From 45f8de98379e6200fc1fa5008eaed6fe47022e7c Mon Sep 17 00:00:00 2001
From: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Date: Mon, 18 Dec 2023 18:30:50 -0500
Subject: [PATCH 1/2] Start to document different software

---
 doc/run/fp-software.md   | 55 ++++++++++++++++++++++++++++++++++++++++
 doc/run/index.rst        |  2 ++
 doc/run/md-software.md   | 25 ++++++++++++++++++
 doc/simplify/simplify.md |  2 +-
 4 files changed, 83 insertions(+), 1 deletion(-)
 create mode 100644 doc/run/fp-software.md
 create mode 100644 doc/run/md-software.md

diff --git a/doc/run/fp-software.md b/doc/run/fp-software.md
new file mode 100644
index 000000000..1c8055629
--- /dev/null
+++ b/doc/run/fp-software.md
@@ -0,0 +1,55 @@
+# Supported FP software
+
+## VASP
+
+{dargs:argument}fp_style <run_jdata/fp_style>: vasp
+
+TODO
+
+## Gaussian
+
+{dargs:argument}fp_style <run_jdata/fp_style>: gaussian
+
+TODO
+
+## Siesta
+
+{dargs:argument}fp_style <run_jdata/fp_style>: siesta
+
+TODO
+
+## CP2k
+
+{dargs:argument}fp_style <run_jdata/fp_style>: cp2k
+
+TODO
+
+## ABACUS
+
+{dargs:argument}fp_style <run_jdata/fp_style>: abacus
+
+TODO
+
+## AMBER DPRc
+
+{dargs:argument}fp_style <run_jdata/fp_style>: amber/diff
+
+TODO
+
+## PWmat
+
+{dargs:argument}fp_style <run_jdata/fp_style>: pwmat
+
+TODO
+
+## PWSCF
+
+{dargs:argument}fp_style <run_jdata/fp_style>: pwscf
+
+TODO
+
+## Customized
+
+{dargs:argument}fp_style <run_jdata/fp_style>: custom
+
+TODO
\ No newline at end of file
diff --git a/doc/run/index.rst b/doc/run/index.rst
index 04e304892..38767cd3f 100644
--- a/doc/run/index.rst
+++ b/doc/run/index.rst
@@ -6,6 +6,8 @@ Run
    :maxdepth: 2
 
    overview-of-the-run-process.md
+   md-software.md
+   fp-software.md
    example-of-param.md
    example-of-machine.md
    param.rst
diff --git a/doc/run/md-software.md b/doc/run/md-software.md
new file mode 100644
index 000000000..eec1287b7
--- /dev/null
+++ b/doc/run/md-software.md
@@ -0,0 +1,25 @@
+# Supported MD software
+
+## LAMMPS
+
+{dargs:argument}model_devi_engine <run_jdata/model_devi_engine>: lammps
+
+TODO
+
+## Amber
+
+{dargs:argument}model_devi_engine <run_jdata/model_devi_engine>: amber
+
+TODO
+
+## Calypso
+
+{dargs:argument}model_devi_engine <run_jdata/model_devi_engine>: calypso
+
+TODO
+
+## Gromacs
+
+{dargs:argument}model_devi_engine <run_jdata/model_devi_engine>: gromacs
+
+TODO
diff --git a/doc/simplify/simplify.md b/doc/simplify/simplify.md
index 8a1fa6dec..51c12f5b7 100644
--- a/doc/simplify/simplify.md
+++ b/doc/simplify/simplify.md
@@ -117,4 +117,4 @@ Here is an example of `param.json` for QM7 dataset:
 }
 ```
 
-Here {dargs:argument}`pick_data <simplify_jdata/pick_data>` is the directory to data to simplify where the program recursively detects systems `System` with `deepmd/npy` format. {dargs:argument}`init_pick_number <simplify_jdata/init_pick_number>` and {dargs:argument}`iter_pick_number <simplify_jdata/iter_pick_number>` are the numbers of picked frames. {dargs:argument}`model_devi_f_trust_lo <simplify_jdata/model_devi_f_trust_lo>` and {dargs:argument}`model_devi_f_trust_hi <simplify_jdata/model_devi_f_trust_hi>` mean the range of the max deviation of atomic forces in a frame. {dargs:argument}`fp_style <simplify_jdata/fp_style>` can be either `gaussian` or `vasp` currently. Other parameters are as the same as those of generator.
+Here {dargs:argument}`pick_data <simplify_jdata/pick_data>` is the directory to data to simplify where the program recursively detects systems `System` with `deepmd/npy` format. {dargs:argument}`init_pick_number <simplify_jdata/init_pick_number>` and {dargs:argument}`iter_pick_number <simplify_jdata/iter_pick_number>` are the numbers of picked frames. {dargs:argument}`model_devi_f_trust_lo <simplify_jdata/model_devi_f_trust_lo>` and {dargs:argument}`model_devi_f_trust_hi <simplify_jdata/model_devi_f_trust_hi>` mean the range of the max deviation of atomic forces in a frame. {dargs:argument}`fp_style <simplify_jdata/fp_style>` supports various software as described in the [Supported FP software](../run/fp-software.md) section. Other parameters are as the same as those of generator.

From ad9d9891593a0ac0123fb486b13a32195c3a7c87 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 18 Dec 2023 23:33:20 +0000
Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 doc/run/fp-software.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/run/fp-software.md b/doc/run/fp-software.md
index 1c8055629..da797b0b2 100644
--- a/doc/run/fp-software.md
+++ b/doc/run/fp-software.md
@@ -52,4 +52,4 @@ TODO
 
 {dargs:argument}fp_style <run_jdata/fp_style>: custom
 
-TODO
\ No newline at end of file
+TODO