NEPAdapters
NEPAdapters 为 NEP 模型提供统一的推理运行时:同一个模型可以通过 Python、C/C++ 或 LAMMPS 调用,并显式选择 CPU 或 CUDA 后端。
如果选中的后端不可用,或该后端不支持当前模型,接口会明确报错,不会静默改用其他后端。普通 NEP、qNEP、spin NEP、dipole、polarizability 和 DFT-D3 使用各自明确的接口,避免输出含义或形状随模型类型悄悄变化。
项目来源与致谢
NEPAdapters 最初从 NepTrainKit 内置的 NEP 运行时中拆分而来。拆分的目的不是重新包装 NEP,也不是替代 GPUMD,而是让计算后端能够脱离桌面应用独立维护、测试和发布,使 NepTrainKit 可以按需更新运行时,也让同一套能力能够被 Python、C/C++ 和 LAMMPS 复用。
各部分的来源和关系如下:
- CPU 后端以 Zheyong Fan、Junjie Wang、Eric Lindgren 等作者维护的 NEP_CPU 独立 C++ 实现为基础,在保留原版权和 GPL 许可证声明的前提下,继续进行接口适配、正确性修复、OpenMP 并行和性能优化。
- CUDA 后端由 NEPAdapters 独立实现,没有直接引入 GPUMD 的 CUDA 源码树。它遵循 NEP 论文和 GPUMD 的模型格式、数学定义与结果语义,并以 NEP_CPU 参考结果和 CPU/CUDA 一致性测试约束正确性。这里的“独立实现”指代码和数据流设计独立,不代表重新发明了 NEP 方法。
- 适配层与前端源自 NepTrainKit 的实际使用需求,负责稳定 API、跨平台打包、运行时能力检查,以及 Python、C/C++ 和 LAMMPS 集成。
NEP 方法及其科学贡献来自 Zheyong Fan 等作者的原创工作,并在 GPUMD 中持续发展。NEPAdapters 的工作重点是工程实现与集成;它不是新的势函数方法,也不是 NEP_CPU 或 GPUMD 的官方发行组成部分。
感谢 NEP 与 GPUMD 作者和社区长期公开算法、代码、文档与验证工作。没有这些基础,NEPAdapters 和 NepTrainKit 都无从建立。GPUMD 的正式文档见 gpumd.org。
先选你要的入口
| 使用场景 | 从这里开始 |
|---|---|
| Python / NumPy / ASE | Python 接口指南 |
| CMake 构建、测试和安装 | 构建与安装 |
| LAMMPS CPU 或 CUDA | LAMMPS 前端指南 |
| C/C++ API | 公共头文件 与 架构说明 |
| 测试和正确性验证 | 测试说明 |
Python 快速开始
仅使用 NumPy 接口:
python -m pip install nep-adapters
同时使用 ASE:
python -m pip install 'nep-adapters[ase]'
使用 ASE 做一次普通 NEP 计算:
from ase import Atoms
from nep_adapters.ase import NepAseCalculator
atoms = Atoms(
"Fe2",
positions=[[0.0, 0.0, 0.0], [1.43, 1.43, 1.43]],
cell=[2.86, 2.86, 2.86],
pbc=True,
)
atoms.calc = NepAseCalculator("nep.txt", backend="cpu")
print(atoms.get_potential_energy())
print(atoms.get_forces())
预编译 wheel 支持 CPython 3.10–3.14:
| 平台 | wheel 包含的后端 | 运行要求 |
|---|---|---|
| Linux x86_64 | CPU + CUDA | CPU 可直接使用;CUDA 需要 NVIDIA 驱动和受支持的 GPU |
| Windows x86_64 | CPU + CUDA | CPU 可直接使用;CUDA 需要 NVIDIA 驱动和受支持的 GPU |
| macOS x86_64 / arm64 | CPU | 不提供 CUDA 后端 |
Linux 和 Windows 的预编译 wheel 已包含 CUDA 运行时,不要求另外安装 CUDA Toolkit。普通 import nep_adapters 或选择 backend="cpu" 不会初始化 CUDA;只有显式选择 backend="cuda" 或检查 CUDA 状态时才会加载 GPU 扩展。CUDA 加载或计算失败时不会改用 CPU。
CUDA wheel 内置 sm_60 和 sm_89 SASS,并保留 compute_60 PTX。没有对应 SASS 的较新架构会在驱动支持时通过 PTX 即时编译运行,因此兼容范围更广,但可能增加首次加载时间或产生一定性能损失。
可以运行下面的命令检查扩展、驱动、设备,并实际完成一次 CUDA 内存分配、核函数启动、同步和结果回传:
python -c "from nep_adapters import backend_status; s=backend_status('cuda'); print(s); assert s.installed and s.available, s"
需要修改源码或只为本机 GPU 编译时,从仓库安装:
git clone https://github.com/MagTheoryLab/NEPAdapters.git
cd NEPAdapters
python -m pip install '.[ase]'
源码安装会依次查找 CUDACXX、CUDAToolkit_ROOT、CUDA_PATH、
CUDA_HOME 和 PATH 中的 NVCC。检测到 CUDA Toolkit 时自动构建
CPU+CUDA,否则只构建 CPU。不指定 CMAKE_CUDA_ARCHITECTURES 时使用
native,只为构建机器上的 GPU 编译。NEP_CUDA=1 和 NEP_CUDA=0
可分别强制启用或禁用 CUDA。
更多 NumPy batch、qNEP、spin、descriptor 和错误处理示例见 Python 接口指南。
CMake 快速开始
只构建 CPU core 和测试:
cmake -S . -B .build/release \
