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Merge pull request #3350 from lammps/doc-page-dump-style-table

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add a table with list of dump styles
This commit is contained in:
Axel Kohlmeyer
2022-07-16 06:45:04 -04:00
committed by GitHub
parent f478ca3b4d db9731bf3b
commit beebaea160
14 changed files with 101 additions and 2 deletions
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1
doc/src/Commands.rst
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@ -21,6 +21,7 @@ commands in it are used to define a LAMMPS simulation.
Commands_pair
Commands_bond
Commands_kspace
Commands_dump
.. toctree::
:maxdepth: 1

1
doc/src/Commands_all.rst
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@ -10,6 +10,7 @@
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
General commands
================

1
doc/src/Commands_bond.rst
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@ -10,6 +10,7 @@
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
.. _bond:

1
doc/src/Commands_compute.rst
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@ -10,6 +10,7 @@
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
Compute commands
================

56
doc/src/Commands_dump.rst Normal file
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@ -0,0 +1,56 @@
.. 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>`
* :doc:`Dump styles <Commands_dump>`
Dump commands
=============
An alphabetic list of all LAMMPS :doc:`dump <dump>` commands.
.. table_from_list::
:columns: 5
* :doc:`atom <dump>`
* :doc:`atom/adios <dump_adios>`
* :doc:`atom/gz <dump>`
* :doc:`atom/mpiio <dump>`
* :doc:`atom/zstd <dump>`
* :doc:`cfg <dump>`
* :doc:`cfg/gz <dump>`
* :doc:`cfg/mpiio <dump>`
* :doc:`cfg/uef <dump_cfg_uef>`
* :doc:`cfg/zstd <dump>`
* :doc:`custom <dump>`
* :doc:`custom/adios <dump_adios>`
* :doc:`custom/gz <dump>`
* :doc:`custom/mpiio <dump>`
* :doc:`custom/zstd <dump>`
* :doc:`dcd <dump>`
* :doc:`deprecated <dump>`
* :doc:`h5md <dump_h5md>`
* :doc:`image <dump_image>`
* :doc:`local <dump>`
* :doc:`local/gz <dump>`
* :doc:`local/zstd <dump>`
* :doc:`molfile <dump_molfile>`
* :doc:`movie <dump_image>`
* :doc:`netcdf <dump_netcdf>`
* :doc:`netcdf/mpiio <dump>`
* :doc:`vtk <dump_vtk>`
* :doc:`xtc <dump>`
* :doc:`xyz <dump>`
* :doc:`xyz/gz <dump>`
* :doc:`xyz/mpiio <dump>`
* :doc:`xyz/zstd <dump>`
* :doc:`yaml <dump>`

1
doc/src/Commands_fix.rst
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@ -10,6 +10,7 @@
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
Fix commands
============

1
doc/src/Commands_kspace.rst
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@ -10,6 +10,7 @@
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
KSpace solvers
==============

1
doc/src/Commands_pair.rst
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@ -10,6 +10,7 @@
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
Pair_style potentials
======================

1
doc/src/Manual.rst
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@ -110,6 +110,7 @@ Command Reference
angles
dihedrals
impropers
dumps
fix_modify_atc_commands
Bibliography

22
doc/src/dump.rst
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@ -1,4 +1,26 @@
.. index:: dump
.. index:: dump atom
.. index:: dump cfg
.. index:: dump custom
.. index:: dump dcd
.. index:: dump local
.. index:: dump xtc
.. index:: dump yaml
.. index:: dump xyz
.. index:: dump atom/gz
.. index:: dump cfg/gz
.. index:: dump custom/gz
.. index:: dump local/gz
.. index:: dump xyz/gz
.. index:: dump atom/mpiio
.. index:: dump cfg/mpiio
.. index:: dump custom/mpiio
.. index:: dump xyz/mpiio
.. index:: dump atom/zstd
.. index:: dump cfg/zstd
.. index:: dump custom/zstd
.. index:: dump xyz/zstd
.. index:: dump local/zstd
dump command
============

1
doc/src/dump_image.rst
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@ -1,4 +1,5 @@
.. index:: dump image
.. index:: dump movie
dump image command
==================

1
doc/src/dump_netcdf.rst
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@ -1,4 +1,5 @@
.. index:: dump netcdf
.. index:: dump netcdf/mpiio
dump netcdf command
===================

8
doc/src/dumps.rst Normal file
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@ -0,0 +1,8 @@
Dump Styles
###############
.. toctree::
:maxdepth: 1
:glob:
dump*

7
doc/utils/check-styles.py
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@ -60,7 +60,7 @@ reader = {}
region = {}
total = 0
index_pattern = re.compile(r"^.. index:: (compute|fix|pair_style|angle_style|bond_style|dihedral_style|improper_style|kspace_style)\s+([a-zA-Z0-9/_]+)$")
index_pattern = re.compile(r"^.. index:: (compute|fix|pair_style|angle_style|bond_style|dihedral_style|improper_style|kspace_style|dump)\s+([a-zA-Z0-9/_]+)$")
style_pattern = re.compile(r"(.+)Style\((.+),(.+)\)")
upper = re.compile("[A-Z]+")
gpu = re.compile("(.+)/gpu$")
@ -84,7 +84,8 @@ def load_index_entries_in_file(path):
def load_index_entries():
index = {'compute': set(), 'fix': set(), 'pair_style': set(), 'angle_style': set(),
'bond_style': set(), 'dihedral_style': set(), 'improper_style': set(), 'kspace_style': set()}
'bond_style': set(), 'dihedral_style': set(), 'improper_style': set(),
'kspace_style': set(), 'dump': set()}
rst_files = glob(os.path.join(doc_dir, '*.rst'))
for f in rst_files:
for command_type, style in load_index_entries_in_file(f):
@ -277,6 +278,7 @@ counter += check_style('dihedral_style.rst', doc_dir, ":doc:`(.+) <dihedral.+>`
counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) <improper.+>`",improper,'Improper',suffix=True)
counter += check_style('improper_style.rst', doc_dir, ":doc:`(.+) <improper.+>` -",improper,'Improper',suffix=False)
counter += check_style('Commands_kspace.rst', doc_dir, ":doc:`(.+) <kspace_style>`",kspace,'KSpace',suffix=True)
counter += check_style('Commands_dump.rst', doc_dir, ":doc:`(.+) <dump.*>`",dump,'Dump',suffix=True)
if counter:
print(f"Found {counter} issue(s) with style lists")
@ -290,6 +292,7 @@ counter += check_style_index("bond_style", bond, index["bond_style"])
counter += check_style_index("dihedral_style", dihedral, index["dihedral_style"])
counter += check_style_index("improper_style", improper, index["improper_style"])
counter += check_style_index("kspace_style", kspace, index["kspace_style"])
counter += check_style_index("dump", dump, index["dump"])
counter += check_style_index("pair_style", pair, index["pair_style"], skip=['meam/c','lj/sf','reax/c','lj/sdk','lj/sdk/coul/long','lj/sdk/coul/msm'])
if counter: