deepmd-kit 2.2.8__tar.gz → 2.2.10__tar.gz

deepmd_kit-2.2.10/.pre-commit-config.yaml

@@ -0,0 +1,121 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: trailing-whitespace
+        exclude: "^.+\\.pbtxt$"
+      - id: end-of-file-fixer
+        exclude: "^.+\\.pbtxt$"
+      - id: check-yaml
+      - id: check-json
+      - id: check-added-large-files
+        args: ["--maxkb=1024", "--enforce-all"]
+        exclude: |
+          (?x)^(
+              source/tests/infer/dipolecharge_e.pbtxt|
+              source/tests/infer/deeppolar_new.pbtxt
+          )$
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: check-toml
+  # Python
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.13.2
+    hooks:
+      - id: isort
+        files: \.py$
+        exclude: ^source/3rdparty
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.3.5
+    hooks:
+      - id: ruff
+        args: ["--fix"]
+        exclude: ^source/3rdparty
+        types_or: [python, pyi, jupyter]
+      - id: ruff-format
+        exclude: ^source/3rdparty
+        types_or: [python, pyi, jupyter]
+  # numpydoc
+  - repo: https://github.com/Carreau/velin
+    rev: 0.0.12
+    hooks:
+      - id: velin
+        args: ["--write"]
+        exclude: ^source/3rdparty
+  # Python inside docs
+  - repo: https://github.com/asottile/blacken-docs
+    rev: 1.16.0
+    hooks:
+      - id: blacken-docs
+  # C++
+  - repo: https://github.com/pre-commit/mirrors-clang-format
+    rev: v18.1.2
+    hooks:
+      - id: clang-format
+        exclude: ^source/3rdparty|source/lib/src/gpu/cudart/.+\.inc
+  # markdown, yaml, CSS, javascript
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v4.0.0-alpha.8
+    hooks:
+      - id: prettier
+        types_or: [markdown, yaml, css]
+        # workflow files cannot be modified by pre-commit.ci
+        exclude: ^(source/3rdparty|\.github/workflows|\.clang-format)
+  # Shell
+  - repo: https://github.com/scop/pre-commit-shfmt
+    rev: v3.8.0-1
+    hooks:
+      - id: shfmt
+  # CMake
+  - repo: https://github.com/cheshirekow/cmake-format-precommit
+    rev: v0.6.13
+    hooks:
+      - id: cmake-format
+      #- id: cmake-lint
+  # license header
+  - repo: https://github.com/Lucas-C/pre-commit-hooks
+    rev: v1.5.5
+    hooks:
+      # C++, js
+      - id: insert-license
+        files: \.(c|cc|cpp|js|ts|h|hpp)$
+        args:
+          - --license-filepath
+          - .license-header.txt
+          - --comment-style
+          - //
+          - --no-extra-eol
+        exclude: ^source/3rdparty|source/lib/src/gpu/cudart/.+\.inc
+      # CSS
+      - id: insert-license
+        files: \.(css|scss)$
+        args:
+          - --license-filepath
+          - .license-header.txt
+          - --comment-style
+          - /*| *| */
+          - --no-extra-eol
+      # Python
+      - id: insert-license
+        files: \.(py|pyx)$
+        args:
+          - --license-filepath
+          - .license-header.txt
+          - --comment-style
+          - "#"
+          - --no-extra-eol
+        exclude: ^source/3rdparty
+      # HTML
+      - id: insert-license
+        files: \.(html|vue|xml)$
+        args:
+          - --license-filepath
+          - .license-header.txt
+          - --comment-style
+          - <!--|  ~|  -->
+          - --no-extra-eol
+ci:
+  autoupdate_branch: devel

{deepmd_kit-2.2.8 → deepmd_kit-2.2.10}/CONTRIBUTING.md

@@ -7,6 +7,7 @@ Welcome to [DeePMD-kit](https://github.com/deepmodeling/deepmd-kit)!
 You can either make a code contribution, help improve our document or offer help to other users. Your help is always appreciated. Come and have fun!
 
 ### Code contribution
+
 You can start from any one of the following items to help improve deepmd-kit
 
 - Smash a bug
@@ -18,6 +19,7 @@ See [here](#before-you-contribute) for some before-hand heads-up.
 See [here](#how-to-contribute) to learn how to contribute.
 
