (atom->nextra_grow)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
}
/* ----------------------------------------------------------------------
@@ -136,28 +136,28 @@ void AtomVecSMD::grow(int n) {
------------------------------------------------------------------------- */
void AtomVecSMD::grow_reset() {
- tag = atom->tag;
- type = atom->type;
- mask = atom->mask;
- image = atom->image;
- x = atom->x;
- v = atom->v;
- f = atom->f;
- radius = atom->radius;
- rmass = atom->rmass;
-
- vfrac = atom->vfrac;
- x0 = atom->x0;
- contact_radius = atom->contact_radius;
- molecule = atom->molecule;
- smd_data_9 = atom->smd_data_9;
- e = atom->e;
- de = atom->de;
- tlsph_stress = atom->smd_stress;
- eff_plastic_strain = atom->eff_plastic_strain;
- eff_plastic_strain_rate = atom->eff_plastic_strain_rate;
- damage = atom->damage;
- vest = atom->vest;
+ tag = atom->tag;
+ type = atom->type;
+ mask = atom->mask;
+ image = atom->image;
+ x = atom->x;
+ v = atom->v;
+ f = atom->f;
+ radius = atom->radius;
+ rmass = atom->rmass;
+
+ vfrac = atom->vfrac;
+ x0 = atom->x0;
+ contact_radius = atom->contact_radius;
+ molecule = atom->molecule;
+ smd_data_9 = atom->smd_data_9;
+ e = atom->e;
+ de = atom->de;
+ tlsph_stress = atom->smd_stress;
+ eff_plastic_strain = atom->eff_plastic_strain;
+ eff_plastic_strain_rate = atom->eff_plastic_strain_rate;
+ damage = atom->damage;
+ vest = atom->vest;
}
/* ----------------------------------------------------------------------
@@ -165,555 +165,555 @@ void AtomVecSMD::grow_reset() {
------------------------------------------------------------------------- */
void AtomVecSMD::copy(int i, int j, int delflag) {
- tag[j] = tag[i];
- type[j] = type[i];
- mask[j] = mask[i];
- image[j] = image[i];
- x[j][0] = x[i][0];
- x[j][1] = x[i][1];
- x[j][2] = x[i][2];
- v[j][0] = v[i][0];
- v[j][1] = v[i][1];
- v[j][2] = v[i][2];
-
- vfrac[j] = vfrac[i];
- rmass[j] = rmass[i];
- x0[j][0] = x0[i][0];
- x0[j][1] = x0[i][1];
- x0[j][2] = x0[i][2];
- radius[j] = radius[i];
- contact_radius[j] = contact_radius[i];
- molecule[j] = molecule[i];
- e[j] = e[i];
- eff_plastic_strain[j] = eff_plastic_strain[i];
- eff_plastic_strain_rate[j] = eff_plastic_strain_rate[i];
- vest[j][0] = vest[i][0];
- vest[j][1] = vest[i][1];
- vest[j][2] = vest[i][2];
-
- for (int k = 0; k < NMAT_FULL; k++) {
- smd_data_9[j][k] = smd_data_9[i][k];
- }
-
- for (int k = 0; k < NMAT_SYMM; k++) {
- tlsph_stress[j][k] = tlsph_stress[i][k];
- }
-
- damage[j] = damage[i];
-
- if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
- modify->fix[atom->extra_grow[iextra]]->copy_arrays(i, j, delflag);
+ tag[j] = tag[i];
+ type[j] = type[i];
+ mask[j] = mask[i];
+ image[j] = image[i];
+ x[j][0] = x[i][0];
+ x[j][1] = x[i][1];
+ x[j][2] = x[i][2];
+ v[j][0] = v[i][0];
+ v[j][1] = v[i][1];
+ v[j][2] = v[i][2];
+
+ vfrac[j] = vfrac[i];
+ rmass[j] = rmass[i];
+ x0[j][0] = x0[i][0];
+ x0[j][1] = x0[i][1];
+ x0[j][2] = x0[i][2];
+ radius[j] = radius[i];
+ contact_radius[j] = contact_radius[i];
+ molecule[j] = molecule[i];
+ e[j] = e[i];
+ eff_plastic_strain[j] = eff_plastic_strain[i];
+ eff_plastic_strain_rate[j] = eff_plastic_strain_rate[i];
+ vest[j][0] = vest[i][0];
+ vest[j][1] = vest[i][1];
+ vest[j][2] = vest[i][2];
+
+ for (int k = 0; k < NMAT_FULL; k++) {
+ smd_data_9[j][k] = smd_data_9[i][k];
+ }
+
+ for (int k = 0; k < NMAT_SYMM; k++) {
+ tlsph_stress[j][k] = tlsph_stress[i][k];
+ }
+
+ damage[j] = damage[i];
+
+ if (atom->nextra_grow)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ modify->fix[atom->extra_grow[iextra]]->copy_arrays(i, j, delflag);
}
/* ---------------------------------------------------------------------- */
int AtomVecSMD::pack_comm(int n, int *list, double *buf, int pbc_flag, int *pbc) {
- error->one(FLERR, "atom vec tlsph can only be used with ghost velocities turned on");
- return -1;
+ error->one(FLERR, "atom vec tlsph can only be used with ghost velocities turned on");
+ return -1;
}
/* ---------------------------------------------------------------------- */
int AtomVecSMD::pack_comm_vel(int n, int *list, double *buf, int pbc_flag, int *pbc) {
- // communicate quantities to ghosts, which are changed by time-integration AND are required on ghost atoms.
-
- //no need to pack stress or defgrad information here, as these quantities are not required for ghost atoms.
- // Inside pair_style tlsph, these quantities are computed and communicated to ghosts.
-
- // no need to communicate x0 here, as it is not changed by time integration
- // if x0 is changed when the ref config is updated, this communication is performed in the fix_integrate/tlsph
- // similarily, rmass could be removed here.
- // radius should be communicated here for future time-integration of the radius with ulsph (not implemented yet)
- int i, j, m;
- double dx, dy, dz, dvx, dvy, dvz;
-
- m = 0;
- if (pbc_flag == 0) {
- for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0];
- buf[m++] = x[j][1];
- buf[m++] = x[j][2]; //3
- buf[m++] = radius[j];
- buf[m++] = vfrac[j]; // 5
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2]; // 8
-
- buf[m++] = vest[j][0];
- buf[m++] = vest[j][1];
- buf[m++] = vest[j][2]; // 11
- buf[m++] = e[j]; // 12
-
- }
- } else {
- if (domain->triclinic == 0) {
- dx = pbc[0] * domain->xprd;
- dy = pbc[1] * domain->yprd;
- dz = pbc[2] * domain->zprd;
- } else {
- dx = pbc[0] * domain->xprd + pbc[5] * domain->xy + pbc[4] * domain->xz;
- dy = pbc[1] * domain->yprd + pbc[3] * domain->yz;
- dz = pbc[2] * domain->zprd;
- }
- if (!deform_vremap) {
- for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- buf[m++] = radius[j];
- buf[m++] = vfrac[j];
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2]; // 8
-
- buf[m++] = vest[j][0];
- buf[m++] = vest[j][1];
- buf[m++] = vest[j][2]; // 11
- buf[m++] = e[j]; // 12
-
- }
- } else {
- dvx = pbc[0] * h_rate[0] + pbc[5] * h_rate[5] + pbc[4] * h_rate[4];
- dvy = pbc[1] * h_rate[1] + pbc[3] * h_rate[3];
- dvz = pbc[2] * h_rate[2];
-// printf("\ndvx = %f, dvy=%f, dvz=%f\n", dvx, dvy, dvz);
-// printf("dx = %f, dy=%f, dz=%f\n", dx, dy, dz);
- for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz;
- buf[m++] = radius[j];
- buf[m++] = vfrac[j];
- if (mask[i] & deform_groupbit) {
- buf[m++] = v[j][0] + dvx;
- buf[m++] = v[j][1] + dvy;
- buf[m++] = v[j][2] + dvz;
- buf[m++] = vest[j][0] + dvx;
- buf[m++] = vest[j][1] + dvy;
- buf[m++] = vest[j][2] + dvz;
- } else {
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2]; // 8
- buf[m++] = vest[j][0];
- buf[m++] = vest[j][1];
- buf[m++] = vest[j][2]; // 11
- }
-
- buf[m++] = e[j]; // 12
-
- }
- }
- }
-
- return m;
+ // communicate quantities to ghosts, which are changed by time-integration AND are required on ghost atoms.
+
+ //no need to pack stress or defgrad information here, as these quantities are not required for ghost atoms.
+ // Inside pair_style tlsph, these quantities are computed and communicated to ghosts.
+
+ // no need to communicate x0 here, as it is not changed by time integration
+ // if x0 is changed when the ref config is updated, this communication is performed in the fix_integrate/tlsph
+ // similarily, rmass could be removed here.
+ // radius should be communicated here for future time-integration of the radius with ulsph (not implemented yet)
+ int i, j, m;
+ double dx, dy, dz, dvx, dvy, dvz;
+
+ m = 0;
+ if (pbc_flag == 0) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = x[j][0];
+ buf[m++] = x[j][1];
+ buf[m++] = x[j][2]; //3
+ buf[m++] = radius[j];
+ buf[m++] = vfrac[j]; // 5
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2]; // 8
+
+ buf[m++] = vest[j][0];
+ buf[m++] = vest[j][1];
+ buf[m++] = vest[j][2]; // 11
+ buf[m++] = e[j]; // 12
+
+ }
+ } else {
+ if (domain->triclinic == 0) {
+ dx = pbc[0] * domain->xprd;
+ dy = pbc[1] * domain->yprd;
+ dz = pbc[2] * domain->zprd;
+ } else {
+ dx = pbc[0] * domain->xprd + pbc[5] * domain->xy + pbc[4] * domain->xz;
+ dy = pbc[1] * domain->yprd + pbc[3] * domain->yz;
+ dz = pbc[2] * domain->zprd;
+ }
+ if (!deform_vremap) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = radius[j];
+ buf[m++] = vfrac[j];
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2]; // 8
+
+ buf[m++] = vest[j][0];
+ buf[m++] = vest[j][1];
+ buf[m++] = vest[j][2]; // 11
+ buf[m++] = e[j]; // 12
+
+ }
+ } else {
+ dvx = pbc[0] * h_rate[0] + pbc[5] * h_rate[5] + pbc[4] * h_rate[4];
+ dvy = pbc[1] * h_rate[1] + pbc[3] * h_rate[3];
+ dvz = pbc[2] * h_rate[2];
+// printf("\ndvx = %f, dvy=%f, dvz=%f\n", dvx, dvy, dvz);
+// printf("dx = %f, dy=%f, dz=%f\n", dx, dy, dz);
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = radius[j];
+ buf[m++] = vfrac[j];
+ if (mask[i] & deform_groupbit) {
+ buf[m++] = v[j][0] + dvx;
+ buf[m++] = v[j][1] + dvy;
+ buf[m++] = v[j][2] + dvz;
+ buf[m++] = vest[j][0] + dvx;
+ buf[m++] = vest[j][1] + dvy;
+ buf[m++] = vest[j][2] + dvz;
+ } else {
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2]; // 8
+ buf[m++] = vest[j][0];
+ buf[m++] = vest[j][1];
+ buf[m++] = vest[j][2]; // 11
+ }
+
+ buf[m++] = e[j]; // 12
+
+ }
+ }
+ }
+
+ return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecSMD::pack_comm_hybrid(int n, int *list, double *buf) {
- int i, j, m;
-
- m = 0;
- for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = radius[j];
- buf[m++] = vfrac[j];
- buf[m++] = vest[j][0];
- buf[m++] = vest[j][1];
- buf[m++] = vest[j][2];
- buf[m++] = e[j];
- }
- return m;
+ int i, j, m;
+
+ m = 0;
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = radius[j];
+ buf[m++] = vfrac[j];
+ buf[m++] = vest[j][0];
+ buf[m++] = vest[j][1];
+ buf[m++] = vest[j][2];
+ buf[m++] = e[j];
+ }
+ return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecSMD::unpack_comm(int n, int first, double *buf) {
- error->one(FLERR, "atom vec tlsph can only be used with ghost velocities turned on");
+ error->one(FLERR, "atom vec tlsph can only be used with ghost velocities turned on");
}
/* ---------------------------------------------------------------------- */
void AtomVecSMD::unpack_comm_vel(int n, int first, double *buf) {
- int i, m, last;
-
- m = 0;
- last = first + n;
- for (i = first; i < last; i++) {
- x[i][0] = buf[m++];
- x[i][1] = buf[m++];
- x[i][2] = buf[m++]; //3
- radius[i] = buf[m++];
- vfrac[i] = buf[m++]; // 5
- v[i][0] = buf[m++];
- v[i][1] = buf[m++];
- v[i][2] = buf[m++]; // 8
-
- vest[i][0] = buf[m++];
- vest[i][1] = buf[m++];
- vest[i][2] = buf[m++]; // 11
- e[i] = buf[m++];
-
- }
+ int i, m, last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ x[i][0] = buf[m++];
+ x[i][1] = buf[m++];
+ x[i][2] = buf[m++]; //3
+ radius[i] = buf[m++];
+ vfrac[i] = buf[m++]; // 5
+ v[i][0] = buf[m++];
+ v[i][1] = buf[m++];
+ v[i][2] = buf[m++]; // 8
+
+ vest[i][0] = buf[m++];
+ vest[i][1] = buf[m++];
+ vest[i][2] = buf[m++]; // 11
+ e[i] = buf[m++];
+
+ }
}
/* ---------------------------------------------------------------------- */
int AtomVecSMD::unpack_comm_hybrid(int n, int first, double *buf) {
- int i, m, last;
-
- m = 0;
- last = first + n;
- for (i = first; i < last; i++) {
- radius[i] = buf[m++];
- vfrac[i] = buf[m++];
- vest[i][0] = buf[m++];
- vest[i][1] = buf[m++];
- vest[i][2] = buf[m++];
- e[i] = buf[m++];
- }
- return m;
+ int i, m, last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ radius[i] = buf[m++];
+ vfrac[i] = buf[m++];
+ vest[i][0] = buf[m++];
+ vest[i][1] = buf[m++];
+ vest[i][2] = buf[m++];
+ e[i] = buf[m++];
+ }
+ return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecSMD::pack_reverse(int n, int first, double *buf) {
- int i, m, last;
-
- printf("in pack_reverse\n");
-
- m = 0;
- last = first + n;
- for (i = first; i < last; i++) {
- buf[m++] = f[i][0];
- buf[m++] = f[i][1];
- buf[m++] = f[i][2];
- buf[m++] = de[i];
- }
- return m;
+ int i, m, last;
+
+ printf("in pack_reverse\n");
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ buf[m++] = f[i][0];
+ buf[m++] = f[i][1];
+ buf[m++] = f[i][2];
+ buf[m++] = de[i];
+ }
+ return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecSMD::pack_reverse_hybrid(int n, int first, double *buf) {
- int i, m, last;
-
- m = 0;
- last = first + n;
- for (i = first; i < last; i++) {
- buf[m++] = de[i];
- }
- return m;
+ int i, m, last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ buf[m++] = de[i];
+ }
+ return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecSMD::unpack_reverse(int n, int *list, double *buf) {
- int i, j, m;
-
- m = 0;
- for (i = 0; i < n; i++) {
- j = list[i];
- f[j][0] += buf[m++];
- f[j][1] += buf[m++];
- f[j][2] += buf[m++];
- de[j] += buf[m++];
- }
+ int i, j, m;
+
+ m = 0;
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ f[j][0] += buf[m++];
+ f[j][1] += buf[m++];
+ f[j][2] += buf[m++];
+ de[j] += buf[m++];
+ }
}
/* ---------------------------------------------------------------------- */
int AtomVecSMD::unpack_reverse_hybrid(int n, int *list, double *buf) {
- int i, j, m;
-
- m = 0;
- for (i = 0; i < n; i++) {
- j = list[i];
- de[j] += buf[m++];
- }
- return m;
+ int i, j, m;
+
+ m = 0;
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ de[j] += buf[m++];
+ }
+ return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecSMD::pack_border(int n, int *list, double *buf, int pbc_flag, int *pbc) {
- error->one(FLERR, "atom vec tlsph can only be used with ghost velocities turned on");
- return -1;
+ error->one(FLERR, "atom vec tlsph can only be used with ghost velocities turned on");
+ return -1;
}
/* ---------------------------------------------------------------------- */
int AtomVecSMD::pack_border_vel(int n, int *list, double *buf, int pbc_flag, int *pbc) {
- int i, j, m;
- double dx, dy, dz, dvx, dvy, dvz;
-
- //printf("AtomVecSMD::pack_border_vel\n");
-
- m = 0;
- if (pbc_flag == 0) {
- for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0];
- buf[m++] = x[j][1];
- buf[m++] = x[j][2]; // 3
- buf[m++] = x0[j][0];
- buf[m++] = x0[j][1];
- buf[m++] = x0[j][2]; // 6
- buf[m++] = ubuf(tag[j]).d;
- buf[m++] = ubuf(type[j]).d;
- buf[m++] = ubuf(mask[j]).d;
- buf[m++] = ubuf(molecule[j]).d; // 10
- buf[m++] = radius[j];
- buf[m++] = rmass[j];
- buf[m++] = vfrac[j];
- buf[m++] = contact_radius[j];
- buf[m++] = e[j];
- buf[m++] = eff_plastic_strain[j]; // 16
-
- for (int k = 0; k < NMAT_FULL; k++) {
- buf[m++] = smd_data_9[j][k];
- } // 25
-
- for (int k = 0; k < NMAT_SYMM; k++) {
- buf[m++] = tlsph_stress[j][k];
- } // 31
-
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2]; // 34
- buf[m++] = vest[j][0];
- buf[m++] = vest[j][1];
- buf[m++] = vest[j][2]; // 37
- }
- } else {
-
- if (domain->triclinic == 0) {
- dx = pbc[0] * domain->xprd;
- dy = pbc[1] * domain->yprd;
- dz = pbc[2] * domain->zprd;
- } else {
- dx = pbc[0];
- dy = pbc[1];
- dz = pbc[2];
- }
- if (!deform_vremap) {
- //printf("dx = %f\n", dx);
- for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz; // 3
- buf[m++] = x0[j][0]; // this is correct
- buf[m++] = x0[j][1];
- buf[m++] = x0[j][2]; // 6
- buf[m++] = ubuf(tag[j]).d;
- buf[m++] = ubuf(type[j]).d;
- buf[m++] = ubuf(mask[j]).d;
- buf[m++] = ubuf(molecule[j]).d; // 10
- buf[m++] = radius[j];
- buf[m++] = rmass[j];
- buf[m++] = vfrac[j];
- buf[m++] = contact_radius[j];
- buf[m++] = e[j];
- buf[m++] = eff_plastic_strain[j]; // 17
-
- for (int k = 0; k < NMAT_FULL; k++) {
- buf[m++] = smd_data_9[j][k];
- } // 26
-
- for (int k = 0; k < NMAT_SYMM; k++) {
- buf[m++] = tlsph_stress[j][k];
- } // 32
-
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2]; // 35
- buf[m++] = vest[j][0];
- buf[m++] = vest[j][1];
- buf[m++] = vest[j][2]; // 38
-
- }
- } else {
- dvx = pbc[0] * h_rate[0] + pbc[5] * h_rate[5] + pbc[4] * h_rate[4];
- dvy = pbc[1] * h_rate[1] + pbc[3] * h_rate[3];
- dvz = pbc[2] * h_rate[2];
-// printf("\ndvx = %f, dvy=%f, dvz=%f\n", dvx, dvy, dvz);
-// printf("dx = %f, dy=%f, dz=%f\n", dx, dy, dz);
- for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x[j][0] + dx;
- buf[m++] = x[j][1] + dy;
- buf[m++] = x[j][2] + dz; // 3
- buf[m++] = x0[j][0];
- buf[m++] = x0[j][1];
- buf[m++] = x0[j][2]; // 6
- buf[m++] = ubuf(tag[j]).d;
- buf[m++] = ubuf(type[j]).d;
- buf[m++] = ubuf(mask[j]).d;
- buf[m++] = ubuf(molecule[j]).d; // 10
- buf[m++] = radius[j];
- buf[m++] = rmass[j];
- buf[m++] = vfrac[j];
- buf[m++] = contact_radius[j];
- buf[m++] = e[j];
- buf[m++] = eff_plastic_strain[j]; // 16
-
- for (int k = 0; k < NMAT_FULL; k++) {
- buf[m++] = smd_data_9[j][k];
- } // 25
-
- for (int k = 0; k < NMAT_SYMM; k++) {
- buf[m++] = tlsph_stress[j][k];
- } // 31
-
- if (mask[i] & deform_groupbit) {
- buf[m++] = v[j][0] + dvx;
- buf[m++] = v[j][1] + dvy;
- buf[m++] = v[j][2] + dvz; // 34
- buf[m++] = vest[j][0] + dvx;
- buf[m++] = vest[j][1] + dvy;
- buf[m++] = vest[j][2] + dvz; // 37
-
- } else {
- buf[m++] = v[j][0];
- buf[m++] = v[j][1];
- buf[m++] = v[j][2]; // 34
- buf[m++] = vest[j][0];
- buf[m++] = vest[j][1];
- buf[m++] = vest[j][2]; // 37
- }
-
- }
- }
- }
-
- if (atom->nextra_border)
- for (int iextra = 0; iextra < atom->nextra_border; iextra++)
- m += modify->fix[atom->extra_border[iextra]]->pack_border(n, list, &buf[m]);
-
- return m;
+ int i, j, m;
+ double dx, dy, dz, dvx, dvy, dvz;
+
+ //printf("AtomVecSMD::pack_border_vel\n");
+
+ m = 0;
+ if (pbc_flag == 0) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = x[j][0];
+ buf[m++] = x[j][1];
+ buf[m++] = x[j][2]; // 3
+ buf[m++] = x0[j][0];
+ buf[m++] = x0[j][1];
+ buf[m++] = x0[j][2]; // 6
+ buf[m++] = ubuf(tag[j]).d;
+ buf[m++] = ubuf(type[j]).d;
+ buf[m++] = ubuf(mask[j]).d;
+ buf[m++] = ubuf(molecule[j]).d; // 10
+ buf[m++] = radius[j];
+ buf[m++] = rmass[j];
+ buf[m++] = vfrac[j];
+ buf[m++] = contact_radius[j];
+ buf[m++] = e[j];
+ buf[m++] = eff_plastic_strain[j]; // 16
+
+ for (int k = 0; k < NMAT_FULL; k++) {
+ buf[m++] = smd_data_9[j][k];
+ } // 25
+
+ for (int k = 0; k < NMAT_SYMM; k++) {
+ buf[m++] = tlsph_stress[j][k];
+ } // 31
+
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2]; // 34
+ buf[m++] = vest[j][0];
+ buf[m++] = vest[j][1];
+ buf[m++] = vest[j][2]; // 37
+ }
+ } else {
+
+ if (domain->triclinic == 0) {
+ dx = pbc[0] * domain->xprd;
+ dy = pbc[1] * domain->yprd;
+ dz = pbc[2] * domain->zprd;
+ } else {
+ dx = pbc[0];
+ dy = pbc[1];
+ dz = pbc[2];
+ }
+ if (!deform_vremap) {
+ //printf("dx = %f\n", dx);
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz; // 3
+ buf[m++] = x0[j][0]; // this is correct
+ buf[m++] = x0[j][1];
+ buf[m++] = x0[j][2]; // 6
+ buf[m++] = ubuf(tag[j]).d;
+ buf[m++] = ubuf(type[j]).d;
+ buf[m++] = ubuf(mask[j]).d;
+ buf[m++] = ubuf(molecule[j]).d; // 10
+ buf[m++] = radius[j];
+ buf[m++] = rmass[j];
+ buf[m++] = vfrac[j];
+ buf[m++] = contact_radius[j];
+ buf[m++] = e[j];
+ buf[m++] = eff_plastic_strain[j]; // 17
+
+ for (int k = 0; k < NMAT_FULL; k++) {
+ buf[m++] = smd_data_9[j][k];
+ } // 26
+
+ for (int k = 0; k < NMAT_SYMM; k++) {
+ buf[m++] = tlsph_stress[j][k];
+ } // 32
+
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2]; // 35
+ buf[m++] = vest[j][0];
+ buf[m++] = vest[j][1];
+ buf[m++] = vest[j][2]; // 38
+
+ }
+ } else {
+ dvx = pbc[0] * h_rate[0] + pbc[5] * h_rate[5] + pbc[4] * h_rate[4];
+ dvy = pbc[1] * h_rate[1] + pbc[3] * h_rate[3];
+ dvz = pbc[2] * h_rate[2];
+// printf("\ndvx = %f, dvy=%f, dvz=%f\n", dvx, dvy, dvz);
+// printf("dx = %f, dy=%f, dz=%f\n", dx, dy, dz);
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz; // 3
+ buf[m++] = x0[j][0];
+ buf[m++] = x0[j][1];
+ buf[m++] = x0[j][2]; // 6
+ buf[m++] = ubuf(tag[j]).d;
+ buf[m++] = ubuf(type[j]).d;
+ buf[m++] = ubuf(mask[j]).d;
+ buf[m++] = ubuf(molecule[j]).d; // 10
+ buf[m++] = radius[j];
+ buf[m++] = rmass[j];
+ buf[m++] = vfrac[j];
+ buf[m++] = contact_radius[j];
+ buf[m++] = e[j];
+ buf[m++] = eff_plastic_strain[j]; // 16
+
+ for (int k = 0; k < NMAT_FULL; k++) {
+ buf[m++] = smd_data_9[j][k];
+ } // 25
+
+ for (int k = 0; k < NMAT_SYMM; k++) {
+ buf[m++] = tlsph_stress[j][k];
+ } // 31
+
+ if (mask[i] & deform_groupbit) {
+ buf[m++] = v[j][0] + dvx;
+ buf[m++] = v[j][1] + dvy;
+ buf[m++] = v[j][2] + dvz; // 34
+ buf[m++] = vest[j][0] + dvx;
+ buf[m++] = vest[j][1] + dvy;
+ buf[m++] = vest[j][2] + dvz; // 37
+
+ } else {
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2]; // 34
+ buf[m++] = vest[j][0];
+ buf[m++] = vest[j][1];
+ buf[m++] = vest[j][2]; // 37
+ }
+
+ }
+ }
+ }
+
+ if (atom->nextra_border)
+ for (int iextra = 0; iextra < atom->nextra_border; iextra++)
+ m += modify->fix[atom->extra_border[iextra]]->pack_border(n, list, &buf[m]);
+
+ return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecSMD::pack_border_hybrid(int n, int *list, double *buf) {
- int i, j, m;
-
- m = 0;
- for (i = 0; i < n; i++) {
- j = list[i];
-
- buf[m++] = x0[j][0];
- buf[m++] = x0[j][1];
- buf[m++] = x0[j][2]; // 3
- buf[m++] = ubuf(molecule[j]).d; // 4
- buf[m++] = radius[j];
- buf[m++] = rmass[j];
- buf[m++] = vfrac[j];
- buf[m++] = contact_radius[j];
- buf[m++] = e[j];
- buf[m++] = eff_plastic_strain[j]; // 11
-
- for (int k = 0; k < NMAT_FULL; k++) {
- buf[m++] = smd_data_9[j][k];
- } // 20
-
- for (int k = 0; k < NMAT_SYMM; k++) {
- buf[m++] = tlsph_stress[j][k];
- } // 26
-
- }
- return m;
+ int i, j, m;
+
+ m = 0;
+ for (i = 0; i < n; i++) {
+ j = list[i];
+
+ buf[m++] = x0[j][0];
+ buf[m++] = x0[j][1];
+ buf[m++] = x0[j][2]; // 3
+ buf[m++] = ubuf(molecule[j]).d; // 4
+ buf[m++] = radius[j];
+ buf[m++] = rmass[j];
+ buf[m++] = vfrac[j];
+ buf[m++] = contact_radius[j];
+ buf[m++] = e[j];
+ buf[m++] = eff_plastic_strain[j]; // 11
+
+ for (int k = 0; k < NMAT_FULL; k++) {
+ buf[m++] = smd_data_9[j][k];
+ } // 20
+
+ for (int k = 0; k < NMAT_SYMM; k++) {
+ buf[m++] = tlsph_stress[j][k];
+ } // 26
+
+ }
+ return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecSMD::unpack_border(int n, int first, double *buf) {
- error->one(FLERR, "atom vec tlsph can only be used with ghost velocities turned on");
+ error->one(FLERR, "atom vec tlsph can only be used with ghost velocities turned on");
}
/* ---------------------------------------------------------------------- */
void AtomVecSMD::unpack_border_vel(int n, int first, double *buf) {
- int i, m, last;
-
- m = 0;
- last = first + n;
- for (i = first; i < last; i++) {
- if (i == nmax)
- grow(0);
- x[i][0] = buf[m++];
- x[i][1] = buf[m++];
- x[i][2] = buf[m++]; // 3
- x0[i][0] = buf[m++];
- x0[i][1] = buf[m++];
- x0[i][2] = buf[m++]; // 6
- tag[i] = (tagint) ubuf(buf[m++]).i;
- type[i] = (int) ubuf(buf[m++]).i;
- mask[i] = (int) ubuf(buf[m++]).i;
- molecule[i] = (tagint) ubuf(buf[m++]).i; // 10
-
- radius[i] = buf[m++];
- rmass[i] = buf[m++];
- vfrac[i] = buf[m++];
- contact_radius[i] = buf[m++];
- e[i] = buf[m++];
- eff_plastic_strain[i] = buf[m++]; // 16
-
- for (int k = 0; k < NMAT_FULL; k++) {
- smd_data_9[i][k] = buf[m++];
- } // 25
-
- for (int k = 0; k < NMAT_SYMM; k++) {
- tlsph_stress[i][k] = buf[m++];
- } // 31
-
- v[i][0] = buf[m++];
- v[i][1] = buf[m++];
- v[i][2] = buf[m++]; // 34
- vest[i][0] = buf[m++];
- vest[i][1] = buf[m++];
- vest[i][2] = buf[m++]; // 37
- }
-
- if (atom->nextra_border)
- for (int iextra = 0; iextra < atom->nextra_border; iextra++)
- m += modify->fix[atom->extra_border[iextra]]->unpack_border(n, first, &buf[m]);
+ int i, m, last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ if (i == nmax)
+ grow(0);
+ x[i][0] = buf[m++];
+ x[i][1] = buf[m++];
+ x[i][2] = buf[m++]; // 3
+ x0[i][0] = buf[m++];
+ x0[i][1] = buf[m++];
+ x0[i][2] = buf[m++]; // 6
+ tag[i] = (tagint) ubuf(buf[m++]).i;
+ type[i] = (int) ubuf(buf[m++]).i;
+ mask[i] = (int) ubuf(buf[m++]).i;
+ molecule[i] = (tagint) ubuf(buf[m++]).i; // 10
+
+ radius[i] = buf[m++];
+ rmass[i] = buf[m++];
+ vfrac[i] = buf[m++];
+ contact_radius[i] = buf[m++];
+ e[i] = buf[m++];
+ eff_plastic_strain[i] = buf[m++]; // 16
+
+ for (int k = 0; k < NMAT_FULL; k++) {
+ smd_data_9[i][k] = buf[m++];
+ } // 25
+
+ for (int k = 0; k < NMAT_SYMM; k++) {
+ tlsph_stress[i][k] = buf[m++];
+ } // 31
+
+ v[i][0] = buf[m++];
+ v[i][1] = buf[m++];
+ v[i][2] = buf[m++]; // 34
+ vest[i][0] = buf[m++];
+ vest[i][1] = buf[m++];
+ vest[i][2] = buf[m++]; // 37
+ }
+
+ if (atom->nextra_border)
+ for (int iextra = 0; iextra < atom->nextra_border; iextra++)
+ m += modify->fix[atom->extra_border[iextra]]->unpack_border(n, first, &buf[m]);
}
/* ---------------------------------------------------------------------- */
int AtomVecSMD::unpack_border_hybrid(int n, int first, double *buf) {
- int i, m, last;
-
- m = 0;
- last = first + n;
- for (i = first; i < last; i++) {
- x0[i][0] = buf[m++];
- x0[i][1] = buf[m++];
- x0[i][2] = buf[m++]; // 3
- molecule[i] = (tagint) ubuf(buf[m++]).i; // 4
- radius[i] = buf[m++];
- rmass[i] = buf[m++];
- vfrac[i] = buf[m++];
- contact_radius[i] = buf[m++];
- e[i] = buf[m++];
- eff_plastic_strain[i] = buf[m++]; // 11
-
- for (int k = 0; k < NMAT_FULL; k++) {
- smd_data_9[i][k] = buf[m++];
- } // 20
-
- for (int k = 0; k < NMAT_SYMM; k++) {
- tlsph_stress[i][k] = buf[m++];
- } // 26
- }
- return m;
+ int i, m, last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ x0[i][0] = buf[m++];
+ x0[i][1] = buf[m++];
+ x0[i][2] = buf[m++]; // 3
+ molecule[i] = (tagint) ubuf(buf[m++]).i; // 4
+ radius[i] = buf[m++];
+ rmass[i] = buf[m++];
+ vfrac[i] = buf[m++];
+ contact_radius[i] = buf[m++];
+ e[i] = buf[m++];
+ eff_plastic_strain[i] = buf[m++]; // 11
+
+ for (int k = 0; k < NMAT_FULL; k++) {
+ smd_data_9[i][k] = buf[m++];
+ } // 20
+
+ for (int k = 0; k < NMAT_SYMM; k++) {
+ tlsph_stress[i][k] = buf[m++];
+ } // 26
+ }
+ return m;
}
/* ----------------------------------------------------------------------
@@ -722,106 +722,106 @@ int AtomVecSMD::unpack_border_hybrid(int n, int first, double *buf) {
------------------------------------------------------------------------- */
int AtomVecSMD::pack_exchange(int i, double *buf) {
- int m = 1;
-
- //printf("in AtomVecSMD::pack_exchange tag %d\n", tag[i]);
-
- buf[m++] = x[i][0];
- buf[m++] = x[i][1];
- buf[m++] = x[i][2]; // 3
- buf[m++] = x0[i][0];
- buf[m++] = x0[i][1];
- buf[m++] = x0[i][2]; // 6
- buf[m++] = ubuf(tag[i]).d;
- buf[m++] = ubuf(type[i]).d;
- buf[m++] = ubuf(mask[i]).d;
- buf[m++] = ubuf(image[i]).d;
- buf[m++] = ubuf(molecule[i]).d; // 11
- buf[m++] = radius[i];
- buf[m++] = rmass[i];
- buf[m++] = vfrac[i];
- buf[m++] = contact_radius[i];
- buf[m++] = e[i];
- buf[m++] = eff_plastic_strain[i]; // 18
- buf[m++] = eff_plastic_strain_rate[i]; // 19
-
- for (int k = 0; k < NMAT_FULL; k++) {
- buf[m++] = smd_data_9[i][k];
- } // 27
-
- for (int k = 0; k < NMAT_SYMM; k++) {
- buf[m++] = tlsph_stress[i][k];
- } // 33
-
- buf[m++] = v[i][0];
- buf[m++] = v[i][1];
- buf[m++] = v[i][2]; // 36
- buf[m++] = vest[i][0];
- buf[m++] = vest[i][1];
- buf[m++] = vest[i][2]; // 39
-
- buf[m++] = damage[i];
-
- if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
- m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i, &buf[m]);
-
- buf[0] = m;
- return m;
+ int m = 1;
+
+ //printf("in AtomVecSMD::pack_exchange tag %d\n", tag[i]);
+
+ buf[m++] = x[i][0];
+ buf[m++] = x[i][1];
+ buf[m++] = x[i][2]; // 3
+ buf[m++] = x0[i][0];
+ buf[m++] = x0[i][1];
+ buf[m++] = x0[i][2]; // 6
+ buf[m++] = ubuf(tag[i]).d;
+ buf[m++] = ubuf(type[i]).d;
+ buf[m++] = ubuf(mask[i]).d;
+ buf[m++] = ubuf(image[i]).d;
+ buf[m++] = ubuf(molecule[i]).d; // 11
+ buf[m++] = radius[i];
+ buf[m++] = rmass[i];
+ buf[m++] = vfrac[i];
+ buf[m++] = contact_radius[i];
+ buf[m++] = e[i];
+ buf[m++] = eff_plastic_strain[i]; // 18
+ buf[m++] = eff_plastic_strain_rate[i]; // 19
+
+ for (int k = 0; k < NMAT_FULL; k++) {
+ buf[m++] = smd_data_9[i][k];
+ } // 27
+
+ for (int k = 0; k < NMAT_SYMM; k++) {
+ buf[m++] = tlsph_stress[i][k];
+ } // 33
+
+ buf[m++] = v[i][0];
+ buf[m++] = v[i][1];
+ buf[m++] = v[i][2]; // 36
+ buf[m++] = vest[i][0];
+ buf[m++] = vest[i][1];
+ buf[m++] = vest[i][2]; // 39
+
+ buf[m++] = damage[i];
+
+ if (atom->nextra_grow)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i, &buf[m]);
+
+ buf[0] = m;
+ return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecSMD::unpack_exchange(double *buf) {
- int nlocal = atom->nlocal;
- if (nlocal == nmax)
- grow(0);
-
- int m = 1;
-
- x[nlocal][0] = buf[m++];
- x[nlocal][1] = buf[m++];
- x[nlocal][2] = buf[m++]; // 3
- x0[nlocal][0] = buf[m++];
- x0[nlocal][1] = buf[m++];
- x0[nlocal][2] = buf[m++]; // 6
- tag[nlocal] = (tagint) ubuf(buf[m++]).i;
- type[nlocal] = (int) ubuf(buf[m++]).i;
- mask[nlocal] = (int) ubuf(buf[m++]).i;
- image[nlocal] = (imageint) ubuf(buf[m++]).i;
- molecule[nlocal] = (tagint) ubuf(buf[m++]).i; // 11
-
- radius[nlocal] = buf[m++];
- rmass[nlocal] = buf[m++];
- vfrac[nlocal] = buf[m++];
- contact_radius[nlocal] = buf[m++];
- e[nlocal] = buf[m++];
- eff_plastic_strain[nlocal] = buf[m++]; // 18
- eff_plastic_strain_rate[nlocal] = buf[m++]; // 19
-
- for (int k = 0; k < NMAT_FULL; k++) {
- smd_data_9[nlocal][k] = buf[m++];
- } // 27
-
- for (int k = 0; k < NMAT_SYMM; k++) {
- tlsph_stress[nlocal][k] = buf[m++];
- } // 33
-
- v[nlocal][0] = buf[m++];
- v[nlocal][1] = buf[m++];
- v[nlocal][2] = buf[m++]; // 36
- vest[nlocal][0] = buf[m++];
- vest[nlocal][1] = buf[m++];
- vest[nlocal][2] = buf[m++]; // 39
-
- damage[nlocal] = buf[m++]; //40
-
- if (atom->nextra_grow)
- for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
- m += modify->fix[atom->extra_grow[iextra]]->unpack_exchange(nlocal, &buf[m]);
-
- atom->nlocal++;
- return m;
+ int nlocal = atom->nlocal;
+ if (nlocal == nmax)
+ grow(0);
+
+ int m = 1;
+
+ x[nlocal][0] = buf[m++];
+ x[nlocal][1] = buf[m++];
+ x[nlocal][2] = buf[m++]; // 3
+ x0[nlocal][0] = buf[m++];
+ x0[nlocal][1] = buf[m++];
+ x0[nlocal][2] = buf[m++]; // 6
+ tag[nlocal] = (tagint) ubuf(buf[m++]).i;
+ type[nlocal] = (int) ubuf(buf[m++]).i;
+ mask[nlocal] = (int) ubuf(buf[m++]).i;
+ image[nlocal] = (imageint) ubuf(buf[m++]).i;
+ molecule[nlocal] = (tagint) ubuf(buf[m++]).i; // 11
+
+ radius[nlocal] = buf[m++];
+ rmass[nlocal] = buf[m++];
+ vfrac[nlocal] = buf[m++];
+ contact_radius[nlocal] = buf[m++];
+ e[nlocal] = buf[m++];
+ eff_plastic_strain[nlocal] = buf[m++]; // 18
+ eff_plastic_strain_rate[nlocal] = buf[m++]; // 19
+
+ for (int k = 0; k < NMAT_FULL; k++) {
+ smd_data_9[nlocal][k] = buf[m++];
+ } // 27
+
+ for (int k = 0; k < NMAT_SYMM; k++) {
+ tlsph_stress[nlocal][k] = buf[m++];
+ } // 33
+
+ v[nlocal][0] = buf[m++];
+ v[nlocal][1] = buf[m++];
+ v[nlocal][2] = buf[m++]; // 36
+ vest[nlocal][0] = buf[m++];
+ vest[nlocal][1] = buf[m++];
+ vest[nlocal][2] = buf[m++]; // 39
+
+ damage[nlocal] = buf[m++]; //40
+
+ if (atom->nextra_grow)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ m += modify->fix[atom->extra_grow[iextra]]->unpack_exchange(nlocal, &buf[m]);
+
+ atom->nlocal++;
+ return m;
}
/* ----------------------------------------------------------------------
@@ -830,17 +830,17 @@ int AtomVecSMD::unpack_exchange(double *buf) {
------------------------------------------------------------------------- */
int AtomVecSMD::size_restart() {
- int i;
+ int i;
- int nlocal = atom->nlocal;
- int n = 43 * nlocal; // count pack_restart + 1 (size of buffer)
+ int nlocal = atom->nlocal;
+ int n = 43 * nlocal; // count pack_restart + 1 (size of buffer)
- if (atom->nextra_restart)
- for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
- for (i = 0; i < nlocal; i++)
- n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
+ if (atom->nextra_restart)
+ for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
+ for (i = 0; i < nlocal; i++)
+ n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
- return n;
+ return n;
}
/* ----------------------------------------------------------------------
@@ -849,50 +849,50 @@ int AtomVecSMD::size_restart() {
molecular types may be negative, but write as positive
------------------------------------------------------------------------- */
int AtomVecSMD::pack_restart(int i, double *buf) {
- int m = 1; // 1
-
- buf[m++] = x[i][0];
- buf[m++] = x[i][1];
- buf[m++] = x[i][2]; // 4
- buf[m++] = x0[i][0];
- buf[m++] = x0[i][1];
- buf[m++] = x0[i][2]; // 7
- buf[m++] = ubuf(tag[i]).d;
- buf[m++] = ubuf(type[i]).d;
- buf[m++] = ubuf(mask[i]).d; // 10
- buf[m++] = ubuf(image[i]).d;
- buf[m++] = ubuf(molecule[i]).d;
- buf[m++] = radius[i];
- buf[m++] = rmass[i];
- buf[m++] = vfrac[i]; // 15
- buf[m++] = contact_radius[i];
- buf[m++] = e[i];
- buf[m++] = eff_plastic_strain[i];
- buf[m++] = eff_plastic_strain_rate[i]; // 19
-
- for (int k = 0; k < NMAT_FULL; k++) {
- buf[m++] = smd_data_9[i][k];
- } // 28
-
- for (int k = 0; k < NMAT_SYMM; k++) {
- buf[m++] = tlsph_stress[i][k];
- } // 34
-
- buf[m++] = v[i][0];
- buf[m++] = v[i][1];
- buf[m++] = v[i][2]; // 37
- buf[m++] = vest[i][0];
- buf[m++] = vest[i][1];
- buf[m++] = vest[i][2]; // 40
-
- buf[m++] = damage[i]; // 41
-
- if (atom->nextra_restart)
- for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
- m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i, &buf[m]);
-
- buf[0] = m;
- return m;
+ int m = 1; // 1
+
+ buf[m++] = x[i][0];
+ buf[m++] = x[i][1];
+ buf[m++] = x[i][2]; // 4
+ buf[m++] = x0[i][0];
+ buf[m++] = x0[i][1];
+ buf[m++] = x0[i][2]; // 7
+ buf[m++] = ubuf(tag[i]).d;
+ buf[m++] = ubuf(type[i]).d;
+ buf[m++] = ubuf(mask[i]).d; // 10
+ buf[m++] = ubuf(image[i]).d;
+ buf[m++] = ubuf(molecule[i]).d;
+ buf[m++] = radius[i];
+ buf[m++] = rmass[i];
+ buf[m++] = vfrac[i]; // 15
+ buf[m++] = contact_radius[i];
+ buf[m++] = e[i];
+ buf[m++] = eff_plastic_strain[i];
+ buf[m++] = eff_plastic_strain_rate[i]; // 19
+
+ for (int k = 0; k < NMAT_FULL; k++) {
+ buf[m++] = smd_data_9[i][k];
+ } // 28
+
+ for (int k = 0; k < NMAT_SYMM; k++) {
+ buf[m++] = tlsph_stress[i][k];
+ } // 34
+
+ buf[m++] = v[i][0];
+ buf[m++] = v[i][1];
+ buf[m++] = v[i][2]; // 37
+ buf[m++] = vest[i][0];
+ buf[m++] = vest[i][1];
+ buf[m++] = vest[i][2]; // 40
+
+ buf[m++] = damage[i]; // 41
+
+ if (atom->nextra_restart)
+ for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
+ m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i, &buf[m]);
+
+ buf[0] = m;
+ return m;
}
/* ----------------------------------------------------------------------
@@ -900,66 +900,66 @@ int AtomVecSMD::pack_restart(int i, double *buf) {
------------------------------------------------------------------------- */
int AtomVecSMD::unpack_restart(double *buf) {
- int nlocal = atom->nlocal;
- if (nlocal == nmax) {
- grow(0);
- if (atom->nextra_store)
- memory->grow(atom->extra, nmax, atom->nextra_store, "atom:extra");
- }
-
- int m = 1;
-
- x[nlocal][0] = buf[m++];
- x[nlocal][1] = buf[m++];
- x[nlocal][2] = buf[m++]; // 3
- x0[nlocal][0] = buf[m++];
- x0[nlocal][1] = buf[m++];
- x0[nlocal][2] = buf[m++]; // 6
- tag[nlocal] = (tagint) ubuf(buf[m++]).i;
- type[nlocal] = (int) ubuf(buf[m++]).i;
- mask[nlocal] = (int) ubuf(buf[m++]).i;
- image[nlocal] = (imageint) ubuf(buf[m++]).i;
- molecule[nlocal] = (tagint) ubuf(buf[m++]).i; // 11
-
- radius[nlocal] = buf[m++];
- rmass[nlocal] = buf[m++];
- vfrac[nlocal] = buf[m++]; //14
- contact_radius[nlocal] = buf[m++]; //15
- e[nlocal] = buf[m++];
- eff_plastic_strain[nlocal] = buf[m++]; // 18
- eff_plastic_strain_rate[nlocal] = buf[m++]; // 29
-
- for (int k = 0; k < NMAT_FULL; k++) {
- smd_data_9[nlocal][k] = buf[m++];
- } // 28
-
- for (int k = 0; k < NMAT_SYMM; k++) {
- tlsph_stress[nlocal][k] = buf[m++];
- } // 34
-
- v[nlocal][0] = buf[m++];
- v[nlocal][1] = buf[m++];
- v[nlocal][2] = buf[m++]; // 37
- vest[nlocal][0] = buf[m++];
- vest[nlocal][1] = buf[m++];
- vest[nlocal][2] = buf[m++]; // 40
-
- damage[nlocal] = buf[m++]; //41
-
- //printf("nlocal in restart is %d\n", nlocal);
-
- double **extra = atom->extra;
- if (atom->nextra_store) {
- int size = static_cast<int>(buf[0]) - m;
- for (int i = 0; i < size; i++)
- extra[nlocal][i] = buf[m++];
- }
-
- atom->nlocal++;
-
- //printf("returning m=%d in unpack_restart\n", m);
-
- return m;
+ int nlocal = atom->nlocal;
+ if (nlocal == nmax) {
+ grow(0);
+ if (atom->nextra_store)
+ memory->grow(atom->extra, nmax, atom->nextra_store, "atom:extra");
+ }
+
+ int m = 1;
+
+ x[nlocal][0] = buf[m++];
+ x[nlocal][1] = buf[m++];
+ x[nlocal][2] = buf[m++]; // 3
+ x0[nlocal][0] = buf[m++];
+ x0[nlocal][1] = buf[m++];
+ x0[nlocal][2] = buf[m++]; // 6
+ tag[nlocal] = (tagint) ubuf(buf[m++]).i;
+ type[nlocal] = (int) ubuf(buf[m++]).i;
+ mask[nlocal] = (int) ubuf(buf[m++]).i;
+ image[nlocal] = (imageint) ubuf(buf[m++]).i;
+ molecule[nlocal] = (tagint) ubuf(buf[m++]).i; // 11
+
+ radius[nlocal] = buf[m++];
+ rmass[nlocal] = buf[m++];
+ vfrac[nlocal] = buf[m++]; //14
+ contact_radius[nlocal] = buf[m++]; //15
+ e[nlocal] = buf[m++];
+ eff_plastic_strain[nlocal] = buf[m++]; // 18
+ eff_plastic_strain_rate[nlocal] = buf[m++]; // 29
+
+ for (int k = 0; k < NMAT_FULL; k++) {
+ smd_data_9[nlocal][k] = buf[m++];
+ } // 28
+
+ for (int k = 0; k < NMAT_SYMM; k++) {
+ tlsph_stress[nlocal][k] = buf[m++];
+ } // 34
+
+ v[nlocal][0] = buf[m++];
+ v[nlocal][1] = buf[m++];
+ v[nlocal][2] = buf[m++]; // 37
+ vest[nlocal][0] = buf[m++];
+ vest[nlocal][1] = buf[m++];
+ vest[nlocal][2] = buf[m++]; // 40
+
+ damage[nlocal] = buf[m++]; //41
+
+ //printf("nlocal in restart is %d\n", nlocal);
+
+ double **extra = atom->extra;
+ if (atom->nextra_store) {
+ int size = static_cast<int>(buf[0]) - m;
+ for (int i = 0; i < size; i++)
+ extra[nlocal][i] = buf[m++];
+ }
+
+ atom->nlocal++;
+
+ //printf("returning m=%d in unpack_restart\n", m);
+
+ return m;
}
/* ----------------------------------------------------------------------
@@ -968,53 +968,53 @@ int AtomVecSMD::unpack_restart(double *buf) {
------------------------------------------------------------------------- */
void AtomVecSMD::create_atom(int itype, double *coord) {
- int nlocal = atom->nlocal;
- if (nlocal == nmax) {
- printf("nlocal = %d, nmax = %d, calling grow\n", nlocal, nmax);
- grow(0);
- printf("... finished growing\n");
- }
-
- tag[nlocal] = 0;
- type[nlocal] = itype;
- x[nlocal][0] = coord[0];
- x[nlocal][1] = coord[1];
- x[nlocal][2] = coord[2];
- x0[nlocal][0] = coord[0];
- x0[nlocal][1] = coord[1];
- x0[nlocal][2] = coord[2];
- mask[nlocal] = 1;
- image[nlocal] = ((imageint) IMGMAX << IMG2BITS) | ((imageint) IMGMAX << IMGBITS) | IMGMAX;
- v[nlocal][0] = 0.0;
- v[nlocal][1] = 0.0;
- v[nlocal][2] = 0.0;
- vest[nlocal][0] = 0.0;
- vest[nlocal][1] = 0.0;
- vest[nlocal][2] = 0.0;
-
- vfrac[nlocal] = 1.0;
- rmass[nlocal] = 1.0;
- radius[nlocal] = 0.5;
- contact_radius[nlocal] = 0.5;
- molecule[nlocal] = 1;
- e[nlocal] = 0.0;
- eff_plastic_strain[nlocal] = 0.0;
- eff_plastic_strain_rate[nlocal] = 0.0;
-
- for (int k = 0; k < NMAT_FULL; k++) {
- smd_data_9[nlocal][k] = 0.0;
- }
- smd_data_9[nlocal][0] = 1.0; // xx
- smd_data_9[nlocal][4] = 1.0; // yy
- smd_data_9[nlocal][8] = 1.0; // zz
-
- for (int k = 0; k < NMAT_SYMM; k++) {
- tlsph_stress[nlocal][k] = 0.0;
- }
-
- damage[nlocal] = 0.0;
-
- atom->nlocal++;
+ int nlocal = atom->nlocal;
+ if (nlocal == nmax) {
+ printf("nlocal = %d, nmax = %d, calling grow\n", nlocal, nmax);
+ grow(0);
+ printf("... finished growing\n");
+ }
+
+ tag[nlocal] = 0;
+ type[nlocal] = itype;
+ x[nlocal][0] = coord[0];
+ x[nlocal][1] = coord[1];
+ x[nlocal][2] = coord[2];
+ x0[nlocal][0] = coord[0];
+ x0[nlocal][1] = coord[1];
+ x0[nlocal][2] = coord[2];
+ mask[nlocal] = 1;
+ image[nlocal] = ((imageint) IMGMAX << IMG2BITS) | ((imageint) IMGMAX << IMGBITS) | IMGMAX;
+ v[nlocal][0] = 0.0;
+ v[nlocal][1] = 0.0;
+ v[nlocal][2] = 0.0;
+ vest[nlocal][0] = 0.0;
+ vest[nlocal][1] = 0.0;
+ vest[nlocal][2] = 0.0;
+
+ vfrac[nlocal] = 1.0;
+ rmass[nlocal] = 1.0;
+ radius[nlocal] = 0.5;
+ contact_radius[nlocal] = 0.5;
+ molecule[nlocal] = 1;
+ e[nlocal] = 0.0;
+ eff_plastic_strain[nlocal] = 0.0;
+ eff_plastic_strain_rate[nlocal] = 0.0;
+
+ for (int k = 0; k < NMAT_FULL; k++) {
+ smd_data_9[nlocal][k] = 0.0;
+ }
+ smd_data_9[nlocal][0] = 1.0; // xx
+ smd_data_9[nlocal][4] = 1.0; // yy
+ smd_data_9[nlocal][8] = 1.0; // zz
+
+ for (int k = 0; k < NMAT_SYMM; k++) {
+ tlsph_stress[nlocal][k] = 0.0;
+ }
+
+ damage[nlocal] = 0.0;
+
+ atom->nlocal++;
}
/* ----------------------------------------------------------------------
@@ -1023,74 +1023,74 @@ void AtomVecSMD::create_atom(int itype, double *coord) {
------------------------------------------------------------------------- */
void AtomVecSMD::data_atom(double *coord, imageint imagetmp, char **values) {
- int nlocal = atom->nlocal;
- if (nlocal == nmax)
- grow(0);
+ int nlocal = atom->nlocal;
+ if (nlocal == nmax)
+ grow(0);
- tag[nlocal] = ATOTAGINT(values[0]);
+ tag[nlocal] = ATOTAGINT(values[0]);
- type[nlocal] = atoi(values[1]);
- if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
- error->one(FLERR, "Invalid atom type in Atoms section of data file");
+ type[nlocal] = atoi(values[1]);
+ if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
+ error->one(FLERR, "Invalid atom type in Atoms section of data file");
- molecule[nlocal] = ATOTAGINT(values[2]);
- if (molecule[nlocal] <= 0)
- error->one(FLERR, "Invalid molecule in Atoms section of data file");
+ molecule[nlocal] = ATOTAGINT(values[2]);
+ if (molecule[nlocal] <= 0)
+ error->one(FLERR, "Invalid molecule in Atoms section of data file");
- vfrac[nlocal] = atof(values[3]);
- if (vfrac[nlocal] < 0.0)
- error->one(FLERR, "Invalid volume in Atoms section of data file");
+ vfrac[nlocal] = atof(values[3]);
+ if (vfrac[nlocal] < 0.0)
+ error->one(FLERR, "Invalid volume in Atoms section of data file");
- rmass[nlocal] = atof(values[4]);
- if (rmass[nlocal] == 0.0)
- error->one(FLERR, "Invalid mass in Atoms section of data file");
+ rmass[nlocal] = atof(values[4]);
+ if (rmass[nlocal] == 0.0)
+ error->one(FLERR, "Invalid mass in Atoms section of data file");
- radius[nlocal] = atof(values[5]);
- if (radius[nlocal] < 0.0)
- error->one(FLERR, "Invalid radius in Atoms section of data file");
+ radius[nlocal] = atof(values[5]);
+ if (radius[nlocal] < 0.0)
+ error->one(FLERR, "Invalid radius in Atoms section of data file");
- contact_radius[nlocal] = atof(values[6]);
- if (contact_radius[nlocal] < 0.0)
- error->one(FLERR, "Invalid contact radius in Atoms section of data file");
+ contact_radius[nlocal] = atof(values[6]);
+ if (contact_radius[nlocal] < 0.0)
+ error->one(FLERR, "Invalid contact radius in Atoms section of data file");
- e[nlocal] = 0.0;
+ e[nlocal] = 0.0;
- x0[nlocal][0] = atof(values[7]);
- x0[nlocal][1] = atof(values[8]);
- x0[nlocal][2] = atof(values[9]);
+ x0[nlocal][0] = atof(values[7]);
+ x0[nlocal][1] = atof(values[8]);
+ x0[nlocal][2] = atof(values[9]);
- x[nlocal][0] = coord[0];
- x[nlocal][1] = coord[1];
- x[nlocal][2] = coord[2];
+ x[nlocal][0] = coord[0];
+ x[nlocal][1] = coord[1];
+ x[nlocal][2] = coord[2];
- image[nlocal] = imagetmp;
+ image[nlocal] = imagetmp;
- mask[nlocal] = 1;
- v[nlocal][0] = 0.0;
- v[nlocal][1] = 0.0;
- v[nlocal][2] = 0.0;
- vest[nlocal][0] = 0.0;
- vest[nlocal][1] = 0.0;
- vest[nlocal][2] = 0.0;
+ mask[nlocal] = 1;
+ v[nlocal][0] = 0.0;
+ v[nlocal][1] = 0.0;
+ v[nlocal][2] = 0.0;
+ vest[nlocal][0] = 0.0;
+ vest[nlocal][1] = 0.0;
+ vest[nlocal][2] = 0.0;
- damage[nlocal] = 0.0;
+ damage[nlocal] = 0.0;
- eff_plastic_strain[nlocal] = 0.0;
- eff_plastic_strain_rate[nlocal] = 0.0;
+ eff_plastic_strain[nlocal] = 0.0;
+ eff_plastic_strain_rate[nlocal] = 0.0;
- for (int k = 0; k < NMAT_FULL; k++) {
- smd_data_9[nlocal][k] = 0.0;
- }
+ for (int k = 0; k < NMAT_FULL; k++) {
+ smd_data_9[nlocal][k] = 0.0;
+ }
- for (int k = 0; k < NMAT_SYMM; k++) {
- tlsph_stress[nlocal][k] = 0.0;
- }
+ for (int k = 0; k < NMAT_SYMM; k++) {
+ tlsph_stress[nlocal][k] = 0.0;
+ }
- smd_data_9[nlocal][0] = 1.0; // xx
- smd_data_9[nlocal][4] = 1.0; // yy
- smd_data_9[nlocal][8] = 1.0; // zz
+ smd_data_9[nlocal][0] = 1.0; // xx
+ smd_data_9[nlocal][4] = 1.0; // yy
+ smd_data_9[nlocal][8] = 1.0; // zz
- atom->nlocal++;
+ atom->nlocal++;
}
/* ----------------------------------------------------------------------
@@ -1099,8 +1099,8 @@ void AtomVecSMD::data_atom(double *coord, imageint imagetmp, char **values) {
------------------------------------------------------------------------- */
int AtomVecSMD::data_atom_hybrid(int nlocal, char **values) {
- error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style smd");
- return -1;
+ error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style smd");
+ return -1;
}
/* ----------------------------------------------------------------------
@@ -1108,12 +1108,12 @@ int AtomVecSMD::data_atom_hybrid(int nlocal, char **values) {
------------------------------------------------------------------------- */
void AtomVecSMD::data_vel(int m, char **values) {
- v[m][0] = atof(values[0]);
- v[m][1] = atof(values[1]);
- v[m][2] = atof(values[2]);
- vest[m][0] = atof(values[0]);
- vest[m][1] = atof(values[1]);
- vest[m][2] = atof(values[2]);
+ v[m][0] = atof(values[0]);
+ v[m][1] = atof(values[1]);
+ v[m][2] = atof(values[2]);
+ vest[m][0] = atof(values[0]);
+ vest[m][1] = atof(values[1]);
+ vest[m][2] = atof(values[2]);
}
/* ----------------------------------------------------------------------
@@ -1121,8 +1121,8 @@ void AtomVecSMD::data_vel(int m, char **values) {
------------------------------------------------------------------------- */
int AtomVecSMD::data_vel_hybrid(int m, char **values) {
- error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style smd");
- return 0;
+ error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style smd");
+ return 0;
}
/* ----------------------------------------------------------------------
@@ -1130,28 +1130,28 @@ int AtomVecSMD::data_vel_hybrid(int m, char **values) {
------------------------------------------------------------------------- */
void AtomVecSMD::pack_data(double **buf) {
- int nlocal = atom->nlocal;
- for (int i = 0; i < nlocal; i++) {
- buf[i][0] = ubuf(tag[i]).d;
- buf[i][1] = ubuf(type[i]).d;
- buf[i][2] = ubuf(molecule[i]).d;
- buf[i][3] = vfrac[i];
- buf[i][4] = rmass[i];
- buf[i][5] = radius[i];
- buf[i][6] = contact_radius[i];
-
- buf[i][7] = x[i][0];
- buf[i][8] = x[i][1];
- buf[i][9] = x[i][2];
-
+ int nlocal = atom->nlocal;
+ for (int i = 0; i < nlocal; i++) {
+ buf[i][0] = ubuf(tag[i]).d;
+ buf[i][1] = ubuf(type[i]).d;
+ buf[i][2] = ubuf(molecule[i]).d;
+ buf[i][3] = vfrac[i];
+ buf[i][4] = rmass[i];
+ buf[i][5] = radius[i];
+ buf[i][6] = contact_radius[i];
+
+ buf[i][7] = x[i][0];
+ buf[i][8] = x[i][1];
+ buf[i][9] = x[i][2];
+
buf[i][10] = x0[i][0];
buf[i][11] = x0[i][1];
buf[i][12] = x0[i][2];
- buf[i][13] = ubuf((image[i] & IMGMASK) - IMGMAX).d;
- buf[i][14] = ubuf((image[i] >> IMGBITS & IMGMASK) - IMGMAX).d;
- buf[i][15] = ubuf((image[i] >> IMG2BITS) - IMGMAX).d;
- }
+ buf[i][13] = ubuf((image[i] & IMGMASK) - IMGMAX).d;
+ buf[i][14] = ubuf((image[i] >> IMGBITS & IMGMASK) - IMGMAX).d;
+ buf[i][15] = ubuf((image[i] >> IMG2BITS) - IMGMAX).d;
+ }
}
/* ----------------------------------------------------------------------
@@ -1159,8 +1159,8 @@ void AtomVecSMD::pack_data(double **buf) {
------------------------------------------------------------------------- */
int AtomVecSMD::pack_data_hybrid(int i, double *buf) {
- error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style smd");
- return -1;
+ error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style smd");
+ return -1;
}
/* ----------------------------------------------------------------------
@@ -1168,12 +1168,12 @@ int AtomVecSMD::pack_data_hybrid(int i, double *buf) {
------------------------------------------------------------------------- */
void AtomVecSMD::write_data(FILE *fp, int n, double **buf) {
- for (int i = 0; i < n; i++)
- fprintf(fp,
- TAGINT_FORMAT
- " %d %d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e\n", (tagint) ubuf(buf[i][0]).i,
- (int) ubuf(buf[i][1]).i, (int) ubuf(buf[i][2]).i, buf[i][3], buf[i][4], buf[i][5], buf[i][6], buf[i][7], buf[i][8],
- buf[i][9], buf[i][10], buf[i][11], buf[i][12]);
+ for (int i = 0; i < n; i++)
+ fprintf(fp,
+ TAGINT_FORMAT
+ " %d %d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e\n", (tagint) ubuf(buf[i][0]).i,
+ (int) ubuf(buf[i][1]).i, (int) ubuf(buf[i][2]).i, buf[i][3], buf[i][4], buf[i][5], buf[i][6], buf[i][7], buf[i][8],
+ buf[i][9], buf[i][10], buf[i][11], buf[i][12]);
}
/* ----------------------------------------------------------------------
@@ -1181,8 +1181,8 @@ void AtomVecSMD::write_data(FILE *fp, int n, double **buf) {
------------------------------------------------------------------------- */
int AtomVecSMD::write_data_hybrid(FILE *fp, double *buf) {
- error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style smd");
- return -1;
+ error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style smd");
+ return -1;
}
/* ----------------------------------------------------------------------
@@ -1190,13 +1190,13 @@ int AtomVecSMD::write_data_hybrid(FILE *fp, double *buf) {
------------------------------------------------------------------------- */
void AtomVecSMD::pack_vel(double **buf) {
- int nlocal = atom->nlocal;
- for (int i = 0; i < nlocal; i++) {
- buf[i][0] = ubuf(tag[i]).d;
- buf[i][1] = v[i][0];
- buf[i][2] = v[i][1];
- buf[i][3] = v[i][2];
- }
+ int nlocal = atom->nlocal;
+ for (int i = 0; i < nlocal; i++) {
+ buf[i][0] = ubuf(tag[i]).d;
+ buf[i][1] = v[i][0];
+ buf[i][2] = v[i][1];
+ buf[i][3] = v[i][2];
+ }
}
/* ----------------------------------------------------------------------
@@ -1204,8 +1204,8 @@ void AtomVecSMD::pack_vel(double **buf) {
------------------------------------------------------------------------- */
int AtomVecSMD::pack_vel_hybrid(int i, double *buf) {
- error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style smd");
- return 0;
+ error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style smd");
+ return 0;
}
/* ----------------------------------------------------------------------
@@ -1213,9 +1213,9 @@ int AtomVecSMD::pack_vel_hybrid(int i, double *buf) {
------------------------------------------------------------------------- */
void AtomVecSMD::write_vel(FILE *fp, int n, double **buf) {
- for (int i = 0; i < n; i++)
- fprintf(fp, TAGINT_FORMAT
- " %-1.16e %-1.16e %-1.16e\n", (tagint) ubuf(buf[i][0]).i, buf[i][1], buf[i][2], buf[i][3]);
+ for (int i = 0; i < n; i++)
+ fprintf(fp, TAGINT_FORMAT
+ " %-1.16e %-1.16e %-1.16e\n", (tagint) ubuf(buf[i][0]).i, buf[i][1], buf[i][2], buf[i][3]);
}
/* ----------------------------------------------------------------------
@@ -1223,8 +1223,8 @@ void AtomVecSMD::write_vel(FILE *fp, int n, double **buf) {
------------------------------------------------------------------------- */
int AtomVecSMD::write_vel_hybrid(FILE *fp, double *buf) {
- error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style smd");
- return 3;
+ error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style smd");
+ return 3;
}
/* ----------------------------------------------------------------------
@@ -1232,59 +1232,59 @@ int AtomVecSMD::write_vel_hybrid(FILE *fp, double *buf) {
------------------------------------------------------------------------- */
bigint AtomVecSMD::memory_usage() {
- bigint bytes = 0;
-
- if (atom->memcheck("tag"))
- bytes += memory->usage(tag, nmax);
- if (atom->memcheck("type"))
- bytes += memory->usage(type, nmax);
- if (atom->memcheck("molecule"))
- bytes += memory->usage(molecule, nmax);
- if (atom->memcheck("mask"))
- bytes += memory->usage(mask, nmax);
- if (atom->memcheck("image"))
- bytes += memory->usage(image, nmax);
- if (atom->memcheck("x"))
- bytes += memory->usage(x, nmax, 3);
- if (atom->memcheck("v"))
- bytes += memory->usage(v, nmax, 3);
- if (atom->memcheck("vest"))
- bytes += memory->usage(vest, nmax, 3);
- if (atom->memcheck("f"))
- bytes += memory->usage(f, nmax * comm->nthreads, 3);
-
- if (atom->memcheck("radius"))
- bytes += memory->usage(radius, nmax);
- if (atom->memcheck("contact_radius"))
- bytes += memory->usage(contact_radius, nmax);
- if (atom->memcheck("vfrac"))
- bytes += memory->usage(vfrac, nmax);
- if (atom->memcheck("rmass"))
- bytes += memory->usage(rmass, nmax);
- if (atom->memcheck("eff_plastic_strain"))
- bytes += memory->usage(eff_plastic_strain, nmax);
- if (atom->memcheck("eff_plastic_strain_rate"))
- bytes += memory->usage(eff_plastic_strain_rate, nmax);
- if (atom->memcheck("e"))
- bytes += memory->usage(e, nmax);
- if (atom->memcheck("de"))
- bytes += memory->usage(de, nmax);
-
- if (atom->memcheck("smd_data_9"))
- bytes += memory->usage(smd_data_9, nmax, NMAT_FULL);
- if (atom->memcheck("tlsph_stress"))
- bytes += memory->usage(tlsph_stress, nmax, NMAT_SYMM);
-
- if (atom->memcheck("damage"))
- bytes += memory->usage(damage, nmax);
-
- return bytes;
+ bigint bytes = 0;
+
+ if (atom->memcheck("tag"))
+ bytes += memory->usage(tag, nmax);
+ if (atom->memcheck("type"))
+ bytes += memory->usage(type, nmax);
+ if (atom->memcheck("molecule"))
+ bytes += memory->usage(molecule, nmax);
+ if (atom->memcheck("mask"))
+ bytes += memory->usage(mask, nmax);
+ if (atom->memcheck("image"))
+ bytes += memory->usage(image, nmax);
+ if (atom->memcheck("x"))
+ bytes += memory->usage(x, nmax, 3);
+ if (atom->memcheck("v"))
+ bytes += memory->usage(v, nmax, 3);
+ if (atom->memcheck("vest"))
+ bytes += memory->usage(vest, nmax, 3);
+ if (atom->memcheck("f"))
+ bytes += memory->usage(f, nmax * comm->nthreads, 3);
+
+ if (atom->memcheck("radius"))
+ bytes += memory->usage(radius, nmax);
+ if (atom->memcheck("contact_radius"))
+ bytes += memory->usage(contact_radius, nmax);
+ if (atom->memcheck("vfrac"))
+ bytes += memory->usage(vfrac, nmax);
+ if (atom->memcheck("rmass"))
+ bytes += memory->usage(rmass, nmax);
+ if (atom->memcheck("eff_plastic_strain"))
+ bytes += memory->usage(eff_plastic_strain, nmax);
+ if (atom->memcheck("eff_plastic_strain_rate"))
+ bytes += memory->usage(eff_plastic_strain_rate, nmax);
+ if (atom->memcheck("e"))
+ bytes += memory->usage(e, nmax);
+ if (atom->memcheck("de"))
+ bytes += memory->usage(de, nmax);
+
+ if (atom->memcheck("smd_data_9"))
+ bytes += memory->usage(smd_data_9, nmax, NMAT_FULL);
+ if (atom->memcheck("tlsph_stress"))
+ bytes += memory->usage(tlsph_stress, nmax, NMAT_SYMM);
+
+ if (atom->memcheck("damage"))
+ bytes += memory->usage(damage, nmax);
+
+ return bytes;
}
/* ---------------------------------------------------------------------- */
void AtomVecSMD::force_clear(int n, size_t nbytes) {
- //printf("clearing force on atom %d", n);
- memset(&de[n], 0, nbytes);
- memset(&f[0][0], 0, 3 * nbytes);
+ //printf("clearing force on atom %d", n);
+ memset(&de[n], 0, nbytes);
+ memset(&f[0][0], 0, 3 * nbytes);
}
diff --git a/src/USER-SMD/compute_smd_hourglass_error.cpp b/src/USER-SMD/compute_smd_hourglass_error.cpp
index cf0f67bfbb..1502f7ccb5 100644
--- a/src/USER-SMD/compute_smd_hourglass_error.cpp
+++ b/src/USER-SMD/compute_smd_hourglass_error.cpp
@@ -39,67 +39,67 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeSMDHourglassError::ComputeSMDHourglassError(LAMMPS *lmp, int narg, char **arg) :
- Compute(lmp, narg, arg) {
- if (narg != 3)
- error->all(FLERR, "Illegal compute smd/hourglass_error command");
- if (atom->smd_flag != 1)
- error->all(FLERR, "compute smd/hourglass_error command requires atom_style with hourglass_error (e.g. smd)");
+ Compute(lmp, narg, arg) {
+ if (narg != 3)
+ error->all(FLERR, "Illegal compute smd/hourglass_error command");
+ if (atom->smd_flag != 1)
+ error->all(FLERR, "compute smd/hourglass_error command requires atom_style with hourglass_error (e.g. smd)");
- peratom_flag = 1;
- size_peratom_cols = 0;
+ peratom_flag = 1;
+ size_peratom_cols = 0;
- nmax = 0;
- hourglass_error_vector = NULL;
+ nmax = 0;
+ hourglass_error_vector = NULL;
}
/* ---------------------------------------------------------------------- */
ComputeSMDHourglassError::~ComputeSMDHourglassError() {
- memory->sfree(hourglass_error_vector);
+ memory->sfree(hourglass_error_vector);
}
/* ---------------------------------------------------------------------- */
void ComputeSMDHourglassError::init() {
- int count = 0;
- for (int i = 0; i < modify->ncompute; i++)
- if (strcmp(modify->compute[i]->style, "smd/hourglass_error") == 0)
- count++;
- if (count > 1 && comm->me == 0)
- error->warning(FLERR, "More than one compute smd/hourglass_error");
+ int count = 0;
+ for (int i = 0; i < modify->ncompute; i++)
+ if (strcmp(modify->compute[i]->style, "smd/hourglass_error") == 0)
+ count++;
+ if (count > 1 && comm->me == 0)
+ error->warning(FLERR, "More than one compute smd/hourglass_error");
}
/* ---------------------------------------------------------------------- */
void ComputeSMDHourglassError::compute_peratom() {
- invoked_peratom = update->ntimestep;
-
- // grow output Vector array if necessary
-
- if (atom->nmax > nmax) {
- memory->sfree(hourglass_error_vector);
- nmax = atom->nmax;
- hourglass_error_vector = (double *) memory->smalloc(nmax * sizeof(double), "atom:hourglass_error_vector");
- vector_atom = hourglass_error_vector;
- }
-
- int itmp = 0;
- double *hourglass_error = (double *) force->pair->extract("smd/tlsph/hourglass_error_ptr", itmp);
- if (hourglass_error == NULL) {
- error->all(FLERR, "compute smd/hourglass_error failed to access hourglass_error array");
- }
-
- int *mask = atom->mask;
- int nlocal = atom->nlocal;
-
- for (int i = 0; i < nlocal; i++) {
- if (mask[i] & groupbit) {
- hourglass_error_vector[i] = hourglass_error[i];
- } else {
- hourglass_error_vector[i] = 0.0;
- }
- }
+ invoked_peratom = update->ntimestep;
+
+ // grow output Vector array if necessary
+
+ if (atom->nmax > nmax) {
+ memory->sfree(hourglass_error_vector);
+ nmax = atom->nmax;
+ hourglass_error_vector = (double *) memory->smalloc(nmax * sizeof(double), "atom:hourglass_error_vector");
+ vector_atom = hourglass_error_vector;
+ }
+
+ int itmp = 0;
+ double *hourglass_error = (double *) force->pair->extract("smd/tlsph/hourglass_error_ptr", itmp);
+ if (hourglass_error == NULL) {
+ error->all(FLERR, "compute smd/hourglass_error failed to access hourglass_error array");
+ }
+
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+
+ for (int i = 0; i < nlocal; i++) {
+ if (mask[i] & groupbit) {
+ hourglass_error_vector[i] = hourglass_error[i];
+ } else {
+ hourglass_error_vector[i] = 0.0;
+ }
+ }
}
/* ----------------------------------------------------------------------
@@ -107,6 +107,6 @@ void ComputeSMDHourglassError::compute_peratom() {
------------------------------------------------------------------------- */
double ComputeSMDHourglassError::memory_usage() {
- double bytes = nmax * sizeof(double);
- return bytes;
+ double bytes = nmax * sizeof(double);
+ return bytes;
}
diff --git a/src/USER-SMD/compute_smd_rho.cpp b/src/USER-SMD/compute_smd_rho.cpp
index 91b75d9003..cb97755aca 100644
--- a/src/USER-SMD/compute_smd_rho.cpp
+++ b/src/USER-SMD/compute_smd_rho.cpp
@@ -37,63 +37,63 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeSMDRho::ComputeSMDRho(LAMMPS *lmp, int narg, char **arg) :
- Compute(lmp, narg, arg) {
- if (narg != 3)
- error->all(FLERR, "Illegal compute smd/rho command");
- if (atom->vfrac_flag != 1)
- error->all(FLERR, "compute smd/rho command requires atom_style with volume (e.g. smd)");
+ Compute(lmp, narg, arg) {
+ if (narg != 3)
+ error->all(FLERR, "Illegal compute smd/rho command");
+ if (atom->vfrac_flag != 1)
+ error->all(FLERR, "compute smd/rho command requires atom_style with volume (e.g. smd)");
- peratom_flag = 1;
- size_peratom_cols = 0;
+ peratom_flag = 1;
+ size_peratom_cols = 0;
- nmax = 0;
- rhoVector = NULL;
+ nmax = 0;
+ rhoVector = NULL;
}
/* ---------------------------------------------------------------------- */
ComputeSMDRho::~ComputeSMDRho() {
- memory->sfree(rhoVector);
+ memory->sfree(rhoVector);
}
/* ---------------------------------------------------------------------- */
void ComputeSMDRho::init() {
- int count = 0;
- for (int i = 0; i < modify->ncompute; i++)
- if (strcmp(modify->compute[i]->style, "smd/rho") == 0)
- count++;
- if (count > 1 && comm->me == 0)
- error->warning(FLERR, "More than one compute smd/rho");
+ int count = 0;
+ for (int i = 0; i < modify->ncompute; i++)
+ if (strcmp(modify->compute[i]->style, "smd/rho") == 0)
+ count++;
+ if (count > 1 && comm->me == 0)
+ error->warning(FLERR, "More than one compute smd/rho");
}
/* ---------------------------------------------------------------------- */
void ComputeSMDRho::compute_peratom() {
- invoked_peratom = update->ntimestep;
-
- // grow rhoVector array if necessary
-
- if (atom->nmax > nmax) {
- memory->sfree(rhoVector);
- nmax = atom->nmax;
- rhoVector = (double *) memory->smalloc(nmax * sizeof(double), "atom:rhoVector");
- vector_atom = rhoVector;
- }
-
- double *vfrac = atom->vfrac;
- double *rmass = atom->rmass;
- int *mask = atom->mask;
- int nlocal = atom->nlocal;
-
- for (int i = 0; i < nlocal; i++) {
- if (mask[i] & groupbit) {
- rhoVector[i] = rmass[i] / vfrac[i];
- } else {
- rhoVector[i] = 0.0;
- }
- }
+ invoked_peratom = update->ntimestep;
+
+ // grow rhoVector array if necessary
+
+ if (atom->nmax > nmax) {
+ memory->sfree(rhoVector);
+ nmax = atom->nmax;
+ rhoVector = (double *) memory->smalloc(nmax * sizeof(double), "atom:rhoVector");
+ vector_atom = rhoVector;
+ }
+
+ double *vfrac = atom->vfrac;
+ double *rmass = atom->rmass;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+
+ for (int i = 0; i < nlocal; i++) {
+ if (mask[i] & groupbit) {
+ rhoVector[i] = rmass[i] / vfrac[i];
+ } else {
+ rhoVector[i] = 0.0;
+ }
+ }
}
@@ -102,6 +102,6 @@ void ComputeSMDRho::compute_peratom() {
------------------------------------------------------------------------- */
double ComputeSMDRho::memory_usage() {
- double bytes = nmax * sizeof(double);
- return bytes;
+ double bytes = nmax * sizeof(double);
+ return bytes;
}
diff --git a/src/USER-SMD/compute_smd_tlsph_defgrad.cpp b/src/USER-SMD/compute_smd_tlsph_defgrad.cpp
index c2ed667ef6..3ba66a656c 100644
--- a/src/USER-SMD/compute_smd_tlsph_defgrad.cpp
+++ b/src/USER-SMD/compute_smd_tlsph_defgrad.cpp
@@ -44,88 +44,88 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeSMDTLSPHDefgrad::ComputeSMDTLSPHDefgrad(LAMMPS *lmp, int narg, char **arg) :
- Compute(lmp, narg, arg) {
- if (narg != 3)
- error->all(FLERR, "Illegal compute smd/tlsph_defgrad command");
+ Compute(lmp, narg, arg) {
+ if (narg != 3)
+ error->all(FLERR, "Illegal compute smd/tlsph_defgrad command");
- peratom_flag = 1;
- size_peratom_cols = 10;
+ peratom_flag = 1;
+ size_peratom_cols = 10;
- nmax = 0;
- defgradVector = NULL;
+ nmax = 0;
+ defgradVector = NULL;
}
/* ---------------------------------------------------------------------- */
ComputeSMDTLSPHDefgrad::~ComputeSMDTLSPHDefgrad() {
- memory->sfree(defgradVector);
+ memory->sfree(defgradVector);
}
/* ---------------------------------------------------------------------- */
void ComputeSMDTLSPHDefgrad::init() {
- int count = 0;
- for (int i = 0; i < modify->ncompute; i++)
- if (strcmp(modify->compute[i]->style, "smd/tlsph_defgrad") == 0)
- count++;
- if (count > 1 && comm->me == 0)
- error->warning(FLERR, "More than one compute smd/tlsph_defgrad");
+ int count = 0;
+ for (int i = 0; i < modify->ncompute; i++)
+ if (strcmp(modify->compute[i]->style, "smd/tlsph_defgrad") == 0)
+ count++;
+ if (count > 1 && comm->me == 0)
+ error->warning(FLERR, "More than one compute smd/tlsph_defgrad");
}
/* ---------------------------------------------------------------------- */
void ComputeSMDTLSPHDefgrad::compute_peratom() {
- double **defgrad = atom->smd_data_9;
- Matrix3d F;
- invoked_peratom = update->ntimestep;
-
- // grow vector array if necessary
- if (atom->nmax > nmax) {
- memory->destroy(defgradVector);
- nmax = atom->nmax;
- memory->create(defgradVector, nmax, size_peratom_cols, "defgradVector");
- array_atom = defgradVector;
- }
-
- int *mask = atom->mask;
- int nlocal = atom->nlocal;
-
- for (int i = 0; i < nlocal; i++) {
- if (mask[i] & groupbit) {
- F(0, 0) = defgrad[i][0];
- F(0, 1) = defgrad[i][1];
- F(0, 2) = defgrad[i][2];
- F(1, 0) = defgrad[i][3];
- F(1, 1) = defgrad[i][4];
- F(1, 2) = defgrad[i][5];
- F(2, 0) = defgrad[i][6];
- F(2, 1) = defgrad[i][7];
- F(2, 2) = defgrad[i][8];
-
- defgradVector[i][0] = F(0, 0);
- defgradVector[i][1] = F(0, 1);
- defgradVector[i][2] = F(0, 2);
- defgradVector[i][3] = F(1, 0);
- defgradVector[i][4] = F(1, 1);
- defgradVector[i][5] = F(1, 2);
- defgradVector[i][6] = F(2, 0);
- defgradVector[i][7] = F(2, 1);
- defgradVector[i][8] = F(2, 2);
- defgradVector[i][9] = F.determinant();
- } else {
- defgradVector[i][0] = 1.0;
- defgradVector[i][1] = 0.0;
- defgradVector[i][2] = 0.0;
- defgradVector[i][3] = 0.0;
- defgradVector[i][4] = 1.0;
- defgradVector[i][5] = 0.0;
- defgradVector[i][6] = 0.0;
- defgradVector[i][7] = 0.0;
- defgradVector[i][8] = 1.0;
- defgradVector[i][9] = 1.0;
- }
- }
+ double **defgrad = atom->smd_data_9;
+ Matrix3d F;
+ invoked_peratom = update->ntimestep;
+
+ // grow vector array if necessary
+ if (atom->nmax > nmax) {
+ memory->destroy(defgradVector);
+ nmax = atom->nmax;
+ memory->create(defgradVector, nmax, size_peratom_cols, "defgradVector");
+ array_atom = defgradVector;
+ }
+
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+
+ for (int i = 0; i < nlocal; i++) {
+ if (mask[i] & groupbit) {
+ F(0, 0) = defgrad[i][0];
+ F(0, 1) = defgrad[i][1];
+ F(0, 2) = defgrad[i][2];
+ F(1, 0) = defgrad[i][3];
+ F(1, 1) = defgrad[i][4];
+ F(1, 2) = defgrad[i][5];
+ F(2, 0) = defgrad[i][6];
+ F(2, 1) = defgrad[i][7];
+ F(2, 2) = defgrad[i][8];
+
+ defgradVector[i][0] = F(0, 0);
+ defgradVector[i][1] = F(0, 1);
+ defgradVector[i][2] = F(0, 2);
+ defgradVector[i][3] = F(1, 0);
+ defgradVector[i][4] = F(1, 1);
+ defgradVector[i][5] = F(1, 2);
+ defgradVector[i][6] = F(2, 0);
+ defgradVector[i][7] = F(2, 1);
+ defgradVector[i][8] = F(2, 2);
+ defgradVector[i][9] = F.determinant();
+ } else {
+ defgradVector[i][0] = 1.0;
+ defgradVector[i][1] = 0.0;
+ defgradVector[i][2] = 0.0;
+ defgradVector[i][3] = 0.0;
+ defgradVector[i][4] = 1.0;
+ defgradVector[i][5] = 0.0;
+ defgradVector[i][6] = 0.0;
+ defgradVector[i][7] = 0.0;
+ defgradVector[i][8] = 1.0;
+ defgradVector[i][9] = 1.0;
+ }
+ }
}
/* ----------------------------------------------------------------------
@@ -133,6 +133,6 @@ void ComputeSMDTLSPHDefgrad::compute_peratom() {
------------------------------------------------------------------------- */
double ComputeSMDTLSPHDefgrad::memory_usage() {
- double bytes = size_peratom_cols * nmax * sizeof(double);
- return bytes;
+ double bytes = size_peratom_cols * nmax * sizeof(double);
+ return bytes;
}
diff --git a/src/USER-SMD/compute_smd_tlsph_dt.cpp b/src/USER-SMD/compute_smd_tlsph_dt.cpp
index 54b4f497fb..6d573775fa 100644
--- a/src/USER-SMD/compute_smd_tlsph_dt.cpp
+++ b/src/USER-SMD/compute_smd_tlsph_dt.cpp
@@ -38,71 +38,71 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeSMDTlsphDt::ComputeSMDTlsphDt(LAMMPS *lmp, int narg, char **arg) :
- Compute(lmp, narg, arg) {
- if (narg != 3)
- error->all(FLERR, "Illegal compute smd/tlsph_dt command");
- if (atom->contact_radius_flag != 1)
- error->all(FLERR,
- "compute smd/tlsph_dt command requires atom_style with contact_radius (e.g. smd)");
-
- peratom_flag = 1;
- size_peratom_cols = 0;
-
- nmax = 0;
- dt_vector = NULL;
+ Compute(lmp, narg, arg) {
+ if (narg != 3)
+ error->all(FLERR, "Illegal compute smd/tlsph_dt command");
+ if (atom->contact_radius_flag != 1)
+ error->all(FLERR,
+ "compute smd/tlsph_dt command requires atom_style with contact_radius (e.g. smd)");
+
+ peratom_flag = 1;
+ size_peratom_cols = 0;
+
+ nmax = 0;
+ dt_vector = NULL;
}
/* ---------------------------------------------------------------------- */
ComputeSMDTlsphDt::~ComputeSMDTlsphDt() {
- memory->sfree(dt_vector);
+ memory->sfree(dt_vector);
}
/* ---------------------------------------------------------------------- */
void ComputeSMDTlsphDt::init() {
- int count = 0;
- for (int i = 0; i < modify->ncompute; i++)
- if (strcmp(modify->compute[i]->style, "smd/tlsph_dt") == 0)
- count++;
- if (count > 1 && comm->me == 0)
- error->warning(FLERR, "More than one compute smd/tlsph_dt");
+ int count = 0;
+ for (int i = 0; i < modify->ncompute; i++)
+ if (strcmp(modify->compute[i]->style, "smd/tlsph_dt") == 0)
+ count++;
+ if (count > 1 && comm->me == 0)
+ error->warning(FLERR, "More than one compute smd/tlsph_dt");
}
/* ---------------------------------------------------------------------- */
void ComputeSMDTlsphDt::compute_peratom() {
- invoked_peratom = update->ntimestep;
-
- // grow rhoVector array if necessary
-
- if (atom->nmax > nmax) {
- memory->sfree(dt_vector);
- nmax = atom->nmax;
- dt_vector = (double *) memory->smalloc(nmax * sizeof(double),
- "atom:tlsph_dt_vector");
- vector_atom = dt_vector;
- }
-
- int itmp = 0;
- double *particle_dt = (double *) force->pair->extract("smd/tlsph/particle_dt_ptr",
- itmp);
- if (particle_dt == NULL) {
- error->all(FLERR,
- "compute smd/tlsph_dt failed to access particle_dt array");
- }
-
- int *mask = atom->mask;
- int nlocal = atom->nlocal;
-
- for (int i = 0; i < nlocal; i++) {
- if (mask[i] & groupbit) {
- dt_vector[i] = particle_dt[i];
- } else {
- dt_vector[i] = 0.0;
- }
- }
+ invoked_peratom = update->ntimestep;
+
+ // grow rhoVector array if necessary
+
+ if (atom->nmax > nmax) {
+ memory->sfree(dt_vector);
+ nmax = atom->nmax;
+ dt_vector = (double *) memory->smalloc(nmax * sizeof(double),
+ "atom:tlsph_dt_vector");
+ vector_atom = dt_vector;
+ }
+
+ int itmp = 0;
+ double *particle_dt = (double *) force->pair->extract("smd/tlsph/particle_dt_ptr",
+ itmp);
+ if (particle_dt == NULL) {
+ error->all(FLERR,
+ "compute smd/tlsph_dt failed to access particle_dt array");
+ }
+
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+
+ for (int i = 0; i < nlocal; i++) {
+ if (mask[i] & groupbit) {
+ dt_vector[i] = particle_dt[i];
+ } else {
+ dt_vector[i] = 0.0;
+ }
+ }
}
/* ----------------------------------------------------------------------
@@ -110,6 +110,6 @@ void ComputeSMDTlsphDt::compute_peratom() {
------------------------------------------------------------------------- */
double ComputeSMDTlsphDt::memory_usage() {
- double bytes = nmax * sizeof(double);
- return bytes;
+ double bytes = nmax * sizeof(double);
+ return bytes;
}
diff --git a/src/USER-SMD/compute_smd_tlsph_shape.cpp b/src/USER-SMD/compute_smd_tlsph_shape.cpp
index cec773b5c3..d9dc070f6b 100644
--- a/src/USER-SMD/compute_smd_tlsph_shape.cpp
+++ b/src/USER-SMD/compute_smd_tlsph_shape.cpp
@@ -45,86 +45,86 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeSmdTlsphShape::ComputeSmdTlsphShape(LAMMPS *lmp, int narg, char **arg) :
- Compute(lmp, narg, arg) {
- if (narg != 3)
- error->all(FLERR, "Illegal compute smd/tlsph_strain command");
+ Compute(lmp, narg, arg) {
+ if (narg != 3)
+ error->all(FLERR, "Illegal compute smd/tlsph_strain command");
- peratom_flag = 1;
- size_peratom_cols = 7;
+ peratom_flag = 1;
+ size_peratom_cols = 7;
- nmax = 0;
- strainVector = NULL;
+ nmax = 0;
+ strainVector = NULL;
}
/* ---------------------------------------------------------------------- */
ComputeSmdTlsphShape::~ComputeSmdTlsphShape() {
- memory->sfree(strainVector);
+ memory->sfree(strainVector);
}
/* ---------------------------------------------------------------------- */
void ComputeSmdTlsphShape::init() {
- int count = 0;
- for (int i = 0; i < modify->ncompute; i++)
- if (strcmp(modify->compute[i]->style, "smd/tlsph_strain") == 0)
- count++;
- if (count > 1 && comm->me == 0)
- error->warning(FLERR, "More than one compute smd/tlsph_strain");
+ int count = 0;
+ for (int i = 0; i < modify->ncompute; i++)
+ if (strcmp(modify->compute[i]->style, "smd/tlsph_strain") == 0)
+ count++;
+ if (count > 1 && comm->me == 0)
+ error->warning(FLERR, "More than one compute smd/tlsph_strain");
}
/* ---------------------------------------------------------------------- */
void ComputeSmdTlsphShape::compute_peratom() {
- double *contact_radius = atom->contact_radius;
- invoked_peratom = update->ntimestep;
-
- // grow vector array if necessary
-
- if (atom->nmax > nmax) {
- memory->destroy(strainVector);
- nmax = atom->nmax;
- memory->create(strainVector, nmax, size_peratom_cols, "strainVector");
- array_atom = strainVector;
- }
-
- int itmp = 0;
- Matrix3d *R = (Matrix3d *) force->pair->extract("smd/tlsph/rotation_ptr", itmp);
- if (R == NULL) {
- error->all(FLERR, "compute smd/tlsph_shape failed to access rotation array");
- }
-
- Matrix3d *F = (Matrix3d *) force->pair->extract("smd/tlsph/Fincr_ptr", itmp);
- if (F == NULL) {
- error->all(FLERR, "compute smd/tlsph_shape failed to access deformation gradient array");
- }
-
- int *mask = atom->mask;
- int nlocal = atom->nlocal;
- Matrix3d E, eye;
- eye.setIdentity();
- Quaterniond q;
-
- for (int i = 0; i < nlocal; i++) {
- if (mask[i] & groupbit) {
-
- E = 0.5 * (F[i].transpose() * F[i] - eye); // Green-Lagrange strain
- strainVector[i][0] = contact_radius[i] * (1.0 + E(0, 0));
- strainVector[i][1] = contact_radius[i] * (1.0 + E(1, 1));
- strainVector[i][2] = contact_radius[i] * (1.0 + E(2, 2));
-
- q = R[i]; // convert pure rotation matrix to quaternion
- strainVector[i][3] = q.w();
- strainVector[i][4] = q.x();
- strainVector[i][5] = q.y();
- strainVector[i][6] = q.z();
- } else {
- for (int j = 0; j < size_peratom_cols; j++) {
- strainVector[i][j] = 0.0;
- }
- }
- }
+ double *contact_radius = atom->contact_radius;
+ invoked_peratom = update->ntimestep;
+
+ // grow vector array if necessary
+
+ if (atom->nmax > nmax) {
+ memory->destroy(strainVector);
+ nmax = atom->nmax;
+ memory->create(strainVector, nmax, size_peratom_cols, "strainVector");
+ array_atom = strainVector;
+ }
+
+ int itmp = 0;
+ Matrix3d *R = (Matrix3d *) force->pair->extract("smd/tlsph/rotation_ptr", itmp);
+ if (R == NULL) {
+ error->all(FLERR, "compute smd/tlsph_shape failed to access rotation array");
+ }
+
+ Matrix3d *F = (Matrix3d *) force->pair->extract("smd/tlsph/Fincr_ptr", itmp);
+ if (F == NULL) {
+ error->all(FLERR, "compute smd/tlsph_shape failed to access deformation gradient array");
+ }
+
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+ Matrix3d E, eye;
+ eye.setIdentity();
+ Quaterniond q;
+
+ for (int i = 0; i < nlocal; i++) {
+ if (mask[i] & groupbit) {
+
+ E = 0.5 * (F[i].transpose() * F[i] - eye); // Green-Lagrange strain
+ strainVector[i][0] = contact_radius[i] * (1.0 + E(0, 0));
+ strainVector[i][1] = contact_radius[i] * (1.0 + E(1, 1));
+ strainVector[i][2] = contact_radius[i] * (1.0 + E(2, 2));
+
+ q = R[i]; // convert pure rotation matrix to quaternion
+ strainVector[i][3] = q.w();
+ strainVector[i][4] = q.x();
+ strainVector[i][5] = q.y();
+ strainVector[i][6] = q.z();
+ } else {
+ for (int j = 0; j < size_peratom_cols; j++) {
+ strainVector[i][j] = 0.0;
+ }
+ }
+ }
}
/* ----------------------------------------------------------------------
@@ -132,6 +132,6 @@ void ComputeSmdTlsphShape::compute_peratom() {
------------------------------------------------------------------------- */
double ComputeSmdTlsphShape::memory_usage() {
- double bytes = size_peratom_cols * nmax * sizeof(double);
- return bytes;
+ double bytes = size_peratom_cols * nmax * sizeof(double);
+ return bytes;
}
diff --git a/src/USER-SMD/compute_smd_tlsph_strain.cpp b/src/USER-SMD/compute_smd_tlsph_strain.cpp
index 2037d6c354..ea137d5b2a 100644
--- a/src/USER-SMD/compute_smd_tlsph_strain.cpp
+++ b/src/USER-SMD/compute_smd_tlsph_strain.cpp
@@ -45,94 +45,94 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeSMDTLSPHstrain::ComputeSMDTLSPHstrain(LAMMPS *lmp, int narg, char **arg) :
- Compute(lmp, narg, arg) {
- if (narg != 3)
- error->all(FLERR, "Illegal compute smd/tlsph_strain command");
+ Compute(lmp, narg, arg) {
+ if (narg != 3)
+ error->all(FLERR, "Illegal compute smd/tlsph_strain command");
- peratom_flag = 1;
- size_peratom_cols = 6;
+ peratom_flag = 1;
+ size_peratom_cols = 6;
- nmax = 0;
- strainVector = NULL;
+ nmax = 0;
+ strainVector = NULL;
}
/* ---------------------------------------------------------------------- */
ComputeSMDTLSPHstrain::~ComputeSMDTLSPHstrain() {
- memory->sfree(strainVector);
+ memory->sfree(strainVector);
}
/* ---------------------------------------------------------------------- */
void ComputeSMDTLSPHstrain::init() {
- int count = 0;
- for (int i = 0; i < modify->ncompute; i++)
- if (strcmp(modify->compute[i]->style, "smd/tlsph_strain") == 0)
- count++;
- if (count > 1 && comm->me == 0)
- error->warning(FLERR, "More than one compute smd/tlsph_strain");
+ int count = 0;
+ for (int i = 0; i < modify->ncompute; i++)
+ if (strcmp(modify->compute[i]->style, "smd/tlsph_strain") == 0)
+ count++;
+ if (count > 1 && comm->me == 0)
+ error->warning(FLERR, "More than one compute smd/tlsph_strain");
}
/* ---------------------------------------------------------------------- */
void ComputeSMDTLSPHstrain::compute_peratom() {
- double **defgrad0 = atom->smd_data_9;
-
- invoked_peratom = update->ntimestep;
-
- // grow vector array if necessary
-
- if (atom->nmax > nmax) {
- memory->destroy(strainVector);
- nmax = atom->nmax;
- memory->create(strainVector, nmax, size_peratom_cols, "strainVector");
- array_atom = strainVector;
- }
-
- // copy data to output array
- int itmp = 0;
- Matrix3d *Fincr = (Matrix3d *) force->pair->extract("smd/tlsph/Fincr_ptr", itmp);
- if (Fincr == NULL) {
- error->all(FLERR, "compute smd/tlsph_strain failed to access Fincr array");
- }
-
- int *mask = atom->mask;
- int nlocal = atom->nlocal;
- Matrix3d E, eye, Ftotal, F0;
- eye.setIdentity();
-
- for (int i = 0; i < nlocal; i++) {
- if (mask[i] & groupbit) {
-
- // old deformation gradient
- F0(0, 0) = defgrad0[i][0];
- F0(0, 1) = defgrad0[i][1];
- F0(0, 2) = defgrad0[i][2];
- F0(1, 0) = defgrad0[i][3];
- F0(1, 1) = defgrad0[i][4];
- F0(1, 2) = defgrad0[i][5];
- F0(2, 0) = defgrad0[i][6];
- F0(2, 1) = defgrad0[i][7];
- F0(2, 2) = defgrad0[i][8];
-
- // compute current total deformation gradient
- Ftotal = F0 * Fincr[i]; // this is the total deformation gradient: reference deformation times incremental deformation
-
-
- E = 0.5 * (Ftotal.transpose() * Ftotal - eye); // Green-Lagrange strain
- strainVector[i][0] = E(0, 0);
- strainVector[i][1] = E(1, 1);
- strainVector[i][2] = E(2, 2);
- strainVector[i][3] = E(0, 1);
- strainVector[i][4] = E(0, 2);
- strainVector[i][5] = E(1, 2);
- } else {
- for (int j = 0; j < size_peratom_cols; j++) {
- strainVector[i][j] = 0.0;
- }
- }
- }
+ double **defgrad0 = atom->smd_data_9;
+
+ invoked_peratom = update->ntimestep;
+
+ // grow vector array if necessary
+
+ if (atom->nmax > nmax) {
+ memory->destroy(strainVector);
+ nmax = atom->nmax;
+ memory->create(strainVector, nmax, size_peratom_cols, "strainVector");
+ array_atom = strainVector;
+ }
+
+ // copy data to output array
+ int itmp = 0;
+ Matrix3d *Fincr = (Matrix3d *) force->pair->extract("smd/tlsph/Fincr_ptr", itmp);
+ if (Fincr == NULL) {
+ error->all(FLERR, "compute smd/tlsph_strain failed to access Fincr array");
+ }
+
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+ Matrix3d E, eye, Ftotal, F0;
+ eye.setIdentity();
+
+ for (int i = 0; i < nlocal; i++) {
+ if (mask[i] & groupbit) {
+
+ // old deformation gradient
+ F0(0, 0) = defgrad0[i][0];
+ F0(0, 1) = defgrad0[i][1];
+ F0(0, 2) = defgrad0[i][2];
+ F0(1, 0) = defgrad0[i][3];
+ F0(1, 1) = defgrad0[i][4];
+ F0(1, 2) = defgrad0[i][5];
+ F0(2, 0) = defgrad0[i][6];
+ F0(2, 1) = defgrad0[i][7];
+ F0(2, 2) = defgrad0[i][8];
+
+ // compute current total deformation gradient
+ Ftotal = F0 * Fincr[i]; // this is the total deformation gradient: reference deformation times incremental deformation
+
+
+ E = 0.5 * (Ftotal.transpose() * Ftotal - eye); // Green-Lagrange strain
+ strainVector[i][0] = E(0, 0);
+ strainVector[i][1] = E(1, 1);
+ strainVector[i][2] = E(2, 2);
+ strainVector[i][3] = E(0, 1);
+ strainVector[i][4] = E(0, 2);
+ strainVector[i][5] = E(1, 2);
+ } else {
+ for (int j = 0; j < size_peratom_cols; j++) {
+ strainVector[i][j] = 0.0;
+ }
+ }
+ }
}
/* ----------------------------------------------------------------------
@@ -140,6 +140,6 @@ void ComputeSMDTLSPHstrain::compute_peratom() {
------------------------------------------------------------------------- */
double ComputeSMDTLSPHstrain::memory_usage() {
- double bytes = size_peratom_cols * nmax * sizeof(double);
- return bytes;
+ double bytes = size_peratom_cols * nmax * sizeof(double);
+ return bytes;
}
diff --git a/src/USER-SMD/compute_smd_tlsph_strain_rate.cpp b/src/USER-SMD/compute_smd_tlsph_strain_rate.cpp
index db91b080ba..ed3525f4ad 100644
--- a/src/USER-SMD/compute_smd_tlsph_strain_rate.cpp
+++ b/src/USER-SMD/compute_smd_tlsph_strain_rate.cpp
@@ -41,67 +41,67 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeSMDTLSPHStrainRate::ComputeSMDTLSPHStrainRate(LAMMPS *lmp, int narg, char **arg) :
- Compute(lmp, narg, arg) {
- if (narg != 3)
- error->all(FLERR, "Illegal compute smd/ulsph_strain_rate command");
+ Compute(lmp, narg, arg) {
+ if (narg != 3)
+ error->all(FLERR, "Illegal compute smd/ulsph_strain_rate command");
- peratom_flag = 1;
- size_peratom_cols = 6;
+ peratom_flag = 1;
+ size_peratom_cols = 6;
- nmax = 0;
- strain_rate_array = NULL;
+ nmax = 0;
+ strain_rate_array = NULL;
}
/* ---------------------------------------------------------------------- */
ComputeSMDTLSPHStrainRate::~ComputeSMDTLSPHStrainRate() {
- memory->sfree(strain_rate_array);
+ memory->sfree(strain_rate_array);
}
/* ---------------------------------------------------------------------- */
void ComputeSMDTLSPHStrainRate::init() {
- int count = 0;
- for (int i = 0; i < modify->ncompute; i++)
- if (strcmp(modify->compute[i]->style, "smd/ulsph_strain_rate") == 0)
