diff --git a/doc/src/Commands.txt b/doc/src/Commands.txt
new file mode 100644
index 0000000000000000000000000000000000000000..30e3343bd21c1203b8182f5f42dbab92a15c723b
--- /dev/null
+++ b/doc/src/Commands.txt
@@ -0,0 +1,51 @@
+"Previous Section"_Run.html - "LAMMPS WWW Site"_lws -
+"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
+Section"_Packages.html :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html#comm)
+
+:line
+
+Commands :h2
+
+These pages describe how a LAMMPS input script is formatted and the
+commands in it are used to define a LAMMPS simulation.
+
+<!-- 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 -->
+
diff --git a/doc/src/Commands_all.txt b/doc/src/Commands_all.txt
new file mode 100644
index 0000000000000000000000000000000000000000..13db1272b928e558ceda0853df22162945e6c6e5
--- /dev/null
+++ b/doc/src/Commands_all.txt
@@ -0,0 +1,128 @@
+"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+"All commands"_Commands_all.html,
+"Fix styles"_Commands_fix.html,
+"Compute styles"_Commands_compute.html,
+"Pair styles"_Commands_pair.html,
+"Bond styles"_Commands_bond.html,
+"Angle styles"_Commands_bond.html#angle,
+"Dihedral styles"_Commands_bond.html#dihedral,
+"Improper styles"_Commands_bond.html#improper,
+"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
+
+All commands :h3
+
+An alphabetic list of all LAMMPS commmands.
+
+"angle_coeff"_angle_coeff.html,
+"angle_style"_angle_style.html,
+"atom_modify"_atom_modify.html,
+"atom_style"_atom_style.html,
+"balance"_balance.html,
+"bond_coeff"_bond_coeff.html,
+"bond_style"_bond_style.html,
+"bond_write"_bond_write.html,
+"boundary"_boundary.html,
+"box"_box.html,
+"change_box"_change_box.html,
+"clear"_clear.html,
+"comm_modify"_comm_modify.html,
+"comm_style"_comm_style.html,
+"compute"_compute.html,
+"compute_modify"_compute_modify.html,
+"create_atoms"_create_atoms.html,
+"create_bonds"_create_bonds.html,
+"create_box"_create_box.html,
+"delete_atoms"_delete_atoms.html,
+"delete_bonds"_delete_bonds.html,
+"dielectric"_dielectric.html,
+"dihedral_coeff"_dihedral_coeff.html,
+"dihedral_style"_dihedral_style.html,
+"dimension"_dimension.html,
+"displace_atoms"_displace_atoms.html,
+"dump"_dump.html,
+"dump image"_dump_image.html,
+"dump_modify"_dump_modify.html,
+"dump movie"_dump_image.html,
+"dump netcdf"_dump_netcdf.html,
+"dump netcdf/mpiio"_dump_netcdf.html,
+"dump vtk"_dump_vtk.html,
+"echo"_echo.html,
+"fix"_fix.html,
+"fix_modify"_fix_modify.html,
+"group"_group.html,
+"group2ndx"_group2ndx.html,
+"if"_if.html,
+"info"_info.html,
+"improper_coeff"_improper_coeff.html,
+"improper_style"_improper_style.html,
+"include"_include.html,
+"jump"_jump.html,
+"kspace_modify"_kspace_modify.html,
+"kspace_style"_kspace_style.html,
+"label"_label.html,
+"lattice"_lattice.html,
+"log"_log.html,
+"mass"_mass.html,
+"minimize"_minimize.html,
+"min_modify"_min_modify.html,
+"min_style"_min_style.html,
+"molecule"_molecule.html,
+"ndx2group"_group2ndx.html,
+"neb"_neb.html,
+"neigh_modify"_neigh_modify.html,
+"neighbor"_neighbor.html,
+"newton"_newton.html,
+"next"_next.html,
+"package"_package.html,
+"pair_coeff"_pair_coeff.html,
+"pair_modify"_pair_modify.html,
+"pair_style"_pair_style.html,
+"pair_write"_pair_write.html,
+"partition"_partition.html,
+"prd"_prd.html,
+"print"_print.html,
+"processors"_processors.html,
+"python"_python.html,
+"quit"_quit.html,
+"read_data"_read_data.html,
+"read_dump"_read_dump.html,
+"read_restart"_read_restart.html,
+"region"_region.html,
+"replicate"_replicate.html,
+"rerun"_rerun.html,
+"reset_ids"_reset_ids.html,
+"reset_timestep"_reset_timestep.html,
+"restart"_restart.html,
+"run"_run.html,
+"run_style"_run_style.html,
+"set"_set.html,
+"shell"_shell.html,
+"special_bonds"_special_bonds.html,
+"suffix"_suffix.html,
+"tad"_tad.html,
+"temper"_temper.html,
+"temper/grem"_temper_grem.html,
+"temper/npt"_temper_npt.html,
+"thermo"_thermo.html,
+"thermo_modify"_thermo_modify.html,
+"thermo_style"_thermo_style.html,
+"timer"_timer.html,
+"timestep"_timestep.html,
+"uncompute"_uncompute.html,
+"undump"_undump.html,
+"unfix"_unfix.html,
+"units"_units.html,
+"variable"_variable.html,
+"velocity"_velocity.html,
+"write_coeff"_write_coeff.html,
+"write_data"_write_data.html,
+"write_dump"_write_dump.html,
+"write_restart"_write_restart.html :tb(c=6,ea=c)
diff --git a/doc/src/Commands_bond.txt b/doc/src/Commands_bond.txt
new file mode 100644
index 0000000000000000000000000000000000000000..314260cb14bc582a5791912ac055ec50260878f1
--- /dev/null
+++ b/doc/src/Commands_bond.txt
@@ -0,0 +1,124 @@
+"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+"All commands"_Commands_all.html,
+"Fix styles"_Commands_fix.html,
+"Compute styles"_Commands_compute.html,
+"Pair styles"_Commands_pair.html,
+"Bond styles"_Commands_bond.html,
+"Angle styles"_Commands_bond.html#angle,
+"Dihedral styles"_Commands_bond.html#dihedral,
+"Improper styles"_Commands_bond.html#improper,
+"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
+
+Bond, angle, dihedral, and improper commands :h3
+
+:line
+
+Bond_style potentials :h3,link(bond)
+
+All LAMMPS "bond_style"_bond_style.html commands.  Some styles have
+accelerated versions.  This is indicated by additional letters in
+parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+OPT.
+
+"none"_bond_none.html,
+"zero"_bond_zero.html,
+"hybrid"_bond_hybrid.html :tb(c=3,ea=c)
+
+"class2 (ko)"_bond_class2.html,
+"fene (iko)"_bond_fene.html,
+"fene/expand (o)"_bond_fene_expand.html,
+"gromos (o)"_bond_gromos.html,
+"harmonic (ko)"_bond_harmonic.html,
+"harmonic/shift (o)"_bond_harmonic_shift.html,
+"harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html,
+"morse (o)"_bond_morse.html,
+"nonlinear (o)"_bond_nonlinear.html,
+"oxdna/fene"_bond_oxdna.html,
+"oxdna2/fene"_bond_oxdna.html,
+"quartic (o)"_bond_quartic.html,
+"table (o)"_bond_table.html :tb(c=4,ea=c)
+
+:line
+
+Angle_style potentials :h3,link(angle)
+
+All LAMMPS "angle_style"_angle_style.html commands.  Some styles have
+accelerated versions.  This is indicated by additional letters in
+parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+OPT.
+
+"none"_angle_none.html,
+"zero"_angle_zero.html,
+"hybrid"_angle_hybrid.html :tb(c=3,ea=c)
+
+"charmm (ko)"_angle_charmm.html,
+"class2 (ko)"_angle_class2.html,
+"cosine (o)"_angle_cosine.html,
+"cosine/delta (o)"_angle_cosine_delta.html,
+"cosine/periodic (o)"_angle_cosine_periodic.html,
+"cosine/shift (o)"_angle_cosine_shift.html,
+"cosine/shift/exp (o)"_angle_cosine_shift_exp.html,
+"cosine/squared (o)"_angle_cosine_squared.html,
+"dipole (o)"_angle_dipole.html,
+"fourier (o)"_angle_fourier.html,
+"fourier/simple (o)"_angle_fourier_simple.html,
+"harmonic (iko)"_angle_harmonic.html,
+"quartic (o)"_angle_quartic.html,
+"sdk"_angle_sdk.html,
+"table (o)"_angle_table.html :tb(c=4,ea=c)
+
+:line
+
+Dihedral_style potentials :h3,link(dihedral)
+
+All LAMMPS "dihedral_style"_dihedral_style.html commands.  Some styles
+have accelerated versions.  This is indicated by additional letters in
+parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+OPT.
+
+"none"_dihedral_none.html,
+"zero"_dihedral_zero.html,
+"hybrid"_dihedral_hybrid.html :tb(c=3,ea=c)
+
+"charmm (iko)"_dihedral_charmm.html,
+"charmmfsw"_dihedral_charmm.html,
+"class2 (ko)"_dihedral_class2.html,
+"cosine/shift/exp (o)"_dihedral_cosine_shift_exp.html,
+"fourier (io)"_dihedral_fourier.html,
+"harmonic (io)"_dihedral_harmonic.html,
+"helix (o)"_dihedral_helix.html,
+"multi/harmonic (o)"_dihedral_multi_harmonic.html,
+"nharmonic (o)"_dihedral_nharmonic.html,
+"opls (iko)"_dihedral_opls.htm;,
+"quadratic (o)"_dihedral_quadratic.html,
+"spherical (o)"_dihedral_spherical.html,
+"table (o)"_dihedral_table.html,
+"table/cut"_dihedral_table_cut.html :tb(c=4,ea=c)
+
+:line
+
+Improper_style potentials :h3,link(improper)
+
+All LAMMPS "improper_style"_improper_style.html commands.  Some styles
+have accelerated versions.  This is indicated by additional letters in
+parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+OPT.
+
+"none"_improper_none.html,
+"zero"_improper_zero.html,
+"hybrid"_improper_hybrid.html  :tb(c=3,ea=c)
+
+"class2 (ko)"_improper_class2.html,
+"cossq (o)"_improper_cossq.html,
+"cvff (io)"_improper_cvff.html,
+"distance"_improper_distance.html,
+"fourier (o)"_improper_fourier.html,
+"harmonic (iko)"_improper_harmonic.html,
+"ring (o)"_improper_ring.html,
+"umbrella (o)"_improper_umbrella.html :tb(c=4,ea=c)
diff --git a/doc/src/Commands_category.txt b/doc/src/Commands_category.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5d047c67272ef0e8bedb1d2d9e52260ee4be0b2e
--- /dev/null
+++ b/doc/src/Commands_category.txt
@@ -0,0 +1,141 @@
+"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Commands by category :h3
+
+This page lists most of the LAMMPS commands, grouped by category.  The
+"Commands all"_Commands_all.html doc page lists all commands
+alphabetically.  It also includes long lists of style options for
+entries that appear in the following categories as a single command
+(fix, compute, pair, etc).
+
+Initialization:
+
+"newton"_newton.html,
+"package"_package.html,
+"processors"_processors.html,
+"suffix"_suffix.html,
+"units"_units.html :ul
+
+Setup simulation box:
+
+"boundary"_boundary.html,
+"box"_box.html,
+"change_box"_change_box.html,
+"create_box"_create_box.html,
+"dimension"_dimension.html,
+"lattice"_lattice.html,
+"region"_region.html :ul
+
+Setup atoms:
+
+"atom_modify"_atom_modify.html,
+"atom_style"_atom_style.html,
+"balance"_balance.html,
+"create_atoms"_create_atoms.html,
+"create_bonds"_create_bonds.html,
+"delete_atoms"_delete_atoms.html,
+"delete_bonds"_delete_bonds.html,
+"displace_atoms"_displace_atoms.html,
+"group"_group.html,
+"mass"_mass.html,
+"molecule"_molecule.html,
+"read_data"_read_data.html,
+"read_dump"_read_dump.html,
+"read_restart"_read_restart.html,
+"replicate"_replicate.html,
+"set"_set.html,
+"velocity"_velocity.html :ul
+
+Force fields:
+
+"angle_coeff"_angle_coeff.html,
+"angle_style"_angle_style.html,
+"bond_coeff"_bond_coeff.html,
+"bond_style"_bond_style.html,
+"bond_write"_bond_write.html,
+"dielectric"_dielectric.html,
+"dihedral_coeff"_dihedral_coeff.html,
+"dihedral_style"_dihedral_style.html,
+"improper_coeff"_improper_coeff.html,
+"improper_style"_improper_style.html,
+"kspace_modify"_kspace_modify.html,
+"kspace_style"_kspace_style.html,
+"pair_coeff"_pair_coeff.html,
+"pair_modify"_pair_modify.html,
+"pair_style"_pair_style.html,
+"pair_write"_pair_write.html,
+"special_bonds"_special_bonds.html :ul
+
+Settings:
+
+"comm_modify"_comm_modify.html,
+"comm_style"_comm_style.html,
+"info"_info.html,
+"min_modify"_min_modify.html,
+"min_style"_min_style.html,
+"neigh_modify"_neigh_modify.html,
+"neighbor"_neighbor.html,
+"partition"_partition.html,
+"reset_timestep"_reset_timestep.html,
+"run_style"_run_style.html,
+"timer"_timer.html,
+"timestep"_timestep.html :ul
+
+Operations within timestepping (fixes) and diagnostics (computes):
+
+"compute"_compute.html,
+"compute_modify"_compute_modify.html,
+"fix"_fix.html,
+"fix_modify"_fix_modify.html,
+"uncompute"_uncompute.html,
+"unfix"_unfix.html :ul
+
+Output:
+
+"dump image"_dump_image.html,
+"dump movie"_dump_image.html,
+"dump"_dump.html,
+"dump_modify"_dump_modify.html,
+"restart"_restart.html,
+"thermo"_thermo.html,
+"thermo_modify"_thermo_modify.html,
+"thermo_style"_thermo_style.html,
+"undump"_undump.html,
+"write_coeff"_write_coeff.html,
+"write_data"_write_data.html,
+"write_dump"_write_dump.html,
+"write_restart"_write_restart.html :ul
+
+Actions:
+
+"minimize"_minimize.html,
+"neb"_neb.html,
+"prd"_prd.html,
+"rerun"_rerun.html,
+"run"_run.html,
+"tad"_tad.html,
+"temper"_temper.html :ul
+
+Input script control:
+
+"clear"_clear.html,
+"echo"_echo.html,
+"if"_if.html,
+"include"_include.html,
+"jump"_jump.html,
+"label"_label.html,
+"log"_log.html,
+"next"_next.html,
+"print"_print.html,
+"python"_python.html,
+"quit"_quit.html,
+"shell"_shell.html,
+"variable"_variable.html :ul
+
diff --git a/doc/src/Commands_compute.txt b/doc/src/Commands_compute.txt
new file mode 100644
index 0000000000000000000000000000000000000000..028e274c9be4a80555dfcab5a417d738b763bfda
--- /dev/null
+++ b/doc/src/Commands_compute.txt
@@ -0,0 +1,153 @@
+"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+"All commands"_Commands_all.html,
+"Fix styles"_Commands_fix.html,
+"Compute styles"_Commands_compute.html,
+"Pair styles"_Commands_pair.html,
+"Bond styles"_Commands_bond.html,
+"Angle styles"_Commands_bond.html#angle,
+"Dihedral styles"_Commands_bond.html#dihedral,
+"Improper styles"_Commands_bond.html#improper,
+"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
+
+Compute commands :h3
+
+An alphabetic list of all LAMMPS "compute"_compute.html commands.
+Some styles have accelerated versions.  This is indicated by
+additional letters in parenthesis: g = GPU, i = USER-INTEL, k =
+KOKKOS, o = USER-OMP, t = OPT.
+
+"ackland/atom"_compute_ackland_atom.html,
+"aggregate/atom"_compute_cluster_atom.html,
+"angle"_compute_angle.html,
+"angle/local"_compute_angle_local.html,
+"angmom/chunk"_compute_angmom_chunk.html,
+"basal/atom"_compute_basal_atom.html,
+"body/local"_compute_body_local.html,
+"bond"_compute_bond.html,
+"bond/local"_compute_bond_local.html,
+"centro/atom"_compute_centro_atom.html,
+"chunk/atom"_compute_chunk_atom.html,
+"cluster/atom"_compute_cluster_atom.html,
+"cna/atom"_compute_cna_atom.html,
+"cnp/atom"_compute_cnp_atom.html,
+"com"_compute_com.html,
+"com/chunk"_compute_com_chunk.html,
+"contact/atom"_compute_contact_atom.html,
+"coord/atom"_compute_coord_atom.html,
+"damage/atom"_compute_damage_atom.html,
+"dihedral"_compute_dihedral.html,
+"dihedral/local"_compute_dihedral_local.html,
+"dilatation/atom"_compute_dilatation_atom.html,
+"dipole/chunk"_compute_dipole_chunk.html,
+"displace/atom"_compute_displace_atom.html,
+"dpd"_compute_dpd.html,
+"dpd/atom"_compute_dpd_atom.html,
+"edpd/temp/atom"_compute_edpd_temp_atom.html,
+"entropy/atom"_compute_entropy_atom.html,
+"erotate/asphere"_compute_erotate_asphere.html,
+"erotate/rigid"_compute_erotate_rigid.html,
+"erotate/sphere"_compute_erotate_sphere.html,
+"erotate/sphere/atom"_compute_erotate_sphere_atom.html,
+"event/displace"_compute_event_displace.html,
+"fep"_compute_fep.html,
+"force/tally"_compute_tally.html,
+"fragment/atom"_compute_cluster_atom.html,
+"global/atom"_compute_global_atom.html,
+"group/group"_compute_group_group.html,
+"gyration"_compute_gyration.html,
+"gyration/chunk"_compute_gyration_chunk.html,
+"heat/flux"_compute_heat_flux.html,
+"heat/flux/tally"_compute_tally.html,
+"hexorder/atom"_compute_hexorder_atom.html,
+"improper"_compute_improper.html,
+"improper/local"_compute_improper_local.html,
+"inertia/chunk"_compute_inertia_chunk.html,
+"ke"_compute_ke.html,
+"ke/atom"_compute_ke_atom.html,
+"ke/atom/eff"_compute_ke_atom_eff.html,
+"ke/eff"_compute_ke_eff.html,
+"ke/rigid"_compute_ke_rigid.html,
+"meso/e/atom"_compute_meso_e_atom.html,
+"meso/rho/atom"_compute_meso_rho_atom.html,
+"meso/t/atom"_compute_meso_t_atom.html,
+"msd"_compute_msd.html,
+"msd/chunk"_compute_msd_chunk.html,
+"msd/nongauss"_compute_msd_nongauss.html,
+"omega/chunk"_compute_omega_chunk.html,
+"orientorder/atom"_compute_orientorder_atom.html,
+"pair"_compute_pair.html,
+"pair/local"_compute_pair_local.html,
+"pe"_compute_pe.html,
+"pe/atom"_compute_pe_atom.html,
+"pe/mol/tally"_compute_tally.html,
+"pe/tally"_compute_tally.html,
+"plasticity/atom"_compute_plasticity_atom.html,
+"pressure"_compute_pressure.html,
+"pressure/uef"_compute_pressure_uef.html,
+"property/atom"_compute_property_atom.html,
+"property/chunk"_compute_property_chunk.html,
+"property/local"_compute_property_local.html,
+"rdf"_compute_rdf.html,
+"reduce"_compute_reduce.html,
+"reduce/region"_compute_reduce.html,
+"rigid/local"_compute_rigid_local.html,
+"saed"_compute_saed.html,
+"slice"_compute_slice.html,
+"smd/contact/radius"_compute_smd_contact_radius.html,
+"smd/damage"_compute_smd_damage.html,
+"smd/hourglass/error"_compute_smd_hourglass_error.html,
+"smd/internal/energy"_compute_smd_internal_energy.html,
+"smd/plastic/strain"_compute_smd_plastic_strain.html,
+"smd/plastic/strain/rate"_compute_smd_plastic_strain_rate.html,
+"smd/rho"_compute_smd_rho.html,
+"smd/tlsph/defgrad"_compute_smd_tlsph_defgrad.html,
+"smd/tlsph/dt"_compute_smd_tlsph_dt.html,
+"smd/tlsph/num/neighs"_compute_smd_tlsph_num_neighs.html,
+"smd/tlsph/shape"_compute_smd_tlsph_shape.html,
+"smd/tlsph/strain"_compute_smd_tlsph_strain.html,
+"smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html,
+"smd/tlsph/stress"_compute_smd_tlsph_stress.html,
+"smd/triangle/mesh/vertices"_compute_smd_triangle_mesh_vertices.html,
+"smd/ulsph/num/neighs"_compute_smd_ulsph_num_neighs.html,
+"smd/ulsph/strain"_compute_smd_ulsph_strain.html,
+"smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html,
+"smd/ulsph/stress"_compute_smd_ulsph_stress.html,
+"smd/vol"_compute_smd_vol.html,
+"sna/atom"_compute_sna_atom.html,
+"snad/atom"_compute_sna_atom.html,
+"snav/atom"_compute_sna_atom.html,
+"spin"_compute_spin.html,
+"stress/atom"_compute_stress_atom.html,
+"stress/tally"_compute_tally.html,
+"tdpd/cc/atom"_compute_tdpd_cc_atom.html,
+"temp (k)"_compute_temp.html,
+"temp/asphere"_compute_temp_asphere.html,
+"temp/body"_compute_temp_body.html,
+"temp/chunk"_compute_temp_chunk.html,
+"temp/com"_compute_temp_com.html,
+"temp/deform"_compute_temp_deform.html,
+"temp/deform/eff"_compute_temp_deform_eff.html,
+"temp/drude"_compute_temp_drude.html,
+"temp/eff"_compute_temp_eff.html,
+"temp/partial"_compute_temp_partial.html,
+"temp/profile"_compute_temp_profile.html,
+"temp/ramp"_compute_temp_ramp.html,
+"temp/region"_compute_temp_region.html,
+"temp/region/eff"_compute_temp_region_eff.html,
+"temp/rotate"_compute_temp_rotate.html,
+"temp/sphere"_compute_temp_sphere.html,
+"temp/uef"_compute_temp_uef.html,
+"ti"_compute_ti.html,
+"torque/chunk"_compute_torque_chunk.html,
+"vacf"_compute_vacf.html,
+"vcm/chunk"_compute_vcm_chunk.html,
+"voronoi/atom"_compute_voronoi_atom.html,
+"xrd"_compute_xrd.html :tb(c=6,ea=c)
diff --git a/doc/src/Commands_fix.txt b/doc/src/Commands_fix.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e002c117701110fc6dd33e83865386f52d2bae3e
--- /dev/null
+++ b/doc/src/Commands_fix.txt
@@ -0,0 +1,229 @@
+"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+"All commands"_Commands_all.html,
+"Fix styles"_Commands_fix.html,
+"Compute styles"_Commands_compute.html,
+"Pair styles"_Commands_pair.html,
+"Bond styles"_Commands_bond.html,
+"Angle styles"_Commands_bond.html#angle,
+"Dihedral styles"_Commands_bond.html#dihedral,
+"Improper styles"_Commands_bond.html#improper,
+"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
+
+Fix commands :h3
+
+An alphabetic list of all LAMMPS "fix"_fix.html commands.  Some styles
+have accelerated versions.  This is indicated by additional letters in
+parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+OPT.
+
+"adapt"_fix_adapt.html,
+"adapt/fep"_fix_adapt_fep.html,
+"addforce"_fix_addforce.html,
+"addtorque"_fix_addtorque.html,
+"append/atoms"_fix_append_atoms.html,
+"atc"_fix_atc.html,
+"atom/swap"_fix_atom_swap.html,
+"ave/atom"_fix_ave_atom.html,
+"ave/chunk"_fix_ave_chunk.html,
+"ave/correlate"_fix_ave_correlate.html,
+"ave/correlate/long"_fix_ave_correlate_long.html,
+"ave/histo"_fix_ave_histo.html,
+"ave/histo/weight"_fix_ave_histo.html,
+"ave/time"_fix_ave_time.html,
+"aveforce"_fix_aveforce.html,
+"balance"_fix_balance.html,
+"bond/break"_fix_bond_break.html,
+"bond/create"_fix_bond_create.html,
+"bond/react"_fix_bond_react.html,
+"bond/swap"_fix_bond_swap.html,
+"box/relax"_fix_box_relax.html,
+"cmap"_fix_cmap.html,
+"colvars"_fix_colvars.html,
+"controller"_fix_controller.html,
+"deform (k)"_fix_deform.html,
+"deposit"_fix_deposit.html,
+"dpd/energy (k)"_fix_dpd_energy.html,
+"drag"_fix_drag.html,
+"drude"_fix_drude.html,
+"drude/transform/direct"_fix_drude_transform.html,
+"drude/transform/reverse"_fix_drude_transform.html,
+"dt/reset"_fix_dt_reset.html,
+"edpd/source"_fix_dpd_source.html,
+"efield"_fix_efield.html,
+"ehex"_fix_ehex.html,
+"enforce2d (k)"_fix_enforce2d.html,
+"eos/cv"_fix_eos_cv.html,
+"eos/table"_fix_eos_table.html,
+"eos/table/rx (k)"_fix_eos_table_rx.html,
+"evaporate"_fix_evaporate.html,
+"external"_fix_external.html,
+"filter/corotate"_fix_filter_corotate.html,
+"flow/gauss"_fix_flow_gauss.html,
+"freeze"_fix_freeze.html,
+"gcmc"_fix_gcmc.html,
+"gld"_fix_gld.html,
+"gle"_fix_gle.html,
+"gravity (o)"_fix_gravity.html,
+"grem"_fix_grem.html,
+"halt"_fix_halt.html,
+"heat"_fix_heat.html,
+"imd"_fix_imd.html,
+"indent"_fix_indent.html,
+"ipi"_fix_ipi.html,
+"langevin (k)"_fix_langevin.html,
+"langevin/drude"_fix_langevin_drude.html,
+"langevin/eff"_fix_langevin_eff.html,
+"langevin/spin"_fix_langevin_spin.html,
+"latte"_fix_latte.html,
+"lb/fluid"_fix_lb_fluid.html,
+"lb/momentum"_fix_lb_momentum.html,
+"lb/pc"_fix_lb_pc.html,
+"lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html,
+"lb/viscous"_fix_lb_viscous.html,
+"lineforce"_fix_lineforce.html,
+"manifoldforce"_fix_manifoldforce.html,
+"meso"_fix_meso.html,
+"meso/stationary"_fix_meso_stationary.html,
+"momentum (k)"_fix_momentum.html,
+"move"_fix_move.html,
+"mscg"_fix_mscg.html,
+"msst"_fix_msst.html,
+"mvv/dpd"_fix_mvv_dpd.html,
+"mvv/edpd"_fix_mvv_dpd.html,
+"mvv/tdpd"_fix_mvv_dpd.html,
+"neb"_fix_neb.html,
+"nph (ko)"_fix_nh.html,
+"nph/asphere (o)"_fix_nph_asphere.html,
+"nph/body"_fix_nph_body.html,
+"nph/eff"_fix_nh_eff.html,
+"nph/sphere (o)"_fix_nph_sphere.html,
+"nphug (o)"_fix_nphug.html,
+"npt (kio)"_fix_nh.html,
+"npt/asphere (o)"_fix_npt_asphere.html,
+"npt/body"_fix_npt_body.html,
+"npt/eff"_fix_nh_eff.html,
+"npt/sphere (o)"_fix_npt_sphere.html,
+"npt/uef"_fix_nh_uef.html,
+"nve (kio)"_fix_nve.html,
+"nve/asphere (i)"_fix_nve_asphere.html,
+"nve/asphere/noforce"_fix_nve_asphere_noforce.html,
+"nve/body"_fix_nve_body.html,
+"nve/dot"_fix_nve_dot.html,
+"nve/dotc/langevin"_fix_nve_dotc_langevin.html,
+"nve/eff"_fix_nve_eff.html,
+"nve/limit"_fix_nve_limit.html,
+"nve/line"_fix_nve_line.html,
+"nve/manifold/rattle"_fix_nve_manifold_rattle.html,
+"nve/noforce"_fix_nve_noforce.html,
+"nve/sphere (o)"_fix_nve_sphere.html,
+"nve/spin"_fix_nve_spin.html,
+"nve/tri"_fix_nve_tri.html,
+"nvk"_fix_nvk.html,
+"nvt (iko)"_fix_nh.html,
+"nvt/asphere (o)"_fix_nvt_asphere.html,
+"nvt/body"_fix_nvt_body.html,
+"nvt/eff"_fix_nh_eff.html,
+"nvt/manifold/rattle"_fix_nvt_manifold_rattle.html,
+"nvt/sllod (io)"_fix_nvt_sllod.html,
+"nvt/sllod/eff"_fix_nvt_sllod_eff.html,
+"nvt/sphere (o)"_fix_nvt_sphere.html,
+"nvt/uef"_fix_nh_uef.html,
+"oneway"_fix_oneway.html,
+"orient/bcc"_fix_orient.html,
+"orient/fcc"_fix_orient.html,
+"phonon"_fix_phonon.html,
+"pimd"_fix_pimd.html,
+"planeforce"_fix_planeforce.html,
+"poems"_fix_poems.html,
+"pour"_fix_pour.html,
+"precession/spin"_fix_precession_spin.html,
+"press/berendsen"_fix_press_berendsen.html,
+"print"_fix_print.html,
+"property/atom (k)"_fix_property_atom.html,
+"python/invoke"_fix_python_invoke.html,
+"python/move"_fix_python_move.html,
+"qbmsst"_fix_qbmsst.html,
+"qeq/comb (o)"_fix_qeq_comb.html,
+"qeq/dynamic"_fix_qeq.html,
+"qeq/fire"_fix_qeq.html,
+"qeq/point"_fix_qeq.html,
+"qeq/reax (ko)"_fix_qeq_reax.html,
+"qeq/shielded"_fix_qeq.html,
+"qeq/slater"_fix_qeq.html,
+"qmmm"_fix_qmmm.html,
+"qtb"_fix_qtb.html,
+"rattle"_fix_shake.html,
+"reax/bonds"_fix_reax_bonds.html,
+"reax/c/bonds (k)"_fix_reax_bonds.html,
+"reax/c/species (k)"_fix_reaxc_species.html,
+"recenter"_fix_recenter.html,
+"restrain"_fix_restrain.html,
+"rhok"_fix_rhok.html,
+"rigid (o)"_fix_rigid.html,
+"rigid/nph (o)"_fix_rigid.html,
+"rigid/npt (o)"_fix_rigid.html,
+"rigid/nve (o)"_fix_rigid.html,
+"rigid/nvt (o)"_fix_rigid.html,
+"rigid/small (o)"_fix_rigid.html,
+"rigid/small/nph"_fix_rigid.html,
+"rigid/small/npt"_fix_rigid.html,
+"rigid/small/nve"_fix_rigid.html,
+"rigid/small/nvt"_fix_rigid.html,
+"rx (k)"_fix_rx.html,
+"saed/vtk"_fix_saed_vtk.html,
+"setforce (k)"_fix_setforce.html,
+"shake"_fix_shake.html,
+"shardlow (k)"_fix_shardlow.html,
+"smd"_fix_smd.html,
+"smd/adjust/dt"_fix_smd_adjust_dt.html,
+"smd/integrate/tlsph"_fix_smd_integrate_tlsph.html,
+"smd/integrate/ulsph"_fix_smd_integrate_ulsph.html,
+"smd/move/triangulated/surface"_fix_smd_move_triangulated_surface.html,
+"smd/setvel"_fix_smd_setvel.html,
+"smd/wall/surface"_fix_smd_wall_surface.html,
+"spring"_fix_spring.html,
+"spring/chunk"_fix_spring_chunk.html,
+"spring/rg"_fix_spring_rg.html,
+"spring/self"_fix_spring_self.html,
+"srd"_fix_srd.html,
+"store/force"_fix_store_force.html,
+"store/state"_fix_store_state.html,
+"tdpd/source"_fix_dpd_source.html,
+"temp/berendsen"_fix_temp_berendsen.html,
+"temp/csld"_fix_temp_csvr.html,
+"temp/csvr"_fix_temp_csvr.html,
+"temp/rescale"_fix_temp_rescale.html,
+"temp/rescale/eff"_fix_temp_rescale_eff.html,
+"tfmc"_fix_tfmc.html,
+"thermal/conductivity"_fix_thermal_conductivity.html,
+"ti/spring"_fix_ti_spring.html,
+"tmd"_fix_tmd.html,
+"ttm"_fix_ttm.html,
+"ttm/mod"_fix_ttm.html,
+"tune/kspace"_fix_tune_kspace.html,
+"vector"_fix_vector.html,
+"viscosity"_fix_viscosity.html,
+"viscous"_fix_viscous.html,
+"wall/body/polygon"_fix_wall_body_polygon.html,
+"wall/body/polyhedron"_fix_wall_body_polyhedron.html,
+"wall/colloid"_fix_wall.html,
+"wall/ees"_fix_wall_ees.html,
+"wall/gran"_fix_wall_gran.html,
+"wall/gran/region"_fix_wall_gran_region.html,
+"wall/harmonic"_fix_wall.html,
+"wall/lj1043"_fix_wall.html,
+"wall/lj126"_fix_wall.html,
+"wall/lj93 (k)"_fix_wall.html,
+"wall/piston"_fix_wall_piston.html,
+"wall/reflect (k)"_fix_wall_reflect.html,
+"wall/region"_fix_wall_region.html,
+"wall/region/ees"_fix_wall_ees.html,
+"wall/srd"_fix_wall_srd.html :tb(c=8,ea=c)
diff --git a/doc/src/Commands_input.txt b/doc/src/Commands_input.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8b3dda741b42dd03bcca359e654ef0ab1ae6a043
--- /dev/null
+++ b/doc/src/Commands_input.txt
@@ -0,0 +1,60 @@
+"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+LAMMPS input scripts :h3
+
+LAMMPS executes by reading commands from a input script (text file),
+one line at a time.  When the input script ends, LAMMPS exits.  Each
+command causes LAMMPS to take some action.  It may set an internal
+variable, read in a file, or run a simulation.  Most commands have
+default settings, which means you only need to use the command if you
+wish to change the default.
+
+In many cases, the ordering of commands in an input script is not
+important.  However the following rules apply:
+
+(1) LAMMPS does not read your entire input script and then perform a
+simulation with all the settings.  Rather, the input script is read
+one line at a time and each command takes effect when it is read.
+Thus this sequence of commands:
+
+timestep 0.5
+run      100
+run      100 :pre
+
+does something different than this sequence:
+
+run      100
+timestep 0.5
+run      100 :pre
+
+In the first case, the specified timestep (0.5 fs) is used for two
+simulations of 100 timesteps each.  In the 2nd case, the default
+timestep (1.0 fs) is used for the 1st 100 step simulation and a 0.5 fs
+timestep is used for the 2nd one.
+
+(2) Some commands are only valid when they follow other commands.  For
+example you cannot set the temperature of a group of atoms until atoms
+have been defined and a group command is used to define which atoms
+belong to the group.
+
+(3) Sometimes command B will use values that can be set by command A.
+This means command A must precede command B in the input script if it
+is to have the desired effect.  For example, the
+"read_data"_read_data.html command initializes the system by setting
+up the simulation box and assigning atoms to processors.  If default
+values are not desired, the "processors"_processors.html and
+"boundary"_boundary.html commands need to be used before read_data to
+tell LAMMPS how to map processors to the simulation box.
+
+Many input script errors are detected by LAMMPS and an ERROR or
+WARNING message is printed.  The "Errors"_Errors.html doc page gives
+more information on what errors mean.  The documentation for each
+command lists restrictions on how the command can be used.
+
diff --git a/doc/src/Commands_kspace.txt b/doc/src/Commands_kspace.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a1263445050bda692218aa311831d3565d22155c
--- /dev/null
+++ b/doc/src/Commands_kspace.txt
@@ -0,0 +1,36 @@
+"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands.html)
+
+:line
+
+"All commands"_Commands_all.html,
+"Fix styles"_Commands_fix.html,
+"Compute styles"_Commands_compute.html,
+"Pair styles"_Commands_pair.html,
+"Bond styles"_Commands_bond.html,
+"Angle styles"_Commands_bond.html#angle,
+"Dihedral styles"_Commands_bond.html#dihedral,
+"Improper styles"_Commands_bond.html#improper,
+"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
+
+KSpace solvers :h3
+
+All LAMMPS "kspace_style"_kspace_style.html solvers.  Some styles have
+accelerated versions.  This is indicated by additional letters in
+parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+OPT.
+
+"ewald (o)"_kspace_style.html,
+"ewald/disp"_kspace_style.html,
+"msm (o)"_kspace_style.html,
+"msm/cg (o)"_kspace_style.html,
+"pppm (gok)"_kspace_style.html,
+"pppm/cg (o)"_kspace_style.html,
+"pppm/disp (i)"_kspace_style.html,
+"pppm/disp/tip4p"_kspace_style.html,
+"pppm/stagger"_kspace_style.html,
+"pppm/tip4p (o)"_kspace_style.html :tb(c=4,ea=c)
diff --git a/doc/src/Commands_pair.txt b/doc/src/Commands_pair.txt
new file mode 100644
index 0000000000000000000000000000000000000000..02b22942ae1601bf8e97ceb818f445e88e13cfe0
--- /dev/null
+++ b/doc/src/Commands_pair.txt
@@ -0,0 +1,231 @@
+"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+"All commands"_Commands_all.html,
+"Fix styles"_Commands_fix.html,
+"Compute styles"_Commands_compute.html,
+"Pair styles"_Commands_pair.html,
+"Bond styles"_Commands_bond.html,
+"Angle styles"_Commands_bond.html#angle,
+"Dihedral styles"_Commands_bond.html#dihedral,
+"Improper styles"_Commands_bond.html#improper,
+"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
+
+Pair_style potentials :h3
+
+All LAMMPS "pair_style"_pair_style.html commands.  Some styles have
+accelerated versions.  This is indicated by additional letters in
+parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+OPT.
+
+"none"_pair_none.html,
+"zero"_pair_zero.html,
+"hybrid"_pair_hybrid.html,
+"hybrid/overlay (k)"_pair_hybrid.html :tb(c=4,ea=c)
+
+"adp (o)"_pair_adp.html,
+"agni (o)"_pair_agni.html,
+"airebo (oi)"_pair_airebo.html,
+"airebo/morse (oi)"_pair_airebo.html,
+"awpmd/cut"_pair_awpmd.html,
+"beck (go)"_pair_beck.html,
+"body/nparticle"_pair_body_nparticle.html,
+"body/rounded/polygon"_pair_body_rounded/polygon.html,
+"body/rounded/polyhedron"_pair_body_rounded/polyhedron.html,
+"bop"_pair_bop.html,
+"born (go)"_pair_born.html,
+"born/coul/dsf"_pair_born.html,
+"born/coul/dsf/cs"_pair_born.html,
+"born/coul/long (go)"_pair_born.html,
+"born/coul/long/cs"_pair_born.html,
+"born/coul/msm (o)"_pair_born.html,
+"born/coul/wolf (go)"_pair_born.html,
+"born/coul/wolf/cs"_pair_born.html,
+"brownian (o)"_pair_brownian.html,
+"brownian/poly (o)"_pair_brownian.html,
+"buck (giko)"_pair_buck.html,
+"buck/coul/cut (giko)"_pair_buck.html,
+"buck/coul/long (giko)"_pair_buck.html,
+"buck/coul/long/cs"_pair_buck.html,
+"buck/coul/msm (o)"_pair_buck.html,
+"buck/long/coul/long (o)"_pair_buck_long.html,
+"buck/mdf"_pair_mdf.html,
+"colloid (go)"_pair_colloid.html,
+"comb (o)"_pair_comb.html,
+"comb3"_pair_comb.html,
+"coul/cut (gko)"_pair_coul.html,
+"coul/cut/soft (o)"_pair_lj_soft.html,
+"coul/debye (gko)"_pair_coul.html,
+"coul/diel (o)"_pair_coul_diel.html,
+"coul/dsf (gko)"_pair_coul.html,
+"coul/long (gko)"_pair_coul.html,
+"coul/long/cs"_pair_coul.html,
+"coul/long/soft (o)"_pair_lj_soft.html,
+"coul/msm"_pair_coul.html,
+"coul/shield"_pair_coul_shield.html,
+"coul/streitz"_pair_coul.html,
+"coul/wolf (ko)"_pair_coul.html,
+"coul/wolf/cs"_pair_coul.html,
+"dpd (gio)"_pair_dpd.html,
+"dpd/fdt"_pair_dpd_fdt.html,
+"dpd/fdt/energy (k)"_pair_dpd_fdt.html,
+"dpd/tstat (go)"_pair_dpd.html,
+"dsmc"_pair_dsmc.html,
+"eam (gikot)"_pair_eam.html,
+"eam/alloy (gikot)"_pair_eam.html,
+"eam/cd (o)"_pair_eam.html,
+"eam/fs (gikot)"_pair_eam.html,
+"edip (o)"_pair_edip.html,
+"edip/multi"_pair_edip.html,
+"edpd"_pair_meso.html,
+"eff/cut"_pair_eff.html,
+"eim (o)"_pair_eim.html,
+"exp6/rx (k)"_pair_exp6_rx.html,
+"extep"_pair_extep.html,
+"gauss (go)"_pair_gauss.html,
+"gauss/cut"_pair_gauss.html,
+"gayberne (gio)"_pair_gayberne.html,
+"gran/hertz/history (o)"_pair_gran.html,
+"gran/hooke (o)"_pair_gran.html,
+"gran/hooke/history (o)"_pair_gran.html,
+"gw"_pair_gw.html,
+"gw/zbl"_pair_gw.html,
+"hbond/dreiding/lj (o)"_pair_hbond_dreiding.html,
+"hbond/dreiding/morse (o)"_pair_hbond_dreiding.html,
+"ilp/graphene/hbn"_pair_ilp_graphene_hbn.html,
+"kim"_pair_kim.html,
+"kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html,
+"kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html,
+"lcbop"_pair_lcbop.html,
+"lennard/mdf"_pair_mdf.html,
+"line/lj"_pair_line_lj.html,
+"list"_pair_list.html,
+"lj/charmm/coul/charmm (iko)"_pair_charmm.html,
+"lj/charmm/coul/charmm/implicit (ko)"_pair_charmm.html,
+"lj/charmm/coul/long (giko)"_pair_charmm.html,
+"lj/charmm/coul/long/soft (o)"_pair_charmm.html,
+"lj/charmm/coul/msm"_pair_charmm.html,
+"lj/charmmfsw/coul/charmmfsh"_pair_charmm.html,
+"lj/charmmfsw/coul/long"_pair_charmm.html,
+"lj/class2 (gko)"_pair_class2.html,
+"lj/class2/coul/cut (ko)"_pair_class2.html,
+"lj/class2/coul/long (gko)"_pair_class2.html,
+"lj/cubic (go)"_pair_lj_cubic.html,
+"lj/cut (gikot)"_pair_lj.html,
+"lj/cut/coul/cut (gko)"_pair_lj.html,
+"lj/cut/coul/cut/soft (o)"_pair_lj_soft.html,
+"lj/cut/coul/debye (gko)"_pair_lj.html,
+"lj/cut/coul/dsf (gko)"_pair_lj.html,
+"lj/cut/coul/long (gikot)"_pair_lj.html,
+"lj/cut/coul/long/cs"_pair_lj.html,
+"lj/cut/coul/long/soft (o)"_pair_lj_soft.html,
+"lj/cut/coul/msm (go)"_pair_lj.html,
+"lj/cut/coul/wolf (o)"_pair_lj.html,
+"lj/cut/dipole/cut (go)"_pair_dipole.html,
+"lj/cut/dipole/long"_pair_dipole.html,
+"lj/cut/dipole/sf (go)"_pair_dipole.html,
+"lj/cut/soft (o)"_pair_lj_soft.html,
+"lj/cut/thole/long (o)"_pair_thole.html,
+"lj/cut/tip4p/cut (o)"_pair_lj.html,
+"lj/cut/tip4p/long (ot)"_pair_lj.html,
+"lj/cut/tip4p/long/soft (o)"_pair_lj_soft.html,
+"lj/expand (gko)"_pair_lj_expand.html,
+"lj/gromacs (gko)"_pair_gromacs.html,
+"lj/gromacs/coul/gromacs (ko)"_pair_gromacs.html,
+"lj/long/coul/long (io)"_pair_lj_long.html,
+"lj/long/dipole/long"_pair_dipole.html,
+"lj/long/tip4p/long"_pair_lj_long.html,
+"lj/mdf"_pair_mdf.html,
+"lj/sdk (gko)"_pair_sdk.html,
+"lj/sdk/coul/long (go)"_pair_sdk.html,
+"lj/sdk/coul/msm (o)"_pair_sdk.html,
+"lj/smooth (o)"_pair_lj_smooth.html,
+"lj/smooth/linear (o)"_pair_lj_smooth_linear.html,
+"lj96/cut (go)"_pair_lj96.html,
+"lubricate (o)"_pair_lubricate.html,
+"lubricate/poly (o)"_pair_lubricate.html,
+"lubricateU"_pair_lubricateU.html,
+"lubricateU/poly"_pair_lubricateU.html,
+"mdpd"_pair_meso.html,
+"mdpd/rhosum"_pair_meso.html,
+"meam"_pair_meam.html,
+"meam/c"_pair_meam.html,
+"meam/spline (o)"_pair_meam_spline.html,
+"meam/sw/spline"_pair_meam_sw_spline.html,
+"mgpt"_pair_mgpt.html,
+"mie/cut (o)"_pair_mie.html,
+"momb"_pair_momb.html,
+"morse (gkot)"_pair_morse.html,
+"morse/smooth/linear"_pair_morse.html,
+"morse/soft"_pair_morse.html,
+"multi/lucy"_pair_multi_lucy.html,
+"multi/lucy/rx (k)"_pair_multi_lucy_rx.html,
+"nb3b/harmonic (o)"_pair_nb3b_harmonic.html,
+"nm/cut (o)"_pair_nm.html,
+"nm/cut/coul/cut (o)"_pair_nm.html,
+"nm/cut/coul/long (o)"_pair_nm.html,
+"oxdna/coaxstk"_pair_oxdna.html,
+"oxdna/excv"_pair_oxdna.html,
+"oxdna/hbond"_pair_oxdna.html,
+"oxdna/stk"_pair_oxdna.html,
+"oxdna/xstk"_pair_oxdna.html,
+"oxdna2/coaxstk"_pair_oxdna2.html,
+"oxdna2/dh"_pair_oxdna2.html,
+"oxdna2/excv"_pair_oxdna2.html,
+"oxdna2/stk"_pair_oxdna2.html,
+"peri/eps"_pair_peri.html,
+"peri/lps (o)"_pair_peri.html,
+"peri/pmb (o)"_pair_peri.html,
+"peri/ves"_pair_peri.html,
+"polymorphic"_pair_polymorphic.html,
+"python"_pair_python.html,
+"quip"_pair_quip.html,
+"reax"_pair_reax.html,
+"reax/c (ko)"_pair_reaxc.html,
+"rebo (oi)"_pair_airebo.html,
+"resquared (go)"_pair_resquared.html,
+"smd/hertz"_pair_smd_hertz.html,
+"smd/tlsph"_pair_smd_tlsph.html,
+"smd/triangulated/surface"_pair_smd_triangulated_surface.html,
+"smd/ulsph"_pair_smd_ulsph.html,
+"smtbq"_pair_smtbq.html,
+"snap (k)"_pair_snap.html,
+"snap (k)"_pair_snap.html,
+"soft (go)"_pair_soft.html,
+"sph/heatconduction"_pair_sph_heatconduction.html,
+"sph/idealgas"_pair_sph_idealgas.html,
+"sph/lj"_pair_sph_lj.html,
+"sph/rhosum"_pair_sph_rhosum.html,
+"sph/taitwater"_pair_sph_taitwater.html,
+"sph/taitwater/morris"_pair_sph_taitwater_morris.html,
+"spin/dmi"_pair_spin_dmi.html,
+"spin/exchange"_pair_spin_exchange.html,
+"spin/magelec"_pair_spin_magelec.html,
+"spin/neel"_pair_spin_neel.html,
+"srp"_pair_srp.html,
+"sw (giko)"_pair_sw.html,
+"table (gko)"_pair_table.html,
+"table/rx (k)"_pair_table_rx.html,
+"tdpd"_pair_meso.html,
+"tersoff (giko)"_pair_tersoff.html,
+"tersoff/mod (gko)"_pair_tersoff_mod.html,
+"tersoff/mod/c (o)"_pair_tersoff_mod.html,
+"tersoff/table (o)"_pair_tersoff.html,
+"tersoff/zbl (gko)"_pair_tersoff_zbl.html,
+"thole"_pair_thole.html,
+"tip4p/cut (o)"_pair_coul.html,
+"tip4p/long (o)"_pair_coul.html,
+"tip4p/long/soft (o)"_pair_lj_soft.html,
+"tri/lj"_pair_tri_lj.html,
+"ufm (got)"_pair_ufm.html,
+"vashishta (ko)"_pair_vashishta.html,
+"vashishta/table (o)"_pair_vashishta.html,
+"yukawa (gok)"_pair_yukawa.html,
+"yukawa/colloid (go)"_pair_yukawa_colloid.html,
+"zbl (gok)"_pair_zbl.html :tb(c=4,ea=c)
diff --git a/doc/src/Commands_parse.txt b/doc/src/Commands_parse.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cbe2261986bb8f8f96089dac3dff3a03dc39dd42
--- /dev/null
+++ b/doc/src/Commands_parse.txt
@@ -0,0 +1,136 @@
+"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Parsing rules for input scripts :h3
+
+Each non-blank line in the input script is treated as a command.
+LAMMPS commands are case sensitive.  Command names are lower-case, as
+are specified command arguments.  Upper case letters may be used in
+file names or user-chosen ID strings.
+
+Here are 6 rulse for how each line in the input script is parsed by
+LAMMPS:
+
+(1) If the last printable character on the line is a "&" character,
+the command is assumed to continue on the next line.  The next line is
+concatenated to the previous line by removing the "&" character and
+line break.  This allows long commands to be continued across two or
+more lines.  See the discussion of triple quotes in (6) for how to
+continue a command across multiple line without using "&" characters.
+
+(2) All characters from the first "#" character onward are treated as
+comment and discarded.  See an exception in (6).  Note that a
+comment after a trailing "&" character will prevent the command from
+continuing on the next line.  Also note that for multi-line commands a
+single leading "#" will comment out the entire command.
+
+(3) The line is searched repeatedly for $ characters, which indicate
+variables that are replaced with a text string.  See an exception in
+(6).
+
+If the $ is followed by curly brackets, then the variable name is the
+text inside the curly brackets.  If no curly brackets follow the $,
+then the variable name is the single character immediately following
+the $.  Thus $\{myTemp\} and $x refer to variable names "myTemp" and
+"x".
+
+How the variable is converted to a text string depends on what style
+of variable it is; see the "variable"_variable.html doc page for details.
+It can be a variable that stores multiple text strings, and return one
+of them.  The returned text string can be multiple "words" (space
+separated) which will then be interpreted as multiple arguments in the
+input command.  The variable can also store a numeric formula which
+will be evaluated and its numeric result returned as a string.
+
+As a special case, if the $ is followed by parenthesis, then the text
+inside the parenthesis is treated as an "immediate" variable and
+evaluated as an "equal-style variable"_variable.html.  This is a way
+to use numeric formulas in an input script without having to assign
+them to variable names.  For example, these 3 input script lines:
+
+variable X equal (xlo+xhi)/2+sqrt(v_area)
+region 1 block $X 2 INF INF EDGE EDGE
+variable X delete :pre
+
+can be replaced by
+
+region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE :pre
+
+so that you do not have to define (or discard) a temporary variable X.
+
+Additionally, the "immediate" variable expression may be followed by a
+colon, followed by a C-style format string, e.g. ":%f" or ":%.10g".
+The format string must be appropriate for a double-precision
+floating-point value.  The format string is used to output the result
+of the variable expression evaluation.  If a format string is not
+specified a high-precision "%.20g" is used as the default.
+
+This can be useful for formatting print output to a desired precion:
+
+print "Final energy per atom: $(pe/atoms:%10.3f) eV/atom" :pre
+
+Note that neither the curly-bracket or immediate form of variables can
+contain nested $ characters for other variables to substitute for.
+Thus you cannot do this:
+
+variable        a equal 2
+variable        b2 equal 4
+print           "B2 = $\{b$a\}" :pre
+
+Nor can you specify this $($x-1.0) for an immediate variable, but
+you could use $(v_x-1.0), since the latter is valid syntax for an
+"equal-style variable"_variable.html.
+
+See the "variable"_variable.html command for more details of how
+strings are assigned to variables and evaluated, and how they can be
+used in input script commands.
+
+(4) The line is broken into "words" separated by whitespace (tabs,
+spaces).  Note that words can thus contain letters, digits,
+underscores, or punctuation characters.
+
+(5) The first word is the command name.  All successive words in the
+line are arguments.
+
+(6) If you want text with spaces to be treated as a single argument,
+it can be enclosed in either single or double or triple quotes.  A
+long single argument enclosed in single or double quotes can span
+multiple lines if the "&" character is used, as described above.  When
+the lines are concatenated together (and the "&" characters and line
+breaks removed), the text will become a single line.  If you want
+multiple lines of an argument to retain their line breaks, the text
+can be enclosed in triple quotes, in which case "&" characters are not
+needed.  For example:
+
+print "Volume = $v"
+print 'Volume = $v'
+if "$\{steps\} > 1000" then quit
+variable a string "red green blue &
+                   purple orange cyan"
+print """
+System volume = $v
+System temperature = $t
+""" :pre
+
+In each case, the single, double, or triple quotes are removed when
+the single argument they enclose is stored internally.
+
+See the "dump modify format"_dump_modify.html, "print"_print.html,
+"if"_if.html, and "python"_python.html commands for examples.
+
+A "#" or "$" character that is between quotes will not be treated as a
+comment indicator in (2) or substituted for as a variable in (3).
+
+NOTE: If the argument is itself a command that requires a quoted
+argument (e.g. using a "print"_print.html command as part of an
+"if"_if.html or "run every"_run.html command), then single, double, or
+triple quotes can be nested in the usual manner.  See the doc pages
+for those commands for examples.  Only one of level of nesting is
+allowed, but that should be sufficient for most use cases.
+
diff --git a/doc/src/Commands_structure.txt b/doc/src/Commands_structure.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b5d2c7b07b1f8b4afdb2d255f4953cfbba0e330b
--- /dev/null
+++ b/doc/src/Commands_structure.txt
@@ -0,0 +1,95 @@
+"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Input script structure :h3
+
+This page describes the structure of a typical LAMMPS input script.
+The examples directory in the LAMMPS distribution contains many sample
+input scripts; it is discussed on the "Examples"_Examples.html doc
+page.
+
+A LAMMPS input script typically has 4 parts:
+
+Initialization
+Atom definition
+Settings
+Run a simulation :ol
+
+The last 2 parts can be repeated as many times as desired.  I.e. run a
+simulation, change some settings, run some more, etc.  Each of the 4
+parts is now described in more detail.  Remember that almost all
+commands need only be used if a non-default value is desired.
+
+(1) Initialization
+
+Set parameters that need to be defined before atoms are created or
+read-in from a file.
+
+The relevant commands are "units"_units.html,
+"dimension"_dimension.html, "newton"_newton.html,
+"processors"_processors.html, "boundary"_boundary.html,
+"atom_style"_atom_style.html, "atom_modify"_atom_modify.html.
+
+If force-field parameters appear in the files that will be read, these
+commands tell LAMMPS what kinds of force fields are being used:
+"pair_style"_pair_style.html, "bond_style"_bond_style.html,
+"angle_style"_angle_style.html, "dihedral_style"_dihedral_style.html,
+"improper_style"_improper_style.html.
+
+(2) Atom definition
+
+There are 3 ways to define atoms in LAMMPS.  Read them in from a data
+or restart file via the "read_data"_read_data.html or
+"read_restart"_read_restart.html commands.  These files can contain
+molecular topology information.  Or create atoms on a lattice (with no
+molecular topology), using these commands: "lattice"_lattice.html,
+"region"_region.html, "create_box"_create_box.html,
+"create_atoms"_create_atoms.html.  The entire set of atoms can be
+duplicated to make a larger simulation using the
+"replicate"_replicate.html command.
+
+(3) Settings
+
+Once atoms and molecular topology are defined, a variety of settings
+can be specified: force field coefficients, simulation parameters,
+output options, etc.
+
+Force field coefficients are set by these commands (they can also be
+set in the read-in files): "pair_coeff"_pair_coeff.html,
+"bond_coeff"_bond_coeff.html, "angle_coeff"_angle_coeff.html,
+"dihedral_coeff"_dihedral_coeff.html,
+"improper_coeff"_improper_coeff.html,
+"kspace_style"_kspace_style.html, "dielectric"_dielectric.html,
+"special_bonds"_special_bonds.html.
+
+Various simulation parameters are set by these commands:
+"neighbor"_neighbor.html, "neigh_modify"_neigh_modify.html,
+"group"_group.html, "timestep"_timestep.html,
+"reset_timestep"_reset_timestep.html, "run_style"_run_style.html,
+"min_style"_min_style.html, "min_modify"_min_modify.html.
+
+Fixes impose a variety of boundary conditions, time integration, and
+diagnostic options.  The "fix"_fix.html command comes in many flavors.
+
+Various computations can be specified for execution during a
+simulation using the "compute"_compute.html,
+"compute_modify"_compute_modify.html, and "variable"_variable.html
+commands.
+
+Output options are set by the "thermo"_thermo.html, "dump"_dump.html,
+and "restart"_restart.html commands.
+
+(4) Run a simulation
+
+A molecular dynamics simulation is run using the "run"_run.html
+command.  Energy minimization (molecular statics) is performed using
+the "minimize"_minimize.html command.  A parallel tempering
+(replica-exchange) simulation can be run using the
+"temper"_temper.html command.
+
diff --git a/doc/src/Errors.txt b/doc/src/Errors.txt
index 92a577c5f26fe57d83a66d32c7b14d135f7025d4..1b6206c780e7a8e02ea5303ad09889dd070e44a0 100644
--- a/doc/src/Errors.txt
+++ b/doc/src/Errors.txt
@@ -4,7 +4,7 @@ Section"_Manual.html :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Errors_bugs.txt b/doc/src/Errors_bugs.txt
index c0a94c7a44b124bc6d987b40d9f0b25ca9b520b5..4a8e62e77546206de35b1132a3484d731db61af3 100644
--- a/doc/src/Errors_bugs.txt
+++ b/doc/src/Errors_bugs.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Errors_common.txt b/doc/src/Errors_common.txt
index 86a25f7e7d4b262fc4e730b42a5584ce76133d12..43d1a85a7bd0ff2772c5dfeb690073d93d50bb10 100644
--- a/doc/src/Errors_common.txt
+++ b/doc/src/Errors_common.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Errors_messages.txt b/doc/src/Errors_messages.txt
index 39eabbd232dcaf447eed51a8ff9a682c08d6106d..03fc25b5618c3b6803c719cdbb5473edad5cbf6a 100644
--- a/doc/src/Errors_messages.txt
+++ b/doc/src/Errors_messages.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Errors_warnings.txt b/doc/src/Errors_warnings.txt
index 1da777043c975de136d486fac100485d51e25367..dd3402ba8641c487f1a6a4210fa27f1b6ae062ff 100644
--- a/doc/src/Errors_warnings.txt
+++ b/doc/src/Errors_warnings.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Examples.txt b/doc/src/Examples.txt
index b01b289d5e2926577ce8e63d755a6c52281d56fd..5bd8da2409185873b745cc87b1ae95b5a0b6ac1b 100644
--- a/doc/src/Examples.txt
+++ b/doc/src/Examples.txt
@@ -4,7 +4,7 @@ Section"_Tools.html :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Howto_2d.txt b/doc/src/Howto_2d.txt
index ea11a7d54666114a2d2c78a99ed64228e879b0b8..e1758c05d5ff9fc771e239ba6007f98d3abbbf63 100644
--- a/doc/src/Howto_2d.txt
+++ b/doc/src/Howto_2d.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Howto_barostat.txt b/doc/src/Howto_barostat.txt
index b289ebfc4c5156d72a71f4b84992f3e36b35dc1c..7c3db891524379f49fe38134186764e07eeff959 100644
--- a/doc/src/Howto_barostat.txt
+++ b/doc/src/Howto_barostat.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Howto_bash.txt b/doc/src/Howto_bash.txt
index 572157ab554ab5624a108fe22d4ac5d0752cfc79..f1438418e78b2bf97118992dea972e73513e0e29 100755
--- a/doc/src/Howto_bash.txt
+++ b/doc/src/Howto_bash.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Howto_bioFF.txt b/doc/src/Howto_bioFF.txt
index 91d6eb0a8e190fbdb7f8380501d5f3e67a1c8072..afb8a84f2e32ac4397054054c4032ab339629290 100644
--- a/doc/src/Howto_bioFF.txt
+++ b/doc/src/Howto_bioFF.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Howto_body.txt b/doc/src/Howto_body.txt
index 3031563f98e7bb9b9cb9c3337778b64f54321503..3535349b461589aa6ddafdf4e9a3d684a546c2e1 100644
--- a/doc/src/Howto_body.txt
+++ b/doc/src/Howto_body.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
@@ -17,9 +17,9 @@ surface meshes of discrete points, collections of sub-particles,
 deformable objects, etc.  Note that other kinds of finite-size
 spherical and aspherical particles are also supported by LAMMPS, such
 as spheres, ellipsoids, line segments, and triangles, but they are
-simpler entities that body particles.  See "Section
-6.14"_Section_howto.html#howto_14 for a general overview of all these
-particle types.
+simpler entities that body particles.  See the "Howto
+spherical"_Howto_spherical.html doc page for a general overview of all
+these particle types.
 
