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Add Sphinx extension to generate tables from lists #1786

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Dec 2, 2019
Merged

Add Sphinx extension to generate tables from lists #1786

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65381d7
Add new table_from_list extension
rbberger Nov 25, 2019
2c33b55
Remove txt/Commands*.txt
rbberger Nov 25, 2019
7d28906
Update src/Command*.rst files
rbberger Nov 25, 2019
4c13001
Add extension errors that stop the build
rbberger Nov 25, 2019
acf02bb
Revert split of Commands_bond.rst as requested by @sjplimp
rbberger Dec 1, 2019
73a4c58
Merge branch 'master' into doc_command_tables
rbberger Dec 1, 2019
dfcb4ed
Fix trailing whitespace
rbberger Dec 1, 2019
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5 changes: 0 additions & 5 deletions doc/src/Commands.rst
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Expand Up @@ -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 changes: 128 additions & 52 deletions doc/src/Commands_all.rst
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215 changes: 136 additions & 79 deletions 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>` | |
+--------------------------------------+-----------------------------------------+-------------------------------------------+---------------------------------------------------------+


.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html
.. table_from_list::
:columns: 4

* :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 changes: 0 additions & 5 deletions doc/src/Commands_category.rst
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Expand Up @@ -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
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