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Merge pull request #1786 from rbberger/doc_command_tables 

Add Sphinx extension to generate tables from lists
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5
doc/src/Commands.rst
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@ -27,8 +27,3 @@ commands in it are used to define a LAMMPS simulation.
:maxdepth: 1
Commands_removed
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

180
doc/src/Commands_all.rst
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@ -1,59 +1,135 @@
+----------------------------------------+------------------------------------+------------------------------------------+
| :doc:`General commands <Commands_all>` | :doc:`Fix styles <Commands_fix>` | :doc:`Compute styles <Commands_compute>` |
+----------------------------------------+------------------------------------+------------------------------------------+
| :doc:`Pair styles <Commands_pair>` | :doc:`Bond styles <Commands_bond>` | :ref:`Angle styles <angle>` |
+----------------------------------------+------------------------------------+------------------------------------------+
| :ref:`Dihedral styles <dihedral>` | :ref:`Improper styles <improper>` | :doc:`KSpace styles <Commands_kspace>` |
+----------------------------------------+------------------------------------+------------------------------------------+
.. table_from_list::
:columns: 3
* :doc:`General commands <Commands_all>`
* :doc:`Fix styles <Commands_fix>`
* :doc:`Compute styles <Commands_compute>`
* :doc:`Pair styles <Commands_pair>`
* :ref:`Bond styles <bond>`
* :ref:`Angle styles <angle>`
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
General commands
================
An alphabetic list of all general LAMMPS commands.
+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
| :doc:`angle\_coeff <angle_coeff>` | :doc:`angle\_style <angle_style>` | :doc:`atom\_modify <atom_modify>` | :doc:`atom\_style <atom_style>` | :doc:`balance <balance>` | :doc:`bond\_coeff <bond_coeff>` |
+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
| :doc:`bond\_style <bond_style>` | :doc:`bond\_write <bond_write>` | :doc:`boundary <boundary>` | :doc:`box <box>` | :doc:`change\_box <change_box>` | :doc:`clear <clear>` |
+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
| :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:`dielectric <dielectric>` | :doc:`dihedral\_coeff <dihedral_coeff>` | :doc:`dihedral\_style <dihedral_style>` |
+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
| :doc:`dimension <dimension>` | :doc:`displace\_atoms <displace_atoms>` | :doc:`dump <dump>` | :doc:`dump adios <dump_adios>` | :doc:`dump image <dump_image>` | :doc:`dump movie <dump_image>` |
+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
| :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:`echo <echo>` |
+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
| :doc:`fix <fix>` | :doc:`fix\_modify <fix_modify>` | :doc:`group <group>` | :doc:`group2ndx <group2ndx>` | :doc:`hyper <hyper>` | :doc:`if <if>` |
+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
| :doc:`info <info>` | :doc:`improper\_coeff <improper_coeff>` | :doc:`improper\_style <improper_style>` | :doc:`include <include>` | :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:`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:`molecule <molecule>` | :doc:`ndx2group <group2ndx>` | :doc:`neb <neb>` | :doc:`neb/spin <neb_spin>` | :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\_style <pair_style>` | :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:`region <region>` |
+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
| :doc:`replicate <replicate>` | :doc:`rerun <rerun>` | :doc:`reset\_ids <reset_ids>` | :doc:`reset\_timestep <reset_timestep>` | :doc:`restart <restart>` | :doc:`run <run>` |
+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
| :doc:`run\_style <run_style>` | :doc:`server <server>` | :doc:`set <set>` | :doc:`shell <shell>` | :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:`timer <timer>` | :doc:`timestep <timestep>` | :doc:`uncompute <uncompute>` | :doc:`undump <undump>` |
+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
| :doc:`unfix <unfix>` | :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>` | | | | |
+-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
.. table_from_list::
:columns: 6
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html
* :doc:`angle_coeff <angle_coeff>`
* :doc:`angle_style <angle_style>`
* :doc:`atom_modify <atom_modify>`
* :doc:`atom_style <atom_style>`
* :doc:`balance <balance>`
* :doc:`bond_coeff <bond_coeff>`
* :doc:`bond\_style <bond_style>`
* :doc:`bond\_write <bond_write>`
* :doc:`boundary <boundary>`
* :doc:`box <box>`
* :doc:`change\_box <change_box>`
* :doc:`clear <clear>`
* :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:`dielectric <dielectric>`
* :doc:`dihedral\_coeff <dihedral_coeff>`
* :doc:`dihedral\_style <dihedral_style>`
* :doc:`dimension <dimension>`
* :doc:`displace\_atoms <displace_atoms>`
* :doc:`dump <dump>`
* :doc:`dump adios <dump_adios>`
* :doc:`dump image <dump_image>`
* :doc:`dump movie <dump_image>`
* :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:`echo <echo>`
* :doc:`fix <fix>`
* :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:`include <include>`
* :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:`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:`molecule <molecule>`
* :doc:`ndx2group <group2ndx>`
* :doc:`neb <neb>`
* :doc:`neb/spin <neb_spin>`
* :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:`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:`region <region>`
* :doc:`replicate <replicate>`
* :doc:`rerun <rerun>`
* :doc:`reset\_ids <reset_ids>`
* :doc:`reset\_timestep <reset_timestep>`
* :doc:`restart <restart>`
* :doc:`run <run>`
* :doc:`run\_style <run_style>`
* :doc:`server <server>`
* :doc:`set <set>`
* :doc:`shell <shell>`
* :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:`timer <timer>`
* :doc:`timestep <timestep>`
* :doc:`uncompute <uncompute>`
* :doc:`undump <undump>`
* :doc:`unfix <unfix>`
* :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>`

203
doc/src/Commands_bond.rst
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@ -1,112 +1,169 @@
.. table_from_list::
:columns: 3
* :doc:`General commands <Commands_all>`
* :doc:`Fix styles <Commands_fix>`
* :doc:`Compute styles <Commands_compute>`
* :doc:`Pair styles <Commands_pair>`
* :ref:`Bond styles <bond>`
* :ref:`Angle styles <angle>`
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
.. _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
accelerated versions. This is indicated by additional letters in
parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
OPT.
+---------------------------------------+-------------------------------------------------+---------------------------------------------------------+---------------------------------+
| :doc:`none <bond_none>` | :doc:`zero <bond_zero>` | :doc:`hybrid <bond_hybrid>` | |
+---------------------------------------+-------------------------------------------------+---------------------------------------------------------+---------------------------------+
| | | | |
+---------------------------------------+-------------------------------------------------+---------------------------------------------------------+---------------------------------+
| :doc:`class2 (ko) <bond_class2>` | :doc:`fene (iko) <bond_fene>` | :doc:`fene/expand (o) <bond_fene_expand>` | :doc:`gromos (o) <bond_gromos>` |
+---------------------------------------+-------------------------------------------------+---------------------------------------------------------+---------------------------------+
| :doc:`harmonic (iko) <bond_harmonic>` | :doc:`harmonic/shift (o) <bond_harmonic_shift>` | :doc:`harmonic/shift/cut (o) <bond_harmonic_shift_cut>` | :doc:`mm3 <bond_mm3>` |
+---------------------------------------+-------------------------------------------------+---------------------------------------------------------+---------------------------------+
| :doc:`morse (o) <bond_morse>` | :doc:`nonlinear (o) <bond_nonlinear>` | :doc:`oxdna/fene <bond_oxdna>` | :doc:`oxdna2/fene <bond_oxdna>` |
+---------------------------------------+-------------------------------------------------+---------------------------------------------------------+---------------------------------+
| :doc:`quartic (o) <bond_quartic>` | :doc:`table (o) <bond_table>` | | |
+---------------------------------------+-------------------------------------------------+---------------------------------------------------------+---------------------------------+
.. table_from_list::
:columns: 4
* :doc:`none <bond_none>`
* :doc:`zero <bond_zero>`
* :doc:`hybrid <bond_hybrid>`
*
*
*
*
*
* :doc:`class2 (ko) <bond_class2>`
* :doc:`fene (iko) <bond_fene>`
* :doc:`fene/expand (o) <bond_fene_expand>`
* :doc:`gromos (o) <bond_gromos>`
* :doc:`harmonic (iko) <bond_harmonic>`
* :doc:`harmonic/shift (o) <bond_harmonic_shift>`
* :doc:`harmonic/shift/cut (o) <bond_harmonic_shift_cut>`
* :doc:`mm3 <bond_mm3>`
* :doc:`morse (o) <bond_morse>`
* :doc:`nonlinear (o) <bond_nonlinear>`
* :doc:`oxdna/fene <bond_oxdna>`
* :doc:`oxdna2/fene <bond_oxdna>`
* :doc:`quartic (o) <bond_quartic>`
* :doc:`table (o) <bond_table>`
*
*
----------
---
.. _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
accelerated versions. This is indicated by additional letters in
parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
OPT.
+------------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------+
| :doc:`none <angle_none>` | :doc:`zero <angle_zero>` | :doc:`hybrid <angle_hybrid>` | |
+------------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------+
| | | | |
+------------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------+
| :doc:`charmm (iko) <angle_charmm>` | :doc:`class2 (ko) <angle_class2>` | :doc:`class2/p6 <angle_class2>` | :doc:`cosine (ko) <angle_cosine>` |
+------------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------+
| :doc:`cosine/buck6d <angle_cosine_buck6d>` | :doc:`cosine/delta (o) <angle_cosine_delta>` | :doc:`cosine/periodic (o) <angle_cosine_periodic>` | :doc:`cosine/shift (o) <angle_cosine_shift>` |
+------------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------+
| :doc:`cosine/shift/exp (o) <angle_cosine_shift_exp>` | :doc:`cosine/squared (o) <angle_cosine_squared>` | :doc:`cross <angle_cross>` | :doc:`dipole (o) <angle_dipole>` |
+------------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------+
| :doc:`fourier (o) <angle_fourier>` | :doc:`fourier/simple (o) <angle_fourier_simple>` | :doc:`harmonic (iko) <angle_harmonic>` | :doc:`mm3 <angle_mm3>` |
+------------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------+
| :doc:`quartic (o) <angle_quartic>` | :doc:`sdk (o) <angle_sdk>` | :doc:`table (o) <angle_table>` | |
+------------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------+
.. table_from_list::
:columns: 4
* :doc:`none <angle_none>`
* :doc:`zero <angle_zero>`
* :doc:`hybrid <angle_hybrid>`
*
*
*
*
*
* :doc:`charmm (iko) <angle_charmm>`
* :doc:`class2 (ko) <angle_class2>`
* :doc:`class2/p6 <angle_class2>`
* :doc:`cosine (ko) <angle_cosine>`
* :doc:`cosine/buck6d <angle_cosine_buck6d>`
* :doc:`cosine/delta (o) <angle_cosine_delta>`
* :doc:`cosine/periodic (o) <angle_cosine_periodic>`
* :doc:`cosine/shift (o) <angle_cosine_shift>`
* :doc:`cosine/shift/exp (o) <angle_cosine_shift_exp>`
* :doc:`cosine/squared (o) <angle_cosine_squared>`
* :doc:`cross <angle_cross>`
* :doc:`dipole (o) <angle_dipole>`
* :doc:`fourier (o) <angle_fourier>`
* :doc:`fourier/simple (o) <angle_fourier_simple>`
* :doc:`harmonic (iko) <angle_harmonic>`
* :doc:`mm3 <angle_mm3>`
* :doc:`quartic (o) <angle_quartic>`
* :doc:`sdk (o) <angle_sdk>`
* :doc:`table (o) <angle_table>`
*
----------
---
.. _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
have accelerated versions. This is indicated by additional letters in
parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
OPT.
+-------------------------------------------+-------------------------------------------+-------------------------------------------+---------------------------------------------------------+
| :doc:`none <dihedral_none>` | :doc:`zero <dihedral_zero>` | :doc:`hybrid <dihedral_hybrid>` | |
+-------------------------------------------+-------------------------------------------+-------------------------------------------+---------------------------------------------------------+
| | | | |
+-------------------------------------------+-------------------------------------------+-------------------------------------------+---------------------------------------------------------+
| :doc:`charmm (iko) <dihedral_charmm>` | :doc:`charmmfsw <dihedral_charmm>` | :doc:`class2 (ko) <dihedral_class2>` | :doc:`cosine/shift/exp (o) <dihedral_cosine_shift_exp>` |
+-------------------------------------------+-------------------------------------------+-------------------------------------------+---------------------------------------------------------+
| :doc:`fourier (io) <dihedral_fourier>` | :doc:`harmonic (iko) <dihedral_harmonic>` | :doc:`helix (o) <dihedral_helix>` | :doc:`multi/harmonic (o) <dihedral_multi_harmonic>` |
+-------------------------------------------+-------------------------------------------+-------------------------------------------+---------------------------------------------------------+
| :doc:`nharmonic (o) <dihedral_nharmonic>` | :doc:`opls (iko) <dihedral_opls>` | :doc:`quadratic (o) <dihedral_quadratic>` | :doc:`spherical <dihedral_spherical>` |
+-------------------------------------------+-------------------------------------------+-------------------------------------------+---------------------------------------------------------+
| :doc:`table (o) <dihedral_table>` | :doc:`table/cut <dihedral_table_cut>` | | |
+-------------------------------------------+-------------------------------------------+-------------------------------------------+---------------------------------------------------------+
.. table_from_list::
:columns: 4
----------
* :doc:`none <dihedral_none>`
* :doc:`zero <dihedral_zero>`
* :doc:`hybrid <dihedral_hybrid>`
*
*
*
*
*
* :doc:`charmm (iko) <dihedral_charmm>`
* :doc:`charmmfsw <dihedral_charmm>`
* :doc:`class2 (ko) <dihedral_class2>`
* :doc:`cosine/shift/exp (o) <dihedral_cosine_shift_exp>`
* :doc:`fourier (io) <dihedral_fourier>`
* :doc:`harmonic (iko) <dihedral_harmonic>`
* :doc:`helix (o) <dihedral_helix>`
* :doc:`multi/harmonic (o) <dihedral_multi_harmonic>`
* :doc:`nharmonic (o) <dihedral_nharmonic>`
* :doc:`opls (iko) <dihedral_opls>`
* :doc:`quadratic (o) <dihedral_quadratic>`
* :doc:`spherical <dihedral_spherical>`
* :doc:`table (o) <dihedral_table>`
* :doc:`table/cut <dihedral_table_cut>`
*
*
.. _improper:
Improper\_style potentials
=========================================
improper_style potentials
=========================
All LAMMPS :doc:`improper\_style <improper_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.
+--------------------------------------+-----------------------------------------+-------------------------------------------+---------------------------------------------------------+
| :doc:`none <improper_none>` | :doc:`zero <improper_zero>` | :doc:`hybrid <improper_hybrid>` | |
+--------------------------------------+-----------------------------------------+-------------------------------------------+---------------------------------------------------------+
| | | | |
+--------------------------------------+-----------------------------------------+-------------------------------------------+---------------------------------------------------------+
| :doc:`class2 (ko) <improper_class2>` | :doc:`cossq (o) <improper_cossq>` | :doc:`cvff (io) <improper_cvff>` | :doc:`distance <improper_distance>` |
+--------------------------------------+-----------------------------------------+-------------------------------------------+---------------------------------------------------------+
| :doc:`distharm <improper_distharm>` | :doc:`fourier (o) <improper_fourier>` | :doc:`harmonic (iko) <improper_harmonic>` | :doc:`inversion/harmonic <improper_inversion_harmonic>` |
+--------------------------------------+-----------------------------------------+-------------------------------------------+---------------------------------------------------------+
| :doc:`ring (o) <improper_ring>` | :doc:`sqdistharm <improper_sqdistharm>` | :doc:`umbrella (o) <improper_umbrella>` | |
+--------------------------------------+-----------------------------------------+-------------------------------------------+---------------------------------------------------------+
.. table_from_list::
:columns: 4
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html
* :doc:`none <improper_none>`
* :doc:`zero <improper_zero>`
* :doc:`hybrid <improper_hybrid>`
*
*
*
*
*
* :doc:`class2 (ko) <improper_class2>`
* :doc:`cossq (o) <improper_cossq>`
* :doc:`cvff (io) <improper_cvff>`
* :doc:`distance <improper_distance>`
* :doc:`distharm <improper_distharm>`
* :doc:`fourier (o) <improper_fourier>`
* :doc:`harmonic (iko) <improper_harmonic>`
* :doc:`inversion/harmonic <improper_inversion_harmonic>`
* :doc:`ring (o) <improper_ring>`
* :doc:`sqdistharm <improper_sqdistharm>`
* :doc:`umbrella (o) <improper_umbrella>`
*