 Body particles are used via the "atom_style body"_atom_style.html
 command.  It takes a body style as an argument.  The current body
diff --git a/doc/src/Howto_chunk.txt b/doc/src/Howto_chunk.txt
index 9d757b2729cb732178161d2add46c68f77b0d641..8e52acf4b8693569bac54304bb5f2c0ffd56d0fb 100644
--- a/doc/src/Howto_chunk.txt
+++ b/doc/src/Howto_chunk.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Howto_coreshell.txt b/doc/src/Howto_coreshell.txt
index 273568418b2a4ce6b397adce4c32b9357fcac35c..4f1cd64384e696dbf00eccf023a3a10be8f40cc9 100644
--- a/doc/src/Howto_coreshell.txt
+++ b/doc/src/Howto_coreshell.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Howto_couple.txt b/doc/src/Howto_couple.txt
index ec45bd129046b4f32497876059a5bde68a1c400f..38595a9d1641ddb869cf5606ce003c2189690813 100644
--- a/doc/src/Howto_couple.txt
+++ b/doc/src/Howto_couple.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Howto_diffusion.txt b/doc/src/Howto_diffusion.txt
index e0e16e1042039f72ac66c0edf052df693590c153..401c1e359c05ee83ef37ecbae44073cdd4ecfacf 100644
--- a/doc/src/Howto_diffusion.txt
+++ b/doc/src/Howto_diffusion.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Howto_dispersion.txt b/doc/src/Howto_dispersion.txt
index 000f45076db1a458b279af52fa62d6302177c462..4ea286258e11a38aa07e6e93df4c3e22cb0aca0a 100644
--- a/doc/src/Howto_dispersion.txt
+++ b/doc/src/Howto_dispersion.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Howto_drude.txt b/doc/src/Howto_drude.txt
index e9c30db772caa8dfa01473259b7c41e675daeb2a..ebdf5f865824a365220f1a58214fd06f111dcae2 100644
--- a/doc/src/Howto_drude.txt
+++ b/doc/src/Howto_drude.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Howto_drude2.txt b/doc/src/Howto_drude2.txt
index f6e7eed40bd84cde46e30213c0a14c22244eae86..a342d4a87d1deec93cbb9820a39099aaf5fb75a6 100644
--- a/doc/src/Howto_drude2.txt
+++ b/doc/src/Howto_drude2.txt
@@ -9,7 +9,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Howto_elastic.txt b/doc/src/Howto_elastic.txt
index 4dda13fa53245a17bd887a8c9ab08e1b4cf49597..68b30970ca33a84308b32bb1516081f49470367e 100644
--- a/doc/src/Howto_elastic.txt
+++ b/doc/src/Howto_elastic.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Howto_github.txt b/doc/src/Howto_github.txt
index 191242205ea9c7742087bb3fe7e96aa3cc282f4c..720b3317f012eb3eaf3f32f65fc1542185359721 100644
--- a/doc/src/Howto_github.txt
+++ b/doc/src/Howto_github.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Howto_granular.txt b/doc/src/Howto_granular.txt
index cfa01bcb632ba10b31fbadf8362772edbaad6f56..8027369501eb0730dd4008b56503d95642ee9380 100644
--- a/doc/src/Howto_granular.txt
+++ b/doc/src/Howto_granular.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Howto_kappa.txt b/doc/src/Howto_kappa.txt
index 949901f21a8639a5f78c8330bd23ad46595a49c6..b2a57ef49b82461b89a72cda29c9785297a877f0 100644
--- a/doc/src/Howto_kappa.txt
+++ b/doc/src/Howto_kappa.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Howto_library.txt b/doc/src/Howto_library.txt
index b15aadd2145082ca39e9451a30f5f6a45147002e..0d4852fbf247adee92be56045d7b98af7e5a3542 100644
--- a/doc/src/Howto_library.txt
+++ b/doc/src/Howto_library.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Howto_manifold.txt b/doc/src/Howto_manifold.txt
index c9bb1ce57f850242b8940365a4a4cebfff4fa162..09a936f7d3adec5cec22b820be9e9c54a2e4dfd0 100644
--- a/doc/src/Howto_manifold.txt
+++ b/doc/src/Howto_manifold.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Howto_multiple.txt b/doc/src/Howto_multiple.txt
index 3516debb71df6a1da7eabc4960f83d3cc26346dc..edcb8196cf015543db85b6ab83411d4d13373758 100644
--- a/doc/src/Howto_multiple.txt
+++ b/doc/src/Howto_multiple.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Howto_nemd.txt b/doc/src/Howto_nemd.txt
index efb3a5cd735f745eb52c7b2ca7aecb28693fbad3..f787801c36745d934abbfb1c26462734014d1c0c 100644
--- a/doc/src/Howto_nemd.txt
+++ b/doc/src/Howto_nemd.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Howto_output.txt b/doc/src/Howto_output.txt
index ed2a78ee19de4a1380fef40180e51024df080727..a204a3cc96c3a0f2cebdc97fbc4ac7d2b78e8420 100644
--- a/doc/src/Howto_output.txt
+++ b/doc/src/Howto_output.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Howto_polarizable.txt b/doc/src/Howto_polarizable.txt
index ec96ddc9a9daab076fc6fb04584408cdc8bec51f..b2653b117e9caed203f1a9127575278f1747fcb4 100644
--- a/doc/src/Howto_polarizable.txt
+++ b/doc/src/Howto_polarizable.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Howto_pylammps.txt b/doc/src/Howto_pylammps.txt
index abf7c52d05b4f61e903c3cb9959e225c8667d970..8be4b66e78a511b404987929d247ce3836a40086 100644
--- a/doc/src/Howto_pylammps.txt
+++ b/doc/src/Howto_pylammps.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Howto_replica.txt b/doc/src/Howto_replica.txt
index b2f0faa209306f11618b31be220f331bc55f548a..1b44fe53748d4dc1adf35aebe333b97bea4c33ac 100644
--- a/doc/src/Howto_replica.txt
+++ b/doc/src/Howto_replica.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Howto_restart.txt b/doc/src/Howto_restart.txt
index d2a993fcd335863271cb6d0e4ade4c264c5dbf17..b211775479bfc367301a408ef15e45f8bd46cca0 100644
--- a/doc/src/Howto_restart.txt
+++ b/doc/src/Howto_restart.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Howto_spc.txt b/doc/src/Howto_spc.txt
index 6a63c1f6a65a61852770baad356c36bc89a79823..2cbf16547be6f318794d837d832d3651edd072be 100644
--- a/doc/src/Howto_spc.txt
+++ b/doc/src/Howto_spc.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Howto_spherical.txt b/doc/src/Howto_spherical.txt
index c239f72c2ab1e4178613ae70edaae442a2eeb9ae..1e737df655462c2fc0e1059ac7bc56ecdb120287 100644
--- a/doc/src/Howto_spherical.txt
+++ b/doc/src/Howto_spherical.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Howto_spins.txt b/doc/src/Howto_spins.txt
index 3cb9e480b205535d4fed5969baf479e9282b38f9..1b9adb49a5701789dafc9f86cebc23a87623411c 100644
--- a/doc/src/Howto_spins.txt
+++ b/doc/src/Howto_spins.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Howto_temperature.txt b/doc/src/Howto_temperature.txt
index 3d1bd8a2d605cecb04bab5ae87819971fff8bdf0..7a318250cffa956692693e601638e749cc4d6df4 100644
--- a/doc/src/Howto_temperature.txt
+++ b/doc/src/Howto_temperature.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Howto_thermostat.txt b/doc/src/Howto_thermostat.txt
index c1887d9738ddfc062a3da1f37ddc6a386fa3a74c..0e2feb18699cd993abf78df4542b599431d8512a 100644
--- a/doc/src/Howto_thermostat.txt
+++ b/doc/src/Howto_thermostat.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Howto_tip3p.txt b/doc/src/Howto_tip3p.txt
index 23ab604d1f676decfcf5bc62ae0bc996f3b3b051..942b42aea16ea63d2541ca839646f4b77dc9c079 100644
--- a/doc/src/Howto_tip3p.txt
+++ b/doc/src/Howto_tip3p.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Howto_tip4p.txt b/doc/src/Howto_tip4p.txt
index a471bdc91896df0d495702efae46a5525fc36834..f9e548e26896c1143f1cead59e3c0a1effb015c3 100644
--- a/doc/src/Howto_tip4p.txt
+++ b/doc/src/Howto_tip4p.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Howto_triclinic.txt b/doc/src/Howto_triclinic.txt
index 10bcc5e9d1cae14a63de8c60bbb2f6278dcf557c..4b299e5ae1ecc024c3be42bbc019bc8d9550c54d 100644
--- a/doc/src/Howto_triclinic.txt
+++ b/doc/src/Howto_triclinic.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 Triclinic (non-orthogonal) simulation boxes :h3
 
diff --git a/doc/src/Howto_viscosity.txt b/doc/src/Howto_viscosity.txt
index 4760607fd574a5d8bc094675236d1f47394f50d6..8bcab6dd247f02de5dbb3135e67fe76cc32efb01 100644
--- a/doc/src/Howto_viscosity.txt
+++ b/doc/src/Howto_viscosity.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Howto_viz.txt b/doc/src/Howto_viz.txt
index 53635442c8ca5afb4fa802a506b609d6f88ff7d2..00c329c50b1a7f5685d31b4f9a59b3affa2dcb4f 100644
--- a/doc/src/Howto_viz.txt
+++ b/doc/src/Howto_viz.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Howto_walls.txt b/doc/src/Howto_walls.txt
index 7b0f8c0cfa751cf534ffcb657e219241c0860939..75221185829cfbb3c6b4f9489ee1a3cd47764b43 100644
--- a/doc/src/Howto_walls.txt
+++ b/doc/src/Howto_walls.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Intro_authors.txt b/doc/src/Intro_authors.txt
index 96b4b861ca399a47f10a98a3339d6098fd9eb606..b48c1eb59a5e71b11892f69e6316bcda02a698b4 100644
--- a/doc/src/Intro_authors.txt
+++ b/doc/src/Intro_authors.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Intro_features.txt b/doc/src/Intro_features.txt
index 2a405ebf775ba3b1174c66b0ac70ee3f4ab6006b..4b7d1d41e2d0b1d066277b8d21dd1f12fa10eb30 100644
--- a/doc/src/Intro_features.txt
+++ b/doc/src/Intro_features.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
@@ -74,8 +74,8 @@ commands)
   long-range interactions for charge, point-dipoles, and LJ dispersion: \
     Ewald, Wolf, PPPM (similar to particle-mesh Ewald)
   polarization models: "QEq"_fix_qeq.html, \
-    "core/shell model"_Section_howto.html#howto_26, \
-    "Drude dipole model"_Section_howto.html#howto_27
+    "core/shell model"_Howto_coreshell.html, \
+    "Drude dipole model"_Howto_drude.html
   charge equilibration (QEq via dynamic, point, shielded, Slater methods)
   coarse-grained potentials: DPD, GayBerne, REsquared, colloidal, DLVO
   mesoscopic potentials: granular, Peridynamics, SPH
diff --git a/doc/src/Intro_nonfeatures.txt b/doc/src/Intro_nonfeatures.txt
index 29b2eacf083e92d7a587fb8d96ebc109a1b76ea5..41f001fc8b675de6c1e3624b1695dd3bfc5ca96c 100644
--- a/doc/src/Intro_nonfeatures.txt
+++ b/doc/src/Intro_nonfeatures.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Intro_opensource.txt b/doc/src/Intro_opensource.txt
index 83384a22a2690bdd80ef9fd44f88b330f936e2dd..e0d57f7ce199b35ffa8abab06e9e0217b3a54304 100644
--- a/doc/src/Intro_opensource.txt
+++ b/doc/src/Intro_opensource.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Intro_overview.txt b/doc/src/Intro_overview.txt
index 51ad21821621ed2499ef61b95ecb6cd878a88abd..49c14bc5f06d463037d294d28873b43fdf6c7f14 100644
--- a/doc/src/Intro_overview.txt
+++ b/doc/src/Intro_overview.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Intro_website.txt b/doc/src/Intro_website.txt
index 61c9babe1c493ac40b8029f8a936eb915ae18955..a8af94157ceb9545be2c6ddd22bcb928115b63d8 100644
--- a/doc/src/Intro_website.txt
+++ b/doc/src/Intro_website.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt
index ddb9b152ec1dea0ad8168a5865bb8088960c0f05..a5e8b63640be29f7212d66e1d6b42ceb66747a41 100644
--- a/doc/src/Manual.txt
+++ b/doc/src/Manual.txt
@@ -14,7 +14,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html#comm)
 
 :line
 
@@ -73,7 +73,7 @@ every LAMMPS command.
 
    Intro
    Section_start
-   Section_commands
+   Commands
    Packages
    Speed
    Howto
@@ -116,12 +116,7 @@ END_RST -->
   2.6 "Command-line options"_start_6 :b
   2.7 "Screen output"_start_7 :b
   2.8 "Tips for users of previous versions"_start_8 :ule,b
-"Commands"_Section_commands.html :l
-  3.1 "LAMMPS input script"_cmd_1 :ulb,b
-  3.2 "Parsing rules"_cmd_2 :b
-  3.3 "Input script structure"_cmd_3 :b
-  3.4 "Commands listed by category"_cmd_4 :b
-  3.5 "Commands listed alphabetically"_cmd_5 :ule,b
+"Commands"_Commands.html :l
 "Optional packages"_Packages.html :l
 "Accelerate performance"_Speed.html :l
 "How-to discussions"_Howto.html :l
@@ -141,12 +136,6 @@ END_RST -->
 :link(start_7,Section_start.html#start_7)
 :link(start_8,Section_start.html#start_8)
 
-:link(cmd_1,Section_commands.html#cmd_1)
-:link(cmd_2,Section_commands.html#cmd_2)
-:link(cmd_3,Section_commands.html#cmd_3)
-:link(cmd_4,Section_commands.html#cmd_4)
-:link(cmd_5,Section_commands.html#cmd_5)
-
 <!-- END_HTML_ONLY -->
 
 </BODY>
diff --git a/doc/src/Manual_version.txt b/doc/src/Manual_version.txt
index db4301b6ea960ebc63eae6cc80b31e9c9a58b5e5..8583eabf865afc3b9b9aeaae76d3acb34028fc85 100644
--- a/doc/src/Manual_version.txt
+++ b/doc/src/Manual_version.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Modify.txt b/doc/src/Modify.txt
index ae0b0dc6bdf2371f9a205c39fbc267b91ecd11b3..f828bd5d74db99ceb5c0dfffd93062d93228ef4c 100644
--- a/doc/src/Modify.txt
+++ b/doc/src/Modify.txt
@@ -4,7 +4,7 @@ Section"_Python.html :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Modify_atom.txt b/doc/src/Modify_atom.txt
index afa1c319d25539594bb65f9dcb1f146023623ff8..60c7dccb29a38e4c628752f87c58a84532eb7c24 100644
--- a/doc/src/Modify_atom.txt
+++ b/doc/src/Modify_atom.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Modify_body.txt b/doc/src/Modify_body.txt
index a0627ebddaade42e44b1f6fbce694dde042680d8..0114ae10c885c2cbd78cd1d2067ad2751ac997fd 100644
--- a/doc/src/Modify_body.txt
+++ b/doc/src/Modify_body.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Modify_bond.txt b/doc/src/Modify_bond.txt
index f0828a0c3b8544c84fa8539c7eb9f30e63489cfb..7ceea3f910121c4191b27cd0aaa8256e421281e3 100644
--- a/doc/src/Modify_bond.txt
+++ b/doc/src/Modify_bond.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Modify_command.txt b/doc/src/Modify_command.txt
index 6fc9aad1fc55174fa3be29eda559966b34db2259..4576f6c8067684ca95b94b7ae022ec0df6166f76 100644
--- a/doc/src/Modify_command.txt
+++ b/doc/src/Modify_command.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Modify_compute.txt b/doc/src/Modify_compute.txt
index b02b8a983ec4c32f0935c7b00b1c3c3dd59e7f5d..2f6481dbd5be934fd8dcfa7f1abed50bd57cc3c3 100644
--- a/doc/src/Modify_compute.txt
+++ b/doc/src/Modify_compute.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Modify_contribute.txt b/doc/src/Modify_contribute.txt
index 9d47b082511a9a2097c553ecc855687937fc3376..ef9fe6a7174eed7d41a74908b49b21e8ecfa6f6d 100644
--- a/doc/src/Modify_contribute.txt
+++ b/doc/src/Modify_contribute.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Modify_dump.txt b/doc/src/Modify_dump.txt
index 81af54e0039a3ad9f95f34f7f0498457914a6f6d..cfe96f5d3d0bc25402b73beef55261f8e7679eb1 100644
--- a/doc/src/Modify_dump.txt
+++ b/doc/src/Modify_dump.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Modify_fix.txt b/doc/src/Modify_fix.txt
index ba985475cc9e72721b7dd50bf3bc9268f97f60c0..b095ebc4b5fa8b549fbfb411c2558e5c6bb14c4d 100644
--- a/doc/src/Modify_fix.txt
+++ b/doc/src/Modify_fix.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Modify_kspace.txt b/doc/src/Modify_kspace.txt
index 21407bf2e9af32f5aa836889ca40824845eb5b98..d5f018411d8d280d679b7a7940403b1658a20726 100644
--- a/doc/src/Modify_kspace.txt
+++ b/doc/src/Modify_kspace.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Modify_min.txt b/doc/src/Modify_min.txt
index 5dcf0f1e6751899be88458220e188dde5e6f716a..8252a576f3b01b7d58461a5bf200c0ddc1405c19 100644
--- a/doc/src/Modify_min.txt
+++ b/doc/src/Modify_min.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Modify_overview.txt b/doc/src/Modify_overview.txt
index f9964d964b14d0ae81d219aab6891278e37a3f36..cf94b40281417805515700d697dc84cbd476fc38 100644
--- a/doc/src/Modify_overview.txt
+++ b/doc/src/Modify_overview.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Modify_pair.txt b/doc/src/Modify_pair.txt
index 8c234dc62135f635bccc3e96ce93179cb901c569..0ebf2daa30baab30e377cb5df9cae40d5e0f5a36 100644
--- a/doc/src/Modify_pair.txt
+++ b/doc/src/Modify_pair.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Modify_region.txt b/doc/src/Modify_region.txt
index 9fbf359292b3e2edd95a3e1b6bd616c4336831a2..cdf192323ac50a8f5d771a4ea80822ec2bc6d3bf 100644
--- a/doc/src/Modify_region.txt
+++ b/doc/src/Modify_region.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Modify_thermo.txt b/doc/src/Modify_thermo.txt
index 001a9f99e108e2fb26285ee8a672f0a54d9f0097..1772bae87a185846f941e0b540d8df2a904a1208 100644
--- a/doc/src/Modify_thermo.txt
+++ b/doc/src/Modify_thermo.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Modify_variable.txt b/doc/src/Modify_variable.txt
index 3c5b29cd1af5d234dd76b2d573bcc07d2eb8087f..b163272f3ebc225522467d08fe144b725dc22a27 100644
--- a/doc/src/Modify_variable.txt
+++ b/doc/src/Modify_variable.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Packages.txt b/doc/src/Packages.txt
index 6498d030634a184f04d2a8a489a81949740789f2..a7f45a99b7fa8f3d33e3c8d2e771f069139a0249 100644
--- a/doc/src/Packages.txt
+++ b/doc/src/Packages.txt
@@ -1,10 +1,10 @@
-"Previous Section"_Section_commands.html - "LAMMPS WWW Site"_lws -
+"Previous Section"_Commands.html - "LAMMPS WWW Site"_lws -
 "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
 Section"_Speed.html :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt
index 2b8980972178b97ba55086ec3dfb5d23b06c660c..eb92fe4dc4c27506cf41b250f7a3dce49e159941 100644
--- a/doc/src/Packages_details.txt
+++ b/doc/src/Packages_details.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
@@ -396,7 +396,7 @@ lib/gpu/README
 "Section 2.6 -sf gpu"_Section_start.html#start_6
 "Section 2.6 -pk gpu"_Section_start.html#start_6
 "package gpu"_package.html
-Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5 for pair styles followed by (g)
+"Commands all"_Commands_all.html pages (pair,kspace) for styles followed by (g)
 "Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
 
 :line
@@ -487,8 +487,8 @@ See the list of all KIM models here:
 https://openkim.org/kim-items/models/by-model-drivers
 
 See the list of example KIM models included by default here:
-https://openkim.org/kim-api in the "What is in the KIM API source
-package?" section
+https://openkim.org/kim-api on the "What is in the KIM API source
+package?" page.
 
 You can then install/un-install the package and build LAMMPS in the
 usual manner:
@@ -593,7 +593,7 @@ lib/kokkos/README
 "Section 2.6 -sf kk"_Section_start.html#start_6
 "Section 2.6 -pk kokkos"_Section_start.html#start_6
 "package kokkos"_package.html
-Styles sections of "Section 3.5"_Section_commands.html#cmd_5 for styles followed by (k)
+"Commands all"_Commands_all.html pages (fix,compute,pair,etc) for styles followed by (k)
 "Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
 
 :line
@@ -631,7 +631,7 @@ src/KSPACE: filenames -> commands
 "Howto tip4p"_Howto_tip4p.html
 "Howto spc"_Howto_spc.html
 "pair_style coul"_pair_coul.html
-Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5 with "long" or "msm" in pair style name
+"Commands pair"_Commands_pair.html page for styles with "long" or "msm" in name
 examples/peptide
 bench/in.rhodo :ul
 
@@ -715,7 +715,7 @@ make machine :pre
 [Supporting info:]
 
 src/MANYBODY: filenames -> commands
-Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5
+"Commands pair"_Commands_pair.html page
 examples/comb
 examples/eim
 examples/nb3d
@@ -1017,7 +1017,7 @@ src/OPT: filenames -> commands
 "Speed packages"_Speed_packages.html
 "Speed opt"_Speed_opt.html
 "Section 2.6 -sf opt"_Section_start.html#start_6
-Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5 for pair styles followed by (t)
+"Commands pair"_Commands_pair.html for styles followed by (t)
 "Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
 
 :line
@@ -2072,7 +2072,7 @@ src/USER-INTEL/README
 "Section 2.6 -sf intel"_Section_start.html#start_6
 "Section 2.6 -pk intel"_Section_start.html#start_6
 "package intel"_package.html
-Styles sections of "Section 3.5"_Section_commands.html#cmd_5 for styles followed by (i)
+"Commands all"_Commands_all.html pages (fix,compute,pair,etc) for styles followed by (i)
 src/USER-INTEL/TEST
 "Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
 
@@ -2457,7 +2457,7 @@ src/USER-OMP/README
 "Section 2.6 -sf omp"_Section_start.html#start_6
 "Section 2.6 -pk omp"_Section_start.html#start_6
 "package omp"_package.html
-Styles sections of "Section 3.5"_Section_commands.html#cmd_5 for styles followed by (o)
+"Commands all"_Commands_all.html pages (fix,compute,pair,etc) for styles followed by (o)
 "Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
 
