deepmd-kit 3.1.3__tar.gz → 3.2.0b0__tar.gz

deepmd_kit-3.2.0b0/.gitignore

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+*~
+*.d
+*.o
+*.aux
+*.dvi
+*.pdf
+*.so
+*.bin
+*.intbin
+*.meta
+*.log
+*.gz
+*.bz2
+*.pyc
+*.pb
+*.DS_Store
+tmp*
+CMakeCache.txt
+CMakeFiles
+*.bk
+build
+_skbuild
+deepmd_kit.egg-info/
+dist
+.eggs
+/deepmd/_version.py
+venv*
+.vscode/**
+_build
+_templates
+doc/API_CC/
+doc/api_py/
+doc/api_core/
+doc/api_c/
+dp/
+dp_test/
+dp_test_cc/
+dp_test_c/
+dp_c/
+build_lammps/
+.idea/
+build_tests/
+build_cc_tests
+build_c_tests
+build_c/
+libdeepmd_c/
+.uv/
+libtorch/
+uv.lock
+buildcxx/
+node_modules/
+*.bib.original
+
+# Coverage files
+.coverage
+.coverage.*
+
+# Test output files (temporary)
+test_dp_test/
+test_dp_test_*.out
+*_detail.out
+
+# Training and model output files
+*.pth
+*.pte
+*.pt2
+*.ckpt*
+checkpoint
+lcurve.out
+out.json
+input_v2_compat.json
+frozen_model.*
+
+# Test system directories
+system/
+*.expected

deepmd_kit-3.2.0b0/.pre-commit-config.yaml

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+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+exclude: ^source/3rdparty/.+/
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+      - id: trailing-whitespace
+        exclude: "^.+\\.pbtxt$"
+      - id: end-of-file-fixer
+        exclude: "^.+\\.pbtxt$|deeppot_sea.*\\.json$"
+      - id: check-yaml
+      - id: check-json
+      - id: check-added-large-files
+        args: ["--maxkb=1024", "--enforce-all"]
+        exclude: |
+          (?x)^(
+              source/tests/infer/dipolecharge_e.pbtxt|
+              source/tests/infer/deeppolar_new.pbtxt
+          )$
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: check-toml
+  # Python
+  - repo: https://github.com/PyCQA/isort
+    rev: 9.0.0a3
+    hooks:
+      - id: isort
+        files: \.py$
+        exclude: ^source/3rdparty
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.15.15
+    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
+  # markdown
+  - repo: https://github.com/hukkin/mdformat
+    rev: 1.0.0
+    hooks:
+      - id: mdformat
+        additional_dependencies:
+          # - mdformat-myst==0.3.0
+          # See https://github.com/executablebooks/mdformat-myst/issues/13
+          - "git+https://github.com/njzjz-bothub/mdformat-myst@d9c414e#egg=mdformat-myst"
+          - mdformat-ruff==0.1.3
+          - mdformat-web==0.2.0
+          - mdformat-config==0.2.1
+          - mdformat-beautysh==1.0.0
+          - mdformat-gfm-alerts==2.0.0
+  # C++
+  - repo: https://github.com/pre-commit/mirrors-clang-format
+    rev: v22.1.5
+    hooks:
+      - id: clang-format
+        exclude: ^(source/3rdparty|source/lib/src/gpu/cudart/.+\.inc|.+\.ipynb$|source/tests/infer/.+\.json$)
+  # yaml, CSS, javascript
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v4.0.0-alpha.8
+    hooks:
+      - id: prettier
+        types_or: [yaml, css]
+        # workflow files cannot be modified by pre-commit.ci
+        exclude: ^(source/3rdparty|\.clang-format)
+  # Shell
+  - repo: https://github.com/scop/pre-commit-shfmt
+    rev: v3.13.1-1
+    hooks:
+      - id: shfmt
+  # CMake
+  - repo: https://github.com/cheshirekow/cmake-format-precommit
+    rev: v0.6.13
+    hooks:
+      - id: cmake-format
+      #- id: cmake-lint
+  - repo: https://github.com/njzjz/mirrors-bibtex-tidy
+    rev: v1.14.0
+    hooks:
+      - id: bibtex-tidy
+        args:
+          - --curly
+          - --numeric
+          - --align=13
+          - --blank-lines
+          # disable sort: the order of keys and fields has explict meanings
+          #- --sort=key
+          - --duplicates=key,doi,citation,abstract
+          - --merge=combine
+          #- --sort-fields
+          #- --strip-comments
