From cfc1b3a82399f636197d3271deeaaf522519f681 Mon Sep 17 00:00:00 2001
From: "Steven J. Plimpton" <sjplimp@singsing.sandia.gov>
Date: Thu, 9 Aug 2018 10:20:02 -0600
Subject: [PATCH] more changes induced by removing Section_start.txt
---
doc/src/Errors_common.txt | 6 +-
doc/src/Errors_messages.txt | 4 +-
doc/src/Examples.txt | 8 +-
doc/src/Howto.txt | 6 +-
doc/src/Howto_couple.txt | 21 +-
doc/src/Howto_library.txt | 19 +-
doc/src/Howto_multiple.txt | 3 +-
doc/src/Howto_replica.txt | 17 +-
doc/src/Howto_restart.txt | 4 +-
doc/src/Howto_temperature.txt | 11 +-
doc/src/Manual.txt | 25 +-
doc/src/Modify_contribute.txt | 15 +-
doc/src/Packages.txt | 8 +-
doc/src/Packages_details.txt | 1175 ++---------------
doc/src/Python_shlib.txt | 13 +-
doc/src/Python_test.txt | 8 +-
doc/src/Speed_gpu.txt | 18 +-
doc/src/Speed_intel.txt | 71 +-
doc/src/Speed_kokkos.txt | 73 +-
doc/src/Speed_measure.txt | 4 +-
doc/src/Speed_omp.txt | 21 +-
doc/src/Speed_opt.txt | 4 +-
doc/src/Speed_packages.txt | 6 +-
doc/src/angle_charmm.txt | 12 +-
doc/src/angle_class2.txt | 12 +-
doc/src/angle_cosine.txt | 12 +-
doc/src/angle_cosine_buck6d.txt | 4 +-
doc/src/angle_cosine_delta.txt | 12 +-
doc/src/angle_cosine_periodic.txt | 12 +-
doc/src/angle_cosine_shift.txt | 19 +-
doc/src/angle_cosine_shift_exp.txt | 12 +-
doc/src/angle_cosine_squared.txt | 12 +-
doc/src/angle_dipole.txt | 12 +-
doc/src/angle_fourier.txt | 12 +-
doc/src/angle_fourier_simple.txt | 12 +-
doc/src/angle_harmonic.txt | 12 +-
doc/src/angle_hybrid.txt | 4 +-
doc/src/angle_quartic.txt | 12 +-
doc/src/angle_sdk.txt | 4 +-
doc/src/angle_style.txt | 7 +-
doc/src/angle_table.txt | 12 +-
doc/src/atom_modify.txt | 6 +-
doc/src/atom_style.txt | 12 +-
doc/src/balance.txt | 10 +-
doc/src/bond_class2.txt | 12 +-
doc/src/bond_fene.txt | 14 +-
doc/src/bond_fene_expand.txt | 14 +-
doc/src/bond_gromos.txt | 14 +-
doc/src/bond_harmonic.txt | 14 +-
doc/src/bond_harmonic_shift.txt | 12 +-
doc/src/bond_harmonic_shift_cut.txt | 12 +-
doc/src/bond_hybrid.txt | 6 +-
doc/src/bond_morse.txt | 14 +-
doc/src/bond_nonlinear.txt | 14 +-
doc/src/bond_oxdna.txt | 4 +-
doc/src/bond_quartic.txt | 14 +-
doc/src/bond_style.txt | 7 +-
doc/src/bond_table.txt | 14 +-
doc/src/compute_ackland_atom.txt | 4 +-
doc/src/compute_basal_atom.txt | 4 +-
doc/src/compute_cnp_atom.txt | 4 +-
doc/src/compute_damage_atom.txt | 4 +-
doc/src/compute_dilatation_atom.txt | 4 +-
doc/src/compute_dpd.txt | 4 +-
doc/src/compute_dpd_atom.txt | 4 +-
doc/src/compute_edpd_temp_atom.txt | 4 +-
doc/src/compute_entropy_atom.txt | 4 +-
doc/src/compute_erotate_rigid.txt | 4 +-
doc/src/compute_event_displace.txt | 4 +-
doc/src/compute_fep.txt | 4 +-
doc/src/compute_ke_atom_eff.txt | 4 +-
doc/src/compute_ke_eff.txt | 4 +-
doc/src/compute_ke_rigid.txt | 4 +-
doc/src/compute_meso_e_atom.txt | 4 +-
doc/src/compute_meso_rho_atom.txt | 4 +-
doc/src/compute_meso_t_atom.txt | 4 +-
doc/src/compute_msd_nongauss.txt | 6 +-
doc/src/compute_plasticity_atom.txt | 4 +-
doc/src/compute_pressure.txt | 8 +-
doc/src/compute_pressure_uef.txt | 6 +-
doc/src/compute_rigid_local.txt | 4 +-
doc/src/compute_saed.txt | 4 +-
doc/src/compute_smd_contact_radius.txt | 4 +-
doc/src/compute_smd_damage.txt | 4 +-
doc/src/compute_smd_hourglass_error.txt | 4 +-
doc/src/compute_smd_internal_energy.txt | 8 +-
doc/src/compute_smd_plastic_strain.txt | 8 +-
doc/src/compute_smd_plastic_strain_rate.txt | 8 +-
doc/src/compute_smd_rho.txt | 4 +-
doc/src/compute_smd_tlsph_defgrad.txt | 8 +-
doc/src/compute_smd_tlsph_dt.txt | 4 +-
doc/src/compute_smd_tlsph_num_neighs.txt | 4 +-
doc/src/compute_smd_tlsph_shape.txt | 4 +-
doc/src/compute_smd_tlsph_strain.txt | 4 +-
doc/src/compute_smd_tlsph_strain_rate.txt | 4 +-
doc/src/compute_smd_tlsph_stress.txt | 4 +-
.../compute_smd_triangle_mesh_vertices.txt | 4 +-
doc/src/compute_smd_ulsph_num_neighs.txt | 8 +-
doc/src/compute_smd_ulsph_strain.txt | 8 +-
doc/src/compute_smd_ulsph_strain_rate.txt | 9 +-
doc/src/compute_smd_ulsph_stress.txt | 8 +-
doc/src/compute_smd_vol.txt | 4 +-
doc/src/compute_sna_atom.txt | 4 +-
doc/src/compute_spin.txt | 8 +-
doc/src/compute_tally.txt | 6 +-
doc/src/compute_tdpd_cc_atom.txt | 4 +-
doc/src/compute_temp.txt | 8 +-
doc/src/compute_temp_asphere.txt | 4 +-
doc/src/compute_temp_body.txt | 4 +-
doc/src/compute_temp_deform_eff.txt | 4 +-
doc/src/compute_temp_eff.txt | 4 +-
doc/src/compute_temp_partial.txt | 8 +-
doc/src/compute_temp_region_eff.txt | 4 +-
doc/src/compute_temp_rotate.txt | 4 +-
doc/src/compute_temp_uef.txt | 6 +-
doc/src/compute_ti.txt | 4 +-
doc/src/compute_voronoi_atom.txt | 4 +-
doc/src/compute_xrd.txt | 4 +-
doc/src/dihedral_charmm.txt | 12 +-
doc/src/dihedral_class2.txt | 12 +-
doc/src/dihedral_cosine_shift_exp.txt | 12 +-
doc/src/dihedral_fourier.txt | 12 +-
doc/src/dihedral_harmonic.txt | 12 +-
doc/src/dihedral_helix.txt | 12 +-
doc/src/dihedral_hybrid.txt | 4 +-
doc/src/dihedral_multi_harmonic.txt | 12 +-
doc/src/dihedral_nharmonic.txt | 12 +-
doc/src/dihedral_opls.txt | 12 +-
doc/src/dihedral_quadratic.txt | 12 +-
doc/src/dihedral_spherical.txt | 4 +-
doc/src/dihedral_style.txt | 7 +-
doc/src/dihedral_table.txt | 12 +-
doc/src/dihedral_table_cut.txt | 4 +-
doc/src/dump.txt | 21 +-
doc/src/dump_cfg_uef.txt | 6 +-
doc/src/dump_h5md.txt | 14 +-
doc/src/dump_image.txt | 7 +-
doc/src/dump_molfile.txt | 4 +-
doc/src/dump_netcdf.txt | 4 +-
doc/src/dump_vtk.txt | 6 +-
doc/src/echo.txt | 4 +-
doc/src/fix.txt | 6 +-
doc/src/fix_addforce.txt | 8 +-
doc/src/fix_addtorque.txt | 4 +-
doc/src/fix_append_atoms.txt | 4 +-
doc/src/fix_atom_swap.txt | 4 +-
doc/src/fix_ave_correlate_long.txt | 4 +-
doc/src/fix_aveforce.txt | 8 +-
doc/src/fix_bocs.txt | 4 +-
doc/src/fix_bond_break.txt | 4 +-
doc/src/fix_bond_create.txt | 4 +-
doc/src/fix_bond_react.txt | 4 +-
doc/src/fix_bond_swap.txt | 4 +-
doc/src/fix_cmap.txt | 4 +-
doc/src/fix_colvars.txt | 4 +-
doc/src/fix_deform.txt | 8 +-
doc/src/fix_deposit.txt | 4 +-
doc/src/fix_dpd_energy.txt | 12 +-
doc/src/fix_dpd_source.txt | 4 +-
doc/src/fix_efield.txt | 4 +-
doc/src/fix_ehex.txt | 4 +-
doc/src/fix_enforce2d.txt | 8 +-
doc/src/fix_eos_cv.txt | 4 +-
doc/src/fix_eos_table.txt | 4 +-
doc/src/fix_eos_table_rx.txt | 12 +-
doc/src/fix_evaporate.txt | 4 +-
doc/src/fix_filter_corotate.txt | 4 +-
doc/src/fix_flow_gauss.txt | 4 +-
doc/src/fix_freeze.txt | 12 +-
doc/src/fix_gcmc.txt | 4 +-
doc/src/fix_gld.txt | 4 +-
doc/src/fix_gle.txt | 6 +-
doc/src/fix_gravity.txt | 8 +-
doc/src/fix_grem.txt | 4 +-
doc/src/fix_imd.txt | 4 +-
doc/src/fix_ipi.txt | 6 +-
doc/src/fix_langevin.txt | 8 +-
doc/src/fix_langevin_eff.txt | 4 +-
doc/src/fix_langevin_spin.txt | 6 +-
doc/src/fix_latte.txt | 8 +-
doc/src/fix_lb_fluid.txt | 4 +-
doc/src/fix_lb_momentum.txt | 4 +-
doc/src/fix_lb_pc.txt | 4 +-
doc/src/fix_lb_rigid_pc_sphere.txt | 4 +-
doc/src/fix_lb_viscous.txt | 4 +-
doc/src/fix_manifoldforce.txt | 27 +-
doc/src/fix_meso.txt | 4 +-
doc/src/fix_meso_stationary.txt | 4 +-
doc/src/fix_momentum.txt | 8 +-
doc/src/fix_mscg.txt | 4 +-
doc/src/fix_msst.txt | 4 +-
doc/src/fix_mvv_dpd.txt | 4 +-
doc/src/fix_neb.txt | 4 +-
doc/src/fix_nh.txt | 8 +-
doc/src/fix_nh_eff.txt | 4 +-
doc/src/fix_nh_uef.txt | 4 +-
doc/src/fix_nph_asphere.txt | 12 +-
doc/src/fix_nph_body.txt | 12 +-
doc/src/fix_nph_sphere.txt | 8 +-
doc/src/fix_nphug.txt | 12 +-
doc/src/fix_npt_asphere.txt | 12 +-
doc/src/fix_npt_body.txt | 12 +-
doc/src/fix_npt_sphere.txt | 8 +-
doc/src/fix_nve.txt | 8 +-
doc/src/fix_nve_asphere.txt | 12 +-
doc/src/fix_nve_asphere_noforce.txt | 4 +-
doc/src/fix_nve_body.txt | 4 +-
doc/src/fix_nve_dot.txt | 4 +-
doc/src/fix_nve_dotc_langevin.txt | 4 +-
doc/src/fix_nve_eff.txt | 4 +-
doc/src/fix_nve_line.txt | 4 +-
doc/src/fix_nve_manifold_rattle.txt | 4 +-
doc/src/fix_nve_sphere.txt | 8 +-
doc/src/fix_nve_spin.txt | 6 +-
doc/src/fix_nve_tri.txt | 4 +-
doc/src/fix_nvk.txt | 6 +-
doc/src/fix_nvt_asphere.txt | 12 +-
doc/src/fix_nvt_body.txt | 12 +-
doc/src/fix_nvt_manifold_rattle.txt | 14 +-
doc/src/fix_nvt_sllod.txt | 8 +-
doc/src/fix_nvt_sllod_eff.txt | 4 +-
doc/src/fix_nvt_sphere.txt | 8 +-
doc/src/fix_orient.txt | 4 +-
doc/src/fix_phonon.txt | 8 +-
doc/src/fix_pimd.txt | 4 +-
doc/src/fix_poems.txt | 4 +-
doc/src/fix_pour.txt | 4 +-
doc/src/fix_precession_spin.txt | 8 +-
doc/src/fix_python_invoke.txt | 6 +-
doc/src/fix_python_move.txt | 4 +-
doc/src/fix_qbmsst.txt | 4 +-
doc/src/fix_qeq.txt | 4 +-
doc/src/fix_qeq_comb.txt | 8 +-
doc/src/fix_qeq_reax.txt | 12 +-
doc/src/fix_qmmm.txt | 4 +-
doc/src/fix_qtb.txt | 4 +-
doc/src/fix_reax_bonds.txt | 12 +-
doc/src/fix_reaxc_species.txt | 16 +-
doc/src/fix_rhok.txt | 4 +-
doc/src/fix_rigid.txt | 12 +-
doc/src/fix_rx.txt | 12 +-
doc/src/fix_setforce.txt | 8 +-
doc/src/fix_shake.txt | 12 +-
doc/src/fix_shardlow.txt | 12 +-
doc/src/fix_smd.txt | 4 +-
doc/src/fix_smd_adjust_dt.txt | 27 +-
doc/src/fix_smd_integrate_tlsph.txt | 18 +-
doc/src/fix_smd_integrate_ulsph.txt | 28 +-
doc/src/fix_smd_move_triangulated_surface.txt | 34 +-
doc/src/fix_smd_setvel.txt | 4 +-
doc/src/fix_smd_wall_surface.txt | 45 +-
doc/src/fix_srd.txt | 4 +-
doc/src/fix_temp_rescale_eff.txt | 4 +-
doc/src/fix_tfmc.txt | 4 +-
doc/src/fix_thermal_conductivity.txt | 4 +-
doc/src/fix_ti_spring.txt | 4 +-
doc/src/fix_tmd.txt | 4 +-
doc/src/fix_ttm.txt | 3 +-
doc/src/fix_tune_kspace.txt | 6 +-
doc/src/fix_viscosity.txt | 4 +-
doc/src/fix_wall.txt | 8 +-
doc/src/fix_wall_body_polygon.txt | 4 +-
doc/src/fix_wall_body_polyhedron.txt | 6 +-
doc/src/fix_wall_ees.txt | 4 +-
doc/src/fix_wall_gran.txt | 4 +-
doc/src/fix_wall_gran_region.txt | 4 +-
doc/src/fix_wall_piston.txt | 4 +-
doc/src/fix_wall_reflect.txt | 8 +-
doc/src/group2ndx.txt | 4 +-
doc/src/improper_class2.txt | 12 +-
doc/src/improper_cossq.txt | 12 +-
doc/src/improper_cvff.txt | 12 +-
doc/src/improper_distance.txt | 4 +-
doc/src/improper_fourier.txt | 12 +-
doc/src/improper_harmonic.txt | 12 +-
doc/src/improper_hybrid.txt | 4 +-
doc/src/improper_inversion_harmonic.txt | 4 +-
doc/src/improper_ring.txt | 12 +-
doc/src/improper_style.txt | 7 +-
doc/src/improper_umbrella.txt | 12 +-
doc/src/jump.txt | 11 +-
doc/src/kspace_style.txt | 20 +-
doc/src/lammps.book | 22 +-
doc/src/log.txt | 5 +-
doc/src/neb.txt | 20 +-
doc/src/neighbor.txt | 4 +-
doc/src/next.txt | 10 +-
doc/src/package.txt | 95 +-
doc/src/pair_adp.txt | 8 +-
doc/src/pair_agni.txt | 25 +-
doc/src/pair_airebo.txt | 12 +-
doc/src/pair_beck.txt | 8 +-
doc/src/pair_body_nparticle.txt | 4 +-
doc/src/pair_body_rounded_polygon.txt | 4 +-
doc/src/pair_body_rounded_polyhedron.txt | 4 +-
doc/src/pair_bop.txt | 5 +-
doc/src/pair_born.txt | 12 +-
doc/src/pair_brownian.txt | 12 +-
doc/src/pair_buck.txt | 12 +-
doc/src/pair_buck6d_coul_gauss.txt | 6 +-
doc/src/pair_buck_long.txt | 14 +-
doc/src/pair_charmm.txt | 14 +-
doc/src/pair_class2.txt | 12 +-
doc/src/pair_colloid.txt | 12 +-
doc/src/pair_comb.txt | 14 +-
doc/src/pair_coul.txt | 10 +-
doc/src/pair_coul_diel.txt | 9 +-
doc/src/pair_coul_shield.txt | 6 +-
doc/src/pair_cs.txt | 4 +-
doc/src/pair_dipole.txt | 16 +-
doc/src/pair_dpd.txt | 8 +-
doc/src/pair_dpd_fdt.txt | 12 +-
doc/src/pair_dsmc.txt | 4 +-
doc/src/pair_eam.txt | 12 +-
doc/src/pair_edip.txt | 12 +-
doc/src/pair_eff.txt | 4 +-
doc/src/pair_eim.txt | 8 +-
doc/src/pair_exp6_rx.txt | 12 +-
doc/src/pair_gauss.txt | 12 +-
doc/src/pair_gayberne.txt | 12 +-
doc/src/pair_gran.txt | 12 +-
doc/src/pair_gromacs.txt | 8 +-
doc/src/pair_gw.txt | 4 +-
doc/src/pair_hbond_dreiding.txt | 8 +-
doc/src/pair_hybrid.txt | 12 +-
doc/src/pair_ilp_graphene_hbn.txt | 4 +-
doc/src/pair_kim.txt | 4 +-
doc/src/pair_kolmogorov_crespi_full.txt | 4 +-
doc/src/pair_kolmogorov_crespi_z.txt | 4 +-
doc/src/pair_lcbop.txt | 4 +-
doc/src/pair_line_lj.txt | 4 +-
doc/src/pair_list.txt | 4 +-
doc/src/pair_lj.txt | 14 +-
doc/src/pair_lj96.txt | 8 +-
doc/src/pair_lj_cubic.txt | 8 +-
doc/src/pair_lj_expand.txt | 8 +-
doc/src/pair_lj_long.txt | 14 +-
doc/src/pair_lj_smooth.txt | 8 +-
doc/src/pair_lj_smooth_linear.txt | 8 +-
doc/src/pair_lj_soft.txt | 10 +-
doc/src/pair_lubricate.txt | 12 +-
doc/src/pair_lubricateU.txt | 4 +-
doc/src/pair_mdf.txt | 4 +-
doc/src/pair_meam.txt | 14 +-
doc/src/pair_meam_spline.txt | 12 +-
doc/src/pair_meam_sw_spline.txt | 5 +-
doc/src/pair_meso.txt | 4 +-
doc/src/pair_mgpt.txt | 4 +-
doc/src/pair_momb.txt | 4 +-
doc/src/pair_morse.txt | 16 +-
doc/src/pair_multi_lucy.txt | 4 +-
doc/src/pair_multi_lucy_rx.txt | 12 +-
doc/src/pair_nb3b_harmonic.txt | 12 +-
doc/src/pair_nm.txt | 12 +-
doc/src/pair_oxdna.txt | 4 +-
doc/src/pair_oxdna2.txt | 4 +-
doc/src/pair_peri.txt | 12 +-
doc/src/pair_polymorphic.txt | 4 +-
doc/src/pair_python.txt | 4 +-
doc/src/pair_quip.txt | 4 +-
doc/src/pair_reaxc.txt | 12 +-
doc/src/pair_resquared.txt | 12 +-
doc/src/pair_sdk.txt | 18 +-
doc/src/pair_smd_hertz.txt | 30 +-
doc/src/pair_smd_tlsph.txt | 46 +-
doc/src/pair_smd_triangulated_surface.txt | 24 +-
doc/src/pair_smd_ulsph.txt | 54 +-
doc/src/pair_smtbq.txt | 4 +-
doc/src/pair_snap.txt | 14 +-
doc/src/pair_soft.txt | 8 +-
doc/src/pair_sph_heatconduction.txt | 4 +-
doc/src/pair_sph_idealgas.txt | 4 +-
doc/src/pair_sph_lj.txt | 4 +-
doc/src/pair_sph_rhosum.txt | 4 +-
doc/src/pair_sph_taitwater.txt | 4 +-
doc/src/pair_sph_taitwater_morris.txt | 4 +-
doc/src/pair_spin_dmi.txt | 8 +-
doc/src/pair_spin_exchange.txt | 8 +-
doc/src/pair_spin_magelec.txt | 8 +-
doc/src/pair_spin_neel.txt | 8 +-
doc/src/pair_style.txt | 7 +-
doc/src/pair_sw.txt | 12 +-
doc/src/pair_table.txt | 8 +-
doc/src/pair_table_rx.txt | 12 +-
doc/src/pair_tersoff.txt | 12 +-
doc/src/pair_tersoff_mod.txt | 12 +-
doc/src/pair_tersoff_zbl.txt | 12 +-
doc/src/pair_thole.txt | 12 +-
doc/src/pair_tri_lj.txt | 4 +-
doc/src/pair_ufm.txt | 8 +-
doc/src/pair_vashishta.txt | 12 +-
doc/src/pair_yukawa.txt | 8 +-
doc/src/pair_yukawa_colloid.txt | 12 +-
doc/src/pair_zbl.txt | 8 +-
doc/src/partition.txt | 7 +-
doc/src/prd.txt | 22 +-
doc/src/processors.txt | 29 +-
doc/src/python.txt | 4 +-
doc/src/read_data.txt | 8 +-
doc/src/read_dump.txt | 6 +-
doc/src/read_restart.txt | 3 +-
doc/src/region.txt | 8 +-
doc/src/rerun.txt | 4 +-
doc/src/restart.txt | 3 +-
doc/src/run_style.txt | 22 +-
doc/src/suffix.txt | 16 +-
doc/src/tad.txt | 4 +-
doc/src/temper.txt | 25 +-
doc/src/temper_grem.txt | 4 +-
doc/src/temper_npt.txt | 4 +-
doc/src/thermo_style.txt | 6 +-
doc/src/timer.txt | 4 +-
doc/src/variable.txt | 49 +-
doc/src/write_data.txt | 2 +-
doc/src/write_restart.txt | 3 +-
415 files changed, 2033 insertions(+), 2894 deletions(-)
diff --git a/doc/src/Errors_common.txt b/doc/src/Errors_common.txt
index 43d1a85a7b..8f26b22b3a 100644
--- a/doc/src/Errors_common.txt
+++ b/doc/src/Errors_common.txt
@@ -58,9 +58,9 @@ style", with ... being fix, compute, pair, etc, it means that you
mistyped the style name or that the command is part of an optional
package which was not compiled into your executable. The list of
available styles in your executable can be listed by using "the -h
-command-line argument"_Section_start.html#start_6. The installation
-and compilation of optional packages is explained in the "installation
-instructions"_Section_start.html#start_3.
+command-line swith"_Run_options.html. The installation and
+compilation of optional packages is explained on the "Build
+packages"_Build_packages.html doc page.
For a given command, LAMMPS expects certain arguments in a specified
order. If you mess this up, LAMMPS will often flag the error, but it
diff --git a/doc/src/Errors_messages.txt b/doc/src/Errors_messages.txt
index 03fc25b561..d279b5e975 100644
--- a/doc/src/Errors_messages.txt
+++ b/doc/src/Errors_messages.txt
@@ -7911,8 +7911,8 @@ Atom IDs must be positive integers. :dd
{One or more atom IDs is too big} :dt
The limit on atom IDs is set by the SMALLBIG, BIGBIG, SMALLSMALL
-setting in your Makefile. See Section_start 2.2 of the manual for
-more details. :dd
+setting in your LAMMPS build. See the "Build
+settings"_Build_settings.html doc page for more info. :dd
{One or more atom IDs is zero} :dt
diff --git a/doc/src/Examples.txt b/doc/src/Examples.txt
index 5bd8da2409..4b6db8a047 100644
--- a/doc/src/Examples.txt
+++ b/doc/src/Examples.txt
@@ -112,10 +112,10 @@ web site.
If you uncomment the "dump image"_dump_image.html line(s) in the input
script a series of JPG images will be produced by the run (assuming
-you built LAMMPS with JPG support; see "Section
-2.2"_Section_start.html#start_2 for details). These can be viewed
-individually or turned into a movie or animated by tools like
-ImageMagick or QuickTime or various Windows-based tools. See the
+you built LAMMPS with JPG support; see the
+"Build_settings"_Build_settings.html doc page for details). These can
+be viewed individually or turned into a movie or animated by tools
+like ImageMagick or QuickTime or various Windows-based tools. See the
"dump image"_dump_image.html doc page for more details. E.g. this
Imagemagick command would create a GIF file suitable for viewing in a
browser.
diff --git a/doc/src/Howto.txt b/doc/src/Howto.txt
index d9a60d1ef4..6e434552e7 100644
--- a/doc/src/Howto.txt
+++ b/doc/src/Howto.txt
@@ -84,7 +84,7 @@ END_RST -->
"Using GitHub with LAMMPS"_Howto_github.html
"PyLAMMPS interface to LAMMPS"_Howto_pylammps.html
-"Using LAMMPS with bash on Windows"_Howto_bash.html
+"Using LAMMPS with bash on Windows"_Howto_bash.html :all(b)
"Restart a simulation"_Howto_restart.html
"Visualize LAMMPS snapshots"_Howto_viz.html
@@ -121,8 +121,8 @@ END_RST -->
"Polarizable models"_Howto_polarizable.html
"Adiabatic core/shell model"_Howto_coreshell.html
"Drude induced dipoles"_Howto_drude.html
-"Drude induced dipoles (extended)"_Howto_drude2.html :all(b)
+"Drude induced dipoles (extended)"_Howto_drude2.html
"Manifolds (surfaces)"_Howto_manifold.html
-"Magnetic spins"_Howto_spins.html
+"Magnetic spins"_Howto_spins.html :all(b)
<!-- END_HTML_ONLY -->
diff --git a/doc/src/Howto_couple.txt b/doc/src/Howto_couple.txt
index 38595a9d16..4c0f72a806 100644
--- a/doc/src/Howto_couple.txt
+++ b/doc/src/Howto_couple.txt
@@ -77,17 +77,16 @@ strain induced across grain boundaries :l
:link(quest,http://dft.sandia.gov/Quest)
:link(spparks,http://www.sandia.gov/~sjplimp/spparks.html)
-"This section"_Section_start.html#start_5 of the documentation
-describes how to build LAMMPS as a library. Once this is done, you
-can interface with LAMMPS either via C++, C, Fortran, or Python (or
-any other language that supports a vanilla C-like interface). For
-example, from C++ you could create one (or more) "instances" of
-LAMMPS, pass it an input script to process, or execute individual
-commands, all by invoking the correct class methods in LAMMPS. From C
-or Fortran you can make function calls to do the same things. See the
-"Python"_Python.html doc pages for a description of the Python wrapper
-provided with LAMMPS that operates through the LAMMPS library
-interface.
+The "Build basics"_Build_basics.html doc page describes how to build
+LAMMPS as a library. Once this is done, you can interface with LAMMPS
+either via C++, C, Fortran, or Python (or any other language that
+supports a vanilla C-like interface). For example, from C++ you could
+create one (or more) "instances" of LAMMPS, pass it an input script to
+process, or execute individual commands, all by invoking the correct
+class methods in LAMMPS. From C or Fortran you can make function
+calls to do the same things. See the "Python"_Python.html doc pages
+for a description of the Python wrapper provided with LAMMPS that
+operates through the LAMMPS library interface.
The files src/library.cpp and library.h contain the C-style interface
to LAMMPS. See the "Howto library"_Howto_library.html doc page for a
diff --git a/doc/src/Howto_library.txt b/doc/src/Howto_library.txt
index 0d4852fbf2..8e99182f87 100644
--- a/doc/src/Howto_library.txt
+++ b/doc/src/Howto_library.txt
@@ -9,10 +9,10 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
Library interface to LAMMPS :h3
-As described in "Section 2.5"_Section_start.html#start_5, LAMMPS can
-be built as a library, so that it can be called by another code, used
-in a "coupled manner"_Howto_couple.html with other codes, or driven
-through a "Python interface"_Python.html.
+As described on the "Build basics"_Build_basics.html doc page, LAMMPS
+can be built as a library, so that it can be called by another code,
+used in a "coupled manner"_Howto_couple.html with other codes, or
+driven through a "Python interface"_Python.html.
All of these methodologies use a C-style interface to LAMMPS that is
provided in the files src/library.cpp and src/library.h. The
@@ -51,12 +51,11 @@ void lammps_free(void *) :pre
The lammps_open() function is used to initialize LAMMPS, passing in a
list of strings as if they were "command-line
-arguments"_Section_start.html#start_6 when LAMMPS is run in
-stand-alone mode from the command line, and a MPI communicator for
-LAMMPS to run under. It returns a ptr to the LAMMPS object that is
-created, and which is used in subsequent library calls. The
-lammps_open() function can be called multiple times, to create
-multiple instances of LAMMPS.
+arguments"_Run_options.html when LAMMPS is run in stand-alone mode
+from the command line, and a MPI communicator for LAMMPS to run under.
+It returns a ptr to the LAMMPS object that is created, and which is
+used in subsequent library calls. The lammps_open() function can be
+called multiple times, to create multiple instances of LAMMPS.
LAMMPS will run on the set of processors in the communicator. This
means the calling code can run LAMMPS on all or a subset of
diff --git a/doc/src/Howto_multiple.txt b/doc/src/Howto_multiple.txt
index edcb8196cf..9ad872fedc 100644
--- a/doc/src/Howto_multiple.txt
+++ b/doc/src/Howto_multiple.txt
@@ -80,8 +80,7 @@ jump in.polymer :pre
All of the above examples work whether you are running on 1 or
multiple processors, but assumed you are running LAMMPS on a single
partition of processors. LAMMPS can be run on multiple partitions via
-the "-partition" command-line switch as described in "this
-section"_Section_start.html#start_6 of the manual.
+the "-partition command-line switch"_Run_options.html.
In the last 2 examples, if LAMMPS were run on 3 partitions, the same
scripts could be used if the "index" and "loop" variables were
diff --git a/doc/src/Howto_replica.txt b/doc/src/Howto_replica.txt
index 1b44fe5374..2135e52e0e 100644
--- a/doc/src/Howto_replica.txt
+++ b/doc/src/Howto_replica.txt
@@ -29,29 +29,28 @@ runs different replicas at a series of temperature to facilitate
rare-event sampling.
These commands can only be used if LAMMPS was built with the REPLICA
-package. See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info on packages.
+package. See the "Build package"_Build_package.html doc page for more
+info.
PIMD runs different replicas whose individual particles are coupled
together by springs to model a system or ring-polymers.
This commands can only be used if LAMMPS was built with the USER-MISC
-package. See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info on packages.
+package. See the "Build package"_Build_package.html doc page for more
+info.
In all these cases, you must run with one or more processors per
replica. The processors assigned to each replica are determined at
run-time by using the "-partition command-line
-switch"_Section_start.html#start_6 to launch LAMMPS on multiple
-partitions, which in this context are the same as replicas. E.g.
-these commands:
+switch"_Run_options.html to launch LAMMPS on multiple partitions,
+which in this context are the same as replicas. E.g. these commands:
mpirun -np 16 lmp_linux -partition 8x2 -in in.temper
mpirun -np 8 lmp_linux -partition 8x1 -in in.neb :pre
would each run 8 replicas, on either 16 or 8 processors. Note the use
-of the "-in command-line switch"_Section_start.html#start_6 to specify
-the input script which is required when running in multi-replica mode.
+of the "-in command-line switch"_Run_options.html to specify the input
+script which is required when running in multi-replica mode.
Also note that with MPI installed on a machine (e.g. your desktop),
you can run on more (virtual) processors than you have physical
diff --git a/doc/src/Howto_restart.txt b/doc/src/Howto_restart.txt
index b211775479..bc67daa78e 100644
--- a/doc/src/Howto_restart.txt
+++ b/doc/src/Howto_restart.txt
@@ -16,8 +16,8 @@ restart files can be saved to disk using the "restart"_restart.html
command. At a later time, these binary files can be read via a
"read_restart"_read_restart.html command in a new script. Or they can
be converted to text data files using the "-r command-line
-switch"_Section_start.html#start_6 and read by a
-"read_data"_read_data.html command in a new script.
+switch"_Run_options.html and read by a "read_data"_read_data.html
+command in a new script.
Here we give examples of 2 scripts that read either a binary restart
file or a converted data file and then issue a new run command to
diff --git a/doc/src/Howto_temperature.txt b/doc/src/Howto_temperature.txt
index 7a318250cf..8a9e262da1 100644
--- a/doc/src/Howto_temperature.txt
+++ b/doc/src/Howto_temperature.txt
@@ -17,7 +17,10 @@ aggregate motion of particles) and its thermal velocity. The sum of
the two is the particle's total velocity, but the latter is often what
is wanted to compute a temperature.
-LAMMPS has several options for computing temperatures, any of which can be used in "thermostatting"_Howto_thermostat.html and "barostatting"_Howto_barostat.html. These "compute commands"_compute.html calculate temperature:
+LAMMPS has several options for computing temperatures, any of which
+can be used in "thermostatting"_Howto_thermostat.html and
+"barostatting"_Howto_barostat.html. These "compute
+commands"_compute.html calculate temperature:
"compute temp"_compute_temp.html
"compute temp/sphere"_compute_temp_sphere.html
@@ -35,6 +38,6 @@ velocities) that are removed when computing the thermal temperature.
temp/asphere"_compute_temp_asphere.html compute kinetic energy for
finite-size particles that includes rotational degrees of freedom.
They both allow for velocity biases indirectly, via an optional extra
-argument which is another temperature compute that subtracts a velocity bias.
-This allows the translational velocity of spherical or aspherical
-particles to be adjusted in prescribed ways.
+argument which is another temperature compute that subtracts a
+velocity bias. This allows the translational velocity of spherical or
+aspherical particles to be adjusted in prescribed ways.
diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt
index a5e8b63640..a3747465cd 100644
--- a/doc/src/Manual.txt
+++ b/doc/src/Manual.txt
@@ -72,7 +72,9 @@ every LAMMPS command.
:includehidden:
Intro
- Section_start
+ Install
+ Build
+ Run
Commands
Packages
Speed
@@ -107,15 +109,9 @@ END_RST -->
<!-- HTML_ONLY -->
"Introduction"_Intro.html :olb,l
-"Getting started"_Section_start.html :l
- 2.1 "What's in the LAMMPS distribution"_start_1 :ulb,b
- 2.2 "Making LAMMPS"_start_2 :b
- 2.3 "Making LAMMPS with optional packages"_start_3 :b
- 2.4 "Building LAMMPS as a library"_start_4 :b
- 2.5 "Running LAMMPS"_start_5 :b
- 2.6 "Command-line options"_start_6 :b
- 2.7 "Screen output"_start_7 :b
- 2.8 "Tips for users of previous versions"_start_8 :ule,b
+"Install LAMMPS"_Install.html :l
+"Build LAMMPS"_Build.html :l
+"Run LAMMPS"_Run.html :l
"Commands"_Commands.html :l
"Optional packages"_Packages.html :l
"Accelerate performance"_Speed.html :l
@@ -127,15 +123,6 @@ END_RST -->
"Errors"_Errors.html :l
:ole
-:link(start_1,Section_start.html#start_1)
-:link(start_2,Section_start.html#start_2)
-:link(start_3,Section_start.html#start_3)
-:link(start_4,Section_start.html#start_4)
-:link(start_5,Section_start.html#start_5)
-:link(start_6,Section_start.html#start_6)
-:link(start_7,Section_start.html#start_7)
-:link(start_8,Section_start.html#start_8)
-
<!-- END_HTML_ONLY -->
</BODY>
diff --git a/doc/src/Modify_contribute.txt b/doc/src/Modify_contribute.txt
index ef9fe6a717..8cbea8bb31 100644
--- a/doc/src/Modify_contribute.txt
+++ b/doc/src/Modify_contribute.txt
@@ -44,13 +44,14 @@ compression, as this works well on all platforms.
If the new features/files are broadly useful we may add them as core
files to LAMMPS or as part of a "standard
-package"_Section_start.html#start_3. Else we will add them as a
-user-contributed file or package. Examples of user packages are in
-src sub-directories that start with USER. The USER-MISC package is
-simply a collection of (mostly) unrelated single files, which is the
-simplest way to have your contribution quickly added to the LAMMPS
-distribution. You can see a list of the both standard and user
-packages by typing "make package" in the LAMMPS src directory.
+package"_Packages_standard.html. Else we will add them as a
+user-contributed file or "user package"_Packages_user.html. Examples
+of user packages are in src sub-directories that start with USER. The
+USER-MISC package is simply a collection of (mostly) unrelated single
+files, which is the simplest way to have your contribution quickly
+added to the LAMMPS distribution. All the standard and user packages
+are listed and described on the "Packages
+details"_Packages_details.html doc page.
Note that by providing us files to release, you are agreeing to make
them open-source, i.e. we can release them under the terms of the GPL,
diff --git a/doc/src/Packages.txt b/doc/src/Packages.txt
index a7f45a99b7..e48c947be3 100644
--- a/doc/src/Packages.txt
+++ b/doc/src/Packages.txt
@@ -13,12 +13,12 @@ Optional packages :h2
This section gives an overview of the optional packages that extend
LAMMPS functionality. Packages are groups of files that enable a
specific set of features. For example, force fields for molecular
-systems or rigid-body constraint are in packages. You can see the
+systems or rigid-body constraints are in packages. You can see the
list of all packages and "make" commands to manage them by typing
"make package" from within the src directory of the LAMMPS
-distribution. "Section 2.3"_Section_start.html#start_3 gives general
-info on how to install and un-install packages as part of the LAMMPS
-build process.
+distribution. The "Build package"_Build_package.html doc page gives
+general info on how to install and un-install packages as part of the
+LAMMPS build process.
<!-- RST
diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt
index eb92fe4dc4..1dbde273b4 100644
--- a/doc/src/Packages_details.txt
+++ b/doc/src/Packages_details.txt
@@ -17,6 +17,13 @@ library it requires. It also gives links to documentation, example
scripts, and pictures/movies (if available) that illustrate use of the
package.
+The majority of packages can be included in a LAMMPS build with a
+single setting (-D PGK_NAME for CMake) or command ("make yes-name" for
+make). See the "Build package"_Build_package.html doc page for more
+info. A few packages may require additional steps; this is indicated
+in the descriptions below. The "Build extras"_Build_extras.html doc
+page gives those details.
+
NOTE: To see the complete list of commands a package adds to LAMMPS,
you can examine the files in its src directory, e.g. "ls
src/GRANULAR". Files with names that start with fix, compute, atom,
@@ -102,14 +109,6 @@ ASPHERE package :link(ASPHERE),h4
Computes, time-integration fixes, and pair styles for aspherical
particle models including ellipsoids, 2d lines, and 3d triangles.
-[Install or un-install:]
-
-make yes-asphere
-make machine :pre
-
-make no-asphere
-make machine :pre
-
[Supporting info:]
src/ASPHERE: filenames -> commands
@@ -134,14 +133,6 @@ time-integration fixes, pair styles, as well as the body styles
themselves. See the "Howto body"_Howto_body.html doc page for an
overview.
-[Install or un-install:]
-
-make yes-body
-make machine :pre
-
-make no-body
-make machine :pre
-
[Supporting info:]
src/BODY filenames -> commands
@@ -160,14 +151,6 @@ CLASS2 package :link(CLASS2),h4
Bond, angle, dihedral, improper, and pair styles for the COMPASS
CLASS2 molecular force field.
-[Install or un-install:]
-
-make yes-class2
-make machine :pre
-
-make no-class2
-make machine :pre
-
[Supporting info:]
src/CLASS2: filenames -> commands
@@ -192,14 +175,6 @@ simplified approximation to Stokesian dynamics.
which were created by Amit Kumar and Michael Bybee from Jonathan
Higdon's group at UIUC.
-[Install or un-install:]
-
-make yes-colloid
-make machine :pre
-
-make no-colloid
-make machine :pre
-
[Supporting info:]
src/COLLOID: filenames -> commands
@@ -226,19 +201,11 @@ available on your system.
[Author:] Axel Kohlmeyer (Temple U).
-[Install or un-install:]
-
-Note that building with this package assumes you have the zlib
-compression library available on your system. The LAMMPS build uses
-the settings in the lib/compress/Makefile.lammps file in the
-compile/link process. You should only need to edit this file if the
-LAMMPS build fails on your system.
+[Install:]
-make yes-compress
-make machine :pre
-
-make no-compress
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -266,14 +233,6 @@ this package.
[Author:] Hendrik Heenen (Technical U of Munich).
-[Install or un-install:]
-
-make yes-coreshell
-make machine :pre
-
-make no-coreshell
-make machine :pre
-
[Supporting info:]
src/CORESHELL: filenames -> commands
@@ -294,14 +253,6 @@ DIPOLE package :link(DIPOLE),h4
An atom style and several pair styles for point dipole models with
short-range or long-range interactions.
-[Install or un-install:]
-
-make yes-dipole
-make machine :pre
-
-make no-dipole
-make machine :pre
-
[Supporting info:]
src/DIPOLE: filenames -> commands
@@ -325,66 +276,17 @@ and only the CUDA versions are regularly tested. The "Speed
gpu"_Speed_gpu.html doc page gives details of what hardware and GPU
software is required on your system, and details on how to build and
use this package. Its styles can be invoked at run time via the "-sf
-gpu" or "-suffix gpu" "command-line
-switches"_Section_start.html#start_6. See also the "KOKKOS"_#KOKKOS
-package, which has GPU-enabled styles.