- count++;
- if (count > 1 && comm->me == 0)
- error->warning(FLERR, "More than one compute smd/ulsph_strain_rate");
+ int count = 0;
+ for (int i = 0; i < modify->ncompute; i++)
+ if (strcmp(modify->compute[i]->style, "smd/ulsph_strain_rate") == 0)
+ count++;
+ if (count > 1 && comm->me == 0)
+ error->warning(FLERR, "More than one compute smd/ulsph_strain_rate");
}
/* ---------------------------------------------------------------------- */
void ComputeSMDTLSPHStrainRate::compute_peratom() {
- invoked_peratom = update->ntimestep;
-
- // grow vector array if necessary
-
- if (atom->nmax > nmax) {
- memory->destroy(strain_rate_array);
- nmax = atom->nmax;
- memory->create(strain_rate_array, nmax, size_peratom_cols, "stresstensorVector");
- array_atom = strain_rate_array;
- }
-
- int itmp = 0;
- Matrix3d *D = (Matrix3d *) force->pair->extract("smd/tlsph/strain_rate_ptr", itmp);
- if (D == NULL) {
- error->all(FLERR,
- "compute smd/tlsph_strain_rate could not access strain rate. Are the matching pair styles present?");
- }
-
- int nlocal = atom->nlocal;
-
- for (int i = 0; i < nlocal; i++) {
-
- strain_rate_array[i][0] = D[i](0, 0); // xx
- strain_rate_array[i][1] = D[i](1, 1); // yy
- strain_rate_array[i][2] = D[i](2, 2); // zz
- strain_rate_array[i][3] = D[i](0, 1); // xy
- strain_rate_array[i][4] = D[i](0, 2); // xz
- strain_rate_array[i][5] = D[i](1, 2); // yz
- }
+ invoked_peratom = update->ntimestep;
+
+ // grow vector array if necessary
+
+ if (atom->nmax > nmax) {
+ memory->destroy(strain_rate_array);
+ nmax = atom->nmax;
+ memory->create(strain_rate_array, nmax, size_peratom_cols, "stresstensorVector");
+ array_atom = strain_rate_array;
+ }
+
+ int itmp = 0;
+ Matrix3d *D = (Matrix3d *) force->pair->extract("smd/tlsph/strain_rate_ptr", itmp);
+ if (D == NULL) {
+ error->all(FLERR,
+ "compute smd/tlsph_strain_rate could not access strain rate. Are the matching pair styles present?");
+ }
+
+ int nlocal = atom->nlocal;
+
+ for (int i = 0; i < nlocal; i++) {
+
+ strain_rate_array[i][0] = D[i](0, 0); // xx
+ strain_rate_array[i][1] = D[i](1, 1); // yy
+ strain_rate_array[i][2] = D[i](2, 2); // zz
+ strain_rate_array[i][3] = D[i](0, 1); // xy
+ strain_rate_array[i][4] = D[i](0, 2); // xz
+ strain_rate_array[i][5] = D[i](1, 2); // yz
+ }
}
/* ----------------------------------------------------------------------
@@ -109,6 +109,6 @@ void ComputeSMDTLSPHStrainRate::compute_peratom() {
------------------------------------------------------------------------- */
double ComputeSMDTLSPHStrainRate::memory_usage() {
- double bytes = size_peratom_cols * nmax * sizeof(double);
- return bytes;
+ double bytes = size_peratom_cols * nmax * sizeof(double);
+ return bytes;
}
diff --git a/src/USER-SMD/compute_smd_tlsph_stress.cpp b/src/USER-SMD/compute_smd_tlsph_stress.cpp
index d1fce57f92..cbcb4c45af 100644
--- a/src/USER-SMD/compute_smd_tlsph_stress.cpp
+++ b/src/USER-SMD/compute_smd_tlsph_stress.cpp
@@ -41,85 +41,85 @@ using namespace LAMMPS_NS;
* deviator of a tensor
*/
static Matrix3d Deviator(Matrix3d M) {
- Matrix3d eye;
- eye.setIdentity();
- eye *= M.trace() / 3.0;
- return M - eye;
+ Matrix3d eye;
+ eye.setIdentity();
+ eye *= M.trace() / 3.0;
+ return M - eye;
}
/* ---------------------------------------------------------------------- */
ComputeSMDTLSPHStress::ComputeSMDTLSPHStress(LAMMPS *lmp, int narg, char **arg) :
- Compute(lmp, narg, arg) {
- if (narg != 3)
- error->all(FLERR, "Illegal compute smd/tlsph_stress command");
+ Compute(lmp, narg, arg) {
+ if (narg != 3)
+ error->all(FLERR, "Illegal compute smd/tlsph_stress command");
- peratom_flag = 1;
- size_peratom_cols = 7;
+ peratom_flag = 1;
+ size_peratom_cols = 7;
- nmax = 0;
- stress_array = NULL;
+ nmax = 0;
+ stress_array = NULL;
}
/* ---------------------------------------------------------------------- */
ComputeSMDTLSPHStress::~ComputeSMDTLSPHStress() {
- memory->sfree(stress_array);
+ memory->sfree(stress_array);
}
/* ---------------------------------------------------------------------- */
void ComputeSMDTLSPHStress::init() {
- int count = 0;
- for (int i = 0; i < modify->ncompute; i++)
- if (strcmp(modify->compute[i]->style, "smd/tlsph_stress") == 0)
- count++;
- if (count > 1 && comm->me == 0)
- error->warning(FLERR, "More than one compute smd/tlsph_stress");
+ int count = 0;
+ for (int i = 0; i < modify->ncompute; i++)
+ if (strcmp(modify->compute[i]->style, "smd/tlsph_stress") == 0)
+ count++;
+ if (count > 1 && comm->me == 0)
+ error->warning(FLERR, "More than one compute smd/tlsph_stress");
}
/* ---------------------------------------------------------------------- */
void ComputeSMDTLSPHStress::compute_peratom() {
- invoked_peratom = update->ntimestep;
- Matrix3d stress_deviator;
- double von_mises_stress;
-
- // grow vector array if necessary
-
- if (atom->nmax > nmax) {
- memory->destroy(stress_array);
- nmax = atom->nmax;
- memory->create(stress_array, nmax, size_peratom_cols, "stresstensorVector");
- array_atom = stress_array;
- }
-
- int itmp = 0;
- Matrix3d *T = (Matrix3d *) force->pair->extract("smd/tlsph/stressTensor_ptr", itmp);
- if (T == NULL) {
- error->all(FLERR, "compute smd/tlsph_stress could not access stress tensors. Are the matching pair styles present?");
- }
- int nlocal = atom->nlocal;
- int *mask = atom->mask;
-
- for (int i = 0; i < nlocal; i++) {
- if (mask[i] & groupbit) {
- stress_deviator = Deviator(T[i]);
- von_mises_stress = sqrt(3. / 2.) * stress_deviator.norm();
- stress_array[i][0] = T[i](0, 0); // xx
- stress_array[i][1] = T[i](1, 1); // yy
- stress_array[i][2] = T[i](2, 2); // zz
- stress_array[i][3] = T[i](0, 1); // xy
- stress_array[i][4] = T[i](0, 2); // xz
- stress_array[i][5] = T[i](1, 2); // yz
- stress_array[i][6] = von_mises_stress;
- } else {
- for (int j = 0; j < size_peratom_cols; j++) {
- stress_array[i][j] = 0.0;
- }
- }
- }
+ invoked_peratom = update->ntimestep;
+ Matrix3d stress_deviator;
+ double von_mises_stress;
+
+ // grow vector array if necessary
+
+ if (atom->nmax > nmax) {
+ memory->destroy(stress_array);
+ nmax = atom->nmax;
+ memory->create(stress_array, nmax, size_peratom_cols, "stresstensorVector");
+ array_atom = stress_array;
+ }
+
+ int itmp = 0;
+ Matrix3d *T = (Matrix3d *) force->pair->extract("smd/tlsph/stressTensor_ptr", itmp);
+ if (T == NULL) {
+ error->all(FLERR, "compute smd/tlsph_stress could not access stress tensors. Are the matching pair styles present?");
+ }
+ int nlocal = atom->nlocal;
+ int *mask = atom->mask;
+
+ for (int i = 0; i < nlocal; i++) {
+ if (mask[i] & groupbit) {
+ stress_deviator = Deviator(T[i]);
+ von_mises_stress = sqrt(3. / 2.) * stress_deviator.norm();
+ stress_array[i][0] = T[i](0, 0); // xx
+ stress_array[i][1] = T[i](1, 1); // yy
+ stress_array[i][2] = T[i](2, 2); // zz
+ stress_array[i][3] = T[i](0, 1); // xy
+ stress_array[i][4] = T[i](0, 2); // xz
+ stress_array[i][5] = T[i](1, 2); // yz
+ stress_array[i][6] = von_mises_stress;
+ } else {
+ for (int j = 0; j < size_peratom_cols; j++) {
+ stress_array[i][j] = 0.0;
+ }
+ }
+ }
}
/* ----------------------------------------------------------------------
@@ -127,6 +127,6 @@ void ComputeSMDTLSPHStress::compute_peratom() {
------------------------------------------------------------------------- */
double ComputeSMDTLSPHStress::memory_usage() {
- double bytes = size_peratom_cols * nmax * sizeof(double);
- return bytes;
+ double bytes = size_peratom_cols * nmax * sizeof(double);
+ return bytes;
}
diff --git a/src/USER-SMD/compute_smd_triangle_mesh_vertices.cpp b/src/USER-SMD/compute_smd_triangle_mesh_vertices.cpp
index 822d62d6db..e43dadb47a 100644
--- a/src/USER-SMD/compute_smd_triangle_mesh_vertices.cpp
+++ b/src/USER-SMD/compute_smd_triangle_mesh_vertices.cpp
@@ -78,8 +78,8 @@ void ComputeSMDTriangleVertices::init() {
void ComputeSMDTriangleVertices::compute_peratom() {
- double **smd_data_9 = atom->smd_data_9;
- tagint *mol = atom->molecule;
+ double **smd_data_9 = atom->smd_data_9;
+ tagint *mol = atom->molecule;
invoked_peratom = update->ntimestep;
diff --git a/src/USER-SMD/compute_smd_ulsph_effm.cpp b/src/USER-SMD/compute_smd_ulsph_effm.cpp
index 87de3df256..9453d8cfa6 100644
--- a/src/USER-SMD/compute_smd_ulsph_effm.cpp
+++ b/src/USER-SMD/compute_smd_ulsph_effm.cpp
@@ -38,71 +38,71 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeSMD_Ulsph_Effm::ComputeSMD_Ulsph_Effm(LAMMPS *lmp, int narg, char **arg) :
- Compute(lmp, narg, arg) {
- if (narg != 3)
- error->all(FLERR, "Illegal compute smd/ulsph_effm command");
- if (atom->contact_radius_flag != 1)
- error->all(FLERR,
- "compute smd/ulsph_effm command requires atom_style with contact_radius (e.g. smd)");
-
- peratom_flag = 1;
- size_peratom_cols = 0;
-
- nmax = 0;
- dt_vector = NULL;
+ Compute(lmp, narg, arg) {
+ if (narg != 3)
+ error->all(FLERR, "Illegal compute smd/ulsph_effm command");
+ if (atom->contact_radius_flag != 1)
+ error->all(FLERR,
+ "compute smd/ulsph_effm command requires atom_style with contact_radius (e.g. smd)");
+
+ peratom_flag = 1;
+ size_peratom_cols = 0;
+
+ nmax = 0;
+ dt_vector = NULL;
}
/* ---------------------------------------------------------------------- */
ComputeSMD_Ulsph_Effm::~ComputeSMD_Ulsph_Effm() {
- memory->sfree(dt_vector);
+ memory->sfree(dt_vector);
}
/* ---------------------------------------------------------------------- */
void ComputeSMD_Ulsph_Effm::init() {
- int count = 0;
- for (int i = 0; i < modify->ncompute; i++)
- if (strcmp(modify->compute[i]->style, "smd/ulsph_effm") == 0)
- count++;
- if (count > 1 && comm->me == 0)
- error->warning(FLERR, "More than one compute smd/ulsph_effm");
+ int count = 0;
+ for (int i = 0; i < modify->ncompute; i++)
+ if (strcmp(modify->compute[i]->style, "smd/ulsph_effm") == 0)
+ count++;
+ if (count > 1 && comm->me == 0)
+ error->warning(FLERR, "More than one compute smd/ulsph_effm");
}
/* ---------------------------------------------------------------------- */
void ComputeSMD_Ulsph_Effm::compute_peratom() {
- invoked_peratom = update->ntimestep;
-
- // grow rhoVector array if necessary
-
- if (atom->nmax > nmax) {
- memory->sfree(dt_vector);
- nmax = atom->nmax;
- dt_vector = (double *) memory->smalloc(nmax * sizeof(double),
- "atom:tlsph_dt_vector");
- vector_atom = dt_vector;
- }
-
- int itmp = 0;
- double *particle_dt = (double *) force->pair->extract("smd/ulsph/effective_modulus_ptr",
- itmp);
- if (particle_dt == NULL) {
- error->all(FLERR,
- "compute smd/ulsph_effm failed to access particle_dt array");
- }
-
- int *mask = atom->mask;
- int nlocal = atom->nlocal;
-
- for (int i = 0; i < nlocal; i++) {
- if (mask[i] & groupbit) {
- dt_vector[i] = particle_dt[i];
- } else {
- dt_vector[i] = 0.0;
- }
- }
+ invoked_peratom = update->ntimestep;
+
+ // grow rhoVector array if necessary
+
+ if (atom->nmax > nmax) {
+ memory->sfree(dt_vector);
+ nmax = atom->nmax;
+ dt_vector = (double *) memory->smalloc(nmax * sizeof(double),
+ "atom:tlsph_dt_vector");
+ vector_atom = dt_vector;
+ }
+
+ int itmp = 0;
+ double *particle_dt = (double *) force->pair->extract("smd/ulsph/effective_modulus_ptr",
+ itmp);
+ if (particle_dt == NULL) {
+ error->all(FLERR,
+ "compute smd/ulsph_effm failed to access particle_dt array");
+ }
+
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+
+ for (int i = 0; i < nlocal; i++) {
+ if (mask[i] & groupbit) {
+ dt_vector[i] = particle_dt[i];
+ } else {
+ dt_vector[i] = 0.0;
+ }
+ }
}
/* ----------------------------------------------------------------------
@@ -110,6 +110,6 @@ void ComputeSMD_Ulsph_Effm::compute_peratom() {
------------------------------------------------------------------------- */
double ComputeSMD_Ulsph_Effm::memory_usage() {
- double bytes = nmax * sizeof(double);
- return bytes;
+ double bytes = nmax * sizeof(double);
+ return bytes;
}
diff --git a/src/USER-SMD/compute_smd_ulsph_strain.cpp b/src/USER-SMD/compute_smd_ulsph_strain.cpp
index 2ecb79e670..c7fcc909f3 100644
--- a/src/USER-SMD/compute_smd_ulsph_strain.cpp
+++ b/src/USER-SMD/compute_smd_ulsph_strain.cpp
@@ -45,69 +45,69 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeSMDULSPHstrain::ComputeSMDULSPHstrain(LAMMPS *lmp, int narg, char **arg) :
- Compute(lmp, narg, arg) {
- if (narg != 3)
- error->all(FLERR, "Illegal compute smd/tlsph_strain command");
+ Compute(lmp, narg, arg) {
+ if (narg != 3)
+ error->all(FLERR, "Illegal compute smd/tlsph_strain command");
- peratom_flag = 1;
- size_peratom_cols = 6;
+ peratom_flag = 1;
+ size_peratom_cols = 6;
- nmax = 0;
- strainVector = NULL;
+ nmax = 0;
+ strainVector = NULL;
}
/* ---------------------------------------------------------------------- */
ComputeSMDULSPHstrain::~ComputeSMDULSPHstrain() {
- memory->sfree(strainVector);
+ memory->sfree(strainVector);
}
/* ---------------------------------------------------------------------- */
void ComputeSMDULSPHstrain::init() {
- int count = 0;
- for (int i = 0; i < modify->ncompute; i++)
- if (strcmp(modify->compute[i]->style, "smd/tlsph_strain") == 0)
- count++;
- if (count > 1 && comm->me == 0)
- error->warning(FLERR, "More than one compute smd/tlsph_strain");
+ int count = 0;
+ for (int i = 0; i < modify->ncompute; i++)
+ if (strcmp(modify->compute[i]->style, "smd/tlsph_strain") == 0)
+ count++;
+ if (count > 1 && comm->me == 0)
+ error->warning(FLERR, "More than one compute smd/tlsph_strain");
}
/* ---------------------------------------------------------------------- */
void ComputeSMDULSPHstrain::compute_peratom() {
- double **atom_data9 = atom->smd_data_9; // ULSPH strain is stored in the first 6 entries of this data field
-
- invoked_peratom = update->ntimestep;
-
- // grow vector array if necessary
-
- if (atom->nmax > nmax) {
- memory->destroy(strainVector);
- nmax = atom->nmax;
- memory->create(strainVector, nmax, size_peratom_cols, "strainVector");
- array_atom = strainVector;
- }
-
- int *mask = atom->mask;
- int nlocal = atom->nlocal;
-
- for (int i = 0; i < nlocal; i++) {
- if (mask[i] & groupbit) {
-
- strainVector[i][0] = atom_data9[i][0];
- strainVector[i][1] = atom_data9[i][1];
- strainVector[i][2] = atom_data9[i][2];
- strainVector[i][3] = atom_data9[i][3];
- strainVector[i][4] = atom_data9[i][4];
- strainVector[i][5] = atom_data9[i][5];
- } else {
- for (int j = 0; j < size_peratom_cols; j++) {
- strainVector[i][j] = 0.0;
- }
- }
- }
+ double **atom_data9 = atom->smd_data_9; // ULSPH strain is stored in the first 6 entries of this data field
+
+ invoked_peratom = update->ntimestep;
+
+ // grow vector array if necessary
+
+ if (atom->nmax > nmax) {
+ memory->destroy(strainVector);
+ nmax = atom->nmax;
+ memory->create(strainVector, nmax, size_peratom_cols, "strainVector");
+ array_atom = strainVector;
+ }
+
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+
+ for (int i = 0; i < nlocal; i++) {
+ if (mask[i] & groupbit) {
+
+ strainVector[i][0] = atom_data9[i][0];
+ strainVector[i][1] = atom_data9[i][1];
+ strainVector[i][2] = atom_data9[i][2];
+ strainVector[i][3] = atom_data9[i][3];
+ strainVector[i][4] = atom_data9[i][4];
+ strainVector[i][5] = atom_data9[i][5];
+ } else {
+ for (int j = 0; j < size_peratom_cols; j++) {
+ strainVector[i][j] = 0.0;
+ }
+ }
+ }
}
/* ----------------------------------------------------------------------
@@ -115,6 +115,6 @@ void ComputeSMDULSPHstrain::compute_peratom() {
------------------------------------------------------------------------- */
double ComputeSMDULSPHstrain::memory_usage() {
- double bytes = size_peratom_cols * nmax * sizeof(double);
- return bytes;
+ double bytes = size_peratom_cols * nmax * sizeof(double);
+ return bytes;
}
diff --git a/src/USER-SMD/compute_smd_ulsph_strain_rate.cpp b/src/USER-SMD/compute_smd_ulsph_strain_rate.cpp
index 4ba4c6c520..0d472a368a 100644
--- a/src/USER-SMD/compute_smd_ulsph_strain_rate.cpp
+++ b/src/USER-SMD/compute_smd_ulsph_strain_rate.cpp
@@ -40,77 +40,77 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeSMDULSPHStrainRate::ComputeSMDULSPHStrainRate(LAMMPS *lmp, int narg, char **arg) :
- Compute(lmp, narg, arg) {
- if (narg != 3)
- error->all(FLERR, "Illegal compute smd/ulsph_strain_rate command");
+ Compute(lmp, narg, arg) {
+ if (narg != 3)
+ error->all(FLERR, "Illegal compute smd/ulsph_strain_rate command");
- peratom_flag = 1;
- size_peratom_cols = 6;
+ peratom_flag = 1;
+ size_peratom_cols = 6;
- nmax = 0;
- strain_rate_array = NULL;
+ nmax = 0;
+ strain_rate_array = NULL;
}
/* ---------------------------------------------------------------------- */
ComputeSMDULSPHStrainRate::~ComputeSMDULSPHStrainRate() {
- memory->sfree(strain_rate_array);
+ memory->sfree(strain_rate_array);
}
/* ---------------------------------------------------------------------- */
void ComputeSMDULSPHStrainRate::init() {
- int count = 0;
- for (int i = 0; i < modify->ncompute; i++)
- if (strcmp(modify->compute[i]->style, "smd/ulsph_strain_rate") == 0)
- count++;
- if (count > 1 && comm->me == 0)
- error->warning(FLERR, "More than one compute smd/ulsph_strain_rate");
+ int count = 0;
+ for (int i = 0; i < modify->ncompute; i++)
+ if (strcmp(modify->compute[i]->style, "smd/ulsph_strain_rate") == 0)
+ count++;
+ if (count > 1 && comm->me == 0)
+ error->warning(FLERR, "More than one compute smd/ulsph_strain_rate");
}
/* ---------------------------------------------------------------------- */
void ComputeSMDULSPHStrainRate::compute_peratom() {
- invoked_peratom = update->ntimestep;
- int *mask = atom->mask;
-
- // grow vector array if necessary
-
- if (atom->nmax > nmax) {
- memory->destroy(strain_rate_array);
- nmax = atom->nmax;
- memory->create(strain_rate_array, nmax, size_peratom_cols, "stresstensorVector");
- array_atom = strain_rate_array;
- }
-
- int itmp = 0;
- Matrix3d *L = (Matrix3d *) force->pair->extract("smd/ulsph/velocityGradient_ptr", itmp);
- if (L == NULL) {
- error->all(FLERR,
- "compute smd/ulsph_strain_rate could not access any velocity gradients. Are the matching pair styles present?");
- }
- int nlocal = atom->nlocal;
- Matrix3d D;
-
- for (int i = 0; i < nlocal; i++) {
- if (mask[i] & groupbit) {
- D = 0.5 * (L[i] + L[i].transpose());
- strain_rate_array[i][0] = D(0, 0); // xx
- strain_rate_array[i][1] = D(1, 1); // yy
- strain_rate_array[i][2] = D(2, 2); // zz
- strain_rate_array[i][3] = D(0, 1); // xy
- strain_rate_array[i][4] = D(0, 2); // xz
- strain_rate_array[i][5] = D(1, 2); // yz
- } else {
- strain_rate_array[i][0] = 0.0;
- strain_rate_array[i][1] = 0.0;
- strain_rate_array[i][2] = 0.0;
- strain_rate_array[i][3] = 0.0;
- strain_rate_array[i][4] = 0.0;
- strain_rate_array[i][5] = 0.0;
- }
- }
+ invoked_peratom = update->ntimestep;
+ int *mask = atom->mask;
+
+ // grow vector array if necessary
+
+ if (atom->nmax > nmax) {
+ memory->destroy(strain_rate_array);
+ nmax = atom->nmax;
+ memory->create(strain_rate_array, nmax, size_peratom_cols, "stresstensorVector");
+ array_atom = strain_rate_array;
+ }
+
+ int itmp = 0;
+ Matrix3d *L = (Matrix3d *) force->pair->extract("smd/ulsph/velocityGradient_ptr", itmp);
+ if (L == NULL) {
+ error->all(FLERR,
+ "compute smd/ulsph_strain_rate could not access any velocity gradients. Are the matching pair styles present?");
+ }
+ int nlocal = atom->nlocal;
+ Matrix3d D;
+
+ for (int i = 0; i < nlocal; i++) {
+ if (mask[i] & groupbit) {
+ D = 0.5 * (L[i] + L[i].transpose());
+ strain_rate_array[i][0] = D(0, 0); // xx
+ strain_rate_array[i][1] = D(1, 1); // yy
+ strain_rate_array[i][2] = D(2, 2); // zz
+ strain_rate_array[i][3] = D(0, 1); // xy
+ strain_rate_array[i][4] = D(0, 2); // xz
+ strain_rate_array[i][5] = D(1, 2); // yz
+ } else {
+ strain_rate_array[i][0] = 0.0;
+ strain_rate_array[i][1] = 0.0;
+ strain_rate_array[i][2] = 0.0;
+ strain_rate_array[i][3] = 0.0;
+ strain_rate_array[i][4] = 0.0;
+ strain_rate_array[i][5] = 0.0;
+ }
+ }
}
/* ----------------------------------------------------------------------
@@ -118,6 +118,6 @@ void ComputeSMDULSPHStrainRate::compute_peratom() {
------------------------------------------------------------------------- */
double ComputeSMDULSPHStrainRate::memory_usage() {
- double bytes = size_peratom_cols * nmax * sizeof(double);
- return bytes;
+ double bytes = size_peratom_cols * nmax * sizeof(double);
+ return bytes;
}
diff --git a/src/USER-SMD/compute_smd_ulsph_stress.cpp b/src/USER-SMD/compute_smd_ulsph_stress.cpp
index e26e0c12f2..7069feced3 100644
--- a/src/USER-SMD/compute_smd_ulsph_stress.cpp
+++ b/src/USER-SMD/compute_smd_ulsph_stress.cpp
@@ -40,87 +40,87 @@ using namespace LAMMPS_NS;
* deviator of a tensor
*/
static Matrix3d Deviator(Matrix3d M) {
- Matrix3d eye;
- eye.setIdentity();
- eye *= M.trace() / 3.0;
- return M - eye;
+ Matrix3d eye;
+ eye.setIdentity();
+ eye *= M.trace() / 3.0;
+ return M - eye;
}
/* ---------------------------------------------------------------------- */
ComputeSMDULSPHStress::ComputeSMDULSPHStress(LAMMPS *lmp, int narg, char **arg) :
- Compute(lmp, narg, arg) {
- if (narg != 3)
- error->all(FLERR, "Illegal compute smd/ulsph_stress command");
+ Compute(lmp, narg, arg) {
+ if (narg != 3)
+ error->all(FLERR, "Illegal compute smd/ulsph_stress command");
- peratom_flag = 1;
- size_peratom_cols = 7;
+ peratom_flag = 1;
+ size_peratom_cols = 7;
- nmax = 0;
- stress_array = NULL;
+ nmax = 0;
+ stress_array = NULL;
}
/* ---------------------------------------------------------------------- */
ComputeSMDULSPHStress::~ComputeSMDULSPHStress() {
- memory->sfree(stress_array);
+ memory->sfree(stress_array);
}
/* ---------------------------------------------------------------------- */
void ComputeSMDULSPHStress::init() {
- int count = 0;
- for (int i = 0; i < modify->ncompute; i++)
- if (strcmp(modify->compute[i]->style, "smd/ulsph_stress") == 0)
- count++;
- if (count > 1 && comm->me == 0)
- error->warning(FLERR, "More than one compute smd/ulsph_stress");
+ int count = 0;
+ for (int i = 0; i < modify->ncompute; i++)
+ if (strcmp(modify->compute[i]->style, "smd/ulsph_stress") == 0)
+ count++;
+ if (count > 1 && comm->me == 0)
+ error->warning(FLERR, "More than one compute smd/ulsph_stress");
}
/* ---------------------------------------------------------------------- */
void ComputeSMDULSPHStress::compute_peratom() {
- invoked_peratom = update->ntimestep;
- int *mask = atom->mask;
- Matrix3d stress_deviator;
- double von_mises_stress;
-
- // grow vector array if necessary
-
- if (atom->nmax > nmax) {
- memory->destroy(stress_array);
- nmax = atom->nmax;
- memory->create(stress_array, nmax, size_peratom_cols, "stresstensorVector");
- array_atom = stress_array;
- }
-
- int itmp = 0;
- Matrix3d *T = (Matrix3d *) force->pair->extract("smd/ulsph/stressTensor_ptr", itmp);
- if (T == NULL) {
- error->all(FLERR, "compute smd/ulsph_stress could not access stress tensors. Are the matching pair styles present?");
- }
- int nlocal = atom->nlocal;
-
- for (int i = 0; i < nlocal; i++) {
-
- if (mask[i] & groupbit) {
- stress_deviator = Deviator(T[i]);
- von_mises_stress = sqrt(3. / 2.) * stress_deviator.norm();
- stress_array[i][0] = T[i](0, 0); // xx
- stress_array[i][1] = T[i](1, 1); // yy
- stress_array[i][2] = T[i](2, 2); // zz
- stress_array[i][3] = T[i](0, 1); // xy
- stress_array[i][4] = T[i](0, 2); // xz
- stress_array[i][5] = T[i](1, 2); // yz
- stress_array[i][6] = von_mises_stress;
-
- } else {
- for (int j = 0; j < size_peratom_cols; j++) {
- stress_array[i][j] = 0.0;
- }
- }
- }
+ invoked_peratom = update->ntimestep;
+ int *mask = atom->mask;
+ Matrix3d stress_deviator;
+ double von_mises_stress;
+
+ // grow vector array if necessary
+
+ if (atom->nmax > nmax) {
+ memory->destroy(stress_array);
+ nmax = atom->nmax;
+ memory->create(stress_array, nmax, size_peratom_cols, "stresstensorVector");
+ array_atom = stress_array;
+ }
+
+ int itmp = 0;
+ Matrix3d *T = (Matrix3d *) force->pair->extract("smd/ulsph/stressTensor_ptr", itmp);
+ if (T == NULL) {
+ error->all(FLERR, "compute smd/ulsph_stress could not access stress tensors. Are the matching pair styles present?");
+ }
+ int nlocal = atom->nlocal;
+
+ for (int i = 0; i < nlocal; i++) {
+
+ if (mask[i] & groupbit) {
+ stress_deviator = Deviator(T[i]);
+ von_mises_stress = sqrt(3. / 2.) * stress_deviator.norm();
+ stress_array[i][0] = T[i](0, 0); // xx
+ stress_array[i][1] = T[i](1, 1); // yy
+ stress_array[i][2] = T[i](2, 2); // zz
+ stress_array[i][3] = T[i](0, 1); // xy
+ stress_array[i][4] = T[i](0, 2); // xz
+ stress_array[i][5] = T[i](1, 2); // yz
+ stress_array[i][6] = von_mises_stress;
+
+ } else {
+ for (int j = 0; j < size_peratom_cols; j++) {
+ stress_array[i][j] = 0.0;
+ }
+ }
+ }
}
/* ----------------------------------------------------------------------
@@ -128,7 +128,7 @@ void ComputeSMDULSPHStress::compute_peratom() {
------------------------------------------------------------------------- */
double ComputeSMDULSPHStress::memory_usage() {
- double bytes = size_peratom_cols * nmax * sizeof(double);
- return bytes;
+ double bytes = size_peratom_cols * nmax * sizeof(double);
+ return bytes;
}
diff --git a/src/USER-SMD/compute_smd_vol.cpp b/src/USER-SMD/compute_smd_vol.cpp
index a12164d9e2..3573ee6a6c 100644
--- a/src/USER-SMD/compute_smd_vol.cpp
+++ b/src/USER-SMD/compute_smd_vol.cpp
@@ -37,86 +37,86 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeSMDVol::ComputeSMDVol(LAMMPS *lmp, int narg, char **arg) :
- Compute(lmp, narg, arg) {
- if (narg != 3)
- error->all(FLERR, "Illegal compute smd/volume command");
- if (atom->vfrac_flag != 1)
- error->all(FLERR, "compute smd/volume command requires atom_style with density (e.g. smd)");
-
- scalar_flag = 1;
- peratom_flag = 1;
- size_peratom_cols = 0;
-
- nmax = 0;
- volVector = NULL;
+ Compute(lmp, narg, arg) {
+ if (narg != 3)
+ error->all(FLERR, "Illegal compute smd/volume command");
+ if (atom->vfrac_flag != 1)
+ error->all(FLERR, "compute smd/volume command requires atom_style with density (e.g. smd)");
+
+ scalar_flag = 1;
+ peratom_flag = 1;
+ size_peratom_cols = 0;
+
+ nmax = 0;
+ volVector = NULL;
}
/* ---------------------------------------------------------------------- */
ComputeSMDVol::~ComputeSMDVol() {
- memory->sfree(volVector);
+ memory->sfree(volVector);
}
/* ---------------------------------------------------------------------- */
void ComputeSMDVol::init() {
- int count = 0;
- for (int i = 0; i < modify->ncompute; i++)
- if (strcmp(modify->compute[i]->style, "smd/volume") == 0)
- count++;
- if (count > 1 && comm->me == 0)
- error->warning(FLERR, "More than one compute smd/volume");
+ int count = 0;
+ for (int i = 0; i < modify->ncompute; i++)
+ if (strcmp(modify->compute[i]->style, "smd/volume") == 0)
+ count++;
+ if (count > 1 && comm->me == 0)
+ error->warning(FLERR, "More than one compute smd/volume");
}
/* ---------------------------------------------------------------------- */
void ComputeSMDVol::compute_peratom() {
- invoked_peratom = update->ntimestep;
-
- // grow volVector array if necessary
-
- if (atom->nmax > nmax) {
- memory->sfree(volVector);
- nmax = atom->nmax;
- volVector = (double *) memory->smalloc(nmax * sizeof(double), "atom:volVector");
- vector_atom = volVector;
- }
-
- double *vfrac = atom->vfrac;
- int *mask = atom->mask;
- int nlocal = atom->nlocal;
-
- for (int i = 0; i < nlocal; i++) {
- if (mask[i] & groupbit) {
- volVector[i] = vfrac[i];
- } else {
- volVector[i] = 0.0;
- }
- }
+ invoked_peratom = update->ntimestep;
+
+ // grow volVector array if necessary
+
+ if (atom->nmax > nmax) {
+ memory->sfree(volVector);
+ nmax = atom->nmax;
+ volVector = (double *) memory->smalloc(nmax * sizeof(double), "atom:volVector");
+ vector_atom = volVector;
+ }
+
+ double *vfrac = atom->vfrac;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+
+ for (int i = 0; i < nlocal; i++) {
+ if (mask[i] & groupbit) {
+ volVector[i] = vfrac[i];
+ } else {
+ volVector[i] = 0.0;
+ }
+ }
}
/* ---------------------------------------------------------------------- */
double ComputeSMDVol::compute_scalar() {
- invoked_scalar = update->ntimestep;
- double *vfrac = atom->vfrac;
- int *mask = atom->mask;
- int nlocal = atom->nlocal;
+ invoked_scalar = update->ntimestep;
+ double *vfrac = atom->vfrac;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
- double this_proc_sum_volumes = 0.0;
- for (int i = 0; i < nlocal; i++) {
- if (mask[i] & groupbit) {
- this_proc_sum_volumes += vfrac[i];
- }
- }
+ double this_proc_sum_volumes = 0.0;
+ for (int i = 0; i < nlocal; i++) {
+ if (mask[i] & groupbit) {
+ this_proc_sum_volumes += vfrac[i];
+ }
+ }
- //printf("this_proc_sum_volumes = %g\n", this_proc_sum_volumes);
- MPI_Allreduce(&this_proc_sum_volumes, &scalar, 1, MPI_DOUBLE, MPI_SUM, world);
- //if (comm->me == 0) printf("global sum_volumes = %g\n", scalar);
+ //printf("this_proc_sum_volumes = %g\n", this_proc_sum_volumes);
+ MPI_Allreduce(&this_proc_sum_volumes, &scalar, 1, MPI_DOUBLE, MPI_SUM, world);
+ //if (comm->me == 0) printf("global sum_volumes = %g\n", scalar);
- return scalar;
+ return scalar;
}
@@ -125,6 +125,6 @@ double ComputeSMDVol::compute_scalar() {
------------------------------------------------------------------------- */
double ComputeSMDVol::memory_usage() {
- double bytes = nmax * sizeof(double);
- return bytes;
+ double bytes = nmax * sizeof(double);
+ return bytes;
}
diff --git a/src/USER-SMD/fix_smd_adjust_dt.cpp b/src/USER-SMD/fix_smd_adjust_dt.cpp
index 4920160a30..d2570b6bdc 100644
--- a/src/USER-SMD/fix_smd_adjust_dt.cpp
+++ b/src/USER-SMD/fix_smd_adjust_dt.cpp
@@ -48,161 +48,161 @@ using namespace FixConst;
/* ---------------------------------------------------------------------- */
FixSMDTlsphDtReset::FixSMDTlsphDtReset(LAMMPS *lmp, int narg, char **arg) :
- Fix(lmp, narg, arg) {
- if (narg != 4)
- error->all(FLERR, "Illegal fix smd/adjust_dt command");
+ Fix(lmp, narg, arg) {
+ if (narg != 4)
+ error->all(FLERR, "Illegal fix smd/adjust_dt command");
- // set time_depend, else elapsed time accumulation can be messed up
+ // set time_depend, else elapsed time accumulation can be messed up
- time_depend = 1;
- scalar_flag = 1;
- vector_flag = 1;
- size_vector = 2;
- global_freq = 1;
- extscalar = 0;
- extvector = 0;
- restart_global = 1; // this fix stores global (i.e., not per-atom) info: elaspsed time
+ time_depend = 1;
+ scalar_flag = 1;
+ vector_flag = 1;
+ size_vector = 2;
+ global_freq = 1;
+ extscalar = 0;
+ extvector = 0;
+ restart_global = 1; // this fix stores global (i.e., not per-atom) info: elaspsed time
- safety_factor = atof(arg[3]);
+ safety_factor = atof(arg[3]);
- // initializations
- t_elapsed = 0.0;
+ // initializations
+ t_elapsed = 0.0;
}
/* ---------------------------------------------------------------------- */
int FixSMDTlsphDtReset::setmask() {
- int mask = 0;
- mask |= INITIAL_INTEGRATE;
- mask |= END_OF_STEP;
- return mask;
+ int mask = 0;
+ mask |= INITIAL_INTEGRATE;
+ mask |= END_OF_STEP;
+ return mask;
}
/* ---------------------------------------------------------------------- */
void FixSMDTlsphDtReset::init() {
- dt = update->dt;
+ dt = update->dt;
}
/* ---------------------------------------------------------------------- */
void FixSMDTlsphDtReset::setup(int vflag) {
- end_of_step();
+ end_of_step();
}
/* ---------------------------------------------------------------------- */
void FixSMDTlsphDtReset::initial_integrate(int vflag) {
- //printf("in adjust_dt: dt = %20.10f\n", update->dt);
+ //printf("in adjust_dt: dt = %20.10f\n", update->dt);
- t_elapsed += update->dt;
+ t_elapsed += update->dt;
}
/* ---------------------------------------------------------------------- */
void FixSMDTlsphDtReset::end_of_step() {
- double dtmin = BIG;
- int itmp = 0;
-
- /*
- * extract minimum CFL timestep from TLSPH and ULSPH pair styles
- */
-
- double *dtCFL_TLSPH = (double *) force->pair->extract("smd/tlsph/dtCFL_ptr", itmp);
- double *dtCFL_ULSPH = (double *) force->pair->extract("smd/ulsph/dtCFL_ptr", itmp);
- double *dt_TRI = (double *) force->pair->extract("smd/tri_surface/stable_time_increment_ptr", itmp);
- double *dt_HERTZ = (double *) force->pair->extract("smd/hertz/stable_time_increment_ptr", itmp);
- double *dt_PERI_IPMB = (double *) force->pair->extract("smd/peri_ipmb/stable_time_increment_ptr", itmp);
-
- if ((dtCFL_TLSPH == NULL) && (dtCFL_ULSPH == NULL) && (dt_TRI == NULL) && (dt_HERTZ == NULL)
- && (dt_PERI_IPMB == NULL)) {
- error->all(FLERR, "fix smd/adjust_dt failed to access a valid dtCFL");
- }
-
- if (dtCFL_TLSPH != NULL) {
- dtmin = MIN(dtmin, *dtCFL_TLSPH);
- }
-
- if (dtCFL_ULSPH != NULL) {
- dtmin = MIN(dtmin, *dtCFL_ULSPH);
- }
-
- if (dt_TRI != NULL) {
- dtmin = MIN(dtmin, *dt_TRI);
- }
-
- if (dt_HERTZ != NULL) {
- dtmin = MIN(dtmin, *dt_HERTZ);
- }
-
- if (dt_PERI_IPMB != NULL) {
- dtmin = MIN(dtmin, *dt_PERI_IPMB);
- }
-
-// double **v = atom->v;
-// double **f = atom->f;
-// double *rmass = atom->rmass;
-// double *radius = atom->radius;
-// int *mask = atom->mask;
-// int nlocal = atom->nlocal;
-// double dtv, dtf, dtsq;
-// double vsq, fsq, massinv, xmax;
-// double delx, dely, delz, delr;
-
-// for (int i = 0; i < nlocal; i++) {
-// if (mask[i] & groupbit) {
-// xmax = 0.005 * radius[i];
-// massinv = 1.0 / rmass[i];
-// vsq = v[i][0] * v[i][0] + v[i][1] * v[i][1] + v[i][2] * v[i][2];
-// fsq = f[i][0] * f[i][0] + f[i][1] * f[i][1] + f[i][2] * f[i][2];
-// dtv = dtf = BIG;
-// if (vsq > 0.0)
-// dtv = xmax / sqrt(vsq);
-// if (fsq > 0.0)
-// dtf = sqrt(2.0 * xmax / (sqrt(fsq) * massinv));
-// dt = MIN(dtv, dtf);
-// dtmin = MIN(dtmin, dt);
-// dtsq = dt * dt;
-// delx = dt * v[i][0] + 0.5 * dtsq * massinv * f[i][0];
-// dely = dt * v[i][1] + 0.5 * dtsq * massinv * f[i][1];
-// delz = dt * v[i][2] + 0.5 * dtsq * massinv * f[i][2];
-// delr = sqrt(delx * delx + dely * dely + delz * delz);
-// if (delr > xmax)
-// dt *= xmax / delr;
-// dtmin = MIN(dtmin, dt);
+ double dtmin = BIG;
+ int itmp = 0;
+
+ /*
+ * extract minimum CFL timestep from TLSPH and ULSPH pair styles
+ */
+
+ double *dtCFL_TLSPH = (double *) force->pair->extract("smd/tlsph/dtCFL_ptr", itmp);
+ double *dtCFL_ULSPH = (double *) force->pair->extract("smd/ulsph/dtCFL_ptr", itmp);
+ double *dt_TRI = (double *) force->pair->extract("smd/tri_surface/stable_time_increment_ptr", itmp);
+ double *dt_HERTZ = (double *) force->pair->extract("smd/hertz/stable_time_increment_ptr", itmp);
+ double *dt_PERI_IPMB = (double *) force->pair->extract("smd/peri_ipmb/stable_time_increment_ptr", itmp);
+
+ if ((dtCFL_TLSPH == NULL) && (dtCFL_ULSPH == NULL) && (dt_TRI == NULL) && (dt_HERTZ == NULL)
+ && (dt_PERI_IPMB == NULL)) {
+ error->all(FLERR, "fix smd/adjust_dt failed to access a valid dtCFL");
+ }
+
+ if (dtCFL_TLSPH != NULL) {
+ dtmin = MIN(dtmin, *dtCFL_TLSPH);
+ }
+
+ if (dtCFL_ULSPH != NULL) {
+ dtmin = MIN(dtmin, *dtCFL_ULSPH);
+ }
+
+ if (dt_TRI != NULL) {
+ dtmin = MIN(dtmin, *dt_TRI);
+ }
+
+ if (dt_HERTZ != NULL) {
+ dtmin = MIN(dtmin, *dt_HERTZ);
+ }
+
+ if (dt_PERI_IPMB != NULL) {
+ dtmin = MIN(dtmin, *dt_PERI_IPMB);
+ }
+
+// double **v = atom->v;
+// double **f = atom->f;
+// double *rmass = atom->rmass;
+// double *radius = atom->radius;
+// int *mask = atom->mask;
+// int nlocal = atom->nlocal;
+// double dtv, dtf, dtsq;
+// double vsq, fsq, massinv, xmax;
+// double delx, dely, delz, delr;
+
+// for (int i = 0; i < nlocal; i++) {
+// if (mask[i] & groupbit) {
+// xmax = 0.005 * radius[i];
+// massinv = 1.0 / rmass[i];
+// vsq = v[i][0] * v[i][0] + v[i][1] * v[i][1] + v[i][2] * v[i][2];
+// fsq = f[i][0] * f[i][0] + f[i][1] * f[i][1] + f[i][2] * f[i][2];
+// dtv = dtf = BIG;
+// if (vsq > 0.0)
+// dtv = xmax / sqrt(vsq);
+// if (fsq > 0.0)
+// dtf = sqrt(2.0 * xmax / (sqrt(fsq) * massinv));
+// dt = MIN(dtv, dtf);
+// dtmin = MIN(dtmin, dt);
+// dtsq = dt * dt;
+// delx = dt * v[i][0] + 0.5 * dtsq * massinv * f[i][0];
+// dely = dt * v[i][1] + 0.5 * dtsq * massinv * f[i][1];
+// delz = dt * v[i][2] + 0.5 * dtsq * massinv * f[i][2];
+// delr = sqrt(delx * delx + dely * dely + delz * delz);
+// if (delr > xmax)
+// dt *= xmax / delr;
+// dtmin = MIN(dtmin, dt);
//
-//// xmax = 0.05 * radius[i];
-//// massinv = 1.0 / rmass[i];
-//// fsq = f[i][0] * f[i][0] + f[i][1] * f[i][1] + f[i][2] * f[i][2];
-//// dtf = BIG;
-//// if (fsq > 0.0)
-//// dtf = sqrt(2.0 * xmax / (sqrt(fsq) * massinv));
-//// dtmin = MIN(dtmin, dtf);
-// }
-// }
-
- dtmin *= safety_factor; // apply safety factor
- MPI_Allreduce(&dtmin, &dt, 1, MPI_DOUBLE, MPI_MIN, world);
-
- if (update->ntimestep == 0) {
- dt = 1.0e-16;
- }
-
- //printf("dtmin is now: %f, dt is now%f\n", dtmin, dt);
-
-
- update->dt = dt;
- if (force->pair)
- force->pair->reset_dt();
- for (int i = 0; i < modify->nfix; i++)
- modify->fix[i]->reset_dt();
+//// xmax = 0.05 * radius[i];
+//// massinv = 1.0 / rmass[i];
+//// fsq = f[i][0] * f[i][0] + f[i][1] * f[i][1] + f[i][2] * f[i][2];
+//// dtf = BIG;
+//// if (fsq > 0.0)
+//// dtf = sqrt(2.0 * xmax / (sqrt(fsq) * massinv));
+//// dtmin = MIN(dtmin, dtf);
+// }
+// }
+
+ dtmin *= safety_factor; // apply safety factor
+ MPI_Allreduce(&dtmin, &dt, 1, MPI_DOUBLE, MPI_MIN, world);
+
+ if (update->ntimestep == 0) {
+ dt = 1.0e-16;
+ }
+
+ //printf("dtmin is now: %f, dt is now%f\n", dtmin, dt);
+
+
+ update->dt = dt;
+ if (force->pair)
+ force->pair->reset_dt();
+ for (int i = 0; i < modify->nfix; i++)
+ modify->fix[i]->reset_dt();
}
/* ---------------------------------------------------------------------- */
double FixSMDTlsphDtReset::compute_scalar() {
- return t_elapsed;
+ return t_elapsed;
}
/* ----------------------------------------------------------------------
@@ -210,15 +210,15 @@ double FixSMDTlsphDtReset::compute_scalar() {
------------------------------------------------------------------------- */
void FixSMDTlsphDtReset::write_restart(FILE *fp) {
- int n = 0;
- double list[1];
- list[n++] = t_elapsed;
-
- if (comm->me == 0) {
- int size = n * sizeof(double);
- fwrite(&size, sizeof(int), 1, fp);
- fwrite(list, sizeof(double), n, fp);
- }
+ int n = 0;
+ double list[1];
+ list[n++] = t_elapsed;
+
+ if (comm->me == 0) {
+ int size = n * sizeof(double);
+ fwrite(&size, sizeof(int), 1, fp);
+ fwrite(list, sizeof(double), n, fp);
+ }
}
/* ----------------------------------------------------------------------
@@ -226,8 +226,8 @@ void FixSMDTlsphDtReset::write_restart(FILE *fp) {
------------------------------------------------------------------------- */
void FixSMDTlsphDtReset::restart(char *buf) {
- int n = 0;
- double *list = (double *) buf;
- t_elapsed = list[n++];
+ int n = 0;
+ double *list = (double *) buf;
+ t_elapsed = list[n++];
}
diff --git a/src/USER-SMD/fix_smd_adjust_dt.h b/src/USER-SMD/fix_smd_adjust_dt.h
index d7d8c922f2..b89c136082 100644
--- a/src/USER-SMD/fix_smd_adjust_dt.h
+++ b/src/USER-SMD/fix_smd_adjust_dt.h
@@ -37,21 +37,21 @@ namespace LAMMPS_NS {
class FixSMDTlsphDtReset: public Fix {
public:
- FixSMDTlsphDtReset(class LAMMPS *, int, char **);
- ~FixSMDTlsphDtReset() {
- }
- int setmask();
- void init();
- void setup(int);
- void initial_integrate(int);
- void end_of_step();
- double compute_scalar();
- void write_restart(FILE *);
- void restart(char *);
+ FixSMDTlsphDtReset(class LAMMPS *, int, char **);
+ ~FixSMDTlsphDtReset() {
+ }
+ int setmask();
+ void init();
+ void setup(int);
+ void initial_integrate(int);
+ void end_of_step();
+ double compute_scalar();
+ void write_restart(FILE *);
+ void restart(char *);
private:
- double safety_factor;
- double dt, t_elapsed;
+ double safety_factor;
+ double dt, t_elapsed;
};
}
diff --git a/src/USER-SMD/fix_smd_integrate_tlsph.cpp b/src/USER-SMD/fix_smd_integrate_tlsph.cpp
index b364c4813d..2744211d87 100644
--- a/src/USER-SMD/fix_smd_integrate_tlsph.cpp
+++ b/src/USER-SMD/fix_smd_integrate_tlsph.cpp
@@ -48,207 +48,207 @@ using namespace std;
/* ---------------------------------------------------------------------- */
FixSMDIntegrateTlsph::FixSMDIntegrateTlsph(LAMMPS *lmp, int narg, char **arg) :
- Fix(lmp, narg, arg) {
- if (narg < 3) {
- printf("narg=%d\n", narg);
- error->all(FLERR, "Illegal fix smd/integrate_tlsph command");
- }
-
- xsphFlag = false;
- vlimit = -1.0;
- int iarg = 3;
-
- if (comm->me == 0) {
- printf("\n>>========>>========>>========>>========>>========>>========>>========>>========\n");
- printf("fix smd/integrate_tlsph is active for group: %s \n", arg[1]);
- }
-
- while (true) {
-
- if (iarg >= narg) {
- break;
- }
-
- if (strcmp(arg[iarg], "xsph") == 0) {
- xsphFlag = true;
- if (comm->me == 0) {
- error->one(FLERR, "XSPH is currently not available");
- printf("... will use XSPH time integration\n");
- }
- } else if (strcmp(arg[iarg], "limit_velocity") == 0) {
- iarg++;
- if (iarg == narg) {
- error->all(FLERR, "expected number following limit_velocity");
- }
-
- vlimit = force->numeric(FLERR, arg[iarg]);
- if (comm->me == 0) {
- printf("... will limit velocities to <= %g\n", vlimit);
- }
- } else {
- char msg[128];
- sprintf(msg, "Illegal keyword for smd/integrate_tlsph: %s\n", arg[iarg]);
- error->all(FLERR, msg);
- }
-
- iarg++;
- }
-
- if (comm->me == 0) {
- printf(">>========>>========>>========>>========>>========>>========>>========>>========\n");
- }
-
- time_integrate = 1;
-
- // set comm sizes needed by this fix
-
- atom->add_callback(0);
+ Fix(lmp, narg, arg) {
+ if (narg < 3) {
+ printf("narg=%d\n", narg);
+ error->all(FLERR, "Illegal fix smd/integrate_tlsph command");
+ }
+
+ xsphFlag = false;
+ vlimit = -1.0;
+ int iarg = 3;
+
+ if (comm->me == 0) {
+ printf("\n>>========>>========>>========>>========>>========>>========>>========>>========\n");
+ printf("fix smd/integrate_tlsph is active for group: %s \n", arg[1]);
+ }
+
+ while (true) {
+
+ if (iarg >= narg) {
+ break;
+ }
+
+ if (strcmp(arg[iarg], "xsph") == 0) {
+ xsphFlag = true;
+ if (comm->me == 0) {
+ error->one(FLERR, "XSPH is currently not available");
+ printf("... will use XSPH time integration\n");
+ }
+ } else if (strcmp(arg[iarg], "limit_velocity") == 0) {
+ iarg++;
+ if (iarg == narg) {
+ error->all(FLERR, "expected number following limit_velocity");
+ }
+
+ vlimit = force->numeric(FLERR, arg[iarg]);
+ if (comm->me == 0) {
+ printf("... will limit velocities to <= %g\n", vlimit);
+ }
+ } else {
+ char msg[128];
+ sprintf(msg, "Illegal keyword for smd/integrate_tlsph: %s\n", arg[iarg]);
+ error->all(FLERR, msg);
+ }
+
+ iarg++;
+ }
+
+ if (comm->me == 0) {
+ printf(">>========>>========>>========>>========>>========>>========>>========>>========\n");
+ }
+
+ time_integrate = 1;
+
+ // set comm sizes needed by this fix
+
+ atom->add_callback(0);
}
/* ---------------------------------------------------------------------- */
int FixSMDIntegrateTlsph::setmask() {
- int mask = 0;
- mask |= INITIAL_INTEGRATE;
- mask |= FINAL_INTEGRATE;
- return mask;
+ int mask = 0;
+ mask |= INITIAL_INTEGRATE;
+ mask |= FINAL_INTEGRATE;
+ return mask;
}
/* ---------------------------------------------------------------------- */
void FixSMDIntegrateTlsph::init() {
- dtv = update->dt;
- dtf = 0.5 * update->dt * force->ftm2v;
- vlimitsq = vlimit * vlimit;
+ dtv = update->dt;
+ dtf = 0.5 * update->dt * force->ftm2v;
+ vlimitsq = vlimit * vlimit;
}
/* ----------------------------------------------------------------------
------------------------------------------------------------------------- */
void FixSMDIntegrateTlsph::initial_integrate(int vflag) {
- double dtfm, vsq, scale;
-
- // update v and x of atoms in group
-
- double **x = atom->x;
- double **v = atom->v;
- double **vest = atom->vest;
- double **f = atom->f;
- double *rmass = atom->rmass;
- int *mask = atom->mask;
- int nlocal = atom->nlocal;
- int itmp;
- double vxsph_x, vxsph_y, vxsph_z;
- if (igroup == atom->firstgroup)
- nlocal = atom->nfirst;
-
- Vector3d *smoothVelDifference = (Vector3d *) force->pair->extract("smd/tlsph/smoothVel_ptr", itmp);
-
- if (xsphFlag) {
- if (smoothVelDifference == NULL) {
- error->one(FLERR,
- "fix smd/integrate_tlsph failed to access smoothVel array. Check if a pair style exist which calculates this quantity.");
- }
- }
-
- for (int i = 0; i < nlocal; i++) {
- if (mask[i] & groupbit) {
- dtfm = dtf / rmass[i];
-
- // 1st part of Velocity_Verlet: push velocties 1/2 time increment ahead
- v[i][0] += dtfm * f[i][0];
- v[i][1] += dtfm * f[i][1];
- v[i][2] += dtfm * f[i][2];
-
- if (vlimit > 0.0) {
- vsq = v[i][0] * v[i][0] + v[i][1] * v[i][1] + v[i][2] * v[i][2];
- if (vsq > vlimitsq) {
- scale = sqrt(vlimitsq / vsq);
- v[i][0] *= scale;
- v[i][1] *= scale;
- v[i][2] *= scale;
- }
- }
-
- if (xsphFlag) {
-
- // construct XSPH velocity
- vxsph_x = v[i][0] + 0.5 * smoothVelDifference[i](0);
- vxsph_y = v[i][1] + 0.5 * smoothVelDifference[i](1);
- vxsph_z = v[i][2] + 0.5 * smoothVelDifference[i](2);
-
- vest[i][0] = vxsph_x + dtfm * f[i][0];
- vest[i][1] = vxsph_y + dtfm * f[i][1];
- vest[i][2] = vxsph_z + dtfm * f[i][2];
-
- x[i][0] += dtv * vxsph_x;
- x[i][1] += dtv * vxsph_y;
- x[i][2] += dtv * vxsph_z;
- } else {
-
- // extrapolate velocity from half- to full-step
- vest[i][0] = v[i][0] + dtfm * f[i][0];
- vest[i][1] = v[i][1] + dtfm * f[i][1];
- vest[i][2] = v[i][2] + dtfm * f[i][2];
-
- x[i][0] += dtv * v[i][0]; // 2nd part of Velocity-Verlet: push positions one full time increment ahead
- x[i][1] += dtv * v[i][1];
- x[i][2] += dtv * v[i][2];
- }
- }
- }
+ double dtfm, vsq, scale;
+
+ // update v and x of atoms in group
+
+ double **x = atom->x;
+ double **v = atom->v;
+ double **vest = atom->vest;
+ double **f = atom->f;
+ double *rmass = atom->rmass;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+ int itmp;
+ double vxsph_x, vxsph_y, vxsph_z;
+ if (igroup == atom->firstgroup)
+ nlocal = atom->nfirst;
+
+ Vector3d *smoothVelDifference = (Vector3d *) force->pair->extract("smd/tlsph/smoothVel_ptr", itmp);
+
+ if (xsphFlag) {
+ if (smoothVelDifference == NULL) {
+ error->one(FLERR,
+ "fix smd/integrate_tlsph failed to access smoothVel array. Check if a pair style exist which calculates this quantity.");
+ }
+ }
+
+ for (int i = 0; i < nlocal; i++) {
+ if (mask[i] & groupbit) {
+ dtfm = dtf / rmass[i];
+
+ // 1st part of Velocity_Verlet: push velocties 1/2 time increment ahead
+ v[i][0] += dtfm * f[i][0];
+ v[i][1] += dtfm * f[i][1];
+ v[i][2] += dtfm * f[i][2];
+
+ if (vlimit > 0.0) {
+ vsq = v[i][0] * v[i][0] + v[i][1] * v[i][1] + v[i][2] * v[i][2];
+ if (vsq > vlimitsq) {
+ scale = sqrt(vlimitsq / vsq);
+ v[i][0] *= scale;
+ v[i][1] *= scale;
+ v[i][2] *= scale;
+ }
+ }
+
+ if (xsphFlag) {
+
+ // construct XSPH velocity
+ vxsph_x = v[i][0] + 0.5 * smoothVelDifference[i](0);
+ vxsph_y = v[i][1] + 0.5 * smoothVelDifference[i](1);
+ vxsph_z = v[i][2] + 0.5 * smoothVelDifference[i](2);
+
+ vest[i][0] = vxsph_x + dtfm * f[i][0];
+ vest[i][1] = vxsph_y + dtfm * f[i][1];
+ vest[i][2] = vxsph_z + dtfm * f[i][2];
+
+ x[i][0] += dtv * vxsph_x;
+ x[i][1] += dtv * vxsph_y;
+ x[i][2] += dtv * vxsph_z;
+ } else {
+
+ // extrapolate velocity from half- to full-step
+ vest[i][0] = v[i][0] + dtfm * f[i][0];
+ vest[i][1] = v[i][1] + dtfm * f[i][1];
+ vest[i][2] = v[i][2] + dtfm * f[i][2];
+
+ x[i][0] += dtv * v[i][0]; // 2nd part of Velocity-Verlet: push positions one full time increment ahead
+ x[i][1] += dtv * v[i][1];
+ x[i][2] += dtv * v[i][2];
+ }
+ }
+ }
}
/* ---------------------------------------------------------------------- */
void FixSMDIntegrateTlsph::final_integrate() {
- double dtfm, vsq, scale;
+ double dtfm, vsq, scale;
// update v of atoms in group
- double **v = atom->v;
- double **f = atom->f;
- double *e = atom->e;
- double *de = atom->de;
- double *rmass = atom->rmass;
- int *mask = atom->mask;
- int nlocal = atom->nlocal;
- if (igroup == atom->firstgroup)
- nlocal = atom->nfirst;
- int i;
-
- for (i = 0; i < nlocal; i++) {
- if (mask[i] & groupbit) {
- dtfm = dtf / rmass[i];
-
- v[i][0] += dtfm * f[i][0]; // 3rd part of Velocity-Verlet: push velocities another half time increment ahead
- v[i][1] += dtfm * f[i][1]; // both positions and velocities are now defined at full time-steps.
- v[i][2] += dtfm * f[i][2];
-
- // limit velocity
- if (vlimit > 0.0) {
- vsq = v[i][0] * v[i][0] + v[i][1] * v[i][1] + v[i][2] * v[i][2];
- if (vsq > vlimitsq) {
- scale = sqrt(vlimitsq / vsq);
- v[i][0] *= scale;
- v[i][1] *= scale;
- v[i][2] *= scale;
- }
- }
-
- e[i] += dtv * de[i];
- }
- }
+ double **v = atom->v;
+ double **f = atom->f;
+ double *e = atom->e;
+ double *de = atom->de;
+ double *rmass = atom->rmass;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+ if (igroup == atom->firstgroup)
+ nlocal = atom->nfirst;
+ int i;
+
+ for (i = 0; i < nlocal; i++) {
+ if (mask[i] & groupbit) {
+ dtfm = dtf / rmass[i];
+
+ v[i][0] += dtfm * f[i][0]; // 3rd part of Velocity-Verlet: push velocities another half time increment ahead
+ v[i][1] += dtfm * f[i][1]; // both positions and velocities are now defined at full time-steps.
+ v[i][2] += dtfm * f[i][2];
+
+ // limit velocity
+ if (vlimit > 0.0) {
+ vsq = v[i][0] * v[i][0] + v[i][1] * v[i][1] + v[i][2] * v[i][2];
+ if (vsq > vlimitsq) {
+ scale = sqrt(vlimitsq / vsq);
+ v[i][0] *= scale;
+ v[i][1] *= scale;
+ v[i][2] *= scale;
+ }
+ }
+
+ e[i] += dtv * de[i];
+ }
+ }
}
/* ---------------------------------------------------------------------- */
void FixSMDIntegrateTlsph::reset_dt() {
- dtv = update->dt;
- dtf = 0.5 * update->dt * force->ftm2v;
- vlimitsq = vlimit * vlimit;
+ dtv = update->dt;
+ dtf = 0.5 * update->dt * force->ftm2v;
+ vlimitsq = vlimit * vlimit;
}
/* ---------------------------------------------------------------------- */
diff --git a/src/USER-SMD/fix_smd_integrate_tlsph.h b/src/USER-SMD/fix_smd_integrate_tlsph.h
index ca047f2dfd..6c152e6fe3 100644
--- a/src/USER-SMD/fix_smd_integrate_tlsph.h
+++ b/src/USER-SMD/fix_smd_integrate_tlsph.h
@@ -37,8 +37,8 @@ FixStyle(smd/integrate_tlsph,FixSMDIntegrateTlsph)
namespace LAMMPS_NS {
class FixSMDIntegrateTlsph: public Fix {
- friend class Neighbor;
- friend class PairTlsph;
+ friend class Neighbor;
+ friend class PairTlsph;
public:
FixSMDIntegrateTlsph(class LAMMPS *, int, char **);
virtual ~FixSMDIntegrateTlsph() {
diff --git a/src/USER-SMD/fix_smd_integrate_ulsph.cpp b/src/USER-SMD/fix_smd_integrate_ulsph.cpp
index 3dbf453349..9b892bf259 100644
--- a/src/USER-SMD/fix_smd_integrate_ulsph.cpp
+++ b/src/USER-SMD/fix_smd_integrate_ulsph.cpp
@@ -50,109 +50,109 @@ using namespace FixConst;
/* ---------------------------------------------------------------------- */
FixSMDIntegrateUlsph::FixSMDIntegrateUlsph(LAMMPS *lmp, int narg, char **arg) :
- Fix(lmp, narg, arg) {
-
- if ((atom->e_flag != 1) || (atom->vfrac_flag != 1))
- error->all(FLERR, "fix smd/integrate_ulsph command requires atom_style with both energy and volume");
-
- if (narg < 3)
- error->all(FLERR, "Illegal number of arguments for fix smd/integrate_ulsph command");
-
- adjust_radius_flag = false;
- xsphFlag = false;
- vlimit = -1.0;
- int iarg = 3;
-
- if (comm->me == 0) {
- printf("\n>>========>>========>>========>>========>>========>>========>>========>>========\n");
- printf("fix smd/integrate_ulsph is active for group: %s \n", arg[1]);
- }
- while (true) {
-
- if (iarg >= narg) {
- break;
- }
-
- if (strcmp(arg[iarg], "xsph") == 0) {
- xsphFlag = true;
- if (comm->me == 0) {
- error->one(FLERR, "XSPH is currently not available");
- printf("... will use XSPH time integration\n");
- }
- } else if (strcmp(arg[iarg], "adjust_radius") == 0) {
- adjust_radius_flag = true;
-
- iarg++;
- if (iarg == narg) {
- error->all(FLERR, "expected three numbers following adjust_radius: factor, min, max");
- }
-
- adjust_radius_factor = force->numeric(FLERR, arg[iarg]);
-
- iarg++;
- if (iarg == narg) {
- error->all(FLERR, "expected three numbers following adjust_radius: factor, min, max");
- }
-
- min_nn = force->inumeric(FLERR, arg[iarg]);
-
- iarg++;
- if (iarg == narg) {
- error->all(FLERR, "expected three numbers following adjust_radius: factor, min, max");
- }
-
- max_nn = force->inumeric(FLERR, arg[iarg]);
-
- if (comm->me == 0) {
- printf("... will adjust smoothing length dynamically with factor %g to achieve %d to %d neighbors per particle.\n ",
- adjust_radius_factor, min_nn, max_nn);
- }
-
- } else if (strcmp(arg[iarg], "limit_velocity") == 0) {
- iarg++;
- if (iarg == narg) {
- error->all(FLERR, "expected number following limit_velocity");
- }
- vlimit = force->numeric(FLERR, arg[iarg]);
-
- if (comm->me == 0) {
- printf("... will limit velocities to <= %g\n", vlimit);
- }
- } else {
- char msg[128];
- sprintf(msg, "Illegal keyword for smd/integrate_ulsph: %s\n", arg[iarg]);
- error->all(FLERR, msg);
- }
-
- iarg++;
-
- }
-
- if (comm->me == 0) {
- printf(">>========>>========>>========>>========>>========>>========>>========>>========\n\n");
- }
-
- // set comm sizes needed by this fix
- atom->add_callback(0);
-
- time_integrate = 1;
+ Fix(lmp, narg, arg) {
+
+ if ((atom->e_flag != 1) || (atom->vfrac_flag != 1))
+ error->all(FLERR, "fix smd/integrate_ulsph command requires atom_style with both energy and volume");
+
+ if (narg < 3)
+ error->all(FLERR, "Illegal number of arguments for fix smd/integrate_ulsph command");
+
+ adjust_radius_flag = false;
+ xsphFlag = false;
+ vlimit = -1.0;
+ int iarg = 3;
+
+ if (comm->me == 0) {
+ printf("\n>>========>>========>>========>>========>>========>>========>>========>>========\n");
+ printf("fix smd/integrate_ulsph is active for group: %s \n", arg[1]);
+ }
+ while (true) {
+
+ if (iarg >= narg) {
+ break;
+ }
+
+ if (strcmp(arg[iarg], "xsph") == 0) {
+ xsphFlag = true;
+ if (comm->me == 0) {
+ error->one(FLERR, "XSPH is currently not available");
+ printf("... will use XSPH time integration\n");
+ }
+ } else if (strcmp(arg[iarg], "adjust_radius") == 0) {
+ adjust_radius_flag = true;
+
+ iarg++;
+ if (iarg == narg) {
+ error->all(FLERR, "expected three numbers following adjust_radius: factor, min, max");
+ }
+
+ adjust_radius_factor = force->numeric(FLERR, arg[iarg]);
+
+ iarg++;
+ if (iarg == narg) {
+ error->all(FLERR, "expected three numbers following adjust_radius: factor, min, max");
+ }
+
+ min_nn = force->inumeric(FLERR, arg[iarg]);
+
+ iarg++;
+ if (iarg == narg) {
+ error->all(FLERR, "expected three numbers following adjust_radius: factor, min, max");
+ }
+
+ max_nn = force->inumeric(FLERR, arg[iarg]);
+
+ if (comm->me == 0) {
+ printf("... will adjust smoothing length dynamically with factor %g to achieve %d to %d neighbors per particle.\n ",
+ adjust_radius_factor, min_nn, max_nn);
+ }
+
+ } else if (strcmp(arg[iarg], "limit_velocity") == 0) {
+ iarg++;
+ if (iarg == narg) {
+ error->all(FLERR, "expected number following limit_velocity");
+ }
+ vlimit = force->numeric(FLERR, arg[iarg]);
+
+ if (comm->me == 0) {
+ printf("... will limit velocities to <= %g\n", vlimit);
+ }
+ } else {
+ char msg[128];
+ sprintf(msg, "Illegal keyword for smd/integrate_ulsph: %s\n", arg[iarg]);
+ error->all(FLERR, msg);
+ }
+
+ iarg++;
+
+ }
+
+ if (comm->me == 0) {
+ printf(">>========>>========>>========>>========>>========>>========>>========>>========\n\n");
+ }
+
+ // set comm sizes needed by this fix
+ atom->add_callback(0);
+
+ time_integrate = 1;
}
/* ---------------------------------------------------------------------- */
int FixSMDIntegrateUlsph::setmask() {
- int mask = 0;
- mask |= INITIAL_INTEGRATE;
- mask |= FINAL_INTEGRATE;
- return mask;
+ int mask = 0;
+ mask |= INITIAL_INTEGRATE;
+ mask |= FINAL_INTEGRATE;
+ return mask;
}
/* ---------------------------------------------------------------------- */
void FixSMDIntegrateUlsph::init() {
- dtv = update->dt;
- dtf = 0.5 * update->dt * force->ftm2v;
- vlimitsq = vlimit * vlimit;
+ dtv = update->dt;
+ dtf = 0.5 * update->dt * force->ftm2v;
+ vlimitsq = vlimit * vlimit;
}
/* ----------------------------------------------------------------------
@@ -160,166 +160,166 @@ void FixSMDIntegrateUlsph::init() {
------------------------------------------------------------------------- */
void FixSMDIntegrateUlsph::initial_integrate(int vflag) {
- double **x = atom->x;
- double **v = atom->v;
- double **f = atom->f;
- double **vest = atom->vest;
- double *rmass = atom->rmass;
+ double **x = atom->x;
+ double **v = atom->v;
+ double **f = atom->f;
+ double **vest = atom->vest;
+ double *rmass = atom->rmass;
- int *mask = atom->mask;
- int nlocal = atom->nlocal;
- int i, itmp;
- double dtfm, vsq, scale;
- double vxsph_x, vxsph_y, vxsph_z;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+ int i, itmp;
+ double dtfm, vsq, scale;
+ double vxsph_x, vxsph_y, vxsph_z;
- //printf("initial_integrate at timestep %d\n", update->ntimestep);
+ //printf("initial_integrate at timestep %d\n", update->ntimestep);
- /*
- * get smoothed velocities from ULSPH pair style
- */
+ /*
+ * get smoothed velocities from ULSPH pair style
+ */
- Vector3d *smoothVel = (Vector3d *) force->pair->extract("smd/ulsph/smoothVel_ptr", itmp);
+ Vector3d *smoothVel = (Vector3d *) force->pair->extract("smd/ulsph/smoothVel_ptr", itmp);
- if (xsphFlag) {
- if (smoothVel == NULL) {
- error->one(FLERR, "fix smd/integrate_ulsph failed to access smoothVel array");
- }
- }
+ if (xsphFlag) {
+ if (smoothVel == NULL) {
+ error->one(FLERR, "fix smd/integrate_ulsph failed to access smoothVel array");
+ }
+ }
- if (igroup == atom->firstgroup)
- nlocal = atom->nfirst;
+ if (igroup == atom->firstgroup)
+ nlocal = atom->nfirst;
- for (i = 0; i < nlocal; i++) {
- if (mask[i] & groupbit) {
- dtfm = dtf / rmass[i];
+ for (i = 0; i < nlocal; i++) {
+ if (mask[i] & groupbit) {
+ dtfm = dtf / rmass[i];
- v[i][0] += dtfm * f[i][0];
- v[i][1] += dtfm * f[i][1];
- v[i][2] += dtfm * f[i][2];
+ v[i][0] += dtfm * f[i][0];
+ v[i][1] += dtfm * f[i][1];
+ v[i][2] += dtfm * f[i][2];
- if (vlimit > 0.0) {
- vsq = v[i][0] * v[i][0] + v[i][1] * v[i][1] + v[i][2] * v[i][2];
- if (vsq > vlimitsq) {
- scale = sqrt(vlimitsq / vsq);
- v[i][0] *= scale;
- v[i][1] *= scale;
- v[i][2] *= scale;
+ if (vlimit > 0.0) {
+ vsq = v[i][0] * v[i][0] + v[i][1] * v[i][1] + v[i][2] * v[i][2];
+ if (vsq > vlimitsq) {
+ scale = sqrt(vlimitsq / vsq);
+ v[i][0] *= scale;
+ v[i][1] *= scale;
+ v[i][2] *= scale;
- vest[i][0] = v[i][0];
- vest[i][1] = v[i][1];
- vest[i][2] = v[i][2];
- }
- }
+ vest[i][0] = v[i][0];
+ vest[i][1] = v[i][1];
+ vest[i][2] = v[i][2];
+ }
+ }
- if (xsphFlag) {
+ if (xsphFlag) {
- // construct XSPH velocity
- vxsph_x = v[i][0] - 0.5 * smoothVel[i](0);
- vxsph_y = v[i][1] - 0.5 * smoothVel[i](1);
- vxsph_z = v[i][2] - 0.5 * smoothVel[i](2);
+ // construct XSPH velocity
+ vxsph_x = v[i][0] - 0.5 * smoothVel[i](0);
+ vxsph_y = v[i][1] - 0.5 * smoothVel[i](1);
+ vxsph_z = v[i][2] - 0.5 * smoothVel[i](2);
- vest[i][0] = vxsph_x + dtfm * f[i][0];
- vest[i][1] = vxsph_y + dtfm * f[i][1];
- vest[i][2] = vxsph_z + dtfm * f[i][2];
+ vest[i][0] = vxsph_x + dtfm * f[i][0];
+ vest[i][1] = vxsph_y + dtfm * f[i][1];
+ vest[i][2] = vxsph_z + dtfm * f[i][2];
- x[i][0] += dtv * vxsph_x;
- x[i][1] += dtv * vxsph_y;
- x[i][2] += dtv * vxsph_z;
+ x[i][0] += dtv * vxsph_x;
+ x[i][1] += dtv * vxsph_y;
+ x[i][2] += dtv * vxsph_z;
- } else {
+ } else {
- // extrapolate velocity from half- to full-step
- vest[i][0] = v[i][0] + dtfm * f[i][0];
- vest[i][1] = v[i][1] + dtfm * f[i][1];
- vest[i][2] = v[i][2] + dtfm * f[i][2];
+ // extrapolate velocity from half- to full-step
+ vest[i][0] = v[i][0] + dtfm * f[i][0];
+ vest[i][1] = v[i][1] + dtfm * f[i][1];
+ vest[i][2] = v[i][2] + dtfm * f[i][2];
- x[i][0] += dtv * v[i][0];
- x[i][1] += dtv * v[i][1];
- x[i][2] += dtv * v[i][2];
- }
- }
- }
+ x[i][0] += dtv * v[i][0];
+ x[i][1] += dtv * v[i][1];
+ x[i][2] += dtv * v[i][2];
+ }
+ }
+ }
}
/* ---------------------------------------------------------------------- */
void FixSMDIntegrateUlsph::final_integrate() {
- double **v = atom->v;
- double **f = atom->f;
- double *e = atom->e;
- double *de = atom->de;
- double *vfrac = atom->vfrac;
- double *radius = atom->radius;
- double *contact_radius = atom->contact_radius;
- int *mask = atom->mask;
- int nlocal = atom->nlocal;
- if (igroup == atom->firstgroup)
- nlocal = atom->nfirst;
- double dtfm, vsq, scale;
- double *rmass = atom->rmass;
- double vol_increment;
- Matrix3d D;
-
- /*
- * get current number of SPH neighbors from ULSPH pair style
- */
-
- int itmp;
- int *nn = (int *) force->pair->extract("smd/ulsph/numNeighs_ptr", itmp);
- if (nn == NULL) {
- error->one(FLERR, "fix smd/integrate_ulsph failed to accesss num_neighs array");
- }
-
- Matrix3d *L = (Matrix3d *) force->pair->extract("smd/ulsph/velocityGradient_ptr", itmp);
- if (L == NULL) {
- error->one(FLERR, "fix smd/integrate_ulsph failed to accesss velocityGradient array");
- }
-
- for (int i = 0; i < nlocal; i++) {
- if (mask[i] & groupbit) {
-
- dtfm = dtf / rmass[i];
- v[i][0] += dtfm * f[i][0];
- v[i][1] += dtfm * f[i][1];
- v[i][2] += dtfm * f[i][2];
-
- if (vlimit > 0.0) {
- vsq = v[i][0] * v[i][0] + v[i][1] * v[i][1] + v[i][2] * v[i][2];
- if (vsq > vlimitsq) {
- scale = sqrt(vlimitsq / vsq);
- v[i][0] *= scale;
- v[i][1] *= scale;
- v[i][2] *= scale;
- }
- }
-
- e[i] += dtf * de[i];
-
- if (adjust_radius_flag) {
- if (nn[i] < min_nn) {
- radius[i] *= adjust_radius_factor;
- } else if (nn[i] > max_nn) {
- radius[i] /= adjust_radius_factor;
- }
- radius[i] = MAX(radius[i], 1.25 * contact_radius[i]);
- radius[i] = MIN(radius[i], 4.0 * contact_radius[i]);
-
- }
-
- D = 0.5 * (L[i] + L[i].transpose());
- vol_increment = vfrac[i] * update->dt * D.trace(); // Jacobian of deformation
- vfrac[i] += vol_increment;
- }
- }
+ double **v = atom->v;
+ double **f = atom->f;
+ double *e = atom->e;
+ double *de = atom->de;
+ double *vfrac = atom->vfrac;
+ double *radius = atom->radius;
+ double *contact_radius = atom->contact_radius;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+ if (igroup == atom->firstgroup)
+ nlocal = atom->nfirst;
+ double dtfm, vsq, scale;
+ double *rmass = atom->rmass;
+ double vol_increment;
+ Matrix3d D;
+
+ /*
+ * get current number of SPH neighbors from ULSPH pair style
+ */
+
+ int itmp;
+ int *nn = (int *) force->pair->extract("smd/ulsph/numNeighs_ptr", itmp);
+ if (nn == NULL) {
+ error->one(FLERR, "fix smd/integrate_ulsph failed to accesss num_neighs array");
+ }
+
+ Matrix3d *L = (Matrix3d *) force->pair->extract("smd/ulsph/velocityGradient_ptr", itmp);
+ if (L == NULL) {
+ error->one(FLERR, "fix smd/integrate_ulsph failed to accesss velocityGradient array");
+ }
+
+ for (int i = 0; i < nlocal; i++) {
+ if (mask[i] & groupbit) {
+
+ dtfm = dtf / rmass[i];
+ v[i][0] += dtfm * f[i][0];
+ v[i][1] += dtfm * f[i][1];
+ v[i][2] += dtfm * f[i][2];
+
+ if (vlimit > 0.0) {
+ vsq = v[i][0] * v[i][0] + v[i][1] * v[i][1] + v[i][2] * v[i][2];
+ if (vsq > vlimitsq) {
+ scale = sqrt(vlimitsq / vsq);
+ v[i][0] *= scale;
+ v[i][1] *= scale;
+ v[i][2] *= scale;
+ }
+ }
+
+ e[i] += dtf * de[i];
+
+ if (adjust_radius_flag) {
+ if (nn[i] < min_nn) {
+ radius[i] *= adjust_radius_factor;
+ } else if (nn[i] > max_nn) {
+ radius[i] /= adjust_radius_factor;
+ }
+ radius[i] = MAX(radius[i], 1.25 * contact_radius[i]);
+ radius[i] = MIN(radius[i], 4.0 * contact_radius[i]);
+
+ }
+
+ D = 0.5 * (L[i] + L[i].transpose());
+ vol_increment = vfrac[i] * update->dt * D.trace(); // Jacobian of deformation
+ vfrac[i] += vol_increment;
+ }
+ }
}
/* ---------------------------------------------------------------------- */
void FixSMDIntegrateUlsph::reset_dt() {
- dtv = update->dt;
- dtf = 0.5 * update->dt * force->ftm2v;
+ dtv = update->dt;
+ dtf = 0.5 * update->dt * force->ftm2v;
}
diff --git a/src/USER-SMD/fix_smd_move_triangulated_surface.cpp b/src/USER-SMD/fix_smd_move_triangulated_surface.cpp
index e452923bd4..d8a0bda4d0 100644
--- a/src/USER-SMD/fix_smd_move_triangulated_surface.cpp
+++ b/src/USER-SMD/fix_smd_move_triangulated_surface.cpp
@@ -53,173 +53,173 @@ using namespace std;
/* ---------------------------------------------------------------------- */
FixSMDMoveTriSurf::FixSMDMoveTriSurf(LAMMPS *lmp, int narg, char **arg) :
- Fix(lmp, narg, arg) {
-
- if (atom->smd_flag != 1) {
- error->all(FLERR, "fix fix smd/move_tri_surf command requires atom_style smd");
- }
-
- if (narg < 3)
- error->all(FLERR, "Illegal number of arguments for fix fix smd/move_tri_surf command");
-
- rotateFlag = linearFlag = wiggleFlag = false;
- wiggle_direction = 1.0;
- wiggle_max_travel = 0.0;
-
- int iarg = 3;
-
- if (comm->me == 0) {
- printf("\n>>========>>========>>========>>========>>========>>========>>========>>========\n");
- printf("fix fix smd/move_tri_surf is active for group: %s \n", arg[1]);
- }
- while (true) {
-
- if (iarg >= narg) {
- break;
- }
-
- if (strcmp(arg[iarg], "*LINEAR") == 0) {
- linearFlag = true;
- if (comm->me == 0) {
- printf("... will move surface in a linear fashion\n");
- }
-
- iarg++;
- if (iarg == narg) {
- error->all(FLERR, "expected three floats for velocity following *LINEAR");
- }
- vx = force->numeric(FLERR, arg[iarg]);
-
- iarg++;
- if (iarg == narg) {
- error->all(FLERR, "expected three floats for velocity following *LINEAR");
- }
- vy = force->numeric(FLERR, arg[iarg]);
-
- iarg++;
- if (iarg == narg) {
- error->all(FLERR, "expected three floats for velocity following *LINEAR");
- }
- vz = force->numeric(FLERR, arg[iarg]);
-
- } else if (strcmp(arg[iarg], "*WIGGLE") == 0) {
- wiggleFlag = true;
- if (comm->me == 0) {
- printf("... will move surface in wiggle fashion\n");
- }
-
- iarg++;
- if (iarg == narg) {
- error->all(FLERR, "expected 4 floats following *WIGGLE : vx vy vz max_travel");
- }
- vx = force->numeric(FLERR, arg[iarg]);
-
- iarg++;
- if (iarg == narg) {
- error->all(FLERR, "expected 4 floats following *WIGGLE : vx vy vz max_travel");
- }
- vy = force->numeric(FLERR, arg[iarg]);
-
- iarg++;
- if (iarg == narg) {
- error->all(FLERR, "expected 4 floats following *WIGGLE : vx vy vz max_travel");
- }
- vz = force->numeric(FLERR, arg[iarg]);
-
- iarg++;
- if (iarg == narg) {
- error->all(FLERR, "expected 4 floats following *WIGGLE : vx vy vz max_travel");
- }
- wiggle_max_travel = force->numeric(FLERR, arg[iarg]);
-
- } else if (strcmp(arg[iarg], "*ROTATE") == 0) {
- rotateFlag = true;
-
- iarg++;
- if (iarg == narg) {
- error->all(FLERR, "expected 7 floats following *ROTATE: origin, rotation axis, and rotation period");
- }
- origin(0) = force->numeric(FLERR, arg[iarg]);
-
- iarg++;
- if (iarg == narg) {
- error->all(FLERR, "expected 7 floats following *ROTATE: origin, rotation axis, and rotation period");
- }
- origin(1) = force->numeric(FLERR, arg[iarg]);
-
- iarg++;
- if (iarg == narg) {
- error->all(FLERR, "expected 7 floats following *ROTATE: origin, rotation axis, and rotation period");
- }
- origin(2) = force->numeric(FLERR, arg[iarg]);
-
- iarg++;
- if (iarg == narg) {
- error->all(FLERR, "expected 7 floats following *ROTATE: origin, rotation axis, and rotation period");
- }
- rotation_axis(0) = force->numeric(FLERR, arg[iarg]);
-
- iarg++;
- if (iarg == narg) {
- error->all(FLERR, "expected 7 floats following *ROTATE: origin, rotation axis, and rotation period");
- }
- rotation_axis(1) = force->numeric(FLERR, arg[iarg]);
-
- iarg++;
- if (iarg == narg) {
- error->all(FLERR, "expected 7 floats following *ROTATE: origin, rotation axis, and rotation period");
- }
- rotation_axis(2) = force->numeric(FLERR, arg[iarg]);
-
- iarg++;
- if (iarg == narg) {
- error->all(FLERR, "expected 7 floats following *ROTATE: origin, rotation axis, and rotation period");
- }
- rotation_period = force->numeric(FLERR, arg[iarg]);
-
- /*
- * construct rotation matrix
- */
-
- u_cross(0, 0) = 0.0;
- u_cross(0, 1) = -rotation_axis(2);
- u_cross(0, 2) = rotation_axis(1);
-
- u_cross(1, 0) = rotation_axis(2);
- u_cross(1, 1) = 0.0;
- u_cross(1, 2) = -rotation_axis(0);
-
- u_cross(2, 0) = -rotation_axis(1);
- u_cross(2, 1) = rotation_axis(0);
- u_cross(2, 2) = 0.0;
-
- uxu = rotation_axis * rotation_axis.transpose();
-
- if (comm->me == 0) {
- printf("will rotate with period %f\n", rotation_period);
- }
-
- } else {
- char msg[128];
- sprintf(msg, "Illegal keyword for fix smd/move_tri_surf: %s\n", arg[iarg]);
- error->all(FLERR, msg);
- }
-
- iarg++;
-
- }
-
- if (comm->me == 0) {
- printf(">>========>>========>>========>>========>>========>>========>>========>>========\n\n");
- }
-
- // set comm sizes needed by this fix
- comm_forward = 12;
-
- //atom->add_callback(0);
- //atom->add_callback(1);
-
- time_integrate = 1;
+ Fix(lmp, narg, arg) {
+
+ if (atom->smd_flag != 1) {
+ error->all(FLERR, "fix fix smd/move_tri_surf command requires atom_style smd");
+ }
+
+ if (narg < 3)
+ error->all(FLERR, "Illegal number of arguments for fix fix smd/move_tri_surf command");
+
+ rotateFlag = linearFlag = wiggleFlag = false;
+ wiggle_direction = 1.0;
+ wiggle_max_travel = 0.0;
+
+ int iarg = 3;
+
+ if (comm->me == 0) {
+ printf("\n>>========>>========>>========>>========>>========>>========>>========>>========\n");
+ printf("fix fix smd/move_tri_surf is active for group: %s \n", arg[1]);
+ }
+ while (true) {
+
+ if (iarg >= narg) {
+ break;
+ }
+
+ if (strcmp(arg[iarg], "*LINEAR") == 0) {
+ linearFlag = true;
+ if (comm->me == 0) {
+ printf("... will move surface in a linear fashion\n");
+ }
+
+ iarg++;
+ if (iarg == narg) {
+ error->all(FLERR, "expected three floats for velocity following *LINEAR");
+ }
+ vx = force->numeric(FLERR, arg[iarg]);
+
+ iarg++;
+ if (iarg == narg) {
+ error->all(FLERR, "expected three floats for velocity following *LINEAR");
+ }
+ vy = force->numeric(FLERR, arg[iarg]);
+
+ iarg++;
+ if (iarg == narg) {
+ error->all(FLERR, "expected three floats for velocity following *LINEAR");
+ }
+ vz = force->numeric(FLERR, arg[iarg]);
+
+ } else if (strcmp(arg[iarg], "*WIGGLE") == 0) {
+ wiggleFlag = true;
+ if (comm->me == 0) {
+ printf("... will move surface in wiggle fashion\n");
+ }
+
+ iarg++;
+ if (iarg == narg) {
+ error->all(FLERR, "expected 4 floats following *WIGGLE : vx vy vz max_travel");
+ }
+ vx = force->numeric(FLERR, arg[iarg]);
+
+ iarg++;
+ if (iarg == narg) {
+ error->all(FLERR, "expected 4 floats following *WIGGLE : vx vy vz max_travel");
+ }
+ vy = force->numeric(FLERR, arg[iarg]);
+
+ iarg++;
+ if (iarg == narg) {
+ error->all(FLERR, "expected 4 floats following *WIGGLE : vx vy vz max_travel");
+ }
+ vz = force->numeric(FLERR, arg[iarg]);
+
+ iarg++;
+ if (iarg == narg) {
+ error->all(FLERR, "expected 4 floats following *WIGGLE : vx vy vz max_travel");
+ }
+ wiggle_max_travel = force->numeric(FLERR, arg[iarg]);
+
+ } else if (strcmp(arg[iarg], "*ROTATE") == 0) {
+ rotateFlag = true;
+
+ iarg++;
+ if (iarg == narg) {
+ error->all(FLERR, "expected 7 floats following *ROTATE: origin, rotation axis, and rotation period");
+ }
+ origin(0) = force->numeric(FLERR, arg[iarg]);
+
+ iarg++;
+ if (iarg == narg) {
+ error->all(FLERR, "expected 7 floats following *ROTATE: origin, rotation axis, and rotation period");
+ }
+ origin(1) = force->numeric(FLERR, arg[iarg]);
+
+ iarg++;
+ if (iarg == narg) {
+ error->all(FLERR, "expected 7 floats following *ROTATE: origin, rotation axis, and rotation period");
+ }
+ origin(2) = force->numeric(FLERR, arg[iarg]);
+
+ iarg++;
+ if (iarg == narg) {
+ error->all(FLERR, "expected 7 floats following *ROTATE: origin, rotation axis, and rotation period");
+ }
+ rotation_axis(0) = force->numeric(FLERR, arg[iarg]);
+
+ iarg++;
+ if (iarg == narg) {
+ error->all(FLERR, "expected 7 floats following *ROTATE: origin, rotation axis, and rotation period");
+ }
+ rotation_axis(1) = force->numeric(FLERR, arg[iarg]);
+
+ iarg++;
+ if (iarg == narg) {
+ error->all(FLERR, "expected 7 floats following *ROTATE: origin, rotation axis, and rotation period");
+ }
+ rotation_axis(2) = force->numeric(FLERR, arg[iarg]);
+
+ iarg++;
+ if (iarg == narg) {
+ error->all(FLERR, "expected 7 floats following *ROTATE: origin, rotation axis, and rotation period");
+ }
+ rotation_period = force->numeric(FLERR, arg[iarg]);
+
+ /*
+ * construct rotation matrix
+ */
+
+ u_cross(0, 0) = 0.0;
+ u_cross(0, 1) = -rotation_axis(2);
+ u_cross(0, 2) = rotation_axis(1);
+
+ u_cross(1, 0) = rotation_axis(2);
+ u_cross(1, 1) = 0.0;
+ u_cross(1, 2) = -rotation_axis(0);
+
+ u_cross(2, 0) = -rotation_axis(1);
+ u_cross(2, 1) = rotation_axis(0);
+ u_cross(2, 2) = 0.0;
+
+ uxu = rotation_axis * rotation_axis.transpose();
+
+ if (comm->me == 0) {
+ printf("will rotate with period %f\n", rotation_period);
+ }
+
+ } else {
+ char msg[128];
+ sprintf(msg, "Illegal keyword for fix smd/move_tri_surf: %s\n", arg[iarg]);
+ error->all(FLERR, msg);
+ }
+
+ iarg++;
+
+ }
+
+ if (comm->me == 0) {
+ printf(">>========>>========>>========>>========>>========>>========>>========>>========\n\n");
+ }
+
+ // set comm sizes needed by this fix
+ comm_forward = 12;
+
+ //atom->add_callback(0);
+ //atom->add_callback(1);
+
+ time_integrate = 1;
}
/* ---------------------------------------------------------------------- */
@@ -234,284 +234,284 @@ FixSMDMoveTriSurf::~FixSMDMoveTriSurf()
/* ---------------------------------------------------------------------- */
int FixSMDMoveTriSurf::setmask() {
- int mask = 0;
- mask |= INITIAL_INTEGRATE;
- //mask |= PRE_EXCHANGE;
- return mask;
+ int mask = 0;
+ mask |= INITIAL_INTEGRATE;
+ //mask |= PRE_EXCHANGE;
+ return mask;
}
/* ---------------------------------------------------------------------- */
void FixSMDMoveTriSurf::init() {
- dtv = update->dt;
+ dtv = update->dt;
}
/* ----------------------------------------------------------------------
------------------------------------------------------------------------- */
void FixSMDMoveTriSurf::initial_integrate(int vflag) {
- double **x = atom->x;
- double **x0 = atom->x0;
- double **v = atom->v;
- double **vest = atom->vest;
- double **smd_data_9 = atom->smd_data_9;
- tagint *mol = atom->molecule;
-
- int *mask = atom->mask;
- int nlocal = atom->nlocal;
- double phi;
- int i;
- Matrix3d eye, Rot;
- eye.setIdentity();
-
- Vector3d v1, v2, v3, n, point, rotated_point, R, vel;
-
- if (igroup == atom->firstgroup)
- nlocal = atom->nfirst;
+ double **x = atom->x;
+ double **x0 = atom->x0;
+ double **v = atom->v;
+ double **vest = atom->vest;
+ double **smd_data_9 = atom->smd_data_9;
+ tagint *mol = atom->molecule;
+
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+ double phi;
+ int i;
+ Matrix3d eye, Rot;
+ eye.setIdentity();
+
+ Vector3d v1, v2, v3, n, point, rotated_point, R, vel;
+
+ if (igroup == atom->firstgroup)
+ nlocal = atom->nfirst;
- if (linearFlag) { // translate particles
- for (i = 0; i < nlocal; i++) {
- if (mask[i] & groupbit) {
+ if (linearFlag) { // translate particles
+ for (i = 0; i < nlocal; i++) {
+ if (mask[i] & groupbit) {
- v[i][0] = vx;
- v[i][1] = vy;
- v[i][2] = vz;
-
- vest[i][0] = vx;
- vest[i][1] = vy;
- vest[i][2] = vz;
-
- x[i][0] += dtv * vx;
- x[i][1] += dtv * vy;
- x[i][2] += dtv * vz;
-
- /*
- * if this is a triangle, move the vertices as well
- */
-
- if (mol[i] >= 65535) {
- smd_data_9[i][0] += dtv * vx;
- smd_data_9[i][1] += dtv * vy;
- smd_data_9[i][2] += dtv * vz;
-
- smd_data_9[i][3] += dtv * vx;
- smd_data_9[i][4] += dtv * vy;
- smd_data_9[i][5] += dtv * vz;
-
- smd_data_9[i][6] += dtv * vx;
- smd_data_9[i][7] += dtv * vy;
- smd_data_9[i][8] += dtv * vz;
- }
-
- }
- }
- }
-
- if (wiggleFlag) { // wiggle particles forward and backward
-
- wiggle_travel += sqrt(vx * vx + vy * vy + vz * vz ) * dtv;
- double wiggle_vx = wiggle_direction * vx;
- double wiggle_vy = wiggle_direction * vy;
- double wiggle_vz = wiggle_direction * vz;
-
- //printf("wiggle vz is %f, wiggle_max_travel is %f, dir=%f\n", wiggle_vz, wiggle_max_travel, wiggle_direction);
-
- for (i = 0; i < nlocal; i++) {
- if (mask[i] & groupbit) {
-
- v[i][0] = wiggle_vx;
- v[i][1] = wiggle_vy;
- v[i][2] = wiggle_vz;
-
- vest[i][0] = wiggle_vx;
- vest[i][1] = wiggle_vy;
- vest[i][2] = wiggle_vz;
-
- x[i][0] += dtv * wiggle_vx;
- x[i][1] += dtv * wiggle_vy;
- x[i][2] += dtv * wiggle_vz;
-
- /*
- * if this is a triangle, move the vertices as well
- */
-
- if (mol[i] >= 65535) {
- smd_data_9[i][0] += dtv * wiggle_vx;
- smd_data_9[i][1] += dtv * wiggle_vy;
- smd_data_9[i][2] += dtv * wiggle_vz;
-
- smd_data_9[i][3] += dtv * wiggle_vx;
- smd_data_9[i][4] += dtv * wiggle_vy;
- smd_data_9[i][5] += dtv * wiggle_vz;
-
- smd_data_9[i][6] += dtv * wiggle_vx;
- smd_data_9[i][7] += dtv * wiggle_vy;
- smd_data_9[i][8] += dtv * wiggle_vz;
- }
-
- }
- }
-
- if (wiggle_travel >= wiggle_max_travel) {
- wiggle_direction *= -1.0;
- wiggle_travel = 0.0;
- }
- }
-
- if (rotateFlag) { // rotate particles
- Vector3d xnew, R_new, x_correct;
-
- /*
- * rotation angle and matrix form of Rodrigues' rotation formula
- */
-
- phi = MY_2PI * dtv / rotation_period;
- //printf("dt=%f, phi =%f, T=%f\n", dtv, phi, rotation_period);
- Rot = cos(phi) * eye + sin(phi) * u_cross + (1.0 - cos(phi)) * uxu;
-
- for (i = 0; i < nlocal; i++) {
- if (mask[i] & groupbit) {
-
- /*
- * generate vector R from origin to point which is to be rotated
- */
- point << x[i][0], x[i][1], x[i][2];
- R = point - origin;
-
- /*
- * rotate vector and shift away from origin
- */
- rotated_point = Rot * R + origin;
-
- /*
- * determine velocity
- */
- vel = (rotated_point - point) / update->dt;
-
- /*
- * assign new velocities and coordinates
- */
- v[i][0] = vel(0);
- v[i][1] = vel(1);
- v[i][2] = vel(2);
-
- vest[i][0] = vel(0);
- vest[i][1] = vel(1);
- vest[i][2] = vel(2);
-
- x[i][0] = rotated_point(0);
- x[i][1] = rotated_point(1);
- x[i][2] = rotated_point(2);
-
- /*
- * if this is a triangle, rotate the vertices as well
- */
-
- if (mol[i] >= 65535) {
-
- v1 << smd_data_9[i][0], smd_data_9[i][1], smd_data_9[i][2];
- R = v1 - origin;
- rotated_point = Rot * R + origin;
- vel = (rotated_point - v1) / update->dt;
- smd_data_9[i][0] = rotated_point(0);
- smd_data_9[i][1] = rotated_point(1);
- smd_data_9[i][2] = rotated_point(2);
- v1 = rotated_point;
-
- v2 << smd_data_9[i][3], smd_data_9[i][4], smd_data_9[i][5];
- R = v2 - origin;
- rotated_point = Rot * R + origin;
- vel = (rotated_point - v2) / update->dt;
- smd_data_9[i][3] = rotated_point(0);
- smd_data_9[i][4] = rotated_point(1);
- smd_data_9[i][5] = rotated_point(2);
- v2 = rotated_point;
-
- v3 << smd_data_9[i][6], smd_data_9[i][7], smd_data_9[i][8];
- R = v3 - origin;
- rotated_point = Rot * R + origin;
- vel = (rotated_point - v3) / update->dt;
- smd_data_9[i][6] = rotated_point(0);
- smd_data_9[i][7] = rotated_point(1);
- smd_data_9[i][8] = rotated_point(2);
- v3 = rotated_point;
-
- // recalculate triangle normal
- n = (v2 - v1).cross(v2 - v3);
- n /= n.norm();
- x0[i][0] = n(0);
- x0[i][1] = n(1);
- x0[i][2] = n(2);
-
- }
-
- }
- }
- }
-
- // we changed smd_data_9, x0. perform communication to ghosts
- comm->forward_comm_fix(this);
+ v[i][0] = vx;
+ v[i][1] = vy;
+ v[i][2] = vz;
+
+ vest[i][0] = vx;
+ vest[i][1] = vy;
+ vest[i][2] = vz;
+
+ x[i][0] += dtv * vx;
+ x[i][1] += dtv * vy;
+ x[i][2] += dtv * vz;
+
+ /*
+ * if this is a triangle, move the vertices as well
+ */
+
+ if (mol[i] >= 65535) {
+ smd_data_9[i][0] += dtv * vx;
+ smd_data_9[i][1] += dtv * vy;
+ smd_data_9[i][2] += dtv * vz;
+
+ smd_data_9[i][3] += dtv * vx;
+ smd_data_9[i][4] += dtv * vy;
+ smd_data_9[i][5] += dtv * vz;
+
+ smd_data_9[i][6] += dtv * vx;
+ smd_data_9[i][7] += dtv * vy;
+ smd_data_9[i][8] += dtv * vz;
+ }
+
+ }
+ }
+ }
+
+ if (wiggleFlag) { // wiggle particles forward and backward
+
+ wiggle_travel += sqrt(vx * vx + vy * vy + vz * vz ) * dtv;
+ double wiggle_vx = wiggle_direction * vx;
+ double wiggle_vy = wiggle_direction * vy;
+ double wiggle_vz = wiggle_direction * vz;
+
+ //printf("wiggle vz is %f, wiggle_max_travel is %f, dir=%f\n", wiggle_vz, wiggle_max_travel, wiggle_direction);
+
+ for (i = 0; i < nlocal; i++) {
+ if (mask[i] & groupbit) {
+
+ v[i][0] = wiggle_vx;
+ v[i][1] = wiggle_vy;
+ v[i][2] = wiggle_vz;
+
+ vest[i][0] = wiggle_vx;
+ vest[i][1] = wiggle_vy;
+ vest[i][2] = wiggle_vz;
+
+ x[i][0] += dtv * wiggle_vx;
+ x[i][1] += dtv * wiggle_vy;
+ x[i][2] += dtv * wiggle_vz;
+
+ /*
+ * if this is a triangle, move the vertices as well
+ */
+
+ if (mol[i] >= 65535) {
+ smd_data_9[i][0] += dtv * wiggle_vx;
+ smd_data_9[i][1] += dtv * wiggle_vy;
+ smd_data_9[i][2] += dtv * wiggle_vz;
+
+ smd_data_9[i][3] += dtv * wiggle_vx;
+ smd_data_9[i][4] += dtv * wiggle_vy;
+ smd_data_9[i][5] += dtv * wiggle_vz;
+
+ smd_data_9[i][6] += dtv * wiggle_vx;
+ smd_data_9[i][7] += dtv * wiggle_vy;
+ smd_data_9[i][8] += dtv * wiggle_vz;
+ }
+
+ }
+ }
+
+ if (wiggle_travel >= wiggle_max_travel) {
+ wiggle_direction *= -1.0;
+ wiggle_travel = 0.0;
+ }
+ }
+
+ if (rotateFlag) { // rotate particles
+ Vector3d xnew, R_new, x_correct;
+
+ /*
+ * rotation angle and matrix form of Rodrigues' rotation formula
+ */
+
+ phi = MY_2PI * dtv / rotation_period;
+ //printf("dt=%f, phi =%f, T=%f\n", dtv, phi, rotation_period);
+ Rot = cos(phi) * eye + sin(phi) * u_cross + (1.0 - cos(phi)) * uxu;
+
+ for (i = 0; i < nlocal; i++) {
+ if (mask[i] & groupbit) {
+
+ /*
+ * generate vector R from origin to point which is to be rotated
+ */
+ point << x[i][0], x[i][1], x[i][2];
+ R = point - origin;
+
+ /*
+ * rotate vector and shift away from origin
+ */
+ rotated_point = Rot * R + origin;
+
+ /*
+ * determine velocity
+ */
+ vel = (rotated_point - point) / update->dt;
+
+ /*
+ * assign new velocities and coordinates
+ */
+ v[i][0] = vel(0);
+ v[i][1] = vel(1);
+ v[i][2] = vel(2);
+
+ vest[i][0] = vel(0);
+ vest[i][1] = vel(1);
+ vest[i][2] = vel(2);
+
+ x[i][0] = rotated_point(0);
+ x[i][1] = rotated_point(1);
+ x[i][2] = rotated_point(2);
+
+ /*
+ * if this is a triangle, rotate the vertices as well
+ */
+
+ if (mol[i] >= 65535) {
+
+ v1 << smd_data_9[i][0], smd_data_9[i][1], smd_data_9[i][2];
+ R = v1 - origin;