 :line
diff --git a/doc/src/Packages_standard.txt b/doc/src/Packages_standard.txt
index cff2d38273ae131ba7c8a12c35652462feb32cf3..7e6434560244abfce710c182af2c4fb6cad31da6 100644
--- a/doc/src/Packages_standard.txt
+++ b/doc/src/Packages_standard.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Packages_user.txt b/doc/src/Packages_user.txt
index 046529698049a756e27fa9f971eeba9e09c2de8f..c8728148f9c1a83f0c900524e3b49bc586101aa6 100644
--- a/doc/src/Packages_user.txt
+++ b/doc/src/Packages_user.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Python.txt b/doc/src/Python.txt
index 169670d669da6bbfcbdcb9adb491276819685f9f..2c9c6872bbf21e5704088b46752603f7349cd3e6 100644
--- a/doc/src/Python.txt
+++ b/doc/src/Python.txt
@@ -4,7 +4,7 @@ Section"_Errors.html :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Python_call.txt b/doc/src/Python_call.txt
index 3e30a5a7c7e7d831413c1e532de421d40555fdd0..621f1fe2410f7f7d58e193466481cc3cd19a4578 100644
--- a/doc/src/Python_call.txt
+++ b/doc/src/Python_call.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Python_examples.txt b/doc/src/Python_examples.txt
index fbca381e8b0f1cc4084e491162f2dad6dd7ddb36..46e5fee2b97da5d4f46644883434729c6e5406ad 100644
--- a/doc/src/Python_examples.txt
+++ b/doc/src/Python_examples.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Python_install.txt b/doc/src/Python_install.txt
index 631f6c4a7f1a3a40245e3d7ab98b7b195bb4fefc..6591360ae2535935f0c9e88e8bf6bc2c830f6cb0 100644
--- a/doc/src/Python_install.txt
+++ b/doc/src/Python_install.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Python_library.txt b/doc/src/Python_library.txt
index db16c39a478830911f522051f895549803c9da1d..8d0c724a45992294f7860612e5042387efc150ec 100644
--- a/doc/src/Python_library.txt
+++ b/doc/src/Python_library.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Python_mpi.txt b/doc/src/Python_mpi.txt
index 8377bbb3d0a0ac058c1f97274ba7fe7ba054b648..6e0a2ce3198fd79bb98d1bf24fe0e60675de72ce 100644
--- a/doc/src/Python_mpi.txt
+++ b/doc/src/Python_mpi.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Python_pylammps.txt b/doc/src/Python_pylammps.txt
index cdc8e2c086c37ddefa3a0d7c3bdbecaa4a4eb932..d7baa93e2e69154b20fdc2f7f4666f500f2d6a02 100644
--- a/doc/src/Python_pylammps.txt
+++ b/doc/src/Python_pylammps.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Python_run.txt b/doc/src/Python_run.txt
index 03ab2ed3d7dc3e6b4703c78950978323835c394d..a94dc07f2d7368ec8086fc1535337ed3c245f82f 100644
--- a/doc/src/Python_run.txt
+++ b/doc/src/Python_run.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Python_shlib.txt b/doc/src/Python_shlib.txt
index 1aafbe2e847e3b486f10b7991b85bbea9009d45b..1a921e4025cde5cc1376c603a4beb2cf5c4c58fb 100644
--- a/doc/src/Python_shlib.txt
+++ b/doc/src/Python_shlib.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Python_test.txt b/doc/src/Python_test.txt
index 5f361a500b6c8ba12748fed18b61af3c81d9028b..4a05d5c4680df053cd563f5e09d017e64fe4bb1f 100644
--- a/doc/src/Python_test.txt
+++ b/doc/src/Python_test.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt
deleted file mode 100644
index daedb00a0a6f6b431356d04fece2dfaeddbb9f23..0000000000000000000000000000000000000000
--- a/doc/src/Section_commands.txt
+++ /dev/null
@@ -1,1292 +0,0 @@
-"Previous Section"_Section_start.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Packages.html :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
-
-:line
-
-3. Commands :h2
-
-This section describes how a LAMMPS input script is formatted and the
-input script commands used to define a LAMMPS simulation.
-
-3.1 "LAMMPS input script"_#cmd_1
-3.2 "Parsing rules"_#cmd_2
-3.3 "Input script structure"_#cmd_3
-3.4 "Commands listed by category"_#cmd_4
-3.5 "Commands listed alphabetically"_#cmd_5 :all(b)
-
-:line
-:line
-
-3.1 LAMMPS input script :link(cmd_1),h4
-
-LAMMPS executes by reading commands from a input script (text file),
-one line at a time.  When the input script ends, LAMMPS exits.  Each
-command causes LAMMPS to take some action.  It may set an internal
-variable, read in a file, or run a simulation.  Most commands have
-default settings, which means you only need to use the command if you
-wish to change the default.
-
-In many cases, the ordering of commands in an input script is not
-important.  However the following rules apply:
-
-(1) LAMMPS does not read your entire input script and then perform a
-simulation with all the settings.  Rather, the input script is read
-one line at a time and each command takes effect when it is read.
-Thus this sequence of commands:
-
-timestep 0.5
-run      100
-run      100 :pre
-
-does something different than this sequence:
-
-run      100
-timestep 0.5
-run      100 :pre
-
-In the first case, the specified timestep (0.5 fmsec) is used for two
-simulations of 100 timesteps each.  In the 2nd case, the default
-timestep (1.0 fmsec) is used for the 1st 100 step simulation and a 0.5
-fmsec timestep is used for the 2nd one.
-
-(2) Some commands are only valid when they follow other commands.  For
-example you cannot set the temperature of a group of atoms until atoms
-have been defined and a group command is used to define which atoms
-belong to the group.
-
-(3) Sometimes command B will use values that can be set by command A.
-This means command A must precede command B in the input script if it
-is to have the desired effect.  For example, the
-"read_data"_read_data.html command initializes the system by setting
-up the simulation box and assigning atoms to processors.  If default
-values are not desired, the "processors"_processors.html and
-"boundary"_boundary.html commands need to be used before read_data to
-tell LAMMPS how to map processors to the simulation box.
-
-Many input script errors are detected by LAMMPS and an ERROR or
-WARNING message is printed.  The "Errors"_Errors.html doc page gives
-more information on what errors mean.  The documentation for each
-command lists restrictions on how the command can be used.
-
-:line
-
-3.2 Parsing rules :link(cmd_2),h4
-
-Each non-blank line in the input script is treated as a command.
-LAMMPS commands are case sensitive.  Command names are lower-case, as
-are specified command arguments.  Upper case letters may be used in
-file names or user-chosen ID strings.
-
-Here is how each line in the input script is parsed by LAMMPS:
-
-(1) If the last printable character on the line is a "&" character,
-the command is assumed to continue on the next line.  The next line is
-concatenated to the previous line by removing the "&" character and
-line break.  This allows long commands to be continued across two or
-more lines.  See the discussion of triple quotes in (6) for how to
-continue a command across multiple line without using "&" characters.
-
-(2) All characters from the first "#" character onward are treated as
-comment and discarded.  See an exception in (6).  Note that a
-comment after a trailing "&" character will prevent the command from
-continuing on the next line.  Also note that for multi-line commands a
-single leading "#" will comment out the entire command.
-
-(3) The line is searched repeatedly for $ characters, which indicate
-variables that are replaced with a text string.  See an exception in
-(6).
-
-If the $ is followed by curly brackets, then the variable name is the
-text inside the curly brackets.  If no curly brackets follow the $,
-then the variable name is the single character immediately following
-the $.  Thus $\{myTemp\} and $x refer to variable names "myTemp" and
-"x".
-
-How the variable is converted to a text string depends on what style
-of variable it is; see the "variable"_variable.html doc page for details.
-It can be a variable that stores multiple text strings, and return one
-of them.  The returned text string can be multiple "words" (space
-separated) which will then be interpreted as multiple arguments in the
-input command.  The variable can also store a numeric formula which
-will be evaluated and its numeric result returned as a string.
-
-As a special case, if the $ is followed by parenthesis, then the text
-inside the parenthesis is treated as an "immediate" variable and
-evaluated as an "equal-style variable"_variable.html.  This is a way
-to use numeric formulas in an input script without having to assign
-them to variable names.  For example, these 3 input script lines:
-
-variable X equal (xlo+xhi)/2+sqrt(v_area)
-region 1 block $X 2 INF INF EDGE EDGE
-variable X delete :pre
-
-can be replaced by
-
-region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE :pre
-
-so that you do not have to define (or discard) a temporary variable X.
-
-Additionally, the "immediate" variable expression may be followed by a
-colon, followed by a C-style format string, e.g. ":%f" or ":%.10g".
-The format string must be appropriate for a double-precision
-floating-point value.  The format string is used to output the result
-of the variable expression evaluation.  If a format string is not
-specified a high-precision "%.20g" is used as the default.
-
-This can be useful for formatting print output to a desired precion:
-
-print "Final energy per atom: $(pe/atoms:%10.3f) eV/atom" :pre
-
-Note that neither the curly-bracket or immediate form of variables can
-contain nested $ characters for other variables to substitute for.
-Thus you cannot do this:
-
-variable        a equal 2
-variable        b2 equal 4
-print           "B2 = $\{b$a\}" :pre
-
-Nor can you specify this $($x-1.0) for an immediate variable, but
-you could use $(v_x-1.0), since the latter is valid syntax for an
-"equal-style variable"_variable.html.
-
-See the "variable"_variable.html command for more details of how
-strings are assigned to variables and evaluated, and how they can be
-used in input script commands.
-
-(4) The line is broken into "words" separated by whitespace (tabs,
-spaces).  Note that words can thus contain letters, digits,
-underscores, or punctuation characters.
-
-(5) The first word is the command name.  All successive words in the
-line are arguments.
-
-(6) If you want text with spaces to be treated as a single argument,
-it can be enclosed in either single or double or triple quotes.  A
-long single argument enclosed in single or double quotes can span
-multiple lines if the "&" character is used, as described above.  When
-the lines are concatenated together (and the "&" characters and line
-breaks removed), the text will become a single line.  If you want
-multiple lines of an argument to retain their line breaks, the text
-can be enclosed in triple quotes, in which case "&" characters are not
-needed.  For example:
-
-print "Volume = $v"
-print 'Volume = $v'
-if "$\{steps\} > 1000" then quit
-variable a string "red green blue &
-                   purple orange cyan"
-print """
-System volume = $v
-System temperature = $t
-""" :pre
-
-In each case, the single, double, or triple quotes are removed when
-the single argument they enclose is stored internally.
-
-See the "dump modify format"_dump_modify.html, "print"_print.html,
-"if"_if.html, and "python"_python.html commands for examples.
-
-A "#" or "$" character that is between quotes will not be treated as a
-comment indicator in (2) or substituted for as a variable in (3).
-
-NOTE: If the argument is itself a command that requires a quoted
-argument (e.g. using a "print"_print.html command as part of an
-"if"_if.html or "run every"_run.html command), then single, double, or
-triple quotes can be nested in the usual manner.  See the doc pages
-for those commands for examples.  Only one of level of nesting is
-allowed, but that should be sufficient for most use cases.
-
-:line
-
-3.3 Input script structure :h3,link(cmd_3)
-
-This section describes the structure of a typical LAMMPS input script.
-The examples directory in the LAMMPS distribution contains many sample
-input scripts; the corresponding problems are discussed on the
-"Examples"_Examples.html doc page, and animated on the "LAMMPS WWW
-Site"_lws.
-
-A LAMMPS input script typically has 4 parts:
-
-Initialization
-Atom definition
-Settings
-Run a simulation :ol
-
-The last 2 parts can be repeated as many times as desired.  I.e. run a
-simulation, change some settings, run some more, etc.  Each of the 4
-parts is now described in more detail.  Remember that almost all the
-commands need only be used if a non-default value is desired.
-
-(1) Initialization
-
-Set parameters that need to be defined before atoms are created or
-read-in from a file.
-
-The relevant commands are "units"_units.html,
-"dimension"_dimension.html, "newton"_newton.html,
-"processors"_processors.html, "boundary"_boundary.html,
-"atom_style"_atom_style.html, "atom_modify"_atom_modify.html.
-
-If force-field parameters appear in the files that will be read, these
-commands tell LAMMPS what kinds of force fields are being used:
-"pair_style"_pair_style.html, "bond_style"_bond_style.html,
-"angle_style"_angle_style.html, "dihedral_style"_dihedral_style.html,
-"improper_style"_improper_style.html.
-
-(2) Atom definition
-
-There are 3 ways to define atoms in LAMMPS.  Read them in from a data
-or restart file via the "read_data"_read_data.html or
-"read_restart"_read_restart.html commands.  These files can contain
-molecular topology information.  Or create atoms on a lattice (with no
-molecular topology), using these commands: "lattice"_lattice.html,
-"region"_region.html, "create_box"_create_box.html,
-"create_atoms"_create_atoms.html.  The entire set of atoms can be
-duplicated to make a larger simulation using the
-"replicate"_replicate.html command.
-
-(3) Settings
-
-Once atoms and molecular topology are defined, a variety of settings
-can be specified: force field coefficients, simulation parameters,
-output options, etc.
-
-Force field coefficients are set by these commands (they can also be
-set in the read-in files): "pair_coeff"_pair_coeff.html,
-"bond_coeff"_bond_coeff.html, "angle_coeff"_angle_coeff.html,
-"dihedral_coeff"_dihedral_coeff.html,
-"improper_coeff"_improper_coeff.html,
-"kspace_style"_kspace_style.html, "dielectric"_dielectric.html,
-"special_bonds"_special_bonds.html.
-
-Various simulation parameters are set by these commands:
-"neighbor"_neighbor.html, "neigh_modify"_neigh_modify.html,
-"group"_group.html, "timestep"_timestep.html,
-"reset_timestep"_reset_timestep.html, "run_style"_run_style.html,
-"min_style"_min_style.html, "min_modify"_min_modify.html.
-
-Fixes impose a variety of boundary conditions, time integration, and
-diagnostic options.  The "fix"_fix.html command comes in many flavors.
-
-Various computations can be specified for execution during a
-simulation using the "compute"_compute.html,
-"compute_modify"_compute_modify.html, and "variable"_variable.html
-commands.
-
-Output options are set by the "thermo"_thermo.html, "dump"_dump.html,
-and "restart"_restart.html commands.
-
-(4) Run a simulation
-
-A molecular dynamics simulation is run using the "run"_run.html
-command.  Energy minimization (molecular statics) is performed using
-the "minimize"_minimize.html command.  A parallel tempering
-(replica-exchange) simulation can be run using the
-"temper"_temper.html command.
-
-:line
-
-3.4 Commands listed by category :link(cmd_4),h4
-
-This section lists core LAMMPS commands, grouped by category.
-The "next section"_#cmd_5 lists all commands alphabetically.  The
-next section also includes (long) lists of style options for entries
-that appear in the following categories as a single command (fix,
-compute, pair, etc).  Commands that are added by user packages are not
-included in the categories here, but they are in the next section.
-
-Initialization:
-
-"newton"_newton.html,
-"package"_package.html,
-"processors"_processors.html,
-"suffix"_suffix.html,
-"units"_units.html
-
-Setup simulation box:
-
-"boundary"_boundary.html,
-"box"_box.html,
-"change_box"_change_box.html,
-"create_box"_create_box.html,
-"dimension"_dimension.html,
-"lattice"_lattice.html,
-"region"_region.html
-
-Setup atoms:
-
-"atom_modify"_atom_modify.html,
-"atom_style"_atom_style.html,
-"balance"_balance.html,
-"create_atoms"_create_atoms.html,
-"create_bonds"_create_bonds.html,
-"delete_atoms"_delete_atoms.html,
-"delete_bonds"_delete_bonds.html,
-"displace_atoms"_displace_atoms.html,
-"group"_group.html,
-"mass"_mass.html,
-"molecule"_molecule.html,
-"read_data"_read_data.html,
-"read_dump"_read_dump.html,
-"read_restart"_read_restart.html,
-"replicate"_replicate.html,
-"set"_set.html,
-"velocity"_velocity.html
-
-Force fields:
-
-"angle_coeff"_angle_coeff.html,
-"angle_style"_angle_style.html,
-"bond_coeff"_bond_coeff.html,
-"bond_style"_bond_style.html,
-"bond_write"_bond_write.html,
-"dielectric"_dielectric.html,
-"dihedral_coeff"_dihedral_coeff.html,
-"dihedral_style"_dihedral_style.html,
-"improper_coeff"_improper_coeff.html,
-"improper_style"_improper_style.html,
-"kspace_modify"_kspace_modify.html,
-"kspace_style"_kspace_style.html,
-"pair_coeff"_pair_coeff.html,
-"pair_modify"_pair_modify.html,
-"pair_style"_pair_style.html,
-"pair_write"_pair_write.html,
-"special_bonds"_special_bonds.html
-
-Settings:
-
-"comm_modify"_comm_modify.html,
-"comm_style"_comm_style.html,
-"info"_info.html,
-"min_modify"_min_modify.html,
-"min_style"_min_style.html,
-"neigh_modify"_neigh_modify.html,
-"neighbor"_neighbor.html,
-"partition"_partition.html,
-"reset_timestep"_reset_timestep.html,
-"run_style"_run_style.html,
-"timer"_timer.html,
-"timestep"_timestep.html
-
-Operations within timestepping (fixes) and diagnostics (computes):
-
-"compute"_compute.html,
-"compute_modify"_compute_modify.html,
-"fix"_fix.html,
-"fix_modify"_fix_modify.html,
-"uncompute"_uncompute.html,
-"unfix"_unfix.html
-
-Output:
-
-"dump image"_dump_image.html,
-"dump movie"_dump_image.html,
-"dump"_dump.html,
-"dump_modify"_dump_modify.html,
-"restart"_restart.html,
-"thermo"_thermo.html,
-"thermo_modify"_thermo_modify.html,
-"thermo_style"_thermo_style.html,
-"undump"_undump.html,
-"write_coeff"_write_coeff.html,
-"write_data"_write_data.html,
-"write_dump"_write_dump.html,
-"write_restart"_write_restart.html
-
-Actions:
-
-"minimize"_minimize.html,
-"neb"_neb.html,
-"prd"_prd.html,
-"rerun"_rerun.html,
-"run"_run.html,
-"tad"_tad.html,
-"temper"_temper.html
-
-Input script control:
-
-"clear"_clear.html,
-"echo"_echo.html,
-"if"_if.html,
-"include"_include.html,
-"jump"_jump.html,
-"label"_label.html,
-"log"_log.html,
-"next"_next.html,
-"print"_print.html,
-"python"_python.html,
-"quit"_quit.html,
-"shell"_shell.html,
-"variable"_variable.html
-
-:line
-
-3.5 Individual commands :h3,link(cmd_5),link(comm)
-
-This section lists all LAMMPS commands alphabetically, with a separate
-listing below of styles within certain commands.  The "previous
-section"_#cmd_4 lists the same commands, grouped by category.  Note
-that some style options for some commands are part of specific LAMMPS
-packages, which means they cannot be used unless the package was
-included when LAMMPS was built.  Not all packages are included in a
-default LAMMPS build.  These dependencies are listed as Restrictions
-in the command's documentation.
-
-"angle_coeff"_angle_coeff.html,
-"angle_style"_angle_style.html,
-"atom_modify"_atom_modify.html,
-"atom_style"_atom_style.html,
-"balance"_balance.html,
-"bond_coeff"_bond_coeff.html,
-"bond_style"_bond_style.html,
-"bond_write"_bond_write.html,
-"boundary"_boundary.html,
-"box"_box.html,
-"change_box"_change_box.html,
-"clear"_clear.html,
-"comm_modify"_comm_modify.html,
-"comm_style"_comm_style.html,
-"compute"_compute.html,
-"compute_modify"_compute_modify.html,
-"create_atoms"_create_atoms.html,
-"create_bonds"_create_bonds.html,
-"create_box"_create_box.html,
-"delete_atoms"_delete_atoms.html,
-"delete_bonds"_delete_bonds.html,
-"dielectric"_dielectric.html,
-"dihedral_coeff"_dihedral_coeff.html,
-"dihedral_style"_dihedral_style.html,
-"dimension"_dimension.html,
-"displace_atoms"_displace_atoms.html,
-"dump"_dump.html,
-"dump image"_dump_image.html,
-"dump_modify"_dump_modify.html,
-"dump movie"_dump_image.html,
-"echo"_echo.html,
-"fix"_fix.html,
-"fix_modify"_fix_modify.html,
-"group"_group.html,
-"if"_if.html,
-"info"_info.html,
-"improper_coeff"_improper_coeff.html,
-"improper_style"_improper_style.html,
-"include"_include.html,
-"jump"_jump.html,
-"kspace_modify"_kspace_modify.html,
-"kspace_style"_kspace_style.html,
-"label"_label.html,
-"lattice"_lattice.html,
-"log"_log.html,
-"mass"_mass.html,
-"minimize"_minimize.html,
-"min_modify"_min_modify.html,
-"min_style"_min_style.html,
-"molecule"_molecule.html,
-"neb"_neb.html,
-"neigh_modify"_neigh_modify.html,
-"neighbor"_neighbor.html,
-"newton"_newton.html,
-"next"_next.html,
-"package"_package.html,
-"pair_coeff"_pair_coeff.html,
-"pair_modify"_pair_modify.html,
-"pair_style"_pair_style.html,
-"pair_write"_pair_write.html,
-"partition"_partition.html,
-"prd"_prd.html,
-"print"_print.html,
-"processors"_processors.html,
-"python"_python.html,
-"quit"_quit.html,
-"read_data"_read_data.html,
-"read_dump"_read_dump.html,
-"read_restart"_read_restart.html,
-"region"_region.html,
-"replicate"_replicate.html,
-"rerun"_rerun.html,
-"reset_ids"_reset_ids.html,
-"reset_timestep"_reset_timestep.html,
-"restart"_restart.html,
-"run"_run.html,
-"run_style"_run_style.html,
-"set"_set.html,
-"shell"_shell.html,
-"special_bonds"_special_bonds.html,
-"suffix"_suffix.html,
-"tad"_tad.html,
-"temper"_temper.html,
-"thermo"_thermo.html,
-"thermo_modify"_thermo_modify.html,
-"thermo_style"_thermo_style.html,
-"timer"_timer.html,
-"timestep"_timestep.html,
-"uncompute"_uncompute.html,
-"undump"_undump.html,
-"unfix"_unfix.html,
-"units"_units.html,
-"variable"_variable.html,
-"velocity"_velocity.html,
-"write_coeff"_write_coeff.html,
-"write_data"_write_data.html,
-"write_dump"_write_dump.html,
-"write_restart"_write_restart.html :tb(c=6,ea=c)
-
-These are additional commands in USER packages, which can be used if
-"LAMMPS is built with the appropriate
-package"_Section_start.html#start_3.
-
-"dump netcdf"_dump_netcdf.html,
-"dump netcdf/mpiio"_dump_netcdf.html,
-"dump vtk"_dump_vtk.html,
-"group2ndx"_group2ndx.html,
-"ndx2group"_group2ndx.html,
-"temper/grem"_temper_grem.html,
-"temper/npt"_temper_npt.html :tb(c=3,ea=c)
-
-:line
-
-Fix styles :h3
-
-See the "fix"_fix.html command for one-line descriptions of each style
-or click on the style itself for a full description.  Some of the
-styles have accelerated versions, which can be used if LAMMPS is built
-with the "appropriate accelerated package"_Speed_packages.html.  This
-is indicated by additional letters in parenthesis: g = GPU, i =
-USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
-
-"adapt"_fix_adapt.html,
-"addforce"_fix_addforce.html,
-"append/atoms"_fix_append_atoms.html,
-"atom/swap"_fix_atom_swap.html,
-"aveforce"_fix_aveforce.html,
-"ave/atom"_fix_ave_atom.html,
-"ave/chunk"_fix_ave_chunk.html,
-"ave/correlate"_fix_ave_correlate.html,
-"ave/histo"_fix_ave_histo.html,
-"ave/histo/weight"_fix_ave_histo.html,
-"ave/time"_fix_ave_time.html,
-"balance"_fix_balance.html,
-"bond/break"_fix_bond_break.html,
-"bond/create"_fix_bond_create.html,
-"bond/swap"_fix_bond_swap.html,
-"box/relax"_fix_box_relax.html,
-"cmap"_fix_cmap.html,
-"controller"_fix_controller.html,
-"deform (k)"_fix_deform.html,
-"deposit"_fix_deposit.html,
-"drag"_fix_drag.html,
-"dt/reset"_fix_dt_reset.html,
-"efield"_fix_efield.html,
-"ehex"_fix_ehex.html,
-"enforce2d (k)"_fix_enforce2d.html,
-"evaporate"_fix_evaporate.html,
-"external"_fix_external.html,
-"freeze"_fix_freeze.html,
-"gcmc"_fix_gcmc.html,
-"gld"_fix_gld.html,
-"gravity (o)"_fix_gravity.html,
-"halt"_fix_halt.html,
-"heat"_fix_heat.html,
-"indent"_fix_indent.html,
-"latte"_fix_latte.html,
-"langevin (k)"_fix_langevin.html,
-"langevin/spin"_fix_langevin_spin.hmtl,
-"lineforce"_fix_lineforce.html,
-"momentum (k)"_fix_momentum.html,
-"move"_fix_move.html,
-"mscg"_fix_mscg.html,
-"msst"_fix_msst.html,
-"neb"_fix_neb.html,
-"nph (ko)"_fix_nh.html,
-"nphug (o)"_fix_nphug.html,
-"nph/asphere (o)"_fix_nph_asphere.html,
-"nph/body"_fix_nph_body.html,
-"nph/sphere (o)"_fix_nph_sphere.html,
-"npt (kio)"_fix_nh.html,
-"npt/asphere (o)"_fix_npt_asphere.html,
-"npt/body"_fix_npt_body.html,
-"npt/sphere (o)"_fix_npt_sphere.html,
-"nve (kio)"_fix_nve.html,
-"nve/asphere (i)"_fix_nve_asphere.html,
-"nve/asphere/noforce"_fix_nve_asphere_noforce.html,
-"nve/body"_fix_nve_body.html,
-"nve/limit"_fix_nve_limit.html,
-"nve/line"_fix_nve_line.html,
-"nve/noforce"_fix_nve_noforce.html,
-"nve/sphere (o)"_fix_nve_sphere.html,
-"nve/spin"_fix_nve_spin.html,
-"nve/tri"_fix_nve_tri.html,
-"nvt (iko)"_fix_nh.html,
-"nvt/asphere (o)"_fix_nvt_asphere.html,
-"nvt/body"_fix_nvt_body.html,
-"nvt/sllod (io)"_fix_nvt_sllod.html,
-"nvt/sphere (o)"_fix_nvt_sphere.html,
-"oneway"_fix_oneway.html,
-"orient/bcc"_fix_orient.html,
-"orient/fcc"_fix_orient.html,
-"planeforce"_fix_planeforce.html,
-"poems"_fix_poems.html,
-"pour"_fix_pour.html,
-"precession/spin"_fix_precession_spin.html,
-"press/berendsen"_fix_press_berendsen.html,
-"print"_fix_print.html,
-"property/atom (k)"_fix_property_atom.html,
-"python/invoke"_fix_python_invoke.html,
-"python/move"_fix_python_move.html,
-"qeq/comb (o)"_fix_qeq_comb.html,
-"qeq/dynamic"_fix_qeq.html,
-"qeq/fire"_fix_qeq.html,
-"qeq/point"_fix_qeq.html,
-"qeq/shielded"_fix_qeq.html,
-"qeq/slater"_fix_qeq.html,
-"rattle"_fix_shake.html,
-"reax/bonds"_fix_reax_bonds.html,
-"recenter"_fix_recenter.html,
-"restrain"_fix_restrain.html,
-"rigid (o)"_fix_rigid.html,
-"rigid/nph (o)"_fix_rigid.html,
-"rigid/npt (o)"_fix_rigid.html,
-"rigid/nve (o)"_fix_rigid.html,
-"rigid/nvt (o)"_fix_rigid.html,
-"rigid/small (o)"_fix_rigid.html,
-"rigid/small/nph"_fix_rigid.html,
-"rigid/small/npt"_fix_rigid.html,
-"rigid/small/nve"_fix_rigid.html,
-"rigid/small/nvt"_fix_rigid.html,
-"setforce (k)"_fix_setforce.html,
-"shake"_fix_shake.html,
-"spring"_fix_spring.html,
-"spring/chunk"_fix_spring_chunk.html,
-"spring/rg"_fix_spring_rg.html,
-"spring/self"_fix_spring_self.html,
-"srd"_fix_srd.html,
-"store/force"_fix_store_force.html,
-"store/state"_fix_store_state.html,
-"temp/berendsen"_fix_temp_berendsen.html,
-"temp/csld"_fix_temp_csvr.html,
-"temp/csvr"_fix_temp_csvr.html,
-"temp/rescale"_fix_temp_rescale.html,
-"tfmc"_fix_tfmc.html,
-"thermal/conductivity"_fix_thermal_conductivity.html,
-"tmd"_fix_tmd.html,
-"ttm"_fix_ttm.html,
-"tune/kspace"_fix_tune_kspace.html,
-"vector"_fix_vector.html,
-"viscosity"_fix_viscosity.html,
-"viscous"_fix_viscous.html,
-"wall/body/polygon"_fix_wall_body_polygon.html,
-"wall/body/polyhedron"_fix_wall_body_polyhedron.html,
-"wall/colloid"_fix_wall.html,
-"wall/gran"_fix_wall_gran.html,
-"wall/gran/region"_fix_wall_gran_region.html,
-"wall/harmonic"_fix_wall.html,
-"wall/lj1043"_fix_wall.html,
-"wall/lj126"_fix_wall.html,
-"wall/lj93 (k)"_fix_wall.html,
-"wall/piston"_fix_wall_piston.html,
-"wall/reflect (k)"_fix_wall_reflect.html,
-"wall/region"_fix_wall_region.html,
-"wall/srd"_fix_wall_srd.html :tb(c=8,ea=c)
-
-These are additional fix styles in USER packages, which can be used if
-"LAMMPS is built with the appropriate
-package"_Section_start.html#start_3.
-
-"adapt/fep"_fix_adapt_fep.html,
-"addtorque"_fix_addtorque.html,
-"atc"_fix_atc.html,
-"ave/correlate/long"_fix_ave_correlate_long.html,
-"bond/react"_fix_bond_react.html,
-"colvars"_fix_colvars.html,
-"dpd/energy (k)"_fix_dpd_energy.html,
-"drude"_fix_drude.html,
-"drude/transform/direct"_fix_drude_transform.html,
-"drude/transform/reverse"_fix_drude_transform.html,
-"edpd/source"_fix_dpd_source.html,
-"eos/cv"_fix_eos_cv.html,
-"eos/table"_fix_eos_table.html,
-"eos/table/rx (k)"_fix_eos_table_rx.html,
-"filter/corotate"_fix_filter_corotate.html,
-"flow/gauss"_fix_flow_gauss.html,
-"gle"_fix_gle.html,
-"grem"_fix_grem.html,
-"imd"_fix_imd.html,
-"ipi"_fix_ipi.html,
-"langevin/drude"_fix_langevin_drude.html,
-"langevin/eff"_fix_langevin_eff.html,
-"lb/fluid"_fix_lb_fluid.html,
-"lb/momentum"_fix_lb_momentum.html,
-"lb/pc"_fix_lb_pc.html,
-"lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html,
-"lb/viscous"_fix_lb_viscous.html,
-"meso"_fix_meso.html,
-"manifoldforce"_fix_manifoldforce.html,
-"meso/stationary"_fix_meso_stationary.html,
-"mvv/dpd"_fix_mvv_dpd.html,
-"mvv/edpd"_fix_mvv_dpd.html,
-"mvv/tdpd"_fix_mvv_dpd.html,
-"nph/eff"_fix_nh_eff.html,
-"npt/eff"_fix_nh_eff.html,
-"npt/uef"_fix_nh_uef.html,
-"nve/dot"_fix_nve_dot.html,
-"nve/dotc/langevin"_fix_nve_dotc_langevin.html,
-"nve/eff"_fix_nve_eff.html,
-"nve/manifold/rattle"_fix_nve_manifold_rattle.html,
-"nvk"_fix_nvk.html,
-"nvt/eff"_fix_nh_eff.html,
-"nvt/manifold/rattle"_fix_nvt_manifold_rattle.html,
-"nvt/sllod/eff"_fix_nvt_sllod_eff.html,
-"nvt/uef"_fix_nh_uef.html,
-"phonon"_fix_phonon.html,
-"pimd"_fix_pimd.html,
-"qbmsst"_fix_qbmsst.html,
-"qeq/reax (ko)"_fix_qeq_reax.html,
-"qmmm"_fix_qmmm.html,
-"qtb"_fix_qtb.html,
-"reax/c/bonds (k)"_fix_reax_bonds.html,
-"reax/c/species (k)"_fix_reaxc_species.html,
-"rhok"_fix_rhok.html,
-"rx (k)"_fix_rx.html,
-"saed/vtk"_fix_saed_vtk.html,
-"shardlow (k)"_fix_shardlow.html,
-"smd"_fix_smd.html,
-"smd/adjust/dt"_fix_smd_adjust_dt.html,
-"smd/integrate/tlsph"_fix_smd_integrate_tlsph.html,
-"smd/integrate/ulsph"_fix_smd_integrate_ulsph.html,
-"smd/move/triangulated/surface"_fix_smd_move_triangulated_surface.html,
-"smd/setvel"_fix_smd_setvel.html,
-"smd/wall/surface"_fix_smd_wall_surface.html,
-"tdpd/source"_fix_dpd_source.html,
-"temp/rescale/eff"_fix_temp_rescale_eff.html,
-"ti/spring"_fix_ti_spring.html,
-"ttm/mod"_fix_ttm.html,
-"wall/ees"_fix_wall_ees.html,
-"wall/region/ees"_fix_wall_ees.html :tb(c=6,ea=c)
-
-:line
-
-Compute styles :h3
-
-See the "compute"_compute.html command for one-line descriptions of
-each style or click on the style itself for a full description.  Some
-of the styles have accelerated versions, which can be used if LAMMPS
-is built with the "appropriate accelerated
-package"_Speed_packages.html.  This is indicated by additional letters
-in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
-OPT.
-
-"aggregate/atom"_compute_cluster_atom.html,
-"angle"_compute_angle.html,
-"angle/local"_compute_angle_local.html,
-"angmom/chunk"_compute_angmom_chunk.html,
-"body/local"_compute_body_local.html,
-"bond"_compute_bond.html,
-"bond/local"_compute_bond_local.html,
-"centro/atom"_compute_centro_atom.html,
-"chunk/atom"_compute_chunk_atom.html,
-"cluster/atom"_compute_cluster_atom.html,
-"cna/atom"_compute_cna_atom.html,
-"com"_compute_com.html,
-"com/chunk"_compute_com_chunk.html,
-"contact/atom"_compute_contact_atom.html,
-"coord/atom"_compute_coord_atom.html,
-"damage/atom"_compute_damage_atom.html,
-"dihedral"_compute_dihedral.html,
-"dihedral/local"_compute_dihedral_local.html,
-"dilatation/atom"_compute_dilatation_atom.html,
-"dipole/chunk"_compute_dipole_chunk.html,
-"displace/atom"_compute_displace_atom.html,
-"erotate/asphere"_compute_erotate_asphere.html,
-"erotate/rigid"_compute_erotate_rigid.html,
-"erotate/sphere"_compute_erotate_sphere.html,
-"erotate/sphere/atom"_compute_erotate_sphere_atom.html,
-"event/displace"_compute_event_displace.html,
-"fragment/atom"_compute_cluster_atom.html,
-"global/atom"_compute_global_atom.html,
-"group/group"_compute_group_group.html,
-"gyration"_compute_gyration.html,
-"gyration/chunk"_compute_gyration_chunk.html,
-"heat/flux"_compute_heat_flux.html,
-"hexorder/atom"_compute_hexorder_atom.html,
-"improper"_compute_improper.html,
-"improper/local"_compute_improper_local.html,
-"inertia/chunk"_compute_inertia_chunk.html,
-"ke"_compute_ke.html,
-"ke/atom"_compute_ke_atom.html,
-"ke/rigid"_compute_ke_rigid.html,
-"msd"_compute_msd.html,
-"msd/chunk"_compute_msd_chunk.html,
-"msd/nongauss"_compute_msd_nongauss.html,
-"omega/chunk"_compute_omega_chunk.html,
-"orientorder/atom"_compute_orientorder_atom.html,
-"pair"_compute_pair.html,
-"pair/local"_compute_pair_local.html,
-"pe"_compute_pe.html,
-"pe/atom"_compute_pe_atom.html,
-"plasticity/atom"_compute_plasticity_atom.html,
-"pressure"_compute_pressure.html,
-"property/atom"_compute_property_atom.html,
-"property/local"_compute_property_local.html,
-"property/chunk"_compute_property_chunk.html,
-"rdf"_compute_rdf.html,
-"reduce"_compute_reduce.html,
-"reduce/region"_compute_reduce.html,
-"rigid/local"_compute_rigid_local.html,
-"slice"_compute_slice.html,
-"sna/atom"_compute_sna_atom.html,
-"snad/atom"_compute_sna_atom.html,
-"snav/atom"_compute_sna_atom.html,
-"spin"_compute_spin.html,
-"stress/atom"_compute_stress_atom.html,
-"temp (k)"_compute_temp.html,
-"temp/asphere"_compute_temp_asphere.html,
-"temp/body"_compute_temp_body.html,
-"temp/chunk"_compute_temp_chunk.html,
-"temp/com"_compute_temp_com.html,
-"temp/deform"_compute_temp_deform.html,
-"temp/partial"_compute_temp_partial.html,
-"temp/profile"_compute_temp_profile.html,
-"temp/ramp"_compute_temp_ramp.html,
-"temp/region"_compute_temp_region.html,
-"temp/sphere"_compute_temp_sphere.html,
-"ti"_compute_ti.html,
-"torque/chunk"_compute_torque_chunk.html,
-"vacf"_compute_vacf.html,
-"vcm/chunk"_compute_vcm_chunk.html,
-"voronoi/atom"_compute_voronoi_atom.html :tb(c=6,ea=c)
-
-These are additional compute styles in USER packages, which can be
-used if "LAMMPS is built with the appropriate
-package"_Section_start.html#start_3.
-
-"ackland/atom"_compute_ackland_atom.html,
-"basal/atom"_compute_basal_atom.html,
-"cnp/atom"_compute_cnp_atom.html,
-"dpd"_compute_dpd.html,
-"dpd/atom"_compute_dpd_atom.html,
-"edpd/temp/atom"_compute_edpd_temp_atom.html,
-"entropy/atom"_compute_entropy_atom.html,
-"fep"_compute_fep.html,
-"force/tally"_compute_tally.html,
-"heat/flux/tally"_compute_tally.html,
-"ke/eff"_compute_ke_eff.html,
-"ke/atom/eff"_compute_ke_atom_eff.html,
-"meso/e/atom"_compute_meso_e_atom.html,
-"meso/rho/atom"_compute_meso_rho_atom.html,
-"meso/t/atom"_compute_meso_t_atom.html,
-"pe/tally"_compute_tally.html,
-"pe/mol/tally"_compute_tally.html,
-"pressure/uef"_compute_pressure_uef.html,
-"saed"_compute_saed.html,
-"smd/contact/radius"_compute_smd_contact_radius.html,
-"smd/damage"_compute_smd_damage.html,
-"smd/hourglass/error"_compute_smd_hourglass_error.html,
-"smd/internal/energy"_compute_smd_internal_energy.html,
-"smd/plastic/strain"_compute_smd_plastic_strain.html,
-"smd/plastic/strain/rate"_compute_smd_plastic_strain_rate.html,
-"smd/rho"_compute_smd_rho.html,
-"smd/tlsph/defgrad"_compute_smd_tlsph_defgrad.html,
-"smd/tlsph/dt"_compute_smd_tlsph_dt.html,
-"smd/tlsph/num/neighs"_compute_smd_tlsph_num_neighs.html,
-"smd/tlsph/shape"_compute_smd_tlsph_shape.html,
-"smd/tlsph/strain"_compute_smd_tlsph_strain.html,
-"smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html,
-"smd/tlsph/stress"_compute_smd_tlsph_stress.html,
-"smd/triangle/mesh/vertices"_compute_smd_triangle_mesh_vertices.html,
-"smd/ulsph/num/neighs"_compute_smd_ulsph_num_neighs.html,
-"smd/ulsph/strain"_compute_smd_ulsph_strain.html,
-"smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html,
-"smd/ulsph/stress"_compute_smd_ulsph_stress.html,
-"smd/vol"_compute_smd_vol.html,
-"stress/tally"_compute_tally.html,
-"tdpd/cc/atom"_compute_tdpd_cc_atom.html,
-"temp/drude"_compute_temp_drude.html,
-"temp/eff"_compute_temp_eff.html,
-"temp/deform/eff"_compute_temp_deform_eff.html,
-"temp/region/eff"_compute_temp_region_eff.html,
-"temp/rotate"_compute_temp_rotate.html,
-"temp/uef"_compute_temp_uef.html,
-"xrd"_compute_xrd.html :tb(c=6,ea=c)
-
-:line
-
-Pair_style potentials :h3
-
-See the "pair_style"_pair_style.html command for an overview of pair
-potentials.  Click on the style itself for a full description.  Many
-of the styles have accelerated versions, which can be used if LAMMPS
-is built with the "appropriate accelerated
-package"_Speed_packages.html.  This is indicated by additional letters
-in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
-OPT.
-
-"none"_pair_none.html,
-"zero"_pair_zero.html,
-"hybrid"_pair_hybrid.html,
-"hybrid/overlay (k)"_pair_hybrid.html,
-"adp (o)"_pair_adp.html,
-"airebo (oi)"_pair_airebo.html,
-"airebo/morse (oi)"_pair_airebo.html,
-"beck (go)"_pair_beck.html,
-"body/nparticle"_pair_body_nparticle.html,
-"body/rounded/polygon"_pair_body_rounded/polygon.html,
-"body/rounded/polyhedron"_pair_body_rounded/polyhedron.html,
-"bop"_pair_bop.html,
-"born (go)"_pair_born.html,
-"born/coul/dsf"_pair_born.html,
-"born/coul/dsf/cs"_pair_born.html,
-"born/coul/long (go)"_pair_born.html,
-"born/coul/long/cs"_pair_born.html,
-"born/coul/msm (o)"_pair_born.html,
-"born/coul/wolf (go)"_pair_born.html,
-"born/coul/wolf/cs"_pair_born.html,
-"brownian (o)"_pair_brownian.html,
-"brownian/poly (o)"_pair_brownian.html,
-"buck (giko)"_pair_buck.html,
-"buck/coul/cut (giko)"_pair_buck.html,
-"buck/coul/long (giko)"_pair_buck.html,
-"buck/coul/long/cs"_pair_buck.html,
-"buck/coul/msm (o)"_pair_buck.html,
-"buck/long/coul/long (o)"_pair_buck_long.html,
-"colloid (go)"_pair_colloid.html,
-"comb (o)"_pair_comb.html,
-"comb3"_pair_comb.html,
-"coul/cut (gko)"_pair_coul.html,
-"coul/debye (gko)"_pair_coul.html,
-"coul/dsf (gko)"_pair_coul.html,
-"coul/long (gko)"_pair_coul.html,
-"coul/long/cs"_pair_coul.html,
-"coul/msm"_pair_coul.html,
-"coul/streitz"_pair_coul.html,
-"coul/wolf (ko)"_pair_coul.html,
-"coul/wolf/cs"_pair_coul.html,
-"dpd (gio)"_pair_dpd.html,
-"dpd/tstat (go)"_pair_dpd.html,
-"dsmc"_pair_dsmc.html,
-"eam (gikot)"_pair_eam.html,
-"eam/alloy (gikot)"_pair_eam.html,
-"eam/cd (o)"_pair_eam.html,
-"eam/fs (gikot)"_pair_eam.html,
-"eim (o)"_pair_eim.html,
-"gauss (go)"_pair_gauss.html,
-"gayberne (gio)"_pair_gayberne.html,
-"gran/hertz/history (o)"_pair_gran.html,
-"gran/hooke (o)"_pair_gran.html,
-"gran/hooke/history (o)"_pair_gran.html,
-"gw"_pair_gw.html,
-"gw/zbl"_pair_gw.html,
-"hbond/dreiding/lj (o)"_pair_hbond_dreiding.html,
-"hbond/dreiding/morse (o)"_pair_hbond_dreiding.html,
-"kim"_pair_kim.html,
-"lcbop"_pair_lcbop.html,
-"line/lj"_pair_line_lj.html,
-"lj/charmm/coul/charmm (iko)"_pair_charmm.html,
-"lj/charmm/coul/charmm/implicit (ko)"_pair_charmm.html,
-"lj/charmm/coul/long (giko)"_pair_charmm.html,
-"lj/charmm/coul/msm"_pair_charmm.html,
-"lj/charmmfsw/coul/charmmfsh"_pair_charmm.html,
-"lj/charmmfsw/coul/long"_pair_charmm.html,
-"lj/class2 (gko)"_pair_class2.html,
-"lj/class2/coul/cut (ko)"_pair_class2.html,
-"lj/class2/coul/long (gko)"_pair_class2.html,
-"lj/cubic (go)"_pair_lj_cubic.html,
-"lj/cut (gikot)"_pair_lj.html,
-"lj/cut/coul/cut (gko)"_pair_lj.html,
-"lj/cut/coul/debye (gko)"_pair_lj.html,
-"lj/cut/coul/dsf (gko)"_pair_lj.html,
-"lj/cut/coul/long (gikot)"_pair_lj.html,
-"lj/cut/coul/long/cs"_pair_lj.html,
-"lj/cut/coul/msm (go)"_pair_lj.html,
-"lj/cut/coul/wolf (o)"_pair_lj.html,
-"lj/cut/dipole/cut (go)"_pair_dipole.html,
-"lj/cut/dipole/long"_pair_dipole.html,
-"lj/cut/tip4p/cut (o)"_pair_lj.html,
-"lj/cut/tip4p/long (ot)"_pair_lj.html,
-"lj/expand (gko)"_pair_lj_expand.html,
-"lj/gromacs (gko)"_pair_gromacs.html,
-"lj/gromacs/coul/gromacs (ko)"_pair_gromacs.html,
-"lj/long/coul/long (io)"_pair_lj_long.html,
-"lj/long/dipole/long"_pair_dipole.html,
-"lj/long/tip4p/long"_pair_lj_long.html,
-"lj/smooth (o)"_pair_lj_smooth.html,
-"lj/smooth/linear (o)"_pair_lj_smooth_linear.html,
-"lj96/cut (go)"_pair_lj96.html,
-"lubricate (o)"_pair_lubricate.html,
-"lubricate/poly (o)"_pair_lubricate.html,
-"lubricateU"_pair_lubricateU.html,
-"lubricateU/poly"_pair_lubricateU.html,
-"meam"_pair_meam.html,
-"mie/cut (o)"_pair_mie.html,
-"morse (gkot)"_pair_morse.html,
-"nb3b/harmonic (o)"_pair_nb3b_harmonic.html,
-"nm/cut (o)"_pair_nm.html,
-"nm/cut/coul/cut (o)"_pair_nm.html,
-"nm/cut/coul/long (o)"_pair_nm.html,
-"peri/eps"_pair_peri.html,
-"peri/lps (o)"_pair_peri.html,
-"peri/pmb (o)"_pair_peri.html,
-"peri/ves"_pair_peri.html,
-"polymorphic"_pair_polymorphic.html,
-"python"_pair_python.html,
-"reax"_pair_reax.html,
-"rebo (oi)"_pair_airebo.html,
-"resquared (go)"_pair_resquared.html,
-"snap (k)"_pair_snap.html,
-"soft (go)"_pair_soft.html,
-"sw (giko)"_pair_sw.html,
-"spin/dmi"_pair_spin_dmi.html,
-"spin/exchange"_pair_spin_exchange.html,
-"spin/magelec"_pair_spin_magelec.html,
-"spin/neel"_pair_spin_neel.html,
-"table (gko)"_pair_table.html,
-"tersoff (giko)"_pair_tersoff.html,
-"tersoff/mod (gko)"_pair_tersoff_mod.html,
-"tersoff/mod/c (o)"_pair_tersoff_mod.html,
-"tersoff/zbl (gko)"_pair_tersoff_zbl.html,
-"tip4p/cut (o)"_pair_coul.html,
-"tip4p/long (o)"_pair_coul.html,
-"tri/lj"_pair_tri_lj.html,
-"ufm (got)"_pair_ufm.html,
-"vashishta (ko)"_pair_vashishta.html,
-"vashishta/table (o)"_pair_vashishta.html,
-"yukawa (gok)"_pair_yukawa.html,
-"yukawa/colloid (go)"_pair_yukawa_colloid.html,
-"zbl (gok)"_pair_zbl.html :tb(c=4,ea=c)
-
-These are additional pair styles in USER packages, which can be used
-if "LAMMPS is built with the appropriate
-package"_Section_start.html#start_3.
-
-"agni (o)"_pair_agni.html,
-"awpmd/cut"_pair_awpmd.html,
-"buck/mdf"_pair_mdf.html,
-"coul/cut/soft (o)"_pair_lj_soft.html,
-"coul/diel (o)"_pair_coul_diel.html,
-"coul/long/soft (o)"_pair_lj_soft.html,
-"coul/shield"_pair_coul_shield.html,
-"dpd/fdt"_pair_dpd_fdt.html,
-"dpd/fdt/energy (k)"_pair_dpd_fdt.html,
-"edip (o)"_pair_edip.html,
-"edip/multi"_pair_edip.html,
-"edpd"_pair_meso.html,
-"eff/cut"_pair_eff.html,
-"exp6/rx (k)"_pair_exp6_rx.html,
-"extep"_pair_extep.html,
-"gauss/cut"_pair_gauss.html,
-"ilp/graphene/hbn"_pair_ilp_graphene_hbn.html,
-"kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html,
-"kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html,
-"lennard/mdf"_pair_mdf.html,
-"list"_pair_list.html,
-"lj/charmm/coul/long/soft (o)"_pair_charmm.html,
-"lj/cut/coul/cut/soft (o)"_pair_lj_soft.html,
-"lj/cut/coul/long/soft (o)"_pair_lj_soft.html,
-"lj/cut/dipole/sf (go)"_pair_dipole.html,
-"lj/cut/soft (o)"_pair_lj_soft.html,
-"lj/cut/thole/long (o)"_pair_thole.html,
-"lj/cut/tip4p/long/soft (o)"_pair_lj_soft.html,
-"lj/mdf"_pair_mdf.html,
-"lj/sdk (gko)"_pair_sdk.html,
-"lj/sdk/coul/long (go)"_pair_sdk.html,
-"lj/sdk/coul/msm (o)"_pair_sdk.html,
-"mdpd"_pair_meso.html,
-"mdpd/rhosum"_pair_meso.html,
-"meam/c"_pair_meam.html,
-"meam/spline (o)"_pair_meam_spline.html,
-"meam/sw/spline"_pair_meam_sw_spline.html,
-"mgpt"_pair_mgpt.html,
-"momb"_pair_momb.html,
-"morse/smooth/linear"_pair_morse.html,
-"morse/soft"_pair_morse.html,
-"multi/lucy"_pair_multi_lucy.html,
-"multi/lucy/rx (k)"_pair_multi_lucy_rx.html,
-"oxdna/coaxstk"_pair_oxdna.html,
-"oxdna/excv"_pair_oxdna.html,
-"oxdna/hbond"_pair_oxdna.html,
-"oxdna/stk"_pair_oxdna.html,
-"oxdna/xstk"_pair_oxdna.html,
-"oxdna2/coaxstk"_pair_oxdna2.html,
-"oxdna2/dh"_pair_oxdna2.html,
-"oxdna2/excv"_pair_oxdna2.html,
-"oxdna2/stk"_pair_oxdna2.html,
-"quip"_pair_quip.html,
-"reax/c (ko)"_pair_reaxc.html,
-"smd/hertz"_pair_smd_hertz.html,
-"smd/tlsph"_pair_smd_tlsph.html,
-"smd/triangulated/surface"_pair_smd_triangulated_surface.html,
-"smd/ulsph"_pair_smd_ulsph.html,
-"smtbq"_pair_smtbq.html,
-"snap (k)"_pair_snap.html,
-"sph/heatconduction"_pair_sph_heatconduction.html,
-"sph/idealgas"_pair_sph_idealgas.html,
-"sph/lj"_pair_sph_lj.html,
-"sph/rhosum"_pair_sph_rhosum.html,
-"sph/taitwater"_pair_sph_taitwater.html,
-"sph/taitwater/morris"_pair_sph_taitwater_morris.html,
-"srp"_pair_srp.html,
-"table/rx (k)"_pair_table_rx.html,
-"tdpd"_pair_meso.html,
-"tersoff/table (o)"_pair_tersoff.html,
-"thole"_pair_thole.html,
-"tip4p/long/soft (o)"_pair_lj_soft.html :tb(c=4,ea=c)
-
-:line
-
-Bond_style potentials :h3
-
-See the "bond_style"_bond_style.html command for an overview of bond
-potentials.  Click on the style itself for a full description.  Some
-of the styles have accelerated versions, which can be used if LAMMPS
-is built with the "appropriate accelerated
-package"_Speed_packages.html.  This is indicated by additional letters
-in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
-OPT.
-
-"none"_bond_none.html,
-"zero"_bond_zero.html,
-"hybrid"_bond_hybrid.html,
-"class2 (ko)"_bond_class2.html,
-"fene (iko)"_bond_fene.html,
-"fene/expand (o)"_bond_fene_expand.html,
-"gromos (o)"_bond_gromos.html,
-"harmonic (ko)"_bond_harmonic.html,
-"morse (o)"_bond_morse.html,
-"nonlinear (o)"_bond_nonlinear.html,
-"quartic (o)"_bond_quartic.html,
-"table (o)"_bond_table.html :tb(c=4,ea=c)
-
-These are additional bond styles in USER packages, which can be used
-if "LAMMPS is built with the appropriate
-package"_Section_start.html#start_3.
-
-"harmonic/shift (o)"_bond_harmonic_shift.html,
-"harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html,
-"oxdna/fene"_bond_oxdna.html,
-"oxdna2/fene"_bond_oxdna.html :tb(c=4,ea=c)
-
-:line
-
-Angle_style potentials :h3
-
-See the "angle_style"_angle_style.html command for an overview of
-angle potentials.  Click on the style itself for a full description.
-Some of the styles have accelerated versions, which can be used if
-LAMMPS is built with the "appropriate accelerated
-package"_Speed_packages.html.  This is indicated by additional letters
-in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
-OPT.
-
-"none"_angle_none.html,
-"zero"_angle_zero.html,
-"hybrid"_angle_hybrid.html,
-"charmm (ko)"_angle_charmm.html,
-"class2 (ko)"_angle_class2.html,
-"cosine (o)"_angle_cosine.html,
-"cosine/delta (o)"_angle_cosine_delta.html,
-"cosine/periodic (o)"_angle_cosine_periodic.html,
-"cosine/squared (o)"_angle_cosine_squared.html,
-"harmonic (iko)"_angle_harmonic.html,
-"table (o)"_angle_table.html :tb(c=4,ea=c)
-
-These are additional angle styles in USER packages, which can be used
-if "LAMMPS is built with the appropriate
-package"_Section_start.html#start_3.
-
-"cosine/shift (o)"_angle_cosine_shift.html,
-"cosine/shift/exp (o)"_angle_cosine_shift_exp.html,
-"dipole (o)"_angle_dipole.html,
-"fourier (o)"_angle_fourier.html,
-"fourier/simple (o)"_angle_fourier_simple.html,
-"quartic (o)"_angle_quartic.html,
-"sdk"_angle_sdk.html :tb(c=4,ea=c)
-
-:line
-
-Dihedral_style potentials :h3
-
-See the "dihedral_style"_dihedral_style.html command for an overview
-of dihedral potentials.  Click on the style itself for a full
-description.  Some of the styles have accelerated versions, which can
-be used if LAMMPS is built with the "appropriate accelerated
-package"_Speed_packages.html.  This is indicated by additional
-letters in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o =
-USER-OMP, t = OPT.
-
-"none"_dihedral_none.html,
-"zero"_dihedral_zero.html,
-"hybrid"_dihedral_hybrid.html,
-"charmm (iko)"_dihedral_charmm.html,
-"charmmfsw"_dihedral_charmm.html,
-"class2 (ko)"_dihedral_class2.html,
-"harmonic (io)"_dihedral_harmonic.html,
-"helix (o)"_dihedral_helix.html,
-"multi/harmonic (o)"_dihedral_multi_harmonic.html,
-"opls (iko)"_dihedral_opls.html :tb(c=4,ea=c)
-
-These are additional dihedral styles in USER packages, which can be
-used if "LAMMPS is built with the appropriate
-package"_Section_start.html#start_3.
-
-"cosine/shift/exp (o)"_dihedral_cosine_shift_exp.html,
-"fourier (io)"_dihedral_fourier.html,
-"nharmonic (o)"_dihedral_nharmonic.html,
-"quadratic (o)"_dihedral_quadratic.html,
-"spherical (o)"_dihedral_spherical.html,
-"table (o)"_dihedral_table.html,
-"table/cut"_dihedral_table_cut.html :tb(c=4,ea=c)
-
-:line
-
-Improper_style potentials :h3
-
-See the "improper_style"_improper_style.html command for an overview
-of improper potentials.  Click on the style itself for a full
-description.  Some of the styles have accelerated versions, which can
-be used if LAMMPS is built with the "appropriate accelerated
-package"_Speed_packages.html.  This is indicated by additional letters
-in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
-OPT.
-
-"none"_improper_none.html,
-"zero"_improper_zero.html,
-"hybrid"_improper_hybrid.html,
-"class2 (ko)"_improper_class2.html,
-"cvff (io)"_improper_cvff.html,
-"harmonic (iko)"_improper_harmonic.html,
-"umbrella (o)"_improper_umbrella.html :tb(c=4,ea=c)
-
-These are additional improper styles in USER packages, which can be
-used if "LAMMPS is built with the appropriate
-package"_Section_start.html#start_3.
-
-"cossq (o)"_improper_cossq.html,
-"distance"_improper_distance.html,
-"fourier (o)"_improper_fourier.html,
-"ring (o)"_improper_ring.html :tb(c=4,ea=c)
-
-:line
-
-Kspace solvers :h3
-
-See the "kspace_style"_kspace_style.html command for an overview of
-Kspace solvers.  Click on the style itself for a full description.
-Some of the styles have accelerated versions, which can be used if
-LAMMPS is built with the "appropriate accelerated
-package"_Speed_packages.html.  This is indicated by additional letters
-in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
-OPT.
-
-"ewald (o)"_kspace_style.html,
-"ewald/disp"_kspace_style.html,
-"msm (o)"_kspace_style.html,
-"msm/cg (o)"_kspace_style.html,
-"pppm (gok)"_kspace_style.html,
-"pppm/cg (o)"_kspace_style.html,
-"pppm/disp (i)"_kspace_style.html,
-"pppm/disp/tip4p"_kspace_style.html,
-"pppm/stagger"_kspace_style.html,
-"pppm/tip4p (o)"_kspace_style.html :tb(c=4,ea=c)
diff --git a/doc/src/Section_start.txt b/doc/src/Section_start.txt
index 4176432328f0eb02cd6264576d2c770659092874..19a798d5dfddbbb14e2d9ccbf9e66b943392d920 100644
--- a/doc/src/Section_start.txt
+++ b/doc/src/Section_start.txt
@@ -1,10 +1,10 @@
 "Previous Section"_Intro.html - "LAMMPS WWW Site"_lws -
 "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
-Section"_Section_commands.html :c
+Section"_Commands.html :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
@@ -1070,7 +1070,7 @@ the '-in' command-line switch, e.g.
 