+          - --trailing-commas
+          - --encode-urls
+          - --remove-empty-fields
+          - --wrap=80
+  # license header
+  - repo: https://github.com/Lucas-C/pre-commit-hooks
+    rev: v1.5.6
+    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
+  - repo: local
+    hooks:
+      - id: disallow-caps
+        name: Disallow improper capitalization
+        language: pygrep
+        entry: DeepMD|DeepMd|Pytorch|Tensorflow|Numpy|Github|Lammps|I-Pi|I-PI|i-Pi
+        # unclear why PairDeepMD is used instead of PairDeePMD
+        exclude: .pre-commit-config.yaml|source/lmp
+  # customized pylint rules
+  - repo: https://github.com/pylint-dev/pylint/
+    rev: v4.0.5
+    hooks:
+      - id: pylint
+        entry: env PYTHONPATH=source/checker pylint
+        files: ^deepmd/

deepmd_kit-3.2.0b0/.readthedocs.yml

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+version: 2
+build:
+  os: ubuntu-26.04
+  tools:
+    python: "3.11"
+  jobs:
+    post_create_environment:
+      - pip install uv
+    post_install:
+      - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH uv pip install -r doc/requirements.txt
+  apt_packages:
+    - inkscape
+sphinx:
+  configuration: doc/conf.py
+formats:
+  - pdf

deepmd_kit-3.2.0b0/AGENTS.md

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+# DeePMD-kit
+
+DeePMD-kit is a deep learning package for many-body potential energy representation and molecular dynamics. It supports multiple backends (TensorFlow, PyTorch, JAX, Paddle) and integrates with MD packages like LAMMPS and i-PI.
+
+**Always reference these instructions first and fallback to search or bash commands only when you encounter unexpected information that does not match the info here.**
+
+## Working Effectively
+
+### Bootstrap and Build Repository
+
+- Create virtual environment: `uv venv venv && source venv/bin/activate`
+- Install base dependencies: `uv pip install tensorflow-cpu` (takes ~8 seconds)
+- Install PyTorch: `uv pip install torch --index-url https://download.pytorch.org/whl/cpu` (takes ~5 seconds)
+- Build Python package: `uv pip install -e .[cpu,test]` -- takes 67 seconds. **NEVER CANCEL. Set timeout to 120+ seconds.**
+- Build C++ components: `export TENSORFLOW_ROOT=$(python -c 'import importlib.util,pathlib;print(pathlib.Path(importlib.util.find_spec("tensorflow").origin).parent)')` then `export PYTORCH_ROOT=$(python -c 'import torch;print(torch.__path__[0])')` then `./source/install/build_cc.sh` -- takes 164 seconds. **NEVER CANCEL. Set timeout to 300+ seconds.**
+
+### Test Repository
+
+- Run single test: `pytest source/tests/tf/test_dp_test.py::TestDPTestEner::test_1frame -v` -- takes 8-13 seconds
+- Run test subset: `pytest source/tests/tf/test_dp_test.py -v` -- takes 15 seconds. **NEVER CANCEL. Set timeout to 60+ seconds.**
+- **Recommended: Use single test cases for validation instead of full test suite** -- full suite has 314 test files and takes 60+ minutes
+
+### Lint and Format Code
+
+- Install linter: `uv pip install ruff`
+- Run linting: `ruff check .` -- takes \<1 second
+- Format code: `ruff format .` -- takes \<1 second
+- **Always run `ruff check .` and `ruff format .` before committing changes or the CI will fail.**
+
+### Training and Validation
+
+- Test TensorFlow training: `cd examples/water/se_e2_a && dp train input.json --skip-neighbor-stat` -- training proceeds but is slow on CPU
+- Test PyTorch training: `cd examples/water/se_e2_a && dp --pt train input_torch.json --skip-neighbor-stat` -- training proceeds but is slow on CPU
+- **Training examples are for validation only. Real training takes hours/days. Timeout training tests after 60 seconds for validation.**
+
+## Validation Scenarios
+
+**ALWAYS manually validate any new code through at least one complete scenario:**