+ rotated_point = Rot * R + origin;
+ vel = (rotated_point - v1) / update->dt;
+ smd_data_9[i][0] = rotated_point(0);
+ smd_data_9[i][1] = rotated_point(1);
+ smd_data_9[i][2] = rotated_point(2);
+ v1 = rotated_point;
+
+ v2 << smd_data_9[i][3], smd_data_9[i][4], smd_data_9[i][5];
+ R = v2 - origin;
+ rotated_point = Rot * R + origin;
+ vel = (rotated_point - v2) / update->dt;
+ smd_data_9[i][3] = rotated_point(0);
+ smd_data_9[i][4] = rotated_point(1);
+ smd_data_9[i][5] = rotated_point(2);
+ v2 = rotated_point;
+
+ v3 << smd_data_9[i][6], smd_data_9[i][7], smd_data_9[i][8];
+ R = v3 - origin;
+ rotated_point = Rot * R + origin;
+ vel = (rotated_point - v3) / update->dt;
+ smd_data_9[i][6] = rotated_point(0);
+ smd_data_9[i][7] = rotated_point(1);
+ smd_data_9[i][8] = rotated_point(2);
+ v3 = rotated_point;
+
+ // recalculate triangle normal
+ n = (v2 - v1).cross(v2 - v3);
+ n /= n.norm();
+ x0[i][0] = n(0);
+ x0[i][1] = n(1);
+ x0[i][2] = n(2);
+
+ }
+
+ }
+ }
+ }
+
+ // we changed smd_data_9, x0. perform communication to ghosts
+ comm->forward_comm_fix(this);
}
/* ---------------------------------------------------------------------- */
void FixSMDMoveTriSurf::reset_dt() {
- dtv = update->dt;
+ dtv = update->dt;
}
/* ---------------------------------------------------------------------- */
int FixSMDMoveTriSurf::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc) {
- int i, j, m;
- double **x0 = atom->x0;
- double **smd_data_9 = atom->smd_data_9;
-
- //printf("in FixSMDIntegrateTlsph::pack_forward_comm\n");
- m = 0;
- for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x0[j][0];
- buf[m++] = x0[j][1];
- buf[m++] = x0[j][2];
-
- buf[m++] = smd_data_9[j][0];
- buf[m++] = smd_data_9[j][1];
- buf[m++] = smd_data_9[j][2];
- buf[m++] = smd_data_9[j][3];
- buf[m++] = smd_data_9[j][4];
- buf[m++] = smd_data_9[j][5];
- buf[m++] = smd_data_9[j][6];
- buf[m++] = smd_data_9[j][7];
- buf[m++] = smd_data_9[j][8];
-
- }
- return m;
+ int i, j, m;
+ double **x0 = atom->x0;
+ double **smd_data_9 = atom->smd_data_9;
+
+ //printf("in FixSMDIntegrateTlsph::pack_forward_comm\n");
+ m = 0;
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = x0[j][0];
+ buf[m++] = x0[j][1];
+ buf[m++] = x0[j][2];
+
+ buf[m++] = smd_data_9[j][0];
+ buf[m++] = smd_data_9[j][1];
+ buf[m++] = smd_data_9[j][2];
+ buf[m++] = smd_data_9[j][3];
+ buf[m++] = smd_data_9[j][4];
+ buf[m++] = smd_data_9[j][5];
+ buf[m++] = smd_data_9[j][6];
+ buf[m++] = smd_data_9[j][7];
+ buf[m++] = smd_data_9[j][8];
+
+ }
+ return m;
}
/* ---------------------------------------------------------------------- */
void FixSMDMoveTriSurf::unpack_forward_comm(int n, int first, double *buf) {
- int i, m, last;
- double **x0 = atom->x0;
- double **smd_data_9 = atom->smd_data_9;
-
- //printf("in FixSMDMoveTriSurf::unpack_forward_comm\n");
- m = 0;
- last = first + n;
- for (i = first; i < last; i++) {
- x0[i][0] = buf[m++];
- x0[i][1] = buf[m++];
- x0[i][2] = buf[m++];
-
- smd_data_9[i][0] = buf[m++];
- smd_data_9[i][1] = buf[m++];
- smd_data_9[i][2] = buf[m++];
- smd_data_9[i][3] = buf[m++];
- smd_data_9[i][4] = buf[m++];
- smd_data_9[i][5] = buf[m++];
- smd_data_9[i][6] = buf[m++];
- smd_data_9[i][7] = buf[m++];
- smd_data_9[i][8] = buf[m++];
- }
+ int i, m, last;
+ double **x0 = atom->x0;
+ double **smd_data_9 = atom->smd_data_9;
+
+ //printf("in FixSMDMoveTriSurf::unpack_forward_comm\n");
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ x0[i][0] = buf[m++];
+ x0[i][1] = buf[m++];
+ x0[i][2] = buf[m++];
+
+ smd_data_9[i][0] = buf[m++];
+ smd_data_9[i][1] = buf[m++];
+ smd_data_9[i][2] = buf[m++];
+ smd_data_9[i][3] = buf[m++];
+ smd_data_9[i][4] = buf[m++];
+ smd_data_9[i][5] = buf[m++];
+ smd_data_9[i][6] = buf[m++];
+ smd_data_9[i][7] = buf[m++];
+ smd_data_9[i][8] = buf[m++];
+ }
}
diff --git a/src/USER-SMD/fix_smd_move_triangulated_surface.h b/src/USER-SMD/fix_smd_move_triangulated_surface.h
index c851d490c5..ec58a8bac1 100644
--- a/src/USER-SMD/fix_smd_move_triangulated_surface.h
+++ b/src/USER-SMD/fix_smd_move_triangulated_surface.h
@@ -38,23 +38,23 @@ namespace LAMMPS_NS {
class FixSMDMoveTriSurf: public Fix {
public:
- FixSMDMoveTriSurf(class LAMMPS *, int, char **);
- ~FixSMDMoveTriSurf();
- int setmask();
- virtual void init();
- virtual void initial_integrate(int);
- void reset_dt();
- int pack_forward_comm(int, int *, double *, int, int *);
- void unpack_forward_comm(int, int, double *);
+ FixSMDMoveTriSurf(class LAMMPS *, int, char **);
+ ~FixSMDMoveTriSurf();
+ int setmask();
+ virtual void init();
+ virtual void initial_integrate(int);
+ void reset_dt();
+ int pack_forward_comm(int, int *, double *, int, int *);
+ void unpack_forward_comm(int, int, double *);
protected:
- double dtv;
- bool linearFlag, wiggleFlag, rotateFlag;
- double vx, vy, vz;
- Eigen::Vector3d rotation_axis, origin;
- double rotation_period;
- Eigen::Matrix3d u_cross, uxu;
- double wiggle_travel, wiggle_max_travel, wiggle_direction;
+ double dtv;
+ bool linearFlag, wiggleFlag, rotateFlag;
+ double vx, vy, vz;
+ Eigen::Vector3d rotation_axis, origin;
+ double rotation_period;
+ Eigen::Matrix3d u_cross, uxu;
+ double wiggle_travel, wiggle_max_travel, wiggle_direction;
};
}
diff --git a/src/USER-SMD/fix_smd_setvel.cpp b/src/USER-SMD/fix_smd_setvel.cpp
index 92c4a00581..0c2dc31f45 100644
--- a/src/USER-SMD/fix_smd_setvel.cpp
+++ b/src/USER-SMD/fix_smd_setvel.cpp
@@ -41,304 +41,304 @@ using namespace LAMMPS_NS;
using namespace FixConst;
enum {
- NONE, CONSTANT, EQUAL, ATOM
+ NONE, CONSTANT, EQUAL, ATOM
};
/* ---------------------------------------------------------------------- */
FixSMDSetVel::FixSMDSetVel(LAMMPS *lmp, int narg, char **arg) :
- Fix(lmp, narg, arg) {
- if (narg < 6)
- error->all(FLERR, "Illegal fix setvelocity command");
-
- dynamic_group_allow = 1;
- vector_flag = 1;
- size_vector = 3;
- global_freq = 1;
- extvector = 1;
-
- xstr = ystr = zstr = NULL;
-
- if (strstr(arg[3], "v_") == arg[3]) {
- int n = strlen(&arg[3][2]) + 1;
- xstr = new char[n];
- strcpy(xstr, &arg[3][2]);
- } else if (strcmp(arg[3], "NULL") == 0) {
- xstyle = NONE;
- } else {
- xvalue = force->numeric(FLERR, arg[3]);
- xstyle = CONSTANT;
- }
- if (strstr(arg[4], "v_") == arg[4]) {
- int n = strlen(&arg[4][2]) + 1;
- ystr = new char[n];
- strcpy(ystr, &arg[4][2]);
- } else if (strcmp(arg[4], "NULL") == 0) {
- ystyle = NONE;
- } else {
- yvalue = force->numeric(FLERR, arg[4]);
- ystyle = CONSTANT;
- }
- if (strstr(arg[5], "v_") == arg[5]) {
- int n = strlen(&arg[5][2]) + 1;
- zstr = new char[n];
- strcpy(zstr, &arg[5][2]);
- } else if (strcmp(arg[5], "NULL") == 0) {
- zstyle = NONE;
- } else {
- zvalue = force->numeric(FLERR, arg[5]);
- zstyle = CONSTANT;
- }
-
- // optional args
-
- iregion = -1;
- idregion = NULL;
-
- int iarg = 6;
- while (iarg < narg) {
- if (strcmp(arg[iarg], "region") == 0) {
- if (iarg + 2 > narg)
- error->all(FLERR, "Illegal fix setvelocity command");
- iregion = domain->find_region(arg[iarg + 1]);
- if (iregion == -1)
- error->all(FLERR, "Region ID for fix setvelocity does not exist");
- int n = strlen(arg[iarg + 1]) + 1;
- idregion = new char[n];
- strcpy(idregion, arg[iarg + 1]);
- iarg += 2;
- } else
- error->all(FLERR, "Illegal fix setvelocity command");
- }
-
- force_flag = 0;
- foriginal[0] = foriginal[1] = foriginal[2] = 0.0;
-
- maxatom = atom->nmax;
- memory->create(sforce, maxatom, 3, "setvelocity:sforce");
+ Fix(lmp, narg, arg) {
+ if (narg < 6)
+ error->all(FLERR, "Illegal fix setvelocity command");
+
+ dynamic_group_allow = 1;
+ vector_flag = 1;
+ size_vector = 3;
+ global_freq = 1;
+ extvector = 1;
+
+ xstr = ystr = zstr = NULL;
+
+ if (strstr(arg[3], "v_") == arg[3]) {
+ int n = strlen(&arg[3][2]) + 1;
+ xstr = new char[n];
+ strcpy(xstr, &arg[3][2]);
+ } else if (strcmp(arg[3], "NULL") == 0) {
+ xstyle = NONE;
+ } else {
+ xvalue = force->numeric(FLERR, arg[3]);
+ xstyle = CONSTANT;
+ }
+ if (strstr(arg[4], "v_") == arg[4]) {
+ int n = strlen(&arg[4][2]) + 1;
+ ystr = new char[n];
+ strcpy(ystr, &arg[4][2]);
+ } else if (strcmp(arg[4], "NULL") == 0) {
+ ystyle = NONE;
+ } else {
+ yvalue = force->numeric(FLERR, arg[4]);
+ ystyle = CONSTANT;
+ }
+ if (strstr(arg[5], "v_") == arg[5]) {
+ int n = strlen(&arg[5][2]) + 1;
+ zstr = new char[n];
+ strcpy(zstr, &arg[5][2]);
+ } else if (strcmp(arg[5], "NULL") == 0) {
+ zstyle = NONE;
+ } else {
+ zvalue = force->numeric(FLERR, arg[5]);
+ zstyle = CONSTANT;
+ }
+
+ // optional args
+
+ iregion = -1;
+ idregion = NULL;
+
+ int iarg = 6;
+ while (iarg < narg) {
+ if (strcmp(arg[iarg], "region") == 0) {
+ if (iarg + 2 > narg)
+ error->all(FLERR, "Illegal fix setvelocity command");
+ iregion = domain->find_region(arg[iarg + 1]);
+ if (iregion == -1)
+ error->all(FLERR, "Region ID for fix setvelocity does not exist");
+ int n = strlen(arg[iarg + 1]) + 1;
+ idregion = new char[n];
+ strcpy(idregion, arg[iarg + 1]);
+ iarg += 2;
+ } else
+ error->all(FLERR, "Illegal fix setvelocity command");
+ }
+
+ force_flag = 0;
+ foriginal[0] = foriginal[1] = foriginal[2] = 0.0;
+
+ maxatom = atom->nmax;
+ memory->create(sforce, maxatom, 3, "setvelocity:sforce");
}
/* ---------------------------------------------------------------------- */
FixSMDSetVel::~FixSMDSetVel() {
- delete[] xstr;
- delete[] ystr;
- delete[] zstr;
- delete[] idregion;
- memory->destroy(sforce);
+ delete[] xstr;
+ delete[] ystr;
+ delete[] zstr;
+ delete[] idregion;
+ memory->destroy(sforce);
}
/* ---------------------------------------------------------------------- */
int FixSMDSetVel::setmask() {
- int mask = 0;
- //mask |= INITIAL_INTEGRATE;
- mask |= POST_FORCE;
- return mask;
+ int mask = 0;
+ //mask |= INITIAL_INTEGRATE;
+ mask |= POST_FORCE;
+ return mask;
}
/* ---------------------------------------------------------------------- */
void FixSMDSetVel::init() {
- // check variables
-
- if (xstr) {
- xvar = input->variable->find(xstr);
- if (xvar < 0)
- error->all(FLERR, "Variable name for fix setvelocity does not exist");
- if (input->variable->equalstyle(xvar))
- xstyle = EQUAL;
- else if (input->variable->atomstyle(xvar))
- xstyle = ATOM;
- else
- error->all(FLERR, "Variable for fix setvelocity is invalid style");
- }
- if (ystr) {
- yvar = input->variable->find(ystr);
- if (yvar < 0)
- error->all(FLERR, "Variable name for fix setvelocity does not exist");
- if (input->variable->equalstyle(yvar))
- ystyle = EQUAL;
- else if (input->variable->atomstyle(yvar))
- ystyle = ATOM;
- else
- error->all(FLERR, "Variable for fix setvelocity is invalid style");
- }
- if (zstr) {
- zvar = input->variable->find(zstr);
- if (zvar < 0)
- error->all(FLERR, "Variable name for fix setvelocity does not exist");
- if (input->variable->equalstyle(zvar))
- zstyle = EQUAL;
- else if (input->variable->atomstyle(zvar))
- zstyle = ATOM;
- else
- error->all(FLERR, "Variable for fix setvelocity is invalid style");
- }
-
- // set index and check validity of region
-
- if (iregion >= 0) {
- iregion = domain->find_region(idregion);
- if (iregion == -1)
- error->all(FLERR, "Region ID for fix setvelocity does not exist");
- }
-
- if (xstyle == ATOM || ystyle == ATOM || zstyle == ATOM)
- varflag = ATOM;
- else if (xstyle == EQUAL || ystyle == EQUAL || zstyle == EQUAL)
- varflag = EQUAL;
- else
- varflag = CONSTANT;
-
- // cannot use non-zero forces for a minimization since no energy is integrated
- // use fix addforce instead
-
- int flag = 0;
- if (update->whichflag == 2) {
- if (xstyle == EQUAL || xstyle == ATOM)
- flag = 1;
- if (ystyle == EQUAL || ystyle == ATOM)
- flag = 1;
- if (zstyle == EQUAL || zstyle == ATOM)
- flag = 1;
- if (xstyle == CONSTANT && xvalue != 0.0)
- flag = 1;
- if (ystyle == CONSTANT && yvalue != 0.0)
- flag = 1;
- if (zstyle == CONSTANT && zvalue != 0.0)
- flag = 1;
- }
- if (flag)
- error->all(FLERR, "Cannot use non-zero forces in an energy minimization");
+ // check variables
+
+ if (xstr) {
+ xvar = input->variable->find(xstr);
+ if (xvar < 0)
+ error->all(FLERR, "Variable name for fix setvelocity does not exist");
+ if (input->variable->equalstyle(xvar))
+ xstyle = EQUAL;
+ else if (input->variable->atomstyle(xvar))
+ xstyle = ATOM;
+ else
+ error->all(FLERR, "Variable for fix setvelocity is invalid style");
+ }
+ if (ystr) {
+ yvar = input->variable->find(ystr);
+ if (yvar < 0)
+ error->all(FLERR, "Variable name for fix setvelocity does not exist");
+ if (input->variable->equalstyle(yvar))
+ ystyle = EQUAL;
+ else if (input->variable->atomstyle(yvar))
+ ystyle = ATOM;
+ else
+ error->all(FLERR, "Variable for fix setvelocity is invalid style");
+ }
+ if (zstr) {
+ zvar = input->variable->find(zstr);
+ if (zvar < 0)
+ error->all(FLERR, "Variable name for fix setvelocity does not exist");
+ if (input->variable->equalstyle(zvar))
+ zstyle = EQUAL;
+ else if (input->variable->atomstyle(zvar))
+ zstyle = ATOM;
+ else
+ error->all(FLERR, "Variable for fix setvelocity is invalid style");
+ }
+
+ // set index and check validity of region
+
+ if (iregion >= 0) {
+ iregion = domain->find_region(idregion);
+ if (iregion == -1)
+ error->all(FLERR, "Region ID for fix setvelocity does not exist");
+ }
+
+ if (xstyle == ATOM || ystyle == ATOM || zstyle == ATOM)
+ varflag = ATOM;
+ else if (xstyle == EQUAL || ystyle == EQUAL || zstyle == EQUAL)
+ varflag = EQUAL;
+ else
+ varflag = CONSTANT;
+
+ // cannot use non-zero forces for a minimization since no energy is integrated
+ // use fix addforce instead
+
+ int flag = 0;
+ if (update->whichflag == 2) {
+ if (xstyle == EQUAL || xstyle == ATOM)
+ flag = 1;
+ if (ystyle == EQUAL || ystyle == ATOM)
+ flag = 1;
+ if (zstyle == EQUAL || zstyle == ATOM)
+ flag = 1;
+ if (xstyle == CONSTANT && xvalue != 0.0)
+ flag = 1;
+ if (ystyle == CONSTANT && yvalue != 0.0)
+ flag = 1;
+ if (zstyle == CONSTANT && zvalue != 0.0)
+ flag = 1;
+ }
+ if (flag)
+ error->all(FLERR, "Cannot use non-zero forces in an energy minimization");
}
/* ---------------------------------------------------------------------- */
void FixSMDSetVel::setup(int vflag) {
- if (strstr(update->integrate_style, "verlet"))
- post_force(vflag);
- else
+ if (strstr(update->integrate_style, "verlet"))
+ post_force(vflag);
+ else
error->all(FLERR,"Fix smd/setvel does not support RESPA");
}
/* ---------------------------------------------------------------------- */
void FixSMDSetVel::min_setup(int vflag) {
- post_force(vflag);
+ post_force(vflag);
}
/* ---------------------------------------------------------------------- */
//void FixSMDSetVel::initial_integrate(int vflag) {
void FixSMDSetVel::post_force(int vflag) {
- double **x = atom->x;
- double **f = atom->f;
- double **v = atom->v;
- double **vest = atom->vest;
- int *mask = atom->mask;
- int nlocal = atom->nlocal;
-
- // update region if necessary
-
- Region *region = NULL;
- if (iregion >= 0) {
- region = domain->regions[iregion];
- region->prematch();
- }
-
- // reallocate sforce array if necessary
-
- if (varflag == ATOM && atom->nmax > maxatom) {
- maxatom = atom->nmax;
- memory->destroy(sforce);
- memory->create(sforce, maxatom, 3, "setvelocity:sforce");
- }
-
- foriginal[0] = foriginal[1] = foriginal[2] = 0.0;
- force_flag = 0;
-
- if (varflag == CONSTANT) {
- for (int i = 0; i < nlocal; i++)
- if (mask[i] & groupbit) {
- if (region && !region->match(x[i][0], x[i][1], x[i][2]))
- continue;
- foriginal[0] += f[i][0];
- foriginal[1] += f[i][1];
- foriginal[2] += f[i][2];
- if (xstyle) {
- v[i][0] = xvalue;
- vest[i][0] = xvalue;
- f[i][0] = 0.0;
- }
- if (ystyle) {
- v[i][1] = yvalue;
- vest[i][1] = yvalue;
- f[i][1] = 0.0;
- }
- if (zstyle) {
- v[i][2] = zvalue;
- vest[i][2] = zvalue;
- f[i][2] = 0.0;
- }
- }
-
- // variable force, wrap with clear/add
-
- } else {
-
- modify->clearstep_compute();
-
- if (xstyle == EQUAL)
- xvalue = input->variable->compute_equal(xvar);
- else if (xstyle == ATOM)
- input->variable->compute_atom(xvar, igroup, &sforce[0][0], 3, 0);
- if (ystyle == EQUAL)
- yvalue = input->variable->compute_equal(yvar);
- else if (ystyle == ATOM)
- input->variable->compute_atom(yvar, igroup, &sforce[0][1], 3, 0);
- if (zstyle == EQUAL)
- zvalue = input->variable->compute_equal(zvar);
- else if (zstyle == ATOM)
- input->variable->compute_atom(zvar, igroup, &sforce[0][2], 3, 0);
-
- modify->addstep_compute(update->ntimestep + 1);
-
- //printf("setting velocity at timestep %d\n", update->ntimestep);
-
- for (int i = 0; i < nlocal; i++)
- if (mask[i] & groupbit) {
- if (region && !region->match(x[i][0], x[i][1], x[i][2]))
- continue;
- foriginal[0] += f[i][0];
- foriginal[1] += f[i][1];
- foriginal[2] += f[i][2];
- if (xstyle == ATOM) {
- vest[i][0] = v[i][0] = sforce[i][0];
- f[i][0] = 0.0;
- } else if (xstyle) {
- vest[i][0] = v[i][0] = xvalue;
- f[i][0] = 0.0;
- }
-
- if (ystyle == ATOM) {
- vest[i][1] = v[i][1] = sforce[i][1];
- f[i][1] = 0.0;
- } else if (ystyle) {
- vest[i][1] = v[i][1] = yvalue;
- f[i][1] = 0.0;
- }
-
- if (zstyle == ATOM) {
- vest[i][2] = v[i][2] = sforce[i][2];
- f[i][2] = 0.0;
- } else if (zstyle) {
- vest[i][2] = v[i][2] = zvalue;
- f[i][2] = 0.0;
- }
-
- }
- }
+ double **x = atom->x;
+ double **f = atom->f;
+ double **v = atom->v;
+ double **vest = atom->vest;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+
+ // update region if necessary
+
+ Region *region = NULL;
+ if (iregion >= 0) {
+ region = domain->regions[iregion];
+ region->prematch();
+ }
+
+ // reallocate sforce array if necessary
+
+ if (varflag == ATOM && atom->nmax > maxatom) {
+ maxatom = atom->nmax;
+ memory->destroy(sforce);
+ memory->create(sforce, maxatom, 3, "setvelocity:sforce");
+ }
+
+ foriginal[0] = foriginal[1] = foriginal[2] = 0.0;
+ force_flag = 0;
+
+ if (varflag == CONSTANT) {
+ for (int i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit) {
+ if (region && !region->match(x[i][0], x[i][1], x[i][2]))
+ continue;
+ foriginal[0] += f[i][0];
+ foriginal[1] += f[i][1];
+ foriginal[2] += f[i][2];
+ if (xstyle) {
+ v[i][0] = xvalue;
+ vest[i][0] = xvalue;
+ f[i][0] = 0.0;
+ }
+ if (ystyle) {
+ v[i][1] = yvalue;
+ vest[i][1] = yvalue;
+ f[i][1] = 0.0;
+ }
+ if (zstyle) {
+ v[i][2] = zvalue;
+ vest[i][2] = zvalue;
+ f[i][2] = 0.0;
+ }
+ }
+
+ // variable force, wrap with clear/add
+
+ } else {
+
+ modify->clearstep_compute();
+
+ if (xstyle == EQUAL)
+ xvalue = input->variable->compute_equal(xvar);
+ else if (xstyle == ATOM)
+ input->variable->compute_atom(xvar, igroup, &sforce[0][0], 3, 0);
+ if (ystyle == EQUAL)
+ yvalue = input->variable->compute_equal(yvar);
+ else if (ystyle == ATOM)
+ input->variable->compute_atom(yvar, igroup, &sforce[0][1], 3, 0);
+ if (zstyle == EQUAL)
+ zvalue = input->variable->compute_equal(zvar);
+ else if (zstyle == ATOM)
+ input->variable->compute_atom(zvar, igroup, &sforce[0][2], 3, 0);
+
+ modify->addstep_compute(update->ntimestep + 1);
+
+ //printf("setting velocity at timestep %d\n", update->ntimestep);
+
+ for (int i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit) {
+ if (region && !region->match(x[i][0], x[i][1], x[i][2]))
+ continue;
+ foriginal[0] += f[i][0];
+ foriginal[1] += f[i][1];
+ foriginal[2] += f[i][2];
+ if (xstyle == ATOM) {
+ vest[i][0] = v[i][0] = sforce[i][0];
+ f[i][0] = 0.0;
+ } else if (xstyle) {
+ vest[i][0] = v[i][0] = xvalue;
+ f[i][0] = 0.0;
+ }
+
+ if (ystyle == ATOM) {
+ vest[i][1] = v[i][1] = sforce[i][1];
+ f[i][1] = 0.0;
+ } else if (ystyle) {
+ vest[i][1] = v[i][1] = yvalue;
+ f[i][1] = 0.0;
+ }
+
+ if (zstyle == ATOM) {
+ vest[i][2] = v[i][2] = sforce[i][2];
+ f[i][2] = 0.0;
+ } else if (zstyle) {
+ vest[i][2] = v[i][2] = zvalue;
+ f[i][2] = 0.0;
+ }
+
+ }
+ }
}
/* ----------------------------------------------------------------------
@@ -348,11 +348,11 @@ void FixSMDSetVel::post_force(int vflag) {
double FixSMDSetVel::compute_vector(int n) {
// only sum across procs one time
- if (force_flag == 0) {
- MPI_Allreduce(foriginal, foriginal_all, 3, MPI_DOUBLE, MPI_SUM, world);
- force_flag = 1;
- }
- return foriginal_all[n];
+ if (force_flag == 0) {
+ MPI_Allreduce(foriginal, foriginal_all, 3, MPI_DOUBLE, MPI_SUM, world);
+ force_flag = 1;
+ }
+ return foriginal_all[n];
}
/* ----------------------------------------------------------------------
@@ -360,8 +360,8 @@ double FixSMDSetVel::compute_vector(int n) {
------------------------------------------------------------------------- */
double FixSMDSetVel::memory_usage() {
- double bytes = 0.0;
- if (varflag == ATOM)
- bytes = atom->nmax * 3 * sizeof(double);
- return bytes;
+ double bytes = 0.0;
+ if (varflag == ATOM)
+ bytes = atom->nmax * 3 * sizeof(double);
+ return bytes;
}
diff --git a/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp b/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp
index 76fd8021b6..da0533c88b 100644
--- a/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp
+++ b/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp
@@ -57,141 +57,141 @@ using namespace SMD_Math;
/* ---------------------------------------------------------------------- */
FixSMD_TLSPH_ReferenceConfiguration::FixSMD_TLSPH_ReferenceConfiguration(LAMMPS *lmp, int narg, char **arg) :
- Fix(lmp, narg, arg) {
-
- if (atom->map_style == 0)
- error->all(FLERR, "Pair tlsph with partner list requires an atom map, see atom_modify");
-
- maxpartner = 1;
- npartner = NULL;
- partner = NULL;
- wfd_list = NULL;
- wf_list = NULL;
- energy_per_bond = NULL;
- degradation_ij = NULL;
- grow_arrays(atom->nmax);
- atom->add_callback(0);
-
- // initialize npartner to 0 so neighbor list creation is OK the 1st time
- int nlocal = atom->nlocal;
- for (int i = 0; i < nlocal; i++) {
- npartner[i] = 0;
- }
-
- comm_forward = 14;
- updateFlag = 1;
+ Fix(lmp, narg, arg) {
+
+ if (atom->map_style == 0)
+ error->all(FLERR, "Pair tlsph with partner list requires an atom map, see atom_modify");
+
+ maxpartner = 1;
+ npartner = NULL;
+ partner = NULL;
+ wfd_list = NULL;
+ wf_list = NULL;
+ energy_per_bond = NULL;
+ degradation_ij = NULL;
+ grow_arrays(atom->nmax);
+ atom->add_callback(0);
+
+ // initialize npartner to 0 so neighbor list creation is OK the 1st time
+ int nlocal = atom->nlocal;
+ for (int i = 0; i < nlocal; i++) {
+ npartner[i] = 0;
+ }
+
+ comm_forward = 14;
+ updateFlag = 1;
}
/* ---------------------------------------------------------------------- */
FixSMD_TLSPH_ReferenceConfiguration::~FixSMD_TLSPH_ReferenceConfiguration() {
- // unregister this fix so atom class doesn't invoke it any more
+ // unregister this fix so atom class doesn't invoke it any more
- atom->delete_callback(id, 0);
+ atom->delete_callback(id, 0);
// delete locally stored arrays
- memory->destroy(npartner);
- memory->destroy(partner);
- memory->destroy(wfd_list);
- memory->destroy(wf_list);
- memory->destroy(degradation_ij);
- memory->destroy(energy_per_bond);
+ memory->destroy(npartner);
+ memory->destroy(partner);
+ memory->destroy(wfd_list);
+ memory->destroy(wf_list);
+ memory->destroy(degradation_ij);
+ memory->destroy(energy_per_bond);
}
/* ---------------------------------------------------------------------- */
int FixSMD_TLSPH_ReferenceConfiguration::setmask() {
- int mask = 0;
- mask |= PRE_EXCHANGE;
- return mask;
+ int mask = 0;
+ mask |= PRE_EXCHANGE;
+ return mask;
}
/* ---------------------------------------------------------------------- */
void FixSMD_TLSPH_ReferenceConfiguration::init() {
- if (atom->tag_enable == 0)
- error->all(FLERR, "Pair style tlsph requires atoms have IDs");
+ if (atom->tag_enable == 0)
+ error->all(FLERR, "Pair style tlsph requires atoms have IDs");
}
/* ---------------------------------------------------------------------- */
void FixSMD_TLSPH_ReferenceConfiguration::pre_exchange() {
- //return;
-
- //printf("in FixSMD_TLSPH_ReferenceConfiguration::pre_exchange()\n");
- double **defgrad = atom->smd_data_9;
- double *radius = atom->radius;
- double *rho = atom->rho;
- double *vfrac = atom->vfrac;
- double **x = atom->x;
- double **x0 = atom->x0;
- double *rmass = atom->rmass;
- int nlocal = atom->nlocal;
- int i, itmp;
- int *mask = atom->mask;
- if (igroup == atom->firstgroup) {
- nlocal = atom->nfirst;
- }
-
- int *updateFlag_ptr = (int *) force->pair->extract("smd/tlsph/updateFlag_ptr", itmp);
- if (updateFlag_ptr == NULL) {
- error->one(FLERR,
- "fix FixSMD_TLSPH_ReferenceConfiguration failed to access updateFlag pointer. Check if a pair style exist which calculates this quantity.");
- }
-
- int *nn = (int *) force->pair->extract("smd/tlsph/numNeighsRefConfig_ptr", itmp);
- if (nn == NULL) {
- error->all(FLERR, "FixSMDIntegrateTlsph::updateReferenceConfiguration() failed to access numNeighsRefConfig_ptr array");
- }
-
- // sum all update flag across processors
- MPI_Allreduce(updateFlag_ptr, &updateFlag, 1, MPI_INT, MPI_MAX, world);
-
- if (updateFlag > 0) {
- if (comm->me == 0) {
- printf("**** updating ref config at step: %ld\n", update->ntimestep);
- }
-
- for (i = 0; i < nlocal; i++) {
-
- if (mask[i] & groupbit) {
-
- // re-set x0 coordinates
- x0[i][0] = x[i][0];
- x0[i][1] = x[i][1];
- x0[i][2] = x[i][2];
-
- // re-set deformation gradient
- defgrad[i][0] = 1.0;
- defgrad[i][1] = 0.0;
- defgrad[i][2] = 0.0;
- defgrad[i][3] = 0.0;
- defgrad[i][4] = 1.0;
- defgrad[i][5] = 0.0;
- defgrad[i][6] = 0.0;
- defgrad[i][7] = 0.0;
- defgrad[i][8] = 1.0;
- /*
- * Adjust particle volume as the reference configuration is changed.
- * We safeguard against excessive deformations by limiting the adjustment range
- * to the intervale J \in [0.9..1.1]
- */
- vfrac[i] = rmass[i] / rho[i];
+ //return;
+
+ //printf("in FixSMD_TLSPH_ReferenceConfiguration::pre_exchange()\n");
+ double **defgrad = atom->smd_data_9;
+ double *radius = atom->radius;
+ double *rho = atom->rho;
+ double *vfrac = atom->vfrac;
+ double **x = atom->x;
+ double **x0 = atom->x0;
+ double *rmass = atom->rmass;
+ int nlocal = atom->nlocal;
+ int i, itmp;
+ int *mask = atom->mask;
+ if (igroup == atom->firstgroup) {
+ nlocal = atom->nfirst;
+ }
+
+ int *updateFlag_ptr = (int *) force->pair->extract("smd/tlsph/updateFlag_ptr", itmp);
+ if (updateFlag_ptr == NULL) {
+ error->one(FLERR,
+ "fix FixSMD_TLSPH_ReferenceConfiguration failed to access updateFlag pointer. Check if a pair style exist which calculates this quantity.");
+ }
+
+ int *nn = (int *) force->pair->extract("smd/tlsph/numNeighsRefConfig_ptr", itmp);
+ if (nn == NULL) {
+ error->all(FLERR, "FixSMDIntegrateTlsph::updateReferenceConfiguration() failed to access numNeighsRefConfig_ptr array");
+ }
+
+ // sum all update flag across processors
+ MPI_Allreduce(updateFlag_ptr, &updateFlag, 1, MPI_INT, MPI_MAX, world);
+
+ if (updateFlag > 0) {
+ if (comm->me == 0) {
+ printf("**** updating ref config at step: %ld\n", update->ntimestep);
+ }
+
+ for (i = 0; i < nlocal; i++) {
+
+ if (mask[i] & groupbit) {
+
+ // re-set x0 coordinates
+ x0[i][0] = x[i][0];
+ x0[i][1] = x[i][1];
+ x0[i][2] = x[i][2];
+
+ // re-set deformation gradient
+ defgrad[i][0] = 1.0;
+ defgrad[i][1] = 0.0;
+ defgrad[i][2] = 0.0;
+ defgrad[i][3] = 0.0;
+ defgrad[i][4] = 1.0;
+ defgrad[i][5] = 0.0;
+ defgrad[i][6] = 0.0;
+ defgrad[i][7] = 0.0;
+ defgrad[i][8] = 1.0;
+ /*
+ * Adjust particle volume as the reference configuration is changed.
+ * We safeguard against excessive deformations by limiting the adjustment range
+ * to the intervale J \in [0.9..1.1]
+ */
+ vfrac[i] = rmass[i] / rho[i];
//
- if (nn[i] < 15) {
- radius[i] *= 1.2;
- } // else //{
- // radius[i] *= pow(J, 1.0 / domain->dimension);
- //}
- }
- }
-
- // update of reference config could have changed x0, vfrac, radius
- // communicate these quantities now to ghosts: x0, vfrac, radius
- comm->forward_comm_fix(this);
-
- setup(0);
- }
+ if (nn[i] < 15) {
+ radius[i] *= 1.2;
+ } // else //{
+ // radius[i] *= pow(J, 1.0 / domain->dimension);
+ //}
+ }
+ }
+
+ // update of reference config could have changed x0, vfrac, radius
+ // communicate these quantities now to ghosts: x0, vfrac, radius
+ comm->forward_comm_fix(this);
+
+ setup(0);
+ }
}
/* ----------------------------------------------------------------------
@@ -200,155 +200,155 @@ void FixSMD_TLSPH_ReferenceConfiguration::pre_exchange() {
------------------------------------------------------------------------- */
void FixSMD_TLSPH_ReferenceConfiguration::setup(int vflag) {
- int i, j, ii, jj, n, inum, jnum;
- int *ilist, *jlist, *numneigh, **firstneigh;
- double r, h, wf, wfd;
- Vector3d dx;
+ int i, j, ii, jj, n, inum, jnum;
+ int *ilist, *jlist, *numneigh, **firstneigh;
+ double r, h, wf, wfd;
+ Vector3d dx;
- if (updateFlag == 0)
- return;
+ if (updateFlag == 0)
+ return;
- int nlocal = atom->nlocal;
- nmax = atom->nmax;
- grow_arrays(nmax);
+ int nlocal = atom->nlocal;
+ nmax = atom->nmax;
+ grow_arrays(nmax);
// 1st loop over neighbor list
// calculate npartner for each owned atom
// nlocal_neigh = nlocal when neigh list was built, may be smaller than nlocal
- double **x0 = atom->x;
- double *radius = atom->radius;
- int *mask = atom->mask;
- tagint *tag = atom->tag;
- NeighList *list = pair->list;
- inum = list->inum;
- ilist = list->ilist;
- numneigh = list->numneigh;
- firstneigh = list->firstneigh;
-
- // zero npartner for all current atoms
- for (i = 0; i < nlocal; i++)
- npartner[i] = 0;
-
- for (ii = 0; ii < inum; ii++) {
- i = ilist[ii];
- jlist = firstneigh[i];
- jnum = numneigh[i];
-
- for (jj = 0; jj < jnum; jj++) {
- j = jlist[jj];
- j &= NEIGHMASK;
-
- if (INSERT_PREDEFINED_CRACKS) {
- if (!crack_exclude(i, j))
- continue;
- }
-
- dx(0) = x0[i][0] - x0[j][0];
- dx(1) = x0[i][1] - x0[j][1];
- dx(2) = x0[i][2] - x0[j][2];
- r = dx.norm();
- h = radius[i] + radius[j];
-
- if (r <= h) {
- npartner[i]++;
- if (j < nlocal) {
- npartner[j]++;
- }
- }
- }
- }
-
- maxpartner = 0;
- for (i = 0; i < nlocal; i++)
- maxpartner = MAX(maxpartner, npartner[i]);
- int maxall;
- MPI_Allreduce(&maxpartner, &maxall, 1, MPI_INT, MPI_MAX, world);
- maxpartner = maxall;
-
- grow_arrays(nmax);
-
- for (i = 0; i < nlocal; i++) {
- npartner[i] = 0;
- for (jj = 0; jj < maxpartner; jj++) {
- wfd_list[i][jj] = 0.0;
- wf_list[i][jj] = 0.0;
- degradation_ij[i][jj] = 0.0;
- energy_per_bond[i][jj] = 0.0;
- }
- }
-
- for (ii = 0; ii < inum; ii++) {
- i = ilist[ii];
- jlist = firstneigh[i];
- jnum = numneigh[i];
-
- for (jj = 0; jj < jnum; jj++) {
- j = jlist[jj];
- j &= NEIGHMASK;
-
- dx(0) = x0[i][0] - x0[j][0];
- dx(1) = x0[i][1] - x0[j][1];
- dx(2) = x0[i][2] - x0[j][2];
- r = dx.norm();
- h = radius[i] + radius[j];
-
- if (INSERT_PREDEFINED_CRACKS) {
- if (!crack_exclude(i, j))
- continue;
- }
-
- if (r < h) {
- spiky_kernel_and_derivative(h, r, domain->dimension, wf, wfd);
-
- partner[i][npartner[i]] = tag[j];
- wfd_list[i][npartner[i]] = wfd;
- wf_list[i][npartner[i]] = wf;
- npartner[i]++;
- if (j < nlocal) {
- partner[j][npartner[j]] = tag[i];
- wfd_list[j][npartner[j]] = wfd;
- wf_list[j][npartner[j]] = wf;
- npartner[j]++;
- }
- }
- }
- }
-
- // count number of particles for which this group is active
-
- // bond statistics
- if (update->ntimestep > -1) {
- n = 0;
- int count = 0;
- for (i = 0; i < nlocal; i++) {
- if (mask[i] & groupbit) {
- n += npartner[i];
- count += 1;
- }
- }
- int nall, countall;
- MPI_Allreduce(&n, &nall, 1, MPI_INT, MPI_SUM, world);
- MPI_Allreduce(&count, &countall, 1, MPI_INT, MPI_SUM, world);
+ double **x0 = atom->x;
+ double *radius = atom->radius;
+ int *mask = atom->mask;
+ tagint *tag = atom->tag;
+ NeighList *list = pair->list;
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
+
+ // zero npartner for all current atoms
+ for (i = 0; i < nlocal; i++)
+ npartner[i] = 0;
+
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
+ j &= NEIGHMASK;
+
+ if (INSERT_PREDEFINED_CRACKS) {
+ if (!crack_exclude(i, j))
+ continue;
+ }
+
+ dx(0) = x0[i][0] - x0[j][0];
+ dx(1) = x0[i][1] - x0[j][1];
+ dx(2) = x0[i][2] - x0[j][2];
+ r = dx.norm();
+ h = radius[i] + radius[j];
+
+ if (r <= h) {
+ npartner[i]++;
+ if (j < nlocal) {
+ npartner[j]++;
+ }
+ }
+ }
+ }
+
+ maxpartner = 0;
+ for (i = 0; i < nlocal; i++)
+ maxpartner = MAX(maxpartner, npartner[i]);
+ int maxall;
+ MPI_Allreduce(&maxpartner, &maxall, 1, MPI_INT, MPI_MAX, world);
+ maxpartner = maxall;
+
+ grow_arrays(nmax);
+
+ for (i = 0; i < nlocal; i++) {
+ npartner[i] = 0;
+ for (jj = 0; jj < maxpartner; jj++) {
+ wfd_list[i][jj] = 0.0;
+ wf_list[i][jj] = 0.0;
+ degradation_ij[i][jj] = 0.0;
+ energy_per_bond[i][jj] = 0.0;
+ }
+ }
+
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
+ j &= NEIGHMASK;
+
+ dx(0) = x0[i][0] - x0[j][0];
+ dx(1) = x0[i][1] - x0[j][1];
+ dx(2) = x0[i][2] - x0[j][2];
+ r = dx.norm();
+ h = radius[i] + radius[j];
+
+ if (INSERT_PREDEFINED_CRACKS) {
+ if (!crack_exclude(i, j))
+ continue;
+ }
+
+ if (r < h) {
+ spiky_kernel_and_derivative(h, r, domain->dimension, wf, wfd);
+
+ partner[i][npartner[i]] = tag[j];
+ wfd_list[i][npartner[i]] = wfd;
+ wf_list[i][npartner[i]] = wf;
+ npartner[i]++;
+ if (j < nlocal) {
+ partner[j][npartner[j]] = tag[i];
+ wfd_list[j][npartner[j]] = wfd;
+ wf_list[j][npartner[j]] = wf;
+ npartner[j]++;
+ }
+ }
+ }
+ }
+
+ // count number of particles for which this group is active
+
+ // bond statistics
+ if (update->ntimestep > -1) {
+ n = 0;
+ int count = 0;
+ for (i = 0; i < nlocal; i++) {
+ if (mask[i] & groupbit) {
+ n += npartner[i];
+ count += 1;
+ }
+ }
+ int nall, countall;
+ MPI_Allreduce(&n, &nall, 1, MPI_INT, MPI_SUM, world);
+ MPI_Allreduce(&count, &countall, 1, MPI_INT, MPI_SUM, world);
if (countall < 1) countall = 1;
- if (comm->me == 0) {
- if (screen) {
- printf("\n>>========>>========>>========>>========>>========>>========>>========>>========\n");
- fprintf(screen, "TLSPH neighbors:\n");
- fprintf(screen, " max # of neighbors for a single particle = %d\n", maxpartner);
- fprintf(screen, " average # of neighbors/particle in group tlsph = %g\n", (double) nall / countall);
- printf(">>========>>========>>========>>========>>========>>========>>========>>========\n\n");
- }
- if (logfile) {
- fprintf(logfile, "\nTLSPH neighbors:\n");
- fprintf(logfile, " max # of neighbors for a single particle = %d\n", maxpartner);
- fprintf(logfile, " average # of neighbors/particle in group tlsph = %g\n", (double) nall / countall);
- }
- }
- }
-
- updateFlag = 0; // set update flag to zero after the update
+ if (comm->me == 0) {
+ if (screen) {
+ printf("\n>>========>>========>>========>>========>>========>>========>>========>>========\n");
+ fprintf(screen, "TLSPH neighbors:\n");
+ fprintf(screen, " max # of neighbors for a single particle = %d\n", maxpartner);
+ fprintf(screen, " average # of neighbors/particle in group tlsph = %g\n", (double) nall / countall);
+ printf(">>========>>========>>========>>========>>========>>========>>========>>========\n\n");
+ }
+ if (logfile) {
+ fprintf(logfile, "\nTLSPH neighbors:\n");
+ fprintf(logfile, " max # of neighbors for a single particle = %d\n", maxpartner);
+ fprintf(logfile, " average # of neighbors/particle in group tlsph = %g\n", (double) nall / countall);
+ }
+ }
+ }
+
+ updateFlag = 0; // set update flag to zero after the update
}
@@ -357,14 +357,14 @@ void FixSMD_TLSPH_ReferenceConfiguration::setup(int vflag) {
------------------------------------------------------------------------- */
double FixSMD_TLSPH_ReferenceConfiguration::memory_usage() {
- int nmax = atom->nmax;
- int bytes = nmax * sizeof(int);
- bytes += nmax * maxpartner * sizeof(tagint); // partner array
- bytes += nmax * maxpartner * sizeof(float); // wf_list
- bytes += nmax * maxpartner * sizeof(float); // wfd_list
- bytes += nmax * maxpartner * sizeof(float); // damage_per_interaction array
- bytes += nmax * sizeof(int); // npartner array
- return bytes;
+ int nmax = atom->nmax;
+ int bytes = nmax * sizeof(int);
+ bytes += nmax * maxpartner * sizeof(tagint); // partner array
+ bytes += nmax * maxpartner * sizeof(float); // wf_list
+ bytes += nmax * maxpartner * sizeof(float); // wfd_list
+ bytes += nmax * maxpartner * sizeof(float); // damage_per_interaction array
+ bytes += nmax * sizeof(int); // npartner array
+ return bytes;
}
@@ -373,13 +373,13 @@ double FixSMD_TLSPH_ReferenceConfiguration::memory_usage() {
------------------------------------------------------------------------- */
void FixSMD_TLSPH_ReferenceConfiguration::grow_arrays(int nmax) {
- //printf("in FixSMD_TLSPH_ReferenceConfiguration::grow_arrays\n");
- memory->grow(npartner, nmax, "tlsph_refconfig_neigh:npartner");
- memory->grow(partner, nmax, maxpartner, "tlsph_refconfig_neigh:partner");
- memory->grow(wfd_list, nmax, maxpartner, "tlsph_refconfig_neigh:wfd");
- memory->grow(wf_list, nmax, maxpartner, "tlsph_refconfig_neigh:wf");
- memory->grow(degradation_ij, nmax, maxpartner, "tlsph_refconfig_neigh:degradation_ij");
- memory->grow(energy_per_bond, nmax, maxpartner, "tlsph_refconfig_neigh:damage_onset_strain");
+ //printf("in FixSMD_TLSPH_ReferenceConfiguration::grow_arrays\n");
+ memory->grow(npartner, nmax, "tlsph_refconfig_neigh:npartner");
+ memory->grow(partner, nmax, maxpartner, "tlsph_refconfig_neigh:partner");
+ memory->grow(wfd_list, nmax, maxpartner, "tlsph_refconfig_neigh:wfd");
+ memory->grow(wf_list, nmax, maxpartner, "tlsph_refconfig_neigh:wf");
+ memory->grow(degradation_ij, nmax, maxpartner, "tlsph_refconfig_neigh:degradation_ij");
+ memory->grow(energy_per_bond, nmax, maxpartner, "tlsph_refconfig_neigh:damage_onset_strain");
}
/* ----------------------------------------------------------------------
@@ -387,14 +387,14 @@ void FixSMD_TLSPH_ReferenceConfiguration::grow_arrays(int nmax) {
------------------------------------------------------------------------- */
void FixSMD_TLSPH_ReferenceConfiguration::copy_arrays(int i, int j, int delflag) {
- npartner[j] = npartner[i];
- for (int m = 0; m < npartner[j]; m++) {
- partner[j][m] = partner[i][m];
- wfd_list[j][m] = wfd_list[i][m];
- wf_list[j][m] = wf_list[i][m];
- degradation_ij[j][m] = degradation_ij[i][m];
- energy_per_bond[j][m] = energy_per_bond[i][m];
- }
+ npartner[j] = npartner[i];
+ for (int m = 0; m < npartner[j]; m++) {
+ partner[j][m] = partner[i][m];
+ wfd_list[j][m] = wfd_list[i][m];
+ wf_list[j][m] = wf_list[i][m];
+ degradation_ij[j][m] = degradation_ij[i][m];
+ energy_per_bond[j][m] = energy_per_bond[i][m];
+ }
}
/* ----------------------------------------------------------------------
@@ -407,16 +407,16 @@ int FixSMD_TLSPH_ReferenceConfiguration::pack_exchange(int i, double *buf) {
//printf("pack_exchange ...\n");
- int m = 0;
- buf[m++] = npartner[i];
- for (int n = 0; n < npartner[i]; n++) {
- buf[m++] = partner[i][n];
- buf[m++] = wfd_list[i][n];
- buf[m++] = wf_list[i][n];
- buf[m++] = degradation_ij[i][n];
- buf[m++] = energy_per_bond[i][n];
- }
- return m;
+ int m = 0;
+ buf[m++] = npartner[i];
+ for (int n = 0; n < npartner[i]; n++) {
+ buf[m++] = partner[i][n];
+ buf[m++] = wfd_list[i][n];
+ buf[m++] = wf_list[i][n];
+ buf[m++] = degradation_ij[i][n];
+ buf[m++] = energy_per_bond[i][n];
+ }
+ return m;
}
@@ -425,27 +425,27 @@ int FixSMD_TLSPH_ReferenceConfiguration::pack_exchange(int i, double *buf) {
------------------------------------------------------------------------- */
int FixSMD_TLSPH_ReferenceConfiguration::unpack_exchange(int nlocal, double *buf) {
- if (nlocal == nmax) {
- //printf("nlocal=%d, nmax=%d\n", nlocal, nmax);
- nmax = nmax / DELTA * DELTA;
- nmax += DELTA;
- grow_arrays(nmax);
-
- error->message(FLERR,
- "in Fixtlsph_refconfigNeighGCG::unpack_exchange: local arrays too small for receiving partner information; growing arrays");
- }
+ if (nlocal == nmax) {
+ //printf("nlocal=%d, nmax=%d\n", nlocal, nmax);
+ nmax = nmax / DELTA * DELTA;
+ nmax += DELTA;
+ grow_arrays(nmax);
+
+ error->message(FLERR,
+ "in Fixtlsph_refconfigNeighGCG::unpack_exchange: local arrays too small for receiving partner information; growing arrays");
+ }
//printf("nlocal=%d, nmax=%d\n", nlocal, nmax);
- int m = 0;
- npartner[nlocal] = static_cast<int>(buf[m++]);
- for (int n = 0; n < npartner[nlocal]; n++) {
- partner[nlocal][n] = static_cast<tagint>(buf[m++]);
- wfd_list[nlocal][n] = static_cast<float>(buf[m++]);
- wf_list[nlocal][n] = static_cast<float>(buf[m++]);
- degradation_ij[nlocal][n] = static_cast<float>(buf[m++]);
- energy_per_bond[nlocal][n] = static_cast<float>(buf[m++]);
- }
- return m;
+ int m = 0;
+ npartner[nlocal] = static_cast<int>(buf[m++]);
+ for (int n = 0; n < npartner[nlocal]; n++) {
+ partner[nlocal][n] = static_cast<tagint>(buf[m++]);
+ wfd_list[nlocal][n] = static_cast<float>(buf[m++]);
+ wf_list[nlocal][n] = static_cast<float>(buf[m++]);
+ degradation_ij[nlocal][n] = static_cast<float>(buf[m++]);
+ energy_per_bond[nlocal][n] = static_cast<float>(buf[m++]);
+ }
+ return m;
}
/* ----------------------------------------------------------------------
@@ -453,17 +453,17 @@ int FixSMD_TLSPH_ReferenceConfiguration::unpack_exchange(int nlocal, double *buf
------------------------------------------------------------------------- */
int FixSMD_TLSPH_ReferenceConfiguration::pack_restart(int i, double *buf) {
- int m = 0;
- buf[m++] = 4 * npartner[i] + 2;
- buf[m++] = npartner[i];
- for (int n = 0; n < npartner[i]; n++) {
- buf[m++] = partner[i][n];
- buf[m++] = wfd_list[i][n];
- buf[m++] = wf_list[i][n];
- buf[m++] = degradation_ij[i][n];
- buf[m++] = energy_per_bond[i][n];
- }
- return m;
+ int m = 0;
+ buf[m++] = 4 * npartner[i] + 2;
+ buf[m++] = npartner[i];
+ for (int n = 0; n < npartner[i]; n++) {
+ buf[m++] = partner[i][n];
+ buf[m++] = wfd_list[i][n];
+ buf[m++] = wf_list[i][n];
+ buf[m++] = degradation_ij[i][n];
+ buf[m++] = energy_per_bond[i][n];
+ }
+ return m;
}
/* ----------------------------------------------------------------------
@@ -475,19 +475,19 @@ void FixSMD_TLSPH_ReferenceConfiguration::unpack_restart(int nlocal, int nth) {
// skip to Nth set of extra values
-// double **extra = atom->extra;
+// double **extra = atom->extra;
//
-// int m = 0;
-// for (int i = 0; i < nth; i++)
-// m += static_cast<int>(extra[nlocal][m]);
-// m++;
+// int m = 0;
+// for (int i = 0; i < nth; i++)
+// m += static_cast<int>(extra[nlocal][m]);
+// m++;
//
-// // allocate new chunks from ipage,dpage for incoming values
+// // allocate new chunks from ipage,dpage for incoming values
//
-// 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++]);
-// }
+// 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++]);
+// }
}
/* ----------------------------------------------------------------------
@@ -497,9 +497,9 @@ void FixSMD_TLSPH_ReferenceConfiguration::unpack_restart(int nlocal, int nth) {
int FixSMD_TLSPH_ReferenceConfiguration::maxsize_restart() {
// maxtouch_all = max # of touching partners across all procs
- int maxtouch_all;
- MPI_Allreduce(&maxpartner, &maxtouch_all, 1, MPI_INT, MPI_MAX, world);
- return 4 * maxtouch_all + 2;
+ int maxtouch_all;
+ MPI_Allreduce(&maxpartner, &maxtouch_all, 1, MPI_INT, MPI_MAX, world);
+ return 4 * maxtouch_all + 2;
}
/* ----------------------------------------------------------------------
@@ -507,72 +507,72 @@ int FixSMD_TLSPH_ReferenceConfiguration::maxsize_restart() {
------------------------------------------------------------------------- */
int FixSMD_TLSPH_ReferenceConfiguration::size_restart(int nlocal) {
- return 4 * npartner[nlocal] + 2;
+ return 4 * npartner[nlocal] + 2;
}
/* ---------------------------------------------------------------------- */
int FixSMD_TLSPH_ReferenceConfiguration::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc) {
- int i, j, m;
- double *radius = atom->radius;
- double *vfrac = atom->vfrac;
- double **x0 = atom->x0;
- double **defgrad0 = atom->smd_data_9;
-
- //printf("FixSMD_TLSPH_ReferenceConfiguration:::pack_forward_comm\n");
- m = 0;
- for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = x0[j][0];
- buf[m++] = x0[j][1];
- buf[m++] = x0[j][2];
-
- buf[m++] = vfrac[j];
- buf[m++] = radius[j];
-
- buf[m++] = defgrad0[i][0];
- buf[m++] = defgrad0[i][1];
- buf[m++] = defgrad0[i][2];
- buf[m++] = defgrad0[i][3];
- buf[m++] = defgrad0[i][4];
- buf[m++] = defgrad0[i][5];
- buf[m++] = defgrad0[i][6];
- buf[m++] = defgrad0[i][7];
- buf[m++] = defgrad0[i][8];
-
- }
- return m;
+ int i, j, m;
+ double *radius = atom->radius;
+ double *vfrac = atom->vfrac;
+ double **x0 = atom->x0;
+ double **defgrad0 = atom->smd_data_9;
+
+ //printf("FixSMD_TLSPH_ReferenceConfiguration:::pack_forward_comm\n");
+ m = 0;
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = x0[j][0];
+ buf[m++] = x0[j][1];
+ buf[m++] = x0[j][2];
+
+ buf[m++] = vfrac[j];
+ buf[m++] = radius[j];
+
+ buf[m++] = defgrad0[i][0];
+ buf[m++] = defgrad0[i][1];
+ buf[m++] = defgrad0[i][2];
+ buf[m++] = defgrad0[i][3];
+ buf[m++] = defgrad0[i][4];
+ buf[m++] = defgrad0[i][5];
+ buf[m++] = defgrad0[i][6];
+ buf[m++] = defgrad0[i][7];
+ buf[m++] = defgrad0[i][8];
+
+ }
+ return m;
}
/* ---------------------------------------------------------------------- */
void FixSMD_TLSPH_ReferenceConfiguration::unpack_forward_comm(int n, int first, double *buf) {
- int i, m, last;
- double *radius = atom->radius;
- double *vfrac = atom->vfrac;
- double **x0 = atom->x0;
- double **defgrad0 = atom->smd_data_9;
-
- m = 0;
- last = first + n;
- for (i = first; i < last; i++) {
- x0[i][0] = buf[m++];
- x0[i][1] = buf[m++];
- x0[i][2] = buf[m++];
-
- vfrac[i] = buf[m++];
- radius[i] = buf[m++];
-
- defgrad0[i][0] = buf[m++];
- defgrad0[i][1] = buf[m++];
- defgrad0[i][2] = buf[m++];
- defgrad0[i][3] = buf[m++];
- defgrad0[i][4] = buf[m++];
- defgrad0[i][5] = buf[m++];
- defgrad0[i][6] = buf[m++];
- defgrad0[i][7] = buf[m++];
- defgrad0[i][8] = buf[m++];
- }
+ int i, m, last;
+ double *radius = atom->radius;
+ double *vfrac = atom->vfrac;
+ double **x0 = atom->x0;
+ double **defgrad0 = atom->smd_data_9;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ x0[i][0] = buf[m++];
+ x0[i][1] = buf[m++];
+ x0[i][2] = buf[m++];
+
+ vfrac[i] = buf[m++];
+ radius[i] = buf[m++];
+
+ defgrad0[i][0] = buf[m++];
+ defgrad0[i][1] = buf[m++];
+ defgrad0[i][2] = buf[m++];
+ defgrad0[i][3] = buf[m++];
+ defgrad0[i][4] = buf[m++];
+ defgrad0[i][5] = buf[m++];
+ defgrad0[i][6] = buf[m++];
+ defgrad0[i][7] = buf[m++];
+ defgrad0[i][8] = buf[m++];
+ }
}
/* ----------------------------------------------------------------------
@@ -583,26 +583,26 @@ void FixSMD_TLSPH_ReferenceConfiguration::unpack_forward_comm(int n, int first,
bool FixSMD_TLSPH_ReferenceConfiguration::crack_exclude(int i, int j) {
- double **x = atom->x;
- double l0 = domain->lattice->xlattice;
+ double **x = atom->x;
+ double l0 = domain->lattice->xlattice;
- // line between pair of atoms i,j
- double x1 = x[i][0] / l0;
- double y1 = x[i][1] / l0;
+ // line between pair of atoms i,j
+ double x1 = x[i][0] / l0;
+ double y1 = x[i][1] / l0;
- double x2 = x[j][0] / l0;
- double y2 = x[j][1] / l0;
+ double x2 = x[j][0] / l0;
+ double y2 = x[j][1] / l0;
- // hardcoded crack line
- double x3 = -0.1 / l0;
- double y3 = ((int) 1.0 / l0) + 0.5;
- //printf("y3 = %f\n", y3);
- double x4 = 0.1 / l0 - 1.0 + 0.1;
- double y4 = y3;
+ // hardcoded crack line
+ double x3 = -0.1 / l0;
+ double y3 = ((int) 1.0 / l0) + 0.5;
+ //printf("y3 = %f\n", y3);
+ double x4 = 0.1 / l0 - 1.0 + 0.1;
+ double y4 = y3;
- bool retVal = DoLineSegmentsIntersect(x1, y1, x2, y2, x3, y3, x4, y4);
+ bool retVal = DoLineSegmentsIntersect(x1, y1, x2, y2, x3, y3, x4, y4);
- return !retVal;
- //return 1;
+ return !retVal;
+ //return 1;
}
diff --git a/src/USER-SMD/fix_smd_tlsph_reference_configuration.h b/src/USER-SMD/fix_smd_tlsph_reference_configuration.h
index 3ff693e9bb..8549621c2f 100644
--- a/src/USER-SMD/fix_smd_tlsph_reference_configuration.h
+++ b/src/USER-SMD/fix_smd_tlsph_reference_configuration.h
@@ -40,42 +40,42 @@ FixStyle(SMD_TLSPH_NEIGHBORS,FixSMD_TLSPH_ReferenceConfiguration)
namespace LAMMPS_NS {
class FixSMD_TLSPH_ReferenceConfiguration: public Fix {
- friend class Neighbor;
- friend class PairTlsph;
+ friend class Neighbor;
+ friend class PairTlsph;
public:
- FixSMD_TLSPH_ReferenceConfiguration(class LAMMPS *, int, char **);
- ~FixSMD_TLSPH_ReferenceConfiguration();
- int setmask();
- void init();
- void setup(int);
- void pre_exchange();
- int pack_forward_comm(int, int *, double *, int, int *);
- void unpack_forward_comm(int, int, double *);
-
- double memory_usage();
- void grow_arrays(int);
- void copy_arrays(int, int, int);
- int pack_exchange(int, double *);
- int unpack_exchange(int, double *);
- int pack_restart(int, double *);
- void unpack_restart(int, int);
- int size_restart(int);
- int maxsize_restart();
-
- bool crack_exclude(int i, int j);
- bool get_line_intersection(int i, int j);
+ FixSMD_TLSPH_ReferenceConfiguration(class LAMMPS *, int, char **);
+ ~FixSMD_TLSPH_ReferenceConfiguration();
+ int setmask();
+ void init();
+ void setup(int);
+ void pre_exchange();
+ int pack_forward_comm(int, int *, double *, int, int *);
+ void unpack_forward_comm(int, int, double *);
+
+ double memory_usage();
+ void grow_arrays(int);
+ void copy_arrays(int, int, int);
+ int pack_exchange(int, double *);
+ int unpack_exchange(int, double *);
+ int pack_restart(int, double *);
+ void unpack_restart(int, int);
+ int size_restart(int);
+ int maxsize_restart();
+
+ bool crack_exclude(int i, int j);
+ bool get_line_intersection(int i, int j);
protected:
- int updateFlag; // flag to update reference configuration
- int nmax;
- int maxpartner;
- int *npartner; // # of touching partners of each atom
- tagint **partner; // global atom IDs for the partners
- float **wfd_list, **wf_list, **energy_per_bond;
- float **degradation_ij; // per-pair interaction degradation status
-
- class Pair *pair;
+ int updateFlag; // flag to update reference configuration
+ int nmax;
+ int maxpartner;
+ int *npartner; // # of touching partners of each atom
+ tagint **partner; // global atom IDs for the partners
+ float **wfd_list, **wf_list, **energy_per_bond;
+ float **degradation_ij; // per-pair interaction degradation status
+
+ class Pair *pair;
};
diff --git a/src/USER-SMD/fix_smd_wall_surface.cpp b/src/USER-SMD/fix_smd_wall_surface.cpp
index 94cac6e20c..53232af001 100644
--- a/src/USER-SMD/fix_smd_wall_surface.cpp
+++ b/src/USER-SMD/fix_smd_wall_surface.cpp
@@ -41,39 +41,39 @@ using namespace std;
#define DELTA 16384
#define EPSILON 1.0e-6
enum {
- LAYOUT_UNIFORM, LAYOUT_NONUNIFORM, LAYOUT_TILED
+ LAYOUT_UNIFORM, LAYOUT_NONUNIFORM, LAYOUT_TILED
};
// several files
/* ---------------------------------------------------------------------- */
FixSMDWallSurface::FixSMDWallSurface(LAMMPS *lmp, int narg, char **arg) :
- Fix(lmp, narg, arg) {
-
- restart_global = 0;
- restart_peratom = 0;
- first = 1;
-
- //atom->add_callback(0);
- //atom->add_callback(1);
-
- if (narg != 6)
- error->all(FLERR, "Illegal number of arguments for fix smd/wall_surface");
-
- filename = strdup(arg[3]);
- wall_particle_type = force->inumeric(FLERR, arg[4]);
- wall_molecule_id = force->inumeric(FLERR, arg[5]);
- if (wall_molecule_id < 65535) {
- error->one(FLERR, "wall molcule id must be >= 65535\n");
- }
-
- if (comm->me == 0) {
- printf("\n>>========>>========>>========>>========>>========>>========>>========>>========\n");
- printf("fix smd/wall_surface reads trianglulated surface from file: %s\n", filename);
- printf("fix smd/wall_surface has particle type %d \n", wall_particle_type);
- printf("fix smd/wall_surface has molecule id %d \n", wall_molecule_id);
- printf(">>========>>========>>========>>========>>========>>========>>========>>========\n");
- }
+ Fix(lmp, narg, arg) {
+
+ restart_global = 0;
+ restart_peratom = 0;
+ first = 1;
+
+ //atom->add_callback(0);
+ //atom->add_callback(1);
+
+ if (narg != 6)
+ error->all(FLERR, "Illegal number of arguments for fix smd/wall_surface");
+
+ filename = strdup(arg[3]);
+ wall_particle_type = force->inumeric(FLERR, arg[4]);
+ wall_molecule_id = force->inumeric(FLERR, arg[5]);
+ if (wall_molecule_id < 65535) {
+ error->one(FLERR, "wall molcule id must be >= 65535\n");
+ }
+
+ if (comm->me == 0) {
+ printf("\n>>========>>========>>========>>========>>========>>========>>========>>========\n");
+ printf("fix smd/wall_surface reads trianglulated surface from file: %s\n", filename);
+ printf("fix smd/wall_surface has particle type %d \n", wall_particle_type);
+ printf("fix smd/wall_surface has molecule id %d \n", wall_molecule_id);
+ printf(">>========>>========>>========>>========>>========>>========>>========>>========\n");
+ }
}
/* ---------------------------------------------------------------------- */
@@ -81,24 +81,24 @@ FixSMDWallSurface::FixSMDWallSurface(LAMMPS *lmp, int narg, char **arg) :
FixSMDWallSurface::~FixSMDWallSurface() {
free(filename);
filename = NULL;
- // unregister this fix so atom class doesn't invoke it any more
+ // unregister this fix so atom class doesn't invoke it any more
- //atom->delete_callback(id, 0);
- //atom->delete_callback(id, 1);
+ //atom->delete_callback(id, 0);
+ //atom->delete_callback(id, 1);
}
/* ---------------------------------------------------------------------- */
int FixSMDWallSurface::setmask() {
- int mask = 0;
- return mask;
+ int mask = 0;
+ return mask;
}
/* ---------------------------------------------------------------------- */
void FixSMDWallSurface::init() {
- if (!first)
- return;
+ if (!first)
+ return;
}
/* ----------------------------------------------------------------------
@@ -106,7 +106,7 @@ void FixSMDWallSurface::init() {
------------------------------------------------------------------------- */
void FixSMDWallSurface::min_setup(int vflag) {
- setup(vflag);
+ setup(vflag);
}
/* ----------------------------------------------------------------------
@@ -116,83 +116,83 @@ void FixSMDWallSurface::min_setup(int vflag) {
void FixSMDWallSurface::setup(int vflag) {
- if (!first)
- return;
- first = 0;
-
- // set bounds for my proc
- // if periodic and I am lo/hi proc, adjust bounds by EPSILON
- // insures all data atoms will be owned even with round-off
-
- int triclinic = domain->triclinic;
-
- double epsilon[3];
- if (triclinic)
- epsilon[0] = epsilon[1] = epsilon[2] = EPSILON;
- else {
- epsilon[0] = domain->prd[0] * EPSILON;
- epsilon[1] = domain->prd[1] * EPSILON;
- epsilon[2] = domain->prd[2] * EPSILON;
- }
-
- if (triclinic == 0) {
- sublo[0] = domain->sublo[0];
- subhi[0] = domain->subhi[0];
- sublo[1] = domain->sublo[1];
- subhi[1] = domain->subhi[1];
- sublo[2] = domain->sublo[2];
- subhi[2] = domain->subhi[2];
- } else {
- sublo[0] = domain->sublo_lamda[0];
- subhi[0] = domain->subhi_lamda[0];
- sublo[1] = domain->sublo_lamda[1];
- subhi[1] = domain->subhi_lamda[1];
- sublo[2] = domain->sublo_lamda[2];
- subhi[2] = domain->subhi_lamda[2];
- }
-
- if (comm->layout != LAYOUT_TILED) {
- if (domain->xperiodic) {
- if (comm->myloc[0] == 0)
- sublo[0] -= epsilon[0];
- if (comm->myloc[0] == comm->procgrid[0] - 1)
- subhi[0] += epsilon[0];
- }
- if (domain->yperiodic) {
- if (comm->myloc[1] == 0)
- sublo[1] -= epsilon[1];
- if (comm->myloc[1] == comm->procgrid[1] - 1)
- subhi[1] += epsilon[1];
- }
- if (domain->zperiodic) {
- if (comm->myloc[2] == 0)
- sublo[2] -= epsilon[2];
- if (comm->myloc[2] == comm->procgrid[2] - 1)
- subhi[2] += epsilon[2];
- }
-
- } else {
- if (domain->xperiodic) {
- if (comm->mysplit[0][0] == 0.0)
- sublo[0] -= epsilon[0];
- if (comm->mysplit[0][1] == 1.0)
- subhi[0] += epsilon[0];
- }
- if (domain->yperiodic) {
- if (comm->mysplit[1][0] == 0.0)
- sublo[1] -= epsilon[1];
- if (comm->mysplit[1][1] == 1.0)
- subhi[1] += epsilon[1];
- }
- if (domain->zperiodic) {
- if (comm->mysplit[2][0] == 0.0)
- sublo[2] -= epsilon[2];
- if (comm->mysplit[2][1] == 1.0)
- subhi[2] += epsilon[2];
- }
- }
-
- read_triangles(0);
+ if (!first)
+ return;
+ first = 0;
+
+ // set bounds for my proc
+ // if periodic and I am lo/hi proc, adjust bounds by EPSILON
+ // insures all data atoms will be owned even with round-off
+
+ int triclinic = domain->triclinic;
+
+ double epsilon[3];
+ if (triclinic)
+ epsilon[0] = epsilon[1] = epsilon[2] = EPSILON;
+ else {
+ epsilon[0] = domain->prd[0] * EPSILON;
+ epsilon[1] = domain->prd[1] * EPSILON;
+ epsilon[2] = domain->prd[2] * EPSILON;
+ }
+
+ if (triclinic == 0) {
+ sublo[0] = domain->sublo[0];
+ subhi[0] = domain->subhi[0];
+ sublo[1] = domain->sublo[1];
+ subhi[1] = domain->subhi[1];
+ sublo[2] = domain->sublo[2];
+ subhi[2] = domain->subhi[2];
+ } else {
+ sublo[0] = domain->sublo_lamda[0];
+ subhi[0] = domain->subhi_lamda[0];
+ sublo[1] = domain->sublo_lamda[1];
+ subhi[1] = domain->subhi_lamda[1];
+ sublo[2] = domain->sublo_lamda[2];
+ subhi[2] = domain->subhi_lamda[2];
+ }
+
+ if (comm->layout != LAYOUT_TILED) {
+ if (domain->xperiodic) {
+ if (comm->myloc[0] == 0)
+ sublo[0] -= epsilon[0];
+ if (comm->myloc[0] == comm->procgrid[0] - 1)
+ subhi[0] += epsilon[0];
+ }
+ if (domain->yperiodic) {
+ if (comm->myloc[1] == 0)
+ sublo[1] -= epsilon[1];
+ if (comm->myloc[1] == comm->procgrid[1] - 1)
+ subhi[1] += epsilon[1];
+ }
+ if (domain->zperiodic) {
+ if (comm->myloc[2] == 0)
+ sublo[2] -= epsilon[2];
+ if (comm->myloc[2] == comm->procgrid[2] - 1)
+ subhi[2] += epsilon[2];
+ }
+
+ } else {
+ if (domain->xperiodic) {
+ if (comm->mysplit[0][0] == 0.0)
+ sublo[0] -= epsilon[0];
+ if (comm->mysplit[0][1] == 1.0)
+ subhi[0] += epsilon[0];
+ }
+ if (domain->yperiodic) {
+ if (comm->mysplit[1][0] == 0.0)
+ sublo[1] -= epsilon[1];
+ if (comm->mysplit[1][1] == 1.0)
+ subhi[1] += epsilon[1];
+ }
+ if (domain->zperiodic) {
+ if (comm->mysplit[2][0] == 0.0)
+ sublo[2] -= epsilon[2];
+ if (comm->mysplit[2][1] == 1.0)
+ subhi[2] += epsilon[2];
+ }
+ }
+
+ read_triangles(0);
}
/* ----------------------------------------------------------------------
@@ -200,25 +200,25 @@ void FixSMDWallSurface::setup(int vflag) {
------------------------------------------------------------------------- */
int FixSMDWallSurface::count_words(const char *line) {
- int n = strlen(line) + 1;
- char *copy;
- memory->create(copy, n, "atom:copy");
- strcpy(copy, line);
-
- char *ptr;
- if ((ptr = strchr(copy, '#')))
- *ptr = '\0';
-
- if (strtok(copy, " \t\n\r\f") == NULL) {
- memory->destroy(copy);
- return 0;
- }
- n = 1;
- while (strtok(NULL, " \t\n\r\f"))
- n++;
-
- memory->destroy(copy);
- return n;
+ int n = strlen(line) + 1;
+ char *copy;
+ memory->create(copy, n, "atom:copy");
+ strcpy(copy, line);
+
+ char *ptr;
+ if ((ptr = strchr(copy, '#')))
+ *ptr = '\0';
+
+ if (strtok(copy, " \t\n\r\f") == NULL) {
+ memory->destroy(copy);
+ return 0;
+ }
+ n = 1;
+ while (strtok(NULL, " \t\n\r\f"))
+ n++;
+
+ memory->destroy(copy);
+ return n;
}
/* ----------------------------------------------------------------------
@@ -227,283 +227,283 @@ int FixSMDWallSurface::count_words(const char *line) {
void FixSMDWallSurface::read_triangles(int pass) {
- double coord[3];
-
- int nlocal_previous = atom->nlocal;
- int ilocal = nlocal_previous;
- int m;
- int me;
-
- bigint natoms_previous = atom->natoms;
- Vector3d *vert;
- vert = new Vector3d[3];
- Vector3d normal, center;
-
- FILE *fp = fopen(filename, "r");
- if (fp == NULL) {
- char str[128];
- sprintf(str, "Cannot open file %s", filename);
- error->one(FLERR, str);
- }
-
- MPI_Comm_rank(world, &me);
- if (me == 0) {
- if (screen) {
- if (pass == 0) {
- printf("\n>>========>>========>>========>>========>>========>>========>>========>>========\n");
- fprintf(screen, " scanning triangle pairs ...\n");
- } else {
- fprintf(screen, " reading triangle pairs ...\n");
- }
- }
- if (logfile) {
- if (pass == 0) {
- fprintf(logfile, " scanning triangle pairs ...\n");
- } else {
- fprintf(logfile, " reading triangle pairs ...\n");
- }
- }
- }
-
- char str[128];
- char line[256];
- char *retpointer;
- char **values;
- int nwords;
-
- // read STL solid name
- retpointer = fgets(line, sizeof(line), fp);
- if (retpointer == NULL) {
- sprintf(str, "error reading number of triangle pairs");
- error->one(FLERR, str);
- }
-
- nwords = count_words(line);
- if (nwords < 1) {
- sprintf(str, "first line of file is incorrect");
- error->one(FLERR, str);
- }
-
-// values = new char*[nwords];
-// values[0] = strtok(line, " \t\n\r\f");
-// if (values[0] == NULL)
-// error->all(FLERR, "Incorrect atom format in data file");
-// for (m = 1; m < nwords; m++) {
-// values[m] = strtok(NULL, " \t\n\r\f");
-// if (values[m] == NULL)
-// error->all(FLERR, "Incorrect atom format in data file");
-// }
-// delete[] values;
+ double coord[3];
+
+ int nlocal_previous = atom->nlocal;
+ int ilocal = nlocal_previous;
+ int m;
+ int me;
+
+ bigint natoms_previous = atom->natoms;
+ Vector3d *vert;
+ vert = new Vector3d[3];
+ Vector3d normal, center;
+
+ FILE *fp = fopen(filename, "r");
+ if (fp == NULL) {
+ char str[128];
+ sprintf(str, "Cannot open file %s", filename);
+ error->one(FLERR, str);
+ }
+
+ MPI_Comm_rank(world, &me);
+ if (me == 0) {
+ if (screen) {
+ if (pass == 0) {
+ printf("\n>>========>>========>>========>>========>>========>>========>>========>>========\n");
+ fprintf(screen, " scanning triangle pairs ...\n");
+ } else {
+ fprintf(screen, " reading triangle pairs ...\n");
+ }
+ }
+ if (logfile) {
+ if (pass == 0) {
+ fprintf(logfile, " scanning triangle pairs ...\n");
+ } else {
+ fprintf(logfile, " reading triangle pairs ...\n");
+ }
+ }
+ }
+
+ char str[128];
+ char line[256];
+ char *retpointer;
+ char **values;
+ int nwords;
+
+ // read STL solid name
+ retpointer = fgets(line, sizeof(line), fp);
+ if (retpointer == NULL) {
+ sprintf(str, "error reading number of triangle pairs");
+ error->one(FLERR, str);
+ }
+
+ nwords = count_words(line);
+ if (nwords < 1) {
+ sprintf(str, "first line of file is incorrect");
+ error->one(FLERR, str);
+ }
+
+// values = new char*[nwords];
+// values[0] = strtok(line, " \t\n\r\f");
+// if (values[0] == NULL)
+// error->all(FLERR, "Incorrect atom format in data file");
+// for (m = 1; m < nwords; m++) {
+// values[m] = strtok(NULL, " \t\n\r\f");
+// if (values[m] == NULL)
+// error->all(FLERR, "Incorrect atom format in data file");
+// }
+// delete[] values;
//
-// if (comm->me == 0) {
-// cout << "STL file contains solid body with name: " << values[1] << endl;
-// }
-
- // iterate over STL facets util end of body is reached
-
- while (fgets(line, sizeof(line), fp)) { // read a line, should be the facet line
-
- // evaluate facet line
- nwords = count_words(line);
- if (nwords != 5) {
- //sprintf(str, "found end solid line");
- //error->message(FLERR, str);
- break;
- } else {
- // should be facet line
- }
-
- values = new char*[nwords];
- values[0] = strtok(line, " \t\n\r\f");
- if (values[0] == NULL)
- error->all(FLERR, "Incorrect atom format in data file");
- for (m = 1; m < nwords; m++) {
- values[m] = strtok(NULL, " \t\n\r\f");
- if (values[m] == NULL)
- error->all(FLERR, "Incorrect atom format in data file");
- }
-
- normal << force->numeric(FLERR, values[2]), force->numeric(FLERR, values[3]), force->numeric(FLERR, values[4]);
- //cout << "normal is " << normal << endl;
-
- delete[] values;
-
- // read outer loop line
- retpointer = fgets(line, sizeof(line), fp);
- if (retpointer == NULL) {
- sprintf(str, "error reading outer loop");
- error->one(FLERR, str);
- }
-
- nwords = count_words(line);
- if (nwords != 2) {
- sprintf(str, "error reading outer loop");
- error->one(FLERR, str);
- }
-
- // read vertex lines
-
- for (int k = 0; k < 3; k++) {
- retpointer = fgets(line, sizeof(line), fp);
- if (retpointer == NULL) {
- sprintf(str, "error reading vertex line");
- error->one(FLERR, str);
- }
-
- nwords = count_words(line);
- if (nwords != 4) {
- sprintf(str, "error reading vertex line");
- error->one(FLERR, str);
- }
-
- values = new char*[nwords];
- values[0] = strtok(line, " \t\n\r\f");
- if (values[0] == NULL)
- error->all(FLERR, "Incorrect vertex line");
- for (m = 1; m < nwords; m++) {
- values[m] = strtok(NULL, " \t\n\r\f");
- if (values[m] == NULL)
- error->all(FLERR, "Incorrect vertex line");
- }
-
- vert[k] << force->numeric(FLERR, values[1]), force->numeric(FLERR, values[2]), force->numeric(FLERR, values[3]);
- //cout << "vertex is " << vert[k] << endl;
- //printf("%s %s %s\n", values[1], values[2], values[3]);
- delete[] values;
- //exit(1);
-
- }
-
- // read end loop line
- retpointer = fgets(line, sizeof(line), fp);
- if (retpointer == NULL) {
- sprintf(str, "error reading endloop");
- error->one(FLERR, str);
- }
-
- nwords = count_words(line);
- if (nwords != 1) {
- sprintf(str, "error reading endloop");
- error->one(FLERR, str);
- }
-
- // read end facet line
- retpointer = fgets(line, sizeof(line), fp);
- if (retpointer == NULL) {
- sprintf(str, "error reading endfacet");
- error->one(FLERR, str);
- }
-
- nwords = count_words(line);
- if (nwords != 1) {
- sprintf(str, "error reading endfacet");
- error->one(FLERR, str);
- }
-
- // now we have a normal and three vertices ... proceed with adding triangle
-
- center = (vert[0] + vert[1] + vert[2]) / 3.0;
-
- // cout << "center is " << center << endl;
-
- double r1 = (center - vert[0]).norm();
- double r2 = (center - vert[1]).norm();
- double r3 = (center - vert[2]).norm();
- double r = MAX(r1, r2);
- r = MAX(r, r3);
-
- /*
- * if atom/molecule is in my subbox, create it
- * ... use x0 to hold triangle normal.
- * ... use smd_data_9 to hold the three vertices
- * ... use x to hold triangle center
- * ... radius is the mmaximal distance from triangle center to all vertices
- */
-
- // printf("coord: %f %f %f\n", coord[0], coord[1], coord[2]);
- // printf("sublo: %f %f %f\n", sublo[0], sublo[1], sublo[2]);
- // printf("subhi: %f %f %f\n", subhi[0], subhi[1], subhi[2]);
- //printf("ilocal = %d\n", ilocal);
- if (center(0) >= sublo[0] && center(0) < subhi[0] && center(1) >= sublo[1] && center(1) < subhi[1] && center(2) >= sublo[2]
- && center(2) < subhi[2]) {
- //printf("******* KERATIN nlocal=%d ***\n", nlocal);
- coord[0] = center(0);
- coord[1] = center(1);
- coord[2] = center(2);
- atom->avec->create_atom(wall_particle_type, coord);
-
- /*
- * need to initialize pointers to atom vec arrays here, because they could have changed
- * due to calling grow() in create_atoms() above;
- */
-
- tagint *mol = atom->molecule;
- int *type = atom->type;
- double *radius = atom->radius;
- double *contact_radius = atom->contact_radius;
- double **smd_data_9 = atom->smd_data_9;
- double **x0 = atom->x0;
-
- radius[ilocal] = r; //ilocal;
- contact_radius[ilocal] = r; //ilocal;
- mol[ilocal] = wall_molecule_id;
- type[ilocal] = wall_particle_type;
- x0[ilocal][0] = normal(0);
- x0[ilocal][1] = normal(1);
- x0[ilocal][2] = normal(2);
- smd_data_9[ilocal][0] = vert[0](0);
- smd_data_9[ilocal][1] = vert[0](1);
- smd_data_9[ilocal][2] = vert[0](2);
- smd_data_9[ilocal][3] = vert[1](0);
- smd_data_9[ilocal][4] = vert[1](1);
- smd_data_9[ilocal][5] = vert[1](2);
- smd_data_9[ilocal][6] = vert[2](0);
- smd_data_9[ilocal][7] = vert[2](1);
- smd_data_9[ilocal][8] = vert[2](2);
-
- ilocal++;
- }
-
- }
+// if (comm->me == 0) {
+// cout << "STL file contains solid body with name: " << values[1] << endl;
+// }
+
+ // iterate over STL facets util end of body is reached
+
+ while (fgets(line, sizeof(line), fp)) { // read a line, should be the facet line
+
+ // evaluate facet line
+ nwords = count_words(line);
+ if (nwords != 5) {
+ //sprintf(str, "found end solid line");
+ //error->message(FLERR, str);
+ break;
+ } else {
+ // should be facet line
+ }
+
+ values = new char*[nwords];
+ values[0] = strtok(line, " \t\n\r\f");
+ if (values[0] == NULL)
+ error->all(FLERR, "Incorrect atom format in data file");
+ for (m = 1; m < nwords; m++) {
+ values[m] = strtok(NULL, " \t\n\r\f");
+ if (values[m] == NULL)
+ error->all(FLERR, "Incorrect atom format in data file");
+ }
+
+ normal << force->numeric(FLERR, values[2]), force->numeric(FLERR, values[3]), force->numeric(FLERR, values[4]);
+ //cout << "normal is " << normal << endl;
+
+ delete[] values;
+
+ // read outer loop line
+ retpointer = fgets(line, sizeof(line), fp);
+ if (retpointer == NULL) {
+ sprintf(str, "error reading outer loop");
+ error->one(FLERR, str);
+ }
+
+ nwords = count_words(line);
+ if (nwords != 2) {
+ sprintf(str, "error reading outer loop");
+ error->one(FLERR, str);
+ }
+
+ // read vertex lines
+
+ for (int k = 0; k < 3; k++) {
+ retpointer = fgets(line, sizeof(line), fp);
+ if (retpointer == NULL) {
+ sprintf(str, "error reading vertex line");
+ error->one(FLERR, str);
+ }
+
+ nwords = count_words(line);
+ if (nwords != 4) {
+ sprintf(str, "error reading vertex line");
+ error->one(FLERR, str);
+ }
+
+ values = new char*[nwords];
+ values[0] = strtok(line, " \t\n\r\f");
+ if (values[0] == NULL)
+ error->all(FLERR, "Incorrect vertex line");
+ for (m = 1; m < nwords; m++) {
+ values[m] = strtok(NULL, " \t\n\r\f");
+ if (values[m] == NULL)
+ error->all(FLERR, "Incorrect vertex line");
+ }
+
+ vert[k] << force->numeric(FLERR, values[1]), force->numeric(FLERR, values[2]), force->numeric(FLERR, values[3]);
+ //cout << "vertex is " << vert[k] << endl;
+ //printf("%s %s %s\n", values[1], values[2], values[3]);
+ delete[] values;
+ //exit(1);
+
+ }
+
+ // read end loop line
+ retpointer = fgets(line, sizeof(line), fp);
+ if (retpointer == NULL) {
+ sprintf(str, "error reading endloop");
+ error->one(FLERR, str);
+ }
+
+ nwords = count_words(line);
+ if (nwords != 1) {
+ sprintf(str, "error reading endloop");
+ error->one(FLERR, str);
+ }
+
+ // read end facet line
+ retpointer = fgets(line, sizeof(line), fp);
+ if (retpointer == NULL) {
+ sprintf(str, "error reading endfacet");
+ error->one(FLERR, str);
+ }
+
+ nwords = count_words(line);
+ if (nwords != 1) {
+ sprintf(str, "error reading endfacet");
+ error->one(FLERR, str);
+ }
+
+ // now we have a normal and three vertices ... proceed with adding triangle
+
+ center = (vert[0] + vert[1] + vert[2]) / 3.0;
+
+ // cout << "center is " << center << endl;
+
+ double r1 = (center - vert[0]).norm();
+ double r2 = (center - vert[1]).norm();
+ double r3 = (center - vert[2]).norm();
+ double r = MAX(r1, r2);
+ r = MAX(r, r3);
+
+ /*
+ * if atom/molecule is in my subbox, create it
+ * ... use x0 to hold triangle normal.
+ * ... use smd_data_9 to hold the three vertices
+ * ... use x to hold triangle center
+ * ... radius is the mmaximal distance from triangle center to all vertices
+ */
+
+ // printf("coord: %f %f %f\n", coord[0], coord[1], coord[2]);
+ // printf("sublo: %f %f %f\n", sublo[0], sublo[1], sublo[2]);
+ // printf("subhi: %f %f %f\n", subhi[0], subhi[1], subhi[2]);
+ //printf("ilocal = %d\n", ilocal);
+ if (center(0) >= sublo[0] && center(0) < subhi[0] && center(1) >= sublo[1] && center(1) < subhi[1] && center(2) >= sublo[2]
+ && center(2) < subhi[2]) {
+ //printf("******* KERATIN nlocal=%d ***\n", nlocal);
+ coord[0] = center(0);
+ coord[1] = center(1);
+ coord[2] = center(2);
+ atom->avec->create_atom(wall_particle_type, coord);
+
+ /*
+ * need to initialize pointers to atom vec arrays here, because they could have changed
+ * due to calling grow() in create_atoms() above;
+ */
+
+ tagint *mol = atom->molecule;
+ int *type = atom->type;
+ double *radius = atom->radius;
+ double *contact_radius = atom->contact_radius;
+ double **smd_data_9 = atom->smd_data_9;
+ double **x0 = atom->x0;
+
+ radius[ilocal] = r; //ilocal;
+ contact_radius[ilocal] = r; //ilocal;
+ mol[ilocal] = wall_molecule_id;
+ type[ilocal] = wall_particle_type;
+ x0[ilocal][0] = normal(0);
+ x0[ilocal][1] = normal(1);
+ x0[ilocal][2] = normal(2);
+ smd_data_9[ilocal][0] = vert[0](0);
+ smd_data_9[ilocal][1] = vert[0](1);
+ smd_data_9[ilocal][2] = vert[0](2);
+ smd_data_9[ilocal][3] = vert[1](0);
+ smd_data_9[ilocal][4] = vert[1](1);
+ smd_data_9[ilocal][5] = vert[1](2);
+ smd_data_9[ilocal][6] = vert[2](0);
+ smd_data_9[ilocal][7] = vert[2](1);
+ smd_data_9[ilocal][8] = vert[2](2);
+
+ ilocal++;
+ }
+
+ }
// set new total # of atoms and error check
- bigint nblocal = atom->nlocal;
- MPI_Allreduce(&nblocal, &atom->natoms, 1, MPI_LMP_BIGINT, MPI_SUM, world);
- if (atom->natoms < 0 || atom->natoms >= MAXBIGINT)
- error->all(FLERR, "Too many total atoms");
+ bigint nblocal = atom->nlocal;
+ MPI_Allreduce(&nblocal, &atom->natoms, 1, MPI_LMP_BIGINT, MPI_SUM, world);
+ if (atom->natoms < 0 || atom->natoms >= MAXBIGINT)
+ error->all(FLERR, "Too many total atoms");
// add IDs for newly created atoms
// check that atom IDs are valid
- if (atom->tag_enable)
- atom->tag_extend();
- atom->tag_check();
+ if (atom->tag_enable)
+ atom->tag_extend();
+ atom->tag_check();
// create global mapping of atoms
// zero nghost in case are adding new atoms to existing atoms
- if (atom->map_style) {
- atom->nghost = 0;
- atom->map_init();
- atom->map_set();
- }
+ if (atom->map_style) {
+ atom->nghost = 0;
+ atom->map_init();
+ atom->map_set();
+ }
// print status
- if (comm->me == 0) {
- if (screen) {
- printf("... fix smd/wall_surface finished reading triangulated surface\n");
- fprintf(screen, "fix smd/wall_surface created " BIGINT_FORMAT " atoms\n", atom->natoms - natoms_previous);
- printf(">>========>>========>>========>>========>>========>>========>>========>>========\n");
- }
- if (logfile) {
- fprintf(logfile, "... fix smd/wall_surface finished reading triangulated surface\n");
- fprintf(logfile, "fix smd/wall_surface created " BIGINT_FORMAT " atoms\n", atom->natoms - natoms_previous);
- fprintf(logfile, ">>========>>========>>========>>========>>========>>========>>========>>========\n");
- }
- }
-
- delete[] vert;
- fclose(fp);
+ if (comm->me == 0) {
+ if (screen) {
+ printf("... fix smd/wall_surface finished reading triangulated surface\n");
+ fprintf(screen, "fix smd/wall_surface created " BIGINT_FORMAT " atoms\n", atom->natoms - natoms_previous);
+ printf(">>========>>========>>========>>========>>========>>========>>========>>========\n");
+ }
+ if (logfile) {
+ fprintf(logfile, "... fix smd/wall_surface finished reading triangulated surface\n");
+ fprintf(logfile, "fix smd/wall_surface created " BIGINT_FORMAT " atoms\n", atom->natoms - natoms_previous);
+ fprintf(logfile, ">>========>>========>>========>>========>>========>>========>>========>>========\n");
+ }
+ }
+
+ delete[] vert;
+ fclose(fp);
}
diff --git a/src/USER-SMD/fix_smd_wall_surface.h b/src/USER-SMD/fix_smd_wall_surface.h
index a32319f48f..10f80c4ca8 100644
--- a/src/USER-SMD/fix_smd_wall_surface.h
+++ b/src/USER-SMD/fix_smd_wall_surface.h
@@ -27,22 +27,22 @@ namespace LAMMPS_NS {
class FixSMDWallSurface: public Fix {
public:
- FixSMDWallSurface(class LAMMPS *, int, char **);
- virtual ~FixSMDWallSurface();
- int setmask();
- void init();
- void setup(int);
- void min_setup(int);
+ FixSMDWallSurface(class LAMMPS *, int, char **);
+ virtual ~FixSMDWallSurface();
+ int setmask();
+ void init();
+ void setup(int);
+ void min_setup(int);
- int count_words(const char *line);
- void read_triangles(int pass);
+ int count_words(const char *line);
+ void read_triangles(int pass);
private:
- int first; // flag for first time initialization
- double sublo[3], subhi[3]; // epsilon-extended proc sub-box for adding atoms;
- char *filename;
- int wall_particle_type;
- int wall_molecule_id;
+ int first; // flag for first time initialization
+ double sublo[3], subhi[3]; // epsilon-extended proc sub-box for adding atoms;
+ char *filename;
+ int wall_particle_type;
+ int wall_molecule_id;
};
}
diff --git a/src/USER-SMD/pair_smd_hertz.cpp b/src/USER-SMD/pair_smd_hertz.cpp
index b5bae7ef47..9b26382965 100644
--- a/src/USER-SMD/pair_smd_hertz.cpp
+++ b/src/USER-SMD/pair_smd_hertz.cpp
@@ -51,166 +51,166 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairHertz::PairHertz(LAMMPS *lmp) :
- Pair(lmp) {
+ Pair(lmp) {
- onerad_dynamic = onerad_frozen = maxrad_dynamic = maxrad_frozen = NULL;
- bulkmodulus = NULL;
- kn = NULL;
- scale = 1.0;
+ onerad_dynamic = onerad_frozen = maxrad_dynamic = maxrad_frozen = NULL;
+ bulkmodulus = NULL;
+ kn = NULL;
+ scale = 1.0;
}
/* ---------------------------------------------------------------------- */
PairHertz::~PairHertz() {
- if (allocated) {
- memory->destroy(setflag);
- memory->destroy(cutsq);
- memory->destroy(bulkmodulus);
- memory->destroy(kn);
-
- delete[] onerad_dynamic;
- delete[] onerad_frozen;
- delete[] maxrad_dynamic;
- delete[] maxrad_frozen;
- }
+ if (allocated) {
+ memory->destroy(setflag);
+ memory->destroy(cutsq);
+ memory->destroy(bulkmodulus);
+ memory->destroy(kn);
+
+ delete[] onerad_dynamic;
+ delete[] onerad_frozen;
+ delete[] maxrad_dynamic;
+ delete[] maxrad_frozen;
+ }
}
/* ---------------------------------------------------------------------- */
void PairHertz::compute(int eflag, int vflag) {
- int i, j, ii, jj, inum, jnum, itype, jtype;
- double xtmp, ytmp, ztmp, delx, dely, delz;
- double rsq, r, evdwl, fpair;
- int *ilist, *jlist, *numneigh, **firstneigh;
- double rcut, r_geom, delta, ri, rj, dt_crit;
- double *rmass = atom->rmass;
-
- evdwl = 0.0;
- if (eflag || vflag)
- ev_setup(eflag, vflag);
- else
- evflag = vflag_fdotr = 0;
-
- double **f = atom->f;
- double **x = atom->x;
- double **x0 = atom->x0;
- int *type = atom->type;
- int nlocal = atom->nlocal;
- double *radius = atom->contact_radius;
- double *sph_radius = atom->radius;
- double rcutSq;
- double delx0, dely0, delz0, rSq0, sphCut;
-
- int newton_pair = force->newton_pair;
- int periodic = (domain->xperiodic || domain->yperiodic || domain->zperiodic);
-
- inum = list->inum;
- ilist = list->ilist;
- numneigh = list->numneigh;
- firstneigh = list->firstneigh;
-
- stable_time_increment = 1.0e22;
-
- // loop over neighbors of my atoms
- for (ii = 0; ii < inum; ii++) {
- i = ilist[ii];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- itype = type[i];
- ri = scale * radius[i];
- jlist = firstneigh[i];
- jnum = numneigh[i];
-
- for (jj = 0; jj < jnum; jj++) {
- j = jlist[jj];
- j &= NEIGHMASK;
-
- jtype = type[j];
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
-
- rsq = delx * delx + dely * dely + delz * delz;
-
- rj = scale * radius[j];
- rcut = ri + rj;
- rcutSq = rcut * rcut;
-
- if (rsq < rcutSq) {
-
- /*
- * self contact option:
- * if pair of particles was initially close enough to interact via a bulk continuum mechanism (e.g. SPH), exclude pair from contact forces.
- * this approach should work well if no updates of the reference configuration are performed.
- */
-
- if (itype == jtype) {
- delx0 = x0[j][0] - x0[i][0];
- dely0 = x0[j][1] - x0[i][1];
- delz0 = x0[j][2] - x0[i][2];
- if (periodic) {
- domain->minimum_image(delx0, dely0, delz0);
- }
- rSq0 = delx0 * delx0 + dely0 * dely0 + delz0 * delz0; // initial distance
- sphCut = sph_radius[i] + sph_radius[j];
- if (rSq0 < sphCut * sphCut) {
- rcut = 0.5 * rcut;
- rcutSq = rcut * rcut;
- if (rsq > rcutSq) {
- continue;
- }
- }
- }
-
- r = sqrt(rsq);
- //printf("hertz interaction, r=%f, cut=%f, h=%f\n", r, rcut, sqrt(rSq0));
-
- // Hertzian short-range forces
- delta = rcut - r; // overlap distance
- r_geom = ri * rj / rcut;
- //assuming poisson ratio = 1/4 for 3d
- fpair = 1.066666667e0 * bulkmodulus[itype][jtype] * delta * sqrt(delta * r_geom); // units: N
- evdwl = fpair * 0.4e0 * delta; // GCG 25 April: this expression conserves total energy
- dt_crit = 3.14 * sqrt(0.5 * (rmass[i] + rmass[j]) / (fpair / delta));
-
- stable_time_increment = MIN(stable_time_increment, dt_crit);
- if (r > 2.0e-16) {
- fpair /= r; // divide by r and multiply with non-normalized distance vector
- } else {
- fpair = 0.0;
- }
-
- /*
- * contact viscosity -- needs to be done, see GRANULAR package for normal & shear damping
- * for now: no damping and thus no viscous energy deltaE
- */
-
- if (evflag) {
- ev_tally(i, j, nlocal, newton_pair, evdwl, 0.0, fpair, delx, dely, delz);
- }
-
- f[i][0] += delx * fpair;
- f[i][1] += dely * fpair;
- f[i][2] += delz * fpair;
-
- if (newton_pair || j < nlocal) {
- f[j][0] -= delx * fpair;
- f[j][1] -= dely * fpair;
- f[j][2] -= delz * fpair;
- }
-
- }
- }
- }
-
-// double stable_time_increment_all = 0.0;
-// MPI_Allreduce(&stable_time_increment, &stable_time_increment_all, 1, MPI_DOUBLE, MPI_MIN, world);
-// if (comm->me == 0) {
-// printf("stable time step for pair smd/hertz is %f\n", stable_time_increment_all);
-// }
+ int i, j, ii, jj, inum, jnum, itype, jtype;
+ double xtmp, ytmp, ztmp, delx, dely, delz;
+ double rsq, r, evdwl, fpair;
+ int *ilist, *jlist, *numneigh, **firstneigh;
+ double rcut, r_geom, delta, ri, rj, dt_crit;
+ double *rmass = atom->rmass;
+
+ evdwl = 0.0;
+ if (eflag || vflag)
+ ev_setup(eflag, vflag);
+ else
+ evflag = vflag_fdotr = 0;
+
+ double **f = atom->f;
+ double **x = atom->x;
+ double **x0 = atom->x0;
+ int *type = atom->type;
+ int nlocal = atom->nlocal;
+ double *radius = atom->contact_radius;
+ double *sph_radius = atom->radius;
+ double rcutSq;
+ double delx0, dely0, delz0, rSq0, sphCut;
+
+ int newton_pair = force->newton_pair;
+ int periodic = (domain->xperiodic || domain->yperiodic || domain->zperiodic);
+
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
+
+ stable_time_increment = 1.0e22;
+
+ // loop over neighbors of my atoms
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ itype = type[i];
+ ri = scale * radius[i];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
+ j &= NEIGHMASK;
+
+ jtype = type[j];
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+
+ rsq = delx * delx + dely * dely + delz * delz;
+
+ rj = scale * radius[j];
+ rcut = ri + rj;
+ rcutSq = rcut * rcut;
+
+ if (rsq < rcutSq) {
+
+ /*
+ * self contact option:
+ * if pair of particles was initially close enough to interact via a bulk continuum mechanism (e.g. SPH), exclude pair from contact forces.
+ * this approach should work well if no updates of the reference configuration are performed.