 lmp_linux -in in.file :pre
 
-"This section"_Section_commands.html describes how input scripts are
+The "Commands"_Commands.html doc page describes how input scripts are
 structured and what commands they contain.
 
 You can test LAMMPS on any of the sample inputs provided in the
@@ -1615,9 +1615,9 @@ value2 ..."  at the beginning of the input script.  Defining an index
 variable as a command-line argument overrides any setting for the same
 index variable in the input script, since index variables cannot be
 re-defined.  See the "variable"_variable.html command for more info on
-defining index and other kinds of variables and "this
-section"_Section_commands.html#cmd_2 for more info on using variables
-in input scripts.
+defining index and other kinds of variables and the "Commands
+parse"_Commands_parse.html page for more info on using variables in
+input scripts.
 
 NOTE: Currently, the command-line parser looks for arguments that
 start with "-" to indicate new switches.  Thus you cannot specify
diff --git a/doc/src/Speed.txt b/doc/src/Speed.txt
index 6c53d6bcf0d1d98f43c572f3964caa502b570293..091657082ae75a48d53c433a8fd98428ba6180ff 100644
--- a/doc/src/Speed.txt
+++ b/doc/src/Speed.txt
@@ -4,7 +4,7 @@ Section"_Howto.html :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Speed_bench.txt b/doc/src/Speed_bench.txt
index dc76588c11699822e11030b9db676683492794dd..8e407d14ea6bdb7428bff3818a670a9a84244f63 100644
--- a/doc/src/Speed_bench.txt
+++ b/doc/src/Speed_bench.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Speed_compare.txt b/doc/src/Speed_compare.txt
index 6c947b9662dca8be601ce897c2d1a149a812bbe0..1a17b39c79b672e43062770253ae5e82fc1f998d 100644
--- a/doc/src/Speed_compare.txt
+++ b/doc/src/Speed_compare.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Speed_gpu.txt b/doc/src/Speed_gpu.txt
index d6ebbf8069d1adde06b1b52c83fff027a3905377..ab8ec7e9d164b64c269e729e77936cd92fd6dfc0 100644
--- a/doc/src/Speed_gpu.txt
+++ b/doc/src/Speed_gpu.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Speed_intel.txt b/doc/src/Speed_intel.txt
index 08e3fbc4cc110256f91ac70f4bbe99c428e44734..20f49672e02849e2f0b544604bc6a88049eb0f05 100644
--- a/doc/src/Speed_intel.txt
+++ b/doc/src/Speed_intel.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Speed_kokkos.txt b/doc/src/Speed_kokkos.txt
index 8e01db7bdc7b52b3a95f7a5b3e73ccdb97bff1f4..14f4103aed8d6df6e782eba0e63c196c2daf380d 100644
--- a/doc/src/Speed_kokkos.txt
+++ b/doc/src/Speed_kokkos.txt
@@ -3,34 +3,39 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
 KOKKOS package :h3
 
 Kokkos is a templated C++ library that provides abstractions to allow
-a single implementation of an application kernel (e.g. a pair style) to run efficiently on
-different kinds of hardware, such as GPUs, Intel Xeon Phis, or many-core
-CPUs. Kokkos maps the C++ kernel onto different backend languages such as CUDA, OpenMP, or Pthreads.
-The Kokkos library also provides data abstractions to adjust (at
-compile time) the memory layout of data structures like 2d and
-3d arrays to optimize performance on different hardware. For more information on Kokkos, see
-"Github"_https://github.com/kokkos/kokkos. Kokkos is part of
-"Trilinos"_http://trilinos.sandia.gov/packages/kokkos. The Kokkos library was written primarily by Carter Edwards,
-Christian Trott, and Dan Sunderland (all Sandia).
-
-The LAMMPS KOKKOS package contains versions of pair, fix, and atom styles
-that use data structures and macros provided by the Kokkos library,
-which is included with LAMMPS in /lib/kokkos. The KOKKOS package was developed primarily by Christian Trott (Sandia)
-and Stan Moore (Sandia) with contributions of various styles by others, including Sikandar
-Mashayak (UIUC), Ray Shan (Sandia), and Dan Ibanez (Sandia). For more information on developing using Kokkos abstractions
+a single implementation of an application kernel (e.g. a pair style)
+to run efficiently on different kinds of hardware, such as GPUs, Intel
+Xeon Phis, or many-core CPUs. Kokkos maps the C++ kernel onto
+different backend languages such as CUDA, OpenMP, or Pthreads.  The
+Kokkos library also provides data abstractions to adjust (at compile
+time) the memory layout of data structures like 2d and 3d arrays to
+optimize performance on different hardware. For more information on
+Kokkos, see "Github"_https://github.com/kokkos/kokkos. Kokkos is part
+of "Trilinos"_http://trilinos.sandia.gov/packages/kokkos. The Kokkos
+library was written primarily by Carter Edwards, Christian Trott, and
+Dan Sunderland (all Sandia).
+
+The LAMMPS KOKKOS package contains versions of pair, fix, and atom
+styles that use data structures and macros provided by the Kokkos
+library, which is included with LAMMPS in /lib/kokkos. The KOKKOS
+package was developed primarily by Christian Trott (Sandia) and Stan
+Moore (Sandia) with contributions of various styles by others,
+including Sikandar Mashayak (UIUC), Ray Shan (Sandia), and Dan Ibanez
+(Sandia). For more information on developing using Kokkos abstractions
 see the Kokkos programmers' guide at /lib/kokkos/doc/Kokkos_PG.pdf.
 
 Kokkos currently provides support for 3 modes of execution (per MPI
-task). These are Serial (MPI-only for CPUs and Intel Phi), OpenMP (threading
-for many-core CPUs and Intel Phi), and CUDA (for NVIDIA GPUs). You choose the mode at build time to
-produce an executable compatible with specific hardware.
+task). These are Serial (MPI-only for CPUs and Intel Phi), OpenMP
+(threading for many-core CPUs and Intel Phi), and CUDA (for NVIDIA
+GPUs). You choose the mode at build time to produce an executable
+compatible with specific hardware.
 
 [Building LAMMPS with the KOKKOS package:]
 
@@ -38,16 +43,18 @@ NOTE: Kokkos support within LAMMPS must be built with a C++11 compatible
 compiler. This means GCC version 4.7.2 or later, Intel 14.0.4 or later, or
 Clang 3.5.2 or later is required.
 
-The recommended method of building the KOKKOS package is to start with the provided Kokkos
-Makefiles in /src/MAKE/OPTIONS/. You may need to modify the KOKKOS_ARCH variable in the Makefile
-to match your specific hardware. For example:
+The recommended method of building the KOKKOS package is to start with
+the provided Kokkos Makefiles in /src/MAKE/OPTIONS/. You may need to
+modify the KOKKOS_ARCH variable in the Makefile to match your specific
+hardware. For example:
 
 for Sandy Bridge CPUs, set KOKKOS_ARCH=SNB
 for Broadwell CPUs, set KOKKOS_ARCH=BWD
 for K80 GPUs, set KOKKOS_ARCH=Kepler37
 for P100 GPUs and Power8 CPUs, set KOKKOS_ARCH=Pascal60,Power8 :ul
 
-See the [Advanced Kokkos Options] section below for a listing of all KOKKOS_ARCH options.
+See the [Advanced Kokkos Options] section below for a listing of all
+KOKKOS_ARCH options.
 
 [Compile for CPU-only (MPI only, no threading):]
 
@@ -61,11 +68,12 @@ make kokkos_mpi_only :pre
 
 [Compile for CPU-only (MPI plus OpenMP threading):]
 
-NOTE: To build with Kokkos support for OpenMP threading, your compiler must support the
-OpenMP interface. You should have one or more multi-core CPUs so that
-multiple threads can be launched by each MPI task running on a CPU.
+NOTE: To build with Kokkos support for OpenMP threading, your compiler
+must support the OpenMP interface. You should have one or more
+multi-core CPUs so that multiple threads can be launched by each MPI
+task running on a CPU.
 
-use a C++11 compatible compiler and set KOKKOS_ARCH variable in
+Use a C++11 compatible compiler and set KOKKOS_ARCH variable in
 /src/MAKE/OPTIONS/Makefile.kokkos_omp as described above.  Then do the
 following:
 
@@ -88,9 +96,9 @@ software version 7.5 or later must be installed on your system. See
 the discussion for the "GPU package"_Speed_gpu.html for details of how
 to check and do this.
 
-use a C++11 compatible compiler and set KOKKOS_ARCH variable in
-/src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi for both GPU and CPU as described
-above.  Then do the following:
+Use a C++11 compatible compiler and set KOKKOS_ARCH variable in
+/src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi for both GPU and CPU as
+described above.  Then do the following:
 
 cd lammps/src
 make yes-kokkos
@@ -104,24 +112,24 @@ on the make command line. For example:
 make mpi KOKKOS_DEVICES=OpenMP KOKKOS_ARCH=SNB     # set the KOKKOS_DEVICES and KOKKOS_ARCH variable explicitly
 make kokkos_cuda_mpi KOKKOS_ARCH=Pascal60,Power8   # set the KOKKOS_ARCH variable explicitly :pre
 
-Setting the KOKKOS_DEVICES and KOKKOS_ARCH variables on the
-make command line requires a GNU-compatible make command. Try
-"gmake" if your system's standard make complains.
+Setting the KOKKOS_DEVICES and KOKKOS_ARCH variables on the make
+command line requires a GNU-compatible make command. Try "gmake" if
+your system's standard make complains.
 
 NOTE: If you build using make line variables and re-build LAMMPS twice
-with different KOKKOS options and the *same* target, then you *must* perform a "make clean-all"
-or "make clean-machine" before each build. This is to force all the
-KOKKOS-dependent files to be re-compiled with the new options.
+with different KOKKOS options and the *same* target, then you *must*
+perform a "make clean-all" or "make clean-machine" before each
+build. This is to force all the KOKKOS-dependent files to be
+re-compiled with the new options.
 
 [Running LAMMPS with the KOKKOS package:]
 
-All Kokkos operations occur within the
-context of an individual MPI task running on a single node of the
-machine. The total number of MPI tasks used by LAMMPS (one or
-multiple per compute node) is set in the usual manner via the mpirun
-or mpiexec commands, and is independent of Kokkos. E.g. the mpirun
-command in OpenMPI does this via its
--np and -npernode switches. Ditto for MPICH via -np and -ppn.
+All Kokkos operations occur within the context of an individual MPI
+task running on a single node of the machine. The total number of MPI
+tasks used by LAMMPS (one or multiple per compute node) is set in the
+usual manner via the mpirun or mpiexec commands, and is independent of
+Kokkos. E.g. the mpirun command in OpenMPI does this via its -np and
+-npernode switches. Ditto for MPICH via -np and -ppn.
 
 [Running on a multi-core CPU:]
 
@@ -133,8 +141,9 @@ mpirun -np 2 -ppn 1 lmp_kokkos_omp -k on t 16 -sf kk -in in.lj  # 2 nodes, 1 MPI
 mpirun -np 2 lmp_kokkos_omp -k on t 8 -sf kk -in in.lj          # 1 node,  2 MPI tasks/node, 8 threads/task
 mpirun -np 32 -ppn 4 lmp_kokkos_omp -k on t 4 -sf kk -in in.lj  # 8 nodes, 4 MPI tasks/node, 4 threads/task :pre
 
-To run using the KOKKOS package, use the "-k on", "-sf kk" and "-pk kokkos" "command-line switches"_Section_start.html#start_7 in your mpirun command.
-You must use the "-k on" "command-line
+To run using the KOKKOS package, use the "-k on", "-sf kk" and "-pk
+kokkos" "command-line switches"_Section_start.html#start_7 in your
+mpirun command.  You must use the "-k on" "command-line
 switch"_Section_start.html#start_7 to enable the KOKKOS package. It
 takes additional arguments for hardware settings appropriate to your
 system. Those arguments are "documented
@@ -142,32 +151,33 @@ here"_Section_start.html#start_7. For OpenMP use:
 
 -k on t Nt :pre
 
-The "t Nt" option specifies how many OpenMP threads per MPI
-task to use with a node. The default is Nt = 1, which is MPI-only mode.
-Note that the product of MPI tasks * OpenMP
-threads/task should not exceed the physical number of cores (on a
-node), otherwise performance will suffer. If hyperthreading is enabled, then
-the product of MPI tasks * OpenMP threads/task should not exceed the
-physical number of cores * hardware threads.
-The "-k on" switch also issues a "package kokkos" command (with no
-additional arguments) which sets various KOKKOS options to default
-values, as discussed on the "package"_package.html command doc page.
-
-The "-sf kk" "command-line switch"_Section_start.html#start_7
-will automatically append the "/kk" suffix to styles that support it.
-In this manner no modification to the input script is needed. Alternatively,
-one can run with the KOKKOS package by editing the input script as described below.
-
-NOTE: The default for the "package kokkos"_package.html command is
-to use "full" neighbor lists and set the Newton flag to "off" for both
+The "t Nt" option specifies how many OpenMP threads per MPI task to
+use with a node. The default is Nt = 1, which is MPI-only mode.  Note
+that the product of MPI tasks * OpenMP threads/task should not exceed
+the physical number of cores (on a node), otherwise performance will
+suffer. If hyperthreading is enabled, then the product of MPI tasks *
+OpenMP threads/task should not exceed the physical number of cores *
+hardware threads.  The "-k on" switch also issues a "package kokkos"
+command (with no additional arguments) which sets various KOKKOS
+options to default values, as discussed on the "package"_package.html
+command doc page.
+
+The "-sf kk" "command-line switch"_Section_start.html#start_7 will
+automatically append the "/kk" suffix to styles that support it.  In
+this manner no modification to the input script is
+needed. Alternatively, one can run with the KOKKOS package by editing
+the input script as described below.
+
+NOTE: The default for the "package kokkos"_package.html command is to
+use "full" neighbor lists and set the Newton flag to "off" for both
 pairwise and bonded interactions. However, when running on CPUs, it
 will typically be faster to use "half" neighbor lists and set the
 Newton flag to "on", just as is the case for non-accelerated pair
-styles. It can also be faster to use non-threaded communication.
-Use the "-pk kokkos" "command-line switch"_Section_start.html#start_7 to
-change the default "package kokkos"_package.html
-options. See its doc page for details and default settings. Experimenting with
-its options can provide a speed-up for specific calculations. For example:
+styles. It can also be faster to use non-threaded communication.  Use
+the "-pk kokkos" "command-line switch"_Section_start.html#start_7 to
+change the default "package kokkos"_package.html options. See its doc
+page for details and default settings. Experimenting with its options
+can provide a speed-up for specific calculations. For example:
 
 mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk -pk kokkos newton on neigh half comm no -in in.lj       # Newton on, Half neighbor list, non-threaded comm :pre
 
@@ -176,9 +186,9 @@ script, it can also override the Newton flag defaults.
 
 [Core and Thread Affinity:]
 
-When using multi-threading, it is important for
-performance to bind both MPI tasks to physical cores, and threads to
-physical cores, so they do not migrate during a simulation.
+When using multi-threading, it is important for performance to bind
+both MPI tasks to physical cores, and threads to physical cores, so
+they do not migrate during a simulation.
 
 If you are not certain MPI tasks are being bound (check the defaults
 for your MPI installation), binding can be forced with these flags:
@@ -189,24 +199,24 @@ Mvapich2 2.0: mpiexec -np 2 --bind-to socket --map-by socket ./lmp_mvapich ... :
 For binding threads with KOKKOS OpenMP, use thread affinity
 environment variables to force binding. With OpenMP 3.1 (gcc 4.7 or
 later, intel 12 or later) setting the environment variable
-OMP_PROC_BIND=true should be sufficient. In general, for best performance
-with OpenMP 4.0 or better set OMP_PROC_BIND=spread and OMP_PLACES=threads.
-For binding threads with the
-KOKKOS pthreads option, compile LAMMPS the KOKKOS HWLOC=yes option
-as described below.
+OMP_PROC_BIND=true should be sufficient. In general, for best
+performance with OpenMP 4.0 or better set OMP_PROC_BIND=spread and
+OMP_PLACES=threads.  For binding threads with the KOKKOS pthreads
+option, compile LAMMPS the KOKKOS HWLOC=yes option as described below.
 
 [Running on Knight's Landing (KNL) Intel Xeon Phi:]
 
-Here is a quick overview of how to use the KOKKOS package
-for the Intel Knight's Landing (KNL) Xeon Phi:
+Here is a quick overview of how to use the KOKKOS package for the
+Intel Knight's Landing (KNL) Xeon Phi:
 
-KNL Intel Phi chips have 68 physical cores. Typically 1 to 4 cores
-are reserved for the OS, and only 64 or 66 cores are used. Each core
-has 4 hyperthreads,so there are effectively N = 256 (4*64) or
-N = 264 (4*66) cores to run on. The product of MPI tasks * OpenMP threads/task should not exceed this limit,
-otherwise performance will suffer. Note that with the KOKKOS package you do not need to
-specify how many KNLs there are per node; each
-KNL is simply treated as running some number of MPI tasks.
+KNL Intel Phi chips have 68 physical cores. Typically 1 to 4 cores are
+reserved for the OS, and only 64 or 66 cores are used. Each core has 4
+hyperthreads,so there are effectively N = 256 (4*64) or N = 264 (4*66)
+cores to run on. The product of MPI tasks * OpenMP threads/task should
+not exceed this limit, otherwise performance will suffer. Note that
+with the KOKKOS package you do not need to specify how many KNLs there
+are per node; each KNL is simply treated as running some number of MPI
+tasks.
 
 Examples of mpirun commands that follow these rules are shown below.
 
@@ -221,57 +231,60 @@ tasks/node. The "-k on t Nt" command-line switch sets the number of
 threads/task as Nt. The product of these two values should be N, i.e.
 256 or 264.
 
-NOTE: The default for the "package kokkos"_package.html command is
-to use "full" neighbor lists and set the Newton flag to "off" for both
-pairwise and bonded interactions. When running on KNL, this
-will typically be best for pair-wise potentials. For manybody potentials,
-using "half" neighbor lists and setting the
-Newton flag to "on" may be faster. It can also be faster to use non-threaded communication.
-Use the "-pk kokkos" "command-line switch"_Section_start.html#start_7 to
-change the default "package kokkos"_package.html
-options. See its doc page for details and default settings. Experimenting with
-its options can provide a speed-up for specific calculations. For example:
+NOTE: The default for the "package kokkos"_package.html command is to
+use "full" neighbor lists and set the Newton flag to "off" for both
+pairwise and bonded interactions. When running on KNL, this will
+typically be best for pair-wise potentials. For manybody potentials,
+using "half" neighbor lists and setting the Newton flag to "on" may be
+faster. It can also be faster to use non-threaded communication.  Use
+the "-pk kokkos" "command-line switch"_Section_start.html#start_7 to
+change the default "package kokkos"_package.html options. See its doc
+page for details and default settings. Experimenting with its options
+can provide a speed-up for specific calculations. For example:
 
 mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos comm no -in in.lj      #  Newton off, full neighbor list, non-threaded comm
 mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos newton on neigh half comm no -in in.reax      # Newton on, half neighbor list, non-threaded comm :pre
 
-NOTE: MPI tasks and threads should be bound to cores as described above for CPUs.
+NOTE: MPI tasks and threads should be bound to cores as described
+above for CPUs.
 
-NOTE: To build with Kokkos support for Intel Xeon Phi coprocessors such as Knight's Corner (KNC), your
-system must be configured to use them in "native" mode, not "offload"
-mode like the USER-INTEL package supports.
+NOTE: To build with Kokkos support for Intel Xeon Phi coprocessors
+such as Knight's Corner (KNC), your system must be configured to use
+them in "native" mode, not "offload" mode like the USER-INTEL package
+supports.
 
 [Running on GPUs:]
 
-Use the "-k" "command-line switch"_Section_commands.html#start_7 to
-specify the number of GPUs per node. Typically the -np setting
-of the mpirun command should set the number of MPI
-tasks/node to be equal to the # of physical GPUs on the node.
-You can assign multiple MPI tasks to the same GPU with the
-KOKKOS package, but this is usually only faster if significant portions
-of the input script have not been ported to use Kokkos. Using CUDA MPS
-is recommended in this scenario. As above for multi-core CPUs (and no GPU), if N is the number
-of physical cores/node, then the number of MPI tasks/node should not exceed N.
+Use the "-k" "command-line switch"_Section_start.html#start_7 to
+specify the number of GPUs per node. Typically the -np setting of the
+mpirun command should set the number of MPI tasks/node to be equal to
+the # of physical GPUs on the node.  You can assign multiple MPI tasks
+to the same GPU with the KOKKOS package, but this is usually only
+faster if significant portions of the input script have not been
+ported to use Kokkos. Using CUDA MPS is recommended in this
+scenario. As above for multi-core CPUs (and no GPU), if N is the
+number of physical cores/node, then the number of MPI tasks/node
+should not exceed N.
 
 -k on g Ng :pre
 
-Here are examples of how to use the KOKKOS package for GPUs,
-assuming one or more nodes, each with two GPUs:
+Here are examples of how to use the KOKKOS package for GPUs, assuming
+one or more nodes, each with two GPUs:
 
 mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -in in.lj          # 1 node,   2 MPI tasks/node, 2 GPUs/node
 mpirun -np 32 -ppn 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -in in.lj  # 16 nodes, 2 MPI tasks/node, 2 GPUs/node (32 GPUs total) :pre
 
-NOTE: The default for the "package kokkos"_package.html command is
-to use "full" neighbor lists and set the Newton flag to "off" for both
+NOTE: The default for the "package kokkos"_package.html command is to
+use "full" neighbor lists and set the Newton flag to "off" for both
 pairwise and bonded interactions, along with threaded communication.
-When running on Maxwell or Kepler GPUs, this will typically be best. For Pascal GPUs,
-using "half" neighbor lists and setting the
-Newton flag to "on" may be faster. For many pair styles, setting the neighbor binsize
-equal to the ghost atom cutoff will give speedup.
-Use the "-pk kokkos" "command-line switch"_Section_start.html#start_7 to
-change the default "package kokkos"_package.html
-options. See its doc page for details and default settings. Experimenting with
-its options can provide a speed-up for specific calculations. For example:
+When running on Maxwell or Kepler GPUs, this will typically be
+best. For Pascal GPUs, using "half" neighbor lists and setting the
+Newton flag to "on" may be faster. For many pair styles, setting the
+neighbor binsize equal to the ghost atom cutoff will give speedup.
+Use the "-pk kokkos" "command-line switch"_Section_start.html#start_7
+to change the default "package kokkos"_package.html options. See its
+doc page for details and default settings. Experimenting with its
+options can provide a speed-up for specific calculations. For example:
 
 mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos binsize 2.8 -in in.lj      # Set binsize = neighbor ghost cutoff
 mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos newton on neigh half binsize 2.8 -in in.lj      # Newton on, half neighborlist, set binsize = neighbor ghost cutoff :pre
@@ -299,8 +312,8 @@ Alternatively the effect of the "-sf" or "-pk" switches can be
 duplicated by adding the "package kokkos"_package.html or "suffix
 kk"_suffix.html commands to your input script.
 
-The discussion above for building LAMMPS with the KOKKOS package, the mpirun/mpiexec command, and setting
-appropriate thread are the same.
+The discussion above for building LAMMPS with the KOKKOS package, the
+mpirun/mpiexec command, and setting appropriate thread are the same.
 
 You must still use the "-k on" "command-line
 switch"_Section_start.html#start_7 to enable the KOKKOS package, and
@@ -318,17 +331,19 @@ wish to change any of its option defaults, as set by the "-k on"
 
 [Using OpenMP threading and CUDA together (experimental):]
 
-With the KOKKOS package, both OpenMP multi-threading and GPUs can be used
-together in a few special cases. In the Makefile, the KOKKOS_DEVICES variable must
-include both "Cuda" and "OpenMP", as is the case for /src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi
+With the KOKKOS package, both OpenMP multi-threading and GPUs can be
+used together in a few special cases. In the Makefile, the
+KOKKOS_DEVICES variable must include both "Cuda" and "OpenMP", as is
+the case for /src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi
 
 KOKKOS_DEVICES=Cuda,OpenMP :pre
 
 The suffix "/kk" is equivalent to "/kk/device", and for Kokkos CUDA,
-using the "-sf kk" in the command line gives the default CUDA version everywhere.
-However, if the "/kk/host" suffix is added to a specific style in the input
-script, the Kokkos OpenMP (CPU) version of that specific style will be used instead.
-Set the number of OpenMP threads as "t Nt" and the number of GPUs as "g Ng"
+using the "-sf kk" in the command line gives the default CUDA version
+everywhere.  However, if the "/kk/host" suffix is added to a specific
+style in the input script, the Kokkos OpenMP (CPU) version of that
+specific style will be used instead.  Set the number of OpenMP threads
+as "t Nt" and the number of GPUs as "g Ng"
 
 -k on t Nt g Ng :pre
 
@@ -336,18 +351,20 @@ For example, the command to run with 1 GPU and 8 OpenMP threads is then:
 
 mpiexec -np 1 lmp_kokkos_cuda_openmpi -in in.lj -k on g 1 t 8 -sf kk :pre
 
-Conversely, if the "-sf kk/host" is used in the command line and then the
-"/kk" or "/kk/device" suffix is added to a specific style in your input script,
-then only that specific style will run on the GPU while everything else will
-run on the CPU in OpenMP mode. Note that the execution of the CPU and GPU
-styles will NOT overlap, except for a special case:
-
-A kspace style and/or molecular topology (bonds, angles, etc.) running on
-the host CPU can overlap with a pair style running on the GPU. First compile
-with "--default-stream per-thread" added to CCFLAGS in the Kokkos CUDA Makefile.
-Then explicitly use the "/kk/host" suffix for kspace and bonds, angles, etc.
-in the input file and the "kk" suffix (equal to "kk/device") on the command line.
-Also make sure the environment variable CUDA_LAUNCH_BLOCKING is not set to "1"
+Conversely, if the "-sf kk/host" is used in the command line and then
+the "/kk" or "/kk/device" suffix is added to a specific style in your
+input script, then only that specific style will run on the GPU while
+everything else will run on the CPU in OpenMP mode. Note that the
+execution of the CPU and GPU styles will NOT overlap, except for a
+special case:
+
+A kspace style and/or molecular topology (bonds, angles, etc.) running
+on the host CPU can overlap with a pair style running on the
+GPU. First compile with "--default-stream per-thread" added to CCFLAGS
+in the Kokkos CUDA Makefile.  Then explicitly use the "/kk/host"
+suffix for kspace and bonds, angles, etc.  in the input file and the
+"kk" suffix (equal to "kk/device") on the command line.  Also make
+sure the environment variable CUDA_LAUNCH_BLOCKING is not set to "1"
 so CPU/GPU overlap can occur.
 
 [Speed-ups to expect:]
@@ -384,9 +401,8 @@ hardware.
 There are other allowed options when building with the KOKKOS package.
 As above, they can be set either as variables on the make command line
 or in Makefile.machine. This is the full list of options, including
-those discussed above. Each takes a value shown below. The
-default value is listed, which is set in the
-/lib/kokkos/Makefile.kokkos file.
+those discussed above. Each takes a value shown below. The default
+value is listed, which is set in the /lib/kokkos/Makefile.kokkos file.
 
 KOKKOS_DEVICES, values = {Serial}, {OpenMP}, {Pthreads}, {Cuda}, default = {OpenMP}
 KOKKOS_ARCH, values = {KNC}, {SNB}, {HSW}, {Kepler30}, {Kepler32}, {Kepler35}, {Kepler37}, {Maxwell50}, {Maxwell52}, {Maxwell53}, {Pascal60}, {Pascal61}, {ARMv80}, {ARMv81}, {ARMv81}, {ARMv8-ThunderX}, {BGQ}, {Power7}, {Power8}, {Power9}, {KNL}, {BDW}, {SKX}, default = {none}
@@ -444,13 +460,14 @@ within LAMMPS. KOKKOS_DEBUG=yes enables printing of run-time
 debugging information that can be useful. It also enables runtime
 bounds checking on Kokkos data structures.
 
-KOKKOS_CXX_STANDARD and KOKKOS_OPTIONS are typically not changed when building LAMMPS.
+KOKKOS_CXX_STANDARD and KOKKOS_OPTIONS are typically not changed when
+building LAMMPS.
 
-KOKKOS_CUDA_OPTIONS are additional options for CUDA. The LAMMPS KOKKOS package must be compiled
-with the {enable_lambda} option when using GPUs.
+KOKKOS_CUDA_OPTIONS are additional options for CUDA. The LAMMPS KOKKOS
+package must be compiled with the {enable_lambda} option when using
+GPUs.
 
 [Restrictions:]
 
-Currently, there are no precision options with the KOKKOS
-package. All compilation and computation is performed in double
-precision.
+Currently, there are no precision options with the KOKKOS package. All
+compilation and computation is performed in double precision.
diff --git a/doc/src/Speed_measure.txt b/doc/src/Speed_measure.txt
index 03c0345c206c238f3061e714ab935b35a558ccce..78dc220088d3873b241aae6237b84b8426f03776 100644
--- a/doc/src/Speed_measure.txt
+++ b/doc/src/Speed_measure.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Speed_omp.txt b/doc/src/Speed_omp.txt
index 9685b6d349fe730517f07a5906f8802d094ffb36..bcfc406902d0947e2c6d9e0426b2fe8d7406dda3 100644
--- a/doc/src/Speed_omp.txt
+++ b/doc/src/Speed_omp.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Speed_opt.txt b/doc/src/Speed_opt.txt
index 7d0d7169f001682b76fa931a00459df293379101..676a5d84182e90ea4f832c3938bab51e5a3011dc 100644
--- a/doc/src/Speed_opt.txt
+++ b/doc/src/Speed_opt.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Speed_packages.txt b/doc/src/Speed_packages.txt
index 13b5e183dbbfcac153b09377d8e698b2deca3490..f463ed91b85d28cf495db638a401f7c52a5326fe 100644
--- a/doc/src/Speed_packages.txt
+++ b/doc/src/Speed_packages.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
@@ -71,11 +71,12 @@ Lennard-Jones "pair_style lj/cut"_pair_lj.html:
 "pair_style lj/cut/omp"_pair_lj.html
 "pair_style lj/cut/opt"_pair_lj.html :ul
 
-To see what accelerate styles are currently available, see
-"Section 3.5"_Section_commands.html#cmd_5 of the manual.  The
-doc pages for individual commands (e.g. "pair lj/cut"_pair_lj.html or
-"fix nve"_fix_nve.html) also list any accelerated variants available
-for that style.
+To see what accelerate styles are currently available for a particular
+style, find the style name in the "Commands_all"_Commands_all.html
+style pages (fix,compute,pair,etc) and see what suffixes are listed
+(g,i,k,o,t) with it.  The doc pages for individual commands
+(e.g. "pair lj/cut"_pair_lj.html or "fix nve"_fix_nve.html) also list
+any accelerated variants available for that style.
 
 To use an accelerator package in LAMMPS, and one or more of the styles
 it provides, follow these general steps.  Details vary from package to
diff --git a/doc/src/Speed_tips.txt b/doc/src/Speed_tips.txt
index c0d360cd8e2932dd726b19713cb50cf18ef35620..7c950779d5e4864db0802e90369c6acaaf8b6d36 100644
--- a/doc/src/Speed_tips.txt
+++ b/doc/src/Speed_tips.txt
@@ -3,7 +3,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/Tools.txt b/doc/src/Tools.txt
index bf0f9ae134f73015974eeac6d8b81c809b730571..85ee531cfd905371ebef6f17db26713c2a496d6c 100644
--- a/doc/src/Tools.txt
+++ b/doc/src/Tools.txt
@@ -4,7 +4,7 @@ Section"_Modify.html :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/angle_charmm.txt b/doc/src/angle_charmm.txt
index fe109d24fb5fa2fd014f06094da8a60ca077ec9c..f72f0862348328bbd5c62a11d42274bb4f4c14d3 100644
--- a/doc/src/angle_charmm.txt
+++ b/doc/src/angle_charmm.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/angle_class2.txt b/doc/src/angle_class2.txt
index c13a64afb667955a61ca1bc1dae826251f257c85..3e5445d3a3c17200bd5e548791bdbfbb31f4dcbe 100644
--- a/doc/src/angle_class2.txt
+++ b/doc/src/angle_class2.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/angle_coeff.txt b/doc/src/angle_coeff.txt
index 37298ba14591ca28fe4a45952ec5ed80551a8178..4c217bae7d3905298202c2d48592e1bb045e49ef 100644
--- a/doc/src/angle_coeff.txt
+++ b/doc/src/angle_coeff.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
@@ -65,9 +65,9 @@ the style to display the formula it computes and coefficients
 specified by the associated "angle_coeff"_angle_coeff.html command.
 
 Note that there are also additional angle styles submitted by users
-which are included in the LAMMPS distribution.  The list of these with
-links to the individual styles are given in the angle section of "this
-page"_Section_commands.html#cmd_5.
+which are included in the LAMMPS distribution.  The full list of all
+angle styles is on the "Commands bond"_Commands_bond.html#angle doc
+page.
 
 "angle_style none"_angle_none.html - turn off angle interactions
 "angle_style hybrid"_angle_hybrid.html - define multiple styles of angle interactions :ul
diff --git a/doc/src/angle_cosine.txt b/doc/src/angle_cosine.txt
index 99264b02a60adeb79c5f360988edbead0487c66f..5a1fe91c834271bfe883e1b2d5a410f3bb148a23 100644
--- a/doc/src/angle_cosine.txt
+++ b/doc/src/angle_cosine.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/angle_cosine_buck6d.txt b/doc/src/angle_cosine_buck6d.txt
index 7182ffecc849e1c581793add231af6ed1fa03d57..63a451b7631456aa21b870eadf5808e92b052ec9 100644
--- a/doc/src/angle_cosine_buck6d.txt
+++ b/doc/src/angle_cosine_buck6d.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/angle_cosine_delta.txt b/doc/src/angle_cosine_delta.txt
index 052300412f1449a86f636888e101fac170fb086d..b6ac0ed8181ad55b183ab59962e9502c2cd5ab93 100644
--- a/doc/src/angle_cosine_delta.txt
+++ b/doc/src/angle_cosine_delta.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/angle_cosine_periodic.txt b/doc/src/angle_cosine_periodic.txt
index 108b0815333dd9c2948cf4d24cc599b228815ca7..c5b184e0b46b1e5b14efb8b1dd0477740c59ae19 100644
--- a/doc/src/angle_cosine_periodic.txt
+++ b/doc/src/angle_cosine_periodic.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/angle_cosine_shift.txt b/doc/src/angle_cosine_shift.txt
index 185b9f530940d80bf6b63bc5a7cf963ca6f3d590..90ac61fe23c9d45f595c579e937d55bdea284909 100644
--- a/doc/src/angle_cosine_shift.txt
+++ b/doc/src/angle_cosine_shift.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/angle_cosine_shift_exp.txt b/doc/src/angle_cosine_shift_exp.txt
index e5c7fdd7095b029d3618c2d85d6d94f82f1cd74a..f1c4c93c425e0ce8f51d12e39dd34c9493bf0426 100644
--- a/doc/src/angle_cosine_shift_exp.txt
+++ b/doc/src/angle_cosine_shift_exp.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/angle_cosine_squared.txt b/doc/src/angle_cosine_squared.txt
index e85c514d1edf9a5f1c18e4cb818b2299a3d4b620..ba5fd9d4139a4f1142c287e121d3e3e7f002a6d4 100644
--- a/doc/src/angle_cosine_squared.txt
+++ b/doc/src/angle_cosine_squared.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/angle_dipole.txt b/doc/src/angle_dipole.txt
index 31ae2e9464b0bd6c2b9cab81220a94273490358b..c001d9d9206c743222357f1cdcb345934f9a9ead 100644
--- a/doc/src/angle_dipole.txt
+++ b/doc/src/angle_dipole.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/angle_fourier.txt b/doc/src/angle_fourier.txt
index 18eb56b478614bfc51391bd54288f8d330bd801d..e0e32c1eed001fa0d6ecb70f2f2c69542d39d6c0 100644
--- a/doc/src/angle_fourier.txt
+++ b/doc/src/angle_fourier.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/angle_fourier_simple.txt b/doc/src/angle_fourier_simple.txt
index 6faff5f10d60924064badc7b8622541ace5c84f6..3c50536a2cbc0720ec69c4a4b02cdefa15bd48ff 100644
--- a/doc/src/angle_fourier_simple.txt
+++ b/doc/src/angle_fourier_simple.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/angle_harmonic.txt b/doc/src/angle_harmonic.txt
index fe803be62320c156185ee30a7bf227e394fa3214..76c7a491e8943aa7cdd720750394818fc7460b9e 100644
--- a/doc/src/angle_harmonic.txt
+++ b/doc/src/angle_harmonic.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/angle_hybrid.txt b/doc/src/angle_hybrid.txt
index bdd3707ccb80130284817d86a3eec53a698c2a2a..26469034212fe359d66a965e216543404b2d1020 100644
--- a/doc/src/angle_hybrid.txt
+++ b/doc/src/angle_hybrid.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/angle_none.txt b/doc/src/angle_none.txt
index a4a9b07c78e0bf7616ffe4d0ae0dc4ee8c4c9061..1eca5cbbeca786991139f7af6a44547f86d9d821 100644
--- a/doc/src/angle_none.txt
+++ b/doc/src/angle_none.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/angle_quartic.txt b/doc/src/angle_quartic.txt
index a31214f4357c2c0c9d1fb9f911904dcd977fd4f4..294be330b1faab22d868d16b1a78edb048be928c 100644
--- a/doc/src/angle_quartic.txt
+++ b/doc/src/angle_quartic.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/angle_sdk.txt b/doc/src/angle_sdk.txt
index 0cc535e543f878bba02b38b9a5fa18e65da0aea2..9c5630ef3adf62b7688dbbd021555283536b2cff 100644
--- a/doc/src/angle_sdk.txt
+++ b/doc/src/angle_sdk.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/angle_style.txt b/doc/src/angle_style.txt
index f687e9286c40ac37a84566a5ab904c65fb3d30bf..63295faf264d8fee8b2a75fb32143ae710d02586 100644
--- a/doc/src/angle_style.txt
+++ b/doc/src/angle_style.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
@@ -58,9 +58,9 @@ the style to display the formula it computes and coefficients
 specified by the associated "angle_coeff"_angle_coeff.html command.
 
 Note that there are also additional angle styles submitted by users
-which are included in the LAMMPS distribution.  The list of these with
-links to the individual styles are given in the angle section of "this
-page"_Section_commands.html#cmd_5.
+which are included in the LAMMPS distribution.  The full list of all
+angle styles are is on the "Commands bond"_Commands_bond.html#angle
+doc page.
 