+
+### Basic Functionality Validation
+
+1. **CLI Interface**: Run `dp --version` and `dp -h` to verify installation
+1. **Python Interface**: Run `python -c "import deepmd; import deepmd.tf; print('Both interfaces work')"`
+1. **Backend Selection**: Test `dp --tf -h`, `dp --pt -h`, `dp --jax -h`, `dp --pd -h`
+
+### Training Workflow Validation
+
+1. **TensorFlow Training**: `cd examples/water/se_e2_a && timeout 60 dp train input.json --skip-neighbor-stat` -- should start training and show decreasing loss
+1. **PyTorch Training**: `cd examples/water/se_e2_a && timeout 60 dp --pt train input_torch.json --skip-neighbor-stat` -- should start training and show decreasing loss
+1. **Verify training output**: Look for "batch X: trn: rmse" messages showing decreasing error values
+
+### Test-Based Validation
+
+1. **Core Tests**: `pytest source/tests/tf/test_dp_test.py::TestDPTestEner::test_1frame -v` -- should pass in ~10 seconds
+1. **Multi-backend**: Test both TensorFlow and PyTorch components work
+
+## Common Commands and Timing
+
+### Repository Structure
+
+```
+ls -la [repo-root]
+.github/               # GitHub workflows and templates
+CONTRIBUTING.md        # Contributing guide
+README.md             # Project overview
+deepmd/               # Python package source
+doc/                  # Documentation
+examples/             # Training examples and configurations
+pyproject.toml        # Python build configuration
+source/               # C++ source code and tests
+```
+
+### Key Directories and Files
+
+- `deepmd/` - Main Python package with backend implementations
+- `source/lib/` - Core C++ library
+- `source/op/` - Backend-specific operators (TF, PyTorch, etc.)
+- `source/api_cc/` - C++ API
+- `source/api_c/` - C API
+- `source/tests/` - Test suite (314 test files)
+- `examples/water/se_e2_a/` - Basic water training example
+- `examples/` - Various model examples for different scenarios
+
+### Common CLI Commands
+
+- `dp --version` - Show version information
+- `dp -h` - Show help and available commands
+- `dp train input.json` - Train a model (TensorFlow backend)
+- `dp --pt train input.json` - Train with PyTorch backend
+- `dp --jax train input.json` - Train with JAX backend
+- `dp --pd train input.json` - Train with Paddle backend
+- `dp test -m model.pb -s system/` - Test a trained model
+- `dp freeze -o model.pb` - Freeze/save a model
+
+### Build Dependencies and Setup
+
+- **Python 3.10+** required
+- **Virtual environment** strongly recommended: `uv venv venv && source venv/bin/activate`
+- **Backend dependencies**: TensorFlow, PyTorch, JAX, or Paddle (install before building)
+- **Build tools**: CMake, C++ compiler, scikit-build-core
+- **C++ build requires**: Both TensorFlow and PyTorch installed, set TENSORFLOW_ROOT and PYTORCH_ROOT environment variables
+
+### Key Configuration Files
+
+- `pyproject.toml` - Python build configuration and dependencies
+- `source/CMakeLists.txt` - C++ build configuration
+- `examples/water/se_e2_a/input.json` - Basic TensorFlow training config
+- `examples/water/se_e2_a/input_torch.json` - Basic PyTorch training config
+
+## Frequent Patterns and Time Expectations
+
+### Installation and Build Times
+
+- **Virtual environment setup**: ~5 seconds
+- **TensorFlow CPU install**: ~8 seconds
+- **PyTorch CPU install**: ~5 seconds
+- **Python package build**: ~67 seconds. **NEVER CANCEL.**
+- **C++ components build**: ~164 seconds. **NEVER CANCEL.**
+- **Full fresh setup**: ~3-4 minutes total
+
+### Testing Times
+
+- **Single test**: 8-13 seconds
+- **Test file (~5 tests)**: ~15 seconds
+- **Backend-specific test subset**: 15-30 minutes. **Use sparingly.**
+- **Full test suite (314 files)**: 60+ minutes. **Avoid in development - use single tests instead.**
+