5
doc/src/Commands_category.rst
View File

@ -130,8 +130,3 @@ Input script control:
* :doc:`quit <quit>`,
* :doc:`shell <shell>`,
* :doc:`variable <variable>`
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

218
doc/src/Commands_compute.rst
View File

@ -1,10 +1,15 @@
+----------------------------------------+------------------------------------+------------------------------------------+
| :doc:`General commands <Commands_all>` | :doc:`Fix styles <Commands_fix>` | :doc:`Compute styles <Commands_compute>` |
+----------------------------------------+------------------------------------+------------------------------------------+
| :doc:`Pair styles <Commands_pair>` | :doc:`Bond styles <Commands_bond>` | :ref:`Angle styles <angle>` |
+----------------------------------------+------------------------------------+------------------------------------------+
| :ref:`Dihedral styles <dihedral>` | :ref:`Improper styles <improper>` | :doc:`KSpace styles <Commands_kspace>` |
+----------------------------------------+------------------------------------+------------------------------------------+
.. table_from_list::
:columns: 3
* :doc:`General commands <Commands_all>`
* :doc:`Fix styles <Commands_fix>`
* :doc:`Compute styles <Commands_compute>`
* :doc:`Pair styles <Commands_pair>`
* :ref:`Bond styles <bond>`
* :ref:`Angle styles <angle>`
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
Compute commands
================
@ -14,57 +19,150 @@ 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.
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
| :doc:`ackland/atom <compute_ackland_atom>` | :doc:`adf <compute_adf>` | :doc:`aggregate/atom <compute_cluster_atom>` | :doc:`angle <compute_angle>` | :doc:`angle/local <compute_angle_local>` | :doc:`angmom/chunk <compute_angmom_chunk>` |
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
| :doc:`basal/atom <compute_basal_atom>` | :doc:`body/local <compute_body_local>` | :doc:`bond <compute_bond>` | :doc:`bond/local <compute_bond_local>` | :doc:`centro/atom <compute_centro_atom>` | :doc:`centroid/stress/atom <compute_stress_atom>` |
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
| :doc:`chunk/atom <compute_chunk_atom>` | :doc:`chunk/spread/atom <compute_chunk_spread_atom>` | :doc:`cluster/atom <compute_cluster_atom>` | :doc:`cna/atom <compute_cna_atom>` | :doc:`cnp/atom <compute_cnp_atom>` | :doc:`com <compute_com>` |
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
| :doc:`com/chunk <compute_com_chunk>` | :doc:`contact/atom <compute_contact_atom>` | :doc:`coord/atom <compute_coord_atom>` | :doc:`damage/atom <compute_damage_atom>` | :doc:`dihedral <compute_dihedral>` | :doc:`dihedral/local <compute_dihedral_local>` |
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
| :doc:`dilatation/atom <compute_dilatation_atom>` | :doc:`dipole/chunk <compute_dipole_chunk>` | :doc:`displace/atom <compute_displace_atom>` | :doc:`dpd <compute_dpd>` | :doc:`dpd/atom <compute_dpd_atom>` | :doc:`edpd/temp/atom <compute_edpd_temp_atom>` |
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
| :doc:`entropy/atom <compute_entropy_atom>` | :doc:`erotate/asphere <compute_erotate_asphere>` | :doc:`erotate/rigid <compute_erotate_rigid>` | :doc:`erotate/sphere <compute_erotate_sphere>` | :doc:`erotate/sphere/atom <compute_erotate_sphere_atom>` | :doc:`event/displace <compute_event_displace>` |
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
| :doc:`fep <compute_fep>` | :doc:`force/tally <compute_tally>` | :doc:`fragment/atom <compute_cluster_atom>` | :doc:`global/atom <compute_global_atom>` | :doc:`group/group <compute_group_group>` | :doc:`gyration <compute_gyration>` |
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
| :doc:`gyration/chunk <compute_gyration_chunk>` | :doc:`gyration/shape <compute_gyration_shape>` | :doc:`gyration/shape/chunk <compute_gyration_shape_chunk>` | :doc:`heat/flux <compute_heat_flux>` | :doc:`heat/flux/tally <compute_tally>` | :doc:`hexorder/atom <compute_hexorder_atom>` |
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
| :doc:`hma <compute_hma>` | :doc:`improper <compute_improper>` | :doc:`improper/local <compute_improper_local>` | :doc:`inertia/chunk <compute_inertia_chunk>` | :doc:`ke <compute_ke>` | :doc:`ke/atom <compute_ke_atom>` |
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
| :doc:`ke/atom/eff <compute_ke_atom_eff>` | :doc:`ke/eff <compute_ke_eff>` | :doc:`ke/rigid <compute_ke_rigid>` | :doc:`meso/e/atom <compute_meso_e_atom>` | :doc:`meso/rho/atom <compute_meso_rho_atom>` | :doc:`meso/t/atom <compute_meso_t_atom>` |
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
| :doc:`momentum <compute_momentum>` | :doc:`msd <compute_msd>` | :doc:`msd/chunk <compute_msd_chunk>` | :doc:`msd/nongauss <compute_msd_nongauss>` | :doc:`omega/chunk <compute_omega_chunk>` | :doc:`orientorder/atom <compute_orientorder_atom>` |
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
| :doc:`pair <compute_pair>` | :doc:`pair/local <compute_pair_local>` | :doc:`pe <compute_pe>` | :doc:`pe/atom <compute_pe_atom>` | :doc:`pe/mol/tally <compute_tally>` | :doc:`pe/tally <compute_tally>` |
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
| :doc:`plasticity/atom <compute_plasticity_atom>` | :doc:`pressure <compute_pressure>` | :doc:`pressure/cylinder <compute_pressure_cylinder>` | :doc:`pressure/uef <compute_pressure_uef>` | :doc:`property/atom <compute_property_atom>` | :doc:`property/chunk <compute_property_chunk>` |
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
| :doc:`property/local <compute_property_local>` | :doc:`ptm/atom <compute_ptm_atom>` | :doc:`rdf <compute_rdf>` | :doc:`reduce <compute_reduce>` | :doc:`reduce/chunk <compute_reduce_chunk>` | :doc:`reduce/region <compute_reduce>` |
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
| :doc:`rigid/local <compute_rigid_local>` | :doc:`saed <compute_saed>` | :doc:`slice <compute_slice>` | :doc:`smd/contact/radius <compute_smd_contact_radius>` | :doc:`smd/damage <compute_smd_damage>` | :doc:`smd/hourglass/error <compute_smd_hourglass_error>` |
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
| :doc:`smd/internal/energy <compute_smd_internal_energy>` | :doc:`smd/plastic/strain <compute_smd_plastic_strain>` | :doc:`smd/plastic/strain/rate <compute_smd_plastic_strain_rate>` | :doc:`smd/rho <compute_smd_rho>` | :doc:`smd/tlsph/defgrad <compute_smd_tlsph_defgrad>` | :doc:`smd/tlsph/dt <compute_smd_tlsph_dt>` |
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
| :doc:`smd/tlsph/num/neighs <compute_smd_tlsph_num_neighs>` | :doc:`smd/tlsph/shape <compute_smd_tlsph_shape>` | :doc:`smd/tlsph/strain <compute_smd_tlsph_strain>` | :doc:`smd/tlsph/strain/rate <compute_smd_tlsph_strain_rate>` | :doc:`smd/tlsph/stress <compute_smd_tlsph_stress>` | :doc:`smd/triangle/vertices <compute_smd_triangle_vertices>` |
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
| :doc:`smd/ulsph/num/neighs <compute_smd_ulsph_num_neighs>` | :doc:`smd/ulsph/strain <compute_smd_ulsph_strain>` | :doc:`smd/ulsph/strain/rate <compute_smd_ulsph_strain_rate>` | :doc:`smd/ulsph/stress <compute_smd_ulsph_stress>` | :doc:`smd/vol <compute_smd_vol>` | :doc:`snap <compute_sna_atom>` |
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
| :doc:`sna/atom <compute_sna_atom>` | :doc:`snad/atom <compute_sna_atom>` | :doc:`snav/atom <compute_sna_atom>` | :doc:`spin <compute_spin>` | :doc:`stress/atom <compute_stress_atom>` | :doc:`stress/mop <compute_stress_mop>` |
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
| :doc:`stress/mop/profile <compute_stress_mop>` | :doc:`stress/tally <compute_tally>` | :doc:`tdpd/cc/atom <compute_tdpd_cc_atom>` | :doc:`temp (k) <compute_temp>` | :doc:`temp/asphere <compute_temp_asphere>` | :doc:`temp/body <compute_temp_body>` |
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
| :doc:`temp/chunk <compute_temp_chunk>` | :doc:`temp/com <compute_temp_com>` | :doc:`temp/cs <compute_temp_cs>` | :doc:`temp/deform <compute_temp_deform>` | :doc:`temp/deform/eff <compute_temp_deform_eff>` | :doc:`temp/drude <compute_temp_drude>` |
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
| :doc:`temp/eff <compute_temp_eff>` | :doc:`temp/partial <compute_temp_partial>` | :doc:`temp/profile <compute_temp_profile>` | :doc:`temp/ramp <compute_temp_ramp>` | :doc:`temp/region <compute_temp_region>` | :doc:`temp/region/eff <compute_temp_region_eff>` |
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
| :doc:`temp/rotate <compute_temp_rotate>` | :doc:`temp/sphere <compute_temp_sphere>` | :doc:`temp/uef <compute_temp_uef>` | :doc:`ti <compute_ti>` | :doc:`torque/chunk <compute_torque_chunk>` | :doc:`vacf <compute_vacf>` |
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
| :doc:`vcm/chunk <compute_vcm_chunk>` | :doc:`voronoi/atom <compute_voronoi_atom>` | :doc:`xrd <compute_xrd>` | | | |
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
.. table_from_list::
:columns: 6
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html
* :doc:`ackland/atom <compute_ackland_atom>`
* :doc:`adf <compute_adf>`
* :doc:`aggregate/atom <compute_cluster_atom>`
* :doc:`angle <compute_angle>`
* :doc:`angle/local <compute_angle_local>`
* :doc:`angmom/chunk <compute_angmom_chunk>`
* :doc:`basal/atom <compute_basal_atom>`
* :doc:`body/local <compute_body_local>`
* :doc:`bond <compute_bond>`
* :doc:`bond/local <compute_bond_local>`
* :doc:`centro/atom <compute_centro_atom>`
* :doc:`centroid/stress/atom <compute_stress_atom>`
* :doc:`chunk/atom <compute_chunk_atom>`
* :doc:`chunk/spread/atom <compute_chunk_spread_atom>`
* :doc:`cluster/atom <compute_cluster_atom>`
* :doc:`cna/atom <compute_cna_atom>`
* :doc:`cnp/atom <compute_cnp_atom>`
* :doc:`com <compute_com>`
* :doc:`com/chunk <compute_com_chunk>`
* :doc:`contact/atom <compute_contact_atom>`
* :doc:`coord/atom <compute_coord_atom>`
* :doc:`damage/atom <compute_damage_atom>`
* :doc:`dihedral <compute_dihedral>`
* :doc:`dihedral/local <compute_dihedral_local>`
* :doc:`dilatation/atom <compute_dilatation_atom>`
* :doc:`dipole/chunk <compute_dipole_chunk>`
* :doc:`displace/atom <compute_displace_atom>`
* :doc:`dpd <compute_dpd>`
* :doc:`dpd/atom <compute_dpd_atom>`
* :doc:`edpd/temp/atom <compute_edpd_temp_atom>`
* :doc:`entropy/atom <compute_entropy_atom>`
* :doc:`erotate/asphere <compute_erotate_asphere>`
* :doc:`erotate/rigid <compute_erotate_rigid>`
* :doc:`erotate/sphere <compute_erotate_sphere>`
* :doc:`erotate/sphere/atom <compute_erotate_sphere_atom>`
* :doc:`event/displace <compute_event_displace>`
* :doc:`fep <compute_fep>`
* :doc:`force/tally <compute_tally>`
* :doc:`fragment/atom <compute_cluster_atom>`
* :doc:`global/atom <compute_global_atom>`
* :doc:`group/group <compute_group_group>`
* :doc:`gyration <compute_gyration>`
* :doc:`gyration/chunk <compute_gyration_chunk>`
* :doc:`gyration/shape <compute_gyration_shape>`
* :doc:`gyration/shape/chunk <compute_gyration_shape_chunk>`
* :doc:`heat/flux <compute_heat_flux>`
* :doc:`heat/flux/tally <compute_tally>`
* :doc:`hexorder/atom <compute_hexorder_atom>`
* :doc:`hma <compute_hma>`
* :doc:`improper <compute_improper>`
* :doc:`improper/local <compute_improper_local>`
* :doc:`inertia/chunk <compute_inertia_chunk>`
* :doc:`ke <compute_ke>`
* :doc:`ke/atom <compute_ke_atom>`
* :doc:`ke/atom/eff <compute_ke_atom_eff>`
* :doc:`ke/eff <compute_ke_eff>`
* :doc:`ke/rigid <compute_ke_rigid>`
* :doc:`meso/e/atom <compute_meso_e_atom>`
* :doc:`meso/rho/atom <compute_meso_rho_atom>`
* :doc:`meso/t/atom <compute_meso_t_atom>`
* :doc:`momentum <compute_momentum>`
* :doc:`msd <compute_msd>`
* :doc:`msd/chunk <compute_msd_chunk>`
* :doc:`msd/nongauss <compute_msd_nongauss>`
* :doc:`omega/chunk <compute_omega_chunk>`
* :doc:`orientorder/atom <compute_orientorder_atom>`
* :doc:`pair <compute_pair>`
* :doc:`pair/local <compute_pair_local>`
* :doc:`pe <compute_pe>`
* :doc:`pe/atom <compute_pe_atom>`
* :doc:`pe/mol/tally <compute_tally>`
* :doc:`pe/tally <compute_tally>`
* :doc:`plasticity/atom <compute_plasticity_atom>`
* :doc:`pressure <compute_pressure>`
* :doc:`pressure/cylinder <compute_pressure_cylinder>`
* :doc:`pressure/uef <compute_pressure_uef>`
* :doc:`property/atom <compute_property_atom>`
* :doc:`property/chunk <compute_property_chunk>`
* :doc:`property/local <compute_property_local>`
* :doc:`ptm/atom <compute_ptm_atom>`
* :doc:`rdf <compute_rdf>`
* :doc:`reduce <compute_reduce>`
* :doc:`reduce/chunk <compute_reduce_chunk>`
* :doc:`reduce/region <compute_reduce>`
* :doc:`rigid/local <compute_rigid_local>`
* :doc:`saed <compute_saed>`
* :doc:`slice <compute_slice>`
* :doc:`smd/contact/radius <compute_smd_contact_radius>`
* :doc:`smd/damage <compute_smd_damage>`
* :doc:`smd/hourglass/error <compute_smd_hourglass_error>`
* :doc:`smd/internal/energy <compute_smd_internal_energy>`
* :doc:`smd/plastic/strain <compute_smd_plastic_strain>`
* :doc:`smd/plastic/strain/rate <compute_smd_plastic_strain_rate>`
* :doc:`smd/rho <compute_smd_rho>`
* :doc:`smd/tlsph/defgrad <compute_smd_tlsph_defgrad>`
* :doc:`smd/tlsph/dt <compute_smd_tlsph_dt>`
* :doc:`smd/tlsph/num/neighs <compute_smd_tlsph_num_neighs>`
* :doc:`smd/tlsph/shape <compute_smd_tlsph_shape>`
* :doc:`smd/tlsph/strain <compute_smd_tlsph_strain>`
* :doc:`smd/tlsph/strain/rate <compute_smd_tlsph_strain_rate>`
* :doc:`smd/tlsph/stress <compute_smd_tlsph_stress>`
* :doc:`smd/triangle/vertices <compute_smd_triangle_vertices>`
* :doc:`smd/ulsph/num/neighs <compute_smd_ulsph_num_neighs>`
* :doc:`smd/ulsph/strain <compute_smd_ulsph_strain>`
* :doc:`smd/ulsph/strain/rate <compute_smd_ulsph_strain_rate>`
* :doc:`smd/ulsph/stress <compute_smd_ulsph_stress>`
* :doc:`smd/vol <compute_smd_vol>`
* :doc:`snap <compute_sna_atom>`
* :doc:`sna/atom <compute_sna_atom>`
* :doc:`snad/atom <compute_sna_atom>`
* :doc:`snav/atom <compute_sna_atom>`
* :doc:`spin <compute_spin>`
* :doc:`stress/atom <compute_stress_atom>`
* :doc:`stress/mop <compute_stress_mop>`
* :doc:`stress/mop/profile <compute_stress_mop>`
* :doc:`stress/tally <compute_tally>`
* :doc:`tdpd/cc/atom <compute_tdpd_cc_atom>`
* :doc:`temp (k) <compute_temp>`
* :doc:`temp/asphere <compute_temp_asphere>`
* :doc:`temp/body <compute_temp_body>`
* :doc:`temp/chunk <compute_temp_chunk>`
* :doc:`temp/com <compute_temp_com>`
* :doc:`temp/cs <compute_temp_cs>`
* :doc:`temp/deform <compute_temp_deform>`
* :doc:`temp/deform/eff <compute_temp_deform_eff>`
* :doc:`temp/drude <compute_temp_drude>`
* :doc:`temp/eff <compute_temp_eff>`
* :doc:`temp/partial <compute_temp_partial>`
* :doc:`temp/profile <compute_temp_profile>`
* :doc:`temp/ramp <compute_temp_ramp>`
* :doc:`temp/region <compute_temp_region>`
* :doc:`temp/region/eff <compute_temp_region_eff>`
* :doc:`temp/rotate <compute_temp_rotate>`
* :doc:`temp/sphere <compute_temp_sphere>`
* :doc:`temp/uef <compute_temp_uef>`
* :doc:`ti <compute_ti>`
* :doc:`torque/chunk <compute_torque_chunk>`
* :doc:`vacf <compute_vacf>`
* :doc:`vcm/chunk <compute_vcm_chunk>`
* :doc:`voronoi/atom <compute_voronoi_atom>`
* :doc:`xrd <compute_xrd>`
*
*
*

