diff --git a/doc/src/Commands.txt b/doc/src/Commands.txt new file mode 100644 index 0000000000..30e3343bd2 --- /dev/null +++ b/doc/src/Commands.txt @@ -0,0 +1,51 @@ +"Previous Section"_Run.html - "LAMMPS WWW Site"_lws - +"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next +Section"_Packages.html :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html#comm) + +:line + +Commands :h2 + +These pages describe how a LAMMPS input script is formatted and the +commands in it are used to define a LAMMPS simulation. + + + + + +"LAMMPS input scripts"_Commands_input.html +"Parsing rules for input scripts"_Commands_parse.html +"Input script structure"_Commands_structure.html +"Commands by category"_Commands_category.html :all(b) + +"All commands"_Commands_all.html +"Fix commands"_Commands_fix.html +"Compute commands"_Commands_compute.html +"Pair commands"_Commands_pair.html +"Bond, angle, dihedral, improper commands"_Commands_bond.html +"KSpace solvers"_Commands_kspace.html :all(b) + + + diff --git a/doc/src/Commands_all.txt b/doc/src/Commands_all.txt new file mode 100644 index 0000000000..13db1272b9 --- /dev/null +++ b/doc/src/Commands_all.txt @@ -0,0 +1,128 @@ +"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +"All commands"_Commands_all.html, +"Fix styles"_Commands_fix.html, +"Compute styles"_Commands_compute.html, +"Pair styles"_Commands_pair.html, +"Bond styles"_Commands_bond.html, +"Angle styles"_Commands_bond.html#angle, +"Dihedral styles"_Commands_bond.html#dihedral, +"Improper styles"_Commands_bond.html#improper, +"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c) + +All commands :h3 + +An alphabetic list of all LAMMPS commmands. + +"angle_coeff"_angle_coeff.html, +"angle_style"_angle_style.html, +"atom_modify"_atom_modify.html, +"atom_style"_atom_style.html, +"balance"_balance.html, +"bond_coeff"_bond_coeff.html, +"bond_style"_bond_style.html, +"bond_write"_bond_write.html, +"boundary"_boundary.html, +"box"_box.html, +"change_box"_change_box.html, +"clear"_clear.html, +"comm_modify"_comm_modify.html, +"comm_style"_comm_style.html, +"compute"_compute.html, +"compute_modify"_compute_modify.html, +"create_atoms"_create_atoms.html, +"create_bonds"_create_bonds.html, +"create_box"_create_box.html, +"delete_atoms"_delete_atoms.html, +"delete_bonds"_delete_bonds.html, +"dielectric"_dielectric.html, +"dihedral_coeff"_dihedral_coeff.html, +"dihedral_style"_dihedral_style.html, +"dimension"_dimension.html, +"displace_atoms"_displace_atoms.html, +"dump"_dump.html, +"dump image"_dump_image.html, +"dump_modify"_dump_modify.html, +"dump movie"_dump_image.html, +"dump netcdf"_dump_netcdf.html, +"dump netcdf/mpiio"_dump_netcdf.html, +"dump vtk"_dump_vtk.html, +"echo"_echo.html, +"fix"_fix.html, +"fix_modify"_fix_modify.html, +"group"_group.html, +"group2ndx"_group2ndx.html, +"if"_if.html, +"info"_info.html, +"improper_coeff"_improper_coeff.html, +"improper_style"_improper_style.html, +"include"_include.html, +"jump"_jump.html, +"kspace_modify"_kspace_modify.html, +"kspace_style"_kspace_style.html, +"label"_label.html, +"lattice"_lattice.html, +"log"_log.html, +"mass"_mass.html, +"minimize"_minimize.html, +"min_modify"_min_modify.html, +"min_style"_min_style.html, +"molecule"_molecule.html, +"ndx2group"_group2ndx.html, +"neb"_neb.html, +"neigh_modify"_neigh_modify.html, +"neighbor"_neighbor.html, +"newton"_newton.html, +"next"_next.html, +"package"_package.html, +"pair_coeff"_pair_coeff.html, +"pair_modify"_pair_modify.html, +"pair_style"_pair_style.html, +"pair_write"_pair_write.html, +"partition"_partition.html, +"prd"_prd.html, +"print"_print.html, +"processors"_processors.html, +"python"_python.html, +"quit"_quit.html, +"read_data"_read_data.html, +"read_dump"_read_dump.html, +"read_restart"_read_restart.html, +"region"_region.html, +"replicate"_replicate.html, +"rerun"_rerun.html, +"reset_ids"_reset_ids.html, +"reset_timestep"_reset_timestep.html, +"restart"_restart.html, +"run"_run.html, +"run_style"_run_style.html, +"set"_set.html, +"shell"_shell.html, +"special_bonds"_special_bonds.html, +"suffix"_suffix.html, +"tad"_tad.html, +"temper"_temper.html, +"temper/grem"_temper_grem.html, +"temper/npt"_temper_npt.html, +"thermo"_thermo.html, +"thermo_modify"_thermo_modify.html, +"thermo_style"_thermo_style.html, +"timer"_timer.html, +"timestep"_timestep.html, +"uncompute"_uncompute.html, +"undump"_undump.html, +"unfix"_unfix.html, +"units"_units.html, +"variable"_variable.html, +"velocity"_velocity.html, +"write_coeff"_write_coeff.html, +"write_data"_write_data.html, +"write_dump"_write_dump.html, +"write_restart"_write_restart.html :tb(c=6,ea=c) diff --git a/doc/src/Commands_bond.txt b/doc/src/Commands_bond.txt new file mode 100644 index 0000000000..314260cb14 --- /dev/null +++ b/doc/src/Commands_bond.txt @@ -0,0 +1,124 @@ +"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +"All commands"_Commands_all.html, +"Fix styles"_Commands_fix.html, +"Compute styles"_Commands_compute.html, +"Pair styles"_Commands_pair.html, +"Bond styles"_Commands_bond.html, +"Angle styles"_Commands_bond.html#angle, +"Dihedral styles"_Commands_bond.html#dihedral, +"Improper styles"_Commands_bond.html#improper, +"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c) + +Bond, angle, dihedral, and improper commands :h3 + +:line + +Bond_style potentials :h3,link(bond) + +All LAMMPS "bond_style"_bond_style.html commands. Some styles have +accelerated versions. This is indicated by additional letters in +parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = +OPT. + +"none"_bond_none.html, +"zero"_bond_zero.html, +"hybrid"_bond_hybrid.html :tb(c=3,ea=c) + +"class2 (ko)"_bond_class2.html, +"fene (iko)"_bond_fene.html, +"fene/expand (o)"_bond_fene_expand.html, +"gromos (o)"_bond_gromos.html, +"harmonic (ko)"_bond_harmonic.html, +"harmonic/shift (o)"_bond_harmonic_shift.html, +"harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html, +"morse (o)"_bond_morse.html, +"nonlinear (o)"_bond_nonlinear.html, +"oxdna/fene"_bond_oxdna.html, +"oxdna2/fene"_bond_oxdna.html, +"quartic (o)"_bond_quartic.html, +"table (o)"_bond_table.html :tb(c=4,ea=c) + +:line + +Angle_style potentials :h3,link(angle) + +All LAMMPS "angle_style"_angle_style.html commands. Some styles have +accelerated versions. This is indicated by additional letters in +parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = +OPT. + +"none"_angle_none.html, +"zero"_angle_zero.html, +"hybrid"_angle_hybrid.html :tb(c=3,ea=c) + +"charmm (ko)"_angle_charmm.html, +"class2 (ko)"_angle_class2.html, +"cosine (o)"_angle_cosine.html, +"cosine/delta (o)"_angle_cosine_delta.html, +"cosine/periodic (o)"_angle_cosine_periodic.html, +"cosine/shift (o)"_angle_cosine_shift.html, +"cosine/shift/exp (o)"_angle_cosine_shift_exp.html, +"cosine/squared (o)"_angle_cosine_squared.html, +"dipole (o)"_angle_dipole.html, +"fourier (o)"_angle_fourier.html, +"fourier/simple (o)"_angle_fourier_simple.html, +"harmonic (iko)"_angle_harmonic.html, +"quartic (o)"_angle_quartic.html, +"sdk"_angle_sdk.html, +"table (o)"_angle_table.html :tb(c=4,ea=c) + +:line + +Dihedral_style potentials :h3,link(dihedral) + +All LAMMPS "dihedral_style"_dihedral_style.html commands. Some styles +have accelerated versions. This is indicated by additional letters in +parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = +OPT. + +"none"_dihedral_none.html, +"zero"_dihedral_zero.html, +"hybrid"_dihedral_hybrid.html :tb(c=3,ea=c) + +"charmm (iko)"_dihedral_charmm.html, +"charmmfsw"_dihedral_charmm.html, +"class2 (ko)"_dihedral_class2.html, +"cosine/shift/exp (o)"_dihedral_cosine_shift_exp.html, +"fourier (io)"_dihedral_fourier.html, +"harmonic (io)"_dihedral_harmonic.html, +"helix (o)"_dihedral_helix.html, +"multi/harmonic (o)"_dihedral_multi_harmonic.html, +"nharmonic (o)"_dihedral_nharmonic.html, +"opls (iko)"_dihedral_opls.htm;, +"quadratic (o)"_dihedral_quadratic.html, +"spherical (o)"_dihedral_spherical.html, +"table (o)"_dihedral_table.html, +"table/cut"_dihedral_table_cut.html :tb(c=4,ea=c) + +:line + +Improper_style potentials :h3,link(improper) + +All LAMMPS "improper_style"_improper_style.html commands. Some styles +have accelerated versions. This is indicated by additional letters in +parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = +OPT. + +"none"_improper_none.html, +"zero"_improper_zero.html, +"hybrid"_improper_hybrid.html :tb(c=3,ea=c) + +"class2 (ko)"_improper_class2.html, +"cossq (o)"_improper_cossq.html, +"cvff (io)"_improper_cvff.html, +"distance"_improper_distance.html, +"fourier (o)"_improper_fourier.html, +"harmonic (iko)"_improper_harmonic.html, +"ring (o)"_improper_ring.html, +"umbrella (o)"_improper_umbrella.html :tb(c=4,ea=c) diff --git a/doc/src/Commands_category.txt b/doc/src/Commands_category.txt new file mode 100644 index 0000000000..5d047c6727 --- /dev/null +++ b/doc/src/Commands_category.txt @@ -0,0 +1,141 @@ +"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Commands by category :h3 + +This page lists most of the LAMMPS commands, grouped by category. The +"Commands all"_Commands_all.html doc page lists all commands +alphabetically. It also includes long lists of style options for +entries that appear in the following categories as a single command +(fix, compute, pair, etc). + +Initialization: + +"newton"_newton.html, +"package"_package.html, +"processors"_processors.html, +"suffix"_suffix.html, +"units"_units.html :ul + +Setup simulation box: + +"boundary"_boundary.html, +"box"_box.html, +"change_box"_change_box.html, +"create_box"_create_box.html, +"dimension"_dimension.html, +"lattice"_lattice.html, +"region"_region.html :ul + +Setup atoms: + +"atom_modify"_atom_modify.html, +"atom_style"_atom_style.html, +"balance"_balance.html, +"create_atoms"_create_atoms.html, +"create_bonds"_create_bonds.html, +"delete_atoms"_delete_atoms.html, +"delete_bonds"_delete_bonds.html, +"displace_atoms"_displace_atoms.html, +"group"_group.html, +"mass"_mass.html, +"molecule"_molecule.html, +"read_data"_read_data.html, +"read_dump"_read_dump.html, +"read_restart"_read_restart.html, +"replicate"_replicate.html, +"set"_set.html, +"velocity"_velocity.html :ul + +Force fields: + +"angle_coeff"_angle_coeff.html, +"angle_style"_angle_style.html, +"bond_coeff"_bond_coeff.html, +"bond_style"_bond_style.html, +"bond_write"_bond_write.html, +"dielectric"_dielectric.html, +"dihedral_coeff"_dihedral_coeff.html, +"dihedral_style"_dihedral_style.html, +"improper_coeff"_improper_coeff.html, +"improper_style"_improper_style.html, +"kspace_modify"_kspace_modify.html, +"kspace_style"_kspace_style.html, +"pair_coeff"_pair_coeff.html, +"pair_modify"_pair_modify.html, +"pair_style"_pair_style.html, +"pair_write"_pair_write.html, +"special_bonds"_special_bonds.html :ul + +Settings: + +"comm_modify"_comm_modify.html, +"comm_style"_comm_style.html, +"info"_info.html, +"min_modify"_min_modify.html, +"min_style"_min_style.html, +"neigh_modify"_neigh_modify.html, +"neighbor"_neighbor.html, +"partition"_partition.html, +"reset_timestep"_reset_timestep.html, +"run_style"_run_style.html, +"timer"_timer.html, +"timestep"_timestep.html :ul + +Operations within timestepping (fixes) and diagnostics (computes): + +"compute"_compute.html, +"compute_modify"_compute_modify.html, +"fix"_fix.html, +"fix_modify"_fix_modify.html, +"uncompute"_uncompute.html, +"unfix"_unfix.html :ul + +Output: + +"dump image"_dump_image.html, +"dump movie"_dump_image.html, +"dump"_dump.html, +"dump_modify"_dump_modify.html, +"restart"_restart.html, +"thermo"_thermo.html, +"thermo_modify"_thermo_modify.html, +"thermo_style"_thermo_style.html, +"undump"_undump.html, +"write_coeff"_write_coeff.html, +"write_data"_write_data.html, +"write_dump"_write_dump.html, +"write_restart"_write_restart.html :ul + +Actions: + +"minimize"_minimize.html, +"neb"_neb.html, +"prd"_prd.html, +"rerun"_rerun.html, +"run"_run.html, +"tad"_tad.html, +"temper"_temper.html :ul + +Input script control: + +"clear"_clear.html, +"echo"_echo.html, +"if"_if.html, +"include"_include.html, +"jump"_jump.html, +"label"_label.html, +"log"_log.html, +"next"_next.html, +"print"_print.html, +"python"_python.html, +"quit"_quit.html, +"shell"_shell.html, +"variable"_variable.html :ul + diff --git a/doc/src/Commands_compute.txt b/doc/src/Commands_compute.txt new file mode 100644 index 0000000000..028e274c9b --- /dev/null +++ b/doc/src/Commands_compute.txt @@ -0,0 +1,153 @@ +"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +"All commands"_Commands_all.html, +"Fix styles"_Commands_fix.html, +"Compute styles"_Commands_compute.html, +"Pair styles"_Commands_pair.html, +"Bond styles"_Commands_bond.html, +"Angle styles"_Commands_bond.html#angle, +"Dihedral styles"_Commands_bond.html#dihedral, +"Improper styles"_Commands_bond.html#improper, +"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c) + +Compute commands :h3 + +An alphabetic list of all LAMMPS "compute"_compute.html commands. +Some styles have accelerated versions. This is indicated by +additional letters in parenthesis: g = GPU, i = USER-INTEL, k = +KOKKOS, o = USER-OMP, t = OPT. + +"ackland/atom"_compute_ackland_atom.html, +"aggregate/atom"_compute_cluster_atom.html, +"angle"_compute_angle.html, +"angle/local"_compute_angle_local.html, +"angmom/chunk"_compute_angmom_chunk.html, +"basal/atom"_compute_basal_atom.html, +"body/local"_compute_body_local.html, +"bond"_compute_bond.html, +"bond/local"_compute_bond_local.html, +"centro/atom"_compute_centro_atom.html, +"chunk/atom"_compute_chunk_atom.html, +"cluster/atom"_compute_cluster_atom.html, +"cna/atom"_compute_cna_atom.html, +"cnp/atom"_compute_cnp_atom.html, +"com"_compute_com.html, +"com/chunk"_compute_com_chunk.html, +"contact/atom"_compute_contact_atom.html, +"coord/atom"_compute_coord_atom.html, +"damage/atom"_compute_damage_atom.html, +"dihedral"_compute_dihedral.html, +"dihedral/local"_compute_dihedral_local.html, +"dilatation/atom"_compute_dilatation_atom.html, +"dipole/chunk"_compute_dipole_chunk.html, +"displace/atom"_compute_displace_atom.html, +"dpd"_compute_dpd.html, +"dpd/atom"_compute_dpd_atom.html, +"edpd/temp/atom"_compute_edpd_temp_atom.html, +"entropy/atom"_compute_entropy_atom.html, +"erotate/asphere"_compute_erotate_asphere.html, +"erotate/rigid"_compute_erotate_rigid.html, +"erotate/sphere"_compute_erotate_sphere.html, +"erotate/sphere/atom"_compute_erotate_sphere_atom.html, +"event/displace"_compute_event_displace.html, +"fep"_compute_fep.html, +"force/tally"_compute_tally.html, +"fragment/atom"_compute_cluster_atom.html, +"global/atom"_compute_global_atom.html, +"group/group"_compute_group_group.html, +"gyration"_compute_gyration.html, +"gyration/chunk"_compute_gyration_chunk.html, +"heat/flux"_compute_heat_flux.html, +"heat/flux/tally"_compute_tally.html, +"hexorder/atom"_compute_hexorder_atom.html, +"improper"_compute_improper.html, +"improper/local"_compute_improper_local.html, +"inertia/chunk"_compute_inertia_chunk.html, +"ke"_compute_ke.html, +"ke/atom"_compute_ke_atom.html, +"ke/atom/eff"_compute_ke_atom_eff.html, +"ke/eff"_compute_ke_eff.html, +"ke/rigid"_compute_ke_rigid.html, +"meso/e/atom"_compute_meso_e_atom.html, +"meso/rho/atom"_compute_meso_rho_atom.html, +"meso/t/atom"_compute_meso_t_atom.html, +"msd"_compute_msd.html, +"msd/chunk"_compute_msd_chunk.html, +"msd/nongauss"_compute_msd_nongauss.html, +"omega/chunk"_compute_omega_chunk.html, +"orientorder/atom"_compute_orientorder_atom.html, +"pair"_compute_pair.html, +"pair/local"_compute_pair_local.html, +"pe"_compute_pe.html, +"pe/atom"_compute_pe_atom.html, +"pe/mol/tally"_compute_tally.html, +"pe/tally"_compute_tally.html, +"plasticity/atom"_compute_plasticity_atom.html, +"pressure"_compute_pressure.html, +"pressure/uef"_compute_pressure_uef.html, +"property/atom"_compute_property_atom.html, +"property/chunk"_compute_property_chunk.html, +"property/local"_compute_property_local.html, +"rdf"_compute_rdf.html, +"reduce"_compute_reduce.html, +"reduce/region"_compute_reduce.html, +"rigid/local"_compute_rigid_local.html, +"saed"_compute_saed.html, +"slice"_compute_slice.html, +"smd/contact/radius"_compute_smd_contact_radius.html, +"smd/damage"_compute_smd_damage.html, +"smd/hourglass/error"_compute_smd_hourglass_error.html, +"smd/internal/energy"_compute_smd_internal_energy.html, +"smd/plastic/strain"_compute_smd_plastic_strain.html, +"smd/plastic/strain/rate"_compute_smd_plastic_strain_rate.html, +"smd/rho"_compute_smd_rho.html, +"smd/tlsph/defgrad"_compute_smd_tlsph_defgrad.html, +"smd/tlsph/dt"_compute_smd_tlsph_dt.html, +"smd/tlsph/num/neighs"_compute_smd_tlsph_num_neighs.html, +"smd/tlsph/shape"_compute_smd_tlsph_shape.html, +"smd/tlsph/strain"_compute_smd_tlsph_strain.html, +"smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html, +"smd/tlsph/stress"_compute_smd_tlsph_stress.html, +"smd/triangle/mesh/vertices"_compute_smd_triangle_mesh_vertices.html, +"smd/ulsph/num/neighs"_compute_smd_ulsph_num_neighs.html, +"smd/ulsph/strain"_compute_smd_ulsph_strain.html, +"smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html, +"smd/ulsph/stress"_compute_smd_ulsph_stress.html, +"smd/vol"_compute_smd_vol.html, +"sna/atom"_compute_sna_atom.html, +"snad/atom"_compute_sna_atom.html, +"snav/atom"_compute_sna_atom.html, +"spin"_compute_spin.html, +"stress/atom"_compute_stress_atom.html, +"stress/tally"_compute_tally.html, +"tdpd/cc/atom"_compute_tdpd_cc_atom.html, +"temp (k)"_compute_temp.html, +"temp/asphere"_compute_temp_asphere.html, +"temp/body"_compute_temp_body.html, +"temp/chunk"_compute_temp_chunk.html, +"temp/com"_compute_temp_com.html, +"temp/deform"_compute_temp_deform.html, +"temp/deform/eff"_compute_temp_deform_eff.html, +"temp/drude"_compute_temp_drude.html, +"temp/eff"_compute_temp_eff.html, +"temp/partial"_compute_temp_partial.html, +"temp/profile"_compute_temp_profile.html, +"temp/ramp"_compute_temp_ramp.html, +"temp/region"_compute_temp_region.html, +"temp/region/eff"_compute_temp_region_eff.html, +"temp/rotate"_compute_temp_rotate.html, +"temp/sphere"_compute_temp_sphere.html, +"temp/uef"_compute_temp_uef.html, +"ti"_compute_ti.html, +"torque/chunk"_compute_torque_chunk.html, +"vacf"_compute_vacf.html, +"vcm/chunk"_compute_vcm_chunk.html, +"voronoi/atom"_compute_voronoi_atom.html, +"xrd"_compute_xrd.html :tb(c=6,ea=c) diff --git a/doc/src/Commands_fix.txt b/doc/src/Commands_fix.txt new file mode 100644 index 0000000000..e002c11770 --- /dev/null +++ b/doc/src/Commands_fix.txt @@ -0,0 +1,229 @@ +"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +"All commands"_Commands_all.html, +"Fix styles"_Commands_fix.html, +"Compute styles"_Commands_compute.html, +"Pair styles"_Commands_pair.html, +"Bond styles"_Commands_bond.html, +"Angle styles"_Commands_bond.html#angle, +"Dihedral styles"_Commands_bond.html#dihedral, +"Improper styles"_Commands_bond.html#improper, +"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c) + +Fix commands :h3 + +An alphabetic list of all LAMMPS "fix"_fix.html commands. Some styles +have accelerated versions. This is indicated by additional letters in +parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = +OPT. + +"adapt"_fix_adapt.html, +"adapt/fep"_fix_adapt_fep.html, +"addforce"_fix_addforce.html, +"addtorque"_fix_addtorque.html, +"append/atoms"_fix_append_atoms.html, +"atc"_fix_atc.html, +"atom/swap"_fix_atom_swap.html, +"ave/atom"_fix_ave_atom.html, +"ave/chunk"_fix_ave_chunk.html, +"ave/correlate"_fix_ave_correlate.html, +"ave/correlate/long"_fix_ave_correlate_long.html, +"ave/histo"_fix_ave_histo.html, +"ave/histo/weight"_fix_ave_histo.html, +"ave/time"_fix_ave_time.html, +"aveforce"_fix_aveforce.html, +"balance"_fix_balance.html, +"bond/break"_fix_bond_break.html, +"bond/create"_fix_bond_create.html, +"bond/react"_fix_bond_react.html, +"bond/swap"_fix_bond_swap.html, +"box/relax"_fix_box_relax.html, +"cmap"_fix_cmap.html, +"colvars"_fix_colvars.html, +"controller"_fix_controller.html, +"deform (k)"_fix_deform.html, +"deposit"_fix_deposit.html, +"dpd/energy (k)"_fix_dpd_energy.html, +"drag"_fix_drag.html, +"drude"_fix_drude.html, +"drude/transform/direct"_fix_drude_transform.html, +"drude/transform/reverse"_fix_drude_transform.html, +"dt/reset"_fix_dt_reset.html, +"edpd/source"_fix_dpd_source.html, +"efield"_fix_efield.html, +"ehex"_fix_ehex.html, +"enforce2d (k)"_fix_enforce2d.html, +"eos/cv"_fix_eos_cv.html, +"eos/table"_fix_eos_table.html, +"eos/table/rx (k)"_fix_eos_table_rx.html, +"evaporate"_fix_evaporate.html, +"external"_fix_external.html, +"filter/corotate"_fix_filter_corotate.html, +"flow/gauss"_fix_flow_gauss.html, +"freeze"_fix_freeze.html, +"gcmc"_fix_gcmc.html, +"gld"_fix_gld.html, +"gle"_fix_gle.html, +"gravity (o)"_fix_gravity.html, +"grem"_fix_grem.html, +"halt"_fix_halt.html, +"heat"_fix_heat.html, +"imd"_fix_imd.html, +"indent"_fix_indent.html, +"ipi"_fix_ipi.html, +"langevin (k)"_fix_langevin.html, +"langevin/drude"_fix_langevin_drude.html, +"langevin/eff"_fix_langevin_eff.html, +"langevin/spin"_fix_langevin_spin.html, +"latte"_fix_latte.html, +"lb/fluid"_fix_lb_fluid.html, +"lb/momentum"_fix_lb_momentum.html, +"lb/pc"_fix_lb_pc.html, +"lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html, +"lb/viscous"_fix_lb_viscous.html, +"lineforce"_fix_lineforce.html, +"manifoldforce"_fix_manifoldforce.html, +"meso"_fix_meso.html, +"meso/stationary"_fix_meso_stationary.html, +"momentum (k)"_fix_momentum.html, +"move"_fix_move.html, +"mscg"_fix_mscg.html, +"msst"_fix_msst.html, +"mvv/dpd"_fix_mvv_dpd.html, +"mvv/edpd"_fix_mvv_dpd.html, +"mvv/tdpd"_fix_mvv_dpd.html, +"neb"_fix_neb.html, +"nph (ko)"_fix_nh.html, +"nph/asphere (o)"_fix_nph_asphere.html, +"nph/body"_fix_nph_body.html, +"nph/eff"_fix_nh_eff.html, +"nph/sphere (o)"_fix_nph_sphere.html, +"nphug (o)"_fix_nphug.html, +"npt (kio)"_fix_nh.html, +"npt/asphere (o)"_fix_npt_asphere.html, +"npt/body"_fix_npt_body.html, +"npt/eff"_fix_nh_eff.html, +"npt/sphere (o)"_fix_npt_sphere.html, +"npt/uef"_fix_nh_uef.html, +"nve (kio)"_fix_nve.html, +"nve/asphere (i)"_fix_nve_asphere.html, +"nve/asphere/noforce"_fix_nve_asphere_noforce.html, +"nve/body"_fix_nve_body.html, +"nve/dot"_fix_nve_dot.html, +"nve/dotc/langevin"_fix_nve_dotc_langevin.html, +"nve/eff"_fix_nve_eff.html, +"nve/limit"_fix_nve_limit.html, +"nve/line"_fix_nve_line.html, +"nve/manifold/rattle"_fix_nve_manifold_rattle.html, +"nve/noforce"_fix_nve_noforce.html, +"nve/sphere (o)"_fix_nve_sphere.html, +"nve/spin"_fix_nve_spin.html, +"nve/tri"_fix_nve_tri.html, +"nvk"_fix_nvk.html, +"nvt (iko)"_fix_nh.html, +"nvt/asphere (o)"_fix_nvt_asphere.html, +"nvt/body"_fix_nvt_body.html, +"nvt/eff"_fix_nh_eff.html, +"nvt/manifold/rattle"_fix_nvt_manifold_rattle.html, +"nvt/sllod (io)"_fix_nvt_sllod.html, +"nvt/sllod/eff"_fix_nvt_sllod_eff.html, +"nvt/sphere (o)"_fix_nvt_sphere.html, +"nvt/uef"_fix_nh_uef.html, +"oneway"_fix_oneway.html, +"orient/bcc"_fix_orient.html, +"orient/fcc"_fix_orient.html, +"phonon"_fix_phonon.html, +"pimd"_fix_pimd.html, +"planeforce"_fix_planeforce.html, +"poems"_fix_poems.html, +"pour"_fix_pour.html, +"precession/spin"_fix_precession_spin.html, +"press/berendsen"_fix_press_berendsen.html, +"print"_fix_print.html, +"property/atom (k)"_fix_property_atom.html, +"python/invoke"_fix_python_invoke.html, +"python/move"_fix_python_move.html, +"qbmsst"_fix_qbmsst.html, +"qeq/comb (o)"_fix_qeq_comb.html, +"qeq/dynamic"_fix_qeq.html, +"qeq/fire"_fix_qeq.html, +"qeq/point"_fix_qeq.html, +"qeq/reax (ko)"_fix_qeq_reax.html, +"qeq/shielded"_fix_qeq.html, +"qeq/slater"_fix_qeq.html, +"qmmm"_fix_qmmm.html, +"qtb"_fix_qtb.html, +"rattle"_fix_shake.html, +"reax/bonds"_fix_reax_bonds.html, +"reax/c/bonds (k)"_fix_reax_bonds.html, +"reax/c/species (k)"_fix_reaxc_species.html, +"recenter"_fix_recenter.html, +"restrain"_fix_restrain.html, +"rhok"_fix_rhok.html, +"rigid (o)"_fix_rigid.html, +"rigid/nph (o)"_fix_rigid.html, +"rigid/npt (o)"_fix_rigid.html, +"rigid/nve (o)"_fix_rigid.html, +"rigid/nvt (o)"_fix_rigid.html, +"rigid/small (o)"_fix_rigid.html, +"rigid/small/nph"_fix_rigid.html, +"rigid/small/npt"_fix_rigid.html, +"rigid/small/nve"_fix_rigid.html, +"rigid/small/nvt"_fix_rigid.html, +"rx (k)"_fix_rx.html, +"saed/vtk"_fix_saed_vtk.html, +"setforce (k)"_fix_setforce.html, +"shake"_fix_shake.html, +"shardlow (k)"_fix_shardlow.html, +"smd"_fix_smd.html, +"smd/adjust/dt"_fix_smd_adjust_dt.html, +"smd/integrate/tlsph"_fix_smd_integrate_tlsph.html, +"smd/integrate/ulsph"_fix_smd_integrate_ulsph.html, +"smd/move/triangulated/surface"_fix_smd_move_triangulated_surface.html, +"smd/setvel"_fix_smd_setvel.html, +"smd/wall/surface"_fix_smd_wall_surface.html, +"spring"_fix_spring.html, +"spring/chunk"_fix_spring_chunk.html, +"spring/rg"_fix_spring_rg.html, +"spring/self"_fix_spring_self.html, +"srd"_fix_srd.html, +"store/force"_fix_store_force.html, +"store/state"_fix_store_state.html, +"tdpd/source"_fix_dpd_source.html, +"temp/berendsen"_fix_temp_berendsen.html, +"temp/csld"_fix_temp_csvr.html, +"temp/csvr"_fix_temp_csvr.html, +"temp/rescale"_fix_temp_rescale.html, +"temp/rescale/eff"_fix_temp_rescale_eff.html, +"tfmc"_fix_tfmc.html, +"thermal/conductivity"_fix_thermal_conductivity.html, +"ti/spring"_fix_ti_spring.html, +"tmd"_fix_tmd.html, +"ttm"_fix_ttm.html, +"ttm/mod"_fix_ttm.html, +"tune/kspace"_fix_tune_kspace.html, +"vector"_fix_vector.html, +"viscosity"_fix_viscosity.html, +"viscous"_fix_viscous.html, +"wall/body/polygon"_fix_wall_body_polygon.html, +"wall/body/polyhedron"_fix_wall_body_polyhedron.html, +"wall/colloid"_fix_wall.html, +"wall/ees"_fix_wall_ees.html, +"wall/gran"_fix_wall_gran.html, +"wall/gran/region"_fix_wall_gran_region.html, +"wall/harmonic"_fix_wall.html, +"wall/lj1043"_fix_wall.html, +"wall/lj126"_fix_wall.html, +"wall/lj93 (k)"_fix_wall.html, +"wall/piston"_fix_wall_piston.html, +"wall/reflect (k)"_fix_wall_reflect.html, +"wall/region"_fix_wall_region.html, +"wall/region/ees"_fix_wall_ees.html, +"wall/srd"_fix_wall_srd.html :tb(c=8,ea=c) diff --git a/doc/src/Commands_input.txt b/doc/src/Commands_input.txt new file mode 100644 index 0000000000..8b3dda741b --- /dev/null +++ b/doc/src/Commands_input.txt @@ -0,0 +1,60 @@ +"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +LAMMPS input scripts :h3 + +LAMMPS executes by reading commands from a input script (text file), +one line at a time. When the input script ends, LAMMPS exits. Each +command causes LAMMPS to take some action. It may set an internal +variable, read in a file, or run a simulation. Most commands have +default settings, which means you only need to use the command if you +wish to change the default. + +In many cases, the ordering of commands in an input script is not +important. However the following rules apply: + +(1) LAMMPS does not read your entire input script and then perform a +simulation with all the settings. Rather, the input script is read +one line at a time and each command takes effect when it is read. +Thus this sequence of commands: + +timestep 0.5 +run 100 +run 100 :pre + +does something different than this sequence: + +run 100 +timestep 0.5 +run 100 :pre + +In the first case, the specified timestep (0.5 fs) is used for two +simulations of 100 timesteps each. In the 2nd case, the default +timestep (1.0 fs) is used for the 1st 100 step simulation and a 0.5 fs +timestep is used for the 2nd one. + +(2) Some commands are only valid when they follow other commands. For +example you cannot set the temperature of a group of atoms until atoms +have been defined and a group command is used to define which atoms +belong to the group. + +(3) Sometimes command B will use values that can be set by command A. +This means command A must precede command B in the input script if it +is to have the desired effect. For example, the +"read_data"_read_data.html command initializes the system by setting +up the simulation box and assigning atoms to processors. If default +values are not desired, the "processors"_processors.html and +"boundary"_boundary.html commands need to be used before read_data to +tell LAMMPS how to map processors to the simulation box. + +Many input script errors are detected by LAMMPS and an ERROR or +WARNING message is printed. The "Errors"_Errors.html doc page gives +more information on what errors mean. The documentation for each +command lists restrictions on how the command can be used. + diff --git a/doc/src/Commands_kspace.txt b/doc/src/Commands_kspace.txt new file mode 100644 index 0000000000..a126344505 --- /dev/null +++ b/doc/src/Commands_kspace.txt @@ -0,0 +1,36 @@ +"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands.html) + +:line + +"All commands"_Commands_all.html, +"Fix styles"_Commands_fix.html, +"Compute styles"_Commands_compute.html, +"Pair styles"_Commands_pair.html, +"Bond styles"_Commands_bond.html, +"Angle styles"_Commands_bond.html#angle, +"Dihedral styles"_Commands_bond.html#dihedral, +"Improper styles"_Commands_bond.html#improper, +"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c) + +KSpace solvers :h3 + +All LAMMPS "kspace_style"_kspace_style.html solvers. Some styles have +accelerated versions. This is indicated by additional letters in +parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = +OPT. + +"ewald (o)"_kspace_style.html, +"ewald/disp"_kspace_style.html, +"msm (o)"_kspace_style.html, +"msm/cg (o)"_kspace_style.html, +"pppm (gok)"_kspace_style.html, +"pppm/cg (o)"_kspace_style.html, +"pppm/disp (i)"_kspace_style.html, +"pppm/disp/tip4p"_kspace_style.html, +"pppm/stagger"_kspace_style.html, +"pppm/tip4p (o)"_kspace_style.html :tb(c=4,ea=c) diff --git a/doc/src/Commands_pair.txt b/doc/src/Commands_pair.txt new file mode 100644 index 0000000000..02b22942ae --- /dev/null +++ b/doc/src/Commands_pair.txt @@ -0,0 +1,231 @@ +"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +"All commands"_Commands_all.html, +"Fix styles"_Commands_fix.html, +"Compute styles"_Commands_compute.html, +"Pair styles"_Commands_pair.html, +"Bond styles"_Commands_bond.html, +"Angle styles"_Commands_bond.html#angle, +"Dihedral styles"_Commands_bond.html#dihedral, +"Improper styles"_Commands_bond.html#improper, +"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c) + +Pair_style potentials :h3 + +All LAMMPS "pair_style"_pair_style.html commands. Some styles have +accelerated versions. This is indicated by additional letters in +parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = +OPT. + +"none"_pair_none.html, +"zero"_pair_zero.html, +"hybrid"_pair_hybrid.html, +"hybrid/overlay (k)"_pair_hybrid.html :tb(c=4,ea=c) + +"adp (o)"_pair_adp.html, +"agni (o)"_pair_agni.html, +"airebo (oi)"_pair_airebo.html, +"airebo/morse (oi)"_pair_airebo.html, +"awpmd/cut"_pair_awpmd.html, +"beck (go)"_pair_beck.html, +"body/nparticle"_pair_body_nparticle.html, +"body/rounded/polygon"_pair_body_rounded/polygon.html, +"body/rounded/polyhedron"_pair_body_rounded/polyhedron.html, +"bop"_pair_bop.html, +"born (go)"_pair_born.html, +"born/coul/dsf"_pair_born.html, +"born/coul/dsf/cs"_pair_born.html, +"born/coul/long (go)"_pair_born.html, +"born/coul/long/cs"_pair_born.html, +"born/coul/msm (o)"_pair_born.html, +"born/coul/wolf (go)"_pair_born.html, +"born/coul/wolf/cs"_pair_born.html, +"brownian (o)"_pair_brownian.html, +"brownian/poly (o)"_pair_brownian.html, +"buck (giko)"_pair_buck.html, +"buck/coul/cut (giko)"_pair_buck.html, +"buck/coul/long (giko)"_pair_buck.html, +"buck/coul/long/cs"_pair_buck.html, +"buck/coul/msm (o)"_pair_buck.html, +"buck/long/coul/long (o)"_pair_buck_long.html, +"buck/mdf"_pair_mdf.html, +"colloid (go)"_pair_colloid.html, +"comb (o)"_pair_comb.html, +"comb3"_pair_comb.html, +"coul/cut (gko)"_pair_coul.html, +"coul/cut/soft (o)"_pair_lj_soft.html, +"coul/debye (gko)"_pair_coul.html, +"coul/diel (o)"_pair_coul_diel.html, +"coul/dsf (gko)"_pair_coul.html, +"coul/long (gko)"_pair_coul.html, +"coul/long/cs"_pair_coul.html, +"coul/long/soft (o)"_pair_lj_soft.html, +"coul/msm"_pair_coul.html, +"coul/shield"_pair_coul_shield.html, +"coul/streitz"_pair_coul.html, +"coul/wolf (ko)"_pair_coul.html, +"coul/wolf/cs"_pair_coul.html, +"dpd (gio)"_pair_dpd.html, +"dpd/fdt"_pair_dpd_fdt.html, +"dpd/fdt/energy (k)"_pair_dpd_fdt.html, +"dpd/tstat (go)"_pair_dpd.html, +"dsmc"_pair_dsmc.html, +"eam (gikot)"_pair_eam.html, +"eam/alloy (gikot)"_pair_eam.html, +"eam/cd (o)"_pair_eam.html, +"eam/fs (gikot)"_pair_eam.html, +"edip (o)"_pair_edip.html, +"edip/multi"_pair_edip.html, +"edpd"_pair_meso.html, +"eff/cut"_pair_eff.html, +"eim (o)"_pair_eim.html, +"exp6/rx (k)"_pair_exp6_rx.html, +"extep"_pair_extep.html, +"gauss (go)"_pair_gauss.html, +"gauss/cut"_pair_gauss.html, +"gayberne (gio)"_pair_gayberne.html, +"gran/hertz/history (o)"_pair_gran.html, +"gran/hooke (o)"_pair_gran.html, +"gran/hooke/history (o)"_pair_gran.html, +"gw"_pair_gw.html, +"gw/zbl"_pair_gw.html, +"hbond/dreiding/lj (o)"_pair_hbond_dreiding.html, +"hbond/dreiding/morse (o)"_pair_hbond_dreiding.html, +"ilp/graphene/hbn"_pair_ilp_graphene_hbn.html, +"kim"_pair_kim.html, +"kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html, +"kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html, +"lcbop"_pair_lcbop.html, +"lennard/mdf"_pair_mdf.html, +"line/lj"_pair_line_lj.html, +"list"_pair_list.html, +"lj/charmm/coul/charmm (iko)"_pair_charmm.html, +"lj/charmm/coul/charmm/implicit (ko)"_pair_charmm.html, +"lj/charmm/coul/long (giko)"_pair_charmm.html, +"lj/charmm/coul/long/soft (o)"_pair_charmm.html, +"lj/charmm/coul/msm"_pair_charmm.html, +"lj/charmmfsw/coul/charmmfsh"_pair_charmm.html, +"lj/charmmfsw/coul/long"_pair_charmm.html, +"lj/class2 (gko)"_pair_class2.html, +"lj/class2/coul/cut (ko)"_pair_class2.html, +"lj/class2/coul/long (gko)"_pair_class2.html, +"lj/cubic (go)"_pair_lj_cubic.html, +"lj/cut (gikot)"_pair_lj.html, +"lj/cut/coul/cut (gko)"_pair_lj.html, +"lj/cut/coul/cut/soft (o)"_pair_lj_soft.html, +"lj/cut/coul/debye (gko)"_pair_lj.html, +"lj/cut/coul/dsf (gko)"_pair_lj.html, +"lj/cut/coul/long (gikot)"_pair_lj.html, +"lj/cut/coul/long/cs"_pair_lj.html, +"lj/cut/coul/long/soft (o)"_pair_lj_soft.html, +"lj/cut/coul/msm (go)"_pair_lj.html, +"lj/cut/coul/wolf (o)"_pair_lj.html, +"lj/cut/dipole/cut (go)"_pair_dipole.html, +"lj/cut/dipole/long"_pair_dipole.html, +"lj/cut/dipole/sf (go)"_pair_dipole.html, +"lj/cut/soft (o)"_pair_lj_soft.html, +"lj/cut/thole/long (o)"_pair_thole.html, +"lj/cut/tip4p/cut (o)"_pair_lj.html, +"lj/cut/tip4p/long (ot)"_pair_lj.html, +"lj/cut/tip4p/long/soft (o)"_pair_lj_soft.html, +"lj/expand (gko)"_pair_lj_expand.html, +"lj/gromacs (gko)"_pair_gromacs.html, +"lj/gromacs/coul/gromacs (ko)"_pair_gromacs.html, +"lj/long/coul/long (io)"_pair_lj_long.html, +"lj/long/dipole/long"_pair_dipole.html, +"lj/long/tip4p/long"_pair_lj_long.html, +"lj/mdf"_pair_mdf.html, +"lj/sdk (gko)"_pair_sdk.html, +"lj/sdk/coul/long (go)"_pair_sdk.html, +"lj/sdk/coul/msm (o)"_pair_sdk.html, +"lj/smooth (o)"_pair_lj_smooth.html, +"lj/smooth/linear (o)"_pair_lj_smooth_linear.html, +"lj96/cut (go)"_pair_lj96.html, +"lubricate (o)"_pair_lubricate.html, +"lubricate/poly (o)"_pair_lubricate.html, +"lubricateU"_pair_lubricateU.html, +"lubricateU/poly"_pair_lubricateU.html, +"mdpd"_pair_meso.html, +"mdpd/rhosum"_pair_meso.html, +"meam"_pair_meam.html, +"meam/c"_pair_meam.html, +"meam/spline (o)"_pair_meam_spline.html, +"meam/sw/spline"_pair_meam_sw_spline.html, +"mgpt"_pair_mgpt.html, +"mie/cut (o)"_pair_mie.html, +"momb"_pair_momb.html, +"morse (gkot)"_pair_morse.html, +"morse/smooth/linear"_pair_morse.html, +"morse/soft"_pair_morse.html, +"multi/lucy"_pair_multi_lucy.html, +"multi/lucy/rx (k)"_pair_multi_lucy_rx.html, +"nb3b/harmonic (o)"_pair_nb3b_harmonic.html, +"nm/cut (o)"_pair_nm.html, +"nm/cut/coul/cut (o)"_pair_nm.html, +"nm/cut/coul/long (o)"_pair_nm.html, +"oxdna/coaxstk"_pair_oxdna.html, +"oxdna/excv"_pair_oxdna.html, +"oxdna/hbond"_pair_oxdna.html, +"oxdna/stk"_pair_oxdna.html, +"oxdna/xstk"_pair_oxdna.html, +"oxdna2/coaxstk"_pair_oxdna2.html, +"oxdna2/dh"_pair_oxdna2.html, +"oxdna2/excv"_pair_oxdna2.html, +"oxdna2/stk"_pair_oxdna2.html, +"peri/eps"_pair_peri.html, +"peri/lps (o)"_pair_peri.html, +"peri/pmb (o)"_pair_peri.html, +"peri/ves"_pair_peri.html, +"polymorphic"_pair_polymorphic.html, +"python"_pair_python.html, +"quip"_pair_quip.html, +"reax"_pair_reax.html, +"reax/c (ko)"_pair_reaxc.html, +"rebo (oi)"_pair_airebo.html, +"resquared (go)"_pair_resquared.html, +"smd/hertz"_pair_smd_hertz.html, +"smd/tlsph"_pair_smd_tlsph.html, +"smd/triangulated/surface"_pair_smd_triangulated_surface.html, +"smd/ulsph"_pair_smd_ulsph.html, +"smtbq"_pair_smtbq.html, +"snap (k)"_pair_snap.html, +"snap (k)"_pair_snap.html, +"soft (go)"_pair_soft.html, +"sph/heatconduction"_pair_sph_heatconduction.html, +"sph/idealgas"_pair_sph_idealgas.html, +"sph/lj"_pair_sph_lj.html, +"sph/rhosum"_pair_sph_rhosum.html, +"sph/taitwater"_pair_sph_taitwater.html, +"sph/taitwater/morris"_pair_sph_taitwater_morris.html, +"spin/dmi"_pair_spin_dmi.html, +"spin/exchange"_pair_spin_exchange.html, +"spin/magelec"_pair_spin_magelec.html, +"spin/neel"_pair_spin_neel.html, +"srp"_pair_srp.html, +"sw (giko)"_pair_sw.html, +"table (gko)"_pair_table.html, +"table/rx (k)"_pair_table_rx.html, +"tdpd"_pair_meso.html, +"tersoff (giko)"_pair_tersoff.html, +"tersoff/mod (gko)"_pair_tersoff_mod.html, +"tersoff/mod/c (o)"_pair_tersoff_mod.html, +"tersoff/table (o)"_pair_tersoff.html, +"tersoff/zbl (gko)"_pair_tersoff_zbl.html, +"thole"_pair_thole.html, +"tip4p/cut (o)"_pair_coul.html, +"tip4p/long (o)"_pair_coul.html, +"tip4p/long/soft (o)"_pair_lj_soft.html, +"tri/lj"_pair_tri_lj.html, +"ufm (got)"_pair_ufm.html, +"vashishta (ko)"_pair_vashishta.html, +"vashishta/table (o)"_pair_vashishta.html, +"yukawa (gok)"_pair_yukawa.html, +"yukawa/colloid (go)"_pair_yukawa_colloid.html, +"zbl (gok)"_pair_zbl.html :tb(c=4,ea=c) diff --git a/doc/src/Commands_parse.txt b/doc/src/Commands_parse.txt new file mode 100644 index 0000000000..cbe2261986 --- /dev/null +++ b/doc/src/Commands_parse.txt @@ -0,0 +1,136 @@ +"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Parsing rules for input scripts :h3 + +Each non-blank line in the input script is treated as a command. +LAMMPS commands are case sensitive. Command names are lower-case, as +are specified command arguments. Upper case letters may be used in +file names or user-chosen ID strings. + +Here are 6 rulse for how each line in the input script is parsed by +LAMMPS: + +(1) If the last printable character on the line is a "&" character, +the command is assumed to continue on the next line. The next line is +concatenated to the previous line by removing the "&" character and +line break. This allows long commands to be continued across two or +more lines. See the discussion of triple quotes in (6) for how to +continue a command across multiple line without using "&" characters. + +(2) All characters from the first "#" character onward are treated as +comment and discarded. See an exception in (6). Note that a +comment after a trailing "&" character will prevent the command from +continuing on the next line. Also note that for multi-line commands a +single leading "#" will comment out the entire command. + +(3) The line is searched repeatedly for $ characters, which indicate +variables that are replaced with a text string. See an exception in +(6). + +If the $ is followed by curly brackets, then the variable name is the +text inside the curly brackets. If no curly brackets follow the $, +then the variable name is the single character immediately following +the $. Thus $\{myTemp\} and $x refer to variable names "myTemp" and +"x". + +How the variable is converted to a text string depends on what style +of variable it is; see the "variable"_variable.html doc page for details. +It can be a variable that stores multiple text strings, and return one +of them. The returned text string can be multiple "words" (space +separated) which will then be interpreted as multiple arguments in the +input command. The variable can also store a numeric formula which +will be evaluated and its numeric result returned as a string. + +As a special case, if the $ is followed by parenthesis, then the text +inside the parenthesis is treated as an "immediate" variable and +evaluated as an "equal-style variable"_variable.html. This is a way +to use numeric formulas in an input script without having to assign +them to variable names. For example, these 3 input script lines: + +variable X equal (xlo+xhi)/2+sqrt(v_area) +region 1 block $X 2 INF INF EDGE EDGE +variable X delete :pre + +can be replaced by + +region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE :pre + +so that you do not have to define (or discard) a temporary variable X. + +Additionally, the "immediate" variable expression may be followed by a +colon, followed by a C-style format string, e.g. ":%f" or ":%.10g". +The format string must be appropriate for a double-precision +floating-point value. The format string is used to output the result +of the variable expression evaluation. If a format string is not +specified a high-precision "%.20g" is used as the default. + +This can be useful for formatting print output to a desired precion: + +print "Final energy per atom: $(pe/atoms:%10.3f) eV/atom" :pre + +Note that neither the curly-bracket or immediate form of variables can +contain nested $ characters for other variables to substitute for. +Thus you cannot do this: + +variable a equal 2 +variable b2 equal 4 +print "B2 = $\{b$a\}" :pre + +Nor can you specify this $($x-1.0) for an immediate variable, but +you could use $(v_x-1.0), since the latter is valid syntax for an +"equal-style variable"_variable.html. + +See the "variable"_variable.html command for more details of how +strings are assigned to variables and evaluated, and how they can be +used in input script commands. + +(4) The line is broken into "words" separated by whitespace (tabs, +spaces). Note that words can thus contain letters, digits, +underscores, or punctuation characters. + +(5) The first word is the command name. All successive words in the +line are arguments. + +(6) If you want text with spaces to be treated as a single argument, +it can be enclosed in either single or double or triple quotes. A +long single argument enclosed in single or double quotes can span +multiple lines if the "&" character is used, as described above. When +the lines are concatenated together (and the "&" characters and line +breaks removed), the text will become a single line. If you want +multiple lines of an argument to retain their line breaks, the text +can be enclosed in triple quotes, in which case "&" characters are not +needed. For example: + +print "Volume = $v" +print 'Volume = $v' +if "$\{steps\} > 1000" then quit +variable a string "red green blue & + purple orange cyan" +print """ +System volume = $v +System temperature = $t +""" :pre + +In each case, the single, double, or triple quotes are removed when +the single argument they enclose is stored internally. + +See the "dump modify format"_dump_modify.html, "print"_print.html, +"if"_if.html, and "python"_python.html commands for examples. + +A "#" or "$" character that is between quotes will not be treated as a +comment indicator in (2) or substituted for as a variable in (3). + +NOTE: If the argument is itself a command that requires a quoted +argument (e.g. using a "print"_print.html command as part of an +"if"_if.html or "run every"_run.html command), then single, double, or +triple quotes can be nested in the usual manner. See the doc pages +for those commands for examples. Only one of level of nesting is +allowed, but that should be sufficient for most use cases. + diff --git a/doc/src/Commands_structure.txt b/doc/src/Commands_structure.txt new file mode 100644 index 0000000000..b5d2c7b07b --- /dev/null +++ b/doc/src/Commands_structure.txt @@ -0,0 +1,95 @@ +"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Input script structure :h3 + +This page describes the structure of a typical LAMMPS input script. +The examples directory in the LAMMPS distribution contains many sample +input scripts; it is discussed on the "Examples"_Examples.html doc +page. + +A LAMMPS input script typically has 4 parts: + +Initialization +Atom definition +Settings +Run a simulation :ol + +The last 2 parts can be repeated as many times as desired. I.e. run a +simulation, change some settings, run some more, etc. Each of the 4 +parts is now described in more detail. Remember that almost all +commands need only be used if a non-default value is desired. + +(1) Initialization + +Set parameters that need to be defined before atoms are created or +read-in from a file. + +The relevant commands are "units"_units.html, +"dimension"_dimension.html, "newton"_newton.html, +"processors"_processors.html, "boundary"_boundary.html, +"atom_style"_atom_style.html, "atom_modify"_atom_modify.html. + +If force-field parameters appear in the files that will be read, these +commands tell LAMMPS what kinds of force fields are being used: +"pair_style"_pair_style.html, "bond_style"_bond_style.html, +"angle_style"_angle_style.html, "dihedral_style"_dihedral_style.html, +"improper_style"_improper_style.html. + +(2) Atom definition + +There are 3 ways to define atoms in LAMMPS. Read them in from a data +or restart file via the "read_data"_read_data.html or +"read_restart"_read_restart.html commands. These files can contain +molecular topology information. Or create atoms on a lattice (with no +molecular topology), using these commands: "lattice"_lattice.html, +"region"_region.html, "create_box"_create_box.html, +"create_atoms"_create_atoms.html. The entire set of atoms can be +duplicated to make a larger simulation using the +"replicate"_replicate.html command. + +(3) Settings + +Once atoms and molecular topology are defined, a variety of settings +can be specified: force field coefficients, simulation parameters, +output options, etc. + +Force field coefficients are set by these commands (they can also be +set in the read-in files): "pair_coeff"_pair_coeff.html, +"bond_coeff"_bond_coeff.html, "angle_coeff"_angle_coeff.html, +"dihedral_coeff"_dihedral_coeff.html, +"improper_coeff"_improper_coeff.html, +"kspace_style"_kspace_style.html, "dielectric"_dielectric.html, +"special_bonds"_special_bonds.html. + +Various simulation parameters are set by these commands: +"neighbor"_neighbor.html, "neigh_modify"_neigh_modify.html, +"group"_group.html, "timestep"_timestep.html, +"reset_timestep"_reset_timestep.html, "run_style"_run_style.html, +"min_style"_min_style.html, "min_modify"_min_modify.html. + +Fixes impose a variety of boundary conditions, time integration, and +diagnostic options. The "fix"_fix.html command comes in many flavors. + +Various computations can be specified for execution during a +simulation using the "compute"_compute.html, +"compute_modify"_compute_modify.html, and "variable"_variable.html +commands. + +Output options are set by the "thermo"_thermo.html, "dump"_dump.html, +and "restart"_restart.html commands. + +(4) Run a simulation + +A molecular dynamics simulation is run using the "run"_run.html +command. Energy minimization (molecular statics) is performed using +the "minimize"_minimize.html command. A parallel tempering +(replica-exchange) simulation can be run using the +"temper"_temper.html command. + diff --git a/doc/src/Errors.txt b/doc/src/Errors.txt index 92a577c5f2..1b6206c780 100644 --- a/doc/src/Errors.txt +++ b/doc/src/Errors.txt @@ -4,7 +4,7 @@ Section"_Manual.html :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Errors_bugs.txt b/doc/src/Errors_bugs.txt index c0a94c7a44..4a8e62e775 100644 --- a/doc/src/Errors_bugs.txt +++ b/doc/src/Errors_bugs.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Errors_common.txt b/doc/src/Errors_common.txt index 86a25f7e7d..43d1a85a7b 100644 --- a/doc/src/Errors_common.txt +++ b/doc/src/Errors_common.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Errors_messages.txt b/doc/src/Errors_messages.txt index 39eabbd232..03fc25b561 100644 --- a/doc/src/Errors_messages.txt +++ b/doc/src/Errors_messages.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Errors_warnings.txt b/doc/src/Errors_warnings.txt index 1da777043c..dd3402ba86 100644 --- a/doc/src/Errors_warnings.txt +++ b/doc/src/Errors_warnings.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Examples.txt b/doc/src/Examples.txt index b01b289d5e..5bd8da2409 100644 --- a/doc/src/Examples.txt +++ b/doc/src/Examples.txt @@ -4,7 +4,7 @@ Section"_Tools.html :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Howto_2d.txt b/doc/src/Howto_2d.txt index ea11a7d546..e1758c05d5 100644 --- a/doc/src/Howto_2d.txt +++ b/doc/src/Howto_2d.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Howto_barostat.txt b/doc/src/Howto_barostat.txt index b289ebfc4c..7c3db89152 100644 --- a/doc/src/Howto_barostat.txt +++ b/doc/src/Howto_barostat.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Howto_bash.txt b/doc/src/Howto_bash.txt index 572157ab55..f1438418e7 100755 --- a/doc/src/Howto_bash.txt +++ b/doc/src/Howto_bash.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Howto_bioFF.txt b/doc/src/Howto_bioFF.txt index 91d6eb0a8e..afb8a84f2e 100644 --- a/doc/src/Howto_bioFF.txt +++ b/doc/src/Howto_bioFF.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Howto_body.txt b/doc/src/Howto_body.txt index 3031563f98..3535349b46 100644 --- a/doc/src/Howto_body.txt +++ b/doc/src/Howto_body.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -17,9 +17,9 @@ surface meshes of discrete points, collections of sub-particles, deformable objects, etc. Note that other kinds of finite-size spherical and aspherical particles are also supported by LAMMPS, such as spheres, ellipsoids, line segments, and triangles, but they are -simpler entities that body particles. See "Section -6.14"_Section_howto.html#howto_14 for a general overview of all these -particle types. +simpler entities that body particles. See the "Howto +spherical"_Howto_spherical.html doc page for a general overview of all +these particle types. Body particles are used via the "atom_style body"_atom_style.html command. It takes a body style as an argument. The current body diff --git a/doc/src/Howto_chunk.txt b/doc/src/Howto_chunk.txt index 9d757b2729..8e52acf4b8 100644 --- a/doc/src/Howto_chunk.txt +++ b/doc/src/Howto_chunk.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Howto_coreshell.txt b/doc/src/Howto_coreshell.txt index 273568418b..4f1cd64384 100644 --- a/doc/src/Howto_coreshell.txt +++ b/doc/src/Howto_coreshell.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Howto_couple.txt b/doc/src/Howto_couple.txt index ec45bd1290..38595a9d16 100644 --- a/doc/src/Howto_couple.txt +++ b/doc/src/Howto_couple.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Howto_diffusion.txt b/doc/src/Howto_diffusion.txt index e0e16e1042..401c1e359c 100644 --- a/doc/src/Howto_diffusion.txt +++ b/doc/src/Howto_diffusion.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Howto_dispersion.txt b/doc/src/Howto_dispersion.txt index 000f45076d..4ea286258e 100644 --- a/doc/src/Howto_dispersion.txt +++ b/doc/src/Howto_dispersion.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Howto_drude.txt b/doc/src/Howto_drude.txt index e9c30db772..ebdf5f8658 100644 --- a/doc/src/Howto_drude.txt +++ b/doc/src/Howto_drude.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Howto_drude2.txt b/doc/src/Howto_drude2.txt index f6e7eed40b..a342d4a87d 100644 --- a/doc/src/Howto_drude2.txt +++ b/doc/src/Howto_drude2.txt @@ -9,7 +9,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Howto_elastic.txt b/doc/src/Howto_elastic.txt index 4dda13fa53..68b30970ca 100644 --- a/doc/src/Howto_elastic.txt +++ b/doc/src/Howto_elastic.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Howto_github.txt b/doc/src/Howto_github.txt index 191242205e..720b3317f0 100644 --- a/doc/src/Howto_github.txt +++ b/doc/src/Howto_github.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Howto_granular.txt b/doc/src/Howto_granular.txt index cfa01bcb63..8027369501 100644 --- a/doc/src/Howto_granular.txt +++ b/doc/src/Howto_granular.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Howto_kappa.txt b/doc/src/Howto_kappa.txt index 949901f21a..b2a57ef49b 100644 --- a/doc/src/Howto_kappa.txt +++ b/doc/src/Howto_kappa.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Howto_library.txt b/doc/src/Howto_library.txt index b15aadd214..0d4852fbf2 100644 --- a/doc/src/Howto_library.txt +++ b/doc/src/Howto_library.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Howto_manifold.txt b/doc/src/Howto_manifold.txt index c9bb1ce57f..09a936f7d3 100644 --- a/doc/src/Howto_manifold.txt +++ b/doc/src/Howto_manifold.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Howto_multiple.txt b/doc/src/Howto_multiple.txt index 3516debb71..edcb8196cf 100644 --- a/doc/src/Howto_multiple.txt +++ b/doc/src/Howto_multiple.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Howto_nemd.txt b/doc/src/Howto_nemd.txt index efb3a5cd73..f787801c36 100644 --- a/doc/src/Howto_nemd.txt +++ b/doc/src/Howto_nemd.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Howto_output.txt b/doc/src/Howto_output.txt index ed2a78ee19..a204a3cc96 100644 --- a/doc/src/Howto_output.txt +++ b/doc/src/Howto_output.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Howto_polarizable.txt b/doc/src/Howto_polarizable.txt index ec96ddc9a9..b2653b117e 100644 --- a/doc/src/Howto_polarizable.txt +++ b/doc/src/Howto_polarizable.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Howto_pylammps.txt b/doc/src/Howto_pylammps.txt index abf7c52d05..8be4b66e78 100644 --- a/doc/src/Howto_pylammps.txt +++ b/doc/src/Howto_pylammps.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Howto_replica.txt b/doc/src/Howto_replica.txt index b2f0faa209..1b44fe5374 100644 --- a/doc/src/Howto_replica.txt +++ b/doc/src/Howto_replica.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Howto_restart.txt b/doc/src/Howto_restart.txt index d2a993fcd3..b211775479 100644 --- a/doc/src/Howto_restart.txt +++ b/doc/src/Howto_restart.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Howto_spc.txt b/doc/src/Howto_spc.txt index 6a63c1f6a6..2cbf16547b 100644 --- a/doc/src/Howto_spc.txt +++ b/doc/src/Howto_spc.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Howto_spherical.txt b/doc/src/Howto_spherical.txt index c239f72c2a..1e737df655 100644 --- a/doc/src/Howto_spherical.txt +++ b/doc/src/Howto_spherical.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Howto_spins.txt b/doc/src/Howto_spins.txt index 3cb9e480b2..1b9adb49a5 100644 --- a/doc/src/Howto_spins.txt +++ b/doc/src/Howto_spins.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Howto_temperature.txt b/doc/src/Howto_temperature.txt index 3d1bd8a2d6..7a318250cf 100644 --- a/doc/src/Howto_temperature.txt +++ b/doc/src/Howto_temperature.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Howto_thermostat.txt b/doc/src/Howto_thermostat.txt index c1887d9738..0e2feb1869 100644 --- a/doc/src/Howto_thermostat.txt +++ b/doc/src/Howto_thermostat.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Howto_tip3p.txt b/doc/src/Howto_tip3p.txt index 23ab604d1f..942b42aea1 100644 --- a/doc/src/Howto_tip3p.txt +++ b/doc/src/Howto_tip3p.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Howto_tip4p.txt b/doc/src/Howto_tip4p.txt index a471bdc918..f9e548e268 100644 --- a/doc/src/Howto_tip4p.txt +++ b/doc/src/Howto_tip4p.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Howto_triclinic.txt b/doc/src/Howto_triclinic.txt index 10bcc5e9d1..4b299e5ae1 100644 --- a/doc/src/Howto_triclinic.txt +++ b/doc/src/Howto_triclinic.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) Triclinic (non-orthogonal) simulation boxes :h3 diff --git a/doc/src/Howto_viscosity.txt b/doc/src/Howto_viscosity.txt index 4760607fd5..8bcab6dd24 100644 --- a/doc/src/Howto_viscosity.txt +++ b/doc/src/Howto_viscosity.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Howto_viz.txt b/doc/src/Howto_viz.txt index 53635442c8..00c329c50b 100644 --- a/doc/src/Howto_viz.txt +++ b/doc/src/Howto_viz.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Howto_walls.txt b/doc/src/Howto_walls.txt index 7b0f8c0cfa..7522118582 100644 --- a/doc/src/Howto_walls.txt +++ b/doc/src/Howto_walls.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Intro_authors.txt b/doc/src/Intro_authors.txt index 96b4b861ca..b48c1eb59a 100644 --- a/doc/src/Intro_authors.txt +++ b/doc/src/Intro_authors.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Intro_features.txt b/doc/src/Intro_features.txt index 2a405ebf77..4b7d1d41e2 100644 --- a/doc/src/Intro_features.txt +++ b/doc/src/Intro_features.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -74,8 +74,8 @@ commands) long-range interactions for charge, point-dipoles, and LJ dispersion: \ Ewald, Wolf, PPPM (similar to particle-mesh Ewald) polarization models: "QEq"_fix_qeq.html, \ - "core/shell model"_Section_howto.html#howto_26, \ - "Drude dipole model"_Section_howto.html#howto_27 + "core/shell model"_Howto_coreshell.html, \ + "Drude dipole model"_Howto_drude.html charge equilibration (QEq via dynamic, point, shielded, Slater methods) coarse-grained potentials: DPD, GayBerne, REsquared, colloidal, DLVO mesoscopic potentials: granular, Peridynamics, SPH diff --git a/doc/src/Intro_nonfeatures.txt b/doc/src/Intro_nonfeatures.txt index 29b2eacf08..41f001fc8b 100644 --- a/doc/src/Intro_nonfeatures.txt +++ b/doc/src/Intro_nonfeatures.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Intro_opensource.txt b/doc/src/Intro_opensource.txt index 83384a22a2..e0d57f7ce1 100644 --- a/doc/src/Intro_opensource.txt +++ b/doc/src/Intro_opensource.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Intro_overview.txt b/doc/src/Intro_overview.txt index 51ad218216..49c14bc5f0 100644 --- a/doc/src/Intro_overview.txt +++ b/doc/src/Intro_overview.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Intro_website.txt b/doc/src/Intro_website.txt index 61c9babe1c..a8af94157c 100644 --- a/doc/src/Intro_website.txt +++ b/doc/src/Intro_website.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt index ddb9b152ec..a5e8b63640 100644 --- a/doc/src/Manual.txt +++ b/doc/src/Manual.txt @@ -14,7 +14,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html#comm) :line @@ -73,7 +73,7 @@ every LAMMPS command. Intro Section_start - Section_commands + Commands Packages Speed Howto @@ -116,12 +116,7 @@ END_RST --> 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 -"Commands"_Section_commands.html :l - 3.1 "LAMMPS input script"_cmd_1 :ulb,b - 3.2 "Parsing rules"_cmd_2 :b - 3.3 "Input script structure"_cmd_3 :b - 3.4 "Commands listed by category"_cmd_4 :b - 3.5 "Commands listed alphabetically"_cmd_5 :ule,b +"Commands"_Commands.html :l "Optional packages"_Packages.html :l "Accelerate performance"_Speed.html :l "How-to discussions"_Howto.html :l @@ -141,12 +136,6 @@ END_RST --> :link(start_7,Section_start.html#start_7) :link(start_8,Section_start.html#start_8) -:link(cmd_1,Section_commands.html#cmd_1) -:link(cmd_2,Section_commands.html#cmd_2) -:link(cmd_3,Section_commands.html#cmd_3) -:link(cmd_4,Section_commands.html#cmd_4) -:link(cmd_5,Section_commands.html#cmd_5) - diff --git a/doc/src/Manual_version.txt b/doc/src/Manual_version.txt index db4301b6ea..8583eabf86 100644 --- a/doc/src/Manual_version.txt +++ b/doc/src/Manual_version.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Modify.txt b/doc/src/Modify.txt index ae0b0dc6bd..f828bd5d74 100644 --- a/doc/src/Modify.txt +++ b/doc/src/Modify.txt @@ -4,7 +4,7 @@ Section"_Python.html :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Modify_atom.txt b/doc/src/Modify_atom.txt index afa1c319d2..60c7dccb29 100644 --- a/doc/src/Modify_atom.txt +++ b/doc/src/Modify_atom.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Modify_body.txt b/doc/src/Modify_body.txt index a0627ebdda..0114ae10c8 100644 --- a/doc/src/Modify_body.txt +++ b/doc/src/Modify_body.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Modify_bond.txt b/doc/src/Modify_bond.txt index f0828a0c3b..7ceea3f910 100644 --- a/doc/src/Modify_bond.txt +++ b/doc/src/Modify_bond.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Modify_command.txt b/doc/src/Modify_command.txt index 6fc9aad1fc..4576f6c806 100644 --- a/doc/src/Modify_command.txt +++ b/doc/src/Modify_command.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Modify_compute.txt b/doc/src/Modify_compute.txt index b02b8a983e..2f6481dbd5 100644 --- a/doc/src/Modify_compute.txt +++ b/doc/src/Modify_compute.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Modify_contribute.txt b/doc/src/Modify_contribute.txt index 9d47b08251..ef9fe6a717 100644 --- a/doc/src/Modify_contribute.txt +++ b/doc/src/Modify_contribute.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Modify_dump.txt b/doc/src/Modify_dump.txt index 81af54e003..cfe96f5d3d 100644 --- a/doc/src/Modify_dump.txt +++ b/doc/src/Modify_dump.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Modify_fix.txt b/doc/src/Modify_fix.txt index ba985475cc..b095ebc4b5 100644 --- a/doc/src/Modify_fix.txt +++ b/doc/src/Modify_fix.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Modify_kspace.txt b/doc/src/Modify_kspace.txt index 21407bf2e9..d5f018411d 100644 --- a/doc/src/Modify_kspace.txt +++ b/doc/src/Modify_kspace.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Modify_min.txt b/doc/src/Modify_min.txt index 5dcf0f1e67..8252a576f3 100644 --- a/doc/src/Modify_min.txt +++ b/doc/src/Modify_min.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Modify_overview.txt b/doc/src/Modify_overview.txt index f9964d964b..cf94b40281 100644 --- a/doc/src/Modify_overview.txt +++ b/doc/src/Modify_overview.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Modify_pair.txt b/doc/src/Modify_pair.txt index 8c234dc621..0ebf2daa30 100644 --- a/doc/src/Modify_pair.txt +++ b/doc/src/Modify_pair.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Modify_region.txt b/doc/src/Modify_region.txt index 9fbf359292..cdf192323a 100644 --- a/doc/src/Modify_region.txt +++ b/doc/src/Modify_region.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Modify_thermo.txt b/doc/src/Modify_thermo.txt index 001a9f99e1..1772bae87a 100644 --- a/doc/src/Modify_thermo.txt +++ b/doc/src/Modify_thermo.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Modify_variable.txt b/doc/src/Modify_variable.txt index 3c5b29cd1a..b163272f3e 100644 --- a/doc/src/Modify_variable.txt +++ b/doc/src/Modify_variable.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Packages.txt b/doc/src/Packages.txt index 6498d03063..a7f45a99b7 100644 --- a/doc/src/Packages.txt +++ b/doc/src/Packages.txt @@ -1,10 +1,10 @@ -"Previous Section"_Section_commands.html - "LAMMPS WWW Site"_lws - +"Previous Section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Speed.html :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt index 2b89809721..eb92fe4dc4 100644 --- a/doc/src/Packages_details.txt +++ b/doc/src/Packages_details.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -396,7 +396,7 @@ lib/gpu/README "Section 2.6 -sf gpu"_Section_start.html#start_6 "Section 2.6 -pk gpu"_Section_start.html#start_6 "package gpu"_package.html -Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5 for pair styles followed by (g) +"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 :line @@ -487,8 +487,8 @@ 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 in the "What is in the KIM API source -package?" section +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: @@ -593,7 +593,7 @@ lib/kokkos/README "Section 2.6 -sf kk"_Section_start.html#start_6 "Section 2.6 -pk kokkos"_Section_start.html#start_6 "package kokkos"_package.html -Styles sections of "Section 3.5"_Section_commands.html#cmd_5 for styles followed by (k) +"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 :line @@ -631,7 +631,7 @@ src/KSPACE: filenames -> commands "Howto tip4p"_Howto_tip4p.html "Howto spc"_Howto_spc.html "pair_style coul"_pair_coul.html -Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5 with "long" or "msm" in pair style name +"Commands pair"_Commands_pair.html page for styles with "long" or "msm" in name examples/peptide bench/in.rhodo :ul @@ -715,7 +715,7 @@ make machine :pre [Supporting info:] src/MANYBODY: filenames -> commands -Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5 +"Commands pair"_Commands_pair.html page examples/comb examples/eim examples/nb3d @@ -1017,7 +1017,7 @@ src/OPT: filenames -> commands "Speed packages"_Speed_packages.html "Speed opt"_Speed_opt.html "Section 2.6 -sf opt"_Section_start.html#start_6 -Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5 for pair styles followed by (t) +"Commands pair"_Commands_pair.html for styles followed by (t) "Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul :line @@ -2072,7 +2072,7 @@ src/USER-INTEL/README "Section 2.6 -sf intel"_Section_start.html#start_6 "Section 2.6 -pk intel"_Section_start.html#start_6 "package intel"_package.html -Styles sections of "Section 3.5"_Section_commands.html#cmd_5 for styles followed by (i) +"Commands all"_Commands_all.html pages (fix,compute,pair,etc) for styles followed by (i) src/USER-INTEL/TEST "Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul @@ -2457,7 +2457,7 @@ src/USER-OMP/README "Section 2.6 -sf omp"_Section_start.html#start_6 "Section 2.6 -pk omp"_Section_start.html#start_6 "package omp"_package.html -Styles sections of "Section 3.5"_Section_commands.html#cmd_5 for styles followed by (o) +"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 :line diff --git a/doc/src/Packages_standard.txt b/doc/src/Packages_standard.txt index cff2d38273..7e64345602 100644 --- a/doc/src/Packages_standard.txt +++ b/doc/src/Packages_standard.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Packages_user.txt b/doc/src/Packages_user.txt index 0465296980..c8728148f9 100644 --- a/doc/src/Packages_user.txt +++ b/doc/src/Packages_user.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Python.txt b/doc/src/Python.txt index 169670d669..2c9c6872bb 100644 --- a/doc/src/Python.txt +++ b/doc/src/Python.txt @@ -4,7 +4,7 @@ Section"_Errors.html :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Python_call.txt b/doc/src/Python_call.txt index 3e30a5a7c7..621f1fe241 100644 --- a/doc/src/Python_call.txt +++ b/doc/src/Python_call.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Python_examples.txt b/doc/src/Python_examples.txt index fbca381e8b..46e5fee2b9 100644 --- a/doc/src/Python_examples.txt +++ b/doc/src/Python_examples.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Python_install.txt b/doc/src/Python_install.txt index 631f6c4a7f..6591360ae2 100644 --- a/doc/src/Python_install.txt +++ b/doc/src/Python_install.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Python_library.txt b/doc/src/Python_library.txt index db16c39a47..8d0c724a45 100644 --- a/doc/src/Python_library.txt +++ b/doc/src/Python_library.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Python_mpi.txt b/doc/src/Python_mpi.txt index 8377bbb3d0..6e0a2ce319 100644 --- a/doc/src/Python_mpi.txt +++ b/doc/src/Python_mpi.