+ */
+
+ if (itype == jtype) {
+ delx0 = x0[j][0] - x0[i][0];
+ dely0 = x0[j][1] - x0[i][1];
+ delz0 = x0[j][2] - x0[i][2];
+ if (periodic) {
+ domain->minimum_image(delx0, dely0, delz0);
+ }
+ rSq0 = delx0 * delx0 + dely0 * dely0 + delz0 * delz0; // initial distance
+ sphCut = sph_radius[i] + sph_radius[j];
+ if (rSq0 < sphCut * sphCut) {
+ rcut = 0.5 * rcut;
+ rcutSq = rcut * rcut;
+ if (rsq > rcutSq) {
+ continue;
+ }
+ }
+ }
+
+ r = sqrt(rsq);
+ //printf("hertz interaction, r=%f, cut=%f, h=%f\n", r, rcut, sqrt(rSq0));
+
+ // Hertzian short-range forces
+ delta = rcut - r; // overlap distance
+ r_geom = ri * rj / rcut;
+ //assuming poisson ratio = 1/4 for 3d
+ fpair = 1.066666667e0 * bulkmodulus[itype][jtype] * delta * sqrt(delta * r_geom); // units: N
+ evdwl = fpair * 0.4e0 * delta; // GCG 25 April: this expression conserves total energy
+ dt_crit = 3.14 * sqrt(0.5 * (rmass[i] + rmass[j]) / (fpair / delta));
+
+ stable_time_increment = MIN(stable_time_increment, dt_crit);
+ if (r > 2.0e-16) {
+ fpair /= r; // divide by r and multiply with non-normalized distance vector
+ } else {
+ fpair = 0.0;
+ }
+
+ /*
+ * contact viscosity -- needs to be done, see GRANULAR package for normal & shear damping
+ * for now: no damping and thus no viscous energy deltaE
+ */
+
+ if (evflag) {
+ ev_tally(i, j, nlocal, newton_pair, evdwl, 0.0, fpair, delx, dely, delz);
+ }
+
+ f[i][0] += delx * fpair;
+ f[i][1] += dely * fpair;
+ f[i][2] += delz * fpair;
+
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx * fpair;
+ f[j][1] -= dely * fpair;
+ f[j][2] -= delz * fpair;
+ }
+
+ }
+ }
+ }
+
+// double stable_time_increment_all = 0.0;
+// MPI_Allreduce(&stable_time_increment, &stable_time_increment_all, 1, MPI_DOUBLE, MPI_MIN, world);
+// if (comm->me == 0) {
+// printf("stable time step for pair smd/hertz is %f\n", stable_time_increment_all);
+// }
}
/* ----------------------------------------------------------------------
@@ -218,23 +218,23 @@ void PairHertz::compute(int eflag, int vflag) {
------------------------------------------------------------------------- */
void PairHertz::allocate() {
- allocated = 1;
- int n = atom->ntypes;
+ allocated = 1;
+ int n = atom->ntypes;
- memory->create(setflag, n + 1, n + 1, "pair:setflag");
- for (int i = 1; i <= n; i++)
- for (int j = i; j <= n; j++)
- setflag[i][j] = 0;
+ memory->create(setflag, n + 1, n + 1, "pair:setflag");
+ for (int i = 1; i <= n; i++)
+ for (int j = i; j <= n; j++)
+ setflag[i][j] = 0;
- memory->create(bulkmodulus, n + 1, n + 1, "pair:kspring");
- memory->create(kn, n + 1, n + 1, "pair:kn");
+ memory->create(bulkmodulus, n + 1, n + 1, "pair:kspring");
+ memory->create(kn, n + 1, n + 1, "pair:kn");
- memory->create(cutsq, n + 1, n + 1, "pair:cutsq"); // always needs to be allocated, even with granular neighborlist
+ memory->create(cutsq, n + 1, n + 1, "pair:cutsq"); // always needs to be allocated, even with granular neighborlist
- onerad_dynamic = new double[n + 1];
- onerad_frozen = new double[n + 1];
- maxrad_dynamic = new double[n + 1];
- maxrad_frozen = new double[n + 1];
+ onerad_dynamic = new double[n + 1];
+ onerad_frozen = new double[n + 1];
+ maxrad_dynamic = new double[n + 1];
+ maxrad_frozen = new double[n + 1];
}
/* ----------------------------------------------------------------------
@@ -242,16 +242,16 @@ void PairHertz::allocate() {
------------------------------------------------------------------------- */
void PairHertz::settings(int narg, char **arg) {
- if (narg != 1)
- error->all(FLERR, "Illegal number of args for pair_style hertz");
+ if (narg != 1)
+ error->all(FLERR, "Illegal number of args for pair_style hertz");
- scale = force->numeric(FLERR, arg[0]);
- if (comm->me == 0) {
- printf("\n>>========>>========>>========>>========>>========>>========>>========>>========\n");
- printf("SMD/HERTZ CONTACT SETTINGS:\n");
- printf("... effective contact radius is scaled by %f\n", scale);
- printf(">>========>>========>>========>>========>>========>>========>>========>>========\n");
- }
+ scale = force->numeric(FLERR, arg[0]);
+ if (comm->me == 0) {
+ printf("\n>>========>>========>>========>>========>>========>>========>>========>>========\n");
+ printf("SMD/HERTZ CONTACT SETTINGS:\n");
+ printf("... effective contact radius is scaled by %f\n", scale);
+ printf(">>========>>========>>========>>========>>========>>========>>========>>========\n");
+ }
}
@@ -260,37 +260,37 @@ void PairHertz::settings(int narg, char **arg) {
------------------------------------------------------------------------- */
void PairHertz::coeff(int narg, char **arg) {
- if (narg != 3)
- error->all(FLERR, "Incorrect args for pair coefficients");
- if (!allocated)
- allocate();
-
- int ilo, ihi, jlo, jhi;
- force->bounds(FLERR,arg[0], atom->ntypes, ilo, ihi);
- force->bounds(FLERR,arg[1], atom->ntypes, jlo, jhi);
-
- double bulkmodulus_one = atof(arg[2]);
-
- // set short-range force constant
- double kn_one = 0.0;
- if (domain->dimension == 3) {
- kn_one = (16. / 15.) * bulkmodulus_one; //assuming poisson ratio = 1/4 for 3d
- } else {
- kn_one = 0.251856195 * (2. / 3.) * bulkmodulus_one; //assuming poisson ratio = 1/3 for 2d
- }
-
- int count = 0;
- for (int i = ilo; i <= ihi; i++) {
- for (int j = MAX(jlo, i); j <= jhi; j++) {
- bulkmodulus[i][j] = bulkmodulus_one;
- kn[i][j] = kn_one;
- setflag[i][j] = 1;
- count++;
- }
- }
-
- if (count == 0)
- error->all(FLERR, "Incorrect args for pair coefficients");
+ if (narg != 3)
+ error->all(FLERR, "Incorrect args for pair coefficients");
+ if (!allocated)
+ allocate();
+
+ int ilo, ihi, jlo, jhi;
+ force->bounds(FLERR,arg[0], atom->ntypes, ilo, ihi);
+ force->bounds(FLERR,arg[1], atom->ntypes, jlo, jhi);
+
+ double bulkmodulus_one = atof(arg[2]);
+
+ // set short-range force constant
+ double kn_one = 0.0;
+ if (domain->dimension == 3) {
+ kn_one = (16. / 15.) * bulkmodulus_one; //assuming poisson ratio = 1/4 for 3d
+ } else {
+ kn_one = 0.251856195 * (2. / 3.) * bulkmodulus_one; //assuming poisson ratio = 1/3 for 2d
+ }
+
+ int count = 0;
+ for (int i = ilo; i <= ihi; i++) {
+ for (int j = MAX(jlo, i); j <= jhi; j++) {
+ bulkmodulus[i][j] = bulkmodulus_one;
+ kn[i][j] = kn_one;
+ setflag[i][j] = 1;
+ count++;
+ }
+ }
+
+ if (count == 0)
+ error->all(FLERR, "Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
@@ -299,26 +299,26 @@ void PairHertz::coeff(int narg, char **arg) {
double PairHertz::init_one(int i, int j) {
- if (!allocated)
- allocate();
+ if (!allocated)
+ allocate();
- if (setflag[i][j] == 0)
- error->all(FLERR, "All pair coeffs are not set");
+ if (setflag[i][j] == 0)
+ error->all(FLERR, "All pair coeffs are not set");
- bulkmodulus[j][i] = bulkmodulus[i][j];
- kn[j][i] = kn[i][j];
+ bulkmodulus[j][i] = bulkmodulus[i][j];
+ kn[j][i] = kn[i][j];
- // cutoff = sum of max I,J radii for
- // dynamic/dynamic & dynamic/frozen interactions, but not frozen/frozen
+ // cutoff = sum of max I,J radii for
+ // dynamic/dynamic & dynamic/frozen interactions, but not frozen/frozen
- double cutoff = maxrad_dynamic[i] + maxrad_dynamic[j];
- cutoff = MAX(cutoff, maxrad_frozen[i] + maxrad_dynamic[j]);
- cutoff = MAX(cutoff, maxrad_dynamic[i] + maxrad_frozen[j]);
+ double cutoff = maxrad_dynamic[i] + maxrad_dynamic[j];
+ cutoff = MAX(cutoff, maxrad_frozen[i] + maxrad_dynamic[j]);
+ cutoff = MAX(cutoff, maxrad_dynamic[i] + maxrad_frozen[j]);
- if (comm->me == 0) {
- printf("cutoff for pair smd/hertz = %f\n", cutoff);
- }
- return cutoff;
+ if (comm->me == 0) {
+ printf("cutoff for pair smd/hertz = %f\n", cutoff);
+ }
+ return cutoff;
}
/* ----------------------------------------------------------------------
@@ -326,32 +326,32 @@ double PairHertz::init_one(int i, int j) {
------------------------------------------------------------------------- */
void PairHertz::init_style() {
- int i;
+ int i;
- // error checks
+ // error checks
- if (!atom->contact_radius_flag)
- error->all(FLERR, "Pair style smd/hertz requires atom style with contact_radius");
+ if (!atom->contact_radius_flag)
+ error->all(FLERR, "Pair style smd/hertz requires atom style with contact_radius");
- int irequest = neighbor->request(this);
- neighbor->requests[irequest]->size = 1;
+ int irequest = neighbor->request(this);
+ neighbor->requests[irequest]->size = 1;
- // set maxrad_dynamic and maxrad_frozen for each type
- // include future Fix pour particles as dynamic
+ // set maxrad_dynamic and maxrad_frozen for each type
+ // include future Fix pour particles as dynamic
- for (i = 1; i <= atom->ntypes; i++)
- onerad_dynamic[i] = onerad_frozen[i] = 0.0;
+ for (i = 1; i <= atom->ntypes; i++)
+ onerad_dynamic[i] = onerad_frozen[i] = 0.0;
- double *radius = atom->radius;
- int *type = atom->type;
- int nlocal = atom->nlocal;
+ double *radius = atom->radius;
+ int *type = atom->type;
+ int nlocal = atom->nlocal;
- for (i = 0; i < nlocal; i++) {
- onerad_dynamic[type[i]] = MAX(onerad_dynamic[type[i]], radius[i]);
- }
+ for (i = 0; i < nlocal; i++) {
+ onerad_dynamic[type[i]] = MAX(onerad_dynamic[type[i]], radius[i]);
+ }
- MPI_Allreduce(&onerad_dynamic[1], &maxrad_dynamic[1], atom->ntypes, MPI_DOUBLE, MPI_MAX, world);
- MPI_Allreduce(&onerad_frozen[1], &maxrad_frozen[1], atom->ntypes, MPI_DOUBLE, MPI_MAX, world);
+ MPI_Allreduce(&onerad_dynamic[1], &maxrad_dynamic[1], atom->ntypes, MPI_DOUBLE, MPI_MAX, world);
+ MPI_Allreduce(&onerad_frozen[1], &maxrad_frozen[1], atom->ntypes, MPI_DOUBLE, MPI_MAX, world);
}
/* ----------------------------------------------------------------------
@@ -360,8 +360,8 @@ void PairHertz::init_style() {
------------------------------------------------------------------------- */
void PairHertz::init_list(int id, NeighList *ptr) {
- if (id == 0)
- list = ptr;
+ if (id == 0)
+ list = ptr;
}
/* ----------------------------------------------------------------------
@@ -370,15 +370,15 @@ void PairHertz::init_list(int id, NeighList *ptr) {
double PairHertz::memory_usage() {
- return 0.0;
+ return 0.0;
}
void *PairHertz::extract(const char *str, int &i) {
- //printf("in PairTriSurf::extract\n");
- if (strcmp(str, "smd/hertz/stable_time_increment_ptr") == 0) {
- return (void *) &stable_time_increment;
- }
+ //printf("in PairTriSurf::extract\n");
+ if (strcmp(str, "smd/hertz/stable_time_increment_ptr") == 0) {
+ return (void *) &stable_time_increment;
+ }
- return NULL;
+ return NULL;
}
diff --git a/src/USER-SMD/pair_smd_tlsph.cpp b/src/USER-SMD/pair_smd_tlsph.cpp
index 8dac846017..1a600b393e 100644
--- a/src/USER-SMD/pair_smd_tlsph.cpp
+++ b/src/USER-SMD/pair_smd_tlsph.cpp
@@ -65,68 +65,68 @@ using namespace SMD_Math;
/* ---------------------------------------------------------------------- */
PairTlsph::PairTlsph(LAMMPS *lmp) :
- Pair(lmp) {
+ Pair(lmp) {
- onerad_dynamic = onerad_frozen = maxrad_dynamic = maxrad_frozen = NULL;
+ onerad_dynamic = onerad_frozen = maxrad_dynamic = maxrad_frozen = NULL;
- failureModel = NULL;
- strengthModel = eos = NULL;
+ failureModel = NULL;
+ strengthModel = eos = NULL;
- nmax = 0; // make sure no atom on this proc such that initial memory allocation is correct
- Fdot = Fincr = K = PK1 = NULL;
- R = FincrInv = W = D = NULL;
- detF = NULL;
- smoothVelDifference = NULL;
- numNeighsRefConfig = NULL;
- CauchyStress = NULL;
- hourglass_error = NULL;
- Lookup = NULL;
- particle_dt = NULL;
+ nmax = 0; // make sure no atom on this proc such that initial memory allocation is correct
+ Fdot = Fincr = K = PK1 = NULL;
+ R = FincrInv = W = D = NULL;
+ detF = NULL;
+ smoothVelDifference = NULL;
+ numNeighsRefConfig = NULL;
+ CauchyStress = NULL;
+ hourglass_error = NULL;
+ Lookup = NULL;
+ particle_dt = NULL;
- updateFlag = 0;
- first = true;
- dtCFL = 0.0; // initialize dtCFL so it is set to safe value if extracted on zero-th timestep
+ updateFlag = 0;
+ first = true;
+ dtCFL = 0.0; // initialize dtCFL so it is set to safe value if extracted on zero-th timestep
- comm_forward = 22; // this pair style communicates 20 doubles to ghost atoms : PK1 tensor + F tensor + shepardWeight
- fix_tlsph_reference_configuration = NULL;
+ comm_forward = 22; // this pair style communicates 20 doubles to ghost atoms : PK1 tensor + F tensor + shepardWeight
+ fix_tlsph_reference_configuration = NULL;
- cut_comm = MAX(neighbor->cutneighmax, comm->cutghostuser); // cutoff radius within which ghost atoms are communicated.
+ cut_comm = MAX(neighbor->cutneighmax, comm->cutghostuser); // cutoff radius within which ghost atoms are communicated.
}
/* ---------------------------------------------------------------------- */
PairTlsph::~PairTlsph() {
- //printf("in PairTlsph::~PairTlsph()\n");
-
- if (allocated) {
- memory->destroy(setflag);
- memory->destroy(cutsq);
- memory->destroy(strengthModel);
- memory->destroy(eos);
- memory->destroy(Lookup);
-
- delete[] onerad_dynamic;
- delete[] onerad_frozen;
- delete[] maxrad_dynamic;
- delete[] maxrad_frozen;
-
- delete[] Fdot;
- delete[] Fincr;
- delete[] K;
- delete[] detF;
- delete[] PK1;
- delete[] smoothVelDifference;
- delete[] R;
- delete[] FincrInv;
- delete[] W;
- delete[] D;
- delete[] numNeighsRefConfig;
- delete[] CauchyStress;
- delete[] hourglass_error;
- delete[] particle_dt;
-
- delete[] failureModel;
- }
+ //printf("in PairTlsph::~PairTlsph()\n");
+
+ if (allocated) {
+ memory->destroy(setflag);
+ memory->destroy(cutsq);
+ memory->destroy(strengthModel);
+ memory->destroy(eos);
+ memory->destroy(Lookup);
+
+ delete[] onerad_dynamic;
+ delete[] onerad_frozen;
+ delete[] maxrad_dynamic;
+ delete[] maxrad_frozen;
+
+ delete[] Fdot;
+ delete[] Fincr;
+ delete[] K;
+ delete[] detF;
+ delete[] PK1;
+ delete[] smoothVelDifference;
+ delete[] R;
+ delete[] FincrInv;
+ delete[] W;
+ delete[] D;
+ delete[] numNeighsRefConfig;
+ delete[] CauchyStress;
+ delete[] hourglass_error;
+ delete[] particle_dt;
+
+ delete[] failureModel;
+ }
}
/* ----------------------------------------------------------------------
@@ -136,563 +136,563 @@ PairTlsph::~PairTlsph() {
---------------------------------------------------------------------- */
void PairTlsph::PreCompute() {
- tagint *mol = atom->molecule;
- double *vfrac = atom->vfrac;
- double *radius = atom->radius;
- double **x0 = atom->x0;
- double **x = atom->x;
- double **v = atom->vest; // extrapolated velocities corresponding to current positions
- double **vint = atom->v; // Velocity-Verlet algorithm velocities
- double *damage = atom->damage;
- tagint *tag = atom->tag;
- int *type = atom->type;
- int nlocal = atom->nlocal;
- int jnum, jj, i, j, itype, idim;
-
- tagint **partner = ((FixSMD_TLSPH_ReferenceConfiguration *) modify->fix[ifix_tlsph])->partner;
- int *npartner = ((FixSMD_TLSPH_ReferenceConfiguration *) modify->fix[ifix_tlsph])->npartner;
- float **wfd_list = ((FixSMD_TLSPH_ReferenceConfiguration *) modify->fix[ifix_tlsph])->wfd_list;
- float **wf_list = ((FixSMD_TLSPH_ReferenceConfiguration *) modify->fix[ifix_tlsph])->wf_list;
- float **degradation_ij = ((FixSMD_TLSPH_ReferenceConfiguration *) modify->fix[ifix_tlsph])->degradation_ij;
- double r0, r0Sq, wf, wfd, h, irad, voli, volj, scale, shepardWeight;
- Vector3d dx, dx0, dv, g;
- Matrix3d Ktmp, Ftmp, Fdottmp, L, U, eye;
- Vector3d vi, vj, vinti, vintj, xi, xj, x0i, x0j, dvint;
- int periodic = (domain->xperiodic || domain->yperiodic || domain->zperiodic);
- bool status;
- Matrix3d F0;
-
- eye.setIdentity();
-
- for (i = 0; i < nlocal; i++) {
-
- itype = type[i];
- if (setflag[itype][itype] == 1) {
-
- K[i].setZero();
- Fincr[i].setZero();
- Fdot[i].setZero();
- numNeighsRefConfig[i] = 0;
- smoothVelDifference[i].setZero();
- hourglass_error[i] = 0.0;
-
- if (mol[i] < 0) { // valid SPH particle have mol > 0
- continue;
- }
-
- // initialize aveage mass density
- h = 2.0 * radius[i];
- r0 = 0.0;
- spiky_kernel_and_derivative(h, r0, domain->dimension, wf, wfd);
- shepardWeight = wf * voli;
-
- jnum = npartner[i];
- irad = radius[i];
- voli = vfrac[i];
-
- // initialize Eigen data structures from LAMMPS data structures
- for (idim = 0; idim < 3; idim++) {
- xi(idim) = x[i][idim];
- x0i(idim) = x0[i][idim];
- vi(idim) = v[i][idim];
- vinti(idim) = vint[i][idim];
- }
-
- for (jj = 0; jj < jnum; jj++) {
-
- if (partner[i][jj] == 0)
- continue;
- j = atom->map(partner[i][jj]);
- if (j < 0) { // // check if lost a partner without first breaking bond
- partner[i][jj] = 0;
- continue;
- }
-
- if (mol[j] < 0) { // particle has failed. do not include it for computing any property
- continue;
- }
-
- if (mol[i] != mol[j]) {
- continue;
- }
-
- // initialize Eigen data structures from LAMMPS data structures
- for (idim = 0; idim < 3; idim++) {
- xj(idim) = x[j][idim];
- x0j(idim) = x0[j][idim];
- vj(idim) = v[j][idim];
- vintj(idim) = vint[j][idim];
- }
- dx0 = x0j - x0i;
- dx = xj - xi;
-
- if (periodic)
- domain->minimum_image(dx0(0), dx0(1), dx0(2));
-
- r0Sq = dx0.squaredNorm();
- h = irad + radius[j];
-
- r0 = sqrt(r0Sq);
- volj = vfrac[j];
-
- // distance vectors in current and reference configuration, velocity difference
- dv = vj - vi;
- dvint = vintj - vinti;
-
- // scale the interaction according to the damage variable
- scale = 1.0 - degradation_ij[i][jj];
- wf = wf_list[i][jj] * scale;
- wfd = wfd_list[i][jj] * scale;
- g = (wfd / r0) * dx0;
-
- /* build matrices */
- Ktmp = -g * dx0.transpose();
- Fdottmp = -dv * g.transpose();
- Ftmp = -(dx - dx0) * g.transpose();
-
- K[i] += volj * Ktmp;
- Fdot[i] += volj * Fdottmp;
- Fincr[i] += volj * Ftmp;
- shepardWeight += volj * wf;
- smoothVelDifference[i] += volj * wf * dvint;
- numNeighsRefConfig[i]++;
- } // end loop over j
-
- // normalize average velocity field around an integration point
- if (shepardWeight > 0.0) {
- smoothVelDifference[i] /= shepardWeight;
- } else {
- smoothVelDifference[i].setZero();
- }
-
- pseudo_inverse_SVD(K[i]);
- Fdot[i] *= K[i];
- Fincr[i] *= K[i];
- Fincr[i] += eye;
-
- if (JAUMANN) {
- R[i].setIdentity(); // for Jaumann stress rate, we do not need a subsequent rotation back into the reference configuration
- } else {
- status = PolDec(Fincr[i], R[i], U, false); // polar decomposition of the deformation gradient, F = R * U
- if (!status) {
- error->message(FLERR, "Polar decomposition of deformation gradient failed.\n");
- mol[i] = -1;
- } else {
- Fincr[i] = R[i] * U;
- }
- }
-
- detF[i] = Fincr[i].determinant();
- FincrInv[i] = Fincr[i].inverse();
-
- // velocity gradient
- L = Fdot[i] * FincrInv[i];
-
- // symmetric (D) and asymmetric (W) parts of L
- D[i] = 0.5 * (L + L.transpose());
- W[i] = 0.5 * (L - L.transpose()); // spin tensor:: need this for Jaumann rate
-
- // unrotated rate-of-deformation tensor d, see right side of Pronto2d, eqn.(2.1.7)
- // convention: unrotated frame is that one, where the true rotation of an integration point has been subtracted.
- // stress in the unrotated frame of reference is denoted sigma (stress seen by an observer doing rigid body rotations along with the material)
- // stress in the true frame of reference (a stationary observer) is denoted by T, "true stress"
- D[i] = (R[i].transpose() * D[i] * R[i]).eval();
-
- // limit strain rate
- //double limit = 1.0e-3 * Lookup[SIGNAL_VELOCITY][itype] / radius[i];
- //D[i] = LimitEigenvalues(D[i], limit);
-
- /*
- * make sure F stays within some limits
- */
-
- if ((detF[i] < DETF_MIN) || (detF[i] > DETF_MAX) || (numNeighsRefConfig[i] == 0)) {
- printf("deleting particle [%d] because det(F)=%f is outside stable range %f -- %f \n", tag[i],
- Fincr[i].determinant(),
- DETF_MIN, DETF_MAX);
- printf("nn = %d, damage=%f\n", numNeighsRefConfig[i], damage[i]);
- cout << "Here is matrix F:" << endl << Fincr[i] << endl;
- cout << "Here is matrix F-1:" << endl << FincrInv[i] << endl;
- cout << "Here is matrix K-1:" << endl << K[i] << endl;
- cout << "Here is matrix K:" << endl << K[i].inverse() << endl;
- cout << "Here is det of K" << endl << (K[i].inverse()).determinant() << endl;
- cout << "Here is matrix R:" << endl << R[i] << endl;
- cout << "Here is det of R" << endl << R[i].determinant() << endl;
- cout << "Here is matrix U:" << endl << U << endl;
- mol[i] = -1;
- //error->one(FLERR, "");
- }
-
- if (mol[i] < 0) {
- D[i].setZero();
- Fdot[i].setZero();
- Fincr[i].setIdentity();
- smoothVelDifference[i].setZero();
- detF[i] = 1.0;
- K[i].setIdentity();
-
- vint[i][0] = 0.0;
- vint[i][1] = 0.0;
- vint[i][2] = 0.0;
- }
- } // end loop over i
- } // end check setflag
+ tagint *mol = atom->molecule;
+ double *vfrac = atom->vfrac;
+ double *radius = atom->radius;
+ double **x0 = atom->x0;
+ double **x = atom->x;
+ double **v = atom->vest; // extrapolated velocities corresponding to current positions
+ double **vint = atom->v; // Velocity-Verlet algorithm velocities
+ double *damage = atom->damage;
+ tagint *tag = atom->tag;
+ int *type = atom->type;
+ int nlocal = atom->nlocal;
+ int jnum, jj, i, j, itype, idim;
+
+ tagint **partner = ((FixSMD_TLSPH_ReferenceConfiguration *) modify->fix[ifix_tlsph])->partner;
+ int *npartner = ((FixSMD_TLSPH_ReferenceConfiguration *) modify->fix[ifix_tlsph])->npartner;
+ float **wfd_list = ((FixSMD_TLSPH_ReferenceConfiguration *) modify->fix[ifix_tlsph])->wfd_list;
+ float **wf_list = ((FixSMD_TLSPH_ReferenceConfiguration *) modify->fix[ifix_tlsph])->wf_list;
+ float **degradation_ij = ((FixSMD_TLSPH_ReferenceConfiguration *) modify->fix[ifix_tlsph])->degradation_ij;
+ double r0, r0Sq, wf, wfd, h, irad, voli, volj, scale, shepardWeight;
+ Vector3d dx, dx0, dv, g;
+ Matrix3d Ktmp, Ftmp, Fdottmp, L, U, eye;
+ Vector3d vi, vj, vinti, vintj, xi, xj, x0i, x0j, dvint;
+ int periodic = (domain->xperiodic || domain->yperiodic || domain->zperiodic);
+ bool status;
+ Matrix3d F0;
+
+ eye.setIdentity();
+
+ for (i = 0; i < nlocal; i++) {
+
+ itype = type[i];
+ if (setflag[itype][itype] == 1) {
+
+ K[i].setZero();
+ Fincr[i].setZero();
+ Fdot[i].setZero();
+ numNeighsRefConfig[i] = 0;
+ smoothVelDifference[i].setZero();
+ hourglass_error[i] = 0.0;
+
+ if (mol[i] < 0) { // valid SPH particle have mol > 0
+ continue;
+ }
+
+ // initialize aveage mass density
+ h = 2.0 * radius[i];
+ r0 = 0.0;
+ spiky_kernel_and_derivative(h, r0, domain->dimension, wf, wfd);
+ shepardWeight = wf * voli;
+
+ jnum = npartner[i];
+ irad = radius[i];
+ voli = vfrac[i];
+
+ // initialize Eigen data structures from LAMMPS data structures
+ for (idim = 0; idim < 3; idim++) {
+ xi(idim) = x[i][idim];
+ x0i(idim) = x0[i][idim];
+ vi(idim) = v[i][idim];
+ vinti(idim) = vint[i][idim];
+ }
+
+ for (jj = 0; jj < jnum; jj++) {
+
+ if (partner[i][jj] == 0)
+ continue;
+ j = atom->map(partner[i][jj]);
+ if (j < 0) { // // check if lost a partner without first breaking bond
+ partner[i][jj] = 0;
+ continue;
+ }
+
+ if (mol[j] < 0) { // particle has failed. do not include it for computing any property
+ continue;
+ }
+
+ if (mol[i] != mol[j]) {
+ continue;
+ }
+
+ // initialize Eigen data structures from LAMMPS data structures
+ for (idim = 0; idim < 3; idim++) {
+ xj(idim) = x[j][idim];
+ x0j(idim) = x0[j][idim];
+ vj(idim) = v[j][idim];
+ vintj(idim) = vint[j][idim];
+ }
+ dx0 = x0j - x0i;
+ dx = xj - xi;
+
+ if (periodic)
+ domain->minimum_image(dx0(0), dx0(1), dx0(2));
+
+ r0Sq = dx0.squaredNorm();
+ h = irad + radius[j];
+
+ r0 = sqrt(r0Sq);
+ volj = vfrac[j];
+
+ // distance vectors in current and reference configuration, velocity difference
+ dv = vj - vi;
+ dvint = vintj - vinti;
+
+ // scale the interaction according to the damage variable
+ scale = 1.0 - degradation_ij[i][jj];
+ wf = wf_list[i][jj] * scale;
+ wfd = wfd_list[i][jj] * scale;
+ g = (wfd / r0) * dx0;
+
+ /* build matrices */
+ Ktmp = -g * dx0.transpose();
+ Fdottmp = -dv * g.transpose();
+ Ftmp = -(dx - dx0) * g.transpose();
+
+ K[i] += volj * Ktmp;
+ Fdot[i] += volj * Fdottmp;
+ Fincr[i] += volj * Ftmp;
+ shepardWeight += volj * wf;
+ smoothVelDifference[i] += volj * wf * dvint;
+ numNeighsRefConfig[i]++;
+ } // end loop over j
+
+ // normalize average velocity field around an integration point
+ if (shepardWeight > 0.0) {
+ smoothVelDifference[i] /= shepardWeight;
+ } else {
+ smoothVelDifference[i].setZero();
+ }
+
+ pseudo_inverse_SVD(K[i]);
+ Fdot[i] *= K[i];
+ Fincr[i] *= K[i];
+ Fincr[i] += eye;
+
+ if (JAUMANN) {
+ R[i].setIdentity(); // for Jaumann stress rate, we do not need a subsequent rotation back into the reference configuration
+ } else {
+ status = PolDec(Fincr[i], R[i], U, false); // polar decomposition of the deformation gradient, F = R * U
+ if (!status) {
+ error->message(FLERR, "Polar decomposition of deformation gradient failed.\n");
+ mol[i] = -1;
+ } else {
+ Fincr[i] = R[i] * U;
+ }
+ }
+
+ detF[i] = Fincr[i].determinant();
+ FincrInv[i] = Fincr[i].inverse();
+
+ // velocity gradient
+ L = Fdot[i] * FincrInv[i];
+
+ // symmetric (D) and asymmetric (W) parts of L
+ D[i] = 0.5 * (L + L.transpose());
+ W[i] = 0.5 * (L - L.transpose()); // spin tensor:: need this for Jaumann rate
+
+ // unrotated rate-of-deformation tensor d, see right side of Pronto2d, eqn.(2.1.7)
+ // convention: unrotated frame is that one, where the true rotation of an integration point has been subtracted.
+ // stress in the unrotated frame of reference is denoted sigma (stress seen by an observer doing rigid body rotations along with the material)
+ // stress in the true frame of reference (a stationary observer) is denoted by T, "true stress"
+ D[i] = (R[i].transpose() * D[i] * R[i]).eval();
+
+ // limit strain rate
+ //double limit = 1.0e-3 * Lookup[SIGNAL_VELOCITY][itype] / radius[i];
+ //D[i] = LimitEigenvalues(D[i], limit);
+
+ /*
+ * make sure F stays within some limits
+ */
+
+ if ((detF[i] < DETF_MIN) || (detF[i] > DETF_MAX) || (numNeighsRefConfig[i] == 0)) {
+ printf("deleting particle [%d] because det(F)=%f is outside stable range %f -- %f \n", tag[i],
+ Fincr[i].determinant(),
+ DETF_MIN, DETF_MAX);
+ printf("nn = %d, damage=%f\n", numNeighsRefConfig[i], damage[i]);
+ cout << "Here is matrix F:" << endl << Fincr[i] << endl;
+ cout << "Here is matrix F-1:" << endl << FincrInv[i] << endl;
+ cout << "Here is matrix K-1:" << endl << K[i] << endl;
+ cout << "Here is matrix K:" << endl << K[i].inverse() << endl;
+ cout << "Here is det of K" << endl << (K[i].inverse()).determinant() << endl;
+ cout << "Here is matrix R:" << endl << R[i] << endl;
+ cout << "Here is det of R" << endl << R[i].determinant() << endl;
+ cout << "Here is matrix U:" << endl << U << endl;
+ mol[i] = -1;
+ //error->one(FLERR, "");
+ }
+
+ if (mol[i] < 0) {
+ D[i].setZero();
+ Fdot[i].setZero();
+ Fincr[i].setIdentity();
+ smoothVelDifference[i].setZero();
+ detF[i] = 1.0;
+ K[i].setIdentity();
+
+ vint[i][0] = 0.0;
+ vint[i][1] = 0.0;
+ vint[i][2] = 0.0;
+ }
+ } // end loop over i
+ } // end check setflag
}
/* ---------------------------------------------------------------------- */
void PairTlsph::compute(int eflag, int vflag) {
- if (atom->nmax > nmax) {
- nmax = atom->nmax;
- delete[] Fdot;
- Fdot = new Matrix3d[nmax]; // memory usage: 9 doubles
- delete[] Fincr;
- Fincr = new Matrix3d[nmax]; // memory usage: 9 doubles
- delete[] K;
- K = new Matrix3d[nmax]; // memory usage: 9 doubles
- delete[] PK1;
- PK1 = new Matrix3d[nmax]; // memory usage: 9 doubles; total 5*9=45 doubles
- delete[] detF;
- detF = new double[nmax]; // memory usage: 1 double; total 46 doubles
- delete[] smoothVelDifference;
- smoothVelDifference = new Vector3d[nmax]; // memory usage: 3 doubles; total 49 doubles
- delete[] R;
- R = new Matrix3d[nmax]; // memory usage: 9 doubles; total 67 doubles
- delete[] FincrInv;
- FincrInv = new Matrix3d[nmax]; // memory usage: 9 doubles; total 85 doubles
- delete[] W;
- W = new Matrix3d[nmax]; // memory usage: 9 doubles; total 94 doubles
- delete[] D;
- D = new Matrix3d[nmax]; // memory usage: 9 doubles; total 103 doubles
- delete[] numNeighsRefConfig;
- numNeighsRefConfig = new int[nmax]; // memory usage: 1 int; total 108 doubles
- delete[] CauchyStress;
- CauchyStress = new Matrix3d[nmax]; // memory usage: 9 doubles; total 118 doubles
- delete[] hourglass_error;
- hourglass_error = new double[nmax];
- delete[] particle_dt;
- particle_dt = new double[nmax];
- }
-
- if (first) { // return on first call, because reference connectivity lists still needs to be built. Also zero quantities which are otherwise undefined.
- first = false;
-
- for (int i = 0; i < atom->nlocal; i++) {
- Fincr[i].setZero();
- detF[i] = 0.0;
- smoothVelDifference[i].setZero();
- D[i].setZero();
- numNeighsRefConfig[i] = 0;
- CauchyStress[i].setZero();
- hourglass_error[i] = 0.0;
- particle_dt[i] = 0.0;
- }
-
- return;
- }
-
- /*
- * calculate deformations and rate-of-deformations
- */
- PairTlsph::PreCompute();
-
- /*
- * calculate stresses from constitutive models
- */
- PairTlsph::AssembleStress();
-
- /*
- * QUANTITIES ABOVE HAVE ONLY BEEN CALCULATED FOR NLOCAL PARTICLES.
- * NEED TO DO A FORWARD COMMUNICATION TO GHOST ATOMS NOW
- */
- comm->forward_comm_pair(this);
-
- /*
- * compute forces between particles
- */
- updateFlag = 0;
- ComputeForces(eflag, vflag);
+ if (atom->nmax > nmax) {
+ nmax = atom->nmax;
+ delete[] Fdot;
+ Fdot = new Matrix3d[nmax]; // memory usage: 9 doubles
+ delete[] Fincr;
+ Fincr = new Matrix3d[nmax]; // memory usage: 9 doubles
+ delete[] K;
+ K = new Matrix3d[nmax]; // memory usage: 9 doubles
+ delete[] PK1;
+ PK1 = new Matrix3d[nmax]; // memory usage: 9 doubles; total 5*9=45 doubles
+ delete[] detF;
+ detF = new double[nmax]; // memory usage: 1 double; total 46 doubles
+ delete[] smoothVelDifference;
+ smoothVelDifference = new Vector3d[nmax]; // memory usage: 3 doubles; total 49 doubles
+ delete[] R;
+ R = new Matrix3d[nmax]; // memory usage: 9 doubles; total 67 doubles
+ delete[] FincrInv;
+ FincrInv = new Matrix3d[nmax]; // memory usage: 9 doubles; total 85 doubles
+ delete[] W;
+ W = new Matrix3d[nmax]; // memory usage: 9 doubles; total 94 doubles
+ delete[] D;
+ D = new Matrix3d[nmax]; // memory usage: 9 doubles; total 103 doubles
+ delete[] numNeighsRefConfig;
+ numNeighsRefConfig = new int[nmax]; // memory usage: 1 int; total 108 doubles
+ delete[] CauchyStress;
+ CauchyStress = new Matrix3d[nmax]; // memory usage: 9 doubles; total 118 doubles
+ delete[] hourglass_error;
+ hourglass_error = new double[nmax];
+ delete[] particle_dt;
+ particle_dt = new double[nmax];
+ }
+
+ if (first) { // return on first call, because reference connectivity lists still needs to be built. Also zero quantities which are otherwise undefined.
+ first = false;
+
+ for (int i = 0; i < atom->nlocal; i++) {
+ Fincr[i].setZero();
+ detF[i] = 0.0;
+ smoothVelDifference[i].setZero();
+ D[i].setZero();
+ numNeighsRefConfig[i] = 0;
+ CauchyStress[i].setZero();
+ hourglass_error[i] = 0.0;
+ particle_dt[i] = 0.0;
+ }
+
+ return;
+ }
+
+ /*
+ * calculate deformations and rate-of-deformations
+ */
+ PairTlsph::PreCompute();
+
+ /*
+ * calculate stresses from constitutive models
+ */
+ PairTlsph::AssembleStress();
+
+ /*
+ * QUANTITIES ABOVE HAVE ONLY BEEN CALCULATED FOR NLOCAL PARTICLES.
+ * NEED TO DO A FORWARD COMMUNICATION TO GHOST ATOMS NOW
+ */
+ comm->forward_comm_pair(this);
+
+ /*
+ * compute forces between particles
+ */
+ updateFlag = 0;
+ ComputeForces(eflag, vflag);
}
void PairTlsph::ComputeForces(int eflag, int vflag) {
- tagint *mol = atom->molecule;
- double **x = atom->x;
- double **v = atom->vest;
- double **x0 = atom->x0;
- double **f = atom->f;
- double *vfrac = atom->vfrac;
- double *de = atom->de;
- double *rmass = atom->rmass;
- double *radius = atom->radius;
- double *damage = atom->damage;
- double *plastic_strain = atom->eff_plastic_strain;
- int *type = atom->type;
- int nlocal = atom->nlocal;
- int i, j, jj, jnum, itype, idim;
- double r, hg_mag, wf, wfd, h, r0, r0Sq, voli, volj;
- double delVdotDelR, visc_magnitude, deltaE, mu_ij, hg_err, gamma_dot_dx, delta, scale;
- double strain1d, strain1d_max, softening_strain, shepardWeight;
- char str[128];
- Vector3d fi, fj, dx0, dx, dv, f_stress, f_hg, dxp_i, dxp_j, gamma, g, gamma_i, gamma_j, x0i, x0j;
- Vector3d xi, xj, vi, vj, f_visc, sumForces, f_spring;
- int periodic = (domain->xperiodic || domain->yperiodic || domain->zperiodic);
-
- tagint **partner = ((FixSMD_TLSPH_ReferenceConfiguration *) modify->fix[ifix_tlsph])->partner;
- int *npartner = ((FixSMD_TLSPH_ReferenceConfiguration *) modify->fix[ifix_tlsph])->npartner;
- float **wfd_list = ((FixSMD_TLSPH_ReferenceConfiguration *) modify->fix[ifix_tlsph])->wfd_list;
- float **wf_list = ((FixSMD_TLSPH_ReferenceConfiguration *) modify->fix[ifix_tlsph])->wf_list;
- float **degradation_ij = ((FixSMD_TLSPH_ReferenceConfiguration *) modify->fix[ifix_tlsph])->degradation_ij;
- float **energy_per_bond = ((FixSMD_TLSPH_ReferenceConfiguration *) modify->fix[ifix_tlsph])->energy_per_bond;
- Matrix3d eye;
- eye.setIdentity();
-
- if (eflag || vflag)
- ev_setup(eflag, vflag);
- else
- evflag = vflag_fdotr = 0;
-
- /*
- * iterate over pairs of particles i, j and assign forces using PK1 stress tensor
- */
-
- //updateFlag = 0;
- hMin = 1.0e22;
- dtRelative = 1.0e22;
-
- for (i = 0; i < nlocal; i++) {
-
- if (mol[i] < 0) {
- continue; // Particle i is not a valid SPH particle (anymore). Skip all interactions with this particle.
- }
-
- itype = type[i];
- jnum = npartner[i];
- voli = vfrac[i];
-
- // initialize aveage mass density
- h = 2.0 * radius[i];
- r = 0.0;
- spiky_kernel_and_derivative(h, r, domain->dimension, wf, wfd);
- shepardWeight = wf * voli;
-
- for (idim = 0; idim < 3; idim++) {
- x0i(idim) = x0[i][idim];
- xi(idim) = x[i][idim];
- vi(idim) = v[i][idim];
- }
-
- for (jj = 0; jj < jnum; jj++) {
- if (partner[i][jj] == 0)
- continue;
- j = atom->map(partner[i][jj]);
- if (j < 0) { // // check if lost a partner without first breaking bond
- partner[i][jj] = 0;
- continue;
- }
-
- if (mol[j] < 0) {
- continue; // Particle j is not a valid SPH particle (anymore). Skip all interactions with this particle.
- }
-
- if (mol[i] != mol[j]) {
- continue;
- }
-
- if (type[j] != itype) {
- sprintf(str, "particle pair is not of same type!");
- error->all(FLERR, str);
- }
-
- for (idim = 0; idim < 3; idim++) {
- x0j(idim) = x0[j][idim];
- xj(idim) = x[j][idim];
- vj(idim) = v[j][idim];
- }
-
- if (periodic)
- domain->minimum_image(dx0(0), dx0(1), dx0(2));
-
- // check that distance between i and j (in the reference config) is less than cutoff
- dx0 = x0j - x0i;
- r0Sq = dx0.squaredNorm();
- h = radius[i] + radius[j];
- hMin = MIN(hMin, h);
- r0 = sqrt(r0Sq);
- volj = vfrac[j];
-
- // distance vectors in current and reference configuration, velocity difference
- dx = xj - xi;
- dv = vj - vi;
- r = dx.norm(); // current distance
-
- // scale the interaction according to the damage variable
- scale = 1.0 - degradation_ij[i][jj];
- wf = wf_list[i][jj] * scale;
- wfd = wfd_list[i][jj] * scale;
-
- g = (wfd / r0) * dx0; // uncorrected kernel gradient
-
- /*
- * force contribution -- note that the kernel gradient correction has been absorbed into PK1
- */
-
- f_stress = -voli * volj * (PK1[i] + PK1[j]) * g;
-
- /*
- * artificial viscosity
- */
- delVdotDelR = dx.dot(dv) / (r + 0.1 * h); // project relative velocity onto unit particle distance vector [m/s]
- LimitDoubleMagnitude(delVdotDelR, 0.01 * Lookup[SIGNAL_VELOCITY][itype]);
- mu_ij = h * delVdotDelR / (r + 0.1 * h); // units: [m * m/s / m = m/s]
- visc_magnitude = (-Lookup[VISCOSITY_Q1][itype] * Lookup[SIGNAL_VELOCITY][itype] * mu_ij
- + Lookup[VISCOSITY_Q2][itype] * mu_ij * mu_ij) / Lookup[REFERENCE_DENSITY][itype]; // units: m^5/(s^2 kg))
- f_visc = rmass[i] * rmass[j] * visc_magnitude * wfd * dx / (r + 1.0e-2 * h); // units: kg^2 * m^5/(s^2 kg) * m^-4 = kg m / s^2 = N
-
- /*
- * hourglass deviation of particles i and j
- */
-
- gamma = 0.5 * (Fincr[i] + Fincr[j]) * dx0 - dx;
- hg_err = gamma.norm() / r0;
- hourglass_error[i] += volj * wf * hg_err;
-
- /* SPH-like hourglass formulation */
-
- if (MAX(plastic_strain[i], plastic_strain[j]) > 1.0e-3) {
- /*
- * viscous hourglass formulation for particles with plastic deformation
- */
- delta = gamma.dot(dx);
- if (delVdotDelR * delta < 0.0) {
- hg_err = MAX(hg_err, 0.05); // limit hg_err to avoid numerical instabilities
- hg_mag = -hg_err * Lookup[HOURGLASS_CONTROL_AMPLITUDE][itype] * Lookup[SIGNAL_VELOCITY][itype] * mu_ij
- / Lookup[REFERENCE_DENSITY][itype]; // this has units of pressure
- } else {
- hg_mag = 0.0;
- }
- f_hg = rmass[i] * rmass[j] * hg_mag * wfd * dx / (r + 1.0e-2 * h);
-
- } else {
- /*
- * stiffness hourglass formulation for particle in the elastic regime
- */
-
- gamma_dot_dx = gamma.dot(dx); // project hourglass error vector onto pair distance vector
- LimitDoubleMagnitude(gamma_dot_dx, 0.1 * r); // limit projected vector to avoid numerical instabilities
- delta = 0.5 * gamma_dot_dx / (r + 0.1 * h); // delta has dimensions of [m]
- hg_mag = Lookup[HOURGLASS_CONTROL_AMPLITUDE][itype] * delta / (r0Sq + 0.01 * h * h); // hg_mag has dimensions [m^(-1)]
- hg_mag *= -voli * volj * wf * Lookup[YOUNGS_MODULUS][itype]; // hg_mag has dimensions [J*m^(-1)] = [N]
- f_hg = (hg_mag / (r + 0.01 * h)) * dx;
- }
-
- // scale hourglass force with damage
- f_hg *= (1.0 - damage[i]) * (1.0 - damage[j]);
-
- // sum stress, viscous, and hourglass forces
- sumForces = f_stress + f_visc + f_hg; // + f_spring;
-
- // energy rate -- project velocity onto force vector
- deltaE = 0.5 * sumForces.dot(dv);
-
- // apply forces to pair of particles
- f[i][0] += sumForces(0);
- f[i][1] += sumForces(1);
- f[i][2] += sumForces(2);
- de[i] += deltaE;
-
- // tally atomistic stress tensor
- if (evflag) {
- ev_tally_xyz(i, j, nlocal, 0, 0.0, 0.0, sumForces(0), sumForces(1), sumForces(2), dx(0), dx(1), dx(2));
- }
-
- shepardWeight += wf * volj;
-
- // check if a particle has moved too much w.r.t another particle
- if (r > r0) {
- if (update_method == UPDATE_CONSTANT_THRESHOLD) {
- if (r - r0 > update_threshold) {
- updateFlag = 1;
- }
- } else if (update_method == UPDATE_PAIRWISE_RATIO) {
- if ((r - r0) / h > update_threshold) {
- updateFlag = 1;
- }
- }
- }
-
- if (failureModel[itype].failure_max_pairwise_strain) {
-
- strain1d = (r - r0) / r0;
- strain1d_max = Lookup[FAILURE_MAX_PAIRWISE_STRAIN_THRESHOLD][itype];
- softening_strain = 2.0 * strain1d_max;
-
- if (strain1d > strain1d_max) {
- degradation_ij[i][jj] = (strain1d - strain1d_max) / softening_strain;
- } else {
- degradation_ij[i][jj] = 0.0;
- }
-
- if (degradation_ij[i][jj] >= 1.0) { // delete interaction if fully damaged
- partner[i][jj] = 0;
- }
- }
-
- if (failureModel[itype].failure_energy_release_rate) {
-
- // integration approach
- energy_per_bond[i][jj] += update->dt * f_stress.dot(dv) / (voli * volj);
- double Vic = (2.0 / 3.0) * h * h * h; // interaction volume for 2d plane strain
- double critical_energy_per_bond = Lookup[CRITICAL_ENERGY_RELEASE_RATE][itype] / (2.0 * Vic);
-
- if (energy_per_bond[i][jj] > critical_energy_per_bond) {
- //degradation_ij[i][jj] = 1.0;
- partner[i][jj] = 0;
- }
- }
-
- if (failureModel[itype].integration_point_wise) {
-
- strain1d = (r - r0) / r0;
-
- if (strain1d > 0.0) {
-
- if ((damage[i] == 1.0) && (damage[j] == 1.0)) {
- // check if damage_onset is already defined
- if (energy_per_bond[i][jj] == 0.0) { // pair damage not defined yet
- energy_per_bond[i][jj] = strain1d;
- } else { // damage initiation strain already defined
- strain1d_max = energy_per_bond[i][jj];
- softening_strain = 2.0 * strain1d_max;
-
- if (strain1d > strain1d_max) {
- degradation_ij[i][jj] = (strain1d - strain1d_max) / softening_strain;
- } else {
- degradation_ij[i][jj] = 0.0;
- }
- }
- }
-
- if (degradation_ij[i][jj] >= 1.0) { // delete interaction if fully damaged
- partner[i][jj] = 0;
- }
-
- } else {
- degradation_ij[i][jj] = 0.0;
- } // end failureModel[itype].integration_point_wise
-
- }
-
- } // end loop over jj neighbors of i
-
- if (shepardWeight != 0.0) {
- hourglass_error[i] /= shepardWeight;
- }
-
- } // end loop over i
-
- if (vflag_fdotr)
- virial_fdotr_compute();
+ tagint *mol = atom->molecule;
+ double **x = atom->x;
+ double **v = atom->vest;
+ double **x0 = atom->x0;
+ double **f = atom->f;
+ double *vfrac = atom->vfrac;
+ double *de = atom->de;
+ double *rmass = atom->rmass;
+ double *radius = atom->radius;
+ double *damage = atom->damage;
+ double *plastic_strain = atom->eff_plastic_strain;
+ int *type = atom->type;
+ int nlocal = atom->nlocal;
+ int i, j, jj, jnum, itype, idim;
+ double r, hg_mag, wf, wfd, h, r0, r0Sq, voli, volj;
+ double delVdotDelR, visc_magnitude, deltaE, mu_ij, hg_err, gamma_dot_dx, delta, scale;
+ double strain1d, strain1d_max, softening_strain, shepardWeight;
+ char str[128];
+ Vector3d fi, fj, dx0, dx, dv, f_stress, f_hg, dxp_i, dxp_j, gamma, g, gamma_i, gamma_j, x0i, x0j;
+ Vector3d xi, xj, vi, vj, f_visc, sumForces, f_spring;
+ int periodic = (domain->xperiodic || domain->yperiodic || domain->zperiodic);
+
+ tagint **partner = ((FixSMD_TLSPH_ReferenceConfiguration *) modify->fix[ifix_tlsph])->partner;
+ int *npartner = ((FixSMD_TLSPH_ReferenceConfiguration *) modify->fix[ifix_tlsph])->npartner;
+ float **wfd_list = ((FixSMD_TLSPH_ReferenceConfiguration *) modify->fix[ifix_tlsph])->wfd_list;
+ float **wf_list = ((FixSMD_TLSPH_ReferenceConfiguration *) modify->fix[ifix_tlsph])->wf_list;
+ float **degradation_ij = ((FixSMD_TLSPH_ReferenceConfiguration *) modify->fix[ifix_tlsph])->degradation_ij;
+ float **energy_per_bond = ((FixSMD_TLSPH_ReferenceConfiguration *) modify->fix[ifix_tlsph])->energy_per_bond;
+ Matrix3d eye;
+ eye.setIdentity();
+
+ if (eflag || vflag)
+ ev_setup(eflag, vflag);
+ else
+ evflag = vflag_fdotr = 0;
+
+ /*
+ * iterate over pairs of particles i, j and assign forces using PK1 stress tensor
+ */
+
+ //updateFlag = 0;
+ hMin = 1.0e22;
+ dtRelative = 1.0e22;
+
+ for (i = 0; i < nlocal; i++) {
+
+ if (mol[i] < 0) {
+ continue; // Particle i is not a valid SPH particle (anymore). Skip all interactions with this particle.
+ }
+
+ itype = type[i];
+ jnum = npartner[i];
+ voli = vfrac[i];
+
+ // initialize aveage mass density
+ h = 2.0 * radius[i];
+ r = 0.0;
+ spiky_kernel_and_derivative(h, r, domain->dimension, wf, wfd);
+ shepardWeight = wf * voli;
+
+ for (idim = 0; idim < 3; idim++) {
+ x0i(idim) = x0[i][idim];
+ xi(idim) = x[i][idim];
+ vi(idim) = v[i][idim];
+ }
+
+ for (jj = 0; jj < jnum; jj++) {
+ if (partner[i][jj] == 0)
+ continue;
+ j = atom->map(partner[i][jj]);
+ if (j < 0) { // // check if lost a partner without first breaking bond
+ partner[i][jj] = 0;
+ continue;
+ }
+
+ if (mol[j] < 0) {
+ continue; // Particle j is not a valid SPH particle (anymore). Skip all interactions with this particle.
+ }
+
+ if (mol[i] != mol[j]) {
+ continue;
+ }
+
+ if (type[j] != itype) {
+ sprintf(str, "particle pair is not of same type!");
+ error->all(FLERR, str);
+ }
+
+ for (idim = 0; idim < 3; idim++) {
+ x0j(idim) = x0[j][idim];
+ xj(idim) = x[j][idim];
+ vj(idim) = v[j][idim];
+ }
+
+ if (periodic)
+ domain->minimum_image(dx0(0), dx0(1), dx0(2));
+
+ // check that distance between i and j (in the reference config) is less than cutoff
+ dx0 = x0j - x0i;
+ r0Sq = dx0.squaredNorm();
+ h = radius[i] + radius[j];
+ hMin = MIN(hMin, h);
+ r0 = sqrt(r0Sq);
+ volj = vfrac[j];
+
+ // distance vectors in current and reference configuration, velocity difference
+ dx = xj - xi;
+ dv = vj - vi;
+ r = dx.norm(); // current distance
+
+ // scale the interaction according to the damage variable
+ scale = 1.0 - degradation_ij[i][jj];
+ wf = wf_list[i][jj] * scale;
+ wfd = wfd_list[i][jj] * scale;
+
+ g = (wfd / r0) * dx0; // uncorrected kernel gradient
+
+ /*
+ * force contribution -- note that the kernel gradient correction has been absorbed into PK1
+ */
+
+ f_stress = -voli * volj * (PK1[i] + PK1[j]) * g;
+
+ /*
+ * artificial viscosity
+ */
+ delVdotDelR = dx.dot(dv) / (r + 0.1 * h); // project relative velocity onto unit particle distance vector [m/s]
+ LimitDoubleMagnitude(delVdotDelR, 0.01 * Lookup[SIGNAL_VELOCITY][itype]);
+ mu_ij = h * delVdotDelR / (r + 0.1 * h); // units: [m * m/s / m = m/s]
+ visc_magnitude = (-Lookup[VISCOSITY_Q1][itype] * Lookup[SIGNAL_VELOCITY][itype] * mu_ij
+ + Lookup[VISCOSITY_Q2][itype] * mu_ij * mu_ij) / Lookup[REFERENCE_DENSITY][itype]; // units: m^5/(s^2 kg))
+ f_visc = rmass[i] * rmass[j] * visc_magnitude * wfd * dx / (r + 1.0e-2 * h); // units: kg^2 * m^5/(s^2 kg) * m^-4 = kg m / s^2 = N
+
+ /*
+ * hourglass deviation of particles i and j
+ */
+
+ gamma = 0.5 * (Fincr[i] + Fincr[j]) * dx0 - dx;
+ hg_err = gamma.norm() / r0;
+ hourglass_error[i] += volj * wf * hg_err;
+
+ /* SPH-like hourglass formulation */
+
+ if (MAX(plastic_strain[i], plastic_strain[j]) > 1.0e-3) {
+ /*
+ * viscous hourglass formulation for particles with plastic deformation
+ */
+ delta = gamma.dot(dx);
+ if (delVdotDelR * delta < 0.0) {
+ hg_err = MAX(hg_err, 0.05); // limit hg_err to avoid numerical instabilities
+ hg_mag = -hg_err * Lookup[HOURGLASS_CONTROL_AMPLITUDE][itype] * Lookup[SIGNAL_VELOCITY][itype] * mu_ij
+ / Lookup[REFERENCE_DENSITY][itype]; // this has units of pressure
+ } else {
+ hg_mag = 0.0;
+ }
+ f_hg = rmass[i] * rmass[j] * hg_mag * wfd * dx / (r + 1.0e-2 * h);
+
+ } else {
+ /*
+ * stiffness hourglass formulation for particle in the elastic regime
+ */
+
+ gamma_dot_dx = gamma.dot(dx); // project hourglass error vector onto pair distance vector
+ LimitDoubleMagnitude(gamma_dot_dx, 0.1 * r); // limit projected vector to avoid numerical instabilities
+ delta = 0.5 * gamma_dot_dx / (r + 0.1 * h); // delta has dimensions of [m]
+ hg_mag = Lookup[HOURGLASS_CONTROL_AMPLITUDE][itype] * delta / (r0Sq + 0.01 * h * h); // hg_mag has dimensions [m^(-1)]
+ hg_mag *= -voli * volj * wf * Lookup[YOUNGS_MODULUS][itype]; // hg_mag has dimensions [J*m^(-1)] = [N]
+ f_hg = (hg_mag / (r + 0.01 * h)) * dx;
+ }
+
+ // scale hourglass force with damage
+ f_hg *= (1.0 - damage[i]) * (1.0 - damage[j]);
+
+ // sum stress, viscous, and hourglass forces
+ sumForces = f_stress + f_visc + f_hg; // + f_spring;
+
+ // energy rate -- project velocity onto force vector
+ deltaE = 0.5 * sumForces.dot(dv);
+
+ // apply forces to pair of particles
+ f[i][0] += sumForces(0);
+ f[i][1] += sumForces(1);
+ f[i][2] += sumForces(2);
+ de[i] += deltaE;
+
+ // tally atomistic stress tensor
+ if (evflag) {
+ ev_tally_xyz(i, j, nlocal, 0, 0.0, 0.0, sumForces(0), sumForces(1), sumForces(2), dx(0), dx(1), dx(2));
+ }
+
+ shepardWeight += wf * volj;
+
+ // check if a particle has moved too much w.r.t another particle
+ if (r > r0) {
+ if (update_method == UPDATE_CONSTANT_THRESHOLD) {
+ if (r - r0 > update_threshold) {
+ updateFlag = 1;
+ }
+ } else if (update_method == UPDATE_PAIRWISE_RATIO) {
+ if ((r - r0) / h > update_threshold) {
+ updateFlag = 1;
+ }
+ }
+ }
+
+ if (failureModel[itype].failure_max_pairwise_strain) {
+
+ strain1d = (r - r0) / r0;
+ strain1d_max = Lookup[FAILURE_MAX_PAIRWISE_STRAIN_THRESHOLD][itype];
+ softening_strain = 2.0 * strain1d_max;
+
+ if (strain1d > strain1d_max) {
+ degradation_ij[i][jj] = (strain1d - strain1d_max) / softening_strain;
+ } else {
+ degradation_ij[i][jj] = 0.0;
+ }
+
+ if (degradation_ij[i][jj] >= 1.0) { // delete interaction if fully damaged
+ partner[i][jj] = 0;
+ }
+ }
+
+ if (failureModel[itype].failure_energy_release_rate) {
+
+ // integration approach
+ energy_per_bond[i][jj] += update->dt * f_stress.dot(dv) / (voli * volj);
+ double Vic = (2.0 / 3.0) * h * h * h; // interaction volume for 2d plane strain
+ double critical_energy_per_bond = Lookup[CRITICAL_ENERGY_RELEASE_RATE][itype] / (2.0 * Vic);
+
+ if (energy_per_bond[i][jj] > critical_energy_per_bond) {
+ //degradation_ij[i][jj] = 1.0;
+ partner[i][jj] = 0;
+ }
+ }
+
+ if (failureModel[itype].integration_point_wise) {
+
+ strain1d = (r - r0) / r0;
+
+ if (strain1d > 0.0) {
+
+ if ((damage[i] == 1.0) && (damage[j] == 1.0)) {
+ // check if damage_onset is already defined
+ if (energy_per_bond[i][jj] == 0.0) { // pair damage not defined yet
+ energy_per_bond[i][jj] = strain1d;
+ } else { // damage initiation strain already defined
+ strain1d_max = energy_per_bond[i][jj];
+ softening_strain = 2.0 * strain1d_max;
+
+ if (strain1d > strain1d_max) {
+ degradation_ij[i][jj] = (strain1d - strain1d_max) / softening_strain;
+ } else {
+ degradation_ij[i][jj] = 0.0;
+ }
+ }
+ }
+
+ if (degradation_ij[i][jj] >= 1.0) { // delete interaction if fully damaged
+ partner[i][jj] = 0;
+ }
+
+ } else {
+ degradation_ij[i][jj] = 0.0;
+ } // end failureModel[itype].integration_point_wise
+
+ }
+
+ } // end loop over jj neighbors of i
+
+ if (shepardWeight != 0.0) {
+ hourglass_error[i] /= shepardWeight;
+ }
+
+ } // end loop over i
+
+ if (vflag_fdotr)
+ virial_fdotr_compute();
}
/* ----------------------------------------------------------------------
@@ -701,181 +701,181 @@ void PairTlsph::ComputeForces(int eflag, int vflag) {
shape matrix correction
------------------------------------------------------------------------- */
void PairTlsph::AssembleStress() {
- tagint *mol = atom->molecule;
- double *eff_plastic_strain = atom->eff_plastic_strain;
- double *eff_plastic_strain_rate = atom->eff_plastic_strain_rate;
- double **tlsph_stress = atom->smd_stress;
- int *type = atom->type;
- double *radius = atom->radius;
- double *damage = atom->damage;
- double *rmass = atom->rmass;
- double *vfrac = atom->vfrac;
- double *e = atom->e;
- double pInitial, d_iso, pFinal, p_rate, plastic_strain_increment;
- int i, itype;
- int nlocal = atom->nlocal;
- double dt = update->dt;
- double M_eff, p_wave_speed, mass_specific_energy, vol_specific_energy, rho;
- Matrix3d sigma_rate, eye, sigmaInitial, sigmaFinal, T, T_damaged, Jaumann_rate, sigma_rate_check;
- Matrix3d d_dev, sigmaInitial_dev, sigmaFinal_dev, sigma_dev_rate, strain;
- Vector3d x0i, xi, xp;
-
- eye.setIdentity();
- dtCFL = 1.0e22;
- pFinal = 0.0;
-
- for (i = 0; i < nlocal; i++) {
- particle_dt[i] = 0.0;
-
- itype = type[i];
- if (setflag[itype][itype] == 1) {
- if (mol[i] > 0) { // only do the following if particle has not failed -- mol < 0 means particle has failed
-
- /*
- * initial stress state: given by the unrotateted Cauchy stress.
- * Assemble Eigen 3d matrix from stored stress state
- */
- sigmaInitial(0, 0) = tlsph_stress[i][0];
- sigmaInitial(0, 1) = tlsph_stress[i][1];
- sigmaInitial(0, 2) = tlsph_stress[i][2];
- sigmaInitial(1, 1) = tlsph_stress[i][3];
- sigmaInitial(1, 2) = tlsph_stress[i][4];
- sigmaInitial(2, 2) = tlsph_stress[i][5];
- sigmaInitial(1, 0) = sigmaInitial(0, 1);
- sigmaInitial(2, 0) = sigmaInitial(0, 2);
- sigmaInitial(2, 1) = sigmaInitial(1, 2);
-
- //cout << "this is sigma initial" << endl << sigmaInitial << endl;
-
- pInitial = sigmaInitial.trace() / 3.0; // isotropic part of initial stress
- sigmaInitial_dev = Deviator(sigmaInitial);
- d_iso = D[i].trace(); // volumetric part of stretch rate
- d_dev = Deviator(D[i]); // deviatoric part of stretch rate
- strain = 0.5 * (Fincr[i].transpose() * Fincr[i] - eye);
- mass_specific_energy = e[i] / rmass[i]; // energy per unit mass
- rho = rmass[i] / (detF[i] * vfrac[i]);
- vol_specific_energy = mass_specific_energy * rho; // energy per current volume
-
- /*
- * pressure: compute pressure rate p_rate and final pressure pFinal
- */
-
- ComputePressure(i, rho, mass_specific_energy, vol_specific_energy, pInitial, d_iso, pFinal, p_rate);
-
- /*
- * material strength
- */
-
- //cout << "this is the strain deviator rate" << endl << d_dev << endl;
- ComputeStressDeviator(i, sigmaInitial_dev, d_dev, sigmaFinal_dev, sigma_dev_rate, plastic_strain_increment);
- //cout << "this is the stress deviator rate" << endl << sigma_dev_rate << endl;
-
- // keep a rolling average of the plastic strain rate over the last 100 or so timesteps
- eff_plastic_strain[i] += plastic_strain_increment;
-
- // compute a characteristic time over which to average the plastic strain
- double tav = 1000 * radius[i] / (Lookup[SIGNAL_VELOCITY][itype]);
- eff_plastic_strain_rate[i] -= eff_plastic_strain_rate[i] * dt / tav;
+ tagint *mol = atom->molecule;
+ double *eff_plastic_strain = atom->eff_plastic_strain;
+ double *eff_plastic_strain_rate = atom->eff_plastic_strain_rate;
+ double **tlsph_stress = atom->smd_stress;
+ int *type = atom->type;
+ double *radius = atom->radius;
+ double *damage = atom->damage;
+ double *rmass = atom->rmass;
+ double *vfrac = atom->vfrac;
+ double *e = atom->e;
+ double pInitial, d_iso, pFinal, p_rate, plastic_strain_increment;
+ int i, itype;
+ int nlocal = atom->nlocal;
+ double dt = update->dt;
+ double M_eff, p_wave_speed, mass_specific_energy, vol_specific_energy, rho;
+ Matrix3d sigma_rate, eye, sigmaInitial, sigmaFinal, T, T_damaged, Jaumann_rate, sigma_rate_check;
+ Matrix3d d_dev, sigmaInitial_dev, sigmaFinal_dev, sigma_dev_rate, strain;
+ Vector3d x0i, xi, xp;
+
+ eye.setIdentity();
+ dtCFL = 1.0e22;
+ pFinal = 0.0;
+
+ for (i = 0; i < nlocal; i++) {
+ particle_dt[i] = 0.0;
+
+ itype = type[i];
+ if (setflag[itype][itype] == 1) {
+ if (mol[i] > 0) { // only do the following if particle has not failed -- mol < 0 means particle has failed
+
+ /*
+ * initial stress state: given by the unrotateted Cauchy stress.
+ * Assemble Eigen 3d matrix from stored stress state
+ */
+ sigmaInitial(0, 0) = tlsph_stress[i][0];
+ sigmaInitial(0, 1) = tlsph_stress[i][1];
+ sigmaInitial(0, 2) = tlsph_stress[i][2];
+ sigmaInitial(1, 1) = tlsph_stress[i][3];
+ sigmaInitial(1, 2) = tlsph_stress[i][4];
+ sigmaInitial(2, 2) = tlsph_stress[i][5];
+ sigmaInitial(1, 0) = sigmaInitial(0, 1);
+ sigmaInitial(2, 0) = sigmaInitial(0, 2);
+ sigmaInitial(2, 1) = sigmaInitial(1, 2);
+
+ //cout << "this is sigma initial" << endl << sigmaInitial << endl;
+
+ pInitial = sigmaInitial.trace() / 3.0; // isotropic part of initial stress
+ sigmaInitial_dev = Deviator(sigmaInitial);
+ d_iso = D[i].trace(); // volumetric part of stretch rate
+ d_dev = Deviator(D[i]); // deviatoric part of stretch rate
+ strain = 0.5 * (Fincr[i].transpose() * Fincr[i] - eye);
+ mass_specific_energy = e[i] / rmass[i]; // energy per unit mass
+ rho = rmass[i] / (detF[i] * vfrac[i]);
+ vol_specific_energy = mass_specific_energy * rho; // energy per current volume
+
+ /*
+ * pressure: compute pressure rate p_rate and final pressure pFinal
+ */
+
+ ComputePressure(i, rho, mass_specific_energy, vol_specific_energy, pInitial, d_iso, pFinal, p_rate);
+
+ /*
+ * material strength
+ */
+
+ //cout << "this is the strain deviator rate" << endl << d_dev << endl;
+ ComputeStressDeviator(i, sigmaInitial_dev, d_dev, sigmaFinal_dev, sigma_dev_rate, plastic_strain_increment);
+ //cout << "this is the stress deviator rate" << endl << sigma_dev_rate << endl;
+
+ // keep a rolling average of the plastic strain rate over the last 100 or so timesteps
+ eff_plastic_strain[i] += plastic_strain_increment;
+
+ // compute a characteristic time over which to average the plastic strain
+ double tav = 1000 * radius[i] / (Lookup[SIGNAL_VELOCITY][itype]);
+ eff_plastic_strain_rate[i] -= eff_plastic_strain_rate[i] * dt / tav;
eff_plastic_strain_rate[i] += plastic_strain_increment / tav;
eff_plastic_strain_rate[i] = MAX(0.0, eff_plastic_strain_rate[i]);
- /*
- * assemble total stress from pressure and deviatoric stress
- */
- sigmaFinal = pFinal * eye + sigmaFinal_dev; // this is the stress that is kept
-
- if (JAUMANN) {
- /*
- * sigma is already the co-rotated Cauchy stress.
- * The stress rate, however, needs to be made objective.
- */
-
- if (dt > 1.0e-16) {
- sigma_rate = (1.0 / dt) * (sigmaFinal - sigmaInitial);
- } else {
- sigma_rate.setZero();
- }
-
- Jaumann_rate = sigma_rate + W[i] * sigmaInitial + sigmaInitial * W[i].transpose();
- sigmaFinal = sigmaInitial + dt * Jaumann_rate;
- T = sigmaFinal;
- } else {
- /*
- * sigma is the unrotated stress.
- * need to do forward rotation of the unrotated stress sigma to the current configuration
- */
- T = R[i] * sigmaFinal * R[i].transpose();
- }
-
- /*
- * store unrotated stress in atom vector
- * symmetry is exploited
- */
- tlsph_stress[i][0] = sigmaFinal(0, 0);
- tlsph_stress[i][1] = sigmaFinal(0, 1);
- tlsph_stress[i][2] = sigmaFinal(0, 2);
- tlsph_stress[i][3] = sigmaFinal(1, 1);
- tlsph_stress[i][4] = sigmaFinal(1, 2);
- tlsph_stress[i][5] = sigmaFinal(2, 2);
-
- /*
- * Damage due to failure criteria.
- */
-
- if (failureModel[itype].integration_point_wise) {
- ComputeDamage(i, strain, T, T_damaged);
- //T = T_damaged; Do not do this, it is undefined as of now
- }
-
- // store rotated, "true" Cauchy stress
- CauchyStress[i] = T;
-
- /*
- * We have the corotational Cauchy stress.
- * Convert to PK1. Note that reference configuration used for computing the forces is linked via
- * the incremental deformation gradient, not the full deformation gradient.
- */
- PK1[i] = detF[i] * T * FincrInv[i].transpose();
-
- /*
- * pre-multiply stress tensor with shape matrix to save computation in force loop
- */
- PK1[i] = PK1[i] * K[i];
-
- /*
- * compute stable time step according to Pronto 2d
- */
-
- Matrix3d deltaSigma;
- deltaSigma = sigmaFinal - sigmaInitial;
- p_rate = deltaSigma.trace() / (3.0 * dt + 1.0e-16);
- sigma_dev_rate = Deviator(deltaSigma) / (dt + 1.0e-16);
-
- double K_eff, mu_eff;
- effective_longitudinal_modulus(itype, dt, d_iso, p_rate, d_dev, sigma_dev_rate, damage[i], K_eff, mu_eff, M_eff);
- p_wave_speed = sqrt(M_eff / rho);
-
- if (mol[i] < 0) {
- error->one(FLERR, "this should not happen");
- }
-
- particle_dt[i] = 2.0 * radius[i] / p_wave_speed;
- dtCFL = MIN(dtCFL, particle_dt[i]);
-
- } else { // end if mol > 0
- PK1[i].setZero();
- K[i].setIdentity();
- CauchyStress[i].setZero();
- sigma_rate.setZero();
- tlsph_stress[i][0] = 0.0;
- tlsph_stress[i][1] = 0.0;
- tlsph_stress[i][2] = 0.0;
- tlsph_stress[i][3] = 0.0;
- tlsph_stress[i][4] = 0.0;
- tlsph_stress[i][5] = 0.0;
- } // end if mol > 0
- } // end setflag
- } // end for
+ /*
+ * assemble total stress from pressure and deviatoric stress
+ */
+ sigmaFinal = pFinal * eye + sigmaFinal_dev; // this is the stress that is kept
+
+ if (JAUMANN) {
+ /*
+ * sigma is already the co-rotated Cauchy stress.
+ * The stress rate, however, needs to be made objective.
+ */
+
+ if (dt > 1.0e-16) {
+ sigma_rate = (1.0 / dt) * (sigmaFinal - sigmaInitial);
+ } else {
+ sigma_rate.setZero();
+ }
+
+ Jaumann_rate = sigma_rate + W[i] * sigmaInitial + sigmaInitial * W[i].transpose();
+ sigmaFinal = sigmaInitial + dt * Jaumann_rate;
+ T = sigmaFinal;
+ } else {
+ /*
+ * sigma is the unrotated stress.
+ * need to do forward rotation of the unrotated stress sigma to the current configuration
+ */
+ T = R[i] * sigmaFinal * R[i].transpose();
+ }
+
+ /*
+ * store unrotated stress in atom vector
+ * symmetry is exploited
+ */
+ tlsph_stress[i][0] = sigmaFinal(0, 0);
+ tlsph_stress[i][1] = sigmaFinal(0, 1);
+ tlsph_stress[i][2] = sigmaFinal(0, 2);
+ tlsph_stress[i][3] = sigmaFinal(1, 1);
+ tlsph_stress[i][4] = sigmaFinal(1, 2);
+ tlsph_stress[i][5] = sigmaFinal(2, 2);
+
+ /*
+ * Damage due to failure criteria.
+ */
+
+ if (failureModel[itype].integration_point_wise) {
+ ComputeDamage(i, strain, T, T_damaged);
+ //T = T_damaged; Do not do this, it is undefined as of now
+ }
+
+ // store rotated, "true" Cauchy stress
+ CauchyStress[i] = T;
+
+ /*
+ * We have the corotational Cauchy stress.
+ * Convert to PK1. Note that reference configuration used for computing the forces is linked via
+ * the incremental deformation gradient, not the full deformation gradient.
+ */
+ PK1[i] = detF[i] * T * FincrInv[i].transpose();
+
+ /*
+ * pre-multiply stress tensor with shape matrix to save computation in force loop
+ */
+ PK1[i] = PK1[i] * K[i];
+
+ /*
+ * compute stable time step according to Pronto 2d
+ */
+
+ Matrix3d deltaSigma;
+ deltaSigma = sigmaFinal - sigmaInitial;
+ p_rate = deltaSigma.trace() / (3.0 * dt + 1.0e-16);
+ sigma_dev_rate = Deviator(deltaSigma) / (dt + 1.0e-16);
+
+ double K_eff, mu_eff;
+ effective_longitudinal_modulus(itype, dt, d_iso, p_rate, d_dev, sigma_dev_rate, damage[i], K_eff, mu_eff, M_eff);
+ p_wave_speed = sqrt(M_eff / rho);
+
+ if (mol[i] < 0) {
+ error->one(FLERR, "this should not happen");
+ }
+
+ particle_dt[i] = 2.0 * radius[i] / p_wave_speed;
+ dtCFL = MIN(dtCFL, particle_dt[i]);
+
+ } else { // end if mol > 0
+ PK1[i].setZero();
+ K[i].setIdentity();
+ CauchyStress[i].setZero();
+ sigma_rate.setZero();
+ tlsph_stress[i][0] = 0.0;
+ tlsph_stress[i][1] = 0.0;
+ tlsph_stress[i][2] = 0.0;
+ tlsph_stress[i][3] = 0.0;
+ tlsph_stress[i][4] = 0.0;
+ tlsph_stress[i][5] = 0.0;
+ } // end if mol > 0
+ } // end setflag
+ } // end for
}
/* ----------------------------------------------------------------------
@@ -883,25 +883,25 @@ void PairTlsph::AssembleStress() {
------------------------------------------------------------------------- */
void PairTlsph::allocate() {
- allocated = 1;
- int n = atom->ntypes;
+ allocated = 1;
+ int n = atom->ntypes;
- memory->create(setflag, n + 1, n + 1, "pair:setflag");
- for (int i = 1; i <= n; i++)
- for (int j = i; j <= n; j++)
- setflag[i][j] = 0;
+ memory->create(setflag, n + 1, n + 1, "pair:setflag");
+ for (int i = 1; i <= n; i++)
+ for (int j = i; j <= n; j++)
+ setflag[i][j] = 0;
- memory->create(strengthModel, n + 1, "pair:strengthmodel");
- memory->create(eos, n + 1, "pair:eosmodel");
- failureModel = new failure_types[n + 1];
- memory->create(Lookup, MAX_KEY_VALUE, n + 1, "pair:LookupTable");
+ memory->create(strengthModel, n + 1, "pair:strengthmodel");
+ memory->create(eos, n + 1, "pair:eosmodel");
+ failureModel = new failure_types[n + 1];
+ memory->create(Lookup, MAX_KEY_VALUE, n + 1, "pair:LookupTable");
- memory->create(cutsq, n + 1, n + 1, "pair:cutsq"); // always needs to be allocated, even with granular neighborlist
+ memory->create(cutsq, n + 1, n + 1, "pair:cutsq"); // always needs to be allocated, even with granular neighborlist
- onerad_dynamic = new double[n + 1];
- onerad_frozen = new double[n + 1];
- maxrad_dynamic = new double[n + 1];
- maxrad_frozen = new double[n + 1];
+ onerad_dynamic = new double[n + 1];
+ onerad_frozen = new double[n + 1];
+ maxrad_dynamic = new double[n + 1];
+ maxrad_frozen = new double[n + 1];
}
@@ -911,82 +911,82 @@ void PairTlsph::allocate() {
void PairTlsph::settings(int narg, char **arg) {
- if (comm->me == 0) {
- printf(
- "\n>>========>>========>>========>>========>>========>>========>>========>>========>>========>>========>>========>>========\n");
- printf("TLSPH settings\n");
- }
-
- /*
- * default value for update_threshold for updates of reference configuration:
- * The maximum relative displacement which is tracked by the construction of LAMMPS' neighborlists
- * is the folowing.
- */
-
- cut_comm = MAX(neighbor->cutneighmax, comm->cutghostuser); // cutoff radius within which ghost atoms are communicated.
- update_threshold = cut_comm;
- update_method = UPDATE_NONE;
-
- int iarg = 0;
-
- while (true) {
-
- if (iarg >= narg) {
- break;
- }
-
- if (strcmp(arg[iarg], "*UPDATE_CONSTANT") == 0) {
- iarg++;
- if (iarg == narg) {
- error->all(FLERR, "expected number following *UPDATE_CONSTANT keyword");
- }
-
- update_method = UPDATE_CONSTANT_THRESHOLD;
- update_threshold = force->numeric(FLERR, arg[iarg]);
-
- } else if (strcmp(arg[iarg], "*UPDATE_PAIRWISE") == 0) {
- iarg++;
- if (iarg == narg) {
- error->all(FLERR, "expected number following *UPDATE_PAIRWISE keyword");
- }
-
- update_method = UPDATE_PAIRWISE_RATIO;
- update_threshold = force->numeric(FLERR, arg[iarg]);
-
- } else {
- char msg[128];
- sprintf(msg, "Illegal keyword for smd/integrate_tlsph: %s\n", arg[iarg]);
- error->all(FLERR, msg);
- }
-
- iarg++;
- }
-
- if ((update_threshold > cut_comm) && (update_method == UPDATE_CONSTANT_THRESHOLD)) {
- if (comm->me == 0) {
- printf("\n ***** WARNING ***\n");
- printf("requested reference configuration update threshold is %g length units\n", update_threshold);
- printf("This value exceeds the maximum value %g beyond which TLSPH displacements can be tracked at current settings.\n",
- cut_comm);
- printf("Expect loss of neighbors!\n");
- }
- }
-
- if (comm->me == 0) {
-
- if (update_method == UPDATE_CONSTANT_THRESHOLD) {
- printf("... will update reference configuration if magnitude of relative displacement exceeds %g length units\n",
- update_threshold);
- } else if (update_method == UPDATE_PAIRWISE_RATIO) {
- printf("... will update reference configuration if ratio pairwise distance / smoothing length exceeds %g\n",
- update_threshold);
- } else if (update_method == UPDATE_NONE) {
- printf("... will never update reference configuration");
- }
- printf(
- ">>========>>========>>========>>========>>========>>========>>========>>========>>========>>========>>========>>========\n");
-
- }
+ if (comm->me == 0) {
+ printf(
+ "\n>>========>>========>>========>>========>>========>>========>>========>>========>>========>>========>>========>>========\n");
+ printf("TLSPH settings\n");
+ }
+
+ /*
+ * default value for update_threshold for updates of reference configuration:
+ * The maximum relative displacement which is tracked by the construction of LAMMPS' neighborlists
+ * is the folowing.
+ */
+
+ cut_comm = MAX(neighbor->cutneighmax, comm->cutghostuser); // cutoff radius within which ghost atoms are communicated.
+ update_threshold = cut_comm;
+ update_method = UPDATE_NONE;
+
+ int iarg = 0;
+
+ while (true) {
+
+ if (iarg >= narg) {
+ break;
+ }
+
+ if (strcmp(arg[iarg], "*UPDATE_CONSTANT") == 0) {
+ iarg++;
+ if (iarg == narg) {
+ error->all(FLERR, "expected number following *UPDATE_CONSTANT keyword");
+ }
+
+ update_method = UPDATE_CONSTANT_THRESHOLD;
+ update_threshold = force->numeric(FLERR, arg[iarg]);
+
+ } else if (strcmp(arg[iarg], "*UPDATE_PAIRWISE") == 0) {
+ iarg++;
+ if (iarg == narg) {
+ error->all(FLERR, "expected number following *UPDATE_PAIRWISE keyword");
+ }
+
+ update_method = UPDATE_PAIRWISE_RATIO;
+ update_threshold = force->numeric(FLERR, arg[iarg]);
+
+ } else {
+ char msg[128];
+ sprintf(msg, "Illegal keyword for smd/integrate_tlsph: %s\n", arg[iarg]);
+ error->all(FLERR, msg);
+ }
+
+ iarg++;
+ }
+
+ if ((update_threshold > cut_comm) && (update_method == UPDATE_CONSTANT_THRESHOLD)) {
+ if (comm->me == 0) {
+ printf("\n ***** WARNING ***\n");
+ printf("requested reference configuration update threshold is %g length units\n", update_threshold);
+ printf("This value exceeds the maximum value %g beyond which TLSPH displacements can be tracked at current settings.\n",
+ cut_comm);
+ printf("Expect loss of neighbors!\n");
+ }
+ }
+
+ if (comm->me == 0) {
+
+ if (update_method == UPDATE_CONSTANT_THRESHOLD) {
+ printf("... will update reference configuration if magnitude of relative displacement exceeds %g length units\n",
+ update_threshold);
+ } else if (update_method == UPDATE_PAIRWISE_RATIO) {
+ printf("... will update reference configuration if ratio pairwise distance / smoothing length exceeds %g\n",
+ update_threshold);
+ } else if (update_method == UPDATE_NONE) {
+ printf("... will never update reference configuration");
+ }
+ printf(
+ ">>========>>========>>========>>========>>========>>========>>========>>========>>========>>========>>========>>========\n");
+
+ }
}
@@ -995,701 +995,701 @@ void PairTlsph::settings(int narg, char **arg) {
------------------------------------------------------------------------- */
void PairTlsph::coeff(int narg, char **arg) {
- int ioffset, iarg, iNextKwd, itype;
- char str[128];
- std::string s, t;
-
- if (narg < 3) {
- sprintf(str, "number of arguments for pair tlsph is too small!");
- error->all(FLERR, str);
- }
- if (!allocated)
- allocate();
-
- /*
- * check that TLSPH parameters are given only in i,i form
- */
- if (force->inumeric(FLERR, arg[0]) != force->inumeric(FLERR, arg[1])) {
- sprintf(str, "TLSPH coefficients can only be specified between particles of same type!");
- error->all(FLERR, str);
- }
- itype = force->inumeric(FLERR, arg[0]);
+ int ioffset, iarg, iNextKwd, itype;
+ char str[128];
+ std::string s, t;
+
+ if (narg < 3) {
+ sprintf(str, "number of arguments for pair tlsph is too small!");
+ error->all(FLERR, str);
+ }
+ if (!allocated)
+ allocate();
+
+ /*
+ * check that TLSPH parameters are given only in i,i form
+ */
+ if (force->inumeric(FLERR, arg[0]) != force->inumeric(FLERR, arg[1])) {
+ sprintf(str, "TLSPH coefficients can only be specified between particles of same type!");
+ error->all(FLERR, str);
+ }
+ itype = force->inumeric(FLERR, arg[0]);
// set all eos, strength and failure models to inactive by default
- eos[itype] = EOS_NONE;
- strengthModel[itype] = STRENGTH_NONE;
-
- if (comm->me == 0) {
- printf(
- "\n>>========>>========>>========>>========>>========>>========>>========>>========>>========>>========>>========>>========\n");
- printf("SMD / TLSPH PROPERTIES OF PARTICLE TYPE %d:\n", itype);
- }
-
- /*
- * read parameters which are common -- regardless of material / eos model
- */
-
- ioffset = 2;
- if (strcmp(arg[ioffset], "*COMMON") != 0) {
- sprintf(str, "common keyword missing!");
- error->all(FLERR, str);
- }
-
- t = string("*");
- iNextKwd = -1;
- for (iarg = ioffset + 1; iarg < narg; iarg++) {
- s = string(arg[iarg]);
- if (s.compare(0, t.length(), t) == 0) {
- iNextKwd = iarg;
- break;
- }
- }
+ eos[itype] = EOS_NONE;
+ strengthModel[itype] = STRENGTH_NONE;
+
+ if (comm->me == 0) {
+ printf(
+ "\n>>========>>========>>========>>========>>========>>========>>========>>========>>========>>========>>========>>========\n");
+ printf("SMD / TLSPH PROPERTIES OF PARTICLE TYPE %d:\n", itype);
+ }
+
+ /*
+ * read parameters which are common -- regardless of material / eos model
+ */
+
+ ioffset = 2;
+ if (strcmp(arg[ioffset], "*COMMON") != 0) {
+ sprintf(str, "common keyword missing!");
+ error->all(FLERR, str);
+ }
+
+ t = string("*");
+ iNextKwd = -1;
+ for (iarg = ioffset + 1; iarg < narg; iarg++) {
+ s = string(arg[iarg]);
+ if (s.compare(0, t.length(), t) == 0) {
+ iNextKwd = iarg;
+ break;
+ }
+ }
//printf("keyword following *COMMON is %s\n", arg[iNextKwd]);
- if (iNextKwd < 0) {
- sprintf(str, "no *KEYWORD terminates *COMMON");
- error->all(FLERR, str);
- }
-
- if (iNextKwd - ioffset != 7 + 1) {
- sprintf(str, "expected 7 arguments following *COMMON but got %d\n", iNextKwd - ioffset - 1);
- error->all(FLERR, str);
- }
-
- Lookup[REFERENCE_DENSITY][itype] = force->numeric(FLERR, arg[ioffset + 1]);
- Lookup[YOUNGS_MODULUS][itype] = force->numeric(FLERR, arg[ioffset + 2]);
- Lookup[POISSON_RATIO][itype] = force->numeric(FLERR, arg[ioffset + 3]);
- Lookup[VISCOSITY_Q1][itype] = force->numeric(FLERR, arg[ioffset + 4]);
- Lookup[VISCOSITY_Q2][itype] = force->numeric(FLERR, arg[ioffset + 5]);
- Lookup[HOURGLASS_CONTROL_AMPLITUDE][itype] = force->numeric(FLERR, arg[ioffset + 6]);
- Lookup[HEAT_CAPACITY][itype] = force->numeric(FLERR, arg[ioffset + 7]);
-
- Lookup[LAME_LAMBDA][itype] = Lookup[YOUNGS_MODULUS][itype] * Lookup[POISSON_RATIO][itype]
- / ((1.0 + Lookup[POISSON_RATIO][itype]) * (1.0 - 2.0 * Lookup[POISSON_RATIO][itype]));
- Lookup[SHEAR_MODULUS][itype] = Lookup[YOUNGS_MODULUS][itype] / (2.0 * (1.0 + Lookup[POISSON_RATIO][itype]));
- Lookup[M_MODULUS][itype] = Lookup[LAME_LAMBDA][itype] + 2.0 * Lookup[SHEAR_MODULUS][itype];
- Lookup[SIGNAL_VELOCITY][itype] = sqrt(
- (Lookup[LAME_LAMBDA][itype] + 2.0 * Lookup[SHEAR_MODULUS][itype]) / Lookup[REFERENCE_DENSITY][itype]);
- Lookup[BULK_MODULUS][itype] = Lookup[LAME_LAMBDA][itype] + 2.0 * Lookup[SHEAR_MODULUS][itype] / 3.0;
-
- if (comm->me == 0) {
- printf("\n material unspecific properties for SMD/TLSPH definition of particle type %d:\n", itype);
- printf("%60s : %g\n", "reference density", Lookup[REFERENCE_DENSITY][itype]);
- printf("%60s : %g\n", "Young's modulus", Lookup[YOUNGS_MODULUS][itype]);
- printf("%60s : %g\n", "Poisson ratio", Lookup[POISSON_RATIO][itype]);
- printf("%60s : %g\n", "linear viscosity coefficient", Lookup[VISCOSITY_Q1][itype]);
- printf("%60s : %g\n", "quadratic viscosity coefficient", Lookup[VISCOSITY_Q2][itype]);
- printf("%60s : %g\n", "hourglass control coefficient", Lookup[HOURGLASS_CONTROL_AMPLITUDE][itype]);
- printf("%60s : %g\n", "heat capacity [energy / (mass * temperature)]", Lookup[HEAT_CAPACITY][itype]);
- printf("%60s : %g\n", "Lame constant lambda", Lookup[LAME_LAMBDA][itype]);
- printf("%60s : %g\n", "shear modulus", Lookup[SHEAR_MODULUS][itype]);
- printf("%60s : %g\n", "bulk modulus", Lookup[BULK_MODULUS][itype]);
- printf("%60s : %g\n", "signal velocity", Lookup[SIGNAL_VELOCITY][itype]);
-
- }
-
- /*
- * read following material cards
- */
+ if (iNextKwd < 0) {
+ sprintf(str, "no *KEYWORD terminates *COMMON");
+ error->all(FLERR, str);
+ }
+
+ if (iNextKwd - ioffset != 7 + 1) {
+ sprintf(str, "expected 7 arguments following *COMMON but got %d\n", iNextKwd - ioffset - 1);
+ error->all(FLERR, str);
+ }
+
+ Lookup[REFERENCE_DENSITY][itype] = force->numeric(FLERR, arg[ioffset + 1]);
+ Lookup[YOUNGS_MODULUS][itype] = force->numeric(FLERR, arg[ioffset + 2]);
+ Lookup[POISSON_RATIO][itype] = force->numeric(FLERR, arg[ioffset + 3]);
+ Lookup[VISCOSITY_Q1][itype] = force->numeric(FLERR, arg[ioffset + 4]);
+ Lookup[VISCOSITY_Q2][itype] = force->numeric(FLERR, arg[ioffset + 5]);
+ Lookup[HOURGLASS_CONTROL_AMPLITUDE][itype] = force->numeric(FLERR, arg[ioffset + 6]);
+ Lookup[HEAT_CAPACITY][itype] = force->numeric(FLERR, arg[ioffset + 7]);
+
+ Lookup[LAME_LAMBDA][itype] = Lookup[YOUNGS_MODULUS][itype] * Lookup[POISSON_RATIO][itype]
+ / ((1.0 + Lookup[POISSON_RATIO][itype]) * (1.0 - 2.0 * Lookup[POISSON_RATIO][itype]));
+ Lookup[SHEAR_MODULUS][itype] = Lookup[YOUNGS_MODULUS][itype] / (2.0 * (1.0 + Lookup[POISSON_RATIO][itype]));
+ Lookup[M_MODULUS][itype] = Lookup[LAME_LAMBDA][itype] + 2.0 * Lookup[SHEAR_MODULUS][itype];
+ Lookup[SIGNAL_VELOCITY][itype] = sqrt(
+ (Lookup[LAME_LAMBDA][itype] + 2.0 * Lookup[SHEAR_MODULUS][itype]) / Lookup[REFERENCE_DENSITY][itype]);
+ Lookup[BULK_MODULUS][itype] = Lookup[LAME_LAMBDA][itype] + 2.0 * Lookup[SHEAR_MODULUS][itype] / 3.0;
+
+ if (comm->me == 0) {
+ printf("\n material unspecific properties for SMD/TLSPH definition of particle type %d:\n", itype);
+ printf("%60s : %g\n", "reference density", Lookup[REFERENCE_DENSITY][itype]);
+ printf("%60s : %g\n", "Young's modulus", Lookup[YOUNGS_MODULUS][itype]);
+ printf("%60s : %g\n", "Poisson ratio", Lookup[POISSON_RATIO][itype]);
+ printf("%60s : %g\n", "linear viscosity coefficient", Lookup[VISCOSITY_Q1][itype]);
+ printf("%60s : %g\n", "quadratic viscosity coefficient", Lookup[VISCOSITY_Q2][itype]);
+ printf("%60s : %g\n", "hourglass control coefficient", Lookup[HOURGLASS_CONTROL_AMPLITUDE][itype]);
+ printf("%60s : %g\n", "heat capacity [energy / (mass * temperature)]", Lookup[HEAT_CAPACITY][itype]);
+ printf("%60s : %g\n", "Lame constant lambda", Lookup[LAME_LAMBDA][itype]);
+ printf("%60s : %g\n", "shear modulus", Lookup[SHEAR_MODULUS][itype]);
+ printf("%60s : %g\n", "bulk modulus", Lookup[BULK_MODULUS][itype]);
+ printf("%60s : %g\n", "signal velocity", Lookup[SIGNAL_VELOCITY][itype]);
+
+ }
+
+ /*
+ * read following material cards
+ */
//printf("next kwd is %s\n", arg[iNextKwd]);
- eos[itype] = EOS_NONE;
- strengthModel[itype] = STRENGTH_NONE;
-
- while (true) {
- if (strcmp(arg[iNextKwd], "*END") == 0) {
- if (comm->me == 0) {
- printf("found *END keyword");
- printf(
- "\n>>========>>========>>========>>========>>========>>========>>========>>========>>========>>========>>========>>========\n\n");
- }
- break;
- }
-
- /*
- * Linear Elasticity model based on deformation gradient
- */
- ioffset = iNextKwd;
- if (strcmp(arg[ioffset], "*LINEAR_DEFGRAD") == 0) {
- strengthModel[itype] = LINEAR_DEFGRAD;
-
- if (comm->me == 0) {
- printf("reading *LINEAR_DEFGRAD\n");
- }
-
- t = string("*");
- iNextKwd = -1;
- for (iarg = ioffset + 1; iarg < narg; iarg++) {
- s = string(arg[iarg]);
- if (s.compare(0, t.length(), t) == 0) {
- iNextKwd = iarg;
- break;
- }
- }
-
- if (iNextKwd < 0) {
- sprintf(str, "no *KEYWORD terminates *LINEAR_DEFGRAD");
- error->all(FLERR, str);
- }
-
- if (iNextKwd - ioffset != 1) {
- sprintf(str, "expected 0 arguments following *LINEAR_DEFGRAD but got %d\n", iNextKwd - ioffset - 1);
- error->all(FLERR, str);
- }
-
- if (comm->me == 0) {
- printf("\n%60s\n", "Linear Elasticity model based on deformation gradient");
- }
- } else if (strcmp(arg[ioffset], "*STRENGTH_LINEAR") == 0) {
-
- /*
- * Linear Elasticity strength only model based on strain rate
- */
-
- strengthModel[itype] = STRENGTH_LINEAR;
- if (comm->me == 0) {
- printf("reading *STRENGTH_LINEAR\n");
- }
-
- t = string("*");
- iNextKwd = -1;
- for (iarg = ioffset + 1; iarg < narg; iarg++) {
- s = string(arg[iarg]);
- if (s.compare(0, t.length(), t) == 0) {
- iNextKwd = iarg;
- break;
- }
- }
-
- if (iNextKwd < 0) {
- sprintf(str, "no *KEYWORD terminates *STRENGTH_LINEAR");
- error->all(FLERR, str);
- }
-
- if (iNextKwd - ioffset != 1) {
- sprintf(str, "expected 0 arguments following *STRENGTH_LINEAR but got %d\n", iNextKwd - ioffset - 1);
- error->all(FLERR, str);
- }
-
- if (comm->me == 0) {
- printf("%60s\n", "Linear Elasticity strength based on strain rate");
- }
- } // end Linear Elasticity strength only model based on strain rate
-
- else if (strcmp(arg[ioffset], "*STRENGTH_LINEAR_PLASTIC") == 0) {
-
- /*
- * Linear Elastic / perfectly plastic strength only model based on strain rate
- */
-
- strengthModel[itype] = STRENGTH_LINEAR_PLASTIC;
- if (comm->me == 0) {
- printf("reading *STRENGTH_LINEAR_PLASTIC\n");
- }
-
- t = string("*");
- iNextKwd = -1;
- for (iarg = ioffset + 1; iarg < narg; iarg++) {
- s = string(arg[iarg]);
- if (s.compare(0, t.length(), t) == 0) {
- iNextKwd = iarg;
- break;
- }
- }
-
- if (iNextKwd < 0) {
- sprintf(str, "no *KEYWORD terminates *STRENGTH_LINEAR_PLASTIC");
- error->all(FLERR, str);
- }
-
- if (iNextKwd - ioffset != 2 + 1) {
- sprintf(str, "expected 2 arguments following *STRENGTH_LINEAR_PLASTIC but got %d\n", iNextKwd - ioffset - 1);
- error->all(FLERR, str);
- }
-
- Lookup[YIELD_STRESS][itype] = force->numeric(FLERR, arg[ioffset + 1]);
- Lookup[HARDENING_PARAMETER][itype] = force->numeric(FLERR, arg[ioffset + 2]);
-
- if (comm->me == 0) {
- printf("%60s\n", "Linear elastic / perfectly plastic strength based on strain rate");
- printf("%60s : %g\n", "Young's modulus", Lookup[YOUNGS_MODULUS][itype]);
- printf("%60s : %g\n", "Poisson ratio", Lookup[POISSON_RATIO][itype]);
- printf("%60s : %g\n", "shear modulus", Lookup[SHEAR_MODULUS][itype]);
- printf("%60s : %g\n", "constant yield stress", Lookup[YIELD_STRESS][itype]);
- printf("%60s : %g\n", "constant hardening parameter", Lookup[HARDENING_PARAMETER][itype]);
- }
- } // end Linear Elastic / perfectly plastic strength only model based on strain rate
-
- else if (strcmp(arg[ioffset], "*JOHNSON_COOK") == 0) {
-
- /*
- * JOHNSON - COOK
- */
-
- strengthModel[itype] = STRENGTH_JOHNSON_COOK;
- if (comm->me == 0) {
- printf("reading *JOHNSON_COOK\n");
- }
-
- t = string("*");
- iNextKwd = -1;
- for (iarg = ioffset + 1; iarg < narg; iarg++) {
- s = string(arg[iarg]);
- if (s.compare(0, t.length(), t) == 0) {
- iNextKwd = iarg;
- break;
- }
- }
-
- if (iNextKwd < 0) {
- sprintf(str, "no *KEYWORD terminates *JOHNSON_COOK");
- error->all(FLERR, str);
- }
-
- if (iNextKwd - ioffset != 8 + 1) {
- sprintf(str, "expected 8 arguments following *JOHNSON_COOK but got %d\n", iNextKwd - ioffset - 1);
- error->all(FLERR, str);
- }
-
- Lookup[JC_A][itype] = force->numeric(FLERR, arg[ioffset + 1]);
- Lookup[JC_B][itype] = force->numeric(FLERR, arg[ioffset + 2]);
- Lookup[JC_a][itype] = force->numeric(FLERR, arg[ioffset + 3]);
- Lookup[JC_C][itype] = force->numeric(FLERR, arg[ioffset + 4]);
- Lookup[JC_epdot0][itype] = force->numeric(FLERR, arg[ioffset + 5]);
- Lookup[JC_T0][itype] = force->numeric(FLERR, arg[ioffset + 6]);
- Lookup[JC_Tmelt][itype] = force->numeric(FLERR, arg[ioffset + 7]);
- Lookup[JC_M][itype] = force->numeric(FLERR, arg[ioffset + 8]);
-
- if (comm->me == 0) {
- printf("%60s\n", "Johnson Cook material strength model");
- printf("%60s : %g\n", "A: initial yield stress", Lookup[JC_A][itype]);
- printf("%60s : %g\n", "B : proportionality factor for plastic strain dependency", Lookup[JC_B][itype]);
- printf("%60s : %g\n", "a : exponent for plastic strain dependency", Lookup[JC_a][itype]);
- printf("%60s : %g\n", "C : proportionality factor for logarithmic plastic strain rate dependency",
- Lookup[JC_C][itype]);
- printf("%60s : %g\n", "epdot0 : dimensionality factor for plastic strain rate dependency",
- Lookup[JC_epdot0][itype]);
- printf("%60s : %g\n", "T0 : reference (room) temperature", Lookup[JC_T0][itype]);
- printf("%60s : %g\n", "Tmelt : melting temperature", Lookup[JC_Tmelt][itype]);
- printf("%60s : %g\n", "M : exponent for temperature dependency", Lookup[JC_M][itype]);
- }
-
- } else if (strcmp(arg[ioffset], "*EOS_NONE") == 0) {
-
- /*
- * no eos
- */
-
- eos[itype] = EOS_NONE;
- if (comm->me == 0) {
- printf("reading *EOS_NONE\n");
- }
-
- t = string("*");
- iNextKwd = -1;
- for (iarg = ioffset + 1; iarg < narg; iarg++) {
- s = string(arg[iarg]);
- if (s.compare(0, t.length(), t) == 0) {
- iNextKwd = iarg;
- break;
- }
- }
-
- if (iNextKwd < 0) {
- sprintf(str, "no *KEYWORD terminates *EOS_NONE");
- error->all(FLERR, str);
- }
-
- if (iNextKwd - ioffset != 1) {
- sprintf(str, "expected 0 arguments following *EOS_NONE but got %d\n", iNextKwd - ioffset - 1);
- error->all(FLERR, str);
- }
-
- if (comm->me == 0) {
- printf("\n%60s\n", "no EOS selected");
- }
-
- } else if (strcmp(arg[ioffset], "*EOS_LINEAR") == 0) {
-
- /*
- * linear eos
- */
-
- eos[itype] = EOS_LINEAR;
- if (comm->me == 0) {
- printf("reading *EOS_LINEAR\n");
- }
-
- t = string("*");
- iNextKwd = -1;
- for (iarg = ioffset + 1; iarg < narg; iarg++) {
- s = string(arg[iarg]);
- if (s.compare(0, t.length(), t) == 0) {
- iNextKwd = iarg;
- break;
- }
- }
-
- if (iNextKwd < 0) {
- sprintf(str, "no *KEYWORD terminates *EOS_LINEAR");
- error->all(FLERR, str);
- }
-
- if (iNextKwd - ioffset != 1) {
- sprintf(str, "expected 0 arguments following *EOS_LINEAR but got %d\n", iNextKwd - ioffset - 1);
- error->all(FLERR, str);
- }
-
- if (comm->me == 0) {
- printf("\n%60s\n", "linear EOS based on strain rate");
- printf("%60s : %g\n", "bulk modulus", Lookup[BULK_MODULUS][itype]);
- }
- } // end linear eos
- else if (strcmp(arg[ioffset], "*EOS_SHOCK") == 0) {
-
- /*
- * shock eos
- */
-
- eos[itype] = EOS_SHOCK;
- if (comm->me == 0) {
- printf("reading *EOS_SHOCK\n");
- }
-
- t = string("*");
- iNextKwd = -1;
- for (iarg = ioffset + 1; iarg < narg; iarg++) {
- s = string(arg[iarg]);
- if (s.compare(0, t.length(), t) == 0) {
- iNextKwd = iarg;
- break;
- }
- }
-
- if (iNextKwd < 0) {
- sprintf(str, "no *KEYWORD terminates *EOS_SHOCK");
- error->all(FLERR, str);
- }
-
- if (iNextKwd - ioffset != 3 + 1) {
- sprintf(str, "expected 3 arguments (c0, S, Gamma) following *EOS_SHOCK but got %d\n", iNextKwd - ioffset - 1);
- error->all(FLERR, str);
- }
-
- Lookup[EOS_SHOCK_C0][itype] = force->numeric(FLERR, arg[ioffset + 1]);
- Lookup[EOS_SHOCK_S][itype] = force->numeric(FLERR, arg[ioffset + 2]);
- Lookup[EOS_SHOCK_GAMMA][itype] = force->numeric(FLERR, arg[ioffset + 3]);
- if (comm->me == 0) {
- printf("\n%60s\n", "shock EOS based on strain rate");
- printf("%60s : %g\n", "reference speed of sound", Lookup[EOS_SHOCK_C0][itype]);
- printf("%60s : %g\n", "Hugoniot parameter S", Lookup[EOS_SHOCK_S][itype]);
- printf("%60s : %g\n", "Grueneisen Gamma", Lookup[EOS_SHOCK_GAMMA][itype]);
- }
- } // end shock eos
-
- else if (strcmp(arg[ioffset], "*EOS_POLYNOMIAL") == 0) {
- /*
- * polynomial eos
- */
-
- eos[itype] = EOS_POLYNOMIAL;
- if (comm->me == 0) {
- printf("reading *EOS_POLYNOMIAL\n");
- }
-
- t = string("*");
- iNextKwd = -1;
- for (iarg = ioffset + 1; iarg < narg; iarg++) {
- s = string(arg[iarg]);
- if (s.compare(0, t.length(), t) == 0) {
- iNextKwd = iarg;
- break;
- }
- }
-
- if (iNextKwd < 0) {
- sprintf(str, "no *KEYWORD terminates *EOS_POLYNOMIAL");
- error->all(FLERR, str);
- }
-
- if (iNextKwd - ioffset != 7 + 1) {
- sprintf(str, "expected 7 arguments following *EOS_POLYNOMIAL but got %d\n", iNextKwd - ioffset - 1);
- error->all(FLERR, str);
- }
-
- Lookup[EOS_POLYNOMIAL_C0][itype] = force->numeric(FLERR, arg[ioffset + 1]);
- Lookup[EOS_POLYNOMIAL_C1][itype] = force->numeric(FLERR, arg[ioffset + 2]);
- Lookup[EOS_POLYNOMIAL_C2][itype] = force->numeric(FLERR, arg[ioffset + 3]);
- Lookup[EOS_POLYNOMIAL_C3][itype] = force->numeric(FLERR, arg[ioffset + 4]);
- Lookup[EOS_POLYNOMIAL_C4][itype] = force->numeric(FLERR, arg[ioffset + 5]);
- Lookup[EOS_POLYNOMIAL_C5][itype] = force->numeric(FLERR, arg[ioffset + 6]);
- Lookup[EOS_POLYNOMIAL_C6][itype] = force->numeric(FLERR, arg[ioffset + 7]);
- if (comm->me == 0) {
- printf("\n%60s\n", "polynomial EOS based on strain rate");
- printf("%60s : %g\n", "parameter c0", Lookup[EOS_POLYNOMIAL_C0][itype]);
- printf("%60s : %g\n", "parameter c1", Lookup[EOS_POLYNOMIAL_C1][itype]);
- printf("%60s : %g\n", "parameter c2", Lookup[EOS_POLYNOMIAL_C2][itype]);
- printf("%60s : %g\n", "parameter c3", Lookup[EOS_POLYNOMIAL_C3][itype]);
- printf("%60s : %g\n", "parameter c4", Lookup[EOS_POLYNOMIAL_C4][itype]);
- printf("%60s : %g\n", "parameter c5", Lookup[EOS_POLYNOMIAL_C5][itype]);
- printf("%60s : %g\n", "parameter c6", Lookup[EOS_POLYNOMIAL_C6][itype]);
- }
- } // end polynomial eos
-
- else if (strcmp(arg[ioffset], "*FAILURE_MAX_PLASTIC_STRAIN") == 0) {
-
- /*
- * maximum plastic strain failure criterion
- */
-
- if (comm->me == 0) {
- printf("reading *FAILURE_MAX_PLASTIC_SRTRAIN\n");
- }
-
- t = string("*");
- iNextKwd = -1;
- for (iarg = ioffset + 1; iarg < narg; iarg++) {
- s = string(arg[iarg]);
- if (s.compare(0, t.length(), t) == 0) {
- iNextKwd = iarg;
- break;
- }
- }
-
- if (iNextKwd < 0) {
- sprintf(str, "no *KEYWORD terminates *FAILURE_MAX_PLASTIC_STRAIN");
- error->all(FLERR, str);
- }
-
- if (iNextKwd - ioffset != 1 + 1) {
- sprintf(str, "expected 1 arguments following *FAILURE_MAX_PLASTIC_STRAIN but got %d\n", iNextKwd - ioffset - 1);
- error->all(FLERR, str);
- }
-
- failureModel[itype].failure_max_plastic_strain = true;
- failureModel[itype].integration_point_wise = true;
- Lookup[FAILURE_MAX_PLASTIC_STRAIN_THRESHOLD][itype] = force->numeric(FLERR, arg[ioffset + 1]);
-
- if (comm->me == 0) {
- printf("\n%60s\n", "maximum plastic strain failure criterion");
- printf("%60s : %g\n", "failure occurs when plastic strain reaches limit",
- Lookup[FAILURE_MAX_PLASTIC_STRAIN_THRESHOLD][itype]);
- }
- } // end maximum plastic strain failure criterion
- else if (strcmp(arg[ioffset], "*FAILURE_MAX_PAIRWISE_STRAIN") == 0) {
-
- /*
- * failure criterion based on maximum strain between a pair of TLSPH particles.
- */
-
- if (comm->me == 0) {
- printf("reading *FAILURE_MAX_PAIRWISE_STRAIN\n");
- }
-
- if (update_method != UPDATE_NONE) {
- error->all(FLERR, "cannot use *FAILURE_MAX_PAIRWISE_STRAIN with updated Total-Lagrangian formalism");
- }
-
- t = string("*");
- iNextKwd = -1;
- for (iarg = ioffset + 1; iarg < narg; iarg++) {
- s = string(arg[iarg]);
- if (s.compare(0, t.length(), t) == 0) {
- iNextKwd = iarg;
- break;
- }
- }
-
- if (iNextKwd < 0) {
- sprintf(str, "no *KEYWORD terminates *FAILURE_MAX_PAIRWISE_STRAIN");
- error->all(FLERR, str);
- }
-
- if (iNextKwd - ioffset != 1 + 1) {
- sprintf(str, "expected 1 arguments following *FAILURE_MAX_PAIRWISE_STRAIN but got %d\n", iNextKwd - ioffset - 1);
- error->all(FLERR, str);
- }
-
- failureModel[itype].failure_max_pairwise_strain = true;
- failureModel[itype].integration_point_wise = true;
- Lookup[FAILURE_MAX_PAIRWISE_STRAIN_THRESHOLD][itype] = force->numeric(FLERR, arg[ioffset + 1]);
-
- if (comm->me == 0) {
- printf("\n%60s\n", "maximum pairwise strain failure criterion");
- printf("%60s : %g\n", "failure occurs when pairwise strain reaches limit",
- Lookup[FAILURE_MAX_PAIRWISE_STRAIN_THRESHOLD][itype]);
- }
- } // end pair based maximum strain failure criterion
- else if (strcmp(arg[ioffset], "*FAILURE_MAX_PRINCIPAL_STRAIN") == 0) {
- error->all(FLERR, "this failure model is currently unsupported");
-
- /*
- * maximum principal strain failure criterion
- */
- if (comm->me == 0) {
- printf("reading *FAILURE_MAX_PRINCIPAL_STRAIN\n");
- }
-
- t = string("*");
- iNextKwd = -1;
- for (iarg = ioffset + 1; iarg < narg; iarg++) {
- s = string(arg[iarg]);
- if (s.compare(0, t.length(), t) == 0) {
- iNextKwd = iarg;
- break;
- }
- }
-
- if (iNextKwd < 0) {
- sprintf(str, "no *KEYWORD terminates *FAILURE_MAX_PRINCIPAL_STRAIN");
- error->all(FLERR, str);
- }
-
- if (iNextKwd - ioffset != 1 + 1) {
- sprintf(str, "expected 1 arguments following *FAILURE_MAX_PRINCIPAL_STRAIN but got %d\n", iNextKwd - ioffset - 1);
- error->all(FLERR, str);
- }
-
- failureModel[itype].failure_max_principal_strain = true;
- failureModel[itype].integration_point_wise = true;
- Lookup[FAILURE_MAX_PRINCIPAL_STRAIN_THRESHOLD][itype] = force->numeric(FLERR, arg[ioffset + 1]);
-
- if (comm->me == 0) {
- printf("\n%60s\n", "maximum principal strain failure criterion");
- printf("%60s : %g\n", "failure occurs when principal strain reaches limit",
- Lookup[FAILURE_MAX_PRINCIPAL_STRAIN_THRESHOLD][itype]);
- }
- } // end maximum principal strain failure criterion
- else if (strcmp(arg[ioffset], "*FAILURE_JOHNSON_COOK") == 0) {
- error->all(FLERR, "this failure model is currently unsupported");
- if (comm->me == 0) {
- printf("reading *FAILURE_JOHNSON_COOK\n");
- }
-
- t = string("*");
- iNextKwd = -1;
- for (iarg = ioffset + 1; iarg < narg; iarg++) {
- s = string(arg[iarg]);
- if (s.compare(0, t.length(), t) == 0) {
- iNextKwd = iarg;
- break;
- }
- }
-
- if (iNextKwd < 0) {
- sprintf(str, "no *KEYWORD terminates *FAILURE_JOHNSON_COOK");
- error->all(FLERR, str);
- }
-
- if (iNextKwd - ioffset != 5 + 1) {
- sprintf(str, "expected 5 arguments following *FAILURE_JOHNSON_COOK but got %d\n", iNextKwd - ioffset - 1);
- error->all(FLERR, str);
- }
-
- failureModel[itype].failure_johnson_cook = true;
- failureModel[itype].integration_point_wise = true;
-
- Lookup[FAILURE_JC_D1][itype] = force->numeric(FLERR, arg[ioffset + 1]);
- Lookup[FAILURE_JC_D2][itype] = force->numeric(FLERR, arg[ioffset + 2]);
- Lookup[FAILURE_JC_D3][itype] = force->numeric(FLERR, arg[ioffset + 3]);
- Lookup[FAILURE_JC_D4][itype] = force->numeric(FLERR, arg[ioffset + 4]);
- Lookup[FAILURE_JC_EPDOT0][itype] = force->numeric(FLERR, arg[ioffset + 5]);
-
- if (comm->me == 0) {
- printf("\n%60s\n", "Johnson-Cook failure criterion");
- printf("%60s : %g\n", "parameter d1", Lookup[FAILURE_JC_D1][itype]);
- printf("%60s : %g\n", "parameter d2", Lookup[FAILURE_JC_D2][itype]);
- printf("%60s : %g\n", "parameter d3", Lookup[FAILURE_JC_D3][itype]);
- printf("%60s : %g\n", "parameter d4", Lookup[FAILURE_JC_D4][itype]);
- printf("%60s : %g\n", "reference plastic strain rate", Lookup[FAILURE_JC_EPDOT0][itype]);
- }
-
- } else if (strcmp(arg[ioffset], "*FAILURE_MAX_PRINCIPAL_STRESS") == 0) {
- error->all(FLERR, "this failure model is currently unsupported");
-
- /*
- * maximum principal stress failure criterion
- */
-
- if (comm->me == 0) {
- printf("reading *FAILURE_MAX_PRINCIPAL_STRESS\n");
- }
-
- t = string("*");
- iNextKwd = -1;
- for (iarg = ioffset + 1; iarg < narg; iarg++) {
- s = string(arg[iarg]);
- if (s.compare(0, t.length(), t) == 0) {
- iNextKwd = iarg;
- break;
- }
- }
-
- if (iNextKwd < 0) {
- sprintf(str, "no *KEYWORD terminates *FAILURE_MAX_PRINCIPAL_STRESS");
- error->all(FLERR, str);
- }
-
- if (iNextKwd - ioffset != 1 + 1) {
- sprintf(str, "expected 1 arguments following *FAILURE_MAX_PRINCIPAL_STRESS but got %d\n", iNextKwd - ioffset - 1);
- error->all(FLERR, str);
- }
-
- failureModel[itype].failure_max_principal_stress = true;
- failureModel[itype].integration_point_wise = true;
- Lookup[FAILURE_MAX_PRINCIPAL_STRESS_THRESHOLD][itype] = force->numeric(FLERR, arg[ioffset + 1]);
-
- if (comm->me == 0) {
- printf("\n%60s\n", "maximum principal stress failure criterion");
- printf("%60s : %g\n", "failure occurs when principal stress reaches limit",
- Lookup[FAILURE_MAX_PRINCIPAL_STRESS_THRESHOLD][itype]);
- }
- } // end maximum principal stress failure criterion
-
- else if (strcmp(arg[ioffset], "*FAILURE_ENERGY_RELEASE_RATE") == 0) {
- if (comm->me == 0) {
- printf("reading *FAILURE_ENERGY_RELEASE_RATE\n");
- }
-
- t = string("*");
- iNextKwd = -1;
- for (iarg = ioffset + 1; iarg < narg; iarg++) {
- s = string(arg[iarg]);
- if (s.compare(0, t.length(), t) == 0) {
- iNextKwd = iarg;
- break;
- }
- }
-
- if (iNextKwd < 0) {
- sprintf(str, "no *KEYWORD terminates *FAILURE_ENERGY_RELEASE_RATE");
- error->all(FLERR, str);
- }
-
- if (iNextKwd - ioffset != 1 + 1) {
- sprintf(str, "expected 1 arguments following *FAILURE_ENERGY_RELEASE_RATE but got %d\n", iNextKwd - ioffset - 1);
- error->all(FLERR, str);
- }
-
- failureModel[itype].failure_energy_release_rate = true;
- Lookup[CRITICAL_ENERGY_RELEASE_RATE][itype] = force->numeric(FLERR, arg[ioffset + 1]);
-
- if (comm->me == 0) {
- printf("\n%60s\n", "critical energy release rate failure criterion");
- printf("%60s : %g\n", "failure occurs when energy release rate reaches limit",
- Lookup[CRITICAL_ENERGY_RELEASE_RATE][itype]);
- }
- } // end energy release rate failure criterion
-
- else {
- sprintf(str, "unknown *KEYWORD: %s", arg[ioffset]);
- error->all(FLERR, str);
- }
-
- }
-
- setflag[itype][itype] = 1;
+ eos[itype] = EOS_NONE;
+ strengthModel[itype] = STRENGTH_NONE;
+
+ while (true) {
+ if (strcmp(arg[iNextKwd], "*END") == 0) {
+ if (comm->me == 0) {
+ printf("found *END keyword");
+ printf(
+ "\n>>========>>========>>========>>========>>========>>========>>========>>========>>========>>========>>========>>========\n\n");
+ }
+ break;
+ }
+
+ /*
+ * Linear Elasticity model based on deformation gradient
+ */
+ ioffset = iNextKwd;
+ if (strcmp(arg[ioffset], "*LINEAR_DEFGRAD") == 0) {
+ strengthModel[itype] = LINEAR_DEFGRAD;
+
+ if (comm->me == 0) {
+ printf("reading *LINEAR_DEFGRAD\n");
+ }
+
+ t = string("*");
+ iNextKwd = -1;
+ for (iarg = ioffset + 1; iarg < narg; iarg++) {
+ s = string(arg[iarg]);
+ if (s.compare(0, t.length(), t) == 0) {
+ iNextKwd = iarg;
+ break;
+ }
+ }
+
+ if (iNextKwd < 0) {
+ sprintf(str, "no *KEYWORD terminates *LINEAR_DEFGRAD");
+ error->all(FLERR, str);
+ }
+
+ if (iNextKwd - ioffset != 1) {
+ sprintf(str, "expected 0 arguments following *LINEAR_DEFGRAD but got %d\n", iNextKwd - ioffset - 1);
+ error->all(FLERR, str);
+ }
+
+ if (comm->me == 0) {
+ printf("\n%60s\n", "Linear Elasticity model based on deformation gradient");
+ }
+ } else if (strcmp(arg[ioffset], "*STRENGTH_LINEAR") == 0) {
+
+ /*
+ * Linear Elasticity strength only model based on strain rate
+ */
+
+ strengthModel[itype] = STRENGTH_LINEAR;
+ if (comm->me == 0) {
+ printf("reading *STRENGTH_LINEAR\n");
+ }
+
+ t = string("*");
+ iNextKwd = -1;
+ for (iarg = ioffset + 1; iarg < narg; iarg++) {
+ s = string(arg[iarg]);
+ if (s.compare(0, t.length(), t) == 0) {
+ iNextKwd = iarg;
+ break;
+ }
+ }
+
+ if (iNextKwd < 0) {
+ sprintf(str, "no *KEYWORD terminates *STRENGTH_LINEAR");
+ error->all(FLERR, str);
+ }
+
+ if (iNextKwd - ioffset != 1) {
+ sprintf(str, "expected 0 arguments following *STRENGTH_LINEAR but got %d\n", iNextKwd - ioffset - 1);
+ error->all(FLERR, str);
+ }
+
+ if (comm->me == 0) {
+ printf("%60s\n", "Linear Elasticity strength based on strain rate");
+ }
+ } // end Linear Elasticity strength only model based on strain rate
+
+ else if (strcmp(arg[ioffset], "*STRENGTH_LINEAR_PLASTIC") == 0) {
+
+ /*
+ * Linear Elastic / perfectly plastic strength only model based on strain rate
+ */
+
+ strengthModel[itype] = STRENGTH_LINEAR_PLASTIC;
+ if (comm->me == 0) {
+ printf("reading *STRENGTH_LINEAR_PLASTIC\n");
+ }
+
+ t = string("*");
+ iNextKwd = -1;
+ for (iarg = ioffset + 1; iarg < narg; iarg++) {
+ s = string(arg[iarg]);
+ if (s.compare(0, t.length(), t) == 0) {
+ iNextKwd = iarg;
+ break;
+ }
+ }
+
+ if (iNextKwd < 0) {
+ sprintf(str, "no *KEYWORD terminates *STRENGTH_LINEAR_PLASTIC");
+ error->all(FLERR, str);
+ }
+
+ if (iNextKwd - ioffset != 2 + 1) {
+ sprintf(str, "expected 2 arguments following *STRENGTH_LINEAR_PLASTIC but got %d\n", iNextKwd - ioffset - 1);
+ error->all(FLERR, str);
+ }
+
+ Lookup[YIELD_STRESS][itype] = force->numeric(FLERR, arg[ioffset + 1]);
+ Lookup[HARDENING_PARAMETER][itype] = force->numeric(FLERR, arg[ioffset + 2]);
+
+ if (comm->me == 0) {
+ printf("%60s\n", "Linear elastic / perfectly plastic strength based on strain rate");
+ printf("%60s : %g\n", "Young's modulus", Lookup[YOUNGS_MODULUS][itype]);
+ printf("%60s : %g\n", "Poisson ratio", Lookup[POISSON_RATIO][itype]);
+ printf("%60s : %g\n", "shear modulus", Lookup[SHEAR_MODULUS][itype]);
+ printf("%60s : %g\n", "constant yield stress", Lookup[YIELD_STRESS][itype]);
+ printf("%60s : %g\n", "constant hardening parameter", Lookup[HARDENING_PARAMETER][itype]);
+ }
+ } // end Linear Elastic / perfectly plastic strength only model based on strain rate
+
+ else if (strcmp(arg[ioffset], "*JOHNSON_COOK") == 0) {
+
+ /*
+ * JOHNSON - COOK
+ */
+
+ strengthModel[itype] = STRENGTH_JOHNSON_COOK;
+ if (comm->me == 0) {
+ printf("reading *JOHNSON_COOK\n");
+ }
+
+ t = string("*");
+ iNextKwd = -1;
+ for (iarg = ioffset + 1; iarg < narg; iarg++) {
+ s = string(arg[iarg]);
+ if (s.compare(0, t.length(), t) == 0) {
+ iNextKwd = iarg;
+ break;
+ }
+ }
+
+ if (iNextKwd < 0) {
+ sprintf(str, "no *KEYWORD terminates *JOHNSON_COOK");
+ error->all(FLERR, str);
+ }
+
+ if (iNextKwd - ioffset != 8 + 1) {
+ sprintf(str, "expected 8 arguments following *JOHNSON_COOK but got %d\n", iNextKwd - ioffset - 1);
+ error->all(FLERR, str);
+ }
+
+ Lookup[JC_A][itype] = force->numeric(FLERR, arg[ioffset + 1]);
+ Lookup[JC_B][itype] = force->numeric(FLERR, arg[ioffset + 2]);
+ Lookup[JC_a][itype] = force->numeric(FLERR, arg[ioffset + 3]);
+ Lookup[JC_C][itype] = force->numeric(FLERR, arg[ioffset + 4]);
+ Lookup[JC_epdot0][itype] = force->numeric(FLERR, arg[ioffset + 5]);
+ Lookup[JC_T0][itype] = force->numeric(FLERR, arg[ioffset + 6]);
+ Lookup[JC_Tmelt][itype] = force->numeric(FLERR, arg[ioffset + 7]);
+ Lookup[JC_M][itype] = force->numeric(FLERR, arg[ioffset + 8]);
+
+ if (comm->me == 0) {
+ printf("%60s\n", "Johnson Cook material strength model");
+ printf("%60s : %g\n", "A: initial yield stress", Lookup[JC_A][itype]);
+ printf("%60s : %g\n", "B : proportionality factor for plastic strain dependency", Lookup[JC_B][itype]);
+ printf("%60s : %g\n", "a : exponent for plastic strain dependency", Lookup[JC_a][itype]);
+ printf("%60s : %g\n", "C : proportionality factor for logarithmic plastic strain rate dependency",
+ Lookup[JC_C][itype]);
+ printf("%60s : %g\n", "epdot0 : dimensionality factor for plastic strain rate dependency",
+ Lookup[JC_epdot0][itype]);
+ printf("%60s : %g\n", "T0 : reference (room) temperature", Lookup[JC_T0][itype]);
+ printf("%60s : %g\n", "Tmelt : melting temperature", Lookup[JC_Tmelt][itype]);
+ printf("%60s : %g\n", "M : exponent for temperature dependency", Lookup[JC_M][itype]);
+ }
+
+ } else if (strcmp(arg[ioffset], "*EOS_NONE") == 0) {
+
+ /*
+ * no eos
+ */
+
+ eos[itype] = EOS_NONE;
+ if (comm->me == 0) {
+ printf("reading *EOS_NONE\n");
+ }
+
+ t = string("*");
+ iNextKwd = -1;
+ for (iarg = ioffset + 1; iarg < narg; iarg++) {
+ s = string(arg[iarg]);
+ if (s.compare(0, t.length(), t) == 0) {
+ iNextKwd = iarg;
+ break;
+ }
+ }
+
+ if (iNextKwd < 0) {
+ sprintf(str, "no *KEYWORD terminates *EOS_NONE");
+ error->all(FLERR, str);
+ }
+
+ if (iNextKwd - ioffset != 1) {
+ sprintf(str, "expected 0 arguments following *EOS_NONE but got %d\n", iNextKwd - ioffset - 1);
+ error->all(FLERR, str);
+ }
+
+ if (comm->me == 0) {
+ printf("\n%60s\n", "no EOS selected");
+ }
+
+ } else if (strcmp(arg[ioffset], "*EOS_LINEAR") == 0) {
+
+ /*
+ * linear eos
+ */
+
+ eos[itype] = EOS_LINEAR;
+ if (comm->me == 0) {
+ printf("reading *EOS_LINEAR\n");
+ }
+
+ t = string("*");
+ iNextKwd = -1;
+ for (iarg = ioffset + 1; iarg < narg; iarg++) {
+ s = string(arg[iarg]);
+ if (s.compare(0, t.length(), t) == 0) {
+ iNextKwd = iarg;
+ break;
+ }
+ }
+
+ if (iNextKwd < 0) {
+ sprintf(str, "no *KEYWORD terminates *EOS_LINEAR");
+ error->all(FLERR, str);
+ }
+
+ if (iNextKwd - ioffset != 1) {
+ sprintf(str, "expected 0 arguments following *EOS_LINEAR but got %d\n", iNextKwd - ioffset - 1);
+ error->all(FLERR, str);
+ }
+
+ if (comm->me == 0) {
+ printf("\n%60s\n", "linear EOS based on strain rate");
+ printf("%60s : %g\n", "bulk modulus", Lookup[BULK_MODULUS][itype]);
+ }
+ } // end linear eos
+ else if (strcmp(arg[ioffset], "*EOS_SHOCK") == 0) {
+
+ /*
+ * shock eos
+ */
+
+ eos[itype] = EOS_SHOCK;
+ if (comm->me == 0) {
+ printf("reading *EOS_SHOCK\n");
+ }
+
+ t = string("*");
+ iNextKwd = -1;
+ for (iarg = ioffset + 1; iarg < narg; iarg++) {
+ s = string(arg[iarg]);
+ if (s.compare(0, t.length(), t) == 0) {
+ iNextKwd = iarg;
+ break;
+ }
+ }
+
+ if (iNextKwd < 0) {
+ sprintf(str, "no *KEYWORD terminates *EOS_SHOCK");
+ error->all(FLERR, str);
+ }
+
+ if (iNextKwd - ioffset != 3 + 1) {
+ sprintf(str, "expected 3 arguments (c0, S, Gamma) following *EOS_SHOCK but got %d\n", iNextKwd - ioffset - 1);
+ error->all(FLERR, str);
+ }
+
+ Lookup[EOS_SHOCK_C0][itype] = force->numeric(FLERR, arg[ioffset + 1]);
+ Lookup[EOS_SHOCK_S][itype] = force->numeric(FLERR, arg[ioffset + 2]);
+ Lookup[EOS_SHOCK_GAMMA][itype] = force->numeric(FLERR, arg[ioffset + 3]);
+ if (comm->me == 0) {
+ printf("\n%60s\n", "shock EOS based on strain rate");
+ printf("%60s : %g\n", "reference speed of sound", Lookup[EOS_SHOCK_C0][itype]);
+ printf("%60s : %g\n", "Hugoniot parameter S", Lookup[EOS_SHOCK_S][itype]);
+ printf("%60s : %g\n", "Grueneisen Gamma", Lookup[EOS_SHOCK_GAMMA][itype]);
+ }
+ } // end shock eos
+
+ else if (strcmp(arg[ioffset], "*EOS_POLYNOMIAL") == 0) {
+ /*
+ * polynomial eos
+ */
+
+ eos[itype] = EOS_POLYNOMIAL;
+ if (comm->me == 0) {
+ printf("reading *EOS_POLYNOMIAL\n");
+ }
+
+ t = string("*");
+ iNextKwd = -1;
+ for (iarg = ioffset + 1; iarg < narg; iarg++) {
+ s = string(arg[iarg]);
+ if (s.compare(0, t.length(), t) == 0) {
+ iNextKwd = iarg;
+ break;
+ }
+ }
+
+ if (iNextKwd < 0) {
+ sprintf(str, "no *KEYWORD terminates *EOS_POLYNOMIAL");
+ error->all(FLERR, str);
+ }
+
+ if (iNextKwd - ioffset != 7 + 1) {
+ sprintf(str, "expected 7 arguments following *EOS_POLYNOMIAL but got %d\n", iNextKwd - ioffset - 1);
+ error->all(FLERR, str);
+ }
+
+ Lookup[EOS_POLYNOMIAL_C0][itype] = force->numeric(FLERR, arg[ioffset + 1]);
+ Lookup[EOS_POLYNOMIAL_C1][itype] = force->numeric(FLERR, arg[ioffset + 2]);
+ Lookup[EOS_POLYNOMIAL_C2][itype] = force->numeric(FLERR, arg[ioffset + 3]);
+ Lookup[EOS_POLYNOMIAL_C3][itype] = force->numeric(FLERR, arg[ioffset + 4]);
+ Lookup[EOS_POLYNOMIAL_C4][itype] = force->numeric(FLERR, arg[ioffset + 5]);
+ Lookup[EOS_POLYNOMIAL_C5][itype] = force->numeric(FLERR, arg[ioffset + 6]);
+ Lookup[EOS_POLYNOMIAL_C6][itype] = force->numeric(FLERR, arg[ioffset + 7]);
+ if (comm->me == 0) {
+ printf("\n%60s\n", "polynomial EOS based on strain rate");
+ printf("%60s : %g\n", "parameter c0", Lookup[EOS_POLYNOMIAL_C0][itype]);
+ printf("%60s : %g\n", "parameter c1", Lookup[EOS_POLYNOMIAL_C1][itype]);
+ printf("%60s : %g\n", "parameter c2", Lookup[EOS_POLYNOMIAL_C2][itype]);
+ printf("%60s : %g\n", "parameter c3", Lookup[EOS_POLYNOMIAL_C3][itype]);
+ printf("%60s : %g\n", "parameter c4", Lookup[EOS_POLYNOMIAL_C4][itype]);
+ printf("%60s : %g\n", "parameter c5", Lookup[EOS_POLYNOMIAL_C5][itype]);
+ printf("%60s : %g\n", "parameter c6", Lookup[EOS_POLYNOMIAL_C6][itype]);
+ }
+ } // end polynomial eos
+
+ else if (strcmp(arg[ioffset], "*FAILURE_MAX_PLASTIC_STRAIN") == 0) {
+
+ /*
+ * maximum plastic strain failure criterion
+ */
+
+ if (comm->me == 0) {
+ printf("reading *FAILURE_MAX_PLASTIC_SRTRAIN\n");
+ }
+
+ t = string("*");
+ iNextKwd = -1;
+ for (iarg = ioffset + 1; iarg < narg; iarg++) {
+ s = string(arg[iarg]);
+ if (s.compare(0, t.length(), t) == 0) {
+ iNextKwd = iarg;
+ break;
+ }
+ }
+
+ if (iNextKwd < 0) {
+ sprintf(str, "no *KEYWORD terminates *FAILURE_MAX_PLASTIC_STRAIN");
+ error->all(FLERR, str);
+ }
+
+ if (iNextKwd - ioffset != 1 + 1) {
+ sprintf(str, "expected 1 arguments following *FAILURE_MAX_PLASTIC_STRAIN but got %d\n", iNextKwd - ioffset - 1);
+ error->all(FLERR, str);
+ }
+
+ failureModel[itype].failure_max_plastic_strain = true;
+ failureModel[itype].integration_point_wise = true;
+ Lookup[FAILURE_MAX_PLASTIC_STRAIN_THRESHOLD][itype] = force->numeric(FLERR, arg[ioffset + 1]);
+
+ if (comm->me == 0) {
+ printf("\n%60s\n", "maximum plastic strain failure criterion");
+ printf("%60s : %g\n", "failure occurs when plastic strain reaches limit",
+ Lookup[FAILURE_MAX_PLASTIC_STRAIN_THRESHOLD][itype]);
+ }
+ } // end maximum plastic strain failure criterion
+ else if (strcmp(arg[ioffset], "*FAILURE_MAX_PAIRWISE_STRAIN") == 0) {
+
+ /*
+ * failure criterion based on maximum strain between a pair of TLSPH particles.
+ */
+
+ if (comm->me == 0) {
+ printf("reading *FAILURE_MAX_PAIRWISE_STRAIN\n");
+ }
+
+ if (update_method != UPDATE_NONE) {
+ error->all(FLERR, "cannot use *FAILURE_MAX_PAIRWISE_STRAIN with updated Total-Lagrangian formalism");
+ }
+
+ t = string("*");
+ iNextKwd = -1;
+ for (iarg = ioffset + 1; iarg < narg; iarg++) {
+ s = string(arg[iarg]);
+ if (s.compare(0, t.length(), t) == 0) {
+ iNextKwd = iarg;
+ break;
+ }
+ }
+
+ if (iNextKwd < 0) {
+ sprintf(str, "no *KEYWORD terminates *FAILURE_MAX_PAIRWISE_STRAIN");
+ error->all(FLERR, str);
+ }
+
+ if (iNextKwd - ioffset != 1 + 1) {
+ sprintf(str, "expected 1 arguments following *FAILURE_MAX_PAIRWISE_STRAIN but got %d\n", iNextKwd - ioffset - 1);
+ error->all(FLERR, str);
+ }
+
+ failureModel[itype].failure_max_pairwise_strain = true;
+ failureModel[itype].integration_point_wise = true;
+ Lookup[FAILURE_MAX_PAIRWISE_STRAIN_THRESHOLD][itype] = force->numeric(FLERR, arg[ioffset + 1]);
+
+ if (comm->me == 0) {
+ printf("\n%60s\n", "maximum pairwise strain failure criterion");
+ printf("%60s : %g\n", "failure occurs when pairwise strain reaches limit",
+ Lookup[FAILURE_MAX_PAIRWISE_STRAIN_THRESHOLD][itype]);
+ }
+ } // end pair based maximum strain failure criterion
+ else if (strcmp(arg[ioffset], "*FAILURE_MAX_PRINCIPAL_STRAIN") == 0) {
+ error->all(FLERR, "this failure model is currently unsupported");
+
+ /*
+ * maximum principal strain failure criterion
+ */
+ if (comm->me == 0) {
+ printf("reading *FAILURE_MAX_PRINCIPAL_STRAIN\n");
+ }
+
+ t = string("*");
+ iNextKwd = -1;
+ for (iarg = ioffset + 1; iarg < narg; iarg++) {
+ s = string(arg[iarg]);
+ if (s.compare(0, t.length(), t) == 0) {
+ iNextKwd = iarg;
+ break;
+ }
+ }
+
+ if (iNextKwd < 0) {
+ sprintf(str, "no *KEYWORD terminates *FAILURE_MAX_PRINCIPAL_STRAIN");
+ error->all(FLERR, str);
+ }
+
+ if (iNextKwd - ioffset != 1 + 1) {
+ sprintf(str, "expected 1 arguments following *FAILURE_MAX_PRINCIPAL_STRAIN but got %d\n", iNextKwd - ioffset - 1);
+ error->all(FLERR, str);
+ }
+
+ failureModel[itype].failure_max_principal_strain = true;
+ failureModel[itype].integration_point_wise = true;
+ Lookup[FAILURE_MAX_PRINCIPAL_STRAIN_THRESHOLD][itype] = force->numeric(FLERR, arg[ioffset + 1]);
+
+ if (comm->me == 0) {
+ printf("\n%60s\n", "maximum principal strain failure criterion");
+ printf("%60s : %g\n", "failure occurs when principal strain reaches limit",
+ Lookup[FAILURE_MAX_PRINCIPAL_STRAIN_THRESHOLD][itype]);
+ }
+ } // end maximum principal strain failure criterion
+ else if (strcmp(arg[ioffset], "*FAILURE_JOHNSON_COOK") == 0) {
+ error->all(FLERR, "this failure model is currently unsupported");
+ if (comm->me == 0) {
+ printf("reading *FAILURE_JOHNSON_COOK\n");
+ }
+
+ t = string("*");
+ iNextKwd = -1;
+ for (iarg = ioffset + 1; iarg < narg; iarg++) {
+ s = string(arg[iarg]);
+ if (s.compare(0, t.length(), t) == 0) {
+ iNextKwd = iarg;
+ break;
+ }
+ }
+
+ if (iNextKwd < 0) {
+ sprintf(str, "no *KEYWORD terminates *FAILURE_JOHNSON_COOK");
+ error->all(FLERR, str);
+ }
+
+ if (iNextKwd - ioffset != 5 + 1) {
+ sprintf(str, "expected 5 arguments following *FAILURE_JOHNSON_COOK but got %d\n", iNextKwd - ioffset - 1);
+ error->all(FLERR, str);
+ }
+
+ failureModel[itype].failure_johnson_cook = true;
+ failureModel[itype].integration_point_wise = true;
+
+ Lookup[FAILURE_JC_D1][itype] = force->numeric(FLERR, arg[ioffset + 1]);
+ Lookup[FAILURE_JC_D2][itype] = force->numeric(FLERR, arg[ioffset + 2]);
+ Lookup[FAILURE_JC_D3][itype] = force->numeric(FLERR, arg[ioffset + 3]);
+ Lookup[FAILURE_JC_D4][itype] = force->numeric(FLERR, arg[ioffset + 4]);
+ Lookup[FAILURE_JC_EPDOT0][itype] = force->numeric(FLERR, arg[ioffset + 5]);
+
+ if (comm->me == 0) {
+ printf("\n%60s\n", "Johnson-Cook failure criterion");
+ printf("%60s : %g\n", "parameter d1", Lookup[FAILURE_JC_D1][itype]);
+ printf("%60s : %g\n", "parameter d2", Lookup[FAILURE_JC_D2][itype]);
+ printf("%60s : %g\n", "parameter d3", Lookup[FAILURE_JC_D3][itype]);
+ printf("%60s : %g\n", "parameter d4", Lookup[FAILURE_JC_D4][itype]);
+ printf("%60s : %g\n", "reference plastic strain rate", Lookup[FAILURE_JC_EPDOT0][itype]);
+ }
+
+ } else if (strcmp(arg[ioffset], "*FAILURE_MAX_PRINCIPAL_STRESS") == 0) {
+ error->all(FLERR, "this failure model is currently unsupported");
+
+ /*
+ * maximum principal stress failure criterion
+ */
+
+ if (comm->me == 0) {
+ printf("reading *FAILURE_MAX_PRINCIPAL_STRESS\n");
+ }
+
+ t = string("*");
+ iNextKwd = -1;
+ for (iarg = ioffset + 1; iarg < narg; iarg++) {
+ s = string(arg[iarg]);
+ if (s.compare(0, t.length(), t) == 0) {
+ iNextKwd = iarg;
+ break;
+ }
+ }
+
+ if (iNextKwd < 0) {
+ sprintf(str, "no *KEYWORD terminates *FAILURE_MAX_PRINCIPAL_STRESS");
+ error->all(FLERR, str);
+ }
+
+ if (iNextKwd - ioffset != 1 + 1) {
+ sprintf(str, "expected 1 arguments following *FAILURE_MAX_PRINCIPAL_STRESS but got %d\n", iNextKwd - ioffset - 1);
+ error->all(FLERR, str);
+ }
+
+ failureModel[itype].failure_max_principal_stress = true;
+ failureModel[itype].integration_point_wise = true;
+ Lookup[FAILURE_MAX_PRINCIPAL_STRESS_THRESHOLD][itype] = force->numeric(FLERR, arg[ioffset + 1]);
+
+ if (comm->me == 0) {
+ printf("\n%60s\n", "maximum principal stress failure criterion");
+ printf("%60s : %g\n", "failure occurs when principal stress reaches limit",
+ Lookup[FAILURE_MAX_PRINCIPAL_STRESS_THRESHOLD][itype]);
+ }
+ } // end maximum principal stress failure criterion
+
+ else if (strcmp(arg[ioffset], "*FAILURE_ENERGY_RELEASE_RATE") == 0) {
+ if (comm->me == 0) {
+ printf("reading *FAILURE_ENERGY_RELEASE_RATE\n");
+ }
+
+ t = string("*");
+ iNextKwd = -1;
+ for (iarg = ioffset + 1; iarg < narg; iarg++) {
+ s = string(arg[iarg]);
+ if (s.compare(0, t.length(), t) == 0) {
+ iNextKwd = iarg;
+ break;
+ }
+ }
+
+ if (iNextKwd < 0) {
+ sprintf(str, "no *KEYWORD terminates *FAILURE_ENERGY_RELEASE_RATE");
+ error->all(FLERR, str);
+ }
+
+ if (iNextKwd - ioffset != 1 + 1) {
+ sprintf(str, "expected 1 arguments following *FAILURE_ENERGY_RELEASE_RATE but got %d\n", iNextKwd - ioffset - 1);
+ error->all(FLERR, str);
+ }
+
+ failureModel[itype].failure_energy_release_rate = true;
+ Lookup[CRITICAL_ENERGY_RELEASE_RATE][itype] = force->numeric(FLERR, arg[ioffset + 1]);
+
+ if (comm->me == 0) {
+ printf("\n%60s\n", "critical energy release rate failure criterion");
+ printf("%60s : %g\n", "failure occurs when energy release rate reaches limit",
+ Lookup[CRITICAL_ENERGY_RELEASE_RATE][itype]);
+ }
+ } // end energy release rate failure criterion
+
+ else {
+ sprintf(str, "unknown *KEYWORD: %s", arg[ioffset]);
+ error->all(FLERR, str);
+ }
+
+ }
+
+ setflag[itype][itype] = 1;
}
@@ -1699,23 +1699,23 @@ void PairTlsph::coeff(int narg, char **arg) {
double PairTlsph::init_one(int i, int j) {
- if (!allocated)
- allocate();
+ if (!allocated)
+ allocate();
- if (setflag[i][j] == 0)
- error->all(FLERR, "All pair coeffs are not set");
+ if (setflag[i][j] == 0)
+ error->all(FLERR, "All pair coeffs are not set");
- if (force->newton == 1)
- error->all(FLERR, "Pair style tlsph requires newton off");
+ if (force->newton == 1)
+ error->all(FLERR, "Pair style tlsph requires newton off");
// cutoff = sum of max I,J radii for
// dynamic/dynamic & dynamic/frozen interactions, but not frozen/frozen
- double cutoff = maxrad_dynamic[i] + maxrad_dynamic[j];
- cutoff = MAX(cutoff, maxrad_frozen[i] + maxrad_dynamic[j]);
- cutoff = MAX(cutoff, maxrad_dynamic[i] + maxrad_frozen[j]);
+ double cutoff = maxrad_dynamic[i] + maxrad_dynamic[j];
+ cutoff = MAX(cutoff, maxrad_frozen[i] + maxrad_dynamic[j]);
+ cutoff = MAX(cutoff, maxrad_dynamic[i] + maxrad_frozen[j]);
//printf("cutoff for pair pair tlsph = %f\n", cutoff);
- return cutoff;
+ return cutoff;
}
/* ----------------------------------------------------------------------
@@ -1723,58 +1723,58 @@ double PairTlsph::init_one(int i, int j) {
------------------------------------------------------------------------- */
void PairTlsph::init_style() {
- int i;
+ int i;
- if (force->newton_pair == 1) {
- error->all(FLERR, "Pair style tlsph requires newton pair off");
- }
+ if (force->newton_pair == 1) {
+ error->all(FLERR, "Pair style tlsph requires newton pair off");
+ }
// request a granular neighbor list
- int irequest = neighbor->request(this);
- neighbor->requests[irequest]->size = 1;
+ int irequest = neighbor->request(this);
+ neighbor->requests[irequest]->size = 1;
// set maxrad_dynamic and maxrad_frozen for each type
// include future Fix pour particles as dynamic
- for (i = 1; i <= atom->ntypes; i++)
- onerad_dynamic[i] = onerad_frozen[i] = 0.0;
+ for (i = 1; i <= atom->ntypes; i++)
+ onerad_dynamic[i] = onerad_frozen[i] = 0.0;
- double *radius = atom->radius;
- int *type = atom->type;
- int nlocal = atom->nlocal;
+ double *radius = atom->radius;
+ int *type = atom->type;
+ int nlocal = atom->nlocal;
- for (i = 0; i < nlocal; i++)
- onerad_dynamic[type[i]] = MAX(onerad_dynamic[type[i]], radius[i]);
+ for (i = 0; i < nlocal; i++)
+ onerad_dynamic[type[i]] = MAX(onerad_dynamic[type[i]], radius[i]);
- MPI_Allreduce(&onerad_dynamic[1], &maxrad_dynamic[1], atom->ntypes, MPI_DOUBLE, MPI_MAX, world);
- MPI_Allreduce(&onerad_frozen[1], &maxrad_frozen[1], atom->ntypes, MPI_DOUBLE, MPI_MAX, world);
+ MPI_Allreduce(&onerad_dynamic[1], &maxrad_dynamic[1], atom->ntypes, MPI_DOUBLE, MPI_MAX, world);
+ MPI_Allreduce(&onerad_frozen[1], &maxrad_frozen[1], atom->ntypes, MPI_DOUBLE, MPI_MAX, world);
// if first init, create Fix needed for storing reference configuration neighbors
- int igroup = group->find("tlsph");
- if (igroup == -1)
- error->all(FLERR, "Pair style tlsph requires its particles to be part of a group named tlsph. This group does not exist.");
-
- if (fix_tlsph_reference_configuration == NULL) {
- char **fixarg = new char*[3];
- fixarg[0] = (char *) "SMD_TLSPH_NEIGHBORS";
- fixarg[1] = (char *) "tlsph";
- fixarg[2] = (char *) "SMD_TLSPH_NEIGHBORS";
- modify->add_fix(3, fixarg);
- delete[] fixarg;
- fix_tlsph_reference_configuration = (FixSMD_TLSPH_ReferenceConfiguration *) modify->fix[modify->nfix - 1];
- fix_tlsph_reference_configuration->pair = this;
- }
+ int igroup = group->find("tlsph");
+ if (igroup == -1)
+ error->all(FLERR, "Pair style tlsph requires its particles to be part of a group named tlsph. This group does not exist.");
+
+ if (fix_tlsph_reference_configuration == NULL) {
+ char **fixarg = new char*[3];
+ fixarg[0] = (char *) "SMD_TLSPH_NEIGHBORS";
+ fixarg[1] = (char *) "tlsph";
+ fixarg[2] = (char *) "SMD_TLSPH_NEIGHBORS";
+ modify->add_fix(3, fixarg);
+ delete[] fixarg;
+ fix_tlsph_reference_configuration = (FixSMD_TLSPH_ReferenceConfiguration *) modify->fix[modify->nfix - 1];
+ fix_tlsph_reference_configuration->pair = this;
+ }
// find associated SMD_TLSPH_NEIGHBORS fix that must exist
// could have changed locations in fix list since created
- ifix_tlsph = -1;
- for (int i = 0; i < modify->nfix; i++)
- if (strcmp(modify->fix[i]->style, "SMD_TLSPH_NEIGHBORS") == 0)
- ifix_tlsph = i;
- if (ifix_tlsph == -1)
- error->all(FLERR, "Fix SMD_TLSPH_NEIGHBORS does not exist");
+ ifix_tlsph = -1;
+ for (int i = 0; i < modify->nfix; i++)
+ if (strcmp(modify->fix[i]->style, "SMD_TLSPH_NEIGHBORS") == 0)
+ ifix_tlsph = i;
+ if (ifix_tlsph == -1)
+ error->all(FLERR, "Fix SMD_TLSPH_NEIGHBORS does not exist");
}
@@ -1784,8 +1784,8 @@ void PairTlsph::init_style() {
------------------------------------------------------------------------- */
void PairTlsph::init_list(int id, NeighList *ptr) {
- if (id == 0)
- list = ptr;
+ if (id == 0)
+ list = ptr;
}
/* ----------------------------------------------------------------------
@@ -1794,7 +1794,7 @@ void PairTlsph::init_list(int id, NeighList *ptr) {
double PairTlsph::memory_usage() {
- return 118 * nmax * sizeof(double);
+ return 118 * nmax * sizeof(double);
}
/* ----------------------------------------------------------------------
@@ -1803,122 +1803,122 @@ double PairTlsph::memory_usage() {
void *PairTlsph::extract(const char *str, int &i) {
//printf("in PairTlsph::extract\n");
- if (strcmp(str, "smd/tlsph/Fincr_ptr") == 0) {
- return (void *) Fincr;
- } else if (strcmp(str, "smd/tlsph/detF_ptr") == 0) {
- return (void *) detF;
- } else if (strcmp(str, "smd/tlsph/PK1_ptr") == 0) {
- return (void *) PK1;
- } else if (strcmp(str, "smd/tlsph/smoothVel_ptr") == 0) {
- return (void *) smoothVelDifference;
- } else if (strcmp(str, "smd/tlsph/numNeighsRefConfig_ptr") == 0) {
- return (void *) numNeighsRefConfig;
- } else if (strcmp(str, "smd/tlsph/stressTensor_ptr") == 0) {
- return (void *) CauchyStress;
- } else if (strcmp(str, "smd/tlsph/updateFlag_ptr") == 0) {
- return (void *) &updateFlag;
- } else if (strcmp(str, "smd/tlsph/strain_rate_ptr") == 0) {
- return (void *) D;
- } else if (strcmp(str, "smd/tlsph/hMin_ptr") == 0) {
- return (void *) &hMin;
- } else if (strcmp(str, "smd/tlsph/dtCFL_ptr") == 0) {
- return (void *) &dtCFL;
- } else if (strcmp(str, "smd/tlsph/dtRelative_ptr") == 0) {
- return (void *) &dtRelative;
- } else if (strcmp(str, "smd/tlsph/hourglass_error_ptr") == 0) {
- return (void *) hourglass_error;
- } else if (strcmp(str, "smd/tlsph/particle_dt_ptr") == 0) {
- return (void *) particle_dt;
- } else if (strcmp(str, "smd/tlsph/rotation_ptr") == 0) {
- return (void *) R;
- }
-
- return NULL;
+ if (strcmp(str, "smd/tlsph/Fincr_ptr") == 0) {
+ return (void *) Fincr;
+ } else if (strcmp(str, "smd/tlsph/detF_ptr") == 0) {
+ return (void *) detF;
+ } else if (strcmp(str, "smd/tlsph/PK1_ptr") == 0) {
+ return (void *) PK1;
+ } else if (strcmp(str, "smd/tlsph/smoothVel_ptr") == 0) {
+ return (void *) smoothVelDifference;
+ } else if (strcmp(str, "smd/tlsph/numNeighsRefConfig_ptr") == 0) {
+ return (void *) numNeighsRefConfig;
+ } else if (strcmp(str, "smd/tlsph/stressTensor_ptr") == 0) {
+ return (void *) CauchyStress;
+ } else if (strcmp(str, "smd/tlsph/updateFlag_ptr") == 0) {
+ return (void *) &updateFlag;
+ } else if (strcmp(str, "smd/tlsph/strain_rate_ptr") == 0) {
+ return (void *) D;
+ } else if (strcmp(str, "smd/tlsph/hMin_ptr") == 0) {
+ return (void *) &hMin;
+ } else if (strcmp(str, "smd/tlsph/dtCFL_ptr") == 0) {
+ return (void *) &dtCFL;
+ } else if (strcmp(str, "smd/tlsph/dtRelative_ptr") == 0) {
+ return (void *) &dtRelative;
+ } else if (strcmp(str, "smd/tlsph/hourglass_error_ptr") == 0) {
+ return (void *) hourglass_error;
+ } else if (strcmp(str, "smd/tlsph/particle_dt_ptr") == 0) {
+ return (void *) particle_dt;
+ } else if (strcmp(str, "smd/tlsph/rotation_ptr") == 0) {
+ return (void *) R;
+ }
+
+ return NULL;
}
/* ---------------------------------------------------------------------- */
int PairTlsph::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc) {
- int i, j, m;
- tagint *mol = atom->molecule;
- double *damage = atom->damage;
- double *eff_plastic_strain = atom->eff_plastic_strain;
- double *eff_plastic_strain_rate = atom->eff_plastic_strain_rate;
+ int i, j, m;
+ tagint *mol = atom->molecule;
+ double *damage = atom->damage;
+ double *eff_plastic_strain = atom->eff_plastic_strain;
+ double *eff_plastic_strain_rate = atom->eff_plastic_strain_rate;
//printf("in PairTlsph::pack_forward_comm\n");
- m = 0;
- for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = PK1[j](0, 0); // PK1 is not symmetric
- buf[m++] = PK1[j](0, 1);
- buf[m++] = PK1[j](0, 2);
- buf[m++] = PK1[j](1, 0);
- buf[m++] = PK1[j](1, 1);
- buf[m++] = PK1[j](1, 2);
- buf[m++] = PK1[j](2, 0);
- buf[m++] = PK1[j](2, 1);
- buf[m++] = PK1[j](2, 2); // 9
-
- buf[m++] = Fincr[j](0, 0); // Fincr is not symmetric
- buf[m++] = Fincr[j](0, 1);
- buf[m++] = Fincr[j](0, 2);
- buf[m++] = Fincr[j](1, 0);
- buf[m++] = Fincr[j](1, 1);
- buf[m++] = Fincr[j](1, 2);
- buf[m++] = Fincr[j](2, 0);
- buf[m++] = Fincr[j](2, 1);
- buf[m++] = Fincr[j](2, 2); // 9 + 9 = 18
-
- buf[m++] = mol[j]; //19
- buf[m++] = damage[j]; //20
- buf[m++] = eff_plastic_strain[j]; //21
- buf[m++] = eff_plastic_strain_rate[j]; //22
-
- }
- return m;
+ m = 0;
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = PK1[j](0, 0); // PK1 is not symmetric
+ buf[m++] = PK1[j](0, 1);
+ buf[m++] = PK1[j](0, 2);
+ buf[m++] = PK1[j](1, 0);
+ buf[m++] = PK1[j](1, 1);
+ buf[m++] = PK1[j](1, 2);
+ buf[m++] = PK1[j](2, 0);
+ buf[m++] = PK1[j](2, 1);
+ buf[m++] = PK1[j](2, 2); // 9
+
+ buf[m++] = Fincr[j](0, 0); // Fincr is not symmetric
+ buf[m++] = Fincr[j](0, 1);
+ buf[m++] = Fincr[j](0, 2);
+ buf[m++] = Fincr[j](1, 0);
+ buf[m++] = Fincr[j](1, 1);
+ buf[m++] = Fincr[j](1, 2);
+ buf[m++] = Fincr[j](2, 0);
+ buf[m++] = Fincr[j](2, 1);
+ buf[m++] = Fincr[j](2, 2); // 9 + 9 = 18
+
+ buf[m++] = mol[j]; //19
+ buf[m++] = damage[j]; //20
+ buf[m++] = eff_plastic_strain[j]; //21
+ buf[m++] = eff_plastic_strain_rate[j]; //22
+
+ }
+ return m;
}
/* ---------------------------------------------------------------------- */
void PairTlsph::unpack_forward_comm(int n, int first, double *buf) {
- int i, m, last;
- tagint *mol = atom->molecule;
- double *damage = atom->damage;
- double *eff_plastic_strain = atom->eff_plastic_strain;
- double *eff_plastic_strain_rate = atom->eff_plastic_strain_rate;
+ int i, m, last;
+ tagint *mol = atom->molecule;
+ double *damage = atom->damage;
+ double *eff_plastic_strain = atom->eff_plastic_strain;
+ double *eff_plastic_strain_rate = atom->eff_plastic_strain_rate;
//printf("in PairTlsph::unpack_forward_comm\n");
- m = 0;
- last = first + n;
- for (i = first; i < last; i++) {
-
- PK1[i](0, 0) = buf[m++]; // PK1 is not symmetric
- PK1[i](0, 1) = buf[m++];
- PK1[i](0, 2) = buf[m++];
- PK1[i](1, 0) = buf[m++];
- PK1[i](1, 1) = buf[m++];
- PK1[i](1, 2) = buf[m++];
- PK1[i](2, 0) = buf[m++];
- PK1[i](2, 1) = buf[m++];
- PK1[i](2, 2) = buf[m++];
-
- Fincr[i](0, 0) = buf[m++];
- Fincr[i](0, 1) = buf[m++];
- Fincr[i](0, 2) = buf[m++];
- Fincr[i](1, 0) = buf[m++];
- Fincr[i](1, 1) = buf[m++];
- Fincr[i](1, 2) = buf[m++];
- Fincr[i](2, 0) = buf[m++];
- Fincr[i](2, 1) = buf[m++];
- Fincr[i](2, 2) = buf[m++];
-
- mol[i] = static_cast<int>(buf[m++]);
- damage[i] = buf[m++];
- eff_plastic_strain[i] = buf[m++]; //22
- eff_plastic_strain_rate[i] = buf[m++]; //23
- }
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+
+ PK1[i](0, 0) = buf[m++]; // PK1 is not symmetric
+ PK1[i](0, 1) = buf[m++];
+ PK1[i](0, 2) = buf[m++];
+ PK1[i](1, 0) = buf[m++];
+ PK1[i](1, 1) = buf[m++];
+ PK1[i](1, 2) = buf[m++];
+ PK1[i](2, 0) = buf[m++];
+ PK1[i](2, 1) = buf[m++];
+ PK1[i](2, 2) = buf[m++];
+
+ Fincr[i](0, 0) = buf[m++];
+ Fincr[i](0, 1) = buf[m++];
+ Fincr[i](0, 2) = buf[m++];
+ Fincr[i](1, 0) = buf[m++];
+ Fincr[i](1, 1) = buf[m++];
+ Fincr[i](1, 2) = buf[m++];
+ Fincr[i](2, 0) = buf[m++];
+ Fincr[i](2, 1) = buf[m++];
+ Fincr[i](2, 2) = buf[m++];
+
+ mol[i] = static_cast<int>(buf[m++]);
+ damage[i] = buf[m++];
+ eff_plastic_strain[i] = buf[m++]; //22
+ eff_plastic_strain_rate[i] = buf[m++]; //23
+ }
}
/* ----------------------------------------------------------------------
@@ -1927,166 +1927,166 @@ void PairTlsph::unpack_forward_comm(int n, int first, double *buf) {
------------------------------------------------------------------------- */
void PairTlsph::effective_longitudinal_modulus(const int itype, const double dt, const double d_iso, const double p_rate,
- const Matrix3d d_dev, const Matrix3d sigma_dev_rate, const double damage, double &K_eff, double &mu_eff, double &M_eff) {
- double M0; // initial longitudinal modulus
- double shear_rate_sq;
-
-// if (damage >= 0.5) {
-// M_eff = Lookup[M_MODULUS][itype];
-// K_eff = Lookup[BULK_MODULUS][itype];
-// mu_eff = Lookup[SHEAR_MODULUS][itype];
-// return;
-// }
-
- M0 = Lookup[M_MODULUS][itype];
-
- if (dt * d_iso > 1.0e-6) {
- K_eff = p_rate / d_iso;
- if (K_eff < 0.0) { // it is possible for K_eff to become negative due to strain softening
-// if (damage == 0.0) {
-// error->one(FLERR, "computed a negative effective bulk modulus but particle is not damaged.");
-// }
- K_eff = Lookup[BULK_MODULUS][itype];
- }
- } else {
- K_eff = Lookup[BULK_MODULUS][itype];
- }
-
- if (domain->dimension == 3) {
+ const Matrix3d d_dev, const Matrix3d sigma_dev_rate, const double damage, double &K_eff, double &mu_eff, double &M_eff) {
+ double M0; // initial longitudinal modulus
+ double shear_rate_sq;
+
+// if (damage >= 0.5) {
+// M_eff = Lookup[M_MODULUS][itype];
+// K_eff = Lookup[BULK_MODULUS][itype];
+// mu_eff = Lookup[SHEAR_MODULUS][itype];
+// return;
+// }
+
+ M0 = Lookup[M_MODULUS][itype];
+
+ if (dt * d_iso > 1.0e-6) {
+ K_eff = p_rate / d_iso;
+ if (K_eff < 0.0) { // it is possible for K_eff to become negative due to strain softening
+// if (damage == 0.0) {
+// error->one(FLERR, "computed a negative effective bulk modulus but particle is not damaged.");
+// }
+ K_eff = Lookup[BULK_MODULUS][itype];
+ }
+ } else {
+ K_eff = Lookup[BULK_MODULUS][itype];
+ }
+
+ if (domain->dimension == 3) {
// Calculate 2 mu by looking at ratio shear stress / shear strain. Use numerical softening to avoid divide-by-zero.
- mu_eff = 0.5
- * (sigma_dev_rate(0, 1) / (d_dev(0, 1) + 1.0e-16) + sigma_dev_rate(0, 2) / (d_dev(0, 2) + 1.0e-16)
- + sigma_dev_rate(1, 2) / (d_dev(1, 2) + 1.0e-16));
+ mu_eff = 0.5
+ * (sigma_dev_rate(0, 1) / (d_dev(0, 1) + 1.0e-16) + sigma_dev_rate(0, 2) / (d_dev(0, 2) + 1.0e-16)
+ + sigma_dev_rate(1, 2) / (d_dev(1, 2) + 1.0e-16));
// Calculate magnitude of deviatoric strain rate. This is used for deciding if shear modulus should be computed from current rate or be taken as the initial value.
- shear_rate_sq = d_dev(0, 1) * d_dev(0, 1) + d_dev(0, 2) * d_dev(0, 2) + d_dev(1, 2) * d_dev(1, 2);
- } else {
- mu_eff = 0.5 * (sigma_dev_rate(0, 1) / (d_dev(0, 1) + 1.0e-16));
- shear_rate_sq = d_dev(0, 1) * d_dev(0, 1);
- }
-
- if (dt * dt * shear_rate_sq < 1.0e-8) {
- mu_eff = Lookup[SHEAR_MODULUS][itype];
- }
-
- if (mu_eff < Lookup[SHEAR_MODULUS][itype]) { // it is possible for mu_eff to become negative due to strain softening
-// if (damage == 0.0) {
-// printf("mu_eff = %f, tau=%f, gamma=%f\n", mu_eff, sigma_dev_rate(0, 1), d_dev(0, 1));
-// error->message(FLERR, "computed a negative effective shear modulus but particle is not damaged.");
-// }
- mu_eff = Lookup[SHEAR_MODULUS][itype];
- }
+ shear_rate_sq = d_dev(0, 1) * d_dev(0, 1) + d_dev(0, 2) * d_dev(0, 2) + d_dev(1, 2) * d_dev(1, 2);
+ } else {
+ mu_eff = 0.5 * (sigma_dev_rate(0, 1) / (d_dev(0, 1) + 1.0e-16));
+ shear_rate_sq = d_dev(0, 1) * d_dev(0, 1);
+ }
+
+ if (dt * dt * shear_rate_sq < 1.0e-8) {
+ mu_eff = Lookup[SHEAR_MODULUS][itype];
+ }
+
+ if (mu_eff < Lookup[SHEAR_MODULUS][itype]) { // it is possible for mu_eff to become negative due to strain softening
+// if (damage == 0.0) {
+// printf("mu_eff = %f, tau=%f, gamma=%f\n", mu_eff, sigma_dev_rate(0, 1), d_dev(0, 1));
+// error->message(FLERR, "computed a negative effective shear modulus but particle is not damaged.");
+// }
+ mu_eff = Lookup[SHEAR_MODULUS][itype];
+ }
//mu_eff = Lookup[SHEAR_MODULUS][itype];
- if (K_eff < 0.0) {
- printf("K_eff = %f, p_rate=%f, vol_rate=%f\n", K_eff, p_rate, d_iso);
- }
+ if (K_eff < 0.0) {
+ printf("K_eff = %f, p_rate=%f, vol_rate=%f\n", K_eff, p_rate, d_iso);
+ }
- if (mu_eff < 0.0) {
- printf("mu_eff = %f, tau=%f, gamma=%f\n", mu_eff, sigma_dev_rate(0, 1), d_dev(0, 1));
- error->one(FLERR, "");
- }
+ if (mu_eff < 0.0) {
+ printf("mu_eff = %f, tau=%f, gamma=%f\n", mu_eff, sigma_dev_rate(0, 1), d_dev(0, 1));
+ error->one(FLERR, "");
+ }
- M_eff = (K_eff + 4.0 * mu_eff / 3.0); // effective dilational modulus, see Pronto 2d eqn 3.4.8
+ M_eff = (K_eff + 4.0 * mu_eff / 3.0); // effective dilational modulus, see Pronto 2d eqn 3.4.8
- if (M_eff < M0) { // do not allow effective dilatational modulus to decrease beyond its initial value
- M_eff = M0;
- }
+ if (M_eff < M0) { // do not allow effective dilatational modulus to decrease beyond its initial value
+ M_eff = M0;
+ }
}
/* ----------------------------------------------------------------------
compute pressure. Called from AssembleStress().
------------------------------------------------------------------------- */
void PairTlsph::ComputePressure(const int i, const double rho, const double mass_specific_energy, const double vol_specific_energy,
- const double pInitial, const double d_iso, double &pFinal, double &p_rate) {
- int *type = atom->type;
- double dt = update->dt;
-
- int itype;
-
- itype = type[i];
-
- switch (eos[itype]) {
- case EOS_LINEAR:
- LinearEOS(Lookup[BULK_MODULUS][itype], pInitial, d_iso, dt, pFinal, p_rate);
- break;
- case EOS_NONE:
- pFinal = 0.0;
- p_rate = 0.0;
- break;
- case EOS_SHOCK:
+ const double pInitial, const double d_iso, double &pFinal, double &p_rate) {
+ int *type = atom->type;
+ double dt = update->dt;
+
+ int itype;
+
+ itype = type[i];
+
+ switch (eos[itype]) {
+ case EOS_LINEAR:
+ LinearEOS(Lookup[BULK_MODULUS][itype], pInitial, d_iso, dt, pFinal, p_rate);
+ break;
+ case EOS_NONE:
+ pFinal = 0.0;
+ p_rate = 0.0;
+ break;
+ case EOS_SHOCK:
// rho, rho0, e, e0, c0, S, Gamma, pInitial, dt, &pFinal, &p_rate);
- ShockEOS(rho, Lookup[REFERENCE_DENSITY][itype], mass_specific_energy, 0.0, Lookup[EOS_SHOCK_C0][itype],
- Lookup[EOS_SHOCK_S][itype], Lookup[EOS_SHOCK_GAMMA][itype], pInitial, dt, pFinal, p_rate);
- break;
- case EOS_POLYNOMIAL:
- polynomialEOS(rho, Lookup[REFERENCE_DENSITY][itype], vol_specific_energy, Lookup[EOS_POLYNOMIAL_C0][itype],
- Lookup[EOS_POLYNOMIAL_C1][itype], Lookup[EOS_POLYNOMIAL_C2][itype], Lookup[EOS_POLYNOMIAL_C3][itype],
- Lookup[EOS_POLYNOMIAL_C4][itype], Lookup[EOS_POLYNOMIAL_C5][itype], Lookup[EOS_POLYNOMIAL_C6][itype], pInitial, dt,
- pFinal, p_rate);
-
- break;
- default:
- error->one(FLERR, "unknown EOS.");
- break;
- }
+ ShockEOS(rho, Lookup[REFERENCE_DENSITY][itype], mass_specific_energy, 0.0, Lookup[EOS_SHOCK_C0][itype],
+ Lookup[EOS_SHOCK_S][itype], Lookup[EOS_SHOCK_GAMMA][itype], pInitial, dt, pFinal, p_rate);
+ break;
+ case EOS_POLYNOMIAL:
+ polynomialEOS(rho, Lookup[REFERENCE_DENSITY][itype], vol_specific_energy, Lookup[EOS_POLYNOMIAL_C0][itype],
+ Lookup[EOS_POLYNOMIAL_C1][itype], Lookup[EOS_POLYNOMIAL_C2][itype], Lookup[EOS_POLYNOMIAL_C3][itype],
+ Lookup[EOS_POLYNOMIAL_C4][itype], Lookup[EOS_POLYNOMIAL_C5][itype], Lookup[EOS_POLYNOMIAL_C6][itype], pInitial, dt,
+ pFinal, p_rate);
+
+ break;
+ default:
+ error->one(FLERR, "unknown EOS.");
+ break;
+ }
}
/* ----------------------------------------------------------------------
Compute stress deviator. Called from AssembleStress().
------------------------------------------------------------------------- */
void PairTlsph::ComputeStressDeviator(const int i, const Matrix3d sigmaInitial_dev, const Matrix3d d_dev, Matrix3d &sigmaFinal_dev,
- Matrix3d &sigma_dev_rate, double &plastic_strain_increment) {
- double *eff_plastic_strain = atom->eff_plastic_strain;
- double *eff_plastic_strain_rate = atom->eff_plastic_strain_rate;
- int *type = atom->type;
- double *rmass = atom->rmass;
+ Matrix3d &sigma_dev_rate, double &plastic_strain_increment) {
+ double *eff_plastic_strain = atom->eff_plastic_strain;
+ double *eff_plastic_strain_rate = atom->eff_plastic_strain_rate;
+ int *type = atom->type;
+ double *rmass = atom->rmass;
//double *vfrac = atom->vfrac;
- double *e = atom->e;
- double dt = update->dt;
- double yieldStress;
- int itype;
+ double *e = atom->e;
+ double dt = update->dt;
+ double yieldStress;
+ int itype;
- double mass_specific_energy = e[i] / rmass[i]; // energy per unit mass
- plastic_strain_increment = 0.0;
- itype = type[i];
+ double mass_specific_energy = e[i] / rmass[i]; // energy per unit mass
+ plastic_strain_increment = 0.0;
+ itype = type[i];
- switch (strengthModel[itype]) {
- case STRENGTH_LINEAR:
+ switch (strengthModel[itype]) {
+ case STRENGTH_LINEAR:
- sigma_dev_rate = 2.0 * Lookup[SHEAR_MODULUS][itype] * d_dev;
- sigmaFinal_dev = sigmaInitial_dev + dt * sigma_dev_rate;
+ sigma_dev_rate = 2.0 * Lookup[SHEAR_MODULUS][itype] * d_dev;
+ sigmaFinal_dev = sigmaInitial_dev + dt * sigma_dev_rate;
- break;
- case LINEAR_DEFGRAD:
+ break;
+ case LINEAR_DEFGRAD:
//LinearStrengthDefgrad(Lookup[LAME_LAMBDA][itype], Lookup[SHEAR_MODULUS][itype], Fincr[i], &sigmaFinal_dev);
//eff_plastic_strain[i] = 0.0;
//p_rate = pInitial - sigmaFinal_dev.trace() / 3.0;
//sigma_dev_rate = sigmaInitial_dev - Deviator(sigmaFinal_dev);
- error->one(FLERR, "LINEAR_DEFGRAD is only for debugging purposes and currently deactivated.");
- R[i].setIdentity();
- break;
- case STRENGTH_LINEAR_PLASTIC:
-
- yieldStress = Lookup[YIELD_STRESS][itype] + Lookup[HARDENING_PARAMETER][itype] * eff_plastic_strain[i];
- LinearPlasticStrength(Lookup[SHEAR_MODULUS][itype], yieldStress, sigmaInitial_dev, d_dev, dt, sigmaFinal_dev,
- sigma_dev_rate, plastic_strain_increment);
- break;
- case STRENGTH_JOHNSON_COOK:
- JohnsonCookStrength(Lookup[SHEAR_MODULUS][itype], Lookup[HEAT_CAPACITY][itype], mass_specific_energy, Lookup[JC_A][itype],
- Lookup[JC_B][itype], Lookup[JC_a][itype], Lookup[JC_C][itype], Lookup[JC_epdot0][itype], Lookup[JC_T0][itype],
- Lookup[JC_Tmelt][itype], Lookup[JC_M][itype], dt, eff_plastic_strain[i], eff_plastic_strain_rate[i],
- sigmaInitial_dev, d_dev, sigmaFinal_dev, sigma_dev_rate, plastic_strain_increment);
- break;
- case STRENGTH_NONE:
- sigmaFinal_dev.setZero();
- sigma_dev_rate.setZero();
- break;
- default:
- error->one(FLERR, "unknown strength model.");
- break;
- }
+ error->one(FLERR, "LINEAR_DEFGRAD is only for debugging purposes and currently deactivated.");
+ R[i].setIdentity();
+ break;
+ case STRENGTH_LINEAR_PLASTIC:
+
+ yieldStress = Lookup[YIELD_STRESS][itype] + Lookup[HARDENING_PARAMETER][itype] * eff_plastic_strain[i];
+ LinearPlasticStrength(Lookup[SHEAR_MODULUS][itype], yieldStress, sigmaInitial_dev, d_dev, dt, sigmaFinal_dev,
+ sigma_dev_rate, plastic_strain_increment);
+ break;
+ case STRENGTH_JOHNSON_COOK:
+ JohnsonCookStrength(Lookup[SHEAR_MODULUS][itype], Lookup[HEAT_CAPACITY][itype], mass_specific_energy, Lookup[JC_A][itype],
+ Lookup[JC_B][itype], Lookup[JC_a][itype], Lookup[JC_C][itype], Lookup[JC_epdot0][itype], Lookup[JC_T0][itype],
+ Lookup[JC_Tmelt][itype], Lookup[JC_M][itype], dt, eff_plastic_strain[i], eff_plastic_strain_rate[i],
+ sigmaInitial_dev, d_dev, sigmaFinal_dev, sigma_dev_rate, plastic_strain_increment);
+ break;
+ case STRENGTH_NONE:
+ sigmaFinal_dev.setZero();
+ sigma_dev_rate.setZero();
+ break;
+ default:
+ error->one(FLERR, "unknown strength model.");
+ break;
+ }
}
@@ -2094,67 +2094,67 @@ void PairTlsph::ComputeStressDeviator(const int i, const Matrix3d sigmaInitial_d
Compute damage. Called from AssembleStress().
------------------------------------------------------------------------- */
void PairTlsph::ComputeDamage(const int i, const Matrix3d strain, const Matrix3d stress, Matrix3d &stress_damaged) {
- double *eff_plastic_strain = atom->eff_plastic_strain;
- double *eff_plastic_strain_rate = atom->eff_plastic_strain_rate;
- double *radius = atom->radius;
- double *damage = atom->damage;
- int *type = atom->type;
- int itype = type[i];
- double jc_failure_strain;
+ double *eff_plastic_strain = atom->eff_plastic_strain;
+ double *eff_plastic_strain_rate = atom->eff_plastic_strain_rate;
+ double *radius = atom->radius;
+ double *damage = atom->damage;
+ int *type = atom->type;
+ int itype = type[i];
+ double jc_failure_strain;
//double damage_gap, damage_rate;
- Matrix3d eye, stress_deviator;
-
- eye.setIdentity();
- stress_deviator = Deviator(stress);
- double pressure = -stress.trace() / 3.0;
-
- if (failureModel[itype].failure_max_principal_stress) {
- error->one(FLERR, "not yet implemented");
- /*
- * maximum stress failure criterion:
- */
- IsotropicMaxStressDamage(stress, Lookup[FAILURE_MAX_PRINCIPAL_STRESS_THRESHOLD][itype]);
- } else if (failureModel[itype].failure_max_principal_strain) {
- error->one(FLERR, "not yet implemented");
- /*
- * maximum strain failure criterion:
- */
- IsotropicMaxStrainDamage(strain, Lookup[FAILURE_MAX_PRINCIPAL_STRAIN_THRESHOLD][itype]);
- } else if (failureModel[itype].failure_max_plastic_strain) {
- if (eff_plastic_strain[i] >= Lookup[FAILURE_MAX_PLASTIC_STRAIN_THRESHOLD][itype]) {
- damage[i] = 1.0;
- //double damage_gap = 0.5 * Lookup[FAILURE_MAX_PLASTIC_STRAIN_THRESHOLD][itype];
- //damage[i] = (eff_plastic_strain[i] - Lookup[FAILURE_MAX_PLASTIC_STRAIN_THRESHOLD][itype]) / damage_gap;
- }
- } else if (failureModel[itype].failure_johnson_cook) {
-
- //cout << "this is stress deviator" << stress_deviator << endl;
-
- jc_failure_strain = JohnsonCookFailureStrain(pressure, stress_deviator, Lookup[FAILURE_JC_D1][itype],
- Lookup[FAILURE_JC_D2][itype], Lookup[FAILURE_JC_D3][itype], Lookup[FAILURE_JC_D4][itype],
- Lookup[FAILURE_JC_EPDOT0][itype], eff_plastic_strain_rate[i]);
-
- //cout << "plastic strain increment is " << plastic_strain_increment << " jc fs is " << jc_failure_strain << endl;
- //printf("JC failure strain is: %f\n", jc_failure_strain);
-
- if (eff_plastic_strain[i] >= jc_failure_strain) {
- double damage_rate = Lookup[SIGNAL_VELOCITY][itype] / (100.0 * radius[i]);
- damage[i] += damage_rate * update->dt;
- //damage[i] = 1.0;
- }
- }
-
- /*
- * Apply damage to integration point
- */
-
-// damage[i] = MIN(damage[i], 0.8);
+ Matrix3d eye, stress_deviator;
+
+ eye.setIdentity();
+ stress_deviator = Deviator(stress);
+ double pressure = -stress.trace() / 3.0;
+
+ if (failureModel[itype].failure_max_principal_stress) {
+ error->one(FLERR, "not yet implemented");
+ /*
+ * maximum stress failure criterion:
+ */
+ IsotropicMaxStressDamage(stress, Lookup[FAILURE_MAX_PRINCIPAL_STRESS_THRESHOLD][itype]);
+ } else if (failureModel[itype].failure_max_principal_strain) {
+ error->one(FLERR, "not yet implemented");
+ /*
+ * maximum strain failure criterion:
+ */
+ IsotropicMaxStrainDamage(strain, Lookup[FAILURE_MAX_PRINCIPAL_STRAIN_THRESHOLD][itype]);
+ } else if (failureModel[itype].failure_max_plastic_strain) {
+ if (eff_plastic_strain[i] >= Lookup[FAILURE_MAX_PLASTIC_STRAIN_THRESHOLD][itype]) {
+ damage[i] = 1.0;
+ //double damage_gap = 0.5 * Lookup[FAILURE_MAX_PLASTIC_STRAIN_THRESHOLD][itype];
+ //damage[i] = (eff_plastic_strain[i] - Lookup[FAILURE_MAX_PLASTIC_STRAIN_THRESHOLD][itype]) / damage_gap;
+ }
+ } else if (failureModel[itype].failure_johnson_cook) {
+
+ //cout << "this is stress deviator" << stress_deviator << endl;
+
+ jc_failure_strain = JohnsonCookFailureStrain(pressure, stress_deviator, Lookup[FAILURE_JC_D1][itype],
+ Lookup[FAILURE_JC_D2][itype], Lookup[FAILURE_JC_D3][itype], Lookup[FAILURE_JC_D4][itype],
+ Lookup[FAILURE_JC_EPDOT0][itype], eff_plastic_strain_rate[i]);
+
+ //cout << "plastic strain increment is " << plastic_strain_increment << " jc fs is " << jc_failure_strain << endl;
+ //printf("JC failure strain is: %f\n", jc_failure_strain);
+
+ if (eff_plastic_strain[i] >= jc_failure_strain) {
+ double damage_rate = Lookup[SIGNAL_VELOCITY][itype] / (100.0 * radius[i]);
+ damage[i] += damage_rate * update->dt;
+ //damage[i] = 1.0;
+ }
+ }
+
+ /*
+ * Apply damage to integration point
+ */
+
+// damage[i] = MIN(damage[i], 0.8);
//
-// if (pressure > 0.0) { // compression: particle can carry compressive load but reduced shear
-// stress_damaged = -pressure * eye + (1.0 - damage[i]) * Deviator(stress);
-// } else { // tension: particle has reduced tensile and shear load bearing capability
-// stress_damaged = (1.0 - damage[i]) * (-pressure * eye + Deviator(stress));
-// }
+// if (pressure > 0.0) { // compression: particle can carry compressive load but reduced shear
+// stress_damaged = -pressure * eye + (1.0 - damage[i]) * Deviator(stress);
+// } else { // tension: particle has reduced tensile and shear load bearing capability
+// stress_damaged = (1.0 - damage[i]) * (-pressure * eye + Deviator(stress));
+// }
}
diff --git a/src/USER-SMD/pair_smd_tlsph.h b/src/USER-SMD/pair_smd_tlsph.h
index 4c9db9209b..62e7ce2295 100644
--- a/src/USER-SMD/pair_smd_tlsph.h
+++ b/src/USER-SMD/pair_smd_tlsph.h
@@ -39,163 +39,163 @@ namespace LAMMPS_NS {
class PairTlsph: public Pair {
public:
- PairTlsph(class LAMMPS *);
- virtual ~PairTlsph();
- virtual void compute(int, int);
- void settings(int, char **);
- void coeff(int, char **);
- double init_one(int, int);
- void init_style();
- void init_list(int, class NeighList *);
- void write_restart_settings(FILE *) {
- }
- void read_restart_settings(FILE *) {
- }
- virtual double memory_usage();
- void compute_shape_matrix(void);
- void material_model(void);
- void *extract(const char *, int &);
- int pack_forward_comm(int, int *, double *, int, int *);
- void unpack_forward_comm(int, int, double *);
- void AssembleStress();
-
- void PreCompute();
- void ComputeForces(int eflag, int vflag);
- void effective_longitudinal_modulus(const int itype, const double dt, const double d_iso, const double p_rate,
- const Eigen::Matrix3d d_dev, const Eigen::Matrix3d sigma_dev_rate, const double damage, double &K_eff, double &mu_eff, double &M_eff);
-
- void ComputePressure(const int i, const double rho, const double mass_specific_energy, const double vol_specific_energy,
- const double pInitial, const double d_iso, double &pFinal, double &p_rate);
- void ComputeStressDeviator(const int i, const Eigen::Matrix3d sigmaInitial_dev, const Eigen::Matrix3d d_dev, Eigen::Matrix3d &sigmaFinal_dev,
- Eigen::Matrix3d &sigma_dev_rate, double &plastic_strain_increment);
- void ComputeDamage(const int i, const Eigen::Matrix3d strain, const Eigen::Matrix3d sigmaFinal, Eigen::Matrix3d &sigma_damaged);
+ PairTlsph(class LAMMPS *);
+ virtual ~PairTlsph();
+ virtual void compute(int, int);
+ void settings(int, char **);
+ void coeff(int, char **);
+ double init_one(int, int);
+ void init_style();
+ void init_list(int, class NeighList *);
+ void write_restart_settings(FILE *) {
+ }
+ void read_restart_settings(FILE *) {
+ }
+ virtual double memory_usage();
+ void compute_shape_matrix(void);
+ void material_model(void);
+ void *extract(const char *, int &);
+ int pack_forward_comm(int, int *, double *, int, int *);
+ void unpack_forward_comm(int, int, double *);
+ void AssembleStress();
+
+ void PreCompute();
+ void ComputeForces(int eflag, int vflag);
+ void effective_longitudinal_modulus(const int itype, const double dt, const double d_iso, const double p_rate,
+ const Eigen::Matrix3d d_dev, const Eigen::Matrix3d sigma_dev_rate, const double damage, double &K_eff, double &mu_eff, double &M_eff);
+
+ void ComputePressure(const int i, const double rho, const double mass_specific_energy, const double vol_specific_energy,
+ const double pInitial, const double d_iso, double &pFinal, double &p_rate);
+ void ComputeStressDeviator(const int i, const Eigen::Matrix3d sigmaInitial_dev, const Eigen::Matrix3d d_dev, Eigen::Matrix3d &sigmaFinal_dev,
+ Eigen::Matrix3d &sigma_dev_rate, double &plastic_strain_increment);
+ void ComputeDamage(const int i, const Eigen::Matrix3d strain, const Eigen::Matrix3d sigmaFinal, Eigen::Matrix3d &sigma_damaged);
protected:
- void allocate();
- char *suffix;
-
- /*
- * per-type arrays
- */
- int *strengthModel, *eos;
- double *onerad_dynamic, *onerad_frozen, *maxrad_dynamic, *maxrad_frozen;
-
- /*
- * per atom arrays
- */
- Eigen::Matrix3d *K, *PK1, *Fdot, *Fincr;
- Eigen::Matrix3d *R; // rotation matrix
- Eigen::Matrix3d *FincrInv;
- Eigen::Matrix3d *D, *W; // strain rate and spin tensor
- Eigen::Vector3d *smoothVelDifference;
- Eigen::Matrix3d *CauchyStress;
- double *detF, *particle_dt;
- double *hourglass_error;
- int *numNeighsRefConfig;
-
- int nmax; // max number of atoms on this proc
- double hMin; // minimum kernel radius for two particles
- double dtCFL;
- double dtRelative; // relative velocity of two particles, divided by sound speed
- int updateFlag;
- double update_threshold; // updateFlage is set to one if the relative displacement of a pair exceeds update_threshold
- double cut_comm;
-
- enum {
- UPDATE_NONE = 5000, UPDATE_CONSTANT_THRESHOLD = 5001, UPDATE_PAIRWISE_RATIO = 5002,
- };
-
- enum {
- LINEAR_DEFGRAD = 0,
- STRENGTH_LINEAR = 1,
- STRENGTH_LINEAR_PLASTIC = 2,
- STRENGTH_JOHNSON_COOK = 3,
- STRENGTH_NONE = 4,
- EOS_LINEAR = 5,
- EOS_SHOCK = 6,
- EOS_POLYNOMIAL = 7,
- EOS_NONE = 8,
- REFERENCE_DENSITY = 9,
- YOUNGS_MODULUS = 10,
- POISSON_RATIO = 11,
- HOURGLASS_CONTROL_AMPLITUDE = 12,
- HEAT_CAPACITY = 13,
- LAME_LAMBDA = 14,
- SHEAR_MODULUS = 15,
- M_MODULUS = 16,
- SIGNAL_VELOCITY = 17,
- BULK_MODULUS = 18,
- VISCOSITY_Q1 = 19,
- VISCOSITY_Q2 = 20,
- YIELD_STRESS = 21,
- FAILURE_MAX_PLASTIC_STRAIN_THRESHOLD = 22,
- JC_A = 23,
- JC_B = 24,
- JC_a = 25,
- JC_C = 26,
- JC_epdot0 = 27,
- JC_T0 = 28,
- JC_Tmelt = 29,
- JC_M = 30,
- EOS_SHOCK_C0 = 31,
- EOS_SHOCK_S = 32,
- EOS_SHOCK_GAMMA = 33,
- HARDENING_PARAMETER = 34,
- FAILURE_MAX_PRINCIPAL_STRAIN_THRESHOLD = 35,
- FAILURE_MAX_PRINCIPAL_STRESS_THRESHOLD = 36,
- FAILURE_MAX_PAIRWISE_STRAIN_THRESHOLD = 37,
- EOS_POLYNOMIAL_C0 = 38,
- EOS_POLYNOMIAL_C1 = 39,
- EOS_POLYNOMIAL_C2 = 40,
- EOS_POLYNOMIAL_C3 = 41,
- EOS_POLYNOMIAL_C4 = 42,
- EOS_POLYNOMIAL_C5 = 43,
- EOS_POLYNOMIAL_C6 = 44,
-
- FAILURE_JC_D1 = 45,
- FAILURE_JC_D2 = 46,
- FAILURE_JC_D3 = 47,
- FAILURE_JC_D4 = 48,
- FAILURE_JC_EPDOT0 = 49,
-
- CRITICAL_ENERGY_RELEASE_RATE = 50,
-
- MAX_KEY_VALUE = 51
- };
-
- struct failure_types { // this is defined per type and determines which failure/damage model is active
- bool failure_none;
- bool failure_max_principal_strain;
- bool failure_max_principal_stress;
- bool failure_max_plastic_strain;
- bool failure_johnson_cook;
- bool failure_max_pairwise_strain;
- bool integration_point_wise; // true if failure model applies to stress/strain state of integration point
- bool failure_energy_release_rate;
-
- failure_types() {
- failure_none = true;
- failure_max_principal_strain = false;
- failure_max_principal_stress = false;
- failure_max_plastic_strain = false;
- failure_johnson_cook = false;
- failure_max_pairwise_strain = false;
- integration_point_wise = false;
- failure_energy_release_rate = false;
- //printf("constructed failure type\n");
- }
- };
- failure_types *failureModel;
-
- int ifix_tlsph;
- int update_method;
-
- class FixSMD_TLSPH_ReferenceConfiguration *fix_tlsph_reference_configuration;
+ void allocate();
+ char *suffix;
+
+ /*
+ * per-type arrays
+ */
+ int *strengthModel, *eos;
+ double *onerad_dynamic, *onerad_frozen, *maxrad_dynamic, *maxrad_frozen;
+
+ /*
+ * per atom arrays
+ */
+ Eigen::Matrix3d *K, *PK1, *Fdot, *Fincr;
+ Eigen::Matrix3d *R; // rotation matrix
+ Eigen::Matrix3d *FincrInv;
+ Eigen::Matrix3d *D, *W; // strain rate and spin tensor
+ Eigen::Vector3d *smoothVelDifference;
+ Eigen::Matrix3d *CauchyStress;
+ double *detF, *particle_dt;
+ double *hourglass_error;
+ int *numNeighsRefConfig;
+
+ int nmax; // max number of atoms on this proc
+ double hMin; // minimum kernel radius for two particles
+ double dtCFL;
+ double dtRelative; // relative velocity of two particles, divided by sound speed
+ int updateFlag;
+ double update_threshold; // updateFlage is set to one if the relative displacement of a pair exceeds update_threshold
+ double cut_comm;
+
+ enum {
+ UPDATE_NONE = 5000, UPDATE_CONSTANT_THRESHOLD = 5001, UPDATE_PAIRWISE_RATIO = 5002,
+ };
+
+ enum {
+ LINEAR_DEFGRAD = 0,
+ STRENGTH_LINEAR = 1,
+ STRENGTH_LINEAR_PLASTIC = 2,
+ STRENGTH_JOHNSON_COOK = 3,
+ STRENGTH_NONE = 4,
+ EOS_LINEAR = 5,
+ EOS_SHOCK = 6,
+ EOS_POLYNOMIAL = 7,
+ EOS_NONE = 8,
+ REFERENCE_DENSITY = 9,
+ YOUNGS_MODULUS = 10,
+ POISSON_RATIO = 11,
+ HOURGLASS_CONTROL_AMPLITUDE = 12,
+ HEAT_CAPACITY = 13,
+ LAME_LAMBDA = 14,
+ SHEAR_MODULUS = 15,
+ M_MODULUS = 16,
+ SIGNAL_VELOCITY = 17,
+ BULK_MODULUS = 18,
+ VISCOSITY_Q1 = 19,
+ VISCOSITY_Q2 = 20,
+ YIELD_STRESS = 21,
+ FAILURE_MAX_PLASTIC_STRAIN_THRESHOLD = 22,
+ JC_A = 23,
+ JC_B = 24,
+ JC_a = 25,
+ JC_C = 26,
+ JC_epdot0 = 27,
+ JC_T0 = 28,
+ JC_Tmelt = 29,
+ JC_M = 30,
+ EOS_SHOCK_C0 = 31,
+ EOS_SHOCK_S = 32,
+ EOS_SHOCK_GAMMA = 33,
+ HARDENING_PARAMETER = 34,
+ FAILURE_MAX_PRINCIPAL_STRAIN_THRESHOLD = 35,
+ FAILURE_MAX_PRINCIPAL_STRESS_THRESHOLD = 36,
+ FAILURE_MAX_PAIRWISE_STRAIN_THRESHOLD = 37,
+ EOS_POLYNOMIAL_C0 = 38,
+ EOS_POLYNOMIAL_C1 = 39,
+ EOS_POLYNOMIAL_C2 = 40,
+ EOS_POLYNOMIAL_C3 = 41,
+ EOS_POLYNOMIAL_C4 = 42,
+ EOS_POLYNOMIAL_C5 = 43,
+ EOS_POLYNOMIAL_C6 = 44,
+
+ FAILURE_JC_D1 = 45,
+ FAILURE_JC_D2 = 46,
+ FAILURE_JC_D3 = 47,
+ FAILURE_JC_D4 = 48,
+ FAILURE_JC_EPDOT0 = 49,
+
+ CRITICAL_ENERGY_RELEASE_RATE = 50,
+
+ MAX_KEY_VALUE = 51
+ };
+
+ struct failure_types { // this is defined per type and determines which failure/damage model is active
+ bool failure_none;
+ bool failure_max_principal_strain;
+ bool failure_max_principal_stress;
+ bool failure_max_plastic_strain;
+ bool failure_johnson_cook;
+ bool failure_max_pairwise_strain;
+ bool integration_point_wise; // true if failure model applies to stress/strain state of integration point
+ bool failure_energy_release_rate;
+
+ failure_types() {
+ failure_none = true;
+ failure_max_principal_strain = false;
+ failure_max_principal_stress = false;
+ failure_max_plastic_strain = false;
+ failure_johnson_cook = false;
+ failure_max_pairwise_strain = false;
+ integration_point_wise = false;
+ failure_energy_release_rate = false;
+ //printf("constructed failure type\n");
+ }
+ };
+ failure_types *failureModel;
+
+ int ifix_tlsph;
+ int update_method;
+
+ class FixSMD_TLSPH_ReferenceConfiguration *fix_tlsph_reference_configuration;
private:
- double **Lookup; // holds per-type material parameters for the quantities defined in enum statement above.
- bool first; // if first is true, do not perform any computations, beacuse reference configuration is not ready yet.
+ double **Lookup; // holds per-type material parameters for the quantities defined in enum statement above.
+ bool first; // if first is true, do not perform any computations, beacuse reference configuration is not ready yet.
};
}
diff --git a/src/USER-SMD/pair_smd_triangulated_surface.cpp b/src/USER-SMD/pair_smd_triangulated_surface.cpp
index eec9e517ea..a62e262b7a 100644
--- a/src/USER-SMD/pair_smd_triangulated_surface.cpp
+++ b/src/USER-SMD/pair_smd_triangulated_surface.cpp
@@ -56,245 +56,245 @@ using namespace Eigen;
/* ---------------------------------------------------------------------- */
PairTriSurf::PairTriSurf(LAMMPS *lmp) :
- Pair(lmp) {
+ Pair(lmp) {
- onerad_dynamic = onerad_frozen = maxrad_dynamic = maxrad_frozen = NULL;
- bulkmodulus = NULL;
- kn = NULL;
- scale = 1.0;
+ onerad_dynamic = onerad_frozen = maxrad_dynamic = maxrad_frozen = NULL;
+ bulkmodulus = NULL;
+ kn = NULL;
+ scale = 1.0;
}
/* ---------------------------------------------------------------------- */
PairTriSurf::~PairTriSurf() {
- if (allocated) {
- memory->destroy(setflag);
- memory->destroy(cutsq);
- memory->destroy(bulkmodulus);
- memory->destroy(kn);
-
- delete[] onerad_dynamic;
- delete[] onerad_frozen;
- delete[] maxrad_dynamic;
- delete[] maxrad_frozen;
- }
+ if (allocated) {
+ memory->destroy(setflag);
+ memory->destroy(cutsq);
+ memory->destroy(bulkmodulus);
+ memory->destroy(kn);
+
+ delete[] onerad_dynamic;
+ delete[] onerad_frozen;
+ delete[] maxrad_dynamic;
+ delete[] maxrad_frozen;
+ }
}
/* ---------------------------------------------------------------------- */
void PairTriSurf::compute(int eflag, int vflag) {
- int i, j, ii, jj, inum, jnum, itype, jtype;
- double rsq, r, evdwl, fpair;
- int *ilist, *jlist, *numneigh, **firstneigh;
- double rcut, r_geom, delta, r_tri, r_particle, touch_distance, dt_crit;
- int tri, particle;
- Vector3d normal, x1, x2, x3, x4, x13, x23, x43, w, cp, x4cp, vnew, v_old;
- ;
- Vector3d xi, x_center, dx;
- Matrix2d C;
- Vector2d w2d, rhs;
-
- evdwl = 0.0;
- if (eflag || vflag)
- ev_setup(eflag, vflag);
- else
- evflag = vflag_fdotr = 0;
-
- tagint *mol = atom->molecule;
- double **f = atom->f;
- double **smd_data_9 = atom->smd_data_9;
- double **x = atom->x;
- double **x0 = atom->x0;
- double **v = atom->v;
- double *rmass = atom->rmass;
- int *type = atom->type;
- int nlocal = atom->nlocal;
- double *radius = atom->contact_radius;
- double rcutSq;
- Vector3d offset;
-
- int newton_pair = force->newton_pair;
- int periodic = (domain->xperiodic || domain->yperiodic || domain->zperiodic);
-
- inum = list->inum;
- ilist = list->ilist;
- numneigh = list->numneigh;
- firstneigh = list->firstneigh;
-
- int max_neighs = 0;
- stable_time_increment = 1.0e22;
-
- // loop over neighbors of my atoms using a half neighbor list
- for (ii = 0; ii < inum; ii++) {
- i = ilist[ii];
- itype = type[i];
- jlist = firstneigh[i];
- jnum = numneigh[i];
- max_neighs = MAX(max_neighs, jnum);
-
- for (jj = 0; jj < jnum; jj++) {
- j = jlist[jj];
-
- j &= NEIGHMASK;
-
- jtype = type[j];
-
- /*
- * decide which one of i, j is triangle and which is particle
- */
- if ((mol[i] < 65535) && (mol[j] >= 65535)) {
- particle = i;
- tri = j;
- } else if ((mol[j] < 65535) && (mol[i] >= 65535)) {
- particle = j;
- tri = i;
- } else {
- error->one(FLERR, "unknown case");
- }
-
- //x_center << x[tri][0], x[tri][1], x[tri][2]; // center of triangle
- x_center(0) = x[tri][0];
- x_center(1) = x[tri][1];
- x_center(2) = x[tri][2];
- //x4 << x[particle][0], x[particle][1], x[particle][2];
- x4(0) = x[particle][0];
- x4(1) = x[particle][1];
- x4(2) = x[particle][2];
- dx = x_center - x4; //
- if (periodic) {
- domain->minimum_image(dx(0), dx(1), dx(2));
- }
- rsq = dx.squaredNorm();
-
- r_tri = scale * radius[tri];
- r_particle = scale * radius[particle];
- rcut = r_tri + r_particle;
- rcutSq = rcut * rcut;
-
- //printf("type i=%d, type j=%d, r=%f, ri=%f, rj=%f\n", itype, jtype, sqrt(rsq), ri, rj);
-
- if (rsq < rcutSq) {
-
- /*
- * gather triangle information
- */
- normal(0) = x0[tri][0];
- normal(1) = x0[tri][1];
- normal(2) = x0[tri][2];
-
- /*
- * distance check: is particle closer than its radius to the triangle plane?
- */
- if (fabs(dx.dot(normal)) < radius[particle]) {
- /*
- * get other two triangle vertices
- */
- x1(0) = smd_data_9[tri][0];
- x1(1) = smd_data_9[tri][1];
- x1(2) = smd_data_9[tri][2];
- x2(0) = smd_data_9[tri][3];
- x2(1) = smd_data_9[tri][4];
- x2(2) = smd_data_9[tri][5];
- x3(0) = smd_data_9[tri][6];
- x3(1) = smd_data_9[tri][7];
- x3(2) = smd_data_9[tri][8];
-
- PointTriangleDistance(x4, x1, x2, x3, cp, r);
-
- /*
- * distance to closest point
- */
- x4cp = x4 - cp;
-
- /*
- * flip normal to point in direction of x4cp
- */
-
- if (x4cp.dot(normal) < 0.0) {
- normal *= -1.0;
- }
-
- /*
- * penalty force pushes particle away from triangle
- */
- if (r < 1.0 * radius[particle]) {
-
- delta = radius[particle] - r; // overlap distance
- r_geom = radius[particle];
- fpair = 1.066666667e0 * bulkmodulus[itype][jtype] * delta * sqrt(delta * r_geom);
- dt_crit = 3.14 * sqrt(rmass[particle] / (fpair / delta));
- stable_time_increment = MIN(stable_time_increment, dt_crit);
-
- evdwl = r * fpair * 0.4e0 * delta; // GCG 25 April: this expression conserves total energy
-
- fpair /= (r + 1.0e-2 * radius[particle]); // divide by r + softening and multiply with non-normalized distance vector
-
- if (particle < nlocal) {
- f[particle][0] += x4cp(0) * fpair;
- f[particle][1] += x4cp(1) * fpair;
- f[particle][2] += x4cp(2) * fpair;
- }
-
- if (tri < nlocal) {
- f[tri][0] -= x4cp(0) * fpair;
- f[tri][1] -= x4cp(1) * fpair;
- f[tri][2] -= x4cp(2) * fpair;
- }
-
- if (evflag) {
- ev_tally(i, j, nlocal, newton_pair, evdwl, 0.0, fpair, x4cp(0), x4cp(1), x4cp(2));
- }
-
- }
-
- /*
- * if particle comes too close to triangle, reflect its velocity and explicitly move it away
- */
-
- touch_distance = 1.0 * radius[particle];
- if (r < touch_distance) {
-
- /*
- * reflect velocity if it points toward triangle
- */
-
- normal = x4cp / r;
-
- //v_old << v[particle][0], v[particle][1], v[particle][2];
- v_old(0) = v[particle][0];
- v_old(1) = v[particle][1];
- v_old(2) = v[particle][2];
- if (v_old.dot(normal) < 0.0) {
- //printf("flipping velocity\n");
- vnew = 1.0 * (-2.0 * v_old.dot(normal) * normal + v_old);
- v[particle][0] = vnew(0);
- v[particle][1] = vnew(1);
- v[particle][2] = vnew(2);
- }
-
- //printf("moving particle on top of triangle\n");
- x[particle][0] = cp(0) + touch_distance * normal(0);
- x[particle][1] = cp(1) + touch_distance * normal(1);
- x[particle][2] = cp(2) + touch_distance * normal(2);
- }
-
- }
- }
- }
- }
-
-// int max_neighs_all = 0;
-// MPI_Allreduce(&max_neighs, &max_neighs_all, 1, MPI_INT, MPI_MAX, world);
-// if (comm->me == 0) {
-// printf("max. neighs in tri pair is %d\n", max_neighs_all);
-// }
+ int i, j, ii, jj, inum, jnum, itype, jtype;
+ double rsq, r, evdwl, fpair;
+ int *ilist, *jlist, *numneigh, **firstneigh;
+ double rcut, r_geom, delta, r_tri, r_particle, touch_distance, dt_crit;
+ int tri, particle;
+ Vector3d normal, x1, x2, x3, x4, x13, x23, x43, w, cp, x4cp, vnew, v_old;
+ ;
+ Vector3d xi, x_center, dx;
+ Matrix2d C;
+ Vector2d w2d, rhs;
+
+ evdwl = 0.0;
+ if (eflag || vflag)
+ ev_setup(eflag, vflag);
+ else
+ evflag = vflag_fdotr = 0;
+
+ tagint *mol = atom->molecule;
+ double **f = atom->f;
+ double **smd_data_9 = atom->smd_data_9;
+ double **x = atom->x;
+ double **x0 = atom->x0;
+ double **v = atom->v;
+ double *rmass = atom->rmass;
+ int *type = atom->type;
+ int nlocal = atom->nlocal;
+ double *radius = atom->contact_radius;
+ double rcutSq;
+ Vector3d offset;
+
+ int newton_pair = force->newton_pair;
+ int periodic = (domain->xperiodic || domain->yperiodic || domain->zperiodic);
+
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
+
+ int max_neighs = 0;
+ stable_time_increment = 1.0e22;
+
+ // loop over neighbors of my atoms using a half neighbor list
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+ itype = type[i];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+ max_neighs = MAX(max_neighs, jnum);
+
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
+
+ j &= NEIGHMASK;
+
+ jtype = type[j];
+
+ /*
+ * decide which one of i, j is triangle and which is particle
+ */
+ if ((mol[i] < 65535) && (mol[j] >= 65535)) {
+ particle = i;
+ tri = j;
+ } else if ((mol[j] < 65535) && (mol[i] >= 65535)) {
+ particle = j;
+ tri = i;
+ } else {
+ error->one(FLERR, "unknown case");
+ }
+
+ //x_center << x[tri][0], x[tri][1], x[tri][2]; // center of triangle
+ x_center(0) = x[tri][0];
+ x_center(1) = x[tri][1];
+ x_center(2) = x[tri][2];
+ //x4 << x[particle][0], x[particle][1], x[particle][2];
+ x4(0) = x[particle][0];
+ x4(1) = x[particle][1];
+ x4(2) = x[particle][2];
+ dx = x_center - x4; //
+ if (periodic) {
+ domain->minimum_image(dx(0), dx(1), dx(2));
+ }
+ rsq = dx.squaredNorm();
+
+ r_tri = scale * radius[tri];
+ r_particle = scale * radius[particle];
+ rcut = r_tri + r_particle;
+ rcutSq = rcut * rcut;
+
+ //printf("type i=%d, type j=%d, r=%f, ri=%f, rj=%f\n", itype, jtype, sqrt(rsq), ri, rj);
+
+ if (rsq < rcutSq) {
+
+ /*
+ * gather triangle information
+ */
+ normal(0) = x0[tri][0];
+ normal(1) = x0[tri][1];
+ normal(2) = x0[tri][2];
+
+ /*
+ * distance check: is particle closer than its radius to the triangle plane?