 ### Document improvement
+
 You can start from any one of the following items to help improve [DeePMD-kit Docs](https://deepmd.readthedocs.io/en/latest/?badge=latest):
 
 - Fix typos or format (punctuation, space, indentation, code block, etc.)
@@ -26,21 +28,27 @@ You can start from any one of the following items to help improve [DeePMD-kit Do
 - Translate docs changes from English to Chinese
 
 ### Offer help
+
 You can help other users of deepmd-kit in the following way
 
 - Submit, reply to, and resolve [issues](https://github.com/deepmodeling/deepmd-kit/issues)
 - (Advanced) Review Pull Requests created by others
 
 ## Before you contribute
+
 ### Overview of DeePMD-kit
+
 Currently, we maintain two main branch:
+
 - master: stable branch with version tag
-- devel :  branch for developers
+- devel : branch for developers
 
 ### Developer guide
-See [here](doc/development/index.md) for coding conventions, API and other needs-to-know of the code.
+
+See [documentation](https://deepmd.readthedocs.io/) for coding conventions, API and other needs-to-know of the code.
 
 ## How to contribute
+
 Please perform the following steps to create your Pull Request to this repository. If don't like to use commands, you can also use [GitHub Desktop](https://desktop.github.com/), which is easier to get started. Go to [git documentation](https://git-scm.com/doc) if you want to really master git.
 
 ### Step 1: Fork the repository
@@ -51,79 +59,82 @@ Please perform the following steps to create your Pull Request to this repositor
 ### Step 2: Clone the forked repository to local storage and set configurations
 
 1. Clone your own repo, not the public repo (from deepmodeling) ! And change the branch to devel.
-    ```bash
-    git clone https://github.com/$username/deepmd-kit.git
-    # Replace `$username` with your GitHub ID
 
-    git checkout devel
-    ```
+   ```bash
+   git clone https://github.com/$username/deepmd-kit.git
+   # Replace `$username` with your GitHub ID
+
+   git checkout devel
+   ```
 
 2. Add deepmodeling's repo as your remote repo, we can name it "upstream". And fetch upstream's latest codes to your workstation.
-    ```bash
-    git remote add upstream https://github.com/deepmodeling/deepmd-kit.git
-    # After you add a remote repo, your local repo will be automatically named "origin".
 
-    git fetch upstream
+   ```bash
+   git remote add upstream https://github.com/deepmodeling/deepmd-kit.git
+   # After you add a remote repo, your local repo will be automatically named "origin".
 
-    # If your current codes are behind the latest codes, you should merge latest codes first.
-    # Notice you should merge from "devel"!
-    git merge upstream/devel
-    ```
+   git fetch upstream
+
+   # If your current codes are behind the latest codes, you should merge latest codes first.
+   # Notice you should merge from "devel"!
+   git merge upstream/devel
+   ```
 
 3. Modify your codes and design unit tests.
 
 4. Commit your changes
-    ```bash
-    git status # Checks the local status
-    git add <file> ... # Adds the file(s) you want to commit. If you want to commit all changes, you can directly use `git add.`
-    git commit -m "commit-message: update the xx"
-    ```
+
+   ```bash
+   git status # Checks the local status
+   git add <file> ... # Adds the file(s) you want to commit. If you want to commit all changes, you can directly use `git add.`
+   git commit -m "commit-message: update the xx"
+   ```
 
 5. Push the changed codes to your original repo on github.
-    ```bash
-    git push origin devel
-    ```
+   ```bash
+   git push origin devel
+   ```
 
 ### Alternatively: Create a new branch
 
 1. Get your local master up-to-date with upstream/master.
 
-    ```bash
-    cd $working_dir/deepmd-kit
-    git fetch upstream
-    git checkout master
-    git rebase upstream/master
-    ```
+   ```bash
+   cd $working_dir/deepmd-kit
+   git fetch upstream
+   git checkout master
+   git rebase upstream/master
+   ```
 
 2. Create a new branch based on the master branch.
 
-    ```bash
-    git checkout -b new-branch-name
-    ```
+   ```bash
+   git checkout -b new-branch-name
+   ```
 
 3. Modify your codes and design unit tests.
 
 4. Commit your changes
 
-    ```bash
-    git status # Checks the local status
-    git add <file> ... # Adds the file(s) you want to commit. If you want to commit all changes, you can directly use `git add.`
-    git commit -m "commit-message: update the xx"
-    ```
+   ```bash
+   git status # Checks the local status
+   git add <file> ... # Adds the file(s) you want to commit. If you want to commit all changes, you can directly use `git add.`
+   git commit -m "commit-message: update the xx"
+   ```
 
