Unverified Commit 587fc9d9 authored by Axel Kohlmeyer's avatar Axel Kohlmeyer Committed by GitHub
Browse files

Merge pull request #1828 from lammps/post-patch-tweaks 

minor omissions in recent patch release
parents 7ebddb60 b2c43856

doc/src/Build_extras.rst

+1 −1
Original line number Original line 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

your system (in a location CMake cannot find it), set the PKG\_CONFIG\_PATH

environment variable so that libkim-api can be found.

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

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

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

doc/src/Commands_all.rst

+51 −45
Original line number Original line Diff line number Diff line
@@ -25,26 +25,26 @@ An alphabetic list of all general LAMMPS commands. 
   * :doc:`atom_style <atom_style>`

   * :doc:`atom_style <atom_style>`

   * :doc:`balance <balance>`

   * :doc:`balance <balance>`

   * :doc:`bond_coeff <bond_coeff>`

   * :doc:`bond_coeff <bond_coeff>`

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

   * :doc:`bond_style <bond_style>`

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

   * :doc:`bond_write <bond_write>`

   * :doc:`boundary <boundary>`

   * :doc:`boundary <boundary>`

   * :doc:`box <box>`

   * :doc:`box <box>`

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

   * :doc:`change_box <change_box>`

   * :doc:`clear <clear>`

   * :doc:`clear <clear>`

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

   * :doc:`comm_modify <comm_modify>`

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

   * :doc:`comm_style <comm_style>`

   * :doc:`compute <compute>`

   * :doc:`compute <compute>`

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

   * :doc:`compute_modify <compute_modify>`

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

   * :doc:`create_atoms <create_atoms>`

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

   * :doc:`create_bonds <create_bonds>`

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

   * :doc:`create_box <create_box>`

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

   * :doc:`delete_atoms <delete_atoms>`

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

   * :doc:`delete_bonds <delete_bonds>`

   * :doc:`dielectric <dielectric>`

   * :doc:`dielectric <dielectric>`

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

   * :doc:`dihedral_coeff <dihedral_coeff>`

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

   * :doc:`dihedral_style <dihedral_style>`

   * :doc:`dimension <dimension>`

   * :doc:`dimension <dimension>`

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

   * :doc:`displace_atoms <displace_atoms>`

   * :doc:`dump <dump>`

   * :doc:`dump <dump>`

   * :doc:`dump adios <dump_adios>`

   * :doc:`dump adios <dump_adios>`

   * :doc:`dump image <dump_image>`

   * :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 <dump_netcdf>`

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

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

   * :doc:`dump vtk <dump_vtk>`

   * :doc:`dump vtk <dump_vtk>`

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

   * :doc:`dump_modify <dump_modify>`

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

   * :doc:`dynamical_matrix <dynamical_matrix>`

   * :doc:`echo <echo>`

   * :doc:`echo <echo>`

   * :doc:`fix <fix>`

   * :doc:`fix <fix>`

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

   * :doc:`fix_modify <fix_modify>`

   * :doc:`group <group>`

   * :doc:`group <group>`

   * :doc:`group2ndx <group2ndx>`

   * :doc:`group2ndx <group2ndx>`

   * :doc:`hyper <hyper>`

   * :doc:`hyper <hyper>`

   * :doc:`if <if>`

   * :doc:`if <if>`

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

   * :doc:`improper_coeff <improper_coeff>`

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

   * :doc:`improper_style <improper_style>`

   * :doc:`include <include>`

   * :doc:`include <include>`

   * :doc:`info <info>`

   * :doc:`jump <jump>`

   * :doc:`jump <jump>`

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

   * :doc:`kim_init <kim_commands>`

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

   * :doc:`kim_interactions <kim_commands>`

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

   * :doc:`kim_param <kim_commands>`

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

   * :doc:`kim_query <kim_commands>`

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

   * :doc:`kspace_modify <kspace_modify>`

   * :doc:`kspace_style <kspace_style>`

   * :doc:`label <label>`

   * :doc:`label <label>`

   * :doc:`lattice <lattice>`

   * :doc:`lattice <lattice>`

   * :doc:`log <log>`

   * :doc:`log <log>`

   * :doc:`mass <mass>`

   * :doc:`mass <mass>`

   * :doc:`message <message>`

   * :doc:`message <message>`

   * :doc:`minimize <minimize>`

   * :doc:`minimize <minimize>`

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

   * :doc:`min_modify <min_modify>`

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

   * :doc:`min_style <min_style>`

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

   * :doc:`min_style spin <min_spin>`

   * :doc:`molecule <molecule>`

   * :doc:`molecule <molecule>`

   * :doc:`ndx2group <group2ndx>`

   * :doc:`ndx2group <group2ndx>`

   * :doc:`neb <neb>`

   * :doc:`neb <neb>`

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

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

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

   * :doc:`neigh_modify <neigh_modify>`

   * :doc:`neighbor <neighbor>`

   * :doc:`neighbor <neighbor>`

   * :doc:`newton <newton>`

   * :doc:`newton <newton>`