+### Linting and Formatting
+
+- **Ruff check**: \<1 second
+- **Ruff format**: \<1 second
+- **Pre-commit hooks**: May have network issues, use individual tools
+
+### Commit Messages and PR Titles
+
+**All commit messages and PR titles must follow [conventional commit specification](https://www.conventionalcommits.org/):**
+
+- **Format**: `type(scope): description`
+- **Common types**: `feat`, `fix`, `docs`, `style`, `refactor`, `test`, `chore`, `ci`
+- **Examples**:
+  - `feat(core): add new descriptor type`
+  - `fix(tf): resolve memory leak in training`
+  - `docs: update installation guide`
+  - `ci: add workflow for testing`
+
+### Training and Model Operations
+
+- **Training initialization**: 10-30 seconds
+- **Training per batch**: 0.1-1 second (CPU), much faster on GPU
+- **Model freezing**: 5-15 seconds
+- **Model testing**: 10-30 seconds
+
+## Backend-Specific Notes
+
+### TensorFlow Backend
+
+- **Default backend** when no flag specified
+- **Configuration**: Use `input.json` format
+- **Training**: `dp train input.json`
+- **Requirements**: `tensorflow` or `tensorflow-cpu` package
+
+### PyTorch Backend
+
+- **Activation**: Use `--pt` flag or `export DP_BACKEND=pytorch`
+- **Configuration**: Use `input_torch.json` format typically
+- **Training**: `dp --pt train input_torch.json`
+- **Requirements**: `torch` package
+
+### JAX Backend
+
+- **Activation**: Use `--jax` flag
+- **Training**: `dp --jax train input.json`
+- **Requirements**: `jax` and related packages
+- **Note**: Experimental backend, may have limitations
+
+### Paddle Backend
+
+- **Activation**: Use `--pd` flag
+- **Training**: `dp --pd train input.json`
+- **Requirements**: `paddlepaddle` package
+- **Note**: Less commonly used
+
+## Critical Warnings
+
+- **NEVER CANCEL BUILD OPERATIONS**: Python build takes 67 seconds, C++ build takes 164 seconds
+- **USE SINGLE TESTS FOR VALIDATION**: Run individual tests instead of full test suite for faster feedback
+- **ALWAYS activate virtual environment**: Build and runtime failures occur without proper environment
+- **ALWAYS install backend dependencies first**: TensorFlow/PyTorch required before building C++ components
+- **ALWAYS run linting before commits**: `ruff check . && ruff format .` or CI will fail
+- **ALWAYS test both Python and C++ components**: Some features require both to be built
+- **ALWAYS follow conventional commit format**: All commit messages and PR titles must use conventional commit specification (`type(scope): description`)

deepmd_kit-3.2.0b0/PKG-INFO

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+Metadata-Version: 2.4
+Name: deepmd-kit
+Version: 3.2.0b0
+Summary: A deep learning package for many-body potential energy representation and molecular dynamics
+Keywords: deepmd
+Author: DeepModeling
+Author-Email: Han Wang <wang_han@iapcm.ac.cn>
+License-Expression: LGPL-3.0-or-later
+License-File: LICENSE
+Classifier: Natural Language :: English
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Operating System :: Microsoft :: Windows
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Programming Language :: C
+Classifier: Programming Language :: C++
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Environment :: GPU :: NVIDIA CUDA :: 12 :: 12.2
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
+Classifier: Topic :: Scientific/Engineering :: Physics
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Classifier: Environment :: Console
+Project-URL: Homepage, https://github.com/deepmodeling/deepmd-kit
+Project-URL: documentation, https://docs.deepmodeling.com/projects/deepmd
+Project-URL: repository, https://github.com/deepmodeling/deepmd-kit
+Requires-Python: >=3.10
+Requires-Dist: numpy>=1.21
+Requires-Dist: scipy
+Requires-Dist: pyyaml