314
doc/src/Commands_fix.rst
View File

@ -1,10 +1,15 @@
+----------------------------------------+------------------------------------+------------------------------------------+
| :doc:`General commands <Commands_all>` | :doc:`Fix styles <Commands_fix>` | :doc:`Compute styles <Commands_compute>` |
+----------------------------------------+------------------------------------+------------------------------------------+
| :doc:`Pair styles <Commands_pair>` | :doc:`Bond styles <Commands_bond>` | :ref:`Angle styles <angle>` |
+----------------------------------------+------------------------------------+------------------------------------------+
| :ref:`Dihedral styles <dihedral>` | :ref:`Improper styles <improper>` | :doc:`KSpace styles <Commands_kspace>` |
+----------------------------------------+------------------------------------+------------------------------------------+
.. table_from_list::
:columns: 3
* :doc:`General commands <Commands_all>`
* :doc:`Fix styles <Commands_fix>`
* :doc:`Compute styles <Commands_compute>`
* :doc:`Pair styles <Commands_pair>`
* :ref:`Bond styles <bond>`
* :ref:`Angle styles <angle>`
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
Fix commands
============
@ -14,81 +19,222 @@ have accelerated versions. This is indicated by additional letters in
parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
OPT.
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
| :doc:`adapt <fix_adapt>` | :doc:`adapt/fep <fix_adapt_fep>` | :doc:`addforce <fix_addforce>` | :doc:`addtorque <fix_addtorque>` | :doc:`append/atoms <fix_append_atoms>` | :doc:`atc <fix_atc>` |
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
| :doc:`atom/swap <fix_atom_swap>` | :doc:`ave/atom <fix_ave_atom>` | :doc:`ave/chunk <fix_ave_chunk>` | :doc:`ave/correlate <fix_ave_correlate>` | :doc:`ave/correlate/long <fix_ave_correlate_long>` | :doc:`ave/histo <fix_ave_histo>` |
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
| :doc:`ave/histo/weight <fix_ave_histo>` | :doc:`ave/time <fix_ave_time>` | :doc:`aveforce <fix_aveforce>` | :doc:`balance <fix_balance>` | :doc:`bocs <fix_bocs>` | :doc:`bond/break <fix_bond_break>` |
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
| :doc:`bond/create <fix_bond_create>` | :doc:`bond/react <fix_bond_react>` | :doc:`bond/swap <fix_bond_swap>` | :doc:`box/relax <fix_box_relax>` | :doc:`client/md <fix_client_md>` | :doc:`cmap <fix_cmap>` |
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
| :doc:`colvars <fix_colvars>` | :doc:`controller <fix_controller>` | :doc:`deform (k) <fix_deform>` | :doc:`deposit <fix_deposit>` | :doc:`dpd/energy (k) <fix_dpd_energy>` | :doc:`drag <fix_drag>` |
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
| :doc:`drude <fix_drude>` | :doc:`drude/transform/direct <fix_drude_transform>` | :doc:`drude/transform/inverse <fix_drude_transform>` | :doc:`dt/reset <fix_dt_reset>` | :doc:`edpd/source <fix_dpd_source>` | :doc:`efield <fix_efield>` |
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
| :doc:`ehex <fix_ehex>` | :doc:`electron/stopping <fix_electron_stopping>` | :doc:`enforce2d (k) <fix_enforce2d>` | :doc:`eos/cv <fix_eos_cv>` | :doc:`eos/table <fix_eos_table>` | :doc:`eos/table/rx (k) <fix_eos_table_rx>` |
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
| :doc:`evaporate <fix_evaporate>` | :doc:`external <fix_external>` | :doc:`ffl <fix_ffl>` | :doc:`filter/corotate <fix_filter_corotate>` | :doc:`flow/gauss <fix_flow_gauss>` | :doc:`freeze (k) <fix_freeze>` |
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
| :doc:`gcmc <fix_gcmc>` | :doc:`gld <fix_gld>` | :doc:`gle <fix_gle>` | :doc:`gravity (ko) <fix_gravity>` | :doc:`grem <fix_grem>` | :doc:`halt <fix_halt>` |
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
| :doc:`heat <fix_heat>` | :doc:`hyper/global <fix_hyper_global>` | :doc:`hyper/local <fix_hyper_local>` | :doc:`imd <fix_imd>` | :doc:`indent <fix_indent>` | :doc:`ipi <fix_ipi>` |
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
| :doc:`langevin (k) <fix_langevin>` | :doc:`langevin/drude <fix_langevin_drude>` | :doc:`langevin/eff <fix_langevin_eff>` | :doc:`langevin/spin <fix_langevin_spin>` | :doc:`latte <fix_latte>` | :doc:`lb/fluid <fix_lb_fluid>` |
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
| :doc:`lb/momentum <fix_lb_momentum>` | :doc:`lb/pc <fix_lb_pc>` | :doc:`lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>` | :doc:`lb/viscous <fix_lb_viscous>` | :doc:`lineforce <fix_lineforce>` | :doc:`manifoldforce <fix_manifoldforce>` |
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
| :doc:`meso <fix_meso>` | :doc:`meso/move <fix_meso_move>` | :doc:`meso/stationary <fix_meso_stationary>` | :doc:`momentum (k) <fix_momentum>` | :doc:`move <fix_move>` | :doc:`mscg <fix_mscg>` |
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
| :doc:`msst <fix_msst>` | :doc:`mvv/dpd <fix_mvv_dpd>` | :doc:`mvv/edpd <fix_mvv_dpd>` | :doc:`mvv/tdpd <fix_mvv_dpd>` | :doc:`neb <fix_neb>` | :doc:`neb\_spin <fix_neb_spin>` |
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
| :doc:`nph (ko) <fix_nh>` | :doc:`nph/asphere (o) <fix_nph_asphere>` | :doc:`nph/body <fix_nph_body>` | :doc:`nph/eff <fix_nh_eff>` | :doc:`nph/sphere (o) <fix_nph_sphere>` | :doc:`nphug (o) <fix_nphug>` |
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
| :doc:`npt (iko) <fix_nh>` | :doc:`npt/asphere (o) <fix_npt_asphere>` | :doc:`npt/body <fix_npt_body>` | :doc:`npt/eff <fix_nh_eff>` | :doc:`npt/sphere (o) <fix_npt_sphere>` | :doc:`npt/uef <fix_nh_uef>` |
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
| :doc:`nve (iko) <fix_nve>` | :doc:`nve/asphere (i) <fix_nve_asphere>` | :doc:`nve/asphere/noforce <fix_nve_asphere_noforce>` | :doc:`nve/awpmd <fix_nve_awpmd>` | :doc:`nve/body <fix_nve_body>` | :doc:`nve/dot <fix_nve_dot>` |
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
| :doc:`nve/dotc/langevin <fix_nve_dotc_langevin>` | :doc:`nve/eff <fix_nve_eff>` | :doc:`nve/limit <fix_nve_limit>` | :doc:`nve/line <fix_nve_line>` | :doc:`nve/manifold/rattle <fix_nve_manifold_rattle>` | :doc:`nve/noforce <fix_nve_noforce>` |
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
| :doc:`nve/sphere (ko) <fix_nve_sphere>` | :doc:`nve/spin <fix_nve_spin>` | :doc:`nve/tri <fix_nve_tri>` | :doc:`nvk <fix_nvk>` | :doc:`nvt (iko) <fix_nh>` | :doc:`nvt/asphere (o) <fix_nvt_asphere>` |
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
| :doc:`nvt/body <fix_nvt_body>` | :doc:`nvt/eff <fix_nh_eff>` | :doc:`nvt/manifold/rattle <fix_nvt_manifold_rattle>` | :doc:`nvt/sllod (io) <fix_nvt_sllod>` | :doc:`nvt/sllod/eff <fix_nvt_sllod_eff>` | :doc:`nvt/sphere (o) <fix_nvt_sphere>` |
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
| :doc:`nvt/uef <fix_nh_uef>` | :doc:`oneway <fix_oneway>` | :doc:`orient/bcc <fix_orient>` | :doc:`orient/fcc <fix_orient>` | :doc:`phonon <fix_phonon>` | :doc:`pimd <fix_pimd>` |
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
| :doc:`planeforce <fix_planeforce>` | :doc:`plumed <fix_plumed>` | :doc:`poems <fix_poems>` | :doc:`pour <fix_pour>` | :doc:`precession/spin <fix_precession_spin>` | :doc:`press/berendsen <fix_press_berendsen>` |
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
| :doc:`print <fix_print>` | :doc:`property/atom (k) <fix_property_atom>` | :doc:`python/invoke <fix_python_invoke>` | :doc:`python/move <fix_python_move>` | :doc:`qbmsst <fix_qbmsst>` | :doc:`qeq/comb (o) <fix_qeq_comb>` |
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
| :doc:`qeq/dynamic <fix_qeq>` | :doc:`qeq/fire <fix_qeq>` | :doc:`qeq/point <fix_qeq>` | :doc:`qeq/reax (ko) <fix_qeq_reax>` | :doc:`qeq/shielded <fix_qeq>` | :doc:`qeq/slater <fix_qeq>` |
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
| :doc:`qmmm <fix_qmmm>` | :doc:`qtb <fix_qtb>` | :doc:`rattle <fix_shake>` | :doc:`reax/c/bonds (k) <fix_reaxc_bonds>` | :doc:`reax/c/species (k) <fix_reaxc_species>` | :doc:`recenter <fix_recenter>` |
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
| :doc:`restrain <fix_restrain>` | :doc:`rhok <fix_rhok>` | :doc:`rigid (o) <fix_rigid>` | :doc:`rigid/meso <fix_rigid_meso>` | :doc:`rigid/nph (o) <fix_rigid>` | :doc:`rigid/nph/small <fix_rigid>` |
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
| :doc:`rigid/npt (o) <fix_rigid>` | :doc:`rigid/npt/small <fix_rigid>` | :doc:`rigid/nve (o) <fix_rigid>` | :doc:`rigid/nve/small <fix_rigid>` | :doc:`rigid/nvt (o) <fix_rigid>` | :doc:`rigid/nvt/small <fix_rigid>` |
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
| :doc:`rigid/small (o) <fix_rigid>` | :doc:`rx (k) <fix_rx>` | :doc:`saed/vtk <fix_saed_vtk>` | :doc:`setforce (k) <fix_setforce>` | :doc:`shake <fix_shake>` | :doc:`shardlow (k) <fix_shardlow>` |
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
| :doc:`smd <fix_smd>` | :doc:`smd/adjust\_dt <fix_smd_adjust_dt>` | :doc:`smd/integrate\_tlsph <fix_smd_integrate_tlsph>` | :doc:`smd/integrate\_ulsph <fix_smd_integrate_ulsph>` | :doc:`smd/move\_tri\_surf <fix_smd_move_triangulated_surface>` | :doc:`smd/setvel <fix_smd_setvel>` |
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
| :doc:`smd/wall\_surface <fix_smd_wall_surface>` | :doc:`spring <fix_spring>` | :doc:`spring/chunk <fix_spring_chunk>` | :doc:`spring/rg <fix_spring_rg>` | :doc:`spring/self <fix_spring_self>` | :doc:`srd <fix_srd>` |
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
| :doc:`store/force <fix_store_force>` | :doc:`store/state <fix_store_state>` | :doc:`tdpd/source <fix_dpd_source>` | :doc:`temp/berendsen <fix_temp_berendsen>` | :doc:`temp/csld <fix_temp_csvr>` | :doc:`temp/csvr <fix_temp_csvr>` |
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
| :doc:`temp/rescale <fix_temp_rescale>` | :doc:`temp/rescale/eff <fix_temp_rescale_eff>` | :doc:`tfmc <fix_tfmc>` | :doc:`thermal/conductivity <fix_thermal_conductivity>` | :doc:`ti/spring <fix_ti_spring>` | :doc:`tmd <fix_tmd>` |
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
| :doc:`ttm <fix_ttm>` | :doc:`ttm/mod <fix_ttm>` | :doc:`tune/kspace <fix_tune_kspace>` | :doc:`vector <fix_vector>` | :doc:`viscosity <fix_viscosity>` | :doc:`viscous <fix_viscous>` |
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
| :doc:`wall/body/polygon <fix_wall_body_polygon>` | :doc:`wall/body/polyhedron <fix_wall_body_polyhedron>` | :doc:`wall/colloid <fix_wall>` | :doc:`wall/ees <fix_wall_ees>` | :doc:`wall/gran <fix_wall_gran>` | :doc:`wall/gran/region <fix_wall_gran_region>` |
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
| :doc:`wall/harmonic <fix_wall>` | :doc:`wall/lj1043 <fix_wall>` | :doc:`wall/lj126 <fix_wall>` | :doc:`wall/lj93 (k) <fix_wall>` | :doc:`wall/morse <fix_wall>` | :doc:`wall/piston <fix_wall_piston>` |
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
| :doc:`wall/reflect (k) <fix_wall_reflect>` | :doc:`wall/region <fix_wall_region>` | :doc:`wall/region/ees <fix_wall_ees>` | :doc:`wall/srd <fix_wall_srd>` | | |
+--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
.. table_from_list::
:columns: 6
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html
* :doc:`adapt <fix_adapt>`
* :doc:`adapt/fep <fix_adapt_fep>`
* :doc:`addforce <fix_addforce>`
* :doc:`addtorque <fix_addtorque>`
* :doc:`append/atoms <fix_append_atoms>`
* :doc:`atc <fix_atc>`
* :doc:`atom/swap <fix_atom_swap>`
* :doc:`ave/atom <fix_ave_atom>`
* :doc:`ave/chunk <fix_ave_chunk>`
* :doc:`ave/correlate <fix_ave_correlate>`
* :doc:`ave/correlate/long <fix_ave_correlate_long>`
* :doc:`ave/histo <fix_ave_histo>`
* :doc:`ave/histo/weight <fix_ave_histo>`
* :doc:`ave/time <fix_ave_time>`
* :doc:`aveforce <fix_aveforce>`
* :doc:`balance <fix_balance>`
* :doc:`bocs <fix_bocs>`
* :doc:`bond/break <fix_bond_break>`
* :doc:`bond/create <fix_bond_create>`
* :doc:`bond/react <fix_bond_react>`
* :doc:`bond/swap <fix_bond_swap>`
* :doc:`box/relax <fix_box_relax>`
* :doc:`client/md <fix_client_md>`
* :doc:`cmap <fix_cmap>`
* :doc:`colvars <fix_colvars>`
* :doc:`controller <fix_controller>`
* :doc:`deform (k) <fix_deform>`
* :doc:`deposit <fix_deposit>`
* :doc:`dpd/energy (k) <fix_dpd_energy>`
* :doc:`drag <fix_drag>`
* :doc:`drude <fix_drude>`
* :doc:`drude/transform/direct <fix_drude_transform>`
* :doc:`drude/transform/inverse <fix_drude_transform>`
* :doc:`dt/reset <fix_dt_reset>`
* :doc:`edpd/source <fix_dpd_source>`
* :doc:`efield <fix_efield>`
* :doc:`ehex <fix_ehex>`
* :doc:`electron/stopping <fix_electron_stopping>`
* :doc:`enforce2d (k) <fix_enforce2d>`
* :doc:`eos/cv <fix_eos_cv>`
* :doc:`eos/table <fix_eos_table>`
* :doc:`eos/table/rx (k) <fix_eos_table_rx>`
* :doc:`evaporate <fix_evaporate>`
* :doc:`external <fix_external>`
* :doc:`ffl <fix_ffl>`
* :doc:`filter/corotate <fix_filter_corotate>`
* :doc:`flow/gauss <fix_flow_gauss>`
* :doc:`freeze (k) <fix_freeze>`
* :doc:`gcmc <fix_gcmc>`
* :doc:`gld <fix_gld>`
* :doc:`gle <fix_gle>`
* :doc:`gravity (ko) <fix_gravity>`
* :doc:`grem <fix_grem>`
* :doc:`halt <fix_halt>`
* :doc:`heat <fix_heat>`
* :doc:`hyper/global <fix_hyper_global>`
* :doc:`hyper/local <fix_hyper_local>`
* :doc:`imd <fix_imd>`
* :doc:`indent <fix_indent>`
* :doc:`ipi <fix_ipi>`
* :doc:`langevin (k) <fix_langevin>`
* :doc:`langevin/drude <fix_langevin_drude>`
* :doc:`langevin/eff <fix_langevin_eff>`
* :doc:`langevin/spin <fix_langevin_spin>`
* :doc:`latte <fix_latte>`
* :doc:`lb/fluid <fix_lb_fluid>`
* :doc:`lb/momentum <fix_lb_momentum>`
* :doc:`lb/pc <fix_lb_pc>`
* :doc:`lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>`
* :doc:`lb/viscous <fix_lb_viscous>`
* :doc:`lineforce <fix_lineforce>`
* :doc:`manifoldforce <fix_manifoldforce>`
* :doc:`meso <fix_meso>`
* :doc:`meso/move <fix_meso_move>`
* :doc:`meso/stationary <fix_meso_stationary>`
* :doc:`momentum (k) <fix_momentum>`
* :doc:`move <fix_move>`
* :doc:`mscg <fix_mscg>`
* :doc:`msst <fix_msst>`
* :doc:`mvv/dpd <fix_mvv_dpd>`
* :doc:`mvv/edpd <fix_mvv_dpd>`
* :doc:`mvv/tdpd <fix_mvv_dpd>`
* :doc:`neb <fix_neb>`
* :doc:`neb\_spin <fix_neb_spin>`
* :doc:`nph (ko) <fix_nh>`
* :doc:`nph/asphere (o) <fix_nph_asphere>`
* :doc:`nph/body <fix_nph_body>`
* :doc:`nph/eff <fix_nh_eff>`
* :doc:`nph/sphere (o) <fix_nph_sphere>`
* :doc:`nphug (o) <fix_nphug>`
* :doc:`npt (iko) <fix_nh>`
* :doc:`npt/asphere (o) <fix_npt_asphere>`
* :doc:`npt/body <fix_npt_body>`
* :doc:`npt/eff <fix_nh_eff>`
* :doc:`npt/sphere (o) <fix_npt_sphere>`
* :doc:`npt/uef <fix_nh_uef>`
* :doc:`nve (iko) <fix_nve>`
* :doc:`nve/asphere (i) <fix_nve_asphere>`
* :doc:`nve/asphere/noforce <fix_nve_asphere_noforce>`
* :doc:`nve/awpmd <fix_nve_awpmd>`
* :doc:`nve/body <fix_nve_body>`
* :doc:`nve/dot <fix_nve_dot>`
* :doc:`nve/dotc/langevin <fix_nve_dotc_langevin>`
* :doc:`nve/eff <fix_nve_eff>`
* :doc:`nve/limit <fix_nve_limit>`
* :doc:`nve/line <fix_nve_line>`
* :doc:`nve/manifold/rattle <fix_nve_manifold_rattle>`
* :doc:`nve/noforce <fix_nve_noforce>`
* :doc:`nve/sphere (ko) <fix_nve_sphere>`
* :doc:`nve/spin <fix_nve_spin>`
* :doc:`nve/tri <fix_nve_tri>`
* :doc:`nvk <fix_nvk>`
* :doc:`nvt (iko) <fix_nh>`
* :doc:`nvt/asphere (o) <fix_nvt_asphere>`
* :doc:`nvt/body <fix_nvt_body>`
* :doc:`nvt/eff <fix_nh_eff>`
* :doc:`nvt/manifold/rattle <fix_nvt_manifold_rattle>`
* :doc:`nvt/sllod (io) <fix_nvt_sllod>`
* :doc:`nvt/sllod/eff <fix_nvt_sllod_eff>`
* :doc:`nvt/sphere (o) <fix_nvt_sphere>`
* :doc:`nvt/uef <fix_nh_uef>`
* :doc:`oneway <fix_oneway>`
* :doc:`orient/bcc <fix_orient>`
* :doc:`orient/fcc <fix_orient>`
* :doc:`phonon <fix_phonon>`
* :doc:`pimd <fix_pimd>`
* :doc:`planeforce <fix_planeforce>`
* :doc:`plumed <fix_plumed>`
* :doc:`poems <fix_poems>`
* :doc:`pour <fix_pour>`
* :doc:`precession/spin <fix_precession_spin>`
* :doc:`press/berendsen <fix_press_berendsen>`
* :doc:`print <fix_print>`
* :doc:`property/atom (k) <fix_property_atom>`
* :doc:`python/invoke <fix_python_invoke>`
* :doc:`python/move <fix_python_move>`
* :doc:`qbmsst <fix_qbmsst>`
* :doc:`qeq/comb (o) <fix_qeq_comb>`
* :doc:`qeq/dynamic <fix_qeq>`
* :doc:`qeq/fire <fix_qeq>`
* :doc:`qeq/point <fix_qeq>`
* :doc:`qeq/reax (ko) <fix_qeq_reax>`
* :doc:`qeq/shielded <fix_qeq>`
* :doc:`qeq/slater <fix_qeq>`
* :doc:`qmmm <fix_qmmm>`
* :doc:`qtb <fix_qtb>`
* :doc:`rattle <fix_shake>`
* :doc:`reax/c/bonds (k) <fix_reaxc_bonds>`
* :doc:`reax/c/species (k) <fix_reaxc_species>`
* :doc:`recenter <fix_recenter>`
* :doc:`restrain <fix_restrain>`
* :doc:`rhok <fix_rhok>`
* :doc:`rigid (o) <fix_rigid>`
* :doc:`rigid/meso <fix_rigid_meso>`
* :doc:`rigid/nph (o) <fix_rigid>`
* :doc:`rigid/nph/small <fix_rigid>`
* :doc:`rigid/npt (o) <fix_rigid>`
* :doc:`rigid/npt/small <fix_rigid>`
* :doc:`rigid/nve (o) <fix_rigid>`
* :doc:`rigid/nve/small <fix_rigid>`
* :doc:`rigid/nvt (o) <fix_rigid>`
* :doc:`rigid/nvt/small <fix_rigid>`
* :doc:`rigid/small (o) <fix_rigid>`
* :doc:`rx (k) <fix_rx>`
* :doc:`saed/vtk <fix_saed_vtk>`
* :doc:`setforce (k) <fix_setforce>`
* :doc:`shake <fix_shake>`
* :doc:`shardlow (k) <fix_shardlow>`
* :doc:`smd <fix_smd>`
* :doc:`smd/adjust\_dt <fix_smd_adjust_dt>`
* :doc:`smd/integrate\_tlsph <fix_smd_integrate_tlsph>`
* :doc:`smd/integrate\_ulsph <fix_smd_integrate_ulsph>`
* :doc:`smd/move\_tri\_surf <fix_smd_move_triangulated_surface>`
* :doc:`smd/setvel <fix_smd_setvel>`
* :doc:`smd/wall\_surface <fix_smd_wall_surface>`
* :doc:`spring <fix_spring>`
* :doc:`spring/chunk <fix_spring_chunk>`
* :doc:`spring/rg <fix_spring_rg>`
* :doc:`spring/self <fix_spring_self>`
* :doc:`srd <fix_srd>`
* :doc:`store/force <fix_store_force>`
* :doc:`store/state <fix_store_state>`
* :doc:`tdpd/source <fix_dpd_source>`
* :doc:`temp/berendsen <fix_temp_berendsen>`
* :doc:`temp/csld <fix_temp_csvr>`
* :doc:`temp/csvr <fix_temp_csvr>`
* :doc:`temp/rescale <fix_temp_rescale>`
* :doc:`temp/rescale/eff <fix_temp_rescale_eff>`
* :doc:`tfmc <fix_tfmc>`
* :doc:`thermal/conductivity <fix_thermal_conductivity>`
* :doc:`ti/spring <fix_ti_spring>`
* :doc:`tmd <fix_tmd>`
* :doc:`ttm <fix_ttm>`
* :doc:`ttm/mod <fix_ttm>`
* :doc:`tune/kspace <fix_tune_kspace>`
* :doc:`vector <fix_vector>`
* :doc:`viscosity <fix_viscosity>`
* :doc:`viscous <fix_viscous>`
* :doc:`wall/body/polygon <fix_wall_body_polygon>`
* :doc:`wall/body/polyhedron <fix_wall_body_polyhedron>`
* :doc:`wall/colloid <fix_wall>`
* :doc:`wall/ees <fix_wall_ees>`
* :doc:`wall/gran <fix_wall_gran>`
* :doc:`wall/gran/region <fix_wall_gran_region>`
* :doc:`wall/harmonic <fix_wall>`
* :doc:`wall/lj1043 <fix_wall>`
* :doc:`wall/lj126 <fix_wall>`
* :doc:`wall/lj93 (k) <fix_wall>`
* :doc:`wall/morse <fix_wall>`
* :doc:`wall/piston <fix_wall_piston>`
* :doc:`wall/reflect (k) <fix_wall_reflect>`
* :doc:`wall/region <fix_wall_region>`
* :doc:`wall/region/ees <fix_wall_ees>`
* :doc:`wall/srd <fix_wall_srd>`
*
*

