From f36653caebd893eaa61dbedb0fddadd080110f11 Mon Sep 17 00:00:00 2001
From: Steve Plimpton <sjplimp@sandia.gov>
Date: Fri, 15 Jul 2022 14:47:45 -0600
Subject: [PATCH 1/5] add a table with list of dump styles

---
 doc/src/Commands_all.rst     |  1 +
 doc/src/Commands_bond.rst    |  1 +
 doc/src/Commands_compute.rst |  1 +
 doc/src/Commands_dump.rst    | 56 ++++++++++++++++++++++++++++++++++++
 doc/src/Commands_fix.rst     |  1 +
 doc/src/Commands_kspace.rst  |  1 +
 doc/src/Commands_pair.rst    |  1 +
 7 files changed, 62 insertions(+)
 create mode 100644 doc/src/Commands_dump.rst

diff --git a/doc/src/Commands_all.rst b/doc/src/Commands_all.rst
index a868ad84fc..5e309c3ed0 100644
--- a/doc/src/Commands_all.rst
+++ b/doc/src/Commands_all.rst
@@ -10,6 +10,7 @@
    * :ref:`Dihedral styles <dihedral>`
    * :ref:`Improper styles <improper>`
    * :doc:`KSpace styles <Commands_kspace>`
+   * :doc:`Dump styles <Commands_dump>`
 
 General commands
 ================
diff --git a/doc/src/Commands_bond.rst b/doc/src/Commands_bond.rst
index dcedbb72b4..e230426ab9 100644
--- a/doc/src/Commands_bond.rst
+++ b/doc/src/Commands_bond.rst
@@ -10,6 +10,7 @@
    * :ref:`Dihedral styles <dihedral>`
    * :ref:`Improper styles <improper>`
    * :doc:`KSpace styles <Commands_kspace>`
+   * :doc:`Dump styles <Commands_dump>`
 
 .. _bond:
 
diff --git a/doc/src/Commands_compute.rst b/doc/src/Commands_compute.rst
index bb0c3e9c2a..682a75f201 100644
--- a/doc/src/Commands_compute.rst
+++ b/doc/src/Commands_compute.rst
@@ -10,6 +10,7 @@
    * :ref:`Dihedral styles <dihedral>`
    * :ref:`Improper styles <improper>`
    * :doc:`KSpace styles <Commands_kspace>`
+   * :doc:`Dump styles <Commands_dump>`
 
 Compute commands
 ================
diff --git a/doc/src/Commands_dump.rst b/doc/src/Commands_dump.rst
new file mode 100644
index 0000000000..2867a2194d
--- /dev/null
+++ b/doc/src/Commands_dump.rst
@@ -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>`
+
diff --git a/doc/src/Commands_fix.rst b/doc/src/Commands_fix.rst
index 4e40523c44..cb61cbe17b 100644
--- a/doc/src/Commands_fix.rst
+++ b/doc/src/Commands_fix.rst
@@ -10,6 +10,7 @@
    * :ref:`Dihedral styles <dihedral>`
    * :ref:`Improper styles <improper>`
    * :doc:`KSpace styles <Commands_kspace>`
+   * :doc:`Dump styles <Commands_dump>`
 
 Fix commands
 ============
diff --git a/doc/src/Commands_kspace.rst b/doc/src/Commands_kspace.rst
index 0f64338415..088789e321 100644
--- a/doc/src/Commands_kspace.rst
+++ b/doc/src/Commands_kspace.rst
@@ -10,6 +10,7 @@
    * :ref:`Dihedral styles <dihedral>`
    * :ref:`Improper styles <improper>`
    * :doc:`KSpace styles <Commands_kspace>`
+   * :doc:`Dump styles <Commands_dump>`
 
 KSpace solvers
 ==============
diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst
index f9ddecc590..7f14132c9b 100644
--- a/doc/src/Commands_pair.rst
+++ b/doc/src/Commands_pair.rst
@@ -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
 ======================