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Python_pylammps.txt b/doc/src/Python_pylammps.txt index cdc8e2c086..d7baa93e2e 100644 --- a/doc/src/Python_pylammps.txt +++ b/doc/src/Python_pylammps.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Python_run.txt b/doc/src/Python_run.txt index 03ab2ed3d7..a94dc07f2d 100644 --- a/doc/src/Python_run.txt +++ b/doc/src/Python_run.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Python_shlib.txt b/doc/src/Python_shlib.txt index 1aafbe2e84..1a921e4025 100644 --- a/doc/src/Python_shlib.txt +++ b/doc/src/Python_shlib.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Python_test.txt b/doc/src/Python_test.txt index 5f361a500b..4a05d5c468 100644 --- a/doc/src/Python_test.txt +++ b/doc/src/Python_test.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt deleted file mode 100644 index daedb00a0a..0000000000 --- a/doc/src/Section_commands.txt +++ /dev/null @@ -1,1292 +0,0 @@ -"Previous Section"_Section_start.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Packages.html :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Section_commands.html#comm) - -:line - -3. Commands :h2 - -This section describes how a LAMMPS input script is formatted and the -input script commands used to define a LAMMPS simulation. - -3.1 "LAMMPS input script"_#cmd_1 -3.2 "Parsing rules"_#cmd_2 -3.3 "Input script structure"_#cmd_3 -3.4 "Commands listed by category"_#cmd_4 -3.5 "Commands listed alphabetically"_#cmd_5 :all(b) - -:line -:line - -3.1 LAMMPS input script :link(cmd_1),h4 - -LAMMPS executes by reading commands from a input script (text file), -one line at a time. When the input script ends, LAMMPS exits. Each -command causes LAMMPS to take some action. It may set an internal -variable, read in a file, or run a simulation. Most commands have -default settings, which means you only need to use the command if you -wish to change the default. - -In many cases, the ordering of commands in an input script is not -important. However the following rules apply: - -(1) LAMMPS does not read your entire input script and then perform a -simulation with all the settings. Rather, the input script is read -one line at a time and each command takes effect when it is read. -Thus this sequence of commands: - -timestep 0.5 -run 100 -run 100 :pre - -does something different than this sequence: - -run 100 -timestep 0.5 -run 100 :pre - -In the first case, the specified timestep (0.5 fmsec) is used for two -simulations of 100 timesteps each. In the 2nd case, the default -timestep (1.0 fmsec) is used for the 1st 100 step simulation and a 0.5 -fmsec timestep is used for the 2nd one. - -(2) Some commands are only valid when they follow other commands. For -example you cannot set the temperature of a group of atoms until atoms -have been defined and a group command is used to define which atoms -belong to the group. - -(3) Sometimes command B will use values that can be set by command A. -This means command A must precede command B in the input script if it -is to have the desired effect. For example, the -"read_data"_read_data.html command initializes the system by setting -up the simulation box and assigning atoms to processors. If default -values are not desired, the "processors"_processors.html and -"boundary"_boundary.html commands need to be used before read_data to -tell LAMMPS how to map processors to the simulation box. - -Many input script errors are detected by LAMMPS and an ERROR or -WARNING message is printed. The "Errors"_Errors.html doc page gives -more information on what errors mean. The documentation for each -command lists restrictions on how the command can be used. - -:line - -3.2 Parsing rules :link(cmd_2),h4 - -Each non-blank line in the input script is treated as a command. -LAMMPS commands are case sensitive. Command names are lower-case, as -are specified command arguments. Upper case letters may be used in -file names or user-chosen ID strings. - -Here is how each line in the input script is parsed by LAMMPS: - -(1) If the last printable character on the line is a "&" character, -the command is assumed to continue on the next line. The next line is -concatenated to the previous line by removing the "&" character and -line break. This allows long commands to be continued across two or -more lines. See the discussion of triple quotes in (6) for how to -continue a command across multiple line without using "&" characters. - -(2) All characters from the first "#" character onward are treated as -comment and discarded. See an exception in (6). Note that a -comment after a trailing "&" character will prevent the command from -continuing on the next line. Also note that for multi-line commands a -single leading "#" will comment out the entire command. - -(3) The line is searched repeatedly for $ characters, which indicate -variables that are replaced with a text string. See an exception in -(6). - -If the $ is followed by curly brackets, then the variable name is the -text inside the curly brackets. If no curly brackets follow the $, -then the variable name is the single character immediately following -the $. Thus $\{myTemp\} and $x refer to variable names "myTemp" and -"x". - -How the variable is converted to a text string depends on what style -of variable it is; see the "variable"_variable.html doc page for details. -It can be a variable that stores multiple text strings, and return one -of them. The returned text string can be multiple "words" (space -separated) which will then be interpreted as multiple arguments in the -input command. The variable can also store a numeric formula which -will be evaluated and its numeric result returned as a string. - -As a special case, if the $ is followed by parenthesis, then the text -inside the parenthesis is treated as an "immediate" variable and -evaluated as an "equal-style variable"_variable.html. This is a way -to use numeric formulas in an input script without having to assign -them to variable names. For example, these 3 input script lines: - -variable X equal (xlo+xhi)/2+sqrt(v_area) -region 1 block $X 2 INF INF EDGE EDGE -variable X delete :pre - -can be replaced by - -region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE :pre - -so that you do not have to define (or discard) a temporary variable X. - -Additionally, the "immediate" variable expression may be followed by a -colon, followed by a C-style format string, e.g. ":%f" or ":%.10g". -The format string must be appropriate for a double-precision -floating-point value. The format string is used to output the result -of the variable expression evaluation. If a format string is not -specified a high-precision "%.20g" is used as the default. - -This can be useful for formatting print output to a desired precion: - -print "Final energy per atom: $(pe/atoms:%10.3f) eV/atom" :pre - -Note that neither the curly-bracket or immediate form of variables can -contain nested $ characters for other variables to substitute for. -Thus you cannot do this: - -variable a equal 2 -variable b2 equal 4 -print "B2 = $\{b$a\}" :pre - -Nor can you specify this $($x-1.0) for an immediate variable, but -you could use $(v_x-1.0), since the latter is valid syntax for an -"equal-style variable"_variable.html. - -See the "variable"_variable.html command for more details of how -strings are assigned to variables and evaluated, and how they can be -used in input script commands. - -(4) The line is broken into "words" separated by whitespace (tabs, -spaces). Note that words can thus contain letters, digits, -underscores, or punctuation characters. - -(5) The first word is the command name. All successive words in the -line are arguments. - -(6) If you want text with spaces to be treated as a single argument, -it can be enclosed in either single or double or triple quotes. A -long single argument enclosed in single or double quotes can span -multiple lines if the "&" character is used, as described above. When -the lines are concatenated together (and the "&" characters and line -breaks removed), the text will become a single line. If you want -multiple lines of an argument to retain their line breaks, the text -can be enclosed in triple quotes, in which case "&" characters are not -needed. For example: - -print "Volume = $v" -print 'Volume = $v' -if "$\{steps\} > 1000" then quit -variable a string "red green blue & - purple orange cyan" -print """ -System volume = $v -System temperature = $t -""" :pre - -In each case, the single, double, or triple quotes are removed when -the single argument they enclose is stored internally. - -See the "dump modify format"_dump_modify.html, "print"_print.html, -"if"_if.html, and "python"_python.html commands for examples. - -A "#" or "$" character that is between quotes will not be treated as a -comment indicator in (2) or substituted for as a variable in (3). - -NOTE: If the argument is itself a command that requires a quoted -argument (e.g. using a "print"_print.html command as part of an -"if"_if.html or "run every"_run.html command), then single, double, or -triple quotes can be nested in the usual manner. See the doc pages -for those commands for examples. Only one of level of nesting is -allowed, but that should be sufficient for most use cases. - -:line - -3.3 Input script structure :h3,link(cmd_3) - -This section describes the structure of a typical LAMMPS input script. -The examples directory in the LAMMPS distribution contains many sample -input scripts; the corresponding problems are discussed on the -"Examples"_Examples.html doc page, and animated on the "LAMMPS WWW -Site"_lws. - -A LAMMPS input script typically has 4 parts: - -Initialization -Atom definition -Settings -Run a simulation :ol - -The last 2 parts can be repeated as many times as desired. I.e. run a -simulation, change some settings, run some more, etc. Each of the 4 -parts is now described in more detail. Remember that almost all the -commands need only be used if a non-default value is desired. - -(1) Initialization - -Set parameters that need to be defined before atoms are created or -read-in from a file. - -The relevant commands are "units"_units.html, -"dimension"_dimension.html, "newton"_newton.html, -"processors"_processors.html, "boundary"_boundary.html, -"atom_style"_atom_style.html, "atom_modify"_atom_modify.html. - -If force-field parameters appear in the files that will be read, these -commands tell LAMMPS what kinds of force fields are being used: -"pair_style"_pair_style.html, "bond_style"_bond_style.html, -"angle_style"_angle_style.html, "dihedral_style"_dihedral_style.html, -"improper_style"_improper_style.html. - -(2) Atom definition - -There are 3 ways to define atoms in LAMMPS. Read them in from a data -or restart file via the "read_data"_read_data.html or -"read_restart"_read_restart.html commands. These files can contain -molecular topology information. Or create atoms on a lattice (with no -molecular topology), using these commands: "lattice"_lattice.html, -"region"_region.html, "create_box"_create_box.html, -"create_atoms"_create_atoms.html. The entire set of atoms can be -duplicated to make a larger simulation using the -"replicate"_replicate.html command. - -(3) Settings - -Once atoms and molecular topology are defined, a variety of settings -can be specified: force field coefficients, simulation parameters, -output options, etc. - -Force field coefficients are set by these commands (they can also be -set in the read-in files): "pair_coeff"_pair_coeff.html, -"bond_coeff"_bond_coeff.html, "angle_coeff"_angle_coeff.html, -"dihedral_coeff"_dihedral_coeff.html, -"improper_coeff"_improper_coeff.html, -"kspace_style"_kspace_style.html, "dielectric"_dielectric.html, -"special_bonds"_special_bonds.html. - -Various simulation parameters are set by these commands: -"neighbor"_neighbor.html, "neigh_modify"_neigh_modify.html, -"group"_group.html, "timestep"_timestep.html, -"reset_timestep"_reset_timestep.html, "run_style"_run_style.html, -"min_style"_min_style.html, "min_modify"_min_modify.html. - -Fixes impose a variety of boundary conditions, time integration, and -diagnostic options. The "fix"_fix.html command comes in many flavors. - -Various computations can be specified for execution during a -simulation using the "compute"_compute.html, -"compute_modify"_compute_modify.html, and "variable"_variable.html -commands. - -Output options are set by the "thermo"_thermo.html, "dump"_dump.html, -and "restart"_restart.html commands. - -(4) Run a simulation - -A molecular dynamics simulation is run using the "run"_run.html -command. Energy minimization (molecular statics) is performed using -the "minimize"_minimize.html command. A parallel tempering -(replica-exchange) simulation can be run using the -"temper"_temper.html command. - -:line - -3.4 Commands listed by category :link(cmd_4),h4 - -This section lists core LAMMPS commands, grouped by category. -The "next section"_#cmd_5 lists all commands alphabetically. The -next section also includes (long) lists of style options for entries -that appear in the following categories as a single command (fix, -compute, pair, etc). Commands that are added by user packages are not -included in the categories here, but they are in the next section. - -Initialization: - -"newton"_newton.html, -"package"_package.html, -"processors"_processors.html, -"suffix"_suffix.html, -"units"_units.html - -Setup simulation box: - -"boundary"_boundary.html, -"box"_box.html, -"change_box"_change_box.html, -"create_box"_create_box.html, -"dimension"_dimension.html, -"lattice"_lattice.html, -"region"_region.html - -Setup atoms: - -"atom_modify"_atom_modify.html, -"atom_style"_atom_style.html, -"balance"_balance.html, -"create_atoms"_create_atoms.html, -"create_bonds"_create_bonds.html, -"delete_atoms"_delete_atoms.html, -"delete_bonds"_delete_bonds.html, -"displace_atoms"_displace_atoms.html, -"group"_group.html, -"mass"_mass.html, -"molecule"_molecule.html, -"read_data"_read_data.html, -"read_dump"_read_dump.html, -"read_restart"_read_restart.html, -"replicate"_replicate.html, -"set"_set.html, -"velocity"_velocity.html - -Force fields: - -"angle_coeff"_angle_coeff.html, -"angle_style"_angle_style.html, -"bond_coeff"_bond_coeff.html, -"bond_style"_bond_style.html, -"bond_write"_bond_write.html, -"dielectric"_dielectric.html, -"dihedral_coeff"_dihedral_coeff.html, -"dihedral_style"_dihedral_style.html, -"improper_coeff"_improper_coeff.html, -"improper_style"_improper_style.html, -"kspace_modify"_kspace_modify.html, -"kspace_style"_kspace_style.html, -"pair_coeff"_pair_coeff.html, -"pair_modify"_pair_modify.html, -"pair_style"_pair_style.html, -"pair_write"_pair_write.html, -"special_bonds"_special_bonds.html - -Settings: - -"comm_modify"_comm_modify.html, -"comm_style"_comm_style.html, -"info"_info.html, -"min_modify"_min_modify.html, -"min_style"_min_style.html, -"neigh_modify"_neigh_modify.html, -"neighbor"_neighbor.html, -"partition"_partition.html, -"reset_timestep"_reset_timestep.html, -"run_style"_run_style.html, -"timer"_timer.html, -"timestep"_timestep.html - -Operations within timestepping (fixes) and diagnostics (computes): - -"compute"_compute.html, -"compute_modify"_compute_modify.html, -"fix"_fix.html, -"fix_modify"_fix_modify.html, -"uncompute"_uncompute.html, -"unfix"_unfix.html - -Output: - -"dump image"_dump_image.html, -"dump movie"_dump_image.html, -"dump"_dump.html, -"dump_modify"_dump_modify.html, -"restart"_restart.html, -"thermo"_thermo.html, -"thermo_modify"_thermo_modify.html, -"thermo_style"_thermo_style.html, -"undump"_undump.html, -"write_coeff"_write_coeff.html, -"write_data"_write_data.html, -"write_dump"_write_dump.html, -"write_restart"_write_restart.html - -Actions: - -"minimize"_minimize.html, -"neb"_neb.html, -"prd"_prd.html, -"rerun"_rerun.html, -"run"_run.html, -"tad"_tad.html, -"temper"_temper.html - -Input script control: - -"clear"_clear.html, -"echo"_echo.html, -"if"_if.html, -"include"_include.html, -"jump"_jump.html, -"label"_label.html, -"log"_log.html, -"next"_next.html, -"print"_print.html, -"python"_python.html, -"quit"_quit.html, -"shell"_shell.html, -"variable"_variable.html - -:line - -3.5 Individual commands :h3,link(cmd_5),link(comm) - -This section lists all LAMMPS commands alphabetically, with a separate -listing below of styles within certain commands. The "previous -section"_#cmd_4 lists the same commands, grouped by category. Note -that some style options for some commands are part of specific LAMMPS -packages, which means they cannot be used unless the package was -included when LAMMPS was built. Not all packages are included in a -default LAMMPS build. These dependencies are listed as Restrictions -in the command's documentation. - -"angle_coeff"_angle_coeff.html, -"angle_style"_angle_style.html, -"atom_modify"_atom_modify.html, -"atom_style"_atom_style.html, -"balance"_balance.html, -"bond_coeff"_bond_coeff.html, -"bond_style"_bond_style.html, -"bond_write"_bond_write.html, -"boundary"_boundary.html, -"box"_box.html, -"change_box"_change_box.html, -"clear"_clear.html, -"comm_modify"_comm_modify.html, -"comm_style"_comm_style.html, -"compute"_compute.html, -"compute_modify"_compute_modify.html, -"create_atoms"_create_atoms.html, -"create_bonds"_create_bonds.html, -"create_box"_create_box.html, -"delete_atoms"_delete_atoms.html, -"delete_bonds"_delete_bonds.html, -"dielectric"_dielectric.html, -"dihedral_coeff"_dihedral_coeff.html, -"dihedral_style"_dihedral_style.html, -"dimension"_dimension.html, -"displace_atoms"_displace_atoms.html, -"dump"_dump.html, -"dump image"_dump_image.html, -"dump_modify"_dump_modify.html, -"dump movie"_dump_image.html, -"echo"_echo.html, -"fix"_fix.html, -"fix_modify"_fix_modify.html, -"group"_group.html, -"if"_if.html, -"info"_info.html, -"improper_coeff"_improper_coeff.html, -"improper_style"_improper_style.html, -"include"_include.html, -"jump"_jump.html, -"kspace_modify"_kspace_modify.html, -"kspace_style"_kspace_style.html, -"label"_label.html, -"lattice"_lattice.html, -"log"_log.html, -"mass"_mass.html, -"minimize"_minimize.html, -"min_modify"_min_modify.html, -"min_style"_min_style.html, -"molecule"_molecule.html, -"neb"_neb.html, -"neigh_modify"_neigh_modify.html, -"neighbor"_neighbor.html, -"newton"_newton.html, -"next"_next.html, -"package"_package.html, -"pair_coeff"_pair_coeff.html, -"pair_modify"_pair_modify.html, -"pair_style"_pair_style.html, -"pair_write"_pair_write.html, -"partition"_partition.html, -"prd"_prd.html, -"print"_print.html, -"processors"_processors.html, -"python"_python.html, -"quit"_quit.html, -"read_data"_read_data.html, -"read_dump"_read_dump.html, -"read_restart"_read_restart.html, -"region"_region.html, -"replicate"_replicate.html, -"rerun"_rerun.html, -"reset_ids"_reset_ids.html, -"reset_timestep"_reset_timestep.html, -"restart"_restart.html, -"run"_run.html, -"run_style"_run_style.html, -"set"_set.html, -"shell"_shell.html, -"special_bonds"_special_bonds.html, -"suffix"_suffix.html, -"tad"_tad.html, -"temper"_temper.html, -"thermo"_thermo.html, -"thermo_modify"_thermo_modify.html, -"thermo_style"_thermo_style.html, -"timer"_timer.html, -"timestep"_timestep.html, -"uncompute"_uncompute.html, -"undump"_undump.html, -"unfix"_unfix.html, -"units"_units.html, -"variable"_variable.html, -"velocity"_velocity.html, -"write_coeff"_write_coeff.html, -"write_data"_write_data.html, -"write_dump"_write_dump.html, -"write_restart"_write_restart.html :tb(c=6,ea=c) - -These are additional commands in USER packages, which can be used if -"LAMMPS is built with the appropriate -package"_Section_start.html#start_3. - -"dump netcdf"_dump_netcdf.html, -"dump netcdf/mpiio"_dump_netcdf.html, -"dump vtk"_dump_vtk.html, -"group2ndx"_group2ndx.html, -"ndx2group"_group2ndx.html, -"temper/grem"_temper_grem.html, -"temper/npt"_temper_npt.html :tb(c=3,ea=c) - -:line - -Fix styles :h3 - -See the "fix"_fix.html command for one-line descriptions of each style -or click on the style itself for a full description. Some of the -styles have accelerated versions, which can be used if LAMMPS is built -with the "appropriate accelerated package"_Speed_packages.html. This -is indicated by additional letters in parenthesis: g = GPU, i = -USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. - -"adapt"_fix_adapt.html, -"addforce"_fix_addforce.html, -"append/atoms"_fix_append_atoms.html, -"atom/swap"_fix_atom_swap.html, -"aveforce"_fix_aveforce.html, -"ave/atom"_fix_ave_atom.html, -"ave/chunk"_fix_ave_chunk.html, -"ave/correlate"_fix_ave_correlate.html, -"ave/histo"_fix_ave_histo.html, -"ave/histo/weight"_fix_ave_histo.html, -"ave/time"_fix_ave_time.html, -"balance"_fix_balance.html, -"bond/break"_fix_bond_break.html, -"bond/create"_fix_bond_create.html, -"bond/swap"_fix_bond_swap.html, -"box/relax"_fix_box_relax.html, -"cmap"_fix_cmap.html, -"controller"_fix_controller.html, -"deform (k)"_fix_deform.html, -"deposit"_fix_deposit.html, -"drag"_fix_drag.html, -"dt/reset"_fix_dt_reset.html, -"efield"_fix_efield.html, -"ehex"_fix_ehex.html, -"enforce2d (k)"_fix_enforce2d.html, -"evaporate"_fix_evaporate.html, -"external"_fix_external.html, -"freeze"_fix_freeze.html, -"gcmc"_fix_gcmc.html, -"gld"_fix_gld.html, -"gravity (o)"_fix_gravity.html, -"halt"_fix_halt.html, -"heat"_fix_heat.html, -"indent"_fix_indent.html, -"latte"_fix_latte.html, -"langevin (k)"_fix_langevin.html, -"langevin/spin"_fix_langevin_spin.hmtl, -"lineforce"_fix_lineforce.html, -"momentum (k)"_fix_momentum.html, -"move"_fix_move.html, -"mscg"_fix_mscg.html, -"msst"_fix_msst.html, -"neb"_fix_neb.html, -"nph (ko)"_fix_nh.html, -"nphug (o)"_fix_nphug.html, -"nph/asphere (o)"_fix_nph_asphere.html, -"nph/body"_fix_nph_body.html, -"nph/sphere (o)"_fix_nph_sphere.html, -"npt (kio)"_fix_nh.html, -"npt/asphere (o)"_fix_npt_asphere.html, -"npt/body"_fix_npt_body.html, -"npt/sphere (o)"_fix_npt_sphere.html, -"nve (kio)"_fix_nve.html, -"nve/asphere (i)"_fix_nve_asphere.html, -"nve/asphere/noforce"_fix_nve_asphere_noforce.html, -"nve/body"_fix_nve_body.html, -"nve/limit"_fix_nve_limit.html, -"nve/line"_fix_nve_line.html, -"nve/noforce"_fix_nve_noforce.html, -"nve/sphere (o)"_fix_nve_sphere.html, -"nve/spin"_fix_nve_spin.html, -"nve/tri"_fix_nve_tri.html, -"nvt (iko)"_fix_nh.html, -"nvt/asphere (o)"_fix_nvt_asphere.html, -"nvt/body"_fix_nvt_body.html, -"nvt/sllod (io)"_fix_nvt_sllod.html, -"nvt/sphere (o)"_fix_nvt_sphere.html, -"oneway"_fix_oneway.html, -"orient/bcc"_fix_orient.html, -"orient/fcc"_fix_orient.html, -"planeforce"_fix_planeforce.html, -"poems"_fix_poems.html, -"pour"_fix_pour.html, -"precession/spin"_fix_precession_spin.html, -"press/berendsen"_fix_press_berendsen.html, -"print"_fix_print.html, -"property/atom (k)"_fix_property_atom.html, -"python/invoke"_fix_python_invoke.html, -"python/move"_fix_python_move.html, -"qeq/comb (o)"_fix_qeq_comb.html, -"qeq/dynamic"_fix_qeq.html, -"qeq/fire"_fix_qeq.html, -"qeq/point"_fix_qeq.html, -"qeq/shielded"_fix_qeq.html, -"qeq/slater"_fix_qeq.html, -"rattle"_fix_shake.html, -"reax/bonds"_fix_reax_bonds.html, -"recenter"_fix_recenter.html, -"restrain"_fix_restrain.html, -"rigid (o)"_fix_rigid.html, -"rigid/nph (o)"_fix_rigid.html, -"rigid/npt (o)"_fix_rigid.html, -"rigid/nve (o)"_fix_rigid.html, -"rigid/nvt (o)"_fix_rigid.html, -"rigid/small (o)"_fix_rigid.html, -"rigid/small/nph"_fix_rigid.html, -"rigid/small/npt"_fix_rigid.html, -"rigid/small/nve"_fix_rigid.html, -"rigid/small/nvt"_fix_rigid.html, -"setforce (k)"_fix_setforce.html, -"shake"_fix_shake.html, -"spring"_fix_spring.html, -"spring/chunk"_fix_spring_chunk.html, -"spring/rg"_fix_spring_rg.html, -"spring/self"_fix_spring_self.html, -"srd"_fix_srd.html, -"store/force"_fix_store_force.html, -"store/state"_fix_store_state.html, -"temp/berendsen"_fix_temp_berendsen.html, -"temp/csld"_fix_temp_csvr.html, -"temp/csvr"_fix_temp_csvr.html, -"temp/rescale"_fix_temp_rescale.html, -"tfmc"_fix_tfmc.html, -"thermal/conductivity"_fix_thermal_conductivity.html, -"tmd"_fix_tmd.html, -"ttm"_fix_ttm.html, -"tune/kspace"_fix_tune_kspace.html, -"vector"_fix_vector.html, -"viscosity"_fix_viscosity.html, -"viscous"_fix_viscous.html, -"wall/body/polygon"_fix_wall_body_polygon.html, -"wall/body/polyhedron"_fix_wall_body_polyhedron.html, -"wall/colloid"_fix_wall.html, -"wall/gran"_fix_wall_gran.html, -"wall/gran/region"_fix_wall_gran_region.html, -"wall/harmonic"_fix_wall.html, -"wall/lj1043"_fix_wall.html, -"wall/lj126"_fix_wall.html, -"wall/lj93 (k)"_fix_wall.html, -"wall/piston"_fix_wall_piston.html, -"wall/reflect (k)"_fix_wall_reflect.html, -"wall/region"_fix_wall_region.html, -"wall/srd"_fix_wall_srd.html :tb(c=8,ea=c) - -These are additional fix styles in USER packages, which can be used if -"LAMMPS is built with the appropriate -package"_Section_start.html#start_3. - -"adapt/fep"_fix_adapt_fep.html, -"addtorque"_fix_addtorque.html, -"atc"_fix_atc.html, -"ave/correlate/long"_fix_ave_correlate_long.html, -"bond/react"_fix_bond_react.html, -"colvars"_fix_colvars.html, -"dpd/energy (k)"_fix_dpd_energy.html, -"drude"_fix_drude.html, -"drude/transform/direct"_fix_drude_transform.html, -"drude/transform/reverse"_fix_drude_transform.html, -"edpd/source"_fix_dpd_source.html, -"eos/cv"_fix_eos_cv.html, -"eos/table"_fix_eos_table.html, -"eos/table/rx (k)"_fix_eos_table_rx.html, -"filter/corotate"_fix_filter_corotate.html, -"flow/gauss"_fix_flow_gauss.html, -"gle"_fix_gle.html, -"grem"_fix_grem.html, -"imd"_fix_imd.html, -"ipi"_fix_ipi.html, -"langevin/drude"_fix_langevin_drude.html, -"langevin/eff"_fix_langevin_eff.html, -"lb/fluid"_fix_lb_fluid.html, -"lb/momentum"_fix_lb_momentum.html, -"lb/pc"_fix_lb_pc.html, -"lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html, -"lb/viscous"_fix_lb_viscous.html, -"meso"_fix_meso.html, -"manifoldforce"_fix_manifoldforce.html, -"meso/stationary"_fix_meso_stationary.html, -"mvv/dpd"_fix_mvv_dpd.html, -"mvv/edpd"_fix_mvv_dpd.html, -"mvv/tdpd"_fix_mvv_dpd.html, -"nph/eff"_fix_nh_eff.html, -"npt/eff"_fix_nh_eff.html, -"npt/uef"_fix_nh_uef.html, -"nve/dot"_fix_nve_dot.html, -"nve/dotc/langevin"_fix_nve_dotc_langevin.html, -"nve/eff"_fix_nve_eff.html, -"nve/manifold/rattle"_fix_nve_manifold_rattle.html, -"nvk"_fix_nvk.html, -"nvt/eff"_fix_nh_eff.html, -"nvt/manifold/rattle"_fix_nvt_manifold_rattle.html, -"nvt/sllod/eff"_fix_nvt_sllod_eff.html, -"nvt/uef"_fix_nh_uef.html, -"phonon"_fix_phonon.html, -"pimd"_fix_pimd.html, -"qbmsst"_fix_qbmsst.html, -"qeq/reax (ko)"_fix_qeq_reax.html, -"qmmm"_fix_qmmm.html, -"qtb"_fix_qtb.html, -"reax/c/bonds (k)"_fix_reax_bonds.html, -"reax/c/species (k)"_fix_reaxc_species.html, -"rhok"_fix_rhok.html, -"rx (k)"_fix_rx.html, -"saed/vtk"_fix_saed_vtk.html, -"shardlow (k)"_fix_shardlow.html, -"smd"_fix_smd.html, -"smd/adjust/dt"_fix_smd_adjust_dt.html, -"smd/integrate/tlsph"_fix_smd_integrate_tlsph.html, -"smd/integrate/ulsph"_fix_smd_integrate_ulsph.html, -"smd/move/triangulated/surface"_fix_smd_move_triangulated_surface.html, -"smd/setvel"_fix_smd_setvel.html, -"smd/wall/surface"_fix_smd_wall_surface.html, -"tdpd/source"_fix_dpd_source.html, -"temp/rescale/eff"_fix_temp_rescale_eff.html, -"ti/spring"_fix_ti_spring.html, -"ttm/mod"_fix_ttm.html, -"wall/ees"_fix_wall_ees.html, -"wall/region/ees"_fix_wall_ees.html :tb(c=6,ea=c) - -:line - -Compute styles :h3 - -See the "compute"_compute.html command for one-line descriptions of -each style or click on the style itself for a full description. Some -of the styles have accelerated versions, which can be used if LAMMPS -is built with the "appropriate accelerated -package"_Speed_packages.html. This is indicated by additional letters -in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = -OPT. - -"aggregate/atom"_compute_cluster_atom.html, -"angle"_compute_angle.html, -"angle/local"_compute_angle_local.html, -"angmom/chunk"_compute_angmom_chunk.html, -"body/local"_compute_body_local.html, -"bond"_compute_bond.html, -"bond/local"_compute_bond_local.html, -"centro/atom"_compute_centro_atom.html, -"chunk/atom"_compute_chunk_atom.html, -"cluster/atom"_compute_cluster_atom.html, -"cna/atom"_compute_cna_atom.html, -"com"_compute_com.html, -"com/chunk"_compute_com_chunk.html, -"contact/atom"_compute_contact_atom.html, -"coord/atom"_compute_coord_atom.html, -"damage/atom"_compute_damage_atom.html, -"dihedral"_compute_dihedral.html, -"dihedral/local"_compute_dihedral_local.html, -"dilatation/atom"_compute_dilatation_atom.html, -"dipole/chunk"_compute_dipole_chunk.html, -"displace/atom"_compute_displace_atom.html, -"erotate/asphere"_compute_erotate_asphere.html, -"erotate/rigid"_compute_erotate_rigid.html, -"erotate/sphere"_compute_erotate_sphere.html, -"erotate/sphere/atom"_compute_erotate_sphere_atom.html, -"event/displace"_compute_event_displace.html, -"fragment/atom"_compute_cluster_atom.html, -"global/atom"_compute_global_atom.html, -"group/group"_compute_group_group.html, -"gyration"_compute_gyration.html, -"gyration/chunk"_compute_gyration_chunk.html, -"heat/flux"_compute_heat_flux.html, -"hexorder/atom"_compute_hexorder_atom.html, -"improper"_compute_improper.html, -"improper/local"_compute_improper_local.html, -"inertia/chunk"_compute_inertia_chunk.html, -"ke"_compute_ke.html, -"ke/atom"_compute_ke_atom.html, -"ke/rigid"_compute_ke_rigid.html, -"msd"_compute_msd.html, -"msd/chunk"_compute_msd_chunk.html, -"msd/nongauss"_compute_msd_nongauss.html, -"omega/chunk"_compute_omega_chunk.html, -"orientorder/atom"_compute_orientorder_atom.html, -"pair"_compute_pair.html, -"pair/local"_compute_pair_local.html, -"pe"_compute_pe.html, -"pe/atom"_compute_pe_atom.html, -"plasticity/atom"_compute_plasticity_atom.html, -"pressure"_compute_pressure.html, -"property/atom"_compute_property_atom.html, -"property/local"_compute_property_local.html, -"property/chunk"_compute_property_chunk.html, -"rdf"_compute_rdf.html, -"reduce"_compute_reduce.html, -"reduce/region"_compute_reduce.html, -"rigid/local"_compute_rigid_local.html, -"slice"_compute_slice.html, -"sna/atom"_compute_sna_atom.html, -"snad/atom"_compute_sna_atom.html, -"snav/atom"_compute_sna_atom.html, -"spin"_compute_spin.html, -"stress/atom"_compute_stress_atom.html, -"temp (k)"_compute_temp.html, -"temp/asphere"_compute_temp_asphere.html, -"temp/body"_compute_temp_body.html, -"temp/chunk"_compute_temp_chunk.html, -"temp/com"_compute_temp_com.html, -"temp/deform"_compute_temp_deform.html, -"temp/partial"_compute_temp_partial.html, -"temp/profile"_compute_temp_profile.html, -"temp/ramp"_compute_temp_ramp.html, -"temp/region"_compute_temp_region.html, -"temp/sphere"_compute_temp_sphere.html, -"ti"_compute_ti.html, -"torque/chunk"_compute_torque_chunk.html, -"vacf"_compute_vacf.html, -"vcm/chunk"_compute_vcm_chunk.html, -"voronoi/atom"_compute_voronoi_atom.html :tb(c=6,ea=c) - -These are additional compute styles in USER packages, which can be -used if "LAMMPS is built with the appropriate -package"_Section_start.html#start_3. - -"ackland/atom"_compute_ackland_atom.html, -"basal/atom"_compute_basal_atom.html, -"cnp/atom"_compute_cnp_atom.html, -"dpd"_compute_dpd.html, -"dpd/atom"_compute_dpd_atom.html, -"edpd/temp/atom"_compute_edpd_temp_atom.html, -"entropy/atom"_compute_entropy_atom.html, -"fep"_compute_fep.html, -"force/tally"_compute_tally.html, -"heat/flux/tally"_compute_tally.html, -"ke/eff"_compute_ke_eff.html, -"ke/atom/eff"_compute_ke_atom_eff.html, -"meso/e/atom"_compute_meso_e_atom.html, -"meso/rho/atom"_compute_meso_rho_atom.html, -"meso/t/atom"_compute_meso_t_atom.html, -"pe/tally"_compute_tally.html, -"pe/mol/tally"_compute_tally.html, -"pressure/uef"_compute_pressure_uef.html, -"saed"_compute_saed.html, -"smd/contact/radius"_compute_smd_contact_radius.html, -"smd/damage"_compute_smd_damage.html, -"smd/hourglass/error"_compute_smd_hourglass_error.html, -"smd/internal/energy"_compute_smd_internal_energy.html, -"smd/plastic/strain"_compute_smd_plastic_strain.html, -"smd/plastic/strain/rate"_compute_smd_plastic_strain_rate.html, -"smd/rho"_compute_smd_rho.html, -"smd/tlsph/defgrad"_compute_smd_tlsph_defgrad.html, -"smd/tlsph/dt"_compute_smd_tlsph_dt.html, -"smd/tlsph/num/neighs"_compute_smd_tlsph_num_neighs.html, -"smd/tlsph/shape"_compute_smd_tlsph_shape.html, -"smd/tlsph/strain"_compute_smd_tlsph_strain.html, -"smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html, -"smd/tlsph/stress"_compute_smd_tlsph_stress.html, -"smd/triangle/mesh/vertices"_compute_smd_triangle_mesh_vertices.html, -"smd/ulsph/num/neighs"_compute_smd_ulsph_num_neighs.html, -"smd/ulsph/strain"_compute_smd_ulsph_strain.html, -"smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html, -"smd/ulsph/stress"_compute_smd_ulsph_stress.html, -"smd/vol"_compute_smd_vol.html, -"stress/tally"_compute_tally.html, -"tdpd/cc/atom"_compute_tdpd_cc_atom.html, -"temp/drude"_compute_temp_drude.html, -"temp/eff"_compute_temp_eff.html, -"temp/deform/eff"_compute_temp_deform_eff.html, -"temp/region/eff"_compute_temp_region_eff.html, -"temp/rotate"_compute_temp_rotate.html, -"temp/uef"_compute_temp_uef.html, -"xrd"_compute_xrd.html :tb(c=6,ea=c) - -:line - -Pair_style potentials :h3 - -See the "pair_style"_pair_style.html command for an overview of pair -potentials. Click on the style itself for a full description. Many -of the styles have accelerated versions, which can be used if LAMMPS -is built with the "appropriate accelerated -package"_Speed_packages.html. This is indicated by additional letters -in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = -OPT. - -"none"_pair_none.html, -"zero"_pair_zero.html, -"hybrid"_pair_hybrid.html, -"hybrid/overlay (k)"_pair_hybrid.html, -"adp (o)"_pair_adp.html, -"airebo (oi)"_pair_airebo.html, -"airebo/morse (oi)"_pair_airebo.html, -"beck (go)"_pair_beck.html, -"body/nparticle"_pair_body_nparticle.html, -"body/rounded/polygon"_pair_body_rounded/polygon.html, -"body/rounded/polyhedron"_pair_body_rounded/polyhedron.html, -"bop"_pair_bop.html, -"born (go)"_pair_born.html, -"born/coul/dsf"_pair_born.html, -"born/coul/dsf/cs"_pair_born.html, -"born/coul/long (go)"_pair_born.html, -"born/coul/long/cs"_pair_born.html, -"born/coul/msm (o)"_pair_born.html, -"born/coul/wolf (go)"_pair_born.html, -"born/coul/wolf/cs"_pair_born.html, -"brownian (o)"_pair_brownian.html, -"brownian/poly (o)"_pair_brownian.html, -"buck (giko)"_pair_buck.html, -"buck/coul/cut (giko)"_pair_buck.html, -"buck/coul/long (giko)"_pair_buck.html, -"buck/coul/long/cs"_pair_buck.html, -"buck/coul/msm (o)"_pair_buck.html, -"buck/long/coul/long (o)"_pair_buck_long.html, -"colloid (go)"_pair_colloid.html, -"comb (o)"_pair_comb.html, -"comb3"_pair_comb.html, -"coul/cut (gko)"_pair_coul.html, -"coul/debye (gko)"_pair_coul.html, -"coul/dsf (gko)"_pair_coul.html, -"coul/long (gko)"_pair_coul.html, -"coul/long/cs"_pair_coul.html, -"coul/msm"_pair_coul.html, -"coul/streitz"_pair_coul.html, -"coul/wolf (ko)"_pair_coul.html, -"coul/wolf/cs"_pair_coul.html, -"dpd (gio)"_pair_dpd.html, -"dpd/tstat (go)"_pair_dpd.html, -"dsmc"_pair_dsmc.html, -"eam (gikot)"_pair_eam.html, -"eam/alloy (gikot)"_pair_eam.html, -"eam/cd (o)"_pair_eam.html, -"eam/fs (gikot)"_pair_eam.html, -"eim (o)"_pair_eim.html, -"gauss (go)"_pair_gauss.html, -"gayberne (gio)"_pair_gayberne.html, -"gran/hertz/history (o)"_pair_gran.html, -"gran/hooke (o)"_pair_gran.html, -"gran/hooke/history (o)"_pair_gran.html, -"gw"_pair_gw.html, -"gw/zbl"_pair_gw.html, -"hbond/dreiding/lj (o)"_pair_hbond_dreiding.html, -"hbond/dreiding/morse (o)"_pair_hbond_dreiding.html, -"kim"_pair_kim.html, -"lcbop"_pair_lcbop.html, -"line/lj"_pair_line_lj.html, -"lj/charmm/coul/charmm (iko)"_pair_charmm.html, -"lj/charmm/coul/charmm/implicit (ko)"_pair_charmm.html, -"lj/charmm/coul/long (giko)"_pair_charmm.html, -"lj/charmm/coul/msm"_pair_charmm.html, -"lj/charmmfsw/coul/charmmfsh"_pair_charmm.html, -"lj/charmmfsw/coul/long"_pair_charmm.html, -"lj/class2 (gko)"_pair_class2.html, -"lj/class2/coul/cut (ko)"_pair_class2.html, -"lj/class2/coul/long (gko)"_pair_class2.html, -"lj/cubic (go)"_pair_lj_cubic.html, -"lj/cut (gikot)"_pair_lj.html, -"lj/cut/coul/cut (gko)"_pair_lj.html, -"lj/cut/coul/debye (gko)"_pair_lj.html, -"lj/cut/coul/dsf (gko)"_pair_lj.html, -"lj/cut/coul/long (gikot)"_pair_lj.html, -"lj/cut/coul/long/cs"_pair_lj.html, -"lj/cut/coul/msm (go)"_pair_lj.html, -"lj/cut/coul/wolf (o)"_pair_lj.html, -"lj/cut/dipole/cut (go)"_pair_dipole.html, -"lj/cut/dipole/long"_pair_dipole.html, -"lj/cut/tip4p/cut (o)"_pair_lj.html, -"lj/cut/tip4p/long (ot)"_pair_lj.html, -"lj/expand (gko)"_pair_lj_expand.html, -"lj/gromacs (gko)"_pair_gromacs.html, -"lj/gromacs/coul/gromacs (ko)"_pair_gromacs.html, -"lj/long/coul/long (io)"_pair_lj_long.html, -"lj/long/dipole/long"_pair_dipole.html, -"lj/long/tip4p/long"_pair_lj_long.html, -"lj/smooth (o)"_pair_lj_smooth.html, -"lj/smooth/linear (o)"_pair_lj_smooth_linear.html, -"lj96/cut (go)"_pair_lj96.html, -"lubricate (o)"_pair_lubricate.html, -"lubricate/poly (o)"_pair_lubricate.html, -"lubricateU"_pair_lubricateU.html, -"lubricateU/poly"_pair_lubricateU.html, -"meam"_pair_meam.html, -"mie/cut (o)"_pair_mie.html, -"morse (gkot)"_pair_morse.html, -"nb3b/harmonic (o)"_pair_nb3b_harmonic.html, -"nm/cut (o)"_pair_nm.html, -"nm/cut/coul/cut (o)"_pair_nm.html, -"nm/cut/coul/long (o)"_pair_nm.html, -"peri/eps"_pair_peri.html, -"peri/lps (o)"_pair_peri.html, -"peri/pmb (o)"_pair_peri.html, -"peri/ves"_pair_peri.html, -"polymorphic"_pair_polymorphic.html, -"python"_pair_python.html, -"reax"_pair_reax.html, -"rebo (oi)"_pair_airebo.html, -"resquared (go)"_pair_resquared.html, -"snap (k)"_pair_snap.html, -"soft (go)"_pair_soft.html, -"sw (giko)"_pair_sw.html, -"spin/dmi"_pair_spin_dmi.html, -"spin/exchange"_pair_spin_exchange.html, -"spin/magelec"_pair_spin_magelec.html, -"spin/neel"_pair_spin_neel.html, -"table (gko)"_pair_table.html, -"tersoff (giko)"_pair_tersoff.html, -"tersoff/mod (gko)"_pair_tersoff_mod.html, -"tersoff/mod/c (o)"_pair_tersoff_mod.html, -"tersoff/zbl (gko)"_pair_tersoff_zbl.html, -"tip4p/cut (o)"_pair_coul.html, -"tip4p/long (o)"_pair_coul.html, -"tri/lj"_pair_tri_lj.html, -"ufm (got)"_pair_ufm.html, -"vashishta (ko)"_pair_vashishta.html, -"vashishta/table (o)"_pair_vashishta.html, -"yukawa (gok)"_pair_yukawa.html, -"yukawa/colloid (go)"_pair_yukawa_colloid.html, -"zbl (gok)"_pair_zbl.html :tb(c=4,ea=c) - -These are additional pair styles in USER packages, which can be used -if "LAMMPS is built with the appropriate -package"_Section_start.html#start_3. - -"agni (o)"_pair_agni.html, -"awpmd/cut"_pair_awpmd.html, -"buck/mdf"_pair_mdf.html, -"coul/cut/soft (o)"_pair_lj_soft.html, -"coul/diel (o)"_pair_coul_diel.html, -"coul/long/soft (o)"_pair_lj_soft.html, -"coul/shield"_pair_coul_shield.html, -"dpd/fdt"_pair_dpd_fdt.html, -"dpd/fdt/energy (k)"_pair_dpd_fdt.html, -"edip (o)"_pair_edip.html, -"edip/multi"_pair_edip.html, -"edpd"_pair_meso.html, -"eff/cut"_pair_eff.html, -"exp6/rx (k)"_pair_exp6_rx.html, -"extep"_pair_extep.html, -"gauss/cut"_pair_gauss.html, -"ilp/graphene/hbn"_pair_ilp_graphene_hbn.html, -"kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html, -"kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html, -"lennard/mdf"_pair_mdf.html, -"list"_pair_list.html, -"lj/charmm/coul/long/soft (o)"_pair_charmm.html, -"lj/cut/coul/cut/soft (o)"_pair_lj_soft.html, -"lj/cut/coul/long/soft (o)"_pair_lj_soft.html, -"lj/cut/dipole/sf (go)"_pair_dipole.html, -"lj/cut/soft (o)"_pair_lj_soft.html, -"lj/cut/thole/long (o)"_pair_thole.html, -"lj/cut/tip4p/long/soft (o)"_pair_lj_soft.html, -"lj/mdf"_pair_mdf.html, -"lj/sdk (gko)"_pair_sdk.html, -"lj/sdk/coul/long (go)"_pair_sdk.html, -"lj/sdk/coul/msm (o)"_pair_sdk.html, -"mdpd"_pair_meso.html, -"mdpd/rhosum"_pair_meso.html, -"meam/c"_pair_meam.html, -"meam/spline (o)"_pair_meam_spline.html, -"meam/sw/spline"_pair_meam_sw_spline.html, -"mgpt"_pair_mgpt.html, -"momb"_pair_momb.html, -"morse/smooth/linear"_pair_morse.html, -"morse/soft"_pair_morse.html, -"multi/lucy"_pair_multi_lucy.html, -"multi/lucy/rx (k)"_pair_multi_lucy_rx.html, -"oxdna/coaxstk"_pair_oxdna.html, -"oxdna/excv"_pair_oxdna.html, -"oxdna/hbond"_pair_oxdna.html, -"oxdna/stk"_pair_oxdna.html, -"oxdna/xstk"_pair_oxdna.html, -"oxdna2/coaxstk"_pair_oxdna2.html, -"oxdna2/dh"_pair_oxdna2.html, -"oxdna2/excv"_pair_oxdna2.html, -"oxdna2/stk"_pair_oxdna2.html, -"quip"_pair_quip.html, -"reax/c (ko)"_pair_reaxc.html, -"smd/hertz"_pair_smd_hertz.html, -"smd/tlsph"_pair_smd_tlsph.html, -"smd/triangulated/surface"_pair_smd_triangulated_surface.html, -"smd/ulsph"_pair_smd_ulsph.html, -"smtbq"_pair_smtbq.html, -"snap (k)"_pair_snap.html, -"sph/heatconduction"_pair_sph_heatconduction.html, -"sph/idealgas"_pair_sph_idealgas.html, -"sph/lj"_pair_sph_lj.html, -"sph/rhosum"_pair_sph_rhosum.html, -"sph/taitwater"_pair_sph_taitwater.html, -"sph/taitwater/morris"_pair_sph_taitwater_morris.html, -"srp"_pair_srp.html, -"table/rx (k)"_pair_table_rx.html, -"tdpd"_pair_meso.html, -"tersoff/table (o)"_pair_tersoff.html, -"thole"_pair_thole.html, -"tip4p/long/soft (o)"_pair_lj_soft.html :tb(c=4,ea=c) - -:line - -Bond_style potentials :h3 - -See the "bond_style"_bond_style.html command for an overview of bond -potentials. Click on the style itself for a full description. Some -of the styles have accelerated versions, which can be used if LAMMPS -is built with the "appropriate accelerated -package"_Speed_packages.html. This is indicated by additional letters -in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = -OPT. - -"none"_bond_none.html, -"zero"_bond_zero.html, -"hybrid"_bond_hybrid.html, -"class2 (ko)"_bond_class2.html, -"fene (iko)"_bond_fene.html, -"fene/expand (o)"_bond_fene_expand.html, -"gromos (o)"_bond_gromos.html, -"harmonic (ko)"_bond_harmonic.html, -"morse (o)"_bond_morse.html, -"nonlinear (o)"_bond_nonlinear.html, -"quartic (o)"_bond_quartic.html, -"table (o)"_bond_table.html :tb(c=4,ea=c) - -These are additional bond styles in USER packages, which can be used -if "LAMMPS is built with the appropriate -package"_Section_start.html#start_3. - -"harmonic/shift (o)"_bond_harmonic_shift.html, -"harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html, -"oxdna/fene"_bond_oxdna.html, -"oxdna2/fene"_bond_oxdna.html :tb(c=4,ea=c) - -:line - -Angle_style potentials :h3 - -See the "angle_style"_angle_style.html command for an overview of -angle potentials. Click on the style itself for a full description. -Some of the styles have accelerated versions, which can be used if -LAMMPS is built with the "appropriate accelerated -package"_Speed_packages.html. This is indicated by additional letters -in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = -OPT. - -"none"_angle_none.html, -"zero"_angle_zero.html, -"hybrid"_angle_hybrid.html, -"charmm (ko)"_angle_charmm.html, -"class2 (ko)"_angle_class2.html, -"cosine (o)"_angle_cosine.html, -"cosine/delta (o)"_angle_cosine_delta.html, -"cosine/periodic (o)"_angle_cosine_periodic.html, -"cosine/squared (o)"_angle_cosine_squared.html, -"harmonic (iko)"_angle_harmonic.html, -"table (o)"_angle_table.html :tb(c=4,ea=c) - -These are additional angle styles in USER packages, which can be used -if "LAMMPS is built with the appropriate -package"_Section_start.html#start_3. - -"cosine/shift (o)"_angle_cosine_shift.html, -"cosine/shift/exp (o)"_angle_cosine_shift_exp.html, -"dipole (o)"_angle_dipole.html, -"fourier (o)"_angle_fourier.html, -"fourier/simple (o)"_angle_fourier_simple.html, -"quartic (o)"_angle_quartic.html, -"sdk"_angle_sdk.html :tb(c=4,ea=c) - -:line - -Dihedral_style potentials :h3 - -See the "dihedral_style"_dihedral_style.html command for an overview -of dihedral potentials. Click on the style itself for a full -description. Some of the styles have accelerated versions, which can -be used if LAMMPS is built with the "appropriate accelerated -package"_Speed_packages.html. This is indicated by additional -letters in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = -USER-OMP, t = OPT. - -"none"_dihedral_none.html, -"zero"_dihedral_zero.html, -"hybrid"_dihedral_hybrid.html, -"charmm (iko)"_dihedral_charmm.html, -"charmmfsw"_dihedral_charmm.html, -"class2 (ko)"_dihedral_class2.html, -"harmonic (io)"_dihedral_harmonic.html, -"helix (o)"_dihedral_helix.html, -"multi/harmonic (o)"_dihedral_multi_harmonic.html, -"opls (iko)"_dihedral_opls.html :tb(c=4,ea=c) - -These are additional dihedral styles in USER packages, which can be -used if "LAMMPS is built with the appropriate -package"_Section_start.html#start_3. - -"cosine/shift/exp (o)"_dihedral_cosine_shift_exp.html, -"fourier (io)"_dihedral_fourier.html, -"nharmonic (o)"_dihedral_nharmonic.html, -"quadratic (o)"_dihedral_quadratic.html, -"spherical (o)"_dihedral_spherical.html, -"table (o)"_dihedral_table.html, -"table/cut"_dihedral_table_cut.html :tb(c=4,ea=c) - -:line - -Improper_style potentials :h3 - -See the "improper_style"_improper_style.html command for an overview -of improper potentials. Click on the style itself for a full -description. Some of the styles have accelerated versions, which can -be used if LAMMPS is built with the "appropriate accelerated -package"_Speed_packages.html. This is indicated by additional letters -in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = -OPT. - -"none"_improper_none.html, -"zero"_improper_zero.html, -"hybrid"_improper_hybrid.html, -"class2 (ko)"_improper_class2.html, -"cvff (io)"_improper_cvff.html, -"harmonic (iko)"_improper_harmonic.html, -"umbrella (o)"_improper_umbrella.html :tb(c=4,ea=c) - -These are additional improper styles in USER packages, which can be -used if "LAMMPS is built with the appropriate -package"_Section_start.html#start_3. - -"cossq (o)"_improper_cossq.html, -"distance"_improper_distance.html, -"fourier (o)"_improper_fourier.html, -"ring (o)"_improper_ring.html :tb(c=4,ea=c) - -:line - -Kspace solvers :h3 - -See the "kspace_style"_kspace_style.html command for an overview of -Kspace solvers. Click on the style itself for a full description. -Some of the styles have accelerated versions, which can be used if -LAMMPS is built with the "appropriate accelerated -package"_Speed_packages.html. This is indicated by additional letters -in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = -OPT. - -"ewald (o)"_kspace_style.html, -"ewald/disp"_kspace_style.html, -"msm (o)"_kspace_style.html, -"msm/cg (o)"_kspace_style.html, -"pppm (gok)"_kspace_style.html, -"pppm/cg (o)"_kspace_style.html, -"pppm/disp (i)"_kspace_style.html, -"pppm/disp/tip4p"_kspace_style.html, -"pppm/stagger"_kspace_style.html, -"pppm/tip4p (o)"_kspace_style.html :tb(c=4,ea=c) diff --git a/doc/src/Section_start.txt b/doc/src/Section_start.txt index 4176432328..19a798d5df 100644 --- a/doc/src/Section_start.txt +++ b/doc/src/Section_start.txt @@ -1,10 +1,10 @@ "Previous Section"_Intro.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next -Section"_Section_commands.html :c +Section"_Commands.html :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -1070,7 +1070,7 @@ the '-in' command-line switch, e.g. lmp_linux -in in.file :pre -"This section"_Section_commands.html describes how input scripts are +The "Commands"_Commands.html doc page describes how input scripts are structured and what commands they contain. You can test LAMMPS on any of the sample inputs provided in the @@ -1615,9 +1615,9 @@ value2 ..." at the beginning of the input script. Defining an index variable as a command-line argument overrides any setting for the same index variable in the input script, since index variables cannot be re-defined. See the "variable"_variable.html command for more info on -defining index and other kinds of variables and "this -section"_Section_commands.html#cmd_2 for more info on using variables -in input scripts. +defining index and other kinds of variables and the "Commands +parse"_Commands_parse.html page for more info on using variables in +input scripts. NOTE: Currently, the command-line parser looks for arguments that start with "-" to indicate new switches. Thus you cannot specify diff --git a/doc/src/Speed.txt b/doc/src/Speed.txt index 6c53d6bcf0..091657082a 100644 --- a/doc/src/Speed.txt +++ b/doc/src/Speed.txt @@ -4,7 +4,7 @@ Section"_Howto.html :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Speed_bench.txt b/doc/src/Speed_bench.txt index dc76588c11..8e407d14ea 100644 --- a/doc/src/Speed_bench.txt +++ b/doc/src/Speed_bench.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Speed_compare.txt b/doc/src/Speed_compare.txt index 6c947b9662..1a17b39c79 100644 --- a/doc/src/Speed_compare.txt +++ b/doc/src/Speed_compare.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Speed_gpu.txt b/doc/src/Speed_gpu.txt index d6ebbf8069..ab8ec7e9d1 100644 --- a/doc/src/Speed_gpu.txt +++ b/doc/src/Speed_gpu.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Speed_intel.txt b/doc/src/Speed_intel.txt index 08e3fbc4cc..20f49672e0 100644 --- a/doc/src/Speed_intel.txt +++ b/doc/src/Speed_intel.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Speed_kokkos.txt b/doc/src/Speed_kokkos.txt index 8e01db7bdc..14f4103aed 100644 --- a/doc/src/Speed_kokkos.txt +++ b/doc/src/Speed_kokkos.txt @@ -3,34 +3,39 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line KOKKOS package :h3 Kokkos is a templated C++ library that provides abstractions to allow -a single implementation of an application kernel (e.g. a pair style) to run efficiently on -different kinds of hardware, such as GPUs, Intel Xeon Phis, or many-core -CPUs. Kokkos maps the C++ kernel onto different backend languages such as CUDA, OpenMP, or Pthreads. -The Kokkos library also provides data abstractions to adjust (at -compile time) the memory layout of data structures like 2d and -3d arrays to optimize performance on different hardware. For more information on Kokkos, see -"Github"_https://github.com/kokkos/kokkos. Kokkos is part of -"Trilinos"_http://trilinos.sandia.gov/packages/kokkos. The Kokkos library was written primarily by Carter Edwards, -Christian Trott, and Dan Sunderland (all Sandia). +a single implementation of an application kernel (e.g. a pair style) +to run efficiently on different kinds of hardware, such as GPUs, Intel +Xeon Phis, or many-core CPUs. Kokkos maps the C++ kernel onto +different backend languages such as CUDA, OpenMP, or Pthreads. The +Kokkos library also provides data abstractions to adjust (at compile +time) the memory layout of data structures like 2d and 3d arrays to +optimize performance on different hardware. For more information on +Kokkos, see "Github"_https://github.com/kokkos/kokkos. Kokkos is part +of "Trilinos"_http://trilinos.sandia.gov/packages/kokkos. The Kokkos +library was written primarily by Carter Edwards, Christian Trott, and +Dan Sunderland (all Sandia). -The LAMMPS KOKKOS package contains versions of pair, fix, and atom styles -that use data structures and macros provided by the Kokkos library, -which is included with LAMMPS in /lib/kokkos. The KOKKOS package was developed primarily by Christian Trott (Sandia) -and Stan Moore (Sandia) with contributions of various styles by others, including Sikandar -Mashayak (UIUC), Ray Shan (Sandia), and Dan Ibanez (Sandia). For more information on developing using Kokkos abstractions +The LAMMPS KOKKOS package contains versions of pair, fix, and atom +styles that use data structures and macros provided by the Kokkos +library, which is included with LAMMPS in /lib/kokkos. The KOKKOS +package was developed primarily by Christian Trott (Sandia) and Stan +Moore (Sandia) with contributions of various styles by others, +including Sikandar Mashayak (UIUC), Ray Shan (Sandia), and Dan Ibanez +(Sandia). For more information on developing using Kokkos abstractions see the Kokkos programmers' guide at /lib/kokkos/doc/Kokkos_PG.pdf. Kokkos currently provides support for 3 modes of execution (per MPI -task). These are Serial (MPI-only for CPUs and Intel Phi), OpenMP (threading -for many-core CPUs and Intel Phi), and CUDA (for NVIDIA GPUs). You choose the mode at build time to -produce an executable compatible with specific hardware. +task). These are Serial (MPI-only for CPUs and Intel Phi), OpenMP +(threading for many-core CPUs and Intel Phi), and CUDA (for NVIDIA +GPUs). You choose the mode at build time to produce an executable +compatible with specific hardware. [Building LAMMPS with the KOKKOS package:] @@ -38,16 +43,18 @@ NOTE: Kokkos support within LAMMPS must be built with a C++11 compatible compiler. This means GCC version 4.7.2 or later, Intel 14.0.4 or later, or Clang 3.5.2 or later is required. -The recommended method of building the KOKKOS package is to start with the provided Kokkos -Makefiles in /src/MAKE/OPTIONS/. You may need to modify the KOKKOS_ARCH variable in the Makefile -to match your specific hardware. For example: +The recommended method of building the KOKKOS package is to start with +the provided Kokkos Makefiles in /src/MAKE/OPTIONS/. You may need to +modify the KOKKOS_ARCH variable in the Makefile to match your specific +hardware. For example: for Sandy Bridge CPUs, set KOKKOS_ARCH=SNB for Broadwell CPUs, set KOKKOS_ARCH=BWD for K80 GPUs, set KOKKOS_ARCH=Kepler37 for P100 GPUs and Power8 CPUs, set KOKKOS_ARCH=Pascal60,Power8 :ul -See the [Advanced Kokkos Options] section below for a listing of all KOKKOS_ARCH options. +See the [Advanced Kokkos Options] section below for a listing of all +KOKKOS_ARCH options. [Compile for CPU-only (MPI only, no threading):] @@ -61,11 +68,12 @@ make kokkos_mpi_only :pre [Compile for CPU-only (MPI plus OpenMP threading):] -NOTE: To build with Kokkos support for OpenMP threading, your compiler must support the -OpenMP interface. You should have one or more multi-core CPUs so that -multiple threads can be launched by each MPI task running on a CPU. +NOTE: To build with Kokkos support for OpenMP threading, your compiler +must support the OpenMP interface. You should have one or more +multi-core CPUs so that multiple threads can be launched by each MPI +task running on a CPU. -use a C++11 compatible compiler and set KOKKOS_ARCH variable in +Use a C++11 compatible compiler and set KOKKOS_ARCH variable in /src/MAKE/OPTIONS/Makefile.kokkos_omp as described above. Then do the following: @@ -88,9 +96,9 @@ software version 7.5 or later must be installed on your system. See the discussion for the "GPU package"_Speed_gpu.html for details of how to check and do this. -use a C++11 compatible compiler and set KOKKOS_ARCH variable in -/src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi for both GPU and CPU as described -above. Then do the following: +Use a C++11 compatible compiler and set KOKKOS_ARCH variable in +/src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi for both GPU and CPU as +described above. Then do the following: cd lammps/src make yes-kokkos @@ -104,24 +112,24 @@ on the make command line. For example: make mpi KOKKOS_DEVICES=OpenMP KOKKOS_ARCH=SNB # set the KOKKOS_DEVICES and KOKKOS_ARCH variable explicitly make kokkos_cuda_mpi KOKKOS_ARCH=Pascal60,Power8 # set the KOKKOS_ARCH variable explicitly :pre -Setting the KOKKOS_DEVICES and KOKKOS_ARCH variables on the -make command line requires a GNU-compatible make command. Try -"gmake" if your system's standard make complains. +Setting the KOKKOS_DEVICES and KOKKOS_ARCH variables on the make +command line requires a GNU-compatible make command. Try "gmake" if +your system's standard make complains. NOTE: If you build using make line variables and re-build LAMMPS twice -with different KOKKOS options and the *same* target, then you *must* perform a "make clean-all" -or "make clean-machine" before each build. This is to force all the -KOKKOS-dependent files to be re-compiled with the new options. +with different KOKKOS options and the *same* target, then you *must* +perform a "make clean-all" or "make clean-machine" before each +build. This is to force all the KOKKOS-dependent files to be +re-compiled with the new options. [Running LAMMPS with the KOKKOS package:] -All Kokkos operations occur within the -context of an individual MPI task running on a single node of the -machine. The total number of MPI tasks used by LAMMPS (one or -multiple per compute node) is set in the usual manner via the mpirun -or mpiexec commands, and is independent of Kokkos. E.g. the mpirun -command in OpenMPI does this via its --np and -npernode switches. Ditto for MPICH via -np and -ppn. +All Kokkos operations occur within the context of an individual MPI +task running on a single node of the machine. The total number of MPI +tasks used by LAMMPS (one or multiple per compute node) is set in the +usual manner via the mpirun or mpiexec commands, and is independent of +Kokkos. E.g. the mpirun command in OpenMPI does this via its -np and +-npernode switches. Ditto for MPICH via -np and -ppn. [Running on a multi-core CPU:] @@ -133,8 +141,9 @@ mpirun -np 2 -ppn 1 lmp_kokkos_omp -k on t 16 -sf kk -in in.lj # 2 nodes, 1 MPI mpirun -np 2 lmp_kokkos_omp -k on t 8 -sf kk -in in.lj # 1 node, 2 MPI tasks/node, 8 threads/task 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 +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 @@ -142,32 +151,33 @@ here"_Section_start.html#start_7. For OpenMP use: -k on t Nt :pre -The "t Nt" option specifies how many OpenMP threads per MPI -task to use with a node. The default is Nt = 1, which is MPI-only mode. -Note that the product of MPI tasks * OpenMP -threads/task should not exceed the physical number of cores (on a -node), otherwise performance will suffer. If hyperthreading is enabled, then -the product of MPI tasks * OpenMP threads/task should not exceed the -physical number of cores * hardware threads. -The "-k on" switch also issues a "package kokkos" command (with no -additional arguments) which sets various KOKKOS options to default -values, as discussed on the "package"_package.html command doc page. +The "t Nt" option specifies how many OpenMP threads per MPI task to +use with a node. The default is Nt = 1, which is MPI-only mode. Note +that the product of MPI tasks * OpenMP threads/task should not exceed +the physical number of cores (on a node), otherwise performance will +suffer. If hyperthreading is enabled, then the product of MPI tasks * +OpenMP threads/task should not exceed the physical number of cores * +hardware threads. The "-k on" switch also issues a "package kokkos" +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"_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. -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 +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 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: +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: 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 @@ -176,9 +186,9 @@ script, it can also override the Newton flag defaults. [Core and Thread Affinity:] -When using multi-threading, it is important for -performance to bind both MPI tasks to physical cores, and threads to -physical cores, so they do not migrate during a simulation. +When using multi-threading, it is important for performance to bind +both MPI tasks to physical cores, and threads to physical cores, so +they do not migrate during a simulation. If you are not certain MPI tasks are being bound (check the defaults for your MPI installation), binding can be forced with these flags: @@ -189,24 +199,24 @@ Mvapich2 2.0: mpiexec -np 2 --bind-to socket --map-by socket ./lmp_mvapich ... : For binding threads with KOKKOS OpenMP, use thread affinity environment variables to force binding. With OpenMP 3.1 (gcc 4.7 or later, intel 12 or later) setting the environment variable -OMP_PROC_BIND=true should be sufficient. In general, for best performance -with OpenMP 4.0 or better set OMP_PROC_BIND=spread and OMP_PLACES=threads. -For binding threads with the -KOKKOS pthreads option, compile LAMMPS the KOKKOS HWLOC=yes option -as described below. +OMP_PROC_BIND=true should be sufficient. In general, for best +performance with OpenMP 4.0 or better set OMP_PROC_BIND=spread and +OMP_PLACES=threads. For binding threads with the KOKKOS pthreads +option, compile LAMMPS the KOKKOS HWLOC=yes option as described below. [Running on Knight's Landing (KNL) Intel Xeon Phi:] -Here is a quick overview of how to use the KOKKOS package -for the Intel Knight's Landing (KNL) Xeon Phi: +Here is a quick overview of how to use the KOKKOS package for the +Intel Knight's Landing (KNL) Xeon Phi: -KNL Intel Phi chips have 68 physical cores. Typically 1 to 4 cores -are reserved for the OS, and only 64 or 66 cores are used. Each core -has 4 hyperthreads,so there are effectively N = 256 (4*64) or -N = 264 (4*66) cores to run on. The product of MPI tasks * OpenMP threads/task should not exceed this limit, -otherwise performance will suffer. Note that with the KOKKOS package you do not need to -specify how many KNLs there are per node; each -KNL is simply treated as running some number of MPI tasks. +KNL Intel Phi chips have 68 physical cores. Typically 1 to 4 cores are +reserved for the OS, and only 64 or 66 cores are used. Each core has 4 +hyperthreads,so there are effectively N = 256 (4*64) or N = 264 (4*66) +cores to run on. The product of MPI tasks * OpenMP threads/task should +not exceed this limit, otherwise performance will suffer. Note that +with the KOKKOS package you do not need to specify how many KNLs there +are per node; each KNL is simply treated as running some number of MPI +tasks. Examples of mpirun commands that follow these rules are shown below. @@ -221,57 +231,60 @@ tasks/node. The "-k on t Nt" command-line switch sets the number of threads/task as Nt. The product of these two values should be N, i.e. 256 or 264. -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 -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: +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 +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: 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 -NOTE: MPI tasks and threads should be bound to cores as described above for CPUs. +NOTE: MPI tasks and threads should be bound to cores as described +above for CPUs. -NOTE: To build with Kokkos support for Intel Xeon Phi coprocessors such as Knight's Corner (KNC), your -system must be configured to use them in "native" mode, not "offload" -mode like the USER-INTEL package supports. +NOTE: To build with Kokkos support for Intel Xeon Phi coprocessors +such as Knight's Corner (KNC), your system must be configured to use +them in "native" mode, not "offload" mode like the USER-INTEL package +supports. [Running on GPUs:] -Use the "-k" "command-line switch"_Section_commands.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"_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. -k on g Ng :pre -Here are examples of how to use the KOKKOS package for GPUs, -assuming one or more nodes, each with two GPUs: +Here are examples of how to use the KOKKOS package for GPUs, assuming +one or more nodes, each with two GPUs: mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -in in.lj # 1 node, 2 MPI tasks/node, 2 GPUs/node mpirun -np 32 -ppn 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -in in.lj # 16 nodes, 2 MPI tasks/node, 2 GPUs/node (32 GPUs total) :pre -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 +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 pairwise and bonded interactions, along with threaded communication. -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: +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: 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 @@ -299,8 +312,8 @@ Alternatively the effect of the "-sf" or "-pk" switches can be duplicated by adding the "package kokkos"_package.html or "suffix 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. +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 @@ -318,17 +331,19 @@ wish to change any of its option defaults, as set by the "-k on" [Using OpenMP threading and CUDA together (experimental):] -With the KOKKOS package, both OpenMP multi-threading and GPUs can be used -together in a few special cases. In the Makefile, the KOKKOS_DEVICES variable must -include both "Cuda" and "OpenMP", as is the case for /src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi +With the KOKKOS package, both OpenMP multi-threading and GPUs can be +used together in a few special cases. In the Makefile, the +KOKKOS_DEVICES variable must include both "Cuda" and "OpenMP", as is +the case for /src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi KOKKOS_DEVICES=Cuda,OpenMP :pre The suffix "/kk" is equivalent to "/kk/device", and for Kokkos CUDA, -using the "-sf kk" in the command line gives the default CUDA version everywhere. -However, if the "/kk/host" suffix is added to a specific style in the input -script, the Kokkos OpenMP (CPU) version of that specific style will be used instead. -Set the number of OpenMP threads as "t Nt" and the number of GPUs as "g Ng" +using the "-sf kk" in the command line gives the default CUDA version +everywhere. However, if the "/kk/host" suffix is added to a specific +style in the input script, the Kokkos OpenMP (CPU) version of that +specific style will be used instead. Set the number of OpenMP threads +as "t Nt" and the number of GPUs as "g Ng" -k on t Nt g Ng :pre @@ -336,18 +351,20 @@ For example, the command to run with 1 GPU and 8 OpenMP threads is then: mpiexec -np 1 lmp_kokkos_cuda_openmpi -in in.lj -k on g 1 t 8 -sf kk :pre -Conversely, if the "-sf kk/host" is used in the command line and then the -"/kk" or "/kk/device" suffix is added to a specific style in your input script, -then only that specific style will run on the GPU while everything else will -run on the CPU in OpenMP mode. Note that the execution of the CPU and GPU -styles will NOT overlap, except for a special case: +Conversely, if the "-sf kk/host" is used in the command line and then +the "/kk" or "/kk/device" suffix is added to a specific style in your +input script, then only that specific style will run on the GPU while +everything else will run on the CPU in OpenMP mode. Note that the +execution of the CPU and GPU styles will NOT overlap, except for a +special case: -A kspace style and/or molecular topology (bonds, angles, etc.) running on -the host CPU can overlap with a pair style running on the GPU. First compile -with "--default-stream per-thread" added to CCFLAGS in the Kokkos CUDA Makefile. -Then explicitly use the "/kk/host" suffix for kspace and bonds, angles, etc. -in the input file and the "kk" suffix (equal to "kk/device") on the command line. -Also make sure the environment variable CUDA_LAUNCH_BLOCKING is not set to "1" +A kspace style and/or molecular topology (bonds, angles, etc.) running +on the host CPU can overlap with a pair style running on the +GPU. First compile with "--default-stream per-thread" added to CCFLAGS +in the Kokkos CUDA Makefile. Then explicitly use the "/kk/host" +suffix for kspace and bonds, angles, etc. in the input file and the +"kk" suffix (equal to "kk/device") on the command line. Also make +sure the environment variable CUDA_LAUNCH_BLOCKING is not set to "1" so CPU/GPU overlap can occur. [Speed-ups to expect:] @@ -384,9 +401,8 @@ hardware. There are other allowed options when building with the KOKKOS package. As above, they can be set either as variables on the make command line or in Makefile.machine. This is the full list of options, including -those discussed above. Each takes a value shown below. The -default value is listed, which is set in the -/lib/kokkos/Makefile.kokkos file. +those discussed above. Each takes a value shown below. The default +value is listed, which is set in the /lib/kokkos/Makefile.kokkos file. KOKKOS_DEVICES, values = {Serial}, {OpenMP}, {Pthreads}, {Cuda}, default = {OpenMP} KOKKOS_ARCH, values = {KNC}, {SNB}, {HSW}, {Kepler30}, {Kepler32}, {Kepler35}, {Kepler37}, {Maxwell50}, {Maxwell52}, {Maxwell53}, {Pascal60}, {Pascal61}, {ARMv80}, {ARMv81}, {ARMv81}, {ARMv8-ThunderX}, {BGQ}, {Power7}, {Power8}, {Power9}, {KNL}, {BDW}, {SKX}, default = {none} @@ -444,13 +460,14 @@ within LAMMPS. KOKKOS_DEBUG=yes enables printing of run-time debugging information that can be useful. It also enables runtime bounds checking on Kokkos data structures. -KOKKOS_CXX_STANDARD and KOKKOS_OPTIONS are typically not changed when building LAMMPS. +KOKKOS_CXX_STANDARD and KOKKOS_OPTIONS are typically not changed when +building LAMMPS. -KOKKOS_CUDA_OPTIONS are additional options for CUDA. The LAMMPS KOKKOS package must be compiled -with the {enable_lambda} option when using GPUs. +KOKKOS_CUDA_OPTIONS are additional options for CUDA. The LAMMPS KOKKOS +package must be compiled with the {enable_lambda} option when using +GPUs. [Restrictions:] -Currently, there are no precision options with the KOKKOS -package. All compilation and computation is performed in double -precision. +Currently, there are no precision options with the KOKKOS package. All +compilation and computation is performed in double precision. diff --git a/doc/src/Speed_measure.txt b/doc/src/Speed_measure.txt index 03c0345c20..78dc220088 100644 --- a/doc/src/Speed_measure.txt +++ b/doc/src/Speed_measure.