replace Section_commands.txt file

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.
+
+<!-- RST
+
+.. toctree::
+
+   Commands_input
+   Commands_parse
+   Commands_structure
+   Commands_category
+
+.. toctree::
+
+   Commands_all
+   Commands_fix
+   Commands_compute
+   Commands_pair
+   Commands_bond
+   Commands_kspace
+
+END_RST -->
+
+<!-- HTML_ONLY -->
+
+"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)
+
+<!-- END_HTML_ONLY -->
+

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)

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)

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
+

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)

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)

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.
+

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)

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)

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.
+

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.
+

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
 

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
 

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
 

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
 

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
 

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
 

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
 

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
 

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
 

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
 

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
+simpler entities that body particles.  See the "Howto
-6.14"_Section_howto.html#howto_14 for a general overview of all these
+spherical"_Howto_spherical.html doc page for a general overview of all
-particle types.
+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

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
 

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
 

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
 

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
 

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
 

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
 

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
 

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
 

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
 

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
 

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
 

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
 

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
 

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
 

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
 

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
 

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
 

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
 

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
 

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
 

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
 

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
 

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
 

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
 

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
 

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
 

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
 

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
 

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
 

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
 

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
 

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
 

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, \
+    "core/shell model"_Howto_coreshell.html, \
-    "Drude dipole model"_Section_howto.html#howto_27
+    "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

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
 

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
 

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
 

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
 

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
+"Commands"_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
 "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)
-
 <!-- END_HTML_ONLY -->
 
 </BODY>

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
 

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
 

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
 

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
 

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
 

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
 

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
 

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
 

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
 

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
 

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
 

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
 

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
 

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
 

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
 

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
 

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
 

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
 

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
+https://openkim.org/kim-api on the "What is in the KIM API source
-package?" section
+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

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
 

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
 

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
 

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
 

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
 

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
 

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
 

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
 

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
 

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
 

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
 

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
 

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
+defining index and other kinds of variables and the "Commands
-section"_Section_commands.html#cmd_2 for more info on using variables
+parse"_Commands_parse.html page for more info on using variables in
-in input scripts.
+input scripts.
 
 NOTE: Currently, the command-line parser looks for arguments that
 start with "-" to indicate new switches.  Thus you cannot specify