+gpu" or "-suffix gpu" "command-line switches"_Run_options.html. See
+also the "KOKKOS"_#KOKKOS package, which has GPU-enabled styles.
[Authors:] Mike Brown (Intel) while at Sandia and ORNL and Trung Nguyen
(Northwestern U) while at ORNL.
-[Install or un-install:]
-
-Before building LAMMPS with this package, you must first build the GPU
-library in lib/gpu from a set of provided C and CUDA files. You can
-do this manually if you prefer; follow the instructions in
-lib/gpu/README. Please note, that the GPU library uses MPI calls, so
-you have to make certain to use the same MPI library (or the STUBS
-library) settings as the main LAMMPS code. That same applies to the
--DLAMMPS_BIGBIG, -DLAMMPS_SMALLBIG, or -DLAMMPS_SMALLSMALL define.
-
-You can also do it in one step from the lammps/src
-dir, using a command like these, which simply invoke the
-lib/gpu/Install.py script with the specified args:
-
-make lib-gpu # print help message
-make lib-gpu args="-b" # build GPU library with default Makefile.linux
-make lib-gpu args="-m xk7 -p single -o xk7.single" # create new Makefile.xk7.single, altered for single-precision
-make lib-gpu args="-m mpi -p mixed -b" # build GPU library with mixed precision using settings in Makefile.mpi :pre
+[Install:]
-Note that this procedure through the '-m machine' flag starts with one of
-the existing Makefile.machine files in lib/gpu. For your convenience,
-machine makefiles for "mpi" and "serial" are provided, which have the
-same settings as the corresponding machine makefiles in the main LAMMPS
-source folder. In addition you can alter 4 important settings in that
-Makefile, via the -h, -a, -p, -e switches, and also save a copy of the
-new Makefile, if desired:
-
-CUDA_HOME = where NVIDIA CUDA software is installed on your system
-CUDA_ARCH = what GPU hardware you have (see help message for details)
-CUDA_PRECISION = precision (double, mixed, single)
-EXTRAMAKE = which Makefile.lammps.* file to copy to Makefile.lammps :ul
-
-If the library build is successful, at least 3 files should be created:
-lib/gpu/libgpu.a, lib/gpu/nvc_get_devices, and lib/gpu/Makefile.lammps.
-The latter has settings that enable LAMMPS to link with CUDA libraries.
-If the settings in Makefile.lammps for your machine are not correct,
-the LAMMPS build will fail, and lib/gpu/Makefile.lammps may need to
-be edited.
-
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
-
-make yes-gpu
-make machine :pre
-
-make no-gpu
-make machine :pre
-
-NOTE: If you re-build the GPU library in lib/gpu, you should always
-un-install the GPU package, then re-install it and re-build LAMMPS.
-This is because the compilation of files in the GPU package use the
-library settings from the lib/gpu/Makefile.machine used to build the
-GPU library.
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -393,8 +295,8 @@ src/GPU/README
lib/gpu/README
"Speed packages"_Speed_packages.html
"Speed gpu"_Speed_gpu.html.html
-"Section 2.6 -sf gpu"_Section_start.html#start_6
-"Section 2.6 -pk gpu"_Section_start.html#start_6
+"Section 2.6 -sf gpu"_Run_options.html
+"Section 2.6 -pk gpu"_Run_options.html
"package gpu"_package.html
"Commands all"_Commands_all.html pages (pair,kspace) for styles followed by (g)
"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
@@ -409,14 +311,6 @@ Pair styles and fixes for finite-size granular particles, which
interact with each other and boundaries via frictional and dissipative
potentials.
-[Install or un-install:]
-
-make yes-granular
-make machine :pre
-
-make no-granular
-make machine :pre
-
[Supporting info:]
src/GRANULAR: filenames -> commands
@@ -456,48 +350,11 @@ API which the "pair_style kim"_pair_kim.html command uses. He
developed the pair style in collaboration with Valeriu Smirichinski (U
Minnesota).
-[Install or un-install:]
-
-Before building LAMMPS with this package, you must first download and
-build the KIM library and include the KIM models that you want to
-use. You can do this manually if you prefer; follow the instructions
-in lib/kim/README. You can also do it in one step from the lammps/src
-dir, using a command like these, which simply invoke the
-lib/kim/Install.py script with the specified args.
-
-make lib-kim # print help message
-make lib-kim args="-b " # (re-)install KIM API lib with only example models
-make lib-kim args="-b -a Glue_Ercolessi_Adams_Al__MO_324507536345_001" # ditto plus one model
-make lib-kim args="-b -a everything" # install KIM API lib with all models
-make lib-kim args="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # add one model or model driver
-make lib-kim args="-p /usr/local/kim-api" # use an existing KIM API installation at the provided location
-make lib-kim args="-p /usr/local/kim-api -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver :pre
-
-Note that in LAMMPS lingo, a KIM model driver is a pair style
-(e.g. EAM or Tersoff). A KIM model is a pair style for a particular
-element or alloy and set of parameters, e.g. EAM for Cu with a
-specific EAM potential file. Also note that installing the KIM API
-library with all its models, may take around 30 min to build. Of
-course you only need to do that once.
-
-See the list of KIM model drivers here:
-https://openkim.org/kim-items/model-drivers/alphabetical
-
-See the list of all KIM models here:
-https://openkim.org/kim-items/models/by-model-drivers
-
-See the list of example KIM models included by default here:
-https://openkim.org/kim-api on the "What is in the KIM API source
-package?" page.
-
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
+[Install:]
-make yes-kim
-make machine :pre
-
-make no-kim
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -521,9 +378,9 @@ style name. The "Speed kokkos"_Speed_kokkos.html doc page gives
details of what hardware and software is required on your system, and
how to build and use this package. Its styles can be invoked at run
time via the "-sf kk" or "-suffix kk" "command-line
-switches"_Section_start.html#start_6. Also see the "GPU"_#GPU,
-"OPT"_#OPT, "USER-INTEL"_#USER-INTEL, and "USER-OMP"_#USER-OMP
-packages, which have styles optimized for CPUs, KNLs, and GPUs.
+switches"_Run_options.html. Also see the "GPU"_#GPU, "OPT"_#OPT,
+"USER-INTEL"_#USER-INTEL, and "USER-OMP"_#USER-OMP packages, which
+have styles optimized for CPUs, KNLs, and GPUs.
You must have a C++11 compatible compiler to use this package.
@@ -534,53 +391,11 @@ which was developed by Carter Edwards, Christian Trott, and others at
Sandia, and which is included in the LAMMPS distribution in
lib/kokkos.
-[Install or un-install:]
-
-For the KOKKOS package, you have 3 choices when building. You can
-build with either CPU or KNL or GPU support. Each choice requires
-additional settings in your Makefile.machine for the KOKKOS_DEVICES
-and KOKKOS_ARCH settings. See the src/MAKE/OPTIONS/Makefile.kokkos*
-files for examples.
-
-For multicore CPUs using OpenMP:
-
-KOKKOS_DEVICES = OpenMP
-KOKKOS_ARCH = HSW # HSW = Haswell, SNB = SandyBridge, BDW = Broadwell, etc :pre
-
-For Intel KNLs using OpenMP:
-
-KOKKOS_DEVICES = OpenMP
-KOKKOS_ARCH = KNL :pre
-
-For NVIDIA GPUs using CUDA:
+[Install:]
-KOKKOS_DEVICES = Cuda
-KOKKOS_ARCH = Pascal60,Power8 # P100 hosted by an IBM Power8, etc
-KOKKOS_ARCH = Kepler37,Power8 # K80 hosted by an IBM Power8, etc :pre
-
-For GPUs, you also need these 2 lines in your Makefile.machine before
-the CC line is defined, in this case for use with OpenMPI mpicxx. The
-2 lines define a nvcc wrapper compiler, which will use nvcc for
-compiling CUDA files or use a C++ compiler for non-Kokkos, non-CUDA
-files.
-
-KOKKOS_ABSOLUTE_PATH = $(shell cd $(KOKKOS_PATH); pwd)
-export OMPI_CXX = $(KOKKOS_ABSOLUTE_PATH)/config/nvcc_wrapper
-CC = mpicxx :pre
-
-Once you have an appropriate Makefile.machine, you can
-install/un-install the package and build LAMMPS in the usual manner.
-Note that you cannot build one executable to run on multiple hardware
-targets (CPU or KNL or GPU). You need to build LAMMPS once for each
-hardware target, to produce a separate executable. Also note that we
-do not recommend building with other acceleration packages installed
-(GPU, OPT, USER-INTEL, USER-OMP) when also building with KOKKOS.
-
-make yes-kokkos
-make machine :pre
-
-make no-kokkos
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -589,9 +404,9 @@ src/KOKKOS/README
lib/kokkos/README
"Speed packages"_Speed_packages.html
"Speed kokkos"_Speed_kokkos.html
-"Section 2.6 -k on ..."_Section_start.html#start_6
-"Section 2.6 -sf kk"_Section_start.html#start_6
-"Section 2.6 -pk kokkos"_Section_start.html#start_6
+"Section 2.6 -k on ..."_Run_options.html
+"Section 2.6 -sf kk"_Run_options.html
+"Section 2.6 -pk kokkos"_Run_options.html
"package kokkos"_package.html
"Commands all"_Commands_all.html pages (fix,compute,pair,etc) for styles followed by (k)
"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
@@ -607,20 +422,14 @@ which compute the corresponding short-range pairwise Coulombic
interactions. These include Ewald, particle-particle particle-mesh
(PPPM), and multilevel summation method (MSM) solvers.
-[Install or un-install:]
+[Install:]
Building with this package requires a 1d FFT library be present on
your system for use by the PPPM solvers. This can be the KISS FFT
library provided with LAMMPS, 3rd party libraries like FFTW, or a
-vendor-supplied FFT library. See step 6 of "Section
-2.2.2"_Section_start.html#start_2_2 of the manual for details on how
-to select different FFT options in your machine Makefile.
-
-make yes-kspace
-make machine :pre
-
-make no-kspace
-make machine :pre
+vendor-supplied FFT library. See the "Build
+settings"_Build_settings.html doc page for details on how to select
+different FFT options for your LAMPMS build.
[Supporting info:]
@@ -655,36 +464,11 @@ description is given with the "fix latte"_fix_latte.html command.
itself is developed at Los Alamos National Laboratory by Marc
Cawkwell, Anders Niklasson, and Christian Negre.
-[Install or un-install:]
+[Install:]
-Before building LAMMPS with this package, you must first download and
-build the LATTE library. You can do this manually if you prefer;
-follow the instructions in lib/latte/README. You can also do it in
-one step from the lammps/src dir, using a command like these, which
-simply invokes the lib/latte/Install.py script with the specified
-args:
-
-make lib-latte # print help message
-make lib-latte args="-b" # download and build in lib/latte/LATTE-master
-make lib-latte args="-p $HOME/latte" # use existing LATTE installation in $HOME/latte
-make lib-latte args="-b -m gfortran" # download and build in lib/latte and
- # copy Makefile.lammps.gfortran to Makefile.lammps
-:pre
-
-Note that 3 symbolic (soft) links, "includelink" and "liblink" and
-"filelink.o", are created in lib/latte to point into the LATTE home dir.
-When LAMMPS builds in src it will use these links. You should
-also check that the Makefile.lammps file you create is appropriate
-for the compiler you use on your system to build LATTE.
-
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
-
-make yes-latte
-make machine :pre
-
-make no-latte
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -704,14 +488,6 @@ MANYBODY package :link(MANYBODY),h4
A variety of manybody and bond-order potentials. These include
(AI)REBO, BOP, EAM, EIM, Stillinger-Weber, and Tersoff potentials.
-[Install or un-install:]
-
-make yes-manybody
-make machine :pre
-
-make no-manybody
-make machine :pre
-
[Supporting info:]
src/MANYBODY: filenames -> commands
@@ -735,14 +511,6 @@ attributes. These include fixes for creating, breaking, and swapping
bonds, for performing atomic swaps, and performing grand-canonical MC
(GCMC) in conjuction with dynamics.
-[Install or un-install:]
-
-make yes-mc
-make machine :pre
-
-make no-mc
-make machine :pre
-
[Supporting info:]
src/MC: filenames -> commands
@@ -770,37 +538,11 @@ while providing the identical features and USER interface.
[Author:] Greg Wagner (Northwestern U) while at Sandia.
-[Install or un-install:]
-
-Before building LAMMPS with this package, you must first build the
-MEAM library in lib/meam. You can do this manually if you prefer;
-follow the instructions in lib/meam/README. You can also do it in one
-step from the lammps/src dir, using a command like these, which simply
-invoke the lib/meam/Install.py script with the specified args:
-
-make lib-meam # print help message
-make lib-meam args="-m mpi" # build with default Fortran compiler compatible with your MPI library
-make lib-meam args="-m serial" # build with compiler compatible with "make serial" (GNU Fortran)
-make lib-meam args="-m ifort" # build with Intel Fortran compiler using Makefile.ifort :pre
-
-The build should produce two files: lib/meam/libmeam.a and
-lib/meam/Makefile.lammps. The latter is copied from an existing
-Makefile.lammps.* and has settings needed to link C++ (LAMMPS) with
-Fortran (MEAM library). Typically the two compilers used for LAMMPS
-and the MEAM library need to be consistent (e.g. both Intel or both
-GNU compilers). If necessary, you can edit/create a new
-lib/meam/Makefile.machine file for your system, which should define an
-EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine
-file.
-
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
-
-make yes-meam
-make machine :pre
+[Install:]
-make no-meam
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
NOTE: You should test building the MEAM library with both the Intel
and GNU compilers to see if a simulation runs faster with one versus
@@ -827,14 +569,6 @@ listing, "ls src/MISC", to see the list of commands.
NOTE: the MISC package contains styles that require using the
-restrict flag, when compiling with Intel compilers.
-[Install or un-install:]
-
-make yes-misc
-make machine :pre
-
-make no-misc
-make machine :pre
-
[Supporting info:]
src/MISC: filenames -> commands
@@ -860,14 +594,6 @@ that are used to model molecular systems with fixed covalent bonds.
The pair styles include the Dreiding (hydrogen-bonding) and CHARMM
force fields, and a TIP4P water model.
-[Install or un-install:]
-
-make yes-molecule
-make machine :pre
-
-make no-molecule
-make machine :pre
-
[Supporting info:]
src/MOLECULE: filenames -> commands
@@ -897,18 +623,6 @@ MPIIO library. It adds "dump styles"_dump.html with a "mpiio" in
their style name. Restart files with an ".mpiio" suffix are also
written and read in parallel.
-[Install or un-install:]
-
-Note that MPIIO is part of the standard message-passing interface
-(MPI) library, so you should not need any additional compiler or link
-settings, beyond what LAMMPS normally uses for MPI on your system.
-
-make yes-mpiio
-make machine :pre
-
-make no-mpiio
-make machine :pre
-
[Supporting info:]
src/MPIIO: filenames -> commands
@@ -936,39 +650,11 @@ system.
library was developed by Jacob Wagner in Greg Voth's group at the
University of Chicago.
-[Install or un-install:]
-
-Before building LAMMPS with this package, you must first download and
-build the MS-CG library. Building the MS-CG library and using it from
-LAMMPS requires a C++11 compatible compiler and that the GSL
-(GNU Scientific Library) headers and libraries are installed on your
-machine. See the lib/mscg/README and MSCG/Install files for more details.
-
-Assuming these libraries are in place, you can do the download and
-build of MS-CG manually if you prefer; follow the instructions in
-lib/mscg/README. You can also do it in one step from the lammps/src
-dir, using a command like these, which simply invoke the
-lib/mscg/Install.py script with the specified args:
-
-make lib-mscg # print help message
-make lib-mscg args="-b -m serial" # download and build in lib/mscg/MSCG-release-master
- # with the settings compatible with "make serial"
-make lib-mscg args="-b -m mpi" # download and build in lib/mscg/MSCG-release-master
- # with the settings compatible with "make mpi"
-make lib-mscg args="-p /usr/local/mscg-release" # use the existing MS-CG installation in /usr/local/mscg-release :pre
-
-Note that 2 symbolic (soft) links, "includelink" and "liblink", will be created in lib/mscg
-to point to the MS-CG src/installation dir. When LAMMPS is built in src it will use these links.
-You should not need to edit the lib/mscg/Makefile.lammps file.
-
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
-
-make yes-mscg
-make machine :pre
+[Install:]
-make no-mscg
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -989,34 +675,25 @@ CHARMM, and Morse potentials. The styles have an "opt" suffix in
their style name. The "Speed opt"_Speed_opt.html doc page gives
details of how to build and use this package. Its styles can be
invoked at run time via the "-sf opt" or "-suffix opt" "command-line
-switches"_Section_start.html#start_6. See also the "KOKKOS"_#KOKKOS,
+switches"_Run_options.html. See also the "KOKKOS"_#KOKKOS,
"USER-INTEL"_#USER-INTEL, and "USER-OMP"_#USER-OMP packages, which
have styles optimized for CPU performance.
[Authors:] James Fischer (High Performance Technologies), David Richie,
and Vincent Natoli (Stone Ridge Technolgy).
-[Install or un-install:]
+[Install:]
-make yes-opt
-make machine :pre
-
-make no-opt
-make machine :pre
-
-NOTE: The compile flag "-restrict" must be used to build LAMMPS with
-the OPT package when using Intel compilers. It should be added to
-the CCFLAGS line of your Makefile.machine. See Makefile.opt in
-src/MAKE/OPTIONS for an example.
-
-CCFLAGS: add -restrict for Intel compilers :ul
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
src/OPT: filenames -> commands
"Speed packages"_Speed_packages.html
"Speed opt"_Speed_opt.html
-"Section 2.6 -sf opt"_Section_start.html#start_6
+"Section 2.6 -sf opt"_Run_options.html
"Commands pair"_Commands_pair.html for styles followed by (t)
"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
@@ -1035,14 +712,6 @@ model.
Additional Peridynamics models were added by Rezwanur Rahman and John
Foster (UTSA).
-[Install or un-install:]
-
-make yes-peri
-make machine :pre
-
-make no-peri
-make machine :pre
-
[Supporting info:]
src/PERI: filenames -> commands
@@ -1070,35 +739,11 @@ connections at hinge points.
[Author:] Rudra Mukherjee (JPL) while at RPI.
-[Install or un-install:]
-
-Before building LAMMPS with this package, you must first build the
-POEMS library in lib/poems. You can do this manually if you prefer;
-follow the instructions in lib/poems/README. You can also do it in
-one step from the lammps/src dir, using a command like these, which
-simply invoke the lib/poems/Install.py script with the specified args:
-
-make lib-poems # print help message
-make lib-poems args="-m serial" # build with GNU g++ compiler (settings as with "make serial")
-make lib-poems args="-m mpi" # build with default MPI C++ compiler (settings as with "make mpi")
-make lib-poems args="-m icc" # build with Intel icc compiler :pre
+[Install:]
-The build should produce two files: lib/poems/libpoems.a and
-lib/poems/Makefile.lammps. The latter is copied from an existing
-Makefile.lammps.* and has settings needed to build LAMMPS with the
-POEMS library (though typically the settings are just blank). If
-necessary, you can edit/create a new lib/poems/Makefile.machine file
-for your system, which should define an EXTRAMAKE variable to specify
-a corresponding Makefile.lammps.machine file.
-
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
-
-make yes-poems
-make machine :pre
-
-make no-meam
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -1121,21 +766,16 @@ call"_Python_call.html doc page for an overview of using Python from
LAMMPS in this manner and all the "Python"_Python.html doc pages for
other ways to use LAMMPS and Python together.
-[Install or un-install:]
-
-make yes-python
-make machine :pre
-
-make no-python
-make machine :pre
-
NOTE: Building with the PYTHON package assumes you have a Python
shared library available on your system, which needs to be a Python 2
version, 2.6 or later. Python 3 is not yet supported. See the
-lib/python/README for more details. Note that the build uses the
-lib/python/Makefile.lammps file in the compile/link process. You
-should only need to create a new Makefile.lammps.* file (and copy it
-to Makefile.lammps) if the LAMMPS build fails.
+lib/python/README for more details.
+
+[Install:]
+
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -1154,14 +794,6 @@ Several fixes for performing charge equilibration (QEq) via different
algorithms. These can be used with pair styles that perform QEq as
part of their formulation.
-[Install or un-install:]
-
-make yes-qeq
-make machine :pre
-
-make no-qeq
-make machine :pre
-
[Supporting info:]
src/QEQ: filenames -> commands
@@ -1183,37 +815,11 @@ monitoring molecules as bonds are created and destroyed.
[Author:] Aidan Thompson (Sandia).
-[Install or un-install:]
-
-Before building LAMMPS with this package, you must first build the
-REAX library in lib/reax. You can do this manually if you prefer;
-follow the instructions in lib/reax/README. You can also do it in one
-step from the lammps/src dir, using a command like these, which simply
-invoke the lib/reax/Install.py script with the specified args:
-
-make lib-reax # print help message
-make lib-reax args="-m serial" # build with GNU Fortran compiler (settings as with "make serial")
-make lib-reax args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
-make lib-reax args="-m ifort" # build with Intel ifort compiler :pre
-
-The build should produce two files: lib/reax/libreax.a and
-lib/reax/Makefile.lammps. The latter is copied from an existing
-Makefile.lammps.* and has settings needed to link C++ (LAMMPS) with
-Fortran (REAX library). Typically the two compilers used for LAMMPS
-and the REAX library need to be consistent (e.g. both Intel or both
-GNU compilers). If necessary, you can edit/create a new
-lib/reax/Makefile.machine file for your system, which should define an
-EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine
-file.
-
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
-
-make yes-reax
-make machine :pre
+[Install:]
-make no-reax
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -1239,14 +845,6 @@ verlet/split algorithm for performing long-range Coulombics on one set
of processors, and the remainder of the force field calcalation on
another set.
-[Install or un-install:]
-
-make yes-replica
-make machine :pre
-
-make no-replica
-make machine :pre
-
[Supporting info:]
src/REPLICA: filenames -> commands
@@ -1271,16 +869,6 @@ particles. This includes SHAKE and RATTLE, as well as varous
rigid-body integrators for a few large bodies or many small bodies.
Also several computes which calculate properties of rigid bodies.
-To install/build:
-
-make yes-rigid
-make machine :pre
-
-To un-install/re-build:
-
-make no-rigid
-make machine :pre
-
[Supporting info:]
src/RIGID: filenames -> commands
@@ -1303,14 +891,6 @@ SHOCK package :link(SHOCK),h4
Fixes for running impact simulations where a shock-wave passes through
a material.
-[Install or un-install:]
-
-make yes-shock
-make machine :pre
-
-make no-shock
-make machine :pre
-
[Supporting info:]
src/SHOCK: filenames -> commands
@@ -1334,14 +914,6 @@ computes which analyze attributes of the potential.
[Author:] Aidan Thompson (Sandia).
-[Install or un-install:]
-
-make yes-snap
-make machine :pre
-
-make no-snap
-make machine :pre
-
[Supporting info:]
src/SNAP: filenames -> commands
@@ -1362,14 +934,6 @@ the usual manner via MD. Various pair, fix, and compute styles.
[Author:] Julian Tranchida (Sandia).
-[Install or un-install:]
-
-make yes-spin
-make machine :pre
-
-make no-spin
-make machine :pre
-
[Supporting info:]
src/SPIN: filenames -> commands
@@ -1393,16 +957,6 @@ A pair of fixes which implement the Stochastic Rotation Dynamics (SRD)
method for coarse-graining of a solvent, typically around large
colloidal particles.
-To install/build:
-
-make yes-srd
-make machine :pre
-
-To un-install/re-build:
-
-make no-srd
-make machine :pre
-
[Supporting info:]
src/SRD: filenames -> commands
@@ -1434,33 +988,11 @@ system.
library was written by Chris Rycroft (Harvard U) while at UC Berkeley
and LBNL.
-[Install or un-install:]
-
-Before building LAMMPS with this package, you must first download and
-build the Voro++ library. You can do this manually if you prefer;
-follow the instructions in lib/voronoi/README. You can also do it in
-one step from the lammps/src dir, using a command like these, which
-simply invoke the lib/voronoi/Install.py script with the specified
-args:
-
-make lib-voronoi # print help message
-make lib-voronoi args="-b" # download and build the default version in lib/voronoi/voro++-<version>
-make lib-voronoi args="-p $HOME/voro++" # use existing Voro++ installation in $HOME/voro++
-make lib-voronoi args="-b -v voro++0.4.6" # download and build the 0.4.6 version in lib/voronoi/voro++-0.4.6 :pre
-
-Note that 2 symbolic (soft) links, "includelink" and "liblink", are
-created in lib/voronoi to point to the Voro++ src dir. When LAMMPS
-builds in src it will use these links. You should not need to edit
-the lib/voronoi/Makefile.lammps file.
-
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
+[Install:]
-make yes-voronoi
-make machine :pre
-
-make no-voronoi
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -1484,46 +1016,11 @@ atomic information to continuum fields.
[Authors:] Reese Jones, Jeremy Templeton, Jon Zimmerman (Sandia).
-[Install or un-install:]
-
-Before building LAMMPS with this package, you must first build the ATC
-library in lib/atc. You can do this manually if you prefer; follow
-the instructions in lib/atc/README. You can also do it in one step
-from the lammps/src dir, using a command like these, which simply
-invoke the lib/atc/Install.py script with the specified args:
-
-make lib-atc # print help message
-make lib-atc args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
-make lib-atc args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
-make lib-atc args="-m icc" # build with Intel icc compiler :pre
-
-The build should produce two files: lib/atc/libatc.a and
-lib/atc/Makefile.lammps. The latter is copied from an existing
-Makefile.lammps.* and has settings needed to build LAMMPS with the ATC
-library. If necessary, you can edit/create a new
-lib/atc/Makefile.machine file for your system, which should define an
-EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine
-file.
-
-Note that the Makefile.lammps file has settings for the BLAS and
-LAPACK linear algebra libraries. As explained in lib/atc/README these
-can either exist on your system, or you can use the files provided in
-lib/linalg. In the latter case you also need to build the library
-in lib/linalg with a command like these:
-
-make lib-linalg # print help message
-make lib-linalg args="-m serial" # build with GNU Fortran compiler (settings as with "make serial")
-make lib-linalg args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
-make lib-linalg args="-m gfortran" # build with GNU Fortran compiler :pre
-
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
-
-make yes-user-atc
-make machine :pre
+[Install:]
-make no-user-atc
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -1546,46 +1043,11 @@ model.
[Author:] Ilya Valuev (JIHT, Russia).
-[Install or un-install:]
+[Install:]
-Before building LAMMPS with this package, you must first build the
-AWPMD library in lib/awpmd. You can do this manually if you prefer;
-follow the instructions in lib/awpmd/README. You can also do it in
-one step from the lammps/src dir, using a command like these, which
-simply invoke the lib/awpmd/Install.py script with the specified args:
-
-make lib-awpmd # print help message
-make lib-awpmd args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
-make lib-awpmd args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
-make lib-awpmd args="-m icc" # build with Intel icc compiler :pre
-
-The build should produce two files: lib/awpmd/libawpmd.a and
-lib/awpmd/Makefile.lammps. The latter is copied from an existing
-Makefile.lammps.* and has settings needed to build LAMMPS with the
-AWPMD library. If necessary, you can edit/create a new
-lib/awpmd/Makefile.machine file for your system, which should define
-an EXTRAMAKE variable to specify a corresponding
-Makefile.lammps.machine file.
-
-Note that the Makefile.lammps file has settings for the BLAS and
-LAPACK linear algebra libraries. As explained in lib/awpmd/README
-these can either exist on your system, or you can use the files
-provided in lib/linalg. In the latter case you also need to build the
-library in lib/linalg with a command like these:
-
-make lib-linalg # print help message
-make lib-linalg args="-m serial" # build with GNU Fortran compiler (settings as with "make serial")
-make lib-linalg args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
-make lib-linalg args="-m gfortran" # build with GNU Fortran compiler :pre
-
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
-
-make yes-user-awpmd
-make machine :pre
-
-make no-user-awpmd
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -1608,15 +1070,8 @@ N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that
accurately describe the structure, pressure, and compressibility of
molecular liquids," J. Chem. Phys. 143, 243148 (2015).
-[Authors:] Nicholas J. H. Dunn and Michael R. DeLyser (The Pennsylvania State University)
-
-[Install or un-install:]
-
-make yes-user-bocs
-make machine :pre
-
-make no-user-bocs
-make machine :pre
+[Authors:] Nicholas J. H. Dunn and Michael R. DeLyser (The
+Pennsylvania State University)
[Supporting info:]
@@ -1645,14 +1100,6 @@ stability.
[Author:] Oliver Henrich (University of Strathclyde, Glasgow).
-[Install or un-install:]
-
-make yes-user-cgdna
-make machine :pre
-
-make no-user-cgdna
-make machine :pre
-
[Supporting info:]
src/USER-CGDNA: filenames -> commands
@@ -1676,14 +1123,6 @@ acids.
[Author:] Axel Kohlmeyer (Temple U).
-[Install or un-install:]
-
-make yes-user-cgsdk
-make machine :pre
-
-make no-user-cgsdk
-make machine :pre
-
[Supporting info:]
src/USER-CGSDK: filenames -> commands
@@ -1712,36 +1151,11 @@ and Jerome Henin (LISM, CNRS, Marseille, France), originally for
the NAMD MD code, but with portability in mind. Axel Kohlmeyer
(Temple U) provided the interface to LAMMPS.
-[Install or un-install:]
+[Install:]
-Before building LAMMPS with this package, you must first build the
-COLVARS library in lib/colvars. You can do this manually if you
-prefer; follow the instructions in lib/colvars/README. You can also
-do it in one step from the lammps/src dir, using a command like these,
-which simply invoke the lib/colvars/Install.py script with the
-specified args:
-
-make lib-colvars # print help message
-make lib-colvars args="-m serial" # build with GNU g++ compiler (settings as with "make serial")
-make lib-colvars args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
-make lib-colvars args="-m g++-debug" # build with GNU g++ compiler and colvars debugging enabled :pre
-
-The build should produce two files: lib/colvars/libcolvars.a and
-lib/colvars/Makefile.lammps. The latter is copied from an existing
-Makefile.lammps.* and has settings needed to build LAMMPS with the
-COLVARS library (though typically the settings are just blank). If
-necessary, you can edit/create a new lib/colvars/Makefile.machine file
-for your system, which should define an EXTRAMAKE variable to specify
-a corresponding Makefile.lammps.machine file.
-
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
-
-make yes-user-colvars
-make machine :pre
-
-make no-user-colvars
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -1763,14 +1177,6 @@ intensities based on kinematic diffraction theory.
[Author:] Shawn Coleman while at the U Arkansas.
-[Install or un-install:]
-
-make yes-user-diffraction
-make machine :pre
-
-make no-user-diffraction
-make machine :pre
-
[Supporting info:]
src/USER-DIFFRACTION: filenames -> commands
@@ -1798,14 +1204,6 @@ algorithm.
[Authors:] Jim Larentzos (ARL), Tim Mattox (Engility Corp), and and John
Brennan (ARL).
-[Install or un-install:]
-
-make yes-user-dpd
-make machine :pre
-
-make no-user-dpd
-make machine :pre
-
[Supporting info:]
src/USER-DPD: filenames -> commands
@@ -1840,14 +1238,6 @@ for using this package in tools/drude.
[Authors:] Alain Dequidt (U Blaise Pascal Clermont-Ferrand), Julien
Devemy (CNRS), and Agilio Padua (U Blaise Pascal).
-[Install or un-install:]
-
-make yes-user-drude
-make machine :pre
-
-make no-user-drude
-make machine :pre
-
[Supporting info:]
src/USER-DRUDE: filenames -> commands
@@ -1879,14 +1269,6 @@ tools/eff; see its README file.
[Author:] Andres Jaramillo-Botero (CalTech).
-[Install or un-install:]
-
-make yes-user-eff
-make machine :pre
-
-make no-user-eff
-make machine :pre
-
[Supporting info:]
src/USER-EFF: filenames -> commands
@@ -1918,14 +1300,6 @@ for using this package in tools/fep; see its README file.
[Author:] Agilio Padua (Universite Blaise Pascal Clermont-Ferrand)
-[Install or un-install:]
-
-make yes-user-fep
-make machine :pre
-
-make no-user-fep
-make machine :pre
-
[Supporting info:]
src/USER-FEP: filenames -> commands
@@ -1957,37 +1331,11 @@ system.
[Author:] Pierre de Buyl (KU Leuven) created both the package and the
H5MD format.
-[Install or un-install:]
-
-Note that to follow these steps to compile and link to the CH5MD
-library, you need the standard HDF5 software package installed on your
-system, which should include the h5cc compiler and the HDF5 library.
-
-Before building LAMMPS with this package, you must first build the
-CH5MD library in lib/h5md. You can do this manually if you prefer;
-follow the instructions in lib/h5md/README. You can also do it in one
-step from the lammps/src dir, using a command like these, which simply
-invoke the lib/h5md/Install.py script with the specified args:
-
-make lib-h5md # print help message
-make lib-hm5d args="-m h5cc" # build with h5cc compiler :pre
-
-The build should produce two files: lib/h5md/libch5md.a and
-lib/h5md/Makefile.lammps. The latter is copied from an existing
-Makefile.lammps.* and has settings needed to build LAMMPS with the
-system HDF5 library. If necessary, you can edit/create a new
-lib/h5md/Makefile.machine file for your system, which should define an
-EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine
-file.
+[Install:]
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
-
-make yes-user-h5md
-make machine :pre
-
-make no-user-h5md
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -2008,9 +1356,9 @@ All of them have an "intel" in their style name. The "Speed
intel"_Speed_intel.html doc page gives details of what hardware and
compilers are required on your system, and how to build and use this
package. Its styles can be invoked at run time via the "-sf intel" or
-"-suffix intel" "command-line switches"_Section_start.html#start_6.
-Also see the "KOKKOS"_#KOKKOS, "OPT"_#OPT, and "USER-OMP"_#USER-OMP
-packages, which have styles optimized for CPUs and KNLs.
+"-suffix intel" "command-line switches"_Run_options.html. Also see
+the "KOKKOS"_#KOKKOS, "OPT"_#OPT, and "USER-OMP"_#USER-OMP packages,
+which have styles optimized for CPUs and KNLs.
You need to have an Intel compiler, version 14 or higher to take full
advantage of this package. While compilation with GNU compilers is
@@ -2019,49 +1367,13 @@ supported, performance will be suboptimal.
NOTE: the USER-INTEL package contains styles that require using the
-restrict flag, when compiling with Intel compilers.
-
[Author:] Mike Brown (Intel).
-[Install or un-install:]
-
-For the USER-INTEL package, you have 2 choices when building. You can
-build with either CPU or KNL support. Each choice requires additional
-settings in your Makefile.machine for CCFLAGS and LINKFLAGS and
-optimized malloc libraries. See the
-src/MAKE/OPTIONS/Makefile.intel_cpu and src/MAKE/OPTIONS/Makefile.knl
-files for examples.
+[Install:]
-For CPUs:
-
-OPTFLAGS = -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits
-CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload \
--fno-alias -ansi-alias -restrict $(OPTFLAGS)
-LINKFLAGS = -g -qopenmp $(OPTFLAGS)
-LIB = -ltbbmalloc -ltbbmalloc_proxy :pre
-
-For KNLs:
-
-OPTFLAGS = -xMIC-AVX512 -O2 -fp-model fast=2 -no-prec-div -qoverride-limits
-CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload \
--fno-alias -ansi-alias -restrict $(OPTFLAGS)
-LINKFLAGS = -g -qopenmp $(OPTFLAGS)
-LIB = -ltbbmalloc :pre
-
-Once you have an appropriate Makefile.machine, you can
-install/un-install the package and build LAMMPS in the usual manner.
-Note that you cannot build one executable to run on multiple hardware
-targets (Intel CPUs or KNL). You need to build LAMMPS once for each
-hardware target, to produce a separate executable.
-
-You should also typically install the USER-OMP package, as it can be
-used in tandem with the USER-INTEL package to good effect, as
-explained on the "Speed intel"_Speed_intel.html doc page.
-
-make yes-user-intel yes-user-omp
-make machine :pre
-
-make no-user-intel no-user-omp
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -2069,8 +1381,8 @@ src/USER-INTEL: filenames -> commands
src/USER-INTEL/README
"Speed packages"_Speed_packages.html
"Speed intel"_Speed_intel.html
-"Section 2.6 -sf intel"_Section_start.html#start_6
-"Section 2.6 -pk intel"_Section_start.html#start_6
+"Section 2.6 -sf intel"_Run_options.html
+"Section 2.6 -pk intel"_Run_options.html
"package intel"_package.html
"Commands all"_Commands_all.html pages (fix,compute,pair,etc) for styles followed by (i)
src/USER-INTEL/TEST
@@ -2088,14 +1400,6 @@ can be used to model MD particles influenced by hydrodynamic forces.
[Authors:] Frances Mackay and Colin Denniston (University of Western
Ontario).
-[Install or un-install:]
-
-make yes-user-lb
-make machine :pre
-
-make no-user-lb
-make machine :pre
-
[Supporting info:]
src/USER-LB: filenames -> commands
@@ -2122,14 +1426,6 @@ matrix-MGPT algorithm due to Tomas Oppelstrup at LLNL.
[Authors:] Tomas Oppelstrup and John Moriarty (LLNL).
-[Install or un-install:]
-
-make yes-user-mgpt
-make machine :pre
-
-make no-user-mgpt
-make machine :pre
-
[Supporting info:]
src/USER-MGPT: filenames -> commands
@@ -2150,14 +1446,6 @@ dihedral, improper, or command style.
[Authors:] The author for each style in the package is listed in the
src/USER-MISC/README file.
-[Install or un-install:]
-
-make yes-user-misc
-make machine :pre
-
-make no-user-misc
-make machine :pre
-
[Supporting info:]
src/USER-MISC: filenames -> commands
@@ -2178,16 +1466,9 @@ algorithm to formulate single-particle constraint functions
g(xi,yi,zi) = 0 and their derivative (i.e. the normal of the manifold)
n = grad(g).
-[Author:] Stefan Paquay (until 2017: Eindhoven University of Technology (TU/e), The
-Netherlands; since 2017: Brandeis University, Waltham, MA, USA)
-
-[Install or un-install:]
-
-make yes-user-manifold
-make machine :pre
-
-make no-user-manifold
-make machine :pre
+[Author:] Stefan Paquay (until 2017: Eindhoven University of
+Technology (TU/e), The Netherlands; since 2017: Brandeis University,
+Waltham, MA, USA)
[Supporting info:]
@@ -2216,14 +1497,6 @@ multiple times.
based on the Fortran version of Greg Wagner (Northwestern U) while at
Sandia.
-[Install or un-install:]
-
-make yes-user-meamc
-make machine :pre
-
-make no-user-meamc
-make machine :pre
-
[Supporting info:]
src/USER-MEAMC: filenames -> commands
@@ -2247,14 +1520,6 @@ algorithm.
[Author:] Zhen Li (Division of Applied Mathematics, Brown University)
-[Install or un-install:]
-
-make yes-user-meso
-make machine :pre
-
-make no-user-meso
-make machine :pre
-
[Supporting info:]
src/USER-MESO: filenames -> commands
@@ -2287,14 +1552,6 @@ well as the "MOF+"_MOFplus website.
[Author:] Hendrik Heenen (Technical U of Munich),
Rochus Schmid (Ruhr-University Bochum).
-[Install or un-install:]
-
-make yes-user-mofff
-make machine :pre
-
-make no-user-mofff
-make machine :pre
-
[Supporting info:]
src/USER-MOFFF: filenames -> commands
@@ -2335,20 +1592,11 @@ at
[Author:] Axel Kohlmeyer (Temple U).
-[Install or un-install:]
-
-Note that the lib/molfile/Makefile.lammps file has a setting for a
-dynamic loading library libdl.a that should is typically present on
-all systems, which is required for LAMMPS to link with this package.
-If the setting is not valid for your system, you will need to edit the
-Makefile.lammps file. See lib/molfile/README and
-lib/molfile/Makefile.lammps for details.
+[Install:]
-make yes-user-molfile
-make machine :pre
-
-make no-user-molfile
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -2383,20 +1631,11 @@ tools:
[Author:] Lars Pastewka (Karlsruhe Institute of Technology).
-[Install or un-install:]
-
-Note that to follow these steps, you need the standard NetCDF software
-package installed on your system. The lib/netcdf/Makefile.lammps file
-has settings for NetCDF include and library files that LAMMPS needs to
-compile and linkk with this package. If the settings are not valid
-for your system, you will need to edit the Makefile.lammps file. See
-lib/netcdf/README for details.
+[Install:]
-make yes-user-netcdf
-make machine :pre
-
-make no-user-netcdf
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -2417,10 +1656,9 @@ via OpenMP directives. All of them have an "omp" in their style name.
The "Speed omp"_Speed_omp.html doc page gives details of what hardware
and compilers are required on your system, and how to build and use
this package. Its styles can be invoked at run time via the "-sf omp"
-or "-suffix omp" "command-line switches"_Section_start.html#start_6.
-Also see the "KOKKOS"_#KOKKOS, "OPT"_#OPT, and
-"USER-INTEL"_#USER-INTEL packages, which have styles optimized for
-CPUs.
+or "-suffix omp" "command-line switches"_Run_options.html. Also see
+the "KOKKOS"_#KOKKOS, "OPT"_#OPT, and "USER-INTEL"_#USER-INTEL
+packages, which have styles optimized for CPUs.
[Author:] Axel Kohlmeyer (Temple U).
@@ -2437,16 +1675,11 @@ See src/MAKE/OPTIONS/Makefile.omp for an example.