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Speed_omp.txt b/doc/src/Speed_omp.txt index 9685b6d349..bcfc406902 100644 --- a/doc/src/Speed_omp.txt +++ b/doc/src/Speed_omp.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Speed_opt.txt b/doc/src/Speed_opt.txt index 7d0d7169f0..676a5d8418 100644 --- a/doc/src/Speed_opt.txt +++ b/doc/src/Speed_opt.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Speed_packages.txt b/doc/src/Speed_packages.txt index 13b5e183db..f463ed91b8 100644 --- a/doc/src/Speed_packages.txt +++ b/doc/src/Speed_packages.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -71,11 +71,12 @@ Lennard-Jones "pair_style lj/cut"_pair_lj.html: "pair_style lj/cut/omp"_pair_lj.html "pair_style lj/cut/opt"_pair_lj.html :ul -To see what accelerate styles are currently available, see -"Section 3.5"_Section_commands.html#cmd_5 of the manual. The -doc pages for individual commands (e.g. "pair lj/cut"_pair_lj.html or -"fix nve"_fix_nve.html) also list any accelerated variants available -for that style. +To see what accelerate styles are currently available for a particular +style, find the style name in the "Commands_all"_Commands_all.html +style pages (fix,compute,pair,etc) and see what suffixes are listed +(g,i,k,o,t) with it. The doc pages for individual commands +(e.g. "pair lj/cut"_pair_lj.html or "fix nve"_fix_nve.html) also list +any accelerated variants available for that style. To use an accelerator package in LAMMPS, and one or more of the styles it provides, follow these general steps. Details vary from package to diff --git a/doc/src/Speed_tips.txt b/doc/src/Speed_tips.txt index c0d360cd8e..7c950779d5 100644 --- a/doc/src/Speed_tips.txt +++ b/doc/src/Speed_tips.txt @@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Tools.txt b/doc/src/Tools.txt index bf0f9ae134..85ee531cfd 100644 --- a/doc/src/Tools.txt +++ b/doc/src/Tools.txt @@ -4,7 +4,7 @@ Section"_Modify.html :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/angle_charmm.txt b/doc/src/angle_charmm.txt index fe109d24fb..f72f086234 100644 --- a/doc/src/angle_charmm.txt +++ b/doc/src/angle_charmm.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/angle_class2.txt b/doc/src/angle_class2.txt index c13a64afb6..3e5445d3a3 100644 --- a/doc/src/angle_class2.txt +++ b/doc/src/angle_class2.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/angle_coeff.txt b/doc/src/angle_coeff.txt index 37298ba145..4c217bae7d 100644 --- a/doc/src/angle_coeff.txt +++ b/doc/src/angle_coeff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -65,9 +65,9 @@ the style to display the formula it computes and coefficients specified by the associated "angle_coeff"_angle_coeff.html command. Note that there are also additional angle styles submitted by users -which are included in the LAMMPS distribution. The list of these with -links to the individual styles are given in the angle section of "this -page"_Section_commands.html#cmd_5. +which are included in the LAMMPS distribution. The full list of all +angle styles is on the "Commands bond"_Commands_bond.html#angle doc +page. "angle_style none"_angle_none.html - turn off angle interactions "angle_style hybrid"_angle_hybrid.html - define multiple styles of angle interactions :ul diff --git a/doc/src/angle_cosine.txt b/doc/src/angle_cosine.txt index 99264b02a6..5a1fe91c83 100644 --- a/doc/src/angle_cosine.txt +++ b/doc/src/angle_cosine.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/angle_cosine_buck6d.txt b/doc/src/angle_cosine_buck6d.txt index 7182ffecc8..63a451b763 100644 --- a/doc/src/angle_cosine_buck6d.txt +++ b/doc/src/angle_cosine_buck6d.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/angle_cosine_delta.txt b/doc/src/angle_cosine_delta.txt index 052300412f..b6ac0ed818 100644 --- a/doc/src/angle_cosine_delta.txt +++ b/doc/src/angle_cosine_delta.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/angle_cosine_periodic.txt b/doc/src/angle_cosine_periodic.txt index 108b081533..c5b184e0b4 100644 --- a/doc/src/angle_cosine_periodic.txt +++ b/doc/src/angle_cosine_periodic.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/angle_cosine_shift.txt b/doc/src/angle_cosine_shift.txt index 185b9f5309..90ac61fe23 100644 --- a/doc/src/angle_cosine_shift.txt +++ b/doc/src/angle_cosine_shift.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/angle_cosine_shift_exp.txt b/doc/src/angle_cosine_shift_exp.txt index e5c7fdd709..f1c4c93c42 100644 --- a/doc/src/angle_cosine_shift_exp.txt +++ b/doc/src/angle_cosine_shift_exp.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/angle_cosine_squared.txt b/doc/src/angle_cosine_squared.txt index e85c514d1e..ba5fd9d413 100644 --- a/doc/src/angle_cosine_squared.txt +++ b/doc/src/angle_cosine_squared.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/angle_dipole.txt b/doc/src/angle_dipole.txt index 31ae2e9464..c001d9d920 100644 --- a/doc/src/angle_dipole.txt +++ b/doc/src/angle_dipole.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/angle_fourier.txt b/doc/src/angle_fourier.txt index 18eb56b478..e0e32c1eed 100644 --- a/doc/src/angle_fourier.txt +++ b/doc/src/angle_fourier.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/angle_fourier_simple.txt b/doc/src/angle_fourier_simple.txt index 6faff5f10d..3c50536a2c 100644 --- a/doc/src/angle_fourier_simple.txt +++ b/doc/src/angle_fourier_simple.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/angle_harmonic.txt b/doc/src/angle_harmonic.txt index fe803be623..76c7a491e8 100644 --- a/doc/src/angle_harmonic.txt +++ b/doc/src/angle_harmonic.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/angle_hybrid.txt b/doc/src/angle_hybrid.txt index bdd3707ccb..2646903421 100644 --- a/doc/src/angle_hybrid.txt +++ b/doc/src/angle_hybrid.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/angle_none.txt b/doc/src/angle_none.txt index a4a9b07c78..1eca5cbbec 100644 --- a/doc/src/angle_none.txt +++ b/doc/src/angle_none.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/angle_quartic.txt b/doc/src/angle_quartic.txt index a31214f435..294be330b1 100644 --- a/doc/src/angle_quartic.txt +++ b/doc/src/angle_quartic.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/angle_sdk.txt b/doc/src/angle_sdk.txt index 0cc535e543..9c5630ef3a 100644 --- a/doc/src/angle_sdk.txt +++ b/doc/src/angle_sdk.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/angle_style.txt b/doc/src/angle_style.txt index f687e9286c..63295faf26 100644 --- a/doc/src/angle_style.txt +++ b/doc/src/angle_style.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -58,9 +58,9 @@ the style to display the formula it computes and coefficients specified by the associated "angle_coeff"_angle_coeff.html command. Note that there are also additional angle styles submitted by users -which are included in the LAMMPS distribution. The list of these with -links to the individual styles are given in the angle section of "this -page"_Section_commands.html#cmd_5. +which are included in the LAMMPS distribution. The full list of all +angle styles are is on the "Commands bond"_Commands_bond.html#angle +doc page. "angle_style none"_angle_none.html - turn off angle interactions "angle_style zero"_angle_zero.html - topology but no interactions diff --git a/doc/src/angle_table.txt b/doc/src/angle_table.txt index 29b56875e7..31ab532be1 100644 --- a/doc/src/angle_table.txt +++ b/doc/src/angle_table.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/angle_zero.txt b/doc/src/angle_zero.txt index b8e8ebf953..c6c1958ec8 100644 --- a/doc/src/angle_zero.txt +++ b/doc/src/angle_zero.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/atom_modify.txt b/doc/src/atom_modify.txt index 1dc0fa6bfb..c882d1b0ba 100644 --- a/doc/src/atom_modify.txt +++ b/doc/src/atom_modify.txt @@ -3,7 +3,7 @@ Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/atom_style.txt b/doc/src/atom_style.txt index 063f9e446c..abf05885a3 100644 --- a/doc/src/atom_style.txt +++ b/doc/src/atom_style.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/balance.txt b/doc/src/balance.txt index da6f59900d..06c4eca491 100644 --- a/doc/src/balance.txt +++ b/doc/src/balance.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/body.txt b/doc/src/body.txt index 96aedccf40..4de5b52911 100644 --- a/doc/src/body.txt +++ b/doc/src/body.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/bond_class2.txt b/doc/src/bond_class2.txt index 049482c973..3d8d5007ba 100644 --- a/doc/src/bond_class2.txt +++ b/doc/src/bond_class2.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/bond_coeff.txt b/doc/src/bond_coeff.txt index d93c0b223b..7485fa3d8d 100644 --- a/doc/src/bond_coeff.txt +++ b/doc/src/bond_coeff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -61,9 +61,8 @@ the style to display the formula it computes and coefficients specified by the associated "bond_coeff"_bond_coeff.html command. Note that here are also additional bond styles submitted by users -which are included in the LAMMPS distribution. The list of these with -links to the individual styles are given in the bond section of "this -page"_Section_commands.html#cmd_5. +which are included in the LAMMPS distribution. The full list of all +bond styles is on the "Commands bond"_Commands_bond.html doc page. "bond_style none"_bond_none.html - turn off bonded interactions "bond_style hybrid"_bond_hybrid.html - define multiple styles of bond interactions :ul diff --git a/doc/src/bond_fene.txt b/doc/src/bond_fene.txt index be154a53b1..e16307a710 100644 --- a/doc/src/bond_fene.txt +++ b/doc/src/bond_fene.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/bond_fene_expand.txt b/doc/src/bond_fene_expand.txt index 77ebd977c8..8edd325885 100644 --- a/doc/src/bond_fene_expand.txt +++ b/doc/src/bond_fene_expand.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/bond_gromos.txt b/doc/src/bond_gromos.txt index 7a56cb3afa..275036a421 100644 --- a/doc/src/bond_gromos.txt +++ b/doc/src/bond_gromos.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/bond_harmonic.txt b/doc/src/bond_harmonic.txt index 54e89fcc72..e4b2015fed 100644 --- a/doc/src/bond_harmonic.txt +++ b/doc/src/bond_harmonic.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/bond_harmonic_shift.txt b/doc/src/bond_harmonic_shift.txt index 0213b5cc6f..b6dc18a5fd 100644 --- a/doc/src/bond_harmonic_shift.txt +++ b/doc/src/bond_harmonic_shift.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/bond_harmonic_shift_cut.txt b/doc/src/bond_harmonic_shift_cut.txt index d907bf4a62..b3054437d8 100644 --- a/doc/src/bond_harmonic_shift_cut.txt +++ b/doc/src/bond_harmonic_shift_cut.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/bond_hybrid.txt b/doc/src/bond_hybrid.txt index 400c3e0be4..140fb72378 100644 --- a/doc/src/bond_hybrid.txt +++ b/doc/src/bond_hybrid.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/bond_morse.txt b/doc/src/bond_morse.txt index 66f2d08cab..9b64e8c5c1 100644 --- a/doc/src/bond_morse.txt +++ b/doc/src/bond_morse.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/bond_none.txt b/doc/src/bond_none.txt index 8cb262a50f..cace1919e1 100644 --- a/doc/src/bond_none.txt +++ b/doc/src/bond_none.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/bond_nonlinear.txt b/doc/src/bond_nonlinear.txt index e0aa5629b3..08109bc699 100644 --- a/doc/src/bond_nonlinear.txt +++ b/doc/src/bond_nonlinear.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/bond_oxdna.txt b/doc/src/bond_oxdna.txt index 927fea6403..a0e14a123a 100644 --- a/doc/src/bond_oxdna.txt +++ b/doc/src/bond_oxdna.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/bond_quartic.txt b/doc/src/bond_quartic.txt index 760a5d7f07..87a21eff02 100644 --- a/doc/src/bond_quartic.txt +++ b/doc/src/bond_quartic.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/bond_style.txt b/doc/src/bond_style.txt index 3bd8afda19..41fa1cabb2 100644 --- a/doc/src/bond_style.txt +++ b/doc/src/bond_style.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -66,9 +66,8 @@ the style to display the formula it computes and coefficients specified by the associated "bond_coeff"_bond_coeff.html command. Note that there are also additional bond styles submitted by users -which are included in the LAMMPS distribution. The list of these with -links to the individual styles are given in the bond section of "this -page"_Section_commands.html#cmd_5. +which are included in the LAMMPS distribution. The full list of all +bond styles is on the "Commands bond"_Commands_bond.html doc page. "bond_style none"_bond_none.html - turn off bonded interactions "bond_style zero"_bond_zero.html - topology but no interactions diff --git a/doc/src/bond_table.txt b/doc/src/bond_table.txt index fe0b3ce22b..e53cbdfa9f 100644 --- a/doc/src/bond_table.txt +++ b/doc/src/bond_table.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/bond_write.txt b/doc/src/bond_write.txt index 4797d06cb1..711bd2c296 100644 --- a/doc/src/bond_write.txt +++ b/doc/src/bond_write.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/bond_zero.txt b/doc/src/bond_zero.txt index b599f291b4..554f26e7f0 100644 --- a/doc/src/bond_zero.txt +++ b/doc/src/bond_zero.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/boundary.txt b/doc/src/boundary.txt index 7ee897ffa4..f9685433b2 100644 --- a/doc/src/boundary.txt +++ b/doc/src/boundary.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/box.txt b/doc/src/box.txt index 6dc093ad81..38c874fb78 100644 --- a/doc/src/box.txt +++ b/doc/src/box.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/change_box.txt b/doc/src/change_box.txt index 8f3fda263f..adc5d6bdcb 100644 --- a/doc/src/change_box.txt +++ b/doc/src/change_box.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/clear.txt b/doc/src/clear.txt index 7ac4da5c8d..c4ad4c4030 100644 --- a/doc/src/clear.txt +++ b/doc/src/clear.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/comm_modify.txt b/doc/src/comm_modify.txt index 3e8d0eca4f..489278523b 100644 --- a/doc/src/comm_modify.txt +++ b/doc/src/comm_modify.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/comm_style.txt b/doc/src/comm_style.txt index 8248d654d3..39eb1d4ef5 100644 --- a/doc/src/comm_style.txt +++ b/doc/src/comm_style.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute.txt b/doc/src/compute.txt index 105571b82a..7d9e443e7d 100644 --- a/doc/src/compute.txt +++ b/doc/src/compute.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -161,13 +161,19 @@ calculations accessed in the various ways described above. Each compute style has its own doc page which describes its arguments and what it does. Here is an alphabetic list of compute styles -available in LAMMPS. They are also given in more compact form in the -Compute section of "this page"_Section_commands.html#cmd_5. +available in LAMMPS. They are also listed in more compact form on the +"Commands compute"_Commands_compute.html doc page. There are also additional compute styles (not listed here) submitted -by users which are included in the LAMMPS distribution. The list of -these with links to the individual styles are given in the compute -section of "this page"_Section_commands.html#cmd_5. +by users which are included in the LAMMPS distribution. The full list +of all compute styles is on the "Commands +compute"_Commands_compute.html doc page. + +There are also additional accelerated compute styles included in the +LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs. +The individual style names on the "Commands +compute"_Commands_compute.html doc page are followed by one or more of +(g,i,k,o,t) to indicate which accerlerated styles exist. "aggregate/atom"_compute_cluster_atom.html - aggregate ID for each atom "angle/local"_compute_bond_local.html - theta and energy of each angle @@ -243,16 +249,6 @@ section of "this page"_Section_commands.html#cmd_5. "vcm/chunk"_compute_vcm_chunk.html - velocity of center-of-mass for each chunk "voronoi/atom"_compute_voronoi_atom.html - Voronoi volume and neighbors for each atom :ul -There are also additional compute styles submitted by users which are -included in the LAMMPS distribution. The list of these with links to -the individual styles are given in the compute section of "this -page"_Section_commands.html#cmd_5. - -There are also additional accelerated compute styles included in the -LAMMPS distribution for faster performance on CPUs and GPUs. The list -of these with links to the individual styles are given in the pair -section of "this page"_Section_commands.html#cmd_5. - [Restrictions:] none [Related commands:] diff --git a/doc/src/compute_ackland_atom.txt b/doc/src/compute_ackland_atom.txt index e75ad534eb..485c191313 100644 --- a/doc/src/compute_ackland_atom.txt +++ b/doc/src/compute_ackland_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_angle.txt b/doc/src/compute_angle.txt index 1deb3a4b1b..64eb2f4bb1 100644 --- a/doc/src/compute_angle.txt +++ b/doc/src/compute_angle.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_angle_local.txt b/doc/src/compute_angle_local.txt index 487b41eaf3..3a321965ef 100644 --- a/doc/src/compute_angle_local.txt +++ b/doc/src/compute_angle_local.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_angmom_chunk.txt b/doc/src/compute_angmom_chunk.txt index c97af96f49..7e49ff3024 100644 --- a/doc/src/compute_angmom_chunk.txt +++ b/doc/src/compute_angmom_chunk.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_basal_atom.txt b/doc/src/compute_basal_atom.txt index e0ac6b0a60..067a020c35 100644 --- a/doc/src/compute_basal_atom.txt +++ b/doc/src/compute_basal_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_body_local.txt b/doc/src/compute_body_local.txt index f387e61c78..8ac3f00c55 100644 --- a/doc/src/compute_body_local.txt +++ b/doc/src/compute_body_local.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_bond.txt b/doc/src/compute_bond.txt index ac0e50872b..a87c510538 100644 --- a/doc/src/compute_bond.txt +++ b/doc/src/compute_bond.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_bond_local.txt b/doc/src/compute_bond_local.txt index 868b43caa9..c3dc1cc4af 100644 --- a/doc/src/compute_bond_local.txt +++ b/doc/src/compute_bond_local.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_centro_atom.txt b/doc/src/compute_centro_atom.txt index bace0d8739..183537690f 100644 --- a/doc/src/compute_centro_atom.txt +++ b/doc/src/compute_centro_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_chunk_atom.txt b/doc/src/compute_chunk_atom.txt index fc0de28b6a..95e6e6c010 100644 --- a/doc/src/compute_chunk_atom.txt +++ b/doc/src/compute_chunk_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_cluster_atom.txt b/doc/src/compute_cluster_atom.txt index 12ecb8f173..e6138fe1e8 100644 --- a/doc/src/compute_cluster_atom.txt +++ b/doc/src/compute_cluster_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_cna_atom.txt b/doc/src/compute_cna_atom.txt index 9c4814560d..d69c5e9c46 100644 --- a/doc/src/compute_cna_atom.txt +++ b/doc/src/compute_cna_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_cnp_atom.txt b/doc/src/compute_cnp_atom.txt index aca7e351ec..44a77d23ca 100644 --- a/doc/src/compute_cnp_atom.txt +++ b/doc/src/compute_cnp_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_com.txt b/doc/src/compute_com.txt index 08bb08b142..fdc631a263 100644 --- a/doc/src/compute_com.txt +++ b/doc/src/compute_com.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_com_chunk.txt b/doc/src/compute_com_chunk.txt index f28355d6c5..b982f0d901 100644 --- a/doc/src/compute_com_chunk.txt +++ b/doc/src/compute_com_chunk.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_contact_atom.txt b/doc/src/compute_contact_atom.txt index ea4158e3b1..efe524263a 100644 --- a/doc/src/compute_contact_atom.txt +++ b/doc/src/compute_contact_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_coord_atom.txt b/doc/src/compute_coord_atom.txt index 06b565aedc..66eecd195d 100644 --- a/doc/src/compute_coord_atom.txt +++ b/doc/src/compute_coord_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_damage_atom.txt b/doc/src/compute_damage_atom.txt index e262ee0b1f..74939e2280 100644 --- a/doc/src/compute_damage_atom.txt +++ b/doc/src/compute_damage_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_dihedral.txt b/doc/src/compute_dihedral.txt index 67c97b60f1..aa25f9dd10 100644 --- a/doc/src/compute_dihedral.txt +++ b/doc/src/compute_dihedral.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_dihedral_local.txt b/doc/src/compute_dihedral_local.txt index d2051a51bd..77812699d3 100644 --- a/doc/src/compute_dihedral_local.txt +++ b/doc/src/compute_dihedral_local.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_dilatation_atom.txt b/doc/src/compute_dilatation_atom.txt index 161e73c7ff..498110cf99 100644 --- a/doc/src/compute_dilatation_atom.txt +++ b/doc/src/compute_dilatation_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_dipole_chunk.txt b/doc/src/compute_dipole_chunk.txt index 5f8d6689c4..d45fde9af2 100644 --- a/doc/src/compute_dipole_chunk.txt +++ b/doc/src/compute_dipole_chunk.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_displace_atom.txt b/doc/src/compute_displace_atom.txt index 5636cc02f0..669ab9f7ca 100644 --- a/doc/src/compute_displace_atom.txt +++ b/doc/src/compute_displace_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_dpd.txt b/doc/src/compute_dpd.txt index a5620d34b3..1721456e35 100644 --- a/doc/src/compute_dpd.txt +++ b/doc/src/compute_dpd.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_dpd_atom.txt b/doc/src/compute_dpd_atom.txt index ed0fd2410b..8e502d4a60 100644 --- a/doc/src/compute_dpd_atom.txt +++ b/doc/src/compute_dpd_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_edpd_temp_atom.txt b/doc/src/compute_edpd_temp_atom.txt index 9011c3c823..f33398e03d 100644 --- a/doc/src/compute_edpd_temp_atom.txt +++ b/doc/src/compute_edpd_temp_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_entropy_atom.txt b/doc/src/compute_entropy_atom.txt index 7fdc1f4af2..9c45fd2870 100644 --- a/doc/src/compute_entropy_atom.txt +++ b/doc/src/compute_entropy_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_erotate_asphere.txt b/doc/src/compute_erotate_asphere.txt index 24e6e5e6f7..5cdc099782 100644 --- a/doc/src/compute_erotate_asphere.txt +++ b/doc/src/compute_erotate_asphere.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_erotate_rigid.txt b/doc/src/compute_erotate_rigid.txt index c8527d7073..5b9077870e 100644 --- a/doc/src/compute_erotate_rigid.txt +++ b/doc/src/compute_erotate_rigid.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_erotate_sphere.txt b/doc/src/compute_erotate_sphere.txt index 8abc9a53ad..d0c176b50e 100644 --- a/doc/src/compute_erotate_sphere.txt +++ b/doc/src/compute_erotate_sphere.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_erotate_sphere_atom.txt b/doc/src/compute_erotate_sphere_atom.txt index 0bea315a89..fdd609a0e6 100644 --- a/doc/src/compute_erotate_sphere_atom.txt +++ b/doc/src/compute_erotate_sphere_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_event_displace.txt b/doc/src/compute_event_displace.txt index 17c4288911..561ded35c0 100644 --- a/doc/src/compute_event_displace.txt +++ b/doc/src/compute_event_displace.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_fep.txt b/doc/src/compute_fep.txt index f0ce3fd704..8b4a92e16e 100644 --- a/doc/src/compute_fep.txt +++ b/doc/src/compute_fep.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_global_atom.txt b/doc/src/compute_global_atom.txt index f40810b70c..a26dba72b0 100644 --- a/doc/src/compute_global_atom.txt +++ b/doc/src/compute_global_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_group_group.txt b/doc/src/compute_group_group.txt index 8f992791d2..cff3687354 100644 --- a/doc/src/compute_group_group.txt +++ b/doc/src/compute_group_group.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_gyration.txt b/doc/src/compute_gyration.txt index 3d698609ca..4dc883ad0b 100644 --- a/doc/src/compute_gyration.txt +++ b/doc/src/compute_gyration.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_gyration_chunk.txt b/doc/src/compute_gyration_chunk.txt index ef14a456f3..dcbfc65393 100644 --- a/doc/src/compute_gyration_chunk.txt +++ b/doc/src/compute_gyration_chunk.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_heat_flux.txt b/doc/src/compute_heat_flux.txt index 84c4951328..81a2a3f517 100644 --- a/doc/src/compute_heat_flux.txt +++ b/doc/src/compute_heat_flux.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_hexorder_atom.txt b/doc/src/compute_hexorder_atom.txt index 1ab40b513c..082a3cad7a 100644 --- a/doc/src/compute_hexorder_atom.txt +++ b/doc/src/compute_hexorder_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_improper.txt b/doc/src/compute_improper.txt index 61c4f6cd29..867dd48cc1 100644 --- a/doc/src/compute_improper.txt +++ b/doc/src/compute_improper.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_improper_local.txt b/doc/src/compute_improper_local.txt index 2aec554d2f..f340d5a03f 100644 --- a/doc/src/compute_improper_local.txt +++ b/doc/src/compute_improper_local.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_inertia_chunk.txt b/doc/src/compute_inertia_chunk.txt index 3edd25d69b..d6cdb3fe79 100644 --- a/doc/src/compute_inertia_chunk.txt +++ b/doc/src/compute_inertia_chunk.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_ke.txt b/doc/src/compute_ke.txt index d6f4e1b709..64ab83db48 100644 --- a/doc/src/compute_ke.txt +++ b/doc/src/compute_ke.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_ke_atom.txt b/doc/src/compute_ke_atom.txt index e0e96a80d8..d288ab0236 100644 --- a/doc/src/compute_ke_atom.txt +++ b/doc/src/compute_ke_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_ke_atom_eff.txt b/doc/src/compute_ke_atom_eff.txt index aa188a411b..f665f35055 100644 --- a/doc/src/compute_ke_atom_eff.txt +++ b/doc/src/compute_ke_atom_eff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_ke_eff.txt b/doc/src/compute_ke_eff.txt index 334b4121ed..d6d7fdb10f 100644 --- a/doc/src/compute_ke_eff.txt +++ b/doc/src/compute_ke_eff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_ke_rigid.txt b/doc/src/compute_ke_rigid.txt index 69cf4a598e..45ba2673b0 100644 --- a/doc/src/compute_ke_rigid.txt +++ b/doc/src/compute_ke_rigid.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_meso_e_atom.txt b/doc/src/compute_meso_e_atom.txt index 70a8969386..9a9c7fae11 100644 --- a/doc/src/compute_meso_e_atom.txt +++ b/doc/src/compute_meso_e_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_meso_rho_atom.txt b/doc/src/compute_meso_rho_atom.txt index 912587f4a2..30b1142b6c 100644 --- a/doc/src/compute_meso_rho_atom.txt +++ b/doc/src/compute_meso_rho_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_meso_t_atom.txt b/doc/src/compute_meso_t_atom.txt index c9db9bf50e..ab92f05018 100644 --- a/doc/src/compute_meso_t_atom.txt +++ b/doc/src/compute_meso_t_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_modify.txt b/doc/src/compute_modify.txt index 9a2480ec0a..192ea0bc9e 100644 --- a/doc/src/compute_modify.txt +++ b/doc/src/compute_modify.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_msd.txt b/doc/src/compute_msd.txt index 742f7ce113..b54e05bc64 100644 --- a/doc/src/compute_msd.txt +++ b/doc/src/compute_msd.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_msd_chunk.txt b/doc/src/compute_msd_chunk.txt index 3e1d8542ae..264f38d5fd 100644 --- a/doc/src/compute_msd_chunk.txt +++ b/doc/src/compute_msd_chunk.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_msd_nongauss.txt b/doc/src/compute_msd_nongauss.txt index db8788db0b..814159121d 100644 --- a/doc/src/compute_msd_nongauss.txt +++ b/doc/src/compute_msd_nongauss.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_omega_chunk.txt b/doc/src/compute_omega_chunk.txt index 4a7a996d1d..84b25ac6f2 100644 --- a/doc/src/compute_omega_chunk.txt +++ b/doc/src/compute_omega_chunk.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_orientorder_atom.txt b/doc/src/compute_orientorder_atom.txt index a8b4008012..7327a7b1d3 100644 --- a/doc/src/compute_orientorder_atom.txt +++ b/doc/src/compute_orientorder_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_pair.txt b/doc/src/compute_pair.txt index be40d7a550..a2c25fcc8d 100644 --- a/doc/src/compute_pair.txt +++ b/doc/src/compute_pair.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_pair_local.txt b/doc/src/compute_pair_local.txt index bbbc5823f2..7588e92527 100644 --- a/doc/src/compute_pair_local.txt +++ b/doc/src/compute_pair_local.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_pe.txt b/doc/src/compute_pe.txt index f3ce5678b0..37655dfd48 100644 --- a/doc/src/compute_pe.txt +++ b/doc/src/compute_pe.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_pe_atom.txt b/doc/src/compute_pe_atom.txt index e6bc5f9052..400621f8df 100644 --- a/doc/src/compute_pe_atom.txt +++ b/doc/src/compute_pe_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_plasticity_atom.txt b/doc/src/compute_plasticity_atom.txt index c992ca8200..50a51d9937 100644 --- a/doc/src/compute_plasticity_atom.txt +++ b/doc/src/compute_plasticity_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_pressure.txt b/doc/src/compute_pressure.txt index 51d3241ace..dea0a7f05b 100644 --- a/doc/src/compute_pressure.txt +++ b/doc/src/compute_pressure.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_pressure_uef.txt b/doc/src/compute_pressure_uef.txt index 5b252b369d..61cc85ad80 100644 --- a/doc/src/compute_pressure_uef.txt +++ b/doc/src/compute_pressure_uef.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_property_atom.txt b/doc/src/compute_property_atom.txt index 88bdf5a453..512009093c 100644 --- a/doc/src/compute_property_atom.txt +++ b/doc/src/compute_property_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_property_chunk.txt b/doc/src/compute_property_chunk.txt index ad131a8a60..a30b5a1f0a 100644 --- a/doc/src/compute_property_chunk.txt +++ b/doc/src/compute_property_chunk.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_property_local.txt b/doc/src/compute_property_local.txt index 74595f00f6..b0ec088cf7 100644 --- a/doc/src/compute_property_local.txt +++ b/doc/src/compute_property_local.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_rdf.txt b/doc/src/compute_rdf.txt index c2d2c379fe..04b38682cc 100644 --- a/doc/src/compute_rdf.txt +++ b/doc/src/compute_rdf.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_reduce.txt b/doc/src/compute_reduce.txt index 614ef50581..ef3c7c6489 100644 --- a/doc/src/compute_reduce.txt +++ b/doc/src/compute_reduce.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_rigid_local.txt b/doc/src/compute_rigid_local.txt index 380713d091..b5e6954ab9 100644 --- a/doc/src/compute_rigid_local.txt +++ b/doc/src/compute_rigid_local.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_saed.txt b/doc/src/compute_saed.txt index 419ad3c489..8c17a30fca 100644 --- a/doc/src/compute_saed.txt +++ b/doc/src/compute_saed.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_slice.txt b/doc/src/compute_slice.txt index 69eb7976ad..51031aeab3 100644 --- a/doc/src/compute_slice.txt +++ b/doc/src/compute_slice.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_smd_contact_radius.txt b/doc/src/compute_smd_contact_radius.txt index 5e043a1390..cd13816047 100644 --- a/doc/src/compute_smd_contact_radius.txt +++ b/doc/src/compute_smd_contact_radius.