   * :doc:`next <next>`

   * :doc:`next <next>`

   * :doc:`package <package>`

   * :doc:`package <package>`

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

   * :doc:`pair_coeff <pair_coeff>`

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

   * :doc:`pair_modify <pair_modify>`

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

   * :doc:`pair_write <pair_write>`

   * :doc:`partition <partition>`

   * :doc:`partition <partition>`

   * :doc:`prd <prd>`

   * :doc:`prd <prd>`

   * :doc:`print <print>`

   * :doc:`print <print>`

   * :doc:`processors <processors>`

   * :doc:`processors <processors>`

   * :doc:`python <python>`

   * :doc:`python <python>`

   * :doc:`quit <quit>`

   * :doc:`quit <quit>`

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

   * :doc:`read_data <read_data>`

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

   * :doc:`read_dump <read_dump>`

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

   * :doc:`read_restart <read_restart>`

   * :doc:`region <region>`

   * :doc:`region <region>`

   * :doc:`replicate <replicate>`

   * :doc:`replicate <replicate>`

   * :doc:`rerun <rerun>`

   * :doc:`rerun <rerun>`

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

   * :doc:`reset_ids <reset_ids>`

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

   * :doc:`reset_timestep <reset_timestep>`

   * :doc:`restart <restart>`

   * :doc:`restart <restart>`

   * :doc:`run <run>`

   * :doc:`run <run>`

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

   * :doc:`run_style <run_style>`

   * :doc:`server <server>`

   * :doc:`server <server>`

   * :doc:`set <set>`

   * :doc:`set <set>`

   * :doc:`shell <shell>`

   * :doc:`shell <shell>`

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

   * :doc:`special_bonds <special_bonds>`

   * :doc:`suffix <suffix>`

   * :doc:`suffix <suffix>`

   * :doc:`tad <tad>`

   * :doc:`tad <tad>`

   * :doc:`temper <temper>`

   * :doc:`temper <temper>`

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

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

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

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

   * :doc:`thermo <thermo>`

   * :doc:`thermo <thermo>`

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

   * :doc:`thermo_modify <thermo_modify>`

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

   * :doc:`thermo_style <thermo_style>`

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

   * :doc:`third_order <third_order>`

   * :doc:`timer <timer>`

   * :doc:`timer <timer>`

   * :doc:`timestep <timestep>`

   * :doc:`timestep <timestep>`

   * :doc:`uncompute <uncompute>`

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

   * :doc:`units <units>`

   * :doc:`variable <variable>`

   * :doc:`variable <variable>`

   * :doc:`velocity <velocity>`

   * :doc:`velocity <velocity>`

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

   * :doc:`write_coeff <write_coeff>`

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

   * :doc:`write_data <write_data>`

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

   * :doc:`write_dump <write_dump>`

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

   *

   *

   *

   *

doc/src/Commands_bond.rst

+5 −9
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@@ -13,7 +13,7 @@ 




.. _bond:

.. _bond:





bond_style potentials

Bond_style potentials

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

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





All LAMMPS :doc:`bond_style <bond_style>` commands.  Some styles have

All LAMMPS :doc:`bond_style <bond_style>` commands.  Some styles have
@@ -44,16 +44,14 @@ OPT. 
   * :doc:`nonlinear (o) <bond_nonlinear>`

   * :doc:`nonlinear (o) <bond_nonlinear>`

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

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

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

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

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

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

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

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

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

   *

   *

   *



---





.. _angle:

.. _angle:





angle_style potentials

Angle_style potentials

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

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





All LAMMPS :doc:`angle_style <angle_style>` commands.  Some styles have

All LAMMPS :doc:`angle_style <angle_style>` commands.  Some styles have
@@ -93,11 +91,9 @@ OPT. 
   * :doc:`table (o) <angle_table>`

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

   *

   *





---



.. _dihedral:

.. _dihedral:





dihedral_style potentials

Dihedral_style potentials

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

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





All LAMMPS :doc:`dihedral_style <dihedral_style>` commands.  Some styles

All LAMMPS :doc:`dihedral_style <dihedral_style>` commands.  Some styles
@@ -136,7 +132,7 @@ OPT. 




.. _improper:

.. _improper:





improper_style potentials

Improper_style potentials

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

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





All LAMMPS :doc:`improper\_style <improper_style>` commands.  Some styles

All LAMMPS :doc:`improper\_style <improper_style>` commands.  Some styles

doc/src/Commands_fix.rst

+8 −8
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@@ -105,13 +105,13 @@ OPT. 
   * :doc:`mvv/edpd <fix_mvv_dpd>`