From c8ca8fb2d60165444f3ffb3e0429e01007ac711f Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 15 Jul 2022 17:51:36 -0400
Subject: [PATCH 2/5] properly integrate the new file into the document toctree

---
 doc/src/Commands.rst      | 1 +
 doc/src/Commands_dump.rst | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/doc/src/Commands.rst b/doc/src/Commands.rst
index 72a98159ff..32920b75fb 100644
--- a/doc/src/Commands.rst
+++ b/doc/src/Commands.rst
@@ -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
diff --git a/doc/src/Commands_dump.rst b/doc/src/Commands_dump.rst
index 2867a2194d..12dd7b2321 100644
--- a/doc/src/Commands_dump.rst
+++ b/doc/src/Commands_dump.rst
@@ -15,7 +15,7 @@
 Dump commands
 =============
 
-An alphabetic list of all LAMMPS :doc:`dump <dump>` commands.  
+An alphabetic list of all LAMMPS :doc:`dump <dump>` commands.
 
 .. table_from_list::
    :columns: 5

From 698d3b06a58b596c2da7c76ffaad911b66377558 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 15 Jul 2022 21:23:08 -0400
Subject: [PATCH 3/5] update style checker script to also check dump styles

---
 doc/utils/check-styles.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/doc/utils/check-styles.py b/doc/utils/check-styles.py
index 47d3dd5e3b..82de537863 100755
--- a/doc/utils/check-styles.py
+++ b/doc/utils/check-styles.py
@@ -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:

From b28f8bc70ea0939e5be46d6df5e2f105a287ea2d Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 15 Jul 2022 21:23:26 -0400
Subject: [PATCH 4/5] add missing index entries for dump style

---
 doc/src/dump.rst        | 22 ++++++++++++++++++++++
 doc/src/dump_image.rst  |  1 +
 doc/src/dump_netcdf.rst |  1 +
 3 files changed, 24 insertions(+)

diff --git a/doc/src/dump.rst b/doc/src/dump.rst
index 843d2e4883..fb291a2bc3 100644
--- a/doc/src/dump.rst
+++ b/doc/src/dump.rst
@@ -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
 ============
diff --git a/doc/src/dump_image.rst b/doc/src/dump_image.rst
index 0aeab34f60..9b16a7c133 100644
--- a/doc/src/dump_image.rst
+++ b/doc/src/dump_image.rst
@@ -1,4 +1,5 @@
 .. index:: dump image
+.. index:: dump movie
 
 dump image command
 ==================
diff --git a/doc/src/dump_netcdf.rst b/doc/src/dump_netcdf.rst
index d53a0a3b12..04790f4986 100644
--- a/doc/src/dump_netcdf.rst
+++ b/doc/src/dump_netcdf.rst
@@ -1,4 +1,5 @@
 .. index:: dump netcdf
+.. index:: dump netcdf/mpiio
 
 dump netcdf command
 ===================

From db9731bf3bb3c1e8997f20f5507ccaac36e92c6b Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 15 Jul 2022 22:58:49 -0400
Subject: [PATCH 5/5] also index dump styles

---
 doc/src/Manual.rst | 1 +
 doc/src/dumps.rst  | 8 ++++++++
 2 files changed, 9 insertions(+)
 create mode 100644 doc/src/dumps.rst

diff --git a/doc/src/Manual.rst b/doc/src/Manual.rst
index 3d7c7ad8dd..962810181f 100644
--- a/doc/src/Manual.rst
+++ b/doc/src/Manual.rst
@@ -110,6 +110,7 @@ Command Reference
    angles
    dihedrals
    impropers
+   dumps
    fix_modify_atc_commands
    Bibliography
 
diff --git a/doc/src/dumps.rst b/doc/src/dumps.rst
new file mode 100644
index 0000000000..4a8f387338
--- /dev/null
+++ b/doc/src/dumps.rst
@@ -0,0 +1,8 @@
+Dump Styles
+###############
+
+.. toctree::
+   :maxdepth: 1
+   :glob:
+
+   dump*