 "angle_style none"_angle_none.html - turn off angle interactions
 "angle_style zero"_angle_zero.html - topology but no interactions
diff --git a/doc/src/angle_table.txt b/doc/src/angle_table.txt
index 29b56875e7e797c06c6a1b1f597118fd4373b603..31ab532be17c95598c2b54f3a34becbf3c966120 100644
--- a/doc/src/angle_table.txt
+++ b/doc/src/angle_table.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/angle_zero.txt b/doc/src/angle_zero.txt
index b8e8ebf953c6b6ba40a583bef0508ab9992f3a6d..c6c1958ec8f35f7d1335b5a9cafaf36b96049c9a 100644
--- a/doc/src/angle_zero.txt
+++ b/doc/src/angle_zero.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/atom_modify.txt b/doc/src/atom_modify.txt
index 1dc0fa6bfb6410df5eaef9abf35cebb3a66749fd..c882d1b0ba0f43a916ee3a954a4b85e41d6c2007 100644
--- a/doc/src/atom_modify.txt
+++ b/doc/src/atom_modify.txt
@@ -3,7 +3,7 @@ Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/atom_style.txt b/doc/src/atom_style.txt
index 063f9e446cd11053eccffabffa540cf5d43de2c4..abf05885a3ee3d96846af804d6ef1caaf42643c6 100644
--- a/doc/src/atom_style.txt
+++ b/doc/src/atom_style.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/balance.txt b/doc/src/balance.txt
index da6f59900d69fb784ee8cdf91cc3bef60921aaa8..06c4eca491d1bd6cdb3c68a5caa2381718159ea7 100644
--- a/doc/src/balance.txt
+++ b/doc/src/balance.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/body.txt b/doc/src/body.txt
index 96aedccf4077e82c22d904aad26ff8b6ec6f2978..4de5b5291132a85cb8ca56196d1c9858b2c2b4ee 100644
--- a/doc/src/body.txt
+++ b/doc/src/body.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/bond_class2.txt b/doc/src/bond_class2.txt
index 049482c97394572d6af86fa598c181ece78af16b..3d8d5007bad145439de155227c8873fcfce616a9 100644
--- a/doc/src/bond_class2.txt
+++ b/doc/src/bond_class2.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/bond_coeff.txt b/doc/src/bond_coeff.txt
index d93c0b223b84a0da9d6f171d9e222847d905ee69..7485fa3d8d1da5da832cc832f69f7ffd6d593696 100644
--- a/doc/src/bond_coeff.txt
+++ b/doc/src/bond_coeff.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
@@ -61,9 +61,8 @@ the style to display the formula it computes and coefficients
 specified by the associated "bond_coeff"_bond_coeff.html command.
 
 Note that here are also additional bond styles submitted by users
-which are included in the LAMMPS distribution.  The list of these with
-links to the individual styles are given in the bond section of "this
-page"_Section_commands.html#cmd_5.
+which are included in the LAMMPS distribution.  The full list of all
+bond styles is on the "Commands bond"_Commands_bond.html doc page.
 
 "bond_style none"_bond_none.html - turn off bonded interactions
 "bond_style hybrid"_bond_hybrid.html - define multiple styles of bond interactions :ul
diff --git a/doc/src/bond_fene.txt b/doc/src/bond_fene.txt
index be154a53b1c88a7cfe8409aa3074e0ba0e1890e1..e16307a71076c6c2c2b6aecd5c660eb4acda8f2a 100644
--- a/doc/src/bond_fene.txt
+++ b/doc/src/bond_fene.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/bond_fene_expand.txt b/doc/src/bond_fene_expand.txt
index 77ebd977c8d7b067ad6feef461c61ec2639e0899..8edd325885e457e039765074ce14be6fe5fe2764 100644
--- a/doc/src/bond_fene_expand.txt
+++ b/doc/src/bond_fene_expand.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/bond_gromos.txt b/doc/src/bond_gromos.txt
index 7a56cb3afa8da3c0f274335c74a84e482eb2425c..275036a421f618085eb25625f87a716cb28876c5 100644
--- a/doc/src/bond_gromos.txt
+++ b/doc/src/bond_gromos.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/bond_harmonic.txt b/doc/src/bond_harmonic.txt
index 54e89fcc72d05d89e01382d7e9d55fd6bae11b2f..e4b2015fed2987dfe52a06e22021fff70bbb6ce6 100644
--- a/doc/src/bond_harmonic.txt
+++ b/doc/src/bond_harmonic.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/bond_harmonic_shift.txt b/doc/src/bond_harmonic_shift.txt
index 0213b5cc6fb5e82b07917a96ce5ad239a251a9bd..b6dc18a5fd69453806968cebd189c4ca7c0d5dd3 100644
--- a/doc/src/bond_harmonic_shift.txt
+++ b/doc/src/bond_harmonic_shift.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/bond_harmonic_shift_cut.txt b/doc/src/bond_harmonic_shift_cut.txt
index d907bf4a629a4ebebde1e8c8552a3f0960d613fa..b3054437d8e8b4a4bda593bb756e7721ff7ebe26 100644
--- a/doc/src/bond_harmonic_shift_cut.txt
+++ b/doc/src/bond_harmonic_shift_cut.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/bond_hybrid.txt b/doc/src/bond_hybrid.txt
index 400c3e0be4c9e1b7fb1fd98936208ad19f384896..140fb723785476a1a09c67360b6865a898f8d1f5 100644
--- a/doc/src/bond_hybrid.txt
+++ b/doc/src/bond_hybrid.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/bond_morse.txt b/doc/src/bond_morse.txt
index 66f2d08cabe033b1864a4558a2a8e058ca8e53ad..9b64e8c5c1d2da41936def16578ba299160121a9 100644
--- a/doc/src/bond_morse.txt
+++ b/doc/src/bond_morse.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/bond_none.txt b/doc/src/bond_none.txt
index 8cb262a50f939617011853d41fe416f1a6e3160a..cace1919e13ff668c51418063f6a2d4a30dbefbc 100644
--- a/doc/src/bond_none.txt
+++ b/doc/src/bond_none.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/bond_nonlinear.txt b/doc/src/bond_nonlinear.txt
index e0aa5629b3ec496c1700009b59615b989a992c8d..08109bc699dfed95d7ad70cff09dbded043627f5 100644
--- a/doc/src/bond_nonlinear.txt
+++ b/doc/src/bond_nonlinear.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/bond_oxdna.txt b/doc/src/bond_oxdna.txt
index 927fea64031d5422615d1251b9332e4e66120d3a..a0e14a123abed8da2728ed13d3ad3b836fc3414b 100644
--- a/doc/src/bond_oxdna.txt
+++ b/doc/src/bond_oxdna.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/bond_quartic.txt b/doc/src/bond_quartic.txt
index 760a5d7f07b65cfab5c8e4cbc99419922c8b0eba..87a21eff02ef4577638e44a5a6932ab181ec5a71 100644
--- a/doc/src/bond_quartic.txt
+++ b/doc/src/bond_quartic.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/bond_style.txt b/doc/src/bond_style.txt
index 3bd8afda196a642c883f7321d7998ed70f98f09c..41fa1cabb213847c51aef2b7acef0b1bb6bee00e 100644
--- a/doc/src/bond_style.txt
+++ b/doc/src/bond_style.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
@@ -66,9 +66,8 @@ the style to display the formula it computes and coefficients
 specified by the associated "bond_coeff"_bond_coeff.html command.
 
 Note that there are also additional bond styles submitted by users
-which are included in the LAMMPS distribution.  The list of these with
-links to the individual styles are given in the bond section of "this
-page"_Section_commands.html#cmd_5.
+which are included in the LAMMPS distribution.  The full list of all
+bond styles is on the "Commands bond"_Commands_bond.html doc page.
 
 "bond_style none"_bond_none.html - turn off bonded interactions
 "bond_style zero"_bond_zero.html - topology but no interactions
diff --git a/doc/src/bond_table.txt b/doc/src/bond_table.txt
index fe0b3ce22bbc388b405e6cce32b7be6466559451..e53cbdfa9f626c0c36377d9ac56a8bea016f958b 100644
--- a/doc/src/bond_table.txt
+++ b/doc/src/bond_table.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/bond_write.txt b/doc/src/bond_write.txt
index 4797d06cb1b5a164a47805840ce38824ea78b6ce..711bd2c2968b7119d80539027feb9deefe991a16 100644
--- a/doc/src/bond_write.txt
+++ b/doc/src/bond_write.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/bond_zero.txt b/doc/src/bond_zero.txt
index b599f291b4cc5fef8b4a77beb893c3b99026d893..554f26e7f00d5eeee62343792b1b3b351ec9f92f 100644
--- a/doc/src/bond_zero.txt
+++ b/doc/src/bond_zero.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/boundary.txt b/doc/src/boundary.txt
index 7ee897ffa497fdfbf17da0c83987a53eb5596349..f9685433b2c4ca35d6f5ebbdaf29b4071514a67f 100644
--- a/doc/src/boundary.txt
+++ b/doc/src/boundary.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/box.txt b/doc/src/box.txt
index 6dc093ad81170aae9c1f545503ddd97147024966..38c874fb78bc68b93ddaf666c6f97c0c147794e4 100644
--- a/doc/src/box.txt
+++ b/doc/src/box.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/change_box.txt b/doc/src/change_box.txt
index 8f3fda263f9f3a0b24fb9647b4eeaa54185cd022..adc5d6bdcb42ee3c8b814ad21480e2ef9496e8d5 100644
--- a/doc/src/change_box.txt
+++ b/doc/src/change_box.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/clear.txt b/doc/src/clear.txt
index 7ac4da5c8d93228e974c48d20b746a3abef2153c..c4ad4c4030ca601cc2c1fa9fde44ce71c21946d2 100644
--- a/doc/src/clear.txt
+++ b/doc/src/clear.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/comm_modify.txt b/doc/src/comm_modify.txt
index 3e8d0eca4ffe2d8c55e0998dd26384619fc712d6..489278523bde3a605053c565405732c55c905825 100644
--- a/doc/src/comm_modify.txt
+++ b/doc/src/comm_modify.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/comm_style.txt b/doc/src/comm_style.txt
index 8248d654d32265924b3e25734fb19d40d2c3b0f5..39eb1d4ef5aece3e2d77f2b6bbd8d16940700ccc 100644
--- a/doc/src/comm_style.txt
+++ b/doc/src/comm_style.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute.txt b/doc/src/compute.txt
index 105571b82acf07695c36b22f32f411ada97d695d..7d9e443e7da7455de147ca1531daab58887e65f8 100644
--- a/doc/src/compute.txt
+++ b/doc/src/compute.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
@@ -161,13 +161,19 @@ calculations accessed in the various ways described above.
 
 Each compute style has its own doc page which describes its arguments
 and what it does.  Here is an alphabetic list of compute styles
-available in LAMMPS.  They are also given in more compact form in the
-Compute section of "this page"_Section_commands.html#cmd_5.
+available in LAMMPS.  They are also listed in more compact form on the
+"Commands compute"_Commands_compute.html doc page.
 
 There are also additional compute styles (not listed here) submitted
-by users which are included in the LAMMPS distribution.  The list of
-these with links to the individual styles are given in the compute
-section of "this page"_Section_commands.html#cmd_5.
+by users which are included in the LAMMPS distribution.  The full list
+of all compute styles is on the "Commands
+compute"_Commands_compute.html doc page.
+
+There are also additional accelerated compute styles included in the
+LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.
+The individual style names on the "Commands
+compute"_Commands_compute.html doc page are followed by one or more of
+(g,i,k,o,t) to indicate which accerlerated styles exist.
 
 "aggregate/atom"_compute_cluster_atom.html - aggregate ID for each atom
 "angle/local"_compute_bond_local.html - theta and energy of each angle
@@ -243,16 +249,6 @@ section of "this page"_Section_commands.html#cmd_5.
 "vcm/chunk"_compute_vcm_chunk.html - velocity of center-of-mass for each chunk
 "voronoi/atom"_compute_voronoi_atom.html - Voronoi volume and neighbors for each atom :ul
 
-There are also additional compute styles submitted by users which are
-included in the LAMMPS distribution.  The list of these with links to
-the individual styles are given in the compute section of "this
-page"_Section_commands.html#cmd_5.
-
-There are also additional accelerated compute styles included in the
-LAMMPS distribution for faster performance on CPUs and GPUs.  The list
-of these with links to the individual styles are given in the pair
-section of "this page"_Section_commands.html#cmd_5.
-
 [Restrictions:] none
 
 [Related commands:]
diff --git a/doc/src/compute_ackland_atom.txt b/doc/src/compute_ackland_atom.txt
index e75ad534eb869325e16e53fccaa28b6d501930d3..485c191313209e46eb2ac979d004f23314678190 100644
--- a/doc/src/compute_ackland_atom.txt
+++ b/doc/src/compute_ackland_atom.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_angle.txt b/doc/src/compute_angle.txt
index 1deb3a4b1b78a9df9b93210550d5633829c1d44b..64eb2f4bb1262828736bb342d3f9fe145f6c4f7b 100644
--- a/doc/src/compute_angle.txt
+++ b/doc/src/compute_angle.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_angle_local.txt b/doc/src/compute_angle_local.txt
index 487b41eaf3fd7e805b19dbbee74c812488600dfa..3a321965ef71135104bdf12f8dc13111dd515564 100644
--- a/doc/src/compute_angle_local.txt
+++ b/doc/src/compute_angle_local.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_angmom_chunk.txt b/doc/src/compute_angmom_chunk.txt
index c97af96f49c756692368f3db73eaa8b6053efc3e..7e49ff302480a753cc5aacefe28b609931d56b06 100644
--- a/doc/src/compute_angmom_chunk.txt
+++ b/doc/src/compute_angmom_chunk.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_basal_atom.txt b/doc/src/compute_basal_atom.txt
index e0ac6b0a604d2e6a1ea0d8f16351192712e43b75..067a020c35ebec8da9acda96b21abb8c68724a30 100644
--- a/doc/src/compute_basal_atom.txt
+++ b/doc/src/compute_basal_atom.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_body_local.txt b/doc/src/compute_body_local.txt
index f387e61c78c8959f2979ef2ad1025d63a790f633..8ac3f00c559345d1de1547542296a9f7b0469c00 100644
--- a/doc/src/compute_body_local.txt
+++ b/doc/src/compute_body_local.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_bond.txt b/doc/src/compute_bond.txt
index ac0e50872bb41f2a7cc4d0d275f467be88665113..a87c510538f6035bf90b75d61cbd886a78c19208 100644
--- a/doc/src/compute_bond.txt
+++ b/doc/src/compute_bond.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_bond_local.txt b/doc/src/compute_bond_local.txt
index 868b43caa9327dd4b0e8adcd02b0d6e9631ecec3..c3dc1cc4afe92ae09118e8f56c0e678a380cee71 100644
--- a/doc/src/compute_bond_local.txt
+++ b/doc/src/compute_bond_local.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_centro_atom.txt b/doc/src/compute_centro_atom.txt
index bace0d873995be48ce5bb6172a9dcbac541d423c..183537690f43f61a5c5099ac3c76c3dd37b8223c 100644
--- a/doc/src/compute_centro_atom.txt
+++ b/doc/src/compute_centro_atom.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_chunk_atom.txt b/doc/src/compute_chunk_atom.txt
index fc0de28b6a46041d241d275a01e7c5e6351ddffa..95e6e6c0104a939af015cecc41a2c2ee3ea5c33c 100644
--- a/doc/src/compute_chunk_atom.txt
+++ b/doc/src/compute_chunk_atom.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_cluster_atom.txt b/doc/src/compute_cluster_atom.txt
index 12ecb8f173edcf1a53dbcadd1105fb22d14c0ecb..e6138fe1e8eb80256cdc317120bcedb8fb7326cb 100644
--- a/doc/src/compute_cluster_atom.txt
+++ b/doc/src/compute_cluster_atom.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_cna_atom.txt b/doc/src/compute_cna_atom.txt
index 9c4814560d435f82fcd4794ad7b0f33c40609046..d69c5e9c467e626017381f6e96268c9ed8aa4b8f 100644
--- a/doc/src/compute_cna_atom.txt
+++ b/doc/src/compute_cna_atom.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_cnp_atom.txt b/doc/src/compute_cnp_atom.txt
index aca7e351ec78d5224a84ba293d514afd493bef84..44a77d23ca0fedade05df5f523302bcdaaa6215a 100644
--- a/doc/src/compute_cnp_atom.txt
+++ b/doc/src/compute_cnp_atom.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_com.txt b/doc/src/compute_com.txt
index 08bb08b1425af6d5d95d289def94f2c3cefeec9a..fdc631a263cb155e437a5f54aa368ffb40ee2d76 100644
--- a/doc/src/compute_com.txt
+++ b/doc/src/compute_com.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_com_chunk.txt b/doc/src/compute_com_chunk.txt
index f28355d6c5d8bf44fb85279727ce342710978c6c..b982f0d9017f4a501d56a9d1696cf6d4a5e51486 100644
--- a/doc/src/compute_com_chunk.txt
+++ b/doc/src/compute_com_chunk.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_contact_atom.txt b/doc/src/compute_contact_atom.txt
index ea4158e3b116749051040e70c960d45e3e53c348..efe524263aa8c399e8771dd7348b52c9ae5cd42c 100644
--- a/doc/src/compute_contact_atom.txt
+++ b/doc/src/compute_contact_atom.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_coord_atom.txt b/doc/src/compute_coord_atom.txt
index 06b565aedc9933ad864c9f4aca9c0f56c0d7bdb7..66eecd195da4fb19851d5d84349c72391e51add6 100644
--- a/doc/src/compute_coord_atom.txt
+++ b/doc/src/compute_coord_atom.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_damage_atom.txt b/doc/src/compute_damage_atom.txt
index e262ee0b1f0592cbc2b9225ef62433ac39b81919..74939e22806077fe5fb274cd17a7630954db9017 100644
--- a/doc/src/compute_damage_atom.txt
+++ b/doc/src/compute_damage_atom.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_dihedral.txt b/doc/src/compute_dihedral.txt
index 67c97b60f10bc1a57875caee57e1f18df4e4c995..aa25f9dd1029af8d7f23ffb938bd7fd6a70e08c8 100644
--- a/doc/src/compute_dihedral.txt
+++ b/doc/src/compute_dihedral.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_dihedral_local.txt b/doc/src/compute_dihedral_local.txt
index d2051a51bd4e54f1ff107368e3f38e87650b47c0..77812699d35fc826c95a344ddc7bf0207caf2ec4 100644
--- a/doc/src/compute_dihedral_local.txt
+++ b/doc/src/compute_dihedral_local.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_dilatation_atom.txt b/doc/src/compute_dilatation_atom.txt
index 161e73c7ffe14568cfbe831090ae7fc11027b996..498110cf99338e56fb24a2b9a362438f03f5f9f3 100644
--- a/doc/src/compute_dilatation_atom.txt
+++ b/doc/src/compute_dilatation_atom.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_dipole_chunk.txt b/doc/src/compute_dipole_chunk.txt
index 5f8d6689c4fe02be20e4fbbb769d700d040fcea8..d45fde9af2dbdd86aedc30abaa55c4b62e82b648 100644
--- a/doc/src/compute_dipole_chunk.txt
+++ b/doc/src/compute_dipole_chunk.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_displace_atom.txt b/doc/src/compute_displace_atom.txt
index 5636cc02f04da1a310a007d505e24245f69db40a..669ab9f7ca3ea74e4a3a8a0b5537c0b09cbd814d 100644
--- a/doc/src/compute_displace_atom.txt
+++ b/doc/src/compute_displace_atom.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_dpd.txt b/doc/src/compute_dpd.txt
index a5620d34b341fb9cc8f198d424e1db0a8bb40f49..1721456e35ab0da5a82d3965f676f35a3d4baa3b 100644
--- a/doc/src/compute_dpd.txt
+++ b/doc/src/compute_dpd.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_dpd_atom.txt b/doc/src/compute_dpd_atom.txt
index ed0fd2410b97d65da7ee518789c2a5bd1bd1fcd6..8e502d4a6060f297da9132013adf5e19d40b565a 100644
--- a/doc/src/compute_dpd_atom.txt
+++ b/doc/src/compute_dpd_atom.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_edpd_temp_atom.txt b/doc/src/compute_edpd_temp_atom.txt
index 9011c3c82307978bda77ef0e4fe4b4417c2bdbbf..f33398e03d68995dc18da4d73fd9537f5e75656d 100644
--- a/doc/src/compute_edpd_temp_atom.txt
+++ b/doc/src/compute_edpd_temp_atom.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_entropy_atom.txt b/doc/src/compute_entropy_atom.txt
index 7fdc1f4af25cdf28c771b54d8299671178210253..9c45fd287099ea6150621a177f55837bbc5855fb 100644
--- a/doc/src/compute_entropy_atom.txt
+++ b/doc/src/compute_entropy_atom.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_erotate_asphere.txt b/doc/src/compute_erotate_asphere.txt
index 24e6e5e6f77c69a8cf2ad58d96d6ca070869dcac..5cdc0997826f3dfbfff0281e85efe3ebb4864bb0 100644
--- a/doc/src/compute_erotate_asphere.txt
+++ b/doc/src/compute_erotate_asphere.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_erotate_rigid.txt b/doc/src/compute_erotate_rigid.txt
index c8527d7073e5adec553e0864c0961eb18caf9123..5b9077870e1d25440827b5a6006b5c6e3233d830 100644
--- a/doc/src/compute_erotate_rigid.txt
+++ b/doc/src/compute_erotate_rigid.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_erotate_sphere.txt b/doc/src/compute_erotate_sphere.txt
index 8abc9a53ad7ff98f0b8908f562a3aacdf1ad0912..d0c176b50eb264ff3431b6bbcdd71ad578092b1a 100644
--- a/doc/src/compute_erotate_sphere.txt
+++ b/doc/src/compute_erotate_sphere.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_erotate_sphere_atom.txt b/doc/src/compute_erotate_sphere_atom.txt
index 0bea315a89f631657841a1723daf4d5d720c64b0..fdd609a0e65ffd71a599a16310b9c1bacdd809b1 100644
--- a/doc/src/compute_erotate_sphere_atom.txt
+++ b/doc/src/compute_erotate_sphere_atom.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_event_displace.txt b/doc/src/compute_event_displace.txt
index 17c42889112ac692769fe7fc938a0c8d7c63c35f..561ded35c052ef3e99e53ea8cb0533e00d3f99e3 100644
--- a/doc/src/compute_event_displace.txt
+++ b/doc/src/compute_event_displace.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_fep.txt b/doc/src/compute_fep.txt
index f0ce3fd704c696d4c6e9f8748b3a94bb61b22ca9..8b4a92e16ea3a0486ca2c7113bf0b1ac87a47399 100644
--- a/doc/src/compute_fep.txt
+++ b/doc/src/compute_fep.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_global_atom.txt b/doc/src/compute_global_atom.txt
index f40810b70c97d4620b2a2832d7c5d58f2c994d72..a26dba72b008de7202aa880c2b6999be67dc56a8 100644
--- a/doc/src/compute_global_atom.txt
+++ b/doc/src/compute_global_atom.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_group_group.txt b/doc/src/compute_group_group.txt
index 8f992791d2c4728106b4dc174ecddf4a07abab9a..cff3687354589ab402cbe03114425ec9baf04985 100644
--- a/doc/src/compute_group_group.txt
+++ b/doc/src/compute_group_group.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_gyration.txt b/doc/src/compute_gyration.txt
index 3d698609cab07ac165323df62862233bad29b0c2..4dc883ad0bd2f2737b4e547b05621da6f39a01d2 100644
--- a/doc/src/compute_gyration.txt
+++ b/doc/src/compute_gyration.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_gyration_chunk.txt b/doc/src/compute_gyration_chunk.txt
index ef14a456f3f6a7040f6f055976df325c248e1e29..dcbfc653938f13b147d5cd58ec85fb3ca392f163 100644
--- a/doc/src/compute_gyration_chunk.txt
+++ b/doc/src/compute_gyration_chunk.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_heat_flux.txt b/doc/src/compute_heat_flux.txt
index 84c49513281cc900aa3bf7c91233f8ad0684b469..81a2a3f51711dc56e4b763de70421fecab1e4a4c 100644
--- a/doc/src/compute_heat_flux.txt
+++ b/doc/src/compute_heat_flux.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_hexorder_atom.txt b/doc/src/compute_hexorder_atom.txt
index 1ab40b513c02955a3ccf224a574efaa0151dde42..082a3cad7a0e62195fa333fd15f5071c2810000c 100644
--- a/doc/src/compute_hexorder_atom.txt
+++ b/doc/src/compute_hexorder_atom.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_improper.txt b/doc/src/compute_improper.txt
index 61c4f6cd2907a14fa444e02d53e3029eabeb92f1..867dd48cc16edc61f5b1cc8d64d4b80234120209 100644
--- a/doc/src/compute_improper.txt
+++ b/doc/src/compute_improper.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_improper_local.txt b/doc/src/compute_improper_local.txt
index 2aec554d2f81f1c8e48c6cdae72d4a6cebf24275..f340d5a03fc472889b22f854480c0563eee0e6dc 100644
--- a/doc/src/compute_improper_local.txt
+++ b/doc/src/compute_improper_local.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_inertia_chunk.txt b/doc/src/compute_inertia_chunk.txt
index 3edd25d69b3e43886b4cf6c696e33655976cafc8..d6cdb3fe79eb950ce3aa3675c9a7d13986d1e957 100644
--- a/doc/src/compute_inertia_chunk.txt
+++ b/doc/src/compute_inertia_chunk.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_ke.txt b/doc/src/compute_ke.txt
index d6f4e1b709ddf14ccda61ba8bc83d4bef09fc4f8..64ab83db48b792aa0bc26dbd60ca0de7800166ae 100644
--- a/doc/src/compute_ke.txt
+++ b/doc/src/compute_ke.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_ke_atom.txt b/doc/src/compute_ke_atom.txt
index e0e96a80d85dc459c7fa232d1e190337e292ea92..d288ab0236d44a40c32805a94e8d1b04a181edd1 100644
--- a/doc/src/compute_ke_atom.txt
+++ b/doc/src/compute_ke_atom.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_ke_atom_eff.txt b/doc/src/compute_ke_atom_eff.txt
index aa188a411b5ba96f325c48304d06638830dab11c..f665f35055f36be914f26aa5c032b2b76233ccf2 100644
--- a/doc/src/compute_ke_atom_eff.txt
+++ b/doc/src/compute_ke_atom_eff.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_ke_eff.txt b/doc/src/compute_ke_eff.txt
index 334b4121ed4823e7a292c346ed1603a3b8ecafa8..d6d7fdb10f5f3667a8443047505e80a775c3b1b6 100644
--- a/doc/src/compute_ke_eff.txt
+++ b/doc/src/compute_ke_eff.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_ke_rigid.txt b/doc/src/compute_ke_rigid.txt
index 69cf4a598ec988dd0ef1b02d0b0ad376b146c244..45ba2673b0283a8106d55ee621103a7f8eb3a7fa 100644
--- a/doc/src/compute_ke_rigid.txt
+++ b/doc/src/compute_ke_rigid.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_meso_e_atom.txt b/doc/src/compute_meso_e_atom.txt
index 70a89693860d6d24a4c4f1fd5b40b320b8097b57..9a9c7fae118d4b6a84636b94a9f83d582c6331c8 100644
--- a/doc/src/compute_meso_e_atom.txt
+++ b/doc/src/compute_meso_e_atom.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_meso_rho_atom.txt b/doc/src/compute_meso_rho_atom.txt
index 912587f4a2065b509113306ffede0002eaa28ce0..30b1142b6cdfef0afb329f7d3be5a360d9487465 100644
--- a/doc/src/compute_meso_rho_atom.txt
+++ b/doc/src/compute_meso_rho_atom.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_meso_t_atom.txt b/doc/src/compute_meso_t_atom.txt
index c9db9bf50ed554005d025a87b5b16aae98719336..ab92f05018a15b6f45edf30d4844b82b2c237493 100644
--- a/doc/src/compute_meso_t_atom.txt
+++ b/doc/src/compute_meso_t_atom.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_modify.txt b/doc/src/compute_modify.txt
index 9a2480ec0ac7fd7b584216a74355ed9b707c877e..192ea0bc9ec96d6c7691214f78f7cf2c080f4ddd 100644
--- a/doc/src/compute_modify.txt
+++ b/doc/src/compute_modify.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_msd.txt b/doc/src/compute_msd.txt
index 742f7ce11311805f0b7770974c27956bf077141e..b54e05bc6498ffd450ce91ff9f5b4c959f9790fd 100644
--- a/doc/src/compute_msd.txt
+++ b/doc/src/compute_msd.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_msd_chunk.txt b/doc/src/compute_msd_chunk.txt
index 3e1d8542ae934cbdc2cb86d05efc8a6ca3a34090..264f38d5fde4a6f587ff97f22ed797b07f3b50bc 100644
--- a/doc/src/compute_msd_chunk.txt
+++ b/doc/src/compute_msd_chunk.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_msd_nongauss.txt b/doc/src/compute_msd_nongauss.txt
index db8788db0bba35babf382f2c1d71239e4e7eab01..814159121d11781bf29850db7c8787ab5644b807 100644
--- a/doc/src/compute_msd_nongauss.txt
+++ b/doc/src/compute_msd_nongauss.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_omega_chunk.txt b/doc/src/compute_omega_chunk.txt
index 4a7a996d1db60d539fc8359ee69c4127d378a07b..84b25ac6f26e014a2258715bf2e7d847642854df 100644
--- a/doc/src/compute_omega_chunk.txt
+++ b/doc/src/compute_omega_chunk.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_orientorder_atom.txt b/doc/src/compute_orientorder_atom.txt
index a8b400801285542c5bf2ca69c2f1d73bb04824ac..7327a7b1d333a5375d033d5d8f88b9e74efc6237 100644
--- a/doc/src/compute_orientorder_atom.txt
+++ b/doc/src/compute_orientorder_atom.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_pair.txt b/doc/src/compute_pair.txt
index be40d7a5503b1bb1cf92ecd8d099ffac1ed25cf9..a2c25fcc8dc0dbe737e3efb76fd1ef57197dd765 100644
--- a/doc/src/compute_pair.txt
+++ b/doc/src/compute_pair.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_pair_local.txt b/doc/src/compute_pair_local.txt
index bbbc5823f230fa3a695201c8e1b2242e16c15d23..7588e92527aa5d32157f4f94207226597a9966f4 100644
--- a/doc/src/compute_pair_local.txt
+++ b/doc/src/compute_pair_local.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_pe.txt b/doc/src/compute_pe.txt
index f3ce5678b0b306ad1a12956a8d37623a0b1ac112..37655dfd480c8bb48b2b722436f5b6b0d15f5e6d 100644
--- a/doc/src/compute_pe.txt
+++ b/doc/src/compute_pe.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_pe_atom.txt b/doc/src/compute_pe_atom.txt
index e6bc5f905238492a70d60afd3198f399d7bed77f..400621f8df1d50b921c2ad870df98b8cdf578784 100644
--- a/doc/src/compute_pe_atom.txt
+++ b/doc/src/compute_pe_atom.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_plasticity_atom.txt b/doc/src/compute_plasticity_atom.txt
index c992ca820020c5ea7917985a80b6c6528d39a559..50a51d99377899c3ed62a81059351ab494968567 100644
--- a/doc/src/compute_plasticity_atom.txt
+++ b/doc/src/compute_plasticity_atom.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_pressure.txt b/doc/src/compute_pressure.txt
index 51d3241acead0255bca6692a9d4190ce42a6d589..dea0a7f05b7f03d209077628f19a07172eb93e0f 100644
--- a/doc/src/compute_pressure.txt
+++ b/doc/src/compute_pressure.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_pressure_uef.txt b/doc/src/compute_pressure_uef.txt
index 5b252b369dd012691e62a3dcf267c6e00cca11c3..61cc85ad8097b3b43ac740cf186b7456f02db707 100644
--- a/doc/src/compute_pressure_uef.txt
+++ b/doc/src/compute_pressure_uef.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_property_atom.txt b/doc/src/compute_property_atom.txt
index 88bdf5a453688c6bd1f97ad82c538fac01c5268e..512009093c0e052e8e7b43f44455d1f61d7e6fb8 100644
--- a/doc/src/compute_property_atom.txt
+++ b/doc/src/compute_property_atom.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_property_chunk.txt b/doc/src/compute_property_chunk.txt
index ad131a8a60a01d972895faa647a1cc8196f1ea45..a30b5a1f0a5526421610cc06946328874c762115 100644
--- a/doc/src/compute_property_chunk.txt
+++ b/doc/src/compute_property_chunk.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_property_local.txt b/doc/src/compute_property_local.txt
index 74595f00f6b831b53425a87c1d19fc6fa5a51af2..b0ec088cf79d009e7c3062907d73dbfe3279e6da 100644
--- a/doc/src/compute_property_local.txt
+++ b/doc/src/compute_property_local.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_rdf.txt b/doc/src/compute_rdf.txt
index c2d2c379fe7c4dd74ad02ce4fb49b3226665215d..04b38682cc4957ac67459b18652249b1dfb75f14 100644
--- a/doc/src/compute_rdf.txt
+++ b/doc/src/compute_rdf.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_reduce.txt b/doc/src/compute_reduce.txt
index 614ef50581b454e5d860efb4afe71341cac4fbe0..ef3c7c6489e03ef3c1056edefd8d4dc419766cdf 100644
--- a/doc/src/compute_reduce.txt
+++ b/doc/src/compute_reduce.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_rigid_local.txt b/doc/src/compute_rigid_local.txt
index 380713d091d8d6828bc75eeb70f52c10e52796a3..b5e6954ab99943f090a3153829ca08a6daa8f0b7 100644
--- a/doc/src/compute_rigid_local.txt
+++ b/doc/src/compute_rigid_local.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_saed.txt b/doc/src/compute_saed.txt
index 419ad3c48966bc66cc0ebbfe30738f7111a9ef77..8c17a30fcaf1acb403a936d4a15938206e89ad4d 100644
--- a/doc/src/compute_saed.txt
+++ b/doc/src/compute_saed.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_slice.txt b/doc/src/compute_slice.txt
index 69eb7976ad7dfc07e7d4e082010373a3d467b02d..51031aeab3017a4bbfee683c0055165d74fd8c03 100644
--- a/doc/src/compute_slice.txt
+++ b/doc/src/compute_slice.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_smd_contact_radius.txt b/doc/src/compute_smd_contact_radius.txt
index 5e043a1390fe65ccd6fe79cd1df338b6426d9f74..cd1381604788bfcd42f00653d2c5e9b46f98d25f 100644
--- a/doc/src/compute_smd_contact_radius.txt
+++ b/doc/src/compute_smd_contact_radius.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_smd_damage.txt b/doc/src/compute_smd_damage.txt
index ea814ba0642842f6583883164171c45c69a820f0..afabe23d7cc1407496463c926ba8adcb9ddc7ff0 100644
--- a/doc/src/compute_smd_damage.txt
+++ b/doc/src/compute_smd_damage.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_smd_hourglass_error.txt b/doc/src/compute_smd_hourglass_error.txt
index 046f7e7f27f1f88efbfb8ea7bc63b438bcc5876c..13fd20a5891cab8bdeeabb570d8343c063a705af 100644
--- a/doc/src/compute_smd_hourglass_error.txt
+++ b/doc/src/compute_smd_hourglass_error.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_smd_internal_energy.txt b/doc/src/compute_smd_internal_energy.txt
index b88bd8a1ce7686901b53bfcb7ef914c62e833f66..6585c3429f27a9c97d17c66a15dff959ebbbe5be 100644
--- a/doc/src/compute_smd_internal_energy.txt
+++ b/doc/src/compute_smd_internal_energy.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_smd_plastic_strain.txt b/doc/src/compute_smd_plastic_strain.txt
index 7fd083726f59b05d38975a0331a4702e82c75688..fb3c5c9138cb5ae444320a5ff9f4a73878780a67 100644
--- a/doc/src/compute_smd_plastic_strain.txt
+++ b/doc/src/compute_smd_plastic_strain.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_smd_plastic_strain_rate.txt b/doc/src/compute_smd_plastic_strain_rate.txt
index b17684e05e691049b7dea288a91bc61e664f56f4..b913ae90976009a7caf916352cbfe9475577d9db 100644
--- a/doc/src/compute_smd_plastic_strain_rate.txt
+++ b/doc/src/compute_smd_plastic_strain_rate.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_smd_rho.txt b/doc/src/compute_smd_rho.txt
index 375513b9c7e32e904cbc700483a97beb5c09aa3a..a1ee1d9c5b95a2971e64a52ad4416e74e54fc226 100644
--- a/doc/src/compute_smd_rho.txt
+++ b/doc/src/compute_smd_rho.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_smd_tlsph_defgrad.txt b/doc/src/compute_smd_tlsph_defgrad.txt
index d07ff99f070c4fc76140acefbea14378fa066fe6..1663c84f65fd3b3c59daf427d4b15fe6a5d27ea9 100644
--- a/doc/src/compute_smd_tlsph_defgrad.txt
+++ b/doc/src/compute_smd_tlsph_defgrad.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_smd_tlsph_dt.txt b/doc/src/compute_smd_tlsph_dt.txt
index 798278661aac5af9440cd38499de124db384b68b..c714f3266bceaf96ea1b86d487cf653cdeeeb47e 100644
--- a/doc/src/compute_smd_tlsph_dt.txt
+++ b/doc/src/compute_smd_tlsph_dt.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_smd_tlsph_num_neighs.txt b/doc/src/compute_smd_tlsph_num_neighs.txt
index 632ab94208f6d3d287df7783cb7306c21fd075b2..af5b0741db6c0c964ab4a73b21bdb928b663fe42 100644
--- a/doc/src/compute_smd_tlsph_num_neighs.txt
+++ b/doc/src/compute_smd_tlsph_num_neighs.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_smd_tlsph_shape.txt b/doc/src/compute_smd_tlsph_shape.txt
index a3daf702228dc9c4a93938e171e16b519467aa7c..927cd7c7aecaa51cc45c095066586899bd37aefb 100644
--- a/doc/src/compute_smd_tlsph_shape.txt
+++ b/doc/src/compute_smd_tlsph_shape.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_smd_tlsph_strain.txt b/doc/src/compute_smd_tlsph_strain.txt
index 899166359c6097e019fe5e923c0f77134b6998bc..4536f26c8ea364d40d306f1ac863f3fc4a278dff 100644
--- a/doc/src/compute_smd_tlsph_strain.txt
+++ b/doc/src/compute_smd_tlsph_strain.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_smd_tlsph_strain_rate.txt b/doc/src/compute_smd_tlsph_strain_rate.txt
index 29246a05d9d65161640b1e7b093de1631ce4fc24..ae2883e4bbedb0e698cac841601984de90af2031 100644
--- a/doc/src/compute_smd_tlsph_strain_rate.txt
+++ b/doc/src/compute_smd_tlsph_strain_rate.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_smd_tlsph_stress.txt b/doc/src/compute_smd_tlsph_stress.txt
index c2c23b6836f45de915daa656e88d4557178dec68..50d6b7f4344ffb585cc27a00d644e803904e5fad 100644
--- a/doc/src/compute_smd_tlsph_stress.txt
+++ b/doc/src/compute_smd_tlsph_stress.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_smd_triangle_mesh_vertices.txt b/doc/src/compute_smd_triangle_mesh_vertices.txt
index 3080ef700edfa0402223e11453b82b9bd85bf54e..9e167924d1401fea40a6ac9b0d9bcc7d257d4355 100644
--- a/doc/src/compute_smd_triangle_mesh_vertices.txt
+++ b/doc/src/compute_smd_triangle_mesh_vertices.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_smd_ulsph_num_neighs.txt b/doc/src/compute_smd_ulsph_num_neighs.txt
index 8550838799248c17a743d17ab780f29fb14bd264..202b8f15e1d95ec3441e272a23b618a0f57f443a 100644
--- a/doc/src/compute_smd_ulsph_num_neighs.txt
+++ b/doc/src/compute_smd_ulsph_num_neighs.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_smd_ulsph_strain.txt b/doc/src/compute_smd_ulsph_strain.txt
index 3813e61f6cdcc41ac7d9123f461a2dab21ee4f66..76c47162a5c85e0def8c8231224ccda416ea6360 100644
--- a/doc/src/compute_smd_ulsph_strain.txt
+++ b/doc/src/compute_smd_ulsph_strain.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_smd_ulsph_strain_rate.txt b/doc/src/compute_smd_ulsph_strain_rate.txt
index 251e5ddbf7247c92256191ea7626f588be964d42..c851e767b34a418a614cfeb537638ec294ae489f 100644
--- a/doc/src/compute_smd_ulsph_strain_rate.txt
+++ b/doc/src/compute_smd_ulsph_strain_rate.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_smd_ulsph_stress.txt b/doc/src/compute_smd_ulsph_stress.txt
index 719cf006c9d89170d95aea0a40e88c53aa795b5e..a5692b2412ce589165a29514c6b199b7d0dd802d 100644
--- a/doc/src/compute_smd_ulsph_stress.txt
+++ b/doc/src/compute_smd_ulsph_stress.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_smd_vol.txt b/doc/src/compute_smd_vol.txt
index 495c09a5f542917d4355096dca7d5bf1fbba05e1..fc4871d6f301157c45fcaf88e99301f20cdff31c 100644
--- a/doc/src/compute_smd_vol.txt
+++ b/doc/src/compute_smd_vol.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_sna_atom.txt b/doc/src/compute_sna_atom.txt
index 6fdd85568b9e9d193a63b0c8e68cfa4c7e621f20..3b302a0a71c65de87fee8ae571e866b3cc19653c 100644
--- a/doc/src/compute_sna_atom.txt
+++ b/doc/src/compute_sna_atom.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_spin.txt b/doc/src/compute_spin.txt
index fcc764c14cb0f7cc88869655bf8d2df1f745c777..792706ecdfae311acd293546d899b51b2bf28d73 100644
--- a/doc/src/compute_spin.txt
+++ b/doc/src/compute_spin.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_stress_atom.txt b/doc/src/compute_stress_atom.txt
index 423c1dcfda4d5a7d92a91b606f8bedf0bd1544ee..222513da61d45e22238a38780c39977ec3900b68 100644
--- a/doc/src/compute_stress_atom.txt
+++ b/doc/src/compute_stress_atom.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_tally.txt b/doc/src/compute_tally.txt
index 95ef4a553b8df78af94dd0d51a7fc48c12d313fb..23fac4309384bac044259f51d128726725fcd3f7 100644
--- a/doc/src/compute_tally.txt
+++ b/doc/src/compute_tally.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_tdpd_cc_atom.txt b/doc/src/compute_tdpd_cc_atom.txt
index ec077a33d10f4df03dc03ecdd7440a30acfbd9c0..9ee4d3da3462fbed0bc3be6b66212d6988fd938d 100644
--- a/doc/src/compute_tdpd_cc_atom.txt
+++ b/doc/src/compute_tdpd_cc_atom.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_temp.txt b/doc/src/compute_temp.txt
index cce40261c6613eaf81f9d2b200e6b0840e66c7b6..9f3a1ca9061feeaab02ac197f5ab15c1844a709a 100644
--- a/doc/src/compute_temp.txt
+++ b/doc/src/compute_temp.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_temp_asphere.txt b/doc/src/compute_temp_asphere.txt
index a5fc0e89275ca46f402c1a5b057206496a703582..6766729ae0c463ce51c6470de27d6966102a0cff 100644
--- a/doc/src/compute_temp_asphere.txt
+++ b/doc/src/compute_temp_asphere.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_temp_body.txt b/doc/src/compute_temp_body.txt
index 580564b059da85c9d57cedd9464868c877c3dcdd..4e3ce3e77f86db797f0222b62d403df6ef82c827 100644
--- a/doc/src/compute_temp_body.txt
+++ b/doc/src/compute_temp_body.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_temp_chunk.txt b/doc/src/compute_temp_chunk.txt
index 5d7d64ce688c4a28c9190bb7fcc4087f544713f2..de8c850a7087329465e84544a2084309602a80d1 100644
--- a/doc/src/compute_temp_chunk.txt
+++ b/doc/src/compute_temp_chunk.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_temp_com.txt b/doc/src/compute_temp_com.txt
index e8b46aec9790f422dea5c6e5046e27043b75055b..12df694e382657c9424e8b0649a4dd677a2630d6 100644
--- a/doc/src/compute_temp_com.txt
+++ b/doc/src/compute_temp_com.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_temp_cs.txt b/doc/src/compute_temp_cs.txt
index 9d2ceabd46f3e20d5afff4d4205fca52b73db189..0236319f547a2a71e5f533f797ffb191e6e8254d 100644
--- a/doc/src/compute_temp_cs.txt
+++ b/doc/src/compute_temp_cs.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_temp_deform.txt b/doc/src/compute_temp_deform.txt
index b81d07babdb1b7b51b8f931dffe78b19e57c197f..26d322589ed70d49d23a0ac8948fc4524e04daef 100644
--- a/doc/src/compute_temp_deform.txt
+++ b/doc/src/compute_temp_deform.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_temp_deform_eff.txt b/doc/src/compute_temp_deform_eff.txt
index 418180d93c0d67203afcd1f89d982ec0ba3275c1..876d492f3446f7294ed295974e20c0f28a2369bd 100644
--- a/doc/src/compute_temp_deform_eff.txt
+++ b/doc/src/compute_temp_deform_eff.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_temp_drude.txt b/doc/src/compute_temp_drude.txt
index 3e86dc8fda0cfd722219f0198caf2db8213b19db..20d9a5c05670a66938a70bb85660cd6b79bc100a 100644
--- a/doc/src/compute_temp_drude.txt
+++ b/doc/src/compute_temp_drude.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_temp_eff.txt b/doc/src/compute_temp_eff.txt
index 42d22a33a7b727a828d4bd9f68660a08f0145ca2..35ddb75b12c30ffac0d1d5fc249f9abe33617a0a 100644
--- a/doc/src/compute_temp_eff.txt
+++ b/doc/src/compute_temp_eff.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_temp_partial.txt b/doc/src/compute_temp_partial.txt
index 0fda274ca0a31efc169dd79c6e03c08a04f8b0e6..2769246532fd55f8cf36df3c076d6d822609d765 100644
--- a/doc/src/compute_temp_partial.txt
+++ b/doc/src/compute_temp_partial.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_temp_profile.txt b/doc/src/compute_temp_profile.txt
index 8f47c8f9f4a54b96194b8a4c54d23abd10770ee4..4ed04ca67e0e0c07ebc3250829ad4f9486c791d2 100644
--- a/doc/src/compute_temp_profile.txt
+++ b/doc/src/compute_temp_profile.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_temp_ramp.txt b/doc/src/compute_temp_ramp.txt
index 1ae0cdfc3e2d36d9b2b373b6ede70fc177810093..15cad9c0cb814ed464f5c9210499a333f6cf576d 100644
--- a/doc/src/compute_temp_ramp.txt
+++ b/doc/src/compute_temp_ramp.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_temp_region.txt b/doc/src/compute_temp_region.txt
index f05fa38e2c56db6689b8b275bd26fb128ec20241..f23901af9861633b83b33d5c172b62f8fe3f681c 100644
--- a/doc/src/compute_temp_region.txt
+++ b/doc/src/compute_temp_region.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_temp_region_eff.txt b/doc/src/compute_temp_region_eff.txt
index 45c01b047fd5e09fcddf31f7fde5cdb75817c82d..95892eb25778eac67c1042de5acf2ed97494c4f1 100644
--- a/doc/src/compute_temp_region_eff.txt
+++ b/doc/src/compute_temp_region_eff.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_temp_rotate.txt b/doc/src/compute_temp_rotate.txt
index 8c5679b83fda4a6f4d95f3b592dc6ebe27f44885..189246d3e47e734b00a63da770e83a0333c9c85e 100644
--- a/doc/src/compute_temp_rotate.txt
+++ b/doc/src/compute_temp_rotate.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_temp_sphere.txt b/doc/src/compute_temp_sphere.txt
index 4d4258182e29ee2ac5fcf6d905a2b11351c70e43..5a55126d121755a60f9705e52189f28dbcca70cf 100644
--- a/doc/src/compute_temp_sphere.txt
+++ b/doc/src/compute_temp_sphere.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_temp_uef.txt b/doc/src/compute_temp_uef.txt
index acd3a6218d9e39d25a73be4d7562ee8127ae9cfa..a94d5db8ed767604c3dd6edac9bf81723d02da1b 100644
--- a/doc/src/compute_temp_uef.txt
+++ b/doc/src/compute_temp_uef.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_ti.txt b/doc/src/compute_ti.txt
index f5d26e1a032643e20025bfa1c3d2bdcbaf767266..e79b594e3f32a252a1ea352a1b3fc113324ebb3d 100644
--- a/doc/src/compute_ti.txt
+++ b/doc/src/compute_ti.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_torque_chunk.txt b/doc/src/compute_torque_chunk.txt
index 254cd0fd85b9df34812ce72404bc82c5dcdb66bc..6484076b37619db625ea585480d1d00b73c455ed 100644
--- a/doc/src/compute_torque_chunk.txt
+++ b/doc/src/compute_torque_chunk.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_vacf.txt b/doc/src/compute_vacf.txt
index d615f70e2269bc6c2ea21b60a5c461460e591f0f..70f1e99490586badb949d7fe6bec0b791a0ebc1c 100644
--- a/doc/src/compute_vacf.txt
+++ b/doc/src/compute_vacf.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_vcm_chunk.txt b/doc/src/compute_vcm_chunk.txt
index af1a4305d83daa7fea51b03f3a733c3866f21ad9..7e8ad712086fe17931a8676179865117aaf41c1f 100644
--- a/doc/src/compute_vcm_chunk.txt
+++ b/doc/src/compute_vcm_chunk.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_voronoi_atom.txt b/doc/src/compute_voronoi_atom.txt
index bbd68b16ea9e7b1526efbe7dd07954be2891db25..a8ce77882ad42069d32d51864cb06ce3566c8bba 100644
--- a/doc/src/compute_voronoi_atom.txt
+++ b/doc/src/compute_voronoi_atom.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/compute_xrd.txt b/doc/src/compute_xrd.txt
index 03fd0ecdc29c547df3ce6d7a3f3b811e05377f4a..609fde3582d9efd03bd9c0ae6fbb63ac3d54db20 100644
--- a/doc/src/compute_xrd.txt
+++ b/doc/src/compute_xrd.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/create_atoms.txt b/doc/src/create_atoms.txt
index 5d824ae1ef2e57815bba64e8596d069048a46f12..d80e2d45f1473d2a4a084b35af0140e6a3e0605a 100644
--- a/doc/src/create_atoms.txt
+++ b/doc/src/create_atoms.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/create_bonds.txt b/doc/src/create_bonds.txt
index 6700ed29d3f3f6d9b3c7d5094b182a1bf6235a82..8596cab51d24c6f0283d5d070192153d6d218534 100644
--- a/doc/src/create_bonds.txt
+++ b/doc/src/create_bonds.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/create_box.txt b/doc/src/create_box.txt
index ed05775591048e7e65651467a7cb9e63e273e1c1..0993b4f927d49a02b8a93328f564c72e16e3fbdb 100644
--- a/doc/src/create_box.txt
+++ b/doc/src/create_box.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/delete_atoms.txt b/doc/src/delete_atoms.txt
index 1aa71d341f83a34a25017b4d123996f22a6fcd16..57faf97ad1bf1d213135707989985a1f866a8f8d 100644
--- a/doc/src/delete_atoms.txt
+++ b/doc/src/delete_atoms.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/delete_bonds.txt b/doc/src/delete_bonds.txt
index b1137a22881213506c8921b9e422d0d9f2e33253..b29fa82f2d0d16c9b1a252073080aba43332605c 100644
--- a/doc/src/delete_bonds.txt
+++ b/doc/src/delete_bonds.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/dielectric.txt b/doc/src/dielectric.txt
index e98badf87b72c94b3a308c806044499966d76463..f93be8cc25823c691b108dce6d8e41b5d6367775 100644
--- a/doc/src/dielectric.txt
+++ b/doc/src/dielectric.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/dihedral_charmm.txt b/doc/src/dihedral_charmm.txt
index f808649a44da0c3ef018ba279c38ec4228e7fc9c..8adef6cf4b5ed1ee5f25ab1d72c7fc12f43078fc 100644
--- a/doc/src/dihedral_charmm.txt
+++ b/doc/src/dihedral_charmm.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/dihedral_class2.txt b/doc/src/dihedral_class2.txt
index 41282b22a3149d59bc72dc1cfb87267a41cde38d..1a2f37abbbd0352fd04bc6e958912c0b17966627 100644
--- a/doc/src/dihedral_class2.txt
+++ b/doc/src/dihedral_class2.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/dihedral_coeff.txt b/doc/src/dihedral_coeff.txt
index 5b43cbbe7f36d937fcb60334bde83a5911a2e61d..1db69e40d5739320b57139e56494749f6661e8d2 100644
--- a/doc/src/dihedral_coeff.txt
+++ b/doc/src/dihedral_coeff.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
@@ -74,9 +74,9 @@ the style to display the formula it computes and coefficients
 specified by the associated "dihedral_coeff"_dihedral_coeff.html command.
 