 5. Keep your branch in sync with upstream/master
 
-    ```bash
-    # While on your new branch
-    git fetch upstream
-    git rebase upstream/master
-    ```
+   ```bash
+   # While on your new branch
+   git fetch upstream
+   git rebase upstream/master
+   ```
 
 6. Push your changes to the remote
 
-    ```bash
-    git push -u origin new-branch-name # "-u" is used to track the remote branch from origin
-    ```
+   ```bash
+   git push -u origin new-branch-name # "-u" is used to track the remote branch from origin
+   ```
 
 ### Step 3: Create a pull request
 
@@ -133,4 +144,5 @@ Please perform the following steps to create your Pull Request to this repositor
 Now, your PR is successfully submitted! After this PR is merged, you will automatically become a contributor to DeePMD-kit.
 
 ## Contact us
+
 E-mail: contact@deepmodeling.org

{deepmd_kit-2.2.8 → deepmd_kit-2.2.10}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: deepmd-kit
-Version: 2.2.8
+Version: 2.2.10
 Summary: A deep learning package for many-body potential energy representation and molecular dynamics
 Keywords: deepmd
 Author: DeepModeling
@@ -199,7 +199,7 @@ Requires-Dist: importlib_metadata>=1.4; python_version < "3.8"
 Requires-Dist: h5py
 Requires-Dist: wcmatch
 Requires-Dist: packaging
-Requires-Dist: dpdata>=0.1.9; extra == "test"
+Requires-Dist: dpdata>=0.2.7; extra == "test"
 Requires-Dist: ase; extra == "test"
 Requires-Dist: pytest; extra == "test"
 Requires-Dist: pytest-cov; extra == "test"
@@ -219,23 +219,16 @@ Requires-Dist: dargs>=0.3.4; extra == "docs"
 Requires-Dist: sphinx-argparse; extra == "docs"
 Requires-Dist: pygments-lammps; extra == "docs"
 Requires-Dist: sphinxcontrib-bibtex; extra == "docs"
-Requires-Dist: lammps~=2023.8.2.2.0; extra == "lmp"
+Requires-Dist: lammps~=2023.8.2.3.0; extra == "lmp"
 Requires-Dist: i-PI; extra == "ipi"
 Requires-Dist: dpgui; extra == "gui"
-Requires-Dist: tensorflow-cpu; platform_machine != "aarch64" and (platform_machine != "arm64" or platform_system != "Darwin") and extra == "cpu"
-Requires-Dist: tensorflow; platform_machine == "aarch64" or (platform_machine == "arm64" and platform_system == "Darwin") and extra == "cpu"
-Requires-Dist: tensorflow-cpu<2.15; platform_system == "Windows" and extra == "cpu"
-Requires-Dist: tensorflow; extra == "gpu"
-Requires-Dist: tensorflow-metal; platform_machine == "arm64" and platform_system == "Darwin" and extra == "gpu"
-Requires-Dist: horovod; extra == "mpi"
-Requires-Dist: mpi4py; extra == "mpi"
 Requires-Dist: nvidia-cuda-runtime-cu11; extra == "cu11"
 Requires-Dist: nvidia-cublas-cu11; extra == "cu11"
 Requires-Dist: nvidia-cufft-cu11; extra == "cu11"
 Requires-Dist: nvidia-curand-cu11; extra == "cu11"
 Requires-Dist: nvidia-cusolver-cu11; extra == "cu11"
 Requires-Dist: nvidia-cusparse-cu11; extra == "cu11"
-Requires-Dist: nvidia-cudnn-cu11; extra == "cu11"
+Requires-Dist: nvidia-cudnn-cu11<9; extra == "cu11"
 Requires-Dist: nvidia-cuda-nvcc-cu11; extra == "cu11"
 Requires-Dist: nvidia-cuda-runtime-cu12; extra == "cu12"
 Requires-Dist: nvidia-cublas-cu12; extra == "cu12"
@@ -243,26 +236,37 @@ Requires-Dist: nvidia-cufft-cu12; extra == "cu12"
 Requires-Dist: nvidia-curand-cu12; extra == "cu12"
 Requires-Dist: nvidia-cusolver-cu12; extra == "cu12"
 Requires-Dist: nvidia-cusparse-cu12; extra == "cu12"
-Requires-Dist: nvidia-cudnn-cu12; extra == "cu12"
+Requires-Dist: nvidia-cudnn-cu12<9; extra == "cu12"
 Requires-Dist: nvidia-cuda-nvcc-cu12; extra == "cu12"
+Requires-Dist: tensorflow-cpu; platform_machine != "aarch64" and (platform_machine != "arm64" or platform_system != "Darwin") and extra == "cpu"
+Requires-Dist: tensorflow; platform_machine == "aarch64" or (platform_machine == "arm64" and platform_system == "Darwin") and extra == "cpu"
+Requires-Dist: tensorflow-cpu<2.15; platform_system == "Windows" and extra == "cpu"
+Requires-Dist: tf-keras; python_version >= "3.9" and extra == "cpu"
+Requires-Dist: tf-keras>=2.16.0rc0; python_version >= "3.12" and extra == "cpu"
+Requires-Dist: tensorflow; extra == "gpu"
+Requires-Dist: tensorflow-metal; platform_machine == "arm64" and platform_system == "Darwin" and extra == "gpu"
+Requires-Dist: tf-keras; python_version >= "3.9" and extra == "gpu"
+Requires-Dist: tf-keras>=2.16.0rc0; python_version >= "3.12" and extra == "gpu"
+Requires-Dist: horovod; extra == "mpi"
+Requires-Dist: mpi4py; extra == "mpi"
 Provides-Extra: test
 Provides-Extra: docs
 Provides-Extra: lmp
 Provides-Extra: ipi
 Provides-Extra: gui
+Provides-Extra: cu11
+Provides-Extra: cu12
 Provides-Extra: cpu
 Provides-Extra: gpu
 Provides-Extra: mpi
-Provides-Extra: cu11
-Provides-Extra: cu12
 Description-Content-Type: text/markdown
 