Once you have an appropriate Makefile.machine, you can
install/un-install the package and build LAMMPS in the usual manner:
-[Install or un-install:]
-
-make yes-user-omp
-make machine :pre
+[Install:]
-make no-user-omp
-make machine :pre
-
-CCFLAGS: add -fopenmp (and -restrict when using Intel compilers)
-LINKFLAGS: add -fopenmp :ul
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -2454,8 +1687,8 @@ src/USER-OMP: filenames -> commands
src/USER-OMP/README
"Speed packages"_Speed_packages.html
"Speed omp"_Speed_omp.html
-"Section 2.6 -sf omp"_Section_start.html#start_6
-"Section 2.6 -pk omp"_Section_start.html#start_6
+"Section 2.6 -sf omp"_Run_options.html
+"Section 2.6 -pk omp"_Run_options.html
"package omp"_package.html
"Commands all"_Commands_all.html pages (fix,compute,pair,etc) for styles followed by (o)
"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
@@ -2472,14 +1705,6 @@ relations, directly from molecular dynamics simulations.
[Author:] Ling-Ti Kong (Shanghai Jiao Tong University).
-[Install or un-install:]
-
-make yes-user-phonon
-make machine :pre
-
-make no-user-phonon
-make machine :pre
-
[Supporting info:]
src/USER-PHONON: filenames -> commands
@@ -2510,42 +1735,11 @@ without changes to LAMMPS itself.
[Author:] Axel Kohlmeyer (Temple U).
-[Install or un-install:]
-
-Before building LAMMPS with this package, you must first build the
-QMMM library in lib/qmmm. You can do this manually if you prefer;
-follow the first two steps explained in lib/qmmm/README. You can
-also do it in one step from the lammps/src dir, using a command like
-these, which simply invoke the lib/qmmm/Install.py script with the
-specified args:
-
-make lib-qmmm # print help message
-make lib-qmmm args="-m serial" # build with GNU Fortran compiler (settings as in "make serial")
-make lib-qmmm args="-m mpi" # build with default MPI compiler (settings as in "make mpi")
-make lib-qmmm args="-m gfortran" # build with GNU Fortran compiler :pre
-
-The build should produce two files: lib/qmmm/libqmmm.a and
-lib/qmmm/Makefile.lammps. The latter is copied from an existing
-Makefile.lammps.* and has settings needed to build LAMMPS with the
-QMMM library (though typically the settings are just blank). If
-necessary, you can edit/create a new lib/qmmm/Makefile.machine file
-for your system, which should define an EXTRAMAKE variable to specify
-a corresponding Makefile.lammps.machine file.
-
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
+[Install:]
-make yes-user-qmmm
-make machine :pre
-
-make no-user-qmmm
-make machine :pre
-
-NOTE: The LAMMPS executable these steps produce is not yet functional
-for a QM/MM simulation. You must also build Quantum ESPRESSO and
-create a new executable which links LAMMPS and Quantum ESPRESSO
-together. These are steps 3 and 4 described in the lib/qmmm/README
-file.
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -2573,14 +1767,6 @@ simulation.
[Author:] Yuan Shen (Stanford U).
-[Install or un-install:]
-
-make yes-user-qtb
-make machine :pre
-
-make no-user-qtb
-make machine :pre
-
[Supporting info:]
src/USER-QTB: filenames -> commands
@@ -2607,26 +1793,11 @@ on your system.
[Author:] Albert Bartok (Cambridge University)
-[Install or un-install:]
-
-Note that to follow these steps to compile and link to the QUIP
-library, you must first download and build QUIP on your systems. It
-can be obtained from GitHub. See step 1 and step 1.1 in the
-lib/quip/README file for details on how to do this. Note that it
-requires setting two environment variables, QUIP_ROOT and QUIP_ARCH,
-which will be accessed by the lib/quip/Makefile.lammps file which is
-used when you compile and link LAMMPS with this package. You should
-only need to edit this file if the LAMMPS build can not use its
-settings to successfully build on your system.
-
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
-
-make yes-user-quip
-make machine :pre
+[Install:]
-make no-user-quip
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -2649,14 +1820,6 @@ for monitoring molecules as bonds are created and destroyed.
[Author:] Hasan Metin Aktulga (MSU) while at Purdue University.
-[Install or un-install:]
-
-make yes-user-reaxc
-make machine :pre
-
-make no-user-reaxc
-make machine :pre
-
[Supporting info:]
src/USER-REAXC: filenames -> commands
@@ -2689,31 +1852,11 @@ specified as surface geometries from *.STL files.
[Author:] Georg Ganzenmuller (Fraunhofer-Institute for High-Speed
Dynamics, Ernst Mach Institute, Germany).
-[Install or un-install:]
-
-Before building LAMMPS with this package, you must first download the
-Eigen library. Eigen is a template library, so you do not need to
-build it, just download it. You can do this manually if you prefer;
-follow the instructions in lib/smd/README. You can also do it in one
-step from the lammps/src dir, using a command like these, which simply
-invoke the lib/smd/Install.py script with the specified args:
-
-make lib-smd # print help message
-make lib-smd args="-b" # download and build in default lib/smd/eigen-eigen-...
-make lib-smd args="-p /usr/include/eigen3" # use existing Eigen installation in /usr/include/eigen3 :pre
-
-Note that a symbolic (soft) link named "includelink" is created in
-lib/smd to point to the Eigen dir. When LAMMPS builds it will use
-this link. You should not need to edit the lib/smd/Makefile.lammps file.
-
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
-
-make yes-user-smd
-make machine :pre
+[Install:]
-make no-user-smd
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -2736,14 +1879,6 @@ ionocovalent bonds in oxides.
[Authors:] Nicolas Salles, Emile Maras, Olivier Politano, and Robert
Tetot (LAAS-CNRS, France).
-[Install or un-install:]
-
-make yes-user-smtbq
-make machine :pre
-
-make no-user-smtbq
-make machine :pre
-
[Supporting info:]
src/USER-SMTBQ: filenames -> commands
@@ -2775,14 +1910,6 @@ property/atom"_compute_property_atom.html command.
[Author:] Georg Ganzenmuller (Fraunhofer-Institute for High-Speed
Dynamics, Ernst Mach Institute, Germany).
-[Install or un-install:]
-
-make yes-user-sph
-make machine :pre
-
-make no-user-sph
-make machine :pre
-
[Supporting info:]
src/USER-SPH: filenames -> commands
@@ -2803,14 +1930,6 @@ stress, etc) about individual interactions.
[Author:] Axel Kohlmeyer (Temple U).
-[Install or un-install:]
-
-make yes-user-tally
-make machine :pre
-
-make no-user-tally
-make machine :pre
-
[Supporting info:]
src/USER-TALLY: filenames -> commands
@@ -2830,14 +1949,6 @@ supporting compute styles and an output option.
[Author:] David Nicholson (MIT).
-[Install or un-install:]
-
-make yes-user-uef
-make machine :pre
-
-make no-user-uef
-make machine :pre
-
[Supporting info:]
src/USER-UEF: filenames -> commands
@@ -2867,23 +1978,11 @@ system.
[Authors:] Richard Berger (JKU) and Daniel Queteschiner (DCS Computing).
-[Install or un-install:]
-
-The lib/vtk/Makefile.lammps file has settings for accessing VTK files
-and its library, which are required for LAMMPS to build and link with
-this package. If the settings are not valid for your system, check if
-one of the other lib/vtk/Makefile.lammps.* files is compatible and
-copy it to Makefile.lammps. If none of the provided files work, you
-will need to edit the Makefile.lammps file.
-
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
-
-make yes-user-vtk
-make machine :pre
+[Install:]
-make no-user-vtk
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
diff --git a/doc/src/Python_shlib.txt b/doc/src/Python_shlib.txt
index 1a921e4025..18775cd2fd 100644
--- a/doc/src/Python_shlib.txt
+++ b/doc/src/Python_shlib.txt
@@ -9,10 +9,11 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
Build LAMMPS as a shared library :h3
-Instructions on how to build LAMMPS as a shared library are given in
-"Section 2.4"_Section_start.html#start_4. A shared library is one
-that is dynamically loadable, which is what Python requires to wrap
-LAMMPS. On Linux this is a library file that ends in ".so", not ".a".
+Instructions on how to build LAMMPS as a shared library are given on
+the "Build_basics"_Build_basics.html doc page. A shared library is
+one that is dynamically loadable, which is what Python requires to
+wrap LAMMPS. On Linux this is a library file that ends in ".so", not
+".a".
From the src directory, type
@@ -29,6 +30,6 @@ NOTE: If you are building LAMMPS with an MPI or FFT library or other
auxiliary libraries (used by various packages), then all of these
extra libraries must also be shared libraries. If the LAMMPS
shared-library build fails with an error complaining about this, see
-"Section 2.4"_Section_start.html#start_4 for more details.
+the "Build_basics"_Build_basics.html doc page.
-Also include CMake info on this
+TODO: Also include CMake info on this
diff --git a/doc/src/Python_test.txt b/doc/src/Python_test.txt
index 4a05d5c468..3d52485aa8 100644
--- a/doc/src/Python_test.txt
+++ b/doc/src/Python_test.txt
@@ -32,10 +32,10 @@ first importing from the lammps.py file:
>>> from ctypes import CDLL
>>> CDLL("liblammps.so") :pre
-If an error occurs, carefully go thru the steps in "Section
-2.4"_Section_start.html#start_4 and above about building a shared
-library and about insuring Python can find the necessary two files
-it needs.
+If an error occurs, carefully go thru the steps on the
+"Build_basics"_Build_basics.html doc page about building a shared
+library and the "Python_install"_Python_install.html doc page about
+insuring Python can find the necessary two files it needs.
[Test LAMMPS and Python in serial:] :h4
diff --git a/doc/src/Speed_gpu.txt b/doc/src/Speed_gpu.txt
index ab8ec7e9d1..cd81c03ba0 100644
--- a/doc/src/Speed_gpu.txt
+++ b/doc/src/Speed_gpu.txt
@@ -52,9 +52,9 @@ specify the # of GPUs per node
use GPU styles in your input script :ul
The latter two steps can be done using the "-pk gpu" and "-sf gpu"
-"command-line switches"_Section_start.html#start_6 respectively. Or
-the effect of the "-pk" or "-sf" switches can be duplicated by adding
-the "package gpu"_package.html or "suffix gpu"_suffix.html commands
+"command-line switches"_Run_options.html respectively. Or the effect
+of the "-pk" or "-sf" switches can be duplicated by adding the
+"package gpu"_package.html or "suffix gpu"_suffix.html commands
respectively to your input script.
[Required hardware/software:]
@@ -143,10 +143,10 @@ automatically if you create more MPI tasks/node than there are
GPUs/mode. E.g. with 8 MPI tasks/node and 2 GPUs, each GPU will be
shared by 4 MPI tasks.
-Use the "-sf gpu" "command-line switch"_Section_start.html#start_6,
-which will automatically append "gpu" to styles that support it. Use
-the "-pk gpu Ng" "command-line switch"_Section_start.html#start_6 to
-set Ng = # of GPUs/node to use.
+Use the "-sf gpu" "command-line switch"_Run_options.html, which will
+automatically append "gpu" to styles that support it. Use the "-pk
+gpu Ng" "command-line switch"_Run_options.html to set Ng = # of
+GPUs/node to use.
lmp_machine -sf gpu -pk gpu 1 -in in.script # 1 MPI task uses 1 GPU
mpirun -np 12 lmp_machine -sf gpu -pk gpu 2 -in in.script # 12 MPI tasks share 2 GPUs on a single 16-core (or whatever) node
@@ -180,8 +180,8 @@ pair_style lj/cut/gpu 2.5 :pre
You must also use the "package gpu"_package.html command to enable the
GPU package, unless the "-sf gpu" or "-pk gpu" "command-line
-switches"_Section_start.html#start_6 were used. It specifies the
-number of GPUs/node to use, as well as other options.
+switches"_Run_options.html were used. It specifies the number of
+GPUs/node to use, as well as other options.
[Speed-ups to expect:]
diff --git a/doc/src/Speed_intel.txt b/doc/src/Speed_intel.txt
index 20f49672e0..2b29ec3b0f 100644
--- a/doc/src/Speed_intel.txt
+++ b/doc/src/Speed_intel.txt
@@ -306,31 +306,31 @@ Hyper-Threading technology disabled.
[Run with the USER-INTEL package from the command line:]
To enable USER-INTEL optimizations for all available styles used in
-the input script, the "-sf intel"
-"command-line switch"_Section_start.html#start_6 can be used without
-any requirement for editing the input script. This switch will
-automatically append "intel" to styles that support it. It also
-invokes a default command: "package intel 1"_package.html. This
-package command is used to set options for the USER-INTEL package.
-The default package command will specify that USER-INTEL calculations
-are performed in mixed precision, that the number of OpenMP threads
-is specified by the OMP_NUM_THREADS environment variable, and that
-if coprocessors are present and the binary was built with offload
-support, that 1 coprocessor per node will be used with automatic
-balancing of work between the CPU and the coprocessor.
+the input script, the "-sf intel" "command-line
+switch"_Run_options.html can be used without any requirement for
+editing the input script. This switch will automatically append
+"intel" to styles that support it. It also invokes a default command:
+"package intel 1"_package.html. This package command is used to set
+options for the USER-INTEL package. The default package command will
+specify that USER-INTEL calculations are performed in mixed precision,
+that the number of OpenMP threads is specified by the OMP_NUM_THREADS
+environment variable, and that if coprocessors are present and the
+binary was built with offload support, that 1 coprocessor per node
+will be used with automatic balancing of work between the CPU and the
+coprocessor.
You can specify different options for the USER-INTEL package by using
-the "-pk intel Nphi" "command-line switch"_Section_start.html#start_6
-with keyword/value pairs as specified in the documentation. Here,
-Nphi = # of Xeon Phi coprocessors/node (ignored without offload
+the "-pk intel Nphi" "command-line switch"_Run_options.html with
+keyword/value pairs as specified in the documentation. Here, Nphi = #
+of Xeon Phi coprocessors/node (ignored without offload
support). Common options to the USER-INTEL package include {omp} to
override any OMP_NUM_THREADS setting and specify the number of OpenMP
-threads, {mode} to set the floating-point precision mode, and
-{lrt} to enable Long-Range Thread mode as described below. See the
-"package intel"_package.html command for details, including the
-default values used for all its options if not specified, and how to
-set the number of OpenMP threads via the OMP_NUM_THREADS environment
-variable if desired.
+threads, {mode} to set the floating-point precision mode, and {lrt} to
+enable Long-Range Thread mode as described below. See the "package
+intel"_package.html command for details, including the default values
+used for all its options if not specified, and how to set the number
+of OpenMP threads via the OMP_NUM_THREADS environment variable if
+desired.
Examples (see documentation for your MPI/Machine for differences in
launching MPI applications):
@@ -390,19 +390,18 @@ lj/cut or when using LRT mode on processors supporting AVX-512.
Not all styles are supported in the USER-INTEL package. You can mix
the USER-INTEL package with styles from the "OPT"_Speed_opt.html
-package or the "USER-OMP package"_Speed_omp.html. Of course,
-this requires that these packages were installed at build time. This
-can performed automatically by using "-sf hybrid intel opt" or
-"-sf hybrid intel omp" command-line options. Alternatively, the "opt"
-and "omp" suffixes can be appended manually in the input script. For
-the latter, the "package omp"_package.html command must be in the
-input script or the "-pk omp Nt" "command-line
-switch"_Section_start.html#start_6 must be used where Nt is the
-number of OpenMP threads. The number of OpenMP threads should not be
-set differently for the different packages. Note that the "suffix
-hybrid intel omp"_suffix.html command can also be used within the
-input script to automatically append the "omp" suffix to styles when
-USER-INTEL styles are not available.
+package or the "USER-OMP package"_Speed_omp.html. Of course, this
+requires that these packages were installed at build time. This can
+performed automatically by using "-sf hybrid intel opt" or "-sf hybrid
+intel omp" command-line options. Alternatively, the "opt" and "omp"
+suffixes can be appended manually in the input script. For the latter,
+the "package omp"_package.html command must be in the input script or
+the "-pk omp Nt" "command-line switch"_Run_options.html must be used
+where Nt is the number of OpenMP threads. The number of OpenMP threads
+should not be set differently for the different packages. Note that
+the "suffix hybrid intel omp"_suffix.html command can also be used
+within the input script to automatically append the "omp" suffix to
+styles when USER-INTEL styles are not available.
NOTE: For simulations on higher node counts, add "processors * * *
grid numa"_processors.html" to the beginning of the input script for
@@ -496,8 +495,8 @@ sorting"_atom_modify.html is changed to 1 so that the per-atom data is
effectively sorted at every rebuild of the neighbor lists. All the
available coprocessor threads on each Phi will be divided among MPI
tasks, unless the {tptask} option of the "-pk intel" "command-line
-switch"_Section_start.html#start_6 is used to limit the coprocessor
-threads per MPI task.
+switch"_Run_options.html is used to limit the coprocessor threads per
+MPI task.
[Restrictions:]
diff --git a/doc/src/Speed_kokkos.txt b/doc/src/Speed_kokkos.txt
index 14f4103aed..f26b2df7e1 100644
--- a/doc/src/Speed_kokkos.txt
+++ b/doc/src/Speed_kokkos.txt
@@ -142,12 +142,11 @@ mpirun -np 2 lmp_kokkos_omp -k on t 8 -sf kk -in in.lj # 1 node, 2 MPI
mpirun -np 32 -ppn 4 lmp_kokkos_omp -k on t 4 -sf kk -in in.lj # 8 nodes, 4 MPI tasks/node, 4 threads/task :pre
To run using the KOKKOS package, use the "-k on", "-sf kk" and "-pk
-kokkos" "command-line switches"_Section_start.html#start_7 in your
-mpirun command. You must use the "-k on" "command-line
-switch"_Section_start.html#start_7 to enable the KOKKOS package. It
-takes additional arguments for hardware settings appropriate to your
-system. Those arguments are "documented
-here"_Section_start.html#start_7. For OpenMP use:
+kokkos" "command-line switches"_Run_options.html in your mpirun
+command. You must use the "-k on" "command-line
+switch"_Run_options.html to enable the KOKKOS package. It takes
+additional arguments for hardware settings appropriate to your system.
+For OpenMP use:
-k on t Nt :pre
@@ -162,11 +161,11 @@ command (with no additional arguments) which sets various KOKKOS
options to default values, as discussed on the "package"_package.html
command doc page.
-The "-sf kk" "command-line switch"_Section_start.html#start_7 will
-automatically append the "/kk" suffix to styles that support it. In
-this manner no modification to the input script is
-needed. Alternatively, one can run with the KOKKOS package by editing
-the input script as described below.
+The "-sf kk" "command-line switch"_Run_options.html will automatically
+append the "/kk" suffix to styles that support it. In this manner no
+modification to the input script is needed. Alternatively, one can run
+with the KOKKOS package by editing the input script as described
+below.
NOTE: The default for the "package kokkos"_package.html command is to
use "full" neighbor lists and set the Newton flag to "off" for both
@@ -174,10 +173,10 @@ pairwise and bonded interactions. However, when running on CPUs, it
will typically be faster to use "half" neighbor lists and set the
Newton flag to "on", just as is the case for non-accelerated pair
styles. It can also be faster to use non-threaded communication. Use
-the "-pk kokkos" "command-line switch"_Section_start.html#start_7 to
-change the default "package kokkos"_package.html options. See its doc
-page for details and default settings. Experimenting with its options
-can provide a speed-up for specific calculations. For example:
+the "-pk kokkos" "command-line switch"_Run_options.html to change the
+default "package kokkos"_package.html options. See its doc page for
+details and default settings. Experimenting with its options can
+provide a speed-up for specific calculations. For example:
mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk -pk kokkos newton on neigh half comm no -in in.lj # Newton on, Half neighbor list, non-threaded comm :pre
@@ -237,10 +236,10 @@ pairwise and bonded interactions. When running on KNL, this will
typically be best for pair-wise potentials. For manybody potentials,
using "half" neighbor lists and setting the Newton flag to "on" may be
faster. It can also be faster to use non-threaded communication. Use
-the "-pk kokkos" "command-line switch"_Section_start.html#start_7 to
-change the default "package kokkos"_package.html options. See its doc
-page for details and default settings. Experimenting with its options
-can provide a speed-up for specific calculations. For example:
+the "-pk kokkos" "command-line switch"_Run_options.html to change the
+default "package kokkos"_package.html options. See its doc page for
+details and default settings. Experimenting with its options can
+provide a speed-up for specific calculations. For example:
mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos comm no -in in.lj # Newton off, full neighbor list, non-threaded comm
mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos newton on neigh half comm no -in in.reax # Newton on, half neighbor list, non-threaded comm :pre
@@ -255,16 +254,15 @@ supports.
[Running on GPUs:]
-Use the "-k" "command-line switch"_Section_start.html#start_7 to
-specify the number of GPUs per node. Typically the -np setting of the
-mpirun command should set the number of MPI tasks/node to be equal to
-the # of physical GPUs on the node. You can assign multiple MPI tasks
-to the same GPU with the KOKKOS package, but this is usually only
-faster if significant portions of the input script have not been
-ported to use Kokkos. Using CUDA MPS is recommended in this
-scenario. As above for multi-core CPUs (and no GPU), if N is the
-number of physical cores/node, then the number of MPI tasks/node
-should not exceed N.
+Use the "-k" "command-line switch"_Run_options.html to specify the
+number of GPUs per node. Typically the -np setting of the mpirun
+command should set the number of MPI tasks/node to be equal to the #
+of physical GPUs on the node. You can assign multiple MPI tasks to
+the same GPU with the KOKKOS package, but this is usually only faster
+if significant portions of the input script have not been ported to
+use Kokkos. Using CUDA MPS is recommended in this scenario. As above
+for multi-core CPUs (and no GPU), if N is the number of physical
+cores/node, then the number of MPI tasks/node should not exceed N.
-k on g Ng :pre
@@ -281,10 +279,10 @@ When running on Maxwell or Kepler GPUs, this will typically be
best. For Pascal GPUs, using "half" neighbor lists and setting the
Newton flag to "on" may be faster. For many pair styles, setting the
neighbor binsize equal to the ghost atom cutoff will give speedup.
-Use the "-pk kokkos" "command-line switch"_Section_start.html#start_7
-to change the default "package kokkos"_package.html options. See its
-doc page for details and default settings. Experimenting with its
-options can provide a speed-up for specific calculations. For example:
+Use the "-pk kokkos" "command-line switch"_Run_options.html to change
+the default "package kokkos"_package.html options. See its doc page
+for details and default settings. Experimenting with its options can
+provide a speed-up for specific calculations. For example:
mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos binsize 2.8 -in in.lj # Set binsize = neighbor ghost cutoff
mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos newton on neigh half binsize 2.8 -in in.lj # Newton on, half neighborlist, set binsize = neighbor ghost cutoff :pre
@@ -315,10 +313,9 @@ kk"_suffix.html commands to your input script.
The discussion above for building LAMMPS with the KOKKOS package, the
mpirun/mpiexec command, and setting appropriate thread are the same.
-You must still use the "-k on" "command-line
-switch"_Section_start.html#start_7 to enable the KOKKOS package, and
-specify its additional arguments for hardware options appropriate to
-your system, as documented above.
+You must still use the "-k on" "command-line switch"_Run_options.html
+to enable the KOKKOS package, and specify its additional arguments for
+hardware options appropriate to your system, as documented above.
You can use the "suffix kk"_suffix.html command, or you can explicitly add a
"kk" suffix to individual styles in your input script, e.g.
@@ -327,7 +324,7 @@ pair_style lj/cut/kk 2.5 :pre
You only need to use the "package kokkos"_package.html command if you
wish to change any of its option defaults, as set by the "-k on"
-"command-line switch"_Section_start.html#start_7.
+"command-line switch"_Run_options.html.
[Using OpenMP threading and CUDA together (experimental):]
diff --git a/doc/src/Speed_measure.txt b/doc/src/Speed_measure.txt
index 78dc220088..647ff71e36 100644
--- a/doc/src/Speed_measure.txt
+++ b/doc/src/Speed_measure.txt
@@ -21,8 +21,8 @@ typically no need to run for 1000s of timesteps to get accurate
timings; you can simply extrapolate from short runs.
For the set of runs, look at the timing data printed to the screen and
-log file at the end of each LAMMPS run. "This
-section"_Section_start.html#start_7 of the manual has an overview.
+log file at the end of each LAMMPS run. The
+"Run_output"_Run_output.html doc page gives an overview.
Running on one (or a few processors) should give a good estimate of
the serial performance and what portions of the timestep are taking
diff --git a/doc/src/Speed_omp.txt b/doc/src/Speed_omp.txt
index bcfc406902..e788d3300c 100644
--- a/doc/src/Speed_omp.txt
+++ b/doc/src/Speed_omp.txt
@@ -57,19 +57,18 @@ threads/task should not exceed the physical number of cores (on a
node), otherwise performance will suffer.
As in the lines above, use the "-sf omp" "command-line
-switch"_Section_start.html#start_6, which will automatically append
-"omp" to styles that support it. The "-sf omp" switch also issues a
-default "package omp 0"_package.html command, which will set the
-number of threads per MPI task via the OMP_NUM_THREADS environment
-variable.
+switch"_Run_options.html, which will automatically append "omp" to
+styles that support it. The "-sf omp" switch also issues a default
+"package omp 0"_package.html command, which will set the number of
+threads per MPI task via the OMP_NUM_THREADS environment variable.
You can also use the "-pk omp Nt" "command-line
-switch"_Section_start.html#start_6, to explicitly set Nt = # of OpenMP
-threads per MPI task to use, as well as additional options. Its
-syntax is the same as the "package omp"_package.html command whose doc
-page gives details, including the default values used if it is not
-specified. It also gives more details on how to set the number of
-threads via the OMP_NUM_THREADS environment variable.
+switch"_Run_options.html, to explicitly set Nt = # of OpenMP threads
+per MPI task to use, as well as additional options. Its syntax is the
+same as the "package omp"_package.html command whose doc page gives
+details, including the default values used if it is not specified. It
+also gives more details on how to set the number of threads via the
+OMP_NUM_THREADS environment variable.
[Or run with the USER-OMP package by editing an input script:]
diff --git a/doc/src/Speed_opt.txt b/doc/src/Speed_opt.txt
index 676a5d8418..bb0bcd255c 100644
--- a/doc/src/Speed_opt.txt
+++ b/doc/src/Speed_opt.txt
@@ -41,8 +41,8 @@ the CCFLAGS setting in your Makefile.machine must include "-restrict".
[Run with the OPT package from the command line:]
As in the lines above, use the "-sf opt" "command-line
-switch"_Section_start.html#start_6, which will automatically append
-"opt" to styles that support it.
+switch"_Run_options.html, which will automatically append "opt" to
+styles that support it.
[Or run with the OPT package by editing an input script:]
diff --git a/doc/src/Speed_packages.txt b/doc/src/Speed_packages.txt
index f463ed91b8..6c837885cd 100644
--- a/doc/src/Speed_packages.txt
+++ b/doc/src/Speed_packages.txt
@@ -93,11 +93,11 @@ re-build LAMMPS |
make machine |
prepare and test a regular LAMMPS simulation |
lmp_machine -in in.script; mpirun -np 32 lmp_machine -in in.script |
-enable specific accelerator support via '-k on' "command-line switch"_Section_start.html#start_6, |
+enable specific accelerator support via '-k on' "command-line switch"_Run_options.html, |
only needed for KOKKOS package |
-set any needed options for the package via "-pk" "command-line switch"_Section_start.html#start_6 or "package"_package.html command, |
+set any needed options for the package via "-pk" "command-line switch"_Run_options.html or "package"_package.html command, |
only if defaults need to be changed |
-use accelerated styles in your input via "-sf" "command-line switch"_Section_start.html#start_6 or "suffix"_suffix.html command | lmp_machine -in in.script -sf gpu
+use accelerated styles in your input via "-sf" "command-line switch"_Run_options.html or "suffix"_suffix.html command | lmp_machine -in in.script -sf gpu
:tb(c=2,s=|)
Note that the first 4 steps can be done as a single command with
diff --git a/doc/src/angle_charmm.txt b/doc/src/angle_charmm.txt
index f72f086234..8b0e298a43 100644
--- a/doc/src/angle_charmm.txt
+++ b/doc/src/angle_charmm.txt
@@ -57,13 +57,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -73,8 +73,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+MOLECULE package. See the "Build package"_Build_package.html doc page
+for more info.
[Related commands:]
diff --git a/doc/src/angle_class2.txt b/doc/src/angle_class2.txt
index 3e5445d3a3..fa5e29582c 100644
--- a/doc/src/angle_class2.txt
+++ b/doc/src/angle_class2.txt
@@ -89,13 +89,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -123,8 +123,8 @@ The bond-bond and bond-angle terms remain unchanged.
This angle style can only be used if LAMMPS was built with the CLASS2
package. For the {class2/p6} style LAMMPS needs to be built with the
-USER-MOFFF package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER-MOFFF package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/angle_cosine.txt b/doc/src/angle_cosine.txt
index 5a1fe91c83..80cf8ae8f1 100644
--- a/doc/src/angle_cosine.txt
+++ b/doc/src/angle_cosine.txt
@@ -44,13 +44,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -60,8 +60,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+MOLECULE package. See the "Build package"_Build_package.html doc page
+for more info.
[Related commands:]
diff --git a/doc/src/angle_cosine_buck6d.txt b/doc/src/angle_cosine_buck6d.txt
index 63a451b763..54709c1370 100644
--- a/doc/src/angle_cosine_buck6d.txt
+++ b/doc/src/angle_cosine_buck6d.txt
@@ -55,8 +55,8 @@ the "special_bonds"_special_bonds.html 1-3 interactions to be weighted
"special_bonds"_special_bonds.html 0.0 weighting of 1-3 interactions.
This angle style can only be used if LAMMPS was built with the
-USER-MOFFF package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+USER-MOFFF package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/angle_cosine_delta.txt b/doc/src/angle_cosine_delta.txt
index b6ac0ed818..1532e39b31 100644
--- a/doc/src/angle_cosine_delta.txt
+++ b/doc/src/angle_cosine_delta.txt
@@ -49,13 +49,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -65,8 +65,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+MOLECULE package. See the "Build package"_Build_package.html doc page
+for more info.
[Related commands:]
diff --git a/doc/src/angle_cosine_periodic.txt b/doc/src/angle_cosine_periodic.txt
index c5b184e0b4..039144797f 100644
--- a/doc/src/angle_cosine_periodic.txt
+++ b/doc/src/angle_cosine_periodic.txt
@@ -57,13 +57,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -73,8 +73,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+MOLECULE package. See the "Build package"_Build_package.html doc page
+for more info.
[Related commands:]
diff --git a/doc/src/angle_cosine_shift.txt b/doc/src/angle_cosine_shift.txt
index 90ac61fe23..8e23e1b49f 100644
--- a/doc/src/angle_cosine_shift.txt
+++ b/doc/src/angle_cosine_shift.txt
@@ -40,20 +40,20 @@ theta (angle) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the "Speed packages"_Speed_packages.html doc
-page. The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
+They have been optimized to run faster, depending on
+your"_Build_package.html doc page kages"_Speed_packages.html doc page.
+The accelerated styles take the same arguments and should produce the
+same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -63,8 +63,7 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER-MISC package.
[Related commands:]
diff --git a/doc/src/angle_cosine_shift_exp.txt b/doc/src/angle_cosine_shift_exp.txt
index f1c4c93c42..3091e83885 100644
--- a/doc/src/angle_cosine_shift_exp.txt
+++ b/doc/src/angle_cosine_shift_exp.txt
@@ -59,13 +59,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -75,8 +75,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER-MISC package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/angle_cosine_squared.txt b/doc/src/angle_cosine_squared.txt
index ba5fd9d413..07fcb1ceb4 100644
--- a/doc/src/angle_cosine_squared.txt
+++ b/doc/src/angle_cosine_squared.txt
@@ -49,13 +49,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -65,8 +65,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+MOLECULE package. See the "Build package"_Build_package.html doc page
+for more info.
[Related commands:]
diff --git a/doc/src/angle_dipole.txt b/doc/src/angle_dipole.txt
index c001d9d920..cdb11972ec 100644
--- a/doc/src/angle_dipole.txt
+++ b/doc/src/angle_dipole.txt
@@ -77,13 +77,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -91,8 +91,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_2_3
-section for more info on packages.
+USER-MISC package. See the "Build package"_Build_package.html doc
+page for more info.
NOTE: In the "Angles" section of the data file, the atom ID 'j'
defining the direction of the dipole vector to restrain must come
diff --git a/doc/src/angle_fourier.txt b/doc/src/angle_fourier.txt
index e0e32c1eed..7dc9975793 100644
--- a/doc/src/angle_fourier.txt
+++ b/doc/src/angle_fourier.txt
@@ -45,13 +45,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -61,8 +61,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-USER_MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER_MISC package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/angle_fourier_simple.txt b/doc/src/angle_fourier_simple.txt
index 3c50536a2c..ae5d308353 100644
--- a/doc/src/angle_fourier_simple.txt
+++ b/doc/src/angle_fourier_simple.txt
@@ -44,13 +44,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -60,8 +60,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-USER_MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER_MISC package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/angle_harmonic.txt b/doc/src/angle_harmonic.txt
index 76c7a491e8..b632f68478 100644
--- a/doc/src/angle_harmonic.txt
+++ b/doc/src/angle_harmonic.txt
@@ -51,13 +51,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -67,8 +67,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+MOLECULE package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/angle_hybrid.txt b/doc/src/angle_hybrid.txt
index 2646903421..0046c161be 100644
--- a/doc/src/angle_hybrid.txt
+++ b/doc/src/angle_hybrid.txt
@@ -76,8 +76,8 @@ for specific angle types.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+MOLECULE package. See the "Build package"_Build_package.html doc page
+for more info.
Unlike other angle styles, the hybrid angle style does not store angle
coefficient info for individual sub-styles in a "binary restart
diff --git a/doc/src/angle_quartic.txt b/doc/src/angle_quartic.txt
index 294be330b1..b20a06eb8d 100644
--- a/doc/src/angle_quartic.txt
+++ b/doc/src/angle_quartic.txt
@@ -51,13 +51,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -67,8 +67,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-USER_MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER_MISC package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/angle_sdk.txt b/doc/src/angle_sdk.txt
index 9c5630ef3a..4de1a6755d 100644
--- a/doc/src/angle_sdk.txt
+++ b/doc/src/angle_sdk.txt
@@ -46,8 +46,8 @@ from the pair_style.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-USER-CGSDK package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+USER-CGSDK package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/angle_style.txt b/doc/src/angle_style.txt
index 63295faf26..756cfc0c60 100644
--- a/doc/src/angle_style.txt
+++ b/doc/src/angle_style.txt
@@ -83,10 +83,9 @@ Angle styles can only be set for atom_styles that allow angles to be
defined.
Most angle styles are part of the MOLECULE package. They are only
-enabled if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
-The doc pages for individual bond potentials tell if it is part of a
-package.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info. The doc pages for
+individual bond potentials tell if it is part of a package.
[Related commands:]
diff --git a/doc/src/angle_table.txt b/doc/src/angle_table.txt
index 31ab532be1..6b9187e512 100644
--- a/doc/src/angle_table.txt
+++ b/doc/src/angle_table.txt
@@ -130,13 +130,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -146,8 +146,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+MOLECULE package. See the "Build package"_Build_package.html doc page
+for more info.
[Related commands:]
diff --git a/doc/src/atom_modify.txt b/doc/src/atom_modify.txt
index c882d1b0ba..4b4ac3862d 100644
--- a/doc/src/atom_modify.txt
+++ b/doc/src/atom_modify.txt
@@ -58,9 +58,9 @@ simulation so large that IDs cannot be uniquely assigned. For a
default LAMMPS build this limit is 2^31 or about 2 billion atoms.
However, even in this case, you can use 64-bit atom IDs, allowing 2^63
or about 9e18 atoms, if you build LAMMPS with the - DLAMMPS_BIGBIG
-switch. This is described in "Section 2.2"_Section_start.html#start_2
-of the manual. If atom IDs are not used, they must be specified as 0
-for all atoms, e.g. in a data or restart file.
+switch. This is described on the "Build_settings"_Build_settings.html
+doc page. If atom IDs are not used, they must be specified as 0 for
+all atoms, e.g. in a data or restart file.
The {map} keyword determines how atoms with specific IDs are found
when required. An example are the bond (angle, etc) methods which
diff --git a/doc/src/atom_style.txt b/doc/src/atom_style.txt
index abf05885a3..db2e285dc4 100644
--- a/doc/src/atom_style.txt
+++ b/doc/src/atom_style.txt
@@ -272,13 +272,13 @@ USER-INTEL, USER-OMP, and OPT packages do not use accelerated atom
styles.
The accelerated styles are part of the KOKKOS package. They are only
-enabled if LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+enabled if LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -289,8 +289,8 @@ This command cannot be used after the simulation box is defined by a
"read_data"_read_data.html or "create_box"_create_box.html command.
Many of the styles listed above are only enabled if LAMMPS was built
-with a specific package, as listed below. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+with a specific package, as listed below. See the "Build
+package"_Build_package.html doc page for more info.
The {angle}, {bond}, {full}, {molecular}, and {template} styles are
part of the MOLECULE package.
diff --git a/doc/src/balance.txt b/doc/src/balance.txt
index 06c4eca491..26e146d89b 100644
--- a/doc/src/balance.txt
+++ b/doc/src/balance.txt
@@ -394,11 +394,11 @@ weights. It assigns the same weight to each particle owned by a
processor based on the total computational time spent by that
processor. See details below on what time window is used. It uses
the same timing information as is used for the "MPI task timing
-breakdown"_Section_start.html#start_7, namely, for sections {Pair},
-{Bond}, {Kspace}, and {Neigh}. The time spent in those portions of
-the timestep are measured for each MPI rank, summed, then divided by
-the number of particles owned by that processor. I.e. the weight is
-an effective CPU time/particle averaged over the particles on that
+breakdown"_Run_output.html, namely, for sections {Pair}, {Bond},
+{Kspace}, and {Neigh}. The time spent in those portions of the
+timestep are measured for each MPI rank, summed, then divided by the
+number of particles owned by that processor. I.e. the weight is an
+effective CPU time/particle averaged over the particles on that
processor.
The {factor} setting is applied as an overall scale factor to the
diff --git a/doc/src/bond_class2.txt b/doc/src/bond_class2.txt
index 3d8d5007ba..4390e3613c 100644
--- a/doc/src/bond_class2.txt
+++ b/doc/src/bond_class2.txt
@@ -50,13 +50,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -66,8 +66,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This bond style can only be used if LAMMPS was built with the CLASS2
-package. See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info on packages.
+package. See the "Build package"_Build_package.html doc page for more
+info.
[Related commands:]
diff --git a/doc/src/bond_fene.txt b/doc/src/bond_fene.txt
index e16307a710..9ec4017d00 100644
--- a/doc/src/bond_fene.txt
+++ b/doc/src/bond_fene.txt
@@ -53,13 +53,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -68,9 +68,9 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
-This bond style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+This bond style can only be used if LAMMPS was built with the MOLECULE
+package. See the "Build package"_Build_package.html doc page for more
+info.
You typically should specify "special_bonds fene"_special_bonds.html
or "special_bonds lj/coul 0 1 1"_special_bonds.html to use this bond
diff --git a/doc/src/bond_fene_expand.txt b/doc/src/bond_fene_expand.txt
index 8edd325885..4d7d2d5438 100644
--- a/doc/src/bond_fene_expand.txt
+++ b/doc/src/bond_fene_expand.txt
@@ -56,13 +56,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -71,9 +71,9 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
-This bond style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+This bond style can only be used if LAMMPS was built with the MOLECULE
+package. See the "Build package"_Build_package.html doc page for more
+info.
You typically should specify "special_bonds fene"_special_bonds.html
or "special_bonds lj/coul 0 1 1"_special_bonds.html to use this bond
diff --git a/doc/src/bond_gromos.txt b/doc/src/bond_gromos.txt
index 275036a421..e039e6c411 100644
--- a/doc/src/bond_gromos.txt
+++ b/doc/src/bond_gromos.txt
@@ -46,13 +46,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -61,9 +61,9 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
-This bond style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+This bond style can only be used if LAMMPS was built with the MOLECULE
+package. See the "Build package"_Build_package.html doc page for more
+info.
[Related commands:]
diff --git a/doc/src/bond_harmonic.txt b/doc/src/bond_harmonic.txt
index e4b2015fed..3afdf4ceba 100644
--- a/doc/src/bond_harmonic.txt
+++ b/doc/src/bond_harmonic.txt
@@ -48,13 +48,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -63,9 +63,9 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
-This bond style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+This bond style can only be used if LAMMPS was built with the MOLECULE
+package. See the "Build package"_Build_package.html doc page for more
+info.
[Related commands:]
diff --git a/doc/src/bond_harmonic_shift.txt b/doc/src/bond_harmonic_shift.txt
index b6dc18a5fd..23d3dcb5d5 100644
--- a/doc/src/bond_harmonic_shift.txt
+++ b/doc/src/bond_harmonic_shift.txt
@@ -49,13 +49,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -65,8 +65,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This bond style can only be used if LAMMPS was built with the
-USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER-MISC package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/bond_harmonic_shift_cut.txt b/doc/src/bond_harmonic_shift_cut.txt
index b3054437d8..13ccb5843b 100644
--- a/doc/src/bond_harmonic_shift_cut.txt
+++ b/doc/src/bond_harmonic_shift_cut.txt
@@ -49,13 +49,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -65,8 +65,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This bond style can only be used if LAMMPS was built with the
-USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER-MISC package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/bond_hybrid.txt b/doc/src/bond_hybrid.txt
index 140fb72378..0996f72ce3 100644
--- a/doc/src/bond_hybrid.txt
+++ b/doc/src/bond_hybrid.txt
@@ -58,9 +58,9 @@ bond types.
[Restrictions:]
-This bond style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+This bond style can only be used if LAMMPS was built with the MOLECULE
+package. See the "Build package"_Build_package.html doc page for more
+info.