 Note that there are also additional dihedral styles submitted by users
-which are included in the LAMMPS distribution.  The list of these with
-links to the individual styles are given in the dihedral section of
-"this page"_Section_commands.html#cmd_5.
+which are included in the LAMMPS distribution.  The full list of all
+dihedral styles is on the "Commands bond"_Commands_bond.html#dihedral
+doc page.
 
 "dihedral_style none"_dihedral_none.html - turn off dihedral interactions
 "dihedral_style hybrid"_dihedral_hybrid.html - define multiple styles of dihedral interactions :ul
diff --git a/doc/src/dihedral_cosine_shift_exp.txt b/doc/src/dihedral_cosine_shift_exp.txt
index 483745be4181cea4d59631f0d7f9711abbdecd0d..7ef27e6bc966b129156159c9714e27a2cc050853 100644
--- a/doc/src/dihedral_cosine_shift_exp.txt
+++ b/doc/src/dihedral_cosine_shift_exp.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/dihedral_fourier.txt b/doc/src/dihedral_fourier.txt
index 0270139f68197e4217fa3f089a1c03dd4de4fbc3..f51cbc9c8cd8e1aeed0248730d7b633a3d636f74 100644
--- a/doc/src/dihedral_fourier.txt
+++ b/doc/src/dihedral_fourier.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/dihedral_harmonic.txt b/doc/src/dihedral_harmonic.txt
index a25a7969fe70b8402c1719caf312fc113ca97544..1eda0c5d02b8f1a7bbba646ad26d684cff7e7806 100644
--- a/doc/src/dihedral_harmonic.txt
+++ b/doc/src/dihedral_harmonic.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/dihedral_helix.txt b/doc/src/dihedral_helix.txt
index 814962a472b7b240ec61eae4ca3dc41762771552..3af4b410bcd24e4469ccdc50e9576fb81cc9539c 100644
--- a/doc/src/dihedral_helix.txt
+++ b/doc/src/dihedral_helix.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/dihedral_hybrid.txt b/doc/src/dihedral_hybrid.txt
index 8cb40eff44a66189d2ff37aadbd0c25ccd5a00c3..c9ca86680c175aca2188891523265ca4d2203f81 100644
--- a/doc/src/dihedral_hybrid.txt
+++ b/doc/src/dihedral_hybrid.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/dihedral_multi_harmonic.txt b/doc/src/dihedral_multi_harmonic.txt
index 62cad4141a6a27283eb725715de91dbbcf4721b7..7c22391923b37a065369b53c0871d20cd90710fe 100644
--- a/doc/src/dihedral_multi_harmonic.txt
+++ b/doc/src/dihedral_multi_harmonic.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/dihedral_nharmonic.txt b/doc/src/dihedral_nharmonic.txt
index a49979fa66ac13a24dbc22e75868337cda771b05..aa8f1e0d7fdc646fa6c06009909b750294e06613 100644
--- a/doc/src/dihedral_nharmonic.txt
+++ b/doc/src/dihedral_nharmonic.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/dihedral_none.txt b/doc/src/dihedral_none.txt
index 3ce2aa1729c6dfb31ad8924b20554f974cbc73b5..4c1ff2ea5d30fadd25949e613b6ec29e4cfa3fdb 100644
--- a/doc/src/dihedral_none.txt
+++ b/doc/src/dihedral_none.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/dihedral_opls.txt b/doc/src/dihedral_opls.txt
index 9b33173da4fe35a9890de29e601d812ff83505ec..f0cf91f30ad67fe914b376aef1c0c94ef5145955 100644
--- a/doc/src/dihedral_opls.txt
+++ b/doc/src/dihedral_opls.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/dihedral_quadratic.txt b/doc/src/dihedral_quadratic.txt
index f90c4b79f159591a0e6d639ae720da32a4be61e3..e65cf2dee86a2b108513f1d83a5cbfe29c8a0034 100644
--- a/doc/src/dihedral_quadratic.txt
+++ b/doc/src/dihedral_quadratic.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/dihedral_spherical.txt b/doc/src/dihedral_spherical.txt
index 7c17fbf5ef1c50aa939642c0eb224835c3721f0d..10a757e8986d6d9c5f450a84bfffc6be81221078 100644
--- a/doc/src/dihedral_spherical.txt
+++ b/doc/src/dihedral_spherical.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/dihedral_style.txt b/doc/src/dihedral_style.txt
index ca592b29b55415fde7c4306fa231ea35e0c5f40a..6aff3f0994777390eba737e8273524f770fd5e8e 100644
--- a/doc/src/dihedral_style.txt
+++ b/doc/src/dihedral_style.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
@@ -81,9 +81,9 @@ the style to display the formula it computes and coefficients
 specified by the associated "dihedral_coeff"_dihedral_coeff.html command.
 
 Note that there are also additional dihedral styles submitted by users
-which are included in the LAMMPS distribution.  The list of these with
-links to the individual styles are given in the dihedral section of
-"this page"_Section_commands.html#cmd_5.
+which are included in the LAMMPS distribution.  The full list of all
+dihedral styles is on the "Commands bond"_Commands_bond.html#dihedral
+doc page.
 
 "dihedral_style none"_dihedral_none.html - turn off dihedral interactions
 "dihedral_style zero"_dihedral_zero.html - topology but no interactions
diff --git a/doc/src/dihedral_table.txt b/doc/src/dihedral_table.txt
index 6a480fec93397fa262f39b42eee0e45c18bcf774..d722ef7c82a76c67ac0353a02b1656b8a8de73c0 100644
--- a/doc/src/dihedral_table.txt
+++ b/doc/src/dihedral_table.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/dihedral_table_cut.txt b/doc/src/dihedral_table_cut.txt
index 1c83d4ffa09f7221ac8c3859594abc754b9b28c4..cc7df8cdf9de397a6a91d9ec89bef542f5b5002a 100644
--- a/doc/src/dihedral_table_cut.txt
+++ b/doc/src/dihedral_table_cut.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/dihedral_zero.txt b/doc/src/dihedral_zero.txt
index 4d33126eeb76330e830fced4f9c55d7b47c86fdf..0c9995a5637c84571297f7b6a28a7162dc75b2fd 100644
--- a/doc/src/dihedral_zero.txt
+++ b/doc/src/dihedral_zero.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/dimension.txt b/doc/src/dimension.txt
index f079f17f996fafc87ec7d7a61f1c6aa15bfff40e..b7dde7652443a10a7199ddc46f9e7e70a21b3a09 100644
--- a/doc/src/dimension.txt
+++ b/doc/src/dimension.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/displace_atoms.txt b/doc/src/displace_atoms.txt
index 634add196b78fe249d4c42177482b69b05f5719e..b4afd5c3a9b9eb4af9666fc4b57f0b0df85810be 100644
--- a/doc/src/displace_atoms.txt
+++ b/doc/src/displace_atoms.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/dump.txt b/doc/src/dump.txt
index cd8bab2e65755be3a87fa38a51dfbafa4cffd10c..5b478b7301960bd536ef29158086c0c8b0f34023 100644
--- a/doc/src/dump.txt
+++ b/doc/src/dump.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/dump_cfg_uef.txt b/doc/src/dump_cfg_uef.txt
index e257f9c4f16d2f768ee4e688f3d71e0a0dd0c1cd..665be14be1330e0b902c73686d430f3ce904a315 100644
--- a/doc/src/dump_cfg_uef.txt
+++ b/doc/src/dump_cfg_uef.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/dump_h5md.txt b/doc/src/dump_h5md.txt
index 93c87d85b7a6064140b6cf320199d3cd99114e10..fbd682dad9cac9c112fc10ee30c31c922e00f4a0 100644
--- a/doc/src/dump_h5md.txt
+++ b/doc/src/dump_h5md.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/dump_image.txt b/doc/src/dump_image.txt
index fcc9b25b62bfd62e295af254be8f7ed40e21e9ef..06332b5dcf92a593ba084c50f9daaacfd7fb4ae3 100644
--- a/doc/src/dump_image.txt
+++ b/doc/src/dump_image.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/dump_modify.txt b/doc/src/dump_modify.txt
index 5365610d640ab7598a11554d6c20bb47de8cf442..73107d07f786e40d60407423551ba839033d7948 100644
--- a/doc/src/dump_modify.txt
+++ b/doc/src/dump_modify.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/dump_molfile.txt b/doc/src/dump_molfile.txt
index 7e68490a68e013c42f13883d9b7d1f9044929ce8..9fa04bd1aeed0de92d8fac59dfe3e8e0d83bee3e 100644
--- a/doc/src/dump_molfile.txt
+++ b/doc/src/dump_molfile.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/dump_netcdf.txt b/doc/src/dump_netcdf.txt
index 70111a36a8b28d9654db6779426090b7e37b507d..b1c63736514d00e4c35e1056aebab49d18f1cc54 100644
--- a/doc/src/dump_netcdf.txt
+++ b/doc/src/dump_netcdf.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/dump_vtk.txt b/doc/src/dump_vtk.txt
index d4d28c81fca69cea2fb65d72e940acf4de0fdcb0..afc6099534eb5c80ffb18461f0f8426ea50bcc67 100644
--- a/doc/src/dump_vtk.txt
+++ b/doc/src/dump_vtk.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/echo.txt b/doc/src/echo.txt
index 3141c7a719bcb0de5d39366183a269f761bd0230..dc6918dc8981af7b971e3e3cd406d29c6aa2e8b7 100644
--- a/doc/src/echo.txt
+++ b/doc/src/echo.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix.txt b/doc/src/fix.txt
index a51dc1637defcc49c51ec1283c891d5f347a98b8..fd966b5bd9916407648f6db1ea7f01d293faef10 100644
--- a/doc/src/fix.txt
+++ b/doc/src/fix.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
@@ -151,16 +151,20 @@ for further info.
 
 :line
 
-Each fix style has its own documentation page which describes its
-arguments and what it does, as listed below.  Here is an alphabetic
-list of fix styles available in LAMMPS.  They are also given in more
-compact form in the Fix section of "this
-page"_Section_commands.html#cmd_5.
+Each fix style has its own doc page which describes its arguments and
+what it does, as listed below.  Here is an alphabetic list of fix
+styles available in LAMMPS.  They are also listed in more compact form
+on the "Commands fix"_Commands_fix.html doc page.
 
 There are also additional fix styles (not listed here) submitted by
-users which are included in the LAMMPS distribution.  The list of
-these with links to the individual styles are given in the fix section
-of "this page"_Section_commands.html#cmd_5.
+users which are included in the LAMMPS distribution.  The full list of
+all fix styles is on the "Commands fix"_Commands_fix.html doc page.
+
+There are also additional accelerated fix styles included in the
+LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.
+The individual style names on the "Commands fix"_Commands_fix.html doc
+page are followed by one or more of (g,i,k,o,t) to indicate which
+accerlerated styles exist.
 
 "adapt"_fix_adapt.html - change a simulation parameter over time
 "addforce"_fix_addforce.html - add a force to each atom
diff --git a/doc/src/fix_adapt.txt b/doc/src/fix_adapt.txt
index 0764d04e6d33cc31530f937b4d72fa23d410bd97..0ca28fb8694c6c5c4d4c2d39ab649dc79a9152a3 100644
--- a/doc/src/fix_adapt.txt
+++ b/doc/src/fix_adapt.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_adapt_fep.txt b/doc/src/fix_adapt_fep.txt
index 43c87a1601d34c4a4ba2d8c0b24b543d85f5476c..7e30a1d29d5b4354b7fae0761f50fc7d8d6e8dd3 100644
--- a/doc/src/fix_adapt_fep.txt
+++ b/doc/src/fix_adapt_fep.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_addforce.txt b/doc/src/fix_addforce.txt
index c77cdb62afa5a1bd278c2cb7b522a7e426b9be0e..51be39fdb2b72156560b0d85c56b6fc1a517056f 100644
--- a/doc/src/fix_addforce.txt
+++ b/doc/src/fix_addforce.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_addtorque.txt b/doc/src/fix_addtorque.txt
index 589cb37cc0c15dea8b83483fe81bd2c9d99ee0b7..c80fad26da1c5e40d8a96f42c034f2f8b18cdb86 100644
--- a/doc/src/fix_addtorque.txt
+++ b/doc/src/fix_addtorque.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_append_atoms.txt b/doc/src/fix_append_atoms.txt
index ba7b4a3e74fae7dd2b357a97b56a8c1b9c6a6423..c6af361afcfe24a5da8cc97c4e917238fe981ab0 100644
--- a/doc/src/fix_append_atoms.txt
+++ b/doc/src/fix_append_atoms.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_atc.txt b/doc/src/fix_atc.txt
index af3270ff528ef9d06696a5beb6ea4692f9d49cec..6de917e5714e6b68537b1180a7f7c5b9769cec81 100644
--- a/doc/src/fix_atc.txt
+++ b/doc/src/fix_atc.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_atom_swap.txt b/doc/src/fix_atom_swap.txt
index 0b3be3ce5e6250be3c5a115d0f06e55cf3ca788f..c1d84dade1954b2a8d1ec15bb699cb99a5d1e1ae 100644
--- a/doc/src/fix_atom_swap.txt
+++ b/doc/src/fix_atom_swap.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_ave_atom.txt b/doc/src/fix_ave_atom.txt
index 05bd0f6fa728c204aefedf2fa40fa3ae1491292c..10deaf64cd2900ee76be741c7a835ed2d0e04175 100644
--- a/doc/src/fix_ave_atom.txt
+++ b/doc/src/fix_ave_atom.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_ave_chunk.txt b/doc/src/fix_ave_chunk.txt
index e9d0ef7e725a28f1dba055f7fa17d87199963f3b..d331e512953b8c32817f0aef973ca99d4289216a 100644
--- a/doc/src/fix_ave_chunk.txt
+++ b/doc/src/fix_ave_chunk.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_ave_correlate.txt b/doc/src/fix_ave_correlate.txt
index 74ce3f340ee23a7b4179d1e6bf1203ce6982bb46..22e8768f1d04444df665513b4d5651c1e31cdbde 100644
--- a/doc/src/fix_ave_correlate.txt
+++ b/doc/src/fix_ave_correlate.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_ave_correlate_long.txt b/doc/src/fix_ave_correlate_long.txt
index 7b4bc53701cf9232ca87cd6cec1ceee38ac67690..ac0ef873aac6ae3cd90fca5077a3cc86e3160645 100644
--- a/doc/src/fix_ave_correlate_long.txt
+++ b/doc/src/fix_ave_correlate_long.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_ave_histo.txt b/doc/src/fix_ave_histo.txt
index e2fd2e04e80d465bca9ab382f1dac799b326591d..f1da130ff7e25c84528bda44cc2e582a8e910274 100644
--- a/doc/src/fix_ave_histo.txt
+++ b/doc/src/fix_ave_histo.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_ave_time.txt b/doc/src/fix_ave_time.txt
index e973a3636054d7565aa1f0406e0c803ea8a4b189..a53e318d3fd83a3aab0382876b305681ed17ee0b 100644
--- a/doc/src/fix_ave_time.txt
+++ b/doc/src/fix_ave_time.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_aveforce.txt b/doc/src/fix_aveforce.txt
index 3497b33ef4d600ac4bf0c7858ac72128a667d466..1fc7e4a18dd8f5efd1b84a21c0a785797be692a1 100644
--- a/doc/src/fix_aveforce.txt
+++ b/doc/src/fix_aveforce.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_balance.txt b/doc/src/fix_balance.txt
index b98fd85c3bf85d4f9a0c65da676020a696f30d44..2de17cdd2a992344886a3eec4d92bc8e3d15b893 100644
--- a/doc/src/fix_balance.txt
+++ b/doc/src/fix_balance.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_bocs.txt b/doc/src/fix_bocs.txt
index f53b7c785c251240a0d325b820545f342ce21c06..f5bbc8a2519dcef980bdce8e3d08eb22a8789867 100644
--- a/doc/src/fix_bocs.txt
+++ b/doc/src/fix_bocs.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_bond_break.txt b/doc/src/fix_bond_break.txt
index b43053c461a41b6de74339ca4327823fdbeeb973..bdb2f2a8624869a8552992b246a111cb3396e7c5 100644
--- a/doc/src/fix_bond_break.txt
+++ b/doc/src/fix_bond_break.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_bond_create.txt b/doc/src/fix_bond_create.txt
index a55ba1ff6ee6dc963f597adb09e02b3205fcfc37..ab34433cecf631fbb8b9cff9fb87d43b87d7c07d 100644
--- a/doc/src/fix_bond_create.txt
+++ b/doc/src/fix_bond_create.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_bond_react.txt b/doc/src/fix_bond_react.txt
index 006f59100f8bb4ad47aca21e35e31cc1c529e211..883968e012557e2ee8d13eddef15b8bc1f6873ef 100644
--- a/doc/src/fix_bond_react.txt
+++ b/doc/src/fix_bond_react.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_bond_swap.txt b/doc/src/fix_bond_swap.txt
index 8d5df7e4e0b99ac66062cae34f6837ab6108d664..a829171f333aa3aa850fbc04c659eae6ac61ad40 100644
--- a/doc/src/fix_bond_swap.txt
+++ b/doc/src/fix_bond_swap.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_box_relax.txt b/doc/src/fix_box_relax.txt
index a625f0c5b84719c2308637cf87d29652b50171c3..8e21ec2c748963302db1fd9876cc855d0d1e35d8 100644
--- a/doc/src/fix_box_relax.txt
+++ b/doc/src/fix_box_relax.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_cmap.txt b/doc/src/fix_cmap.txt
index d352f0e65216a8aad9f932df9bf1a34b62576866..6f3769fafe6a634770dcdedb8908540972ee5d70 100644
--- a/doc/src/fix_cmap.txt
+++ b/doc/src/fix_cmap.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_colvars.txt b/doc/src/fix_colvars.txt
index 2d3000e6ea2649d745b4d4a82cc556bdf34b83e3..4a1d84de64a458dbc56999885ca8246a03ba21ed 100644
--- a/doc/src/fix_colvars.txt
+++ b/doc/src/fix_colvars.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_controller.txt b/doc/src/fix_controller.txt
index 710642c0ea4fc384fd2e00d1847432402e85056c..7458f1bcfa015985158cbb3a1148fe625eb964e4 100644
--- a/doc/src/fix_controller.txt
+++ b/doc/src/fix_controller.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_deform.txt b/doc/src/fix_deform.txt
index 09261e24235affd5544f82febf56f0f53eeecadb..e92d1e6b19c5943d4de785c916738fdd10dc8ef0 100644
--- a/doc/src/fix_deform.txt
+++ b/doc/src/fix_deform.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_deposit.txt b/doc/src/fix_deposit.txt
index 285e720555264bbb623071ad74882783582e4ff6..277ca8777ad7409e586eb16344df34168786c165 100644
--- a/doc/src/fix_deposit.txt
+++ b/doc/src/fix_deposit.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_dpd_energy.txt b/doc/src/fix_dpd_energy.txt
index 4f2b5d573f54679a6f8930f7feeb61f4fc59acfa..f539bc534e76b7e667938ce4dcd78a2f9501ed4e 100644
--- a/doc/src/fix_dpd_energy.txt
+++ b/doc/src/fix_dpd_energy.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_dpd_source.txt b/doc/src/fix_dpd_source.txt
index bbfc99e8c8e1262585fa8a37df286208cf9662bb..04af9a28a184676e1ebc51f67dc13eb5340787a0 100644
--- a/doc/src/fix_dpd_source.txt
+++ b/doc/src/fix_dpd_source.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_drag.txt b/doc/src/fix_drag.txt
index a67ec6aaf2603dd2ddddc897b4705959714df69b..92e68d13a447e07f9f83c4f5c2a1d1666cbdef53 100644
--- a/doc/src/fix_drag.txt
+++ b/doc/src/fix_drag.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_drude.txt b/doc/src/fix_drude.txt
index 4a3d30a9cae982dcccef9c4e6d86063844b5a90d..80eb79201b2a8e5e0222337209bbacb074c6c78e 100644
--- a/doc/src/fix_drude.txt
+++ b/doc/src/fix_drude.txt
@@ -3,7 +3,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_drude_transform.txt b/doc/src/fix_drude_transform.txt
index 54cdfa956ed6dd86a6978338cc82041685906f98..8864cc4eb66242f220bbc50a3e87e2e9abb5385a 100644
--- a/doc/src/fix_drude_transform.txt
+++ b/doc/src/fix_drude_transform.txt
@@ -9,7 +9,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_dt_reset.txt b/doc/src/fix_dt_reset.txt
index 428128fedaa977996ad48875b3595f9f4f46612b..be4fbd255b58983cd52ac8a9fbb1e4144b5a2f6c 100644
--- a/doc/src/fix_dt_reset.txt
+++ b/doc/src/fix_dt_reset.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_efield.txt b/doc/src/fix_efield.txt
index a248a03b07e49137d3b9973769800255bdaeae6d..b5a43f68aa76b5a205f50df3e6ff9325099711bb 100644
--- a/doc/src/fix_efield.txt
+++ b/doc/src/fix_efield.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_ehex.txt b/doc/src/fix_ehex.txt
index 40752a811fdabe06285d0f980ee9cdd253ac10e6..cfcc917d012ba1dca5ff08afd75fb718bb101f82 100644
--- a/doc/src/fix_ehex.txt
+++ b/doc/src/fix_ehex.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_enforce2d.txt b/doc/src/fix_enforce2d.txt
index b0d8c691b5a31cc9b6336f99a174b082ce3620cb..2925e44bda17ef8cf023a9e41c0513694d4c50fa 100644
--- a/doc/src/fix_enforce2d.txt
+++ b/doc/src/fix_enforce2d.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_eos_cv.txt b/doc/src/fix_eos_cv.txt
index 4c973043353c307790aa15447d70ffe77f375e7d..b94e2c64a97ebd8373b3a3dafcee2ab9ecad6ed5 100644
--- a/doc/src/fix_eos_cv.txt
+++ b/doc/src/fix_eos_cv.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_eos_table.txt b/doc/src/fix_eos_table.txt
index 42778d79781c80ced6c90855f7fefe78f62d7207..743c51f4157cfeffc8c59840f9f95ab3132a3d74 100644
--- a/doc/src/fix_eos_table.txt
+++ b/doc/src/fix_eos_table.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_eos_table_rx.txt b/doc/src/fix_eos_table_rx.txt
index f74a838c4776aa955128ce0681a99f95cc391e08..f9deab61c8acebfb5ffe69966b1880e7cacff369 100644
--- a/doc/src/fix_eos_table_rx.txt
+++ b/doc/src/fix_eos_table_rx.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_evaporate.txt b/doc/src/fix_evaporate.txt
index be8b3519862a6f2e029ea81122a431f93f646220..6237a137fd0aa8c719d5f96f7791ebb176b669da 100644
--- a/doc/src/fix_evaporate.txt
+++ b/doc/src/fix_evaporate.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_external.txt b/doc/src/fix_external.txt
index bf80b1b2313f03556f9d65f33c20ddd840a5bd2d..1dec226414c9f7e62b13b3d60a2f34efc6326ccd 100644
--- a/doc/src/fix_external.txt
+++ b/doc/src/fix_external.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_filter_corotate.txt b/doc/src/fix_filter_corotate.txt
index a75a3b7b44f14a5c5000fa6fed75ced2a157b182..d1e5e12f3ef1b764d4d2d9cc35a5d8f504c27a4e 100644
--- a/doc/src/fix_filter_corotate.txt
+++ b/doc/src/fix_filter_corotate.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_flow_gauss.txt b/doc/src/fix_flow_gauss.txt
index 0980076062c123aa796c18c373a7c4df3a0a5b7a..843c2a66a5505d5b3c7051fd9d84897a99ea4138 100644
--- a/doc/src/fix_flow_gauss.txt
+++ b/doc/src/fix_flow_gauss.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_freeze.txt b/doc/src/fix_freeze.txt
index 43714df8023d46dda7aaaa2c3c3414b8b64893b0..76a9fd3b1a2d3f3ffc8372a2cebac2ac85f9fb6f 100644
--- a/doc/src/fix_freeze.txt
+++ b/doc/src/fix_freeze.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_gcmc.txt b/doc/src/fix_gcmc.txt
index 9630d856beaff57a77d8647e8ea30d40e0144976..394690ea5d173b898b51acc6ee9b2094aa5d26b1 100644
--- a/doc/src/fix_gcmc.txt
+++ b/doc/src/fix_gcmc.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_gld.txt b/doc/src/fix_gld.txt
index 06ac5d68cb373a10bdb2a3e1a44d1b604dc1ce81..1c5db6157ddaca593ffc5fc70ebc59613038ae88 100644
--- a/doc/src/fix_gld.txt
+++ b/doc/src/fix_gld.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_gle.txt b/doc/src/fix_gle.txt
index d91dd8dee98c6cbd8d778491e9da181d8b3062c7..9fdc72bf9f206f9b5a6e55267638af159810beeb 100644
--- a/doc/src/fix_gle.txt
+++ b/doc/src/fix_gle.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_gravity.txt b/doc/src/fix_gravity.txt
index 786f1456083fd81dad6f9d616e7f4432d3c82b73..832c677f81559e3893e643dc32330d0e9699a1f7 100644
--- a/doc/src/fix_gravity.txt
+++ b/doc/src/fix_gravity.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_grem.txt b/doc/src/fix_grem.txt
index 661f68ed99cf21d5c5a08514d78dff411a28880e..506e266505a54248fee381d4135802122fd86aba 100644
--- a/doc/src/fix_grem.txt
+++ b/doc/src/fix_grem.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_halt.txt b/doc/src/fix_halt.txt
index 55f313e40f8d57e35eecf1a7542d0ecdf664aa2a..ec117518d285d488b28a78e552280f1ac7b81c17 100644
--- a/doc/src/fix_halt.txt
+++ b/doc/src/fix_halt.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_heat.txt b/doc/src/fix_heat.txt
index a0e9b945fc087047e34f12ad036e43046f0f5499..6db75926091bf4aac4e7fafa5679dab9e58231f4 100644
--- a/doc/src/fix_heat.txt
+++ b/doc/src/fix_heat.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_imd.txt b/doc/src/fix_imd.txt
index 1a1f11c2cf3d3ff8298c9b7ea97396b2657ce2de..8e21a1619b8647b0ba6c497540ac2b7c4973b36a 100644
--- a/doc/src/fix_imd.txt
+++ b/doc/src/fix_imd.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_indent.txt b/doc/src/fix_indent.txt
index 1f67c0b24282f3508d50cf7501824eca7010f80d..9931793c0bffbc1398bee31bf7a5c87cda692d7d 100644
--- a/doc/src/fix_indent.txt
+++ b/doc/src/fix_indent.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_ipi.txt b/doc/src/fix_ipi.txt
index 07e8025d77061db6e41fd3c3e765898664f2ffcd..eba30ef08821d7c55ab06270d18a4300da293de5 100644
--- a/doc/src/fix_ipi.txt
+++ b/doc/src/fix_ipi.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_langevin.txt b/doc/src/fix_langevin.txt
index 769b18860488fbd39d591141f2c342d66bf5fa4c..4d7728cdba4b918d1cc8926f2aaef266bc20a42b 100644
--- a/doc/src/fix_langevin.txt
+++ b/doc/src/fix_langevin.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_langevin_drude.txt b/doc/src/fix_langevin_drude.txt
index bda8ec78811eed5db6bc73f7a8d21c44706d22dd..19a3f87ffc0a20fb66038671e6a76529c5a1db6d 100644
--- a/doc/src/fix_langevin_drude.txt
+++ b/doc/src/fix_langevin_drude.txt
@@ -9,7 +9,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_langevin_eff.txt b/doc/src/fix_langevin_eff.txt
index ef22e99bcf366037b1cdbb543098d793dbda5ad3..cf42f9c036b2dc4da5a9f2afb98296d8a78862d4 100644
--- a/doc/src/fix_langevin_eff.txt
+++ b/doc/src/fix_langevin_eff.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_langevin_spin.txt b/doc/src/fix_langevin_spin.txt
index b089cd7f58148c74a805080cccde0ac2cb600143..1b1936376de0fe29450cf9b4c2db7e298e6d64ab 100644
--- a/doc/src/fix_langevin_spin.txt
+++ b/doc/src/fix_langevin_spin.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_latte.txt b/doc/src/fix_latte.txt
index 4f7e99dea887c421b79d4d523d9702672134dac5..9bc589520bc3689a4ad4370f99e92b9977bb209c 100644
--- a/doc/src/fix_latte.txt
+++ b/doc/src/fix_latte.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_lb_fluid.txt b/doc/src/fix_lb_fluid.txt
index 925ca991c4e95eeba71d5e4c425aaf59670edf9d..5347f0147f4be26b5e3b61877084925003c4fbf4 100644
--- a/doc/src/fix_lb_fluid.txt
+++ b/doc/src/fix_lb_fluid.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_lb_momentum.txt b/doc/src/fix_lb_momentum.txt
index 78a1f497eb50ccc0d8f3dc937d5ac662fc89eb41..a58c5d257eabeb012284a3fd2dd3e2eecd20c1d7 100644
--- a/doc/src/fix_lb_momentum.txt
+++ b/doc/src/fix_lb_momentum.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_lb_pc.txt b/doc/src/fix_lb_pc.txt
index f93d02f677ff434181cef3b666616e44f729e2a5..bd121b7813253cb3b9e547235db88cdc85e5e472 100644
--- a/doc/src/fix_lb_pc.txt
+++ b/doc/src/fix_lb_pc.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_lb_rigid_pc_sphere.txt b/doc/src/fix_lb_rigid_pc_sphere.txt
index 50e91df849fd7666cdf572e6beef9b863282a3a4..bc8fa2ea257212f588dabe01b824d98ff4289a1b 100644
--- a/doc/src/fix_lb_rigid_pc_sphere.txt
+++ b/doc/src/fix_lb_rigid_pc_sphere.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_lb_viscous.txt b/doc/src/fix_lb_viscous.txt
index 27f089496ef61861579d1f113646d84bb2020916..7bbdd204e34d1a4fae91fcf2f4bb2aa4c32fefbf 100644
--- a/doc/src/fix_lb_viscous.txt
+++ b/doc/src/fix_lb_viscous.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_lineforce.txt b/doc/src/fix_lineforce.txt
index ad651862f6f6f55fa10c807d9065c246ad8261d3..3114ed62501e3c3c3581ae06a154c45de0d92996 100644
--- a/doc/src/fix_lineforce.txt
+++ b/doc/src/fix_lineforce.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_manifoldforce.txt b/doc/src/fix_manifoldforce.txt
index fe8a04051b749bce9b152363a41e2face2007b5e..aa32a875bfe2f77de00cdbee7f87085af8443a94 100644
--- a/doc/src/fix_manifoldforce.txt
+++ b/doc/src/fix_manifoldforce.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_meso.txt b/doc/src/fix_meso.txt
index 95f58bedaaf7ab044c2361c6c40829b48cd2cdd7..8f5ad29929313fc6d1b31169b140b5dad0d46959 100644
--- a/doc/src/fix_meso.txt
+++ b/doc/src/fix_meso.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_meso_stationary.txt b/doc/src/fix_meso_stationary.txt
index 3b197c079f0b1d6ab8d0eb8c8dafa667612f6382..38d26b34d67ad7d0a38eec70c7f28583394778eb 100644
--- a/doc/src/fix_meso_stationary.txt
+++ b/doc/src/fix_meso_stationary.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_modify.txt b/doc/src/fix_modify.txt
index 308bba1ac31fdf9a7cbd45ec1da50122cd46bcb9..ddb5f9a4cd4346e6f0d3195a101445c15eaedfde 100644
--- a/doc/src/fix_modify.txt
+++ b/doc/src/fix_modify.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_momentum.txt b/doc/src/fix_momentum.txt
index 28fd2addf2ed44001032df0cccf01f7fb390aed4..f7fe35be2a9fd3825b82db9a0cd3d3cca76dfb56 100644
--- a/doc/src/fix_momentum.txt
+++ b/doc/src/fix_momentum.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_move.txt b/doc/src/fix_move.txt
index 9a1d25b623726e3ebb7205f2f460673b7d026264..08f38d0ed65f2dec91bfec38fd572b8e82e75770 100644
--- a/doc/src/fix_move.txt
+++ b/doc/src/fix_move.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_mscg.txt b/doc/src/fix_mscg.txt
index 7d16967955d1d9988636092d721fe40902386054..aadc3caf5aa909c8ff32f23d51bcac2d3f0919ab 100644
--- a/doc/src/fix_mscg.txt
+++ b/doc/src/fix_mscg.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_msst.txt b/doc/src/fix_msst.txt
index d79b549580c4aa0a9c28d55706494b26059a3d4c..91ffbbb0fa147ea6e520ac75658d114198654da6 100644
--- a/doc/src/fix_msst.txt
+++ b/doc/src/fix_msst.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_mvv_dpd.txt b/doc/src/fix_mvv_dpd.txt
index 7a07642c54788e450e76e96860b75a932e998542..1e9bf631fde813d95546bcc6638b3c24172a0e79 100644
--- a/doc/src/fix_mvv_dpd.txt
+++ b/doc/src/fix_mvv_dpd.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_neb.txt b/doc/src/fix_neb.txt
index 5cfefbf81901b12622f3cde8d0cd726f58c652e1..5341d6999c4e6b0f5220af5d5d77ebd331176fbb 100644
--- a/doc/src/fix_neb.txt
+++ b/doc/src/fix_neb.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_nh.txt b/doc/src/fix_nh.txt
index d18f4a3e166d921dcbda94353d8f2b4b6122ab9c..f6b155e2db2c66bad86e479a8d1ee67d86fd51a7 100644
--- a/doc/src/fix_nh.txt
+++ b/doc/src/fix_nh.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_nh_eff.txt b/doc/src/fix_nh_eff.txt
index 1731f1f3317a6f982a564c256e593439a8f73423..afb319bfa51f6c518b213f63f75cbab14741e0bc 100644
--- a/doc/src/fix_nh_eff.txt
+++ b/doc/src/fix_nh_eff.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_nh_uef.txt b/doc/src/fix_nh_uef.txt
index bde1818371f2c4bcab0bafe11e19c4b04df107b8..0e73c57e089b44643834f1b78fad2c1f046281f4 100644
--- a/doc/src/fix_nh_uef.txt
+++ b/doc/src/fix_nh_uef.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_nph_asphere.txt b/doc/src/fix_nph_asphere.txt
index ff8c300c475d0770e7a345ecfb7e1282a2ea3bbe..6bfd9d3fe26085cff9f1d3c5c0b32fbbd5c5948a 100644
--- a/doc/src/fix_nph_asphere.txt
+++ b/doc/src/fix_nph_asphere.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_nph_body.txt b/doc/src/fix_nph_body.txt
index 9263470e9eba1d609f98969ae880751606d31db7..377e1980eb3cf8c9c46b41baa6a14b2e379c7816 100644
--- a/doc/src/fix_nph_body.txt
+++ b/doc/src/fix_nph_body.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_nph_sphere.txt b/doc/src/fix_nph_sphere.txt
index ba3b2f6c06f67cf2079f022d13a41c05599ba01a..8b7639c4c6a7467e9107db127699efabea8a8993 100644
--- a/doc/src/fix_nph_sphere.txt
+++ b/doc/src/fix_nph_sphere.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_nphug.txt b/doc/src/fix_nphug.txt
index 1276a5697d6c3b8f6e43ffcacc989fc0974de2ec..0bd5153152b4afdcd8a0048b0472df81ad63ed08 100644
--- a/doc/src/fix_nphug.txt
+++ b/doc/src/fix_nphug.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_npt_asphere.txt b/doc/src/fix_npt_asphere.txt
index a21caa1042df33ec57a08e5ffa0eb949b62dadaa..9c95a80d3310a08e3e8ddecd12af471419340773 100644
--- a/doc/src/fix_npt_asphere.txt
+++ b/doc/src/fix_npt_asphere.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_npt_body.txt b/doc/src/fix_npt_body.txt
index 0f678a1b7d422fa910d4b217df7b63698ddaf4d7..0d2b797299dd4d3c803e96cbfb1f4030ac13c032 100644
--- a/doc/src/fix_npt_body.txt
+++ b/doc/src/fix_npt_body.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_npt_sphere.txt b/doc/src/fix_npt_sphere.txt
index 862f95603f8ba3fb2e187a8d567147d0241d965b..dcb25d1c737b39f3a2bcea9a4e01eb1a011fbb60 100644
--- a/doc/src/fix_npt_sphere.txt
+++ b/doc/src/fix_npt_sphere.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_nve.txt b/doc/src/fix_nve.txt
index 8aa4197a60038de6ecea9271876e124d3a6aab55..e446b273977b4dd05865de697b3d10af144bb149 100644
--- a/doc/src/fix_nve.txt
+++ b/doc/src/fix_nve.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_nve_asphere.txt b/doc/src/fix_nve_asphere.txt
index b9ee48f9dd2a635691d343262f38fa136316e0cd..b7fb3e922ce418d666b0cfe9b87170daa7c195ed 100644
--- a/doc/src/fix_nve_asphere.txt
+++ b/doc/src/fix_nve_asphere.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_nve_asphere_noforce.txt b/doc/src/fix_nve_asphere_noforce.txt
index 164e3db10414b4f3ac22284d5519dca946116521..e57417bda5e1657ca69a621840ea82f2199b14b1 100644
--- a/doc/src/fix_nve_asphere_noforce.txt
+++ b/doc/src/fix_nve_asphere_noforce.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_nve_body.txt b/doc/src/fix_nve_body.txt
index 369642537427be0fbde067c230eff0cea039b360..d072bfa1611770921b5e97f7f1fb2bce2128c748 100644
--- a/doc/src/fix_nve_body.txt
+++ b/doc/src/fix_nve_body.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_nve_dot.txt b/doc/src/fix_nve_dot.txt
index 0e0c8f8ecf5d9d02f3a6982ee1ae3e5cd8aa3746..1041a248d8784a0cfae575f1d5a515a4e2c76e35 100644
--- a/doc/src/fix_nve_dot.txt
+++ b/doc/src/fix_nve_dot.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_nve_dotc_langevin.txt b/doc/src/fix_nve_dotc_langevin.txt
index 93d875bca5436127526cdb5f1dad6b170d6c46b3..68c1b4232830fe1a2eaaadaf8ce832474a394f13 100644
--- a/doc/src/fix_nve_dotc_langevin.txt
+++ b/doc/src/fix_nve_dotc_langevin.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_nve_eff.txt b/doc/src/fix_nve_eff.txt
index 608e5e12adadc2dc98de0739a8368f762c0a14e7..7343ddc4292df0f02e7eadef7829ec8041ccae5b 100644
--- a/doc/src/fix_nve_eff.txt
+++ b/doc/src/fix_nve_eff.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_nve_limit.txt b/doc/src/fix_nve_limit.txt
index ffaffd59b798aa98e3026bc6c278942bfdc6c838..8c8c66a0dac92424d08b577ee3957277e81e6ce2 100644
--- a/doc/src/fix_nve_limit.txt
+++ b/doc/src/fix_nve_limit.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_nve_line.txt b/doc/src/fix_nve_line.txt
index a919e648e16d1ec9c7227061b8103359a4a71fe5..dd5101489b00d27a707ac4c044bed5f4a84be643 100644
--- a/doc/src/fix_nve_line.txt
+++ b/doc/src/fix_nve_line.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_nve_manifold_rattle.txt b/doc/src/fix_nve_manifold_rattle.txt
index 89922ea80d3333f4e06504f3c25c8cca303e3505..b333d093fb8eec0ce08d16c8affb3a2cf481c802 100644
--- a/doc/src/fix_nve_manifold_rattle.txt
+++ b/doc/src/fix_nve_manifold_rattle.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_nve_noforce.txt b/doc/src/fix_nve_noforce.txt
index c1a4f76eafbc98c030658b795f6da2ed93c96613..da8d16bbb7c1c49bdee6af72dc4c1bcc2f355a1e 100644
--- a/doc/src/fix_nve_noforce.txt
+++ b/doc/src/fix_nve_noforce.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_nve_sphere.txt b/doc/src/fix_nve_sphere.txt
index 36c4178de99c1ee998aacfdd5e6b257d4c544fef..6e259bdb8e7803482ee894d68d2a354dcefc0e6f 100644
--- a/doc/src/fix_nve_sphere.txt
+++ b/doc/src/fix_nve_sphere.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_nve_spin.txt b/doc/src/fix_nve_spin.txt
index f4b38c270bc4b40b73c570ce590f39fc282bad1f..e31185bc889e785030dbef61a36019a7ba086af0 100644
--- a/doc/src/fix_nve_spin.txt
+++ b/doc/src/fix_nve_spin.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_nve_tri.txt b/doc/src/fix_nve_tri.txt
index 9c03eb872a0ab3cacab0e092ef83aaa745abba84..ebdda19e36428828bdbeb6558b3202cc00982a80 100644
--- a/doc/src/fix_nve_tri.txt
+++ b/doc/src/fix_nve_tri.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_nvk.txt b/doc/src/fix_nvk.txt
index 2106ee52354062d9b2a1d9ce2ddcd7ae68f2b31d..e3189f8e8a3981b76f848f64080b6baa50500738 100644
--- a/doc/src/fix_nvk.txt
+++ b/doc/src/fix_nvk.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_nvt_asphere.txt b/doc/src/fix_nvt_asphere.txt
index 031c60e4becebe29f3279bbfc2b624d54d45ec0d..7b9763717574062e64b9e812bd201d8174cb4880 100644
--- a/doc/src/fix_nvt_asphere.txt
+++ b/doc/src/fix_nvt_asphere.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_nvt_body.txt b/doc/src/fix_nvt_body.txt
index 80de7fd7c3ce275453ecfa3a09b90338dbe6e3c7..4493a892777221ee5c4375769438f8c02cfaf570 100644
--- a/doc/src/fix_nvt_body.txt
+++ b/doc/src/fix_nvt_body.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_nvt_manifold_rattle.txt b/doc/src/fix_nvt_manifold_rattle.txt
index 4261f9a4dbda5c205c940d7b070d7fb5601cec39..1b4ad7916626ea3550b69c4aef84514318acb30e 100644
--- a/doc/src/fix_nvt_manifold_rattle.txt
+++ b/doc/src/fix_nvt_manifold_rattle.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_nvt_sllod.txt b/doc/src/fix_nvt_sllod.txt
index bb3c09293923a9d97d1dbd6469de09c47ffcf4ed..9eb506536910f574867121e26d6dee23ff8071a0 100644
--- a/doc/src/fix_nvt_sllod.txt
+++ b/doc/src/fix_nvt_sllod.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_nvt_sllod_eff.txt b/doc/src/fix_nvt_sllod_eff.txt
index 408eb1da01f99bc026a4581bedbb4ecff2a91b6a..0200d5cb002312980fb21344687676dd06d74fee 100644
--- a/doc/src/fix_nvt_sllod_eff.txt
+++ b/doc/src/fix_nvt_sllod_eff.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_nvt_sphere.txt b/doc/src/fix_nvt_sphere.txt
index 897d5606d717cd668b997b7b59d352cd86c477f4..a87e4abe677ed4c44d6b54470e5d2ee9539d8f7c 100644
--- a/doc/src/fix_nvt_sphere.txt
+++ b/doc/src/fix_nvt_sphere.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_oneway.txt b/doc/src/fix_oneway.txt
index d9217ab14b5428947d7bfc56c7eab7d50c118002..433ceb50f244e7570b83979dffed7c5b34d7a8ca 100644
--- a/doc/src/fix_oneway.txt
+++ b/doc/src/fix_oneway.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_orient.txt b/doc/src/fix_orient.txt
index c57cccd322b7becff9c35e9fc6845fd2695dd961..7552bea8c5bcfb73867322c90f502887276aacf9 100644
--- a/doc/src/fix_orient.txt
+++ b/doc/src/fix_orient.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_phonon.txt b/doc/src/fix_phonon.txt
index 63df4e68012924297236eec9042a9825781e0220..30e5864e3d16af76cdc86ea021c0cf80fda6b2ff 100644
--- a/doc/src/fix_phonon.txt
+++ b/doc/src/fix_phonon.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_pimd.txt b/doc/src/fix_pimd.txt
index 8958063d2e61f4e4ca41ce1c2f5d63dcb1bb2780..b61b3f3065a7c0c57f5994a2a2a23d6ed8778407 100644
--- a/doc/src/fix_pimd.txt
+++ b/doc/src/fix_pimd.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_planeforce.txt b/doc/src/fix_planeforce.txt
index 4a74301066585b0d1b81e53a725fe2b0ef879ed7..ffe1952e31a2f412ce23edf7b36a891b42f70f38 100644
--- a/doc/src/fix_planeforce.txt
+++ b/doc/src/fix_planeforce.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_poems.txt b/doc/src/fix_poems.txt
index 0690923b4549ebd04681b7a36e731868ca8caaf0..1a79c2a048fb75dc04935e978fdc50ae84ab9e69 100644
--- a/doc/src/fix_poems.txt
+++ b/doc/src/fix_poems.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_pour.txt b/doc/src/fix_pour.txt
index 4b86405522f49793b1405af5699f51374aeac79d..e58d8ebc3ad90069a45cfd92ae504ce4656305dc 100644
--- a/doc/src/fix_pour.txt
+++ b/doc/src/fix_pour.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_precession_spin.txt b/doc/src/fix_precession_spin.txt
index bc18fa0e8c277602caa2bb2305267ac48aafdd7d..fafe78448be133680f5b22711403262f1f28086b 100644
--- a/doc/src/fix_precession_spin.txt
+++ b/doc/src/fix_precession_spin.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_press_berendsen.txt b/doc/src/fix_press_berendsen.txt
index 0e41abd1f807ea746407a284eec13668d4ba28a2..7f47a29ba35fa0a1ca9cc0c3aebd51917131564d 100644
--- a/doc/src/fix_press_berendsen.txt
+++ b/doc/src/fix_press_berendsen.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_print.txt b/doc/src/fix_print.txt
index f7a7b333c409ed9a5431cb1ec10879e29f918bf3..d23c1103d3000963e8efcf4600080f79bf3eac20 100644
--- a/doc/src/fix_print.txt
+++ b/doc/src/fix_print.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_property_atom.txt b/doc/src/fix_property_atom.txt
index 624fc5f7dfc3a540017402a618446fdf13e7379a..136ed6c15e6ecb9de65599eb41a821d6487bbf69 100644
--- a/doc/src/fix_property_atom.txt
+++ b/doc/src/fix_property_atom.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_python_invoke.txt b/doc/src/fix_python_invoke.txt
index 787940d9ebc4de8cd334a21454fe58dd6fa7b341..5e0c0369a54b62f81c5c14c6360d182c1f655df0 100644
--- a/doc/src/fix_python_invoke.txt
+++ b/doc/src/fix_python_invoke.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_python_move.txt b/doc/src/fix_python_move.txt
index 2f49427a9ec563ca01003c47ee88fd1251210a2f..a4e0eb39376ea0945bd667ce6625c406b697534a 100644
--- a/doc/src/fix_python_move.txt
+++ b/doc/src/fix_python_move.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_qbmsst.txt b/doc/src/fix_qbmsst.txt
index 56ace85e57c6bc01265689b58cddcf869e8c906a..e96bd97f4587cfa7446b5adc5606a6f4e13df09d 100644
--- a/doc/src/fix_qbmsst.txt
+++ b/doc/src/fix_qbmsst.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_qeq.txt b/doc/src/fix_qeq.txt
index c142d4a06de7015168b9c0e339629c0d5237b9b9..27fb613ef957fc91f280f5eccf7328afcc1cdb35 100644
--- a/doc/src/fix_qeq.txt
+++ b/doc/src/fix_qeq.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_qeq_comb.txt b/doc/src/fix_qeq_comb.txt
index 0eb38fcae62492de87ddbfbd015004ae47f13e2c..99e86df030fb80215b1dfceab6d521fd8f4167f8 100644
--- a/doc/src/fix_qeq_comb.txt
+++ b/doc/src/fix_qeq_comb.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_qeq_reax.txt b/doc/src/fix_qeq_reax.txt
index ea25ddbf57b0424198c2b21641e4ec882f17efaa..cf16daf84731096ec617c9abce809de80764ee73 100644
--- a/doc/src/fix_qeq_reax.txt
+++ b/doc/src/fix_qeq_reax.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_qmmm.txt b/doc/src/fix_qmmm.txt
index 5e730ac8afb20580701dddfa45e413abdcd115e9..657ee841810a25338390cb7c14d6218691dfd6c1 100644
--- a/doc/src/fix_qmmm.txt
+++ b/doc/src/fix_qmmm.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_qtb.txt b/doc/src/fix_qtb.txt
index 07a6af39ba2f81db6ed16cce0eb93d39ac98b65b..5b212934a94780b1d6e34c8c90873519b1bcc543 100644
--- a/doc/src/fix_qtb.txt
+++ b/doc/src/fix_qtb.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_reax_bonds.txt b/doc/src/fix_reax_bonds.txt
index 2f7c38f8154163e052f832a13974728aec42da03..49d61f4db80d45f1993bec664a07bc249f259ca1 100644
--- a/doc/src/fix_reax_bonds.txt
+++ b/doc/src/fix_reax_bonds.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_reaxc_species.txt b/doc/src/fix_reaxc_species.txt
index 4f1249744f1b40fb82498e05e7fa50c330f1a06e..5be1c46230b477e62f07ff70c9dcf02c03ef7da3 100644
--- a/doc/src/fix_reaxc_species.txt
+++ b/doc/src/fix_reaxc_species.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_recenter.txt b/doc/src/fix_recenter.txt
index a2477d11c7a31d1f4a2424a8f381607d36372b56..cfac756cd1659f9d8e7fcc6abc2922104a6b7bb0 100644
--- a/doc/src/fix_recenter.txt
+++ b/doc/src/fix_recenter.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_restrain.txt b/doc/src/fix_restrain.txt
index b8cc7c0d45c6baac526fafb6ca761166f8b711f3..2edc7e32963bb94c3bd60158bd21f94ba123e0a4 100644
--- a/doc/src/fix_restrain.txt
+++ b/doc/src/fix_restrain.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_rhok.txt b/doc/src/fix_rhok.txt
index 2db920ac4bef02c60f95604beb5e6feeb9cb7de6..68cce694e9b46eb71275eb61b5af3ad877eb1fa5 100644
--- a/doc/src/fix_rhok.txt
+++ b/doc/src/fix_rhok.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_rigid.txt b/doc/src/fix_rigid.txt
index a5f00c16e901a99de6cf12b15c3e3678ebeb35e4..d5e3b0166810dd39613d4a9105d9ac0ed43e86b9 100644
--- a/doc/src/fix_rigid.txt
+++ b/doc/src/fix_rigid.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_rx.txt b/doc/src/fix_rx.txt
index aff3303f4353b3889edbfd3e72113609983cade5..d39e41e922d16158b2f643e4b0d4eb60e900493a 100644
--- a/doc/src/fix_rx.txt
+++ b/doc/src/fix_rx.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_saed_vtk.txt b/doc/src/fix_saed_vtk.txt
index 814e17b8e952ad71d3ffe918c99596a0d10dc575..60708cd6962cfa57823d1a3c3d33ba1b50a5f661 100644
--- a/doc/src/fix_saed_vtk.txt
+++ b/doc/src/fix_saed_vtk.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_setforce.txt b/doc/src/fix_setforce.txt
index c6a01e5492d55748ced8500ba7c8a93d68f72e55..14fceb7b49e87a01596f1e8f131c4aecd84d26de 100644
--- a/doc/src/fix_setforce.txt
+++ b/doc/src/fix_setforce.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_shake.txt b/doc/src/fix_shake.txt
index 9297bcc87a28e8ec6e143b8b1d0255dc9341c83b..ea38de41cd1ba8b0ad9f2c759db429666798f524 100644
--- a/doc/src/fix_shake.txt
+++ b/doc/src/fix_shake.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_shardlow.txt b/doc/src/fix_shardlow.txt
index 6d14346334c8beac00d4edbbc206e6213a414ac0..33db2bf7cc9e25d81e6b842e6b8282d6ed5feb07 100644
--- a/doc/src/fix_shardlow.txt
+++ b/doc/src/fix_shardlow.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_smd.txt b/doc/src/fix_smd.txt
index e9403b22ccbc07f840966f81f730a11077048797..2f083dafc337f887ab75da54c4859dd901701844 100644
--- a/doc/src/fix_smd.txt
+++ b/doc/src/fix_smd.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_smd_adjust_dt.txt b/doc/src/fix_smd_adjust_dt.txt
index 86b7363300929bada7f049fae3f3c13cf3cec11f..740b10559d8aced34b4c1428bb355b20c144f325 100644
--- a/doc/src/fix_smd_adjust_dt.txt
+++ b/doc/src/fix_smd_adjust_dt.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_smd_integrate_tlsph.txt b/doc/src/fix_smd_integrate_tlsph.txt
index 17c9c0f400f4cdf5dfc67966d5b1f51d4d0f4672..cd676a51ce3cdc3eb1978e8d8d29ff7f3acc7832 100644
--- a/doc/src/fix_smd_integrate_tlsph.txt
+++ b/doc/src/fix_smd_integrate_tlsph.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_smd_integrate_ulsph.txt b/doc/src/fix_smd_integrate_ulsph.txt
index 28e38c7f970a9d99a07294bd77f4fb66a54ced00..7f16b4b7ceabf7288252e5be36e84bda4c949465 100644
--- a/doc/src/fix_smd_integrate_ulsph.txt
+++ b/doc/src/fix_smd_integrate_ulsph.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_smd_move_triangulated_surface.txt b/doc/src/fix_smd_move_triangulated_surface.txt
index 2cba001267433e921d908bd9d344cb1152886fde..aeabf187686e105a9af292b6e5fd93ab01216095 100644
--- a/doc/src/fix_smd_move_triangulated_surface.txt
+++ b/doc/src/fix_smd_move_triangulated_surface.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_smd_setvel.txt b/doc/src/fix_smd_setvel.txt
index d64726d9b344b5b2314616ead9ff320babab7db9..6634751d6ad9e1ef17333982a7826b1c1e7d724b 100644
--- a/doc/src/fix_smd_setvel.txt
+++ b/doc/src/fix_smd_setvel.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_smd_wall_surface.txt b/doc/src/fix_smd_wall_surface.txt
index feb65b2312823ece1b261e5349750500018b6ed7..a19b2c4cfb7eb2478ca21f684589491127b71eab 100644
--- a/doc/src/fix_smd_wall_surface.txt
+++ b/doc/src/fix_smd_wall_surface.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_spring.txt b/doc/src/fix_spring.txt
index 047e5a6797716cd6f93a60ec87f094d5ffa91da3..690fc3e67c381a9cddd7469e22d9a925f75e4c14 100644
--- a/doc/src/fix_spring.txt
+++ b/doc/src/fix_spring.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_spring_chunk.txt b/doc/src/fix_spring_chunk.txt
index e46f29977137e1b0cfed6262c05d83f37c24acda..9d4e8afd090e3a0ea9bc12af04cf1db4b53b6945 100644
--- a/doc/src/fix_spring_chunk.txt
+++ b/doc/src/fix_spring_chunk.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_spring_rg.txt b/doc/src/fix_spring_rg.txt
index 4afdc02d5a45cf96ea3519ff9fcd34b9a80fc896..b252163958fe5b983faeb2fc25e976bcf602f211 100644
--- a/doc/src/fix_spring_rg.txt
+++ b/doc/src/fix_spring_rg.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_spring_self.txt b/doc/src/fix_spring_self.txt
index e5b5c3dfd00fccb009b78fcb88b3e272e888a9a9..0ac1d5eecb627a363b900d5af01ebef318e200b0 100644
--- a/doc/src/fix_spring_self.txt
+++ b/doc/src/fix_spring_self.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_srd.txt b/doc/src/fix_srd.txt
index 7c5179fb3fc968999de0a8e41d410837f024a063..893557b9acad71bd2f1be0690a3b0694b68022f6 100644
--- a/doc/src/fix_srd.txt
+++ b/doc/src/fix_srd.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_store_force.txt b/doc/src/fix_store_force.txt
index 93437c85b6f637670a699d3087d9a70234afef38..33ebc962d5da9def4a817dbf6a1e9cdb78c5e4ad 100644
--- a/doc/src/fix_store_force.txt
+++ b/doc/src/fix_store_force.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_store_state.txt b/doc/src/fix_store_state.txt
index dee8070bbd55a2a2663cf66c8df79e28a3478a06..df05adc5b9ceb274061dab5bc7a0dbfc5cc395dd 100644
--- a/doc/src/fix_store_state.txt
+++ b/doc/src/fix_store_state.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_surface_global.txt b/doc/src/fix_surface_global.txt
index b470babab72a14f2761805d4719d8bfc92165546..ade64d2056e0e23e58e3e762620077d6ada3f1f1 100644
--- a/doc/src/fix_surface_global.txt
+++ b/doc/src/fix_surface_global.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_temp_berendsen.txt b/doc/src/fix_temp_berendsen.txt
index 9092bbd30e73531cff201ff8556c59845b7654a8..c1f1626782abffb6d380b0faae983b6642d67db0 100644
--- a/doc/src/fix_temp_berendsen.txt
+++ b/doc/src/fix_temp_berendsen.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_temp_csvr.txt b/doc/src/fix_temp_csvr.txt
index 6ce6ad7d9d6c38f5fcf893e2bce0a632376fd793..e50f821bfe9d55339164064ea18a515d4ac58967 100644
--- a/doc/src/fix_temp_csvr.txt
+++ b/doc/src/fix_temp_csvr.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_temp_rescale.txt b/doc/src/fix_temp_rescale.txt
index 89f1777e36ccbfe48a85143add910ce58d299e0b..5640317f1cf68ae357480d2b641441af9acf752a 100644
--- a/doc/src/fix_temp_rescale.txt
+++ b/doc/src/fix_temp_rescale.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_temp_rescale_eff.txt b/doc/src/fix_temp_rescale_eff.txt
index 8a79dc3275998c9e47782993b611eaac8fceead7..0e08e4f1e81c9451e7c50742263f0b0b7b6988b9 100644
--- a/doc/src/fix_temp_rescale_eff.txt
+++ b/doc/src/fix_temp_rescale_eff.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_tfmc.txt b/doc/src/fix_tfmc.txt
index 3c81d62ee0aa7c136765e59267b0a9d85f1a8333..ddfa46261929de1fc4e1ab0c411537e6df97744d 100644
--- a/doc/src/fix_tfmc.txt
+++ b/doc/src/fix_tfmc.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_thermal_conductivity.txt b/doc/src/fix_thermal_conductivity.txt
index 2e10a89738155430b0ea1a62c4c992c3cc00e2dc..86fc6f2c72feba87286126f2b48dacf0983bce69 100644
--- a/doc/src/fix_thermal_conductivity.txt
+++ b/doc/src/fix_thermal_conductivity.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_ti_spring.txt b/doc/src/fix_ti_spring.txt
index b116d8e8a3b56dc79f25a20cee06e4866b2e37ed..afe5373220095b949e9429f41e800f4e2fa6ad79 100644
--- a/doc/src/fix_ti_spring.txt
+++ b/doc/src/fix_ti_spring.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_tmd.txt b/doc/src/fix_tmd.txt
index e1815e61d30105c93f2e3f7ea132e6130dffb204..c2541692f5f4cb2667084e11c5f375132e99abf3 100644
--- a/doc/src/fix_tmd.txt
+++ b/doc/src/fix_tmd.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_ttm.txt b/doc/src/fix_ttm.txt
index d83118d4272b29588b9dac7d8bd8f974a6388f78..6001def5817736192fd0f7ac357a63ce148ca3c1 100644
--- a/doc/src/fix_ttm.txt
+++ b/doc/src/fix_ttm.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_tune_kspace.txt b/doc/src/fix_tune_kspace.txt
index 60a34a26c9c671c291ff9ee77946e43e8c0a7c62..b4e8472591dee2164ddb4ef2550431ce0b575e4e 100644
--- a/doc/src/fix_tune_kspace.txt
+++ b/doc/src/fix_tune_kspace.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_vector.txt b/doc/src/fix_vector.txt
index 69c999fd1a5027e445b3c7926d7d1531f991d901..e1bfbe5738073e466f78f2742ed154e13884dc81 100644
--- a/doc/src/fix_vector.txt
+++ b/doc/src/fix_vector.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_viscosity.txt b/doc/src/fix_viscosity.txt
index 8d73deb7c53b2a8254ace72d12eeeaa4d562abba..934da3efdd7820fff834d01e1daf8354e14c39c2 100644
--- a/doc/src/fix_viscosity.txt
+++ b/doc/src/fix_viscosity.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_viscous.txt b/doc/src/fix_viscous.txt
index 7ff517aec11c8cdc72370569c3a9a5a0a1a09c32..c5a3ede0b24a908ffb9ed5652af2d179400a0dd0 100644
--- a/doc/src/fix_viscous.txt
+++ b/doc/src/fix_viscous.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_wall.txt b/doc/src/fix_wall.txt
index fcd920934fd97f5b608fb4600e45e2a64f1db9f2..2ac59d9588155915370d834c1eb2b0e7727602ca 100644
--- a/doc/src/fix_wall.txt
+++ b/doc/src/fix_wall.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_wall_body_polygon.txt b/doc/src/fix_wall_body_polygon.txt
index ebd25c2bbc71da3667b9bbaee165af3c0d2501b3..0946a85131ae6c003daa63e7af939f9adf442227 100644
--- a/doc/src/fix_wall_body_polygon.txt
+++ b/doc/src/fix_wall_body_polygon.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_wall_body_polyhedron.txt b/doc/src/fix_wall_body_polyhedron.txt
index d3d8bc35a3e9a2faeef5687c76f15575ceb5e3a8..407cf9fb339047e9b881c0e4df9b950280d5cbed 100644
--- a/doc/src/fix_wall_body_polyhedron.txt
+++ b/doc/src/fix_wall_body_polyhedron.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_wall_ees.txt b/doc/src/fix_wall_ees.txt
index f141a194057f30fbb940922bf04d18044c4937b4..ae16ca40d2ab731af1a4b77ac474d3dd8b00f841 100644
--- a/doc/src/fix_wall_ees.txt
+++ b/doc/src/fix_wall_ees.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_wall_gran.txt b/doc/src/fix_wall_gran.txt
index 9796c394597a774b4f89d25adedb44b28d6d56d8..6c2769fc12840c85fdd60248009a45a851d8174a 100644
--- a/doc/src/fix_wall_gran.txt
+++ b/doc/src/fix_wall_gran.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_wall_gran_region.txt b/doc/src/fix_wall_gran_region.txt
index 908bcc39417ac1919858ed613d8e108aae8e3755..187214c1a36ca27c304d291150d16f56d440d204 100644
--- a/doc/src/fix_wall_gran_region.txt
+++ b/doc/src/fix_wall_gran_region.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_wall_piston.txt b/doc/src/fix_wall_piston.txt
index 26018329eb73b05214273e86d075b568eb802e5e..eecf69ebf2b80164672bb2b21cdb48f3ce855a0d 100644
--- a/doc/src/fix_wall_piston.txt
+++ b/doc/src/fix_wall_piston.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_wall_reflect.txt b/doc/src/fix_wall_reflect.txt
index 2956046e2096bd2467269b81fe0dda96485a9352..78be84eb638224ec631841fabc022bf0700a5162 100644
--- a/doc/src/fix_wall_reflect.txt
+++ b/doc/src/fix_wall_reflect.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_wall_region.txt b/doc/src/fix_wall_region.txt
index 8b3b3ff1730b6dd3d616a81aca2f7ba497ff200f..559a2f0d89c0cd8c00cc49be87daf53f793cf6f9 100644
--- a/doc/src/fix_wall_region.txt
+++ b/doc/src/fix_wall_region.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/fix_wall_srd.txt b/doc/src/fix_wall_srd.txt
index 3a8c2e41cd307afcfb5d052b57f5bb2cca55913a..3a50c45ab7592d0c7d3d16dc969423218eaee8b6 100644
--- a/doc/src/fix_wall_srd.txt
+++ b/doc/src/fix_wall_srd.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/group.txt b/doc/src/group.txt
index dddb0459e3711e526e6077318aa6ae51922b0196..847267737286c79b0d99315d20b995907082cf81 100644
--- a/doc/src/group.txt
+++ b/doc/src/group.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/group2ndx.txt b/doc/src/group2ndx.txt
index 94d188399ba6937874f1d579eb4bdf66c840ea2d..242d6a69a4092798fb073f2f89a4c44957b46061 100644
--- a/doc/src/group2ndx.txt
+++ b/doc/src/group2ndx.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/if.txt b/doc/src/if.txt
index 52fad5aea756031760c56e6e7ec4183266f9212c..513e451034da5f2752b96c4cdd81b3ec26ac58c4 100644
--- a/doc/src/if.txt
+++ b/doc/src/if.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
@@ -65,9 +65,9 @@ above.
 NOTE: If a command itself requires a quoted argument (e.g. a
 "print"_print.html command), then double and single quotes can be used
 and nested in the usual manner, as in the examples above and below.
-See "Section 3.2"_Section_commands.html#cmd_2 of the manual for
-more details on using quotes in arguments.  Only one of level of
-nesting is allowed, but that should be sufficient for most use cases.
+The "Commands parse"_Commands_parse.html doc page has more details on
+using quotes in arguments.  Only one of level of nesting is allowed,
+but that should be sufficient for most use cases.
 
