Unverified Commit 8f9c3a3a authored by Axel Kohlmeyer's avatar Axel Kohlmeyer
Browse files

Merge branch 'post-patch-tweaks' into doc-styles-check

parents a38cf075 84a97543

doc/src/Build_extras.rst

+1 −1
Changes for doc/src/Build_extras.rst: 1 added line, 1 removed line.
Original line number Diff line number Diff line
@@ -203,7 +203,7 @@ inside the CMake build directory. If the KIM library is already on 
your system (in a location CMake cannot find it), set the PKG\_CONFIG\_PATH

environment variable so that libkim-api can be found.



For using KIM web queries.

For using OpenKIM web queries in LAMMPS.



If LMP\_DEBUG\_CURL is set, the libcurl verbose mode will be on, and any

libcurl calls within the KIM web query display a lot of information about

doc/src/Commands_all.rst

+51 −45
Changes for doc/src/Commands_all.rst: 51 added lines, 45 removed lines.
Original line number Diff line number Diff line
@@ -25,26 +25,26 @@ An alphabetic list of all general LAMMPS commands. 
   * :doc:`atom_style <atom_style>`

   * :doc:`balance <balance>`

   * :doc:`bond_coeff <bond_coeff>`

   * :doc:`bond\_style <bond_style>`

   * :doc:`bond\_write <bond_write>`

   * :doc:`bond_style <bond_style>`

   * :doc:`bond_write <bond_write>`

   * :doc:`boundary <boundary>`

   * :doc:`box <box>`

   * :doc:`change\_box <change_box>`

   * :doc:`change_box <change_box>`

   * :doc:`clear <clear>`

   * :doc:`comm\_modify <comm_modify>`

   * :doc:`comm\_style <comm_style>`

   * :doc:`comm_modify <comm_modify>`

   * :doc:`comm_style <comm_style>`

   * :doc:`compute <compute>`

   * :doc:`compute\_modify <compute_modify>`

   * :doc:`create\_atoms <create_atoms>`

   * :doc:`create\_bonds <create_bonds>`

   * :doc:`create\_box <create_box>`

   * :doc:`delete\_atoms <delete_atoms>`

   * :doc:`delete\_bonds <delete_bonds>`

   * :doc:`compute_modify <compute_modify>`

   * :doc:`create_atoms <create_atoms>`

   * :doc:`create_bonds <create_bonds>`

   * :doc:`create_box <create_box>`

   * :doc:`delete_atoms <delete_atoms>`

   * :doc:`delete_bonds <delete_bonds>`

   * :doc:`dielectric <dielectric>`

   * :doc:`dihedral\_coeff <dihedral_coeff>`

   * :doc:`dihedral\_style <dihedral_style>`

   * :doc:`dihedral_coeff <dihedral_coeff>`

   * :doc:`dihedral_style <dihedral_style>`

   * :doc:`dimension <dimension>`

   * :doc:`displace\_atoms <displace_atoms>`

   * :doc:`displace_atoms <displace_atoms>`

   * :doc:`dump <dump>`

   * :doc:`dump adios <dump_adios>`

   * :doc:`dump image <dump_image>`
@@ -52,75 +52,77 @@ An alphabetic list of all general LAMMPS commands. 
   * :doc:`dump netcdf <dump_netcdf>`