Unlike other bond styles, the hybrid bond style does not store bond
coefficient info for individual sub-styles in a "binary restart
diff --git a/doc/src/bond_morse.txt b/doc/src/bond_morse.txt
index 9b64e8c5c1..60fd16e17a 100644
--- a/doc/src/bond_morse.txt
+++ b/doc/src/bond_morse.txt
@@ -47,13 +47,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -62,9 +62,9 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
-This bond style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+This bond style can only be used if LAMMPS was built with the MOLECULE
+package. See the "Build package"_Build_package.html doc page for more
+info.
[Related commands:]
diff --git a/doc/src/bond_nonlinear.txt b/doc/src/bond_nonlinear.txt
index 08109bc699..af51383213 100644
--- a/doc/src/bond_nonlinear.txt
+++ b/doc/src/bond_nonlinear.txt
@@ -47,13 +47,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -62,9 +62,9 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
-This bond style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+This bond style can only be used if LAMMPS was built with the MOLECULE
+package. See the "Build package"_Build_package.html doc page for more
+info.
[Related commands:]
diff --git a/doc/src/bond_oxdna.txt b/doc/src/bond_oxdna.txt
index a0e14a123a..1944f7027a 100644
--- a/doc/src/bond_oxdna.txt
+++ b/doc/src/bond_oxdna.txt
@@ -62,8 +62,8 @@ The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf.
[Restrictions:]
This bond style can only be used if LAMMPS was built with the
-USER-CGDNA package and the MOLECULE and ASPHERE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+USER-CGDNA package and the MOLECULE and ASPHERE package. See the
+"Build package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/bond_quartic.txt b/doc/src/bond_quartic.txt
index 87a21eff02..b7b1ee4ce6 100644
--- a/doc/src/bond_quartic.txt
+++ b/doc/src/bond_quartic.txt
@@ -82,13 +82,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -97,9 +97,9 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
-This bond style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+This bond style can only be used if LAMMPS was built with the MOLECULE
+package. See the "Build package"_Build_package.html doc page for more
+info.
The {quartic} style requires that "special_bonds"_special_bonds.html
parameters be set to 1,1,1. Three- and four-body interactions (angle,
diff --git a/doc/src/bond_style.txt b/doc/src/bond_style.txt
index 41fa1cabb2..22fae3e346 100644
--- a/doc/src/bond_style.txt
+++ b/doc/src/bond_style.txt
@@ -90,10 +90,9 @@ Bond styles can only be set for atom styles that allow bonds to be
defined.
Most bond styles are part of the MOLECULE package. They are only
-enabled if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
-The doc pages for individual bond potentials tell if it is part of a
-package.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info. The doc pages for
+individual bond potentials tell if it is part of a package.
[Related commands:]
diff --git a/doc/src/bond_table.txt b/doc/src/bond_table.txt
index e53cbdfa9f..fbf6eb5815 100644
--- a/doc/src/bond_table.txt
+++ b/doc/src/bond_table.txt
@@ -127,13 +127,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -142,9 +142,9 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
-This bond style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+This bond style can only be used if LAMMPS was built with the MOLECULE
+package. See the "Build package"_Build_package.html doc page for more
+info.
[Related commands:]
diff --git a/doc/src/compute_ackland_atom.txt b/doc/src/compute_ackland_atom.txt
index 485c191313..cda4a36b34 100644
--- a/doc/src/compute_ackland_atom.txt
+++ b/doc/src/compute_ackland_atom.txt
@@ -66,8 +66,8 @@ LAMMPS output options.
[Restrictions:]
This compute is part of the USER-MISC package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
The per-atom vector values will be unitless since they are the
integers defined above.
diff --git a/doc/src/compute_basal_atom.txt b/doc/src/compute_basal_atom.txt
index 067a020c35..5c28b8e378 100644
--- a/doc/src/compute_basal_atom.txt
+++ b/doc/src/compute_basal_atom.txt
@@ -55,8 +55,8 @@ components of a unit vector.
[Restrictions:]
This compute is part of the USER-MISC package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
The output of this compute will be meaningless unless the atoms are on
(or near) hcp lattice sites, since the calculation assumes a
diff --git a/doc/src/compute_cnp_atom.txt b/doc/src/compute_cnp_atom.txt
index 44a77d23ca..95dd59089f 100644
--- a/doc/src/compute_cnp_atom.txt
+++ b/doc/src/compute_cnp_atom.txt
@@ -95,8 +95,8 @@ FCC dislocation core ~ 11 :pre
[Restrictions:]
This compute is part of the USER-MISC package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_damage_atom.txt b/doc/src/compute_damage_atom.txt
index 74939e2280..2594dfe356 100644
--- a/doc/src/compute_damage_atom.txt
+++ b/doc/src/compute_damage_atom.txt
@@ -52,8 +52,8 @@ The per-atom vector values are unitless numbers (damage) >= 0.0.
[Restrictions:]
This compute is part of the PERI package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_dilatation_atom.txt b/doc/src/compute_dilatation_atom.txt
index 498110cf99..292638bdf5 100644
--- a/doc/src/compute_dilatation_atom.txt
+++ b/doc/src/compute_dilatation_atom.txt
@@ -56,8 +56,8 @@ The per-atom vector values are unitless numbers (theta) >= 0.0.
[Restrictions:]
This compute is part of the PERI package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_dpd.txt b/doc/src/compute_dpd.txt
index 1721456e35..eccffee9b8 100644
--- a/doc/src/compute_dpd.txt
+++ b/doc/src/compute_dpd.txt
@@ -49,8 +49,8 @@ The vector values will be in energy and temperature "units"_units.html.
[Restrictions:]
This command is part of the USER-DPD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This command also requires use of the "atom_style dpd"_atom_style.html
command.
diff --git a/doc/src/compute_dpd_atom.txt b/doc/src/compute_dpd_atom.txt
index 8e502d4a60..2f9b4098cf 100644
--- a/doc/src/compute_dpd_atom.txt
+++ b/doc/src/compute_dpd_atom.txt
@@ -45,8 +45,8 @@ and temperature (dpdTheta) "units"_units.html.
[Restrictions:]
This command is part of the USER-DPD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This command also requires use of the "atom_style dpd"_atom_style.html
command.
diff --git a/doc/src/compute_edpd_temp_atom.txt b/doc/src/compute_edpd_temp_atom.txt
index f33398e03d..f3c1418d44 100644
--- a/doc/src/compute_edpd_temp_atom.txt
+++ b/doc/src/compute_edpd_temp_atom.txt
@@ -41,8 +41,8 @@ The per-atom vector values will be in temperature "units"_units.html.
[Restrictions:]
This compute is part of the USER-MESO package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_entropy_atom.txt b/doc/src/compute_entropy_atom.txt
index 9c45fd2870..b3891841b8 100644
--- a/doc/src/compute_entropy_atom.txt
+++ b/doc/src/compute_entropy_atom.txt
@@ -109,8 +109,8 @@ ordered environments.
[Restrictions:]
This compute is part of the USER-MISC package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_erotate_rigid.txt b/doc/src/compute_erotate_rigid.txt
index 5b9077870e..fa433c1c97 100644
--- a/doc/src/compute_erotate_rigid.txt
+++ b/doc/src/compute_erotate_rigid.txt
@@ -51,8 +51,8 @@ scalar value will be in energy "units"_units.html.
[Restrictions:]
This compute is part of the RIGID package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_event_displace.txt b/doc/src/compute_event_displace.txt
index 561ded35c0..a36cf2c9c4 100644
--- a/doc/src/compute_event_displace.txt
+++ b/doc/src/compute_event_displace.txt
@@ -52,8 +52,8 @@ scalar value will be a 0 or 1 as explained above.
[Restrictions:]
This command can only be used if LAMMPS was built with the REPLICA
-package. See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info on packages.
+package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/compute_fep.txt b/doc/src/compute_fep.txt
index 8b4a92e16e..5b3a6915dd 100644
--- a/doc/src/compute_fep.txt
+++ b/doc/src/compute_fep.txt
@@ -230,8 +230,8 @@ The values calculated by this compute are "extensive".
[Restrictions:]
This compute is distributed as the USER-FEP package. It is only
-enabled if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_ke_atom_eff.txt b/doc/src/compute_ke_atom_eff.txt
index f665f35055..29905f81d6 100644
--- a/doc/src/compute_ke_atom_eff.txt
+++ b/doc/src/compute_ke_atom_eff.txt
@@ -66,8 +66,8 @@ The per-atom vector values will be in energy "units"_units.html.
[Restrictions:]
This compute is part of the USER-EFF package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_ke_eff.txt b/doc/src/compute_ke_eff.txt
index d6d7fdb10f..fa2c51a032 100644
--- a/doc/src/compute_ke_eff.txt
+++ b/doc/src/compute_ke_eff.txt
@@ -70,8 +70,8 @@ scalar value will be in energy "units"_units.html.
[Restrictions:]
This compute is part of the USER-EFF package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:] none
diff --git a/doc/src/compute_ke_rigid.txt b/doc/src/compute_ke_rigid.txt
index 45ba2673b0..ad6baf567f 100644
--- a/doc/src/compute_ke_rigid.txt
+++ b/doc/src/compute_ke_rigid.txt
@@ -50,8 +50,8 @@ scalar value will be in energy "units"_units.html.
[Restrictions:]
This compute is part of the RIGID package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_meso_e_atom.txt b/doc/src/compute_meso_e_atom.txt
index 9a9c7fae11..0f0cfda2d1 100644
--- a/doc/src/compute_meso_e_atom.txt
+++ b/doc/src/compute_meso_e_atom.txt
@@ -46,8 +46,8 @@ The per-atom vector values will be in energy "units"_units.html.
[Restrictions:]
This compute is part of the USER-SPH package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_meso_rho_atom.txt b/doc/src/compute_meso_rho_atom.txt
index 30b1142b6c..5127ad2c48 100644
--- a/doc/src/compute_meso_rho_atom.txt
+++ b/doc/src/compute_meso_rho_atom.txt
@@ -46,8 +46,8 @@ The per-atom vector values will be in mass/volume "units"_units.html.
[Restrictions:]
This compute is part of the USER-SPH package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_meso_t_atom.txt b/doc/src/compute_meso_t_atom.txt
index ab92f05018..f4ab869ec2 100644
--- a/doc/src/compute_meso_t_atom.txt
+++ b/doc/src/compute_meso_t_atom.txt
@@ -48,8 +48,8 @@ The per-atom vector values will be in temperature "units"_units.html.
[Restrictions:]
This compute is part of the USER-SPH package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_msd_nongauss.txt b/doc/src/compute_msd_nongauss.txt
index 814159121d..c6e89a1061 100644
--- a/doc/src/compute_msd_nongauss.txt
+++ b/doc/src/compute_msd_nongauss.txt
@@ -66,9 +66,9 @@ the 3rd is dimensionless.
[Restrictions:]
-This compute is part of the MISC package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+This compute is part of the MISC package. It is only enabled if
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_plasticity_atom.txt b/doc/src/compute_plasticity_atom.txt
index 50a51d9937..b82179712a 100644
--- a/doc/src/compute_plasticity_atom.txt
+++ b/doc/src/compute_plasticity_atom.txt
@@ -50,8 +50,8 @@ The per-atom vector values are unitless numbers (lambda) >= 0.0.
[Restrictions:]
This compute is part of the PERI package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_pressure.txt b/doc/src/compute_pressure.txt
index dea0a7f05b..6acbaf7d3d 100644
--- a/doc/src/compute_pressure.txt
+++ b/doc/src/compute_pressure.txt
@@ -111,13 +111,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/compute_pressure_uef.txt b/doc/src/compute_pressure_uef.txt
index 61cc85ad80..c4c0fc405f 100644
--- a/doc/src/compute_pressure_uef.txt
+++ b/doc/src/compute_pressure_uef.txt
@@ -38,9 +38,9 @@ The keywords and output information are documented in
[Restrictions:]
-This fix is part of the USER-UEF package. It is only enabled if
-LAMMPS was built with that package. See the
-"Making LAMMPS"_Section_start.html#start_3 section for more info.
+This fix is part of the USER-UEF package. It is only enabled if LAMMPS
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This command can only be used when "fix nvt/uef"_fix_nh_uef.html
or "fix npt/uef"_fix_nh_uef.html is active.
diff --git a/doc/src/compute_rigid_local.txt b/doc/src/compute_rigid_local.txt
index b5e6954ab9..9b829a70fc 100644
--- a/doc/src/compute_rigid_local.txt
+++ b/doc/src/compute_rigid_local.txt
@@ -175,8 +175,8 @@ inertiax,inertiay,inertiaz = mass*distance^2 units :ul
[Restrictions:]
This compute is part of the RIGID package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_saed.txt b/doc/src/compute_saed.txt
index 8c17a30fca..b27c36e318 100644
--- a/doc/src/compute_saed.txt
+++ b/doc/src/compute_saed.txt
@@ -152,8 +152,8 @@ All array values calculated by this compute are "intensive".
[Restrictions:]
This compute is part of the USER-DIFFRACTION package. It is only
-enabled if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
The compute_saed command does not work for triclinic cells.
diff --git a/doc/src/compute_smd_contact_radius.txt b/doc/src/compute_smd_contact_radius.txt
index cd13816047..4ab03e3738 100644
--- a/doc/src/compute_smd_contact_radius.txt
+++ b/doc/src/compute_smd_contact_radius.txt
@@ -45,8 +45,8 @@ The per-particle vector values will be in distance "units"_units.html.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_smd_damage.txt b/doc/src/compute_smd_damage.txt
index afabe23d7c..139fb3ec7b 100644
--- a/doc/src/compute_smd_damage.txt
+++ b/doc/src/compute_smd_damage.txt
@@ -38,8 +38,8 @@ The per-particle values are dimensionless an in the range of zero to one.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info.
+LAMMPS was built with that package. See the "Build
+
[Related commands:]
diff --git a/doc/src/compute_smd_hourglass_error.txt b/doc/src/compute_smd_hourglass_error.txt
index 13fd20a589..5bc3e3a2de 100644
--- a/doc/src/compute_smd_hourglass_error.txt
+++ b/doc/src/compute_smd_hourglass_error.txt
@@ -48,8 +48,8 @@ The per-particle vector values will are dimensionless. See
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This quantity will be computed only for particles which interact with
tlsph pair style.
diff --git a/doc/src/compute_smd_internal_energy.txt b/doc/src/compute_smd_internal_energy.txt
index 6585c3429f..b9d18ce933 100644
--- a/doc/src/compute_smd_internal_energy.txt
+++ b/doc/src/compute_smd_internal_energy.txt
@@ -39,10 +39,10 @@ The per-particle vector values will be given in "units"_units.html of energy.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info. This compute
-can only be used for particles which interact via the updated
-Lagrangian or total Lagrangian SPH pair styles.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info. This compute can
+only be used for particles which interact via the updated Lagrangian
+or total Lagrangian SPH pair styles.
[Related Commands:]
diff --git a/doc/src/compute_smd_plastic_strain.txt b/doc/src/compute_smd_plastic_strain.txt
index fb3c5c9138..d12be7222a 100644
--- a/doc/src/compute_smd_plastic_strain.txt
+++ b/doc/src/compute_smd_plastic_strain.txt
@@ -40,10 +40,10 @@ The per-particle values will be given dimensionless. See "units"_units.html.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info. This compute
-can only be used for particles which interact via the updated
-Lagrangian or total Lagrangian SPH pair styles.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info. This compute can
+only be used for particles which interact via the updated Lagrangian
+or total Lagrangian SPH pair styles.
[Related commands:]
diff --git a/doc/src/compute_smd_plastic_strain_rate.txt b/doc/src/compute_smd_plastic_strain_rate.txt
index b913ae9097..ffc009b2a7 100644
--- a/doc/src/compute_smd_plastic_strain_rate.txt
+++ b/doc/src/compute_smd_plastic_strain_rate.txt
@@ -40,10 +40,10 @@ The per-particle values will be given in "units"_units.html of one over time.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info. This compute
-can only be used for particles which interact via the updated
-Lagrangian or total Lagrangian SPH pair styles.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info. This compute can
+only be used for particles which interact via the updated Lagrangian
+or total Lagrangian SPH pair styles.
[Related commands:]
diff --git a/doc/src/compute_smd_rho.txt b/doc/src/compute_smd_rho.txt
index a1ee1d9c5b..31d7351c92 100644
--- a/doc/src/compute_smd_rho.txt
+++ b/doc/src/compute_smd_rho.txt
@@ -41,8 +41,8 @@ The per-particle values will be in "units"_units.html of mass over volume.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_smd_tlsph_defgrad.txt b/doc/src/compute_smd_tlsph_defgrad.txt
index 1663c84f65..a733a3d6a7 100644
--- a/doc/src/compute_smd_tlsph_defgrad.txt
+++ b/doc/src/compute_smd_tlsph_defgrad.txt
@@ -44,10 +44,10 @@ entry is the determinant of the deformation gradient.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info. TThis
-compute can only be used for particles which interact via the total
-Lagrangian SPH pair style.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info. TThis compute can
+only be used for particles which interact via the total Lagrangian SPH
+pair style.
[Related commands:]
diff --git a/doc/src/compute_smd_tlsph_dt.txt b/doc/src/compute_smd_tlsph_dt.txt
index c714f3266b..92f5923de0 100644
--- a/doc/src/compute_smd_tlsph_dt.txt
+++ b/doc/src/compute_smd_tlsph_dt.txt
@@ -45,8 +45,8 @@ The per-particle values will be given in "units"_units.html of time.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This compute can only be used for particles interacting with the
Total-Lagrangian SPH pair style.
diff --git a/doc/src/compute_smd_tlsph_num_neighs.txt b/doc/src/compute_smd_tlsph_num_neighs.txt
index af5b0741db..db977fe676 100644
--- a/doc/src/compute_smd_tlsph_num_neighs.txt
+++ b/doc/src/compute_smd_tlsph_num_neighs.txt
@@ -40,8 +40,8 @@ The per-particle values are dimensionless. See "units"_units.html.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This quantity will be computed only for particles which interact with
the Total-Lagrangian pair style.
diff --git a/doc/src/compute_smd_tlsph_shape.txt b/doc/src/compute_smd_tlsph_shape.txt
index 927cd7c7ae..9c17194ec1 100644
--- a/doc/src/compute_smd_tlsph_shape.txt
+++ b/doc/src/compute_smd_tlsph_shape.txt
@@ -47,8 +47,8 @@ particle relative to its initial state.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This quantity will be computed only for particles which interact with
the Total-Lagrangian SPH pair style.
diff --git a/doc/src/compute_smd_tlsph_strain.txt b/doc/src/compute_smd_tlsph_strain.txt
index 4536f26c8e..70f996e206 100644
--- a/doc/src/compute_smd_tlsph_strain.txt
+++ b/doc/src/compute_smd_tlsph_strain.txt
@@ -43,8 +43,8 @@ zz, xy, xz, yz components of the symmetric strain tensor.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This quantity will be computed only for particles which interact with
the Total-Lagrangian SPH pair style.
diff --git a/doc/src/compute_smd_tlsph_strain_rate.txt b/doc/src/compute_smd_tlsph_strain_rate.txt
index ae2883e4bb..e6d968c523 100644
--- a/doc/src/compute_smd_tlsph_strain_rate.txt
+++ b/doc/src/compute_smd_tlsph_strain_rate.txt
@@ -42,8 +42,8 @@ zz, xy, xz, yz components of the symmetric strain rate tensor.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This quantity will be computed only for particles which interact with
Total-Lagrangian SPH pair style.
diff --git a/doc/src/compute_smd_tlsph_stress.txt b/doc/src/compute_smd_tlsph_stress.txt
index 50d6b7f434..8340e88536 100644
--- a/doc/src/compute_smd_tlsph_stress.txt
+++ b/doc/src/compute_smd_tlsph_stress.txt
@@ -44,8 +44,8 @@ invariant of the stress tensor, i.e., the von Mises equivalent stress.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This quantity will be computed only for particles which interact with
the Total-Lagrangian SPH pair style.
diff --git a/doc/src/compute_smd_triangle_mesh_vertices.txt b/doc/src/compute_smd_triangle_mesh_vertices.txt
index 9e167924d1..cd1f8fdd9b 100644
--- a/doc/src/compute_smd_triangle_mesh_vertices.txt
+++ b/doc/src/compute_smd_triangle_mesh_vertices.txt
@@ -51,8 +51,8 @@ The values will be given in "units"_units.html of distance.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_smd_ulsph_num_neighs.txt b/doc/src/compute_smd_ulsph_num_neighs.txt
index 202b8f15e1..5157f17e57 100644
--- a/doc/src/compute_smd_ulsph_num_neighs.txt
+++ b/doc/src/compute_smd_ulsph_num_neighs.txt
@@ -40,10 +40,10 @@ The per-particle values will be given dimensionless, see "units"_units.html.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_2 section for more info. This compute
-can only be used for particles which interact with the updated
-Lagrangian SPH pair style.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info. This compute can
+only be used for particles which interact with the updated Lagrangian
+SPH pair style.
[Related commands:]
diff --git a/doc/src/compute_smd_ulsph_strain.txt b/doc/src/compute_smd_ulsph_strain.txt
index 76c47162a5..3dc6bd5249 100644
--- a/doc/src/compute_smd_ulsph_strain.txt
+++ b/doc/src/compute_smd_ulsph_strain.txt
@@ -43,10 +43,10 @@ The per-particle tensor values will be given dimensionless, see
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info. This compute
-can only be used for particles which interact with the updated
-Lagrangian SPH pair style.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info. This compute can
+only be used for particles which interact with the updated Lagrangian
+SPH pair style.
[Related commands:]
diff --git a/doc/src/compute_smd_ulsph_strain_rate.txt b/doc/src/compute_smd_ulsph_strain_rate.txt
index c851e767b3..1ade5ac2d5 100644
--- a/doc/src/compute_smd_ulsph_strain_rate.txt
+++ b/doc/src/compute_smd_ulsph_strain_rate.txt
@@ -43,10 +43,11 @@ zz, xy, xz, yz components of the symmetric strain rate tensor.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_2 section for more info. This compute
-can only be used for particles which interact with the updated
-Lagrangian SPH pair style.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
+
+This compute can only be used for particles which interact with the
+updated Lagrangian SPH pair style.
[Related commands:]
diff --git a/doc/src/compute_smd_ulsph_stress.txt b/doc/src/compute_smd_ulsph_stress.txt
index a5692b2412..ff53e777c5 100644
--- a/doc/src/compute_smd_ulsph_stress.txt
+++ b/doc/src/compute_smd_ulsph_stress.txt
@@ -43,10 +43,10 @@ stress tensor, i.e., the von Mises equivalent stress.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info. This compute
-can only be used for particles which interact with the updated
-Lagrangian SPH pair style.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info. This compute can
+only be used for particles which interact with the updated Lagrangian
+SPH pair style.
[Related commands:]
diff --git a/doc/src/compute_smd_vol.txt b/doc/src/compute_smd_vol.txt
index fc4871d6f3..0edd61f624 100644
--- a/doc/src/compute_smd_vol.txt
+++ b/doc/src/compute_smd_vol.txt
@@ -43,8 +43,8 @@ per-particle volumes of the group for which the fix is defined.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_sna_atom.txt b/doc/src/compute_sna_atom.txt
index 3b302a0a71..95d183937f 100644
--- a/doc/src/compute_sna_atom.txt
+++ b/doc/src/compute_sna_atom.txt
@@ -250,8 +250,8 @@ page for an overview of LAMMPS output options.
[Restrictions:]
These computes are part of the SNAP package. They are only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_spin.txt b/doc/src/compute_spin.txt
index 792706ecdf..787ff8cdcf 100644
--- a/doc/src/compute_spin.txt
+++ b/doc/src/compute_spin.txt
@@ -61,10 +61,10 @@ metal units ("units"_units.html).
[Restrictions:]
-The {spin} compute is part of the SPIN package.
-This compute is only enabled if LAMMPS was built with this package.
-See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
-The atom_style has to be "spin" for this compute to be valid.
+The {spin} compute is part of the SPIN package. This compute is only
+enabled if LAMMPS was built with this package. See the "Build
+package"_Build_package.html doc page for more info. The atom_style
+has to be "spin" for this compute to be valid.
[Related commands:] none
diff --git a/doc/src/compute_tally.txt b/doc/src/compute_tally.txt
index 23fac43093..a4a8441f9e 100644
--- a/doc/src/compute_tally.txt
+++ b/doc/src/compute_tally.txt
@@ -76,9 +76,9 @@ Both the scalar and vector values calculated by this compute are
[Restrictions:]
-This compute is part of the USER-TALLY package. It is only enabled
-if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+This compute is part of the USER-TALLY package. It is only enabled if
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Not all pair styles can be evaluated in a pairwise mode as required by
this compute. For example, 3-body and other many-body potentials,
diff --git a/doc/src/compute_tdpd_cc_atom.txt b/doc/src/compute_tdpd_cc_atom.txt
index 9ee4d3da34..a385bef10b 100644
--- a/doc/src/compute_tdpd_cc_atom.txt
+++ b/doc/src/compute_tdpd_cc_atom.txt
@@ -43,8 +43,8 @@ per unit mass.
[Restrictions:]
This compute is part of the USER-MESO package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_temp.txt b/doc/src/compute_temp.txt
index 9f3a1ca906..757e00c4d2 100644
--- a/doc/src/compute_temp.txt
+++ b/doc/src/compute_temp.txt
@@ -73,13 +73,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/compute_temp_asphere.txt b/doc/src/compute_temp_asphere.txt
index 6766729ae0..eb73891e82 100644
--- a/doc/src/compute_temp_asphere.txt
+++ b/doc/src/compute_temp_asphere.txt
@@ -135,8 +135,8 @@ vector values will be in energy "units"_units.html.
[Restrictions:]
This compute is part of the ASPHERE package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This compute requires that atoms store angular momentum and a
quaternion as defined by the "atom_style ellipsoid"_atom_style.html
diff --git a/doc/src/compute_temp_body.txt b/doc/src/compute_temp_body.txt
index 4e3ce3e77f..341d6d7f79 100644
--- a/doc/src/compute_temp_body.txt
+++ b/doc/src/compute_temp_body.txt
@@ -117,8 +117,8 @@ vector values will be in energy "units"_units.html.
[Restrictions:]
This compute is part of the BODY package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This compute requires that atoms store angular momentum and a
quaternion as defined by the "atom_style body"_atom_style.html
diff --git a/doc/src/compute_temp_deform_eff.txt b/doc/src/compute_temp_deform_eff.txt
index 876d492f34..4af61dc918 100644
--- a/doc/src/compute_temp_deform_eff.txt
+++ b/doc/src/compute_temp_deform_eff.txt
@@ -61,8 +61,8 @@ vector values will be in energy "units"_units.html.
[Restrictions:]
This compute is part of the USER-EFF package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_temp_eff.txt b/doc/src/compute_temp_eff.txt
index 35ddb75b12..415cb77595 100644
--- a/doc/src/compute_temp_eff.txt
+++ b/doc/src/compute_temp_eff.txt
@@ -83,8 +83,8 @@ the simulation.
[Restrictions:]
This compute is part of the USER-EFF package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_temp_partial.txt b/doc/src/compute_temp_partial.txt
index 2769246532..14294842a1 100644
--- a/doc/src/compute_temp_partial.txt
+++ b/doc/src/compute_temp_partial.txt
@@ -80,13 +80,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/compute_temp_region_eff.txt b/doc/src/compute_temp_region_eff.txt
index 95892eb257..f15f3155b0 100644
--- a/doc/src/compute_temp_region_eff.txt
+++ b/doc/src/compute_temp_region_eff.txt
@@ -52,8 +52,8 @@ vector values will be in energy "units"_units.html.
[Restrictions:]
This compute is part of the USER-EFF package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_temp_rotate.txt b/doc/src/compute_temp_rotate.txt
index 189246d3e4..8dac0405b4 100644
--- a/doc/src/compute_temp_rotate.txt
+++ b/doc/src/compute_temp_rotate.txt
@@ -86,8 +86,8 @@ vector values will be in energy "units"_units.html.
[Restrictions:]
This compute is part of the USER-MISC package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_temp_uef.txt b/doc/src/compute_temp_uef.txt
index a94d5db8ed..9a509da450 100644
--- a/doc/src/compute_temp_uef.txt
+++ b/doc/src/compute_temp_uef.txt
@@ -35,9 +35,9 @@ documentation for "compute temp"_compute_temp.html.
[Restrictions:]
-This fix is part of the USER-UEF package. It is only enabled if
-LAMMPS was built with that package. See the
-"Making LAMMPS"_Section_start.html#start_3 section for more info.
+This fix is part of the USER-UEF package. It is only enabled if LAMMPS
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This command can only be used when "fix nvt/uef"_fix_nh_uef.html
or "fix npt/uef"_fix_nh_uef.html is active.
diff --git a/doc/src/compute_ti.txt b/doc/src/compute_ti.txt
index e79b594e3f..9057cab476 100644
--- a/doc/src/compute_ti.txt
+++ b/doc/src/compute_ti.txt
@@ -121,8 +121,8 @@ The scalar value will be in energy "units"_units.html.
[Restrictions:]
This compute is part of the MISC package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_voronoi_atom.txt b/doc/src/compute_voronoi_atom.txt
index a8ce77882a..d01f4df712 100644
--- a/doc/src/compute_voronoi_atom.txt
+++ b/doc/src/compute_voronoi_atom.txt
@@ -212,8 +212,8 @@ The Voronoi face area will be in distance "units"_units.html squared.
[Restrictions:]
This compute is part of the VORONOI package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
It also requires you have a copy of the Voro++ library built and
installed on your system. See instructions on obtaining and
diff --git a/doc/src/compute_xrd.txt b/doc/src/compute_xrd.txt
index 609fde3582..41523f25af 100644
--- a/doc/src/compute_xrd.txt
+++ b/doc/src/compute_xrd.txt
@@ -170,8 +170,8 @@ All array values calculated by this compute are "intensive".
[Restrictions:]
This compute is part of the USER-DIFFRACTION package. It is only
-enabled if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
The compute_xrd command does not work for triclinic cells.
diff --git a/doc/src/dihedral_charmm.txt b/doc/src/dihedral_charmm.txt
index 8adef6cf4b..637a10102d 100644
--- a/doc/src/dihedral_charmm.txt
+++ b/doc/src/dihedral_charmm.txt
@@ -122,13 +122,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -146,8 +146,8 @@ Otherwise non-bonded contributions for these 1-4 pairs will be
computed multiple times.
These dihedral styles can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+MOLECULE package. See the "Build package"_Build_package.html doc page
+for more info.
[Related commands:]
diff --git a/doc/src/dihedral_class2.txt b/doc/src/dihedral_class2.txt
index 1a2f37abbb..9936f3768d 100644
--- a/doc/src/dihedral_class2.txt
+++ b/doc/src/dihedral_class2.txt
@@ -147,13 +147,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -163,8 +163,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This dihedral style can only be used if LAMMPS was built with the
-CLASS2 package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+CLASS2 package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/dihedral_cosine_shift_exp.txt b/doc/src/dihedral_cosine_shift_exp.txt
index 7ef27e6bc9..e2a46d28d8 100644
--- a/doc/src/dihedral_cosine_shift_exp.txt
+++ b/doc/src/dihedral_cosine_shift_exp.txt
@@ -58,13 +58,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -74,8 +74,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This dihedral style can only be used if LAMMPS was built with the
-USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER-MISC package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/dihedral_fourier.txt b/doc/src/dihedral_fourier.txt
index f51cbc9c8c..3045f6824b 100644
--- a/doc/src/dihedral_fourier.txt
+++ b/doc/src/dihedral_fourier.txt
@@ -50,13 +50,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -66,8 +66,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-USER_MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER_MISC package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/dihedral_harmonic.txt b/doc/src/dihedral_harmonic.txt
index 1eda0c5d02..27bc04f9df 100644
--- a/doc/src/dihedral_harmonic.txt
+++ b/doc/src/dihedral_harmonic.txt
@@ -59,13 +59,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -75,8 +75,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This dihedral style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+MOLECULE package. See the "Build package"_Build_package.html doc page
+for more info.
[Related commands:]
diff --git a/doc/src/dihedral_helix.txt b/doc/src/dihedral_helix.txt
index 3af4b410bc..3b3607337b 100644
--- a/doc/src/dihedral_helix.txt
+++ b/doc/src/dihedral_helix.txt
@@ -52,13 +52,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -68,8 +68,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This dihedral style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+MOLECULE package. See the "Build package"_Build_package.html doc page
+for more info.
[Related commands:]
diff --git a/doc/src/dihedral_hybrid.txt b/doc/src/dihedral_hybrid.txt
index c9ca86680c..a4a2a2808e 100644
--- a/doc/src/dihedral_hybrid.txt
+++ b/doc/src/dihedral_hybrid.txt
@@ -77,8 +77,8 @@ for specific dihedral types.
[Restrictions:]
This dihedral style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+MOLECULE package. See the "Build package"_Build_package.html doc page
+for more info.
Unlike other dihedral styles, the hybrid dihedral style does not store
dihedral coefficient info for individual sub-styles in a "binary
diff --git a/doc/src/dihedral_multi_harmonic.txt b/doc/src/dihedral_multi_harmonic.txt
index 7c22391923..74f1f6abc6 100644
--- a/doc/src/dihedral_multi_harmonic.txt
+++ b/doc/src/dihedral_multi_harmonic.txt
@@ -46,13 +46,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -62,8 +62,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This dihedral style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+MOLECULE package. See the "Build package"_Build_package.html doc page
+for more info.
[Related commands:]
diff --git a/doc/src/dihedral_nharmonic.txt b/doc/src/dihedral_nharmonic.txt
index aa8f1e0d7f..7a8bf6cdb7 100644
--- a/doc/src/dihedral_nharmonic.txt
+++ b/doc/src/dihedral_nharmonic.txt
@@ -46,13 +46,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -62,8 +62,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-USER_MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER_MISC package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/dihedral_opls.txt b/doc/src/dihedral_opls.txt
index f0cf91f30a..7fa5d81a14 100644
--- a/doc/src/dihedral_opls.txt
+++ b/doc/src/dihedral_opls.txt
@@ -54,13 +54,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -70,8 +70,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This dihedral style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+MOLECULE package. See the "Build package"_Build_package.html doc page
+for more info.
[Related commands:]
diff --git a/doc/src/dihedral_quadratic.txt b/doc/src/dihedral_quadratic.txt
index e65cf2dee8..dc951e4269 100644
--- a/doc/src/dihedral_quadratic.txt
+++ b/doc/src/dihedral_quadratic.txt
@@ -47,13 +47,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -63,8 +63,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-USER_MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER_MISC package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/dihedral_spherical.txt b/doc/src/dihedral_spherical.txt
index 10a757e898..61949174df 100644
--- a/doc/src/dihedral_spherical.txt
+++ b/doc/src/dihedral_spherical.txt
@@ -78,8 +78,8 @@ wn (typically 0.0 or 1.0) :ul
[Restrictions:]
This dihedral style can only be used if LAMMPS was built with the
-USER_MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER_MISC package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/dihedral_style.txt b/doc/src/dihedral_style.txt
index 6aff3f0994..749f74e399 100644
--- a/doc/src/dihedral_style.txt
+++ b/doc/src/dihedral_style.txt
@@ -104,10 +104,9 @@ Dihedral styles can only be set for atom styles that allow dihedrals
to be defined.
Most dihedral styles are part of the MOLECULE package. They are only
-enabled if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
-The doc pages for individual dihedral potentials tell if it is part of
-a package.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info. The doc pages for
+individual dihedral potentials tell if it is part of a package.
[Related commands:]
diff --git a/doc/src/dihedral_table.txt b/doc/src/dihedral_table.txt
index d722ef7c82..3f679f5709 100644
--- a/doc/src/dihedral_table.txt
+++ b/doc/src/dihedral_table.txt
@@ -180,13 +180,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -194,8 +194,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This dihedral style can only be used if LAMMPS was built with the
-USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER-MISC package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/dihedral_table_cut.txt b/doc/src/dihedral_table_cut.txt
index cc7df8cdf9..b8e0ec64c8 100644
--- a/doc/src/dihedral_table_cut.txt
+++ b/doc/src/dihedral_table_cut.txt
@@ -192,8 +192,8 @@ that matches the specified keyword.
[Restrictions:]
This dihedral style can only be used if LAMMPS was built with the
-USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER-MISC package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/dump.txt b/doc/src/dump.txt
index 5b478b7301..8b630cc706 100644
--- a/doc/src/dump.txt
+++ b/doc/src/dump.txt
@@ -634,23 +634,22 @@ which could then be output into dump files.
[Restrictions:]
To write gzipped dump files, you must either compile LAMMPS with the
--DLAMMPS_GZIP option or use the styles from the COMPRESS package
-- see the "Making LAMMPS"_Section_start.html#start_2 section of
-the documentation.
+-DLAMMPS_GZIP option or use the styles from the COMPRESS package.
+See the "Build settings"_Build_settings.html doc page for details.
-The {atom/gz}, {cfg/gz}, {custom/gz}, and {xyz/gz} styles are part
-of the COMPRESS package. They are only enabled if LAMMPS was built
-with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+The {atom/gz}, {cfg/gz}, {custom/gz}, and {xyz/gz} styles are part of
+the COMPRESS package. They are only enabled if LAMMPS was built with
+that package. See the "Build package"_Build_package.html doc page for
+more info.
The {atom/mpiio}, {cfg/mpiio}, {custom/mpiio}, and {xyz/mpiio} styles
are part of the MPIIO package. They are only enabled if LAMMPS was
-built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+built with that package. See the "Build package"_Build_package.html
+doc page for more info.
The {xtc} style is part of the MISC package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/dump_cfg_uef.txt b/doc/src/dump_cfg_uef.txt
index 665be14be1..16e4aba4c0 100644
--- a/doc/src/dump_cfg_uef.txt
+++ b/doc/src/dump_cfg_uef.txt
@@ -38,9 +38,9 @@ reference frame as the atomic positions.
[Restrictions:]
-This fix is part of the USER-UEF package. It is only enabled if
-LAMMPS was built with that package. See the
-"Making LAMMPS"_Section_start.html#start_3 section for more info.
+This fix is part of the USER-UEF package. It is only enabled if LAMMPS
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This command can only be used when "fix nvt/uef"_fix_nh_uef.html
or "fix npt/uef"_fix_nh_uef.html is active.
diff --git a/doc/src/dump_h5md.txt b/doc/src/dump_h5md.txt
index fbd682dad9..9065e8a648 100644
--- a/doc/src/dump_h5md.txt
+++ b/doc/src/dump_h5md.txt
@@ -98,13 +98,13 @@ note above). Only orthogonal domains are currently supported. This is
a limitation of the present dump h5md command and not of H5MD itself.
The {h5md} dump style is part of the USER-H5MD package. It is only
-enabled if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info. It also
-requires (i) building the ch5md library provided with LAMMPS (See the
-"Making LAMMPS"_Section_start.html#start_3 section for more info.) and
-(ii) having the "HDF5"_HDF5_ws library installed (C bindings are
-sufficient) on your system. The library ch5md is compiled with the
-h5cc wrapper provided by the HDF5 library.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info. It also requires
+(i) building the ch5md library provided with LAMMPS (See the "Build
+package"_Build_package.html doc page for more info.) and (ii) having
+the "HDF5"_HDF5_ws library installed (C bindings are sufficient) on
+your system. The library ch5md is compiled with the h5cc wrapper
+provided by the HDF5 library.
:link(HDF5_ws,http://www.hdfgroup.org/HDF5/)
diff --git a/doc/src/dump_image.txt b/doc/src/dump_image.txt
index 06332b5dcf..9b56dd95a6 100644
--- a/doc/src/dump_image.txt
+++ b/doc/src/dump_image.txt
@@ -142,8 +142,8 @@ framerate can be set using the "dump_modify"_dump_modify.html command.
To write out JPEG and PNG format files, you must build LAMMPS with
support for the corresponding JPEG or PNG library. To convert images
into movies, LAMMPS has to be compiled with the -DLAMMPS_FFMPEG
-flag. See "this section"_Section_start.html#start_2_4 of the manual
-for instructions on how to do this.
+flag. See the "Build settings"_Build_settings.html doc page for
+details.
NOTE: Because periodic boundary conditions are enforced only on
timesteps when neighbor lists are rebuilt, the coordinates of an atom
@@ -624,8 +624,7 @@ building LAMMPS and have the FFmpeg executable available on the
machine where LAMMPS is being run. Typically it's name is lowercase,
i.e. ffmpeg.
-See the "Making LAMMPS"_Section_start.html#start_2_4 section of the
-documentation for details on how to compile with optional switches.
+See the "Build settings"_Build_settings.html doc page for details.
Note that since FFmpeg is run as an external program via a pipe,
LAMMPS has limited control over its execution and no knowledge about
diff --git a/doc/src/dump_molfile.txt b/doc/src/dump_molfile.txt
index 9fa04bd1ae..dd2b212f0b 100644
--- a/doc/src/dump_molfile.txt
+++ b/doc/src/dump_molfile.txt
@@ -90,8 +90,8 @@ determine the sequence of timesteps on which dump files are written.
[Restrictions:]
The {molfile} dump style is part of the USER-MOLFILE package. It is
-only enabled if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+only enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Molfile plugins provide a consistent programming interface to read and
write file formats commonly used in molecular simulations. The
diff --git a/doc/src/dump_netcdf.txt b/doc/src/dump_netcdf.txt
index b1c6373651..52d757eac5 100644
--- a/doc/src/dump_netcdf.txt
+++ b/doc/src/dump_netcdf.txt
@@ -66,8 +66,8 @@ by "thermo_style"_thermo_style.html.
The {netcdf} and {netcdf/mpiio} dump styles are part of the
USER-NETCDF package. They are only enabled if LAMMPS was built with
-that package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info.
+that package. See the "Build package"_Build_package.html doc page for
+more info.
:line
diff --git a/doc/src/dump_vtk.txt b/doc/src/dump_vtk.txt
index afc6099534..7eaa59a795 100644
--- a/doc/src/dump_vtk.txt
+++ b/doc/src/dump_vtk.txt
@@ -156,9 +156,9 @@ write out much faster.