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_smd_damage.txt b/doc/src/compute_smd_damage.txt index ea814ba064..afabe23d7c 100644 --- a/doc/src/compute_smd_damage.txt +++ b/doc/src/compute_smd_damage.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_smd_hourglass_error.txt b/doc/src/compute_smd_hourglass_error.txt index 046f7e7f27..13fd20a589 100644 --- a/doc/src/compute_smd_hourglass_error.txt +++ b/doc/src/compute_smd_hourglass_error.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_smd_internal_energy.txt b/doc/src/compute_smd_internal_energy.txt index b88bd8a1ce..6585c3429f 100644 --- a/doc/src/compute_smd_internal_energy.txt +++ b/doc/src/compute_smd_internal_energy.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_smd_plastic_strain.txt b/doc/src/compute_smd_plastic_strain.txt index 7fd083726f..fb3c5c9138 100644 --- a/doc/src/compute_smd_plastic_strain.txt +++ b/doc/src/compute_smd_plastic_strain.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_smd_plastic_strain_rate.txt b/doc/src/compute_smd_plastic_strain_rate.txt index b17684e05e..b913ae9097 100644 --- a/doc/src/compute_smd_plastic_strain_rate.txt +++ b/doc/src/compute_smd_plastic_strain_rate.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_smd_rho.txt b/doc/src/compute_smd_rho.txt index 375513b9c7..a1ee1d9c5b 100644 --- a/doc/src/compute_smd_rho.txt +++ b/doc/src/compute_smd_rho.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_smd_tlsph_defgrad.txt b/doc/src/compute_smd_tlsph_defgrad.txt index d07ff99f07..1663c84f65 100644 --- a/doc/src/compute_smd_tlsph_defgrad.txt +++ b/doc/src/compute_smd_tlsph_defgrad.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_smd_tlsph_dt.txt b/doc/src/compute_smd_tlsph_dt.txt index 798278661a..c714f3266b 100644 --- a/doc/src/compute_smd_tlsph_dt.txt +++ b/doc/src/compute_smd_tlsph_dt.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_smd_tlsph_num_neighs.txt b/doc/src/compute_smd_tlsph_num_neighs.txt index 632ab94208..af5b0741db 100644 --- a/doc/src/compute_smd_tlsph_num_neighs.txt +++ b/doc/src/compute_smd_tlsph_num_neighs.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_smd_tlsph_shape.txt b/doc/src/compute_smd_tlsph_shape.txt index a3daf70222..927cd7c7ae 100644 --- a/doc/src/compute_smd_tlsph_shape.txt +++ b/doc/src/compute_smd_tlsph_shape.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_smd_tlsph_strain.txt b/doc/src/compute_smd_tlsph_strain.txt index 899166359c..4536f26c8e 100644 --- a/doc/src/compute_smd_tlsph_strain.txt +++ b/doc/src/compute_smd_tlsph_strain.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_smd_tlsph_strain_rate.txt b/doc/src/compute_smd_tlsph_strain_rate.txt index 29246a05d9..ae2883e4bb 100644 --- a/doc/src/compute_smd_tlsph_strain_rate.txt +++ b/doc/src/compute_smd_tlsph_strain_rate.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_smd_tlsph_stress.txt b/doc/src/compute_smd_tlsph_stress.txt index c2c23b6836..50d6b7f434 100644 --- a/doc/src/compute_smd_tlsph_stress.txt +++ b/doc/src/compute_smd_tlsph_stress.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_smd_triangle_mesh_vertices.txt b/doc/src/compute_smd_triangle_mesh_vertices.txt index 3080ef700e..9e167924d1 100644 --- a/doc/src/compute_smd_triangle_mesh_vertices.txt +++ b/doc/src/compute_smd_triangle_mesh_vertices.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_smd_ulsph_num_neighs.txt b/doc/src/compute_smd_ulsph_num_neighs.txt index 8550838799..202b8f15e1 100644 --- a/doc/src/compute_smd_ulsph_num_neighs.txt +++ b/doc/src/compute_smd_ulsph_num_neighs.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_smd_ulsph_strain.txt b/doc/src/compute_smd_ulsph_strain.txt index 3813e61f6c..76c47162a5 100644 --- a/doc/src/compute_smd_ulsph_strain.txt +++ b/doc/src/compute_smd_ulsph_strain.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_smd_ulsph_strain_rate.txt b/doc/src/compute_smd_ulsph_strain_rate.txt index 251e5ddbf7..c851e767b3 100644 --- a/doc/src/compute_smd_ulsph_strain_rate.txt +++ b/doc/src/compute_smd_ulsph_strain_rate.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_smd_ulsph_stress.txt b/doc/src/compute_smd_ulsph_stress.txt index 719cf006c9..a5692b2412 100644 --- a/doc/src/compute_smd_ulsph_stress.txt +++ b/doc/src/compute_smd_ulsph_stress.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_smd_vol.txt b/doc/src/compute_smd_vol.txt index 495c09a5f5..fc4871d6f3 100644 --- a/doc/src/compute_smd_vol.txt +++ b/doc/src/compute_smd_vol.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_sna_atom.txt b/doc/src/compute_sna_atom.txt index 6fdd85568b..3b302a0a71 100644 --- a/doc/src/compute_sna_atom.txt +++ b/doc/src/compute_sna_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_spin.txt b/doc/src/compute_spin.txt index fcc764c14c..792706ecdf 100644 --- a/doc/src/compute_spin.txt +++ b/doc/src/compute_spin.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_stress_atom.txt b/doc/src/compute_stress_atom.txt index 423c1dcfda..222513da61 100644 --- a/doc/src/compute_stress_atom.txt +++ b/doc/src/compute_stress_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_tally.txt b/doc/src/compute_tally.txt index 95ef4a553b..23fac43093 100644 --- a/doc/src/compute_tally.txt +++ b/doc/src/compute_tally.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_tdpd_cc_atom.txt b/doc/src/compute_tdpd_cc_atom.txt index ec077a33d1..9ee4d3da34 100644 --- a/doc/src/compute_tdpd_cc_atom.txt +++ b/doc/src/compute_tdpd_cc_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_temp.txt b/doc/src/compute_temp.txt index cce40261c6..9f3a1ca906 100644 --- a/doc/src/compute_temp.txt +++ b/doc/src/compute_temp.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_temp_asphere.txt b/doc/src/compute_temp_asphere.txt index a5fc0e8927..6766729ae0 100644 --- a/doc/src/compute_temp_asphere.txt +++ b/doc/src/compute_temp_asphere.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_temp_body.txt b/doc/src/compute_temp_body.txt index 580564b059..4e3ce3e77f 100644 --- a/doc/src/compute_temp_body.txt +++ b/doc/src/compute_temp_body.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_temp_chunk.txt b/doc/src/compute_temp_chunk.txt index 5d7d64ce68..de8c850a70 100644 --- a/doc/src/compute_temp_chunk.txt +++ b/doc/src/compute_temp_chunk.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_temp_com.txt b/doc/src/compute_temp_com.txt index e8b46aec97..12df694e38 100644 --- a/doc/src/compute_temp_com.txt +++ b/doc/src/compute_temp_com.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_temp_cs.txt b/doc/src/compute_temp_cs.txt index 9d2ceabd46..0236319f54 100644 --- a/doc/src/compute_temp_cs.txt +++ b/doc/src/compute_temp_cs.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_temp_deform.txt b/doc/src/compute_temp_deform.txt index b81d07babd..26d322589e 100644 --- a/doc/src/compute_temp_deform.txt +++ b/doc/src/compute_temp_deform.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_temp_deform_eff.txt b/doc/src/compute_temp_deform_eff.txt index 418180d93c..876d492f34 100644 --- a/doc/src/compute_temp_deform_eff.txt +++ b/doc/src/compute_temp_deform_eff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_temp_drude.txt b/doc/src/compute_temp_drude.txt index 3e86dc8fda..20d9a5c056 100644 --- a/doc/src/compute_temp_drude.txt +++ b/doc/src/compute_temp_drude.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_temp_eff.txt b/doc/src/compute_temp_eff.txt index 42d22a33a7..35ddb75b12 100644 --- a/doc/src/compute_temp_eff.txt +++ b/doc/src/compute_temp_eff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_temp_partial.txt b/doc/src/compute_temp_partial.txt index 0fda274ca0..2769246532 100644 --- a/doc/src/compute_temp_partial.txt +++ b/doc/src/compute_temp_partial.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_temp_profile.txt b/doc/src/compute_temp_profile.txt index 8f47c8f9f4..4ed04ca67e 100644 --- a/doc/src/compute_temp_profile.txt +++ b/doc/src/compute_temp_profile.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_temp_ramp.txt b/doc/src/compute_temp_ramp.txt index 1ae0cdfc3e..15cad9c0cb 100644 --- a/doc/src/compute_temp_ramp.txt +++ b/doc/src/compute_temp_ramp.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_temp_region.txt b/doc/src/compute_temp_region.txt index f05fa38e2c..f23901af98 100644 --- a/doc/src/compute_temp_region.txt +++ b/doc/src/compute_temp_region.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_temp_region_eff.txt b/doc/src/compute_temp_region_eff.txt index 45c01b047f..95892eb257 100644 --- a/doc/src/compute_temp_region_eff.txt +++ b/doc/src/compute_temp_region_eff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_temp_rotate.txt b/doc/src/compute_temp_rotate.txt index 8c5679b83f..189246d3e4 100644 --- a/doc/src/compute_temp_rotate.txt +++ b/doc/src/compute_temp_rotate.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_temp_sphere.txt b/doc/src/compute_temp_sphere.txt index 4d4258182e..5a55126d12 100644 --- a/doc/src/compute_temp_sphere.txt +++ b/doc/src/compute_temp_sphere.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_temp_uef.txt b/doc/src/compute_temp_uef.txt index acd3a6218d..a94d5db8ed 100644 --- a/doc/src/compute_temp_uef.txt +++ b/doc/src/compute_temp_uef.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_ti.txt b/doc/src/compute_ti.txt index f5d26e1a03..e79b594e3f 100644 --- a/doc/src/compute_ti.txt +++ b/doc/src/compute_ti.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_torque_chunk.txt b/doc/src/compute_torque_chunk.txt index 254cd0fd85..6484076b37 100644 --- a/doc/src/compute_torque_chunk.txt +++ b/doc/src/compute_torque_chunk.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_vacf.txt b/doc/src/compute_vacf.txt index d615f70e22..70f1e99490 100644 --- a/doc/src/compute_vacf.txt +++ b/doc/src/compute_vacf.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_vcm_chunk.txt b/doc/src/compute_vcm_chunk.txt index af1a4305d8..7e8ad71208 100644 --- a/doc/src/compute_vcm_chunk.txt +++ b/doc/src/compute_vcm_chunk.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_voronoi_atom.txt b/doc/src/compute_voronoi_atom.txt index bbd68b16ea..a8ce77882a 100644 --- a/doc/src/compute_voronoi_atom.txt +++ b/doc/src/compute_voronoi_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_xrd.txt b/doc/src/compute_xrd.txt index 03fd0ecdc2..609fde3582 100644 --- a/doc/src/compute_xrd.txt +++ b/doc/src/compute_xrd.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/create_atoms.txt b/doc/src/create_atoms.txt index 5d824ae1ef..d80e2d45f1 100644 --- a/doc/src/create_atoms.txt +++ b/doc/src/create_atoms.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/create_bonds.txt b/doc/src/create_bonds.txt index 6700ed29d3..8596cab51d 100644 --- a/doc/src/create_bonds.txt +++ b/doc/src/create_bonds.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/create_box.txt b/doc/src/create_box.txt index ed05775591..0993b4f927 100644 --- a/doc/src/create_box.txt +++ b/doc/src/create_box.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/delete_atoms.txt b/doc/src/delete_atoms.txt index 1aa71d341f..57faf97ad1 100644 --- a/doc/src/delete_atoms.txt +++ b/doc/src/delete_atoms.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/delete_bonds.txt b/doc/src/delete_bonds.txt index b1137a2288..b29fa82f2d 100644 --- a/doc/src/delete_bonds.txt +++ b/doc/src/delete_bonds.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/dielectric.txt b/doc/src/dielectric.txt index e98badf87b..f93be8cc25 100644 --- a/doc/src/dielectric.txt +++ b/doc/src/dielectric.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/dihedral_charmm.txt b/doc/src/dihedral_charmm.txt index f808649a44..8adef6cf4b 100644 --- a/doc/src/dihedral_charmm.txt +++ b/doc/src/dihedral_charmm.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/dihedral_class2.txt b/doc/src/dihedral_class2.txt index 41282b22a3..1a2f37abbb 100644 --- a/doc/src/dihedral_class2.txt +++ b/doc/src/dihedral_class2.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/dihedral_coeff.txt b/doc/src/dihedral_coeff.txt index 5b43cbbe7f..1db69e40d5 100644 --- a/doc/src/dihedral_coeff.txt +++ b/doc/src/dihedral_coeff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -74,9 +74,9 @@ the style to display the formula it computes and coefficients specified by the associated "dihedral_coeff"_dihedral_coeff.html command. Note that there are also additional dihedral styles submitted by users -which are included in the LAMMPS distribution. The list of these with -links to the individual styles are given in the dihedral section of -"this page"_Section_commands.html#cmd_5. +which are included in the LAMMPS distribution. The full list of all +dihedral styles is on the "Commands bond"_Commands_bond.html#dihedral +doc page. "dihedral_style none"_dihedral_none.html - turn off dihedral interactions "dihedral_style hybrid"_dihedral_hybrid.html - define multiple styles of dihedral interactions :ul diff --git a/doc/src/dihedral_cosine_shift_exp.txt b/doc/src/dihedral_cosine_shift_exp.txt index 483745be41..7ef27e6bc9 100644 --- a/doc/src/dihedral_cosine_shift_exp.txt +++ b/doc/src/dihedral_cosine_shift_exp.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/dihedral_fourier.txt b/doc/src/dihedral_fourier.txt index 0270139f68..f51cbc9c8c 100644 --- a/doc/src/dihedral_fourier.txt +++ b/doc/src/dihedral_fourier.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/dihedral_harmonic.txt b/doc/src/dihedral_harmonic.txt index a25a7969fe..1eda0c5d02 100644 --- a/doc/src/dihedral_harmonic.txt +++ b/doc/src/dihedral_harmonic.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/dihedral_helix.txt b/doc/src/dihedral_helix.txt index 814962a472..3af4b410bc 100644 --- a/doc/src/dihedral_helix.txt +++ b/doc/src/dihedral_helix.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/dihedral_hybrid.txt b/doc/src/dihedral_hybrid.txt index 8cb40eff44..c9ca86680c 100644 --- a/doc/src/dihedral_hybrid.txt +++ b/doc/src/dihedral_hybrid.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/dihedral_multi_harmonic.txt b/doc/src/dihedral_multi_harmonic.txt index 62cad4141a..7c22391923 100644 --- a/doc/src/dihedral_multi_harmonic.txt +++ b/doc/src/dihedral_multi_harmonic.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/dihedral_nharmonic.txt b/doc/src/dihedral_nharmonic.txt index a49979fa66..aa8f1e0d7f 100644 --- a/doc/src/dihedral_nharmonic.txt +++ b/doc/src/dihedral_nharmonic.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/dihedral_none.txt b/doc/src/dihedral_none.txt index 3ce2aa1729..4c1ff2ea5d 100644 --- a/doc/src/dihedral_none.txt +++ b/doc/src/dihedral_none.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/dihedral_opls.txt b/doc/src/dihedral_opls.txt index 9b33173da4..f0cf91f30a 100644 --- a/doc/src/dihedral_opls.txt +++ b/doc/src/dihedral_opls.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/dihedral_quadratic.txt b/doc/src/dihedral_quadratic.txt index f90c4b79f1..e65cf2dee8 100644 --- a/doc/src/dihedral_quadratic.txt +++ b/doc/src/dihedral_quadratic.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/dihedral_spherical.txt b/doc/src/dihedral_spherical.txt index 7c17fbf5ef..10a757e898 100644 --- a/doc/src/dihedral_spherical.txt +++ b/doc/src/dihedral_spherical.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/dihedral_style.txt b/doc/src/dihedral_style.txt index ca592b29b5..6aff3f0994 100644 --- a/doc/src/dihedral_style.txt +++ b/doc/src/dihedral_style.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -81,9 +81,9 @@ the style to display the formula it computes and coefficients specified by the associated "dihedral_coeff"_dihedral_coeff.html command. Note that there are also additional dihedral styles submitted by users -which are included in the LAMMPS distribution. The list of these with -links to the individual styles are given in the dihedral section of -"this page"_Section_commands.html#cmd_5. +which are included in the LAMMPS distribution. The full list of all +dihedral styles is on the "Commands bond"_Commands_bond.html#dihedral +doc page. "dihedral_style none"_dihedral_none.html - turn off dihedral interactions "dihedral_style zero"_dihedral_zero.html - topology but no interactions diff --git a/doc/src/dihedral_table.txt b/doc/src/dihedral_table.txt index 6a480fec93..d722ef7c82 100644 --- a/doc/src/dihedral_table.txt +++ b/doc/src/dihedral_table.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/dihedral_table_cut.txt b/doc/src/dihedral_table_cut.txt index 1c83d4ffa0..cc7df8cdf9 100644 --- a/doc/src/dihedral_table_cut.txt +++ b/doc/src/dihedral_table_cut.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/dihedral_zero.txt b/doc/src/dihedral_zero.txt index 4d33126eeb..0c9995a563 100644 --- a/doc/src/dihedral_zero.txt +++ b/doc/src/dihedral_zero.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/dimension.txt b/doc/src/dimension.txt index f079f17f99..b7dde76524 100644 --- a/doc/src/dimension.txt +++ b/doc/src/dimension.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/displace_atoms.txt b/doc/src/displace_atoms.txt index 634add196b..b4afd5c3a9 100644 --- a/doc/src/displace_atoms.txt +++ b/doc/src/displace_atoms.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/dump.txt b/doc/src/dump.txt index cd8bab2e65..5b478b7301 100644 --- a/doc/src/dump.txt +++ b/doc/src/dump.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/dump_cfg_uef.txt b/doc/src/dump_cfg_uef.txt index e257f9c4f1..665be14be1 100644 --- a/doc/src/dump_cfg_uef.txt +++ b/doc/src/dump_cfg_uef.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/dump_h5md.txt b/doc/src/dump_h5md.txt index 93c87d85b7..fbd682dad9 100644 --- a/doc/src/dump_h5md.txt +++ b/doc/src/dump_h5md.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/dump_image.txt b/doc/src/dump_image.txt index fcc9b25b62..06332b5dcf 100644 --- a/doc/src/dump_image.txt +++ b/doc/src/dump_image.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/dump_modify.txt b/doc/src/dump_modify.txt index 5365610d64..73107d07f7 100644 --- a/doc/src/dump_modify.txt +++ b/doc/src/dump_modify.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/dump_molfile.txt b/doc/src/dump_molfile.txt index 7e68490a68..9fa04bd1ae 100644 --- a/doc/src/dump_molfile.txt +++ b/doc/src/dump_molfile.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/dump_netcdf.txt b/doc/src/dump_netcdf.txt index 70111a36a8..b1c6373651 100644 --- a/doc/src/dump_netcdf.txt +++ b/doc/src/dump_netcdf.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/dump_vtk.txt b/doc/src/dump_vtk.txt index d4d28c81fc..afc6099534 100644 --- a/doc/src/dump_vtk.txt +++ b/doc/src/dump_vtk.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/echo.txt b/doc/src/echo.txt index 3141c7a719..dc6918dc89 100644 --- a/doc/src/echo.txt +++ b/doc/src/echo.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix.txt b/doc/src/fix.txt index a51dc1637d..fd966b5bd9 100644 --- a/doc/src/fix.txt +++ b/doc/src/fix.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -151,16 +151,20 @@ for further info. :line -Each fix style has its own documentation page which describes its -arguments and what it does, as listed below. Here is an alphabetic -list of fix styles available in LAMMPS. They are also given in more -compact form in the Fix section of "this -page"_Section_commands.html#cmd_5. +Each fix style has its own doc page which describes its arguments and +what it does, as listed below. Here is an alphabetic list of fix +styles available in LAMMPS. They are also listed in more compact form +on the "Commands fix"_Commands_fix.html doc page. There are also additional fix styles (not listed here) submitted by -users which are included in the LAMMPS distribution. The list of -these with links to the individual styles are given in the fix section -of "this page"_Section_commands.html#cmd_5. +users which are included in the LAMMPS distribution. The full list of +all fix styles is on the "Commands fix"_Commands_fix.html doc page. + +There are also additional accelerated fix styles included in the +LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs. +The individual style names on the "Commands fix"_Commands_fix.html doc +page are followed by one or more of (g,i,k,o,t) to indicate which +accerlerated styles exist. "adapt"_fix_adapt.html - change a simulation parameter over time "addforce"_fix_addforce.html - add a force to each atom diff --git a/doc/src/fix_adapt.txt b/doc/src/fix_adapt.txt index 0764d04e6d..0ca28fb869 100644 --- a/doc/src/fix_adapt.txt +++ b/doc/src/fix_adapt.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_adapt_fep.txt b/doc/src/fix_adapt_fep.txt index 43c87a1601..7e30a1d29d 100644 --- a/doc/src/fix_adapt_fep.txt +++ b/doc/src/fix_adapt_fep.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_addforce.txt b/doc/src/fix_addforce.txt index c77cdb62af..51be39fdb2 100644 --- a/doc/src/fix_addforce.txt +++ b/doc/src/fix_addforce.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_addtorque.txt b/doc/src/fix_addtorque.txt index 589cb37cc0..c80fad26da 100644 --- a/doc/src/fix_addtorque.txt +++ b/doc/src/fix_addtorque.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_append_atoms.txt b/doc/src/fix_append_atoms.txt index ba7b4a3e74..c6af361afc 100644 --- a/doc/src/fix_append_atoms.txt +++ b/doc/src/fix_append_atoms.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_atc.txt b/doc/src/fix_atc.txt index af3270ff52..6de917e571 100644 --- a/doc/src/fix_atc.txt +++ b/doc/src/fix_atc.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_atom_swap.txt b/doc/src/fix_atom_swap.txt index 0b3be3ce5e..c1d84dade1 100644 --- a/doc/src/fix_atom_swap.txt +++ b/doc/src/fix_atom_swap.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_ave_atom.txt b/doc/src/fix_ave_atom.txt index 05bd0f6fa7..10deaf64cd 100644 --- a/doc/src/fix_ave_atom.txt +++ b/doc/src/fix_ave_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_ave_chunk.txt b/doc/src/fix_ave_chunk.txt index e9d0ef7e72..d331e51295 100644 --- a/doc/src/fix_ave_chunk.txt +++ b/doc/src/fix_ave_chunk.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_ave_correlate.txt b/doc/src/fix_ave_correlate.txt index 74ce3f340e..22e8768f1d 100644 --- a/doc/src/fix_ave_correlate.txt +++ b/doc/src/fix_ave_correlate.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_ave_correlate_long.txt b/doc/src/fix_ave_correlate_long.txt index 7b4bc53701..ac0ef873aa 100644 --- a/doc/src/fix_ave_correlate_long.txt +++ b/doc/src/fix_ave_correlate_long.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_ave_histo.txt b/doc/src/fix_ave_histo.txt index e2fd2e04e8..f1da130ff7 100644 --- a/doc/src/fix_ave_histo.txt +++ b/doc/src/fix_ave_histo.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_ave_time.txt b/doc/src/fix_ave_time.txt index e973a36360..a53e318d3f 100644 --- a/doc/src/fix_ave_time.txt +++ b/doc/src/fix_ave_time.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_aveforce.txt b/doc/src/fix_aveforce.txt index 3497b33ef4..1fc7e4a18d 100644 --- a/doc/src/fix_aveforce.txt +++ b/doc/src/fix_aveforce.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_balance.txt b/doc/src/fix_balance.txt index b98fd85c3b..2de17cdd2a 100644 --- a/doc/src/fix_balance.txt +++ b/doc/src/fix_balance.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_bocs.txt b/doc/src/fix_bocs.txt index f53b7c785c..f5bbc8a251 100644 --- a/doc/src/fix_bocs.txt +++ b/doc/src/fix_bocs.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_bond_break.txt b/doc/src/fix_bond_break.txt index b43053c461..bdb2f2a862 100644 --- a/doc/src/fix_bond_break.txt +++ b/doc/src/fix_bond_break.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_bond_create.txt b/doc/src/fix_bond_create.txt index a55ba1ff6e..ab34433cec 100644 --- a/doc/src/fix_bond_create.txt +++ b/doc/src/fix_bond_create.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_bond_react.txt b/doc/src/fix_bond_react.txt index 006f59100f..883968e012 100644 --- a/doc/src/fix_bond_react.txt +++ b/doc/src/fix_bond_react.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_bond_swap.txt b/doc/src/fix_bond_swap.txt index 8d5df7e4e0..a829171f33 100644 --- a/doc/src/fix_bond_swap.txt +++ b/doc/src/fix_bond_swap.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_box_relax.txt b/doc/src/fix_box_relax.txt index a625f0c5b8..8e21ec2c74 100644 --- a/doc/src/fix_box_relax.txt +++ b/doc/src/fix_box_relax.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_cmap.txt b/doc/src/fix_cmap.txt index d352f0e652..6f3769fafe 100644 --- a/doc/src/fix_cmap.txt +++ b/doc/src/fix_cmap.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_colvars.txt b/doc/src/fix_colvars.txt index 2d3000e6ea..4a1d84de64 100644 --- a/doc/src/fix_colvars.txt +++ b/doc/src/fix_colvars.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_controller.txt b/doc/src/fix_controller.txt index 710642c0ea..7458f1bcfa 100644 --- a/doc/src/fix_controller.txt +++ b/doc/src/fix_controller.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_deform.txt b/doc/src/fix_deform.txt index 09261e2423..e92d1e6b19 100644 --- a/doc/src/fix_deform.txt +++ b/doc/src/fix_deform.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_deposit.txt b/doc/src/fix_deposit.txt index 285e720555..277ca8777a 100644 --- a/doc/src/fix_deposit.txt +++ b/doc/src/fix_deposit.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_dpd_energy.txt b/doc/src/fix_dpd_energy.txt index 4f2b5d573f..f539bc534e 100644 --- a/doc/src/fix_dpd_energy.txt +++ b/doc/src/fix_dpd_energy.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_dpd_source.txt b/doc/src/fix_dpd_source.txt index bbfc99e8c8..04af9a28a1 100644 --- a/doc/src/fix_dpd_source.txt +++ b/doc/src/fix_dpd_source.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_drag.txt b/doc/src/fix_drag.txt index a67ec6aaf2..92e68d13a4 100644 --- a/doc/src/fix_drag.txt +++ b/doc/src/fix_drag.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_drude.txt b/doc/src/fix_drude.txt index 4a3d30a9ca..80eb79201b 100644 --- a/doc/src/fix_drude.txt +++ b/doc/src/fix_drude.txt @@ -3,7 +3,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_drude_transform.txt b/doc/src/fix_drude_transform.txt index 54cdfa956e..8864cc4eb6 100644 --- a/doc/src/fix_drude_transform.txt +++ b/doc/src/fix_drude_transform.txt @@ -9,7 +9,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_dt_reset.txt b/doc/src/fix_dt_reset.txt index 428128feda..be4fbd255b 100644 --- a/doc/src/fix_dt_reset.txt +++ b/doc/src/fix_dt_reset.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_efield.txt b/doc/src/fix_efield.txt index a248a03b07..b5a43f68aa 100644 --- a/doc/src/fix_efield.txt +++ b/doc/src/fix_efield.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_ehex.txt b/doc/src/fix_ehex.txt index 40752a811f..cfcc917d01 100644 --- a/doc/src/fix_ehex.txt +++ b/doc/src/fix_ehex.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_enforce2d.txt b/doc/src/fix_enforce2d.txt index b0d8c691b5..2925e44bda 100644 --- a/doc/src/fix_enforce2d.txt +++ b/doc/src/fix_enforce2d.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_eos_cv.txt b/doc/src/fix_eos_cv.txt index 4c97304335..b94e2c64a9 100644 --- a/doc/src/fix_eos_cv.txt +++ b/doc/src/fix_eos_cv.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_eos_table.txt b/doc/src/fix_eos_table.txt index 42778d7978..743c51f415 100644 --- a/doc/src/fix_eos_table.txt +++ b/doc/src/fix_eos_table.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_eos_table_rx.txt b/doc/src/fix_eos_table_rx.txt index f74a838c47..f9deab61c8 100644 --- a/doc/src/fix_eos_table_rx.txt +++ b/doc/src/fix_eos_table_rx.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_evaporate.txt b/doc/src/fix_evaporate.txt index be8b351986..6237a137fd 100644 --- a/doc/src/fix_evaporate.txt +++ b/doc/src/fix_evaporate.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_external.txt b/doc/src/fix_external.txt index bf80b1b231..1dec226414 100644 --- a/doc/src/fix_external.txt +++ b/doc/src/fix_external.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_filter_corotate.txt b/doc/src/fix_filter_corotate.txt index a75a3b7b44..d1e5e12f3e 100644 --- a/doc/src/fix_filter_corotate.txt +++ b/doc/src/fix_filter_corotate.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_flow_gauss.txt b/doc/src/fix_flow_gauss.txt index 0980076062..843c2a66a5 100644 --- a/doc/src/fix_flow_gauss.txt +++ b/doc/src/fix_flow_gauss.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_freeze.txt b/doc/src/fix_freeze.txt index 43714df802..76a9fd3b1a 100644 --- a/doc/src/fix_freeze.txt +++ b/doc/src/fix_freeze.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_gcmc.txt b/doc/src/fix_gcmc.txt index 9630d856be..394690ea5d 100644 --- a/doc/src/fix_gcmc.txt +++ b/doc/src/fix_gcmc.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_gld.txt b/doc/src/fix_gld.txt index 06ac5d68cb..1c5db6157d 100644 --- a/doc/src/fix_gld.txt +++ b/doc/src/fix_gld.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_gle.txt b/doc/src/fix_gle.txt index d91dd8dee9..9fdc72bf9f 100644 --- a/doc/src/fix_gle.txt +++ b/doc/src/fix_gle.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_gravity.txt b/doc/src/fix_gravity.txt index 786f145608..832c677f81 100644 --- a/doc/src/fix_gravity.txt +++ b/doc/src/fix_gravity.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_grem.txt b/doc/src/fix_grem.txt index 661f68ed99..506e266505 100644 --- a/doc/src/fix_grem.txt +++ b/doc/src/fix_grem.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_halt.txt b/doc/src/fix_halt.txt index 55f313e40f..ec117518d2 100644 --- a/doc/src/fix_halt.txt +++ b/doc/src/fix_halt.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_heat.txt b/doc/src/fix_heat.txt index a0e9b945fc..6db7592609 100644 --- a/doc/src/fix_heat.txt +++ b/doc/src/fix_heat.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_imd.txt b/doc/src/fix_imd.txt index 1a1f11c2cf..8e21a1619b 100644 --- a/doc/src/fix_imd.txt +++ b/doc/src/fix_imd.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_indent.txt b/doc/src/fix_indent.txt index 1f67c0b242..9931793c0b 100644 --- a/doc/src/fix_indent.txt +++ b/doc/src/fix_indent.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_ipi.txt b/doc/src/fix_ipi.txt index 07e8025d77..eba30ef088 100644 --- a/doc/src/fix_ipi.txt +++ b/doc/src/fix_ipi.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_langevin.txt b/doc/src/fix_langevin.txt index 769b188604..4d7728cdba 100644 --- a/doc/src/fix_langevin.txt +++ b/doc/src/fix_langevin.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_langevin_drude.txt b/doc/src/fix_langevin_drude.txt index bda8ec7881..19a3f87ffc 100644 --- a/doc/src/fix_langevin_drude.txt +++ b/doc/src/fix_langevin_drude.txt @@ -9,7 +9,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_langevin_eff.txt b/doc/src/fix_langevin_eff.txt index ef22e99bcf..cf42f9c036 100644 --- a/doc/src/fix_langevin_eff.txt +++ b/doc/src/fix_langevin_eff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_langevin_spin.txt b/doc/src/fix_langevin_spin.txt index b089cd7f58..1b1936376d 100644 --- a/doc/src/fix_langevin_spin.txt +++ b/doc/src/fix_langevin_spin.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_latte.txt b/doc/src/fix_latte.txt index 4f7e99dea8..9bc589520b 100644 --- a/doc/src/fix_latte.txt +++ b/doc/src/fix_latte.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_lb_fluid.txt b/doc/src/fix_lb_fluid.txt index 925ca991c4..5347f0147f 100644 --- a/doc/src/fix_lb_fluid.txt +++ b/doc/src/fix_lb_fluid.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_lb_momentum.txt b/doc/src/fix_lb_momentum.txt index 78a1f497eb..a58c5d257e 100644 --- a/doc/src/fix_lb_momentum.txt +++ b/doc/src/fix_lb_momentum.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_lb_pc.txt b/doc/src/fix_lb_pc.txt index f93d02f677..bd121b7813 100644 --- a/doc/src/fix_lb_pc.txt +++ b/doc/src/fix_lb_pc.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_lb_rigid_pc_sphere.txt b/doc/src/fix_lb_rigid_pc_sphere.txt index 50e91df849..bc8fa2ea25 100644 --- a/doc/src/fix_lb_rigid_pc_sphere.txt +++ b/doc/src/fix_lb_rigid_pc_sphere.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_lb_viscous.txt b/doc/src/fix_lb_viscous.txt index 27f089496e..7bbdd204e3 100644 --- a/doc/src/fix_lb_viscous.txt +++ b/doc/src/fix_lb_viscous.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_lineforce.txt b/doc/src/fix_lineforce.txt index ad651862f6..3114ed6250 100644 --- a/doc/src/fix_lineforce.txt +++ b/doc/src/fix_lineforce.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_manifoldforce.txt b/doc/src/fix_manifoldforce.txt index fe8a04051b..aa32a875bf 100644 --- a/doc/src/fix_manifoldforce.txt +++ b/doc/src/fix_manifoldforce.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_meso.txt b/doc/src/fix_meso.txt index 95f58bedaa..8f5ad29929 100644 --- a/doc/src/fix_meso.txt +++ b/doc/src/fix_meso.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_meso_stationary.txt b/doc/src/fix_meso_stationary.txt index 3b197c079f..38d26b34d6 100644 --- a/doc/src/fix_meso_stationary.txt +++ b/doc/src/fix_meso_stationary.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_modify.txt b/doc/src/fix_modify.txt index 308bba1ac3..ddb5f9a4cd 100644 --- a/doc/src/fix_modify.txt +++ b/doc/src/fix_modify.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_momentum.txt b/doc/src/fix_momentum.txt index 28fd2addf2..f7fe35be2a 100644 --- a/doc/src/fix_momentum.txt +++ b/doc/src/fix_momentum.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_move.txt b/doc/src/fix_move.txt index 9a1d25b623..08f38d0ed6 100644 --- a/doc/src/fix_move.txt +++ b/doc/src/fix_move.