+Requires-Dist: dargs>=0.4.7
+Requires-Dist: typing_extensions>=4.0.0
+Requires-Dist: importlib_metadata>=1.4; python_version < "3.8"
+Requires-Dist: h5py
+Requires-Dist: h5py!=3.11.0,>=3.6.0; platform_system == "Linux" and platform_machine == "aarch64"
+Requires-Dist: wcmatch
+Requires-Dist: einops
+Requires-Dist: packaging
+Requires-Dist: ml_dtypes
+Requires-Dist: mendeleev
+Requires-Dist: array-api-compat
+Requires-Dist: lmdb
+Requires-Dist: msgpack
+Requires-Dist: vesin[torch]
+Provides-Extra: test
+Requires-Dist: dpdata>=0.2.7; extra == "test"
+Requires-Dist: ase>=3.23.0; extra == "test"
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: pytest-cov; extra == "test"
+Requires-Dist: pytest-sugar; extra == "test"
+Requires-Dist: pytest-split; extra == "test"
+Requires-Dist: pytest-timeout; extra == "test"
+Requires-Dist: dpgui; extra == "test"
+Requires-Dist: array-api-strict>=2.2; python_version >= "3.9" and extra == "test"
+Provides-Extra: docs
+Requires-Dist: sphinx>=3.1.1; extra == "docs"
+Requires-Dist: sphinx-book-theme; extra == "docs"
+Requires-Dist: myst-nb>=1.0.0; extra == "docs"
+Requires-Dist: myst-parser>=0.19.2; extra == "docs"
+Requires-Dist: sphinx-design; extra == "docs"
+Requires-Dist: breathe; extra == "docs"
+Requires-Dist: exhale>=0.3.7; extra == "docs"
+Requires-Dist: numpydoc; extra == "docs"
+Requires-Dist: ase; extra == "docs"
+Requires-Dist: deepmodeling-sphinx>=0.3.0; extra == "docs"
+Requires-Dist: dargs>=0.3.4; extra == "docs"
+Requires-Dist: sphinx-argparse<0.5.0; extra == "docs"
+Requires-Dist: pygments-lammps; extra == "docs"
+Requires-Dist: sphinxcontrib-bibtex; extra == "docs"
+Requires-Dist: sphinx-autoapi>=3.0.0; extra == "docs"
+Requires-Dist: sphinxcontrib-programoutput; extra == "docs"
+Requires-Dist: sphinxcontrib-moderncmakedomain; extra == "docs"
+Requires-Dist: sphinx-remove-toctrees; extra == "docs"
+Provides-Extra: lmp
+Requires-Dist: lammps[mpi]~=2025.7.22.2.0; extra == "lmp"
+Provides-Extra: ipi
+Requires-Dist: ipi; extra == "ipi"
+Provides-Extra: gui
+Requires-Dist: dpgui; extra == "gui"
+Provides-Extra: cu12
+Requires-Dist: nvidia-cuda-runtime-cu12; extra == "cu12"
+Requires-Dist: nvidia-cublas-cu12; extra == "cu12"
+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-cuda-nvcc-cu12; extra == "cu12"
+Provides-Extra: jax
+Requires-Dist: jax>=0.4.33; python_version >= "3.10" and extra == "jax"
+Requires-Dist: jax>=0.4.33; python_version >= "3.10" and extra == "jax"
+Requires-Dist: flax>=0.10.0; python_version >= "3.10" and extra == "jax"
+Requires-Dist: flax>=0.10.0; python_version >= "3.10" and extra == "jax"
+Requires-Dist: orbax-checkpoint; python_version >= "3.10" and extra == "jax"
+Requires-Dist: orbax-checkpoint; python_version >= "3.10" and extra == "jax"
+Provides-Extra: cpu
+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.*,<2.20; platform_system == "Windows" and extra == "cpu"
+Requires-Dist: h5py!=3.11.0,>=3.6.0; platform_system == "Linux" and platform_machine == "aarch64" and extra == "cpu"
+Provides-Extra: gpu
+Requires-Dist: tensorflow; extra == "gpu"
+Requires-Dist: tensorflow-metal; platform_machine == "arm64" and platform_system == "Darwin" and extra == "gpu"
+Requires-Dist: h5py!=3.11.0,>=3.6.0; platform_system == "Linux" and platform_machine == "aarch64" and extra == "gpu"
+Provides-Extra: mpi
+Requires-Dist: horovod; extra == "mpi"
+Requires-Dist: mpi4py; extra == "mpi"
+Provides-Extra: torch
+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
+
+[![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)
+[![pip install](https://img.shields.io/pypi/dm/deepmd-kit?label=pip%20install)](https://pypi.org/project/deepmd-kit)
+[![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/)
+
+## 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/).