The {vtk} style does not support writing of gzipped dump files.
-The {vtk} dump style is part of the USER-VTK package. It is
-only enabled if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+The {vtk} dump style is part of the USER-VTK package. It is only
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
To use this dump style, you also must link to the VTK library. See
the info in lib/vtk/README and insure the Makefile.lammps file in that
diff --git a/doc/src/echo.txt b/doc/src/echo.txt
index dc6918dc89..3436737faa 100644
--- a/doc/src/echo.txt
+++ b/doc/src/echo.txt
@@ -26,8 +26,8 @@ command to the screen and/or log file as it is read and processed. If
an input script has errors, it can be useful to look at echoed output
to see the last command processed.
-The "command-line switch"_Section_start.html#start_6 -echo can be used
-in place of this command.
+The "command-line switch"_Run_options.html -echo can be used in place
+of this command.
[Restrictions:] none
diff --git a/doc/src/fix.txt b/doc/src/fix.txt
index fd966b5bd9..9c3a1d0349 100644
--- a/doc/src/fix.txt
+++ b/doc/src/fix.txt
@@ -309,9 +309,9 @@ accerlerated styles exist.
[Restrictions:]
Some fix styles are part of specific packages. They are only enabled
-if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
-The doc pages for individual fixes tell if it is part of a package.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info. The doc pages for
+individual fixes tell if it is part of a package.
[Related commands:]
diff --git a/doc/src/fix_addforce.txt b/doc/src/fix_addforce.txt
index 51be39fdb2..4fdf9a41dd 100644
--- a/doc/src/fix_addforce.txt
+++ b/doc/src/fix_addforce.txt
@@ -112,13 +112,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/fix_addtorque.txt b/doc/src/fix_addtorque.txt
index c80fad26da..0963915e7a 100644
--- a/doc/src/fix_addtorque.txt
+++ b/doc/src/fix_addtorque.txt
@@ -88,8 +88,8 @@ the iteration count during the minimization.
[Restrictions:]
This fix is part of the USER-MISC package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_append_atoms.txt b/doc/src/fix_append_atoms.txt
index c6af361afc..d83f265982 100644
--- a/doc/src/fix_append_atoms.txt
+++ b/doc/src/fix_append_atoms.txt
@@ -95,8 +95,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix style is part of the SHOCK package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
The boundary on which atoms are added with append/atoms must be
shrink/minimum. The opposite boundary may be any boundary type other
diff --git a/doc/src/fix_atom_swap.txt b/doc/src/fix_atom_swap.txt
index c1d84dade1..22091eca00 100644
--- a/doc/src/fix_atom_swap.txt
+++ b/doc/src/fix_atom_swap.txt
@@ -165,8 +165,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the MC package. It is only enabled if LAMMPS was
-built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+built with that package. See the "Build package"_Build_package.html
+doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_ave_correlate_long.txt b/doc/src/fix_ave_correlate_long.txt
index ac0ef873aa..d94bf8af7b 100644
--- a/doc/src/fix_ave_correlate_long.txt
+++ b/doc/src/fix_ave_correlate_long.txt
@@ -120,8 +120,8 @@ the run command. This fix is not invoked during energy minimization.
[Restrictions:]
This compute is part of the USER-MISC package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_aveforce.txt b/doc/src/fix_aveforce.txt
index 1fc7e4a18d..8c759864c6 100644
--- a/doc/src/fix_aveforce.txt
+++ b/doc/src/fix_aveforce.txt
@@ -72,13 +72,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/fix_bocs.txt b/doc/src/fix_bocs.txt
index f5bbc8a251..7acc22d702 100644
--- a/doc/src/fix_bocs.txt
+++ b/doc/src/fix_bocs.txt
@@ -85,8 +85,8 @@ XXXX_press, where XXXX is the ID given to the fix bocs command (in the
example, the ID of the fix bocs command is 1 ).
This fix is part of the USER-BOCS package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related:]
diff --git a/doc/src/fix_bond_break.txt b/doc/src/fix_bond_break.txt
index bdb2f2a862..59fea8f45b 100644
--- a/doc/src/fix_bond_break.txt
+++ b/doc/src/fix_bond_break.txt
@@ -131,8 +131,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the MC package. It is only enabled if LAMMPS was
-built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+built with that package. See the "Build package"_Build_package.html
+doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_bond_create.txt b/doc/src/fix_bond_create.txt
index ab34433cec..02655577fd 100644
--- a/doc/src/fix_bond_create.txt
+++ b/doc/src/fix_bond_create.txt
@@ -226,8 +226,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the MC package. It is only enabled if LAMMPS was
-built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+built with that package. See the "Build package"_Build_package.html
+doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_bond_react.txt b/doc/src/fix_bond_react.txt
index 883968e012..7317dd26bb 100644
--- a/doc/src/fix_bond_react.txt
+++ b/doc/src/fix_bond_react.txt
@@ -312,8 +312,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the USER-MISC package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_bond_swap.txt b/doc/src/fix_bond_swap.txt
index a829171f33..3c90bb53f6 100644
--- a/doc/src/fix_bond_swap.txt
+++ b/doc/src/fix_bond_swap.txt
@@ -165,8 +165,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the MC package. It is only enabled if LAMMPS was
-built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+built with that package. See the "Build package"_Build_package.html
+doc page for more info.
The settings of the "special_bond" command must be 0,1,1 in order to
use this fix, which is typical of bead-spring chains with FENE or
diff --git a/doc/src/fix_cmap.txt b/doc/src/fix_cmap.txt
index 6f3769fafe..ef48e8b51c 100644
--- a/doc/src/fix_cmap.txt
+++ b/doc/src/fix_cmap.txt
@@ -125,8 +125,8 @@ To function as expected this fix command must be issued {before} a
"read_restart"_read_restart.html command.
This fix can only be used if LAMMPS was built with the MOLECULE
-package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+package. See the "Build package"_Build_package.html doc page for more
+info.
[Related commands:]
diff --git a/doc/src/fix_colvars.txt b/doc/src/fix_colvars.txt
index 4a1d84de64..3a64840bdc 100644
--- a/doc/src/fix_colvars.txt
+++ b/doc/src/fix_colvars.txt
@@ -106,8 +106,8 @@ fix is "extensive".
[Restrictions:]
This fix is part of the USER-COLVARS package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
There can only be one colvars fix active at a time. Since the interface
communicates only the minimum amount of information and colvars module
diff --git a/doc/src/fix_deform.txt b/doc/src/fix_deform.txt
index e92d1e6b19..6ba713e662 100644
--- a/doc/src/fix_deform.txt
+++ b/doc/src/fix_deform.txt
@@ -556,13 +556,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/fix_deposit.txt b/doc/src/fix_deposit.txt
index 277ca8777a..265f43bd4b 100644
--- a/doc/src/fix_deposit.txt
+++ b/doc/src/fix_deposit.txt
@@ -271,8 +271,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the MISC package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
The specified insertion region cannot be a "dynamic" region, as
defined by the "region"_region.html command.
diff --git a/doc/src/fix_dpd_energy.txt b/doc/src/fix_dpd_energy.txt
index f539bc534e..5e8e295de9 100644
--- a/doc/src/fix_dpd_energy.txt
+++ b/doc/src/fix_dpd_energy.txt
@@ -56,13 +56,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -72,8 +72,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This command is part of the USER-DPD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This fix must be used with an additional fix that specifies time
integration, e.g. "fix nve"_fix_nve.html.
diff --git a/doc/src/fix_dpd_source.txt b/doc/src/fix_dpd_source.txt
index 04af9a28a1..691cfe86f1 100644
--- a/doc/src/fix_dpd_source.txt
+++ b/doc/src/fix_dpd_source.txt
@@ -71,8 +71,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the USER-MESO package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Fix {edpd/source} must be used with the "pair_style
edpd"_pair_meso.html command. Fix {tdpd/source} must be used with the
diff --git a/doc/src/fix_efield.txt b/doc/src/fix_efield.txt
index b5a43f68aa..cecfb6e6a3 100644
--- a/doc/src/fix_efield.txt
+++ b/doc/src/fix_efield.txt
@@ -156,8 +156,8 @@ system (the quantity being minimized), you MUST enable the
[Restrictions:]
This fix is part of the MISC package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_ehex.txt b/doc/src/fix_ehex.txt
index cfcc917d01..75651e21a4 100644
--- a/doc/src/fix_ehex.txt
+++ b/doc/src/fix_ehex.txt
@@ -156,8 +156,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the RIGID package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_enforce2d.txt b/doc/src/fix_enforce2d.txt
index 2925e44bda..17ac8146fd 100644
--- a/doc/src/fix_enforce2d.txt
+++ b/doc/src/fix_enforce2d.txt
@@ -37,13 +37,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/fix_eos_cv.txt b/doc/src/fix_eos_cv.txt
index b94e2c64a9..b2ac0eb6b9 100644
--- a/doc/src/fix_eos_cv.txt
+++ b/doc/src/fix_eos_cv.txt
@@ -39,8 +39,8 @@ possible.
[Restrictions:]
This command is part of the USER-DPD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This command also requires use of the "atom_style dpd"_atom_style.html
command.
diff --git a/doc/src/fix_eos_table.txt b/doc/src/fix_eos_table.txt
index 743c51f415..53b3204372 100644
--- a/doc/src/fix_eos_table.txt
+++ b/doc/src/fix_eos_table.txt
@@ -99,8 +99,8 @@ one that matches the specified keyword.
[Restrictions:]
This command is part of the USER-DPD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This command also requires use of the "atom_style dpd"_atom_style.html
command.
diff --git a/doc/src/fix_eos_table_rx.txt b/doc/src/fix_eos_table_rx.txt
index f9deab61c8..1a2daa0bc6 100644
--- a/doc/src/fix_eos_table_rx.txt
+++ b/doc/src/fix_eos_table_rx.txt
@@ -162,13 +162,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -178,8 +178,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This command is part of the USER-DPD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This command also requires use of the "atom_style dpd"_atom_style.html
command.
diff --git a/doc/src/fix_evaporate.txt b/doc/src/fix_evaporate.txt
index 6237a137fd..59dab43d9a 100644
--- a/doc/src/fix_evaporate.txt
+++ b/doc/src/fix_evaporate.txt
@@ -84,8 +84,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the MISC package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_filter_corotate.txt b/doc/src/fix_filter_corotate.txt
index d1e5e12f3e..b30966c2f9 100644
--- a/doc/src/fix_filter_corotate.txt
+++ b/doc/src/fix_filter_corotate.txt
@@ -70,8 +70,8 @@ fixes are not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix is part of the USER-MISC package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Currently, it does not support "molecule templates"_molecule.html.
diff --git a/doc/src/fix_flow_gauss.txt b/doc/src/fix_flow_gauss.txt
index 843c2a66a5..46a9477aa2 100644
--- a/doc/src/fix_flow_gauss.txt
+++ b/doc/src/fix_flow_gauss.txt
@@ -111,8 +111,8 @@ flow/gauss fixes, one that specifies {fix_modify respa 3} and one with
[Restart, fix_modify, output, run start/stop, minimize info:]
This fix is part of the USER-MISC package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
No information about this fix is written to "binary restart
files"_restart.html.
diff --git a/doc/src/fix_freeze.txt b/doc/src/fix_freeze.txt
index 76a9fd3b1a..89f2dd8179 100644
--- a/doc/src/fix_freeze.txt
+++ b/doc/src/fix_freeze.txt
@@ -40,13 +40,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -72,8 +72,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the GRANULAR package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
There can only be a single freeze fix defined. This is because other
the "granular pair styles"_pair_gran.html treat frozen particles
diff --git a/doc/src/fix_gcmc.txt b/doc/src/fix_gcmc.txt
index 394690ea5d..6b9a02eeca 100644
--- a/doc/src/fix_gcmc.txt
+++ b/doc/src/fix_gcmc.txt
@@ -403,8 +403,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the MC package. It is only enabled if LAMMPS was
-built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+built with that package. See the "Build package"_Build_package.html
+doc page for more info.
Do not set "neigh_modify once yes" or else this fix will never be
called. Reneighboring is required.
diff --git a/doc/src/fix_gld.txt b/doc/src/fix_gld.txt
index 1c5db6157d..97c3d0e408 100644
--- a/doc/src/fix_gld.txt
+++ b/doc/src/fix_gld.txt
@@ -137,8 +137,8 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix is part of the MISC package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_gle.txt b/doc/src/fix_gle.txt
index 9fdc72bf9f..70a8e7f342 100644
--- a/doc/src/fix_gle.txt
+++ b/doc/src/fix_gle.txt
@@ -132,9 +132,9 @@ In order to perform constant-pressure simulations please use
"fix npt"_fix_nh.html, to avoid duplicate integration of the
equations of motion.
-This fix is part of the USER-MISC package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+This fix is part of the USER-MISC package. It is only enabled if
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_gravity.txt b/doc/src/fix_gravity.txt
index 832c677f81..ea596c8668 100644
--- a/doc/src/fix_gravity.txt
+++ b/doc/src/fix_gravity.txt
@@ -96,13 +96,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/fix_grem.txt b/doc/src/fix_grem.txt
index 506e266505..e096d4bd3c 100644
--- a/doc/src/fix_grem.txt
+++ b/doc/src/fix_grem.txt
@@ -91,8 +91,8 @@ by this fix to add the rescaled kinetic pressure as part of
[Restrictions:]
This fix is part of the USER-MISC package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_imd.txt b/doc/src/fix_imd.txt
index 8e21a1619b..a58cfdb3d3 100644
--- a/doc/src/fix_imd.txt
+++ b/doc/src/fix_imd.txt
@@ -143,8 +143,8 @@ fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix is part of the USER-MISC package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
When used in combination with VMD, a topology or coordinate file has
to be loaded, which matches (in number and ordering of atoms) the
diff --git a/doc/src/fix_ipi.txt b/doc/src/fix_ipi.txt
index eba30ef088..b115aba7df 100644
--- a/doc/src/fix_ipi.txt
+++ b/doc/src/fix_ipi.txt
@@ -81,9 +81,9 @@ define an external potential acting on the atoms that are moved by
i-PI.
This fix is part of the USER-MISC package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info. Because of
-the use of UNIX domain sockets, this fix will only work in a UNIX
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info. Because of the
+use of UNIX domain sockets, this fix will only work in a UNIX
environment.
[Related commands:]
diff --git a/doc/src/fix_langevin.txt b/doc/src/fix_langevin.txt
index 4d7728cdba..e97c7c3c37 100644
--- a/doc/src/fix_langevin.txt
+++ b/doc/src/fix_langevin.txt
@@ -270,13 +270,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/fix_langevin_eff.txt b/doc/src/fix_langevin_eff.txt
index cf42f9c036..e55e40c6c8 100644
--- a/doc/src/fix_langevin_eff.txt
+++ b/doc/src/fix_langevin_eff.txt
@@ -93,8 +93,8 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:] none
This fix is part of the USER-EFF package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_langevin_spin.txt b/doc/src/fix_langevin_spin.txt
index 1b1936376d..7bb25e0a68 100644
--- a/doc/src/fix_langevin_spin.txt
+++ b/doc/src/fix_langevin_spin.txt
@@ -76,9 +76,9 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
-The {langevin/spin} fix is part of the SPIN package.
-This style is only enabled if LAMMPS was built with this package.
-See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+The {langevin/spin} fix is part of the SPIN package. This style is
+only enabled if LAMMPS was built with this package. See the "Build
+package"_Build_package.html doc page for more info.
The numerical integration has to be performed with {fix nve/spin}
when {fix langevin/spin} is enabled.
diff --git a/doc/src/fix_latte.txt b/doc/src/fix_latte.txt
index 9bc589520b..17beb67206 100644
--- a/doc/src/fix_latte.txt
+++ b/doc/src/fix_latte.txt
@@ -136,8 +136,8 @@ quantity being minimized), you MUST enable the
[Restrictions:]
This fix is part of the LATTE package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
You must use metal units, as set by the "units"_units command to use
this fix.
@@ -154,8 +154,8 @@ doing 99% or more of the work to compute quantum-accurate forces.
NOTE: NEB calculations can be done using this fix using multiple
replicas and running LAMMPS in parallel. However, each replica must
be run on a single MPI task. For details, see the "neb"_neb.html
-command and -partition command-line explained in "Section
-2.6"_Section_start.html#start_6 of the manual.
+command doc page and the "-partition command-line
+switch"_Run_options.html
[Related commands:] none
diff --git a/doc/src/fix_lb_fluid.txt b/doc/src/fix_lb_fluid.txt
index 5347f0147f..1a52397822 100644
--- a/doc/src/fix_lb_fluid.txt
+++ b/doc/src/fix_lb_fluid.txt
@@ -307,8 +307,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the USER-LB package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This fix can only be used with an orthogonal simulation domain.
diff --git a/doc/src/fix_lb_momentum.txt b/doc/src/fix_lb_momentum.txt
index a58c5d257e..408978f64c 100644
--- a/doc/src/fix_lb_momentum.txt
+++ b/doc/src/fix_lb_momentum.txt
@@ -61,8 +61,8 @@ Can only be used if a lattice-Boltzmann fluid has been created via the
command.
This fix is part of the USER-LB package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_lb_pc.txt b/doc/src/fix_lb_pc.txt
index bd121b7813..05b5eb20a2 100644
--- a/doc/src/fix_lb_pc.txt
+++ b/doc/src/fix_lb_pc.txt
@@ -42,8 +42,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the USER-LB package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Can only be used if a lattice-Boltzmann fluid has been created via the
"fix lb/fluid"_fix_lb_fluid.html command, and must come after this
diff --git a/doc/src/fix_lb_rigid_pc_sphere.txt b/doc/src/fix_lb_rigid_pc_sphere.txt
index bc8fa2ea25..ddaa552ecc 100644
--- a/doc/src/fix_lb_rigid_pc_sphere.txt
+++ b/doc/src/fix_lb_rigid_pc_sphere.txt
@@ -122,8 +122,8 @@ of the "run"_run.html command. These fixes are not invoked during
[Restrictions:]
This fix is part of the USER-LB package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Can only be used if a lattice-Boltzmann fluid has been created via the
"fix lb/fluid"_fix_lb_fluid.html command, and must come after this
diff --git a/doc/src/fix_lb_viscous.txt b/doc/src/fix_lb_viscous.txt
index 7bbdd204e3..ba91a2cd54 100644
--- a/doc/src/fix_lb_viscous.txt
+++ b/doc/src/fix_lb_viscous.txt
@@ -70,8 +70,8 @@ for details."
[Restrictions:]
This fix is part of the USER-LB package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Can only be used if a lattice-Boltzmann fluid has been created via the
"fix lb/fluid"_fix_lb_fluid.html command, and must come after this
diff --git a/doc/src/fix_manifoldforce.txt b/doc/src/fix_manifoldforce.txt
index aa32a875bf..8dd992170b 100644
--- a/doc/src/fix_manifoldforce.txt
+++ b/doc/src/fix_manifoldforce.txt
@@ -24,10 +24,14 @@ fix constrain all manifoldforce sphere 5.0
[Description:]
-This fix subtracts each time step from the force the component along the normal of the specified "manifold"_manifolds.html.
-This can be used in combination with "minimize"_minimize.html to remove overlap between particles while
-keeping them (roughly) constrained to the given manifold, e.g. to set up a run with "fix nve/manifold/rattle"_fix_nve_manifold_rattle.html.
-I have found that only {hftn} and {quickmin} with a very small time step perform adequately though.
+This fix subtracts each time step from the force the component along
+the normal of the specified "manifold"_manifolds.html. This can be
+used in combination with "minimize"_minimize.html to remove overlap
+between particles while keeping them (roughly) constrained to the
+given manifold, e.g. to set up a run with "fix
+nve/manifold/rattle"_fix_nve_manifold_rattle.html. I have found that
+only {hftn} and {quickmin} with a very small time step perform
+adequately though.
:line
@@ -45,17 +49,18 @@ minimization"_minimize.html.
[Restrictions:]
-This fix is part of the USER-MANIFOLD package. It is only enabled if LAMMPS
-was built with that package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info.
+This fix is part of the USER-MANIFOLD package. It is only enabled if
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
-Only use this with {min_style hftn} or {min_style quickmin}. If not, the constraints
-will not be satisfied very well at all. A warning is generated if the {min_style} is
-incompatible but no error.
+Only use this with {min_style hftn} or {min_style quickmin}. If not,
+the constraints will not be satisfied very well at all. A warning is
+generated if the {min_style} is incompatible but no error.
:line
[Related commands:]
-"fix nve/manifold/rattle"_fix_nve_manifold_rattle.html, "fix nvt/manifold/rattle"_fix_nvt_manifold_rattle.html
+"fix nve/manifold/rattle"_fix_nve_manifold_rattle.html, "fix
+nvt/manifold/rattle"_fix_nvt_manifold_rattle.html
diff --git a/doc/src/fix_meso.txt b/doc/src/fix_meso.txt
index 8f5ad29929..8c0ce5a9b7 100644
--- a/doc/src/fix_meso.txt
+++ b/doc/src/fix_meso.txt
@@ -42,8 +42,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the USER-SPH package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_meso_stationary.txt b/doc/src/fix_meso_stationary.txt
index 38d26b34d6..1a546efec0 100644
--- a/doc/src/fix_meso_stationary.txt
+++ b/doc/src/fix_meso_stationary.txt
@@ -43,8 +43,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the USER-SPH package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_momentum.txt b/doc/src/fix_momentum.txt
index f7fe35be2a..aeedad0719 100644
--- a/doc/src/fix_momentum.txt
+++ b/doc/src/fix_momentum.txt
@@ -67,13 +67,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/fix_mscg.txt b/doc/src/fix_mscg.txt
index aadc3caf5a..1ad7804127 100644
--- a/doc/src/fix_mscg.txt
+++ b/doc/src/fix_mscg.txt
@@ -103,8 +103,8 @@ dihedrals a bead can have in the coarse-grained model.
[Restrictions:]
This fix is part of the MSCG package. It is only enabled if LAMMPS was
-built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+built with that package. See the "Build package"_Build_package.html
+doc page for more info.
The MS-CG library uses C++11, which may not be supported by older
compilers. The MS-CG library also has some additional numeric library
diff --git a/doc/src/fix_msst.txt b/doc/src/fix_msst.txt
index 91ffbbb0fa..e31f61e5f7 100644
--- a/doc/src/fix_msst.txt
+++ b/doc/src/fix_msst.txt
@@ -162,8 +162,8 @@ are "extensive"; the vector values are "intensive".
[Restrictions:]
This fix style is part of the SHOCK package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
All cell dimensions must be periodic. This fix can not be used with a
triclinic cell. The MSST fix has been tested only for the group-ID
diff --git a/doc/src/fix_mvv_dpd.txt b/doc/src/fix_mvv_dpd.txt
index 1e9bf631fd..507f271469 100644
--- a/doc/src/fix_mvv_dpd.txt
+++ b/doc/src/fix_mvv_dpd.txt
@@ -77,8 +77,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the USER-MESO package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_neb.txt b/doc/src/fix_neb.txt
index 5341d6999c..d331d9ad75 100644
--- a/doc/src/fix_neb.txt
+++ b/doc/src/fix_neb.txt
@@ -203,8 +203,8 @@ as invoked by the "minimize"_minimize.html command via the
[Restrictions:]
This command can only be used if LAMMPS was built with the REPLICA
-package. See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info on packages.
+package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/fix_nh.txt b/doc/src/fix_nh.txt
index f6b155e2db..644ced4bdc 100644
--- a/doc/src/fix_nh.txt
+++ b/doc/src/fix_nh.txt
@@ -491,13 +491,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/fix_nh_eff.txt b/doc/src/fix_nh_eff.txt
index afb319bfa5..d7c0457708 100644
--- a/doc/src/fix_nh_eff.txt
+++ b/doc/src/fix_nh_eff.txt
@@ -101,8 +101,8 @@ for details.
[Restrictions:]
This fix is part of the USER-EFF package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Other restriction discussed on the doc page for the "fix nvt, npt, and
nph"_fix_nh.html commands also apply.
diff --git a/doc/src/fix_nh_uef.txt b/doc/src/fix_nh_uef.txt
index 0e73c57e08..ae403cafd1 100644
--- a/doc/src/fix_nh_uef.txt
+++ b/doc/src/fix_nh_uef.txt
@@ -182,8 +182,8 @@ The fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix is part of the USER-UEF package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Due to requirements of the boundary conditions, when the {strain}
keyword is set to zero (or unset), the initial simulation box must be
diff --git a/doc/src/fix_nph_asphere.txt b/doc/src/fix_nph_asphere.txt
index 6bfd9d3fe2..5cabf930e7 100644
--- a/doc/src/fix_nph_asphere.txt
+++ b/doc/src/fix_nph_asphere.txt
@@ -87,13 +87,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -132,8 +132,8 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix is part of the ASPHERE package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This fix requires that atoms store torque and angular momentum and a
quaternion as defined by the "atom_style ellipsoid"_atom_style.html
diff --git a/doc/src/fix_nph_body.txt b/doc/src/fix_nph_body.txt
index 377e1980eb..e04c240de9 100644
--- a/doc/src/fix_nph_body.txt
+++ b/doc/src/fix_nph_body.txt
@@ -86,13 +86,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -131,8 +131,8 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix is part of the BODY package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This fix requires that atoms store torque and angular momentum and a
quaternion as defined by the "atom_style body"_atom_style.html
diff --git a/doc/src/fix_nph_sphere.txt b/doc/src/fix_nph_sphere.txt
index 8b7639c4c6..f94c057c93 100644
--- a/doc/src/fix_nph_sphere.txt
+++ b/doc/src/fix_nph_sphere.txt
@@ -96,13 +96,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/fix_nphug.txt b/doc/src/fix_nphug.txt
index 0bd5153152..855a4c9ae4 100644
--- a/doc/src/fix_nphug.txt
+++ b/doc/src/fix_nphug.txt
@@ -146,13 +146,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -208,8 +208,8 @@ shock calculated from the RH conditions. They have units of distance/time.
[Restrictions:]
This fix style is part of the SHOCK package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
All the usual restrictions for "fix npt"_fix_nh.html apply,
plus the additional ones mentioned above.
diff --git a/doc/src/fix_npt_asphere.txt b/doc/src/fix_npt_asphere.txt
index 9c95a80d33..194f4ff499 100644
--- a/doc/src/fix_npt_asphere.txt
+++ b/doc/src/fix_npt_asphere.txt
@@ -111,13 +111,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -157,8 +157,8 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix is part of the ASPHERE package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This fix requires that atoms store torque and angular momentum and a
quaternion as defined by the "atom_style ellipsoid"_atom_style.html
diff --git a/doc/src/fix_npt_body.txt b/doc/src/fix_npt_body.txt
index 0d2b797299..1d608137b6 100644
--- a/doc/src/fix_npt_body.txt
+++ b/doc/src/fix_npt_body.txt
@@ -110,13 +110,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -156,8 +156,8 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix is part of the BODY package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This fix requires that atoms store torque and angular momentum and a
quaternion as defined by the "atom_style body"_atom_style.html
diff --git a/doc/src/fix_npt_sphere.txt b/doc/src/fix_npt_sphere.txt
index dcb25d1c73..6ebb68e176 100644
--- a/doc/src/fix_npt_sphere.txt
+++ b/doc/src/fix_npt_sphere.txt
@@ -121,13 +121,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/fix_nve.txt b/doc/src/fix_nve.txt
index e446b27397..2347f957ae 100644
--- a/doc/src/fix_nve.txt
+++ b/doc/src/fix_nve.txt
@@ -40,13 +40,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/fix_nve_asphere.txt b/doc/src/fix_nve_asphere.txt
index b7fb3e922c..bd9e4ae873 100644
--- a/doc/src/fix_nve_asphere.txt
+++ b/doc/src/fix_nve_asphere.txt
@@ -51,13 +51,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -67,8 +67,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This fix is part of the ASPHERE package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This fix requires that atoms store torque and angular momentum and a
quaternion as defined by the "atom_style ellipsoid"_atom_style.html
diff --git a/doc/src/fix_nve_asphere_noforce.txt b/doc/src/fix_nve_asphere_noforce.txt
index e57417bda5..94b627bf1b 100644
--- a/doc/src/fix_nve_asphere_noforce.txt
+++ b/doc/src/fix_nve_asphere_noforce.txt
@@ -46,8 +46,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the ASPHERE package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This fix requires that atoms store torque and angular momentum and a
quaternion as defined by the "atom_style ellipsoid"_atom_style.html
diff --git a/doc/src/fix_nve_body.txt b/doc/src/fix_nve_body.txt
index d072bfa161..1a9efb5e13 100644
--- a/doc/src/fix_nve_body.txt
+++ b/doc/src/fix_nve_body.txt
@@ -44,8 +44,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the BODY package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This fix requires that atoms store torque and angular momentum and a
quaternion as defined by the "atom_style body"_atom_style.html
diff --git a/doc/src/fix_nve_dot.txt b/doc/src/fix_nve_dot.txt
index 1041a248d8..54b199c1df 100644
--- a/doc/src/fix_nve_dot.txt
+++ b/doc/src/fix_nve_dot.txt
@@ -44,8 +44,8 @@ A technical report with more information on this integrator can be found
[Restrictions:]
These pair styles can only be used if LAMMPS was built with the
-"USER-CGDNA"_#USER-CGDNA package and the MOLECULE and ASPHERE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+"USER-CGDNA"_#USER-CGDNA package and the MOLECULE and ASPHERE package.
+See the "Build package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_nve_dotc_langevin.txt b/doc/src/fix_nve_dotc_langevin.txt
index 68c1b42328..c6148a7165 100644
--- a/doc/src/fix_nve_dotc_langevin.txt
+++ b/doc/src/fix_nve_dotc_langevin.txt
@@ -122,8 +122,8 @@ A technical report with more information on this integrator can be found
[Restrictions:]
These pair styles can only be used if LAMMPS was built with the
-"USER-CGDNA"_#USER-CGDNA package and the MOLECULE and ASPHERE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+"USER-CGDNA"_#USER-CGDNA package and the MOLECULE and ASPHERE package.
+See the "Build package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_nve_eff.txt b/doc/src/fix_nve_eff.txt
index 7343ddc429..556b95deba 100644
--- a/doc/src/fix_nve_eff.txt
+++ b/doc/src/fix_nve_eff.txt
@@ -43,8 +43,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the USER-EFF package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_nve_line.txt b/doc/src/fix_nve_line.txt
index dd5101489b..896e3b810d 100644
--- a/doc/src/fix_nve_line.txt
+++ b/doc/src/fix_nve_line.txt
@@ -44,8 +44,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the ASPHERE package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This fix requires that particles be line segments as defined by the
"atom_style line"_atom_style.html command.
diff --git a/doc/src/fix_nve_manifold_rattle.txt b/doc/src/fix_nve_manifold_rattle.txt
index b333d093fb..5301ea603c 100644
--- a/doc/src/fix_nve_manifold_rattle.txt
+++ b/doc/src/fix_nve_manifold_rattle.txt
@@ -78,8 +78,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the USER-MANIFOLD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
:line
diff --git a/doc/src/fix_nve_sphere.txt b/doc/src/fix_nve_sphere.txt
index 6e259bdb8e..818940a9bd 100644
--- a/doc/src/fix_nve_sphere.txt
+++ b/doc/src/fix_nve_sphere.txt
@@ -71,13 +71,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/fix_nve_spin.txt b/doc/src/fix_nve_spin.txt
index e31185bc88..08f0eab61d 100644
--- a/doc/src/fix_nve_spin.txt
+++ b/doc/src/fix_nve_spin.txt
@@ -47,9 +47,9 @@ in "(Tranchida)"_#Tranchida1.
[Restrictions:]
-This fix style can only be used if LAMMPS was built with the
-SPIN package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+This fix style can only be used if LAMMPS was built with the SPIN
+package. See the "Build package"_Build_package.html doc page for more
+info.
To use the spin algorithm, it is necessary to define a map with
the atom_modify command. Typically, by adding the command:
diff --git a/doc/src/fix_nve_tri.txt b/doc/src/fix_nve_tri.txt
index ebdda19e36..c14907ca02 100644
--- a/doc/src/fix_nve_tri.txt
+++ b/doc/src/fix_nve_tri.txt
@@ -44,8 +44,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the ASPHERE package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This fix requires that particles be triangles as defined by the
"atom_style tri"_atom_style.html command.
diff --git a/doc/src/fix_nvk.txt b/doc/src/fix_nvk.txt
index e3189f8e8a..98f63487b7 100644
--- a/doc/src/fix_nvk.txt
+++ b/doc/src/fix_nvk.txt
@@ -54,9 +54,9 @@ the simulation box. Therefore, the group must be set to all.
This fix has not yet been implemented to work with the RESPA integrator.
-This fix is part of the USER-MISC package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+This fix is part of the USER-MISC package. It is only enabled if
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:] none
diff --git a/doc/src/fix_nvt_asphere.txt b/doc/src/fix_nvt_asphere.txt
index 7b97637175..a2187f8495 100644
--- a/doc/src/fix_nvt_asphere.txt
+++ b/doc/src/fix_nvt_asphere.txt
@@ -92,13 +92,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -133,8 +133,8 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix is part of the ASPHERE package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This fix requires that atoms store torque and angular momentum and a
quaternion as defined by the "atom_style ellipsoid"_atom_style.html
diff --git a/doc/src/fix_nvt_body.txt b/doc/src/fix_nvt_body.txt
index 4493a89277..62c7cfecf8 100644
--- a/doc/src/fix_nvt_body.txt
+++ b/doc/src/fix_nvt_body.txt
@@ -91,13 +91,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -132,8 +132,8 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix is part of the BODY package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This fix requires that atoms store torque and angular momentum and a
quaternion as defined by the "atom_style body"_atom_style.html
diff --git a/doc/src/fix_nvt_manifold_rattle.txt b/doc/src/fix_nvt_manifold_rattle.txt
index 1b4ad79166..0c4b81aa32 100644
--- a/doc/src/fix_nvt_manifold_rattle.txt
+++ b/doc/src/fix_nvt_manifold_rattle.txt
@@ -27,8 +27,6 @@ keyword = {temp} or {tchain} or {every}
N = length of thermostat chain (1 = single thermostat)
{every} value = N
N = print info about iteration every N steps. N = 0 means no output :pre
-
-
:ule
[Examples:]
@@ -59,20 +57,18 @@ minimization"_minimize.html.
:line
-
[Restrictions:]
-This fix is part of the USER-MANIFOLD package. It is only enabled if LAMMPS
-was built with that package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info.
+This fix is part of the USER-MANIFOLD package. It is only enabled if
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
:line
-
[Related commands:]
-"fix nve/manifold/rattle"_fix_nvt_manifold_rattle.html, "fix manifoldforce"_fix_manifoldforce.html
-[Default:] every = 0
+"fix nve/manifold/rattle"_fix_nvt_manifold_rattle.html, "fix
+manifoldforce"_fix_manifoldforce.html [Default:] every = 0
:line
diff --git a/doc/src/fix_nvt_sllod.txt b/doc/src/fix_nvt_sllod.txt
index 9eb5065369..97a864a231 100644
--- a/doc/src/fix_nvt_sllod.txt
+++ b/doc/src/fix_nvt_sllod.txt
@@ -115,13 +115,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/fix_nvt_sllod_eff.txt b/doc/src/fix_nvt_sllod_eff.txt
index 0200d5cb00..5cba15c8cf 100644
--- a/doc/src/fix_nvt_sllod_eff.txt
+++ b/doc/src/fix_nvt_sllod_eff.txt
@@ -69,8 +69,8 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix is part of the USER-EFF package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This fix works best without Nose-Hoover chain thermostats, i.e. using
tchain = 1. Setting tchain to larger values can result in poor
diff --git a/doc/src/fix_nvt_sphere.txt b/doc/src/fix_nvt_sphere.txt
index a87e4abe67..75222e0de8 100644
--- a/doc/src/fix_nvt_sphere.txt
+++ b/doc/src/fix_nvt_sphere.txt
@@ -102,13 +102,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/fix_orient.txt b/doc/src/fix_orient.txt
index 7552bea8c5..9d8e4e8628 100644
--- a/doc/src/fix_orient.txt
+++ b/doc/src/fix_orient.txt
@@ -151,8 +151,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the MISC package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This fix should only be used with fcc or bcc lattices.
diff --git a/doc/src/fix_phonon.txt b/doc/src/fix_phonon.txt
index 30e5864e3d..0c449899df 100644
--- a/doc/src/fix_phonon.txt
+++ b/doc/src/fix_phonon.txt
@@ -171,11 +171,11 @@ temperature of the system should not exceed the melting temperature to
keep the system in its solid state.
This fix is part of the USER-PHONON package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
-This fix requires LAMMPS be built with an FFT library. See the
-"Making LAMMPS"_Section_start.html#start_2 section for more info.
+This fix requires LAMMPS be built with an FFT library. See the "Build
+settings"_Build_settings.html doc page for details.
[Related commands:]
diff --git a/doc/src/fix_pimd.txt b/doc/src/fix_pimd.txt
index b61b3f3065..a826244973 100644
--- a/doc/src/fix_pimd.txt
+++ b/doc/src/fix_pimd.txt
@@ -136,8 +136,8 @@ read_restart system_$\{ibead\}.restart2 :pre
[Restrictions:]
This fix is part of the USER-MISC package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
A PIMD simulation can be initialized with a single data file read via
the "read_data"_read_data.html command. However, this means all
diff --git a/doc/src/fix_poems.txt b/doc/src/fix_poems.txt
index 1a79c2a048..52ab0ca44d 100644
--- a/doc/src/fix_poems.txt
+++ b/doc/src/fix_poems.txt
@@ -123,8 +123,8 @@ minimization"_minimize.html.
This fix is part of the POEMS package. It is only enabled if LAMMPS
was built with that package, which also requires the POEMS library be
-built and linked with LAMMPS. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+built and linked with LAMMPS. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_pour.txt b/doc/src/fix_pour.txt
index e58d8ebc3a..65f01c00fb 100644
--- a/doc/src/fix_pour.txt
+++ b/doc/src/fix_pour.txt
@@ -245,8 +245,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the GRANULAR package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
For 3d simulations, a gravity fix in the -z direction must be defined
for use in conjunction with this fix. For 2d simulations, gravity
diff --git a/doc/src/fix_precession_spin.txt b/doc/src/fix_precession_spin.txt
index fafe78448b..d58cd622b0 100644
--- a/doc/src/fix_precession_spin.txt
+++ b/doc/src/fix_precession_spin.txt
@@ -75,10 +75,10 @@ files"_restart.html.
[Restrictions:]
-The {precession/spin} style is part of the SPIN package.
-This style is only enabled if LAMMPS was built with this package, and
-if the atom_style "spin" was declared.
-See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+The {precession/spin} style is part of the SPIN package. This style
+is only enabled if LAMMPS was built with this package, and if the
+atom_style "spin" was declared. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_python_invoke.txt b/doc/src/fix_python_invoke.txt
index 5e0c0369a5..2a0124e6bf 100644
--- a/doc/src/fix_python_invoke.txt
+++ b/doc/src/fix_python_invoke.txt
@@ -62,9 +62,9 @@ case not work or in the worst case result in undefined behavior.
[Restrictions:]
-This fix is part of the PYTHON package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+This fix is part of the PYTHON package. It is only enabled if LAMMPS
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Building LAMMPS with the PYTHON package will link LAMMPS with the
Python library on your system. Settings to enable this are in the
diff --git a/doc/src/fix_python_move.txt b/doc/src/fix_python_move.txt
index a4e0eb3937..c64ee788af 100644
--- a/doc/src/fix_python_move.txt
+++ b/doc/src/fix_python_move.txt
@@ -91,8 +91,8 @@ minimization"_minimize.html.
[Restrictions:]
This pair style is part of the PYTHON package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_qbmsst.txt b/doc/src/fix_qbmsst.txt
index e96bd97f45..546d8c0813 100644
--- a/doc/src/fix_qbmsst.txt
+++ b/doc/src/fix_qbmsst.txt
@@ -189,8 +189,8 @@ in the command "fix qtb"_fix_qtb.html.
[Restrictions:]
This fix style is part of the USER-QTB package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
All cell dimensions must be periodic. This fix can not be used with a
triclinic cell. The QBMSST fix has been tested only for the group-ID
diff --git a/doc/src/fix_qeq.txt b/doc/src/fix_qeq.txt
index 27fb613ef9..46d2dd918c 100644
--- a/doc/src/fix_qeq.txt
+++ b/doc/src/fix_qeq.txt
@@ -187,8 +187,8 @@ Thexe fixes are invoked during "energy minimization"_minimize.html.
[Restrictions:]
These fixes are part of the QEQ package. They are only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_qeq_comb.txt b/doc/src/fix_qeq_comb.txt
index 99e86df030..714d03f602 100644
--- a/doc/src/fix_qeq_comb.txt
+++ b/doc/src/fix_qeq_comb.txt
@@ -68,13 +68,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/fix_qeq_reax.txt b/doc/src/fix_qeq_reax.txt
index cf16daf847..b62d46d9de 100644
--- a/doc/src/fix_qeq_reax.txt
+++ b/doc/src/fix_qeq_reax.txt
@@ -86,13 +86,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -102,8 +102,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This fix is part of the USER-REAXC package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This fix does not correctly handle interactions
involving multiple periodic images of the same atom. Hence, it should not
diff --git a/doc/src/fix_qmmm.txt b/doc/src/fix_qmmm.txt
index 657ee84181..2dbf935f93 100644
--- a/doc/src/fix_qmmm.txt
+++ b/doc/src/fix_qmmm.txt
@@ -54,8 +54,8 @@ fix is not invoked during "energy minimization"_minimize.html.
This fix is part of the USER-QMMM package. It is only enabled if
LAMMPS was built with that package. It also requires building a
-library provided with LAMMPS. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+library provided with LAMMPS. See the "Build
+package"_Build_package.html doc page for more info.