+ */
+ if (fabs(dx.dot(normal)) < radius[particle]) {
+ /*
+ * get other two triangle vertices
+ */
+ x1(0) = smd_data_9[tri][0];
+ x1(1) = smd_data_9[tri][1];
+ x1(2) = smd_data_9[tri][2];
+ x2(0) = smd_data_9[tri][3];
+ x2(1) = smd_data_9[tri][4];
+ x2(2) = smd_data_9[tri][5];
+ x3(0) = smd_data_9[tri][6];
+ x3(1) = smd_data_9[tri][7];
+ x3(2) = smd_data_9[tri][8];
+
+ PointTriangleDistance(x4, x1, x2, x3, cp, r);
+
+ /*
+ * distance to closest point
+ */
+ x4cp = x4 - cp;
+
+ /*
+ * flip normal to point in direction of x4cp
+ */
+
+ if (x4cp.dot(normal) < 0.0) {
+ normal *= -1.0;
+ }
+
+ /*
+ * penalty force pushes particle away from triangle
+ */
+ if (r < 1.0 * radius[particle]) {
+
+ delta = radius[particle] - r; // overlap distance
+ r_geom = radius[particle];
+ fpair = 1.066666667e0 * bulkmodulus[itype][jtype] * delta * sqrt(delta * r_geom);
+ dt_crit = 3.14 * sqrt(rmass[particle] / (fpair / delta));
+ stable_time_increment = MIN(stable_time_increment, dt_crit);
+
+ evdwl = r * fpair * 0.4e0 * delta; // GCG 25 April: this expression conserves total energy
+
+ fpair /= (r + 1.0e-2 * radius[particle]); // divide by r + softening and multiply with non-normalized distance vector
+
+ if (particle < nlocal) {
+ f[particle][0] += x4cp(0) * fpair;
+ f[particle][1] += x4cp(1) * fpair;
+ f[particle][2] += x4cp(2) * fpair;
+ }
+
+ if (tri < nlocal) {
+ f[tri][0] -= x4cp(0) * fpair;
+ f[tri][1] -= x4cp(1) * fpair;
+ f[tri][2] -= x4cp(2) * fpair;
+ }
+
+ if (evflag) {
+ ev_tally(i, j, nlocal, newton_pair, evdwl, 0.0, fpair, x4cp(0), x4cp(1), x4cp(2));
+ }
+
+ }
+
+ /*
+ * if particle comes too close to triangle, reflect its velocity and explicitly move it away
+ */
+
+ touch_distance = 1.0 * radius[particle];
+ if (r < touch_distance) {
+
+ /*
+ * reflect velocity if it points toward triangle
+ */
+
+ normal = x4cp / r;
+
+ //v_old << v[particle][0], v[particle][1], v[particle][2];
+ v_old(0) = v[particle][0];
+ v_old(1) = v[particle][1];
+ v_old(2) = v[particle][2];
+ if (v_old.dot(normal) < 0.0) {
+ //printf("flipping velocity\n");
+ vnew = 1.0 * (-2.0 * v_old.dot(normal) * normal + v_old);
+ v[particle][0] = vnew(0);
+ v[particle][1] = vnew(1);
+ v[particle][2] = vnew(2);
+ }
+
+ //printf("moving particle on top of triangle\n");
+ x[particle][0] = cp(0) + touch_distance * normal(0);
+ x[particle][1] = cp(1) + touch_distance * normal(1);
+ x[particle][2] = cp(2) + touch_distance * normal(2);
+ }
+
+ }
+ }
+ }
+ }
+
+// int max_neighs_all = 0;
+// MPI_Allreduce(&max_neighs, &max_neighs_all, 1, MPI_INT, MPI_MAX, world);
+// if (comm->me == 0) {
+// printf("max. neighs in tri pair is %d\n", max_neighs_all);
+// }
//
-// double stable_time_increment_all = 0.0;
-// MPI_Allreduce(&stable_time_increment, &stable_time_increment_all, 1, MPI_DOUBLE, MPI_MIN, world);
-// if (comm->me == 0) {
-// printf("stable time step tri pair is %f\n", stable_time_increment_all);
-// }
+// double stable_time_increment_all = 0.0;
+// MPI_Allreduce(&stable_time_increment, &stable_time_increment_all, 1, MPI_DOUBLE, MPI_MIN, world);
+// if (comm->me == 0) {
+// printf("stable time step tri pair is %f\n", stable_time_increment_all);
+// }
}
/* ----------------------------------------------------------------------
@@ -302,23 +302,23 @@ void PairTriSurf::compute(int eflag, int vflag) {
------------------------------------------------------------------------- */
void PairTriSurf::allocate() {
- allocated = 1;
- int n = atom->ntypes;
+ allocated = 1;
+ int n = atom->ntypes;
- memory->create(setflag, n + 1, n + 1, "pair:setflag");
- for (int i = 1; i <= n; i++)
- for (int j = i; j <= n; j++)
- setflag[i][j] = 0;
+ memory->create(setflag, n + 1, n + 1, "pair:setflag");
+ for (int i = 1; i <= n; i++)
+ for (int j = i; j <= n; j++)
+ setflag[i][j] = 0;
- memory->create(bulkmodulus, n + 1, n + 1, "pair:kspring");
- memory->create(kn, n + 1, n + 1, "pair:kn");
+ memory->create(bulkmodulus, n + 1, n + 1, "pair:kspring");
+ memory->create(kn, n + 1, n + 1, "pair:kn");
- memory->create(cutsq, n + 1, n + 1, "pair:cutsq"); // always needs to be allocated, even with granular neighborlist
+ memory->create(cutsq, n + 1, n + 1, "pair:cutsq"); // always needs to be allocated, even with granular neighborlist
- onerad_dynamic = new double[n + 1];
- onerad_frozen = new double[n + 1];
- maxrad_dynamic = new double[n + 1];
- maxrad_frozen = new double[n + 1];
+ onerad_dynamic = new double[n + 1];
+ onerad_frozen = new double[n + 1];
+ maxrad_dynamic = new double[n + 1];
+ maxrad_frozen = new double[n + 1];
}
/* ----------------------------------------------------------------------
@@ -326,16 +326,16 @@ void PairTriSurf::allocate() {
------------------------------------------------------------------------- */
void PairTriSurf::settings(int narg, char **arg) {
- if (narg != 1)
- error->all(FLERR, "Illegal number of args for pair_style smd/tri_surface");
+ if (narg != 1)
+ error->all(FLERR, "Illegal number of args for pair_style smd/tri_surface");
- scale = force->numeric(FLERR, arg[0]);
- if (comm->me == 0) {
- printf("\n>>========>>========>>========>>========>>========>>========>>========>>========\n");
- printf("SMD/TRI_SURFACE CONTACT SETTINGS:\n");
- printf("... effective contact radius is scaled by %f\n", scale);
- printf(">>========>>========>>========>>========>>========>>========>>========>>========\n");
- }
+ scale = force->numeric(FLERR, arg[0]);
+ if (comm->me == 0) {
+ printf("\n>>========>>========>>========>>========>>========>>========>>========>>========\n");
+ printf("SMD/TRI_SURFACE CONTACT SETTINGS:\n");
+ printf("... effective contact radius is scaled by %f\n", scale);
+ printf(">>========>>========>>========>>========>>========>>========>>========>>========\n");
+ }
}
@@ -344,37 +344,37 @@ void PairTriSurf::settings(int narg, char **arg) {
------------------------------------------------------------------------- */
void PairTriSurf::coeff(int narg, char **arg) {
- if (narg != 3)
- error->all(FLERR, "Incorrect args for pair coefficients");
- if (!allocated)
- allocate();
-
- int ilo, ihi, jlo, jhi;
- force->bounds(FLERR,arg[0], atom->ntypes, ilo, ihi);
- force->bounds(FLERR,arg[1], atom->ntypes, jlo, jhi);
-
- double bulkmodulus_one = atof(arg[2]);
-
- // set short-range force constant
- double kn_one = 0.0;
- if (domain->dimension == 3) {
- kn_one = (16. / 15.) * bulkmodulus_one; //assuming poisson ratio = 1/4 for 3d
- } else {
- kn_one = 0.251856195 * (2. / 3.) * bulkmodulus_one; //assuming poisson ratio = 1/3 for 2d
- }
-
- int count = 0;
- for (int i = ilo; i <= ihi; i++) {
- for (int j = MAX(jlo, i); j <= jhi; j++) {
- bulkmodulus[i][j] = bulkmodulus_one;
- kn[i][j] = kn_one;
- setflag[i][j] = 1;
- count++;
- }
- }
-
- if (count == 0)
- error->all(FLERR, "Incorrect args for pair coefficients");
+ if (narg != 3)
+ error->all(FLERR, "Incorrect args for pair coefficients");
+ if (!allocated)
+ allocate();
+
+ int ilo, ihi, jlo, jhi;
+ force->bounds(FLERR,arg[0], atom->ntypes, ilo, ihi);
+ force->bounds(FLERR,arg[1], atom->ntypes, jlo, jhi);
+
+ double bulkmodulus_one = atof(arg[2]);
+
+ // set short-range force constant
+ double kn_one = 0.0;
+ if (domain->dimension == 3) {
+ kn_one = (16. / 15.) * bulkmodulus_one; //assuming poisson ratio = 1/4 for 3d
+ } else {
+ kn_one = 0.251856195 * (2. / 3.) * bulkmodulus_one; //assuming poisson ratio = 1/3 for 2d
+ }
+
+ int count = 0;
+ for (int i = ilo; i <= ihi; i++) {
+ for (int j = MAX(jlo, i); j <= jhi; j++) {
+ bulkmodulus[i][j] = bulkmodulus_one;
+ kn[i][j] = kn_one;
+ setflag[i][j] = 1;
+ count++;
+ }
+ }
+
+ if (count == 0)
+ error->all(FLERR, "Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
@@ -383,26 +383,26 @@ void PairTriSurf::coeff(int narg, char **arg) {
double PairTriSurf::init_one(int i, int j) {
- if (!allocated)
- allocate();
+ if (!allocated)
+ allocate();
- if (setflag[i][j] == 0)
- error->all(FLERR, "All pair coeffs are not set");
+ if (setflag[i][j] == 0)
+ error->all(FLERR, "All pair coeffs are not set");
- bulkmodulus[j][i] = bulkmodulus[i][j];
- kn[j][i] = kn[i][j];
+ bulkmodulus[j][i] = bulkmodulus[i][j];
+ kn[j][i] = kn[i][j];
- // cutoff = sum of max I,J radii for
- // dynamic/dynamic & dynamic/frozen interactions, but not frozen/frozen
+ // cutoff = sum of max I,J radii for
+ // dynamic/dynamic & dynamic/frozen interactions, but not frozen/frozen
- double cutoff = maxrad_dynamic[i] + maxrad_dynamic[j];
- cutoff = MAX(cutoff, maxrad_frozen[i] + maxrad_dynamic[j]);
- cutoff = MAX(cutoff, maxrad_dynamic[i] + maxrad_frozen[j]);
+ double cutoff = maxrad_dynamic[i] + maxrad_dynamic[j];
+ cutoff = MAX(cutoff, maxrad_frozen[i] + maxrad_dynamic[j]);
+ cutoff = MAX(cutoff, maxrad_dynamic[i] + maxrad_frozen[j]);
- if (comm->me == 0) {
- printf("cutoff for pair smd/smd/tri_surface = %f\n", cutoff);
- }
- return cutoff;
+ if (comm->me == 0) {
+ printf("cutoff for pair smd/smd/tri_surface = %f\n", cutoff);
+ }
+ return cutoff;
}
/* ----------------------------------------------------------------------
@@ -410,38 +410,38 @@ double PairTriSurf::init_one(int i, int j) {
------------------------------------------------------------------------- */
void PairTriSurf::init_style() {
- int i;
+ int i;
- // error checks
+ // error checks
- if (!atom->contact_radius_flag)
- error->all(FLERR, "Pair style smd/smd/tri_surface requires atom style with contact_radius");
+ if (!atom->contact_radius_flag)
+ error->all(FLERR, "Pair style smd/smd/tri_surface requires atom style with contact_radius");
- // old: half list
- int irequest = neighbor->request(this);
- neighbor->requests[irequest]->size = 1;
+ // old: half list
+ int irequest = neighbor->request(this);
+ neighbor->requests[irequest]->size = 1;
- // need a full neighbor list
-// int irequest = neighbor->request(this);
-// neighbor->requests[irequest]->half = 0;
-// neighbor->requests[irequest]->full = 1;
+ // need a full neighbor list
+// int irequest = neighbor->request(this);
+// neighbor->requests[irequest]->half = 0;
+// neighbor->requests[irequest]->full = 1;
- // set maxrad_dynamic and maxrad_frozen for each type
- // include future Fix pour particles as dynamic
+ // set maxrad_dynamic and maxrad_frozen for each type
+ // include future Fix pour particles as dynamic
- for (i = 1; i <= atom->ntypes; i++)
- onerad_dynamic[i] = onerad_frozen[i] = 0.0;
+ for (i = 1; i <= atom->ntypes; i++)
+ onerad_dynamic[i] = onerad_frozen[i] = 0.0;
- double *radius = atom->radius;
- int *type = atom->type;
- int nlocal = atom->nlocal;
+ double *radius = atom->radius;
+ int *type = atom->type;
+ int nlocal = atom->nlocal;
- for (i = 0; i < nlocal; i++) {
- onerad_dynamic[type[i]] = MAX(onerad_dynamic[type[i]], radius[i]);
- }
+ for (i = 0; i < nlocal; i++) {
+ onerad_dynamic[type[i]] = MAX(onerad_dynamic[type[i]], radius[i]);
+ }
- MPI_Allreduce(&onerad_dynamic[1], &maxrad_dynamic[1], atom->ntypes, MPI_DOUBLE, MPI_MAX, world);
- MPI_Allreduce(&onerad_frozen[1], &maxrad_frozen[1], atom->ntypes, MPI_DOUBLE, MPI_MAX, world);
+ MPI_Allreduce(&onerad_dynamic[1], &maxrad_dynamic[1], atom->ntypes, MPI_DOUBLE, MPI_MAX, world);
+ MPI_Allreduce(&onerad_frozen[1], &maxrad_frozen[1], atom->ntypes, MPI_DOUBLE, MPI_MAX, world);
}
/* ----------------------------------------------------------------------
@@ -450,8 +450,8 @@ void PairTriSurf::init_style() {
------------------------------------------------------------------------- */
void PairTriSurf::init_list(int id, NeighList *ptr) {
- if (id == 0)
- list = ptr;
+ if (id == 0)
+ list = ptr;
}
/* ----------------------------------------------------------------------
@@ -460,7 +460,7 @@ void PairTriSurf::init_list(int id, NeighList *ptr) {
double PairTriSurf::memory_usage() {
- return 0.0;
+ return 0.0;
}
/*
@@ -547,199 +547,199 @@ double PairTriSurf::memory_usage() {
*/
//void PairTriSurf::PointTriangleDistance(const Vector3d P, const Vector3d TRI1, const Vector3d TRI2, const Vector3d TRI3,
-// Vector3d &CP, double &dist) {
+// Vector3d &CP, double &dist) {
//
-// Vector3d B, E0, E1, D;
-// double a, b, c, d, e, f;
-// double det, s, t, sqrDistance, tmp0, tmp1, numer, denom, invDet;
+// Vector3d B, E0, E1, D;
+// double a, b, c, d, e, f;
+// double det, s, t, sqrDistance, tmp0, tmp1, numer, denom, invDet;
//
-// // rewrite triangle in normal form
-// B = TRI1;
-// E0 = TRI2 - B;
-// E1 = TRI3 - B;
+// // rewrite triangle in normal form
+// B = TRI1;
+// E0 = TRI2 - B;
+// E1 = TRI3 - B;
//
-// D = B - P;
-// a = E0.dot(E0);
-// b = E0.dot(E1);
-// c = E1.dot(E1);
-// d = E0.dot(D);
-// e = E1.dot(D);
-// f = D.dot(D);
+// D = B - P;
+// a = E0.dot(E0);
+// b = E0.dot(E1);
+// c = E1.dot(E1);
+// d = E0.dot(D);
+// e = E1.dot(D);
+// f = D.dot(D);
//
-// det = a * c - b * b;
-// //% do we have to use abs here?
-// s = b * e - c * d;
-// t = b * d - a * e;
+// det = a * c - b * b;
+// //% do we have to use abs here?
+// s = b * e - c * d;
+// t = b * d - a * e;
//
-// //% Terible tree of conditionals to determine in which region of the diagram
-// //% shown above the projection of the point into the triangle-plane lies.
-// if ((s + t) <= det) {
-// if (s < 0) {
-// if (t < 0) {
-// // %region4
-// if (d < 0) {
-// t = 0;
-// if (-d >= a) {
-// s = 1;
-// sqrDistance = a + 2 * d + f;
-// } else {
-// s = -d / a;
-// sqrDistance = d * s + f;
-// }
-// } else {
-// s = 0;
-// if (e >= 0) {
-// t = 0;
-// sqrDistance = f;
-// } else {
-// if (-e >= c) {
-// t = 1;
-// sqrDistance = c + 2 * e + f;
-// } else {
-// t = -e / c;
-// sqrDistance = e * t + f;
-// }
-// }
-// }
-// // end % of region 4
-// } else {
-// // % region 3
-// s = 0;
-// if (e >= 0) {
-// t = 0;
-// sqrDistance = f;
-// } else {
-// if (-e >= c) {
-// t = 1;
-// sqrDistance = c + 2 * e + f;
-// } else {
-// t = -e / c;
-// sqrDistance = e * t + f;
-// }
-// }
-// }
-// // end of region 3
-// } else {
-// if (t < 0) {
-// //% region 5
-// t = 0;
-// if (d >= 0) {
-// s = 0;
-// sqrDistance = f;
-// } else {
-// if (-d >= a) {
-// s = 1;
-// sqrDistance = a + 2 * d + f;
-// } else {
-// s = -d / a;
-// sqrDistance = d * s + f;
-// }
-// }
-// } else {
-// // region 0
-// invDet = 1 / det;
-// s = s * invDet;
-// t = t * invDet;
-// sqrDistance = s * (a * s + b * t + 2 * d) + t * (b * s + c * t + 2 * e) + f;
-// }
-// }
-// } else {
-// if (s < 0) {
-// // % region 2
-// tmp0 = b + d;
-// tmp1 = c + e;
-// if (tmp1 > tmp0) { //% minimum on edge s+t=1
-// numer = tmp1 - tmp0;
-// denom = a - 2 * b + c;
-// if (numer >= denom) {
-// s = 1;
-// t = 0;
-// sqrDistance = a + 2 * d + f;
-// } else {
-// s = numer / denom;
-// t = 1 - s;
-// sqrDistance = s * (a * s + b * t + 2 * d) + t * (b * s + c * t + 2 * e) + f;
-// }
-// } else
-// // % minimum on edge s=0
-// s = 0;
-// if (tmp1 <= 0) {
-// t = 1;
-// sqrDistance = c + 2 * e + f;
-// } else {
-// if (e >= 0) {
-// t = 0;
-// sqrDistance = f;
-// } else {
-// t = -e / c;
-// sqrDistance = e * t + f;
-// }
-// }
-// } //end % of region 2
-// else {
-// if (t < 0) {
-// // %region6
-// tmp0 = b + e;
-// tmp1 = a + d;
-// if (tmp1 > tmp0) {
-// numer = tmp1 - tmp0;
-// denom = a - 2 * b + c;
-// if (numer >= denom) {
-// t = 1;
-// s = 0;
-// sqrDistance = c + 2 * e + f;
-// } else {
-// t = numer / denom;
-// s = 1 - t;
-// sqrDistance = s * (a * s + b * t + 2 * d) + t * (b * s + c * t + 2 * e) + f;
-// }
-// } else {
-// t = 0;
-// if (tmp1 <= 0) {
-// s = 1;
-// sqrDistance = a + 2 * d + f;
-// } else {
-// if (d >= 0) {
-// s = 0;
-// sqrDistance = f;
-// } else {
-// s = -d / a;
-// sqrDistance = d * s + f;
-// }
-// }
-// } // % end region 6
-// } else {
-// //% region 1
-// numer = c + e - b - d;
-// if (numer <= 0) {
-// s = 0;
-// t = 1;
-// sqrDistance = c + 2 * e + f;
-// } else {
-// denom = a - 2 * b + c;
-// if (numer >= denom) {
-// s = 1;
-// t = 0;
-// sqrDistance = a + 2 * d + f;
-// } else {
-// s = numer / denom;
-// t = 1 - s;
-// sqrDistance = s * (a * s + b * t + 2 * d) + t * (b * s + c * t + 2 * e) + f;
-// }
-// } //% end of region 1
-// }
-// }
-// }
+// //% Terible tree of conditionals to determine in which region of the diagram
+// //% shown above the projection of the point into the triangle-plane lies.
+// if ((s + t) <= det) {
+// if (s < 0) {
+// if (t < 0) {
+// // %region4
+// if (d < 0) {
+// t = 0;
+// if (-d >= a) {
+// s = 1;
+// sqrDistance = a + 2 * d + f;
+// } else {
+// s = -d / a;
+// sqrDistance = d * s + f;
+// }
+// } else {
+// s = 0;
+// if (e >= 0) {
+// t = 0;
+// sqrDistance = f;
+// } else {
+// if (-e >= c) {
+// t = 1;
+// sqrDistance = c + 2 * e + f;
+// } else {
+// t = -e / c;
+// sqrDistance = e * t + f;
+// }
+// }
+// }
+// // end % of region 4
+// } else {
+// // % region 3
+// s = 0;
+// if (e >= 0) {
+// t = 0;
+// sqrDistance = f;
+// } else {
+// if (-e >= c) {
+// t = 1;
+// sqrDistance = c + 2 * e + f;
+// } else {
+// t = -e / c;
+// sqrDistance = e * t + f;
+// }
+// }
+// }
+// // end of region 3
+// } else {
+// if (t < 0) {
+// //% region 5
+// t = 0;
+// if (d >= 0) {
+// s = 0;
+// sqrDistance = f;
+// } else {
+// if (-d >= a) {
+// s = 1;
+// sqrDistance = a + 2 * d + f;
+// } else {
+// s = -d / a;
+// sqrDistance = d * s + f;
+// }
+// }
+// } else {
+// // region 0
+// invDet = 1 / det;
+// s = s * invDet;
+// t = t * invDet;
+// sqrDistance = s * (a * s + b * t + 2 * d) + t * (b * s + c * t + 2 * e) + f;
+// }
+// }
+// } else {
+// if (s < 0) {
+// // % region 2
+// tmp0 = b + d;
+// tmp1 = c + e;
+// if (tmp1 > tmp0) { //% minimum on edge s+t=1
+// numer = tmp1 - tmp0;
+// denom = a - 2 * b + c;
+// if (numer >= denom) {
+// s = 1;
+// t = 0;
+// sqrDistance = a + 2 * d + f;
+// } else {
+// s = numer / denom;
+// t = 1 - s;
+// sqrDistance = s * (a * s + b * t + 2 * d) + t * (b * s + c * t + 2 * e) + f;
+// }
+// } else
+// // % minimum on edge s=0
+// s = 0;
+// if (tmp1 <= 0) {
+// t = 1;
+// sqrDistance = c + 2 * e + f;
+// } else {
+// if (e >= 0) {
+// t = 0;
+// sqrDistance = f;
+// } else {
+// t = -e / c;
+// sqrDistance = e * t + f;
+// }
+// }
+// } //end % of region 2
+// else {
+// if (t < 0) {
+// // %region6
+// tmp0 = b + e;
+// tmp1 = a + d;
+// if (tmp1 > tmp0) {
+// numer = tmp1 - tmp0;
+// denom = a - 2 * b + c;
+// if (numer >= denom) {
+// t = 1;
+// s = 0;
+// sqrDistance = c + 2 * e + f;
+// } else {
+// t = numer / denom;
+// s = 1 - t;
+// sqrDistance = s * (a * s + b * t + 2 * d) + t * (b * s + c * t + 2 * e) + f;
+// }
+// } else {
+// t = 0;
+// if (tmp1 <= 0) {
+// s = 1;
+// sqrDistance = a + 2 * d + f;
+// } else {
+// if (d >= 0) {
+// s = 0;
+// sqrDistance = f;
+// } else {
+// s = -d / a;
+// sqrDistance = d * s + f;
+// }
+// }
+// } // % end region 6
+// } else {
+// //% region 1
+// numer = c + e - b - d;
+// if (numer <= 0) {
+// s = 0;
+// t = 1;
+// sqrDistance = c + 2 * e + f;
+// } else {
+// denom = a - 2 * b + c;
+// if (numer >= denom) {
+// s = 1;
+// t = 0;
+// sqrDistance = a + 2 * d + f;
+// } else {
+// s = numer / denom;
+// t = 1 - s;
+// sqrDistance = s * (a * s + b * t + 2 * d) + t * (b * s + c * t + 2 * e) + f;
+// }
+// } //% end of region 1
+// }
+// }
+// }
//
-// // % account for numerical round-off error
-// if (sqrDistance < 0) {
-// sqrDistance = 0;
-// }
+// // % account for numerical round-off error
+// if (sqrDistance < 0) {
+// sqrDistance = 0;
+// }
//
-// dist = sqrt(sqrDistance);
+// dist = sqrt(sqrDistance);
//
-// // closest point
-// CP = B + s * E0 + t * E1;
+// // closest point
+// CP = B + s * E0 + t * E1;
//
//}
/*
@@ -750,96 +750,96 @@ double PairTriSurf::memory_usage() {
*/
void PairTriSurf::PointTriangleDistance(const Vector3d sourcePosition, const Vector3d TRI0, const Vector3d TRI1,
- const Vector3d TRI2, Vector3d &CP, double &dist) {
-
- Vector3d edge0 = TRI1 - TRI0;
- Vector3d edge1 = TRI2 - TRI0;
- Vector3d v0 = TRI0 - sourcePosition;
-
- double a = edge0.dot(edge0);
- double b = edge0.dot(edge1);
- double c = edge1.dot(edge1);
- double d = edge0.dot(v0);
- double e = edge1.dot(v0);
-
- double det = a * c - b * b;
- double s = b * e - c * d;
- double t = b * d - a * e;
-
- if (s + t < det) {
- if (s < 0.f) {
- if (t < 0.f) {
- if (d < 0.f) {
- s = clamp(-d / a, 0.f, 1.f);
- t = 0.f;
- } else {
- s = 0.f;
- t = clamp(-e / c, 0.f, 1.f);
- }
- } else {
- s = 0.f;
- t = clamp(-e / c, 0.f, 1.f);
- }
- } else if (t < 0.f) {
- s = clamp(-d / a, 0.f, 1.f);
- t = 0.f;
- } else {
- float invDet = 1.f / det;
- s *= invDet;
- t *= invDet;
- }
- } else {
- if (s < 0.f) {
- float tmp0 = b + d;
- float tmp1 = c + e;
- if (tmp1 > tmp0) {
- float numer = tmp1 - tmp0;
- float denom = a - 2 * b + c;
- s = clamp(numer / denom, 0.f, 1.f);
- t = 1 - s;
- } else {
- t = clamp(-e / c, 0.f, 1.f);
- s = 0.f;
- }
- } else if (t < 0.f) {
- if (a + d > b + e) {
- float numer = c + e - b - d;
- float denom = a - 2 * b + c;
- s = clamp(numer / denom, 0.f, 1.f);
- t = 1 - s;
- } else {
- s = clamp(-e / c, 0.f, 1.f);
- t = 0.f;
- }
- } else {
- float numer = c + e - b - d;
- float denom = a - 2 * b + c;
- s = clamp(numer / denom, 0.f, 1.f);
- t = 1.f - s;
- }
- }
-
- CP = TRI0 + s * edge0 + t * edge1;
- dist = (CP - sourcePosition).norm();
+ const Vector3d TRI2, Vector3d &CP, double &dist) {
+
+ Vector3d edge0 = TRI1 - TRI0;
+ Vector3d edge1 = TRI2 - TRI0;
+ Vector3d v0 = TRI0 - sourcePosition;
+
+ double a = edge0.dot(edge0);
+ double b = edge0.dot(edge1);
+ double c = edge1.dot(edge1);
+ double d = edge0.dot(v0);
+ double e = edge1.dot(v0);
+
+ double det = a * c - b * b;
+ double s = b * e - c * d;
+ double t = b * d - a * e;
+
+ if (s + t < det) {
+ if (s < 0.f) {
+ if (t < 0.f) {
+ if (d < 0.f) {
+ s = clamp(-d / a, 0.f, 1.f);
+ t = 0.f;
+ } else {
+ s = 0.f;
+ t = clamp(-e / c, 0.f, 1.f);
+ }
+ } else {
+ s = 0.f;
+ t = clamp(-e / c, 0.f, 1.f);
+ }
+ } else if (t < 0.f) {
+ s = clamp(-d / a, 0.f, 1.f);
+ t = 0.f;
+ } else {
+ float invDet = 1.f / det;
+ s *= invDet;
+ t *= invDet;
+ }
+ } else {
+ if (s < 0.f) {
+ float tmp0 = b + d;
+ float tmp1 = c + e;
+ if (tmp1 > tmp0) {
+ float numer = tmp1 - tmp0;
+ float denom = a - 2 * b + c;
+ s = clamp(numer / denom, 0.f, 1.f);
+ t = 1 - s;
+ } else {
+ t = clamp(-e / c, 0.f, 1.f);
+ s = 0.f;
+ }
+ } else if (t < 0.f) {
+ if (a + d > b + e) {
+ float numer = c + e - b - d;
+ float denom = a - 2 * b + c;
+ s = clamp(numer / denom, 0.f, 1.f);
+ t = 1 - s;
+ } else {
+ s = clamp(-e / c, 0.f, 1.f);
+ t = 0.f;
+ }
+ } else {
+ float numer = c + e - b - d;
+ float denom = a - 2 * b + c;
+ s = clamp(numer / denom, 0.f, 1.f);
+ t = 1.f - s;
+ }
+ }
+
+ CP = TRI0 + s * edge0 + t * edge1;
+ dist = (CP - sourcePosition).norm();
}
double PairTriSurf::clamp(const double a, const double min, const double max) {
- if (a < min) {
- return min;
- } else if (a > max) {
- return max;
- } else {
- return a;
- }
+ if (a < min) {
+ return min;
+ } else if (a > max) {
+ return max;
+ } else {
+ return a;
+ }
}
void *PairTriSurf::extract(const char *str, int &i) {
- //printf("in PairTriSurf::extract\n");
- if (strcmp(str, "smd/tri_surface/stable_time_increment_ptr") == 0) {
- return (void *) &stable_time_increment;
- }
+ //printf("in PairTriSurf::extract\n");
+ if (strcmp(str, "smd/tri_surface/stable_time_increment_ptr") == 0) {
+ return (void *) &stable_time_increment;
+ }
- return NULL;
+ return NULL;
}
diff --git a/src/USER-SMD/pair_smd_ulsph.cpp b/src/USER-SMD/pair_smd_ulsph.cpp
index b983620a02..fcb5e7eeb0 100644
--- a/src/USER-SMD/pair_smd_ulsph.cpp
+++ b/src/USER-SMD/pair_smd_ulsph.cpp
@@ -58,65 +58,65 @@ using namespace Eigen;
#define FORMAT2 "\n.............................. %s \n"
PairULSPH::PairULSPH(LAMMPS *lmp) :
- Pair(lmp) {
-
- // per-type arrays
- Q1 = NULL;
- eos = viscosity = strength = NULL;
- c0_type = NULL;
- c0 = NULL;
- Lookup = NULL;
- artificial_stress = NULL;
- artificial_pressure = NULL;
-
- nmax = 0; // make sure no atom on this proc such that initial memory allocation is correct
- stressTensor = L = K = NULL;
- shepardWeight = NULL;
- smoothVel = NULL;
- numNeighs = NULL;
- F = NULL;
- rho = NULL;
- effm = NULL;
-
- velocity_gradient_required = false; // turn off computation of velocity gradient by default
- density_summation = velocity_gradient = false;
-
- comm_forward = 18; // this pair style communicates 18 doubles to ghost atoms
- updateFlag = 0;
+ Pair(lmp) {
+
+ // per-type arrays
+ Q1 = NULL;
+ eos = viscosity = strength = NULL;
+ c0_type = NULL;
+ c0 = NULL;
+ Lookup = NULL;
+ artificial_stress = NULL;
+ artificial_pressure = NULL;
+
+ nmax = 0; // make sure no atom on this proc such that initial memory allocation is correct
+ stressTensor = L = K = NULL;
+ shepardWeight = NULL;
+ smoothVel = NULL;
+ numNeighs = NULL;
+ F = NULL;
+ rho = NULL;
+ effm = NULL;
+
+ velocity_gradient_required = false; // turn off computation of velocity gradient by default
+ density_summation = velocity_gradient = false;
+
+ comm_forward = 18; // this pair style communicates 18 doubles to ghost atoms
+ updateFlag = 0;
}
/* ---------------------------------------------------------------------- */
PairULSPH::~PairULSPH() {
- if (allocated) {
- //printf("... deallocating\n");
- memory->destroy(Q1);
- memory->destroy(rho0);
- memory->destroy(eos);
- memory->destroy(viscosity);
- memory->destroy(strength);
- memory->destroy(c0_type);
- memory->destroy(Lookup);
- memory->destroy(artificial_pressure);
- memory->destroy(artificial_stress);
-
- delete[] onerad_dynamic;
- delete[] onerad_frozen;
- delete[] maxrad_dynamic;
- delete[] maxrad_frozen;
-
- delete[] K;
- delete[] shepardWeight;
- delete[] c0;
- delete[] smoothVel;
- delete[] stressTensor;
- delete[] L;
- delete[] numNeighs;
- delete[] F;
- delete[] rho;
- delete[] effm;
-
- }
+ if (allocated) {
+ //printf("... deallocating\n");
+ memory->destroy(Q1);
+ memory->destroy(rho0);
+ memory->destroy(eos);
+ memory->destroy(viscosity);
+ memory->destroy(strength);
+ memory->destroy(c0_type);
+ memory->destroy(Lookup);
+ memory->destroy(artificial_pressure);
+ memory->destroy(artificial_stress);
+
+ delete[] onerad_dynamic;
+ delete[] onerad_frozen;
+ delete[] maxrad_dynamic;
+ delete[] maxrad_frozen;
+
+ delete[] K;
+ delete[] shepardWeight;
+ delete[] c0;
+ delete[] smoothVel;
+ delete[] stressTensor;
+ delete[] L;
+ delete[] numNeighs;
+ delete[] F;
+ delete[] rho;
+ delete[] effm;
+
+ }
}
/* ----------------------------------------------------------------------
@@ -127,80 +127,80 @@ PairULSPH::~PairULSPH() {
---------------------------------------------------------------------- */
void PairULSPH::PreCompute_DensitySummation() {
- double *radius = atom->radius;
- double **x = atom->x;
- double *rmass = atom->rmass;
- int *type = atom->type;
- int *ilist, *jlist, *numneigh;
- int **firstneigh;
- int nlocal = atom->nlocal;
- int inum, jnum, ii, jj, i, itype, jtype, j;
- double h, irad, hsq, rSq, wf;
- Vector3d dx, xi, xj;
-
- // set up neighbor list variables
- inum = list->inum;
- ilist = list->ilist;
- numneigh = list->numneigh;
- firstneigh = list->firstneigh;
-
- // zero accumulators
- for (i = 0; i < nlocal; i++) {
- rho[i] = 0.0;
- //shepardWeight[i] = 0.0;
- }
-
- /*
- * only recompute mass density if density summation is used.
- * otherwise, change in mass density is time-integrated
- */
- for (i = 0; i < nlocal; i++) {
- itype = type[i];
- if (setflag[itype][itype] == 1) {
- // initialize particle density with self-contribution.
- h = 2.0 * radius[i];
- hsq = h * h;
- Poly6Kernel(hsq, h, 0.0, domain->dimension, wf);
- rho[i] = wf * rmass[i]; // / shepardWeight[i];
- //printf("SIC to rho is %f\n", rho[i]);
- }
- }
-
- for (ii = 0; ii < inum; ii++) {
- i = ilist[ii];
- itype = type[i];
- jlist = firstneigh[i];
- jnum = numneigh[i];
- irad = radius[i];
-
- xi << x[i][0], x[i][1], x[i][2];
-
- for (jj = 0; jj < jnum; jj++) {
- j = jlist[jj];
- j &= NEIGHMASK;
-
- xj << x[j][0], x[j][1], x[j][2];
- dx = xj - xi;
- rSq = dx.squaredNorm();
- h = irad + radius[j];
- hsq = h * h;
- if (rSq < hsq) {
-
- jtype = type[j];
- Poly6Kernel(hsq, h, rSq, domain->dimension, wf);
-
- if (setflag[itype][itype] == 1) {
- rho[i] += wf * rmass[j]; // / shepardWeight[i];
- }
-
- if (j < nlocal) {
- if (setflag[jtype][jtype] == 1) {
- rho[j] += wf * rmass[i]; // / shepardWeight[j];
- }
- }
- } // end if check distance
- } // end loop over j
- } // end loop over i
+ double *radius = atom->radius;
+ double **x = atom->x;
+ double *rmass = atom->rmass;
+ int *type = atom->type;
+ int *ilist, *jlist, *numneigh;
+ int **firstneigh;
+ int nlocal = atom->nlocal;
+ int inum, jnum, ii, jj, i, itype, jtype, j;
+ double h, irad, hsq, rSq, wf;
+ Vector3d dx, xi, xj;
+
+ // set up neighbor list variables
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
+
+ // zero accumulators
+ for (i = 0; i < nlocal; i++) {
+ rho[i] = 0.0;
+ //shepardWeight[i] = 0.0;
+ }
+
+ /*
+ * only recompute mass density if density summation is used.
+ * otherwise, change in mass density is time-integrated
+ */
+ for (i = 0; i < nlocal; i++) {
+ itype = type[i];
+ if (setflag[itype][itype] == 1) {
+ // initialize particle density with self-contribution.
+ h = 2.0 * radius[i];
+ hsq = h * h;
+ Poly6Kernel(hsq, h, 0.0, domain->dimension, wf);
+ rho[i] = wf * rmass[i]; // / shepardWeight[i];
+ //printf("SIC to rho is %f\n", rho[i]);
+ }
+ }
+
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+ itype = type[i];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+ irad = radius[i];
+
+ xi << x[i][0], x[i][1], x[i][2];
+
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
+ j &= NEIGHMASK;
+
+ xj << x[j][0], x[j][1], x[j][2];
+ dx = xj - xi;
+ rSq = dx.squaredNorm();
+ h = irad + radius[j];
+ hsq = h * h;
+ if (rSq < hsq) {
+
+ jtype = type[j];
+ Poly6Kernel(hsq, h, rSq, domain->dimension, wf);
+
+ if (setflag[itype][itype] == 1) {
+ rho[i] += wf * rmass[j]; // / shepardWeight[i];
+ }
+
+ if (j < nlocal) {
+ if (setflag[jtype][jtype] == 1) {
+ rho[j] += wf * rmass[i]; // / shepardWeight[j];
+ }
+ }
+ } // end if check distance
+ } // end loop over j
+ } // end loop over i
}
/* ----------------------------------------------------------------------
@@ -211,427 +211,427 @@ void PairULSPH::PreCompute_DensitySummation() {
---------------------------------------------------------------------- */
void PairULSPH::PreCompute() {
- double **atom_data9 = atom->smd_data_9;
- double *radius = atom->radius;
- double **x = atom->x;
- double **x0 = atom->x0;
- double **v = atom->vest;
- double *vfrac = atom->vfrac;
- int *type = atom->type;
- int *ilist, *jlist, *numneigh;
- int **firstneigh;
- int nlocal = atom->nlocal;
- int inum, jnum, ii, jj, i, itype, j, idim;
- double wfd, h, irad, r, rSq, wf, ivol, jvol;
- Vector3d dx, dv, g, du;
- Matrix3d Ktmp, Ltmp, Ftmp, K3di, D;
- Vector3d xi, xj, vi, vj, x0i, x0j, dx0;
- Matrix2d K2di, K2d;
-
- // zero accumulators
- for (i = 0; i < nlocal; i++) {
- itype = type[i];
- if (setflag[itype][itype]) {
- if (gradient_correction_flag) {
- K[i].setZero();
- } else {
- K[i].setIdentity();
- }
- L[i].setZero();
- F[i].setZero();
- }
- }
-
- // set up neighbor list variables
- inum = list->inum;
- ilist = list->ilist;
- numneigh = list->numneigh;
- firstneigh = list->firstneigh;
-
- for (ii = 0; ii < inum; ii++) {
- i = ilist[ii];
- itype = type[i];
- jlist = firstneigh[i];
- jnum = numneigh[i];
- irad = radius[i];
- ivol = vfrac[i];
-
- // initialize Eigen data structures from LAMMPS data structures
- for (idim = 0; idim < 3; idim++) {
- x0i(idim) = x0[i][idim];
- xi(idim) = x[i][idim];
- vi(idim) = v[i][idim];
- }
-
- for (jj = 0; jj < jnum; jj++) {
- j = jlist[jj];
- j &= NEIGHMASK;
-
- for (idim = 0; idim < 3; idim++) {
- x0j(idim) = x0[j][idim];
- xj(idim) = x[j][idim];
- vj(idim) = v[j][idim];
- }
-
- dx = xj - xi;
-
- rSq = dx.squaredNorm();
- h = irad + radius[j];
- if (rSq < h * h) {
-
- r = sqrt(rSq);
- jvol = vfrac[j];
-
- // distance vectors in current and reference configuration, velocity difference
- dv = vj - vi;
- dx0 = x0j - x0i;
-
- // kernel and derivative
- spiky_kernel_and_derivative(h, r, domain->dimension, wf, wfd);
- //barbara_kernel_and_derivative(h, r, domain->dimension, wf, wfd);
-
- // uncorrected kernel gradient
- g = (wfd / r) * dx;
-
- /* build correction matrix for kernel derivatives */
- if (gradient_correction_flag) {
- Ktmp = -g * dx.transpose();
- K[i] += jvol * Ktmp;
- }
-
- // velocity gradient L
- Ltmp = -dv * g.transpose();
- L[i] += jvol * Ltmp;
-
- // deformation gradient F in Eulerian frame
- du = dx - dx0;
- Ftmp = dv * g.transpose();
- F[i] += jvol * Ftmp;
-
- if (j < nlocal) {
-
- if (gradient_correction_flag) {
- K[j] += ivol * Ktmp;
- }
-
- L[j] += ivol * Ltmp;
- F[j] += ivol * Ftmp;
- }
- } // end if check distance
- } // end loop over j
- } // end loop over i
-
- /*
- * invert shape matrix and compute corrected quantities
- */
-
- for (i = 0; i < nlocal; i++) {
- itype = type[i];
- if (setflag[itype][itype]) {
- if (gradient_correction_flag) {
- pseudo_inverse_SVD(K[i]);
- K[i] = LimitEigenvalues(K[i], 2.0);
- L[i] *= K[i];
- F[i] *= K[i];
- } // end if (gradient_correction[itype]) {
-
- /*
- * accumulate strain increments
- * we abuse the atom array "atom_data_9" for this purpose, which was originally designed to hold the deformation gradient.
- */
- D = update->dt * 0.5 * (L[i] + L[i].transpose());
- atom_data9[i][0] += D(0, 0); // xx
- atom_data9[i][1] += D(1, 1); // yy
- atom_data9[i][2] += D(2, 2); // zz
- atom_data9[i][3] += D(0, 1); // xy
- atom_data9[i][4] += D(0, 2); // xz
- atom_data9[i][5] += D(1, 2); // yz
-
- } // end if (setflag[itype][itype])
- } // end loop over i = 0 to nlocal
+ double **atom_data9 = atom->smd_data_9;
+ double *radius = atom->radius;
+ double **x = atom->x;
+ double **x0 = atom->x0;
+ double **v = atom->vest;
+ double *vfrac = atom->vfrac;
+ int *type = atom->type;
+ int *ilist, *jlist, *numneigh;
+ int **firstneigh;
+ int nlocal = atom->nlocal;
+ int inum, jnum, ii, jj, i, itype, j, idim;
+ double wfd, h, irad, r, rSq, wf, ivol, jvol;
+ Vector3d dx, dv, g, du;
+ Matrix3d Ktmp, Ltmp, Ftmp, K3di, D;
+ Vector3d xi, xj, vi, vj, x0i, x0j, dx0;
+ Matrix2d K2di, K2d;
+
+ // zero accumulators
+ for (i = 0; i < nlocal; i++) {
+ itype = type[i];
+ if (setflag[itype][itype]) {
+ if (gradient_correction_flag) {
+ K[i].setZero();
+ } else {
+ K[i].setIdentity();
+ }
+ L[i].setZero();
+ F[i].setZero();
+ }
+ }
+
+ // set up neighbor list variables
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
+
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+ itype = type[i];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+ irad = radius[i];
+ ivol = vfrac[i];
+
+ // initialize Eigen data structures from LAMMPS data structures
+ for (idim = 0; idim < 3; idim++) {
+ x0i(idim) = x0[i][idim];
+ xi(idim) = x[i][idim];
+ vi(idim) = v[i][idim];
+ }
+
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
+ j &= NEIGHMASK;
+
+ for (idim = 0; idim < 3; idim++) {
+ x0j(idim) = x0[j][idim];
+ xj(idim) = x[j][idim];
+ vj(idim) = v[j][idim];
+ }
+
+ dx = xj - xi;
+
+ rSq = dx.squaredNorm();
+ h = irad + radius[j];
+ if (rSq < h * h) {
+
+ r = sqrt(rSq);
+ jvol = vfrac[j];
+
+ // distance vectors in current and reference configuration, velocity difference
+ dv = vj - vi;
+ dx0 = x0j - x0i;
+
+ // kernel and derivative
+ spiky_kernel_and_derivative(h, r, domain->dimension, wf, wfd);
+ //barbara_kernel_and_derivative(h, r, domain->dimension, wf, wfd);
+
+ // uncorrected kernel gradient
+ g = (wfd / r) * dx;
+
+ /* build correction matrix for kernel derivatives */
+ if (gradient_correction_flag) {
+ Ktmp = -g * dx.transpose();
+ K[i] += jvol * Ktmp;
+ }
+
+ // velocity gradient L
+ Ltmp = -dv * g.transpose();
+ L[i] += jvol * Ltmp;
+
+ // deformation gradient F in Eulerian frame
+ du = dx - dx0;
+ Ftmp = dv * g.transpose();
+ F[i] += jvol * Ftmp;
+
+ if (j < nlocal) {
+
+ if (gradient_correction_flag) {
+ K[j] += ivol * Ktmp;
+ }
+
+ L[j] += ivol * Ltmp;
+ F[j] += ivol * Ftmp;
+ }
+ } // end if check distance
+ } // end loop over j
+ } // end loop over i
+
+ /*
+ * invert shape matrix and compute corrected quantities
+ */
+
+ for (i = 0; i < nlocal; i++) {
+ itype = type[i];
+ if (setflag[itype][itype]) {
+ if (gradient_correction_flag) {
+ pseudo_inverse_SVD(K[i]);
+ K[i] = LimitEigenvalues(K[i], 2.0);
+ L[i] *= K[i];
+ F[i] *= K[i];
+ } // end if (gradient_correction[itype]) {
+
+ /*
+ * accumulate strain increments
+ * we abuse the atom array "atom_data_9" for this purpose, which was originally designed to hold the deformation gradient.
+ */
+ D = update->dt * 0.5 * (L[i] + L[i].transpose());
+ atom_data9[i][0] += D(0, 0); // xx
+ atom_data9[i][1] += D(1, 1); // yy
+ atom_data9[i][2] += D(2, 2); // zz
+ atom_data9[i][3] += D(0, 1); // xy
+ atom_data9[i][4] += D(0, 2); // xz
+ atom_data9[i][5] += D(1, 2); // yz
+
+ } // end if (setflag[itype][itype])
+ } // end loop over i = 0 to nlocal
}
/* ---------------------------------------------------------------------- */
void PairULSPH::compute(int eflag, int vflag) {
- double **x = atom->x;
- double **v = atom->vest;
- double **vint = atom->v; // Velocity-Verlet algorithm velocities
- double **f = atom->f;
- double *vfrac = atom->vfrac;
- double *de = atom->de;
- double *rmass = atom->rmass;
- double *radius = atom->radius;
- double *contact_radius = atom->contact_radius;
- double **atom_data9 = atom->smd_data_9;
-
- int *type = atom->type;
- int nlocal = atom->nlocal;
- int i, j, ii, jj, jnum, itype, jtype, iDim, inum;
- double r, wf, wfd, h, rSq, ivol, jvol;
- double mu_ij, c_ij, rho_ij;
- double delVdotDelR, visc_magnitude, deltaE;
- int *ilist, *jlist, *numneigh;
- int **firstneigh;
- Vector3d fi, fj, dx, dv, f_stress, g, vinti, vintj, dvint;
- Vector3d xi, xj, vi, vj, f_visc, sumForces, f_stress_new;
- Vector3d gamma, f_hg, dx0, du_est, du;
- double r_ref, weight, p;
- //int periodic = (domain->xperiodic || domain->yperiodic || domain->zperiodic);
-
- double ini_dist;
- Matrix3d S, D, V, eye;
- eye.setIdentity();
- int k;
- SelfAdjointEigenSolver < Matrix3d > es;
-
- if (eflag || vflag)
- ev_setup(eflag, vflag);
- else
- evflag = vflag_fdotr = 0;
-
- if (atom->nmax > nmax) {
+ double **x = atom->x;
+ double **v = atom->vest;
+ double **vint = atom->v; // Velocity-Verlet algorithm velocities
+ double **f = atom->f;
+ double *vfrac = atom->vfrac;
+ double *de = atom->de;
+ double *rmass = atom->rmass;
+ double *radius = atom->radius;
+ double *contact_radius = atom->contact_radius;
+ double **atom_data9 = atom->smd_data_9;
+
+ int *type = atom->type;
+ int nlocal = atom->nlocal;
+ int i, j, ii, jj, jnum, itype, jtype, iDim, inum;
+ double r, wf, wfd, h, rSq, ivol, jvol;
+ double mu_ij, c_ij, rho_ij;
+ double delVdotDelR, visc_magnitude, deltaE;
+ int *ilist, *jlist, *numneigh;
+ int **firstneigh;
+ Vector3d fi, fj, dx, dv, f_stress, g, vinti, vintj, dvint;
+ Vector3d xi, xj, vi, vj, f_visc, sumForces, f_stress_new;
+ Vector3d gamma, f_hg, dx0, du_est, du;
+ double r_ref, weight, p;
+ //int periodic = (domain->xperiodic || domain->yperiodic || domain->zperiodic);
+
+ double ini_dist;
+ Matrix3d S, D, V, eye;
+ eye.setIdentity();
+ int k;
+ SelfAdjointEigenSolver < Matrix3d > es;
+
+ if (eflag || vflag)
+ ev_setup(eflag, vflag);
+ else
+ evflag = vflag_fdotr = 0;
+
+ if (atom->nmax > nmax) {
//printf("... allocating in compute with nmax = %d\n", atom->nmax);
- nmax = atom->nmax;
- delete[] K;
- K = new Matrix3d[nmax];
- delete[] shepardWeight;
- shepardWeight = new double[nmax];
- delete[] c0;
- c0 = new double[nmax];
- delete[] smoothVel;
- smoothVel = new Vector3d[nmax];
- delete[] stressTensor;
- stressTensor = new Matrix3d[nmax];
- delete[] L;
- L = new Matrix3d[nmax];
- delete[] numNeighs;
- numNeighs = new int[nmax];
- delete[] F;
- F = new Matrix3d[nmax];
- delete[] rho;
- rho = new double[nmax];
- delete[] effm;
- effm = new double[nmax];
- }
+ nmax = atom->nmax;
+ delete[] K;
+ K = new Matrix3d[nmax];
+ delete[] shepardWeight;
+ shepardWeight = new double[nmax];
+ delete[] c0;
+ c0 = new double[nmax];
+ delete[] smoothVel;
+ smoothVel = new Vector3d[nmax];
+ delete[] stressTensor;
+ stressTensor = new Matrix3d[nmax];
+ delete[] L;
+ L = new Matrix3d[nmax];
+ delete[] numNeighs;
+ numNeighs = new int[nmax];
+ delete[] F;
+ F = new Matrix3d[nmax];
+ delete[] rho;
+ rho = new double[nmax];
+ delete[] effm;
+ effm = new double[nmax];
+ }
// zero accumulators
- for (i = 0; i < nlocal; i++) {
- shepardWeight[i] = 0.0;
- smoothVel[i].setZero();
- numNeighs[i] = 0;
-
- h = 2.0 * radius[i];
- r = 0.0;
- spiky_kernel_and_derivative(h, r, domain->dimension, wf, wfd);
- }
-
- /*
- * if this is the very first step, zero the array which holds the accumulated strain
- */
- if (update->ntimestep == 0) {
- for (i = 0; i < nlocal; i++) {
- itype = type[i];
- if (setflag[itype][itype]) {
- for (j = 0; j < 9; j++) {
- atom_data9[i][j] = 0.0;
- }
- }
- }
- }
-
- if (density_summation) {
- //printf("dens summ\n");
- PreCompute_DensitySummation();
-
- for (i = 0; i < nlocal; i++) { //compute volumes from rho
- itype = type[i];
- if (setflag[itype][itype]) {
- vfrac[i] = rmass[i] / rho[i];
- }
- }
-
- }
-
- if (velocity_gradient) {
- PairULSPH::PreCompute(); // get velocity gradient and kernel gradient correction
- }
-
- PairULSPH::AssembleStressTensor();
-
- /*
- * QUANTITIES ABOVE HAVE ONLY BEEN CALCULATED FOR NLOCAL PARTICLES.
- * NEED TO DO A FORWARD COMMUNICATION TO GHOST ATOMS NOW
- */
- comm->forward_comm_pair(this);
-
- updateFlag = 0;
-
- /*
- * iterate over pairs of particles i, j and assign forces using pre-computed pressure
- */
+ for (i = 0; i < nlocal; i++) {
+ shepardWeight[i] = 0.0;
+ smoothVel[i].setZero();
+ numNeighs[i] = 0;
+
+ h = 2.0 * radius[i];
+ r = 0.0;
+ spiky_kernel_and_derivative(h, r, domain->dimension, wf, wfd);
+ }
+
+ /*
+ * if this is the very first step, zero the array which holds the accumulated strain
+ */
+ if (update->ntimestep == 0) {
+ for (i = 0; i < nlocal; i++) {
+ itype = type[i];
+ if (setflag[itype][itype]) {
+ for (j = 0; j < 9; j++) {
+ atom_data9[i][j] = 0.0;
+ }
+ }
+ }
+ }
+
+ if (density_summation) {
+ //printf("dens summ\n");
+ PreCompute_DensitySummation();
+
+ for (i = 0; i < nlocal; i++) { //compute volumes from rho
+ itype = type[i];
+ if (setflag[itype][itype]) {
+ vfrac[i] = rmass[i] / rho[i];
+ }
+ }
+
+ }
+
+ if (velocity_gradient) {
+ PairULSPH::PreCompute(); // get velocity gradient and kernel gradient correction
+ }
+
+ PairULSPH::AssembleStressTensor();
+
+ /*
+ * QUANTITIES ABOVE HAVE ONLY BEEN CALCULATED FOR NLOCAL PARTICLES.
+ * NEED TO DO A FORWARD COMMUNICATION TO GHOST ATOMS NOW
+ */
+ comm->forward_comm_pair(this);
+
+ updateFlag = 0;
+
+ /*
+ * iterate over pairs of particles i, j and assign forces using pre-computed pressure
+ */
// set up neighbor list variables
- inum = list->inum;
- ilist = list->ilist;
- numneigh = list->numneigh;
- firstneigh = list->firstneigh;
-
- for (ii = 0; ii < inum; ii++) {
- i = ilist[ii];
- itype = type[i];
- jlist = firstneigh[i];
- jnum = numneigh[i];
- ivol = vfrac[i];
-
- // initialize Eigen data structures from LAMMPS data structures
- for (iDim = 0; iDim < 3; iDim++) {
- xi(iDim) = x[i][iDim];
- vi(iDim) = v[i][iDim];
- vinti(iDim) = vint[i][iDim];
- }
-
- for (jj = 0; jj < jnum; jj++) {
- j = jlist[jj];
- j &= NEIGHMASK;
-
- xj(0) = x[j][0];
- xj(1) = x[j][1];
- xj(2) = x[j][2];
-
- dx = xj - xi;
- rSq = dx.squaredNorm();
- h = radius[i] + radius[j];
- if (rSq < h * h) {
-
- // initialize Eigen data structures from LAMMPS data structures
- for (iDim = 0; iDim < 3; iDim++) {
- vj(iDim) = v[j][iDim];
- vintj(iDim) = vint[j][iDim];
- }
-
- r = sqrt(rSq);
- jtype = type[j];
- jvol = vfrac[j];
-
- // distance vectors in current and reference configuration, velocity difference
- dv = vj - vi;
- dvint = vintj - vinti;
-
- // kernel and derivative
- spiky_kernel_and_derivative(h, r, domain->dimension, wf, wfd);
- //barbara_kernel_and_derivative(h, r, domain->dimension, wf, wfd);
-
- // uncorrected kernel gradient
- g = (wfd / r) * dx;
-
- delVdotDelR = dx.dot(dv) / (r + 0.1 * h); // project relative velocity onto unit particle distance vector [m/s]
-
- S = stressTensor[i] + stressTensor[j];
-
- if (artificial_pressure[itype][jtype] > 0.0) {
- p = S.trace();
- if (p > 0.0) { // we are in tension
- r_ref = contact_radius[i] + contact_radius[j];
- weight = Kernel_Cubic_Spline(r, h) / Kernel_Cubic_Spline(r_ref, h);
- weight = pow(weight, 4.0);
- S -= artificial_pressure[itype][jtype] * weight * p * eye;
- }
- }
-
- /*
- * artificial stress to control tensile instability
- * Only works if particles are uniformly spaced initially.
- */
- if (artificial_stress[itype][jtype] > 0.0) {
- ini_dist = contact_radius[i] + contact_radius[j];
- weight = Kernel_Cubic_Spline(r, h) / Kernel_Cubic_Spline(ini_dist, h);
- weight = pow(weight, 4.0);
-
- es.compute(S);
- D = es.eigenvalues().asDiagonal();
- for (k = 0; k < 3; k++) {
- if (D(k, k) > 0.0) {
- D(k, k) -= weight * artificial_stress[itype][jtype] * D(k, k);
- }
- }
- V = es.eigenvectors();
- S = V * D * V.inverse();
- }
-
- // compute forces
- f_stress = -ivol * jvol * S * g; // DO NOT TOUCH SIGN
-
- /*
- * artificial viscosity -- alpha is dimensionless
- * MonaghanBalsara form of the artificial viscosity
- */
-
- c_ij = 0.5 * (c0[i] + c0[j]);
- LimitDoubleMagnitude(delVdotDelR, 1.1 * c_ij);
-
- mu_ij = h * delVdotDelR / (r + 0.1 * h); // units: [m * m/s / m = m/s]
- rho_ij = 0.5 * (rmass[i] / ivol + rmass[j] / jvol);
- visc_magnitude = 0.5 * (Q1[itype] + Q1[jtype]) * c_ij * mu_ij / rho_ij;
- f_visc = -rmass[i] * rmass[j] * visc_magnitude * g;
-
- if ((Lookup[HOURGLASS_CONTROL_AMPLITUDE][itype] > 0.0) && (Lookup[HOURGLASS_CONTROL_AMPLITUDE][jtype] > 0.0)) {
- f_hg = ComputeHourglassForce(i, itype, j, jtype, dv, dx, g, c_ij, mu_ij, rho_ij);
-
- } else {
- f_hg.setZero();
- }
-
- sumForces = f_stress + f_visc + f_hg;
-
- // energy rate -- project velocity onto force vector
- deltaE = sumForces.dot(dv);
-
- // apply forces to pair of particles
- f[i][0] += sumForces(0);
- f[i][1] += sumForces(1);
- f[i][2] += sumForces(2);
- de[i] += deltaE;
-
- // accumulate smooth velocities
- shepardWeight[i] += jvol * wf;
- smoothVel[i] += jvol * wf * dvint;
- numNeighs[i] += 1;
-
- if (j < nlocal) {
- f[j][0] -= sumForces(0);
- f[j][1] -= sumForces(1);
- f[j][2] -= sumForces(2);
- de[j] += deltaE;
-
- shepardWeight[j] += ivol * wf;
- smoothVel[j] -= ivol * wf * dvint;
- numNeighs[j] += 1;
- }
-
- // tally atomistic stress tensor
- if (evflag) {
- ev_tally_xyz(i, j, nlocal, 0, 0.0, 0.0, sumForces(0), sumForces(1), sumForces(2), dx(0), dx(1), dx(2));
- }
- }
-
- }
- }
-
- for (i = 0; i < nlocal; i++) {
- itype = type[i];
- if (setflag[itype][itype] == 1) {
- if (shepardWeight[i] != 0.0) {
- smoothVel[i] /= shepardWeight[i];
- } else {
- smoothVel[i].setZero();
- }
- } // end check if particle is SPH-type
- } // end loop over i = 0 to nlocal
-
- if (vflag_fdotr)
- virial_fdotr_compute();
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
+
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+ itype = type[i];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+ ivol = vfrac[i];
+
+ // initialize Eigen data structures from LAMMPS data structures
+ for (iDim = 0; iDim < 3; iDim++) {
+ xi(iDim) = x[i][iDim];
+ vi(iDim) = v[i][iDim];
+ vinti(iDim) = vint[i][iDim];
+ }
+
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
+ j &= NEIGHMASK;
+
+ xj(0) = x[j][0];
+ xj(1) = x[j][1];
+ xj(2) = x[j][2];
+
+ dx = xj - xi;
+ rSq = dx.squaredNorm();
+ h = radius[i] + radius[j];
+ if (rSq < h * h) {
+
+ // initialize Eigen data structures from LAMMPS data structures
+ for (iDim = 0; iDim < 3; iDim++) {
+ vj(iDim) = v[j][iDim];
+ vintj(iDim) = vint[j][iDim];
+ }
+
+ r = sqrt(rSq);
+ jtype = type[j];
+ jvol = vfrac[j];
+
+ // distance vectors in current and reference configuration, velocity difference
+ dv = vj - vi;
+ dvint = vintj - vinti;
+
+ // kernel and derivative
+ spiky_kernel_and_derivative(h, r, domain->dimension, wf, wfd);
+ //barbara_kernel_and_derivative(h, r, domain->dimension, wf, wfd);
+
+ // uncorrected kernel gradient
+ g = (wfd / r) * dx;
+
+ delVdotDelR = dx.dot(dv) / (r + 0.1 * h); // project relative velocity onto unit particle distance vector [m/s]
+
+ S = stressTensor[i] + stressTensor[j];
+
+ if (artificial_pressure[itype][jtype] > 0.0) {
+ p = S.trace();
+ if (p > 0.0) { // we are in tension
+ r_ref = contact_radius[i] + contact_radius[j];
+ weight = Kernel_Cubic_Spline(r, h) / Kernel_Cubic_Spline(r_ref, h);
+ weight = pow(weight, 4.0);
+ S -= artificial_pressure[itype][jtype] * weight * p * eye;
+ }
+ }
+
+ /*
+ * artificial stress to control tensile instability
+ * Only works if particles are uniformly spaced initially.
+ */
+ if (artificial_stress[itype][jtype] > 0.0) {
+ ini_dist = contact_radius[i] + contact_radius[j];
+ weight = Kernel_Cubic_Spline(r, h) / Kernel_Cubic_Spline(ini_dist, h);
+ weight = pow(weight, 4.0);
+
+ es.compute(S);
+ D = es.eigenvalues().asDiagonal();
+ for (k = 0; k < 3; k++) {
+ if (D(k, k) > 0.0) {
+ D(k, k) -= weight * artificial_stress[itype][jtype] * D(k, k);
+ }
+ }
+ V = es.eigenvectors();
+ S = V * D * V.inverse();
+ }
+
+ // compute forces
+ f_stress = -ivol * jvol * S * g; // DO NOT TOUCH SIGN
+
+ /*
+ * artificial viscosity -- alpha is dimensionless
+ * MonaghanBalsara form of the artificial viscosity
+ */
+
+ c_ij = 0.5 * (c0[i] + c0[j]);
+ LimitDoubleMagnitude(delVdotDelR, 1.1 * c_ij);
+
+ mu_ij = h * delVdotDelR / (r + 0.1 * h); // units: [m * m/s / m = m/s]
+ rho_ij = 0.5 * (rmass[i] / ivol + rmass[j] / jvol);
+ visc_magnitude = 0.5 * (Q1[itype] + Q1[jtype]) * c_ij * mu_ij / rho_ij;
+ f_visc = -rmass[i] * rmass[j] * visc_magnitude * g;
+
+ if ((Lookup[HOURGLASS_CONTROL_AMPLITUDE][itype] > 0.0) && (Lookup[HOURGLASS_CONTROL_AMPLITUDE][jtype] > 0.0)) {
+ f_hg = ComputeHourglassForce(i, itype, j, jtype, dv, dx, g, c_ij, mu_ij, rho_ij);
+
+ } else {
+ f_hg.setZero();
+ }
+
+ sumForces = f_stress + f_visc + f_hg;
+
+ // energy rate -- project velocity onto force vector
+ deltaE = sumForces.dot(dv);
+
+ // apply forces to pair of particles
+ f[i][0] += sumForces(0);
+ f[i][1] += sumForces(1);
+ f[i][2] += sumForces(2);
+ de[i] += deltaE;
+
+ // accumulate smooth velocities
+ shepardWeight[i] += jvol * wf;
+ smoothVel[i] += jvol * wf * dvint;
+ numNeighs[i] += 1;
+
+ if (j < nlocal) {
+ f[j][0] -= sumForces(0);
+ f[j][1] -= sumForces(1);
+ f[j][2] -= sumForces(2);
+ de[j] += deltaE;
+
+ shepardWeight[j] += ivol * wf;
+ smoothVel[j] -= ivol * wf * dvint;
+ numNeighs[j] += 1;
+ }
+
+ // tally atomistic stress tensor
+ if (evflag) {
+ ev_tally_xyz(i, j, nlocal, 0, 0.0, 0.0, sumForces(0), sumForces(1), sumForces(2), dx(0), dx(1), dx(2));
+ }
+ }
+
+ }
+ }
+
+ for (i = 0; i < nlocal; i++) {
+ itype = type[i];
+ if (setflag[itype][itype] == 1) {
+ if (shepardWeight[i] != 0.0) {
+ smoothVel[i] /= shepardWeight[i];
+ } else {
+ smoothVel[i].setZero();
+ }
+ } // end check if particle is SPH-type
+ } // end loop over i = 0 to nlocal
+
+ if (vflag_fdotr)
+ virial_fdotr_compute();
}
@@ -640,189 +640,189 @@ void PairULSPH::compute(int eflag, int vflag) {
viscosity contributions.
------------------------------------------------------------------------- */
void PairULSPH::AssembleStressTensor() {
- double *radius = atom->radius;
- double *vfrac = atom->vfrac;
- double *rmass = atom->rmass;
- double *eff_plastic_strain = atom->eff_plastic_strain;
- double **tlsph_stress = atom->smd_stress;
- double *e = atom->e;
- int *type = atom->type;
- int i, itype;
- int nlocal = atom->nlocal;
- Matrix3d D, Ddev, W, V, sigma_diag;
- Matrix3d eye, stressRate, StressRateDevJaumann;
- Matrix3d sigmaInitial_dev, d_dev, sigmaFinal_dev, stressRateDev, oldStressDeviator, newStressDeviator;
- double plastic_strain_increment, yieldStress;
- double dt = update->dt;
- double vol, newPressure;
- double G_eff = 0.0; // effective shear modulus
- double K_eff; // effective bulk modulus
- double M, p_wave_speed;
- double rho, effectiveViscosity;
- Matrix3d deltaStressDev;
-
- dtCFL = 1.0e22;
- eye.setIdentity();
-
- for (i = 0; i < nlocal; i++) {
- itype = type[i];
- if (setflag[itype][itype] == 1) {
- newStressDeviator.setZero();
- newPressure = 0.0;
- stressTensor[i].setZero();
- vol = vfrac[i];
- rho = rmass[i] / vfrac[i];
- effectiveViscosity = 0.0;
- K_eff = 0.0;
- G_eff = 0.0;
-
- //printf("rho = %f\n", rho);
-
- switch (eos[itype]) {
- default:
- error->one(FLERR, "unknown EOS.");
- break;
- case NONE:
- c0[i] = 1.0;
- break;
- case EOS_TAIT:
- TaitEOS_density(Lookup[EOS_TAIT_EXPONENT][itype], Lookup[REFERENCE_SOUNDSPEED][itype],
- Lookup[REFERENCE_DENSITY][itype], rho, newPressure, c0[i]);
- //printf("new pressure =%f\n", newPressure);
-
- break;
- case EOS_PERFECT_GAS:
- PerfectGasEOS(Lookup[EOS_PERFECT_GAS_GAMMA][itype], vol, rmass[i], e[i], newPressure, c0[i]);
- break;
- case EOS_LINEAR:
- newPressure = Lookup[BULK_MODULUS][itype] * (rho / Lookup[REFERENCE_DENSITY][itype] - 1.0);
- //printf("p=%f, rho0=%f, rho=%f\n", newPressure, Lookup[REFERENCE_DENSITY][itype], rho);
- c0[i] = Lookup[REFERENCE_SOUNDSPEED][itype];
- break;
- }
-
- K_eff = c0[i] * c0[i] * rho; // effective bulk modulus
-
- /*
- * ******************************* STRENGTH MODELS ************************************************
- */
-
- if (strength[itype] != NONE) {
- /*
- * initial stress state: given by the unrotateted Cauchy stress.
- * Assemble Eigen 3d matrix from stored stress state
- */
- oldStressDeviator(0, 0) = tlsph_stress[i][0];
- oldStressDeviator(0, 1) = tlsph_stress[i][1];
- oldStressDeviator(0, 2) = tlsph_stress[i][2];
- oldStressDeviator(1, 1) = tlsph_stress[i][3];
- oldStressDeviator(1, 2) = tlsph_stress[i][4];
- oldStressDeviator(2, 2) = tlsph_stress[i][5];
- oldStressDeviator(1, 0) = oldStressDeviator(0, 1);
- oldStressDeviator(2, 0) = oldStressDeviator(0, 2);
- oldStressDeviator(2, 1) = oldStressDeviator(1, 2);
-
- D = 0.5 * (L[i] + L[i].transpose());
- W = 0.5 * (L[i] - L[i].transpose()); // spin tensor:: need this for Jaumann rate
- d_dev = Deviator(D);
-
- switch (strength[itype]) {
- default:
- error->one(FLERR, "unknown strength model.");
- break;
- case STRENGTH_LINEAR:
-
- // here in a version with pressure part
-// stressRateDev = Lookup[BULK_MODULUS][itype] * d_iso * eye + 2.0 * Lookup[SHEAR_MODULUS][itype] * d_dev;
-// c0[i] = Lookup[REFERENCE_SOUNDSPEED][itype];
-// newPressure = 0.0;
-
- // here only stress deviator
- stressRateDev = 2.0 * Lookup[SHEAR_MODULUS][itype] * d_dev;
- //cout << "stress rate deviator is " << endl << stressRateDev << endl;
- break;
-
- case STRENGTH_LINEAR_PLASTIC:
- yieldStress = Lookup[YIELD_STRENGTH][itype] + Lookup[HARDENING_PARAMETER][itype] * eff_plastic_strain[i];
- LinearPlasticStrength(Lookup[SHEAR_MODULUS][itype], yieldStress, oldStressDeviator, d_dev, dt,
- newStressDeviator, stressRateDev, plastic_strain_increment);
- eff_plastic_strain[i] += plastic_strain_increment;
-
- break;
- }
-
- //double m = effective_longitudinal_modulus(itype, dt, d_iso, p_rate, d_dev, stressRate_dev, damage);
-
- StressRateDevJaumann = stressRateDev - W * oldStressDeviator + oldStressDeviator * W;
- newStressDeviator = oldStressDeviator + dt * StressRateDevJaumann;
-
- tlsph_stress[i][0] = newStressDeviator(0, 0);
- tlsph_stress[i][1] = newStressDeviator(0, 1);
- tlsph_stress[i][2] = newStressDeviator(0, 2);
- tlsph_stress[i][3] = newStressDeviator(1, 1);
- tlsph_stress[i][4] = newStressDeviator(1, 2);
- tlsph_stress[i][5] = newStressDeviator(2, 2);
-
- // estimate effective shear modulus for time step stability
- deltaStressDev = oldStressDeviator - newStressDeviator;
- G_eff = effective_shear_modulus(d_dev, deltaStressDev, dt, itype);
-
- } // end if (strength[itype] != NONE)
-
- if (viscosity[itype] != NONE) {
- D = 0.5 * (L[i] + L[i].transpose());
- d_dev = Deviator(D);
-
- switch (viscosity[itype]) {
- default:
- error->one(FLERR, "unknown viscosity model.");
- break;
- case VISCOSITY_NEWTON:
- effectiveViscosity = Lookup[VISCOSITY_MU][itype];
-// double shear_rate = 2.0
-// * sqrt(d_dev(0, 1) * d_dev(0, 1) + d_dev(0, 2) * d_dev(0, 2) + d_dev(1, 2) * d_dev(1, 2)); // 3d
- //cout << "shear rate: " << shear_rate << endl;
- //effectiveViscosity = PA6_270C(shear_rate);
- //if (effectiveViscosity > 178.062e-6) {
- // printf("effective visc is %f\n", effectiveViscosity);
- //}
- newStressDeviator = 2.0 * effectiveViscosity * d_dev; // newton original
- //cout << "this is Ddev " << endl << d_dev << endl << endl;
- break;
- }
- } // end if (viscosity[itype] != NONE)
-
- /*
- * assemble stress Tensor from pressure and deviatoric parts
- */
-
- stressTensor[i] = -newPressure * eye + newStressDeviator;
-
- /*
- * stable timestep based on speed-of-sound
- */
-
- M = K_eff + 4.0 * G_eff / 3.0;
- p_wave_speed = sqrt(M / rho);
- effm[i] = G_eff;
- dtCFL = MIN(2 * radius[i] / p_wave_speed, dtCFL);
-
- /*
- * stable timestep based on viscosity
- */
- if (viscosity[itype] != NONE) {
- dtCFL = MIN(4 * radius[i] * radius[i] * rho / effectiveViscosity, dtCFL);
- }
-
- /*
- * kernel gradient correction
- */
- if (gradient_correction_flag) {
- stressTensor[i] *= K[i];
- }
- }
- // end if (setflag[itype][itype] == 1)
- } // end loop over nlocal
+ double *radius = atom->radius;
+ double *vfrac = atom->vfrac;
+ double *rmass = atom->rmass;
+ double *eff_plastic_strain = atom->eff_plastic_strain;
+ double **tlsph_stress = atom->smd_stress;
+ double *e = atom->e;
+ int *type = atom->type;
+ int i, itype;
+ int nlocal = atom->nlocal;
+ Matrix3d D, Ddev, W, V, sigma_diag;
+ Matrix3d eye, stressRate, StressRateDevJaumann;
+ Matrix3d sigmaInitial_dev, d_dev, sigmaFinal_dev, stressRateDev, oldStressDeviator, newStressDeviator;
+ double plastic_strain_increment, yieldStress;
+ double dt = update->dt;
+ double vol, newPressure;
+ double G_eff = 0.0; // effective shear modulus
+ double K_eff; // effective bulk modulus
+ double M, p_wave_speed;
+ double rho, effectiveViscosity;
+ Matrix3d deltaStressDev;
+
+ dtCFL = 1.0e22;
+ eye.setIdentity();
+
+ for (i = 0; i < nlocal; i++) {
+ itype = type[i];
+ if (setflag[itype][itype] == 1) {
+ newStressDeviator.setZero();
+ newPressure = 0.0;
+ stressTensor[i].setZero();
+ vol = vfrac[i];
+ rho = rmass[i] / vfrac[i];
+ effectiveViscosity = 0.0;
+ K_eff = 0.0;
+ G_eff = 0.0;
+
+ //printf("rho = %f\n", rho);
+
+ switch (eos[itype]) {
+ default:
+ error->one(FLERR, "unknown EOS.");
+ break;
+ case NONE:
+ c0[i] = 1.0;
+ break;
+ case EOS_TAIT:
+ TaitEOS_density(Lookup[EOS_TAIT_EXPONENT][itype], Lookup[REFERENCE_SOUNDSPEED][itype],
+ Lookup[REFERENCE_DENSITY][itype], rho, newPressure, c0[i]);
+ //printf("new pressure =%f\n", newPressure);
+
+ break;
+ case EOS_PERFECT_GAS:
+ PerfectGasEOS(Lookup[EOS_PERFECT_GAS_GAMMA][itype], vol, rmass[i], e[i], newPressure, c0[i]);
+ break;
+ case EOS_LINEAR:
+ newPressure = Lookup[BULK_MODULUS][itype] * (rho / Lookup[REFERENCE_DENSITY][itype] - 1.0);
+ //printf("p=%f, rho0=%f, rho=%f\n", newPressure, Lookup[REFERENCE_DENSITY][itype], rho);
+ c0[i] = Lookup[REFERENCE_SOUNDSPEED][itype];
+ break;
+ }
+
+ K_eff = c0[i] * c0[i] * rho; // effective bulk modulus
+
+ /*
+ * ******************************* STRENGTH MODELS ************************************************
+ */
+
+ if (strength[itype] != NONE) {
+ /*
+ * initial stress state: given by the unrotateted Cauchy stress.
+ * Assemble Eigen 3d matrix from stored stress state
+ */
+ oldStressDeviator(0, 0) = tlsph_stress[i][0];
+ oldStressDeviator(0, 1) = tlsph_stress[i][1];
+ oldStressDeviator(0, 2) = tlsph_stress[i][2];
+ oldStressDeviator(1, 1) = tlsph_stress[i][3];
+ oldStressDeviator(1, 2) = tlsph_stress[i][4];
+ oldStressDeviator(2, 2) = tlsph_stress[i][5];
+ oldStressDeviator(1, 0) = oldStressDeviator(0, 1);
+ oldStressDeviator(2, 0) = oldStressDeviator(0, 2);
+ oldStressDeviator(2, 1) = oldStressDeviator(1, 2);
+
+ D = 0.5 * (L[i] + L[i].transpose());
+ W = 0.5 * (L[i] - L[i].transpose()); // spin tensor:: need this for Jaumann rate
+ d_dev = Deviator(D);
+
+ switch (strength[itype]) {
+ default:
+ error->one(FLERR, "unknown strength model.");
+ break;
+ case STRENGTH_LINEAR:
+
+ // here in a version with pressure part
+// stressRateDev = Lookup[BULK_MODULUS][itype] * d_iso * eye + 2.0 * Lookup[SHEAR_MODULUS][itype] * d_dev;
+// c0[i] = Lookup[REFERENCE_SOUNDSPEED][itype];
+// newPressure = 0.0;
+
+ // here only stress deviator
+ stressRateDev = 2.0 * Lookup[SHEAR_MODULUS][itype] * d_dev;
+ //cout << "stress rate deviator is " << endl << stressRateDev << endl;
+ break;
+
+ case STRENGTH_LINEAR_PLASTIC:
+ yieldStress = Lookup[YIELD_STRENGTH][itype] + Lookup[HARDENING_PARAMETER][itype] * eff_plastic_strain[i];
+ LinearPlasticStrength(Lookup[SHEAR_MODULUS][itype], yieldStress, oldStressDeviator, d_dev, dt,
+ newStressDeviator, stressRateDev, plastic_strain_increment);
+ eff_plastic_strain[i] += plastic_strain_increment;
+
+ break;
+ }
+
+ //double m = effective_longitudinal_modulus(itype, dt, d_iso, p_rate, d_dev, stressRate_dev, damage);
+
+ StressRateDevJaumann = stressRateDev - W * oldStressDeviator + oldStressDeviator * W;
+ newStressDeviator = oldStressDeviator + dt * StressRateDevJaumann;
+
+ tlsph_stress[i][0] = newStressDeviator(0, 0);
+ tlsph_stress[i][1] = newStressDeviator(0, 1);
+ tlsph_stress[i][2] = newStressDeviator(0, 2);
+ tlsph_stress[i][3] = newStressDeviator(1, 1);
+ tlsph_stress[i][4] = newStressDeviator(1, 2);
+ tlsph_stress[i][5] = newStressDeviator(2, 2);
+
+ // estimate effective shear modulus for time step stability
+ deltaStressDev = oldStressDeviator - newStressDeviator;
+ G_eff = effective_shear_modulus(d_dev, deltaStressDev, dt, itype);
+
+ } // end if (strength[itype] != NONE)
+
+ if (viscosity[itype] != NONE) {
+ D = 0.5 * (L[i] + L[i].transpose());
+ d_dev = Deviator(D);
+
+ switch (viscosity[itype]) {
+ default:
+ error->one(FLERR, "unknown viscosity model.");
+ break;
+ case VISCOSITY_NEWTON:
+ effectiveViscosity = Lookup[VISCOSITY_MU][itype];
+// double shear_rate = 2.0
+// * sqrt(d_dev(0, 1) * d_dev(0, 1) + d_dev(0, 2) * d_dev(0, 2) + d_dev(1, 2) * d_dev(1, 2)); // 3d
+ //cout << "shear rate: " << shear_rate << endl;
+ //effectiveViscosity = PA6_270C(shear_rate);
+ //if (effectiveViscosity > 178.062e-6) {
+ // printf("effective visc is %f\n", effectiveViscosity);
+ //}
+ newStressDeviator = 2.0 * effectiveViscosity * d_dev; // newton original
+ //cout << "this is Ddev " << endl << d_dev << endl << endl;
+ break;
+ }
+ } // end if (viscosity[itype] != NONE)
+
+ /*
+ * assemble stress Tensor from pressure and deviatoric parts
+ */
+
+ stressTensor[i] = -newPressure * eye + newStressDeviator;
+
+ /*
+ * stable timestep based on speed-of-sound
+ */
+
+ M = K_eff + 4.0 * G_eff / 3.0;
+ p_wave_speed = sqrt(M / rho);
+ effm[i] = G_eff;
+ dtCFL = MIN(2 * radius[i] / p_wave_speed, dtCFL);
+
+ /*
+ * stable timestep based on viscosity
+ */
+ if (viscosity[itype] != NONE) {
+ dtCFL = MIN(4 * radius[i] * radius[i] * rho / effectiveViscosity, dtCFL);
+ }
+
+ /*
+ * kernel gradient correction
+ */
+ if (gradient_correction_flag) {
+ stressTensor[i] *= K[i];
+ }
+ }
+ // end if (setflag[itype][itype] == 1)
+ } // end loop over nlocal
//printf("stable timestep = %g\n", 0.1 * hMin * MaxBulkVelocity);
}
@@ -833,40 +833,40 @@ void PairULSPH::AssembleStressTensor() {
void PairULSPH::allocate() {
- allocated = 1;
- int n = atom->ntypes;
+ allocated = 1;
+ int n = atom->ntypes;
- memory->create(setflag, n + 1, n + 1, "pair:setflag");
+ memory->create(setflag, n + 1, n + 1, "pair:setflag");
- memory->create(Q1, n + 1, "pair:Q1");
- memory->create(rho0, n + 1, "pair:Q2");
- memory->create(c0_type, n + 1, "pair:c0_type");
- memory->create(eos, n + 1, "pair:eosmodel");
- memory->create(viscosity, n + 1, "pair:viscositymodel");
- memory->create(strength, n + 1, "pair:strengthmodel");
+ memory->create(Q1, n + 1, "pair:Q1");
+ memory->create(rho0, n + 1, "pair:Q2");
+ memory->create(c0_type, n + 1, "pair:c0_type");
+ memory->create(eos, n + 1, "pair:eosmodel");
+ memory->create(viscosity, n + 1, "pair:viscositymodel");
+ memory->create(strength, n + 1, "pair:strengthmodel");
- memory->create(Lookup, MAX_KEY_VALUE, n + 1, "pair:LookupTable");
+ memory->create(Lookup, MAX_KEY_VALUE, n + 1, "pair:LookupTable");
- memory->create(artificial_pressure, n + 1, n + 1, "pair:artificial_pressure");
- memory->create(artificial_stress, n + 1, n + 1, "pair:artificial_stress");
- memory->create(cutsq, n + 1, n + 1, "pair:cutsq"); // always needs to be allocated, even with granular neighborlist
+ memory->create(artificial_pressure, n + 1, n + 1, "pair:artificial_pressure");
+ memory->create(artificial_stress, n + 1, n + 1, "pair:artificial_stress");
+ memory->create(cutsq, n + 1, n + 1, "pair:cutsq"); // always needs to be allocated, even with granular neighborlist
- /*
- * initialize arrays to default values
- */
+ /*
+ * initialize arrays to default values
+ */
- for (int i = 1; i <= n; i++) {
- for (int j = i; j <= n; j++) {
- artificial_pressure[i][j] = 0.0;
- artificial_stress[i][j] = 0.0;
- setflag[i][j] = 0;
- }
- }
+ for (int i = 1; i <= n; i++) {
+ for (int j = i; j <= n; j++) {
+ artificial_pressure[i][j] = 0.0;
+ artificial_stress[i][j] = 0.0;
+ setflag[i][j] = 0;
+ }
+ }
- onerad_dynamic = new double[n + 1];
- onerad_frozen = new double[n + 1];
- maxrad_dynamic = new double[n + 1];
- maxrad_frozen = new double[n + 1];
+ onerad_dynamic = new double[n + 1];
+ onerad_frozen = new double[n + 1];
+ maxrad_dynamic = new double[n + 1];
+ maxrad_frozen = new double[n + 1];
}
@@ -875,63 +875,63 @@ void PairULSPH::allocate() {
------------------------------------------------------------------------- */
void PairULSPH::settings(int narg, char **arg) {
- if (narg != 3) {
- printf("narg = %d\n", narg);
- error->all(FLERR, "Illegal number of arguments for pair_style ulsph");
- }
-
- if (comm->me == 0) {
- printf("\n>>========>>========>>========>>========>>========>>========>>========>>========\n");
- printf("... SMD / ULSPH PROPERTIES\n\n");
- }
-
- if (strcmp(arg[0], "*DENSITY_SUMMATION") == 0) {
- density_summation = true;
- density_continuity = false;
- if (comm->me == 0)
- printf("... density summation active\n");
- } else if (strcmp(arg[0], "*DENSITY_CONTINUITY") == 0) {
- density_continuity = true;
- density_summation = false;
- if (comm->me == 0)
- printf("... density continuity active\n");
- } else {
- error->all(FLERR,
- "Illegal settings keyword for first keyword of pair style ulsph. Must be either *DENSITY_SUMMATION or *DENSITY_CONTINUITY");
- }
-
- if (strcmp(arg[1], "*VELOCITY_GRADIENT") == 0) {
- velocity_gradient = true;
- if (comm->me == 0)
- printf("... computation of velocity gradients active\n");
- } else if (strcmp(arg[1], "*NO_VELOCITY_GRADIENT") == 0) {
- velocity_gradient = false;
- if (comm->me == 0)
- printf("... computation of velocity gradients NOT active\n");
- } else {
- error->all(FLERR,
- "Illegal settings keyword for first keyword of pair style ulsph. Must be either *VELOCITY_GRADIENT or *NO_VELOCITY_GRADIENT");
- }
-
- if (strcmp(arg[2], "*GRADIENT_CORRECTION") == 0) {
- gradient_correction_flag = true;
- if (comm->me == 0)
- printf("... first order correction of kernel gradients is active\n");
- } else if (strcmp(arg[2], "*NO_GRADIENT_CORRECTION") == 0) {
- gradient_correction_flag = false;
- if (comm->me == 0)
- printf("... first order correction of kernel gradients is NOT active\n");
- } else {
- error->all(FLERR, "Illegal settings keyword for pair style ulsph");
- }
+ if (narg != 3) {
+ printf("narg = %d\n", narg);
+ error->all(FLERR, "Illegal number of arguments for pair_style ulsph");
+ }
+
+ if (comm->me == 0) {
+ printf("\n>>========>>========>>========>>========>>========>>========>>========>>========\n");
+ printf("... SMD / ULSPH PROPERTIES\n\n");
+ }
+
+ if (strcmp(arg[0], "*DENSITY_SUMMATION") == 0) {
+ density_summation = true;
+ density_continuity = false;
+ if (comm->me == 0)
+ printf("... density summation active\n");
+ } else if (strcmp(arg[0], "*DENSITY_CONTINUITY") == 0) {
+ density_continuity = true;
+ density_summation = false;
+ if (comm->me == 0)
+ printf("... density continuity active\n");
+ } else {
+ error->all(FLERR,
+ "Illegal settings keyword for first keyword of pair style ulsph. Must be either *DENSITY_SUMMATION or *DENSITY_CONTINUITY");
+ }
+
+ if (strcmp(arg[1], "*VELOCITY_GRADIENT") == 0) {
+ velocity_gradient = true;
+ if (comm->me == 0)
+ printf("... computation of velocity gradients active\n");
+ } else if (strcmp(arg[1], "*NO_VELOCITY_GRADIENT") == 0) {
+ velocity_gradient = false;
+ if (comm->me == 0)
+ printf("... computation of velocity gradients NOT active\n");
+ } else {
+ error->all(FLERR,
+ "Illegal settings keyword for first keyword of pair style ulsph. Must be either *VELOCITY_GRADIENT or *NO_VELOCITY_GRADIENT");
+ }
+
+ if (strcmp(arg[2], "*GRADIENT_CORRECTION") == 0) {
+ gradient_correction_flag = true;
+ if (comm->me == 0)
+ printf("... first order correction of kernel gradients is active\n");
+ } else if (strcmp(arg[2], "*NO_GRADIENT_CORRECTION") == 0) {
+ gradient_correction_flag = false;
+ if (comm->me == 0)
+ printf("... first order correction of kernel gradients is NOT active\n");
+ } else {
+ error->all(FLERR, "Illegal settings keyword for pair style ulsph");
+ }
// error check
- //if ((gradient_correction_flag == true) && (density_summation)) {
- // error->all(FLERR, "Cannot use *DENSITY_SUMMATION in combination with *YES_GRADIENT_CORRECTION");
- //}
+ //if ((gradient_correction_flag == true) && (density_summation)) {
+ // error->all(FLERR, "Cannot use *DENSITY_SUMMATION in combination with *YES_GRADIENT_CORRECTION");
+ //}
- if (comm->me == 0)
- printf(">>========>>========>>========>>========>>========>>========>>========>>========\n");
+ if (comm->me == 0)
+ printf(">>========>>========>>========>>========>>========>>========>>========>>========\n");
}
@@ -940,475 +940,475 @@ void PairULSPH::settings(int narg, char **arg) {
------------------------------------------------------------------------- */
void PairULSPH::coeff(int narg, char **arg) {
- int ioffset, iarg, iNextKwd, itype, jtype;
- char str[128];
- std::string s, t;
-
- if (narg < 3) {
- sprintf(str, "number of arguments for pair ulsph is too small!");
- error->all(FLERR, str);
- }
- if (!allocated)
- allocate();
-
- /*
- * if parameters are give in i,i form, i.e., no a cross interaction, set material parameters
- */
-
- if (force->inumeric(FLERR, arg[0]) == force->inumeric(FLERR, arg[1])) {
-
- itype = force->inumeric(FLERR, arg[0]);
- eos[itype] = viscosity[itype] = strength[itype] = NONE;
-
- if (comm->me == 0) {
- printf("\n>>========>>========>>========>>========>>========>>========>>========>>========\n");
- printf("...SMD / ULSPH PROPERTIES OF PARTICLE TYPE %d\n\n", itype);
- }
-
- /*
- * read parameters which are common -- regardless of material / eos model
- */
-
- ioffset = 2;
- if (strcmp(arg[ioffset], "*COMMON") != 0) {
- sprintf(str, "common keyword missing!");
- error->all(FLERR, str);
- } else {
- }
-
- t = string("*");
- iNextKwd = -1;
- for (iarg = ioffset + 1; iarg < narg; iarg++) {
- s = string(arg[iarg]);
- if (s.compare(0, t.length(), t) == 0) {
- iNextKwd = iarg;
- break;
- }
- }
-
- //printf("keyword following *COMMON is %s\n", arg[iNextKwd]);
-
- if (iNextKwd < 0) {
- sprintf(str, "no *KEYWORD terminates *COMMON");
- error->all(FLERR, str);
- }
-
- if (iNextKwd - ioffset != 5 + 1) {
- sprintf(str, "expected 5 arguments following *COMMON but got %d\n", iNextKwd - ioffset - 1);
- error->all(FLERR, str);
- }
-
- Lookup[REFERENCE_DENSITY][itype] = force->numeric(FLERR, arg[ioffset + 1]);
- Lookup[REFERENCE_SOUNDSPEED][itype] = force->numeric(FLERR, arg[ioffset + 2]);
- Q1[itype] = force->numeric(FLERR, arg[ioffset + 3]);
- Lookup[HEAT_CAPACITY][itype] = force->numeric(FLERR, arg[ioffset + 4]);
- Lookup[HOURGLASS_CONTROL_AMPLITUDE][itype] = force->numeric(FLERR, arg[ioffset + 5]);
-
- Lookup[BULK_MODULUS][itype] = Lookup[REFERENCE_SOUNDSPEED][itype] * Lookup[REFERENCE_SOUNDSPEED][itype]
- * Lookup[REFERENCE_DENSITY][itype];
-
- if (comm->me == 0) {
- printf("material unspecific properties for SMD/ULSPH definition of particle type %d:\n", itype);
- printf(FORMAT1, "reference density", Lookup[REFERENCE_DENSITY][itype]);
- printf(FORMAT1, "reference speed of sound", Lookup[REFERENCE_SOUNDSPEED][itype]);
- printf(FORMAT1, "linear viscosity coefficient", Q1[itype]);
- printf(FORMAT1, "heat capacity [energy / (mass * temperature)]", Lookup[HEAT_CAPACITY][itype]);
- printf(FORMAT1, "bulk modulus", Lookup[BULK_MODULUS][itype]);
- printf(FORMAT1, "hourglass control amplitude", Lookup[HOURGLASS_CONTROL_AMPLITUDE][itype]);
- }
-
- /*
- * read following material cards
- */
-
-// if (comm->me == 0) {
-// printf("next kwd is %s\n", arg[iNextKwd]);
-// }
- while (true) {
- if (strcmp(arg[iNextKwd], "*END") == 0) {
-// if (comm->me == 0) {
-// sprintf(str, "found *END");
-// error->message(FLERR, str);
-// }
- break;
- }
-
- ioffset = iNextKwd;
- if (strcmp(arg[ioffset], "*EOS_TAIT") == 0) {
-
- /*
- * Tait EOS
- */
-
- eos[itype] = EOS_TAIT;
- //printf("reading *EOS_TAIT\n");
-
- t = string("*");
- iNextKwd = -1;
- for (iarg = ioffset + 1; iarg < narg; iarg++) {
- s = string(arg[iarg]);
- if (s.compare(0, t.length(), t) == 0) {
- iNextKwd = iarg;
- break;
- }
- }
-
- if (iNextKwd < 0) {
- sprintf(str, "no *KEYWORD terminates *EOS_TAIT");
- error->all(FLERR, str);
- }
-
- if (iNextKwd - ioffset != 1 + 1) {
- sprintf(str, "expected 1 arguments following *EOS_TAIT but got %d\n", iNextKwd - ioffset - 1);
- error->all(FLERR, str);
- }
-
- Lookup[EOS_TAIT_EXPONENT][itype] = force->numeric(FLERR, arg[ioffset + 1]);
-
- if (comm->me == 0) {
- printf(FORMAT2, "Tait EOS");
- printf(FORMAT1, "Exponent", Lookup[EOS_TAIT_EXPONENT][itype]);
- }
- } // end Tait EOS
-
- else if (strcmp(arg[ioffset], "*EOS_PERFECT_GAS") == 0) {
-
- /*
- * Perfect Gas EOS
- */
-
- eos[itype] = EOS_PERFECT_GAS;
- //printf("reading *EOS_PERFECT_GAS\n");
-
- t = string("*");
- iNextKwd = -1;
- for (iarg = ioffset + 1; iarg < narg; iarg++) {
- s = string(arg[iarg]);
- if (s.compare(0, t.length(), t) == 0) {
- iNextKwd = iarg;
- break;
- }
- }
-
- if (iNextKwd < 0) {