+
+### Highlighted features
+
+- **interfaced with multiple backends**, including TensorFlow, PyTorch, JAX, and Paddle, the most popular deep learning frameworks, 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 ABACUS.
+- **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)
+- 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)
+- Jinzhe Zeng, Duo Zhang, Anyang Peng, Xiangyu Zhang, Sensen He, Yan Wang, Xinzijian Liu, Hangrui Bi, Yifan Li, Chun Cai, Chengqian Zhang, Yiming Du, Jia-Xin Zhu, Pinghui Mo, Zhengtao Huang, Qiyu Zeng, Shaochen Shi, Xuejian Qin, Zhaoxi Yu, Chenxing Luo, Ye Ding, Yun-Pei Liu, Ruosong Shi, Zhenyu Wang, Sigbjørn Løland Bore, Junhan Chang, Zhe Deng, Zhaohan Ding, Siyuan Han, Wanrun Jiang, Guolin Ke, Zhaoqing Liu, Denghui Lu, Koki Muraoka, Hananeh Oliaei, Anurag Kumar Singh, Haohui Que, Weihong Xu, Zhangmancang Xu, Yong-Bin Zhuang, Jiayu Dai, Timothy J. Giese, Weile Jia, Ben Xu, Darrin M. York, Linfeng Zhang, Han Wang. "DeePMD-kit v3: A Multiple-Backend Framework for Machine Learning Potentials." J. Chem. Theory Comput. 21 (2025): 4375-4385.
+  [![doi:10.1021/acs.jctc.5c00340](https://img.shields.io/badge/DOI-10.1021%2Facs.jctc.5c00340-blue)](https://doi.org/10.1021/acs.jctc.5c00340)
+  [![Citations](https://citations.njzjz.win/10.1021/acs.jctc.5c00340)](https://badge.dimensions.ai/details/doi/10.1021/acs.jctc.5c00340)
+
+In addition, please follow [the bib file](https://github.com/deepmodeling/deepmd-kit/tree/master/CITATIONS.bib) to cite the methods you used.
+
+### 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.
+
+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.
+
+#### 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 v2 paper](https://doi.org/10.1063/5.0155600) for details of all features until v2.2.3.
+
+#### v3
+
+- Multiple backends supported. Add PyTorch and JAX backends.
+- The DPA2 and DPA3 models.
+- Plugin mechanisms for external models.
+
+See [our v3 paper](https://doi.org/10.1021/acs.jctc.5c00340) for details of all features until v3.0.
+
+## Install and use DeePMD-kit
+
+Just copy and paste in 1s, and let it run.
+
+```sh
+curl -fsSL https://dp1s.deepmodeling.com | bash
+```
+
+Please read the [online documentation](https://deepmd.readthedocs.io/) for details and alternative installation methods.
+
+Then, read on for a brief overview of the usage of DeePMD-kit. You may start with the first step:
+
+```sh
+dp
+```
+
+## Code structure
+
+The code is organized as follows:
+
+- `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.
+
+# 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
+[4]: https://aip.scitation.org/doi/full/10.1063/1.5027645