The fix is only functional when LAMMPS is built as a library and
linked with a compatible QM program and a QM/MM frontend into a QM/MM
diff --git a/doc/src/fix_qtb.txt b/doc/src/fix_qtb.txt
index 5b212934a9..c412146604 100644
--- a/doc/src/fix_qtb.txt
+++ b/doc/src/fix_qtb.txt
@@ -155,8 +155,8 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix style is part of the USER-QTB package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
:line
diff --git a/doc/src/fix_reax_bonds.txt b/doc/src/fix_reax_bonds.txt
index 49d61f4db8..06d30d871a 100644
--- a/doc/src/fix_reax_bonds.txt
+++ b/doc/src/fix_reax_bonds.txt
@@ -79,13 +79,13 @@ issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See "Speed"_Speed.html of the manual for
more instructions on how to use the accelerated styles effectively.
@@ -101,8 +101,8 @@ which also requires the REAX library be built and linked with LAMMPS.
The fix reax/c/bonds command requires that the "pair_style
reax/c"_pair_reaxc.html be invoked. This fix is part of the
USER-REAXC package. It is only enabled if LAMMPS was built with that
-package. See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info.
+package. See the "Build package"_Build_package.html doc page for more
+info.
To write gzipped bond files, you must compile LAMMPS with the
-DLAMMPS_GZIP option.
diff --git a/doc/src/fix_reaxc_species.txt b/doc/src/fix_reaxc_species.txt
index 5be1c46230..980384ff34 100644
--- a/doc/src/fix_reaxc_species.txt
+++ b/doc/src/fix_reaxc_species.txt
@@ -146,13 +146,13 @@ issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See "Speed"_Speed.html of the manual for
more instructions on how to use the accelerated styles effectively.
@@ -161,12 +161,12 @@ more instructions on how to use the accelerated styles effectively.
[Restrictions:]
-The fix species currently only works with
-"pair_style reax/c"_pair_reaxc.html and it requires that the "pair_style
+The fix species currently only works with "pair_style
+reax/c"_pair_reaxc.html and it requires that the "pair_style
reax/c"_pair_reaxc.html be invoked. This fix is part of the
USER-REAXC package. It is only enabled if LAMMPS was built with that
-package. See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info.
+package. See the "Build package"_Build_package.html doc page for more
+info.
To write gzipped species files, you must compile LAMMPS with the
-DLAMMPS_GZIP option.
diff --git a/doc/src/fix_rhok.txt b/doc/src/fix_rhok.txt
index 68cce694e9..a3d1ab702e 100644
--- a/doc/src/fix_rhok.txt
+++ b/doc/src/fix_rhok.txt
@@ -40,8 +40,8 @@ An example of using the interface pinning method is located in the
[Restrictions:]
This fix is part of the MISC package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_rigid.txt b/doc/src/fix_rigid.txt
index d5e3b01668..af4b51948e 100644
--- a/doc/src/fix_rigid.txt
+++ b/doc/src/fix_rigid.txt
@@ -696,13 +696,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -806,8 +806,8 @@ of the "run"_run.html command. These fixes are not invoked during
[Restrictions:]
These fixes are all part of the RIGID package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Assigning a temperature via the "velocity create"_velocity.html
command to a system with "rigid bodies"_fix_rigid.html may not have
diff --git a/doc/src/fix_rx.txt b/doc/src/fix_rx.txt
index d39e41e922..ad42c577aa 100644
--- a/doc/src/fix_rx.txt
+++ b/doc/src/fix_rx.txt
@@ -192,13 +192,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -208,8 +208,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This command is part of the USER-DPD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This command also requires use of the "atom_style dpd"_atom_style.html
command.
diff --git a/doc/src/fix_setforce.txt b/doc/src/fix_setforce.txt
index 14fceb7b49..4b9abba52f 100644
--- a/doc/src/fix_setforce.txt
+++ b/doc/src/fix_setforce.txt
@@ -77,13 +77,13 @@ region must be used. See the region "region"_region.html command for
more information.
These accelerated styles are part of the r Kokkos package. They are
-only enabled if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+only enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/fix_shake.txt b/doc/src/fix_shake.txt
index ea38de41cd..77bb5794f6 100644
--- a/doc/src/fix_shake.txt
+++ b/doc/src/fix_shake.txt
@@ -154,13 +154,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -202,8 +202,8 @@ fixes are not invoked during "energy minimization"_minimize.html.
[Restrictions:]
These fixes are part of the RIGID package. They are only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
For computational efficiency, there can only be one shake or rattle
fix defined in a simulation.
diff --git a/doc/src/fix_shardlow.txt b/doc/src/fix_shardlow.txt
index 33db2bf7cc..c1be146fa6 100644
--- a/doc/src/fix_shardlow.txt
+++ b/doc/src/fix_shardlow.txt
@@ -62,13 +62,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -78,8 +78,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This command is part of the USER-DPD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This fix is currently limited to orthogonal simulation cell
geometries.
diff --git a/doc/src/fix_smd.txt b/doc/src/fix_smd.txt
index 2f083dafc3..644c04eadb 100644
--- a/doc/src/fix_smd.txt
+++ b/doc/src/fix_smd.txt
@@ -130,8 +130,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the USER-MISC package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_smd_adjust_dt.txt b/doc/src/fix_smd_adjust_dt.txt
index 740b10559d..3535ddfcc2 100644
--- a/doc/src/fix_smd_adjust_dt.txt
+++ b/doc/src/fix_smd_adjust_dt.txt
@@ -25,18 +25,23 @@ fix 1 all smd/adjust_dt 0.1 :pre
[Description:]
-The fix calculates a new stable time increment for use with the SMD time integrators.
+The fix calculates a new stable time increment for use with the SMD
+time integrators.
-The stable time increment is based on multiple conditions. For the SPH pair styles, a
-CFL criterion (Courant, Friedrichs & Lewy, 1928) is evaluated, which determines the speed of
-sound cannot propagate further than a typical spacing between particles within a single time step to ensure
-no information is lost. For the contact pair styles, a linear analysis of the pair potential determines a
-stable maximum time step.
+The stable time increment is based on multiple conditions. For the SPH
+pair styles, a CFL criterion (Courant, Friedrichs & Lewy, 1928) is
+evaluated, which determines the speed of sound cannot propagate
+further than a typical spacing between particles within a single time
+step to ensure no information is lost. For the contact pair styles, a
+linear analysis of the pair potential determines a stable maximum time
+step.
-This fix inquires the minimum stable time increment across all particles contained in the group for which this
-fix is defined. An additional safety factor {s_fact} is applied to the time increment.
+This fix inquires the minimum stable time increment across all
+particles contained in the group for which this fix is defined. An
+additional safety factor {s_fact} is applied to the time increment.
-See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth Mach Dynamics in LAMMPS.
+See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth Mach
+Dynamics in LAMMPS.
[Restart, fix_modify, output, run start/stop, minimize info:]
@@ -45,8 +50,8 @@ Currently, no part of USER-SMD supports restarting nor minimization.
[Restrictions:]
This fix is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_smd_integrate_tlsph.txt b/doc/src/fix_smd_integrate_tlsph.txt
index cd676a51ce..029605ff7f 100644
--- a/doc/src/fix_smd_integrate_tlsph.txt
+++ b/doc/src/fix_smd_integrate_tlsph.txt
@@ -27,22 +27,26 @@ fix 1 all smd/integrate_tlsph limit_velocity 1000 :pre
[Description:]
-The fix performs explicit time integration for particles which interact according with the Total-Lagrangian SPH pair style.
+The fix performs explicit time integration for particles which
+interact according with the Total-Lagrangian SPH pair style.
-See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS.
+See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth Mach
+Dynamics in LAMMPS.
-The {limit_velocity} keyword will control the velocity, scaling the norm of
-the velocity vector to max_vel in case it exceeds this velocity limit.
+The {limit_velocity} keyword will control the velocity, scaling the
+norm of the velocity vector to max_vel in case it exceeds this
+velocity limit.
[Restart, fix_modify, output, run start/stop, minimize info:]
-Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs.
+Currently, no part of USER-SMD supports restarting nor
+minimization. This fix has no outputs.
[Restrictions:]
This fix is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_smd_integrate_ulsph.txt b/doc/src/fix_smd_integrate_ulsph.txt
index 7f16b4b7ce..a99574cc85 100644
--- a/doc/src/fix_smd_integrate_ulsph.txt
+++ b/doc/src/fix_smd_integrate_ulsph.txt
@@ -24,7 +24,6 @@ adjust_radius values = adjust_radius_factor min_nn max_nn
limit_velocity values = max_velocity
max_velocity = maximum allowed velocity.
-
[Examples:]
fix 1 all smd/integrate_ulsph adjust_radius 1.02 25 50
@@ -32,28 +31,33 @@ fix 1 all smd/integrate_ulsph limit_velocity 1000 :pre
[Description:]
-The fix performs explicit time integration for particles which interact with the updated Lagrangian SPH pair style.
-See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS.
+The fix performs explicit time integration for particles which
+interact with the updated Lagrangian SPH pair style.
+
+See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth Mach
+Dynamics in LAMMPS.
-The {adjust_radius} keyword activates dynamic adjustment of the per-particle SPH smoothing kernel radius such that the number of neighbors per particles remains
-within the interval {min_nn} to {max_nn}. The parameter {adjust_radius_factor} determines the amount of adjustment per timestep. Typical values are
-{adjust_radius_factor} =1.02, {min_nn} =15, and {max_nn} =20.
+The {adjust_radius} keyword activates dynamic adjustment of the
+per-particle SPH smoothing kernel radius such that the number of
+neighbors per particles remains within the interval {min_nn} to
+{max_nn}. The parameter {adjust_radius_factor} determines the amount
+of adjustment per timestep. Typical values are {adjust_radius_factor}
+=1.02, {min_nn} =15, and {max_nn} =20.
The {limit_velocity} keyword will control the velocity, scaling the norm of
the velocity vector to max_vel in case it exceeds this velocity limit.
[Restart, fix_modify, output, run start/stop, minimize info:]
-Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs.
+Currently, no part of USER-SMD supports restarting nor
+minimization. This fix has no outputs.
[Restrictions:]
This fix is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info.
-
-[Related commands:]
-
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
+[Related commands:] none
[Default:] none
diff --git a/doc/src/fix_smd_move_triangulated_surface.txt b/doc/src/fix_smd_move_triangulated_surface.txt
index aeabf18768..2a998ba8c6 100644
--- a/doc/src/fix_smd_move_triangulated_surface.txt
+++ b/doc/src/fix_smd_move_triangulated_surface.txt
@@ -25,7 +25,6 @@ keyword = {*LINEAR} or {*WIGGLE} or {*ROTATE} :l
Px,Py,Pz = origin point of axis of rotation (distance units)
Rx,Ry,Rz = axis of rotation vector
period = period of rotation (time units) :pre
-
:ule
[Examples:]
@@ -36,9 +35,11 @@ fix 2 tool smd/move_tri_surf *ROTATE 0 0 0 5 2 1 :pre
[Description:]
-This fix applies only to rigid surfaces read from .STL files via fix "smd/wall_surface"_fix_smd_wall_surface.html .
-It updates position and velocity for the particles in the group each timestep without regard to forces on the particles.
-The rigid surfaces can thus be moved along simple trajectories during the simulation.
+This fix applies only to rigid surfaces read from .STL files via fix
+"smd/wall_surface"_fix_smd_wall_surface.html . It updates position
+and velocity for the particles in the group each timestep without
+regard to forces on the particles. The rigid surfaces can thus be
+moved along simple trajectories during the simulation.
The {*LINEAR} style moves particles with the specified constant velocity
vector V = (Vx,Vy,Vz). This style also sets the velocity of each particle
@@ -49,27 +50,30 @@ Particles are moved along (vx, vy, vz) with constant velocity until a
displacement of max_travel is reached. Then, the velocity vector is
reversed. This process is repeated.
-The {*ROTATE} style rotates particles around a rotation axis R = (Rx,Ry,Rz) that
-goes through a point P = (Px,Py,Pz). The period of the rotation is also
-specified. This style also sets the velocity of each particle to (omega cross
-Rperp) where omega is its angular velocity around the rotation axis and
-Rperp is a perpendicular vector from the rotation axis to the particle.
+The {*ROTATE} style rotates particles around a rotation axis R =
+(Rx,Ry,Rz) that goes through a point P = (Px,Py,Pz). The period of the
+rotation is also specified. This style also sets the velocity of each
+particle to (omega cross Rperp) where omega is its angular velocity
+around the rotation axis and Rperp is a perpendicular vector from the
+rotation axis to the particle.
-See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS.
+See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth Mach
+Dynamics in LAMMPS.
[Restart, fix_modify, output, run start/stop, minimize info:]
-Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs.
+Currently, no part of USER-SMD supports restarting nor
+minimization. This fix has no outputs.
[Restrictions:]
This fix is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info.
-
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
-"smd/triangle_mesh_vertices"_compute_smd_triangle_mesh_vertices.html, "smd/wall_surface"_fix_smd_wall_surface.html
+"smd/triangle_mesh_vertices"_compute_smd_triangle_mesh_vertices.html,
+"smd/wall_surface"_fix_smd_wall_surface.html
[Default:] none
diff --git a/doc/src/fix_smd_setvel.txt b/doc/src/fix_smd_setvel.txt
index 6634751d6a..b170eff860 100644
--- a/doc/src/fix_smd_setvel.txt
+++ b/doc/src/fix_smd_setvel.txt
@@ -76,8 +76,8 @@ the "run"_run.html command.
[Restrictions:]
This fix is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:] none
diff --git a/doc/src/fix_smd_wall_surface.txt b/doc/src/fix_smd_wall_surface.txt
index a19b2c4cfb..dc3625e95e 100644
--- a/doc/src/fix_smd_wall_surface.txt
+++ b/doc/src/fix_smd_wall_surface.txt
@@ -17,9 +17,7 @@ smd/wall_surface = style name of this fix command :l
arg = {file} :l
{file} = file name of a triangular mesh in stl format :pre
type = particle type to be given to the new particles created by this fix :l
-mol-ID = molecule-ID to be given to the new particles created by this fix (must be >= 65535) :l
-
-:ule
+mol-ID = molecule-ID to be given to the new particles created by this fix (must be >= 65535) :l,ule
[Examples:]
@@ -27,32 +25,47 @@ fix stl_surf all smd/wall_surface tool.stl 2 65535 :pre
[Description:]
-This fix creates reads a triangulated surface from a file in .STL format.
-For each triangle, a new particle is created which stores the barycenter of the triangle and the vertex positions.
-The radius of the new particle is that of the minimum circle which encompasses the triangle vertices.
+This fix creates reads a triangulated surface from a file in .STL
+format. For each triangle, a new particle is created which stores the
+barycenter of the triangle and the vertex positions. The radius of
+the new particle is that of the minimum circle which encompasses the
+triangle vertices.
-The triangulated surface can be used as a complex rigid wall via the "smd/tri_surface"_pair_smd_triangulated_surface.html pair style.
-It is possible to move the triangulated surface via the "smd/move_tri_surf"_fix_smd_move_triangulated_surface.html fix style.
+The triangulated surface can be used as a complex rigid wall via the
+"smd/tri_surface"_pair_smd_triangulated_surface.html pair style. It
+is possible to move the triangulated surface via the
+"smd/move_tri_surf"_fix_smd_move_triangulated_surface.html fix style.
-Immediately after a .STL file has been read, the simulation needs to be run for 0 timesteps in order to properly register the new particles
-in the system. See the "funnel_flow" example in the USER-SMD examples directory.
+Immediately after a .STL file has been read, the simulation needs to
+be run for 0 timesteps in order to properly register the new particles
+in the system. See the "funnel_flow" example in the USER-SMD examples
+directory.
-See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth Mach Dynamics in LAMMPS.
+See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth Mach
+Dynamics in LAMMPS.
[Restart, fix_modify, output, run start/stop, minimize info:]
-Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs.
+Currently, no part of USER-SMD supports restarting nor
+minimization. This fix has no outputs.
[Restrictions:]
This fix is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info. The molecule ID given to the particles created by this fix have to be equal to or larger than 65535.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
+
+The molecule ID given to the particles created by this fix have to be
+equal to or larger than 65535.
-Within each .STL file, only a single triangulated object must be present, even though the STL format allows for the possibility of multiple objects in one file.
+Within each .STL file, only a single triangulated object must be
+present, even though the STL format allows for the possibility of
+multiple objects in one file.
[Related commands:]
-"smd/triangle_mesh_vertices"_compute_smd_triangle_mesh_vertices.html, "smd/move_tri_surf"_fix_smd_move_triangulated_surface.html, "smd/tri_surface"_pair_smd_triangulated_surface.html
+"smd/triangle_mesh_vertices"_compute_smd_triangle_mesh_vertices.html,
+"smd/move_tri_surf"_fix_smd_move_triangulated_surface.html,
+"smd/tri_surface"_pair_smd_triangulated_surface.html
[Default:] none
diff --git a/doc/src/fix_srd.txt b/doc/src/fix_srd.txt
index 893557b9ac..557eee1cfc 100644
--- a/doc/src/fix_srd.txt
+++ b/doc/src/fix_srd.txt
@@ -371,8 +371,8 @@ minimization"_minimize.html.
[Restrictions:]
This command can only be used if LAMMPS was built with the SRD
-package. See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info on packages.
+package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/fix_temp_rescale_eff.txt b/doc/src/fix_temp_rescale_eff.txt
index 0e08e4f1e8..83b360df85 100644
--- a/doc/src/fix_temp_rescale_eff.txt
+++ b/doc/src/fix_temp_rescale_eff.txt
@@ -64,8 +64,8 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix is part of the USER-EFF package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_tfmc.txt b/doc/src/fix_tfmc.txt
index ddfa462619..2d4f003607 100644
--- a/doc/src/fix_tfmc.txt
+++ b/doc/src/fix_tfmc.txt
@@ -125,8 +125,8 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix is part of the MC package. It is only enabled if LAMMPS was
-built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+built with that package. See the "Build package"_Build_package.html
+doc page for more info.
This fix is not compatible with "fix shake"_fix_shake.html.
diff --git a/doc/src/fix_thermal_conductivity.txt b/doc/src/fix_thermal_conductivity.txt
index 86fc6f2c72..2ab32b25f0 100644
--- a/doc/src/fix_thermal_conductivity.txt
+++ b/doc/src/fix_thermal_conductivity.txt
@@ -123,8 +123,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the MISC package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Swaps conserve both momentum and kinetic energy, even if the masses of
the swapped atoms are not equal. Thus you should not need to
diff --git a/doc/src/fix_ti_spring.txt b/doc/src/fix_ti_spring.txt
index afe5373220..290ee95b9a 100644
--- a/doc/src/fix_ti_spring.txt
+++ b/doc/src/fix_ti_spring.txt
@@ -146,8 +146,8 @@ this fix.
[Restrictions:]
This fix is part of the USER-MISC package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Default:]
diff --git a/doc/src/fix_tmd.txt b/doc/src/fix_tmd.txt
index c2541692f5..73e95ba9fe 100644
--- a/doc/src/fix_tmd.txt
+++ b/doc/src/fix_tmd.txt
@@ -110,8 +110,8 @@ are not multiple competing holonomic constraints applied to the same
atoms.
To read gzipped target files, you must compile LAMMPS with the
--DLAMMPS_GZIP option - see the "Making
-LAMMPS"_Section_start.html#start_2 section of the documentation.
+-DLAMMPS_GZIP option. See the "Build settings"_Build_settings.html
+doc page for details.
[Related commands:] none
diff --git a/doc/src/fix_ttm.txt b/doc/src/fix_ttm.txt
index 6001def581..85407f2466 100644
--- a/doc/src/fix_ttm.txt
+++ b/doc/src/fix_ttm.txt
@@ -295,8 +295,7 @@ of the "run"_run.html command. The fixes are not invoked during
Fix {ttm} is part of the MISC package. It is only enabled if LAMMPS
was built with that package. Fix {ttm/mod} is part of the USER-MISC
package. It is only enabled if LAMMPS was built with that package.
-See the "Making LAMMPS"_Section_start.html#start_3 section for more
-info.
+See the "Build package"_Build_package.html doc page for more info.
These fixes can only be used for 3d simulations and orthogonal
simulation boxes. You must also use periodic
diff --git a/doc/src/fix_tune_kspace.txt b/doc/src/fix_tune_kspace.txt
index b4e8472591..147bb1eb3d 100644
--- a/doc/src/fix_tune_kspace.txt
+++ b/doc/src/fix_tune_kspace.txt
@@ -79,9 +79,9 @@ minimization"_minimize.html.
[Restrictions:]
-This fix is part of the KSPACE package. It is only enabled if LAMMPS was
-built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+This fix is part of the KSPACE package. It is only enabled if LAMMPS
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Do not set "neigh_modify once yes" or else this fix will never be
called. Reneighboring is required.
diff --git a/doc/src/fix_viscosity.txt b/doc/src/fix_viscosity.txt
index 934da3efdd..d86b13d055 100644
--- a/doc/src/fix_viscosity.txt
+++ b/doc/src/fix_viscosity.txt
@@ -129,8 +129,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the MISC package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Swaps conserve both momentum and kinetic energy, even if the masses of
the swapped atoms are not equal. Thus you should not need to
diff --git a/doc/src/fix_wall.txt b/doc/src/fix_wall.txt
index 2ac59d9588..162e32c68c 100644
--- a/doc/src/fix_wall.txt
+++ b/doc/src/fix_wall.txt
@@ -294,13 +294,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/fix_wall_body_polygon.txt b/doc/src/fix_wall_body_polygon.txt
index 0946a85131..45cbb2841d 100644
--- a/doc/src/fix_wall_body_polygon.txt
+++ b/doc/src/fix_wall_body_polygon.txt
@@ -91,8 +91,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the BODY package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Any dimension (xy) that has a wall must be non-periodic.
diff --git a/doc/src/fix_wall_body_polyhedron.txt b/doc/src/fix_wall_body_polyhedron.txt
index 407cf9fb33..231ab1f0fe 100644
--- a/doc/src/fix_wall_body_polyhedron.txt
+++ b/doc/src/fix_wall_body_polyhedron.txt
@@ -89,9 +89,9 @@ minimization"_minimize.html.
[Restrictions:]
-This fix is part of the BODY package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+This fix is part of the BODY package. It is only enabled if LAMMPS
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Any dimension (xyz) that has a wall must be non-periodic.
diff --git a/doc/src/fix_wall_ees.txt b/doc/src/fix_wall_ees.txt
index ae16ca40d2..4cc91f5222 100644
--- a/doc/src/fix_wall_ees.txt
+++ b/doc/src/fix_wall_ees.txt
@@ -97,8 +97,8 @@ of using this fix in the examples/USER/misc/ees/ directory.
[Restrictions:]
This fix is part of the USER-MISC package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This fix requires that atoms be ellipsoids as defined by the
"atom_style ellipsoid"_atom_style.html command.
diff --git a/doc/src/fix_wall_gran.txt b/doc/src/fix_wall_gran.txt
index 6c2769fc12..0ea5b194eb 100644
--- a/doc/src/fix_wall_gran.txt
+++ b/doc/src/fix_wall_gran.txt
@@ -156,8 +156,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the GRANULAR package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Any dimension (xyz) that has a granular wall must be non-periodic.
diff --git a/doc/src/fix_wall_gran_region.txt b/doc/src/fix_wall_gran_region.txt
index 187214c1a3..50d744b305 100644
--- a/doc/src/fix_wall_gran_region.txt
+++ b/doc/src/fix_wall_gran_region.txt
@@ -188,8 +188,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the GRANULAR package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_wall_piston.txt b/doc/src/fix_wall_piston.txt
index eecf69ebf2..b1968e0d49 100644
--- a/doc/src/fix_wall_piston.txt
+++ b/doc/src/fix_wall_piston.txt
@@ -99,8 +99,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix style is part of the SHOCK package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
The face that has the wall/piston must be boundary type 's'
(shrink-wrapped). The opposing face can be
diff --git a/doc/src/fix_wall_reflect.txt b/doc/src/fix_wall_reflect.txt
index 78be84eb63..e4dd7e2fb9 100644
--- a/doc/src/fix_wall_reflect.txt
+++ b/doc/src/fix_wall_reflect.txt
@@ -136,13 +136,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/group2ndx.txt b/doc/src/group2ndx.txt
index 242d6a69a4..ed9bcb003a 100644
--- a/doc/src/group2ndx.txt
+++ b/doc/src/group2ndx.txt
@@ -54,8 +54,8 @@ This command requires that atoms have atom IDs, since this is the
information that is written to the index file.
These commands are part of the USER-COLVARS package. They are only
-enabled if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/improper_class2.txt b/doc/src/improper_class2.txt
index c38f73c64d..704944920e 100644
--- a/doc/src/improper_class2.txt
+++ b/doc/src/improper_class2.txt
@@ -93,13 +93,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -109,8 +109,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This improper style can only be used if LAMMPS was built with the
-CLASS2 package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+CLASS2 package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/improper_cossq.txt b/doc/src/improper_cossq.txt
index 04aa45255c..8bd02afb84 100644
--- a/doc/src/improper_cossq.txt
+++ b/doc/src/improper_cossq.txt
@@ -59,13 +59,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -75,8 +75,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This improper style can only be used if LAMMPS was built with the
-USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER-MISC package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/improper_cvff.txt b/doc/src/improper_cvff.txt
index d01faf2885..d57fddc512 100644
--- a/doc/src/improper_cvff.txt
+++ b/doc/src/improper_cvff.txt
@@ -60,13 +60,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -76,8 +76,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This improper style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+MOLECULE package. See the "Build package"_Build_package.html doc page
+for more info.
[Related commands:]
diff --git a/doc/src/improper_distance.txt b/doc/src/improper_distance.txt
index 93235fe601..bfd92f57ec 100644
--- a/doc/src/improper_distance.txt
+++ b/doc/src/improper_distance.txt
@@ -48,8 +48,8 @@ K_4 (energy/distance^4) :ul
[Restrictions:]
This improper style can only be used if LAMMPS was built with the
-USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER-MISC package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/improper_fourier.txt b/doc/src/improper_fourier.txt
index 78cc1b3f76..8b2021dccd 100644
--- a/doc/src/improper_fourier.txt
+++ b/doc/src/improper_fourier.txt
@@ -54,13 +54,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -70,8 +70,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-USER_MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER_MISC package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/improper_harmonic.txt b/doc/src/improper_harmonic.txt
index f398dc425f..1e9e7172f9 100644
--- a/doc/src/improper_harmonic.txt
+++ b/doc/src/improper_harmonic.txt
@@ -64,13 +64,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -80,8 +80,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This improper style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+MOLECULE package. See the "Build package"_Build_package.html doc page
+for more info.
[Related commands:]
diff --git a/doc/src/improper_hybrid.txt b/doc/src/improper_hybrid.txt
index 42afbe8577..929eec43e1 100644
--- a/doc/src/improper_hybrid.txt
+++ b/doc/src/improper_hybrid.txt
@@ -55,8 +55,8 @@ types.
[Restrictions:]
This improper style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+MOLECULE package. See the "Build package"_Build_package.html doc page
+for more info.
Unlike other improper styles, the hybrid improper style does not store
improper coefficient info for individual sub-styles in a "binary
diff --git a/doc/src/improper_inversion_harmonic.txt b/doc/src/improper_inversion_harmonic.txt
index 2c0f2f0af8..43ffdeb8e9 100644
--- a/doc/src/improper_inversion_harmonic.txt
+++ b/doc/src/improper_inversion_harmonic.txt
@@ -52,8 +52,8 @@ in between.
[Restrictions:]
This improper style can only be used if LAMMPS was built with the
-USER-MOFFF package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+USER-MOFFF package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/improper_ring.txt b/doc/src/improper_ring.txt
index 60bbca170a..8a2ee29e17 100644
--- a/doc/src/improper_ring.txt
+++ b/doc/src/improper_ring.txt
@@ -63,13 +63,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -79,8 +79,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This improper style can only be used if LAMMPS was built with the
-USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER-MISC package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/improper_style.txt b/doc/src/improper_style.txt
index 3d29b28ec4..ef0c524d14 100644
--- a/doc/src/improper_style.txt
+++ b/doc/src/improper_style.txt
@@ -81,10 +81,9 @@ Improper styles can only be set for atom_style choices that allow
impropers to be defined.
Most improper styles are part of the MOLECULE package. They are only
-enabled if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
-The doc pages for individual improper potentials tell if it is part of
-a package.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info. The doc pages for
+individual improper potentials tell if it is part of a package.
[Related commands:]
diff --git a/doc/src/improper_umbrella.txt b/doc/src/improper_umbrella.txt
index b05cf4b181..6c29ec7ac5 100644
--- a/doc/src/improper_umbrella.txt
+++ b/doc/src/improper_umbrella.txt
@@ -57,13 +57,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -73,8 +73,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This improper style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+MOLECULE package. See the "Build package"_Build_package.html doc page
+for more info.
[Related commands:]
diff --git a/doc/src/jump.txt b/doc/src/jump.txt
index b5afeb6559..2e26d32c40 100644
--- a/doc/src/jump.txt
+++ b/doc/src/jump.txt
@@ -40,15 +40,14 @@ lmp_g++ < in.script :pre
since the SELF option invokes the C-library rewind() call, which may
not be supported for stdin on some systems or by some MPI
implementations. This can be worked around by using the "-in
-command-line argument"_Section_start.html#start_6, e.g.
+command-line switch"_Run_options.html, e.g.
lmp_g++ -in in.script :pre
-or by using the "-var command-line
-argument"_Section_start.html#start_6 to pass the script name as a
-variable to the input script. In the latter case, a
-"variable"_variable.html called "fname" could be used in place of
-SELF, e.g.
+or by using the "-var command-line switch"_Run_options.html to pass
+the script name as a variable to the input script. In the latter
+case, a "variable"_variable.html called "fname" could be used in place
+of SELF, e.g.
lmp_g++ -var fname in.script < in.script :pre
diff --git a/doc/src/kspace_style.txt b/doc/src/kspace_style.txt
index 55ad4ab610..7e479c76a6 100644
--- a/doc/src/kspace_style.txt
+++ b/doc/src/kspace_style.txt
@@ -180,9 +180,9 @@ lo-level Makefile. This setting also changes some of the PPPM
operations (e.g. mapping charge to mesh and interpolating electric
fields to particles) to be performed in single precision. This option
can speed-up long-range calculations, particularly in parallel or on
-GPUs. The use of the -DFFT_SINGLE flag is discussed in "this
-section"_Section_start.html#start_2_4 of the manual. MSM does not
-currently support the -DFFT_SINGLE compiler switch.
+GPUs. The use of the -DFFT_SINGLE flag is discussed on the "Build
+settings"_Build_settings.html doc page. MSM does not currently support
+the -DFFT_SINGLE compiler switch.
:line
@@ -286,10 +286,10 @@ The {pppm/kk} style also performs charge assignment and force
interpolation calculations on the GPU while the FFTs themselves are
calculated on the CPU in non-threaded mode.
-These accelerated styles are part of the GPU, USER-INTEL,
-KOKKOS, USER-OMP, and OPT packages respectively. They are only
-enabled if LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP, and OPT packages respectively. They are only enabled if
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -308,9 +308,9 @@ triclinic simulation cells may not yet be supported by suffix versions
of these styles.
All of the kspace styles are part of the KSPACE package. They are
-only enabled if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info. Note that
-the KSPACE package is installed by default.
+only enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info. Note that the
+KSPACE package is installed by default.
For MSM, a simulation must be 3d and one can use any combination of
periodic, non-periodic, or shrink-wrapped boundaries (specified using
diff --git a/doc/src/lammps.book b/doc/src/lammps.book
index c0ca357f21..88ef6d77cb 100644
--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@@ -8,7 +8,27 @@ Intro_nonfeatures.html
Intro_opensource.html
Intro_authors.html
Intro_website.html
-Section_start.html
+Install.html
+Install_linux.html
+Install_mac.html
+Install_windows.html
+Install_tarball.html
+Install_git.html
+Install_svn.html
+Install_patch.html
+Build.html
+Build_cmake.html
+Build_make.html
+Build_link.html
+Build_basics.html
+Build_settings.html
+Build_package.html
+Build_extras.html
+Run.html
+Run_basics.html
+Run_options.html
+Run_output.html
+Run_windows.html
Commands.html
Commands_input.html
Commands_parse.html
diff --git a/doc/src/log.txt b/doc/src/log.txt
index 7603768519..d526158a3c 100644
--- a/doc/src/log.txt
+++ b/doc/src/log.txt
@@ -33,9 +33,8 @@ be a variable, so that different processors do not attempt to write to
the same log file.
The file "log.lammps" is the default log file for a LAMMPS run. The
-name of the initial log file can also be set by the command-line
-switch -log. See "Section 2.6"_Section_start.html#start_6 for
-details.
+name of the initial log file can also be set by the "-log command-line
+switch"_Run_options.html.
[Restrictions:] none
diff --git a/doc/src/neb.txt b/doc/src/neb.txt
index fbd77ee329..57e122fdcd 100644
--- a/doc/src/neb.txt
+++ b/doc/src/neb.txt
@@ -50,14 +50,14 @@ follows the discussion in these 4 papers: "(HenkelmanA)"_#HenkelmanA,
"(HenkelmanB)"_#HenkelmanB, "(Nakano)"_#Nakano3 and "(Maras)"_#Maras2.
Each replica runs on a partition of one or more processors. Processor
-partitions are defined at run-time using the -partition command-line
-switch; see "Section 2.6"_Section_start.html#start_6 of the manual.
-Note that if you have MPI installed, you can run a multi-replica
-simulation with more replicas (partitions) than you have physical
-processors, e.g you can run a 10-replica simulation on just one or two
-processors. You will simply not get the performance speed-up you
-would see with one or more physical processors per replica. See the
-"Howto replica"_Howto_replica.html doc page for further discussion.
+partitions are defined at run-time using the "-partition command-line
+switch"_Run_options.html. Note that if you have MPI installed, you
+can run a multi-replica simulation with more replicas (partitions)
+than you have physical processors, e.g you can run a 10-replica
+simulation on just one or two processors. You will simply not get the
+performance speed-up you would see with one or more physical
+processors per replica. See the "Howto replica"_Howto_replica.html
+doc page for further discussion.
NOTE: As explained below, a NEB calculation perfoms a damped dynamics
minimization across all the replicas. The minimizer uses whatever
@@ -395,8 +395,8 @@ image.
[Restrictions:]
This command can only be used if LAMMPS was built with the REPLICA
-package. See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info on packages.
+package. See the "Build package"_Build_package.html doc
+page for more info.
:line
diff --git a/doc/src/neighbor.txt b/doc/src/neighbor.txt
index 7c7e7b05e5..3e590eaff1 100644
--- a/doc/src/neighbor.txt
+++ b/doc/src/neighbor.txt
@@ -65,8 +65,8 @@ stored in the list.
When a run is finished, counts of the number of neighbors stored in
the pairwise list and the number of times neighbor lists were built
-are printed to the screen and log file. See "this
-section"_Section_start.html#start_7 for details.
+are printed to the screen and log file. See the "Run
+output"_Run_output.html doc page for details.
[Restrictions:] none
diff --git a/doc/src/next.txt b/doc/src/next.txt
index 5a0b30b2a7..aefb2ca594 100644
--- a/doc/src/next.txt
+++ b/doc/src/next.txt
@@ -70,11 +70,11 @@ incrementing is done, using a single lock file for all variables. The
next value (for each variable) is assigned to whichever processor
partition executes the command first. All processors in the partition
are assigned the same value(s). Running LAMMPS on multiple partitions
-of processors via the "-partition" command-line switch is described in
-"this section"_Section_start.html#start_6 of the manual. {Universe}-
-and {uloop}-style variables are incremented using the files
-"tmp.lammps.variable" and "tmp.lammps.variable.lock" which you will
-see in your directory during and after such a LAMMPS run.
+of processors via the "-partition command-line
+switch"_Run_options.html. {Universe}- and {uloop}-style variables are
+incremented using the files "tmp.lammps.variable" and
+"tmp.lammps.variable.lock" which you will see in your directory during
+and after such a LAMMPS run.
Here is an example of running a series of simulations using the next
command with an {index}-style variable. If this input script is named
diff --git a/doc/src/package.txt b/doc/src/package.txt
index c2e7345bb7..76246c22f6 100644
--- a/doc/src/package.txt
+++ b/doc/src/package.txt
@@ -121,8 +121,8 @@ their initialization, before a simulation is defined.
This command can also be specified from the command-line when
launching LAMMPS, using the "-pk" "command-line
-switch"_Section_start.html#start_6. The syntax is exactly the same as
-when used in an input script.
+switch"_Run_options.html. The syntax is exactly the same as when used
+in an input script.
Note that all of the accelerator packages require the package command
to be specified (except the OPT package), if the package is to be used
@@ -132,22 +132,21 @@ a default version of the command is typically invoked by other
accelerator settings.
The KOKKOS package requires a "-k on" "command-line
-switch"_Section_start.html#start_6 respectively, which invokes a
-"package kokkos" command with default settings.
+switch"_Run_options.html respectively, which invokes a "package
+kokkos" command with default settings.
For the GPU, USER-INTEL, and USER-OMP packages, if a "-sf gpu" or "-sf
-intel" or "-sf omp" "command-line switch"_Section_start.html#start_6
-is used to auto-append accelerator suffixes to various styles in the
-input script, then those switches also invoke a "package gpu",
-"package intel", or "package omp" command with default settings.
+intel" or "-sf omp" "command-line switch"_Run_options.html is used to
+auto-append accelerator suffixes to various styles in the input
+script, then those switches also invoke a "package gpu", "package
+intel", or "package omp" command with default settings.
NOTE: A package command for a particular style can be invoked multiple
-times when a simulation is setup, e.g. by the "-c on", "-k on", "-sf",
-and "-pk" "command-line switches"_Section_start.html#start_6, and by
-using this command in an input script. Each time it is used all of
-the style options are set, either to default values or to specified
-settings. I.e. settings from previous invocations do not persist
-across multiple invocations.
+times when a simulation is setup, e.g. by the "-c on, -k on, -sf, and
+-pk command-line switches"_Run_options.html, and by using this command
+in an input script. Each time it is used all of the style options are
+set, either to default values or to specified settings. I.e. settings
+from previous invocations do not persist across multiple invocations.
See the "Speed packages"_Speed_packages.html doc page for more details
about using the various accelerator packages for speeding up LAMMPS
@@ -338,10 +337,10 @@ value via their package commands, but there is only a single global
{Nthreads} value used by OpenMP. Thus if both package commands are
invoked, you should insure the two values are consistent. If they are
not, the last one invoked will take precedence, for both packages.
-Also note that if the "-sf hybrid intel omp" "command-line
-switch"_"_Section_start.html#start_6 is used, it invokes a "package
-intel" command, followed by a "package omp" command, both with a
-setting of {Nthreads} = 0.
+Also note that if the "-sf hybrid intel omp command-line
+switch"_Run_options.html is used, it invokes a "package intel"
+command, followed by a "package omp" command, both with a setting of
+{Nthreads} = 0.
The {mode} keyword determines the precision mode to use for
computing pair style forces, either on the CPU or on the coprocessor,
@@ -568,58 +567,56 @@ This command cannot be used after the simulation box is defined by a
"read_data"_read_data.html or "create_box"_create_box.html command.
The gpu style of this command can only be invoked if LAMMPS was built
-with the GPU package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+with the GPU package. See the "Build package"_Build_package.html doc
+page for more info.
The intel style of this command can only be invoked if LAMMPS was
-built with the USER-INTEL package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+built with the USER-INTEL package. See the "Build
+package"_Build_package.html doc page for more info.
The kk style of this command can only be invoked if LAMMPS was built
-with the KOKKOS package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+with the KOKKOS package. See the "Build package"_Build_package.html
+doc page for more info.
The omp style of this command can only be invoked if LAMMPS was built
-with the USER-OMP package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+with the USER-OMP package. See the "Build package"_Build_package.html
+doc page for more info.
[Related commands:]
-"suffix"_suffix.html, "-pk" "command-line
-setting"_Section_start.html#start_6
+"suffix"_suffix.html, "-pk command-line switch"_Run_options.html
[Default:]
For the GPU package, the default is Ngpu = 1 and the option defaults
are neigh = yes, newton = off, binsize = 0.0, split = 1.0, gpuID = 0
to Ngpu-1, tpa = 1, and device = not used. These settings are made
-automatically if the "-sf gpu" "command-line
-switch"_Section_start.html#start_6 is used. If it is not used, you
-must invoke the package gpu command in your input script or via the
-"-pk gpu" "command-line switch"_Section_start.html#start_6.
+automatically if the "-sf gpu" "command-line switch"_Run_options.html
+is used. If it is not used, you must invoke the package gpu command
+in your input script or via the "-pk gpu" "command-line
+switch"_Run_options.html.
For the USER-INTEL package, the default is Nphi = 1 and the option
defaults are omp = 0, mode = mixed, lrt = no, balance = -1, tpc = 4,
tptask = 240. The default ghost option is determined by the pair
style being used. This value is output to the screen in the offload
report at the end of each run. Note that all of these settings,
-except "omp" and "mode", are ignored if LAMMPS was not built with
-Xeon Phi coprocessor support. These settings are made automatically
-if the "-sf intel" "command-line switch"_Section_start.html#start_6
-is used. If it is not used, you must invoke the package intel
-command in your input script or or via the "-pk intel" "command-line
-switch"_Section_start.html#start_6.
-
-For the KOKKOS package, the option defaults neigh = full,
-neigh/qeq = full, newton = off, binsize = 0.0, and comm = device.
-These settings are made automatically by the required "-k on" "command-line
-switch"_Section_start.html#start_6. You can change them bu using the
-package kokkos command in your input script or via the "-pk kokkos"
-"command-line switch"_Section_start.html#start_6.
+except "omp" and "mode", are ignored if LAMMPS was not built with Xeon
+Phi coprocessor support. These settings are made automatically if the
+"-sf intel" "command-line switch"_Run_options.html is used. If it is
+not used, you must invoke the package intel command in your input
+script or or via the "-pk intel" "command-line
+switch"_Run_options.html.