 Note that by using the line continuation character "&", the if command
 can be spread across many lines, though it is still a single command:
diff --git a/doc/src/improper_class2.txt b/doc/src/improper_class2.txt
index ef2abf5091854d6f75c37100b0c626fca48c7121..c38f73c64dc017d58ce25e86cb431d5c068e9b1e 100644
--- a/doc/src/improper_class2.txt
+++ b/doc/src/improper_class2.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/improper_coeff.txt b/doc/src/improper_coeff.txt
index 5c01a23ae9cda2b729894bb87a8b4108ff4a11b7..8ed65f95350a3a56eb776b5fe5ad67c3257d939d 100644
--- a/doc/src/improper_coeff.txt
+++ b/doc/src/improper_coeff.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
@@ -67,9 +67,9 @@ the style to display the formula it computes and coefficients
 specified by the associated "improper_coeff"_improper_coeff.html command.
 
 Note that there are also additional improper styles submitted by users
-which are included in the LAMMPS distribution.  The list of these with
-links to the individual styles are given in the improper section of
-"this page"_Section_commands.html#cmd_5.
+which are included in the LAMMPS distribution.  The full list of all
+improper styles is on the "Commands bond"_Commands_bond.html#improper
+doc page.
 
 "improper_style none"_improper_none.html - turn off improper interactions
 "improper_style hybrid"_improper_hybrid.html - define multiple styles of improper interactions :ul
diff --git a/doc/src/improper_cossq.txt b/doc/src/improper_cossq.txt
index 22ba990ba4885b4eaba923f5672a86d821c5d22e..04aa45255cb2faf860dcd0493b53e301c6a65bde 100644
--- a/doc/src/improper_cossq.txt
+++ b/doc/src/improper_cossq.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/improper_cvff.txt b/doc/src/improper_cvff.txt
index 1662d93b140420f9b89066a0ba475f6b9b2e224c..d01faf288554e0281f1841e45c9f0c415083c547 100644
--- a/doc/src/improper_cvff.txt
+++ b/doc/src/improper_cvff.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/improper_distance.txt b/doc/src/improper_distance.txt
index 7d49d17c976f262d39ff642380f23aadb0701595..93235fe60197f01fc50297ec4f8d0504c16c6b9a 100644
--- a/doc/src/improper_distance.txt
+++ b/doc/src/improper_distance.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/improper_fourier.txt b/doc/src/improper_fourier.txt
index 99132b893193ba9b7855d4b0a2a75c9dbfd54471..78cc1b3f760fe81de8682983f11bc0f90615f9d4 100644
--- a/doc/src/improper_fourier.txt
+++ b/doc/src/improper_fourier.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/improper_harmonic.txt b/doc/src/improper_harmonic.txt
index f37338e468567487c8409203ae3911e451e2e335..f398dc425f935f605c3446075783df2b91d49c00 100644
--- a/doc/src/improper_harmonic.txt
+++ b/doc/src/improper_harmonic.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/improper_hybrid.txt b/doc/src/improper_hybrid.txt
index 0c2beaef18c07dc3cfcc8ad136a8940486bdeef8..42afbe8577dc30163dcc8e5053de9cc05022b6a2 100644
--- a/doc/src/improper_hybrid.txt
+++ b/doc/src/improper_hybrid.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/improper_inversion_harmonic.txt b/doc/src/improper_inversion_harmonic.txt
index 34683ca2bb0000db8f32f9e93838f344e0287b4c..2c0f2f0af84e1275c8511fc3d65f2508163a89cd 100644
--- a/doc/src/improper_inversion_harmonic.txt
+++ b/doc/src/improper_inversion_harmonic.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/improper_none.txt b/doc/src/improper_none.txt
index af9964c7437af081e5a50ba8daf4359c94882593..f97af101fcffaf64ce4dacc34bc7824e4312d185 100644
--- a/doc/src/improper_none.txt
+++ b/doc/src/improper_none.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/improper_ring.txt b/doc/src/improper_ring.txt
index 84c35f9f5c19f998196ab0044af01bdb4ffccf63..60bbca170a9a3d06cc3d819d847fdf37370691d9 100644
--- a/doc/src/improper_ring.txt
+++ b/doc/src/improper_ring.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/improper_style.txt b/doc/src/improper_style.txt
index 861701590fedcfce745e2542fd7c69c943e4e5a3..3d29b28ec4a69b2200db24e2fb742fdf1c7fabd4 100644
--- a/doc/src/improper_style.txt
+++ b/doc/src/improper_style.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
@@ -60,9 +60,9 @@ specified by the associated "improper_coeff"_improper_coeff.html
 command.
 
 Note that there are also additional improper styles submitted by users
-which are included in the LAMMPS distribution.  The list of these with
-links to the individual styles are given in the improper section of
-"this page"_Section_commands.html#cmd_5.
+which are included in the LAMMPS distribution.  The full list of all
+improper styles is on the "Commands bond"_Commands_bond.html#improper
+doc page.
 
 "improper_style none"_improper_none.html - turn off improper interactions
 "improper_style zero"_improper_zero.html - topology but no interactions
diff --git a/doc/src/improper_umbrella.txt b/doc/src/improper_umbrella.txt
index 59fee0a664cdf08283f237d28fb8a9ab0fcf4f4a..b05cf4b181bfceaed1160cebb650d99922af039a 100644
--- a/doc/src/improper_umbrella.txt
+++ b/doc/src/improper_umbrella.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/improper_zero.txt b/doc/src/improper_zero.txt
index 2a298573d5e359ef1676519ef494526fa14a2bc7..f3f3485b57cf0c6daf81233f1432e9b43f2aeb42 100644
--- a/doc/src/improper_zero.txt
+++ b/doc/src/improper_zero.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/include.txt b/doc/src/include.txt
index 95d08db3522d8d291512e477801860f41f78004a..c11405631365e173f57589d3a11825884a4b0157 100644
--- a/doc/src/include.txt
+++ b/doc/src/include.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/info.txt b/doc/src/info.txt
index d5b5bd97b942842c03a26011d66ce7049b1c3a27..99211de4fb5745edccf401a78f2045c756dee695 100644
--- a/doc/src/info.txt
+++ b/doc/src/info.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/jump.txt b/doc/src/jump.txt
index 4e3799f7b1c48fafa179454b458c2eff588c4453..b5afeb6559f4c80629947cf9376ae455fdde1a63 100644
--- a/doc/src/jump.txt
+++ b/doc/src/jump.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/kspace_modify.txt b/doc/src/kspace_modify.txt
index 37c8c5b1d76736e9d0ad7a9e15317a79f84c405e..dd7b1e8deadfdd3e6defeddaa0cc85d3e4467370 100644
--- a/doc/src/kspace_modify.txt
+++ b/doc/src/kspace_modify.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/kspace_style.txt b/doc/src/kspace_style.txt
index fa717b70ef036a659ff21f4033f0c2bbc7dd3d9d..55ad4ab6107b828fd74e5daa91025063d29c5115 100644
--- a/doc/src/kspace_style.txt
+++ b/doc/src/kspace_style.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/label.txt b/doc/src/label.txt
index c6a573141b205b7dea517f3d24881f84f06e3414..adab44188c8cc3a45cc49139e935c2e7c37a9606 100644
--- a/doc/src/label.txt
+++ b/doc/src/label.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/lammps.book b/doc/src/lammps.book
index a25d6e0629135cd578fb9db5025d82f20380fba7..9cb2d8cd6c7ed04b90d1504e91eea399bf755416 100644
--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@@ -9,7 +9,17 @@ Intro_opensource.html
 Intro_authors.html
 Intro_website.html
 Section_start.html
-Section_commands.html
+Commands.html
+Commands_input.html
+Commands_parse.html
+Commands_structure.html
+Commands_category.html
+Commands_all.html
+Commands_fix.html
+Commands_compute.html
+Commands_pair.html
+Commands_bond.html
+Commands_kspace.html
 Packages.html
 Packages_standard.html
 Packages_user.html
diff --git a/doc/src/lattice.txt b/doc/src/lattice.txt
index 7a90df1f5d553697e7433d4b41cc4a2b241a4531..6f16dc54323ae72ec99eed888f2c1a953e124647 100644
--- a/doc/src/lattice.txt
+++ b/doc/src/lattice.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/log.txt b/doc/src/log.txt
index 92bb12e6dbccf42c9c8d1b80d587088e91bf88c7..76037685194b5ba9b324b02d35ffd0ed34ea26d3 100644
--- a/doc/src/log.txt
+++ b/doc/src/log.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/manifolds.txt b/doc/src/manifolds.txt
index 1013d8fab68f91cb2d5113b0cde132d7fc1f4385..194a75586804a9442114a6d6fd47cd2f59ea1172 100644
--- a/doc/src/manifolds.txt
+++ b/doc/src/manifolds.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/mass.txt b/doc/src/mass.txt
index 4b75132ccfb63a763cb6f238201e19216b736d0a..c6939630441165e80bd0bacb0007e56fedbec7af 100644
--- a/doc/src/mass.txt
+++ b/doc/src/mass.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/min_modify.txt b/doc/src/min_modify.txt
index 73d142f5fabe4556a91064f674e62a37bed26773..9408eea167bbc49274a203b0fe4586f724e8659a 100644
--- a/doc/src/min_modify.txt
+++ b/doc/src/min_modify.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/min_style.txt b/doc/src/min_style.txt
index 245ac5864c1d41bdbce4a42568e5ee555a25bb3d..4948a34864a4424a031e86ab4ace7937c1fd09fe 100644
--- a/doc/src/min_style.txt
+++ b/doc/src/min_style.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 :line
 
 min_style command :h3
diff --git a/doc/src/minimize.txt b/doc/src/minimize.txt
index a3f2c5d0bf5aaa430740076b09ea39fad0b35baa..910fc7f821051bee5f28753442d479e85f7f27e7 100644
--- a/doc/src/minimize.txt
+++ b/doc/src/minimize.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/molecule.txt b/doc/src/molecule.txt
index b2ad547cf053198132f48a2030f89b285e99e133..88c6292d8b6d3bc63f075917f38df9f9482fcbae 100644
--- a/doc/src/molecule.txt
+++ b/doc/src/molecule.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/neb.txt b/doc/src/neb.txt
index 5c6053fca06bd964c771cd5a9b89aa1e484047bd..fbd77ee32903f1d99f4f63232538e0fd88cdde7d 100644
--- a/doc/src/neb.txt
+++ b/doc/src/neb.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/neigh_modify.txt b/doc/src/neigh_modify.txt
index c4544cb29bde3ccf25b708e7d2ad552fc97e7eea..6c4218cff56589fca8b41d6c8c8ab2fa96ee2c5b 100644
--- a/doc/src/neigh_modify.txt
+++ b/doc/src/neigh_modify.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/neighbor.txt b/doc/src/neighbor.txt
index 062f79a5bbba0bc7e9042145dd03cebbf1ceebe3..7c7e7b05e5229b3d1144f251543d5b8ded341c60 100644
--- a/doc/src/neighbor.txt
+++ b/doc/src/neighbor.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/newton.txt b/doc/src/newton.txt
index a3e7f4fa91eec43b623a57f58be483f35ba982e1..fd7b5369203f25c957f62e34d9d68960fee87495 100644
--- a/doc/src/newton.txt
+++ b/doc/src/newton.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/next.txt b/doc/src/next.txt
index 08f73b896cb7ef13f74c5dd982f07d021fe44eea..5a0b30b2a7fe6ff0d824a066376404808702958f 100644
--- a/doc/src/next.txt
+++ b/doc/src/next.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/package.txt b/doc/src/package.txt
index 81e1db9bd8116656f328deb10bc6b449a6f049be..c2e7345bb74c4e25a5dc4861194c704d3017232d 100644
--- a/doc/src/package.txt
+++ b/doc/src/package.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_adp.txt b/doc/src/pair_adp.txt
index 1ba59b7732e164b7f3643100f20d172833b5151b..382a97eceaf93bf844915871d3210a4bca0e7666 100644
--- a/doc/src/pair_adp.txt
+++ b/doc/src/pair_adp.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_agni.txt b/doc/src/pair_agni.txt
index 352e00249a4198506ea9cd5b54f6a34d2dc3cea9..34f99001390ca24026f0ea3218316ab465d68ac0 100644
--- a/doc/src/pair_agni.txt
+++ b/doc/src/pair_agni.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_airebo.txt b/doc/src/pair_airebo.txt
index b5add21f2431c77cb40406ec98e1cba6509771fc..94a692226d608687a094d48455070c1084eed3f4 100644
--- a/doc/src/pair_airebo.txt
+++ b/doc/src/pair_airebo.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_awpmd.txt b/doc/src/pair_awpmd.txt
index fe0e3c952a759234f79234c60d825524b8984023..ec87101d0dc2fa89ed9089e13b37ca061ed3a9d9 100644
--- a/doc/src/pair_awpmd.txt
+++ b/doc/src/pair_awpmd.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_beck.txt b/doc/src/pair_beck.txt
index 1aca4b4f9ac88f93cf20ee110d356db6c7b12c38..ca4186e27b102d8199327d87a3ca0cd9da09f92f 100644
--- a/doc/src/pair_beck.txt
+++ b/doc/src/pair_beck.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_body_nparticle.txt b/doc/src/pair_body_nparticle.txt
index 78a9f2bb3843163c51a0790e87ffd74b4be2be87..9fb88102eb0aece7ace62e32360614fa3bdef106 100644
--- a/doc/src/pair_body_nparticle.txt
+++ b/doc/src/pair_body_nparticle.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_body_rounded_polygon.txt b/doc/src/pair_body_rounded_polygon.txt
index 19807fbe3944063ff14fceec685818139c65a4ca..e724874032afffe0d59f1f6fe2622a1669797b35 100644
--- a/doc/src/pair_body_rounded_polygon.txt
+++ b/doc/src/pair_body_rounded_polygon.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_body_rounded_polyhedron.txt b/doc/src/pair_body_rounded_polyhedron.txt
index d70a86f881b5feaa70c9826bdae1658721ed4121..0f8548d98eab86a6d5e3647f46119162764409cb 100644
--- a/doc/src/pair_body_rounded_polyhedron.txt
+++ b/doc/src/pair_body_rounded_polyhedron.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_bop.txt b/doc/src/pair_bop.txt
index 2a611e4bd038a50685897244936677ba09311cb9..654a7eb0b332dd5efdd4a9ca41410fbf6bd131df 100644
--- a/doc/src/pair_bop.txt
+++ b/doc/src/pair_bop.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_born.txt b/doc/src/pair_born.txt
index 143549cf2d99506448c17c8ac9b2f47de70b9e83..c408de6db6f23b579f2800d7865fdcd35649f9e6 100644
--- a/doc/src/pair_born.txt
+++ b/doc/src/pair_born.txt
@@ -3,7 +3,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_brownian.txt b/doc/src/pair_brownian.txt
index 8d30f0cec65628515add8cab9d6897d06a3301d5..eaff85cbbca374db982add0557f03b57dedceaaf 100644
--- a/doc/src/pair_brownian.txt
+++ b/doc/src/pair_brownian.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_buck.txt b/doc/src/pair_buck.txt
index 2483a6c9e26fa1357dbfb52bf7b09231c8dcc897..cc782c11cf3f551930264316b838c488de4ddb6e 100644
--- a/doc/src/pair_buck.txt
+++ b/doc/src/pair_buck.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_buck6d_coul_gauss.txt b/doc/src/pair_buck6d_coul_gauss.txt
index 879972772ba1aceed1ebe3992725373955840ef1..485c35c6b2fffb04c14fa04469bd33a6400c65d5 100644
--- a/doc/src/pair_buck6d_coul_gauss.txt
+++ b/doc/src/pair_buck6d_coul_gauss.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_buck_long.txt b/doc/src/pair_buck_long.txt
index 94bf6a2d7c4228083f6ed16de5d4a7f82d64f63e..551204f1a7fe97ea559e98c7cfd1ddd92370d328 100644
--- a/doc/src/pair_buck_long.txt
+++ b/doc/src/pair_buck_long.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_charmm.txt b/doc/src/pair_charmm.txt
index af20661bbd3d50b690927d12dc24739b085ddd0e..39c6f29b047fdbf02017352a1e787cc60c79cb78 100644
--- a/doc/src/pair_charmm.txt
+++ b/doc/src/pair_charmm.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_class2.txt b/doc/src/pair_class2.txt
index e62971a64572099caa98854967e90754ba7942f5..104c51474c25764c20a7b064dad9722e548e0809 100644
--- a/doc/src/pair_class2.txt
+++ b/doc/src/pair_class2.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_coeff.txt b/doc/src/pair_coeff.txt
index fe9238f423d22af362c51940a639fbc32312fb7e..63f85f23d5e480a77ccc5f0c673cdde81d5a2d16 100644
--- a/doc/src/pair_coeff.txt
+++ b/doc/src/pair_coeff.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
@@ -111,9 +111,8 @@ Windows:
 :line
 
 The alphabetic list of pair styles defined in LAMMPS is given on the
-"pair_style"_pair_style.html doc page.  They are also given in more
-compact form in the pair section of "this
-page"_Section_commands.html#cmd_5.
+"pair_style"_pair_style.html doc page.  They are also listed in more
+compact form on the "Commands pair"_Commands_pair.html doc page.
 
 Click on the style to display the formula it computes, arguments
 specified in the pair_style command, and coefficients specified by the
@@ -121,15 +120,15 @@ associated "pair_coeff"_pair_coeff.html command.
 
 Note that there are also additional pair styles (not listed on the
 "pair_style"_pair_style.html doc page) submitted by users which are
-included in the LAMMPS distribution.  The list of these with links to
-the individual styles are given in the pair section of "this
-page"_Section_commands.html#cmd_5.
+included in the LAMMPS distribution.  The full list of all pair styles
+is on the "Commands pair"_Commands_pair.html doc page.
 
 There are also additional accelerated pair styles (not listed on the
 "pair_style"_pair_style.html doc page) included in the LAMMPS
-distribution for faster performance on CPUs and GPUs.  The list of
-these with links to the individual styles are given in the pair
-section of "this page"_Section_commands.html#cmd_5.
+distribution for faster performance on CPUs, GPUs, and KNLs.  The
+individual style names on the "Commands pair"_Commands_pair.html doc
+page are followed by one or more of (g,i,k,o,t) to indicate which
+accerlerated styles exist.
 