5
doc/src/Commands_input.rst
View File

@ -55,8 +55,3 @@ Many input script errors are detected by LAMMPS and an ERROR or
WARNING message is printed. The :doc:`Errors <Errors>` doc page gives
more information on what errors mean. The documentation for each
command lists restrictions on how the command can be used.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

44
doc/src/Commands_kspace.rst
View File

@ -1,10 +1,15 @@
+----------------------------------------+------------------------------------+------------------------------------------+
| :doc:`General commands <Commands_all>` | :doc:`Fix styles <Commands_fix>` | :doc:`Compute styles <Commands_compute>` |
+----------------------------------------+------------------------------------+------------------------------------------+
| :doc:`Pair styles <Commands_pair>` | :doc:`Bond styles <Commands_bond>` | :ref:`Angle styles <angle>` |
+----------------------------------------+------------------------------------+------------------------------------------+
| :ref:`Dihedral styles <dihedral>` | :ref:`Improper styles <improper>` | :doc:`KSpace styles <Commands_kspace>` |
+----------------------------------------+------------------------------------+------------------------------------------+
.. table_from_list::
:columns: 3
* :doc:`General commands <Commands_all>`
* :doc:`Fix styles <Commands_fix>`
* :doc:`Compute styles <Commands_compute>`
* :doc:`Pair styles <Commands_pair>`
* :ref:`Bond styles <bond>`
* :ref:`Angle styles <angle>`
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
KSpace solvers
==============
@ -14,15 +19,18 @@ accelerated versions. This is indicated by additional letters in
parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
OPT.
+------------------------------------+--------------------------------------+-------------------------------------+---------------------------------------+
| :doc:`ewald (o) <kspace_style>` | :doc:`ewald/disp <kspace_style>` | :doc:`msm (o) <kspace_style>` | :doc:`msm/cg (o) <kspace_style>` |
+------------------------------------+--------------------------------------+-------------------------------------+---------------------------------------+
| :doc:`pppm (gok) <kspace_style>` | :doc:`pppm/cg (o) <kspace_style>` | :doc:`pppm/disp (i) <kspace_style>` | :doc:`pppm/disp/tip4p <kspace_style>` |
+------------------------------------+--------------------------------------+-------------------------------------+---------------------------------------+
| :doc:`pppm/stagger <kspace_style>` | :doc:`pppm/tip4p (o) <kspace_style>` | :doc:`scafacos <kspace_style>` | |
+------------------------------------+--------------------------------------+-------------------------------------+---------------------------------------+
.. table_from_list::
:columns: 4
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html
* :doc:`ewald (o) <kspace_style>`
* :doc:`ewald/disp <kspace_style>`
* :doc:`msm (o) <kspace_style>`
* :doc:`msm/cg (o) <kspace_style>`
* :doc:`pppm (gok) <kspace_style>`
* :doc:`pppm/cg (o) <kspace_style>`
* :doc:`pppm/disp (i) <kspace_style>`
* :doc:`pppm/disp/tip4p <kspace_style>`
* :doc:`pppm/stagger <kspace_style>`
* :doc:`pppm/tip4p (o) <kspace_style>`
* :doc:`scafacos <kspace_style>`
*