 [<picture><source media="(prefers-color-scheme: dark)" srcset="https://github.com/deepmodeling/deepmd-kit/raw/master/./doc/_static/logo-dark.svg"><source media="(prefers-color-scheme: light)" srcset="https://github.com/deepmodeling/deepmd-kit/raw/master/./doc/_static/logo.svg"><img alt="DeePMD-kit logo" src="https://github.com/deepmodeling/deepmd-kit/raw/master/./doc/_static/logo.svg"></picture>](https://github.com/deepmodeling/deepmd-kit/tree/master/./doc/logo.md)
 
---------------------------------------------------------------------------------
+---
+
+# DeePMD-kit
 
-<span style="font-size:larger;">DeePMD-kit Manual</span>
-========
 [![GitHub release](https://img.shields.io/github/release/deepmodeling/deepmd-kit.svg?maxAge=86400)](https://github.com/deepmodeling/deepmd-kit/releases)
 [![offline packages](https://img.shields.io/github/downloads/deepmodeling/deepmd-kit/total?label=offline%20packages)](https://github.com/deepmodeling/deepmd-kit/releases)
 [![conda-forge](https://img.shields.io/conda/dn/conda-forge/deepmd-kit?color=red&label=conda-forge&logo=conda-forge)](https://anaconda.org/conda-forge/deepmd-kit)
@@ -270,168 +274,88 @@ Description-Content-Type: text/markdown
 [![docker pull](https://img.shields.io/docker/pulls/deepmodeling/deepmd-kit)](https://hub.docker.com/r/deepmodeling/deepmd-kit)
 [![Documentation Status](https://readthedocs.org/projects/deepmd/badge/)](https://deepmd.readthedocs.io/)
 
-# Table of contents
-- [About DeePMD-kit](https://github.com/deepmodeling/deepmd-kit/tree/master/#about-deepmd-kit)
- 	- [Highlights in v2.0](https://github.com/deepmodeling/deepmd-kit/tree/master/#highlights-in-deepmd-kit-v2.0)
- 	- [Highlighted features](https://github.com/deepmodeling/deepmd-kit/tree/master/#highlighted-features)
- 	- [License and credits](https://github.com/deepmodeling/deepmd-kit/tree/master/#license-and-credits)
- 	- [Deep Potential in a nutshell](https://github.com/deepmodeling/deepmd-kit/tree/master/#deep-potential-in-a-nutshell)
-- [Download and install](https://github.com/deepmodeling/deepmd-kit/tree/master/#download-and-install)
-- [Use DeePMD-kit](https://github.com/deepmodeling/deepmd-kit/tree/master/#use-deepmd-kit)
-- [Code structure](https://github.com/deepmodeling/deepmd-kit/tree/master/#code-structure)
-- [Troubleshooting](https://github.com/deepmodeling/deepmd-kit/tree/master/#troubleshooting)
-
-# About DeePMD-kit
+## About DeePMD-kit
+
 DeePMD-kit is a package written in Python/C++, designed to minimize the effort required to build deep learning-based model of interatomic potential energy and force field and to perform molecular dynamics (MD). This brings new hopes to addressing the accuracy-versus-efficiency dilemma in molecular simulations. Applications of DeePMD-kit span from finite molecules to extended systems and from metallic systems to chemically bonded systems.
 