- sprintf(str, "no *KEYWORD terminates *EOS_PERFECT_GAS");
- error->all(FLERR, str);
- }
-
- if (iNextKwd - ioffset != 1 + 1) {
- sprintf(str, "expected 1 arguments following *EOS_PERFECT_GAS but got %d\n", iNextKwd - ioffset - 1);
- error->all(FLERR, str);
- }
-
- Lookup[EOS_PERFECT_GAS_GAMMA][itype] = force->numeric(FLERR, arg[ioffset + 1]);
-
- if (comm->me == 0) {
- printf(FORMAT2, "Perfect Gas EOS");
- printf(FORMAT1, "Heat Capacity Ratio Gamma", Lookup[EOS_PERFECT_GAS_GAMMA][itype]);
- }
- } // end Perfect Gas EOS
- else if (strcmp(arg[ioffset], "*EOS_LINEAR") == 0) {
-
- /*
- * Linear EOS
- */
-
- eos[itype] = EOS_LINEAR;
-
- t = string("*");
- iNextKwd = -1;
- for (iarg = ioffset + 1; iarg < narg; iarg++) {
- s = string(arg[iarg]);
- if (s.compare(0, t.length(), t) == 0) {
- iNextKwd = iarg;
- break;
- }
- }
-
- if (iNextKwd < 0) {
- sprintf(str, "no *KEYWORD terminates *EOS_LINEAR");
- error->all(FLERR, str);
- }
-
- if (iNextKwd - ioffset != 0 + 1) {
- sprintf(str, "expected 0 arguments following *EOS_LINEAR but got %d\n", iNextKwd - ioffset - 1);
- error->all(FLERR, str);
- }
-
- if (comm->me == 0) {
- printf(FORMAT2, "Linear EOS");
- printf(FORMAT1, "Bulk modulus", Lookup[BULK_MODULUS][itype]);
- }
- } // end Linear EOS
- else if (strcmp(arg[ioffset], "*STRENGTH_LINEAR_PLASTIC") == 0) {
-
- if (velocity_gradient != true) {
- error->all(FLERR, "A strength model was requested but *VELOCITY_GRADIENT is not set");
- }
-
- /*
- * linear elastic / ideal plastic material model with strength
- */
-
- strength[itype] = STRENGTH_LINEAR_PLASTIC;
- velocity_gradient_required = true;
- //printf("reading *LINEAR_PLASTIC\n");
-
- t = string("*");
- iNextKwd = -1;
- for (iarg = ioffset + 1; iarg < narg; iarg++) {
- s = string(arg[iarg]);
- if (s.compare(0, t.length(), t) == 0) {
- iNextKwd = iarg;
- break;
- }
- }
-
- if (iNextKwd < 0) {
- sprintf(str, "no *KEYWORD terminates *STRENGTH_LINEAR_PLASTIC");
- error->all(FLERR, str);
- }
-
- if (iNextKwd - ioffset != 3 + 1) {
- sprintf(str, "expected 3 arguments following *STRENGTH_LINEAR_PLASTIC but got %d\n", iNextKwd - ioffset - 1);
- error->all(FLERR, str);
- }
-
- Lookup[SHEAR_MODULUS][itype] = force->numeric(FLERR, arg[ioffset + 1]);
- Lookup[YIELD_STRENGTH][itype] = force->numeric(FLERR, arg[ioffset + 2]);
- Lookup[HARDENING_PARAMETER][itype] = force->numeric(FLERR, arg[ioffset + 3]);
-
- if (comm->me == 0) {
- printf(FORMAT2, "linear elastic / ideal plastic material mode");
- printf(FORMAT1, "yield_strength", Lookup[YIELD_STRENGTH][itype]);
- printf(FORMAT1, "constant hardening parameter", Lookup[HARDENING_PARAMETER][itype]);
- printf(FORMAT1, "shear modulus", Lookup[SHEAR_MODULUS][itype]);
- }
- } // end *STRENGTH_LINEAR_PLASTIC
- else if (strcmp(arg[ioffset], "*STRENGTH_LINEAR") == 0) {
-
- if (velocity_gradient != true) {
- error->all(FLERR, "A strength model was requested but *VELOCITY_GRADIENT is not set");
- }
-
- /*
- * linear elastic / ideal plastic material model with strength
- */
-
- strength[itype] = STRENGTH_LINEAR;
- t = string("*");
- iNextKwd = -1;
- for (iarg = ioffset + 1; iarg < narg; iarg++) {
- s = string(arg[iarg]);
- if (s.compare(0, t.length(), t) == 0) {
- iNextKwd = iarg;
- break;
- }
- }
-
- if (iNextKwd < 0) {
- sprintf(str, "no *KEYWORD terminates *STRENGTH_LINEAR");
- error->all(FLERR, str);
- }
-
- if (iNextKwd - ioffset != 1 + 1) {
- sprintf(str, "expected 1 arguments following *STRENGTH_LINEAR but got %d\n", iNextKwd - ioffset - 1);
- error->all(FLERR, str);
- }
-
- Lookup[SHEAR_MODULUS][itype] = force->numeric(FLERR, arg[ioffset + 1]);
-
- if (comm->me == 0) {
- printf(FORMAT2, "linear elastic strength model");
- printf(FORMAT1, "shear modulus", Lookup[SHEAR_MODULUS][itype]);
- }
- } // end *STRENGTH_LINEAR
- else if (strcmp(arg[ioffset], "*VISCOSITY_NEWTON") == 0) {
-
- if (velocity_gradient != true) {
- error->all(FLERR, "A viscosity model was requested but *VELOCITY_GRADIENT is not set");
- }
-
- /*
- * linear elastic / ideal plastic material model with strength
- */
-
- viscosity[itype] = VISCOSITY_NEWTON;
- t = string("*");
- iNextKwd = -1;
- for (iarg = ioffset + 1; iarg < narg; iarg++) {
- s = string(arg[iarg]);
- if (s.compare(0, t.length(), t) == 0) {
- iNextKwd = iarg;
- break;
- }
- }
-
- if (iNextKwd < 0) {
- sprintf(str, "no *KEYWORD terminates *VISCOSITY_NEWTON");
- error->all(FLERR, str);
- }
-
- if (iNextKwd - ioffset != 1 + 1) {
- sprintf(str, "expected 1 arguments following *VISCOSITY_NEWTON but got %d\n", iNextKwd - ioffset - 1);
- error->all(FLERR, str);
- }
-
- Lookup[VISCOSITY_MU][itype] = force->numeric(FLERR, arg[ioffset + 1]);
-
- if (comm->me == 0) {
- printf(FORMAT2, "Newton viscosity model");
- printf(FORMAT1, "viscosity mu", Lookup[VISCOSITY_MU][itype]);
- }
- } // end *STRENGTH_VISCOSITY_NEWTON
-
- else if (strcmp(arg[ioffset], "*ARTIFICIAL_PRESSURE") == 0) {
-
- /*
- * use Monaghan's artificial pressure to prevent particle clumping
- */
-
- t = string("*");
- iNextKwd = -1;
- for (iarg = ioffset + 1; iarg < narg; iarg++) {
- s = string(arg[iarg]);
- if (s.compare(0, t.length(), t) == 0) {
- iNextKwd = iarg;
- break;
- }
- }
-
- if (iNextKwd < 0) {
- sprintf(str, "no *KEYWORD terminates *ARTIFICIAL_PRESSURE");
- error->all(FLERR, str);
- }
-
- if (iNextKwd - ioffset != 1 + 1) {
- sprintf(str, "expected 1 arguments following *ARTIFICIAL_PRESSURE but got %d\n", iNextKwd - ioffset - 1);
- error->all(FLERR, str);
- }
-
- artificial_pressure[itype][itype] = force->numeric(FLERR, arg[ioffset + 1]);
-
- if (comm->me == 0) {
- printf(FORMAT2, "Artificial Pressure is enabled.");
- printf(FORMAT1, "Artificial Pressure amplitude", artificial_pressure[itype][itype]);
- }
- } // end *ARTIFICIAL_PRESSURE
-
- else if (strcmp(arg[ioffset], "*ARTIFICIAL_STRESS") == 0) {
-
- /*
- * use Monaghan's artificial stress to prevent particle clumping
- */
-
- t = string("*");
- iNextKwd = -1;
- for (iarg = ioffset + 1; iarg < narg; iarg++) {
- s = string(arg[iarg]);
- if (s.compare(0, t.length(), t) == 0) {
- iNextKwd = iarg;
- break;
- }
- }
-
- if (iNextKwd < 0) {
- sprintf(str, "no *KEYWORD terminates *ARTIFICIAL_STRESS");
- error->all(FLERR, str);
- }
-
- if (iNextKwd - ioffset != 1 + 1) {
- sprintf(str, "expected 1 arguments following *ARTIFICIAL_STRESS but got %d\n", iNextKwd - ioffset - 1);
- error->all(FLERR, str);
- }
-
- artificial_stress[itype][itype] = force->numeric(FLERR, arg[ioffset + 1]);
-
- if (comm->me == 0) {
- printf(FORMAT2, "Artificial Stress is enabled.");
- printf(FORMAT1, "Artificial Stress amplitude", artificial_stress[itype][itype]);
- }
- } // end *ARTIFICIAL_STRESS
-
- else {
- sprintf(str, "unknown *KEYWORD: %s", arg[ioffset]);
- error->all(FLERR, str);
- }
-
- }
-
- /*
- * copy data which is looked up in inner pairwise loops from slow maps to fast arrays
- */
-
- rho0[itype] = Lookup[REFERENCE_DENSITY][itype];
- c0_type[itype] = Lookup[REFERENCE_SOUNDSPEED][itype];
- setflag[itype][itype] = 1;
-
- /*
- * error checks
- */
-
- if ((viscosity[itype] != NONE) && (strength[itype] != NONE)) {
- sprintf(str, "cannot have both a strength and viscosity model for particle type %d", itype);
- error->all(FLERR, str);
- }
-
- if (eos[itype] == NONE) {
- sprintf(str, "must specify an EOS for particle type %d", itype);
- error->all(FLERR, str);
- }
-
- } else {
- /*
- * we are reading a cross-interaction line for particle types i, j
- */
-
- itype = force->inumeric(FLERR, arg[0]);
- jtype = force->inumeric(FLERR, arg[1]);
-
- if (strcmp(arg[2], "*CROSS") != 0) {
- sprintf(str, "ulsph cross interaction between particle type %d and %d requested, however, *CROSS keyword is missing",
- itype, jtype);
- error->all(FLERR, str);
- }
-
- if (setflag[itype][itype] != 1) {
- sprintf(str,
- "ulsph cross interaction between particle type %d and %d requested, however, properties of type %d have not yet been specified",
- itype, jtype, itype);
- error->all(FLERR, str);
- }
-
- if (setflag[jtype][jtype] != 1) {
- sprintf(str,
- "ulsph cross interaction between particle type %d and %d requested, however, properties of type %d have not yet been specified",
- itype, jtype, jtype);
- error->all(FLERR, str);
- }
-
- setflag[itype][jtype] = 1;
- setflag[jtype][itype] = 1;
-
- if ((artificial_pressure[itype][itype] > 0.0) && (artificial_pressure[jtype][jtype] > 0.0)) {
- artificial_pressure[itype][jtype] = 0.5 * (artificial_pressure[itype][itype] + artificial_pressure[jtype][jtype]);
- artificial_pressure[jtype][itype] = artificial_pressure[itype][jtype];
- } else {
- artificial_pressure[itype][jtype] = artificial_pressure[jtype][itype] = 0.0;
- }
-
- if ((artificial_stress[itype][itype] > 0.0) && (artificial_stress[jtype][jtype] > 0.0)) {
- artificial_stress[itype][jtype] = 0.5 * (artificial_stress[itype][itype] + artificial_stress[jtype][jtype]);
- artificial_stress[jtype][itype] = artificial_stress[itype][jtype];
- } else {
- artificial_stress[itype][jtype] = artificial_stress[jtype][itype] = 0.0;
- }
-
- if (comm->me == 0) {
- printf(">>========>>========>>========>>========>>========>>========>>========>>========\n");
- }
-
- }
+ int ioffset, iarg, iNextKwd, itype, jtype;
+ char str[128];
+ std::string s, t;
+
+ if (narg < 3) {
+ sprintf(str, "number of arguments for pair ulsph is too small!");
+ error->all(FLERR, str);
+ }
+ if (!allocated)
+ allocate();
+
+ /*
+ * if parameters are give in i,i form, i.e., no a cross interaction, set material parameters
+ */
+
+ if (force->inumeric(FLERR, arg[0]) == force->inumeric(FLERR, arg[1])) {
+
+ itype = force->inumeric(FLERR, arg[0]);
+ eos[itype] = viscosity[itype] = strength[itype] = NONE;
+
+ if (comm->me == 0) {
+ printf("\n>>========>>========>>========>>========>>========>>========>>========>>========\n");
+ printf("...SMD / ULSPH PROPERTIES OF PARTICLE TYPE %d\n\n", itype);
+ }
+
+ /*
+ * read parameters which are common -- regardless of material / eos model
+ */
+
+ ioffset = 2;
+ if (strcmp(arg[ioffset], "*COMMON") != 0) {
+ sprintf(str, "common keyword missing!");
+ error->all(FLERR, str);
+ } else {
+ }
+
+ t = string("*");
+ iNextKwd = -1;
+ for (iarg = ioffset + 1; iarg < narg; iarg++) {
+ s = string(arg[iarg]);
+ if (s.compare(0, t.length(), t) == 0) {
+ iNextKwd = iarg;
+ break;
+ }
+ }
+
+ //printf("keyword following *COMMON is %s\n", arg[iNextKwd]);
+
+ if (iNextKwd < 0) {
+ sprintf(str, "no *KEYWORD terminates *COMMON");
+ error->all(FLERR, str);
+ }
+
+ if (iNextKwd - ioffset != 5 + 1) {
+ sprintf(str, "expected 5 arguments following *COMMON but got %d\n", iNextKwd - ioffset - 1);
+ error->all(FLERR, str);
+ }
+
+ Lookup[REFERENCE_DENSITY][itype] = force->numeric(FLERR, arg[ioffset + 1]);
+ Lookup[REFERENCE_SOUNDSPEED][itype] = force->numeric(FLERR, arg[ioffset + 2]);
+ Q1[itype] = force->numeric(FLERR, arg[ioffset + 3]);
+ Lookup[HEAT_CAPACITY][itype] = force->numeric(FLERR, arg[ioffset + 4]);
+ Lookup[HOURGLASS_CONTROL_AMPLITUDE][itype] = force->numeric(FLERR, arg[ioffset + 5]);
+
+ Lookup[BULK_MODULUS][itype] = Lookup[REFERENCE_SOUNDSPEED][itype] * Lookup[REFERENCE_SOUNDSPEED][itype]
+ * Lookup[REFERENCE_DENSITY][itype];
+
+ if (comm->me == 0) {
+ printf("material unspecific properties for SMD/ULSPH definition of particle type %d:\n", itype);
+ printf(FORMAT1, "reference density", Lookup[REFERENCE_DENSITY][itype]);
+ printf(FORMAT1, "reference speed of sound", Lookup[REFERENCE_SOUNDSPEED][itype]);
+ printf(FORMAT1, "linear viscosity coefficient", Q1[itype]);
+ printf(FORMAT1, "heat capacity [energy / (mass * temperature)]", Lookup[HEAT_CAPACITY][itype]);
+ printf(FORMAT1, "bulk modulus", Lookup[BULK_MODULUS][itype]);
+ printf(FORMAT1, "hourglass control amplitude", Lookup[HOURGLASS_CONTROL_AMPLITUDE][itype]);
+ }
+
+ /*
+ * read following material cards
+ */
+
+// if (comm->me == 0) {
+// printf("next kwd is %s\n", arg[iNextKwd]);
+// }
+ while (true) {
+ if (strcmp(arg[iNextKwd], "*END") == 0) {
+// if (comm->me == 0) {
+// sprintf(str, "found *END");
+// error->message(FLERR, str);
+// }
+ break;
+ }
+
+ ioffset = iNextKwd;
+ if (strcmp(arg[ioffset], "*EOS_TAIT") == 0) {
+
+ /*
+ * Tait EOS
+ */
+
+ eos[itype] = EOS_TAIT;
+ //printf("reading *EOS_TAIT\n");
+
+ t = string("*");
+ iNextKwd = -1;
+ for (iarg = ioffset + 1; iarg < narg; iarg++) {
+ s = string(arg[iarg]);
+ if (s.compare(0, t.length(), t) == 0) {
+ iNextKwd = iarg;
+ break;
+ }
+ }
+
+ if (iNextKwd < 0) {
+ sprintf(str, "no *KEYWORD terminates *EOS_TAIT");
+ error->all(FLERR, str);
+ }
+
+ if (iNextKwd - ioffset != 1 + 1) {
+ sprintf(str, "expected 1 arguments following *EOS_TAIT but got %d\n", iNextKwd - ioffset - 1);
+ error->all(FLERR, str);
+ }
+
+ Lookup[EOS_TAIT_EXPONENT][itype] = force->numeric(FLERR, arg[ioffset + 1]);
+
+ if (comm->me == 0) {
+ printf(FORMAT2, "Tait EOS");
+ printf(FORMAT1, "Exponent", Lookup[EOS_TAIT_EXPONENT][itype]);
+ }
+ } // end Tait EOS
+
+ else if (strcmp(arg[ioffset], "*EOS_PERFECT_GAS") == 0) {
+
+ /*
+ * Perfect Gas EOS
+ */
+
+ eos[itype] = EOS_PERFECT_GAS;
+ //printf("reading *EOS_PERFECT_GAS\n");
+
+ t = string("*");
+ iNextKwd = -1;
+ for (iarg = ioffset + 1; iarg < narg; iarg++) {
+ s = string(arg[iarg]);
+ if (s.compare(0, t.length(), t) == 0) {
+ iNextKwd = iarg;
+ break;
+ }
+ }
+
+ if (iNextKwd < 0) {
+ sprintf(str, "no *KEYWORD terminates *EOS_PERFECT_GAS");
+ error->all(FLERR, str);
+ }
+
+ if (iNextKwd - ioffset != 1 + 1) {
+ sprintf(str, "expected 1 arguments following *EOS_PERFECT_GAS but got %d\n", iNextKwd - ioffset - 1);
+ error->all(FLERR, str);
+ }
+
+ Lookup[EOS_PERFECT_GAS_GAMMA][itype] = force->numeric(FLERR, arg[ioffset + 1]);
+
+ if (comm->me == 0) {
+ printf(FORMAT2, "Perfect Gas EOS");
+ printf(FORMAT1, "Heat Capacity Ratio Gamma", Lookup[EOS_PERFECT_GAS_GAMMA][itype]);
+ }
+ } // end Perfect Gas EOS
+ else if (strcmp(arg[ioffset], "*EOS_LINEAR") == 0) {
+
+ /*
+ * Linear EOS
+ */
+
+ eos[itype] = EOS_LINEAR;
+
+ t = string("*");
+ iNextKwd = -1;
+ for (iarg = ioffset + 1; iarg < narg; iarg++) {
+ s = string(arg[iarg]);
+ if (s.compare(0, t.length(), t) == 0) {
+ iNextKwd = iarg;
+ break;
+ }
+ }
+
+ if (iNextKwd < 0) {
+ sprintf(str, "no *KEYWORD terminates *EOS_LINEAR");
+ error->all(FLERR, str);
+ }
+
+ if (iNextKwd - ioffset != 0 + 1) {
+ sprintf(str, "expected 0 arguments following *EOS_LINEAR but got %d\n", iNextKwd - ioffset - 1);
+ error->all(FLERR, str);
+ }
+
+ if (comm->me == 0) {
+ printf(FORMAT2, "Linear EOS");
+ printf(FORMAT1, "Bulk modulus", Lookup[BULK_MODULUS][itype]);
+ }
+ } // end Linear EOS
+ else if (strcmp(arg[ioffset], "*STRENGTH_LINEAR_PLASTIC") == 0) {
+
+ if (velocity_gradient != true) {
+ error->all(FLERR, "A strength model was requested but *VELOCITY_GRADIENT is not set");
+ }
+
+ /*
+ * linear elastic / ideal plastic material model with strength
+ */
+
+ strength[itype] = STRENGTH_LINEAR_PLASTIC;
+ velocity_gradient_required = true;
+ //printf("reading *LINEAR_PLASTIC\n");
+
+ t = string("*");
+ iNextKwd = -1;
+ for (iarg = ioffset + 1; iarg < narg; iarg++) {
+ s = string(arg[iarg]);
+ if (s.compare(0, t.length(), t) == 0) {
+ iNextKwd = iarg;
+ break;
+ }
+ }
+
+ if (iNextKwd < 0) {
+ sprintf(str, "no *KEYWORD terminates *STRENGTH_LINEAR_PLASTIC");
+ error->all(FLERR, str);
+ }
+
+ if (iNextKwd - ioffset != 3 + 1) {
+ sprintf(str, "expected 3 arguments following *STRENGTH_LINEAR_PLASTIC but got %d\n", iNextKwd - ioffset - 1);
+ error->all(FLERR, str);
+ }
+
+ Lookup[SHEAR_MODULUS][itype] = force->numeric(FLERR, arg[ioffset + 1]);
+ Lookup[YIELD_STRENGTH][itype] = force->numeric(FLERR, arg[ioffset + 2]);
+ Lookup[HARDENING_PARAMETER][itype] = force->numeric(FLERR, arg[ioffset + 3]);
+
+ if (comm->me == 0) {
+ printf(FORMAT2, "linear elastic / ideal plastic material mode");
+ printf(FORMAT1, "yield_strength", Lookup[YIELD_STRENGTH][itype]);
+ printf(FORMAT1, "constant hardening parameter", Lookup[HARDENING_PARAMETER][itype]);
+ printf(FORMAT1, "shear modulus", Lookup[SHEAR_MODULUS][itype]);
+ }
+ } // end *STRENGTH_LINEAR_PLASTIC
+ else if (strcmp(arg[ioffset], "*STRENGTH_LINEAR") == 0) {
+
+ if (velocity_gradient != true) {
+ error->all(FLERR, "A strength model was requested but *VELOCITY_GRADIENT is not set");
+ }
+
+ /*
+ * linear elastic / ideal plastic material model with strength
+ */
+
+ strength[itype] = STRENGTH_LINEAR;
+ t = string("*");
+ iNextKwd = -1;
+ for (iarg = ioffset + 1; iarg < narg; iarg++) {
+ s = string(arg[iarg]);
+ if (s.compare(0, t.length(), t) == 0) {
+ iNextKwd = iarg;
+ break;
+ }
+ }
+
+ if (iNextKwd < 0) {
+ sprintf(str, "no *KEYWORD terminates *STRENGTH_LINEAR");
+ error->all(FLERR, str);
+ }
+
+ if (iNextKwd - ioffset != 1 + 1) {
+ sprintf(str, "expected 1 arguments following *STRENGTH_LINEAR but got %d\n", iNextKwd - ioffset - 1);
+ error->all(FLERR, str);
+ }
+
+ Lookup[SHEAR_MODULUS][itype] = force->numeric(FLERR, arg[ioffset + 1]);
+
+ if (comm->me == 0) {
+ printf(FORMAT2, "linear elastic strength model");
+ printf(FORMAT1, "shear modulus", Lookup[SHEAR_MODULUS][itype]);
+ }
+ } // end *STRENGTH_LINEAR
+ else if (strcmp(arg[ioffset], "*VISCOSITY_NEWTON") == 0) {
+
+ if (velocity_gradient != true) {
+ error->all(FLERR, "A viscosity model was requested but *VELOCITY_GRADIENT is not set");
+ }
+
+ /*
+ * linear elastic / ideal plastic material model with strength
+ */
+
+ viscosity[itype] = VISCOSITY_NEWTON;
+ t = string("*");
+ iNextKwd = -1;
+ for (iarg = ioffset + 1; iarg < narg; iarg++) {
+ s = string(arg[iarg]);
+ if (s.compare(0, t.length(), t) == 0) {
+ iNextKwd = iarg;
+ break;
+ }
+ }
+
+ if (iNextKwd < 0) {
+ sprintf(str, "no *KEYWORD terminates *VISCOSITY_NEWTON");
+ error->all(FLERR, str);
+ }
+
+ if (iNextKwd - ioffset != 1 + 1) {
+ sprintf(str, "expected 1 arguments following *VISCOSITY_NEWTON but got %d\n", iNextKwd - ioffset - 1);
+ error->all(FLERR, str);
+ }
+
+ Lookup[VISCOSITY_MU][itype] = force->numeric(FLERR, arg[ioffset + 1]);
+
+ if (comm->me == 0) {
+ printf(FORMAT2, "Newton viscosity model");
+ printf(FORMAT1, "viscosity mu", Lookup[VISCOSITY_MU][itype]);
+ }
+ } // end *STRENGTH_VISCOSITY_NEWTON
+
+ else if (strcmp(arg[ioffset], "*ARTIFICIAL_PRESSURE") == 0) {
+
+ /*
+ * use Monaghan's artificial pressure to prevent particle clumping
+ */
+
+ t = string("*");
+ iNextKwd = -1;
+ for (iarg = ioffset + 1; iarg < narg; iarg++) {
+ s = string(arg[iarg]);
+ if (s.compare(0, t.length(), t) == 0) {
+ iNextKwd = iarg;
+ break;
+ }
+ }
+
+ if (iNextKwd < 0) {
+ sprintf(str, "no *KEYWORD terminates *ARTIFICIAL_PRESSURE");
+ error->all(FLERR, str);
+ }
+
+ if (iNextKwd - ioffset != 1 + 1) {
+ sprintf(str, "expected 1 arguments following *ARTIFICIAL_PRESSURE but got %d\n", iNextKwd - ioffset - 1);
+ error->all(FLERR, str);
+ }
+
+ artificial_pressure[itype][itype] = force->numeric(FLERR, arg[ioffset + 1]);
+
+ if (comm->me == 0) {
+ printf(FORMAT2, "Artificial Pressure is enabled.");
+ printf(FORMAT1, "Artificial Pressure amplitude", artificial_pressure[itype][itype]);
+ }
+ } // end *ARTIFICIAL_PRESSURE
+
+ else if (strcmp(arg[ioffset], "*ARTIFICIAL_STRESS") == 0) {
+
+ /*
+ * use Monaghan's artificial stress to prevent particle clumping
+ */
+
+ t = string("*");
+ iNextKwd = -1;
+ for (iarg = ioffset + 1; iarg < narg; iarg++) {
+ s = string(arg[iarg]);
+ if (s.compare(0, t.length(), t) == 0) {
+ iNextKwd = iarg;
+ break;
+ }
+ }
+
+ if (iNextKwd < 0) {
+ sprintf(str, "no *KEYWORD terminates *ARTIFICIAL_STRESS");
+ error->all(FLERR, str);
+ }
+
+ if (iNextKwd - ioffset != 1 + 1) {
+ sprintf(str, "expected 1 arguments following *ARTIFICIAL_STRESS but got %d\n", iNextKwd - ioffset - 1);
+ error->all(FLERR, str);
+ }
+
+ artificial_stress[itype][itype] = force->numeric(FLERR, arg[ioffset + 1]);
+
+ if (comm->me == 0) {
+ printf(FORMAT2, "Artificial Stress is enabled.");
+ printf(FORMAT1, "Artificial Stress amplitude", artificial_stress[itype][itype]);
+ }
+ } // end *ARTIFICIAL_STRESS
+
+ else {
+ sprintf(str, "unknown *KEYWORD: %s", arg[ioffset]);
+ error->all(FLERR, str);
+ }
+
+ }
+
+ /*
+ * copy data which is looked up in inner pairwise loops from slow maps to fast arrays
+ */
+
+ rho0[itype] = Lookup[REFERENCE_DENSITY][itype];
+ c0_type[itype] = Lookup[REFERENCE_SOUNDSPEED][itype];
+ setflag[itype][itype] = 1;
+
+ /*
+ * error checks
+ */
+
+ if ((viscosity[itype] != NONE) && (strength[itype] != NONE)) {
+ sprintf(str, "cannot have both a strength and viscosity model for particle type %d", itype);
+ error->all(FLERR, str);
+ }
+
+ if (eos[itype] == NONE) {
+ sprintf(str, "must specify an EOS for particle type %d", itype);
+ error->all(FLERR, str);
+ }
+
+ } else {
+ /*
+ * we are reading a cross-interaction line for particle types i, j
+ */
+
+ itype = force->inumeric(FLERR, arg[0]);
+ jtype = force->inumeric(FLERR, arg[1]);
+
+ if (strcmp(arg[2], "*CROSS") != 0) {
+ sprintf(str, "ulsph cross interaction between particle type %d and %d requested, however, *CROSS keyword is missing",
+ itype, jtype);
+ error->all(FLERR, str);
+ }
+
+ if (setflag[itype][itype] != 1) {
+ sprintf(str,
+ "ulsph cross interaction between particle type %d and %d requested, however, properties of type %d have not yet been specified",
+ itype, jtype, itype);
+ error->all(FLERR, str);
+ }
+
+ if (setflag[jtype][jtype] != 1) {
+ sprintf(str,
+ "ulsph cross interaction between particle type %d and %d requested, however, properties of type %d have not yet been specified",
+ itype, jtype, jtype);
+ error->all(FLERR, str);
+ }
+
+ setflag[itype][jtype] = 1;
+ setflag[jtype][itype] = 1;
+
+ if ((artificial_pressure[itype][itype] > 0.0) && (artificial_pressure[jtype][jtype] > 0.0)) {
+ artificial_pressure[itype][jtype] = 0.5 * (artificial_pressure[itype][itype] + artificial_pressure[jtype][jtype]);
+ artificial_pressure[jtype][itype] = artificial_pressure[itype][jtype];
+ } else {
+ artificial_pressure[itype][jtype] = artificial_pressure[jtype][itype] = 0.0;
+ }
+
+ if ((artificial_stress[itype][itype] > 0.0) && (artificial_stress[jtype][jtype] > 0.0)) {
+ artificial_stress[itype][jtype] = 0.5 * (artificial_stress[itype][itype] + artificial_stress[jtype][jtype]);
+ artificial_stress[jtype][itype] = artificial_stress[itype][jtype];
+ } else {
+ artificial_stress[itype][jtype] = artificial_stress[jtype][itype] = 0.0;
+ }
+
+ if (comm->me == 0) {
+ printf(">>========>>========>>========>>========>>========>>========>>========>>========\n");
+ }
+
+ }
}
/* ----------------------------------------------------------------------
@@ -1417,20 +1417,20 @@ void PairULSPH::coeff(int narg, char **arg) {
double PairULSPH::init_one(int i, int j) {
- if (!allocated)
- allocate();
+ if (!allocated)
+ allocate();
- if (setflag[i][j] == 0)
- error->all(FLERR, "All pair coeffs are not set");
+ if (setflag[i][j] == 0)
+ error->all(FLERR, "All pair coeffs are not set");
// cutoff = sum of max I,J radii for
// dynamic/dynamic & dynamic/frozen interactions, but not frozen/frozen
- double cutoff = maxrad_dynamic[i] + maxrad_dynamic[j];
- cutoff = MAX(cutoff, maxrad_frozen[i] + maxrad_dynamic[j]);
- cutoff = MAX(cutoff, maxrad_dynamic[i] + maxrad_frozen[j]);
+ double cutoff = maxrad_dynamic[i] + maxrad_dynamic[j];
+ cutoff = MAX(cutoff, maxrad_frozen[i] + maxrad_dynamic[j]);
+ cutoff = MAX(cutoff, maxrad_dynamic[i] + maxrad_frozen[j]);
//printf("cutoff for pair sph/fluid = %f\n", cutoff);
- return cutoff;
+ return cutoff;
}
/* ----------------------------------------------------------------------
@@ -1438,28 +1438,28 @@ double PairULSPH::init_one(int i, int j) {
------------------------------------------------------------------------- */
void PairULSPH::init_style() {
- int i;
+ int i;
//printf(" in init style\n");
// request a granular neighbor list
- int irequest = neighbor->request(this);
- neighbor->requests[irequest]->size = 1;
+ int irequest = neighbor->request(this);
+ neighbor->requests[irequest]->size = 1;
// set maxrad_dynamic and maxrad_frozen for each type
// include future Fix pour particles as dynamic
- for (i = 1; i <= atom->ntypes; i++)
- onerad_dynamic[i] = onerad_frozen[i] = 0.0;
+ for (i = 1; i <= atom->ntypes; i++)
+ onerad_dynamic[i] = onerad_frozen[i] = 0.0;
- double *radius = atom->radius;
- int *type = atom->type;
- int nlocal = atom->nlocal;
+ double *radius = atom->radius;
+ int *type = atom->type;
+ int nlocal = atom->nlocal;
- for (i = 0; i < nlocal; i++)
- onerad_dynamic[type[i]] = MAX(onerad_dynamic[type[i]], radius[i]);
+ for (i = 0; i < nlocal; i++)
+ onerad_dynamic[type[i]] = MAX(onerad_dynamic[type[i]], radius[i]);
- MPI_Allreduce(&onerad_dynamic[1], &maxrad_dynamic[1], atom->ntypes, MPI_DOUBLE, MPI_MAX, world);
- MPI_Allreduce(&onerad_frozen[1], &maxrad_frozen[1], atom->ntypes, MPI_DOUBLE, MPI_MAX, world);
+ MPI_Allreduce(&onerad_dynamic[1], &maxrad_dynamic[1], atom->ntypes, MPI_DOUBLE, MPI_MAX, world);
+ MPI_Allreduce(&onerad_frozen[1], &maxrad_frozen[1], atom->ntypes, MPI_DOUBLE, MPI_MAX, world);
}
@@ -1469,8 +1469,8 @@ void PairULSPH::init_style() {
------------------------------------------------------------------------- */
void PairULSPH::init_list(int id, NeighList *ptr) {
- if (id == 0)
- list = ptr;
+ if (id == 0)
+ list = ptr;
}
/* ----------------------------------------------------------------------
@@ -1481,81 +1481,81 @@ double PairULSPH::memory_usage() {
//printf("in memory usage\n");
- return 11 * nmax * sizeof(double);
+ return 11 * nmax * sizeof(double);
}
/* ---------------------------------------------------------------------- */
int PairULSPH::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc) {
- double *vfrac = atom->vfrac;
- double *eff_plastic_strain = atom->eff_plastic_strain;
- int i, j, m;
+ double *vfrac = atom->vfrac;
+ double *eff_plastic_strain = atom->eff_plastic_strain;
+ int i, j, m;
//printf("packing comm\n");
- m = 0;
- for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = vfrac[j];
- buf[m++] = c0[j]; //2
-
- buf[m++] = stressTensor[j](0, 0); // pack symmetric stress tensor
- buf[m++] = stressTensor[j](1, 1);
- buf[m++] = stressTensor[j](2, 2);
- buf[m++] = stressTensor[j](0, 1);
- buf[m++] = stressTensor[j](0, 2);
- buf[m++] = stressTensor[j](1, 2); // 2 + 6 = 8
-
- buf[m++] = F[j](0, 0); // F is not symmetric
- buf[m++] = F[j](0, 1);
- buf[m++] = F[j](0, 2);
- buf[m++] = F[j](1, 0);
- buf[m++] = F[j](1, 1);
- buf[m++] = F[j](1, 2);
- buf[m++] = F[j](2, 0);
- buf[m++] = F[j](2, 1);
- buf[m++] = F[j](2, 2); // 8 + 9 = 17
-
- buf[m++] = eff_plastic_strain[j]; // 18
- }
- return m;
+ m = 0;
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = vfrac[j];
+ buf[m++] = c0[j]; //2
+
+ buf[m++] = stressTensor[j](0, 0); // pack symmetric stress tensor
+ buf[m++] = stressTensor[j](1, 1);
+ buf[m++] = stressTensor[j](2, 2);
+ buf[m++] = stressTensor[j](0, 1);
+ buf[m++] = stressTensor[j](0, 2);
+ buf[m++] = stressTensor[j](1, 2); // 2 + 6 = 8
+
+ buf[m++] = F[j](0, 0); // F is not symmetric
+ buf[m++] = F[j](0, 1);
+ buf[m++] = F[j](0, 2);
+ buf[m++] = F[j](1, 0);
+ buf[m++] = F[j](1, 1);
+ buf[m++] = F[j](1, 2);
+ buf[m++] = F[j](2, 0);
+ buf[m++] = F[j](2, 1);
+ buf[m++] = F[j](2, 2); // 8 + 9 = 17
+
+ buf[m++] = eff_plastic_strain[j]; // 18
+ }
+ return m;
}
/* ---------------------------------------------------------------------- */
void PairULSPH::unpack_forward_comm(int n, int first, double *buf) {
- double *vfrac = atom->vfrac;
- double *eff_plastic_strain = atom->eff_plastic_strain;
- int i, m, last;
-
- m = 0;
- last = first + n;
- for (i = first; i < last; i++) {
- vfrac[i] = buf[m++];
- c0[i] = buf[m++]; // 2
-
- stressTensor[i](0, 0) = buf[m++];
- stressTensor[i](1, 1) = buf[m++];
- stressTensor[i](2, 2) = buf[m++];
- stressTensor[i](0, 1) = buf[m++];
- stressTensor[i](0, 2) = buf[m++];
- stressTensor[i](1, 2) = buf[m++]; // 2 + 6 = 8
- stressTensor[i](1, 0) = stressTensor[i](0, 1);
- stressTensor[i](2, 0) = stressTensor[i](0, 2);
- stressTensor[i](2, 1) = stressTensor[i](1, 2);
-
- F[i](0, 0) = buf[m++];
- F[i](0, 1) = buf[m++];
- F[i](0, 2) = buf[m++];
- F[i](1, 0) = buf[m++];
- F[i](1, 1) = buf[m++];
- F[i](1, 2) = buf[m++];
- F[i](2, 0) = buf[m++];
- F[i](2, 1) = buf[m++];
- F[i](2, 2) = buf[m++]; // 8 + 9 = 17
-
- eff_plastic_strain[i] = buf[m++]; // 18
- }
+ double *vfrac = atom->vfrac;
+ double *eff_plastic_strain = atom->eff_plastic_strain;
+ int i, m, last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ vfrac[i] = buf[m++];
+ c0[i] = buf[m++]; // 2
+
+ stressTensor[i](0, 0) = buf[m++];
+ stressTensor[i](1, 1) = buf[m++];
+ stressTensor[i](2, 2) = buf[m++];
+ stressTensor[i](0, 1) = buf[m++];
+ stressTensor[i](0, 2) = buf[m++];
+ stressTensor[i](1, 2) = buf[m++]; // 2 + 6 = 8
+ stressTensor[i](1, 0) = stressTensor[i](0, 1);
+ stressTensor[i](2, 0) = stressTensor[i](0, 2);
+ stressTensor[i](2, 1) = stressTensor[i](1, 2);
+
+ F[i](0, 0) = buf[m++];
+ F[i](0, 1) = buf[m++];
+ F[i](0, 2) = buf[m++];
+ F[i](1, 0) = buf[m++];
+ F[i](1, 1) = buf[m++];
+ F[i](1, 2) = buf[m++];
+ F[i](2, 0) = buf[m++];
+ F[i](2, 1) = buf[m++];
+ F[i](2, 2) = buf[m++]; // 8 + 9 = 17
+
+ eff_plastic_strain[i] = buf[m++]; // 18
+ }
}
/*
@@ -1564,26 +1564,26 @@ void PairULSPH::unpack_forward_comm(int n, int first, double *buf) {
void *PairULSPH::extract(const char *str, int &i) {
//printf("in extract\n");
- if (strcmp(str, "smd/ulsph/smoothVel_ptr") == 0) {
- return (void *) smoothVel;
- } else if (strcmp(str, "smd/ulsph/stressTensor_ptr") == 0) {
- return (void *) stressTensor;
- } else if (strcmp(str, "smd/ulsph/velocityGradient_ptr") == 0) {
- return (void *) L;
- } else if (strcmp(str, "smd/ulsph/numNeighs_ptr") == 0) {
- return (void *) numNeighs;
- } else if (strcmp(str, "smd/ulsph/dtCFL_ptr") == 0) {
+ if (strcmp(str, "smd/ulsph/smoothVel_ptr") == 0) {
+ return (void *) smoothVel;
+ } else if (strcmp(str, "smd/ulsph/stressTensor_ptr") == 0) {
+ return (void *) stressTensor;
+ } else if (strcmp(str, "smd/ulsph/velocityGradient_ptr") == 0) {
+ return (void *) L;
+ } else if (strcmp(str, "smd/ulsph/numNeighs_ptr") == 0) {
+ return (void *) numNeighs;
+ } else if (strcmp(str, "smd/ulsph/dtCFL_ptr") == 0) {
//printf("dtcfl = %f\n", dtCFL);
- return (void *) &dtCFL;
- } else if (strcmp(str, "smd/ulsph/updateFlag_ptr") == 0) {
- return (void *) &updateFlag;
- } else if (strcmp(str, "smd/ulsph/effective_modulus_ptr") == 0) {
- return (void *) effm;
- } else if (strcmp(str, "smd/ulsph/shape_matrix_ptr") == 0) {
- return (void *) K;
- }
-
- return NULL;
+ return (void *) &dtCFL;
+ } else if (strcmp(str, "smd/ulsph/updateFlag_ptr") == 0) {
+ return (void *) &updateFlag;
+ } else if (strcmp(str, "smd/ulsph/effective_modulus_ptr") == 0) {
+ return (void *) effm;
+ } else if (strcmp(str, "smd/ulsph/shape_matrix_ptr") == 0) {
+ return (void *) K;
+ }
+
+ return NULL;
}
/* ----------------------------------------------------------------------
@@ -1591,31 +1591,31 @@ void *PairULSPH::extract(const char *str, int &i) {
------------------------------------------------------------------------- */
double PairULSPH::effective_shear_modulus(const Matrix3d d_dev, const Matrix3d deltaStressDev, const double dt, const int itype) {
- double G_eff; // effective shear modulus, see Pronto 2d eq. 3.4.7
- double deltaStressDevSum, shearRateSq, strain_increment;
-
- if (domain->dimension == 3) {
- deltaStressDevSum = deltaStressDev(0, 1) * deltaStressDev(0, 1) + deltaStressDev(0, 2) * deltaStressDev(0, 2)
- + deltaStressDev(1, 2) * deltaStressDev(1, 2);
- shearRateSq = d_dev(0, 1) * d_dev(0, 1) + d_dev(0, 2) * d_dev(0, 2) + d_dev(1, 2) * d_dev(1, 2);
- } else {
- deltaStressDevSum = deltaStressDev(0, 1) * deltaStressDev(0, 1);
- shearRateSq = d_dev(0, 1) * d_dev(0, 1);
- }
-
- strain_increment = dt * dt * shearRateSq;
-
- if (strain_increment > 1.0e-12) {
- G_eff = 0.5 * sqrt(deltaStressDevSum / strain_increment);
- } else {
- if (strength[itype] != NONE) {
- G_eff = Lookup[SHEAR_MODULUS][itype];
- } else {
- G_eff = 0.0;
- }
- }
-
- return G_eff;
+ double G_eff; // effective shear modulus, see Pronto 2d eq. 3.4.7
+ double deltaStressDevSum, shearRateSq, strain_increment;
+
+ if (domain->dimension == 3) {
+ deltaStressDevSum = deltaStressDev(0, 1) * deltaStressDev(0, 1) + deltaStressDev(0, 2) * deltaStressDev(0, 2)
+ + deltaStressDev(1, 2) * deltaStressDev(1, 2);
+ shearRateSq = d_dev(0, 1) * d_dev(0, 1) + d_dev(0, 2) * d_dev(0, 2) + d_dev(1, 2) * d_dev(1, 2);
+ } else {
+ deltaStressDevSum = deltaStressDev(0, 1) * deltaStressDev(0, 1);
+ shearRateSq = d_dev(0, 1) * d_dev(0, 1);
+ }
+
+ strain_increment = dt * dt * shearRateSq;
+
+ if (strain_increment > 1.0e-12) {
+ G_eff = 0.5 * sqrt(deltaStressDevSum / strain_increment);
+ } else {
+ if (strength[itype] != NONE) {
+ G_eff = Lookup[SHEAR_MODULUS][itype];
+ } else {
+ G_eff = 0.0;
+ }
+ }
+
+ return G_eff;
}
@@ -1625,26 +1625,26 @@ double PairULSPH::effective_shear_modulus(const Matrix3d d_dev, const Matrix3d d
------------------------------------------------------------------------- */
Vector3d PairULSPH::ComputeHourglassForce(const int i, const int itype, const int j, const int jtype, const Vector3d dv,
- const Vector3d xij, const Vector3d g, const double c_ij, const double mu_ij, const double rho_ij) {
-
- double *rmass = atom->rmass;
- Vector3d dv_est, f_hg;
- double visc_magnitude;
-
- dv_est = -0.5 * (F[i] + F[j]) * xij;
- double hurz = dv_est.dot(dv) / (dv_est.norm() * dv.norm() + 1.0e-16);
- if (hurz < 0.0) {
-
- visc_magnitude = 0.5 * (Q1[itype] + Q1[jtype]) * c_ij * mu_ij / rho_ij;
- f_hg = -rmass[i] * rmass[j] * visc_magnitude * g;
-// printf(" f_hg = %f %f %f\n", f_hg(0), f_hg(1), f_hg(2));
-// printf("\nnegative\n");
-// printf(" dv_est = %f %f %f\n", dv_est(0), dv_est(1), dv_est(2));
-// printf(" dv = %f %f %f\n", dv(0), dv(1), dv(2));
- } else {
- f_hg.setZero();
- }
-
- return f_hg;
+ const Vector3d xij, const Vector3d g, const double c_ij, const double mu_ij, const double rho_ij) {
+
+ double *rmass = atom->rmass;
+ Vector3d dv_est, f_hg;
+ double visc_magnitude;
+
+ dv_est = -0.5 * (F[i] + F[j]) * xij;
+ double hurz = dv_est.dot(dv) / (dv_est.norm() * dv.norm() + 1.0e-16);
+ if (hurz < 0.0) {
+
+ visc_magnitude = 0.5 * (Q1[itype] + Q1[jtype]) * c_ij * mu_ij / rho_ij;
+ f_hg = -rmass[i] * rmass[j] * visc_magnitude * g;
+// printf(" f_hg = %f %f %f\n", f_hg(0), f_hg(1), f_hg(2));
+// printf("\nnegative\n");
+// printf(" dv_est = %f %f %f\n", dv_est(0), dv_est(1), dv_est(2));
+// printf(" dv = %f %f %f\n", dv(0), dv(1), dv(2));
+ } else {
+ f_hg.setZero();
+ }
+
+ return f_hg;
}
diff --git a/src/USER-SMD/pair_smd_ulsph.h b/src/USER-SMD/pair_smd_ulsph.h
index 032079072e..435e0cb5a2 100644
--- a/src/USER-SMD/pair_smd_ulsph.h
+++ b/src/USER-SMD/pair_smd_ulsph.h
@@ -38,94 +38,94 @@ namespace LAMMPS_NS {
class PairULSPH: public Pair {
public:
- PairULSPH(class LAMMPS *);
- virtual ~PairULSPH();
- virtual void compute(int, int);
- void settings(int, char **);
- void coeff(int, char **);
- double init_one(int, int);
- void init_style();
- void init_list(int, class NeighList *);
- virtual double memory_usage();
- int pack_forward_comm(int, int *, double *, int, int *);
- void unpack_forward_comm(int, int, double *);
- void AssembleStressTensor();
- void *extract(const char *, int &);
- void PreCompute();
- void PreCompute_DensitySummation();
- double effective_shear_modulus(const Eigen::Matrix3d d_dev, const Eigen::Matrix3d deltaStressDev, const double dt, const int itype);
-
- Eigen::Vector3d ComputeHourglassForce(const int i, const int itype, const int j, const int jtype, const Eigen::Vector3d dv,
- const Eigen::Vector3d xij, const Eigen::Vector3d g, const double c_ij, const double mu_ij, const double rho_ij);
+ PairULSPH(class LAMMPS *);
+ virtual ~PairULSPH();
+ virtual void compute(int, int);
+ void settings(int, char **);
+ void coeff(int, char **);
+ double init_one(int, int);
+ void init_style();
+ void init_list(int, class NeighList *);
+ virtual double memory_usage();
+ int pack_forward_comm(int, int *, double *, int, int *);
+ void unpack_forward_comm(int, int, double *);
+ void AssembleStressTensor();
+ void *extract(const char *, int &);
+ void PreCompute();
+ void PreCompute_DensitySummation();
+ double effective_shear_modulus(const Eigen::Matrix3d d_dev, const Eigen::Matrix3d deltaStressDev, const double dt, const int itype);
+
+ Eigen::Vector3d ComputeHourglassForce(const int i, const int itype, const int j, const int jtype, const Eigen::Vector3d dv,
+ const Eigen::Vector3d xij, const Eigen::Vector3d g, const double c_ij, const double mu_ij, const double rho_ij);
protected:
- double *c0_type; // reference speed of sound defined per particle type
- double *rho0; // reference mass density per type
- double *Q1; // linear artificial viscosity coeff
- int *eos, *viscosity, *strength; // eos and strength material models
- double **artificial_pressure; // true/false: use Monaghan's artificial pressure correction?
- double **artificial_stress; // artificial stress amplitude
+ double *c0_type; // reference speed of sound defined per particle type
+ double *rho0; // reference mass density per type
+ double *Q1; // linear artificial viscosity coeff
+ int *eos, *viscosity, *strength; // eos and strength material models
+ double **artificial_pressure; // true/false: use Monaghan's artificial pressure correction?
+ double **artificial_stress; // artificial stress amplitude
- double *onerad_dynamic, *onerad_frozen;
- double *maxrad_dynamic, *maxrad_frozen;
+ double *onerad_dynamic, *onerad_frozen;
+ double *maxrad_dynamic, *maxrad_frozen;
- void allocate();
+ void allocate();
- int nmax; // max number of atoms on this proc
- int *numNeighs;
- Eigen::Matrix3d *K;
- double *shepardWeight, *c0, *rho;
- Eigen::Vector3d *smoothVel;
- Eigen::Matrix3d *stressTensor, *L, *F;
+ int nmax; // max number of atoms on this proc
+ int *numNeighs;
+ Eigen::Matrix3d *K;
+ double *shepardWeight, *c0, *rho;
+ Eigen::Vector3d *smoothVel;
+ Eigen::Matrix3d *stressTensor, *L, *F;
- double dtCFL;
+ double dtCFL;
private:
- // enumerate EOSs. MUST BE IN THE RANGE [1000, 2000)
- enum {
- EOS_LINEAR = 1000, EOS_PERFECT_GAS = 1001, EOS_TAIT = 1002,
- };
-
- // enumerate physical viscosity models. MUST BE IN THE RANGE [2000, 3000)
- enum {
- VISCOSITY_NEWTON = 2000
- };
-
- // enumerate strength models. MUST BE IN THE RANGE [3000, 4000)
- enum {
- STRENGTH_LINEAR = 3000, STRENGTH_LINEAR_PLASTIC = 3001
- };
-
- // enumerate some quantitities and associate these with integer values such that they can be used for lookup in an array structure
- enum {
- NONE = 0,
- BULK_MODULUS = 1,
- HOURGLASS_CONTROL_AMPLITUDE = 2,
- EOS_TAIT_EXPONENT = 3,
- REFERENCE_SOUNDSPEED = 4,
- REFERENCE_DENSITY = 5,
- EOS_PERFECT_GAS_GAMMA = 6,
- SHEAR_MODULUS = 7,
- YIELD_STRENGTH = 8,
- YOUNGS_MODULUS = 9,
- POISSON_RATIO = 10,
- LAME_LAMBDA = 11,
- HEAT_CAPACITY = 12,
- M_MODULUS = 13,
- HARDENING_PARAMETER = 14,
- VISCOSITY_MU = 15,
- MAX_KEY_VALUE = 16
- };
- double **Lookup; // holds per-type material parameters for the quantities defined in enum statement above.
-
- bool velocity_gradient_required;
- int updateFlag; // indicates if any relative particle pair movement is significant compared to smoothing length
-
-
- bool density_summation, density_continuity, velocity_gradient, gradient_correction_flag;
- double *effm;
+ // enumerate EOSs. MUST BE IN THE RANGE [1000, 2000)
+ enum {
+ EOS_LINEAR = 1000, EOS_PERFECT_GAS = 1001, EOS_TAIT = 1002,
+ };
+
+ // enumerate physical viscosity models. MUST BE IN THE RANGE [2000, 3000)
+ enum {
+ VISCOSITY_NEWTON = 2000
+ };
+
+ // enumerate strength models. MUST BE IN THE RANGE [3000, 4000)
+ enum {
+ STRENGTH_LINEAR = 3000, STRENGTH_LINEAR_PLASTIC = 3001
+ };
+
+ // enumerate some quantitities and associate these with integer values such that they can be used for lookup in an array structure
+ enum {
+ NONE = 0,
+ BULK_MODULUS = 1,
+ HOURGLASS_CONTROL_AMPLITUDE = 2,
+ EOS_TAIT_EXPONENT = 3,
+ REFERENCE_SOUNDSPEED = 4,
+ REFERENCE_DENSITY = 5,
+ EOS_PERFECT_GAS_GAMMA = 6,
+ SHEAR_MODULUS = 7,
+ YIELD_STRENGTH = 8,
+ YOUNGS_MODULUS = 9,
+ POISSON_RATIO = 10,
+ LAME_LAMBDA = 11,
+ HEAT_CAPACITY = 12,
+ M_MODULUS = 13,
+ HARDENING_PARAMETER = 14,
+ VISCOSITY_MU = 15,
+ MAX_KEY_VALUE = 16
+ };
+ double **Lookup; // holds per-type material parameters for the quantities defined in enum statement above.
+
+ bool velocity_gradient_required;
+ int updateFlag; // indicates if any relative particle pair movement is significant compared to smoothing length
+
+
+ bool density_summation, density_continuity, velocity_gradient, gradient_correction_flag;
+ double *effm;
};
diff --git a/src/USER-SMD/smd_kernels.h b/src/USER-SMD/smd_kernels.h
index 6621881f4b..3bc89b7e64 100644
--- a/src/USER-SMD/smd_kernels.h
+++ b/src/USER-SMD/smd_kernels.h
@@ -14,100 +14,100 @@
namespace SMD_Kernels {
static inline double Kernel_Wendland_Quintic_NotNormalized(const double r, const double h) {
- if (r < h) {
- double q = 2.0 * r / h;
- return pow(1.0 - 0.5 * q, 4) * (2.0 * q + 1.0);
- } else {
- return 0.0;
- }
+ if (r < h) {
+ double q = 2.0 * r / h;
+ return pow(1.0 - 0.5 * q, 4) * (2.0 * q + 1.0);
+ } else {
+ return 0.0;
+ }
}
static inline double Kernel_Cubic_Spline(const double r, const double h) {
- double q = 2.0 * r / h;
- if (q > 2.0) {
- return 0.0;
- } else if ((q <= 2.0) && (q > 1.0)) {
- return pow(2.0 - q, 3.0) / 6.0;
- } else if ((q >= 0.0) && (q <= 1.0)) {
- return 2. / 3. - q * q + 0.5 * q * q * q;
- } else {
- return 0.0;
- }
+ double q = 2.0 * r / h;
+ if (q > 2.0) {
+ return 0.0;
+ } else if ((q <= 2.0) && (q > 1.0)) {
+ return pow(2.0 - q, 3.0) / 6.0;
+ } else if ((q >= 0.0) && (q <= 1.0)) {
+ return 2. / 3. - q * q + 0.5 * q * q * q;
+ } else {
+ return 0.0;
+ }
}
static inline double Kernel_Barbara(const double r, const double h) {
- double arg = (1.570796327 * (r + h)) / h;
- double hsq = h * h;
- //wf = (1.680351548 * (cos(arg) + 1.)) / hsq;
- return -2.639490040 * sin(arg) / (hsq * h);
+ double arg = (1.570796327 * (r + h)) / h;
+ double hsq = h * h;
+ //wf = (1.680351548 * (cos(arg) + 1.)) / hsq;
+ return -2.639490040 * sin(arg) / (hsq * h);
}
static inline void spiky_kernel_and_derivative(const double h, const double r, const int dimension, double &wf, double &wfd) {
- /*
- * Spiky kernel
- */
-
- if (r > h) {
- printf("r=%f > h=%f in Spiky kernel\n", r, h);
- wf = wfd = 0.0;
- return;
- }
-
- double hr = h - r; // [m]
- if (dimension == 2) {
- double n = 0.3141592654e0 * h * h * h * h * h; // [m^5]
- wfd = -3.0e0 * hr * hr / n; // [m*m/m^5] = [1/m^3] ==> correct for dW/dr in 2D
- wf = -0.333333333333e0 * hr * wfd; // [m/m^3] ==> [1/m^2] correct for W in 2D
- } else {
- wfd = -14.0323944878e0 * hr * hr / (h * h * h * h * h * h); // [1/m^4] ==> correct for dW/dr in 3D
- wf = -0.333333333333e0 * hr * wfd; // [m/m^4] ==> [1/m^3] correct for W in 3D
- }
-
- // alternative formulation
-// double hr = h - r;
+ /*
+ * Spiky kernel
+ */
+
+ if (r > h) {
+ printf("r=%f > h=%f in Spiky kernel\n", r, h);
+ wf = wfd = 0.0;
+ return;
+ }
+
+ double hr = h - r; // [m]
+ if (dimension == 2) {
+ double n = 0.3141592654e0 * h * h * h * h * h; // [m^5]
+ wfd = -3.0e0 * hr * hr / n; // [m*m/m^5] = [1/m^3] ==> correct for dW/dr in 2D
+ wf = -0.333333333333e0 * hr * wfd; // [m/m^3] ==> [1/m^2] correct for W in 2D
+ } else {
+ wfd = -14.0323944878e0 * hr * hr / (h * h * h * h * h * h); // [1/m^4] ==> correct for dW/dr in 3D
+ wf = -0.333333333333e0 * hr * wfd; // [m/m^4] ==> [1/m^3] correct for W in 3D
+ }
+
+ // alternative formulation
+// double hr = h - r;
//
-// /*
-// * Spiky kernel
-// */
+// /*
+// * Spiky kernel
+// */
//
-// if (domain->dimension == 2) {
-// double h5 = h * h * h * h * h;
-// wf = 3.183098861e0 * hr * hr * hr / h5;
-// wfd = -9.549296583 * hr * hr / h5;
+// if (domain->dimension == 2) {
+// double h5 = h * h * h * h * h;
+// wf = 3.183098861e0 * hr * hr * hr / h5;
+// wfd = -9.549296583 * hr * hr / h5;
//
-// } else {
-// double h6 = h * h * h * h * h * h;
-// wf = 4.774648292 * hr * hr * hr / h6;
-// wfd = -14.32394487 * hr * hr / h6;
-// }
-// }
+// } else {
+// double h6 = h * h * h * h * h * h;
+// wf = 4.774648292 * hr * hr * hr / h6;
+// wfd = -14.32394487 * hr * hr / h6;
+// }
+// }
}
static inline void barbara_kernel_and_derivative(const double h, const double r, const int dimension, double &wf, double &wfd) {
- /*
- * Barbara kernel
- */
-
- double arg = (1.570796327 * (r + h)) / h;
- double hsq = h * h;
-
- if (r > h) {
- printf("r = %f > h = %f in barbara kernel function\n", r, h);
- exit(1);
- //wf = wfd = 0.0;
- //return;
- }
-
- if (dimension == 2) {
- wf = (1.680351548 * (cos(arg) + 1.)) / hsq;
- wfd = -2.639490040 * sin(arg) / (hsq * h);
- } else {
- wf = 2.051578323 * (cos(arg) + 1.) / (hsq * h);
- wfd = -3.222611694 * sin(arg) / (hsq * hsq);
- }
+ /*
+ * Barbara kernel
+ */
+
+ double arg = (1.570796327 * (r + h)) / h;
+ double hsq = h * h;
+
+ if (r > h) {
+ printf("r = %f > h = %f in barbara kernel function\n", r, h);
+ exit(1);
+ //wf = wfd = 0.0;
+ //return;
+ }
+
+ if (dimension == 2) {
+ wf = (1.680351548 * (cos(arg) + 1.)) / hsq;
+ wfd = -2.639490040 * sin(arg) / (hsq * h);
+ } else {
+ wf = 2.051578323 * (cos(arg) + 1.) / (hsq * h);
+ wfd = -3.222611694 * sin(arg) / (hsq * hsq);
+ }
}
/*
@@ -115,12 +115,12 @@ static inline void barbara_kernel_and_derivative(const double h, const double r,
*/
static inline void Poly6Kernel(const double hsq, const double h, const double rsq, const int dimension, double &wf) {
- double tmp = hsq - rsq;
- if (dimension == 2) {
- wf = tmp * tmp * tmp / (0.7853981635e0 * hsq * hsq * hsq * hsq);
- } else {
- wf = tmp * tmp * tmp / (0.6382918409e0 * hsq * hsq * hsq * hsq * h);
- }
+ double tmp = hsq - rsq;
+ if (dimension == 2) {
+ wf = tmp * tmp * tmp / (0.7853981635e0 * hsq * hsq * hsq * hsq);
+ } else {
+ wf = tmp * tmp * tmp / (0.6382918409e0 * hsq * hsq * hsq * hsq * h);
+ }
}
/*
@@ -128,15 +128,15 @@ static inline void Poly6Kernel(const double hsq, const double h, const double rs
*/
static inline void M4PrimeKernel(const double s, double &wf) {
- if (s < 1.0) {
- //wf = 1.0 - 2.5 * s * s + (3./2.) * s * s * s;
- wf = 1.0 - s * s *(2.5 -1.5 *s);
- } else if (s < 2.0) {
- //wf = 0.5 * (1.0 - s) * ((2.0 - s) * (2.0 - s));
- wf = 2.0 + (-4.0 + (2.5 - 0.5 * s)*s)*s;
- } else {
- wf = 0.0;
- }
+ if (s < 1.0) {
+ //wf = 1.0 - 2.5 * s * s + (3./2.) * s * s * s;
+ wf = 1.0 - s * s *(2.5 -1.5 *s);
+ } else if (s < 2.0) {
+ //wf = 0.5 * (1.0 - s) * ((2.0 - s) * (2.0 - s));
+ wf = 2.0 + (-4.0 + (2.5 - 0.5 * s)*s)*s;
+ } else {
+ wf = 0.0;
+ }
}
}
diff --git a/src/USER-SMD/smd_material_models.cpp b/src/USER-SMD/smd_material_models.cpp
index f1288ae5ca..93228f3724 100644
--- a/src/USER-SMD/smd_material_models.cpp
+++ b/src/USER-SMD/smd_material_models.cpp
@@ -41,13 +41,13 @@ using namespace Eigen;
------------------------------------------------------------------------- */
void LinearEOS(double lambda, double pInitial, double d, double dt, double &pFinal, double &p_rate) {
- /*
- * pressure rate
- */
- p_rate = lambda * d;
+ /*
+ * pressure rate
+ */
+ p_rate = lambda * d;
- pFinal = pInitial + dt * p_rate; // increment pressure using pressure rate
- //cout << "hurz" << endl;
+ pFinal = pInitial + dt * p_rate; // increment pressure using pressure rate
+ //cout << "hurz" << endl;
}
@@ -70,16 +70,16 @@ void LinearEOS(double lambda, double pInitial, double d, double dt, double &pFin
------------------------------------------------------------------------- */
void ShockEOS(double rho, double rho0, double e, double e0, double c0, double S, double Gamma, double pInitial, double dt,
- double &pFinal, double &p_rate) {
+ double &pFinal, double &p_rate) {
- double mu = rho / rho0 - 1.0;
- double pH = rho0 * square(c0) * mu * (1.0 + mu) / square(1.0 - (S - 1.0) * mu);
+ double mu = rho / rho0 - 1.0;
+ double pH = rho0 * square(c0) * mu * (1.0 + mu) / square(1.0 - (S - 1.0) * mu);
- pFinal = (-pH + rho * Gamma * (e - e0));
+ pFinal = (-pH + rho * Gamma * (e - e0));
- //printf("shock EOS: rho = %g, rho0 = %g, Gamma=%f, c0=%f, S=%f, e=%f, e0=%f\n", rho, rho0, Gamma, c0, S, e, e0);
- //printf("pFinal = %f\n", pFinal);
- p_rate = (pFinal - pInitial) / dt;
+ //printf("shock EOS: rho = %g, rho0 = %g, Gamma=%f, c0=%f, S=%f, e=%f, e0=%f\n", rho, rho0, Gamma, c0, S, e, e0);
+ //printf("pFinal = %f\n", pFinal);
+ p_rate = (pFinal - pInitial) / dt;
}
@@ -98,20 +98,20 @@ void ShockEOS(double rho, double rho0, double e, double e0, double c0, double S,
------------------------------------------------------------------------- */
void polynomialEOS(double rho, double rho0, double e, double C0, double C1, double C2, double C3, double C4, double C5, double C6,
- double pInitial, double dt, double &pFinal, double &p_rate) {
+ double pInitial, double dt, double &pFinal, double &p_rate) {
- double mu = rho / rho0 - 1.0;
+ double mu = rho / rho0 - 1.0;
- if (mu > 0.0) {
- pFinal = C0 + C1 * mu + C2 * mu * mu + C3 * mu * mu * mu; // + (C4 + C5 * mu + C6 * mu * mu) * e;
- } else {
- pFinal = C0 + C1 * mu + C3 * mu * mu * mu; // + (C4 + C5 * mu) * e;
- }
- pFinal = -pFinal; // we want the mean stress, not the pressure.
+ if (mu > 0.0) {
+ pFinal = C0 + C1 * mu + C2 * mu * mu + C3 * mu * mu * mu; // + (C4 + C5 * mu + C6 * mu * mu) * e;
+ } else {
+ pFinal = C0 + C1 * mu + C3 * mu * mu * mu; // + (C4 + C5 * mu) * e;
+ }
+ pFinal = -pFinal; // we want the mean stress, not the pressure.
- //printf("pFinal = %f\n", pFinal);
- p_rate = (pFinal - pInitial) / dt;
+ //printf("pFinal = %f\n", pFinal);
+ p_rate = (pFinal - pInitial) / dt;
}
@@ -126,17 +126,17 @@ void polynomialEOS(double rho, double rho0, double e, double C0, double C1, doub
(2) current speed of sound
------------------------------------------------------------------------- */
void TaitEOS_density(const double exponent, const double c0_reference, const double rho_reference, const double rho_current,
- double &pressure, double &sound_speed) {
+ double &pressure, double &sound_speed) {
- double B = rho_reference * c0_reference * c0_reference / exponent;
- double tmp = pow(rho_current / rho_reference, exponent);
- pressure = B * (tmp - 1.0);
- double bulk_modulus = B * tmp * exponent; // computed as rho * d(pressure)/d(rho)
- sound_speed = sqrt(bulk_modulus / rho_current);
+ double B = rho_reference * c0_reference * c0_reference / exponent;
+ double tmp = pow(rho_current / rho_reference, exponent);
+ pressure = B * (tmp - 1.0);
+ double bulk_modulus = B * tmp * exponent; // computed as rho * d(pressure)/d(rho)
+ sound_speed = sqrt(bulk_modulus / rho_current);
-// if (fabs(pressure) > 0.01) {
-// printf("tmp = %f, press=%f, K=%f\n", tmp, pressure, bulk_modulus);
-// }
+// if (fabs(pressure) > 0.01) {
+// printf("tmp = %f, press=%f, K=%f\n", tmp, pressure, bulk_modulus);
+// }
}
@@ -154,20 +154,20 @@ void TaitEOS_density(const double exponent, const double c0_reference, const dou
------------------------------------------------------------------------- */
void PerfectGasEOS(const double gamma, const double vol, const double mass, const double energy, double &pFinal, double &c0) {
- /*
- * perfect gas EOS is p = (gamma - 1) rho e
- */
+ /*
+ * perfect gas EOS is p = (gamma - 1) rho e
+ */
- if (energy > 0.0) {
+ if (energy > 0.0) {
- pFinal = (1.0 - gamma) * energy / vol;
+ pFinal = (1.0 - gamma) * energy / vol;
//printf("gamma = %f, vol%f, e=%g ==> p=%g\n", gamma, vol, energy, *pFinal__/1.0e-9);
- c0 = sqrt((gamma - 1.0) * energy / mass);
+ c0 = sqrt((gamma - 1.0) * energy / mass);
- } else {
- pFinal = c0 = 0.0;
- }
+ } else {
+ pFinal = c0 = 0.0;
+ }
}
@@ -179,17 +179,17 @@ void PerfectGasEOS(const double gamma, const double vol, const double mass, cons
output: sigmaFinal_dev, sigmaFinal_dev_rate__: final stress deviator and its rate.
------------------------------------------------------------------------- */
void LinearStrength(const double mu, const Matrix3d sigmaInitial_dev, const Matrix3d d_dev, const double dt,
- Matrix3d &sigmaFinal_dev__, Matrix3d &sigma_dev_rate__) {
+ Matrix3d &sigmaFinal_dev__, Matrix3d &sigma_dev_rate__) {
- /*
- * deviatoric rate of unrotated stress
- */
- sigma_dev_rate__ = 2.0 * mu * d_dev;
+ /*
+ * deviatoric rate of unrotated stress
+ */
+ sigma_dev_rate__ = 2.0 * mu * d_dev;
- /*
- * elastic update to the deviatoric stress
- */
- sigmaFinal_dev__ = sigmaInitial_dev + dt * sigma_dev_rate__;
+ /*
+ * elastic update to the deviatoric stress
+ */
+ sigmaFinal_dev__ = sigmaInitial_dev + dt * sigma_dev_rate__;
}
/* ----------------------------------------------------------------------
@@ -199,13 +199,13 @@ void LinearStrength(const double mu, const Matrix3d sigmaInitial_dev, const Matr
output: total stress tensor, deviator + pressure
------------------------------------------------------------------------- */
//void PairTlsph::LinearStrengthDefgrad(double lambda, double mu, Matrix3d F, Matrix3d *T) {
-// Matrix3d E, PK2, eye, sigma, S, tau;
+// Matrix3d E, PK2, eye, sigma, S, tau;
//
-// eye.setIdentity();
+// eye.setIdentity();
//
-// E = 0.5 * (F * F.transpose() - eye); // strain measure E = 0.5 * (B - I) = 0.5 * (F * F^T - I)
-// tau = lambda * E.trace() * eye + 2.0 * mu * E; // Kirchhoff stress, work conjugate to above strain
-// sigma = tau / F.determinant(); // convert Kirchhoff stress to Cauchy stress
+// E = 0.5 * (F * F.transpose() - eye); // strain measure E = 0.5 * (B - I) = 0.5 * (F * F^T - I)
+// tau = lambda * E.trace() * eye + 2.0 * mu * E; // Kirchhoff stress, work conjugate to above strain
+// sigma = tau / F.determinant(); // convert Kirchhoff stress to Cauchy stress
//
////printf("l=%f, mu=%f, sigma xy = %f\n", lambda, mu, sigma(0,1));
//
@@ -214,20 +214,20 @@ void LinearStrength(const double mu, const Matrix3d sigmaInitial_dev, const Matr
//// tau = F * S * F.transpose(); // convert PK2 to Kirchhoff stress
//// sigma = tau / F.determinant();
//
-// //*T = sigma;
+// //*T = sigma;
//
-// /*
-// * neo-hookean model due to Bonet
-// */
+// /*
+// * neo-hookean model due to Bonet
+// */
//// lambda = mu = 100.0;
//// // left Cauchy-Green Tensor, b = F.F^T
-// double J = F.determinant();
-// double logJ = log(J);
-// Matrix3d b;
-// b = F * F.transpose();
+// double J = F.determinant();
+// double logJ = log(J);
+// Matrix3d b;
+// b = F * F.transpose();
//
-// sigma = (mu / J) * (b - eye) + (lambda / J) * logJ * eye;
-// *T = sigma;
+// sigma = (mu / J) * (b - eye) + (lambda / J) * logJ * eye;
+// *T = sigma;
//}
/* ----------------------------------------------------------------------
linear strength model for use with linear elasticity
@@ -237,55 +237,55 @@ void LinearStrength(const double mu, const Matrix3d sigmaInitial_dev, const Matr
output: sigmaFinal_dev, sigmaFinal_dev_rate__: final stress deviator and its rate.
------------------------------------------------------------------------- */
void LinearPlasticStrength(const double G, const double yieldStress, const Matrix3d sigmaInitial_dev, const Matrix3d d_dev,
- const double dt, Matrix3d &sigmaFinal_dev__, Matrix3d &sigma_dev_rate__, double &plastic_strain_increment) {
-
- Matrix3d sigmaTrial_dev, dev_rate;
- double J2;
-
- /*
- * deviatoric rate of unrotated stress
- */
- dev_rate = 2.0 * G * d_dev;
-
- /*
- * perform a trial elastic update to the deviatoric stress
- */
- sigmaTrial_dev = sigmaInitial_dev + dt * dev_rate; // increment stress deviator using deviatoric rate
-
- /*
- * check yield condition
- */
- J2 = sqrt(3. / 2.) * sigmaTrial_dev.norm();
-
- if (J2 < yieldStress) {
- /*
- * no yielding has occured.
- * final deviatoric stress is trial deviatoric stress
- */
- sigma_dev_rate__ = dev_rate;
- sigmaFinal_dev__ = sigmaTrial_dev;
- plastic_strain_increment = 0.0;
- //printf("no yield\n");
-
- } else {
- //printf("yiedl\n");
- /*
- * yielding has occured
- */
- plastic_strain_increment = (J2 - yieldStress) / (3.0 * G);
-
- /*
- * new deviatoric stress:
- * obtain by scaling the trial stress deviator
- */
- sigmaFinal_dev__ = (yieldStress / J2) * sigmaTrial_dev;
-
- /*
- * new deviatoric stress rate
- */
- sigma_dev_rate__ = sigmaFinal_dev__ - sigmaInitial_dev;
- //printf("yielding has occured.\n");
- }
+ const double dt, Matrix3d &sigmaFinal_dev__, Matrix3d &sigma_dev_rate__, double &plastic_strain_increment) {
+
+ Matrix3d sigmaTrial_dev, dev_rate;
+ double J2;
+
+ /*
+ * deviatoric rate of unrotated stress
+ */
+ dev_rate = 2.0 * G * d_dev;
+
+ /*
+ * perform a trial elastic update to the deviatoric stress
+ */
+ sigmaTrial_dev = sigmaInitial_dev + dt * dev_rate; // increment stress deviator using deviatoric rate
+
+ /*
+ * check yield condition
+ */
+ J2 = sqrt(3. / 2.) * sigmaTrial_dev.norm();
+
+ if (J2 < yieldStress) {
+ /*
+ * no yielding has occured.
+ * final deviatoric stress is trial deviatoric stress
+ */
+ sigma_dev_rate__ = dev_rate;
+ sigmaFinal_dev__ = sigmaTrial_dev;
+ plastic_strain_increment = 0.0;
+ //printf("no yield\n");
+
+ } else {
+ //printf("yiedl\n");
+ /*
+ * yielding has occured
+ */
+ plastic_strain_increment = (J2 - yieldStress) / (3.0 * G);
+
+ /*
+ * new deviatoric stress:
+ * obtain by scaling the trial stress deviator
+ */
+ sigmaFinal_dev__ = (yieldStress / J2) * sigmaTrial_dev;
+
+ /*
+ * new deviatoric stress rate
+ */
+ sigma_dev_rate__ = sigmaFinal_dev__ - sigmaInitial_dev;
+ //printf("yielding has occured.\n");
+ }
}
/* ----------------------------------------------------------------------
@@ -307,66 +307,66 @@ void LinearPlasticStrength(const double G, const double yieldStress, const Matri
output: sigmaFinal_dev, sigmaFinal_dev_rate__: final stress deviator and its rate.
------------------------------------------------------------------------- */
void JohnsonCookStrength(const double G, const double cp, const double espec, const double A, const double B, const double a,
- const double C, const double epdot0, const double T0, const double Tmelt, const double M, const double dt, const double ep,
- const double epdot, const Matrix3d sigmaInitial_dev, const Matrix3d d_dev, Matrix3d &sigmaFinal_dev__,
- Matrix3d &sigma_dev_rate__, double &plastic_strain_increment) {
-
- Matrix3d sigmaTrial_dev, dev_rate;
- double J2, yieldStress;
-
- double deltaT = espec / cp;
- double TH = deltaT / (Tmelt - T0);
- TH = MAX(TH, 0.0);
- double epdot_ratio = epdot / epdot0;
- epdot_ratio = MAX(epdot_ratio, 1.0);
- //printf("current temperature delta is %f, TH=%f\n", deltaT, TH);
-
- yieldStress = (A + B * pow(ep, a)) * (1.0 + C * log(epdot_ratio)); // * (1.0 - pow(TH, M));
-
- /*
- * deviatoric rate of unrotated stress
- */
- dev_rate = 2.0 * G * d_dev;
-
- /*
- * perform a trial elastic update to the deviatoric stress
- */
- sigmaTrial_dev = sigmaInitial_dev + dt * dev_rate; // increment stress deviator using deviatoric rate
-
- /*
- * check yield condition
- */
- J2 = sqrt(3. / 2.) * sigmaTrial_dev.norm();
-
- if (J2 < yieldStress) {
- /*
- * no yielding has occured.
- * final deviatoric stress is trial deviatoric stress
- */
- sigma_dev_rate__ = dev_rate;
- sigmaFinal_dev__ = sigmaTrial_dev;
- plastic_strain_increment = 0.0;
- //printf("no yield\n");
-
- } else {
- //printf("yiedl\n");
- /*
- * yielding has occured
- */
- plastic_strain_increment = (J2 - yieldStress) / (3.0 * G);
-
- /*
- * new deviatoric stress:
- * obtain by scaling the trial stress deviator
- */
- sigmaFinal_dev__ = (yieldStress / J2) * sigmaTrial_dev;
-
- /*
- * new deviatoric stress rate
- */
- sigma_dev_rate__ = sigmaFinal_dev__ - sigmaInitial_dev;
- //printf("yielding has occured.\n");
- }
+ const double C, const double epdot0, const double T0, const double Tmelt, const double M, const double dt, const double ep,
+ const double epdot, const Matrix3d sigmaInitial_dev, const Matrix3d d_dev, Matrix3d &sigmaFinal_dev__,
+ Matrix3d &sigma_dev_rate__, double &plastic_strain_increment) {
+
+ Matrix3d sigmaTrial_dev, dev_rate;
+ double J2, yieldStress;
+
+ double deltaT = espec / cp;
+ double TH = deltaT / (Tmelt - T0);
+ TH = MAX(TH, 0.0);
+ double epdot_ratio = epdot / epdot0;
+ epdot_ratio = MAX(epdot_ratio, 1.0);
+ //printf("current temperature delta is %f, TH=%f\n", deltaT, TH);
+
+ yieldStress = (A + B * pow(ep, a)) * (1.0 + C * log(epdot_ratio)); // * (1.0 - pow(TH, M));
+
+ /*
+ * deviatoric rate of unrotated stress
+ */
+ dev_rate = 2.0 * G * d_dev;
+
+ /*
+ * perform a trial elastic update to the deviatoric stress
+ */
+ sigmaTrial_dev = sigmaInitial_dev + dt * dev_rate; // increment stress deviator using deviatoric rate
+
+ /*
+ * check yield condition
+ */
+ J2 = sqrt(3. / 2.) * sigmaTrial_dev.norm();
+
+ if (J2 < yieldStress) {
+ /*
+ * no yielding has occured.
+ * final deviatoric stress is trial deviatoric stress
+ */
+ sigma_dev_rate__ = dev_rate;
+ sigmaFinal_dev__ = sigmaTrial_dev;
+ plastic_strain_increment = 0.0;
+ //printf("no yield\n");
+
+ } else {
+ //printf("yiedl\n");
+ /*
+ * yielding has occured
+ */
+ plastic_strain_increment = (J2 - yieldStress) / (3.0 * G);
+
+ /*
+ * new deviatoric stress:
+ * obtain by scaling the trial stress deviator
+ */
+ sigmaFinal_dev__ = (yieldStress / J2) * sigmaTrial_dev;
+
+ /*
+ * new deviatoric stress rate
+ */
+ sigma_dev_rate__ = sigmaFinal_dev__ - sigmaInitial_dev;
+ //printf("yielding has occured.\n");
+ }
}
/* ----------------------------------------------------------------------
@@ -382,19 +382,19 @@ void JohnsonCookStrength(const double G, const double cp, const double espec, co
bool IsotropicMaxStrainDamage(const Matrix3d E, const double maxStrain) {
- /*
- * compute Eigenvalues of strain matrix
- */
- SelfAdjointEigenSolver < Matrix3d > es;
- es.compute(E); // compute eigenvalue and eigenvectors of strain
+ /*
+ * compute Eigenvalues of strain matrix
+ */
+ SelfAdjointEigenSolver < Matrix3d > es;
+ es.compute(E); // compute eigenvalue and eigenvectors of strain
- double max_eigenvalue = es.eigenvalues().maxCoeff();
+ double max_eigenvalue = es.eigenvalues().maxCoeff();
- if (max_eigenvalue > maxStrain) {
- return true;
- } else {
- return false;
- }
+ if (max_eigenvalue > maxStrain) {
+ return true;
+ } else {
+ return false;
+ }
}
/* ----------------------------------------------------------------------
@@ -410,19 +410,19 @@ bool IsotropicMaxStrainDamage(const Matrix3d E, const double maxStrain) {
bool IsotropicMaxStressDamage(const Matrix3d S, const double maxStress) {
- /*
- * compute Eigenvalues of strain matrix
- */
- SelfAdjointEigenSolver < Matrix3d > es;
- es.compute(S); // compute eigenvalue and eigenvectors of strain
+ /*
+ * compute Eigenvalues of strain matrix
+ */
+ SelfAdjointEigenSolver < Matrix3d > es;
+ es.compute(S); // compute eigenvalue and eigenvectors of strain
- double max_eigenvalue = es.eigenvalues().maxCoeff();
+ double max_eigenvalue = es.eigenvalues().maxCoeff();
- if (max_eigenvalue > maxStress) {
- return true;
- } else {
- return false;
- }
+ if (max_eigenvalue > maxStress) {
+ return true;
+ } else {
+ return false;
+ }
}
/* ----------------------------------------------------------------------
@@ -436,39 +436,39 @@ bool IsotropicMaxStressDamage(const Matrix3d S, const double maxStress) {
------------------------------------------------------------------------- */
double JohnsonCookFailureStrain(const double p, const Matrix3d Sdev, const double d1, const double d2, const double d3,
- const double d4, const double epdot0, const double epdot) {
+ const double d4, const double epdot0, const double epdot) {
- double vm = sqrt(3. / 2.) * Sdev.norm(); // von-Mises equivalent stress
- if (vm < 0.0) {
- cout << "this is sdev " << endl << Sdev << endl;
- printf("vm=%f < 0.0, surely must be an error\n", vm);
- exit(1);
- }
+ double vm = sqrt(3. / 2.) * Sdev.norm(); // von-Mises equivalent stress
+ if (vm < 0.0) {
+ cout << "this is sdev " << endl << Sdev << endl;
+ printf("vm=%f < 0.0, surely must be an error\n", vm);
+ exit(1);
+ }
- // determine stress triaxiality
- double triax = p / (vm + 0.01 * fabs(p)); // have softening in denominator to avoid divison by zero
- if (triax < 0.0) {
- triax = 0.0;
- } else if (triax > 3.0) {
- triax = 3.0;
- }
+ // determine stress triaxiality
+ double triax = p / (vm + 0.01 * fabs(p)); // have softening in denominator to avoid divison by zero
+ if (triax < 0.0) {
+ triax = 0.0;
+ } else if (triax > 3.0) {
+ triax = 3.0;
+ }
- // Johnson-Cook failure strain, dependence on stress triaxiality
- double jc_failure_strain = d1 + d2 * exp(d3 * triax);
+ // Johnson-Cook failure strain, dependence on stress triaxiality
+ double jc_failure_strain = d1 + d2 * exp(d3 * triax);
- // include strain rate dependency if parameter d4 is defined and current plastic strain rate exceeds reference strain rate
- if (d4 > 0.0) { //
- if (epdot > epdot0) {
- double epdot_ratio = epdot / epdot0;
- jc_failure_strain *= (1.0 + d4 * log(epdot_ratio));
- //printf("epsdot=%f, epsdot0=%f, factor = %f\n", epdot, epdot0, (1.0 + d4 * log(epdot_ratio)));
- //exit(1);
+ // include strain rate dependency if parameter d4 is defined and current plastic strain rate exceeds reference strain rate
+ if (d4 > 0.0) { //
+ if (epdot > epdot0) {
+ double epdot_ratio = epdot / epdot0;
+ jc_failure_strain *= (1.0 + d4 * log(epdot_ratio));
+ //printf("epsdot=%f, epsdot0=%f, factor = %f\n", epdot, epdot0, (1.0 + d4 * log(epdot_ratio)));
+ //exit(1);
- }
- }
+ }
+ }
- return jc_failure_strain;
+ return jc_failure_strain;
}
diff --git a/src/USER-SMD/smd_material_models.h b/src/USER-SMD/smd_material_models.h
index c6b6f8d94c..acb498c04d 100644
--- a/src/USER-SMD/smd_material_models.h
+++ b/src/USER-SMD/smd_material_models.h
@@ -32,24 +32,24 @@ using namespace Eigen;
*/
void LinearEOS(double lambda, double pInitial, double d, double dt, double &pFinal, double &p_rate);
void ShockEOS(double rho, double rho0, double e, double e0, double c0, double S, double Gamma, double pInitial, double dt,
- double &pFinal, double &p_rate);
+ double &pFinal, double &p_rate);
void polynomialEOS(double rho, double rho0, double e, double C0, double C1, double C2, double C3, double C4, double C5, double C6,
- double pInitial, double dt, double &pFinal, double &p_rate);
+ double pInitial, double dt, double &pFinal, double &p_rate);
void TaitEOS_density(const double exponent, const double c0_reference, const double rho_reference, const double rho_current,
- double &pressure, double &sound_speed);
+ double &pressure, double &sound_speed);
void PerfectGasEOS(const double gamma, const double vol, const double mass, const double energy, double &pFinal__, double &c0);
/*
* Material strength models
*/
void LinearStrength(const double mu, const Matrix3d sigmaInitial_dev, const Matrix3d d_dev, const double dt,
- Matrix3d &sigmaFinal_dev__, Matrix3d &sigma_dev_rate__);
+ Matrix3d &sigmaFinal_dev__, Matrix3d &sigma_dev_rate__);
void LinearPlasticStrength(const double G, const double yieldStress, const Matrix3d sigmaInitial_dev, const Matrix3d d_dev,
- const double dt, Matrix3d &sigmaFinal_dev__, Matrix3d &sigma_dev_rate__, double &plastic_strain_increment);
+ const double dt, Matrix3d &sigmaFinal_dev__, Matrix3d &sigma_dev_rate__, double &plastic_strain_increment);
void JohnsonCookStrength(const double G, const double cp, const double espec, const double A, const double B, const double a,
- const double C, const double epdot0, const double T0, const double Tmelt, const double M, const double dt, const double ep,
- const double epdot, const Matrix3d sigmaInitial_dev, const Matrix3d d_dev, Matrix3d &sigmaFinal_dev__,
- Matrix3d &sigma_dev_rate__, double &plastic_strain_increment);
+ const double C, const double epdot0, const double T0, const double Tmelt, const double M, const double dt, const double ep,
+ const double epdot, const Matrix3d sigmaInitial_dev, const Matrix3d d_dev, Matrix3d &sigmaFinal_dev__,
+ Matrix3d &sigma_dev_rate__, double &plastic_strain_increment);
/*
* Damage models
@@ -58,7 +58,7 @@ void JohnsonCookStrength(const double G, const double cp, const double espec, co
bool IsotropicMaxStrainDamage(const Matrix3d E, const double maxStrain);
bool IsotropicMaxStressDamage(const Matrix3d E, const double maxStrain);
double JohnsonCookFailureStrain(const double p, const Matrix3d Sdev, const double d1, const double d2, const double d3,
- const double d4, const double epdot0, const double epdot);
+ const double d4, const double epdot0, const double epdot);
diff --git a/src/USER-SMD/smd_math.h b/src/USER-SMD/smd_math.h
index b7bf9c112d..23d76f0fdb 100644
--- a/src/USER-SMD/smd_math.h
+++ b/src/USER-SMD/smd_math.h
@@ -20,22 +20,22 @@ using namespace std;
namespace SMD_Math {
static inline void LimitDoubleMagnitude(double &x, const double limit) {
- /*
- * if |x| exceeds limit, set x to limit with the sign of x
- */
- if (fabs(x) > limit) { // limit delVdotDelR to a fraction of speed of sound
- x = limit * copysign(1, x);
- }
+ /*
+ * if |x| exceeds limit, set x to limit with the sign of x
+ */
+ if (fabs(x) > limit) { // limit delVdotDelR to a fraction of speed of sound
+ x = limit * copysign(1, x);
+ }
}
/*
* deviator of a tensor
*/
static inline Matrix3d Deviator(const Matrix3d M) {
- Matrix3d eye;
- eye.setIdentity();
- eye *= M.trace() / 3.0;
- return M - eye;
+ Matrix3d eye;
+ eye.setIdentity();
+ eye *= M.trace() / 3.0;
+ return M - eye;
}
/*
@@ -55,50 +55,50 @@ static inline Matrix3d Deviator(const Matrix3d M) {
static inline bool PolDec(Matrix3d M, Matrix3d &R, Matrix3d &T, bool scaleF) {
- JacobiSVD<Matrix3d> svd(M, ComputeFullU | ComputeFullV); // SVD(A) = U S V*
- Vector3d S_eigenvalues = svd.singularValues();
- Matrix3d S = svd.singularValues().asDiagonal();
- Matrix3d U = svd.matrixU();
- Matrix3d V = svd.matrixV();
- Matrix3d eye;
- eye.setIdentity();
-
- // now do polar decomposition into M = R * T, where R is rotation
- // and T is translation matrix
- R = U * V.transpose();
- T = V * S * V.transpose();
-
- if (R.determinant() < 0.0) { // this is an improper rotation
- // identify the smallest entry in S and flip its sign
- int imin;
- S_eigenvalues.minCoeff(&imin);
- S(imin, imin) *= -1.0;
-
- R = M * V * S.inverse() * V.transpose(); // recompute R using flipped stretch eigenvalues
- }
-
- /*
- * scale S to avoid small principal strains
- */
-
- if (scaleF) {
- double min = 0.3; // 0.3^2 = 0.09, should suffice for most problems
- double max = 2.0;
- for (int i = 0; i < 3; i++) {
- if (S(i, i) < min) {
- S(i, i) = min;
- } else if (S(i, i) > max) {
- S(i, i) = max;
- }
- }
- T = V * S * V.transpose();
- }
-
- if (R.determinant() > 0.0) {
- return true;
- } else {
- return false;
- }
+ JacobiSVD<Matrix3d> svd(M, ComputeFullU | ComputeFullV); // SVD(A) = U S V*
+ Vector3d S_eigenvalues = svd.singularValues();
+ Matrix3d S = svd.singularValues().asDiagonal();
+ Matrix3d U = svd.matrixU();
+ Matrix3d V = svd.matrixV();
+ Matrix3d eye;
+ eye.setIdentity();
+
+ // now do polar decomposition into M = R * T, where R is rotation
+ // and T is translation matrix
+ R = U * V.transpose();
+ T = V * S * V.transpose();
+
+ if (R.determinant() < 0.0) { // this is an improper rotation
+ // identify the smallest entry in S and flip its sign
+ int imin;
+ S_eigenvalues.minCoeff(&imin);
+ S(imin, imin) *= -1.0;
+
+ R = M * V * S.inverse() * V.transpose(); // recompute R using flipped stretch eigenvalues
+ }
+
+ /*
+ * scale S to avoid small principal strains
+ */
+
+ if (scaleF) {
+ double min = 0.3; // 0.3^2 = 0.09, should suffice for most problems
+ double max = 2.0;
+ for (int i = 0; i < 3; i++) {
+ if (S(i, i) < min) {
+ S(i, i) = min;
+ } else if (S(i, i) > max) {
+ S(i, i) = max;
+ }
+ }
+ T = V * S * V.transpose();
+ }
+
+ if (R.determinant() > 0.0) {
+ return true;
+ } else {
+ return false;
+ }
}
/*
@@ -107,44 +107,44 @@ static inline bool PolDec(Matrix3d M, Matrix3d &R, Matrix3d &T, bool scaleF) {
static inline void pseudo_inverse_SVD(Matrix3d &M) {
- //JacobiSVD < Matrix3d > svd(M, ComputeFullU | ComputeFullV);
- JacobiSVD<Matrix3d> svd(M, ComputeFullU); // one Eigevector base is sufficient because matrix is square and symmetric
+ //JacobiSVD < Matrix3d > svd(M, ComputeFullU | ComputeFullV);
+ JacobiSVD<Matrix3d> svd(M, ComputeFullU); // one Eigevector base is sufficient because matrix is square and symmetric
- Vector3d singularValuesInv;
- Vector3d singularValues = svd.singularValues();
+ Vector3d singularValuesInv;
+ Vector3d singularValues = svd.singularValues();
//cout << "Here is the matrix V:" << endl << V * singularValues.asDiagonal() * U << endl;
//cout << "Its singular values are:" << endl << singularValues << endl;
- double pinvtoler = 1.0e-16; // 2d machining example goes unstable if this value is increased (1.0e-16).
- for (int row = 0; row < 3; row++) {
- if (singularValues(row) > pinvtoler) {
- singularValuesInv(row) = 1.0 / singularValues(row);
- } else {
- singularValuesInv(row) = 0.0;
- }
- }
+ double pinvtoler = 1.0e-16; // 2d machining example goes unstable if this value is increased (1.0e-16).
+ for (int row = 0; row < 3; row++) {
+ if (singularValues(row) > pinvtoler) {
+ singularValuesInv(row) = 1.0 / singularValues(row);
+ } else {
+ singularValuesInv(row) = 0.0;
+ }
+ }
- M = svd.matrixU() * singularValuesInv.asDiagonal() * svd.matrixU().transpose();
+ M = svd.matrixU() * singularValuesInv.asDiagonal() * svd.matrixU().transpose();
-// JacobiSVD < Matrix3d > svd(M, ComputeFullU | ComputeFullV);
+// JacobiSVD < Matrix3d > svd(M, ComputeFullU | ComputeFullV);
//
-// Vector3d singularValuesInv;
-// Vector3d singularValues = svd.singularValues();
+// Vector3d singularValuesInv;
+// Vector3d singularValues = svd.singularValues();
//
-// //cout << "Here is the matrix V:" << endl << V * singularValues.asDiagonal() * U << endl;
-// //cout << "Its singular values are:" << endl << singularValues << endl;
+// //cout << "Here is the matrix V:" << endl << V * singularValues.asDiagonal() * U << endl;
+// //cout << "Its singular values are:" << endl << singularValues << endl;
//
-// double pinvtoler = 1.0e-16; // 2d machining example goes unstable if this value is increased (1.0e-16).
-// for (int row = 0; row < 3; row++) {
-// if (singularValues(row) > pinvtoler) {
-// singularValuesInv(row) = 1.0 / singularValues(row);
-// } else {
-// singularValuesInv(row) = 0.0;
-// }
-// }
+// double pinvtoler = 1.0e-16; // 2d machining example goes unstable if this value is increased (1.0e-16).