 :line
 
diff --git a/doc/src/pair_colloid.txt b/doc/src/pair_colloid.txt
index a7bb0db08a4f505ed14897e56199fc0f59ee0472..08540cfee082c761259d3d8e3772015557c21210 100644
--- a/doc/src/pair_colloid.txt
+++ b/doc/src/pair_colloid.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_comb.txt b/doc/src/pair_comb.txt
index 6949ca50c20d7a805d6bb41c77d8e1eb84dacb12..fc4cddbbae1fefa91ce37e930e2a589279f42566 100644
--- a/doc/src/pair_comb.txt
+++ b/doc/src/pair_comb.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_coul.txt b/doc/src/pair_coul.txt
index e2bc78a2e60b5eacc2ffd501305e0e77a0940343..2fd9445785e26a44a3b1f7b070caa7531e61003d 100644
--- a/doc/src/pair_coul.txt
+++ b/doc/src/pair_coul.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_coul_diel.txt b/doc/src/pair_coul_diel.txt
index f651cb4b5e4e927d6d9d230bcfe5e37d9260885f..14932c4835043aa7e93cf7b900672def64f10323 100644
--- a/doc/src/pair_coul_diel.txt
+++ b/doc/src/pair_coul_diel.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_coul_shield.txt b/doc/src/pair_coul_shield.txt
index 19f69688d5b6b1d3da1af094a81340cf8cab1b5d..029e6e5b3b3458ce3fdbab9daaecdad467061dce 100644
--- a/doc/src/pair_coul_shield.txt
+++ b/doc/src/pair_coul_shield.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_cs.txt b/doc/src/pair_cs.txt
index 86eb02b0d74c8404e4319c5cdbb6b489e8db7082..6540c4b8f0d4dd72b704854146d50b4f74815720 100644
--- a/doc/src/pair_cs.txt
+++ b/doc/src/pair_cs.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_dipole.txt b/doc/src/pair_dipole.txt
index e7d196d599985795a484703d90d609337a63c56d..1d8abc4521d2b26d2152d2157081a9d718bc3b47 100644
--- a/doc/src/pair_dipole.txt
+++ b/doc/src/pair_dipole.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_dpd.txt b/doc/src/pair_dpd.txt
index a36029ea63af50a98db8b207c7089317a67f6357..1b636795d962254fed114fd7cad91b2b53fb8bac 100644
--- a/doc/src/pair_dpd.txt
+++ b/doc/src/pair_dpd.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_dpd_fdt.txt b/doc/src/pair_dpd_fdt.txt
index 129d3c84af29af18d35100b27415ec07087c9e40..0d180ba068ffdec47eb78bc7fc7fcdb458aab766 100644
--- a/doc/src/pair_dpd_fdt.txt
+++ b/doc/src/pair_dpd_fdt.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_dsmc.txt b/doc/src/pair_dsmc.txt
index 9e24100ab7cf4ce5d6676060370e75e3ef172aa1..2478a96d5ff183f52d21f817a1205eee6ce99855 100644
--- a/doc/src/pair_dsmc.txt
+++ b/doc/src/pair_dsmc.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_eam.txt b/doc/src/pair_eam.txt
index b3c770179fb948329d4b746b863041a101c83436..361dacb703d41a95c365abd2ce5101e915fe11d3 100644
--- a/doc/src/pair_eam.txt
+++ b/doc/src/pair_eam.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_edip.txt b/doc/src/pair_edip.txt
index f0d1927812b263fdcbeadc8b5e5843492c9f7bea..cce564856e6c2c420771e4c070b23605e0cdafe8 100644
--- a/doc/src/pair_edip.txt
+++ b/doc/src/pair_edip.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_eff.txt b/doc/src/pair_eff.txt
index ee7dc9993296b92e353961284670052624ce11b6..a55860297e609eb106b63cda6655babf3f696966 100644
--- a/doc/src/pair_eff.txt
+++ b/doc/src/pair_eff.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_eim.txt b/doc/src/pair_eim.txt
index 7f94d919f2a62053d6b32142c914b9797f38e607..6490a859c16b361e217faaa3eb04e52386b87143 100644
--- a/doc/src/pair_eim.txt
+++ b/doc/src/pair_eim.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_exp6_rx.txt b/doc/src/pair_exp6_rx.txt
index dec660fd1dbbe2f4ef7c42529a2fac083d120159..08ab1cf3c9b64a40fe70b251500fcecfcd2994f6 100644
--- a/doc/src/pair_exp6_rx.txt
+++ b/doc/src/pair_exp6_rx.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_extep.txt b/doc/src/pair_extep.txt
index 9a784e2501638ecda41031366b0777346115c94f..3acad1132d108f61a70bd4c336b63ee14a919601 100644
--- a/doc/src/pair_extep.txt
+++ b/doc/src/pair_extep.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_gauss.txt b/doc/src/pair_gauss.txt
index 7716f89f174a1d8ce1637c09c13d10c9e4b6b6d5..9662a4f29c743fefb3bddc480b6f70f75045ff88 100644
--- a/doc/src/pair_gauss.txt
+++ b/doc/src/pair_gauss.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_gayberne.txt b/doc/src/pair_gayberne.txt
index e9a98a0b8426f1a980ddd508d57fa06b72951a1f..af41f6879e80ed299050eb6822553e819e22607f 100644
--- a/doc/src/pair_gayberne.txt
+++ b/doc/src/pair_gayberne.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_gran.txt b/doc/src/pair_gran.txt
index 86b04f96dede877734a479a5a6dc8fbfc0f91705..55b00a172f56c4063a20298509cc54856d9b276a 100644
--- a/doc/src/pair_gran.txt
+++ b/doc/src/pair_gran.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_gromacs.txt b/doc/src/pair_gromacs.txt
index 7daf805e2bedff4409f44a66022220f2f2aec371..9f34ac8c43da024cd0123454dfdc2666116379f3 100644
--- a/doc/src/pair_gromacs.txt
+++ b/doc/src/pair_gromacs.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_gw.txt b/doc/src/pair_gw.txt
index 8f1251cf1f3a96aa50e8f9339a69f20b893336bb..809ff008bc86dbaa33e6f899c354957e09a65fef 100644
--- a/doc/src/pair_gw.txt
+++ b/doc/src/pair_gw.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_hbond_dreiding.txt b/doc/src/pair_hbond_dreiding.txt
index d641cb73adec05425860ef39c61bb8992bfeac41..60b0b021743374cc08cfdd5cdc58a8605f02c9b0 100644
--- a/doc/src/pair_hbond_dreiding.txt
+++ b/doc/src/pair_hbond_dreiding.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_hybrid.txt b/doc/src/pair_hybrid.txt
index 9503256d2696919579fce47f655a853e19c08409..9b36109c279e7381ba5a73aea7adad55dee2f3c7 100644
--- a/doc/src/pair_hybrid.txt
+++ b/doc/src/pair_hybrid.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_ilp_graphene_hbn.txt b/doc/src/pair_ilp_graphene_hbn.txt
index dbc9c458e2997d372b58b7aae7a87cca389c2168..9c9304c4a73ba02e35d575331f135ad32187a81e 100644
--- a/doc/src/pair_ilp_graphene_hbn.txt
+++ b/doc/src/pair_ilp_graphene_hbn.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_kim.txt b/doc/src/pair_kim.txt
index fc2c1405af78057496fa7d291e9c3adce7ce0be7..889c1e892fe69202a92ca98b02650b982c68c849 100644
--- a/doc/src/pair_kim.txt
+++ b/doc/src/pair_kim.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_kolmogorov_crespi_full.txt b/doc/src/pair_kolmogorov_crespi_full.txt
index a16d123b89abc938fe172a3a73d123c896687588..8fc6bbff4996ecaefa81e0257048a14c702a7e5d 100644
--- a/doc/src/pair_kolmogorov_crespi_full.txt
+++ b/doc/src/pair_kolmogorov_crespi_full.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_kolmogorov_crespi_z.txt b/doc/src/pair_kolmogorov_crespi_z.txt
index 97f132eacd41e00cd4318cfde24b09e29b4a6ae1..7dad2e3701b852d41a2856e785d80be041f2f5c6 100644
--- a/doc/src/pair_kolmogorov_crespi_z.txt
+++ b/doc/src/pair_kolmogorov_crespi_z.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_lcbop.txt b/doc/src/pair_lcbop.txt
index 148a1d47a067c014d193b14eb3647bbe9c2cd3be..ddf8551d560ff042b8c3d64331db263e5c3d5289 100644
--- a/doc/src/pair_lcbop.txt
+++ b/doc/src/pair_lcbop.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_line_lj.txt b/doc/src/pair_line_lj.txt
index 44cfeb48e96ca4043c8e811d2950ae1243dc126a..c2c6beb97f5490ce4cc11ab6cb3c0634375afc0f 100644
--- a/doc/src/pair_line_lj.txt
+++ b/doc/src/pair_line_lj.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_list.txt b/doc/src/pair_list.txt
index 653e8b0c2d1635c4d10a43889af4b5bd5e99767d..023cc0be4f1c52404fe1f875bdfd86cf03b68e7d 100644
--- a/doc/src/pair_list.txt
+++ b/doc/src/pair_list.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_lj.txt b/doc/src/pair_lj.txt
index a0f7effbb17ff724f1963ffdef6c2c15b7b02632..a55cb348d7568f14dd25c715adf8a7fe382f3a23 100644
--- a/doc/src/pair_lj.txt
+++ b/doc/src/pair_lj.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_lj96.txt b/doc/src/pair_lj96.txt
index a0a9971474ac61c14d25d7eb80aac78338146648..7c68e26acef1c9cf8d21b47fc70ba1109296e502 100644
--- a/doc/src/pair_lj96.txt
+++ b/doc/src/pair_lj96.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_lj_cubic.txt b/doc/src/pair_lj_cubic.txt
index c4e2af506210f3bc1db893101f31239b4698afed..d04a3d8b9d1b6e021ea2df92d2ee16a74ba5e45d 100644
--- a/doc/src/pair_lj_cubic.txt
+++ b/doc/src/pair_lj_cubic.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_lj_expand.txt b/doc/src/pair_lj_expand.txt
index c156fefef250fac814660a90901c948826f70737..3e9996da4d5507158a37cca38cf1db68597dcfdb 100644
--- a/doc/src/pair_lj_expand.txt
+++ b/doc/src/pair_lj_expand.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_lj_long.txt b/doc/src/pair_lj_long.txt
index 0dd55b7e3266d61e3fd681f3ced9f0ec70e458c0..1ba3610f8621801864930acf73a20b4d16bd5a04 100644
--- a/doc/src/pair_lj_long.txt
+++ b/doc/src/pair_lj_long.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_lj_smooth.txt b/doc/src/pair_lj_smooth.txt
index 653520966b512fc5bb7b8e79e87683303f4b0d48..575c023579b4cf5b91927dd241c65d3ee9365c83 100644
--- a/doc/src/pair_lj_smooth.txt
+++ b/doc/src/pair_lj_smooth.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_lj_smooth_linear.txt b/doc/src/pair_lj_smooth_linear.txt
index aebde2e65355a27867903d36d96365a09f925477..0fab768b8fbd9eecc9c80d0760262f9d9ea6111b 100644
--- a/doc/src/pair_lj_smooth_linear.txt
+++ b/doc/src/pair_lj_smooth_linear.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_lj_soft.txt b/doc/src/pair_lj_soft.txt
index 7add9f623d8276855d80c17f4e4fcd434ed651a0..d10fcd0472d24ebd91510e0c4793597292e31127 100644
--- a/doc/src/pair_lj_soft.txt
+++ b/doc/src/pair_lj_soft.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_lubricate.txt b/doc/src/pair_lubricate.txt
index 2a16aa2a9dad961966abc8fd85fbb087bca0b7a2..e9a0a0d2910e5a6036f4993c23e59b0849b88d78 100644
--- a/doc/src/pair_lubricate.txt
+++ b/doc/src/pair_lubricate.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_lubricateU.txt b/doc/src/pair_lubricateU.txt
index 720a8539b890c917ab41aa1f0db151c0520a8280..6b74c208bf2c211ec71b9efff608c2345626505e 100644
--- a/doc/src/pair_lubricateU.txt
+++ b/doc/src/pair_lubricateU.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_mdf.txt b/doc/src/pair_mdf.txt
index ca06f1bf8eb12ad7b4050aaa79359f09a100e6fc..e5a8cac845effe56f019729b2660ad001226923d 100644
--- a/doc/src/pair_mdf.txt
+++ b/doc/src/pair_mdf.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_meam.txt b/doc/src/pair_meam.txt
index c7449428bd05aa010182dc17cb2f9206b69e5303..45f88f0bbec33570565284ab50945076acb85906 100644
--- a/doc/src/pair_meam.txt
+++ b/doc/src/pair_meam.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_meam_spline.txt b/doc/src/pair_meam_spline.txt
index 74242e32b9900d01ef67157dd3ded68cc7d63c9f..96155120419297e54de85192f772f8fcb05216d5 100644
--- a/doc/src/pair_meam_spline.txt
+++ b/doc/src/pair_meam_spline.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_meam_sw_spline.txt b/doc/src/pair_meam_sw_spline.txt
index fa731799ddd450445ee07d19f4b45c7cc44cc866..ba0953a17c3957825fac150f3b373c92a5df44b9 100644
--- a/doc/src/pair_meam_sw_spline.txt
+++ b/doc/src/pair_meam_sw_spline.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_meso.txt b/doc/src/pair_meso.txt
index bcdf717d68cb6d06e84422abffe278f6c382eb94..ad3880e642411c30179bb8a1e9d3b8451cc9c227 100644
--- a/doc/src/pair_meso.txt
+++ b/doc/src/pair_meso.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_mgpt.txt b/doc/src/pair_mgpt.txt
index f8b0c9f0713c99856cbce64bb199ee55068bebbf..09fe61168698455d05fef6b67ed6a80b1b43a962 100644
--- a/doc/src/pair_mgpt.txt
+++ b/doc/src/pair_mgpt.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_mie.txt b/doc/src/pair_mie.txt
index ad602db9f1e02cb1792acb2d1711ad0e189eacdc..818e37272bdd28f962195de66868aee119637d79 100644
--- a/doc/src/pair_mie.txt
+++ b/doc/src/pair_mie.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_modify.txt b/doc/src/pair_modify.txt
index 34dbb5bc3de7acc4f89588d730dc76b407c07d8e..c043fde5a77f7bb68ed0b74dc52d516589ee88f8 100644
--- a/doc/src/pair_modify.txt
+++ b/doc/src/pair_modify.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_momb.txt b/doc/src/pair_momb.txt
index 77c4f184d9380f11848bb7e0deedc719802d130d..545b650f75176e7a32d83ce85312e29720731f0c 100644
--- a/doc/src/pair_momb.txt
+++ b/doc/src/pair_momb.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_morse.txt b/doc/src/pair_morse.txt
index 34876011a1c0553999916fb6ba40c41cd70b782d..85a42986ec87ed45e30fe3fc3120587b4d345492 100644
--- a/doc/src/pair_morse.txt
+++ b/doc/src/pair_morse.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_multi_lucy.txt b/doc/src/pair_multi_lucy.txt
index 38fd1ede4aa2201cb8e2cb2733877272f4b91e5c..31d52a58c89386b5cca80afcd4b585c4e314fc15 100644
--- a/doc/src/pair_multi_lucy.txt
+++ b/doc/src/pair_multi_lucy.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_multi_lucy_rx.txt b/doc/src/pair_multi_lucy_rx.txt
index b043030907f775eb56241b0f3092882e7341f2a0..e09dde3f8051128f22a0817f847b3238061f9ad6 100644
--- a/doc/src/pair_multi_lucy_rx.txt
+++ b/doc/src/pair_multi_lucy_rx.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_nb3b_harmonic.txt b/doc/src/pair_nb3b_harmonic.txt
index e6e103f517855f1a8b37f6e4c8dc028954e138d0..720b9ea2a1f903f42b54525f4481e63f071aa389 100644
--- a/doc/src/pair_nb3b_harmonic.txt
+++ b/doc/src/pair_nb3b_harmonic.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_nm.txt b/doc/src/pair_nm.txt
index 08c3393993bc15e0d6d851b30c30d2ad7165261b..355bfd5573e951c2f28effcc2e4e0aee5c351917 100644
--- a/doc/src/pair_nm.txt
+++ b/doc/src/pair_nm.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_none.txt b/doc/src/pair_none.txt
index f4e9525198413d49fe26c94ce2795ea12d826d9f..960dc05d97be7d7dda8889bb129d348c9578f374 100644
--- a/doc/src/pair_none.txt
+++ b/doc/src/pair_none.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_oxdna.txt b/doc/src/pair_oxdna.txt
index f272d15a8680d6499df5f7164186789426589413..5ec99152978f42f5f603a1c87329ad005093583f 100644
--- a/doc/src/pair_oxdna.txt
+++ b/doc/src/pair_oxdna.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_oxdna2.txt b/doc/src/pair_oxdna2.txt
index 1b55031b2c97dc8c935c0ddb83a567f24d64ab6f..a1d2cfdb7c862f96affbd60ec4d216baef0795bc 100644
--- a/doc/src/pair_oxdna2.txt
+++ b/doc/src/pair_oxdna2.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_peri.txt b/doc/src/pair_peri.txt
index 432700305718db3b0ae720079a7943b7cf81d90f..14abd4541e4b3f33d1dac80119d894f8b758608e 100644
--- a/doc/src/pair_peri.txt
+++ b/doc/src/pair_peri.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_polymorphic.txt b/doc/src/pair_polymorphic.txt
index c088e8bb2242918fe221ab1241cba70129d6c5f7..eb0c30f249cff1b58a11e21dcb2ff5df14a599fb 100644
--- a/doc/src/pair_polymorphic.txt
+++ b/doc/src/pair_polymorphic.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_python.txt b/doc/src/pair_python.txt
index 2f8ed7a27c6702b9e80a82d0a14201f714430bd7..1433557e0388e581c94b2668ecc2721fdeea1928 100644
--- a/doc/src/pair_python.txt
+++ b/doc/src/pair_python.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_quip.txt b/doc/src/pair_quip.txt
index 9436b0c4ed1f71b78d18880d411e64855e727aca..3570a52801852be5207d72ef27a45438518ef6bb 100644
--- a/doc/src/pair_quip.txt
+++ b/doc/src/pair_quip.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_reax.txt b/doc/src/pair_reax.txt
index 1d13f937061c95963165efc936a680ca14415147..a3b84955cd058937fd28cb84732656e2f3f055ef 100644
--- a/doc/src/pair_reax.txt
+++ b/doc/src/pair_reax.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_reaxc.txt b/doc/src/pair_reaxc.txt
index 8d8c7e84e744185c4438a328ad534338d0b6042c..ec575486404904c6b92dd165e4d6ae490e8a7303 100644
--- a/doc/src/pair_reaxc.txt
+++ b/doc/src/pair_reaxc.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_resquared.txt b/doc/src/pair_resquared.txt
index 6ea5c73c0dd1c3cd7036b7aae2d0b492155b81f5..6e72408ebc1a7243f3d01aadaa79dd02afd66553 100644
--- a/doc/src/pair_resquared.txt
+++ b/doc/src/pair_resquared.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_sdk.txt b/doc/src/pair_sdk.txt
index 4cd56bc43d63c88af6a6fb53bfe1e1eede9623c1..ccf704b6f7f85b163fdcdd375b8821146ee37c37 100644
--- a/doc/src/pair_sdk.txt
+++ b/doc/src/pair_sdk.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_smd_hertz.txt b/doc/src/pair_smd_hertz.txt
index eeaa3387a44a834cfe4361a75e40d2610d29bdb6..f2d633903ab99a90ac5485e1f871c994b872f69a 100644
--- a/doc/src/pair_smd_hertz.txt
+++ b/doc/src/pair_smd_hertz.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_smd_tlsph.txt b/doc/src/pair_smd_tlsph.txt
index f73acf74ee5b1a842d2b8cd1a7ed7c632885dd75..3aeaa3155382ee4b0b0b34c0bc8beaa381c68bac 100644
--- a/doc/src/pair_smd_tlsph.txt
+++ b/doc/src/pair_smd_tlsph.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_smd_triangulated_surface.txt b/doc/src/pair_smd_triangulated_surface.txt
index c32bf3a22ea89c35efd3231b0ffbfdd72590a810..65526cfba8cc15a6be2d8dd22510106b5d6a40cf 100644
--- a/doc/src/pair_smd_triangulated_surface.txt
+++ b/doc/src/pair_smd_triangulated_surface.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_smd_ulsph.txt b/doc/src/pair_smd_ulsph.txt
index 268fe78d02294eca17134ff7fcffb276512db2be..a5bda54d5f0c46d792fc23bdbdba13f6168bbeee 100644
--- a/doc/src/pair_smd_ulsph.txt
+++ b/doc/src/pair_smd_ulsph.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_smtbq.txt b/doc/src/pair_smtbq.txt
index c8d6b21b3f1f024421dc56426aa32da817d887f7..c70202c2e13f536307ad84c1f50133490e8bff72 100644
--- a/doc/src/pair_smtbq.txt
+++ b/doc/src/pair_smtbq.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_snap.txt b/doc/src/pair_snap.txt
index c3d6e67e82f24e603fcbe49e77fd9a622ffc78f3..f9bd8910e49ddfe37a044cf9e801f937a1b0cd7e 100644
--- a/doc/src/pair_snap.txt
+++ b/doc/src/pair_snap.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_soft.txt b/doc/src/pair_soft.txt
index adbfa596c9c677506fcc4c273ed5641a7701bed4..374711825b5d4bbf656d15fab9a3753c6f2239ce 100644
--- a/doc/src/pair_soft.txt
+++ b/doc/src/pair_soft.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_sph_heatconduction.txt b/doc/src/pair_sph_heatconduction.txt
index 2387056a1b7b4b06235c3d8d88ad5edec4bccbdf..d19c28a3cb5a0fec2f893d69fc23715abed8ae64 100644
--- a/doc/src/pair_sph_heatconduction.txt
+++ b/doc/src/pair_sph_heatconduction.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_sph_idealgas.txt b/doc/src/pair_sph_idealgas.txt
index 957f901425993d91b248c9a7172a45b0753abd44..a670949a892025d8d30ca9a5d63134020483ddc3 100644
--- a/doc/src/pair_sph_idealgas.txt
+++ b/doc/src/pair_sph_idealgas.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_sph_lj.txt b/doc/src/pair_sph_lj.txt
index ef89c4ad3eaf351d07dad07e953b6dc4ea3eb139..152e6cf8a292cd5b03f895ff84282b9ac6652d63 100644
--- a/doc/src/pair_sph_lj.txt
+++ b/doc/src/pair_sph_lj.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_sph_rhosum.txt b/doc/src/pair_sph_rhosum.txt
index 352e717f76484a2b3c2c993560646fd110869b60..3cd1c5abb2577e0d7c155d7d5cedd9ae1b768307 100644
--- a/doc/src/pair_sph_rhosum.txt
+++ b/doc/src/pair_sph_rhosum.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_sph_taitwater.txt b/doc/src/pair_sph_taitwater.txt
index 9177ca80b868e417e3bf8a23d30f267fd882f3ff..7b9a8188f28b36d30e7a71d64d8b49024ffadd1e 100644
--- a/doc/src/pair_sph_taitwater.txt
+++ b/doc/src/pair_sph_taitwater.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_sph_taitwater_morris.txt b/doc/src/pair_sph_taitwater_morris.txt
index e6c5a6bb20dc302fa3105af4c3c224d9e2411b98..02f16d8982f5af327d25e4ce43fbeb9fa877015b 100644
--- a/doc/src/pair_sph_taitwater_morris.txt
+++ b/doc/src/pair_sph_taitwater_morris.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_spin_dmi.txt b/doc/src/pair_spin_dmi.txt
index a1d0cb2265b9f58a46d33072c9e819acb364c00f..375e59fe89486ebec90679a9a4c08b20f9655bb4 100644
--- a/doc/src/pair_spin_dmi.txt
+++ b/doc/src/pair_spin_dmi.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_spin_exchange.txt b/doc/src/pair_spin_exchange.txt
index a4f37a98eb4e9a205f8c08842d70ef3b6035276d..24eb635b819cd1982c5bc4a37d3e48950e13c28c 100644
--- a/doc/src/pair_spin_exchange.txt
+++ b/doc/src/pair_spin_exchange.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_spin_magelec.txt b/doc/src/pair_spin_magelec.txt
index 8ba24c46af2b98102e872b16f4c423336410338a..b338fae5dcdc3597e16dda8df691a012025114c1 100644
--- a/doc/src/pair_spin_magelec.txt
+++ b/doc/src/pair_spin_magelec.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_spin_neel.txt b/doc/src/pair_spin_neel.txt
index 8551f8d63650f50fd355903028cefd64eb96ed4c..0967632ed2037ccac12228f089b56c31c8272ad1 100644
--- a/doc/src/pair_spin_neel.txt
+++ b/doc/src/pair_spin_neel.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_srp.txt b/doc/src/pair_srp.txt
index e7f1e00d1028635db3c8cce28097cf62d54fa7d3..e784ac3d17d5f8fc0415003a6a084560d3a6a3c3 100644
--- a/doc/src/pair_srp.txt
+++ b/doc/src/pair_srp.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_style.txt b/doc/src/pair_style.txt
index 2763eb3d663689348fc3710a458d7bac13eb1047..cd395133293545306ceb7824e6158b47b5a211fb 100644
--- a/doc/src/pair_style.txt
+++ b/doc/src/pair_style.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
@@ -78,22 +78,22 @@ previously specified pair_coeff values.
 :line
 
 Here is an alphabetic list of pair styles defined in LAMMPS.  They are
-also given in more compact form in the pair section of "this
-page"_Section_commands.html#cmd_5.
+also listed in more compact form on the "Commands
+pair"_Commands_pair.html doc page.
 
 Click on the style to display the formula it computes, arguments
 specified in the pair_style command, and coefficients specified by the
 associated "pair_coeff"_pair_coeff.html command.
 
 There are also additional pair styles (not listed here) submitted by
-users which are included in the LAMMPS distribution.  The list of
-these with links to the individual styles are given in the pair
-section of "this page"_Section_commands.html#cmd_5.
+users which are included in the LAMMPS distribution.  The full list of
+all pair styles is on the "Commands pair"_Commands_pair.html doc page.
 
 There are also additional accelerated pair styles (not listed here)
-included in the LAMMPS distribution for faster performance on CPUs and
-GPUs.  The list of these with links to the individual styles are given
-in the pair section of "this page"_Section_commands.html#cmd_5.
+included in the LAMMPS distribution for faster performance on CPUs,
+GPUs, and KNLs.  The individual style names on the "Commands
+pair"_Commands_pair.html doc page are followed by one or more of
+(g,i,k,o,t) to indicate which accerlerated styles exist.
 
 "pair_style none"_pair_none.html - turn off pairwise interactions
 "pair_style hybrid"_pair_hybrid.html - multiple styles of pairwise interactions
diff --git a/doc/src/pair_sw.txt b/doc/src/pair_sw.txt
index 7c9ce4a4f90728fcc0191caa45fdcfd07ca69723..e6741791dfe8d103ded1dbcfc27a9bcaf70e9527 100644
--- a/doc/src/pair_sw.txt
+++ b/doc/src/pair_sw.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_table.txt b/doc/src/pair_table.txt
index f5e69a6d542110394747848f70a0041d79fe3a79..5e3c1f5ff6f2e1bf58c27589afc653c71c569d18 100644
--- a/doc/src/pair_table.txt
+++ b/doc/src/pair_table.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_table_rx.txt b/doc/src/pair_table_rx.txt
index 52760c396bb2daf15ca8b2d7d004e9c40dadd1a1..41be067bacfcc6eb60286b7f259926c2729e832b 100644
--- a/doc/src/pair_table_rx.txt
+++ b/doc/src/pair_table_rx.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_tersoff.txt b/doc/src/pair_tersoff.txt
index 70fe207f0afa1e69b2414ce802a760b894abf1eb..821c38f3e4174310f43c6ee504ede9b194ebdab8 100644
--- a/doc/src/pair_tersoff.txt
+++ b/doc/src/pair_tersoff.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_tersoff_mod.txt b/doc/src/pair_tersoff_mod.txt
index aced6d40d69ed54e3b1aafb415dbff4b8759f6de..ac1f79a80b772f602f951ed34e373eb3b8bb0f0b 100644
--- a/doc/src/pair_tersoff_mod.txt
+++ b/doc/src/pair_tersoff_mod.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_tersoff_zbl.txt b/doc/src/pair_tersoff_zbl.txt
index 838c2f39cf772b2342681a8e70337be2e7f160ef..a89d4e3ea1fbce4376fa787123d1a98bf25dbbb2 100644
--- a/doc/src/pair_tersoff_zbl.txt
+++ b/doc/src/pair_tersoff_zbl.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_thole.txt b/doc/src/pair_thole.txt
index 42c58e98827f0247f38bc5a164b76a4406beb200..7ce8b7cf4bed33dc699d8c08197b01392d1d6ac3 100644
--- a/doc/src/pair_thole.txt
+++ b/doc/src/pair_thole.txt
@@ -9,7 +9,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_tri_lj.txt b/doc/src/pair_tri_lj.txt
index 42a5bbdfe2285c61c67ad980eecca779666f553b..3915ffc2383c79220f2b403f7e2d43dc0041ab1e 100644
--- a/doc/src/pair_tri_lj.txt
+++ b/doc/src/pair_tri_lj.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_ufm.txt b/doc/src/pair_ufm.txt
index 5af8741502efdf511657435179ed3ea53f8cb0ad..dbc6fd0664b99572fd39dcab68c60003ceef722f 100644
--- a/doc/src/pair_ufm.txt
+++ b/doc/src/pair_ufm.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_vashishta.txt b/doc/src/pair_vashishta.txt
index e90a9d8f5005a0d2bb15658a060800574c79e1eb..2e404e8befcba50b462a0efbb61b48f0ba8cc82e 100644
--- a/doc/src/pair_vashishta.txt
+++ b/doc/src/pair_vashishta.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_write.txt b/doc/src/pair_write.txt
index 9f5970fcbc6c8c406746d752ac281e2eec3ebc9e..48ad76e76eabf624459cb37139e77ef4a09385f0 100644
--- a/doc/src/pair_write.txt
+++ b/doc/src/pair_write.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_yukawa.txt b/doc/src/pair_yukawa.txt
index 979165dda0e97afb88bfb4c1a00e91193589b076..5a8363260a5e31f507d279500ea9eb2c78199758 100644
--- a/doc/src/pair_yukawa.txt
+++ b/doc/src/pair_yukawa.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_yukawa_colloid.txt b/doc/src/pair_yukawa_colloid.txt
index a1752c261ed65c29e4f25644c40c99fc8da3dfb5..515062d9eb679cefc969f91e41c376b265541bd4 100644
--- a/doc/src/pair_yukawa_colloid.txt
+++ b/doc/src/pair_yukawa_colloid.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_zbl.txt b/doc/src/pair_zbl.txt
index 0507083295671c1458a485a311629152b432b2fd..1472c7b6726d970179eeacd97915edabdfcdd55c 100644
--- a/doc/src/pair_zbl.txt
+++ b/doc/src/pair_zbl.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/pair_zero.txt b/doc/src/pair_zero.txt
index e58b33c75f4d0261d43a6eafee975c470e79c627..b324003bd1ca252e6ecaa8a341219dfb11d521cd 100644
--- a/doc/src/pair_zero.txt
+++ b/doc/src/pair_zero.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/partition.txt b/doc/src/partition.txt
index 610eee99b300bd96486991c1841cfde1a2b1d8e5..d4fe06c098fd2de94520c38b96346407a0cbf3b9 100644
--- a/doc/src/partition.txt
+++ b/doc/src/partition.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/prd.txt b/doc/src/prd.txt
index f298d83385fc42f2a89adf9b471ced25c84dab09..b2145ebad1a43ac0037f484f030a945479dd0ecb 100644
--- a/doc/src/prd.txt
+++ b/doc/src/prd.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/print.txt b/doc/src/print.txt
index 77e0c7cfd3d64ed7a6bfeb6dcd17b716f0b1e1f3..476d4104fab9bfcf41aa9ef7b7216523e6faf0d4 100644
--- a/doc/src/print.txt
+++ b/doc/src/print.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/processors.txt b/doc/src/processors.txt
index e54b2cede3b94e8bb13324c22f3352601b8b79d8..df13ae1f617fd9507bdbf7192b52d668c3ca44df 100644
--- a/doc/src/processors.txt
+++ b/doc/src/processors.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/python.txt b/doc/src/python.txt
index d670fcc77f8ef4377c829ae0fa486fa9ba8347a1..4f4faca8f43c5fc6ca5db28f748238798405b862 100644
--- a/doc/src/python.txt
+++ b/doc/src/python.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
@@ -199,9 +199,9 @@ The {here} keyword does the same thing, except that the Python code
 follows as a single argument to the {here} keyword.  This can be done
 using triple quotes as delimiters, as in the examples above.  This
 allows Python code to be listed verbatim in your input script, with
-proper indentation, blank lines, and comments, as desired.  See
-"Section 3.2"_Section_commands.html#cmd_2, for an explanation of how
-triple quotes can be used as part of input script syntax.
+proper indentation, blank lines, and comments, as desired.  See the
+"Commands parse"_Commands_parse.html doc page, for an explanation of
+how triple quotes can be used as part of input script syntax.
 
 The {exists} keyword takes no argument.  It means that Python code
 containing the required Python function defined by the {func} setting,
diff --git a/doc/src/quit.txt b/doc/src/quit.txt
index 843d3de7f3545dfd330f7e7624fe21a3c3c6e430..802df97711e5c4b38e816f12f18043440cb669f3 100644
--- a/doc/src/quit.txt
+++ b/doc/src/quit.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/read_data.txt b/doc/src/read_data.txt
index 4f6a3988b9596ea48c425643f794219ec5217c9c..ded51a4d99855abfd9abc4361c1f0f2b052729dd 100644
--- a/doc/src/read_data.txt
+++ b/doc/src/read_data.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/read_dump.txt b/doc/src/read_dump.txt
index 21c6df5017a50b8bf35ef43198c659f60ae4fb51..a3c0733e07369da85b63f222069ce12b224a3f13 100644
--- a/doc/src/read_dump.txt
+++ b/doc/src/read_dump.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/read_restart.txt b/doc/src/read_restart.txt
index 6f6a82822929d26afd5d0a10ad9c28aa3bd252f7..488c36f02081d5be3c3a9a9067ed2638e4738c63 100644
--- a/doc/src/read_restart.txt
+++ b/doc/src/read_restart.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/region.txt b/doc/src/region.txt
index b32c09ed6fd9c6065a268f895b607a4f1653bbaa..21396ae1fd2b6652fc6928d24f685cfc39bc7031 100644
--- a/doc/src/region.txt
+++ b/doc/src/region.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/replicate.txt b/doc/src/replicate.txt
index 08523ecdd848a58ff04b8b63747fcd6c5c388914..0195dce9114f4a3d0bf30a805a1c0f0e31a70be7 100644
--- a/doc/src/replicate.txt
+++ b/doc/src/replicate.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/rerun.txt b/doc/src/rerun.txt
index edf94cc711c2e5a1ff7b34efed059b7e77327981..8eb3ebd5a19458aec21e3c799ef80cacf936e998 100644
--- a/doc/src/rerun.txt
+++ b/doc/src/rerun.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/reset_ids.txt b/doc/src/reset_ids.txt
index 8655a9d54f3c5b0f7e97512f6553dd6246bfa321..391b51fde99e167d813bef98b3a62f96786ed1de 100644
--- a/doc/src/reset_ids.txt
+++ b/doc/src/reset_ids.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/reset_timestep.txt b/doc/src/reset_timestep.txt
index 79a5812ca1f2a569c23d71e48a6dc8ffcc89d002..0d518655fb774108eb95da66297d854300d945b5 100644
--- a/doc/src/reset_timestep.txt
+++ b/doc/src/reset_timestep.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/restart.txt b/doc/src/restart.txt
index 7c39ae1404eebb9c70d1c7a99730d00200a25af2..6f2dc5ca467c354a9c576d467af4c5d49c1e9301 100644
--- a/doc/src/restart.txt
+++ b/doc/src/restart.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/run.txt b/doc/src/run.txt
index 02860c0b97a7bf73afe215032ed13e23f2169def..c7c73463d92d49bb8e72ca9b549e38d50960f67a 100644
--- a/doc/src/run.txt
+++ b/doc/src/run.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/run_style.txt b/doc/src/run_style.txt
index 6f1f719d6445f0d813c732c24790946359b74c3a..deee51cfd3d6fc0857ea99b5b169d323cbc323c7 100644
--- a/doc/src/run_style.txt
+++ b/doc/src/run_style.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/set.txt b/doc/src/set.txt
index d2235d5c32bc03426c8f7c584c10c5fc2b6a7f1c..b83ad54f4e5fbef3b26a01372e0f3d959db90c9a 100644
--- a/doc/src/set.txt
+++ b/doc/src/set.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/shell.txt b/doc/src/shell.txt
index 205164f874173abd4de45b045e91ec741092acb9..d274f498e595c5abcfca59c182bd36c827016c90 100644
--- a/doc/src/shell.txt
+++ b/doc/src/shell.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/special_bonds.txt b/doc/src/special_bonds.txt
index 1021c4856b02cc7cb91901d429eb8c1fc2ca22c4..a57b61664d56e76b28d3aad9f2059bdbb24a9c31 100644
--- a/doc/src/special_bonds.txt
+++ b/doc/src/special_bonds.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/suffix.txt b/doc/src/suffix.txt
index 74f69b6dfe96296259f536c80e621b23b89edef1..bb0619f1e04af5ab1bafc7772c2e40f09e1f3767 100644
--- a/doc/src/suffix.txt
+++ b/doc/src/suffix.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/tad.txt b/doc/src/tad.txt
index 9ffa24d01245c15dca6a082c596ef3c1d3889e58..a26ff79318ceed4f91cd402bb095a08c546baea5 100644
--- a/doc/src/tad.txt
+++ b/doc/src/tad.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/temper.txt b/doc/src/temper.txt
index e65f59ebedec79dceb144b5ab9a7627df8640d99..c7b482acc6467948a15321a363e138f5fb1962ae 100644
--- a/doc/src/temper.txt
+++ b/doc/src/temper.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/temper_grem.txt b/doc/src/temper_grem.txt
index 6145c8704cc131b96d21464031c9697733be02d1..9cb1bab78465c890c0f6377d9c5fb45d0803b145 100644
--- a/doc/src/temper_grem.txt
+++ b/doc/src/temper_grem.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/temper_npt.txt b/doc/src/temper_npt.txt
index 4ad49f9e3327ded89da41c2fd405929175990a67..4eee225de73cfd0e3ea3b4354a293d902fa8250c 100644
--- a/doc/src/temper_npt.txt
+++ b/doc/src/temper_npt.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 temper/npt command :h3
diff --git a/doc/src/thermo.txt b/doc/src/thermo.txt
index 1d5d34995cd3cc979f3537b529950032be2ea4ba..5f12f987076bc54f50df9cbd5f37aa9c2be40b7e 100644
--- a/doc/src/thermo.txt
+++ b/doc/src/thermo.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/thermo_modify.txt b/doc/src/thermo_modify.txt
index e9aca0f20a1b2ed5c2d90ec3a70714c2dea25bf4..ca2957de776a5d3054da85a0eddfbcaad25bedf9 100644
--- a/doc/src/thermo_modify.txt
+++ b/doc/src/thermo_modify.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/thermo_style.txt b/doc/src/thermo_style.txt
index 64e0785586c76a2838a6d4d9b82ec8bc06d0066d..cbc2612f28c69a49bcd4dcb28b3b1c7a132fd85c 100644
--- a/doc/src/thermo_style.txt
+++ b/doc/src/thermo_style.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/timer.txt b/doc/src/timer.txt
index 768c3e1353fb3e6495f63f2d84830c060b4bf74a..10737dbda0cebfea9b99582c28327168aa55faa6 100644
--- a/doc/src/timer.txt
+++ b/doc/src/timer.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/timestep.txt b/doc/src/timestep.txt
index 639ad6f31136ff9a34f085b8d254b983a9e1ba4d..ee0ace05b9cf7397539cf615e4a87217270f4949 100644
--- a/doc/src/timestep.txt
+++ b/doc/src/timestep.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/uncompute.txt b/doc/src/uncompute.txt
index 49b46781d7ac363156674ef935881dacab2e048f..4c788d472207b302a51f73abddaf34803cae5062 100644
--- a/doc/src/uncompute.txt
+++ b/doc/src/uncompute.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/undump.txt b/doc/src/undump.txt
index a2a371aca5187a9248e8e33e33792087040a66e7..cc3d8b9103ffd2d9eff33bf3dbaefda820c29903 100644
--- a/doc/src/undump.txt
+++ b/doc/src/undump.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/unfix.txt b/doc/src/unfix.txt
index dcc4499b20b4b784779f9038b30c541a5585335e..9608b39c7e2c2056023b9da6607b8e280ed52a11 100644
--- a/doc/src/unfix.txt
+++ b/doc/src/unfix.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/units.txt b/doc/src/units.txt
index 0b856dcc68b67a9f7df9f159e779f8fb5a097379..8df8fe6810ec1163f366a7e53ad4f019418425da 100644
--- a/doc/src/units.txt
+++ b/doc/src/units.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/variable.txt b/doc/src/variable.txt
index 717c77c07908099a76f4f32991697bfcb8294bc6..c6598ccb514d2855259038e99d1560488f7cdff9 100644
--- a/doc/src/variable.txt
+++ b/doc/src/variable.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
@@ -124,8 +124,8 @@ provide, so that the variable gets its value from the evaluation of
 the Python code.  Variables of style {internal} are used by a few
 commands which set their value directly.
 
-NOTE: As discussed in "Section 3.2"_Section_commands.html#cmd_2 of the
-manual, an input script can use "immediate" variables, specified as
+NOTE: As discussed on the "Commands parse"_Commands_parse.html doc
+page, an input script can use "immediate" variables, specified as
 $(formula) with parenthesis, where the formula has the same syntax as
 equal-style variables described on this page.  This is a convenient
 way to evaluate a formula immediately without using the variable
@@ -198,7 +198,7 @@ the same thing.
 
 :line
 
-"This section"_Section_commands.html#cmd_2 of the manual explains how
+The "Commands parse"_Commands_parse.html doc page explains how
 occurrences of a variable name in an input script line are replaced by
 the variable's string.  The variable name can be referenced as $x if
 the name "x" is a single character, or as $\{LoopVar\} if the name
@@ -312,8 +312,8 @@ If you simply wish to print a variable value with desired precision to
 the screen or logfile via the "print"_print.html or "fix
 print"_fix_print.html commands, you can also do this by specifying an
 "immediate" variable with a trailing colon and format string, as part
-of the string argument of those commands.  This is explained in
-"Section 3.2"_Section_commands.html#cmd_2.
+of the string argument of those commands.  This is explained on the
+"Commands parse"_Commands_parse.html doc page.
 
 For the {getenv} style, a single string is assigned to the variable
 which should be the name of an environment variable.  When the
@@ -1119,24 +1119,23 @@ Vectors" discussion above.
 
 If you want an equal-style variable to be evaluated immediately, it
 may be the case that you do not need to define a variable at all.  See
-"Section 3.2"_Section_commands.html#cmd_2 of the manual, which
-describes the use of "immediate" variables in an input script,
-specified as $(formula) with parenthesis, where the formula has the
-same syntax as equal-style variables described on this page.  This
-effectively evaluates a formula immediately without using the variable
-command to define a named variable.
+the "Commands parse"_Commands_parse.html doc page for info on how to
+use "immediate" variables in an input script, specified as $(formula)
+with parenthesis, where the formula has the same syntax as equal-style
+variables described on this page.  This effectively evaluates a
+formula immediately without using the variable command to define a
+named variable.
 
 More generally, there is a difference between referencing a variable
 with a leading $ sign (e.g. $x or $\{abc\}) versus with a leading "v_"
 (e.g. v_x or v_abc).  The former can be used in any input script
 command, including a variable command.  The input script parser
 evaluates the reference variable immediately and substitutes its value
-into the command.  As explained in "Section
-3.2"_Section_commands.html#cmd_2 for "Parsing rules", you can also use
-un-named "immediate" variables for this purpose.  For example, a
-string like this $((xlo+xhi)/2+sqrt(v_area)) in an input script
-command evaluates the string between the parenthesis as an equal-style
-variable formula.
+into the command.  As explained on the "Commands
+parse"_Commands_parse.html doc page, you can also use un-named
+"immediate" variables for this purpose.  For example, a string like
+this $((xlo+xhi)/2+sqrt(v_area)) in an input script command evaluates
+the string between the parenthesis as an equal-style variable formula.
 
 Referencing a variable with a leading "v_" is an optional or required
 kind of argument for some commands (e.g. the "fix
@@ -1180,10 +1179,9 @@ quotes if it contains variables preceded by $ signs.  For example,
 
 variable vratio equal "$\{vfinal\}/$\{v0\}" :pre
 
-This is because the quotes prevent variable substitution (see "this
-section"_Section_commands.html#cmd_2 on parsing input script
-commands), and thus an error will occur when the formula for "vratio"
-is evaluated later.
+This is because the quotes prevent variable substitution (explained on
+the "Commands parse"_Commands_parse.html doc page), and thus an error
+will occur when the formula for "vratio" is evaluated later.
 
 :line
 
diff --git a/doc/src/velocity.txt b/doc/src/velocity.txt
index 057f0054be4e14106c779ee7e374b898152d03fe..96d3fa6dc4fa53e1b7d399fc2d774afbff682de5 100644
--- a/doc/src/velocity.txt
+++ b/doc/src/velocity.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/write_coeff.txt b/doc/src/write_coeff.txt
index 764e119a9d1d310ae5f969a9163d1ec5753ebe1d..5dc4b331dedbe2940286af653c81a76654cb1347 100644
--- a/doc/src/write_coeff.txt
+++ b/doc/src/write_coeff.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/write_data.txt b/doc/src/write_data.txt
index c76f20319c3182a2d9298d8aada887cb806878f3..d8a33f457f2ab15cb38d6922ec54c5b5b8d5d202 100644
--- a/doc/src/write_data.txt
+++ b/doc/src/write_data.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/write_dump.txt b/doc/src/write_dump.txt
index 840716085feff0aaf6b7790befc98b902be87ea3..e67697900129a153801eb53f454641075955189d 100644
--- a/doc/src/write_dump.txt
+++ b/doc/src/write_dump.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
diff --git a/doc/src/write_restart.txt b/doc/src/write_restart.txt
index ff3b652dba75feefdb3841bf764f885cc0b3a9d1..3935a5d5387bfd6118134c605058a146fbc81a43 100644
--- a/doc/src/write_restart.txt
+++ b/doc/src/write_restart.txt
@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line