   * :doc:`mvv/edpd <fix_mvv_dpd>`

   * :doc:`mvv/tdpd <fix_mvv_dpd>`

   * :doc:`mvv/tdpd <fix_mvv_dpd>`

   * :doc:`neb <fix_neb>`

   * :doc:`neb <fix_neb>`

   * :doc:`neb\_spin <fix_neb_spin>`

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

   * :doc:`nph (ko) <fix_nh>`

   * :doc:`nph (ko) <fix_nh>`

   * :doc:`nph/asphere (o) <fix_nph_asphere>`

   * :doc:`nph/asphere (o) <fix_nph_asphere>`

   * :doc:`nph/body <fix_nph_body>`

   * :doc:`nph/body <fix_nph_body>`

   * :doc:`nph/eff <fix_nh_eff>`

   * :doc:`nph/eff <fix_nh_eff>`

   * :doc:`nph/sphere (o) <fix_nph_sphere>`

   * :doc:`nph/sphere (o) <fix_nph_sphere>`

   * :doc:`nphug (o) <fix_nphug>`

   * :doc:`nphug <fix_nphug>`

   * :doc:`npt (iko) <fix_nh>`

   * :doc:`npt (iko) <fix_nh>`

   * :doc:`npt/asphere (o) <fix_npt_asphere>`

   * :doc:`npt/asphere (o) <fix_npt_asphere>`

   * :doc:`npt/body <fix_npt_body>`

   * :doc:`npt/body <fix_npt_body>`
@@ -188,15 +188,16 @@ OPT. 
   * :doc:`rx (k) <fix_rx>`

   * :doc:`rx (k) <fix_rx>`

   * :doc:`saed/vtk <fix_saed_vtk>`

   * :doc:`saed/vtk <fix_saed_vtk>`

   * :doc:`setforce (k) <fix_setforce>`

   * :doc:`setforce (k) <fix_setforce>`

   * :doc:`setforce/spin <fix_setforce>`

   * :doc:`shake <fix_shake>`

   * :doc:`shake <fix_shake>`

   * :doc:`shardlow (k) <fix_shardlow>`

   * :doc:`shardlow (k) <fix_shardlow>`

   * :doc:`smd <fix_smd>`

   * :doc:`smd <fix_smd>`

   * :doc:`smd/adjust\_dt <fix_smd_adjust_dt>`

   * :doc:`smd/adjust_dt <fix_smd_adjust_dt>`

   * :doc:`smd/integrate\_tlsph <fix_smd_integrate_tlsph>`

   * :doc:`smd/integrate_tlsph <fix_smd_integrate_tlsph>`

   * :doc:`smd/integrate\_ulsph <fix_smd_integrate_ulsph>`

   * :doc:`smd/integrate_ulsph <fix_smd_integrate_ulsph>`

   * :doc:`smd/move\_tri\_surf <fix_smd_move_triangulated_surface>`

   * :doc:`smd/move_tri_surf <fix_smd_move_triangulated_surface>`

   * :doc:`smd/setvel <fix_smd_setvel>`

   * :doc:`smd/setvel <fix_smd_setvel>`

   * :doc:`smd/wall\_surface <fix_smd_wall_surface>`

   * :doc:`smd/wall_surface <fix_smd_wall_surface>`

   * :doc:`spring <fix_spring>`

   * :doc:`spring <fix_spring>`

   * :doc:`spring/chunk <fix_spring_chunk>`

   * :doc:`spring/chunk <fix_spring_chunk>`

   * :doc:`spring/rg <fix_spring_rg>`

   * :doc:`spring/rg <fix_spring_rg>`
@@ -237,4 +238,3 @@ OPT. 
   * :doc:`wall/region/ees <fix_wall_ees>`

   * :doc:`wall/region/ees <fix_wall_ees>`

   * :doc:`wall/srd <fix_wall_srd>`

   * :doc:`wall/srd <fix_wall_srd>`

   *
 
   *
 
   *

doc/src/Commands_kspace.rst

+7 −3
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@@ -24,12 +24,16 @@ OPT. 




   * :doc:`ewald (o) <kspace_style>`

   * :doc:`ewald (o) <kspace_style>`

   * :doc:`ewald/disp <kspace_style>`

   * :doc:`ewald/disp <kspace_style>`

   * :doc:`ewald/dipole <kspace_style>`

   * :doc:`ewald/dipole/spin <kspace_style>`

   * :doc:`msm (o) <kspace_style>`

   * :doc:`msm (o) <kspace_style>`

   * :doc:`msm/cg (o) <kspace_style>`

   * :doc:`msm/cg (o) <kspace_style>`

   * :doc:`pppm (gok) <kspace_style>`

   * :doc:`pppm (giko) <kspace_style>`

   * :doc:`pppm/cg (o) <kspace_style>`

   * :doc:`pppm/cg (o) <kspace_style>`

   * :doc:`pppm/disp (i) <kspace_style>`

   * :doc:`pppm/dipole <kspace_style>`

   * :doc:`pppm/disp/tip4p <kspace_style>`

   * :doc:`pppm/dipole/spin <kspace_style>`

   * :doc:`pppm/disp (io) <kspace_style>`

   * :doc:`pppm/disp/tip4p (o) <kspace_style>`

   * :doc:`pppm/stagger <kspace_style>`

   * :doc:`pppm/stagger <kspace_style>`

   * :doc:`pppm/tip4p (o) <kspace_style>`

   * :doc:`pppm/tip4p (o) <kspace_style>`

   * :doc:`scafacos <kspace_style>`

   * :doc:`scafacos <kspace_style>`

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