-DCMAKE_BUILD_TYPE=Release \
-DNEP_ADAPTERS_BUILD_TESTS=ON
cmake --build .build/release -j2
ctest --test-dir .build/release --output-on-failure
Python 源码安装会自动查找 NVCC;独立 CMake 和 LAMMPS 构建仍按目标显式 打开 CUDA,避免有 Toolkit 的机器意外改变 CPU-only 构建。完整组合、安装命令 和选项默认值见 构建与安装。
LAMMPS 安装方式
LAMMPS 有两种支持的安装方式:
- 运行时插件(推荐):单独构建共享库,通过
LAMMPS_PLUGIN_PATH加载,不需要重新编译 LAMMPS; - 源码树内置:运行
tools/install_lammps_source.py,把受管的 pair style 源文件复制到lammps/src/,再通过随附的 CMake 配置把 core 和 engine 静态编入lmp。运行时不需要设置插件环境变量。
不要手工只复制 .cpp 和 .h 文件;安装脚本还会写入连接依赖所需的 CMake 配置、记录文件哈希,并提供安全卸载。两种方式的完整命令见 LAMMPS 前端指南。
当前支持范围
| 前端 / 后端 | 普通 NEP | qNEP | spin NEP | 其他响应模型 |
|---|---|---|---|---|
| Python / CPU | 支持 | charge/BEC 支持 | 支持 | dipole、polarizability、DFT-D3 支持;DFT-D3 仅普通非 spin、非 charge 模型 |
| Python / CUDA | 支持 NEP4/NEP5 | 支持 direct;预编译 wheel 不包含 PPPM | 支持 | 不支持 dipole、polarizability、DFT-D3 |
| LAMMPS / CPU 插件 | 支持,已完成普通模型 MPI 冒烟测试 | 尚未列入已验证支持范围 | 已验证单节点 1/2/4/8 个 MPI 进程,覆盖能量、力、磁力、virial、spin 读回和短程 dynspin | 不适用 |
| LAMMPS / CUDA Kokkos 插件 | 支持 | 不支持,运行时会明确报错 | 已验证单节点 1/2/4/8 个 MPI 进程 | 不适用 |
补充边界:
- 所有 Python batch 接口目前只接受全周期
pbc=(1, 1, 1)。 - LAMMPS spin 不使用单独的
nep/spin/*名称;仍使用nep/cpu或nep/gpu/kk,并配合atom_style spin或spin/kk。 - 构建 LAMMPS CPU plugin 且检测到 MPI launcher 时,CTest 除单 rank 外,还会根据
MPIEXEC_MAX_NUMPROCS自动注册最多 2/4/8 ranks 的 spin 回归;在 Slurm 上应先申请足够的计算资源,再运行ctest -L mpi --output-on-failure。 - qNEP 的 CUDA batch API 可用,但 LAMMPS Kokkos 需要独立的 ghost/charge 数据流,因此当前会明确拒绝该组合,不会静默降级。
- virial 在不同公共入口有不同顺序;调用前请查 Python 接口指南 或 公共 API 契约。
项目结构
include/nep_adapters/:公共 C/C++ API 和数据约定;src/:core 注册、调度和错误处理;engines/cpu/、engines/cuda/:计算后端;frontends/python/、frontends/lammps/:用户前端;tests/:契约、fixture、oracle 和集成测试;benchmarks/:性能与扩展性入口。
LAMMPS 和 Python 都是前端,不是计算后端;算法实现只保留在 engine 层。
科研引用
NEPAdapters 目前没有独立的软件论文。论文方法部分可以记录所用的 NEPAdapters 版本和仓库地址,但这不能替代对 NEP 原始工作的引用。如果 NEPAdapters 用于科研工作,请至少引用 NEP 的基础论文:
- Z. Fan, Z. Zeng, C. Zhang, Y. Wang, K. Song, H. Dong, Y. Chen, and T. Ala-Nissila, “Neuroevolution machine learning potentials: Combining high accuracy and low cost in atomistic simulations and application to heat transport,” Physical Review B 104, 104309 (2021). DOI: 10.1103/PhysRevB.104.104309
如果 NepTrainKit 参与了数据准备、主动学习、训练管理或可视化,也请引用:
- C. Chen, Y. Li, R. Zhao, Z. Liu, Z. Fan, G. Tang, and Z. Wang, “NepTrain and NepTrainKit: Automated active learning and visualization toolkit for neuroevolution potentials,” Computer Physics Communications 317, 109859 (2025). DOI: 10.1016/j.cpc.2025.109859
涉及 GPUMD 的 NEP 训练、实现或分子动力学工作时,建议同时引用 GPUMD 软件论文:
- Z. Fan et al., “GPUMD: A package for constructing accurate machine-learned potentials and performing highly efficient atomistic simulations,” The Journal of Chemical Physics 157, 114801 (2022). DOI: 10.1063/5.0106617
许可证
NEPAdapters 以 GNU GPL v3 或更高版本 发布。
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