+// for (int row = 0; row < 3; row++) {
+// if (singularValues(row) > pinvtoler) {
+// singularValuesInv(row) = 1.0 / singularValues(row);
+// } else {
+// singularValuesInv(row) = 0.0;
+// }
+// }
//
-// M = svd.matrixU() * singularValuesInv.asDiagonal() * svd.matrixV().transpose();
+// M = svd.matrixU() * singularValuesInv.asDiagonal() * svd.matrixV().transpose();
}
@@ -152,15 +152,15 @@ static inline void pseudo_inverse_SVD(Matrix3d &M) {
* test if two matrices are equal
*/
static inline double TestMatricesEqual(Matrix3d A, Matrix3d B, double eps) {
- Matrix3d diff;
- diff = A - B;
- double norm = diff.norm();
- if (norm > eps) {
- printf("Matrices A and B are not equal! The L2-norm difference is: %g\n", norm);
- cout << "Here is matrix A:" << endl << A << endl;
- cout << "Here is matrix B:" << endl << B << endl;
- }
- return norm;
+ Matrix3d diff;
+ diff = A - B;
+ double norm = diff.norm();
+ if (norm > eps) {
+ printf("Matrices A and B are not equal! The L2-norm difference is: %g\n", norm);
+ cout << "Here is matrix A:" << endl << A << endl;
+ cout << "Here is matrix B:" << endl << B << endl;
+ }
+ return norm;
}
/* ----------------------------------------------------------------------
@@ -169,116 +169,116 @@ static inline double TestMatricesEqual(Matrix3d A, Matrix3d B, double eps) {
static inline Matrix3d LimitEigenvalues(Matrix3d S, double limitEigenvalue) {
- /*
- * compute Eigenvalues of matrix S
- */
- SelfAdjointEigenSolver < Matrix3d > es;
- es.compute(S);
-
- double max_eigenvalue = es.eigenvalues().maxCoeff();
- double min_eigenvalue = es.eigenvalues().minCoeff();
- double amax_eigenvalue = fabs(max_eigenvalue);
- double amin_eigenvalue = fabs(min_eigenvalue);
-
- if ((amax_eigenvalue > limitEigenvalue) || (amin_eigenvalue > limitEigenvalue)) {
- if (amax_eigenvalue > amin_eigenvalue) { // need to scale with max_eigenvalue
- double scale = amax_eigenvalue / limitEigenvalue;
- Matrix3d V = es.eigenvectors();
- Matrix3d S_diag = V.inverse() * S * V; // diagonalized input matrix
- S_diag /= scale;
- Matrix3d S_scaled = V * S_diag * V.inverse(); // undiagonalize matrix
- return S_scaled;
- } else { // need to scale using min_eigenvalue
- double scale = amin_eigenvalue / limitEigenvalue;
- Matrix3d V = es.eigenvectors();
- Matrix3d S_diag = V.inverse() * S * V; // diagonalized input matrix
- S_diag /= scale;
- Matrix3d S_scaled = V * S_diag * V.inverse(); // undiagonalize matrix
- return S_scaled;
- }
- } else { // limiting does not apply
- return S;
- }
+ /*
+ * compute Eigenvalues of matrix S
+ */
+ SelfAdjointEigenSolver < Matrix3d > es;
+ es.compute(S);
+
+ double max_eigenvalue = es.eigenvalues().maxCoeff();
+ double min_eigenvalue = es.eigenvalues().minCoeff();
+ double amax_eigenvalue = fabs(max_eigenvalue);
+ double amin_eigenvalue = fabs(min_eigenvalue);
+
+ if ((amax_eigenvalue > limitEigenvalue) || (amin_eigenvalue > limitEigenvalue)) {
+ if (amax_eigenvalue > amin_eigenvalue) { // need to scale with max_eigenvalue
+ double scale = amax_eigenvalue / limitEigenvalue;
+ Matrix3d V = es.eigenvectors();
+ Matrix3d S_diag = V.inverse() * S * V; // diagonalized input matrix
+ S_diag /= scale;
+ Matrix3d S_scaled = V * S_diag * V.inverse(); // undiagonalize matrix
+ return S_scaled;
+ } else { // need to scale using min_eigenvalue
+ double scale = amin_eigenvalue / limitEigenvalue;
+ Matrix3d V = es.eigenvectors();
+ Matrix3d S_diag = V.inverse() * S * V; // diagonalized input matrix
+ S_diag /= scale;
+ Matrix3d S_scaled = V * S_diag * V.inverse(); // undiagonalize matrix
+ return S_scaled;
+ }
+ } else { // limiting does not apply
+ return S;
+ }
}
static inline bool LimitMinMaxEigenvalues(Matrix3d &S, double min, double max) {
- /*
- * compute Eigenvalues of matrix S
- */
- SelfAdjointEigenSolver < Matrix3d > es;
- es.compute(S);
-
- if ((es.eigenvalues().maxCoeff() > max) || (es.eigenvalues().minCoeff() < min)) {
- Matrix3d S_diag = es.eigenvalues().asDiagonal();
- Matrix3d V = es.eigenvectors();
- for (int i = 0; i < 3; i++) {
- if (S_diag(i, i) < min) {
- //printf("limiting eigenvalue %f --> %f\n", S_diag(i, i), min);
- //printf("these are the eigenvalues of U: %f %f %f\n", es.eigenvalues()(0), es.eigenvalues()(1), es.eigenvalues()(2));
- S_diag(i, i) = min;
- } else if (S_diag(i, i) > max) {
- //printf("limiting eigenvalue %f --> %f\n", S_diag(i, i), max);
- S_diag(i, i) = max;
- }
- }
- S = V * S_diag * V.inverse(); // undiagonalize matrix
- return true;
- } else {
- return false;
- }
+ /*
+ * compute Eigenvalues of matrix S
+ */
+ SelfAdjointEigenSolver < Matrix3d > es;
+ es.compute(S);
+
+ if ((es.eigenvalues().maxCoeff() > max) || (es.eigenvalues().minCoeff() < min)) {
+ Matrix3d S_diag = es.eigenvalues().asDiagonal();
+ Matrix3d V = es.eigenvectors();
+ for (int i = 0; i < 3; i++) {
+ if (S_diag(i, i) < min) {
+ //printf("limiting eigenvalue %f --> %f\n", S_diag(i, i), min);
+ //printf("these are the eigenvalues of U: %f %f %f\n", es.eigenvalues()(0), es.eigenvalues()(1), es.eigenvalues()(2));
+ S_diag(i, i) = min;
+ } else if (S_diag(i, i) > max) {
+ //printf("limiting eigenvalue %f --> %f\n", S_diag(i, i), max);
+ S_diag(i, i) = max;
+ }
+ }
+ S = V * S_diag * V.inverse(); // undiagonalize matrix
+ return true;
+ } else {
+ return false;
+ }
}
static inline void reconstruct_rank_deficient_shape_matrix(Matrix3d &K) {
- JacobiSVD<Matrix3d> svd(K, ComputeFullU | ComputeFullV);
- Vector3d singularValues = svd.singularValues();
+ JacobiSVD<Matrix3d> svd(K, ComputeFullU | ComputeFullV);
+ Vector3d singularValues = svd.singularValues();
- for (int i = 0; i < 3; i++) {
- if (singularValues(i) < 1.0e-8) {
- singularValues(i) = 1.0;
- }
- }
+ for (int i = 0; i < 3; i++) {
+ if (singularValues(i) < 1.0e-8) {
+ singularValues(i) = 1.0;
+ }
+ }
-// int imin;
-// double minev = singularValues.minCoeff(&imin);
+// int imin;
+// double minev = singularValues.minCoeff(&imin);
//
-// printf("min eigenvalue=%f has index %d\n", minev, imin);
-// Vector3d singularVec = U.col(0).cross(U.col(1));
-// cout << "the eigenvalues are " << endl << singularValues << endl;
-// cout << "the singular vector is " << endl << singularVec << endl;
+// printf("min eigenvalue=%f has index %d\n", minev, imin);
+// Vector3d singularVec = U.col(0).cross(U.col(1));
+// cout << "the eigenvalues are " << endl << singularValues << endl;
+// cout << "the singular vector is " << endl << singularVec << endl;
//
-// // reconstruct original K
+// // reconstruct original K
//
-// singularValues(2) = 1.0;
+// singularValues(2) = 1.0;
- K = svd.matrixU() * singularValues.asDiagonal() * svd.matrixV().transpose();
- //cout << "the reconstructed K is " << endl << K << endl;
- //exit(1);
+ K = svd.matrixU() * singularValues.asDiagonal() * svd.matrixV().transpose();
+ //cout << "the reconstructed K is " << endl << K << endl;
+ //exit(1);
}
/* ----------------------------------------------------------------------
helper functions for crack_exclude
------------------------------------------------------------------------- */
static inline bool IsOnSegment(double xi, double yi, double xj, double yj, double xk, double yk) {
- return (xi <= xk || xj <= xk) && (xk <= xi || xk <= xj) && (yi <= yk || yj <= yk) && (yk <= yi || yk <= yj);
+ return (xi <= xk || xj <= xk) && (xk <= xi || xk <= xj) && (yi <= yk || yj <= yk) && (yk <= yi || yk <= yj);
}
static inline char ComputeDirection(double xi, double yi, double xj, double yj, double xk, double yk) {
- double a = (xk - xi) * (yj - yi);
- double b = (xj - xi) * (yk - yi);
- return a < b ? -1.0 : a > b ? 1.0 : 0;
+ double a = (xk - xi) * (yj - yi);
+ double b = (xj - xi) * (yk - yi);
+ return a < b ? -1.0 : a > b ? 1.0 : 0;
}
/** Do line segments (x1, y1)--(x2, y2) and (x3, y3)--(x4, y4) intersect? */
static inline bool DoLineSegmentsIntersect(double x1, double y1, double x2, double y2, double x3, double y3, double x4, double y4) {
- char d1 = ComputeDirection(x3, y3, x4, y4, x1, y1);
- char d2 = ComputeDirection(x3, y3, x4, y4, x2, y2);
- char d3 = ComputeDirection(x1, y1, x2, y2, x3, y3);
- char d4 = ComputeDirection(x1, y1, x2, y2, x4, y4);
- return (((d1 > 0 && d2 < 0) || (d1 < 0 && d2 > 0)) && ((d3 > 0 && d4 < 0) || (d3 < 0 && d4 > 0)))
- || (d1 == 0 && IsOnSegment(x3, y3, x4, y4, x1, y1)) || (d2 == 0 && IsOnSegment(x3, y3, x4, y4, x2, y2))
- || (d3 == 0 && IsOnSegment(x1, y1, x2, y2, x3, y3)) || (d4 == 0 && IsOnSegment(x1, y1, x2, y2, x4, y4));
+ char d1 = ComputeDirection(x3, y3, x4, y4, x1, y1);
+ char d2 = ComputeDirection(x3, y3, x4, y4, x2, y2);
+ char d3 = ComputeDirection(x1, y1, x2, y2, x3, y3);
+ char d4 = ComputeDirection(x1, y1, x2, y2, x4, y4);
+ return (((d1 > 0 && d2 < 0) || (d1 < 0 && d2 > 0)) && ((d3 > 0 && d4 < 0) || (d3 < 0 && d4 > 0)))
+ || (d1 == 0 && IsOnSegment(x3, y3, x4, y4, x1, y1)) || (d2 == 0 && IsOnSegment(x3, y3, x4, y4, x2, y2))
+ || (d3 == 0 && IsOnSegment(x1, y1, x2, y2, x3, y3)) || (d4 == 0 && IsOnSegment(x1, y1, x2, y2, x4, y4));
}
}
diff --git a/src/VORONOI/compute_voronoi_atom.cpp b/src/VORONOI/compute_voronoi_atom.cpp
index 5e49b72c66..cd7d73392d 100644
--- a/src/VORONOI/compute_voronoi_atom.cpp
+++ b/src/VORONOI/compute_voronoi_atom.cpp
@@ -80,7 +80,7 @@ ComputeVoronoi::ComputeVoronoi(LAMMPS *lmp, int narg, char **arg) :
}
else if (strcmp(arg[iarg], "radius") == 0) {
if (iarg + 2 > narg || strstr(arg[iarg+1],"v_") != arg[iarg+1] )
- error->all(FLERR,"Illegal compute voronoi/atom command");
+ error->all(FLERR,"Illegal compute voronoi/atom command");
int n = strlen(&arg[iarg+1][2]) + 1;
radstr = new char[n];
strcpy(radstr,&arg[iarg+1][2]);
@@ -274,8 +274,8 @@ void ComputeVoronoi::buildCells()
sublo_bound[i] = sublo_lamda[i]-cut[i]-e;
subhi_bound[i] = subhi_lamda[i]+cut[i]+e;
if (domain->periodicity[i]==0) {
- sublo_bound[i] = MAX(sublo_bound[i],0.0);
- subhi_bound[i] = MIN(subhi_bound[i],1.0);
+ sublo_bound[i] = MAX(sublo_bound[i],0.0);
+ subhi_bound[i] = MIN(subhi_bound[i],1.0);
}
}
if (dim == 2) {
@@ -295,8 +295,8 @@ void ComputeVoronoi::buildCells()
sublo_bound[i] = sublo[i]-cut[i]-e;
subhi_bound[i] = subhi[i]+cut[i]+e;
if (domain->periodicity[i]==0) {
- sublo_bound[i] = MAX(sublo_bound[i],domain->boxlo[i]);
- subhi_bound[i] = MIN(subhi_bound[i],domain->boxhi[i]);
+ sublo_bound[i] = MAX(sublo_bound[i],domain->boxlo[i]);
+ subhi_bound[i] = MIN(subhi_bound[i],domain->boxhi[i]);
}
}
if (dim == 2) {
@@ -345,13 +345,13 @@ void ComputeVoronoi::buildCells()
// polydisperse voro++ container
delete con_poly;
con_poly = new container_poly(sublo_bound[0],
- subhi_bound[0],
- sublo_bound[1],
- subhi_bound[1],
- sublo_bound[2],
- subhi_bound[2],
- int(n[0]),int(n[1]),int(n[2]),
- false,false,false,8);
+ subhi_bound[0],
+ sublo_bound[1],
+ subhi_bound[1],
+ sublo_bound[2],
+ subhi_bound[2],
+ int(n[0]),int(n[1]),int(n[2]),
+ false,false,false,8);
// pass coordinates for local and ghost atoms to voro++
for (i = 0; i < nall; i++) {
@@ -363,13 +363,13 @@ void ComputeVoronoi::buildCells()
delete con_mono;
con_mono = new container(sublo_bound[0],
- subhi_bound[0],
- sublo_bound[1],
- subhi_bound[1],
- sublo_bound[2],
- subhi_bound[2],
- int(n[0]),int(n[1]),int(n[2]),
- false,false,false,8);
+ subhi_bound[0],
+ sublo_bound[1],
+ subhi_bound[1],
+ sublo_bound[2],
+ subhi_bound[2],
+ int(n[0]),int(n[1]),int(n[2]),
+ false,false,false,8);
// pass coordinates for local and ghost atoms to voro++
for (i = 0; i < nall; i++)
@@ -581,9 +581,9 @@ void ComputeVoronoi::processCell(voronoicell_neighbor &c, int i)
if (faces_flag) {
if (nfaces+voro[i][1] > nfacesmax) {
- while (nfacesmax < nfaces+voro[i][1]) nfacesmax += FACESDELTA;
- memory->grow(faces,nfacesmax,size_local_cols,"compute/voronoi/atom:faces");
- array_local = faces;
+ while (nfacesmax < nfaces+voro[i][1]) nfacesmax += FACESDELTA;
+ memory->grow(faces,nfacesmax,size_local_cols,"compute/voronoi/atom:faces");
+ array_local = faces;
}
if (!have_narea) c.face_areas(narea);
@@ -594,19 +594,19 @@ void ComputeVoronoi::processCell(voronoicell_neighbor &c, int i)
tagint *tag = atom->tag;
itag = tag[i];
for (j=0; j<neighs; ++j)
- if (narea[j] > fthresh) {
+ if (narea[j] > fthresh) {
- // external faces assigned the tag 0
+ // external faces assigned the tag 0
- int jj = neigh[j];
- if (jj >= 0) jtag = tag[jj];
- else jtag = 0;
+ int jj = neigh[j];
+ if (jj >= 0) jtag = tag[jj];
+ else jtag = 0;
- faces[nfaces][0] = itag;
- faces[nfaces][1] = jtag;
- faces[nfaces][2] = narea[j];
- nfaces++;
- }
+ faces[nfaces][0] = itag;
+ faces[nfaces][1] = jtag;
+ faces[nfaces][2] = narea[j];
+ nfaces++;
+ }
}
diff --git a/src/atom.cpp b/src/atom.cpp
index fa86046d23..aeb3c1303e 100644
--- a/src/atom.cpp
+++ b/src/atom.cpp
@@ -1387,27 +1387,27 @@ void Atom::data_bodies(int n, char *buf, AtomVecBody *avec_body,
if ((m = map(tagdata)) >= 0) {
if (ninteger > maxint) {
- delete [] ivalues;
- maxint = ninteger;
- ivalues = new int[maxint];
+ delete [] ivalues;
+ maxint = ninteger;
+ ivalues = new int[maxint];
}
if (ndouble > maxdouble) {
- delete [] dvalues;
- maxdouble = ndouble;
- dvalues = new double[maxdouble];
+ delete [] dvalues;
+ maxdouble = ndouble;
+ dvalues = new double[maxdouble];
}
for (j = 0; j < ninteger; j++)
- ivalues[j] = force->inumeric(FLERR,strtok(NULL," \t\n\r\f"));
+ ivalues[j] = force->inumeric(FLERR,strtok(NULL," \t\n\r\f"));
for (j = 0; j < ndouble; j++)
- dvalues[j] = force->numeric(FLERR,strtok(NULL," \t\n\r\f"));
+ dvalues[j] = force->numeric(FLERR,strtok(NULL," \t\n\r\f"));
avec_body->data_body(m,ninteger,ndouble,ivalues,dvalues);
} else {
nvalues = ninteger + ndouble; // number of values to skip
for (j = 0; j < nvalues; j++)
- strtok(NULL," \t\n\r\f");
+ strtok(NULL," \t\n\r\f");
}
}
@@ -1673,7 +1673,7 @@ void Atom::add_molecule_atom(Molecule *onemol, int iatom,
if (onemol->bodyflag) {
body[ilocal] = 0; // as if a body read from data file
onemol->avec_body->data_body(ilocal,onemol->nibody,onemol->ndbody,
- onemol->ibodyparams,onemol->dbodyparams);
+ onemol->ibodyparams,onemol->dbodyparams);
onemol->avec_body->set_quat(ilocal,onemol->quat_external);
}
diff --git a/src/atom_vec_body.cpp b/src/atom_vec_body.cpp
index ca080ff0b6..b7422cf229 100644
--- a/src/atom_vec_body.cpp
+++ b/src/atom_vec_body.cpp
@@ -1055,9 +1055,9 @@ int AtomVecBody::unpack_exchange(double *buf)
bonus[nlocal_bonus].ndouble = (int) ubuf(buf[m++]).i;
// corresponding put() calls are in copy()
bonus[nlocal_bonus].ivalue = icp->get(bonus[nlocal_bonus].ninteger,
- bonus[nlocal_bonus].iindex);
+ bonus[nlocal_bonus].iindex);
bonus[nlocal_bonus].dvalue = dcp->get(bonus[nlocal_bonus].ndouble,
- bonus[nlocal_bonus].dindex);
+ bonus[nlocal_bonus].dindex);
memcpy(bonus[nlocal_bonus].ivalue,&buf[m],
bonus[nlocal_bonus].ninteger*sizeof(int));
if (intdoubleratio == 1) m += bonus[nlocal_bonus].ninteger;
@@ -1209,9 +1209,9 @@ int AtomVecBody::unpack_restart(double *buf)
bonus[nlocal_bonus].ninteger = (int) ubuf(buf[m++]).i;
bonus[nlocal_bonus].ndouble = (int) ubuf(buf[m++]).i;
bonus[nlocal_bonus].ivalue = icp->get(bonus[nlocal_bonus].ninteger,
- bonus[nlocal_bonus].iindex);
+ bonus[nlocal_bonus].iindex);
bonus[nlocal_bonus].dvalue = dcp->get(bonus[nlocal_bonus].ndouble,
- bonus[nlocal_bonus].dindex);
+ bonus[nlocal_bonus].dindex);
memcpy(bonus[nlocal_bonus].ivalue,&buf[m],
bonus[nlocal_bonus].ninteger*sizeof(int));
if (intdoubleratio == 1) m += bonus[nlocal_bonus].ninteger;
@@ -1331,7 +1331,7 @@ int AtomVecBody::data_atom_hybrid(int nlocal, char **values)
------------------------------------------------------------------------- */
void AtomVecBody::data_body(int m, int ninteger, int ndouble,
- int *ivalues, double *dvalues)
+ int *ivalues, double *dvalues)
{
if (body[m]) error->one(FLERR,"Assigning body parameters to non-body atom");
if (nlocal_bonus == nmax_bonus) grow_bonus();
@@ -1482,7 +1482,7 @@ int AtomVecBody::write_vel_hybrid(FILE *fp, double *buf)
------------------------------------------------------------------------- */
double AtomVecBody::radius_body(int ninteger, int ndouble,
- int *ivalues, double *dvalues)
+ int *ivalues, double *dvalues)
{
return bptr->radius_body(ninteger,ndouble,ivalues,dvalues);
}
diff --git a/src/comm.cpp b/src/comm.cpp
index d997c2914f..14d2d70c5a 100644
--- a/src/comm.cpp
+++ b/src/comm.cpp
@@ -743,8 +743,8 @@ int Comm::read_lines_from_file(FILE *fp, int nlines, int maxline, char *buf)
m = 0;
for (int i = 0; i < nlines; i++) {
if (!fgets(&buf[m],maxline,fp)) {
- m = 0;
- break;
+ m = 0;
+ break;
}
m += strlen(&buf[m]);
}
@@ -779,8 +779,8 @@ int Comm::read_lines_from_file_universe(FILE *fp, int nlines, int maxline,
m = 0;
for (int i = 0; i < nlines; i++) {
if (!fgets(&buf[m],maxline,fp)) {
- m = 0;
- break;
+ m = 0;
+ break;
}
m += strlen(&buf[m]);
}
diff --git a/src/compute_chunk_atom.cpp b/src/compute_chunk_atom.cpp
index d08f462907..4463e48fa8 100644
--- a/src/compute_chunk_atom.cpp
+++ b/src/compute_chunk_atom.cpp
@@ -407,14 +407,14 @@ ComputeChunkAtom::ComputeChunkAtom(LAMMPS *lmp, int narg, char **arg) :
if (which == BIN2D) ndim = 2;
if (which == BIN3D) ndim = 3;
for (int idim = 0; idim < ndim; idim++) {
- if (dim[idim] == 0) scale = xscale;
- else if (dim[idim] == 1) scale = yscale;
- else if (dim[idim] == 2) scale = zscale;
- delta[idim] *= scale;
- invdelta[idim] = 1.0/delta[idim];
- if (originflag[idim] == COORD) origin[idim] *= scale;
- if (minflag[idim] == COORD) minvalue[idim] *= scale;
- if (maxflag[idim] == COORD) maxvalue[idim] *= scale;
+ if (dim[idim] == 0) scale = xscale;
+ else if (dim[idim] == 1) scale = yscale;
+ else if (dim[idim] == 2) scale = zscale;
+ delta[idim] *= scale;
+ invdelta[idim] = 1.0/delta[idim];
+ if (originflag[idim] == COORD) origin[idim] *= scale;
+ if (minflag[idim] == COORD) minvalue[idim] *= scale;
+ if (maxflag[idim] == COORD) maxvalue[idim] *= scale;
}
} else if (which == BINSPHERE) {
sorigin_user[0] *= xscale;
diff --git a/src/compute_hexorder_atom.cpp b/src/compute_hexorder_atom.cpp
index 85324651c1..04421dca3e 100644
--- a/src/compute_hexorder_atom.cpp
+++ b/src/compute_hexorder_atom.cpp
@@ -66,11 +66,11 @@ ComputeHexOrderAtom::ComputeHexOrderAtom(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"nnn") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal compute hexorder/atom command");
if (strcmp(arg[iarg+1],"NULL") == 0)
- nnn = 0;
+ nnn = 0;
else {
- nnn = force->numeric(FLERR,arg[iarg+1]);
- if (nnn < 0)
- error->all(FLERR,"Illegal compute hexorder/atom command");
+ nnn = force->numeric(FLERR,arg[iarg+1]);
+ if (nnn < 0)
+ error->all(FLERR,"Illegal compute hexorder/atom command");
}
iarg += 2;
} else if (strcmp(arg[iarg],"cutoff") == 0) {
@@ -212,30 +212,30 @@ void ComputeHexOrderAtom::compute_peratom()
// if not nnn neighbors, order parameter = 0;
if (ncount < nnn) {
- qn[0] = qn[1] = 0.0;
+ qn[0] = qn[1] = 0.0;
continue;
}
// if nnn > 0, use only nearest nnn neighbors
if (nnn > 0) {
- select2(nnn,ncount,distsq,nearest);
- ncount = nnn;
+ select2(nnn,ncount,distsq,nearest);
+ ncount = nnn;
}
double usum = 0.0;
double vsum = 0.0;
for (jj = 0; jj < ncount; jj++) {
- j = nearest[jj];
- j &= NEIGHMASK;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- double u, v;
- calc_qn_complex(delx, dely, u, v);
- usum += u;
- vsum += v;
+ j = nearest[jj];
+ j &= NEIGHMASK;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ double u, v;
+ calc_qn_complex(delx, dely, u, v);
+ usum += u;
+ vsum += v;
}
qn[0] = usum/nnn;
qn[1] = vsum/nnn;
diff --git a/src/compute_msd.cpp b/src/compute_msd.cpp
index f2e82fe239..ac510bca8e 100644
--- a/src/compute_msd.cpp
+++ b/src/compute_msd.cpp
@@ -198,17 +198,17 @@ void ComputeMSD::compute_vector()
xbox = (image[i] & IMGMASK) - IMGMAX;
ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
zbox = (image[i] >> IMG2BITS) - IMGMAX;
- xtmp = x[i][0] + xbox*xprd - cm[0];
- ytmp = x[i][1] + ybox*yprd - cm[1];
- ztmp = x[i][2] + zbox*zprd - cm[2];
+ xtmp = x[i][0] + xbox*xprd - cm[0];
+ ytmp = x[i][1] + ybox*yprd - cm[1];
+ ztmp = x[i][2] + zbox*zprd - cm[2];
- // use running average position for reference if requested
+ // use running average position for reference if requested
- if (avflag) {
- xoriginal[i][0] = (xoriginal[i][0]*naverage + xtmp)*navfac;
- xoriginal[i][1] = (xoriginal[i][1]*naverage + ytmp)*navfac;
- xoriginal[i][2] = (xoriginal[i][2]*naverage + ztmp)*navfac;
- }
+ if (avflag) {
+ xoriginal[i][0] = (xoriginal[i][0]*naverage + xtmp)*navfac;
+ xoriginal[i][1] = (xoriginal[i][1]*naverage + ytmp)*navfac;
+ xoriginal[i][2] = (xoriginal[i][2]*naverage + ztmp)*navfac;
+ }
dx = xtmp - xoriginal[i][0];
dy = ytmp - xoriginal[i][1];
@@ -229,13 +229,13 @@ void ComputeMSD::compute_vector()
ytmp = x[i][1] + h[1]*ybox + h[3]*zbox - cm[1];
ztmp = x[i][2] + h[2]*zbox - cm[2];
- // use running average position for reference if requested
+ // use running average position for reference if requested
- if (avflag) {
- xoriginal[i][0] = (xoriginal[i][0]*naverage + xtmp)*navfac;
- xoriginal[i][1] = (xoriginal[i][0]*naverage + xtmp)*navfac;
- xoriginal[i][2] = (xoriginal[i][0]*naverage + xtmp)*navfac;
- }
+ if (avflag) {
+ xoriginal[i][0] = (xoriginal[i][0]*naverage + xtmp)*navfac;
+ xoriginal[i][1] = (xoriginal[i][0]*naverage + xtmp)*navfac;
+ xoriginal[i][2] = (xoriginal[i][0]*naverage + xtmp)*navfac;
+ }
dx = xtmp - xoriginal[i][0];
dy = ytmp - xoriginal[i][1];
diff --git a/src/compute_orientorder_atom.h b/src/compute_orientorder_atom.h
index eb814e9c1c..d5905df63b 100644
--- a/src/compute_orientorder_atom.h
+++ b/src/compute_orientorder_atom.h
@@ -50,7 +50,7 @@ class ComputeOrientOrderAtom : public Compute {
void select3(int, int, double *, int *, double **);
void calc_boop(double **rlist, int numNeighbors,
- double qn[], int nlist[], int nnlist);
+ double qn[], int nlist[], int nnlist);
double dist(const double r[]);
double polar_prefactor(int, int, double);
diff --git a/src/compute_pressure.cpp b/src/compute_pressure.cpp
index 80289c59b3..99046e864c 100644
--- a/src/compute_pressure.cpp
+++ b/src/compute_pressure.cpp
@@ -99,7 +99,7 @@ ComputePressure::ComputePressure(LAMMPS *lmp, int narg, char **arg) :
if (keflag && id_temp == NULL)
error->all(FLERR,"Compute pressure requires temperature ID "
- "to include kinetic energy");
+ "to include kinetic energy");
vector = new double[6];
nvirial = 0;
@@ -224,7 +224,7 @@ void ComputePressure::compute_vector()
if (force->kspace && kspace_virial && force->kspace->scalar_pressure_flag)
error->all(FLERR,"Must use 'kspace_modify pressure/scalar no' for "
- "tensor components with kspace_style msm");
+ "tensor components with kspace_style msm");
// invoke temperature if it hasn't been already
diff --git a/src/compute_property_chunk.cpp b/src/compute_property_chunk.cpp
index 1461a83ad2..c169e20d73 100644
--- a/src/compute_property_chunk.cpp
+++ b/src/compute_property_chunk.cpp
@@ -53,22 +53,22 @@ ComputePropertyChunk::ComputePropertyChunk(LAMMPS *lmp, int narg, char **arg) :
countflag = 1;
} else if (strcmp(arg[iarg],"id") == 0) {
if (!cchunk->compress)
- error->all(FLERR,"Compute chunk/atom stores no IDs for "
+ error->all(FLERR,"Compute chunk/atom stores no IDs for "
"compute property/chunk");
pack_choice[i] = &ComputePropertyChunk::pack_id;
} else if (strcmp(arg[iarg],"coord1") == 0) {
if (cchunk->ncoord < 1)
- error->all(FLERR,"Compute chunk/atom stores no coord1 for "
+ error->all(FLERR,"Compute chunk/atom stores no coord1 for "
"compute property/chunk");
pack_choice[i] = &ComputePropertyChunk::pack_coord1;
} else if (strcmp(arg[iarg],"coord2") == 0) {
if (cchunk->ncoord < 2)
- error->all(FLERR,"Compute chunk/atom stores no coord2 for "
+ error->all(FLERR,"Compute chunk/atom stores no coord2 for "
"compute property/chunk");
pack_choice[i] = &ComputePropertyChunk::pack_coord2;
} else if (strcmp(arg[iarg],"coord3") == 0) {
if (cchunk->ncoord < 3)
- error->all(FLERR,"Compute chunk/atom stores no coord3 for "
+ error->all(FLERR,"Compute chunk/atom stores no coord3 for "
"compute property/chunk");
pack_choice[i] = &ComputePropertyChunk::pack_coord3;
} else error->all(FLERR,
diff --git a/src/compute_stress_atom.cpp b/src/compute_stress_atom.cpp
index 46ee2ec3c5..fd38f13dba 100644
--- a/src/compute_stress_atom.cpp
+++ b/src/compute_stress_atom.cpp
@@ -61,7 +61,7 @@ ComputeStressAtom::ComputeStressAtom(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,"Could not find compute stress/atom temperature ID");
if (modify->compute[icompute]->tempflag == 0)
error->all(FLERR,
- "Compute stress/atom temperature ID does not "
+ "Compute stress/atom temperature ID does not "
"compute temperature");
}
@@ -263,28 +263,28 @@ void ComputeStressAtom::compute_peratom()
if (biasflag == NOBIAS) {
if (rmass) {
- for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit) {
- onemass = mvv2e * rmass[i];
- stress[i][0] += onemass*v[i][0]*v[i][0];
- stress[i][1] += onemass*v[i][1]*v[i][1];
- stress[i][2] += onemass*v[i][2]*v[i][2];
- stress[i][3] += onemass*v[i][0]*v[i][1];
- stress[i][4] += onemass*v[i][0]*v[i][2];
- stress[i][5] += onemass*v[i][1]*v[i][2];
- }
+ for (i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit) {
+ onemass = mvv2e * rmass[i];
+ stress[i][0] += onemass*v[i][0]*v[i][0];
+ stress[i][1] += onemass*v[i][1]*v[i][1];
+ stress[i][2] += onemass*v[i][2]*v[i][2];
+ stress[i][3] += onemass*v[i][0]*v[i][1];
+ stress[i][4] += onemass*v[i][0]*v[i][2];
+ stress[i][5] += onemass*v[i][1]*v[i][2];
+ }
} else {
- for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit) {
- onemass = mvv2e * mass[type[i]];
- stress[i][0] += onemass*v[i][0]*v[i][0];
- stress[i][1] += onemass*v[i][1]*v[i][1];
- stress[i][2] += onemass*v[i][2]*v[i][2];
- stress[i][3] += onemass*v[i][0]*v[i][1];
- stress[i][4] += onemass*v[i][0]*v[i][2];
- stress[i][5] += onemass*v[i][1]*v[i][2];
- }
+ for (i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit) {
+ onemass = mvv2e * mass[type[i]];
+ stress[i][0] += onemass*v[i][0]*v[i][0];
+ stress[i][1] += onemass*v[i][1]*v[i][1];
+ stress[i][2] += onemass*v[i][2]*v[i][2];
+ stress[i][3] += onemass*v[i][0]*v[i][1];
+ stress[i][4] += onemass*v[i][0]*v[i][2];
+ stress[i][5] += onemass*v[i][1]*v[i][2];
+ }
}
} else {
@@ -293,35 +293,35 @@ void ComputeStressAtom::compute_peratom()
// this insures bias factor is pre-computed
if (keflag && temperature->invoked_scalar != update->ntimestep)
- temperature->compute_scalar();
+ temperature->compute_scalar();
if (rmass) {
- for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit) {
- temperature->remove_bias(i,v[i]);
- onemass = mvv2e * rmass[i];
- stress[i][0] += onemass*v[i][0]*v[i][0];
- stress[i][1] += onemass*v[i][1]*v[i][1];
- stress[i][2] += onemass*v[i][2]*v[i][2];
- stress[i][3] += onemass*v[i][0]*v[i][1];
- stress[i][4] += onemass*v[i][0]*v[i][2];
- stress[i][5] += onemass*v[i][1]*v[i][2];
- temperature->restore_bias(i,v[i]);
- }
+ for (i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit) {
+ temperature->remove_bias(i,v[i]);
+ onemass = mvv2e * rmass[i];
+ stress[i][0] += onemass*v[i][0]*v[i][0];
+ stress[i][1] += onemass*v[i][1]*v[i][1];
+ stress[i][2] += onemass*v[i][2]*v[i][2];
+ stress[i][3] += onemass*v[i][0]*v[i][1];
+ stress[i][4] += onemass*v[i][0]*v[i][2];
+ 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) {
- temperature->remove_bias(i,v[i]);
- onemass = mvv2e * mass[type[i]];
- stress[i][0] += onemass*v[i][0]*v[i][0];
- stress[i][1] += onemass*v[i][1]*v[i][1];
- stress[i][2] += onemass*v[i][2]*v[i][2];
- stress[i][3] += onemass*v[i][0]*v[i][1];
- stress[i][4] += onemass*v[i][0]*v[i][2];
- stress[i][5] += onemass*v[i][1]*v[i][2];
- temperature->restore_bias(i,v[i]);
- }
+ for (i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit) {
+ temperature->remove_bias(i,v[i]);
+ onemass = mvv2e * mass[type[i]];
+ stress[i][0] += onemass*v[i][0]*v[i][0];
+ stress[i][1] += onemass*v[i][1]*v[i][1];
+ stress[i][2] += onemass*v[i][2]*v[i][2];
+ stress[i][3] += onemass*v[i][0]*v[i][1];
+ stress[i][4] += onemass*v[i][0]*v[i][2];
+ stress[i][5] += onemass*v[i][1]*v[i][2];
+ temperature->restore_bias(i,v[i]);
+ }
}
}
}
diff --git a/src/compute_temp_chunk.cpp b/src/compute_temp_chunk.cpp
index 8daaeb0621..7de894d367 100644
--- a/src/compute_temp_chunk.cpp
+++ b/src/compute_temp_chunk.cpp
@@ -342,34 +342,34 @@ void ComputeTempChunk::compute_vector()
if (!comflag) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- index = ichunk[i]-1;
- if (index < 0) continue;
- if (rmass) massone = rmass[i];
- else massone = mass[type[i]];
- t[0] += massone * v[i][0]*v[i][0];
- t[1] += massone * v[i][1]*v[i][1];
- t[2] += massone * v[i][2]*v[i][2];
- t[3] += massone * v[i][0]*v[i][1];
- t[4] += massone * v[i][0]*v[i][2];
- t[5] += massone * v[i][1]*v[i][2];
+ index = ichunk[i]-1;
+ if (index < 0) continue;
+ if (rmass) massone = rmass[i];
+ else massone = mass[type[i]];
+ t[0] += massone * v[i][0]*v[i][0];
+ t[1] += massone * v[i][1]*v[i][1];
+ t[2] += massone * v[i][2]*v[i][2];
+ t[3] += massone * v[i][0]*v[i][1];
+ t[4] += massone * v[i][0]*v[i][2];
+ t[5] += massone * v[i][1]*v[i][2];
}
} else {
double vx,vy,vz;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- index = ichunk[i]-1;
- if (index < 0) continue;
- if (rmass) massone = rmass[i];
- else massone = mass[type[i]];
- vx = v[i][0] - vcmall[index][0];
- vy = v[i][1] - vcmall[index][1];
- vz = v[i][2] - vcmall[index][2];
- t[0] += massone * vx*vx;
- t[1] += massone * vy*vy;
- t[2] += massone * vz*vz;
- t[3] += massone * vx*vy;
- t[4] += massone * vx*vz;
- t[5] += massone * vy*vz;
+ index = ichunk[i]-1;
+ if (index < 0) continue;
+ if (rmass) massone = rmass[i];
+ else massone = mass[type[i]];
+ vx = v[i][0] - vcmall[index][0];
+ vy = v[i][1] - vcmall[index][1];
+ vz = v[i][2] - vcmall[index][2];
+ t[0] += massone * vx*vx;
+ t[1] += massone * vy*vy;
+ t[2] += massone * vz*vz;
+ t[3] += massone * vx*vy;
+ t[4] += massone * vx*vz;
+ t[5] += massone * vy*vz;
}
}
diff --git a/src/compute_vacf.cpp b/src/compute_vacf.cpp
index 6ba272e579..b3f487a4d7 100644
--- a/src/compute_vacf.cpp
+++ b/src/compute_vacf.cpp
@@ -67,9 +67,9 @@ ComputeVACF::ComputeVACF(LAMMPS *lmp, int narg, char **arg) :
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
- voriginal[i][0] = v[i][0];
- voriginal[i][1] = v[i][1];
- voriginal[i][2] = v[i][2];
+ voriginal[i][0] = v[i][0];
+ voriginal[i][1] = v[i][1];
+ voriginal[i][2] = v[i][2];
} else voriginal[i][0] = voriginal[i][1] = voriginal[i][2] = 0.0;
}
diff --git a/src/domain.cpp b/src/domain.cpp
index bad5030373..8522046434 100644
--- a/src/domain.cpp
+++ b/src/domain.cpp
@@ -633,8 +633,8 @@ int Domain::inside(double* x)
hi = boxhi;
if (x[0] < lo[0] || x[0] >= hi[0] ||
- x[1] < lo[1] || x[1] >= hi[1] ||
- x[2] < lo[2] || x[2] >= hi[2]) return 0;
+ x[1] < lo[1] || x[1] >= hi[1] ||
+ x[2] < lo[2] || x[2] >= hi[2]) return 0;
else return 1;
} else {
@@ -644,8 +644,8 @@ int Domain::inside(double* x)
x2lamda(x,lamda);
if (lamda[0] < lo[0] || lamda[0] >= hi[0] ||
- lamda[1] < lo[1] || lamda[1] >= hi[1] ||
- lamda[2] < lo[2] || lamda[2] >= hi[2]) return 0;
+ lamda[1] < lo[1] || lamda[1] >= hi[1] ||
+ lamda[2] < lo[2] || lamda[2] >= hi[2]) return 0;
else return 1;
}
diff --git a/src/dump_cfg.cpp b/src/dump_cfg.cpp
index 8c08bb9edb..6ebdd0f99a 100644
--- a/src/dump_cfg.cpp
+++ b/src/dump_cfg.cpp
@@ -13,7 +13,7 @@
/* ----------------------------------------------------------------------
Contributing author: Liang Wan (Chinese Academy of Sciences)
- Memory efficiency improved by Ray Shan (Sandia)
+ Memory efficiency improved by Ray Shan (Sandia)
------------------------------------------------------------------------- */
#include <math.h>
@@ -177,9 +177,9 @@ int DumpCFG::convert_string(int n, double *mybuf)
for (j = 0; j < size_one; j++) {
if (j == 0) {
- offset += sprintf(&sbuf[offset],"%f \n",mybuf[m]);
+ offset += sprintf(&sbuf[offset],"%f \n",mybuf[m]);
} else if (j == 1) {
- offset += sprintf(&sbuf[offset],"%s \n",typenames[(int) mybuf[m]]);
+ offset += sprintf(&sbuf[offset],"%s \n",typenames[(int) mybuf[m]]);
} else if (j >= 2) {
if (vtype[j] == INT)
offset +=
@@ -209,9 +209,9 @@ int DumpCFG::convert_string(int n, double *mybuf)
for (j = 0; j < size_one; j++) {
if (j == 0) {
- offset += sprintf(&sbuf[offset],"%f \n",mybuf[m]);
+ offset += sprintf(&sbuf[offset],"%f \n",mybuf[m]);
} else if (j == 1) {
- offset += sprintf(&sbuf[offset],"%s \n",typenames[(int) mybuf[m]]);
+ offset += sprintf(&sbuf[offset],"%s \n",typenames[(int) mybuf[m]]);
} else if (j >= 2 && j <= 4) {
unwrap_coord = (mybuf[m] - 0.5)/UNWRAPEXPAND + 0.5;
offset += sprintf(&sbuf[offset],vformat[j],unwrap_coord);
diff --git a/src/dump_custom.cpp b/src/dump_custom.cpp
index 4821171cc9..84ada95975 100644
--- a/src/dump_custom.cpp
+++ b/src/dump_custom.cpp
@@ -937,16 +937,16 @@ int DumpCustom::count()
nstride = 1;
} else if (thresh_array[ithresh] == DNAME) {
- int iwhich,tmp;
+ int iwhich,tmp;
i = nfield + ithresh;
- iwhich = atom->find_custom(id_custom[field2index[i]],tmp);
+ iwhich = atom->find_custom(id_custom[field2index[i]],tmp);
ptr = atom->dvector[iwhich];
nstride = 1;
} else if (thresh_array[ithresh] == INAME) {
- int iwhich,tmp;
+ int iwhich,tmp;
i = nfield + ithresh;
- iwhich = atom->find_custom(id_custom[field2index[i]],tmp);
+ iwhich = atom->find_custom(id_custom[field2index[i]],tmp);
int *ivector = atom->ivector[iwhich];
for (i = 0; i < nlocal; i++)
@@ -960,87 +960,87 @@ int DumpCustom::count()
// copy ptr attribute into thresh_fix if this is first comparison
if (thresh_last[ithresh] < 0) {
- lastflag = 0;
- value = thresh_value[ithresh];
+ lastflag = 0;
+ value = thresh_value[ithresh];
} else {
- lastflag = 1;
- int ilast = thresh_last[ithresh];
- values = thresh_fix[ilast]->vstore;
- ptrhold = ptr;
- if (thresh_first[ilast]) {
- thresh_first[ilast] = 0;
- for (i = 0; i < nlocal; i++, ptr += nstride) values[i] = *ptr;
- ptr = ptrhold;
- }
+ lastflag = 1;
+ int ilast = thresh_last[ithresh];
+ values = thresh_fix[ilast]->vstore;
+ ptrhold = ptr;
+ if (thresh_first[ilast]) {
+ thresh_first[ilast] = 0;
+ for (i = 0; i < nlocal; i++, ptr += nstride) values[i] = *ptr;
+ ptr = ptrhold;
+ }
}
if (thresh_op[ithresh] == LT) {
- if (lastflag) {
- for (i = 0; i < nlocal; i++, ptr += nstride)
- if (choose[i] && *ptr >= values[i]) choose[i] = 0;
- } else {
- for (i = 0; i < nlocal; i++, ptr += nstride)
- if (choose[i] && *ptr >= value) choose[i] = 0;
- }
+ if (lastflag) {
+ for (i = 0; i < nlocal; i++, ptr += nstride)
+ if (choose[i] && *ptr >= values[i]) choose[i] = 0;
+ } else {
+ for (i = 0; i < nlocal; i++, ptr += nstride)
+ if (choose[i] && *ptr >= value) choose[i] = 0;
+ }
} else if (thresh_op[ithresh] == LE) {
- if (lastflag) {
- for (i = 0; i < nlocal; i++, ptr += nstride)
- if (choose[i] && *ptr > values[i]) choose[i] = 0;
- } else {
- for (i = 0; i < nlocal; i++, ptr += nstride)
- if (choose[i] && *ptr > value) choose[i] = 0;
- }
+ if (lastflag) {
+ for (i = 0; i < nlocal; i++, ptr += nstride)
+ if (choose[i] && *ptr > values[i]) choose[i] = 0;
+ } else {
+ for (i = 0; i < nlocal; i++, ptr += nstride)
+ if (choose[i] && *ptr > value) choose[i] = 0;
+ }
} else if (thresh_op[ithresh] == GT) {
- if (lastflag) {
- for (i = 0; i < nlocal; i++, ptr += nstride)
- if (choose[i] && *ptr <= values[i]) choose[i] = 0;
- } else {
- for (i = 0; i < nlocal; i++, ptr += nstride)
- if (choose[i] && *ptr <= value) choose[i] = 0;
- }
+ if (lastflag) {
+ for (i = 0; i < nlocal; i++, ptr += nstride)
+ if (choose[i] && *ptr <= values[i]) choose[i] = 0;
+ } else {
+ for (i = 0; i < nlocal; i++, ptr += nstride)
+ if (choose[i] && *ptr <= value) choose[i] = 0;
+ }
} else if (thresh_op[ithresh] == GE) {
- if (lastflag) {
- for (i = 0; i < nlocal; i++, ptr += nstride)
- if (choose[i] && *ptr < values[i]) choose[i] = 0;
- } else {
- for (i = 0; i < nlocal; i++, ptr += nstride)
- if (choose[i] && *ptr < value) choose[i] = 0;
- }
+ if (lastflag) {
+ for (i = 0; i < nlocal; i++, ptr += nstride)
+ if (choose[i] && *ptr < values[i]) choose[i] = 0;
+ } else {
+ for (i = 0; i < nlocal; i++, ptr += nstride)
+ if (choose[i] && *ptr < value) choose[i] = 0;
+ }
} else if (thresh_op[ithresh] == EQ) {
- if (lastflag) {
- for (i = 0; i < nlocal; i++, ptr += nstride)
- if (choose[i] && *ptr != values[i]) choose[i] = 0;
- } else {
- for (i = 0; i < nlocal; i++, ptr += nstride)
- if (choose[i] && *ptr != value) choose[i] = 0;
- }
+ if (lastflag) {
+ for (i = 0; i < nlocal; i++, ptr += nstride)
+ if (choose[i] && *ptr != values[i]) choose[i] = 0;
+ } else {
+ for (i = 0; i < nlocal; i++, ptr += nstride)
+ if (choose[i] && *ptr != value) choose[i] = 0;
+ }
} else if (thresh_op[ithresh] == NEQ) {
- if (lastflag) {
- for (i = 0; i < nlocal; i++, ptr += nstride)
- if (choose[i] && *ptr == values[i]) choose[i] = 0;
- } else {
- for (i = 0; i < nlocal; i++, ptr += nstride)
- if (choose[i] && *ptr == value) choose[i] = 0;
- }
+ if (lastflag) {
+ for (i = 0; i < nlocal; i++, ptr += nstride)
+ if (choose[i] && *ptr == values[i]) choose[i] = 0;
+ } else {
+ for (i = 0; i < nlocal; i++, ptr += nstride)
+ if (choose[i] && *ptr == value) choose[i] = 0;
+ }
} else if (thresh_op[ithresh] == XOR) {
- if (lastflag) {
- for (i = 0; i < nlocal; i++, ptr += nstride)
- if (choose[i] && (*ptr == 0.0 && values[i] == 0.0) ||
- (*ptr != 0.0 && values[i] != 0.0))
- choose[i] = 0;
- } else {
- for (i = 0; i < nlocal; i++, ptr += nstride)
- if (choose[i] && (*ptr == 0.0 && value == 0.0) ||
- (*ptr != 0.0 && value != 0.0))
- choose[i] = 0;
- }
+ if (lastflag) {
+ for (i = 0; i < nlocal; i++, ptr += nstride)
+ if (choose[i] && (*ptr == 0.0 && values[i] == 0.0) ||
+ (*ptr != 0.0 && values[i] != 0.0))
+ choose[i] = 0;
+ } else {
+ for (i = 0; i < nlocal; i++, ptr += nstride)
+ if (choose[i] && (*ptr == 0.0 && value == 0.0) ||
+ (*ptr != 0.0 && value != 0.0))
+ choose[i] = 0;
+ }
}
// update values stored in threshfix
if (lastflag) {
- ptr = ptrhold;
- for (i = 0; i < nlocal; i++, ptr += nstride) values[i] = *ptr;
+ ptr = ptrhold;
+ for (i = 0; i < nlocal; i++, ptr += nstride) values[i] = *ptr;
}
}
}
@@ -1684,12 +1684,12 @@ int DumpCustom::modify_param(int narg, char **arg)
thresh_op = NULL;
thresh_value = NULL;
thresh_last = NULL;
- for (int i = 0; i < nthreshlast; i++) {
- modify->delete_fix(thresh_fixID[i]);
- delete [] thresh_fixID[i];
- }
- thresh_fix = NULL;
- thresh_fixID = NULL;
+ for (int i = 0; i < nthreshlast; i++) {
+ modify->delete_fix(thresh_fixID[i]);
+ delete [] thresh_fixID[i];
+ }
+ thresh_fix = NULL;
+ thresh_fixID = NULL;
thresh_first = NULL;
}
nthresh = nthreshlast = 0;
@@ -1950,11 +1950,11 @@ int DumpCustom::modify_param(int narg, char **arg)
thresh_last[nthresh] = -1;
} else {
thresh_fix = (FixStore **)
- memory->srealloc(thresh_fix,(nthreshlast+1)*sizeof(FixStore *),
- "dump:thresh_fix");
+ memory->srealloc(thresh_fix,(nthreshlast+1)*sizeof(FixStore *),
+ "dump:thresh_fix");
thresh_fixID = (char **)
- memory->srealloc(thresh_fixID,(nthreshlast+1)*sizeof(char *),
- "dump:thresh_fixID");
+ memory->srealloc(thresh_fixID,(nthreshlast+1)*sizeof(char *),
+ "dump:thresh_fixID");
memory->grow(thresh_first,(nthreshlast+1),"dump:thresh_first");
int n = strlen(id) + strlen("_DUMP_STORE") + 8;
diff --git a/src/fix_adapt.cpp b/src/fix_adapt.cpp
index bc7aa843ef..e34f2dcf55 100644
--- a/src/fix_adapt.cpp
+++ b/src/fix_adapt.cpp
@@ -433,8 +433,8 @@ void FixAdapt::init()
error->all(FLERR,"Fix adapt requires atom attribute diameter");
}
if (ad->aparam == CHARGE) {
- if (!atom->q_flag)
- error->all(FLERR,"Fix adapt requires atom attribute charge");
+ if (!atom->q_flag)
+ error->all(FLERR,"Fix adapt requires atom attribute charge");
}
}
}
@@ -597,12 +597,12 @@ void FixAdapt::change_settings()
}
} else if (ad->aparam == CHARGE) {
double *q = atom->q;
- int *mask = atom->mask;
- int nlocal = atom->nlocal;
+ 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;
+ for (i = 0; i < nall; i++)
+ if (mask[i] & groupbit) q[i] = value;
}
}
}
diff --git a/src/fix_ave_chunk.cpp b/src/fix_ave_chunk.cpp
index 73df50c66c..5b57c7a1f8 100644
--- a/src/fix_ave_chunk.cpp
+++ b/src/fix_ave_chunk.cpp
@@ -176,14 +176,14 @@ FixAveChunk::FixAveChunk(LAMMPS *lmp, int narg, char **arg) :
if (strcmp(arg[iarg],"norm") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/chunk command");
if (strcmp(arg[iarg+1],"all") == 0) {
- normflag = ALL;
- scaleflag = ATOM;
+ normflag = ALL;
+ scaleflag = ATOM;
} else if (strcmp(arg[iarg+1],"sample") == 0) {
- normflag = SAMPLE;
- scaleflag = ATOM;
+ normflag = SAMPLE;
+ scaleflag = ATOM;
} else if (strcmp(arg[iarg+1],"none") == 0) {
- normflag = SAMPLE;
- scaleflag = NOSCALE;
+ normflag = SAMPLE;
+ scaleflag = NOSCALE;
} else error->all(FLERR,"Illegal fix ave/chunk command");
iarg += 2;
} else if (strcmp(arg[iarg],"ave") == 0) {
@@ -686,16 +686,16 @@ void FixAveChunk::end_of_step()
double *rmass = atom->rmass;
if (rmass) {
- for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit && ichunk[i] > 0) {
- index = ichunk[i]-1;
- values_one[index][m] += rmass[i];
+ for (i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit && ichunk[i] > 0) {
+ index = ichunk[i]-1;
+ values_one[index][m] += rmass[i];
}
} else {
for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit && ichunk[i] > 0) {
- index = ichunk[i]-1;
- values_one[index][m] += mass[type[i]];
+ if (mask[i] & groupbit && ichunk[i] > 0) {
+ index = ichunk[i]-1;
+ values_one[index][m] += mass[type[i]];
}
}
diff --git a/src/fix_group.cpp b/src/fix_group.cpp
index 51abebdf29..8479565891 100644
--- a/src/fix_group.cpp
+++ b/src/fix_group.cpp
@@ -75,8 +75,8 @@ idregion(NULL), idvar(NULL), idprop(NULL)
strcpy(idvar,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"property") == 0) {
- if (iarg+2 > narg) error->all(FLERR,"Illegal group command");
- if (atom->find_custom(arg[iarg+1],typeflag) < 0)
+ if (iarg+2 > narg) error->all(FLERR,"Illegal group command");
+ if (atom->find_custom(arg[iarg+1],typeflag) < 0)
error->all(FLERR,"Per atom property for group dynamic does not exist");
propflag = 1;
delete [] idprop;
@@ -84,7 +84,7 @@ idregion(NULL), idvar(NULL), idprop(NULL)
idprop = new char[n];
strcpy(idprop,arg[iarg+1]);
iarg += 2;
- } else if (strcmp(arg[iarg],"every") == 0) {
+ } else if (strcmp(arg[iarg],"every") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal group command");
nevery = force->inumeric(FLERR,arg[iarg+1]);
if (nevery <= 0) error->all(FLERR,"Illegal group command");
diff --git a/src/fix_langevin.cpp b/src/fix_langevin.cpp
index 542d2d6d6f..7afc18b33c 100644
--- a/src/fix_langevin.cpp
+++ b/src/fix_langevin.cpp
@@ -310,132 +310,132 @@ void FixLangevin::post_force(int vflag)
if (tstyle == ATOM)
if (gjfflag)
if (tallyflag)
- if (tbiasflag == BIAS)
- if (rmass)
- if (zeroflag) post_force_templated<1,1,1,1,1,1>();
+ if (tbiasflag == BIAS)
+ if (rmass)
+ if (zeroflag) post_force_templated<1,1,1,1,1,1>();
else post_force_templated<1,1,1,1,1,0>();
- else
- if (zeroflag) post_force_templated<1,1,1,1,0,1>();
+ else
+ if (zeroflag) post_force_templated<1,1,1,1,0,1>();
else post_force_templated<1,1,1,1,0,0>();
- else
- if (rmass)
- if (zeroflag) post_force_templated<1,1,1,0,1,1>();
- else post_force_templated<1,1,1,0,1,0>();
- else
- if (zeroflag) post_force_templated<1,1,1,0,0,1>();
- else post_force_templated<1,1,1,0,0,0>();
+ else
+ if (rmass)
+ if (zeroflag) post_force_templated<1,1,1,0,1,1>();
+ else post_force_templated<1,1,1,0,1,0>();
+ else
+ if (zeroflag) post_force_templated<1,1,1,0,0,1>();
+ else post_force_templated<1,1,1,0,0,0>();
else
- if (tbiasflag == BIAS)
- if (rmass)
- if (zeroflag) post_force_templated<1,1,0,1,1,1>();
- else post_force_templated<1,1,0,1,1,0>();
- else
- if (zeroflag) post_force_templated<1,1,0,1,0,1>();
- else post_force_templated<1,1,0,1,0,0>();
- else
- if (rmass)
- if (zeroflag) post_force_templated<1,1,0,0,1,1>();
- else post_force_templated<1,1,0,0,1,0>();
- else
- if (zeroflag) post_force_templated<1,1,0,0,0,1>();
- else post_force_templated<1,1,0,0,0,0>();
+ if (tbiasflag == BIAS)
+ if (rmass)
+ if (zeroflag) post_force_templated<1,1,0,1,1,1>();
+ else post_force_templated<1,1,0,1,1,0>();
+ else
+ if (zeroflag) post_force_templated<1,1,0,1,0,1>();
+ else post_force_templated<1,1,0,1,0,0>();
+ else
+ if (rmass)
+ if (zeroflag) post_force_templated<1,1,0,0,1,1>();
+ else post_force_templated<1,1,0,0,1,0>();
+ else
+ if (zeroflag) post_force_templated<1,1,0,0,0,1>();
+ else post_force_templated<1,1,0,0,0,0>();
else
if (tallyflag)
- if (tbiasflag == BIAS)
- if (rmass)
- if (zeroflag) post_force_templated<1,0,1,1,1,1>();
- else post_force_templated<1,0,1,1,1,0>();
- else
- if (zeroflag) post_force_templated<1,0,1,1,0,1>();
- else post_force_templated<1,0,1,1,0,0>();
- else
- if (rmass)
- if (zeroflag) post_force_templated<1,0,1,0,1,1>();
- else post_force_templated<1,0,1,0,1,0>();
- else
- if (zeroflag) post_force_templated<1,0,1,0,0,1>();
- else post_force_templated<1,0,1,0,0,0>();
+ if (tbiasflag == BIAS)
+ if (rmass)
+ if (zeroflag) post_force_templated<1,0,1,1,1,1>();
+ else post_force_templated<1,0,1,1,1,0>();
+ else
+ if (zeroflag) post_force_templated<1,0,1,1,0,1>();
+ else post_force_templated<1,0,1,1,0,0>();
+ else
+ if (rmass)
+ if (zeroflag) post_force_templated<1,0,1,0,1,1>();
+ else post_force_templated<1,0,1,0,1,0>();
+ else
+ if (zeroflag) post_force_templated<1,0,1,0,0,1>();
+ else post_force_templated<1,0,1,0,0,0>();
else
- if (tbiasflag == BIAS)
- if (rmass)
- if (zeroflag) post_force_templated<1,0,0,1,1,1>();
- else post_force_templated<1,0,0,1,1,0>();
- else
- if (zeroflag) post_force_templated<1,0,0,1,0,1>();
- else post_force_templated<1,0,0,1,0,0>();
- else
- if (rmass)
- if (zeroflag) post_force_templated<1,0,0,0,1,1>();
- else post_force_templated<1,0,0,0,1,0>();
- else
- if (zeroflag) post_force_templated<1,0,0,0,0,1>();
- else post_force_templated<1,0,0,0,0,0>();
+ if (tbiasflag == BIAS)
+ if (rmass)
+ if (zeroflag) post_force_templated<1,0,0,1,1,1>();
+ else post_force_templated<1,0,0,1,1,0>();
+ else
+ if (zeroflag) post_force_templated<1,0,0,1,0,1>();
+ else post_force_templated<1,0,0,1,0,0>();
+ else
+ if (rmass)
+ if (zeroflag) post_force_templated<1,0,0,0,1,1>();
+ else post_force_templated<1,0,0,0,1,0>();
+ else
+ if (zeroflag) post_force_templated<1,0,0,0,0,1>();
+ else post_force_templated<1,0,0,0,0,0>();
else
if (gjfflag)
if (tallyflag)
- if (tbiasflag == BIAS)
- if (rmass)
- if (zeroflag) post_force_templated<0,1,1,1,1,1>();
- else post_force_templated<0,1,1,1,1,0>();
- else
- if (zeroflag) post_force_templated<0,1,1,1,0,1>();
- else post_force_templated<0,1,1,1,0,0>();
- else
- if (rmass)
- if (zeroflag) post_force_templated<0,1,1,0,1,1>();
- else post_force_templated<0,1,1,0,1,0>();
- else
- if (zeroflag) post_force_templated<0,1,1,0,0,1>();
- else post_force_templated<0,1,1,0,0,0>();
+ if (tbiasflag == BIAS)
+ if (rmass)
+ if (zeroflag) post_force_templated<0,1,1,1,1,1>();
+ else post_force_templated<0,1,1,1,1,0>();
+ else
+ if (zeroflag) post_force_templated<0,1,1,1,0,1>();
+ else post_force_templated<0,1,1,1,0,0>();
+ else
+ if (rmass)
+ if (zeroflag) post_force_templated<0,1,1,0,1,1>();
+ else post_force_templated<0,1,1,0,1,0>();
+ else
+ if (zeroflag) post_force_templated<0,1,1,0,0,1>();
+ else post_force_templated<0,1,1,0,0,0>();
else
- if (tbiasflag == BIAS)
- if (rmass)
- if (zeroflag) post_force_templated<0,1,0,1,1,1>();
- else post_force_templated<0,1,0,1,1,0>();
- else
- if (zeroflag) post_force_templated<0,1,0,1,0,1>();
- else post_force_templated<0,1,0,1,0,0>();
- else
- if (rmass)
- if (zeroflag) post_force_templated<0,1,0,0,1,1>();
- else post_force_templated<0,1,0,0,1,0>();
- else
- if (zeroflag) post_force_templated<0,1,0,0,0,1>();
- else post_force_templated<0,1,0,0,0,0>();
+ if (tbiasflag == BIAS)
+ if (rmass)
+ if (zeroflag) post_force_templated<0,1,0,1,1,1>();
+ else post_force_templated<0,1,0,1,1,0>();
+ else
+ if (zeroflag) post_force_templated<0,1,0,1,0,1>();
+ else post_force_templated<0,1,0,1,0,0>();
+ else
+ if (rmass)
+ if (zeroflag) post_force_templated<0,1,0,0,1,1>();
+ else post_force_templated<0,1,0,0,1,0>();
+ else
+ if (zeroflag) post_force_templated<0,1,0,0,0,1>();
+ else post_force_templated<0,1,0,0,0,0>();
else
if (tallyflag)
- if (tbiasflag == BIAS)
- if (rmass)
- if (zeroflag) post_force_templated<0,0,1,1,1,1>();
- else post_force_templated<0,0,1,1,1,0>();
- else
- if (zeroflag) post_force_templated<0,0,1,1,0,1>();
- else post_force_templated<0,0,1,1,0,0>();
- else
- if (rmass)
- if (zeroflag) post_force_templated<0,0,1,0,1,1>();
- else post_force_templated<0,0,1,0,1,0>();
- else
- if (zeroflag) post_force_templated<0,0,1,0,0,1>();
- else post_force_templated<0,0,1,0,0,0>();
+ if (tbiasflag == BIAS)
+ if (rmass)
+ if (zeroflag) post_force_templated<0,0,1,1,1,1>();
+ else post_force_templated<0,0,1,1,1,0>();
+ else
+ if (zeroflag) post_force_templated<0,0,1,1,0,1>();
+ else post_force_templated<0,0,1,1,0,0>();
+ else
+ if (rmass)
+ if (zeroflag) post_force_templated<0,0,1,0,1,1>();
+ else post_force_templated<0,0,1,0,1,0>();
+ else
+ if (zeroflag) post_force_templated<0,0,1,0,0,1>();
+ else post_force_templated<0,0,1,0,0,0>();
else
- if (tbiasflag == BIAS)
- if (rmass)
- if (zeroflag) post_force_templated<0,0,0,1,1,1>();
- else post_force_templated<0,0,0,1,1,0>();
- else
- if (zeroflag) post_force_templated<0,0,0,1,0,1>();
- else post_force_templated<0,0,0,1,0,0>();
- else
- if (rmass)
- if (zeroflag) post_force_templated<0,0,0,0,1,1>();
- else post_force_templated<0,0,0,0,1,0>();
- else
- if (zeroflag) post_force_templated<0,0,0,0,0,1>();
- else post_force_templated<0,0,0,0,0,0>();
+ if (tbiasflag == BIAS)
+ if (rmass)
+ if (zeroflag) post_force_templated<0,0,0,1,1,1>();
+ else post_force_templated<0,0,0,1,1,0>();
+ else
+ if (zeroflag) post_force_templated<0,0,0,1,0,1>();
+ else post_force_templated<0,0,0,1,0,0>();
+ else
+ if (rmass)
+ if (zeroflag) post_force_templated<0,0,0,0,1,1>();
+ else post_force_templated<0,0,0,0,1,0>();
+ else
+ 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,
- int(tbiasflag==BIAS), int(rmass!=NULL), zeroflag);
+ int(tbiasflag==BIAS), int(rmass!=NULL), zeroflag);
#endif
}
@@ -452,7 +452,7 @@ 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,
- int Tp_BIAS, int Tp_RMASS, int Tp_ZERO >
+ int Tp_BIAS, int Tp_RMASS, int Tp_ZERO >
void FixLangevin::post_force_templated()
#else
void FixLangevin::post_force_untemplated
@@ -525,13 +525,13 @@ void FixLangevin::post_force_untemplated
if (mask[i] & groupbit) {
if (Tp_TSTYLEATOM) tsqrt = sqrt(tforce[i]);
if (Tp_RMASS) {
- gamma1 = -rmass[i] / t_period / ftm2v;
- gamma2 = sqrt(rmass[i]) * sqrt(24.0*boltz/t_period/dt/mvv2e) / ftm2v;
- gamma1 *= 1.0/ratio[type[i]];
- gamma2 *= 1.0/sqrt(ratio[type[i]]) * tsqrt;
+ gamma1 = -rmass[i] / t_period / ftm2v;
+ gamma2 = sqrt(rmass[i]) * sqrt(24.0*boltz/t_period/dt/mvv2e) / ftm2v;
+ gamma1 *= 1.0/ratio[type[i]];
+ gamma2 *= 1.0/sqrt(ratio[type[i]]) * tsqrt;
} else {
- gamma1 = gfactor1[type[i]];
- gamma2 = gfactor2[type[i]] * tsqrt;
+ gamma1 = gfactor1[type[i]];
+ gamma2 = gfactor2[type[i]] * tsqrt;
}
fran[0] = gamma2*(random->uniform()-0.5);
@@ -539,40 +539,40 @@ void FixLangevin::post_force_untemplated
fran[2] = gamma2*(random->uniform()-0.5);
if (Tp_BIAS) {
- temperature->remove_bias(i,v[i]);
- fdrag[0] = gamma1*v[i][0];
- fdrag[1] = gamma1*v[i][1];
- fdrag[2] = gamma1*v[i][2];
- if (v[i][0] == 0.0) fran[0] = 0.0;
- if (v[i][1] == 0.0) fran[1] = 0.0;
- if (v[i][2] == 0.0) fran[2] = 0.0;
- temperature->restore_bias(i,v[i]);
+ temperature->remove_bias(i,v[i]);
+ fdrag[0] = gamma1*v[i][0];
+ fdrag[1] = gamma1*v[i][1];
+ fdrag[2] = gamma1*v[i][2];
+ if (v[i][0] == 0.0) fran[0] = 0.0;
+ if (v[i][1] == 0.0) fran[1] = 0.0;
+ if (v[i][2] == 0.0) fran[2] = 0.0;
+ temperature->restore_bias(i,v[i]);
} else {
- fdrag[0] = gamma1*v[i][0];
- fdrag[1] = gamma1*v[i][1];
- fdrag[2] = gamma1*v[i][2];
+ fdrag[0] = gamma1*v[i][0];
+ fdrag[1] = gamma1*v[i][1];
+ fdrag[2] = gamma1*v[i][2];
}
if (Tp_GJF) {
- fswap = 0.5*(fran[0]+franprev[i][0]);
- franprev[i][0] = fran[0];
- fran[0] = fswap;
- fswap = 0.5*(fran[1]+franprev[i][1]);
- franprev[i][1] = fran[1];
- fran[1] = fswap;
- fswap = 0.5*(fran[2]+franprev[i][2]);
- franprev[i][2] = fran[2];
- fran[2] = fswap;
-
- fdrag[0] *= gjffac;
- fdrag[1] *= gjffac;
- fdrag[2] *= gjffac;
- fran[0] *= gjffac;
- fran[1] *= gjffac;
- fran[2] *= gjffac;
- f[i][0] *= gjffac;
- f[i][1] *= gjffac;
- f[i][2] *= gjffac;
+ fswap = 0.5*(fran[0]+franprev[i][0]);
+ franprev[i][0] = fran[0];
+ fran[0] = fswap;
+ fswap = 0.5*(fran[1]+franprev[i][1]);
+ franprev[i][1] = fran[1];
+ fran[1] = fswap;
+ fswap = 0.5*(fran[2]+franprev[i][2]);
+ franprev[i][2] = fran[2];
+ fran[2] = fswap;
+
+ fdrag[0] *= gjffac;
+ fdrag[1] *= gjffac;
+ fdrag[2] *= gjffac;
+ fran[0] *= gjffac;
+ fran[1] *= gjffac;
+ fran[2] *= gjffac;
+ f[i][0] *= gjffac;
+ f[i][1] *= gjffac;
+ f[i][2] *= gjffac;
}
f[i][0] += fdrag[0] + fran[0];
@@ -580,15 +580,15 @@ void FixLangevin::post_force_untemplated
f[i][2] += fdrag[2] + fran[2];
if (Tp_TALLY) {
- flangevin[i][0] = fdrag[0] + fran[0];
- flangevin[i][1] = fdrag[1] + fran[1];
- flangevin[i][2] = fdrag[2] + fran[2];
+ flangevin[i][0] = fdrag[0] + fran[0];
+ flangevin[i][1] = fdrag[1] + fran[1];
+ flangevin[i][2] = fdrag[2] + fran[2];
}
if (Tp_ZERO) {
- fsum[0] += fran[0];
- fsum[1] += fran[1];
- fsum[2] += fran[2];
+ fsum[0] += fran[0];
+ fsum[1] += fran[1];
+ fsum[2] += fran[2];
}
}
}
diff --git a/src/fix_langevin.h b/src/fix_langevin.h
index 34eec63987..2883ac9ea2 100644
--- a/src/fix_langevin.h
+++ b/src/fix_langevin.h
@@ -76,11 +76,11 @@ class FixLangevin : public Fix {
#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 >
+ int Tp_BIAS, int Tp_RMASS, int Tp_ZERO >
void post_force_templated();
#else
void post_force_untemplated(int, int, int,
- int, int, int);
+ int, int, int);
#endif
void omega_thermostat();
void angmom_thermostat();
diff --git a/src/fix_nh_sphere.cpp b/src/fix_nh_sphere.cpp
index 5307889f5e..28de5490d4 100644
--- a/src/fix_nh_sphere.cpp
+++ b/src/fix_nh_sphere.cpp
@@ -47,7 +47,7 @@ FixNHSphere::FixNHSphere(LAMMPS *lmp, int narg, char **arg) :
if (strcmp(arg[iarg],"disc") == 0){
inertia = 0.5;
if (domain->dimension != 2)
- error->all(FLERR,
+ error->all(FLERR,
"Fix nvt/nph/npt sphere disc option requires 2d simulation");
}
iarg++;
diff --git a/src/fix_nve_sphere.cpp b/src/fix_nve_sphere.cpp
index 8c43800939..7ffd92e232 100644
--- a/src/fix_nve_sphere.cpp
+++ b/src/fix_nve_sphere.cpp
@@ -62,7 +62,7 @@ FixNVESphere::FixNVESphere(LAMMPS *lmp, int narg, char **arg) :
else if (strcmp(arg[iarg],"disc")==0) {
inertia = 0.5;
if (domain->dimension != 2)
- error->all(FLERR,"Fix nve/sphere disc requires 2d simulation");
+ error->all(FLERR,"Fix nve/sphere disc requires 2d simulation");
iarg++;
}
else error->all(FLERR,"Illegal fix nve/sphere command");
diff --git a/src/fix_store_state.cpp b/src/fix_store_state.cpp
index 8b742d5ad4..36f5c6a92e 100644
--- a/src/fix_store_state.cpp
+++ b/src/fix_store_state.cpp
@@ -418,7 +418,7 @@ void FixStoreState::init()
icustom = atom->find_custom(ids[m],iflag);
if ((icustom < 0) || (iflag != 0))
error->all(FLERR,
- "Custom integer vector for fix store/state does not exist");
+ "Custom integer vector for fix store/state does not exist");
value2index[m] = icustom;
} else if (which[m] == DNAME) {
@@ -426,7 +426,7 @@ void FixStoreState::init()
icustom = atom->find_custom(ids[m],iflag);
if ((icustom < 0) || (iflag != 1))
error->all(FLERR,
- "Custom floating point vector for fix store/state does not exist");
+ "Custom floating point vector for fix store/state does not exist");
value2index[m] = icustom;
} else if (which[m] == FIX) {
@@ -1089,7 +1089,7 @@ void FixStoreState::pack_xsu_triclinic(int n)
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit)
vbuf[n] = h_inv[0]*(x[i][0]-boxlo[0]) + h_inv[5]*(x[i][1]-boxlo[1]) +
- h_inv[4]*(x[i][2]-boxlo[2]) + (image[i] & IMGMASK) - IMGMAX;
+ h_inv[4]*(x[i][2]-boxlo[2]) + (image[i] & IMGMASK) - IMGMAX;
else vbuf[n] = 0.0;
n += nvalues;
}
@@ -1110,7 +1110,7 @@ void FixStoreState::pack_ysu_triclinic(int n)
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit)
vbuf[n] = h_inv[1]*(x[i][1]-boxlo[1]) + h_inv[3]*(x[i][2]-boxlo[2]) +
- (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
+ (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
else vbuf[n] = 0.0;
n += nvalues;
}
diff --git a/src/fix_wall_lj1043.cpp b/src/fix_wall_lj1043.cpp
index 064a5a8d60..35bfff1749 100644
--- a/src/fix_wall_lj1043.cpp
+++ b/src/fix_wall_lj1043.cpp
@@ -47,7 +47,7 @@ void FixWallLJ1043::precompute(int m)
double r2inv = rinv*rinv;
double r4inv = r2inv*r2inv;
offset[m] = coeff1[m]*r4inv*r4inv*r2inv - coeff2[m]*r4inv -
- coeff3[m]*pow(cutoff[m]+coeff4[m],-3.0);
+ coeff3[m]*pow(cutoff[m]+coeff4[m],-3.0);
}
/* ---------------------------------------------------------------------- */
@@ -78,10 +78,10 @@ void FixWallLJ1043::wall_particle(int m, int which, double coord)
r10inv = r4inv*r4inv*r2inv;
fwall = side * (coeff5[m]*r10inv*rinv - coeff6[m]*r4inv*rinv -
- coeff7[m]*pow(delta+coeff4[m],-4.0));
+ coeff7[m]*pow(delta+coeff4[m],-4.0));
f[i][dim] -= fwall;
ewall[0] += coeff1[m]*r10inv - coeff2[m]*r4inv -
- coeff3[m]*pow(delta+coeff4[m],-3.0) - offset[m];
+ coeff3[m]*pow(delta+coeff4[m],-3.0) - offset[m];
ewall[m+1] += fwall;
if (evflag) {
diff --git a/src/input.cpp b/src/input.cpp
index 0640327682..3d458c1ea4 100644
--- a/src/input.cpp
+++ b/src/input.cpp
@@ -163,8 +163,8 @@ void Input::file()
while (1) {
if (maxline-m < 2) reallocate(line,maxline,0);
- // end of file reached, so break
- // n == 0 if nothing read, else n = line with str terminator
+ // 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;
@@ -172,23 +172,23 @@ void Input::file()
break;
}
- // continue if last char read was not a newline
- // could happen if line is very long
+ // continue if last char read was not a newline
+ // could happen if line is very long
m = strlen(line);
if (line[m-1] != '\n') continue;
- // continue reading if final printable char is & char
- // or if odd number of triple quotes
- // else break with n = line with str terminator
+ // continue reading if final printable char is & char
+ // or if odd number of triple quotes
+ // else break with n = line with str terminator
m--;
while (m >= 0 && isspace(line[m])) m--;
if (m < 0 || line[m] != '&') {
- if (numtriple(line) % 2) {
- m += 2;
- continue;
- }
+ if (numtriple(line) % 2) {
+ m += 2;
+ continue;
+ }
line[m+1] = '\0';
n = m+2;
break;
@@ -559,17 +559,17 @@ void Input::substitute(char *&str, char *&str2, int &max, int &max2, int flag)
if (quoteflag == 0) {
if (strstr(ptr,"\"\"\"") == ptr) {
- quoteflag = 3;
- *ptr2++ = *ptr++;
- *ptr2++ = *ptr++;
+ quoteflag = 3;
+ *ptr2++ = *ptr++;
+ *ptr2++ = *ptr++;
}
else if (*ptr == '"') quoteflag = 2;
else if (*ptr == '\'') quoteflag = 1;
} else {
if (quoteflag == 3 && strstr(ptr,"\"\"\"") == ptr) {
- quoteflag = 0;
- *ptr2++ = *ptr++;
- *ptr2++ = *ptr++;
+ quoteflag = 0;
+ *ptr2++ = *ptr++;
+ *ptr2++ = *ptr++;
}
else if (quoteflag == 2 && *ptr == '"') quoteflag = 0;
else if (quoteflag == 1 && *ptr == '\'') quoteflag = 0;
@@ -626,62 +626,62 @@ int Input::expand_args(int narg, char **arg, int mode, char **&earg)
ptr1 = strchr(&arg[iarg][2],'[');
if (ptr1) {
- ptr2 = strchr(ptr1,']');
- if (ptr2) {
- *ptr2 = '\0';
- if (strchr(ptr1,'*')) {
- if (arg[iarg][0] == 'c') {
- *ptr1 = '\0';
- icompute = modify->find_compute(&arg[iarg][2]);
- *ptr1 = '[';
+ ptr2 = strchr(ptr1,']');
+ if (ptr2) {
+ *ptr2 = '\0';
+ if (strchr(ptr1,'*')) {
+ if (arg[iarg][0] == 'c') {
+ *ptr1 = '\0';
+ icompute = modify->find_compute(&arg[iarg][2]);
+ *ptr1 = '[';
// check for global vector/array, peratom array, local array
- if (icompute >= 0) {
- if (mode == 0 && modify->compute[icompute]->vector_flag) {
- nmax = modify->compute[icompute]->size_vector;
- expandflag = 1;
- } else if (mode == 1 && modify->compute[icompute]->array_flag) {
- nmax = modify->compute[icompute]->size_array_cols;
- expandflag = 1;
+ if (icompute >= 0) {
+ if (mode == 0 && modify->compute[icompute]->vector_flag) {
+ nmax = modify->compute[icompute]->size_vector;
+ expandflag = 1;
+ } else if (mode == 1 && modify->compute[icompute]->array_flag) {
+ nmax = modify->compute[icompute]->size_array_cols;
+ expandflag = 1;
} else if (modify->compute[icompute]->peratom_flag &&
modify->compute[icompute]->size_peratom_cols) {
- nmax = modify->compute[icompute]->size_peratom_cols;
- expandflag = 1;
+ nmax = modify->compute[icompute]->size_peratom_cols;
+ expandflag = 1;
} else if (modify->compute[icompute]->local_flag &&
modify->compute[icompute]->size_local_cols) {
- nmax = modify->compute[icompute]->size_local_cols;
- expandflag = 1;
- }
- }
- } else if (arg[iarg][0] == 'f') {
- *ptr1 = '\0';
- ifix = modify->find_fix(&arg[iarg][2]);
- *ptr1 = '[';
+ nmax = modify->compute[icompute]->size_local_cols;
+ expandflag = 1;
+ }
+ }
+ } else if (arg[iarg][0] == 'f') {
+ *ptr1 = '\0';
+ ifix = modify->find_fix(&arg[iarg][2]);
+ *ptr1 = '[';
// check for global vector/array, peratom array, local array
- if (ifix >= 0) {
- if (mode == 0 && modify->fix[ifix]->vector_flag) {
- nmax = modify->fix[ifix]->size_vector;
- expandflag = 1;
- } else if (mode == 1 && modify->fix[ifix]->array_flag) {
- nmax = modify->fix[ifix]->size_array_cols;
- expandflag = 1;
+ if (ifix >= 0) {
+ if (mode == 0 && modify->fix[ifix]->vector_flag) {
+ nmax = modify->fix[ifix]->size_vector;
+ expandflag = 1;
+ } else if (mode == 1 && modify->fix[ifix]->array_flag) {
+ nmax = modify->fix[ifix]->size_array_cols;
+ expandflag = 1;
} else if (modify->fix[ifix]->peratom_flag &&
modify->fix[ifix]->size_peratom_cols) {
- nmax = modify->fix[ifix]->size_peratom_cols;
- expandflag = 1;
+ nmax = modify->fix[ifix]->size_peratom_cols;
+ expandflag = 1;
} else if (modify->fix[ifix]->local_flag &&
modify->fix[ifix]->size_local_cols) {
- nmax = modify->fix[ifix]->size_local_cols;
- expandflag = 1;
- }
- }
- }
- }
- *ptr2 = ']';
- }
+ nmax = modify->fix[ifix]->size_local_cols;
+ expandflag = 1;
+ }
+ }
+ }
+ }
+ *ptr2 = ']';
+ }
}
}
@@ -690,23 +690,23 @@ int Input::expand_args(int narg, char **arg, int mode, char **&earg)
force->bounds(FLERR,ptr1+1,nmax,nlo,nhi);
*ptr2 = ']';
if (newarg+nhi-nlo+1 > maxarg) {
- maxarg += nhi-nlo+1;
- earg = (char **)
+ maxarg += nhi-nlo+1;
+ earg = (char **)
memory->srealloc(earg,maxarg*sizeof(char *),"input:earg");
}
for (index = nlo; index <= nhi; index++) {
- n = strlen(arg[iarg]) + 16; // 16 = space for large inserted integer
- str = earg[newarg] = new char[n];
- strncpy(str,arg[iarg],ptr1+1-arg[iarg]);
- sprintf(&str[ptr1+1-arg[iarg]],"%d",index);
- strcat(str,ptr2);
+ n = strlen(arg[iarg]) + 16; // 16 = space for large inserted integer
+ str = earg[newarg] = new char[n];
+ strncpy(str,arg[iarg],ptr1+1-arg[iarg]);
+ sprintf(&str[ptr1+1-arg[iarg]],"%d",index);
+ strcat(str,ptr2);
newarg++;
}
} else {
if (newarg == maxarg) {
- maxarg++;
- earg = (char **)
+ maxarg++;
+ earg = (char **)
memory->srealloc(earg,maxarg*sizeof(char *),"input:earg");
}
n = strlen(arg[iarg]) + 1;
diff --git a/src/kspace.cpp b/src/kspace.cpp
index 07e117e162..b2db585f12 100644
--- a/src/kspace.cpp
+++ b/src/kspace.cpp
@@ -541,11 +541,11 @@ void KSpace::modify_params(int narg, char **arg)
ky_ewald = atoi(arg[iarg+2]);
kz_ewald = atoi(arg[iarg+3]);
if (kx_ewald < 0 || ky_ewald < 0 || kz_ewald < 0)
- error->all(FLERR,"Bad kspace_modify kmax/ewald parameter");
+ error->all(FLERR,"Bad kspace_modify kmax/ewald parameter");
if (kx_ewald > 0 && ky_ewald > 0 && kz_ewald > 0)
- kewaldflag = 1;
+ kewaldflag = 1;
else
- kewaldflag = 0;
+ kewaldflag = 0;
iarg += 4;
} else if (strcmp(arg[iarg],"mix/disp") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal kspace_modify command");
diff --git a/src/lammps.cpp b/src/lammps.cpp
index bde7ca035d..dd91ea7c19 100644
--- a/src/lammps.cpp
+++ b/src/lammps.cpp
@@ -197,18 +197,18 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
if (strcmp(arg[iarg+1],"hybrid") == 0) {
if (iarg+4 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
- int n = strlen(arg[iarg+2]) + 1;
- suffix = new char[n];
- strcpy(suffix,arg[iarg+2]);
- n = strlen(arg[iarg+3]) + 1;
- suffix2 = new char[n];
- strcpy(suffix2,arg[iarg+3]);
- iarg += 4;
+ int n = strlen(arg[iarg+2]) + 1;
+ suffix = new char[n];
+ strcpy(suffix,arg[iarg+2]);
+ n = strlen(arg[iarg+3]) + 1;
+ suffix2 = new char[n];
+ strcpy(suffix2,arg[iarg+3]);
+ iarg += 4;
} else {
- int n = strlen(arg[iarg+1]) + 1;
- suffix = new char[n];
- strcpy(suffix,arg[iarg+1]);
- iarg += 2;
+ int n = strlen(arg[iarg+1]) + 1;
+ suffix = new char[n];
+ strcpy(suffix,arg[iarg+1]);
+ iarg += 2;
}
} else if (strcmp(arg[iarg],"-reorder") == 0 ||
strcmp(arg[iarg],"-ro") == 0) {
diff --git a/src/library.cpp b/src/library.cpp
index 233bb3122c..b30c6e9595 100644
--- a/src/library.cpp
+++ b/src/library.cpp
@@ -1002,7 +1002,7 @@ void lammps_scatter_atoms(void *ptr, char *name,
------------------------------------------------------------------------- */
void lammps_create_atoms(void *ptr, int n, tagint *id, int *type,
- double *x, double *v, imageint *image,
+ double *x, double *v, imageint *image,
int shrinkexceed)
{
LAMMPS *lmp = (LAMMPS *) ptr;
@@ -1044,9 +1044,9 @@ void lammps_create_atoms(void *ptr, int n, tagint *id, int *type,
if (id) atom->tag[nlocal] = id[i];
else atom->tag[nlocal] = i+1;
if (v) {
- atom->v[nlocal][0] = v[3*i];
- atom->v[nlocal][1] = v[3*i+1];
- atom->v[nlocal][2] = v[3*i+2];
+ atom->v[nlocal][0] = v[3*i];
+ atom->v[nlocal][1] = v[3*i+1];
+ atom->v[nlocal][2] = v[3*i+2];
}
if (image) atom->image[nlocal] = image[i];
nlocal++;
diff --git a/src/neighbor.cpp b/src/neighbor.cpp
index 686552656a..82017c8525 100644
--- a/src/neighbor.cpp
+++ b/src/neighbor.cpp
@@ -1455,7 +1455,7 @@ void Neighbor::print_pairwise_info()
nlist,nperpetual,noccasional,nextra);
for (i = 0; i < nlist; i++) {
- rq = requests[i];
+ rq = requests[i];
if (rq->pair) {
char *pname = force->pair_match_ptr((Pair *) rq->requestor);
sprintf(str," (%d) pair %s",i+1,pname);
@@ -1491,12 +1491,12 @@ void Neighbor::print_pairwise_info()
if (rq->half) fprintf(out,"half");
else if (rq->full) fprintf(out,"full");
- if (rq->newton == 0) {
- if (force->newton_pair) fprintf(out,", newton on");
- else fprintf(out,", newton off");
- } else if (rq->newton == 1) fprintf(out,", newton on");
- else if (rq->newton == 2) fprintf(out,", newton off");
-
+ if (rq->newton == 0) {
+ if (force->newton_pair) fprintf(out,", newton on");
+ else fprintf(out,", newton off");
+ } else if (rq->newton == 1) fprintf(out,", newton on");
+ else if (rq->newton == 2) fprintf(out,", newton off");
+
if (rq->ghost) fprintf(out,", ghost");
if (rq->size) fprintf(out,", size");
if (rq->history) fprintf(out,", history");
@@ -2303,7 +2303,7 @@ void Neighbor::modify_params(int narg, char **arg)
iarg += 4;
} else if (strcmp(arg[iarg+1],"molecule/inter") == 0 ||
- strcmp(arg[iarg+1],"molecule/intra") == 0) {
+ strcmp(arg[iarg+1],"molecule/intra") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal neigh_modify command");
if (atom->molecule_flag == 0)
error->all(FLERR,"Neigh_modify exclude molecule "
@@ -2319,13 +2319,13 @@ void Neighbor::modify_params(int narg, char **arg)
ex_mol_group[nex_mol] = group->find(arg[iarg+2]);
if (ex_mol_group[nex_mol] == -1)
error->all(FLERR,"Invalid group ID in neigh_modify command");
- if (strcmp(arg[iarg+1],"molecule/intra") == 0)
- ex_mol_intra[nex_mol] = 1;
- else
- ex_mol_intra[nex_mol] = 0;
+ if (strcmp(arg[iarg+1],"molecule/intra") == 0)
+ ex_mol_intra[nex_mol] = 1;
+ else
+ ex_mol_intra[nex_mol] = 0;
nex_mol++;
iarg += 3;
-
+
} else if (strcmp(arg[iarg+1],"none") == 0) {
nex_type = nex_group = nex_mol = 0;
iarg += 2;
diff --git a/src/pair.h b/src/pair.h
index cfb6576653..94de38ab57 100644
--- a/src/pair.h
+++ b/src/pair.h
@@ -138,7 +138,7 @@ class Pair : protected Pointers {
virtual double single(int, int, int, int,
double, double, double,
- double& fforce) {
+ double& fforce) {
fforce = 0.0;
return 0.0;
}
diff --git a/src/pair_born_coul_dsf.cpp b/src/pair_born_coul_dsf.cpp
index d53e9cf00e..3700aa46d7 100644
--- a/src/pair_born_coul_dsf.cpp
+++ b/src/pair_born_coul_dsf.cpp
@@ -132,7 +132,7 @@ void PairBornCoulDSF::compute(int eflag, int vflag)
if (rsq < cut_coulsq) {
r = sqrt(rsq);
prefactor = qqrd2e*qtmp*q[j]/r;
- arg = alpha * r ;
+ arg = alpha * r ;
erfcd = MathSpecial::expmsq(arg);
erfcc = MathSpecial::my_erfcx(arg) * erfcd;
forcecoul = prefactor * (erfcc/r + 2.0*alpha/MY_PIS * erfcd +
diff --git a/src/pair_coul_streitz.cpp b/src/pair_coul_streitz.cpp
index 6b9ba9df9c..82ecd1d810 100644
--- a/src/pair_coul_streitz.cpp
+++ b/src/pair_coul_streitz.cpp
@@ -189,7 +189,7 @@ void PairCoulStreitz::coeff(int narg, char **arg)
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
if (map[i] >= 0 && map[j] >= 0) {
- scale[i][j] = 1.0;
+ scale[i][j] = 1.0;
setflag[i][j] = 1;
count++;
}
@@ -488,7 +488,7 @@ void PairCoulStreitz::compute(int eflag, int vflag)
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,
- 0.0,ecoul,fpair,delr[0],delr[1],delr[2]);
+ 0.0,ecoul,fpair,delr[0],delr[1],delr[2]);
}
}
@@ -544,7 +544,7 @@ void PairCoulStreitz::compute(int eflag, int vflag)
// Ewald: real-space
ewald_sum(qi, qj, zj, r, ci_jfi, dci_jfi, ci_fifj, dci_fifj,
- ecoul, forcecoul, factor_coul);
+ ecoul, forcecoul, factor_coul);
// Forces
@@ -560,7 +560,7 @@ void PairCoulStreitz::compute(int eflag, int vflag)
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,
- 0.0,ecoul,fpair,delr[0],delr[1],delr[2]);
+ 0.0,ecoul,fpair,delr[0],delr[1],delr[2]);
}
}
}
@@ -585,8 +585,8 @@ 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 &dci_fifj)
+ double &ci_jfi, double &dci_jfi, double &ci_fifj,
+ double &dci_fifj)
{
double rinv = 1.0/r;
double rinv2 = rinv*rinv;
@@ -625,12 +625,12 @@ void PairCoulStreitz::coulomb_integral_wolf(double zei, double zej, double r,
eshift = -exp2zirsh*(rcinv + zei*(sm1 + sm2*zei*rc + sm3*zei2*rc*rc));
fshift = exp2zirsh*(rcinv2 + 2.0*zei*rcinv + zei2*
- (2.0 + 7.0/6.0*zei*rc + 1.0/3.0*zei2*rc*rc));
+ (2.0 + 7.0/6.0*zei*rc + 1.0/3.0*zei2*rc*rc));
ci_fifj = -exp2zir*(rinv + zei*(sm1 + sm2*zei*r + sm3*zei2*r*r))
- - eshift - (r-rc)*fshift;
+ - eshift - (r-rc)*fshift;
dci_fifj = exp2zir*(rinv2 + 2.0*zei*rinv + zei2*
- (2.0 + 7.0/6.0*zei*r + 1.0/3.0*zei2*r*r)) - fshift;
+ (2.0 + 7.0/6.0*zei*r + 1.0/3.0*zei2*r*r)) - fshift;
} else {
@@ -646,7 +646,7 @@ void PairCoulStreitz::coulomb_integral_wolf(double zei, double zej, double r,
+ exp2zjrsh*(2.0*zej*(e2+e4/rc) + e4*rcinv2));
ci_fifj = -exp2zir*(e1+e3/r) - exp2zjr*(e2+e4/r)
- - eshift - (r-rc)*fshift;
+ - eshift - (r-rc)*fshift;
dci_fifj = (exp2zir*(2.0*zei*(e1+e3/r) + e3*rinv2) +
exp2zjr*(2.0*zej*(e2+e4/r) + e4*rinv2)) - fshift;
}
@@ -655,8 +655,8 @@ void PairCoulStreitz::coulomb_integral_wolf(double zei, double zej, double r,
/* ---------------------------------------------------------------------- */
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 ci_jfi, double dci_jfi, double ci_fifj,
+ double dci_fifj, double &etmp, double &ftmp)
{
double a = g_wolf;
double rc = cut_coul;
@@ -688,8 +688,8 @@ 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 &dci_fifj)
+ double &ci_jfi, double &dci_jfi, double &ci_fifj,
+ double &dci_fifj)
{
double rinv = 1.0/r;
double rinv2 = rinv*rinv;
@@ -718,7 +718,7 @@ void PairCoulStreitz::coulomb_integral_ewald(double zei, double zej, double r,
ci_fifj = -exp2zir*(rinv + zei*(sm1 + sm2*zei*r + sm3*zei2*r*r));
dci_fifj = exp2zir*(rinv2 + 2.0*zei*rinv +
- zei2*(2.0 + 7.0/6.0*zei*r + 1.0/3.0*zei2*r*r));
+ 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,
- double dci_fifj, double &etmp, double &ftmp, double fac)
+ double ci_jfi, double dci_jfi, double ci_fifj,
+ double dci_fifj, double &etmp, double &ftmp, double fac)
{
double etmp1, etmp2, etmp3, etmp4;
double ftmp1, ftmp2, ftmp3, ftmp4;
diff --git a/src/pair_coul_streitz.h b/src/pair_coul_streitz.h
index 8e713997f5..c304365270 100644
--- a/src/pair_coul_streitz.h
+++ b/src/pair_coul_streitz.h
@@ -74,11 +74,11 @@ class PairCoulStreitz : public Pair {
void coulomb_integral_wolf(double, double, double, double &, double &,
double &, double &);
void wolf_sum(double, double, double, 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,
- double, double &, double &, double);
+ double, double &, double &, double);
};
diff --git a/src/pair_lj_cut_coul_dsf.cpp b/src/pair_lj_cut_coul_dsf.cpp
index 5d95d06ed7..4290586501 100644
--- a/src/pair_lj_cut_coul_dsf.cpp
+++ b/src/pair_lj_cut_coul_dsf.cpp
@@ -360,7 +360,7 @@ void PairLJCutCoulDSF::write_restart(FILE *fp)
fwrite(&epsilon[i][j],sizeof(double),1,fp);
fwrite(&sigma[i][j],sizeof(double),1,fp);
fwrite(&cut_lj[i][j],sizeof(double),1,fp);
- }
+ }
}
}
diff --git a/src/pair_lj_expand.cpp b/src/pair_lj_expand.cpp
index 785733dccc..f2f49c872d 100644
--- a/src/pair_lj_expand.cpp
+++ b/src/pair_lj_expand.cpp
@@ -282,9 +282,9 @@ double PairLJExpand::init_one(int i, int j)
(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) +
- 3.0*shift2/(11.0*rc2) + shift3/(12.0*rc3))*2.0*sig6/rc9 -
+ 3.0*shift2/(11.0*rc2) + shift3/(12.0*rc3))*2.0*sig6/rc9 -
(1.0/3.0 + 3.0*shift1/(4.0*rc1) +
- 3.0*shift2/(5.0*rc2) + shift3/(6.0*rc3))/rc3);
+ 3.0*shift2/(5.0*rc2) + shift3/(6.0*rc3))/rc3);
}
return cut[i][j] + shift[i][j];
diff --git a/src/pair_morse.h b/src/pair_morse.h
index d1282f8bf1..e7fb9a8cd5 100644
--- a/src/pair_morse.h
+++ b/src/pair_morse.h
@@ -29,7 +29,7 @@ class PairMorse : public Pair {
PairMorse(class LAMMPS *);
virtual ~PairMorse();
virtual void compute(int, int);
-
+
void settings(int, char **);
void coeff(int, char **);
double init_one(int, int);
diff --git a/src/pair_zbl.cpp b/src/pair_zbl.cpp
index ce6c581ced..d2dbaeae70 100644
--- a/src/pair_zbl.cpp
+++ b/src/pair_zbl.cpp
@@ -114,15 +114,15 @@ void PairZBL::compute(int eflag, int vflag)
jtype = type[j];
if (rsq < cut_globalsq) {
- r = sqrt(rsq);
+ r = sqrt(rsq);
fpair = dzbldr(r, itype, jtype);
- if (rsq > cut_innersq) {
- t = r - cut_inner;
- fswitch = t*t *
- (sw1[itype][jtype] + sw2[itype][jtype]*t);
- fpair += fswitch;
- }
+ if (rsq > cut_innersq) {
+ t = r - cut_inner;
+ fswitch = t*t *
+ (sw1[itype][jtype] + sw2[itype][jtype]*t);
+ fpair += fswitch;
+ }
fpair *= -1.0/r;
f[i][0] += delx*fpair;
@@ -136,12 +136,12 @@ void PairZBL::compute(int eflag, int vflag)
if (eflag) {
evdwl = e_zbl(r, itype, jtype);
- evdwl += sw5[itype][jtype];
- if (rsq > cut_innersq) {
- eswitch = t*t*t *
- (sw3[itype][jtype] + sw4[itype][jtype]*t);
- evdwl += eswitch;
- }
+ evdwl += sw5[itype][jtype];
+ if (rsq > cut_innersq) {
+ eswitch = t*t*t *
+ (sw3[itype][jtype] + sw4[itype][jtype]*t);
+ evdwl += eswitch;
+ }
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,
@@ -228,9 +228,9 @@ void PairZBL::coeff(int narg, char **arg)
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
if (i == j) {
- if (z_one != z_two)
- error->all(FLERR,"Incorrect args for pair coefficients");
- z[i] = z_one;
+ if (z_one != z_two)
+ error->all(FLERR,"Incorrect args for pair coefficients");
+ z[i] = z_one;
}
setflag[i][j] = 1;
set_coeff(i, j, z_one, z_two);
@@ -385,7 +385,7 @@ double PairZBL::d2zbldr2(double r, int i, int j) {
sum_pp += c4*e4*d4aij*d4aij;
double result = zzeij*(sum_pp + 2.0*sum_p*rinv +
- 2.0*sum*rinv*rinv)*rinv;
+ 2.0*sum*rinv*rinv)*rinv;
return result;
}
diff --git a/src/rcb.cpp b/src/rcb.cpp
index 7ad1e84d4c..2ef3e0c136 100644
--- a/src/rcb.cpp
+++ b/src/rcb.cpp
@@ -500,8 +500,8 @@ void RCB::compute(int dimension, int n, double **x, double *wt,
if (readnumber) {
MPI_Recv(&incoming,1,MPI_INT,procpartner,0,world,MPI_STATUS_IGNORE);
if (readnumber == 2) {
- MPI_Recv(&incoming2,1,MPI_INT,procpartner2,0,world,MPI_STATUS_IGNORE);
- incoming += incoming2;
+ MPI_Recv(&incoming2,1,MPI_INT,procpartner2,0,world,MPI_STATUS_IGNORE);
+ incoming += incoming2;
}
}
@@ -533,9 +533,9 @@ void RCB::compute(int dimension, int n, double **x, double *wt,
keep = outgoing = 0;
for (i = 0; i < ndot; i++) {
if (dotmark[i] == markactive)
- memcpy(&buf[outgoing++],&dots[i],sizeof(Dot));
+ memcpy(&buf[outgoing++],&dots[i],sizeof(Dot));
else
- memcpy(&dots[keep++],&dots[i],sizeof(Dot));
+ memcpy(&dots[keep++],&dots[i],sizeof(Dot));
}
// post receives for dots
@@ -544,8 +544,8 @@ void RCB::compute(int dimension, int n, double **x, double *wt,
MPI_Irecv(&dots[keep],incoming*sizeof(Dot),MPI_CHAR,
procpartner,1,world,&request);
if (readnumber == 2) {
- keep += incoming - incoming2;
- MPI_Irecv(&dots[keep],incoming2*sizeof(Dot),MPI_CHAR,
+ keep += incoming - incoming2;
+ MPI_Irecv(&dots[keep],incoming2*sizeof(Dot),MPI_CHAR,
procpartner2,1,world,&request2);
}
}
@@ -801,15 +801,15 @@ void RCB::compute_old(int dimension, int n, double **x, double *wt,
// 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);
+ counters[5]++;
+ valuehalf = tree[procmid].cut;
+ if (valuehalf < valuemin || valuehalf > valuemax)
+ valuehalf = 0.5 * (valuemin + valuemax);
} else if (wt)
- valuehalf = valuemin + (targetlo - wtlo) /
- (wttot - wtlo - wthi) * (valuemax - valuemin);
+ valuehalf = valuemin + (targetlo - wtlo) /
+ (wttot - wtlo - wthi) * (valuemax - valuemin);
else
- valuehalf = 0.5 * (valuemin + valuemax);
+ valuehalf = 0.5 * (valuemin + valuemax);
first_iteration = 0;
@@ -827,33 +827,33 @@ void RCB::compute_old(int dimension, int n, double **x, double *wt,
// save indices of closest dots on either side
for (j = 0; j < nlist; j++) {
- i = dotlist[j];
- if (dots[i].x[dim] <= valuehalf) { // in lower part
- medme.totallo += dots[i].wt;
- dotmark[i] = 0;
- if (dots[i].x[dim] > medme.valuelo) { // my closest dot
- medme.valuelo = dots[i].x[dim];
- medme.wtlo = dots[i].wt;
- medme.countlo = 1;
- indexlo = i;
- } else if (dots[i].x[dim] == medme.valuelo) { // tied for closest
- medme.wtlo += dots[i].wt;
- medme.countlo++;
- }
- }
- else { // in upper part
- medme.totalhi += dots[i].wt;
- dotmark[i] = 1;
- if (dots[i].x[dim] < medme.valuehi) { // my closest dot
- medme.valuehi = dots[i].x[dim];
- medme.wthi = dots[i].wt;
- medme.counthi = 1;
- indexhi = i;
- } else if (dots[i].x[dim] == medme.valuehi) { // tied for closest
- medme.wthi += dots[i].wt;
- medme.counthi++;
- }
- }
+ i = dotlist[j];
+ if (dots[i].x[dim] <= valuehalf) { // in lower part
+ medme.totallo += dots[i].wt;
+ dotmark[i] = 0;
+ if (dots[i].x[dim] > medme.valuelo) { // my closest dot
+ medme.valuelo = dots[i].x[dim];
+ medme.wtlo = dots[i].wt;
+ medme.countlo = 1;
+ indexlo = i;
+ } else if (dots[i].x[dim] == medme.valuelo) { // tied for closest
+ medme.wtlo += dots[i].wt;
+ medme.countlo++;
+ }
+ }
+ else { // in upper part
+ medme.totalhi += dots[i].wt;
+ dotmark[i] = 1;
+ if (dots[i].x[dim] < medme.valuehi) { // my closest dot
+ medme.valuehi = dots[i].x[dim];
+ medme.wthi = dots[i].wt;
+ medme.counthi = 1;
+ indexhi = i;
+ } else if (dots[i].x[dim] == medme.valuehi) { // tied for closest
+ medme.wthi += dots[i].wt;
+ medme.counthi++;
+ }
+ }
}
// combine median data struct across current subset of procs
@@ -866,99 +866,99 @@ void RCB::compute_old(int dimension, int n, double **x, double *wt,
if (wtlo + med.totallo < targetlo) { // lower half TOO SMALL
- wtlo += med.totallo;
- valuehalf = med.valuehi;
-
- if (med.counthi == 1) { // only one dot to move
- if (wtlo + med.wthi < targetlo) { // move it, keep iterating
- if (me == med.prochi) dotmark[indexhi] = 0;
- }
- else { // only move if beneficial
- if (wtlo + med.wthi - targetlo < targetlo - wtlo)
- if (me == med.prochi) dotmark[indexhi] = 0;
- break; // all done
- }
- }
- else { // multiple dots to move
- breakflag = 0;
- wtok = 0.0;
- 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;
- if (wtupto > wtmax) wtok = wtok - (wtupto - wtmax);
- breakflag = 1;
- } // wtok = most I can move
- for (j = 0, wtsum = 0.0; j < nlist && wtsum < wtok; j++) {
- i = dotlist[j];
- if (dots[i].x[dim] == med.valuehi) { // only move if better
- if (wtsum + dots[i].wt - wtok < wtok - wtsum)
- dotmark[i] = 0;
- wtsum += dots[i].wt;
- }
- }
- if (breakflag) break; // done if moved enough
- }
-
- wtlo += med.wthi;
- if (targetlo-wtlo <= tolerance) break; // close enough
-
- valuemin = med.valuehi; // iterate again
- markactive = 1;
+ wtlo += med.totallo;
+ valuehalf = med.valuehi;
+
+ if (med.counthi == 1) { // only one dot to move
+ if (wtlo + med.wthi < targetlo) { // move it, keep iterating
+ if (me == med.prochi) dotmark[indexhi] = 0;
+ }
+ else { // only move if beneficial
+ if (wtlo + med.wthi - targetlo < targetlo - wtlo)
+ if (me == med.prochi) dotmark[indexhi] = 0;
+ break; // all done
+ }
+ }
+ else { // multiple dots to move
+ breakflag = 0;
+ wtok = 0.0;
+ 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;
+ if (wtupto > wtmax) wtok = wtok - (wtupto - wtmax);
+ breakflag = 1;
+ } // wtok = most I can move
+ for (j = 0, wtsum = 0.0; j < nlist && wtsum < wtok; j++) {
+ i = dotlist[j];
+ if (dots[i].x[dim] == med.valuehi) { // only move if better
+ if (wtsum + dots[i].wt - wtok < wtok - wtsum)
+ dotmark[i] = 0;
+ wtsum += dots[i].wt;
+ }
+ }
+ if (breakflag) break; // done if moved enough
+ }
+
+ wtlo += med.wthi;
+ if (targetlo-wtlo <= tolerance) break; // close enough
+
+ valuemin = med.valuehi; // iterate again
+ markactive = 1;
}
else if (wthi + med.totalhi < targethi) { // upper half TOO SMALL
- wthi += med.totalhi;
- valuehalf = med.valuelo;
-
- if (med.countlo == 1) { // only one dot to move
- if (wthi + med.wtlo < targethi) { // move it, keep iterating
- if (me == med.proclo) dotmark[indexlo] = 1;
- }
- else { // only move if beneficial
- if (wthi + med.wtlo - targethi < targethi - wthi)
- if (me == med.proclo) dotmark[indexlo] = 1;
- break; // all done
- }
- }
- else { // multiple dots to move
- breakflag = 0;
- wtok = 0.0;
- 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;
- if (wtupto > wtmax) wtok = wtok - (wtupto - wtmax);
- breakflag = 1;
- } // wtok = most I can move
- 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)
- dotmark[i] = 1;
- wtsum += dots[i].wt;
- }
- }
- if (breakflag) break; // done if moved enough
- }
-
- wthi += med.wtlo;
- if (targethi-wthi <= tolerance) break; // close enough
-
- valuemax = med.valuelo; // iterate again
- markactive = 0;
+ wthi += med.totalhi;
+ valuehalf = med.valuelo;
+
+ if (med.countlo == 1) { // only one dot to move
+ if (wthi + med.wtlo < targethi) { // move it, keep iterating
+ if (me == med.proclo) dotmark[indexlo] = 1;
+ }
+ else { // only move if beneficial
+ if (wthi + med.wtlo - targethi < targethi - wthi)
+ if (me == med.proclo) dotmark[indexlo] = 1;
+ break; // all done
+ }
+ }
+ else { // multiple dots to move
+ breakflag = 0;
+ wtok = 0.0;
+ 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;
+ if (wtupto > wtmax) wtok = wtok - (wtupto - wtmax);
+ breakflag = 1;
+ } // wtok = most I can move
+ 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)
+ dotmark[i] = 1;
+ wtsum += dots[i].wt;
+ }
+ }
+ if (breakflag) break; // done if moved enough
+ }
+
+ wthi += med.wtlo;
+ if (targethi-wthi <= tolerance) break; // close enough
+
+ valuemax = med.valuelo; // iterate again
+ markactive = 0;
}
else // Goldilocks result: both partitions just right
- break;
+ break;
// shrink the active list
k = 0;
for (j = 0; j < nlist; j++) {
- i = dotlist[j];
- if (dotmark[i] == markactive) dotlist[k++] = i;
+ i = dotlist[j];
+ if (dotmark[i] == markactive) dotlist[k++] = i;
}
nlist = k;
}
@@ -992,8 +992,8 @@ void RCB::compute_old(int dimension, int n, double **x, double *wt,
if (readnumber) {
MPI_Recv(&incoming,1,MPI_INT,procpartner,0,world,MPI_STATUS_IGNORE);
if (readnumber == 2) {
- MPI_Recv(&incoming2,1,MPI_INT,procpartner2,0,world,MPI_STATUS_IGNORE);
- incoming += incoming2;
+ MPI_Recv(&incoming2,1,MPI_INT,procpartner2,0,world,MPI_STATUS_IGNORE);
+ incoming += incoming2;
}
}
@@ -1025,9 +1025,9 @@ void RCB::compute_old(int dimension, int n, double **x, double *wt,
keep = outgoing = 0;
for (i = 0; i < ndot; i++) {
if (dotmark[i] == markactive)
- memcpy(&buf[outgoing++],&dots[i],sizeof(Dot));
+ memcpy(&buf[outgoing++],&dots[i],sizeof(Dot));
else
- memcpy(&dots[keep++],&dots[i],sizeof(Dot));
+ memcpy(&dots[keep++],&dots[i],sizeof(Dot));
}
// post receives for dots
@@ -1036,8 +1036,8 @@ void RCB::compute_old(int dimension, int n, double **x, double *wt,
MPI_Irecv(&dots[keep],incoming*sizeof(Dot),MPI_CHAR,
procpartner,1,world,&request);
if (readnumber == 2) {
- keep += incoming - incoming2;
- MPI_Irecv(&dots[keep],incoming2*sizeof(Dot),MPI_CHAR,
+ keep += incoming - incoming2;
+ MPI_Irecv(&dots[keep],incoming2*sizeof(Dot),MPI_CHAR,
procpartner2,1,world,&request2);
}
}
@@ -1133,7 +1133,7 @@ void box_merge(void *in, void *inout, int *len, MPI_Datatype *dptr)
wtlo, wthi = total wt of dot(s) at that position
countlo, counthi = total # of dot(s) nearest to cut
proclo, prochi = one unique proc who owns a nearest dot
- all procs must get same proclo,prochi
+ all procs must get same proclo,prochi
------------------------------------------------------------------------- */
void median_merge(void *in, void *inout, int *len, MPI_Datatype *dptr)
@@ -1266,7 +1266,7 @@ void RCB::check()
if (total1 != total2) {
if (me == 0)
printf("ERROR: Points before RCB = %d, Points after RCB = %d\n",
- total1,total2);
+ total1,total2);
}
// check that result is load-balanced within log2(P)*max-wt
@@ -1302,8 +1302,8 @@ void RCB::check()
iflag = 0;
for (i = 0; i < ndot; i++) {
if (dots[i].x[0] < lo[0] || dots[i].x[0] > hi[0] ||
- dots[i].x[1] < lo[1] || dots[i].x[1] > hi[1] ||
- dots[i].x[2] < lo[2] || dots[i].x[2] > hi[2])
+ dots[i].x[1] < lo[1] || dots[i].x[1] > hi[1] ||
+ dots[i].x[2] < lo[2] || dots[i].x[2] > hi[2])
iflag++;
}
if (iflag > 0)
@@ -1330,7 +1330,7 @@ void RCB::stats(int flag)
if (me == 0) {
printf(" Total weight of dots = %g\n",wttot);
printf(" Weight on each proc: ave = %g, max = %g, min = %g\n",
- wttot/nprocs,wtmax,wtmin);
+ wttot/nprocs,wtmax,wtmin);
}
if (flag) {
MPI_Barrier(world);
diff --git a/src/read_data.cpp b/src/read_data.cpp
index 3b93098a6e..bc588051af 100644
--- a/src/read_data.cpp
+++ b/src/read_data.cpp
@@ -1644,9 +1644,9 @@ void ReadData::bodies(int firstpass)
eof = fgets(&buffer[m],MAXLINE,fp);
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
ncount = atom->count_words(&buffer[m],copy);
- if (ncount == 0)
- error->one(FLERR,"Too few values in body lines in data file");
- nword += ncount;
+ if (ncount == 0)
+ error->one(FLERR,"Too few values in body lines in data file");
+ nword += ncount;
m += strlen(&buffer[m]);
onebody++;
}
@@ -1658,9 +1658,9 @@ void ReadData::bodies(int firstpass)
eof = fgets(&buffer[m],MAXLINE,fp);
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
ncount = atom->count_words(&buffer[m],copy);
- if (ncount == 0)
- error->one(FLERR,"Too few values in body lines in data file");
- nword += ncount;
+ if (ncount == 0)
+ error->one(FLERR,"Too few values in body lines in data file");
+ nword += ncount;
m += strlen(&buffer[m]);
onebody++;
}
diff --git a/src/region_cylinder.cpp b/src/region_cylinder.cpp
index 3f2715ea3e..959992f77b 100644
--- a/src/region_cylinder.cpp
+++ b/src/region_cylinder.cpp
@@ -399,13 +399,13 @@ int RegCylinder::surface_exterior(double *x, double cutoff)
yp = c1 + del1*radius/r;
zp = c2 + del2*radius/r;
crad = 2.0*radius;
- varflag = 1;
+ varflag = 1;
} else {
yp = x[1];
zp = x[2];
}
if (x[0] < lo) xp = lo;
- else if (x[0] > hi) xp = hi;
+ else if (x[0] > hi) xp = hi;
else xp = x[0];
}
@@ -493,7 +493,7 @@ int RegCylinder::surface_exterior(double *x, double cutoff)
xp = c1 + del1*radius/r;
zp = c2 + del2*radius/r;
crad = 2.0*radius;
- varflag = 1;
+ varflag = 1;
} else {
xp = x[0];
zp = x[2];
@@ -587,7 +587,7 @@ int RegCylinder::surface_exterior(double *x, double cutoff)
xp = c1 + del1*radius/r;
yp = c2 + del2*radius/r;
crad = 2.0*radius;
- varflag = 1;
+ varflag = 1;
} else {
xp = x[0];
yp = x[1];
diff --git a/src/region_union.cpp b/src/region_union.cpp
index b78ee5580a..abb6f854e3 100644
--- a/src/region_union.cpp
+++ b/src/region_union.cpp
@@ -183,7 +183,7 @@ int RegUnion::surface_interior(double *x, double cutoff)
contact[n].dely = regions[iregion]->contact[m].dely;
contact[n].delz = regions[iregion]->contact[m].delz;
contact[n].iwall = regions[iregion]->contact[m].iwall + walloffset;
- contact[n].varflag = regions[iregion]->contact[m].varflag;
+ contact[n].varflag = regions[iregion]->contact[m].varflag;
n++;
}
}
diff --git a/src/set.cpp b/src/set.cpp
index 11b91df4c4..0565dafb7d 100644
--- a/src/set.cpp
+++ b/src/set.cpp
@@ -780,9 +780,9 @@ void Set::set(int keyword)
else if (keyword == DENSITY) {
if (dvalue <= 0.0) error->one(FLERR,"Invalid density in set command");
if (atom->radius_flag && atom->radius[i] > 0.0)
- if (discflag)
+ if (discflag)
atom->rmass[i] = MY_PI*atom->radius[i]*atom->radius[i] * dvalue;
- else
+ else
atom->rmass[i] = 4.0*MY_PI/3.0 *
atom->radius[i]*atom->radius[i]*atom->radius[i] * dvalue;
else if (atom->ellipsoid_flag && atom->ellipsoid[i] >= 0) {
@@ -791,7 +791,7 @@ void Set::set(int keyword)
// options (fix nve/asphere, fix nh/asphere) are also implemented
// if (discflag)
// atom->rmass[i] = MY_PI*shape[0]*shape[1] * dvalue;
- // else
+ // else
atom->rmass[i] = 4.0*MY_PI/3.0 * shape[0]*shape[1]*shape[2] * dvalue;
} else if (atom->line_flag && atom->line[i] >= 0) {
double length = avec_line->bonus[atom->line[i]].length;
@@ -837,7 +837,7 @@ void Set::set(int keyword)
if (domain->dimension == 2 && (xvalue != 0.0 || yvalue != 0.0))
error->one(FLERR,"Cannot set quaternion with xy components "
"for 2d system");
-
+
double theta2 = MY_PI2 * wvalue/180.0;
double sintheta2 = sin(theta2);
quat[0] = cos(theta2);
@@ -995,8 +995,8 @@ void Set::setrandom(int keyword)
quat = avec_ellipsoid->bonus[atom->ellipsoid[i]].quat;
else if (avec_tri && atom->tri[i] >= 0)
quat = avec_tri->bonus[atom->tri[i]].quat;
- else if (avec_body && atom->body[i] >= 0)
- quat = avec_body->bonus[atom->body[i]].quat;
+ else if (avec_body && atom->body[i] >= 0)
+ quat = avec_body->bonus[atom->body[i]].quat;
else
error->one(FLERR,"Cannot set quaternion for atom that has none");
@@ -1019,8 +1019,8 @@ void Set::setrandom(int keyword)
if (select[i]) {
if (avec_ellipsoid && atom->ellipsoid[i] >= 0)
quat = avec_ellipsoid->bonus[atom->ellipsoid[i]].quat;
- else if (avec_body && atom->body[i] >= 0)
- quat = avec_body->bonus[atom->body[i]].quat;
+ else if (avec_body && atom->body[i] >= 0)
+ quat = avec_body->bonus[atom->body[i]].quat;
else
error->one(FLERR,"Cannot set quaternion for atom that has none");
@@ -1040,11 +1040,11 @@ void Set::setrandom(int keyword)
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) {
if (select[i]) {
- if (atom->line[i] < 0)
- error->one(FLERR,"Cannot set theta for atom that is not a line");
- random->reset(seed,x[i]);
- avec_line->bonus[atom->line[i]].theta = MY_2PI*random->uniform();
- count++;
+ if (atom->line[i] < 0)
+ error->one(FLERR,"Cannot set theta for atom that is not a line");
+ random->reset(seed,x[i]);
+ avec_line->bonus[atom->line[i]].theta = MY_2PI*random->uniform();
+ count++;
}
}
}
diff --git a/src/variable.cpp b/src/variable.cpp
index 399fddeee1..744762dcd4 100644
--- a/src/variable.cpp
+++ b/src/variable.cpp
@@ -889,7 +889,7 @@ char *Variable::retrieve(char *name)
sprintf(data[ivar][0],"%.15g",dvalue[ivar]);
str = data[ivar][0];
} else if (style[ivar] == ATOM || style[ivar] == ATOMFILE ||
- style[ivar] == VECTOR) return NULL;
+ style[ivar] == VECTOR) return NULL;
eval_in_progress[ivar] = 0;
@@ -1279,11 +1279,11 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
print_var_error(FLERR,"Variable evaluation before "
"simulation box is defined",ivar);
- // uppercase used to force access of
- // global vector vs global scalar, and global array vs global vector
+ // uppercase used to force access of
+ // global vector vs global scalar, and global array vs global vector
- int lowercase = 1;
- if (word[0] == 'C') lowercase = 0;
+ int lowercase = 1;
+ if (word[0] == 'C') lowercase = 0;
int icompute = modify->find_compute(word+2);
if (icompute < 0)
@@ -1396,7 +1396,7 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
} else argstack[nargstack++] = value1;
// c_ID = vector from global vector, lowercase or uppercase
-
+
} else if (nbracket == 0 && compute->vector_flag) {
if (tree == NULL)
@@ -1428,7 +1428,7 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
treestack[ntreestack++] = newtree;
// c_ID[i] = vector from global array, lowercase or uppercase
-
+
} else if (nbracket == 1 && compute->array_flag) {
if (tree == NULL)
@@ -1576,11 +1576,11 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
if (domain->box_exist == 0)
print_var_error(FLERR,"Variable evaluation before simulation box is defined",ivar);
- // uppercase used to force access of
- // global vector vs global scalar, and global array vs global vector
+ // uppercase used to force access of
+ // global vector vs global scalar, and global array vs global vector
- int lowercase = 1;
- if (word[0] == 'F') lowercase = 0;
+ int lowercase = 1;
+ if (word[0] == 'F') lowercase = 0;
int ifix = modify->find_fix(word+2);
if (ifix < 0) {
@@ -1686,11 +1686,11 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
if (fix->size_vector == 0)
print_var_error(FLERR,"Variable formula fix vector is zero length",ivar);
- int nvec = fix->size_vector;
- double *vec;
- memory->create(vec,nvec,"variable:values");
- for (int m = 0; m < nvec; m++)
- vec[m] = fix->compute_vector(m);
+ int nvec = fix->size_vector;
+ double *vec;
+ memory->create(vec,nvec,"variable:values");
+ for (int m = 0; m < nvec; m++)
+ vec[m] = fix->compute_vector(m);
Tree *newtree = new Tree();
newtree->type = VECTORARRAY;
@@ -1917,7 +1917,7 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
// v_name = vector from vector-style variable
// evaluate the vector-style variable, put result in newtree
- } else if (nbracket == 0 && style[ivar] == VECTOR) {
+ } else if (nbracket == 0 && style[ivar] == VECTOR) {
if (tree == NULL)
print_var_error(FLERR,"Vector-style variable in "
@@ -1926,18 +1926,18 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
print_var_error(FLERR,"Vector-style variable in "
"atom-style variable formula",ivar);
- double *vec;
- int nvec = compute_vector(ivar,&vec);
+ double *vec;
+ int nvec = compute_vector(ivar,&vec);
- Tree *newtree = new Tree();
- newtree->type = VECTORARRAY;
- newtree->array = vec;
- newtree->nvector = nvec;
- newtree->nstride = 1;
- newtree->selfalloc = 0;
- newtree->first = newtree->second = NULL;
- newtree->nextra = 0;
- treestack[ntreestack++] = newtree;
+ Tree *newtree = new Tree();
+ newtree->type = VECTORARRAY;
+ newtree->array = vec;
+ newtree->nvector = nvec;
+ newtree->nstride = 1;
+ newtree->selfalloc = 0;
+ newtree->first = newtree->second = NULL;
+ newtree->nextra = 0;
+ treestack[ntreestack++] = newtree;
// v_name[N] = scalar from atom-style variable
// compute the per-atom variable in result
@@ -1964,11 +1964,11 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
} else if (nbracket && style[ivar] == VECTOR) {
- double *vec;
- int nvec = compute_vector(ivar,&vec);
- if (index <= 0 || index > nvec)
- print_var_error(FLERR,"Invalid index into vector-style variable",ivar);
- int m = index; // convert from tagint to int
+ double *vec;
+ int nvec = compute_vector(ivar,&vec);
+ if (index <= 0 || index > nvec)
+ print_var_error(FLERR,"Invalid index into vector-style variable",ivar);
+ int m = index; // convert from tagint to int
if (tree) {
Tree *newtree = new Tree();
@@ -2661,9 +2661,9 @@ double Variable::collapse_tree(Tree *tree)
double delta = ivalue1*(ivalue3-1.0)/ivalue2;
int count = 0;
while (update->ntimestep >= tree->value) {
- tree->value += delta;
- count++;
- if (count % ivalue2 == 0) delta *= ivalue3;
+ tree->value += delta;
+ count++;
+ if (count % ivalue2 == 0) delta *= ivalue3;
}
}
tree->value = ceil(tree->value);
@@ -2697,7 +2697,7 @@ double Variable::collapse_tree(Tree *tree)
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[2]->type != VALUE || tree->extra[3]->type != VALUE)
return 0.0;
tree->type = VALUE;
if (ivalue1 < 0 || ivalue2 < 0 || ivalue3 <= 0 || ivalue1 > ivalue2)
@@ -2998,9 +2998,9 @@ double Variable::eval_tree(Tree *tree, int i)
double delta = ivalue1*(ivalue3-1.0)/ivalue2;
int count = 0;
while (update->ntimestep >= arg) {
- arg += delta;
- count++;
- if (count % ivalue2 == 0) delta *= ivalue3;
+ arg += delta;
+ count++;
+ if (count % ivalue2 == 0) delta *= ivalue3;
}
}
arg = ceil(arg);
@@ -3534,13 +3534,13 @@ int Variable::math_function(char *word, char *contents, Tree **tree,
if (update->ntimestep < ivalue1) value = ivalue1;
else {
value = ivalue1;
- double delta = ivalue1*(ivalue3-1.0)/ivalue2;
- int count = 0;
+ double delta = ivalue1*(ivalue3-1.0)/ivalue2;
+ int count = 0;
while (update->ntimestep >= value) {
- value += delta;
- count++;
- if (count % ivalue2 == 0) delta *= ivalue3;
- }
+ value += delta;
+ count++;
+ if (count % ivalue2 == 0) delta *= ivalue3;
+ }
}
argstack[nargstack++] = ceil(value);
}
@@ -3581,7 +3581,7 @@ int Variable::math_function(char *word, char *contents, Tree **tree,
if (ivalue4 < 0 || ivalue5 < 0 || ivalue6 <= 0 || ivalue4 > ivalue5)
error->one(FLERR,"Invalid math function in variable formula");
if (ivalue4 < ivalue1 || ivalue5 > ivalue2)
- error->one(FLERR,"Invalid math function in variable formula");
+ error->one(FLERR,"Invalid math function in variable formula");
bigint istep;
if (update->ntimestep < ivalue1) istep = ivalue1;
else if (update->ntimestep < ivalue2) {
@@ -4117,7 +4117,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
double one;
double *vec = vecs[ivar].values;
for (int i = 0; i < nvec; i++) {
- one = vec[i];
+ one = vec[i];
if (method == SUM) value += one;
else if (method == XMIN) value = MIN(value,one);
else if (method == XMAX) value = MAX(value,one);
--
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