+
+For the KOKKOS package, the option defaults neigh = full, neigh/qeq =
+full, newton = off, binsize = 0.0, and comm = device. These settings
+are made automatically by the required "-k on" "command-line
+switch"_Run_options.html. You can change them bu using the package
+kokkos command in your input script or via the "-pk kokkos"
+"command-line switch"_Run_options.html.
For the OMP package, the default is Nthreads = 0 and the option
defaults are neigh = yes. These settings are made automatically if
-the "-sf omp" "command-line switch"_Section_start.html#start_6 is
-used. If it is not used, you must invoke the package omp command in
-your input script or via the "-pk omp" "command-line
-switch"_Section_start.html#start_6.
+the "-sf omp" "command-line switch"_Run_options.html is used. If it
+is not used, you must invoke the package omp command in your input
+script or via the "-pk omp" "command-line switch"_Run_options.html.
diff --git a/doc/src/pair_adp.txt b/doc/src/pair_adp.txt
index 382a97ecea..fc888ffbff 100644
--- a/doc/src/pair_adp.txt
+++ b/doc/src/pair_adp.txt
@@ -131,13 +131,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/pair_agni.txt b/doc/src/pair_agni.txt
index 34f9900139..74aef41255 100644
--- a/doc/src/pair_agni.txt
+++ b/doc/src/pair_agni.txt
@@ -64,14 +64,14 @@ packages"_Speed_packages.html doc page. The accelerated style takes
the same arguments and should produce the same results, except for
round-off and precision issues.
-The accelerated style is part of the USER-OMP. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+The accelerated style is part of the USER-OMP. They are only enabled
+if LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated style explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -96,13 +96,14 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
-Currently, only elemental systems are implemented. Also, the method only
-provides access to the forces and not energies or stresses. However, one
-can access the energy via thermodynamic integration of the forces as
-discussed in "(Botu3)"_#Botu2016construct. This pair style is part
-of the USER-MISC package. It is only enabled if LAMMPS was built with
-that package. See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info.
+Currently, only elemental systems are implemented. Also, the method
+only provides access to the forces and not energies or
+stresses. However, one can access the energy via thermodynamic
+integration of the forces as discussed in
+"(Botu3)"_#Botu2016construct. This pair style is part of the
+USER-MISC package. It is only enabled if LAMMPS was built with that
+package. See the "Build package"_Build_package.html doc page for more
+info.
The AGNI force field files provided with LAMMPS (see the
potentials directory) are parameterized for metal "units"_units.html.
diff --git a/doc/src/pair_airebo.txt b/doc/src/pair_airebo.txt
index 94a692226d..c090a39af7 100644
--- a/doc/src/pair_airebo.txt
+++ b/doc/src/pair_airebo.txt
@@ -182,13 +182,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -212,8 +212,8 @@ These pair styles can only be used via the {pair} keyword of the
[Restrictions:]
These pair styles are part of the MANYBODY package. They are only
-enabled if LAMMPS was built with that package. See the
-"Making LAMMPS"_Section_start.html#start_3 section for more info.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
These pair potentials require the "newton"_newton.html setting to be
"on" for pair interactions.
diff --git a/doc/src/pair_beck.txt b/doc/src/pair_beck.txt
index ca4186e27b..af60041ff9 100644
--- a/doc/src/pair_beck.txt
+++ b/doc/src/pair_beck.txt
@@ -57,13 +57,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/pair_body_nparticle.txt b/doc/src/pair_body_nparticle.txt
index 9fb88102eb..158eb68ca8 100644
--- a/doc/src/pair_body_nparticle.txt
+++ b/doc/src/pair_body_nparticle.txt
@@ -103,8 +103,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This style is part of the BODY package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_2_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Defining particles to be bodies so they participate in body/body or
body/particle interactions requires the use of the "atom_style
diff --git a/doc/src/pair_body_rounded_polygon.txt b/doc/src/pair_body_rounded_polygon.txt
index e724874032..fc07d8fadd 100644
--- a/doc/src/pair_body_rounded_polygon.txt
+++ b/doc/src/pair_body_rounded_polygon.txt
@@ -116,8 +116,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
These pair styles are part of the BODY package. They are only enabled
-if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This pair style requires the "newton"_newton.html setting to be "on"
for pair interactions.
diff --git a/doc/src/pair_body_rounded_polyhedron.txt b/doc/src/pair_body_rounded_polyhedron.txt
index 0f8548d98e..e650e5138a 100644
--- a/doc/src/pair_body_rounded_polyhedron.txt
+++ b/doc/src/pair_body_rounded_polyhedron.txt
@@ -111,8 +111,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
These pair styles are part of the BODY package. They are only enabled
-if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This pair style requires the "newton"_newton.html setting to be "on"
for pair interactions.
diff --git a/doc/src/pair_bop.txt b/doc/src/pair_bop.txt
index 654a7eb0b3..f9b4262f0c 100644
--- a/doc/src/pair_bop.txt
+++ b/doc/src/pair_bop.txt
@@ -382,9 +382,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
These pair styles are part of the MANYBODY package. They are only
-enabled if LAMMPS was built with that package.
-See the "Making LAMMPS"_Section_start.html#start_3 section for more
-info.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
These pair potentials require the "newtion"_newton.html setting to be
"on" for pair interactions.
diff --git a/doc/src/pair_born.txt b/doc/src/pair_born.txt
index c408de6db6..195d3e6669 100644
--- a/doc/src/pair_born.txt
+++ b/doc/src/pair_born.txt
@@ -151,13 +151,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -193,8 +193,8 @@ respa"_run_style.html command. They do not support the {inner},
[Restrictions:]
The {born/coul/long} style is part of the KSPACE package. It is only
-enabled if LAMMPS was built with that package. See the
-"Making LAMMPS"_Section_start.html#start_3 section for more info.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_brownian.txt b/doc/src/pair_brownian.txt
index eaff85cbbc..52720daa23 100644
--- a/doc/src/pair_brownian.txt
+++ b/doc/src/pair_brownian.txt
@@ -80,13 +80,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See "this section"_Speed.html of the manual for more
instructions on how to use the accelerated styles effectively.
@@ -122,8 +122,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
These styles are part of the COLLOID package. They are only enabled
-if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Only spherical monodisperse particles are allowed for pair_style
brownian.
diff --git a/doc/src/pair_buck.txt b/doc/src/pair_buck.txt
index cc782c11cf..5b1688e868 100644
--- a/doc/src/pair_buck.txt
+++ b/doc/src/pair_buck.txt
@@ -145,13 +145,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -186,8 +186,8 @@ respa"_run_style.html command. They do not support the {inner},
The {buck/coul/long} style is part of the KSPACE package. The
{buck/coul/long/cs} style is part of the CORESHELL package. They are
-only enabled if LAMMPS was built with that package. See the
-"Making LAMMPS"_Section_start.html#start_3 section for more info.
+only enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_buck6d_coul_gauss.txt b/doc/src/pair_buck6d_coul_gauss.txt
index 485c35c6b2..4c43978fe5 100644
--- a/doc/src/pair_buck6d_coul_gauss.txt
+++ b/doc/src/pair_buck6d_coul_gauss.txt
@@ -122,9 +122,9 @@ to be specified in an input script that reads a restart file.
[Restrictions:]
-These styles are part of the USER-MOFFF package. They are only enabled
-if LAMMPS was built with that package. See the
-"Making LAMMPS"_Section_start.html#start_3 section for more info.
+These styles are part of the USER-MOFFF package. They are only
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_buck_long.txt b/doc/src/pair_buck_long.txt
index 551204f1a7..7f3a959ad6 100644
--- a/doc/src/pair_buck_long.txt
+++ b/doc/src/pair_buck_long.txt
@@ -108,13 +108,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -153,9 +153,9 @@ details.
[Restrictions:]
This style is part of the KSPACE package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info. Note that
-the KSPACE package is installed by default.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info. Note that the
+KSPACE package is installed by default.
[Related commands:]
diff --git a/doc/src/pair_charmm.txt b/doc/src/pair_charmm.txt
index 39c6f29b04..dfc87e1bce 100644
--- a/doc/src/pair_charmm.txt
+++ b/doc/src/pair_charmm.txt
@@ -190,13 +190,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -245,9 +245,9 @@ details.
All the styles with {coul/charmm} or {coul/charmmfsh} styles are part
of the MOLECULE package. All the styles with {coul/long} style are
part of the KSPACE package. They are only enabled if LAMMPS was built
-with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info. Note that
-the MOLECULE and KSPACE packages are installed by default.
+with those packages. See the "Build package"_Build_package.html doc
+page for more info. Note that the MOLECULE and KSPACE packages are
+installed by default.
[Related commands:]
diff --git a/doc/src/pair_class2.txt b/doc/src/pair_class2.txt
index 104c51474c..5fc42e78f9 100644
--- a/doc/src/pair_class2.txt
+++ b/doc/src/pair_class2.txt
@@ -108,13 +108,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -154,8 +154,8 @@ support the {inner}, {middle}, {outer} keywords.
[Restrictions:]
These styles are part of the CLASS2 package. They are only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_colloid.txt b/doc/src/pair_colloid.txt
index 08540cfee0..e8a44e1cba 100644
--- a/doc/src/pair_colloid.txt
+++ b/doc/src/pair_colloid.txt
@@ -133,13 +133,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -177,8 +177,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This style is part of the COLLOID package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Normally, this pair style should be used with finite-size particles
which have a diameter, e.g. see the "atom_style
diff --git a/doc/src/pair_comb.txt b/doc/src/pair_comb.txt
index fc4cddbbae..45ce3a3b76 100644
--- a/doc/src/pair_comb.txt
+++ b/doc/src/pair_comb.txt
@@ -118,13 +118,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -154,9 +154,9 @@ These pair styles can only be used via the {pair} keyword of the
[Restrictions:]
-These pair styles are part of the MANYBODY package. It is only enabled
-if LAMMPS was built with that package. See
-the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+These pair styles are part of the MANYBODY package. It is only
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
These pair styles requires the "newton"_newton.html setting to be "on"
for pair interactions.
diff --git a/doc/src/pair_coul.txt b/doc/src/pair_coul.txt
index 2fd9445785..bc0d76a071 100644
--- a/doc/src/pair_coul.txt
+++ b/doc/src/pair_coul.txt
@@ -274,13 +274,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -319,7 +319,7 @@ This pair style can only be used via the {pair} keyword of the
The {coul/long}, {coul/msm} and {tip4p/long} styles are part of the
KSPACE package. The {coul/long/cs} style is part of the CORESHELL
package. They are only enabled if LAMMPS was built with that package.
-See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+See the "Build package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_coul_diel.txt b/doc/src/pair_coul_diel.txt
index 14932c4835..7708287db9 100644
--- a/doc/src/pair_coul_diel.txt
+++ b/doc/src/pair_coul_diel.txt
@@ -67,7 +67,8 @@ The global cutoff (r_c) specified in the pair_style command is used.
[Mixing, shift, table, tail correction, restart, rRESPA info]:
-This pair style does not support parameter mixing. Coefficients must be given explicitly for each type of particle pairs.
+This pair style does not support parameter mixing. Coefficients must
+be given explicitly for each type of particle pairs.
This pair style supports the "pair_modify"_pair_modify.html shift
option for the energy of the Gauss-potential portion of the pair
@@ -86,9 +87,9 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
-This style is part of the "user-misc" package. It is only enabled
-if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_2_3 section for more info.
+This style is part of the "USER-MISC" package. It is only enabled if
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_coul_shield.txt b/doc/src/pair_coul_shield.txt
index 029e6e5b3b..62ac157e76 100644
--- a/doc/src/pair_coul_shield.txt
+++ b/doc/src/pair_coul_shield.txt
@@ -69,9 +69,9 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
-This style is part of the USER-MISC package. It is only enabled
-if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_2_3 section for more info.
+This style is part of the USER-MISC package. It is only enabled if
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_cs.txt b/doc/src/pair_cs.txt
index 6540c4b8f0..8bd4abed68 100644
--- a/doc/src/pair_cs.txt
+++ b/doc/src/pair_cs.txt
@@ -100,8 +100,8 @@ core/shell pair.
[Restrictions:]
These pair styles are part of the CORESHELL package. They are only
-enabled if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_dipole.txt b/doc/src/pair_dipole.txt
index 1d8abc4521..dcb2448949 100644
--- a/doc/src/pair_dipole.txt
+++ b/doc/src/pair_dipole.txt
@@ -192,13 +192,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -240,12 +240,12 @@ This pair style can only be used via the {pair} keyword of the
The {lj/cut/dipole/cut}, {lj/cut/dipole/long}, and
{lj/long/dipole/long} styles are part of the DIPOLE package. They are
-only enabled if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+only enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
The {lj/sf/dipole/sf} style is part of the USER-MISC package. It is
-only enabled if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+only enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Using dipole pair styles with {electron} "units"_units.html is not
currently supported.
diff --git a/doc/src/pair_dpd.txt b/doc/src/pair_dpd.txt
index 1b636795d9..55ae298682 100644
--- a/doc/src/pair_dpd.txt
+++ b/doc/src/pair_dpd.txt
@@ -116,13 +116,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/pair_dpd_fdt.txt b/doc/src/pair_dpd_fdt.txt
index 0d180ba068..4f2459588a 100644
--- a/doc/src/pair_dpd_fdt.txt
+++ b/doc/src/pair_dpd_fdt.txt
@@ -135,13 +135,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -151,8 +151,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
These commands are part of the USER-DPD package. They are only
-enabled if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Pair styles {dpd/fdt} and {dpd/fdt/energy} require use of the
"comm_modify vel yes"_comm_modify.html option so that velocites are
diff --git a/doc/src/pair_dsmc.txt b/doc/src/pair_dsmc.txt
index 2478a96d5f..adaeeb8390 100644
--- a/doc/src/pair_dsmc.txt
+++ b/doc/src/pair_dsmc.txt
@@ -130,8 +130,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This style is part of the MC package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_eam.txt b/doc/src/pair_eam.txt
index 361dacb703..6c3793cb61 100644
--- a/doc/src/pair_eam.txt
+++ b/doc/src/pair_eam.txt
@@ -377,13 +377,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -414,8 +414,8 @@ The eam pair styles can only be used via the {pair} keyword of the
[Restrictions:]
All of these styles are part of the MANYBODY package. They are only
-enabled if LAMMPS was built with that package.
-See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_edip.txt b/doc/src/pair_edip.txt
index cce564856e..053d43b2ba 100644
--- a/doc/src/pair_edip.txt
+++ b/doc/src/pair_edip.txt
@@ -115,13 +115,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -147,8 +147,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This pair style can only be used if LAMMPS was built with the
-USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER-MISC package. See the "Build package"_Build_package.html doc
+page for more info.
This pair style requires the "newton"_newton.html setting to be "on"
for pair interactions.
diff --git a/doc/src/pair_eff.txt b/doc/src/pair_eff.txt
index a55860297e..a665654af0 100644
--- a/doc/src/pair_eff.txt
+++ b/doc/src/pair_eff.txt
@@ -280,8 +280,8 @@ These pair styles can only be used via the {pair} keyword of the
These pair styles will only be enabled if LAMMPS is built with the
USER-EFF package. It will only be enabled if LAMMPS was built with
-that package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info.
+that package. See the "Build package"_Build_package.html doc page for
+more info.
These pair styles require that particles store electron attributes
such as radius, radial velocity, and radial force, as defined by the
diff --git a/doc/src/pair_eim.txt b/doc/src/pair_eim.txt
index 6490a859c1..5f9dcd4c5c 100644
--- a/doc/src/pair_eim.txt
+++ b/doc/src/pair_eim.txt
@@ -142,13 +142,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/pair_exp6_rx.txt b/doc/src/pair_exp6_rx.txt
index 08ab1cf3c9..790674644d 100644
--- a/doc/src/pair_exp6_rx.txt
+++ b/doc/src/pair_exp6_rx.txt
@@ -159,13 +159,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -175,8 +175,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This command is part of the USER-DPD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_gauss.txt b/doc/src/pair_gauss.txt
index 9662a4f29c..ef924b1ef0 100644
--- a/doc/src/pair_gauss.txt
+++ b/doc/src/pair_gauss.txt
@@ -90,13 +90,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch7_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -167,8 +167,8 @@ thermo_style custom step temp epair v_occ :pre
[Restrictions:]
The {gauss/cut} style is part of the "user-misc" package. It is only
-enabled if LAMMPS is build with that package. See the "Making of
-LAMMPS"_Section_start.html#start_3 section for more info.
+enabled if LAMMPS is build with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_gayberne.txt b/doc/src/pair_gayberne.txt
index af41f6879e..426352dc4c 100644
--- a/doc/src/pair_gayberne.txt
+++ b/doc/src/pair_gayberne.txt
@@ -139,13 +139,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -184,8 +184,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
The {gayberne} style is part of the ASPHERE package. It is only
-enabled if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
These pair style require that atoms store torque and a quaternion to
represent their orientation, as defined by the
diff --git a/doc/src/pair_gran.txt b/doc/src/pair_gran.txt
index 55b00a172f..e06d410084 100644
--- a/doc/src/pair_gran.txt
+++ b/doc/src/pair_gran.txt
@@ -185,13 +185,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -232,8 +232,8 @@ pair/local"_compute_pair_local.html command, as {p1}, {p2}, ...,
[Restrictions:]
All the granular pair styles are part of the GRANULAR package. It is
-only enabled if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+only enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
These pair styles require that atoms store torque and angular velocity
(omega) as defined by the "atom_style"_atom_style.html. They also
diff --git a/doc/src/pair_gromacs.txt b/doc/src/pair_gromacs.txt
index 9f34ac8c43..6a36a036c9 100644
--- a/doc/src/pair_gromacs.txt
+++ b/doc/src/pair_gromacs.txt
@@ -97,13 +97,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/pair_gw.txt b/doc/src/pair_gw.txt
index 809ff008bc..ff85955dc0 100644
--- a/doc/src/pair_gw.txt
+++ b/doc/src/pair_gw.txt
@@ -96,8 +96,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This pair style is part of the MANYBODY package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This pair style requires the "newton"_newton.html setting to be "on"
for pair interactions.
diff --git a/doc/src/pair_hbond_dreiding.txt b/doc/src/pair_hbond_dreiding.txt
index 60b0b02174..d4bdcd9258 100644
--- a/doc/src/pair_hbond_dreiding.txt
+++ b/doc/src/pair_hbond_dreiding.txt
@@ -172,13 +172,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/pair_hybrid.txt b/doc/src/pair_hybrid.txt
index 9b36109c27..6e68e820a8 100644
--- a/doc/src/pair_hybrid.txt
+++ b/doc/src/pair_hybrid.txt
@@ -324,15 +324,15 @@ the individual sub-styles, the suffix versions of the {hybrid} and
to all sub-styles, if those versions exist. Otherwise the
non-accelerated version will be used.
-The individual accelerated sub-styles are part of the GPU,
-USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the
-"Making LAMMPS"_Section_start.html#start_3 section for more info.
+The individual accelerated sub-styles are part of the GPU, USER-OMP
+and OPT packages, respectively. They are only enabled if LAMMPS was
+built with those packages. See the "Build package"_Build_package.html
+doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/pair_ilp_graphene_hbn.txt b/doc/src/pair_ilp_graphene_hbn.txt
index 9c9304c4a7..02d0db7af2 100644
--- a/doc/src/pair_ilp_graphene_hbn.txt
+++ b/doc/src/pair_ilp_graphene_hbn.txt
@@ -87,8 +87,8 @@ that reads a restart file.
[Restrictions:]
This fix is part of the USER-MISC package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This pair potential requires the newton setting to be {on} for pair
interactions.
diff --git a/doc/src/pair_kim.txt b/doc/src/pair_kim.txt
index 889c1e892f..e1bde4f10e 100644
--- a/doc/src/pair_kim.txt
+++ b/doc/src/pair_kim.txt
@@ -126,8 +126,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This pair style is part of the KIM package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This current version of pair_style kim is compatible with the
kim-api package version 1.6.0 and higher.
diff --git a/doc/src/pair_kolmogorov_crespi_full.txt b/doc/src/pair_kolmogorov_crespi_full.txt
index 8fc6bbff49..358d2168df 100644
--- a/doc/src/pair_kolmogorov_crespi_full.txt
+++ b/doc/src/pair_kolmogorov_crespi_full.txt
@@ -78,8 +78,8 @@ that reads a restart file.
[Restrictions:]
This fix is part of the USER-MISC package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This pair potential requires the newton setting to be {on} for pair
interactions.
diff --git a/doc/src/pair_kolmogorov_crespi_z.txt b/doc/src/pair_kolmogorov_crespi_z.txt
index 7dad2e3701..f557e6c731 100644
--- a/doc/src/pair_kolmogorov_crespi_z.txt
+++ b/doc/src/pair_kolmogorov_crespi_z.txt
@@ -51,8 +51,8 @@ Other interactions can be set to zero using pair_style {none}.
[Restrictions:]
This fix is part of the USER-MISC package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_lcbop.txt b/doc/src/pair_lcbop.txt
index ddf8551d56..21c809bf6a 100644
--- a/doc/src/pair_lcbop.txt
+++ b/doc/src/pair_lcbop.txt
@@ -72,8 +72,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This pair styles is part of the MANYBODY package. It is only enabled
-if LAMMPS was built with that package. See
-the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This pair potential requires the "newton"_newton.html setting to be
"on" for pair interactions.
diff --git a/doc/src/pair_line_lj.txt b/doc/src/pair_line_lj.txt
index c2c6beb97f..ca5ececa56 100644
--- a/doc/src/pair_line_lj.txt
+++ b/doc/src/pair_line_lj.txt
@@ -130,8 +130,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This style is part of the ASPHERE package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Defining particles to be line segments so they participate in
line/line or line/particle interactions requires the use the
diff --git a/doc/src/pair_list.txt b/doc/src/pair_list.txt
index 023cc0be4f..9500a4c508 100644
--- a/doc/src/pair_list.txt
+++ b/doc/src/pair_list.txt
@@ -130,8 +130,8 @@ atom J (assuming the images are within the cutoff distance), but only
with the nearest image.
This style is part of the USER-MISC package. It is only enabled if
-LAMMPS is build with that package. See the "Making of
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS is build with that package. See the "Build
+package"_Build_package.html doc page on for more info.
[Related commands:]
diff --git a/doc/src/pair_lj.txt b/doc/src/pair_lj.txt
index a55cb348d7..b5a5726182 100644
--- a/doc/src/pair_lj.txt
+++ b/doc/src/pair_lj.txt
@@ -275,13 +275,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -326,9 +326,9 @@ See the "run_style"_run_style.html command for details.
The {lj/cut/coul/long} and {lj/cut/tip4p/long} styles are part of the
KSPACE package. The {lj/cut/tip4p/cut} style is part of the MOLECULE
package. These styles are only enabled if LAMMPS was built with those
-packages. See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info. Note that the KSPACE and MOLECULE packages are
-installed by default.
+packages. See the "Build package"_Build_package.html doc page for
+more info. Note that the KSPACE and MOLECULE packages are installed
+by default.
[Related commands:]
diff --git a/doc/src/pair_lj96.txt b/doc/src/pair_lj96.txt
index 7c68e26ace..19369adc66 100644
--- a/doc/src/pair_lj96.txt
+++ b/doc/src/pair_lj96.txt
@@ -55,13 +55,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/pair_lj_cubic.txt b/doc/src/pair_lj_cubic.txt
index d04a3d8b9d..0a56672d28 100644
--- a/doc/src/pair_lj_cubic.txt
+++ b/doc/src/pair_lj_cubic.txt
@@ -69,13 +69,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/pair_lj_expand.txt b/doc/src/pair_lj_expand.txt
index 3e9996da4d..d26c88e4f7 100644
--- a/doc/src/pair_lj_expand.txt
+++ b/doc/src/pair_lj_expand.txt
@@ -59,13 +59,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/pair_lj_long.txt b/doc/src/pair_lj_long.txt
index 1ba3610f86..2bc2b656ac 100644
--- a/doc/src/pair_lj_long.txt
+++ b/doc/src/pair_lj_long.txt
@@ -162,13 +162,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -209,9 +209,9 @@ different levels of the rRESPA hierarchy. See the
[Restrictions:]
These styles are part of the KSPACE package. They are only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info. Note that
-the KSPACE package is installed by default.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info. Note that the
+KSPACE package is installed by default.
[Related commands:]
diff --git a/doc/src/pair_lj_smooth.txt b/doc/src/pair_lj_smooth.txt
index 575c023579..0c66dd0f66 100644
--- a/doc/src/pair_lj_smooth.txt
+++ b/doc/src/pair_lj_smooth.txt
@@ -68,13 +68,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/pair_lj_smooth_linear.txt b/doc/src/pair_lj_smooth_linear.txt
index 0fab768b8f..9c509515c0 100644
--- a/doc/src/pair_lj_smooth_linear.txt
+++ b/doc/src/pair_lj_smooth_linear.txt
@@ -55,13 +55,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/pair_lj_soft.txt b/doc/src/pair_lj_soft.txt
index d10fcd0472..9bcc83fa66 100644
--- a/doc/src/pair_lj_soft.txt
+++ b/doc/src/pair_lj_soft.txt
@@ -213,13 +213,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -261,7 +261,7 @@ similar substyle can be used via the
All of the plain {soft} pair styles are part of the USER-FEP package.
The {long} styles also requires the KSPACE package to be installed.
They are only enabled if LAMMPS was built with those packages. See
-the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+the "Build package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_lubricate.txt b/doc/src/pair_lubricate.txt
index e9a0a0d291..83a67d0300 100644
--- a/doc/src/pair_lubricate.txt
+++ b/doc/src/pair_lubricate.txt
@@ -149,13 +149,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See "this section"_Speed.html of the manual for more
instructions on how to use the accelerated styles effectively.
@@ -191,8 +191,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
These styles are part of the COLLOID package. They are only enabled
-if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_2_3 section for more info.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Only spherical monodisperse particles are allowed for pair_style
lubricate.
diff --git a/doc/src/pair_lubricateU.txt b/doc/src/pair_lubricateU.txt
index 6b74c208bf..bfc7c36013 100644
--- a/doc/src/pair_lubricateU.txt
+++ b/doc/src/pair_lubricateU.txt
@@ -179,8 +179,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
These styles are part of the COLLOID package. They are only enabled
-if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_2_3 section for more info.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Currently, these pair styles assume that all other types of
forces/torques on the particles have been already been computed when
diff --git a/doc/src/pair_mdf.txt b/doc/src/pair_mdf.txt
index e5a8cac845..8a1551dded 100644
--- a/doc/src/pair_mdf.txt
+++ b/doc/src/pair_mdf.txt
@@ -148,8 +148,8 @@ See the "run_style"_run_style.html command for details.
[Restrictions:]
These pair styles can only be used if LAMMPS was built with the
-USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER-MISC package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/pair_meam.txt b/doc/src/pair_meam.txt
index 45f88f0bbe..0b1c1ac767 100644
--- a/doc/src/pair_meam.txt
+++ b/doc/src/pair_meam.txt
@@ -352,14 +352,14 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
-The {meam} style is part of the MEAM package. It is only enabled if LAMMPS
-was built with that package, which also requires the MEAM library be
-built and linked with LAMMPS.
-The {meam/c} style is provided in the USER-MEAMC package. It is only enabled
-if LAMMPS was built with that package. In contrast to the {meam} style,
-{meam/c} does not require a separate library to be compiled and it can be
+The {meam} style is part of the MEAM package. It is only enabled if
+LAMMPS was built with that package, which also requires the MEAM
+library be built and linked with LAMMPS. The {meam/c} style is
+provided in the USER-MEAMC package. It is only enabled if LAMMPS was
+built with that package. In contrast to the {meam} style, {meam/c}
+does not require a separate library to be compiled and it can be
instantiated multiple times in a "hybrid"_pair_hybrid.html pair style.
-See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+See the "Build package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_meam_spline.txt b/doc/src/pair_meam_spline.txt
index 9615512041..df5db81264 100644
--- a/doc/src/pair_meam_spline.txt
+++ b/doc/src/pair_meam_spline.txt
@@ -112,13 +112,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -147,8 +147,8 @@ This pair style requires the "newton"_newton.html setting to be "on"
for pair interactions.
This pair style is only enabled if LAMMPS was built with the USER-MISC
-package. See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info.
+package. See the "Build package"_Build_package.html doc page for more
+info.
[Related commands:]
diff --git a/doc/src/pair_meam_sw_spline.txt b/doc/src/pair_meam_sw_spline.txt
index ba0953a17c..2e8c26658a 100644
--- a/doc/src/pair_meam_sw_spline.txt
+++ b/doc/src/pair_meam_sw_spline.txt
@@ -111,8 +111,9 @@ support the {inner}, {middle}, {outer} keywords.
This pair style requires the "newton"_newton.html setting to be "on"
for pair interactions.
-This pair style is only enabled if LAMMPS was built with the USER-MISC package.
-See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+This pair style is only enabled if LAMMPS was built with the USER-MISC
+package. See the "Build package"_Build_package.html doc page for more
+info.
[Related commands:]
diff --git a/doc/src/pair_meso.txt b/doc/src/pair_meso.txt
index ad3880e642..005498d8bf 100644
--- a/doc/src/pair_meso.txt
+++ b/doc/src/pair_meso.txt
@@ -245,8 +245,8 @@ that reads a restart file.
The pair styles {edpd}, {mdpd}, {mdpd/rhosum} and {tdpd} are part of
the USER-MESO package. It is only enabled if LAMMPS was built with
-that package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info.
+that package. See the "Build package"_Build_package.html doc page for
+more info.
[Related commands:]
diff --git a/doc/src/pair_mgpt.txt b/doc/src/pair_mgpt.txt
index 09fe611686..bd55d529b8 100644
--- a/doc/src/pair_mgpt.txt
+++ b/doc/src/pair_mgpt.txt
@@ -159,8 +159,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This pair style is part of the USER-MGPT package and is only enabled
-if LAMMPS is built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+if LAMMPS is built with that package. See the "Build
+package"_Build_package.html doc page for more info.
The MGPT potentials require the "newtion"_newton.html setting to be
"on" for pair style interactions.
diff --git a/doc/src/pair_momb.txt b/doc/src/pair_momb.txt
index 545b650f75..f1989f56f4 100644
--- a/doc/src/pair_momb.txt
+++ b/doc/src/pair_momb.txt
@@ -50,8 +50,8 @@ Rr (distance units, typically sum of atomic vdW radii) :ul
[Restrictions:]
This style is part of the USER-MISC package. It is only enabled if
-LAMMPS is built with that package. See the "Making of
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS is built with that package. See the "Build
+package"_Build_package.html doc page on for more info.
[Related commands:]
diff --git a/doc/src/pair_morse.txt b/doc/src/pair_morse.txt
index 85a42986ec..68894f6913 100644
--- a/doc/src/pair_morse.txt
+++ b/doc/src/pair_morse.txt
@@ -107,13 +107,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -148,12 +148,12 @@ These pair styles can only be used via the {pair} keyword of the
[Restrictions:]
The {morse/smooth/linear} pair style is only enabled if LAMMPS was
-built with the USER-MISC package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+built with the USER-MISC package. See the "Build
+package"_Build_package.html doc page for more info.
The {morse/soft} pair style is only enabled if LAMMPS was built with
-the USER-FEP package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+the USER-FEP package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/pair_multi_lucy.txt b/doc/src/pair_multi_lucy.txt
index 31d52a58c8..0b3a430417 100644
--- a/doc/src/pair_multi_lucy.txt
+++ b/doc/src/pair_multi_lucy.txt
@@ -177,8 +177,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This command is part of the USER-DPD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_multi_lucy_rx.txt b/doc/src/pair_multi_lucy_rx.txt
index e09dde3f80..819a15b624 100644
--- a/doc/src/pair_multi_lucy_rx.txt
+++ b/doc/src/pair_multi_lucy_rx.txt
@@ -210,13 +210,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -226,8 +226,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This command is part of the USER-DPD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_nb3b_harmonic.txt b/doc/src/pair_nb3b_harmonic.txt
index 720b9ea2a1..6a119d74e1 100644
--- a/doc/src/pair_nb3b_harmonic.txt
+++ b/doc/src/pair_nb3b_harmonic.txt
@@ -98,13 +98,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -114,8 +114,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This pair style can only be used if LAMMPS was built with the MANYBODY
-package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+package. See the "Build package"_Build_package.html doc page for more
+info.
[Related commands:]
diff --git a/doc/src/pair_nm.txt b/doc/src/pair_nm.txt
index 355bfd5573..a42dfa3c98 100644
--- a/doc/src/pair_nm.txt
+++ b/doc/src/pair_nm.txt
@@ -139,13 +139,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -153,8 +153,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
These pair styles are part of the MISC package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_oxdna.txt b/doc/src/pair_oxdna.txt
index 5ec9915297..b24e3c07df 100644
--- a/doc/src/pair_oxdna.txt
+++ b/doc/src/pair_oxdna.txt
@@ -82,8 +82,8 @@ The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf.
[Restrictions:]
These pair styles can only be used if LAMMPS was built with the
-USER-CGDNA package and the MOLECULE and ASPHERE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+USER-CGDNA package and the MOLECULE and ASPHERE package. See the
+"Build package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_oxdna2.txt b/doc/src/pair_oxdna2.txt
index a1d2cfdb7c..c5662abdeb 100644
--- a/doc/src/pair_oxdna2.txt
+++ b/doc/src/pair_oxdna2.txt
@@ -88,8 +88,8 @@ The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf.
[Restrictions:]
These pair styles can only be used if LAMMPS was built with the
-USER-CGDNA package and the MOLECULE and ASPHERE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+USER-CGDNA package and the MOLECULE and ASPHERE package. See the
+"Build package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_peri.txt b/doc/src/pair_peri.txt
index 14abd4541e..b6baa4edc5 100644
--- a/doc/src/pair_peri.txt
+++ b/doc/src/pair_peri.txt
@@ -145,13 +145,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -182,8 +182,8 @@ These pair styles can only be used via the {pair} keyword of the
[Restrictions:]
All of these styles are part of the PERI package. They are only
-enabled if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_polymorphic.txt b/doc/src/pair_polymorphic.txt
index eb0c30f249..7460044043 100644
--- a/doc/src/pair_polymorphic.txt
+++ b/doc/src/pair_polymorphic.txt
@@ -191,8 +191,8 @@ input script. If using read_data, atomic masses must be defined in the
atomic structure data file.
This pair style is part of the MANYBODY package. It is only enabled if
-LAMMPS was built with that package. See the
-"Making LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This pair potential requires the "newtion"_newton.html setting to be
"on" for pair interactions.
diff --git a/doc/src/pair_python.txt b/doc/src/pair_python.txt
index 1433557e03..23da86fc49 100644
--- a/doc/src/pair_python.txt
+++ b/doc/src/pair_python.txt
@@ -204,8 +204,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This pair style is part of the PYTHON package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_quip.txt b/doc/src/pair_quip.txt
index 3570a52801..1f794d0c84 100644
--- a/doc/src/pair_quip.txt
+++ b/doc/src/pair_quip.txt
@@ -74,8 +74,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This pair style is part of the USER-QUIP package. It is only enabled
-if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
QUIP potentials are parametrized in electron-volts and Angstroms and
therefore should be used with LAMMPS metal "units"_units.html.
diff --git a/doc/src/pair_reaxc.txt b/doc/src/pair_reaxc.txt
index ec57548640..e63f4a90ee 100644
--- a/doc/src/pair_reaxc.txt
+++ b/doc/src/pair_reaxc.txt
@@ -309,13 +309,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -325,8 +325,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This pair style is part of the USER-REAXC package. It is only enabled
-if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
The ReaxFF potential files provided with LAMMPS in the potentials
directory are parameterized for real "units"_units.html. You can use
diff --git a/doc/src/pair_resquared.txt b/doc/src/pair_resquared.txt
index 6e72408ebc..5e760be495 100644
--- a/doc/src/pair_resquared.txt
+++ b/doc/src/pair_resquared.txt
@@ -151,13 +151,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -203,8 +203,8 @@ command"_run_style.html.
[Restrictions:]
This style is part of the ASPHERE package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This pair style requires that atoms be ellipsoids as defined by the
"atom_style ellipsoid"_atom_style.html command.
diff --git a/doc/src/pair_sdk.txt b/doc/src/pair_sdk.txt
index ccf704b6f7..b977aefe88 100644
--- a/doc/src/pair_sdk.txt
+++ b/doc/src/pair_sdk.txt
@@ -91,13 +91,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP, and OPT packages respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -133,11 +133,11 @@ respa"_run_style.html command.
[Restrictions:]
-All of the lj/sdk pair styles are part of the USER-CGSDK package.
-The {lj/sdk/coul/long} style also requires the KSPACE package to be
-built (which is enabled by default). They are only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+All of the lj/sdk pair styles are part of the USER-CGSDK package. The
+{lj/sdk/coul/long} style also requires the KSPACE package to be built
+(which is enabled by default). They are only enabled if LAMMPS was
+built with that package. See the "Build package"_Build_package.html
+doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_smd_hertz.txt b/doc/src/pair_smd_hertz.txt
index f2d633903a..2581c84dc9 100644
--- a/doc/src/pair_smd_hertz.txt
+++ b/doc/src/pair_smd_hertz.txt
@@ -19,32 +19,36 @@ pair_coeff 1 1 <contact_stiffness>
[Description:]
-The {smd/hertz} style calculates contact forces between SPH particles belonging to different physical bodies.
+The {smd/hertz} style calculates contact forces between SPH particles
+belonging to different physical bodies.
-The contact forces are calculated using a Hertz potential, which evaluates the overlap between two particles
-(whose spatial extents are defined via its contact radius).
-The effect is that a particles cannot penetrate into each other.
-The parameter <contact_stiffness> has units of pressure and should equal roughly one half
-of the Young's modulus (or bulk modulus in the case of fluids) of the material model associated with the SPH particles.
+The contact forces are calculated using a Hertz potential, which
+evaluates the overlap between two particles (whose spatial extents are
+defined via its contact radius). The effect is that a particles
+cannot penetrate into each other. The parameter <contact_stiffness>
+has units of pressure and should equal roughly one half of the Young's
+modulus (or bulk modulus in the case of fluids) of the material model
+associated with the SPH particles.
-The parameter {scale_factor} can be used to scale the particles' contact radii. This can be useful to control how close
-particles can approach each other. Usually, {scale_factor} =1.0.
+The parameter {scale_factor} can be used to scale the particles'
+contact radii. This can be useful to control how close particles can
+approach each other. Usually, {scale_factor} =1.0.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
-No mixing is performed automatically.
-Currently, no part of USER-SMD supports restarting nor minimization.
-rRESPA does not apply to this pair style.
+No mixing is performed automatically. Currently, no part of USER-SMD
+supports restarting nor minimization. rRESPA does not apply to this
+pair style.
:line
[Restrictions:]
This fix is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_smd_tlsph.txt b/doc/src/pair_smd_tlsph.txt
index 3aeaa31553..44b0c6cae8 100644
--- a/doc/src/pair_smd_tlsph.txt
+++ b/doc/src/pair_smd_tlsph.txt
@@ -16,10 +16,11 @@ pair_style smd/tlsph args :pre
pair_style smd/tlsph
-
[Description:]
-The {smd/tlsph} style computes particle interactions according to continuum mechanics constitutive laws and a Total-Lagrangian Smooth-Particle Hydrodynamics algorithm.
+The {smd/tlsph} style computes particle interactions according to
+continuum mechanics constitutive laws and a Total-Lagrangian
+Smooth-Particle Hydrodynamics algorithm.
This pair style is invoked with the following command:
@@ -27,35 +28,40 @@ pair_style smd/tlsph
pair_coeff i j *COMMON rho0 E nu Q1 Q2 hg Cp &
*END :pre
-Here, {i} and {j} denote the {LAMMPS} particle types for which this pair style is
-defined. Note that {i} and {j} must be equal, i.e., no {tlsph} cross interactions
-between different particle types are allowed.
-In contrast to the usual {LAMMPS} {pair coeff} definitions, which are given solely a
-number of floats and integers, the {tlsph} {pair coeff} definition is organised using
-keywords. These keywords mark the beginning of different sets of parameters for particle properties,
-material constitutive models, and damage models. The {pair coeff} line must be terminated with
-the {*END} keyword. The use the line continuation operator {&} is recommended. A typical
-invocation of the {tlsph} for a solid body would consist of an equation of state for computing
-the pressure (the diagonal components of the stress tensor), and a material model to compute shear
-stresses (the off-diagonal components of the stress tensor). Damage and failure models can also be added.
-
-Please see the "SMD user guide"_PDF/SMD_LAMMPS_userguide.pdf for a complete listing of the possible keywords and material models.
+Here, {i} and {j} denote the {LAMMPS} particle types for which this
+pair style is defined. Note that {i} and {j} must be equal, i.e., no
+{tlsph} cross interactions between different particle types are
+allowed. In contrast to the usual {LAMMPS} {pair coeff} definitions,
+which are given solely a number of floats and integers, the {tlsph}
+{pair coeff} definition is organised using keywords. These keywords
+mark the beginning of different sets of parameters for particle
+properties, material constitutive models, and damage models. The {pair
+coeff} line must be terminated with the {*END} keyword. The use the
+line continuation operator {&} is recommended. A typical invocation of
+the {tlsph} for a solid body would consist of an equation of state for
+computing the pressure (the diagonal components of the stress tensor),
+and a material model to compute shear stresses (the off-diagonal
+components of the stress tensor). Damage and failure models can also
+be added.
+
+Please see the "SMD user guide"_PDF/SMD_LAMMPS_userguide.pdf for a
+complete listing of the possible keywords and material models.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
-No mixing is performed automatically.
-Currently, no part of USER-SMD supports restarting nor minimization.
-rRESPA does not apply to this pair style.
+No mixing is performed automatically. Currently, no part of USER-SMD
+supports restarting nor minimization. rRESPA does not apply to this
+pair style.