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_mscg.txt b/doc/src/fix_mscg.txt index 7d16967955..aadc3caf5a 100644 --- a/doc/src/fix_mscg.txt +++ b/doc/src/fix_mscg.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_msst.txt b/doc/src/fix_msst.txt index d79b549580..91ffbbb0fa 100644 --- a/doc/src/fix_msst.txt +++ b/doc/src/fix_msst.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_mvv_dpd.txt b/doc/src/fix_mvv_dpd.txt index 7a07642c54..1e9bf631fd 100644 --- a/doc/src/fix_mvv_dpd.txt +++ b/doc/src/fix_mvv_dpd.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_neb.txt b/doc/src/fix_neb.txt index 5cfefbf819..5341d6999c 100644 --- a/doc/src/fix_neb.txt +++ b/doc/src/fix_neb.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_nh.txt b/doc/src/fix_nh.txt index d18f4a3e16..f6b155e2db 100644 --- a/doc/src/fix_nh.txt +++ b/doc/src/fix_nh.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_nh_eff.txt b/doc/src/fix_nh_eff.txt index 1731f1f331..afb319bfa5 100644 --- a/doc/src/fix_nh_eff.txt +++ b/doc/src/fix_nh_eff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_nh_uef.txt b/doc/src/fix_nh_uef.txt index bde1818371..0e73c57e08 100644 --- a/doc/src/fix_nh_uef.txt +++ b/doc/src/fix_nh_uef.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_nph_asphere.txt b/doc/src/fix_nph_asphere.txt index ff8c300c47..6bfd9d3fe2 100644 --- a/doc/src/fix_nph_asphere.txt +++ b/doc/src/fix_nph_asphere.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_nph_body.txt b/doc/src/fix_nph_body.txt index 9263470e9e..377e1980eb 100644 --- a/doc/src/fix_nph_body.txt +++ b/doc/src/fix_nph_body.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_nph_sphere.txt b/doc/src/fix_nph_sphere.txt index ba3b2f6c06..8b7639c4c6 100644 --- a/doc/src/fix_nph_sphere.txt +++ b/doc/src/fix_nph_sphere.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_nphug.txt b/doc/src/fix_nphug.txt index 1276a5697d..0bd5153152 100644 --- a/doc/src/fix_nphug.txt +++ b/doc/src/fix_nphug.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_npt_asphere.txt b/doc/src/fix_npt_asphere.txt index a21caa1042..9c95a80d33 100644 --- a/doc/src/fix_npt_asphere.txt +++ b/doc/src/fix_npt_asphere.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_npt_body.txt b/doc/src/fix_npt_body.txt index 0f678a1b7d..0d2b797299 100644 --- a/doc/src/fix_npt_body.txt +++ b/doc/src/fix_npt_body.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_npt_sphere.txt b/doc/src/fix_npt_sphere.txt index 862f95603f..dcb25d1c73 100644 --- a/doc/src/fix_npt_sphere.txt +++ b/doc/src/fix_npt_sphere.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_nve.txt b/doc/src/fix_nve.txt index 8aa4197a60..e446b27397 100644 --- a/doc/src/fix_nve.txt +++ b/doc/src/fix_nve.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_nve_asphere.txt b/doc/src/fix_nve_asphere.txt index b9ee48f9dd..b7fb3e922c 100644 --- a/doc/src/fix_nve_asphere.txt +++ b/doc/src/fix_nve_asphere.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_nve_asphere_noforce.txt b/doc/src/fix_nve_asphere_noforce.txt index 164e3db104..e57417bda5 100644 --- a/doc/src/fix_nve_asphere_noforce.txt +++ b/doc/src/fix_nve_asphere_noforce.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_nve_body.txt b/doc/src/fix_nve_body.txt index 3696425374..d072bfa161 100644 --- a/doc/src/fix_nve_body.txt +++ b/doc/src/fix_nve_body.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_nve_dot.txt b/doc/src/fix_nve_dot.txt index 0e0c8f8ecf..1041a248d8 100644 --- a/doc/src/fix_nve_dot.txt +++ b/doc/src/fix_nve_dot.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_nve_dotc_langevin.txt b/doc/src/fix_nve_dotc_langevin.txt index 93d875bca5..68c1b42328 100644 --- a/doc/src/fix_nve_dotc_langevin.txt +++ b/doc/src/fix_nve_dotc_langevin.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_nve_eff.txt b/doc/src/fix_nve_eff.txt index 608e5e12ad..7343ddc429 100644 --- a/doc/src/fix_nve_eff.txt +++ b/doc/src/fix_nve_eff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_nve_limit.txt b/doc/src/fix_nve_limit.txt index ffaffd59b7..8c8c66a0da 100644 --- a/doc/src/fix_nve_limit.txt +++ b/doc/src/fix_nve_limit.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_nve_line.txt b/doc/src/fix_nve_line.txt index a919e648e1..dd5101489b 100644 --- a/doc/src/fix_nve_line.txt +++ b/doc/src/fix_nve_line.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_nve_manifold_rattle.txt b/doc/src/fix_nve_manifold_rattle.txt index 89922ea80d..b333d093fb 100644 --- a/doc/src/fix_nve_manifold_rattle.txt +++ b/doc/src/fix_nve_manifold_rattle.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_nve_noforce.txt b/doc/src/fix_nve_noforce.txt index c1a4f76eaf..da8d16bbb7 100644 --- a/doc/src/fix_nve_noforce.txt +++ b/doc/src/fix_nve_noforce.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_nve_sphere.txt b/doc/src/fix_nve_sphere.txt index 36c4178de9..6e259bdb8e 100644 --- a/doc/src/fix_nve_sphere.txt +++ b/doc/src/fix_nve_sphere.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_nve_spin.txt b/doc/src/fix_nve_spin.txt index f4b38c270b..e31185bc88 100644 --- a/doc/src/fix_nve_spin.txt +++ b/doc/src/fix_nve_spin.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_nve_tri.txt b/doc/src/fix_nve_tri.txt index 9c03eb872a..ebdda19e36 100644 --- a/doc/src/fix_nve_tri.txt +++ b/doc/src/fix_nve_tri.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_nvk.txt b/doc/src/fix_nvk.txt index 2106ee5235..e3189f8e8a 100644 --- a/doc/src/fix_nvk.txt +++ b/doc/src/fix_nvk.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_nvt_asphere.txt b/doc/src/fix_nvt_asphere.txt index 031c60e4be..7b97637175 100644 --- a/doc/src/fix_nvt_asphere.txt +++ b/doc/src/fix_nvt_asphere.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_nvt_body.txt b/doc/src/fix_nvt_body.txt index 80de7fd7c3..4493a89277 100644 --- a/doc/src/fix_nvt_body.txt +++ b/doc/src/fix_nvt_body.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_nvt_manifold_rattle.txt b/doc/src/fix_nvt_manifold_rattle.txt index 4261f9a4db..1b4ad79166 100644 --- a/doc/src/fix_nvt_manifold_rattle.txt +++ b/doc/src/fix_nvt_manifold_rattle.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_nvt_sllod.txt b/doc/src/fix_nvt_sllod.txt index bb3c092939..9eb5065369 100644 --- a/doc/src/fix_nvt_sllod.txt +++ b/doc/src/fix_nvt_sllod.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_nvt_sllod_eff.txt b/doc/src/fix_nvt_sllod_eff.txt index 408eb1da01..0200d5cb00 100644 --- a/doc/src/fix_nvt_sllod_eff.txt +++ b/doc/src/fix_nvt_sllod_eff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_nvt_sphere.txt b/doc/src/fix_nvt_sphere.txt index 897d5606d7..a87e4abe67 100644 --- a/doc/src/fix_nvt_sphere.txt +++ b/doc/src/fix_nvt_sphere.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_oneway.txt b/doc/src/fix_oneway.txt index d9217ab14b..433ceb50f2 100644 --- a/doc/src/fix_oneway.txt +++ b/doc/src/fix_oneway.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_orient.txt b/doc/src/fix_orient.txt index c57cccd322..7552bea8c5 100644 --- a/doc/src/fix_orient.txt +++ b/doc/src/fix_orient.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_phonon.txt b/doc/src/fix_phonon.txt index 63df4e6801..30e5864e3d 100644 --- a/doc/src/fix_phonon.txt +++ b/doc/src/fix_phonon.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_pimd.txt b/doc/src/fix_pimd.txt index 8958063d2e..b61b3f3065 100644 --- a/doc/src/fix_pimd.txt +++ b/doc/src/fix_pimd.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_planeforce.txt b/doc/src/fix_planeforce.txt index 4a74301066..ffe1952e31 100644 --- a/doc/src/fix_planeforce.txt +++ b/doc/src/fix_planeforce.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_poems.txt b/doc/src/fix_poems.txt index 0690923b45..1a79c2a048 100644 --- a/doc/src/fix_poems.txt +++ b/doc/src/fix_poems.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_pour.txt b/doc/src/fix_pour.txt index 4b86405522..e58d8ebc3a 100644 --- a/doc/src/fix_pour.txt +++ b/doc/src/fix_pour.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_precession_spin.txt b/doc/src/fix_precession_spin.txt index bc18fa0e8c..fafe78448b 100644 --- a/doc/src/fix_precession_spin.txt +++ b/doc/src/fix_precession_spin.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_press_berendsen.txt b/doc/src/fix_press_berendsen.txt index 0e41abd1f8..7f47a29ba3 100644 --- a/doc/src/fix_press_berendsen.txt +++ b/doc/src/fix_press_berendsen.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_print.txt b/doc/src/fix_print.txt index f7a7b333c4..d23c1103d3 100644 --- a/doc/src/fix_print.txt +++ b/doc/src/fix_print.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_property_atom.txt b/doc/src/fix_property_atom.txt index 624fc5f7df..136ed6c15e 100644 --- a/doc/src/fix_property_atom.txt +++ b/doc/src/fix_property_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_python_invoke.txt b/doc/src/fix_python_invoke.txt index 787940d9eb..5e0c0369a5 100644 --- a/doc/src/fix_python_invoke.txt +++ b/doc/src/fix_python_invoke.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_python_move.txt b/doc/src/fix_python_move.txt index 2f49427a9e..a4e0eb3937 100644 --- a/doc/src/fix_python_move.txt +++ b/doc/src/fix_python_move.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_qbmsst.txt b/doc/src/fix_qbmsst.txt index 56ace85e57..e96bd97f45 100644 --- a/doc/src/fix_qbmsst.txt +++ b/doc/src/fix_qbmsst.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_qeq.txt b/doc/src/fix_qeq.txt index c142d4a06d..27fb613ef9 100644 --- a/doc/src/fix_qeq.txt +++ b/doc/src/fix_qeq.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_qeq_comb.txt b/doc/src/fix_qeq_comb.txt index 0eb38fcae6..99e86df030 100644 --- a/doc/src/fix_qeq_comb.txt +++ b/doc/src/fix_qeq_comb.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_qeq_reax.txt b/doc/src/fix_qeq_reax.txt index ea25ddbf57..cf16daf847 100644 --- a/doc/src/fix_qeq_reax.txt +++ b/doc/src/fix_qeq_reax.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_qmmm.txt b/doc/src/fix_qmmm.txt index 5e730ac8af..657ee84181 100644 --- a/doc/src/fix_qmmm.txt +++ b/doc/src/fix_qmmm.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_qtb.txt b/doc/src/fix_qtb.txt index 07a6af39ba..5b212934a9 100644 --- a/doc/src/fix_qtb.txt +++ b/doc/src/fix_qtb.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_reax_bonds.txt b/doc/src/fix_reax_bonds.txt index 2f7c38f815..49d61f4db8 100644 --- a/doc/src/fix_reax_bonds.txt +++ b/doc/src/fix_reax_bonds.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_reaxc_species.txt b/doc/src/fix_reaxc_species.txt index 4f1249744f..5be1c46230 100644 --- a/doc/src/fix_reaxc_species.txt +++ b/doc/src/fix_reaxc_species.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_recenter.txt b/doc/src/fix_recenter.txt index a2477d11c7..cfac756cd1 100644 --- a/doc/src/fix_recenter.txt +++ b/doc/src/fix_recenter.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_restrain.txt b/doc/src/fix_restrain.txt index b8cc7c0d45..2edc7e3296 100644 --- a/doc/src/fix_restrain.txt +++ b/doc/src/fix_restrain.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_rhok.txt b/doc/src/fix_rhok.txt index 2db920ac4b..68cce694e9 100644 --- a/doc/src/fix_rhok.txt +++ b/doc/src/fix_rhok.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_rigid.txt b/doc/src/fix_rigid.txt index a5f00c16e9..d5e3b01668 100644 --- a/doc/src/fix_rigid.txt +++ b/doc/src/fix_rigid.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_rx.txt b/doc/src/fix_rx.txt index aff3303f43..d39e41e922 100644 --- a/doc/src/fix_rx.txt +++ b/doc/src/fix_rx.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_saed_vtk.txt b/doc/src/fix_saed_vtk.txt index 814e17b8e9..60708cd696 100644 --- a/doc/src/fix_saed_vtk.txt +++ b/doc/src/fix_saed_vtk.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_setforce.txt b/doc/src/fix_setforce.txt index c6a01e5492..14fceb7b49 100644 --- a/doc/src/fix_setforce.txt +++ b/doc/src/fix_setforce.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_shake.txt b/doc/src/fix_shake.txt index 9297bcc87a..ea38de41cd 100644 --- a/doc/src/fix_shake.txt +++ b/doc/src/fix_shake.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_shardlow.txt b/doc/src/fix_shardlow.txt index 6d14346334..33db2bf7cc 100644 --- a/doc/src/fix_shardlow.txt +++ b/doc/src/fix_shardlow.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_smd.txt b/doc/src/fix_smd.txt index e9403b22cc..2f083dafc3 100644 --- a/doc/src/fix_smd.txt +++ b/doc/src/fix_smd.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_smd_adjust_dt.txt b/doc/src/fix_smd_adjust_dt.txt index 86b7363300..740b10559d 100644 --- a/doc/src/fix_smd_adjust_dt.txt +++ b/doc/src/fix_smd_adjust_dt.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_smd_integrate_tlsph.txt b/doc/src/fix_smd_integrate_tlsph.txt index 17c9c0f400..cd676a51ce 100644 --- a/doc/src/fix_smd_integrate_tlsph.txt +++ b/doc/src/fix_smd_integrate_tlsph.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_smd_integrate_ulsph.txt b/doc/src/fix_smd_integrate_ulsph.txt index 28e38c7f97..7f16b4b7ce 100644 --- a/doc/src/fix_smd_integrate_ulsph.txt +++ b/doc/src/fix_smd_integrate_ulsph.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_smd_move_triangulated_surface.txt b/doc/src/fix_smd_move_triangulated_surface.txt index 2cba001267..aeabf18768 100644 --- a/doc/src/fix_smd_move_triangulated_surface.txt +++ b/doc/src/fix_smd_move_triangulated_surface.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_smd_setvel.txt b/doc/src/fix_smd_setvel.txt index d64726d9b3..6634751d6a 100644 --- a/doc/src/fix_smd_setvel.txt +++ b/doc/src/fix_smd_setvel.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_smd_wall_surface.txt b/doc/src/fix_smd_wall_surface.txt index feb65b2312..a19b2c4cfb 100644 --- a/doc/src/fix_smd_wall_surface.txt +++ b/doc/src/fix_smd_wall_surface.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_spring.txt b/doc/src/fix_spring.txt index 047e5a6797..690fc3e67c 100644 --- a/doc/src/fix_spring.txt +++ b/doc/src/fix_spring.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_spring_chunk.txt b/doc/src/fix_spring_chunk.txt index e46f299771..9d4e8afd09 100644 --- a/doc/src/fix_spring_chunk.txt +++ b/doc/src/fix_spring_chunk.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_spring_rg.txt b/doc/src/fix_spring_rg.txt index 4afdc02d5a..b252163958 100644 --- a/doc/src/fix_spring_rg.txt +++ b/doc/src/fix_spring_rg.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_spring_self.txt b/doc/src/fix_spring_self.txt index e5b5c3dfd0..0ac1d5eecb 100644 --- a/doc/src/fix_spring_self.txt +++ b/doc/src/fix_spring_self.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_srd.txt b/doc/src/fix_srd.txt index 7c5179fb3f..893557b9ac 100644 --- a/doc/src/fix_srd.txt +++ b/doc/src/fix_srd.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_store_force.txt b/doc/src/fix_store_force.txt index 93437c85b6..33ebc962d5 100644 --- a/doc/src/fix_store_force.txt +++ b/doc/src/fix_store_force.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_store_state.txt b/doc/src/fix_store_state.txt index dee8070bbd..df05adc5b9 100644 --- a/doc/src/fix_store_state.txt +++ b/doc/src/fix_store_state.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_surface_global.txt b/doc/src/fix_surface_global.txt index b470babab7..ade64d2056 100644 --- a/doc/src/fix_surface_global.txt +++ b/doc/src/fix_surface_global.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_temp_berendsen.txt b/doc/src/fix_temp_berendsen.txt index 9092bbd30e..c1f1626782 100644 --- a/doc/src/fix_temp_berendsen.txt +++ b/doc/src/fix_temp_berendsen.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_temp_csvr.txt b/doc/src/fix_temp_csvr.txt index 6ce6ad7d9d..e50f821bfe 100644 --- a/doc/src/fix_temp_csvr.txt +++ b/doc/src/fix_temp_csvr.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_temp_rescale.txt b/doc/src/fix_temp_rescale.txt index 89f1777e36..5640317f1c 100644 --- a/doc/src/fix_temp_rescale.txt +++ b/doc/src/fix_temp_rescale.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_temp_rescale_eff.txt b/doc/src/fix_temp_rescale_eff.txt index 8a79dc3275..0e08e4f1e8 100644 --- a/doc/src/fix_temp_rescale_eff.txt +++ b/doc/src/fix_temp_rescale_eff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_tfmc.txt b/doc/src/fix_tfmc.txt index 3c81d62ee0..ddfa462619 100644 --- a/doc/src/fix_tfmc.txt +++ b/doc/src/fix_tfmc.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_thermal_conductivity.txt b/doc/src/fix_thermal_conductivity.txt index 2e10a89738..86fc6f2c72 100644 --- a/doc/src/fix_thermal_conductivity.txt +++ b/doc/src/fix_thermal_conductivity.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_ti_spring.txt b/doc/src/fix_ti_spring.txt index b116d8e8a3..afe5373220 100644 --- a/doc/src/fix_ti_spring.txt +++ b/doc/src/fix_ti_spring.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_tmd.txt b/doc/src/fix_tmd.txt index e1815e61d3..c2541692f5 100644 --- a/doc/src/fix_tmd.txt +++ b/doc/src/fix_tmd.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_ttm.txt b/doc/src/fix_ttm.txt index d83118d427..6001def581 100644 --- a/doc/src/fix_ttm.txt +++ b/doc/src/fix_ttm.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_tune_kspace.txt b/doc/src/fix_tune_kspace.txt index 60a34a26c9..b4e8472591 100644 --- a/doc/src/fix_tune_kspace.txt +++ b/doc/src/fix_tune_kspace.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_vector.txt b/doc/src/fix_vector.txt index 69c999fd1a..e1bfbe5738 100644 --- a/doc/src/fix_vector.txt +++ b/doc/src/fix_vector.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_viscosity.txt b/doc/src/fix_viscosity.txt index 8d73deb7c5..934da3efdd 100644 --- a/doc/src/fix_viscosity.txt +++ b/doc/src/fix_viscosity.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_viscous.txt b/doc/src/fix_viscous.txt index 7ff517aec1..c5a3ede0b2 100644 --- a/doc/src/fix_viscous.txt +++ b/doc/src/fix_viscous.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_wall.txt b/doc/src/fix_wall.txt index fcd920934f..2ac59d9588 100644 --- a/doc/src/fix_wall.txt +++ b/doc/src/fix_wall.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_wall_body_polygon.txt b/doc/src/fix_wall_body_polygon.txt index ebd25c2bbc..0946a85131 100644 --- a/doc/src/fix_wall_body_polygon.txt +++ b/doc/src/fix_wall_body_polygon.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_wall_body_polyhedron.txt b/doc/src/fix_wall_body_polyhedron.txt index d3d8bc35a3..407cf9fb33 100644 --- a/doc/src/fix_wall_body_polyhedron.txt +++ b/doc/src/fix_wall_body_polyhedron.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_wall_ees.txt b/doc/src/fix_wall_ees.txt index f141a19405..ae16ca40d2 100644 --- a/doc/src/fix_wall_ees.txt +++ b/doc/src/fix_wall_ees.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_wall_gran.txt b/doc/src/fix_wall_gran.txt index 9796c39459..6c2769fc12 100644 --- a/doc/src/fix_wall_gran.txt +++ b/doc/src/fix_wall_gran.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_wall_gran_region.txt b/doc/src/fix_wall_gran_region.txt index 908bcc3941..187214c1a3 100644 --- a/doc/src/fix_wall_gran_region.txt +++ b/doc/src/fix_wall_gran_region.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_wall_piston.txt b/doc/src/fix_wall_piston.txt index 26018329eb..eecf69ebf2 100644 --- a/doc/src/fix_wall_piston.txt +++ b/doc/src/fix_wall_piston.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_wall_reflect.txt b/doc/src/fix_wall_reflect.txt index 2956046e20..78be84eb63 100644 --- a/doc/src/fix_wall_reflect.txt +++ b/doc/src/fix_wall_reflect.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_wall_region.txt b/doc/src/fix_wall_region.txt index 8b3b3ff173..559a2f0d89 100644 --- a/doc/src/fix_wall_region.txt +++ b/doc/src/fix_wall_region.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_wall_srd.txt b/doc/src/fix_wall_srd.txt index 3a8c2e41cd..3a50c45ab7 100644 --- a/doc/src/fix_wall_srd.txt +++ b/doc/src/fix_wall_srd.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/group.txt b/doc/src/group.txt index dddb0459e3..8472677372 100644 --- a/doc/src/group.txt +++ b/doc/src/group.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/group2ndx.txt b/doc/src/group2ndx.txt index 94d188399b..242d6a69a4 100644 --- a/doc/src/group2ndx.txt +++ b/doc/src/group2ndx.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/if.txt b/doc/src/if.txt index 52fad5aea7..513e451034 100644 --- a/doc/src/if.txt +++ b/doc/src/if.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -65,9 +65,9 @@ above. NOTE: If a command itself requires a quoted argument (e.g. a "print"_print.html command), then double and single quotes can be used and nested in the usual manner, as in the examples above and below. -See "Section 3.2"_Section_commands.html#cmd_2 of the manual for -more details on using quotes in arguments. Only one of level of -nesting is allowed, but that should be sufficient for most use cases. +The "Commands parse"_Commands_parse.html doc page has more details on +using quotes in arguments. Only one of level of nesting is allowed, +but that should be sufficient for most use cases. Note that by using the line continuation character "&", the if command can be spread across many lines, though it is still a single command: diff --git a/doc/src/improper_class2.txt b/doc/src/improper_class2.txt index ef2abf5091..c38f73c64d 100644 --- a/doc/src/improper_class2.txt +++ b/doc/src/improper_class2.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/improper_coeff.txt b/doc/src/improper_coeff.txt index 5c01a23ae9..8ed65f9535 100644 --- a/doc/src/improper_coeff.txt +++ b/doc/src/improper_coeff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -67,9 +67,9 @@ the style to display the formula it computes and coefficients specified by the associated "improper_coeff"_improper_coeff.html command. Note that there are also additional improper styles submitted by users -which are included in the LAMMPS distribution. The list of these with -links to the individual styles are given in the improper section of -"this page"_Section_commands.html#cmd_5. +which are included in the LAMMPS distribution. The full list of all +improper styles is on the "Commands bond"_Commands_bond.html#improper +doc page. "improper_style none"_improper_none.html - turn off improper interactions "improper_style hybrid"_improper_hybrid.html - define multiple styles of improper interactions :ul diff --git a/doc/src/improper_cossq.txt b/doc/src/improper_cossq.txt index 22ba990ba4..04aa45255c 100644 --- a/doc/src/improper_cossq.txt +++ b/doc/src/improper_cossq.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/improper_cvff.txt b/doc/src/improper_cvff.txt index 1662d93b14..d01faf2885 100644 --- a/doc/src/improper_cvff.txt +++ b/doc/src/improper_cvff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/improper_distance.txt b/doc/src/improper_distance.txt index 7d49d17c97..93235fe601 100644 --- a/doc/src/improper_distance.txt +++ b/doc/src/improper_distance.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/improper_fourier.txt b/doc/src/improper_fourier.txt index 99132b8931..78cc1b3f76 100644 --- a/doc/src/improper_fourier.txt +++ b/doc/src/improper_fourier.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/improper_harmonic.txt b/doc/src/improper_harmonic.txt index f37338e468..f398dc425f 100644 --- a/doc/src/improper_harmonic.txt +++ b/doc/src/improper_harmonic.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/improper_hybrid.txt b/doc/src/improper_hybrid.txt index 0c2beaef18..42afbe8577 100644 --- a/doc/src/improper_hybrid.txt +++ b/doc/src/improper_hybrid.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/improper_inversion_harmonic.txt b/doc/src/improper_inversion_harmonic.txt index 34683ca2bb..2c0f2f0af8 100644 --- a/doc/src/improper_inversion_harmonic.txt +++ b/doc/src/improper_inversion_harmonic.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/improper_none.txt b/doc/src/improper_none.txt index af9964c743..f97af101fc 100644 --- a/doc/src/improper_none.txt +++ b/doc/src/improper_none.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/improper_ring.txt b/doc/src/improper_ring.txt index 84c35f9f5c..60bbca170a 100644 --- a/doc/src/improper_ring.txt +++ b/doc/src/improper_ring.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/improper_style.txt b/doc/src/improper_style.txt index 861701590f..3d29b28ec4 100644 --- a/doc/src/improper_style.txt +++ b/doc/src/improper_style.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -60,9 +60,9 @@ specified by the associated "improper_coeff"_improper_coeff.html command. Note that there are also additional improper styles submitted by users -which are included in the LAMMPS distribution. The list of these with -links to the individual styles are given in the improper section of -"this page"_Section_commands.html#cmd_5. +which are included in the LAMMPS distribution. The full list of all +improper styles is on the "Commands bond"_Commands_bond.html#improper +doc page. "improper_style none"_improper_none.html - turn off improper interactions "improper_style zero"_improper_zero.html - topology but no interactions diff --git a/doc/src/improper_umbrella.txt b/doc/src/improper_umbrella.txt index 59fee0a664..b05cf4b181 100644 --- a/doc/src/improper_umbrella.txt +++ b/doc/src/improper_umbrella.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/improper_zero.txt b/doc/src/improper_zero.txt index 2a298573d5..f3f3485b57 100644 --- a/doc/src/improper_zero.txt +++ b/doc/src/improper_zero.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/include.txt b/doc/src/include.txt index 95d08db352..c114056313 100644 --- a/doc/src/include.txt +++ b/doc/src/include.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/info.txt b/doc/src/info.txt index d5b5bd97b9..99211de4fb 100644 --- a/doc/src/info.txt +++ b/doc/src/info.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/jump.txt b/doc/src/jump.txt index 4e3799f7b1..b5afeb6559 100644 --- a/doc/src/jump.txt +++ b/doc/src/jump.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/kspace_modify.txt b/doc/src/kspace_modify.txt index 37c8c5b1d7..dd7b1e8dea 100644 --- a/doc/src/kspace_modify.txt +++ b/doc/src/kspace_modify.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/kspace_style.txt b/doc/src/kspace_style.txt index fa717b70ef..55ad4ab610 100644 --- a/doc/src/kspace_style.txt +++ b/doc/src/kspace_style.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/label.txt b/doc/src/label.txt index c6a573141b..adab44188c 100644 --- a/doc/src/label.txt +++ b/doc/src/label.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/lammps.book b/doc/src/lammps.book index a25d6e0629..9cb2d8cd6c 100644 --- a/doc/src/lammps.book +++ b/doc/src/lammps.book @@ -9,7 +9,17 @@ Intro_opensource.html Intro_authors.html Intro_website.html Section_start.html -Section_commands.html +Commands.html +Commands_input.html +Commands_parse.html +Commands_structure.html +Commands_category.html +Commands_all.html +Commands_fix.html +Commands_compute.html +Commands_pair.html +Commands_bond.html +Commands_kspace.html Packages.html Packages_standard.html Packages_user.html diff --git a/doc/src/lattice.txt b/doc/src/lattice.txt index 7a90df1f5d..6f16dc5432 100644 --- a/doc/src/lattice.txt +++ b/doc/src/lattice.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/log.txt b/doc/src/log.txt index 92bb12e6db..7603768519 100644 --- a/doc/src/log.txt +++ b/doc/src/log.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/manifolds.txt b/doc/src/manifolds.txt index 1013d8fab6..194a755868 100644 --- a/doc/src/manifolds.txt +++ b/doc/src/manifolds.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/mass.txt b/doc/src/mass.txt index 4b75132ccf..c693963044 100644 --- a/doc/src/mass.txt +++ b/doc/src/mass.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/min_modify.txt b/doc/src/min_modify.txt index 73d142f5fa..9408eea167 100644 --- a/doc/src/min_modify.txt +++ b/doc/src/min_modify.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/min_style.txt b/doc/src/min_style.txt index 245ac5864c..4948a34864 100644 --- a/doc/src/min_style.txt +++ b/doc/src/min_style.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line min_style command :h3 diff --git a/doc/src/minimize.txt b/doc/src/minimize.txt index a3f2c5d0bf..910fc7f821 100644 --- a/doc/src/minimize.txt +++ b/doc/src/minimize.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/molecule.txt b/doc/src/molecule.txt index b2ad547cf0..88c6292d8b 100644 --- a/doc/src/molecule.txt +++ b/doc/src/molecule.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/neb.txt b/doc/src/neb.txt index 5c6053fca0..fbd77ee329 100644 --- a/doc/src/neb.txt +++ b/doc/src/neb.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/neigh_modify.txt b/doc/src/neigh_modify.txt index c4544cb29b..6c4218cff5 100644 --- a/doc/src/neigh_modify.txt +++ b/doc/src/neigh_modify.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/neighbor.txt b/doc/src/neighbor.txt index 062f79a5bb..7c7e7b05e5 100644 --- a/doc/src/neighbor.txt +++ b/doc/src/neighbor.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/newton.txt b/doc/src/newton.txt index a3e7f4fa91..fd7b536920 100644 --- a/doc/src/newton.txt +++ b/doc/src/newton.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/next.txt b/doc/src/next.txt index 08f73b896c..5a0b30b2a7 100644 --- a/doc/src/next.txt +++ b/doc/src/next.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/package.txt b/doc/src/package.txt index 81e1db9bd8..c2e7345bb7 100644 --- a/doc/src/package.txt +++ b/doc/src/package.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_adp.txt b/doc/src/pair_adp.txt index 1ba59b7732..382a97ecea 100644 --- a/doc/src/pair_adp.txt +++ b/doc/src/pair_adp.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_agni.txt b/doc/src/pair_agni.txt index 352e00249a..34f9900139 100644 --- a/doc/src/pair_agni.txt +++ b/doc/src/pair_agni.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_airebo.txt b/doc/src/pair_airebo.txt index b5add21f24..94a692226d 100644 --- a/doc/src/pair_airebo.txt +++ b/doc/src/pair_airebo.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_awpmd.txt b/doc/src/pair_awpmd.txt index fe0e3c952a..ec87101d0d 100644 --- a/doc/src/pair_awpmd.txt +++ b/doc/src/pair_awpmd.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_beck.txt b/doc/src/pair_beck.txt index 1aca4b4f9a..ca4186e27b 100644 --- a/doc/src/pair_beck.txt +++ b/doc/src/pair_beck.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_body_nparticle.txt b/doc/src/pair_body_nparticle.txt index 78a9f2bb38..9fb88102eb 100644 --- a/doc/src/pair_body_nparticle.txt +++ b/doc/src/pair_body_nparticle.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_body_rounded_polygon.txt b/doc/src/pair_body_rounded_polygon.txt index 19807fbe39..e724874032 100644 --- a/doc/src/pair_body_rounded_polygon.txt +++ b/doc/src/pair_body_rounded_polygon.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_body_rounded_polyhedron.txt b/doc/src/pair_body_rounded_polyhedron.txt index d70a86f881..0f8548d98e 100644 --- a/doc/src/pair_body_rounded_polyhedron.txt +++ b/doc/src/pair_body_rounded_polyhedron.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_bop.txt b/doc/src/pair_bop.txt index 2a611e4bd0..654a7eb0b3 100644 --- a/doc/src/pair_bop.txt +++ b/doc/src/pair_bop.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_born.txt b/doc/src/pair_born.txt index 143549cf2d..c408de6db6 100644 --- a/doc/src/pair_born.txt +++ b/doc/src/pair_born.txt @@ -3,7 +3,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_brownian.txt b/doc/src/pair_brownian.txt index 8d30f0cec6..eaff85cbbc 100644 --- a/doc/src/pair_brownian.txt +++ b/doc/src/pair_brownian.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_buck.txt b/doc/src/pair_buck.txt index 2483a6c9e2..cc782c11cf 100644 --- a/doc/src/pair_buck.txt +++ b/doc/src/pair_buck.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_buck6d_coul_gauss.txt b/doc/src/pair_buck6d_coul_gauss.txt index 879972772b..485c35c6b2 100644 --- a/doc/src/pair_buck6d_coul_gauss.txt +++ b/doc/src/pair_buck6d_coul_gauss.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_buck_long.txt b/doc/src/pair_buck_long.txt index 94bf6a2d7c..551204f1a7 100644 --- a/doc/src/pair_buck_long.txt +++ b/doc/src/pair_buck_long.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_charmm.txt b/doc/src/pair_charmm.txt index af20661bbd..39c6f29b04 100644 --- a/doc/src/pair_charmm.txt +++ b/doc/src/pair_charmm.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_class2.txt b/doc/src/pair_class2.txt index e62971a645..104c51474c 100644 --- a/doc/src/pair_class2.txt +++ b/doc/src/pair_class2.