 For more information, check the [documentation](https://deepmd.readthedocs.io/).
 
-# Highlights in DeePMD-kit v2.0
-* [Model compression](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/freeze/compress.md). Accelerate the efficiency of model inference 4-15 times.
-* [New descriptors](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/model/overall.md). Including [`se_e2_r`](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/model/train-se-e2-r.md) and [`se_e3`](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/model/train-se-e3.md).
-* [Hybridization of descriptors](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/model/train-hybrid.md). Hybrid descriptor constructed from the concatenation of several descriptors.
-* [Atom type embedding](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/model/train-se-e2-a-tebd.md). Enable atom-type embedding to decline training complexity and refine performance.
-* Training and inference of the dipole (vector) and polarizability (matrix).
-* Split of training and validation dataset.
-* Optimized training on GPUs.
-
-## Highlighted features
-* **interfaced with TensorFlow**, one of the most popular deep learning frameworks, making the training process highly automatic and efficient, in addition, Tensorboard can be used to visualize training procedures.
-* **interfaced with high-performance classical MD and quantum (path-integral) MD packages**, i.e., LAMMPS and i-PI, respectively.
-* **implements the Deep Potential series models**, which have been successfully applied to finite and extended systems including organic molecules, metals, semiconductors, insulators, etc.
-* **implements MPI and GPU supports**, making it highly efficient for high-performance parallel and distributed computing.
-* **highly modularized**, easy to adapt to different descriptors for deep learning-based potential energy models.
-
-## License and credits
+### Highlighted features
+
+- **interfaced with TensorFlow**, making the training process highly automatic and efficient.
+- **interfaced with high-performance classical MD and quantum (path-integral) MD packages**, including LAMMPS, i-PI, AMBER, CP2K, GROMACS, OpenMM, and ABUCUS.
+- **implements the Deep Potential series models**, which have been successfully applied to finite and extended systems, including organic molecules, metals, semiconductors, insulators, etc.
+- **implements MPI and GPU supports**, making it highly efficient for high-performance parallel and distributed computing.
+- **highly modularized**, easy to adapt to different descriptors for deep learning-based potential energy models.
+
+### License and credits
+
 The project DeePMD-kit is licensed under [GNU LGPLv3.0](https://github.com/deepmodeling/deepmd-kit/tree/master/./LICENSE).
 If you use this code in any future publications, please cite the following publications for general purpose:
+
 - Han Wang, Linfeng Zhang, Jiequn Han, and Weinan E. "DeePMD-kit: A deep learning package for many-body potential energy representation and molecular dynamics." Computer Physics Communications 228 (2018): 178-184.
-[![doi:10.1016/j.cpc.2018.03.016](https://img.shields.io/badge/DOI-10.1016%2Fj.cpc.2018.03.016-blue)](https://doi.org/10.1016/j.cpc.2018.03.016)
-[![Citations](https://citations.njzjz.win/10.1016/j.cpc.2018.03.016)](https://badge.dimensions.ai/details/doi/10.1016/j.cpc.2018.03.016)
+  [![doi:10.1016/j.cpc.2018.03.016](https://img.shields.io/badge/DOI-10.1016%2Fj.cpc.2018.03.016-blue)](https://doi.org/10.1016/j.cpc.2018.03.016)
+  [![Citations](https://citations.njzjz.win/10.1016/j.cpc.2018.03.016)](https://badge.dimensions.ai/details/doi/10.1016/j.cpc.2018.03.016)
 - Jinzhe Zeng, Duo Zhang, Denghui Lu, Pinghui Mo, Zeyu Li, Yixiao Chen, Marián Rynik, Li'ang Huang, Ziyao Li, Shaochen Shi, Yingze Wang, Haotian Ye, Ping Tuo, Jiabin Yang, Ye Ding, Yifan Li, Davide Tisi, Qiyu Zeng, Han Bao, Yu Xia, Jiameng Huang, Koki Muraoka, Yibo Wang, Junhan Chang, Fengbo Yuan, Sigbjørn Løland Bore, Chun Cai, Yinnian Lin, Bo Wang, Jiayan Xu, Jia-Xin Zhu, Chenxing Luo, Yuzhi Zhang, Rhys E. A. Goodall, Wenshuo Liang, Anurag Kumar Singh, Sikai Yao, Jingchao Zhang, Renata Wentzcovitch, Jiequn Han, Jie Liu, Weile Jia, Darrin M. York, Weinan E, Roberto Car, Linfeng Zhang, Han Wang. "DeePMD-kit v2: A software package for deep potential models." J. Chem. Phys. 159 (2023): 054801.
-[![doi:10.1063/5.0155600](https://img.shields.io/badge/DOI-10.1063%2F5.0155600-blue)](https://doi.org/10.1063/5.0155600)
-[![Citations](https://citations.njzjz.win/10.1063/5.0155600)](https://badge.dimensions.ai/details/doi/10.1063/5.0155600)
+  [![doi:10.1063/5.0155600](https://img.shields.io/badge/DOI-10.1063%2F5.0155600-blue)](https://doi.org/10.1063/5.0155600)
+  [![Citations](https://citations.njzjz.win/10.1063/5.0155600)](https://badge.dimensions.ai/details/doi/10.1063/5.0155600)
 