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
 

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
 

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
 

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
 

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
 

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
+a single implementation of an application kernel (e.g. a pair style)
-different kinds of hardware, such as GPUs, Intel Xeon Phis, or many-core
+to run efficiently on different kinds of hardware, such as GPUs, Intel
-CPUs. Kokkos maps the C++ kernel onto different backend languages such as CUDA, OpenMP, or Pthreads.
+Xeon Phis, or many-core CPUs. Kokkos maps the C++ kernel onto
-The Kokkos library also provides data abstractions to adjust (at
+different backend languages such as CUDA, OpenMP, or Pthreads.  The
-compile time) the memory layout of data structures like 2d and
+Kokkos library also provides data abstractions to adjust (at compile
-3d arrays to optimize performance on different hardware. For more information on Kokkos, see
+time) the memory layout of data structures like 2d and 3d arrays to
-"Github"_https://github.com/kokkos/kokkos. Kokkos is part of
+optimize performance on different hardware. For more information on
-"Trilinos"_http://trilinos.sandia.gov/packages/kokkos. The Kokkos library was written primarily by Carter Edwards,
+Kokkos, see "Github"_https://github.com/kokkos/kokkos. Kokkos is part
-Christian Trott, and Dan Sunderland (all Sandia).
+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
+The LAMMPS KOKKOS package contains versions of pair, fix, and atom
-that use data structures and macros provided by the Kokkos library,
+styles that use data structures and macros provided by the Kokkos
-which is included with LAMMPS in /lib/kokkos. The KOKKOS package was developed primarily by Christian Trott (Sandia)
+library, which is included with LAMMPS in /lib/kokkos. The KOKKOS
-and Stan Moore (Sandia) with contributions of various styles by others, including Sikandar
+package was developed primarily by Christian Trott (Sandia) and Stan
-Mashayak (UIUC), Ray Shan (Sandia), and Dan Ibanez (Sandia). For more information on developing using Kokkos abstractions
+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
+task). These are Serial (MPI-only for CPUs and Intel Phi), OpenMP
-for many-core CPUs and Intel Phi), and CUDA (for NVIDIA GPUs). You choose the mode at build time to
+(threading for many-core CPUs and Intel Phi), and CUDA (for NVIDIA
-produce an executable compatible with specific hardware.
+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
+The recommended method of building the KOKKOS package is to start with
-Makefiles in /src/MAKE/OPTIONS/. You may need to modify the KOKKOS_ARCH variable in the Makefile
+the provided Kokkos Makefiles in /src/MAKE/OPTIONS/. You may need to
-to match your specific hardware. For example:
+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
+NOTE: To build with Kokkos support for OpenMP threading, your compiler
-OpenMP interface. You should have one or more multi-core CPUs so that
+must support the OpenMP interface. You should have one or more
-multiple threads can be launched by each MPI task running on a CPU.
+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
+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
+/src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi for both GPU and CPU as
-above.  Then do the following:
+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
+Setting the KOKKOS_DEVICES and KOKKOS_ARCH variables on the make
-make command line requires a GNU-compatible make command. Try
+command line requires a GNU-compatible make command. Try "gmake" if
-"gmake" if your system's standard make complains.
+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"
+with different KOKKOS options and the *same* target, then you *must*
-or "make clean-machine" before each build. This is to force all the
+perform a "make clean-all" or "make clean-machine" before each
-KOKKOS-dependent files to be re-compiled with the new options.
+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
+All Kokkos operations occur within the context of an individual MPI
-context of an individual MPI task running on a single node of the
+task running on a single node of the machine. The total number of MPI
-machine. The total number of MPI tasks used by LAMMPS (one or
+tasks used by LAMMPS (one or multiple per compute node) is set in the
-multiple per compute node) is set in the usual manner via the mpirun
+usual manner via the mpirun or mpiexec commands, and is independent of
-or mpiexec commands, and is independent of Kokkos. E.g. the mpirun
+Kokkos. E.g. the mpirun command in OpenMPI does this via its -np and
-command in OpenMPI does this via its
+-npernode switches. Ditto for MPICH via -np and -ppn.
--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.
+To run using the KOKKOS package, use the "-k on", "-sf kk" and "-pk
-You must use the "-k on" "command-line
+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
+The "t Nt" option specifies how many OpenMP threads per MPI task to
-task to use with a node. The default is Nt = 1, which is MPI-only mode.
+use with a node. The default is Nt = 1, which is MPI-only mode.  Note
-Note that the product of MPI tasks * OpenMP
+that the product of MPI tasks * OpenMP threads/task should not exceed
-threads/task should not exceed the physical number of cores (on a
+the physical number of cores (on a node), otherwise performance will
-node), otherwise performance will suffer. If hyperthreading is enabled, then
+suffer. If hyperthreading is enabled, then the product of MPI tasks *
-the product of MPI tasks * OpenMP threads/task should not exceed the
+OpenMP threads/task should not exceed the physical number of cores *
-physical number of cores * hardware threads.
+hardware threads.  The "-k on" switch also issues a "package kokkos"
-The "-k on" switch also issues a "package kokkos" command (with no
+command (with no additional arguments) which sets various KOKKOS
-additional arguments) which sets various KOKKOS options to default
+options to default values, as discussed on the "package"_package.html
-values, as discussed on the "package"_package.html command doc page.
+command doc page.
 