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_coeff.txt b/doc/src/pair_coeff.txt index fe9238f423..63f85f23d5 100644 --- a/doc/src/pair_coeff.txt +++ b/doc/src/pair_coeff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -111,9 +111,8 @@ Windows: :line The alphabetic list of pair styles defined in LAMMPS is given on the -"pair_style"_pair_style.html doc page. They are also given in more -compact form in the pair section of "this -page"_Section_commands.html#cmd_5. +"pair_style"_pair_style.html doc page. They are also listed in more +compact form on the "Commands pair"_Commands_pair.html doc page. Click on the style to display the formula it computes, arguments specified in the pair_style command, and coefficients specified by the @@ -121,15 +120,15 @@ associated "pair_coeff"_pair_coeff.html command. Note that there are also additional pair styles (not listed on the "pair_style"_pair_style.html doc page) submitted by users which are -included in the LAMMPS distribution. The list of these with links to -the individual styles are given in the pair section of "this -page"_Section_commands.html#cmd_5. +included in the LAMMPS distribution. The full list of all pair styles +is on the "Commands pair"_Commands_pair.html doc page. There are also additional accelerated pair styles (not listed on the "pair_style"_pair_style.html doc page) included in the LAMMPS -distribution for faster performance on CPUs and GPUs. The list of -these with links to the individual styles are given in the pair -section of "this page"_Section_commands.html#cmd_5. +distribution for faster performance on CPUs, GPUs, and KNLs. The +individual style names on the "Commands pair"_Commands_pair.html doc +page are followed by one or more of (g,i,k,o,t) to indicate which +accerlerated styles exist. :line diff --git a/doc/src/pair_colloid.txt b/doc/src/pair_colloid.txt index a7bb0db08a..08540cfee0 100644 --- a/doc/src/pair_colloid.txt +++ b/doc/src/pair_colloid.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_comb.txt b/doc/src/pair_comb.txt index 6949ca50c2..fc4cddbbae 100644 --- a/doc/src/pair_comb.txt +++ b/doc/src/pair_comb.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_coul.txt b/doc/src/pair_coul.txt index e2bc78a2e6..2fd9445785 100644 --- a/doc/src/pair_coul.txt +++ b/doc/src/pair_coul.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_coul_diel.txt b/doc/src/pair_coul_diel.txt index f651cb4b5e..14932c4835 100644 --- a/doc/src/pair_coul_diel.txt +++ b/doc/src/pair_coul_diel.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_coul_shield.txt b/doc/src/pair_coul_shield.txt index 19f69688d5..029e6e5b3b 100644 --- a/doc/src/pair_coul_shield.txt +++ b/doc/src/pair_coul_shield.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_cs.txt b/doc/src/pair_cs.txt index 86eb02b0d7..6540c4b8f0 100644 --- a/doc/src/pair_cs.txt +++ b/doc/src/pair_cs.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_dipole.txt b/doc/src/pair_dipole.txt index e7d196d599..1d8abc4521 100644 --- a/doc/src/pair_dipole.txt +++ b/doc/src/pair_dipole.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_dpd.txt b/doc/src/pair_dpd.txt index a36029ea63..1b636795d9 100644 --- a/doc/src/pair_dpd.txt +++ b/doc/src/pair_dpd.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_dpd_fdt.txt b/doc/src/pair_dpd_fdt.txt index 129d3c84af..0d180ba068 100644 --- a/doc/src/pair_dpd_fdt.txt +++ b/doc/src/pair_dpd_fdt.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_dsmc.txt b/doc/src/pair_dsmc.txt index 9e24100ab7..2478a96d5f 100644 --- a/doc/src/pair_dsmc.txt +++ b/doc/src/pair_dsmc.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_eam.txt b/doc/src/pair_eam.txt index b3c770179f..361dacb703 100644 --- a/doc/src/pair_eam.txt +++ b/doc/src/pair_eam.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_edip.txt b/doc/src/pair_edip.txt index f0d1927812..cce564856e 100644 --- a/doc/src/pair_edip.txt +++ b/doc/src/pair_edip.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_eff.txt b/doc/src/pair_eff.txt index ee7dc99932..a55860297e 100644 --- a/doc/src/pair_eff.txt +++ b/doc/src/pair_eff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_eim.txt b/doc/src/pair_eim.txt index 7f94d919f2..6490a859c1 100644 --- a/doc/src/pair_eim.txt +++ b/doc/src/pair_eim.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_exp6_rx.txt b/doc/src/pair_exp6_rx.txt index dec660fd1d..08ab1cf3c9 100644 --- a/doc/src/pair_exp6_rx.txt +++ b/doc/src/pair_exp6_rx.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_extep.txt b/doc/src/pair_extep.txt index 9a784e2501..3acad1132d 100644 --- a/doc/src/pair_extep.txt +++ b/doc/src/pair_extep.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_gauss.txt b/doc/src/pair_gauss.txt index 7716f89f17..9662a4f29c 100644 --- a/doc/src/pair_gauss.txt +++ b/doc/src/pair_gauss.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_gayberne.txt b/doc/src/pair_gayberne.txt index e9a98a0b84..af41f6879e 100644 --- a/doc/src/pair_gayberne.txt +++ b/doc/src/pair_gayberne.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_gran.txt b/doc/src/pair_gran.txt index 86b04f96de..55b00a172f 100644 --- a/doc/src/pair_gran.txt +++ b/doc/src/pair_gran.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_gromacs.txt b/doc/src/pair_gromacs.txt index 7daf805e2b..9f34ac8c43 100644 --- a/doc/src/pair_gromacs.txt +++ b/doc/src/pair_gromacs.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_gw.txt b/doc/src/pair_gw.txt index 8f1251cf1f..809ff008bc 100644 --- a/doc/src/pair_gw.txt +++ b/doc/src/pair_gw.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_hbond_dreiding.txt b/doc/src/pair_hbond_dreiding.txt index d641cb73ad..60b0b02174 100644 --- a/doc/src/pair_hbond_dreiding.txt +++ b/doc/src/pair_hbond_dreiding.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_hybrid.txt b/doc/src/pair_hybrid.txt index 9503256d26..9b36109c27 100644 --- a/doc/src/pair_hybrid.txt +++ b/doc/src/pair_hybrid.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_ilp_graphene_hbn.txt b/doc/src/pair_ilp_graphene_hbn.txt index dbc9c458e2..9c9304c4a7 100644 --- a/doc/src/pair_ilp_graphene_hbn.txt +++ b/doc/src/pair_ilp_graphene_hbn.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_kim.txt b/doc/src/pair_kim.txt index fc2c1405af..889c1e892f 100644 --- a/doc/src/pair_kim.txt +++ b/doc/src/pair_kim.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_kolmogorov_crespi_full.txt b/doc/src/pair_kolmogorov_crespi_full.txt index a16d123b89..8fc6bbff49 100644 --- a/doc/src/pair_kolmogorov_crespi_full.txt +++ b/doc/src/pair_kolmogorov_crespi_full.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_kolmogorov_crespi_z.txt b/doc/src/pair_kolmogorov_crespi_z.txt index 97f132eacd..7dad2e3701 100644 --- a/doc/src/pair_kolmogorov_crespi_z.txt +++ b/doc/src/pair_kolmogorov_crespi_z.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_lcbop.txt b/doc/src/pair_lcbop.txt index 148a1d47a0..ddf8551d56 100644 --- a/doc/src/pair_lcbop.txt +++ b/doc/src/pair_lcbop.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_line_lj.txt b/doc/src/pair_line_lj.txt index 44cfeb48e9..c2c6beb97f 100644 --- a/doc/src/pair_line_lj.txt +++ b/doc/src/pair_line_lj.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_list.txt b/doc/src/pair_list.txt index 653e8b0c2d..023cc0be4f 100644 --- a/doc/src/pair_list.txt +++ b/doc/src/pair_list.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_lj.txt b/doc/src/pair_lj.txt index a0f7effbb1..a55cb348d7 100644 --- a/doc/src/pair_lj.txt +++ b/doc/src/pair_lj.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_lj96.txt b/doc/src/pair_lj96.txt index a0a9971474..7c68e26ace 100644 --- a/doc/src/pair_lj96.txt +++ b/doc/src/pair_lj96.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_lj_cubic.txt b/doc/src/pair_lj_cubic.txt index c4e2af5062..d04a3d8b9d 100644 --- a/doc/src/pair_lj_cubic.txt +++ b/doc/src/pair_lj_cubic.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_lj_expand.txt b/doc/src/pair_lj_expand.txt index c156fefef2..3e9996da4d 100644 --- a/doc/src/pair_lj_expand.txt +++ b/doc/src/pair_lj_expand.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_lj_long.txt b/doc/src/pair_lj_long.txt index 0dd55b7e32..1ba3610f86 100644 --- a/doc/src/pair_lj_long.txt +++ b/doc/src/pair_lj_long.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_lj_smooth.txt b/doc/src/pair_lj_smooth.txt index 653520966b..575c023579 100644 --- a/doc/src/pair_lj_smooth.txt +++ b/doc/src/pair_lj_smooth.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_lj_smooth_linear.txt b/doc/src/pair_lj_smooth_linear.txt index aebde2e653..0fab768b8f 100644 --- a/doc/src/pair_lj_smooth_linear.txt +++ b/doc/src/pair_lj_smooth_linear.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_lj_soft.txt b/doc/src/pair_lj_soft.txt index 7add9f623d..d10fcd0472 100644 --- a/doc/src/pair_lj_soft.txt +++ b/doc/src/pair_lj_soft.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_lubricate.txt b/doc/src/pair_lubricate.txt index 2a16aa2a9d..e9a0a0d291 100644 --- a/doc/src/pair_lubricate.txt +++ b/doc/src/pair_lubricate.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_lubricateU.txt b/doc/src/pair_lubricateU.txt index 720a8539b8..6b74c208bf 100644 --- a/doc/src/pair_lubricateU.txt +++ b/doc/src/pair_lubricateU.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_mdf.txt b/doc/src/pair_mdf.txt index ca06f1bf8e..e5a8cac845 100644 --- a/doc/src/pair_mdf.txt +++ b/doc/src/pair_mdf.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_meam.txt b/doc/src/pair_meam.txt index c7449428bd..45f88f0bbe 100644 --- a/doc/src/pair_meam.txt +++ b/doc/src/pair_meam.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_meam_spline.txt b/doc/src/pair_meam_spline.txt index 74242e32b9..9615512041 100644 --- a/doc/src/pair_meam_spline.txt +++ b/doc/src/pair_meam_spline.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_meam_sw_spline.txt b/doc/src/pair_meam_sw_spline.txt index fa731799dd..ba0953a17c 100644 --- a/doc/src/pair_meam_sw_spline.txt +++ b/doc/src/pair_meam_sw_spline.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_meso.txt b/doc/src/pair_meso.txt index bcdf717d68..ad3880e642 100644 --- a/doc/src/pair_meso.txt +++ b/doc/src/pair_meso.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_mgpt.txt b/doc/src/pair_mgpt.txt index f8b0c9f071..09fe611686 100644 --- a/doc/src/pair_mgpt.txt +++ b/doc/src/pair_mgpt.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_mie.txt b/doc/src/pair_mie.txt index ad602db9f1..818e37272b 100644 --- a/doc/src/pair_mie.txt +++ b/doc/src/pair_mie.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_modify.txt b/doc/src/pair_modify.txt index 34dbb5bc3d..c043fde5a7 100644 --- a/doc/src/pair_modify.txt +++ b/doc/src/pair_modify.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_momb.txt b/doc/src/pair_momb.txt index 77c4f184d9..545b650f75 100644 --- a/doc/src/pair_momb.txt +++ b/doc/src/pair_momb.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_morse.txt b/doc/src/pair_morse.txt index 34876011a1..85a42986ec 100644 --- a/doc/src/pair_morse.txt +++ b/doc/src/pair_morse.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_multi_lucy.txt b/doc/src/pair_multi_lucy.txt index 38fd1ede4a..31d52a58c8 100644 --- a/doc/src/pair_multi_lucy.txt +++ b/doc/src/pair_multi_lucy.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_multi_lucy_rx.txt b/doc/src/pair_multi_lucy_rx.txt index b043030907..e09dde3f80 100644 --- a/doc/src/pair_multi_lucy_rx.txt +++ b/doc/src/pair_multi_lucy_rx.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_nb3b_harmonic.txt b/doc/src/pair_nb3b_harmonic.txt index e6e103f517..720b9ea2a1 100644 --- a/doc/src/pair_nb3b_harmonic.txt +++ b/doc/src/pair_nb3b_harmonic.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_nm.txt b/doc/src/pair_nm.txt index 08c3393993..355bfd5573 100644 --- a/doc/src/pair_nm.txt +++ b/doc/src/pair_nm.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_none.txt b/doc/src/pair_none.txt index f4e9525198..960dc05d97 100644 --- a/doc/src/pair_none.txt +++ b/doc/src/pair_none.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_oxdna.txt b/doc/src/pair_oxdna.txt index f272d15a86..5ec9915297 100644 --- a/doc/src/pair_oxdna.txt +++ b/doc/src/pair_oxdna.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_oxdna2.txt b/doc/src/pair_oxdna2.txt index 1b55031b2c..a1d2cfdb7c 100644 --- a/doc/src/pair_oxdna2.txt +++ b/doc/src/pair_oxdna2.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_peri.txt b/doc/src/pair_peri.txt index 4327003057..14abd4541e 100644 --- a/doc/src/pair_peri.txt +++ b/doc/src/pair_peri.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_polymorphic.txt b/doc/src/pair_polymorphic.txt index c088e8bb22..eb0c30f249 100644 --- a/doc/src/pair_polymorphic.txt +++ b/doc/src/pair_polymorphic.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_python.txt b/doc/src/pair_python.txt index 2f8ed7a27c..1433557e03 100644 --- a/doc/src/pair_python.txt +++ b/doc/src/pair_python.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_quip.txt b/doc/src/pair_quip.txt index 9436b0c4ed..3570a52801 100644 --- a/doc/src/pair_quip.txt +++ b/doc/src/pair_quip.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_reax.txt b/doc/src/pair_reax.txt index 1d13f93706..a3b84955cd 100644 --- a/doc/src/pair_reax.txt +++ b/doc/src/pair_reax.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_reaxc.txt b/doc/src/pair_reaxc.txt index 8d8c7e84e7..ec57548640 100644 --- a/doc/src/pair_reaxc.txt +++ b/doc/src/pair_reaxc.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_resquared.txt b/doc/src/pair_resquared.txt index 6ea5c73c0d..6e72408ebc 100644 --- a/doc/src/pair_resquared.txt +++ b/doc/src/pair_resquared.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_sdk.txt b/doc/src/pair_sdk.txt index 4cd56bc43d..ccf704b6f7 100644 --- a/doc/src/pair_sdk.txt +++ b/doc/src/pair_sdk.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_smd_hertz.txt b/doc/src/pair_smd_hertz.txt index eeaa3387a4..f2d633903a 100644 --- a/doc/src/pair_smd_hertz.txt +++ b/doc/src/pair_smd_hertz.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_smd_tlsph.txt b/doc/src/pair_smd_tlsph.txt index f73acf74ee..3aeaa31553 100644 --- a/doc/src/pair_smd_tlsph.txt +++ b/doc/src/pair_smd_tlsph.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_smd_triangulated_surface.txt b/doc/src/pair_smd_triangulated_surface.txt index c32bf3a22e..65526cfba8 100644 --- a/doc/src/pair_smd_triangulated_surface.txt +++ b/doc/src/pair_smd_triangulated_surface.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_smd_ulsph.txt b/doc/src/pair_smd_ulsph.txt index 268fe78d02..a5bda54d5f 100644 --- a/doc/src/pair_smd_ulsph.txt +++ b/doc/src/pair_smd_ulsph.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_smtbq.txt b/doc/src/pair_smtbq.txt index c8d6b21b3f..c70202c2e1 100644 --- a/doc/src/pair_smtbq.txt +++ b/doc/src/pair_smtbq.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_snap.txt b/doc/src/pair_snap.txt index c3d6e67e82..f9bd8910e4 100644 --- a/doc/src/pair_snap.txt +++ b/doc/src/pair_snap.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_soft.txt b/doc/src/pair_soft.txt index adbfa596c9..374711825b 100644 --- a/doc/src/pair_soft.txt +++ b/doc/src/pair_soft.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_sph_heatconduction.txt b/doc/src/pair_sph_heatconduction.txt index 2387056a1b..d19c28a3cb 100644 --- a/doc/src/pair_sph_heatconduction.txt +++ b/doc/src/pair_sph_heatconduction.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_sph_idealgas.txt b/doc/src/pair_sph_idealgas.txt index 957f901425..a670949a89 100644 --- a/doc/src/pair_sph_idealgas.txt +++ b/doc/src/pair_sph_idealgas.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_sph_lj.txt b/doc/src/pair_sph_lj.txt index ef89c4ad3e..152e6cf8a2 100644 --- a/doc/src/pair_sph_lj.txt +++ b/doc/src/pair_sph_lj.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_sph_rhosum.txt b/doc/src/pair_sph_rhosum.txt index 352e717f76..3cd1c5abb2 100644 --- a/doc/src/pair_sph_rhosum.txt +++ b/doc/src/pair_sph_rhosum.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_sph_taitwater.txt b/doc/src/pair_sph_taitwater.txt index 9177ca80b8..7b9a8188f2 100644 --- a/doc/src/pair_sph_taitwater.txt +++ b/doc/src/pair_sph_taitwater.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_sph_taitwater_morris.txt b/doc/src/pair_sph_taitwater_morris.txt index e6c5a6bb20..02f16d8982 100644 --- a/doc/src/pair_sph_taitwater_morris.txt +++ b/doc/src/pair_sph_taitwater_morris.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_spin_dmi.txt b/doc/src/pair_spin_dmi.txt index a1d0cb2265..375e59fe89 100644 --- a/doc/src/pair_spin_dmi.txt +++ b/doc/src/pair_spin_dmi.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_spin_exchange.txt b/doc/src/pair_spin_exchange.txt index a4f37a98eb..24eb635b81 100644 --- a/doc/src/pair_spin_exchange.txt +++ b/doc/src/pair_spin_exchange.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_spin_magelec.txt b/doc/src/pair_spin_magelec.txt index 8ba24c46af..b338fae5dc 100644 --- a/doc/src/pair_spin_magelec.txt +++ b/doc/src/pair_spin_magelec.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_spin_neel.txt b/doc/src/pair_spin_neel.txt index 8551f8d636..0967632ed2 100644 --- a/doc/src/pair_spin_neel.txt +++ b/doc/src/pair_spin_neel.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_srp.txt b/doc/src/pair_srp.txt index e7f1e00d10..e784ac3d17 100644 --- a/doc/src/pair_srp.txt +++ b/doc/src/pair_srp.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_style.txt b/doc/src/pair_style.txt index 2763eb3d66..cd39513329 100644 --- a/doc/src/pair_style.txt +++ b/doc/src/pair_style.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -78,22 +78,22 @@ previously specified pair_coeff values. :line Here is an alphabetic list of pair styles defined in LAMMPS. They are -also given in more compact form in the pair section of "this -page"_Section_commands.html#cmd_5. +also listed in more compact form on the "Commands +pair"_Commands_pair.html doc page. Click on the style to display the formula it computes, arguments specified in the pair_style command, and coefficients specified by the associated "pair_coeff"_pair_coeff.html command. There are also additional pair styles (not listed here) submitted by -users which are included in the LAMMPS distribution. The list of -these with links to the individual styles are given in the pair -section of "this page"_Section_commands.html#cmd_5. +users which are included in the LAMMPS distribution. The full list of +all pair styles is on the "Commands pair"_Commands_pair.html doc page. There are also additional accelerated pair styles (not listed here) -included in the LAMMPS distribution for faster performance on CPUs and -GPUs. The list of these with links to the individual styles are given -in the pair section of "this page"_Section_commands.html#cmd_5. +included in the LAMMPS distribution for faster performance on CPUs, +GPUs, and KNLs. The individual style names on the "Commands +pair"_Commands_pair.html doc page are followed by one or more of +(g,i,k,o,t) to indicate which accerlerated styles exist. "pair_style none"_pair_none.html - turn off pairwise interactions "pair_style hybrid"_pair_hybrid.html - multiple styles of pairwise interactions diff --git a/doc/src/pair_sw.txt b/doc/src/pair_sw.txt index 7c9ce4a4f9..e6741791df 100644 --- a/doc/src/pair_sw.txt +++ b/doc/src/pair_sw.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_table.txt b/doc/src/pair_table.txt index f5e69a6d54..5e3c1f5ff6 100644 --- a/doc/src/pair_table.txt +++ b/doc/src/pair_table.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_table_rx.txt b/doc/src/pair_table_rx.txt index 52760c396b..41be067bac 100644 --- a/doc/src/pair_table_rx.txt +++ b/doc/src/pair_table_rx.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_tersoff.txt b/doc/src/pair_tersoff.txt index 70fe207f0a..821c38f3e4 100644 --- a/doc/src/pair_tersoff.txt +++ b/doc/src/pair_tersoff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_tersoff_mod.txt b/doc/src/pair_tersoff_mod.txt index aced6d40d6..ac1f79a80b 100644 --- a/doc/src/pair_tersoff_mod.txt +++ b/doc/src/pair_tersoff_mod.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_tersoff_zbl.txt b/doc/src/pair_tersoff_zbl.txt index 838c2f39cf..a89d4e3ea1 100644 --- a/doc/src/pair_tersoff_zbl.txt +++ b/doc/src/pair_tersoff_zbl.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_thole.txt b/doc/src/pair_thole.txt index 42c58e9882..7ce8b7cf4b 100644 --- a/doc/src/pair_thole.txt +++ b/doc/src/pair_thole.txt @@ -9,7 +9,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_tri_lj.txt b/doc/src/pair_tri_lj.txt index 42a5bbdfe2..3915ffc238 100644 --- a/doc/src/pair_tri_lj.txt +++ b/doc/src/pair_tri_lj.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_ufm.txt b/doc/src/pair_ufm.txt index 5af8741502..dbc6fd0664 100644 --- a/doc/src/pair_ufm.txt +++ b/doc/src/pair_ufm.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_vashishta.txt b/doc/src/pair_vashishta.txt index e90a9d8f50..2e404e8bef 100644 --- a/doc/src/pair_vashishta.txt +++ b/doc/src/pair_vashishta.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_write.txt b/doc/src/pair_write.txt index 9f5970fcbc..48ad76e76e 100644 --- a/doc/src/pair_write.txt +++ b/doc/src/pair_write.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_yukawa.txt b/doc/src/pair_yukawa.txt index 979165dda0..5a8363260a 100644 --- a/doc/src/pair_yukawa.txt +++ b/doc/src/pair_yukawa.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_yukawa_colloid.txt b/doc/src/pair_yukawa_colloid.txt index a1752c261e..515062d9eb 100644 --- a/doc/src/pair_yukawa_colloid.txt +++ b/doc/src/pair_yukawa_colloid.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_zbl.txt b/doc/src/pair_zbl.txt index 0507083295..1472c7b672 100644 --- a/doc/src/pair_zbl.txt +++ b/doc/src/pair_zbl.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_zero.txt b/doc/src/pair_zero.txt index e58b33c75f..b324003bd1 100644 --- a/doc/src/pair_zero.txt +++ b/doc/src/pair_zero.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/partition.txt b/doc/src/partition.txt index 610eee99b3..d4fe06c098 100644 --- a/doc/src/partition.txt +++ b/doc/src/partition.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/prd.txt b/doc/src/prd.txt index f298d83385..b2145ebad1 100644 --- a/doc/src/prd.txt +++ b/doc/src/prd.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/print.txt b/doc/src/print.txt index 77e0c7cfd3..476d4104fa 100644 --- a/doc/src/print.txt +++ b/doc/src/print.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/processors.txt b/doc/src/processors.txt index e54b2cede3..df13ae1f61 100644 --- a/doc/src/processors.txt +++ b/doc/src/processors.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/python.txt b/doc/src/python.txt index d670fcc77f..4f4faca8f4 100644 --- a/doc/src/python.txt +++ b/doc/src/python.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -199,9 +199,9 @@ The {here} keyword does the same thing, except that the Python code follows as a single argument to the {here} keyword. This can be done using triple quotes as delimiters, as in the examples above. This allows Python code to be listed verbatim in your input script, with -proper indentation, blank lines, and comments, as desired. See -"Section 3.2"_Section_commands.html#cmd_2, for an explanation of how -triple quotes can be used as part of input script syntax. +proper indentation, blank lines, and comments, as desired. See the +"Commands parse"_Commands_parse.html doc page, for an explanation of +how triple quotes can be used as part of input script syntax. The {exists} keyword takes no argument. It means that Python code containing the required Python function defined by the {func} setting, diff --git a/doc/src/quit.txt b/doc/src/quit.txt index 843d3de7f3..802df97711 100644 --- a/doc/src/quit.txt +++ b/doc/src/quit.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/read_data.txt b/doc/src/read_data.txt index 4f6a3988b9..ded51a4d99 100644 --- a/doc/src/read_data.txt +++ b/doc/src/read_data.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/read_dump.txt b/doc/src/read_dump.txt index 21c6df5017..a3c0733e07 100644 --- a/doc/src/read_dump.txt +++ b/doc/src/read_dump.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/read_restart.txt b/doc/src/read_restart.txt index 6f6a828229..488c36f020 100644 --- a/doc/src/read_restart.txt +++ b/doc/src/read_restart.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/region.txt b/doc/src/region.txt index b32c09ed6f..21396ae1fd 100644 --- a/doc/src/region.txt +++ b/doc/src/region.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/replicate.txt b/doc/src/replicate.txt index 08523ecdd8..0195dce911 100644 --- a/doc/src/replicate.txt +++ b/doc/src/replicate.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/rerun.txt b/doc/src/rerun.txt index edf94cc711..8eb3ebd5a1 100644 --- a/doc/src/rerun.txt +++ b/doc/src/rerun.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/reset_ids.txt b/doc/src/reset_ids.txt index 8655a9d54f..391b51fde9 100644 --- a/doc/src/reset_ids.txt +++ b/doc/src/reset_ids.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/reset_timestep.txt b/doc/src/reset_timestep.txt index 79a5812ca1..0d518655fb 100644 --- a/doc/src/reset_timestep.txt +++ b/doc/src/reset_timestep.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/restart.txt b/doc/src/restart.txt index 7c39ae1404..6f2dc5ca46 100644 --- a/doc/src/restart.txt +++ b/doc/src/restart.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/run.txt b/doc/src/run.txt index 02860c0b97..c7c73463d9 100644 --- a/doc/src/run.txt +++ b/doc/src/run.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/run_style.txt b/doc/src/run_style.txt index 6f1f719d64..deee51cfd3 100644 --- a/doc/src/run_style.txt +++ b/doc/src/run_style.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/set.txt b/doc/src/set.txt index d2235d5c32..b83ad54f4e 100644 --- a/doc/src/set.txt +++ b/doc/src/set.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/shell.txt b/doc/src/shell.txt index 205164f874..d274f498e5 100644 --- a/doc/src/shell.txt +++ b/doc/src/shell.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/special_bonds.txt b/doc/src/special_bonds.txt index 1021c4856b..a57b61664d 100644 --- a/doc/src/special_bonds.txt +++ b/doc/src/special_bonds.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/suffix.txt b/doc/src/suffix.txt index 74f69b6dfe..bb0619f1e0 100644 --- a/doc/src/suffix.txt +++ b/doc/src/suffix.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/tad.txt b/doc/src/tad.txt index 9ffa24d012..a26ff79318 100644 --- a/doc/src/tad.txt +++ b/doc/src/tad.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/temper.txt b/doc/src/temper.txt index e65f59ebed..c7b482acc6 100644 --- a/doc/src/temper.txt +++ b/doc/src/temper.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/temper_grem.txt b/doc/src/temper_grem.txt index 6145c8704c..9cb1bab784 100644 --- a/doc/src/temper_grem.txt +++ b/doc/src/temper_grem.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/temper_npt.txt b/doc/src/temper_npt.txt index 4ad49f9e33..4eee225de7 100644 --- a/doc/src/temper_npt.txt +++ b/doc/src/temper_npt.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line temper/npt command :h3 diff --git a/doc/src/thermo.txt b/doc/src/thermo.txt index 1d5d34995c..5f12f98707 100644 --- a/doc/src/thermo.txt +++ b/doc/src/thermo.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/thermo_modify.txt b/doc/src/thermo_modify.txt index e9aca0f20a..ca2957de77 100644 --- a/doc/src/thermo_modify.txt +++ b/doc/src/thermo_modify.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/thermo_style.txt b/doc/src/thermo_style.txt index 64e0785586..cbc2612f28 100644 --- a/doc/src/thermo_style.txt +++ b/doc/src/thermo_style.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/timer.txt b/doc/src/timer.txt index 768c3e1353..10737dbda0 100644 --- a/doc/src/timer.txt +++ b/doc/src/timer.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/timestep.txt b/doc/src/timestep.txt index 639ad6f311..ee0ace05b9 100644 --- a/doc/src/timestep.txt +++ b/doc/src/timestep.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/uncompute.txt b/doc/src/uncompute.txt index 49b46781d7..4c788d4722 100644 --- a/doc/src/uncompute.txt +++ b/doc/src/uncompute.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/undump.txt b/doc/src/undump.txt index a2a371aca5..cc3d8b9103 100644 --- a/doc/src/undump.txt +++ b/doc/src/undump.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/unfix.txt b/doc/src/unfix.txt index dcc4499b20..9608b39c7e 100644 --- a/doc/src/unfix.txt +++ b/doc/src/unfix.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/units.txt b/doc/src/units.txt index 0b856dcc68..8df8fe6810 100644 --- a/doc/src/units.txt +++ b/doc/src/units.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/variable.txt b/doc/src/variable.txt index 717c77c079..c6598ccb51 100644 --- a/doc/src/variable.txt +++ b/doc/src/variable.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -124,8 +124,8 @@ provide, so that the variable gets its value from the evaluation of the Python code. Variables of style {internal} are used by a few commands which set their value directly. -NOTE: As discussed in "Section 3.2"_Section_commands.html#cmd_2 of the -manual, an input script can use "immediate" variables, specified as +NOTE: As discussed on the "Commands parse"_Commands_parse.html doc +page, an input script can use "immediate" variables, specified as $(formula) with parenthesis, where the formula has the same syntax as equal-style variables described on this page. This is a convenient way to evaluate a formula immediately without using the variable @@ -198,7 +198,7 @@ the same thing. :line -"This section"_Section_commands.html#cmd_2 of the manual explains how +The "Commands parse"_Commands_parse.html doc page explains how occurrences of a variable name in an input script line are replaced by the variable's string. The variable name can be referenced as $x if the name "x" is a single character, or as $\{LoopVar\} if the name @@ -312,8 +312,8 @@ If you simply wish to print a variable value with desired precision to the screen or logfile via the "print"_print.html or "fix print"_fix_print.html commands, you can also do this by specifying an "immediate" variable with a trailing colon and format string, as part -of the string argument of those commands. This is explained in -"Section 3.2"_Section_commands.html#cmd_2. +of the string argument of those commands. This is explained on the +"Commands parse"_Commands_parse.html doc page. For the {getenv} style, a single string is assigned to the variable which should be the name of an environment variable. When the @@ -1119,24 +1119,23 @@ Vectors" discussion above. If you want an equal-style variable to be evaluated immediately, it may be the case that you do not need to define a variable at all. See -"Section 3.2"_Section_commands.html#cmd_2 of the manual, which -describes the use of "immediate" variables in an input script, -specified as $(formula) with parenthesis, where the formula has the -same syntax as equal-style variables described on this page. This -effectively evaluates a formula immediately without using the variable -command to define a named variable. +the "Commands parse"_Commands_parse.html doc page for info on how to +use "immediate" variables in an input script, specified as $(formula) +with parenthesis, where the formula has the same syntax as equal-style +variables described on this page. This effectively evaluates a +formula immediately without using the variable command to define a +named variable. More generally, there is a difference between referencing a variable with a leading $ sign (e.g. $x or $\{abc\}) versus with a leading "v_" (e.g. v_x or v_abc). The former can be used in any input script command, including a variable command. The input script parser evaluates the reference variable immediately and substitutes its value -into the command. As explained in "Section -3.2"_Section_commands.html#cmd_2 for "Parsing rules", you can also use -un-named "immediate" variables for this purpose. For example, a -string like this $((xlo+xhi)/2+sqrt(v_area)) in an input script -command evaluates the string between the parenthesis as an equal-style -variable formula. +into the command. As explained on the "Commands +parse"_Commands_parse.html doc page, you can also use un-named +"immediate" variables for this purpose. For example, a string like +this $((xlo+xhi)/2+sqrt(v_area)) in an input script command evaluates +the string between the parenthesis as an equal-style variable formula. Referencing a variable with a leading "v_" is an optional or required kind of argument for some commands (e.g. the "fix @@ -1180,10 +1179,9 @@ quotes if it contains variables preceded by $ signs. For example, variable vratio equal "$\{vfinal\}/$\{v0\}" :pre -This is because the quotes prevent variable substitution (see "this -section"_Section_commands.html#cmd_2 on parsing input script -commands), and thus an error will occur when the formula for "vratio" -is evaluated later. +This is because the quotes prevent variable substitution (explained on +the "Commands parse"_Commands_parse.html doc page), and thus an error +will occur when the formula for "vratio" is evaluated later. :line diff --git a/doc/src/velocity.txt b/doc/src/velocity.txt index 057f0054be..96d3fa6dc4 100644 --- a/doc/src/velocity.txt +++ b/doc/src/velocity.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/write_coeff.txt b/doc/src/write_coeff.txt index 764e119a9d..5dc4b331de 100644 --- a/doc/src/write_coeff.txt +++ b/doc/src/write_coeff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/write_data.txt b/doc/src/write_data.txt index c76f20319c..d8a33f457f 100644 --- a/doc/src/write_data.txt +++ b/doc/src/write_data.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/write_dump.txt b/doc/src/write_dump.txt index 840716085f..e676979001 100644 --- a/doc/src/write_dump.txt +++ b/doc/src/write_dump.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/write_restart.txt b/doc/src/write_restart.txt index ff3b652dba..3935a5d538 100644 --- a/doc/src/write_restart.txt +++ b/doc/src/write_restart.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line