368
doc/src/Commands_pair.rst
View File

@ -1,10 +1,15 @@
+----------------------------------------+------------------------------------+------------------------------------------+
| :doc:`General commands <Commands_all>` | :doc:`Fix styles <Commands_fix>` | :doc:`Compute styles <Commands_compute>` |
+----------------------------------------+------------------------------------+------------------------------------------+
| :doc:`Pair styles <Commands_pair>` | :doc:`Bond styles <Commands_bond>` | :ref:`Angle styles <angle>` |
+----------------------------------------+------------------------------------+------------------------------------------+
| :ref:`Dihedral styles <dihedral>` | :ref:`Improper styles <improper>` | :doc:`KSpace styles <Commands_kspace>` |
+----------------------------------------+------------------------------------+------------------------------------------+
.. table_from_list::
:columns: 3
* :doc:`General commands <Commands_all>`
* :doc:`Fix styles <Commands_fix>`
* :doc:`Compute styles <Commands_compute>`
* :doc:`Pair styles <Commands_pair>`
* :ref:`Bond styles <bond>`
* :ref:`Angle styles <angle>`
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
Pair\_style potentials
======================
@ -14,123 +19,234 @@ accelerated versions. This is indicated by additional letters in
parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
OPT.
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
| :doc:`none <pair_none>` | :doc:`zero <pair_zero>` | :doc:`hybrid (k) <pair_hybrid>` | :doc:`hybrid/overlay (k) <pair_hybrid>` |
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
| | | | |
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
| :doc:`adp (o) <pair_adp>` | :doc:`agni (o) <pair_agni>` | :doc:`airebo (io) <pair_airebo>` | :doc:`airebo/morse (io) <pair_airebo>` |
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
| :doc:`atm <pair_atm>` | :doc:`awpmd/cut <pair_awpmd>` | :doc:`beck (go) <pair_beck>` | :doc:`body/nparticle <pair_body_nparticle>` |
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
| :doc:`body/rounded/polygon <pair_body_rounded_polygon>` | :doc:`body/rounded/polyhedron <pair_body_rounded_polyhedron>` | :doc:`bop <pair_bop>` | :doc:`born (go) <pair_born>` |
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
| :doc:`born/coul/dsf <pair_born>` | :doc:`born/coul/dsf/cs <pair_cs>` | :doc:`born/coul/long (go) <pair_born>` | :doc:`born/coul/long/cs (g) <pair_cs>` |
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
| :doc:`born/coul/msm (o) <pair_born>` | :doc:`born/coul/wolf (go) <pair_born>` | :doc:`born/coul/wolf/cs (g) <pair_cs>` | :doc:`brownian (o) <pair_brownian>` |
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
| :doc:`brownian/poly (o) <pair_brownian>` | :doc:`buck (giko) <pair_buck>` | :doc:`buck/coul/cut (giko) <pair_buck>` | :doc:`buck/coul/long (giko) <pair_buck>` |
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
| :doc:`buck/coul/long/cs <pair_cs>` | :doc:`buck/coul/msm (o) <pair_buck>` | :doc:`buck/long/coul/long (o) <pair_buck_long>` | :doc:`buck/mdf <pair_mdf>` |
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
| :doc:`buck6d/coul/gauss/dsf <pair_buck6d_coul_gauss>` | :doc:`buck6d/coul/gauss/long <pair_buck6d_coul_gauss>` | :doc:`colloid (go) <pair_colloid>` | :doc:`comb (o) <pair_comb>` |
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
| :doc:`comb3 <pair_comb>` | :doc:`cosine/squared <pair_cosine_squared>` | :doc:`coul/cut (gko) <pair_coul>` | :doc:`coul/cut/soft (o) <pair_fep_soft>` |
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
| :doc:`coul/debye (gko) <pair_coul>` | :doc:`coul/diel (o) <pair_coul_diel>` | :doc:`coul/dsf (gko) <pair_coul>` | :doc:`coul/long (gko) <pair_coul>` |
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
| :doc:`coul/long/cs (g) <pair_cs>` | :doc:`coul/long/soft (o) <pair_fep_soft>` | :doc:`coul/msm (o) <pair_coul>` | :doc:`coul/shield <pair_coul_shield>` |
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
| :doc:`coul/streitz <pair_coul>` | :doc:`coul/wolf (ko) <pair_coul>` | :doc:`coul/wolf/cs <pair_cs>` | :doc:`dpd (gio) <pair_dpd>` |
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
| :doc:`dpd/fdt <pair_dpd_fdt>` | :doc:`dpd/fdt/energy (k) <pair_dpd_fdt>` | :doc:`dpd/tstat (go) <pair_dpd>` | :doc:`dsmc <pair_dsmc>` |
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
| :doc:`e3b <pair_e3b>` | :doc:`drip <pair_drip>` | :doc:`eam (gikot) <pair_eam>` | :doc:`eam/alloy (gikot) <pair_eam>` |
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
| :doc:`eam/cd (o) <pair_eam>` | :doc:`eam/cd/old (o) <pair_eam>` | :doc:`eam/fs (gikot) <pair_eam>` | :doc:`edip (o) <pair_edip>` |
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
| :doc:`edip/multi <pair_edip>` | :doc:`edpd <pair_meso>` | :doc:`eff/cut <pair_eff>` | :doc:`eim (o) <pair_eim>` |
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
| :doc:`exp6/rx (k) <pair_exp6_rx>` | :doc:`extep <pair_extep>` | :doc:`gauss (go) <pair_gauss>` | :doc:`gauss/cut (o) <pair_gauss>` |
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
| :doc:`gayberne (gio) <pair_gayberne>` | :doc:`gran/hertz/history (o) <pair_gran>` | :doc:`gran/hooke (o) <pair_gran>` | :doc:`gran/hooke/history (ko) <pair_gran>` |
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
| :doc:`granular <pair_granular>` | :doc:`gw <pair_gw>` | :doc:`gw/zbl <pair_gw>` | :doc:`hbond/dreiding/lj (o) <pair_hbond_dreiding>` |
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
| :doc:`hbond/dreiding/morse (o) <pair_hbond_dreiding>` | :doc:`ilp/graphene/hbn <pair_ilp_graphene_hbn>` | :doc:`kim <pair_kim>` | :doc:`kolmogorov/crespi/full <pair_kolmogorov_crespi_full>` |
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
| :doc:`kolmogorov/crespi/z <pair_kolmogorov_crespi_z>` | :doc:`lcbop <pair_lcbop>` | :doc:`lebedeva/z <pair_lebedeva_z>` | :doc:`lennard/mdf <pair_mdf>` |
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
| :doc:`line/lj <pair_line_lj>` | :doc:`list <pair_list>` | :doc:`lj/charmm/coul/charmm (iko) <pair_charmm>` | :doc:`lj/charmm/coul/charmm/implicit (ko) <pair_charmm>` |
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
| :doc:`lj/charmm/coul/long (gikot) <pair_charmm>` | :doc:`lj/charmm/coul/long/soft (o) <pair_fep_soft>` | :doc:`lj/charmm/coul/msm (o) <pair_charmm>` | :doc:`lj/charmmfsw/coul/charmmfsh <pair_charmm>` |
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
| :doc:`lj/charmmfsw/coul/long <pair_charmm>` | :doc:`lj/class2 (gko) <pair_class2>` | :doc:`lj/class2/coul/cut (ko) <pair_class2>` | :doc:`lj/class2/coul/cut/soft <pair_fep_soft>` |
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
| :doc:`lj/class2/coul/long (gko) <pair_class2>` | :doc:`lj/class2/coul/long/soft <pair_fep_soft>` | :doc:`lj/class2/soft <pair_fep_soft>` | :doc:`lj/cubic (go) <pair_lj_cubic>` |
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
| :doc:`lj/cut (gikot) <pair_lj>` | :doc:`lj/cut/coul/cut (gko) <pair_lj>` | :doc:`lj/cut/coul/cut/soft (o) <pair_fep_soft>` | :doc:`lj/cut/coul/debye (gko) <pair_lj>` |
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
| :doc:`lj/cut/coul/dsf (gko) <pair_lj>` | :doc:`lj/cut/coul/long (gikot) <pair_lj>` | :doc:`lj/cut/coul/long/cs <pair_cs>` | :doc:`lj/cut/coul/long/soft (o) <pair_fep_soft>` |
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
| :doc:`lj/cut/coul/msm (go) <pair_lj>` | :doc:`lj/cut/coul/wolf (o) <pair_lj>` | :doc:`lj/cut/dipole/cut (go) <pair_dipole>` | :doc:`lj/cut/dipole/long (g) <pair_dipole>` |
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
| :doc:`lj/cut/dipole/sf (go) <pair_dipole>` | :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/soft (o) <pair_fep_soft>` | :doc:`lj/expand (gko) <pair_lj_expand>` | :doc:`lj/expand/coul/long (g) <pair_lj_expand>` |
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
| :doc:`lj/gromacs (gko) <pair_gromacs>` | :doc:`lj/gromacs/coul/gromacs (ko) <pair_gromacs>` | :doc:`lj/long/coul/long (iot) <pair_lj_long>` | :doc:`lj/long/dipole/long <pair_dipole>` |
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
| :doc:`lj/long/tip4p/long (o) <pair_lj_long>` | :doc:`lj/mdf <pair_mdf>` | :doc:`lj/sdk (gko) <pair_sdk>` | :doc:`lj/sdk/coul/long (go) <pair_sdk>` |
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
| :doc:`lj/sdk/coul/msm (o) <pair_sdk>` | :doc:`lj/sf/dipole/sf (go) <pair_dipole>` | :doc:`lj/smooth (o) <pair_lj_smooth>` | :doc:`lj/smooth/linear (o) <pair_lj_smooth_linear>` |
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
| :doc:`lj/switch3/coulgauss/long <pair_lj_switch3_coulgauss>` | :doc:`lj96/cut (go) <pair_lj96>` | :doc:`local/density <pair_local_density>` | :doc:`lubricate (o) <pair_lubricate>` |
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
| :doc:`lubricate/poly (o) <pair_lubricate>` | :doc:`lubricateU <pair_lubricateU>` | :doc:`lubricateU/poly <pair_lubricateU>` | :doc:`mdpd <pair_meso>` |
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
| :doc:`mdpd/rhosum <pair_meso>` | :doc:`meam/c <pair_meamc>` | :doc:`meam/spline (o) <pair_meam_spline>` | :doc:`meam/sw/spline <pair_meam_sw_spline>` |
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
| :doc:`mgpt <pair_mgpt>` | :doc:`mie/cut (g) <pair_mie>` | :doc:`momb <pair_momb>` | :doc:`morse (gkot) <pair_morse>` |
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
| :doc:`morse/smooth/linear (o) <pair_morse>` | :doc:`morse/soft <pair_fep_soft>` | :doc:`multi/lucy <pair_multi_lucy>` | :doc:`multi/lucy/rx (k) <pair_multi_lucy_rx>` |
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
| :doc:`nb3b/harmonic <pair_nb3b_harmonic>` | :doc:`nm/cut (o) <pair_nm>` | :doc:`nm/cut/coul/cut (o) <pair_nm>` | :doc:`nm/cut/coul/long (o) <pair_nm>` |
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
| :doc:`oxdna/coaxstk <pair_oxdna>` | :doc:`oxdna/excv <pair_oxdna>` | :doc:`oxdna/hbond <pair_oxdna>` | :doc:`oxdna/stk <pair_oxdna>` |
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
| :doc:`oxdna/xstk <pair_oxdna>` | :doc:`oxdna2/coaxstk <pair_oxdna2>` | :doc:`oxdna2/dh <pair_oxdna2>` | :doc:`oxdna2/excv <pair_oxdna2>` |
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
| :doc:`oxdna2/hbond <pair_oxdna2>` | :doc:`oxdna2/stk <pair_oxdna2>` | :doc:`oxdna2/xstk <pair_oxdna2>` | :doc:`peri/eps <pair_peri>` |
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
| :doc:`peri/lps (o) <pair_peri>` | :doc:`peri/pmb (o) <pair_peri>` | :doc:`peri/ves <pair_peri>` | :doc:`polymorphic <pair_polymorphic>` |
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