:line
[Restrictions:]
This fix is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_smd_triangulated_surface.txt b/doc/src/pair_smd_triangulated_surface.txt
index 65526cfba8..9eb5e311b8 100644
--- a/doc/src/pair_smd_triangulated_surface.txt
+++ b/doc/src/pair_smd_triangulated_surface.txt
@@ -19,17 +19,21 @@ pair_coeff 1 1 <contact_stiffness>
[Description:]
-The {smd/tri_surface} style calculates contact forces between SPH particles and a rigid wall boundary defined via the
+The {smd/tri_surface} style calculates contact forces between SPH
+particles and a rigid wall boundary defined via the
"smd/wall_surface"_fix_smd_wall_surface.html fix.
-The contact forces are calculated using a Hertz potential, which evaluates the overlap between a particle
-(whose spatial extents are defined via its contact radius) and the triangle.
-The effect is that a particle cannot penetrate into the triangular surface.
-The parameter <contact_stiffness> has units of pressure and should equal roughly one half
-of the Young's modulus (or bulk modulus in the case of fluids) of the material model associated with the SPH particle
+The contact forces are calculated using a Hertz potential, which
+evaluates the overlap between a particle (whose spatial extents are
+defined via its contact radius) and the triangle. The effect is that
+a particle cannot penetrate into the triangular surface. The
+parameter <contact_stiffness> has units of pressure and should equal
+roughly one half of the Young's modulus (or bulk modulus in the case
+of fluids) of the material model associated with the SPH particle
-The parameter {scale_factor} can be used to scale the particles' contact radii. This can be useful to control how close
-particles can approach the triangulated surface. Usually, {scale_factor} =1.0.
+The parameter {scale_factor} can be used to scale the particles'
+contact radii. This can be useful to control how close particles can
+approach the triangulated surface. Usually, {scale_factor} =1.0.
:line
@@ -44,8 +48,8 @@ rRESPA does not apply to this pair style.
[Restrictions:]
This fix is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_smd_ulsph.txt b/doc/src/pair_smd_ulsph.txt
index a5bda54d5f..f28dd9043c 100644
--- a/doc/src/pair_smd_ulsph.txt
+++ b/doc/src/pair_smd_ulsph.txt
@@ -17,11 +17,13 @@ keyword = {*DENSITY_SUMMATION} or {*DENSITY_CONTINUITY} and {*VELOCITY_GRADIENT}
[Examples:]
-pair_style smd/ulsph *DENSITY_CONTINUITY *VELOCITY_GRADIENT *NO_GRADIENT_CORRECTION
+pair_style smd/ulsph *DENSITY_CONTINUITY *VELOCITY_GRADIENT *NO_GRADIENT_CORRECTION :pre
[Description:]
-The {smd/ulsph} style computes particle interactions according to continuum mechanics constitutive laws and an updated Lagrangian Smooth-Particle Hydrodynamics algorithm.
+The {smd/ulsph} style computes particle interactions according to
+continuum mechanics constitutive laws and an updated Lagrangian
+Smooth-Particle Hydrodynamics algorithm.
This pair style is invoked similar to the following command:
@@ -29,37 +31,45 @@ pair_style smd/ulsph *DENSITY_CONTINUITY *VELOCITY_GRADIENT *NO_GRADIENT_CORRECT
pair_coeff i j *COMMON rho0 c0 Q1 Cp hg &
*END :pre
-Here, {i} and {j} denote the {LAMMPS} particle types for which this pair style is
-defined. Note that {i} and {j} can be different, i.e., {ulsph} cross interactions
-between different particle types are allowed. However, {i}--{i} respectively {j}--{j} pair_coeff lines have to precede a cross interaction.
-In contrast to the usual {LAMMPS} {pair coeff} definitions, which are given solely a
-number of floats and integers, the {ulsph} {pair coeff} definition is organised using
-keywords. These keywords mark the beginning of different sets of parameters for particle properties,
-material constitutive models, and damage models. The {pair coeff} line must be terminated with
-the {*END} keyword. The use the line continuation operator {&} is recommended. A typical
-invocation of the {ulsph} for a solid body would consist of an equation of state for computing
-the pressure (the diagonal components of the stress tensor), and a material model to compute shear
-stresses (the off-diagonal components of the stress tensor).
-
-Note that the use of *GRADIENT_CORRECTION can lead to severe numerical instabilities. For a general fluid simulation, *NO_GRADIENT_CORRECTION is recommended.
-
-Please see the "SMD user guide"_PDF/SMD_LAMMPS_userguide.pdf for a complete listing of the possible keywords and material models.
+Here, {i} and {j} denote the {LAMMPS} particle types for which this
+pair style is defined. Note that {i} and {j} can be different, i.e.,
+{ulsph} cross interactions between different particle types are
+allowed. However, {i}--{i} respectively {j}--{j} pair_coeff lines have
+to precede a cross interaction. In contrast to the usual {LAMMPS}
+{pair coeff} definitions, which are given solely a number of floats
+and integers, the {ulsph} {pair coeff} definition is organised using
+keywords. These keywords mark the beginning of different sets of
+parameters for particle properties, material constitutive models, and
+damage models. The {pair coeff} line must be terminated with the
+{*END} keyword. The use the line continuation operator {&} is
+recommended. A typical invocation of the {ulsph} for a solid body
+would consist of an equation of state for computing the pressure (the
+diagonal components of the stress tensor), and a material model to
+compute shear stresses (the off-diagonal components of the stress
+tensor).
+
+Note that the use of *GRADIENT_CORRECTION can lead to severe numerical
+instabilities. For a general fluid simulation, *NO_GRADIENT_CORRECTION
+is recommended.
+
+Please see the "SMD user guide"_PDF/SMD_LAMMPS_userguide.pdf for a
+complete listing of the possible keywords and material models.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
-No mixing is performed automatically.
-Currently, no part of USER-SMD supports restarting nor minimization.
-rRESPA does not apply to this pair style.
+No mixing is performed automatically. Currently, no part of USER-SMD
+supports restarting nor minimization. rRESPA does not apply to this
+pair style.
:line
[Restrictions:]
This fix is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_smtbq.txt b/doc/src/pair_smtbq.txt
index c70202c2e1..e81411678a 100644
--- a/doc/src/pair_smtbq.txt
+++ b/doc/src/pair_smtbq.txt
@@ -219,8 +219,8 @@ This pair style can only be used via the {pair} keyword of the
[Restriction:]
This pair style is part of the USER-SMTBQ package and is only enabled
-if LAMMPS is built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+if LAMMPS is built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This potential requires using atom type 1 for oxygen and atom type
higher than 1 for metal atoms.
diff --git a/doc/src/pair_snap.txt b/doc/src/pair_snap.txt
index f9bd8910e4..6f8cc3d8a8 100644
--- a/doc/src/pair_snap.txt
+++ b/doc/src/pair_snap.txt
@@ -181,13 +181,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -196,9 +196,9 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
-This style is part of the SNAP package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+This style is part of the SNAP package. It is only enabled if LAMMPS
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_soft.txt b/doc/src/pair_soft.txt
index 374711825b..ca0266f34a 100644
--- a/doc/src/pair_soft.txt
+++ b/doc/src/pair_soft.txt
@@ -88,13 +88,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/pair_sph_heatconduction.txt b/doc/src/pair_sph_heatconduction.txt
index d19c28a3cb..78a9cf2b63 100644
--- a/doc/src/pair_sph_heatconduction.txt
+++ b/doc/src/pair_sph_heatconduction.txt
@@ -53,8 +53,8 @@ respa"_run_style.html command. It does not support the {inner},
[Restrictions:]
This pair style is part of the USER-SPH package. It is only enabled
-if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_sph_idealgas.txt b/doc/src/pair_sph_idealgas.txt
index a670949a89..59513e7a73 100644
--- a/doc/src/pair_sph_idealgas.txt
+++ b/doc/src/pair_sph_idealgas.txt
@@ -60,8 +60,8 @@ respa"_run_style.html command. It does not support the {inner},
[Restrictions:]
This pair style is part of the USER-SPH package. It is only enabled
-if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_sph_lj.txt b/doc/src/pair_sph_lj.txt
index 152e6cf8a2..43e77f1aae 100644
--- a/doc/src/pair_sph_lj.txt
+++ b/doc/src/pair_sph_lj.txt
@@ -60,8 +60,8 @@ As noted above, the Lennard-Jones parameters epsilon and sigma are set
to unity.
This pair style is part of the USER-SPH package. It is only enabled
-if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_sph_rhosum.txt b/doc/src/pair_sph_rhosum.txt
index 3cd1c5abb2..9069176f29 100644
--- a/doc/src/pair_sph_rhosum.txt
+++ b/doc/src/pair_sph_rhosum.txt
@@ -54,8 +54,8 @@ respa"_run_style.html command. It does not support the {inner},
[Restrictions:]
This pair style is part of the USER-SPH package. It is only enabled
-if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_sph_taitwater.txt b/doc/src/pair_sph_taitwater.txt
index 7b9a8188f2..dcb9e39603 100644
--- a/doc/src/pair_sph_taitwater.txt
+++ b/doc/src/pair_sph_taitwater.txt
@@ -63,8 +63,8 @@ respa"_run_style.html command. It does not support the {inner},
[Restrictions:]
This pair style is part of the USER-SPH package. It is only enabled
-if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_sph_taitwater_morris.txt b/doc/src/pair_sph_taitwater_morris.txt
index 02f16d8982..b88707d1af 100644
--- a/doc/src/pair_sph_taitwater_morris.txt
+++ b/doc/src/pair_sph_taitwater_morris.txt
@@ -62,8 +62,8 @@ respa"_run_style.html command. It does not support the {inner},
[Restrictions:]
This pair style is part of the USER-SPH package. It is only enabled
-if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_spin_dmi.txt b/doc/src/pair_spin_dmi.txt
index 375e59fe89..bd605bd064 100644
--- a/doc/src/pair_spin_dmi.txt
+++ b/doc/src/pair_spin_dmi.txt
@@ -69,10 +69,10 @@ pair style cannot be used.
[Restrictions:]
-All the {pair/spin} styles are part of the SPIN package.
-These styles are only enabled if LAMMPS was built with this package, and
-if the atom_style "spin" was declared.
-See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+All the {pair/spin} styles are part of the SPIN package. These styles
+are only enabled if LAMMPS was built with this package, and if the
+atom_style "spin" was declared. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_spin_exchange.txt b/doc/src/pair_spin_exchange.txt
index 24eb635b81..2f158704a9 100644
--- a/doc/src/pair_spin_exchange.txt
+++ b/doc/src/pair_spin_exchange.txt
@@ -79,10 +79,10 @@ None of those coefficients is optional. If not specified, the
[Restrictions:]
-All the {pair/spin} styles are part of the SPIN package.
-These styles are only enabled if LAMMPS was built with this package, and
-if the atom_style "spin" was declared.
-See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+All the {pair/spin} styles are part of the SPIN package. These styles
+are only enabled if LAMMPS was built with this package, and if the
+atom_style "spin" was declared. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_spin_magelec.txt b/doc/src/pair_spin_magelec.txt
index b338fae5dc..f552c56a4b 100644
--- a/doc/src/pair_spin_magelec.txt
+++ b/doc/src/pair_spin_magelec.txt
@@ -51,10 +51,10 @@ More details about the derivation of these torques/forces are reported in
[Restrictions:]
-All the {pair/spin} styles are part of the SPIN package.
-These styles are only enabled if LAMMPS was built with this package, and
-if the atom_style "spin" was declared.
-See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+All the {pair/spin} styles are part of the SPIN package. These styles
+are only enabled if LAMMPS was built with this package, and if the
+atom_style "spin" was declared. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_spin_neel.txt b/doc/src/pair_spin_neel.txt
index 0967632ed2..fe3bb1ad14 100644
--- a/doc/src/pair_spin_neel.txt
+++ b/doc/src/pair_spin_neel.txt
@@ -62,10 +62,10 @@ More details about the derivation of these torques/forces are reported in
[Restrictions:]
-All the {pair/spin} styles are part of the SPIN package.
-These styles are only enabled if LAMMPS was built with this package, and
-if the atom_style "spin" was declared.
-See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+All the {pair/spin} styles are part of the SPIN package. These styles
+are only enabled if LAMMPS was built with this package, and if the
+atom_style "spin" was declared. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_style.txt b/doc/src/pair_style.txt
index cd39513329..b33897c5aa 100644
--- a/doc/src/pair_style.txt
+++ b/doc/src/pair_style.txt
@@ -218,10 +218,9 @@ This command must be used before any coefficients are set by the
"read_restart"_read_restart.html commands.
Some pair styles are part of specific packages. They are only enabled
-if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
-The doc pages for individual pair potentials tell if it is part of a
-package.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info. The doc pages for
+individual pair potentials tell if it is part of a package.
[Related commands:]
diff --git a/doc/src/pair_sw.txt b/doc/src/pair_sw.txt
index e6741791df..ff83316419 100644
--- a/doc/src/pair_sw.txt
+++ b/doc/src/pair_sw.txt
@@ -150,13 +150,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
When using the USER-INTEL package with this style, there is an
additional 5 to 10 percent performance improvement when the
@@ -191,8 +191,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This pair style is part of the MANYBODY package. It is only enabled
-if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This pair style requires the "newton"_newton.html setting to be "on"
for pair interactions.
diff --git a/doc/src/pair_table.txt b/doc/src/pair_table.txt
index 5e3c1f5ff6..22c63a1f32 100644
--- a/doc/src/pair_table.txt
+++ b/doc/src/pair_table.txt
@@ -223,13 +223,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/pair_table_rx.txt b/doc/src/pair_table_rx.txt
index 41be067bac..9b9a6abff8 100644
--- a/doc/src/pair_table_rx.txt
+++ b/doc/src/pair_table_rx.txt
@@ -233,13 +233,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -249,8 +249,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This command is part of the USER-DPD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_tersoff.txt b/doc/src/pair_tersoff.txt
index 821c38f3e4..20744bc2a9 100644
--- a/doc/src/pair_tersoff.txt
+++ b/doc/src/pair_tersoff.txt
@@ -185,13 +185,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -221,8 +221,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This pair style is part of the MANYBODY package. It is only enabled
-if LAMMPS was built with that package. See
-the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This pair style requires the "newton"_newton.html setting to be "on"
for pair interactions.
diff --git a/doc/src/pair_tersoff_mod.txt b/doc/src/pair_tersoff_mod.txt
index ac1f79a80b..2df23045a3 100644
--- a/doc/src/pair_tersoff_mod.txt
+++ b/doc/src/pair_tersoff_mod.txt
@@ -137,13 +137,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -169,8 +169,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This pair style is part of the MANYBODY package. It is only enabled
-if LAMMPS was built with that package. See
-the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This pair style requires the "newton"_newton.html setting to be "on"
for pair interactions.
diff --git a/doc/src/pair_tersoff_zbl.txt b/doc/src/pair_tersoff_zbl.txt
index a89d4e3ea1..5f03ffd94e 100644
--- a/doc/src/pair_tersoff_zbl.txt
+++ b/doc/src/pair_tersoff_zbl.txt
@@ -195,13 +195,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -231,8 +231,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This pair style is part of the MANYBODY package. It is only enabled
-if LAMMPS was built with that package. See
-the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This pair style requires the "newton"_newton.html setting to be "on"
for pair interactions.
diff --git a/doc/src/pair_thole.txt b/doc/src/pair_thole.txt
index 7ce8b7cf4b..c7a304ca41 100644
--- a/doc/src/pair_thole.txt
+++ b/doc/src/pair_thole.txt
@@ -136,13 +136,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -161,8 +161,8 @@ are defined using
[Restrictions:]
These pair styles are part of the USER-DRUDE package. They are only
-enabled if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This pair_style should currently not be used with the "charmm dihedral
style"_dihedral_charmm.html if the latter has non-zero 1-4 weighting
diff --git a/doc/src/pair_tri_lj.txt b/doc/src/pair_tri_lj.txt
index 3915ffc238..98bb4e284e 100644
--- a/doc/src/pair_tri_lj.txt
+++ b/doc/src/pair_tri_lj.txt
@@ -101,8 +101,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This style is part of the ASPHERE package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Defining particles to be triangles so they participate in tri/tri or
tri/particle interactions requires the use the "atom_style
diff --git a/doc/src/pair_ufm.txt b/doc/src/pair_ufm.txt
index dbc6fd0664..787c60a1bd 100644
--- a/doc/src/pair_ufm.txt
+++ b/doc/src/pair_ufm.txt
@@ -75,13 +75,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/pair_vashishta.txt b/doc/src/pair_vashishta.txt
index 2e404e8bef..01d089b4de 100644
--- a/doc/src/pair_vashishta.txt
+++ b/doc/src/pair_vashishta.txt
@@ -177,13 +177,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -213,8 +213,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
These pair style are part of the MANYBODY package. They is only
-enabled if LAMMPS was built with that package. See the
-"Making LAMMPS"_Section_start.html#start_3 section for more info.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
These pair styles requires the "newton"_newton.html setting to be "on"
for pair interactions.
diff --git a/doc/src/pair_yukawa.txt b/doc/src/pair_yukawa.txt
index 5a8363260a..154fd3e836 100644
--- a/doc/src/pair_yukawa.txt
+++ b/doc/src/pair_yukawa.txt
@@ -55,13 +55,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/pair_yukawa_colloid.txt b/doc/src/pair_yukawa_colloid.txt
index 515062d9eb..b36c4c235c 100644
--- a/doc/src/pair_yukawa_colloid.txt
+++ b/doc/src/pair_yukawa_colloid.txt
@@ -86,13 +86,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -129,8 +129,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This style is part of the COLLOID package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This pair style requires that atoms be finite-size spheres with a
diameter, as defined by the "atom_style sphere"_atom_style.html
diff --git a/doc/src/pair_zbl.txt b/doc/src/pair_zbl.txt
index 1472c7b672..4c8dfb5455 100644
--- a/doc/src/pair_zbl.txt
+++ b/doc/src/pair_zbl.txt
@@ -77,13 +77,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/partition.txt b/doc/src/partition.txt
index d4fe06c098..86673c226b 100644
--- a/doc/src/partition.txt
+++ b/doc/src/partition.txt
@@ -26,9 +26,8 @@ partition yes 6* fix all nvt temp 1.0 1.0 0.1 :pre
[Description:]
This command invokes the specified command on a subset of the
-partitions of processors you have defined via the -partition
-command-line switch. See "Section 2.6"_Section_start.html#start_6
-for an explanation of the switch.
+partitions of processors you have defined via the "-partition
+command-line switch"_Run_options.html.
Normally, every input script command in your script is invoked by
every partition. This behavior can be modified by defining world- or
@@ -49,7 +48,7 @@ argument.
Partitions are numbered from 1 to Np, where Np is the number of
partitions specified by the "-partition command-line
-switch"_Section_start.html#start_6.
+switch"_Run_options.html.
{N} can be specified in one of two ways. An explicit numeric value
can be used, as in the 1st example above. Or a wild-card asterisk can
diff --git a/doc/src/prd.txt b/doc/src/prd.txt
index b2145ebad1..f71f285336 100644
--- a/doc/src/prd.txt
+++ b/doc/src/prd.txt
@@ -62,15 +62,15 @@ timescale spanned by the multiple simulations, while waiting for an
event to occur.
Each replica runs on a partition of one or more processors. Processor
-partitions are defined at run-time using the -partition command-line
-switch; see "Section 2.6"_Section_start.html#start_6 of the manual.
-Note that if you have MPI installed, you can run a multi-replica
-simulation with more replicas (partitions) than you have physical
-processors, e.g you can run a 10-replica simulation on one or two
-processors. However for PRD, this makes little sense, since running a
-replica on virtual instead of physical processors,offers no effective
-parallel speed-up in searching for infrequent events. See the "Howto
-replica"_Howto_replica.html doc page for further discussion.
+partitions are defined at run-time using the "-partition command-line
+switch"_Run_options.html. Note that if you have MPI installed, you
+can run a multi-replica simulation with more replicas (partitions)
+than you have physical processors, e.g you can run a 10-replica
+simulation on one or two processors. However for PRD, this makes
+little sense, since running a replica on virtual instead of physical
+processors,offers no effective parallel speed-up in searching for
+infrequent events. See the "Howto replica"_Howto_replica.html doc
+page for further discussion.
When a PRD simulation is performed, it is assumed that each replica is
running the same model, though LAMMPS does not check for this.
@@ -285,8 +285,8 @@ value for the first event in the new run will be slightly off.
[Restrictions:]
This command can only be used if LAMMPS was built with the REPLICA
-package. See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info on packages.
+package. See the "Build package"_Build_package.html doc
+page for more info.
The {N} and {t_correlate} settings must be integer multiples of
{t_event}.
diff --git a/doc/src/processors.txt b/doc/src/processors.txt
index df13ae1f61..b9bd927f96 100644
--- a/doc/src/processors.txt
+++ b/doc/src/processors.txt
@@ -81,11 +81,11 @@ communication costs due to the high surface area of each processor's
sub-domain.
Also note that if multiple partitions are being used then P is the
-number of processors in this partition; see "this
-section"_Section_start.html#start_6 for an explanation of the
--partition command-line switch. Also note that you can prefix the
-processors command with the "partition"_partition.html command to
-easily specify different Px,Py,Pz values for different partitions.
+number of processors in this partition; see the "-partition
+command-line switch"_Run_options.html doc page for details. Also note
+that you can prefix the processors command with the
+"partition"_partition.html command to easily specify different
+Px,Py,Pz values for different partitions.
You can use the "partition"_partition.html command to specify
different processor grids for different partitions, e.g.
@@ -249,7 +249,7 @@ partition {Precv} which is enforced when each is setting up their own
mapping of their processors to the simulation box. Each of {Psend}
and {Precv} must be integers from 1 to Np, where Np is the number of
partitions you have defined via the "-partition command-line
-switch"_Section_start.html#start_6.
+switch"_Run_options.html.
A "dependency" means that the sending partition will create its
regular 3d grid as Px by Py by Pz and after it has done this, it will
@@ -286,8 +286,8 @@ processors and their mapping to the 3d grid to the specified file
processors in the manner you desired, which can be tricky to figure
out, especially when running on multiple partitions or on, a multicore
machine or when the processor ranks were reordered by use of the
-"-reorder command-line switch"_Section_start.html#start_6 or due to
-use of MPI-specific launch options such as a config file.
+"-reorder command-line switch"_Run_options.html or due to use of
+MPI-specific launch options such as a config file.
If you have multiple partitions you should insure that each one writes
to a different file, e.g. using a "world-style variable"_variable.html
@@ -300,11 +300,11 @@ The IDs are the processor's rank in this simulation (the world), the
universe (of multiple simulations), and the original MPI communicator
used to instantiate LAMMPS, respectively. The world and universe IDs
will only be different if you are running on more than one partition;
-see the "-partition command-line switch"_Section_start.html#start_6.
-The universe and original IDs will only be different if you used the
-"-reorder command-line switch"_Section_start.html#start_6 to reorder
-the processors differently than their rank in the original
-communicator LAMMPS was instantiated with.
+see the "-partition command-line switch"_Run_options.html. The
+universe and original IDs will only be different if you used the
+"-reorder command-line switch"_Run_options.html to reorder the
+processors differently than their rank in the original communicator
+LAMMPS was instantiated with.
I,J,K are the indices of the processor in the regular 3d grid, each
from 1 to Nd, where Nd is the number of processors in that dimension
@@ -332,7 +332,8 @@ The {part} keyword (for the receiving partition) only works with the
[Related commands:]
-"partition"_partition.html, "-reorder command-line switch"_Section_start.html#start_6
+"partition"_partition.html, "-reorder command-line
+switch"_Run_options.html
[Default:]
diff --git a/doc/src/python.txt b/doc/src/python.txt
index 4f4faca8f4..0c0a203ccd 100644
--- a/doc/src/python.txt
+++ b/doc/src/python.txt
@@ -469,8 +469,8 @@ sys.exit() in the except clause).
[Restrictions:]
This command is part of the PYTHON package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Building LAMMPS with the PYTHON package will link LAMMPS with the
Python library on your system. Settings to enable this are in the
diff --git a/doc/src/read_data.txt b/doc/src/read_data.txt
index ded51a4d99..ef899a15b4 100644
--- a/doc/src/read_data.txt
+++ b/doc/src/read_data.txt
@@ -63,8 +63,8 @@ simulation. The file can be ASCII text or a gzipped text file
atom coordinates; see the "read_restart"_read_restart.html and
"create_atoms"_create_atoms.html commands for alternative methods.
Also see the explanation of the "-restart command-line
-switch"_Section_start.html#start_6 which can convert a restart file to
-a data file.
+switch"_Run_options.html which can convert a restart file to a data
+file.
This command can be used multiple times to add new atoms and their
properties to an existing system by using the {add}, {offset}, and
@@ -1153,8 +1153,8 @@ Translational velocities can also be set by the
[Restrictions:]
To read gzipped data files, you must compile LAMMPS with the
--DLAMMPS_GZIP option - see the "Making
-LAMMPS"_Section_start.html#start_2 section of the documentation.
+-DLAMMPS_GZIP option. See the "Build settings"_Build_settings.html
+doc page for details.
[Related commands:]
diff --git a/doc/src/read_dump.txt b/doc/src/read_dump.txt
index a3c0733e07..db9cfca825 100644
--- a/doc/src/read_dump.txt
+++ b/doc/src/read_dump.txt
@@ -311,12 +311,12 @@ needed to generate absolute, unscaled coordinates.
[Restrictions:]
To read gzipped dump files, you must compile LAMMPS with the
--DLAMMPS_GZIP option - see the "Making
-LAMMPS"_Section_start.html#start_2 section of the documentation.
+-DLAMMPS_GZIP option. See the "Build settings"_Build_settings.html
+doc page for details.
The {molfile} dump file formats are part of the USER-MOLFILE package.
They are only enabled if LAMMPS was built with that packages. See the
-"Making LAMMPS"_Section_start.html#start_3 section for more info.
+"Build package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/read_restart.txt b/doc/src/read_restart.txt
index 488c36f020..08cb6a2e6c 100644
--- a/doc/src/read_restart.txt
+++ b/doc/src/read_restart.txt
@@ -80,8 +80,7 @@ produced the restart file, it could be a LAMMPS bug, so consider
Because restart files are binary, they may not be portable to other
machines. In this case, you can use the "-restart command-line
-switch"_Section_start.html#start_6 to convert a restart file to a data
-file.
+switch"_Run_options.html to convert a restart file to a data file.
Similar to how restart files are written (see the
"write_restart"_write_restart.html and "restart"_restart.html
diff --git a/doc/src/region.txt b/doc/src/region.txt
index 21396ae1fd..acc85dcebb 100644
--- a/doc/src/region.txt
+++ b/doc/src/region.txt
@@ -370,13 +370,13 @@ by Kokkos or no acceleration will occur. Currently, only {block} style
regions are supported by Kokkos.
These accelerated styles are part of the Kokkos package. They are
-only enabled if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+only enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/rerun.txt b/doc/src/rerun.txt
index 8eb3ebd5a1..71ad464bb0 100644
--- a/doc/src/rerun.txt
+++ b/doc/src/rerun.txt
@@ -189,8 +189,8 @@ every 1000 steps, then you will only see thermodynamic output every
[Restrictions:]
To read gzipped dump files, you must compile LAMMPS with the
--DLAMMPS_GZIP option - see the "Making
-LAMMPS"_Section_start.html#start_2 section of the documentation.
+-DLAMMPS_GZIP option. See the "Build settings"_Build_settings.html
+doc page for details.
[Related commands:]
diff --git a/doc/src/restart.txt b/doc/src/restart.txt
index 6f2dc5ca46..7c034f36e0 100644
--- a/doc/src/restart.txt
+++ b/doc/src/restart.txt
@@ -125,8 +125,7 @@ Restart files can be read by a "read_restart"_read_restart.html
command to restart a simulation from a particular state. Because the
file is binary (to enable exact restarts), it may not be readable on
another machine. In this case, you can use the "-r command-line
-switch"_Section_start.html#start_6 to convert a restart file to a data
-file.
+switch"_Run_options.html to convert a restart file to a data file.
NOTE: Although the purpose of restart files is to enable restarting a
simulation from where it left off, not all information about a
diff --git a/doc/src/run_style.txt b/doc/src/run_style.txt
index deee51cfd3..6dd9b56908 100644
--- a/doc/src/run_style.txt
+++ b/doc/src/run_style.txt
@@ -69,8 +69,8 @@ The {verlet} style is a standard velocity-Verlet integrator.
The {verlet/split} style is also a velocity-Verlet integrator, but it
splits the force calculation within each timestep over 2 partitions of
-processors. See "Section 2.6"_Section_start.html#start_6 for an
-explanation of the -partition command-line switch.
+processors. See the "-partition command-line switch"_Run_options.html
+for info on how to run LAMMPS with multiple partitions.
Specifically, this style performs all computation except the
"kspace_style"_kspace_style.html portion of the force field on the 1st
@@ -115,9 +115,9 @@ When you run in 2-partition mode with the {verlet/split} style, the
thermodynamic data for the entire simulation will be output to the log
and screen file of the 1st partition, which are log.lammps.0 and
screen.0 by default; see the "-plog and -pscreen command-line
-switches"_Section_start.html#start_6 to change this. The log and
-screen file for the 2nd partition will not contain thermodynamic
-output beyond the 1st timestep of the run.
+switches"_Run_options.html to change this. The log and screen file
+for the 2nd partition will not contain thermodynamic output beyond the
+1st timestep of the run.
See the "Speed packages"_Speed_packages.html doc page for performance
details of the speed-up offered by the {verlet/split} style. One
@@ -282,10 +282,10 @@ additional operations required for managing {omp} styles. For more on
styles take the same arguments and should produce the same results,
except for round-off and precision issues.
-You can specify {respa/omp} explicitly in your input script, or
-you can use the "-suffix command-line switch"_Section_start.html#start_6
-when you invoke LAMMPS, or you can use the "suffix"_suffix.html
-command in your input script.
+You can specify {respa/omp} explicitly in your input script, or you
+can use the "-suffix command-line switch"_Run_options.html when you
+invoke LAMMPS, or you can use the "suffix"_suffix.html command in your
+input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -296,8 +296,8 @@ instructions on how to use the accelerated styles effectively.
The {verlet/split} style can only be used if LAMMPS was built with the
REPLICA package. Correspondingly the {respa/omp} style is available
-only if the USER-OMP package was included. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+only if the USER-OMP package was included. See the "Build
+package"_Build_package.html doc page for more info.
Whenever using rRESPA, the user should experiment with trade-offs in
speed and accuracy for their system, and verify that they are
diff --git a/doc/src/suffix.txt b/doc/src/suffix.txt
index bb0619f1e0..62e41ed29a 100644
--- a/doc/src/suffix.txt
+++ b/doc/src/suffix.txt
@@ -28,16 +28,16 @@ suffix kk :pre
This command allows you to use variants of various styles if they
exist. In that respect it operates the same as the "-suffix
-command-line switch"_Section_start.html#start_6. It also has options
-to turn off or back on any suffix setting made via the command line.
+command-line switch"_Run_options.html. It also has options to turn
+off or back on any suffix setting made via the command line.
The specified style can be {gpu}, {intel}, {kk}, {omp}, {opt} or
{hybrid}. These refer to optional packages that LAMMPS can be built
-with, as described in "this section of the
-manual"_Section_start.html#start_3. The "gpu" style corresponds to
-the GPU package, the "intel" style to the USER-INTEL package, the "kk"
-style to the KOKKOS package, the "omp" style to the USER-OMP package,
-and the "opt" style to the OPT package.
+with, as described on the "Build package"_Build_package.html doc page.
+The "gpu" style corresponds to the GPU package, the "intel" style to
+the USER-INTEL package, the "kk" style to the KOKKOS package, the
+"omp" style to the USER-OMP package, and the "opt" style to the OPT
+package.
These are the variants these packages provide:
@@ -105,6 +105,6 @@ input script.
[Related commands:]
-"Command-line switch -suffix"_Section_start.html#start_6
+"-suffix command-line switch"_Run_options.html
[Default:] none
diff --git a/doc/src/tad.txt b/doc/src/tad.txt
index a26ff79318..9b34a68636 100644
--- a/doc/src/tad.txt
+++ b/doc/src/tad.txt
@@ -271,8 +271,8 @@ are always monotonically increasing.
[Restrictions:]
This command can only be used if LAMMPS was built with the REPLICA
-package. See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info on packages.
+package. See the "Build package"_Build_package.html doc
+page for more info.
{N} setting must be integer multiple of {t_event}.
diff --git a/doc/src/temper.txt b/doc/src/temper.txt
index c7b482acc6..edd578fbc9 100644
--- a/doc/src/temper.txt
+++ b/doc/src/temper.txt
@@ -31,14 +31,14 @@ Run a parallel tempering or replica exchange simulation using multiple
replicas (ensembles) of a system. Two or more replicas must be used.
Each replica runs on a partition of one or more processors. Processor
-partitions are defined at run-time using the -partition command-line
-switch; see "Section 2.6"_Section_start.html#start_6 of the manual.
-Note that if you have MPI installed, you can run a multi-replica
-simulation with more replicas (partitions) than you have physical
-processors, e.g you can run a 10-replica simulation on one or two
-processors. You will simply not get the performance speed-up you
-would see with one or more physical processors per replica. See the
-"Howto replica"_Howto_replica.html doc page for further discussion.
+partitions are defined at run-time using the "-partition command-line
+switch"_Run_options.html. Note that if you have MPI installed, you
+can run a multi-replica simulation with more replicas (partitions)
+than you have physical processors, e.g you can run a 10-replica
+simulation on one or two processors. You will simply not get the
+performance speed-up you would see with one or more physical
+processors per replica. See the "Howto replica"_Howto_replica.html
+doc page for further discussion.
Each replica's temperature is controlled at a different value by a fix
with {fix-ID} that controls temperature. Most thermostat fix styles
@@ -68,9 +68,8 @@ rejected based on a Boltzmann-weighted Metropolis criterion which uses
As a tempering run proceeds, multiple log files and screen output
files are created, one per replica. By default these files are named
log.lammps.M and screen.M where M is the replica number from 0 to N-1,
-with N = # of replicas. See the "section on command-line
-switches"_Section_start.html#start_6 for info on how to change these
-names.
+with N = # of replicas. See the "-log and -screen command-line
+swiches"_Run_options.html for info on how to change these names.
The main screen and log file (log.lammps) will list information about
which temperature is assigned to each replica at each thermodynamic
@@ -138,8 +137,8 @@ example above with $w as the last argument.
[Restrictions:]
This command can only be used if LAMMPS was built with the REPLICA
-package. See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info on packages.
+package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/temper_grem.txt b/doc/src/temper_grem.txt
index 9cb1bab784..7d22e46403 100644
--- a/doc/src/temper_grem.txt
+++ b/doc/src/temper_grem.txt
@@ -94,8 +94,8 @@ identical to "temper"_temper.html.
[Restrictions:]
This command can only be used if LAMMPS was built with the USER-MISC
-package. See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info on packages.
+package. See the "Build package"_Build_package.html doc
+page for more info.
This command must be used with "fix grem"_fix_grem.html.
diff --git a/doc/src/temper_npt.txt b/doc/src/temper_npt.txt
index 4eee225de7..50ac5615f6 100644
--- a/doc/src/temper_npt.txt
+++ b/doc/src/temper_npt.txt
@@ -48,8 +48,8 @@ on how the parallel tempering is handled in general.
[Restrictions:]
This command can only be used if LAMMPS was built with the USER-MISC
-package. See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info on packages.
+package. See the "Build package"_Build_package.html doc page for more
+info.
This command should be used with a fix that maintains the
isothermal-isobaric (NPT) ensemble.
diff --git a/doc/src/thermo_style.txt b/doc/src/thermo_style.txt
index cbc2612f28..4d294c1df7 100644
--- a/doc/src/thermo_style.txt
+++ b/doc/src/thermo_style.txt
@@ -253,9 +253,9 @@ proceed for the maximum number of allowed iterations.
The {part} keyword is useful for multi-replica or multi-partition
simulations to indicate which partition this output and this file
corresponds to, or for use in a "variable"_variable.html to append to
-a filename for output specific to this partition. See "Section
-2.6"_Section_start.html#start_6 of the manual for details on running
-in multi-partition mode.
+a filename for output specific to this partition. See discussion of
+the "-partition command-line switch"_Run_options.html for details on
+running in multi-partition mode.
The {timeremain} keyword returns the remaining seconds when a
timeout has been configured via the "timer timeout"_timer.html command.
diff --git a/doc/src/timer.txt b/doc/src/timer.txt
index 10737dbda0..4025af9ea6 100644
--- a/doc/src/timer.txt
+++ b/doc/src/timer.txt
@@ -39,8 +39,8 @@ During a simulation run LAMMPS collects information about how much
time is spent in different sections of the code and thus can provide
information for determining performance and load imbalance problems.
This can be done at different levels of detail and accuracy. For more
-information about the timing output, see this "discussion of screen
-output in Section 2.7"_Section_start.html#start_7.
+information about the timing output, see the "Run
+output"_Run_output.html doc page.
The {off} setting will turn all time measurements off. The {loop}
setting will only measure the total time for a run and not collect any
diff --git a/doc/src/variable.txt b/doc/src/variable.txt
index c6598ccb51..a8d50503ac 100644
--- a/doc/src/variable.txt
+++ b/doc/src/variable.txt
@@ -178,9 +178,8 @@ This means variables can NOT be re-defined in an input script (with
two exceptions, read further). This is to allow an input script to be
processed multiple times without resetting the variables; see the
"jump"_jump.html or "include"_include.html commands. It also means
-that using the "command-line switch"_Section_start.html#start_6 -var
-will override a corresponding index variable setting in the input
-script.
+that using the "command-line switch"_Run_options.html -var will
+override a corresponding index variable setting in the input script.
There are two exceptions to this rule. First, variables of style
{string}, {getenv}, {internal}, {equal}, {vector}, {atom}, and
@@ -247,8 +246,7 @@ string is assigned. All processors assign the same string to the
variable.
{Index} style variables with a single string value can also be set by
-using the command-line switch -var; see "this
-section"_Section_start.html#start_6 for details.
+using the "command-line switch -var"_Run_options.html.
The {loop} style is identical to the {index} style except that the
strings are the integers from 1 to N inclusive, if only one argument N
@@ -263,32 +261,31 @@ inclusive, and the string N1 is initially assigned to the variable.
N1 <= N2 and N2 >= 0 is required.
For the {world} style, one or more strings are specified. There must
-be one string for each processor partition or "world". See "this
-section"_Section_start.html#start_6 of the manual for information on
-running LAMMPS with multiple partitions via the "-partition"
-command-line switch. This variable command assigns one string to each
-world. All processors in the world are assigned the same string. The
-next command cannot be used with {equal} style variables, since there
-is only one value per world. This style of variable is useful when
-you wish to run different simulations on different partitions, or when
-performing a parallel tempering simulation (see the
+be one string for each processor partition or "world". LAMMPS can be
+run with multiple partitions via the "-partition command-line
+switch"_Run_options.html. This variable command assigns one string to
+each world. All processors in the world are assigned the same string.
+The next command cannot be used with {equal} style variables, since
+there is only one value per world. This style of variable is useful
+when you wish to run different simulations on different partitions, or
+when performing a parallel tempering simulation (see the
"temper"_temper.html command), to assign different temperatures to
different partitions.
For the {universe} style, one or more strings are specified. There
must be at least as many strings as there are processor partitions or
-"worlds". See "this page"_Section_start.html#start_6 for information
-on running LAMMPS with multiple partitions via the "-partition"
-command-line switch. This variable command initially assigns one
-string to each world. When a "next"_next.html command is encountered
-using this variable, the first processor partition to encounter it, is
-assigned the next available string. This continues until all the
-variable strings are consumed. Thus, this command can be used to run
-50 simulations on 8 processor partitions. The simulations will be run
-one after the other on whatever partition becomes available, until
-they are all finished. {Universe} style variables are incremented
-using the files "tmp.lammps.variable" and "tmp.lammps.variable.lock"
-which you will see in your directory during such a LAMMPS run.
+"worlds". LAMMPS can be run with multiple partitions via the
+"-partition command-line switch"_Run_options.html. This variable
+command initially assigns one string to each world. When a
+"next"_next.html command is encountered using this variable, the first
+processor partition to encounter it, is assigned the next available
+string. This continues until all the variable strings are consumed.
+Thus, this command can be used to run 50 simulations on 8 processor
+partitions. The simulations will be run one after the other on
+whatever partition becomes available, until they are all finished.
+{Universe} style variables are incremented using the files
+"tmp.lammps.variable" and "tmp.lammps.variable.lock" which you will
+see in your directory during such a LAMMPS run.
The {uloop} style is identical to the {universe} style except that the
strings are the integers from 1 to N. This allows generation of long
diff --git a/doc/src/write_data.txt b/doc/src/write_data.txt
index d8a33f457f..b6002b5252 100644
--- a/doc/src/write_data.txt
+++ b/doc/src/write_data.txt
@@ -60,7 +60,7 @@ If you want to do more exact restarts, using binary files, see the
"restart"_restart.html, "write_restart"_write_restart.html, and
"read_restart"_read_restart.html commands. You can also convert
binary restart files to text data files, after a simulation has run,
-using the "-r command-line switch"_Section_start.html#start_6.
+using the "-r command-line switch"_Run_options.html.
NOTE: Only limited information about a simulation is stored in a data
file. For example, no information about atom "groups"_group.html and
diff --git a/doc/src/write_restart.txt b/doc/src/write_restart.txt
index 3935a5d538..c393c7f735 100644
--- a/doc/src/write_restart.txt
+++ b/doc/src/write_restart.txt
@@ -66,8 +66,7 @@ Restart files can be read by a "read_restart"_read_restart.html
command to restart a simulation from a particular state. Because the
file is binary (to enable exact restarts), it may not be readable on
another machine. In this case, you can use the "-r command-line
-switch"_Section_start.html#start_6 to convert a restart file to a data
-file.
+switch"_Run_options.html to convert a restart file to a data file.
NOTE: Although the purpose of restart files is to enable restarting a
simulation from where it left off, not all information about a
--
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