 In addition, please follow [the bib file](https://github.com/deepmodeling/deepmd-kit/tree/master/CITATIONS.bib) to cite the methods you used.
 
-## Deep Potential in a nutshell
-The goal of Deep Potential is to employ deep learning techniques and realize an inter-atomic potential energy model that is general, accurate, computationally efficient and scalable. The key component is to respect the extensive and symmetry-invariant properties of a potential energy model by assigning a local reference frame and a local environment to each atom. Each environment contains a finite number of atoms, whose local coordinates are arranged in a symmetry-preserving way. These local coordinates are then transformed, through a sub-network, to so-called *atomic energy*. Summing up all the atomic energies gives the potential energy of the system.
+### Highlights in major versions
+
+#### Initial version
+
+The goal of Deep Potential is to employ deep learning techniques and realize an inter-atomic potential energy model that is general, accurate, computationally efficient and scalable. The key component is to respect the extensive and symmetry-invariant properties of a potential energy model by assigning a local reference frame and a local environment to each atom. Each environment contains a finite number of atoms, whose local coordinates are arranged in a symmetry-preserving way. These local coordinates are then transformed, through a sub-network, to so-called _atomic energy_. Summing up all the atomic energies gives the potential energy of the system.
 
-The initial proof of concept is in the [Deep Potential][1] paper, which employed an approach that was devised to train the neural network model with the potential energy only. With typical *ab initio* molecular dynamics (AIMD) datasets this is insufficient to reproduce the trajectories. The Deep Potential Molecular Dynamics ([DeePMD][2]) model overcomes this limitation. In addition, the learning process in DeePMD improves significantly over the Deep Potential method thanks to the introduction of a flexible family of loss functions. The NN potential constructed in this way reproduces accurately the AIMD trajectories, both classical and quantum (path integral), in extended and finite systems, at a cost that scales linearly with system size and is always several orders of magnitude lower than that of equivalent AIMD simulations.
+The initial proof of concept is in the [Deep Potential][1] paper, which employed an approach that was devised to train the neural network model with the potential energy only. With typical _ab initio_ molecular dynamics (AIMD) datasets this is insufficient to reproduce the trajectories. The Deep Potential Molecular Dynamics ([DeePMD][2]) model overcomes this limitation. In addition, the learning process in DeePMD improves significantly over the Deep Potential method thanks to the introduction of a flexible family of loss functions. The NN potential constructed in this way reproduces accurately the AIMD trajectories, both classical and quantum (path integral), in extended and finite systems, at a cost that scales linearly with system size and is always several orders of magnitude lower than that of equivalent AIMD simulations.
 
 Although highly efficient, the original Deep Potential model satisfies the extensive and symmetry-invariant properties of a potential energy model at the price of introducing discontinuities in the model. This has negligible influence on a trajectory from canonical sampling but might not be sufficient for calculations of dynamical and mechanical properties. These points motivated us to develop the Deep Potential-Smooth Edition ([DeepPot-SE][3]) model, which replaces the non-smooth local frame with a smooth and adaptive embedding network. DeepPot-SE shows great ability in modeling many kinds of systems that are of interest in the fields of physics, chemistry, biology, and materials science.
 