-The "-sf kk" "command-line switch"_Section_start.html#start_7
+The "-sf kk" "command-line switch"_Section_start.html#start_7 will
-will automatically append the "/kk" suffix to styles that support it.
+automatically append the "/kk" suffix to styles that support it.  In
-In this manner no modification to the input script is needed. Alternatively,
+this manner no modification to the input script is
-one can run with the KOKKOS package by editing the input script as described below.
+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
+NOTE: The default for the "package kokkos"_package.html command is to
-to use "full" neighbor lists and set the Newton flag to "off" for both
+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.
+styles. It can also be faster to use non-threaded communication.  Use
-Use the "-pk kokkos" "command-line switch"_Section_start.html#start_7 to
+the "-pk kokkos" "command-line switch"_Section_start.html#start_7 to
-change the default "package kokkos"_package.html
+change the default "package kokkos"_package.html options. See its doc
-options. See its doc page for details and default settings. Experimenting with
+page for details and default settings. Experimenting with its options
-its options can provide a speed-up for specific calculations. For example:
+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
+When using multi-threading, it is important for performance to bind
-performance to bind both MPI tasks to physical cores, and threads to
+both MPI tasks to physical cores, and threads to physical cores, so
-physical cores, so they do not migrate during a simulation.
+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
+OMP_PROC_BIND=true should be sufficient. In general, for best
-with OpenMP 4.0 or better set OMP_PROC_BIND=spread and OMP_PLACES=threads.
+performance with OpenMP 4.0 or better set OMP_PROC_BIND=spread and
-For binding threads with the
+OMP_PLACES=threads.  For binding threads with the KOKKOS pthreads
-KOKKOS pthreads option, compile LAMMPS the KOKKOS HWLOC=yes option
+option, compile LAMMPS the KOKKOS HWLOC=yes option as described below.
-as described below.
 
 [Running on Knight's Landing (KNL) Intel Xeon Phi:]
 
-Here is a quick overview of how to use the KOKKOS package
+Here is a quick overview of how to use the KOKKOS package for the
-for the Intel Knight's Landing (KNL) Xeon Phi:
+Intel Knight's Landing (KNL) Xeon Phi:
 