   * :doc:`dump netcdf/mpiio <dump_netcdf>`

   * :doc:`dump vtk <dump_vtk>`

   * :doc:`dump\_modify <dump_modify>`

   * :doc:`dynamical\_matrix <dynamical_matrix>`

   * :doc:`dump_modify <dump_modify>`

   * :doc:`dynamical_matrix <dynamical_matrix>`

   * :doc:`echo <echo>`

   * :doc:`fix <fix>`

   * :doc:`fix\_modify <fix_modify>`

   * :doc:`fix_modify <fix_modify>`

   * :doc:`group <group>`

   * :doc:`group2ndx <group2ndx>`

   * :doc:`hyper <hyper>`

   * :doc:`if <if>`

   * :doc:`improper\_coeff <improper_coeff>`

   * :doc:`improper\_style <improper_style>`

   * :doc:`improper_coeff <improper_coeff>`

   * :doc:`improper_style <improper_style>`

   * :doc:`include <include>`

   * :doc:`info <info>`

   * :doc:`jump <jump>`

   * :doc:`kim\_init <kim_commands>`

   * :doc:`kim\_interactions <kim_commands>`

   * :doc:`kim\_query <kim_commands>`

   * :doc:`kspace\_modify <kspace_modify>`

   * :doc:`kspace\_style <kspace_style>`

   * :doc:`kim_init <kim_commands>`

   * :doc:`kim_interactions <kim_commands>`

   * :doc:`kim_param <kim_commands>`

   * :doc:`kim_query <kim_commands>`

   * :doc:`kspace_modify <kspace_modify>`

   * :doc:`kspace_style <kspace_style>`

   * :doc:`label <label>`

   * :doc:`lattice <lattice>`

   * :doc:`log <log>`

   * :doc:`mass <mass>`

   * :doc:`message <message>`

   * :doc:`minimize <minimize>`

   * :doc:`min\_modify <min_modify>`

   * :doc:`min\_style <min_style>`

   * :doc:`min\_style spin <min_spin>`

   * :doc:`min_modify <min_modify>`

   * :doc:`min_style <min_style>`

   * :doc:`min_style spin <min_spin>`

   * :doc:`molecule <molecule>`

   * :doc:`ndx2group <group2ndx>`

   * :doc:`neb <neb>`

   * :doc:`neb/spin <neb_spin>`

   * :doc:`neigh\_modify <neigh_modify>`

   * :doc:`neigh_modify <neigh_modify>`

   * :doc:`neighbor <neighbor>`

   * :doc:`newton <newton>`

   * :doc:`next <next>`

   * :doc:`package <package>`

   * :doc:`pair\_coeff <pair_coeff>`

   * :doc:`pair\_modify <pair_modify>`

   * :doc:`pair\_write <pair_write>`

   * :doc:`pair_coeff <pair_coeff>`

   * :doc:`pair_modify <pair_modify>`

   * :doc:`pair_write <pair_write>`

   * :doc:`partition <partition>`

   * :doc:`prd <prd>`

   * :doc:`print <print>`

   * :doc:`processors <processors>`

   * :doc:`python <python>`

   * :doc:`quit <quit>`

   * :doc:`read\_data <read_data>`

   * :doc:`read\_dump <read_dump>`

   * :doc:`read\_restart <read_restart>`

   * :doc:`read_data <read_data>`

   * :doc:`read_dump <read_dump>`

   * :doc:`read_restart <read_restart>`

   * :doc:`region <region>`

   * :doc:`replicate <replicate>`

   * :doc:`rerun <rerun>`

   * :doc:`reset\_ids <reset_ids>`

   * :doc:`reset\_timestep <reset_timestep>`

   * :doc:`reset_ids <reset_ids>`

   * :doc:`reset_timestep <reset_timestep>`

   * :doc:`restart <restart>`

   * :doc:`run <run>`

   * :doc:`run\_style <run_style>`

   * :doc:`run_style <run_style>`

   * :doc:`server <server>`

   * :doc:`set <set>`

   * :doc:`shell <shell>`

   * :doc:`special\_bonds <special_bonds>`

   * :doc:`special_bonds <special_bonds>`

   * :doc:`suffix <suffix>`

   * :doc:`tad <tad>`

   * :doc:`temper <temper>`

   * :doc:`temper/grem <temper_grem>`

   * :doc:`temper/npt <temper_npt>`

   * :doc:`thermo <thermo>`

   * :doc:`thermo\_modify <thermo_modify>`

   * :doc:`thermo\_style <thermo_style>`

   * :doc:`third\_order <third_order>`

   * :doc:`thermo_modify <thermo_modify>`

   * :doc:`thermo_style <thermo_style>`

   * :doc:`third_order <third_order>`

   * :doc:`timer <timer>`

   * :doc:`timestep <timestep>`

   * :doc:`uncompute <uncompute>`
@@ -129,7 +131,11 @@ An alphabetic list of all general LAMMPS commands. 
   * :doc:`units <units>`