 In addition to building up potential energy models, DeePMD-kit can also be used to build up coarse-grained models. In these models, the quantity that we want to parameterize is the free energy, or the coarse-grained potential, of the coarse-grained particles. See the [DeePCG paper][4] for more details.
 
-See [our latest paper](https://doi.org/10.48550/arXiv.2304.09409) for details of all features.
-
-# Download and install
-
-Please follow our [GitHub](https://github.com/deepmodeling/deepmd-kit) webpage to download the [latest released version](https://github.com/deepmodeling/deepmd-kit/tree/master) and [development version](https://github.com/deepmodeling/deepmd-kit/tree/devel).
-
-DeePMD-kit offers multiple installation methods. It is recommended to use easy methods like [offline packages](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/install/easy-install.md#offline-packages), [conda](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/install/easy-install.md#with-conda) and [docker](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/install/easy-install.md#with-docker).
-
-One may manually install DeePMD-kit by following the instructions on [installing the Python interface](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/install/install-from-source.md#install-the-python-interface) and [installing the C++ interface](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/install/install-from-source.md#install-the-c-interface). The C++ interface is necessary when using DeePMD-kit with LAMMPS, i-PI or GROMACS.
-
-
-# Use DeePMD-kit
-
-A quick start on using DeePMD-kit can be found [here](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/getting-started/quick_start.ipynb).
-
-A full [document](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/train/train-input-auto.rst) on options in the training input script is available.
-
-# Advanced
-
-- [Installation](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/install/index.md)
-    - [Easy install](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/install/easy-install.md)
-    - [Install from source code](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/install/install-from-source.md)
-    - [Install from pre-compiled C library](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/install/install-from-c-library.md)
-    - [Install LAMMPS](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/install/install-lammps.md)
-    - [Install i-PI](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/install/install-ipi.md)
-    - [Install GROMACS](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/install/install-gromacs.md)
-    - [Building conda packages](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/install/build-conda.md)
-    - [Install Node.js interface](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/install/install-nodejs.md)
-    - [Easy install the latest development version](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/install/easy-install-dev.md)
-- [Data](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/data/index.md)
-    - [System](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/data/system.md)
-    - [Formats of a system](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/data/data-conv.md)
-    - [Prepare data with dpdata](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/data/dpdata.md)
-- [Model](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/model/index.md)
-    - [Overall](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/model/overall.md)
-    - [Descriptor `"se_e2_a"`](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/model/train-se-e2-a.md)
-    - [Descriptor `"se_e2_r"`](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/model/train-se-e2-r.md)
-    - [Descriptor `"se_e3"`](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/model/train-se-e3.md)
-    - [Descriptor `"se_atten"`](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/model/train-se-atten.md)
-    - [Descriptor `"se_atten_v2"`](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/model/train-se-atten.md#descriptor-se_atten_v2)
-    - [Descriptor `"hybrid"`](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/model/train-hybrid.md)
-    - [Descriptor `sel`](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/model/sel.md)
-    - [Fit energy](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/model/train-energy.md)
-    - [Fit spin energy](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/model/train-energy-spin.md)
-    - [Fit `tensor` like `Dipole` and `Polarizability`](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/model/train-fitting-tensor.md)
-    - [Fit electronic density of states (DOS)](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/model/train-fitting-dos.md)
-    - [Train a Deep Potential model using `type embedding` approach](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/model/train-se-e2-a-tebd.md)
-    - [Deep potential long-range](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/model/dplr.md)
-    - [Deep Potential - Range Correction (DPRc)](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/model/dprc.md)
-    - [Linear model](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/model/linear.md)
-    - [Interpolation or combination with a pairwise potential](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/model/pairtab.md)
-- [Training](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/train/index.md)
-    - [Training a model](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/train/training.md)
-    - [Advanced options](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/train/training-advanced.md)
-    - [Parallel training](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/train/parallel-training.md)
-    - [Multi-task training](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/train/multi-task-training.md)
-    - [TensorBoard Usage](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/train/tensorboard.md)
-    - [Known limitations of using GPUs](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/train/gpu-limitations.md)
-    - [Training Parameters](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/train-input-auto.rst)
-- [Freeze and Compress](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/freeze/index.rst)
-    - [Freeze a model](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/freeze/freeze.md)
-    - [Compress a model](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/freeze/compress.md)
-- [Test](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/test/index.rst)
-    - [Test a model](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/test/test.md)
-    - [Calculate Model Deviation](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/test/model-deviation.md)
-- [Inference](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/inference/index.rst)
-    - [Python interface](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/inference/python.md)
-    - [C++ interface](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/inference/cxx.md)
-    - [Node.js interface](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/inference/nodejs.md)
-- [Integrate with third-party packages](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/third-party/index.rst)
-    - [Use deep potential with ASE](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/third-party/ase.md)
-    - [Run MD with LAMMPS](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/third-party/lammps-command.md)
-    - [Run path-integral MD with i-PI](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/third-party/ipi.md)
-    - [Run MD with GROMACS](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/third-party/gromacs.md)
-    - [Interfaces out of DeePMD-kit](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/third-party/out-of-deepmd-kit.md)
-- [Use NVNMD](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/nvnmd/index.md)
-
-# Code structure
+#### v1
+
+- Code refactor to make it highly modularized.
+- GPU support for descriptors.
+
+#### v2
+
+- Model compression. Accelerate the efficiency of model inference 4-15 times.
+- New descriptors. Including `se_e2_r`, `se_e3`, and `se_atten` (DPA-1).
+- Hybridization of descriptors. Hybrid descriptor constructed from the concatenation of several descriptors.
+- Atom type embedding. Enable atom-type embedding to decline training complexity and refine performance.
+- Training and inference of the dipole (vector) and polarizability (matrix).
+- Split of training and validation dataset.
+- Optimized training on GPUs, including CUDA and ROCm.
+- Non-von-Neumann.
+- C API to interface with the third-party packages.
+
+See [our latest paper](https://doi.org/10.1063/5.0155600) for details of all features until v2.2.3.
+
+## Install and use DeePMD-kit
+
+Please read the [online documentation](https://deepmd.readthedocs.io/) for how to install and use DeePMD-kit.
+
+## Code structure
 