| :doc:`python <pair_python>` | :doc:`quip <pair_quip>` | :doc:`reax/c (ko) <pair_reaxc>` | :doc:`rebo (io) <pair_airebo>` |
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
| :doc:`resquared (go) <pair_resquared>` | :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/ulsph <pair_smd_ulsph>` | :doc:`smtbq <pair_smtbq>` | :doc:`snap (k) <pair_snap>` |
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
| :doc:`snap (k) <pair_snap>` | :doc:`soft (go) <pair_soft>` | :doc:`sph/heatconduction <pair_sph_heatconduction>` | :doc:`sph/idealgas <pair_sph_idealgas>` |
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
| :doc:`sph/lj <pair_sph_lj>` | :doc:`sph/rhosum <pair_sph_rhosum>` | :doc:`sph/taitwater <pair_sph_taitwater>` | :doc:`sph/taitwater/morris <pair_sph_taitwater_morris>` |
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
| :doc:`spin/dipole/cut <pair_spin_dipole>` | :doc:`spin/dipole/long <pair_spin_dipole>` | :doc:`spin/dmi <pair_spin_dmi>` | :doc:`spin/exchange <pair_spin_exchange>` |
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
| :doc:`spin/magelec <pair_spin_magelec>` | :doc:`spin/neel <pair_spin_neel>` | :doc:`srp <pair_srp>` | :doc:`sw (giko) <pair_sw>` |
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
| :doc:`table (gko) <pair_table>` | :doc:`table/rx (k) <pair_table_rx>` | :doc:`tdpd <pair_meso>` | :doc:`tersoff (giko) <pair_tersoff>` |
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
| :doc:`tersoff/mod (gko) <pair_tersoff_mod>` | :doc:`tersoff/mod/c (o) <pair_tersoff_mod>` | :doc:`tersoff/table (o) <pair_tersoff>` | :doc:`tersoff/zbl (gko) <pair_tersoff_zbl>` |
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
| :doc:`thole <pair_thole>` | :doc:`tip4p/cut (o) <pair_coul>` | :doc:`tip4p/long (o) <pair_coul>` | :doc:`tip4p/long/soft (o) <pair_fep_soft>` |
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
| :doc:`tri/lj <pair_tri_lj>` | :doc:`ufm (got) <pair_ufm>` | :doc:`vashishta (gko) <pair_vashishta>` | :doc:`vashishta/table (o) <pair_vashishta>` |
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
| :doc:`yukawa (gko) <pair_yukawa>` | :doc:`yukawa/colloid (go) <pair_yukawa_colloid>` | :doc:`zbl (gko) <pair_zbl>` | |
+--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
.. table_from_list::
:columns: 4
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html
* :doc:`none <pair_none>`
* :doc:`zero <pair_zero>`
* :doc:`hybrid (k) <pair_hybrid>`
* :doc:`hybrid/overlay (k) <pair_hybrid>`
*
*
*
*
* :doc:`adp (o) <pair_adp>`
* :doc:`agni (o) <pair_agni>`
* :doc:`airebo (io) <pair_airebo>`
* :doc:`airebo/morse (io) <pair_airebo>`
* :doc:`atm <pair_atm>`
* :doc:`awpmd/cut <pair_awpmd>`
* :doc:`beck (go) <pair_beck>`
* :doc:`body/nparticle <pair_body_nparticle>`
* :doc:`body/rounded/polygon <pair_body_rounded_polygon>`
* :doc:`body/rounded/polyhedron <pair_body_rounded_polyhedron>`
* :doc:`bop <pair_bop>`
* :doc:`born (go) <pair_born>`
* :doc:`born/coul/dsf <pair_born>`
* :doc:`born/coul/dsf/cs <pair_cs>`
* :doc:`born/coul/long (go) <pair_born>`
* :doc:`born/coul/long/cs (g) <pair_cs>`
* :doc:`born/coul/msm (o) <pair_born>`
* :doc:`born/coul/wolf (go) <pair_born>`
* :doc:`born/coul/wolf/cs (g) <pair_cs>`
* :doc:`brownian (o) <pair_brownian>`
* :doc:`brownian/poly (o) <pair_brownian>`
* :doc:`buck (giko) <pair_buck>`
* :doc:`buck/coul/cut (giko) <pair_buck>`
* :doc:`buck/coul/long (giko) <pair_buck>`
* :doc:`buck/coul/long/cs <pair_cs>`
* :doc:`buck/coul/msm (o) <pair_buck>`
* :doc:`buck/long/coul/long (o) <pair_buck_long>`
* :doc:`buck/mdf <pair_mdf>`
* :doc:`buck6d/coul/gauss/dsf <pair_buck6d_coul_gauss>`
* :doc:`buck6d/coul/gauss/long <pair_buck6d_coul_gauss>`
* :doc:`colloid (go) <pair_colloid>`
* :doc:`comb (o) <pair_comb>`
* :doc:`comb3 <pair_comb>`
* :doc:`cosine/squared <pair_cosine_squared>`
* :doc:`coul/cut (gko) <pair_coul>`
* :doc:`coul/cut/soft (o) <pair_fep_soft>`
* :doc:`coul/debye (gko) <pair_coul>`
* :doc:`coul/diel (o) <pair_coul_diel>`
* :doc:`coul/dsf (gko) <pair_coul>`
* :doc:`coul/long (gko) <pair_coul>`
* :doc:`coul/long/cs (g) <pair_cs>`
* :doc:`coul/long/soft (o) <pair_fep_soft>`
* :doc:`coul/msm (o) <pair_coul>`
* :doc:`coul/shield <pair_coul_shield>`
* :doc:`coul/streitz <pair_coul>`
* :doc:`coul/wolf (ko) <pair_coul>`
* :doc:`coul/wolf/cs <pair_cs>`
* :doc:`dpd (gio) <pair_dpd>`
* :doc:`dpd/fdt <pair_dpd_fdt>`
* :doc:`dpd/fdt/energy (k) <pair_dpd_fdt>`
* :doc:`dpd/tstat (go) <pair_dpd>`
* :doc:`dsmc <pair_dsmc>`
* :doc:`e3b <pair_e3b>`
* :doc:`drip <pair_drip>`
* :doc:`eam (gikot) <pair_eam>`
* :doc:`eam/alloy (gikot) <pair_eam>`
* :doc:`eam/cd (o) <pair_eam>`
* :doc:`eam/cd/old (o) <pair_eam>`
* :doc:`eam/fs (gikot) <pair_eam>`
* :doc:`edip (o) <pair_edip>`
* :doc:`edip/multi <pair_edip>`
* :doc:`edpd <pair_meso>`
* :doc:`eff/cut <pair_eff>`
* :doc:`eim (o) <pair_eim>`
* :doc:`exp6/rx (k) <pair_exp6_rx>`
* :doc:`extep <pair_extep>`
* :doc:`gauss (go) <pair_gauss>`
* :doc:`gauss/cut (o) <pair_gauss>`
* :doc:`gayberne (gio) <pair_gayberne>`
* :doc:`gran/hertz/history (o) <pair_gran>`
* :doc:`gran/hooke (o) <pair_gran>`
* :doc:`gran/hooke/history (ko) <pair_gran>`
* :doc:`granular <pair_granular>`
* :doc:`gw <pair_gw>`
* :doc:`gw/zbl <pair_gw>`
* :doc:`hbond/dreiding/lj (o) <pair_hbond_dreiding>`
* :doc:`hbond/dreiding/morse (o) <pair_hbond_dreiding>`
* :doc:`ilp/graphene/hbn <pair_ilp_graphene_hbn>`
* :doc:`kim <pair_kim>`
* :doc:`kolmogorov/crespi/full <pair_kolmogorov_crespi_full>`
* :doc:`kolmogorov/crespi/z <pair_kolmogorov_crespi_z>`
* :doc:`lcbop <pair_lcbop>`
* :doc:`lebedeva/z <pair_lebedeva_z>`
* :doc:`lennard/mdf <pair_mdf>`
* :doc:`line/lj <pair_line_lj>`
* :doc:`list <pair_list>`
* :doc:`lj/charmm/coul/charmm (iko) <pair_charmm>`
* :doc:`lj/charmm/coul/charmm/implicit (ko) <pair_charmm>`
* :doc:`lj/charmm/coul/long (gikot) <pair_charmm>`
* :doc:`lj/charmm/coul/long/soft (o) <pair_fep_soft>`
* :doc:`lj/charmm/coul/msm (o) <pair_charmm>`
* :doc:`lj/charmmfsw/coul/charmmfsh <pair_charmm>`
* :doc:`lj/charmmfsw/coul/long <pair_charmm>`
* :doc:`lj/class2 (gko) <pair_class2>`
* :doc:`lj/class2/coul/cut (ko) <pair_class2>`
* :doc:`lj/class2/coul/cut/soft <pair_fep_soft>`
* :doc:`lj/class2/coul/long (gko) <pair_class2>`
* :doc:`lj/class2/coul/long/soft <pair_fep_soft>`
* :doc:`lj/class2/soft <pair_fep_soft>`
* :doc:`lj/cubic (go) <pair_lj_cubic>`
* :doc:`lj/cut (gikot) <pair_lj>`
* :doc:`lj/cut/coul/cut (gko) <pair_lj>`
* :doc:`lj/cut/coul/cut/soft (o) <pair_fep_soft>`
* :doc:`lj/cut/coul/debye (gko) <pair_lj>`
* :doc:`lj/cut/coul/dsf (gko) <pair_lj>`
* :doc:`lj/cut/coul/long (gikot) <pair_lj>`
* :doc:`lj/cut/coul/long/cs <pair_cs>`
* :doc:`lj/cut/coul/long/soft (o) <pair_fep_soft>`
* :doc:`lj/cut/coul/msm (go) <pair_lj>`
* :doc:`lj/cut/coul/wolf (o) <pair_lj>`
* :doc:`lj/cut/dipole/cut (go) <pair_dipole>`
* :doc:`lj/cut/dipole/long (g) <pair_dipole>`
* :doc:`lj/cut/dipole/sf (go) <pair_dipole>`
* :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/soft (o) <pair_fep_soft>`
* :doc:`lj/expand (gko) <pair_lj_expand>`
* :doc:`lj/expand/coul/long (g) <pair_lj_expand>`
* :doc:`lj/gromacs (gko) <pair_gromacs>`
* :doc:`lj/gromacs/coul/gromacs (ko) <pair_gromacs>`
* :doc:`lj/long/coul/long (iot) <pair_lj_long>`
* :doc:`lj/long/dipole/long <pair_dipole>`
* :doc:`lj/long/tip4p/long (o) <pair_lj_long>`
* :doc:`lj/mdf <pair_mdf>`
* :doc:`lj/sdk (gko) <pair_sdk>`
* :doc:`lj/sdk/coul/long (go) <pair_sdk>`
* :doc:`lj/sdk/coul/msm (o) <pair_sdk>`
* :doc:`lj/sf/dipole/sf (go) <pair_dipole>`
* :doc:`lj/smooth (o) <pair_lj_smooth>`
* :doc:`lj/smooth/linear (o) <pair_lj_smooth_linear>`
* :doc:`lj/switch3/coulgauss/long <pair_lj_switch3_coulgauss>`
* :doc:`lj96/cut (go) <pair_lj96>`
* :doc:`local/density <pair_local_density>`
* :doc:`lubricate (o) <pair_lubricate>`
* :doc:`lubricate/poly (o) <pair_lubricate>`
* :doc:`lubricateU <pair_lubricateU>`
* :doc:`lubricateU/poly <pair_lubricateU>`
* :doc:`mdpd <pair_meso>`
* :doc:`mdpd/rhosum <pair_meso>`
* :doc:`meam/c <pair_meamc>`
* :doc:`meam/spline (o) <pair_meam_spline>`
* :doc:`meam/sw/spline <pair_meam_sw_spline>`
* :doc:`mgpt <pair_mgpt>`
* :doc:`mie/cut (g) <pair_mie>`
* :doc:`momb <pair_momb>`
* :doc:`morse (gkot) <pair_morse>`
* :doc:`morse/smooth/linear (o) <pair_morse>`
* :doc:`morse/soft <pair_fep_soft>`
* :doc:`multi/lucy <pair_multi_lucy>`
* :doc:`multi/lucy/rx (k) <pair_multi_lucy_rx>`
* :doc:`nb3b/harmonic <pair_nb3b_harmonic>`
* :doc:`nm/cut (o) <pair_nm>`
* :doc:`nm/cut/coul/cut (o) <pair_nm>`
* :doc:`nm/cut/coul/long (o) <pair_nm>`
* :doc:`oxdna/coaxstk <pair_oxdna>`
* :doc:`oxdna/excv <pair_oxdna>`
* :doc:`oxdna/hbond <pair_oxdna>`
* :doc:`oxdna/stk <pair_oxdna>`
* :doc:`oxdna/xstk <pair_oxdna>`
* :doc:`oxdna2/coaxstk <pair_oxdna2>`
* :doc:`oxdna2/dh <pair_oxdna2>`
* :doc:`oxdna2/excv <pair_oxdna2>`
* :doc:`oxdna2/hbond <pair_oxdna2>`
* :doc:`oxdna2/stk <pair_oxdna2>`
* :doc:`oxdna2/xstk <pair_oxdna2>`
* :doc:`peri/eps <pair_peri>`
* :doc:`peri/lps (o) <pair_peri>`
* :doc:`peri/pmb (o) <pair_peri>`
* :doc:`peri/ves <pair_peri>`
* :doc:`python <pair_python>`
* :doc:`quip <pair_quip>`
* :doc:`reax/c (ko) <pair_reaxc>`
* :doc:`rebo (io) <pair_airebo>`
* :doc:`resquared (go) <pair_resquared>`
* :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/ulsph <pair_smd_ulsph>`
* :doc:`smtbq <pair_smtbq>`
* :doc:`snap (k) <pair_snap>`
* :doc:`snap (k) <pair_snap>`
* :doc:`soft (go) <pair_soft>`
* :doc:`sph/heatconduction <pair_sph_heatconduction>`
* :doc:`sph/idealgas <pair_sph_idealgas>`
* :doc:`sph/lj <pair_sph_lj>`
* :doc:`sph/rhosum <pair_sph_rhosum>`
* :doc:`sph/taitwater <pair_sph_taitwater>`
* :doc:`sph/taitwater/morris <pair_sph_taitwater_morris>`
* :doc:`spin/dipole/cut <pair_spin_dipole>`
* :doc:`spin/dipole/long <pair_spin_dipole>`
* :doc:`spin/dmi <pair_spin_dmi>`
* :doc:`spin/exchange <pair_spin_exchange>`
* :doc:`spin/magelec <pair_spin_magelec>`
* :doc:`spin/neel <pair_spin_neel>`
* :doc:`srp <pair_srp>`
* :doc:`sw (giko) <pair_sw>`
* :doc:`table (gko) <pair_table>`
* :doc:`table/rx (k) <pair_table_rx>`
* :doc:`tdpd <pair_meso>`
* :doc:`tersoff (giko) <pair_tersoff>`
* :doc:`tersoff/mod (gko) <pair_tersoff_mod>`
* :doc:`tersoff/mod/c (o) <pair_tersoff_mod>`
* :doc:`tersoff/table (o) <pair_tersoff>`
* :doc:`tersoff/zbl (gko) <pair_tersoff_zbl>`
* :doc:`thole <pair_thole>`
* :doc:`tip4p/cut (o) <pair_coul>`
* :doc:`tip4p/long (o) <pair_coul>`
* :doc:`tip4p/long/soft (o) <pair_fep_soft>`
* :doc:`tri/lj <pair_tri_lj>`
* :doc:`ufm (got) <pair_ufm>`
* :doc:`vashishta (gko) <pair_vashishta>`
* :doc:`vashishta/table (o) <pair_vashishta>`
* :doc:`yukawa (gko) <pair_yukawa>`
* :doc:`yukawa/colloid (go) <pair_yukawa_colloid>`
* :doc:`zbl (gko) <pair_zbl>`
*
*