-KNL Intel Phi chips have 68 physical cores. Typically 1 to 4 cores
+KNL Intel Phi chips have 68 physical cores. Typically 1 to 4 cores are
-are reserved for the OS, and only 64 or 66 cores are used. Each core
+reserved for the OS, and only 64 or 66 cores are used. Each core has 4
-has 4 hyperthreads,so there are effectively N = 256 (4*64) or
+hyperthreads,so there are effectively N = 256 (4*64) or N = 264 (4*66)
-N = 264 (4*66) cores to run on. The product of MPI tasks * OpenMP threads/task should not exceed this limit,
+cores to run on. The product of MPI tasks * OpenMP threads/task should
-otherwise performance will suffer. Note that with the KOKKOS package you do not need to
+not exceed this limit, otherwise performance will suffer. Note that
-specify how many KNLs there are per node; each
+with the KOKKOS package you do not need to specify how many KNLs there
-KNL is simply treated as running some number of MPI tasks.
+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
+NOTE: The default for the "package kokkos"_package.html command is to
-to use "full" neighbor lists and set the Newton flag to "off" for both
+use "full" neighbor lists and set the Newton flag to "off" for both
-pairwise and bonded interactions. When running on KNL, this
+pairwise and bonded interactions. When running on KNL, this will
-will typically be best for pair-wise potentials. For manybody potentials,
+typically be best for pair-wise potentials. For manybody potentials,
-using "half" neighbor lists and setting the
+using "half" neighbor lists and setting the Newton flag to "on" may be
-Newton flag to "on" may be faster. It can also be faster to use non-threaded communication.
+faster. It can also be faster to use non-threaded communication.  Use
-Use the "-pk kokkos" "command-line switch"_Section_start.html#start_7 to
+the "-pk kokkos" "command-line switch"_Section_start.html#start_7 to
-change the default "package kokkos"_package.html
+change the default "package kokkos"_package.html options. See its doc
-options. See its doc page for details and default settings. Experimenting with
+page for details and default settings. Experimenting with its options
-its options can provide a speed-up for specific calculations. For example:
+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
+NOTE: To build with Kokkos support for Intel Xeon Phi coprocessors
-system must be configured to use them in "native" mode, not "offload"
+such as Knight's Corner (KNC), your system must be configured to use
-mode like the USER-INTEL package supports.
+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
+Use the "-k" "command-line switch"_Section_start.html#start_7 to
-specify the number of GPUs per node. Typically the -np setting
+specify the number of GPUs per node. Typically the -np setting of the
-of the mpirun command should set the number of MPI
+mpirun command should set the number of MPI tasks/node to be equal to
-tasks/node to be equal to the # of physical GPUs on the node.
+the # of physical GPUs on the node.  You can assign multiple MPI tasks
-You can assign multiple MPI tasks to the same GPU with the
+to the same GPU with the KOKKOS package, but this is usually only
-KOKKOS package, but this is usually only faster if significant portions
+faster if significant portions of the input script have not been
-of the input script have not been ported to use Kokkos. Using CUDA MPS
+ported to use Kokkos. Using CUDA MPS is recommended in this
-is recommended in this scenario. As above for multi-core CPUs (and no GPU), if N is the number
+scenario. As above for multi-core CPUs (and no GPU), if N is the
-of physical cores/node, then the number of MPI tasks/node should not exceed N.
+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,
+Here are examples of how to use the KOKKOS package for GPUs, assuming
-assuming one or more nodes, each with two GPUs:
+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
+NOTE: The default for the "package kokkos"_package.html command is to
-to use "full" neighbor lists and set the Newton flag to "off" for both
+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,
+When running on Maxwell or Kepler GPUs, this will typically be
-using "half" neighbor lists and setting the
+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
+Newton flag to "on" may be faster. For many pair styles, setting the
-equal to the ghost atom cutoff will give speedup.
+neighbor binsize equal to the ghost atom cutoff will give speedup.
-Use the "-pk kokkos" "command-line switch"_Section_start.html#start_7 to
+Use the "-pk kokkos" "command-line switch"_Section_start.html#start_7
-change the default "package kokkos"_package.html
+to change the default "package kokkos"_package.html options. See its
-options. See its doc page for details and default settings. Experimenting with
+doc page for details and default settings. Experimenting with its
-its options can provide a speed-up for specific calculations. For example:
+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
+The discussion above for building LAMMPS with the KOKKOS package, the
-appropriate thread are the same.
+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
+With the KOKKOS package, both OpenMP multi-threading and GPUs can be
-together in a few special cases. In the Makefile, the KOKKOS_DEVICES variable must
+used together in a few special cases. In the Makefile, the
-include both "Cuda" and "OpenMP", as is the case for /src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi
+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.
+using the "-sf kk" in the command line gives the default CUDA version
-However, if the "/kk/host" suffix is added to a specific style in the input
+everywhere.  However, if the "/kk/host" suffix is added to a specific
-script, the Kokkos OpenMP (CPU) version of that specific style will be used instead.
+style in the input script, the Kokkos OpenMP (CPU) version of that
-Set the number of OpenMP threads as "t Nt" and the number of GPUs as "g Ng"
+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
+Conversely, if the "-sf kk/host" is used in the command line and then
-"/kk" or "/kk/device" suffix is added to a specific style in your input script,
+the "/kk" or "/kk/device" suffix is added to a specific style in your
-then only that specific style will run on the GPU while everything else will
+input script, then only that specific style will run on the GPU while
-run on the CPU in OpenMP mode. Note that the execution of the CPU and GPU
+everything else will run on the CPU in OpenMP mode. Note that the
-styles will NOT overlap, except for a special case:
+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
+A kspace style and/or molecular topology (bonds, angles, etc.) running
-the host CPU can overlap with a pair style running on the GPU. First compile
+on the host CPU can overlap with a pair style running on the
-with "--default-stream per-thread" added to CCFLAGS in the Kokkos CUDA Makefile.
+GPU. First compile with "--default-stream per-thread" added to CCFLAGS
-Then explicitly use the "/kk/host" suffix for kspace and bonds, angles, etc.
+in the Kokkos CUDA Makefile.  Then explicitly use the "/kk/host"
-in the input file and the "kk" suffix (equal to "kk/device") on the command line.
+suffix for kspace and bonds, angles, etc.  in the input file and the
-Also make sure the environment variable CUDA_LAUNCH_BLOCKING is not set to "1"
+"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
+those discussed above. Each takes a value shown below. The default
-default value is listed, which is set in the
+value is listed, which is set in the /lib/kokkos/Makefile.kokkos file.
-/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
+KOKKOS_CUDA_OPTIONS are additional options for CUDA. The LAMMPS KOKKOS
-with the {enable_lambda} option when using GPUs.
+package must be compiled with the {enable_lambda} option when using
+GPUs.
 
 [Restrictions:]
 
-Currently, there are no precision options with the KOKKOS
+Currently, there are no precision options with the KOKKOS package. All
-package. All compilation and computation is performed in double
+compilation and computation is performed in double precision.
-precision.

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