 The code is organized as follows:
 
-* `data/raw`: tools manipulating the raw data files.
-* `examples`: examples.
-* `deepmd`: DeePMD-kit python modules.
-* `source/api_cc`: source code of DeePMD-kit C++ API.
-* `source/ipi`: source code of i-PI client.
-* `source/lib`: source code of DeePMD-kit library.
-* `source/lmp`: source code of Lammps module.
-* `source/gmx`: source code of Gromacs plugin.
-* `source/op`: TensorFlow op implementation. working with the library.
-
-
-# Troubleshooting
-
-- [Model compatibility](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/troubleshooting/model_compatability.md)
-- [Installation](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/troubleshooting/installation.md)
-- [The temperature undulates violently during the early stages of MD](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/troubleshooting/md_energy_undulation.md)
-- [MD: cannot run LAMMPS after installing a new version of DeePMD-kit](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/troubleshooting/md_version_compatibility.md)
-- [Do we need to set rcut < half boxsize?](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/troubleshooting/howtoset_rcut.md)
-- [How to set sel?](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/troubleshooting/howtoset_sel.md)
-- [How to control the parallelism of a job?](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/troubleshooting/howtoset_num_nodes.md)
-- [How to tune Fitting/embedding-net size?](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/troubleshooting/howtoset_netsize.md)
-- [Why does a model have low precision?](https://github.com/deepmodeling/deepmd-kit/tree/master/doc/troubleshooting/precision.md)
+- `examples`: examples.
+- `deepmd`: DeePMD-kit python modules.
+- `source/lib`: source code of the core library.
+- `source/op`: Operator (OP) implementation.
+- `source/api_cc`: source code of DeePMD-kit C++ API.
+- `source/api_c`: source code of the C API.
+- `source/nodejs`: source code of the Node.js API.
+- `source/ipi`: source code of i-PI client.
+- `source/lmp`: source code of Lammps module.
+- `source/gmx`: source code of Gromacs plugin.
 
 # Contributing
 
 See [DeePMD-kit Contributing Guide](https://github.com/deepmodeling/deepmd-kit/tree/master/CONTRIBUTING.md) to become a contributor! 🤓
 
-
 [1]: https://arxiv.org/abs/1707.01478
 [2]: https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.120.143001
 [3]: https://arxiv.org/abs/1805.09003