5
doc/src/Commands_parse.rst
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@ -146,8 +146,3 @@ comment indicator in (2) or substituted for as a variable in (3).
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.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Commands_structure.rst
View File

@ -84,8 +84,3 @@ command. Energy minimization (molecular statics) is performed using
the :doc:`minimize <minimize>` command. A parallel tempering
(replica-exchange) simulation can be run using the
:doc:`temper <temper>` command.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

61
doc/src/_ext/table_from_list.py Normal file
View File

@ -0,0 +1,61 @@
from docutils import nodes
from sphinx.util.docutils import SphinxDirective
from docutils.nodes import Element, Node
from typing import Any, Dict, List
from sphinx import addnodes
from sphinx.util import logging
from sphinx.errors import SphinxError
class TableFromList(SphinxDirective):
has_content = True
required_arguments = 0
optional_arguments = 0
final_argument_whitespace = False
option_spec = {
'columns': int,
}
def run(self) -> List[Node]:
ncolumns = self.options.get('columns', 2)
node = addnodes.compact_paragraph()
node.document = self.state.document
self.state.nested_parse(self.content, self.content_offset, node)
if len(node.children) != 1 or not isinstance(node.children[0],
nodes.bullet_list):
reporter = self.state.document.reporter
raise SphinxError('table_from_list content is not a list')
fulllist = node.children[0]
if (len(fulllist) % ncolumns) != 0:
raise SphinxError('number of list elements not a multiple of column number')
table = nodes.table()
tgroup = nodes.tgroup(cols=ncolumns)
table += tgroup
for i in range(ncolumns):
tgroup += nodes.colspec(colwidth=1)
tbody = nodes.tbody()
tgroup += tbody
current_row = nodes.row()
for idx, cell in enumerate(fulllist.children):
if len(current_row.children) == ncolumns:
tbody += current_row
current_row = nodes.row()
entry = nodes.entry()
current_row += entry
if len(cell.children) > 0:
entry += cell.children[0]
tbody += current_row
return [table]
def setup(app):
app.add_directive("table_from_list", TableFromList)
return {
'version': '0.1',
'parallel_read_safe': True,
'parallel_write_safe': True,
}

60
doc/txt/Commands.txt
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@ -1,60 +0,0 @@
"Previous Section"_Run_head.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::
:maxdepth: 1
Commands_input
Commands_parse
Commands_structure
Commands_category
.. toctree::
:maxdepth: 1
Commands_all
Commands_fix
Commands_compute
Commands_pair
Commands_bond
Commands_kspace
.. toctree::
:maxdepth: 1
Commands_removed
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)
"General 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)
"Removed commands and packages"_Commands_removed.html :all(b)
<!-- END_HTML_ONLY -->

139
doc/txt/Commands_all.txt
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@ -1,139 +0,0 @@
"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
"General 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)
General commands :h3
An alphabetic list of all general LAMMPS commands.
"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 adios"_dump_adios.html,
"dump image"_dump_image.html,
"dump movie"_dump_image.html,
"dump netcdf"_dump_netcdf.html,
"dump netcdf/mpiio"_dump_netcdf.html,
"dump vtk"_dump_vtk.html,
"dump_modify"_dump_modify.html,
"dynamical_matrix"_dynamical_matrix.html,
"echo"_echo.html,
"fix"_fix.html,
"fix_modify"_fix_modify.html,
"group"_group.html,
"group2ndx"_group2ndx.html,
"hyper"_hyper.html,
"if"_if.html,
"info"_info.html,
"improper_coeff"_improper_coeff.html,
"improper_style"_improper_style.html,
"include"_include.html,
"jump"_jump.html,
"kim_init"_kim_commands.html,
"kim_interactions"_kim_commands.html,
"kim_query"_kim_commands.html,
"kspace_modify"_kspace_modify.html,
"kspace_style"_kspace_style.html,
"label"_label.html,
"lattice"_lattice.html,
"log"_log.html,
"mass"_mass.html,
"message"_message.html,
"minimize"_minimize.html,
"min_modify"_min_modify.html,
"min_style"_min_style.html,
"min_style spin"_min_spin.html,
"molecule"_molecule.html,
"ndx2group"_group2ndx.html,
"neb"_neb.html,
"neb/spin"_neb_spin.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,
"server"_server.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,
"third_order"_third_order.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)