   * :doc:`variable <variable>`

   * :doc:`velocity <velocity>`

   * :doc:`write\_coeff <write_coeff>`

   * :doc:`write\_data <write_data>`

   * :doc:`write\_dump <write_dump>`

   * :doc:`write\_restart <write_restart>`
 
   * :doc:`write_coeff <write_coeff>`

   * :doc:`write_data <write_data>`

   * :doc:`write_dump <write_dump>`

   * :doc:`write_restart <write_restart>`

   *

   *

   *

   *

doc/src/Commands_bond.rst

+1 −5
Changes for doc/src/Commands_bond.rst: 1 added line, 5 removed lines.
Original line number Diff line number Diff line
@@ -44,12 +44,10 @@ OPT. 
   * :doc:`nonlinear (o) <bond_nonlinear>`

   * :doc:`oxdna/fene <bond_oxdna>`

   * :doc:`oxdna2/fene <bond_oxdna>`

   * :doc:`oxrna2/fene <bond_oxdna>`

   * :doc:`quartic (o) <bond_quartic>`

   * :doc:`table (o) <bond_table>`

   *

   *



---



.. _angle:
@@ -93,8 +91,6 @@ OPT. 
   * :doc:`table (o) <angle_table>`

   *



---



.. _dihedral:



dihedral_style potentials

doc/src/Commands_pair.rst

+4 −4
Changes for doc/src/Commands_pair.rst: 4 added lines, 4 removed lines.
Original line number Diff line number Diff line
@@ -11,10 +11,10 @@ 
   * :ref:`Improper styles <improper>`

   * :doc:`KSpace styles <Commands_kspace>`



Pair\_style potentials

Pair_style potentials

======================



All LAMMPS :doc:`pair\_style <pair_style>` commands.  Some styles have

All LAMMPS :doc:`pair_style <pair_style>` 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.
@@ -146,7 +146,7 @@ OPT. 
   * :doc:`lj/cut/soft (o) <pair_fep_soft>`

   * :doc:`lj/cut/thole/long (o) <pair_thole>`

   * :doc:`lj/cut/tip4p/cut (o) <pair_lj>`

   * :doc:`lj/cut/tip4p/long (ot) <pair_lj>`

   * :doc:`lj/cut/tip4p/long (got) <pair_lj>`

   * :doc:`lj/cut/tip4p/long/soft (o) <pair_fep_soft>`

   * :doc:`lj/expand (gko) <pair_lj_expand>`

   * :doc:`lj/expand/coul/long (g) <pair_lj_expand>`
@@ -209,7 +209,7 @@ OPT. 
   * :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>`

   * :doc:`smd/hertz <pair_smd_hertz>`

   * :doc:`smd/tlsph <pair_smd_tlsph>`

   * :doc:`smd/tri\_surface <pair_smd_triangulated_surface>`

   * :doc:`smd/tri_surface <pair_smd_triangulated_surface>`

   * :doc:`smd/ulsph <pair_smd_ulsph>`

   * :doc:`smtbq <pair_smtbq>`

   * :doc:`snap (k) <pair_snap>`

doc/src/pair_lj.rst

+3 −3
Changes for doc/src/pair_lj.rst: 3 added lines, 3 removed lines.
Original line number Diff line number Diff line
@@ -90,6 +90,9 @@ pair\_style lj/cut/coul/wolf/omp command 
pair\_style lj/cut/tip4p/cut command

====================================



pair\_style lj/cut/tip4p/cut/gpu command

========================================



pair\_style lj/cut/tip4p/cut/omp command

========================================
@@ -102,9 +105,6 @@ pair\_style lj/cut/tip4p/long/omp command 
pair\_style lj/cut/tip4p/long/opt command

=========================================



pair\_style lj/cut/tip4p/long/gpu command

=====================================



Syntax

""""""

CRA Git | Maintained and supported by SUSTech CRA and CCSE