148
doc/txt/Commands_bond.txt
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@ -1,148 +0,0 @@
"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)
"General commands"_Commands_all.html,
"Fix styles"_Commands_fix.html,
"Compute styles"_Commands_compute.html,
"Pair styles"_Commands_pair.html,
"Bond styles"_Commands_bond.html#bond,
"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,
,
,
,
,
,
"class2 (ko)"_bond_class2.html,
"fene (iko)"_bond_fene.html,
"fene/expand (o)"_bond_fene_expand.html,
"gromos (o)"_bond_gromos.html,
"harmonic (iko)"_bond_harmonic.html,
"harmonic/shift (o)"_bond_harmonic_shift.html,
"harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html,
"mm3"_bond_mm3.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,
,
,
,
,
,
"charmm (iko)"_angle_charmm.html,
"class2 (ko)"_angle_class2.html,
"class2/p6"_angle_class2.html,
"cosine (ko)"_angle_cosine.html,
"cosine/buck6d"_angle_cosine_buck6d.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,
"cross"_angle_cross.html,
"dipole (o)"_angle_dipole.html,
"fourier (o)"_angle_fourier.html,
"fourier/simple (o)"_angle_fourier_simple.html,
"harmonic (iko)"_angle_harmonic.html,
"mm3"_angle_mm3.html,
"quartic (o)"_angle_quartic.html,
"sdk (o)"_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,
,
,
,
,
,
"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 (iko)"_dihedral_harmonic.html,
"helix (o)"_dihedral_helix.html,
"multi/harmonic (o)"_dihedral_multi_harmonic.html,
"nharmonic (o)"_dihedral_nharmonic.html,
"opls (iko)"_dihedral_opls.html,
"quadratic (o)"_dihedral_quadratic.html,
"spherical"_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,
,
,
,
,
,
"class2 (ko)"_improper_class2.html,
"cossq (o)"_improper_cossq.html,
"cvff (io)"_improper_cvff.html,
"distance"_improper_distance.html,
"distharm"_improper_distharm.html,
"fourier (o)"_improper_fourier.html,
"harmonic (iko)"_improper_harmonic.html,
"inversion/harmonic"_improper_inversion_harmonic.html,
"ring (o)"_improper_ring.html,
"sqdistharm"_improper_sqdistharm.html,
"umbrella (o)"_improper_umbrella.html :tb(c=4,ea=c)

141
doc/txt/Commands_category.txt
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@ -1,141 +0,0 @@
"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
"General commands"_Commands_all.html doc page lists all general commands
alphabetically. Style options for entries like fix, compute, pair etc.
have their own pages where they are listed alphabetically.
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,
"neb_spin"_neb_spin.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

167
doc/txt/Commands_compute.txt
View File

@ -1,167 +0,0 @@
"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
"General 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,
"adf"_compute_adf.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,
"centroid/stress/atom"_compute_stress_atom.html,
"chunk/atom"_compute_chunk_atom.html,
"chunk/spread/atom"_compute_chunk_spread_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,
"gyration/shape"_compute_gyration_shape.html,
"gyration/shape/chunk"_compute_gyration_shape_chunk.html,
"heat/flux"_compute_heat_flux.html,
"heat/flux/tally"_compute_tally.html,
"hexorder/atom"_compute_hexorder_atom.html,
"hma"_compute_hma.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,
"momentum"_compute_momentum.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/cylinder"_compute_pressure_cylinder.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,
"ptm/atom"_compute_ptm_atom.html,
"rdf"_compute_rdf.html,
"reduce"_compute_reduce.html,
"reduce/chunk"_compute_reduce_chunk.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/vertices"_compute_smd_triangle_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,
"snap"_compute_sna_atom.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/mop"_compute_stress_mop.html,
"stress/mop/profile"_compute_stress_mop.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/cs"_compute_temp_cs.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)

240
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@ -1,240 +0,0 @@
"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
"General 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,
"bocs"_fix_bocs.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,
"client/md"_fix_client_md.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/inverse"_fix_drude_transform.html,
"dt/reset"_fix_dt_reset.html,
"edpd/source"_fix_dpd_source.html,
"efield"_fix_efield.html,
"ehex"_fix_ehex.html,
"electron/stopping"_fix_electron_stopping.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,
"ffl"_fix_ffl.html,
"filter/corotate"_fix_filter_corotate.html,
"flow/gauss"_fix_flow_gauss.html,
"freeze (k)"_fix_freeze.html,
"gcmc"_fix_gcmc.html,
"gld"_fix_gld.html,
"gle"_fix_gle.html,
"gravity (ko)"_fix_gravity.html,
"grem"_fix_grem.html,
"halt"_fix_halt.html,
"heat"_fix_heat.html,
"hyper/global"_fix_hyper_global.html,
"hyper/local"_fix_hyper_local.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/move"_fix_meso_move.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,
"neb_spin"_fix_neb_spin.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 (iko)"_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 (iko)"_fix_nve.html,
"nve/asphere (i)"_fix_nve_asphere.html,
"nve/asphere/noforce"_fix_nve_asphere_noforce.html,
"nve/awpmd"_fix_nve_awpmd.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 (ko)"_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,
"plumed"_fix_plumed.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/c/bonds (k)"_fix_reaxc_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/meso"_fix_rigid_meso.html,
"rigid/nph (o)"_fix_rigid.html,
"rigid/nph/small"_fix_rigid.html,
"rigid/npt (o)"_fix_rigid.html,
"rigid/npt/small"_fix_rigid.html,
"rigid/nve (o)"_fix_rigid.html,
"rigid/nve/small"_fix_rigid.html,
"rigid/nvt (o)"_fix_rigid.html,
"rigid/nvt/small"_fix_rigid.html,
"rigid/small (o)"_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_tri_surf"_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/morse"_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=6,ea=c)

37
doc/txt/Commands_kspace.txt
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@ -1,37 +0,0 @@
"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
"General 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,
"scafacos"_kspace_style.html :tb(c=4,ea=c)

253
doc/txt/Commands_pair.txt
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@ -1,253 +0,0 @@
"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
"General 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 (k)"_pair_hybrid.html,
"hybrid/overlay (k)"_pair_hybrid.html,
,
,
,
,
"adp (o)"_pair_adp.html,
"agni (o)"_pair_agni.html,
"airebo (io)"_pair_airebo.html,
"airebo/morse (io)"_pair_airebo.html,
"atm"_pair_atm.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_cs.html,
"born/coul/long (go)"_pair_born.html,
"born/coul/long/cs (g)"_pair_cs.html,
"born/coul/msm (o)"_pair_born.html,
"born/coul/wolf (go)"_pair_born.html,
"born/coul/wolf/cs (g)"_pair_cs.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_cs.html,
"buck/coul/msm (o)"_pair_buck.html,
"buck/long/coul/long (o)"_pair_buck_long.html,
"buck/mdf"_pair_mdf.html,
"buck6d/coul/gauss/dsf"_pair_buck6d_coul_gauss.html,
"buck6d/coul/gauss/long"_pair_buck6d_coul_gauss.html,
"colloid (go)"_pair_colloid.html,
"comb (o)"_pair_comb.html,
"comb3"_pair_comb.html,
"cosine/squared"_pair_cosine_squared.html,
"coul/cut (gko)"_pair_coul.html,
"coul/cut/soft (o)"_pair_fep_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 (g)"_pair_cs.html,
"coul/long/soft (o)"_pair_fep_soft.html,
"coul/msm (o)"_pair_coul.html,
"coul/shield"_pair_coul_shield.html,
"coul/streitz"_pair_coul.html,
"coul/wolf (ko)"_pair_coul.html,
"coul/wolf/cs"_pair_cs.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,
"e3b"_pair_e3b.html,
"drip"_pair_drip.html,
"eam (gikot)"_pair_eam.html,
"eam/alloy (gikot)"_pair_eam.html,
"eam/cd (o)"_pair_eam.html,
"eam/cd/old (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 (o)"_pair_gauss.html,
"gayberne (gio)"_pair_gayberne.html,
"gran/hertz/history (o)"_pair_gran.html,
"gran/hooke (o)"_pair_gran.html,
"gran/hooke/history (ko)"_pair_gran.html,
"granular"_pair_granular.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,
"lebedeva/z"_pair_lebedeva_z.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 (gikot)"_pair_charmm.html,
"lj/charmm/coul/long/soft (o)"_pair_fep_soft.html,
"lj/charmm/coul/msm (o)"_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/cut/soft"_pair_fep_soft.html,
"lj/class2/coul/long (gko)"_pair_class2.html,
"lj/class2/coul/long/soft"_pair_fep_soft.html,
"lj/class2/soft"_pair_fep_soft.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_fep_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_cs.html,
"lj/cut/coul/long/soft (o)"_pair_fep_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 (g)"_pair_dipole.html,
"lj/cut/dipole/sf (go)"_pair_dipole.html,
"lj/cut/soft (o)"_pair_fep_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_fep_soft.html,
"lj/expand (gko)"_pair_lj_expand.html,
"lj/expand/coul/long (g)"_pair_lj_expand.html,
"lj/gromacs (gko)"_pair_gromacs.html,
"lj/gromacs/coul/gromacs (ko)"_pair_gromacs.html,
"lj/long/coul/long (iot)"_pair_lj_long.html,
"lj/long/dipole/long"_pair_dipole.html,
"lj/long/tip4p/long (o)"_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/sf/dipole/sf (go)"_pair_dipole.html,
"lj/smooth (o)"_pair_lj_smooth.html,
"lj/smooth/linear (o)"_pair_lj_smooth_linear.html,
"lj/switch3/coulgauss/long"_pair_lj_switch3_coulgauss.html,
"lj96/cut (go)"_pair_lj96.html,
"local/density"_pair_local_density.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/c"_pair_meamc.html,
"meam/spline (o)"_pair_meam_spline.html,
"meam/sw/spline"_pair_meam_sw_spline.html,
"mgpt"_pair_mgpt.html,
"mie/cut (g)"_pair_mie.html,
"momb"_pair_momb.html,
"morse (gkot)"_pair_morse.html,
"morse/smooth/linear (o)"_pair_morse.html,
"morse/soft"_pair_fep_soft.html,
"multi/lucy"_pair_multi_lucy.html,
"multi/lucy/rx (k)"_pair_multi_lucy_rx.html,
"nb3b/harmonic"_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/hbond"_pair_oxdna2.html,
"oxdna2/stk"_pair_oxdna2.html,
"oxdna2/xstk"_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/c (ko)"_pair_reaxc.html,
"rebo (io)"_pair_airebo.html,
"resquared (go)"_pair_resquared.html,
"sdpd/taitwater/isothermal"_pair_sdpd_taitwater_isothermal.html,
"smd/hertz"_pair_smd_hertz.html,
"smd/tlsph"_pair_smd_tlsph.html,
"smd/tri_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/dipole/cut"_pair_spin_dipole.html,
"spin/dipole/long"_pair_spin_dipole.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_fep_soft.html,
"tri/lj"_pair_tri_lj.html,
"ufm (got)"_pair_ufm.html,
"vashishta (gko)"_pair_vashishta.html,
"vashishta/table (o)"_pair_vashishta.html,
"yukawa (gko)"_pair_yukawa.html,
"yukawa/colloid (go)"_pair_yukawa_colloid.html,
"zbl (gko)"_pair_zbl.html :tb(c=4,ea=c)

66
doc/txt/Commands_removed.txt
View File

@ -1,66 +0,0 @@
"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
Removed commands and packages :h3
This page lists LAMMPS commands and packages that have been removed from
the distribution and provides suggestions for alternatives or replacements.
LAMMPS has special dummy styles implemented, that will stop LAMMPS and
print a suitable error message in most cases, when a style/command is used
that has been removed.
Fix ave/spatial and fix ave/spatial/sphere :h4
The fixes ave/spatial and ave/spatial/sphere have been removed from LAMMPS
since they were superseded by the more general and extensible "chunk
infrastructure". Here the system is partitioned in one of many possible
ways through the "compute chunk/atom"_compute_chunk_atom.html command
and then averaging is done using "fix ave/chunk"_fix_ave_chunk.html.
Please refer to the "chunk HOWTO"_Howto_chunk.html section for an overview.
MEAM package :h4
The MEAM package has been removed since it was superseded by the
"USER-MEAMC package"_Package_details.html#PKG-USER-MEAMC. The code in
the USER-MEAMC package is a translation of the Fortran code of MEAM into C++,
which removes several restrictions (e.g. there can be multiple instances
in hybrid pair styles) and allows for some optimizations leading
to better performance. The new pair style "meam/c"_pair_meamc.html has
the exact same syntax as the old "meam" pair style and thus pair style
"meam"_pair_meamc.html is an alias to the new style and backward
compatibility of old inputs is preserved.
REAX package :h4
The REAX package has been removed since it was superseded by the
"USER-REAXC package"_Package_details.html#PKG-USER-REAXC. The USER-REAXC
package has been tested to yield equivalent results to the REAX package,
offers better performance, supports OpenMP multi-threading via USER-OMP,
and GPU and threading parallelization through KOKKOS. The new pair styles
are not syntax compatible with the removed reax pair style, so input
files will have to be adapted.
USER-CUDA package :h4
The USER-CUDA package had been removed, since it had been unmaintained
for a long time and had known bugs and problems. Significant parts of
the design were transferred to the
"KOKKOS package"_Package_details.html#PKG-KOKKOS, which has similar
performance characteristics on Nvidia GPUs. Both, the KOKKOS
and the "GPU package"_Package_details.html#PKG-GPU are maintained
and allow running LAMMPS with GPU acceleration.
restart2data tool :h4
The functionality of the restart2data tool has been folded into the
LAMMPS executable directly instead of having a separate tool. A
combination of the commands "read_restart"_read_restart.html and
"write_data"_write_data.html can be used to the same effect. For added
convenience this conversion can also be triggered by "command line
flags"_Run_options.html

95
doc/txt/Commands_structure.txt
View File

@ -1,95 +0,0 @@
"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.

5
doc/utils/sphinx-config/conf.py
View File

@ -20,6 +20,7 @@ import os
# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here.
#sys.path.insert(0, os.path.abspath('.'))
sys.path.append(os.path.join(os.path.dirname(__file__), '../../src/_ext'))
# -- General configuration ------------------------------------------------
@ -30,7 +31,9 @@ import os
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
extensions = [
'sphinx.ext.mathjax', 'sphinx.ext.imgmath'
'sphinx.ext.mathjax',
'sphinx.ext.imgmath',
'table_from_list',
]
# 2017-12-07: commented out, since this package is broken with Sphinx 16.x
# yet we can no longer use Sphinx 15.x, since that breaks with