lammps-forcefield-tools 0.1.0__tar.gz

lammps_forcefield_tools-0.1.0/LICENSE

@@ -0,0 +1,339 @@
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lammps_forcefield_tools-0.1.0/MANIFEST.in

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+include README.md
+include LICENSE
+include pyproject.toml
+include lft.config
+include requirements.lock
+recursive-include docs *.md
+recursive-include examples *.md *.mol2 *.xyz *.pdb
+recursive-include tests *.py *.yaml *.json *.mol2 *.pdb *.xyz *.txt
+recursive-include scripts *.py *.sh
+prune _archive
+prune _scratch
+prune references
+prune thirdparty
+prune research
+prune e2e
+global-exclude __pycache__ *.py[cod] *.so *.egg-info

lammps_forcefield_tools-0.1.0/PKG-INFO

@@ -0,0 +1,298 @@
+Metadata-Version: 2.4
+Name: lammps-forcefield-tools
+Version: 0.1.0
+Summary: Automated LAMMPS and GROMACS force-field and topology generation from molecular and crystal structures
+Author: tgraphite
+License-Expression: GPL-2.0-only
+Project-URL: Homepage, https://github.com/tgraphite/LammpsForcefieldTools
+Project-URL: Repository, https://github.com/tgraphite/LammpsForcefieldTools
+Project-URL: Documentation, https://github.com/tgraphite/LammpsForcefieldTools/blob/main/docs/MANUAL.md
+Project-URL: Changelog, https://github.com/tgraphite/LammpsForcefieldTools/blob/main/docs/CHANGELOG.md
+Project-URL: Issues, https://github.com/tgraphite/LammpsForcefieldTools/issues
+Project-URL: PyPI, https://pypi.org/project/lammps-forcefield-tools/
+Keywords: lammps,gromacs,force-field,topology,molecular-dynamics,gaff,am1-bcc,resp,computational-chemistry
+Classifier: Development Status :: 4 - Beta
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Classifier: Topic :: Scientific/Engineering :: Physics
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.26
+Requires-Dist: scipy>=1.11
+Requires-Dist: pyscf>=2.14
+Requires-Dist: dftd3>=1.6
+Requires-Dist: cclib>=1.8
+Requires-Dist: openbabel-wheel>=3.1.1
+Requires-Dist: PyYAML>=6.0
+Provides-Extra: test
+Requires-Dist: pytest>=8; extra == "test"
+Dynamic: license-file
+
+# LammpsForcefieldTools
+
+[![PyPI](https://img.shields.io/pypi/v/lammps-forcefield-tools.svg)](https://pypi.org/project/lammps-forcefield-tools/)
+[![Python](https://img.shields.io/pypi/pyversions/lammps-forcefield-tools.svg)](https://pypi.org/project/lammps-forcefield-tools/)
+[![License: GPL-2.0](https://img.shields.io/badge/license-GPL--2.0-blue.svg)](LICENSE)
+
+把分子/晶体结构自动转换为可运行的 **LAMMPS** 力场与拓扑输入，同时提供 **GROMACS** 兼容输出。命令行入口为 **`lft`**。
+
+```bash
+lft -f molecule.mol2          # 生成 molecule.data + molecule.in
+lmp -in molecule.in           # 直接运行
+```
+
+- GitHub：<https://github.com/tgraphite/LammpsForcefieldTools>
+- PyPI：<https://pypi.org/project/lammps-forcefield-tools/>
+- 使用手册：[docs/MANUAL.md](docs/MANUAL.md)
+
+---
+
+## 功能特性
+
+| 能力 | 说明 |
+|---|---|
+| 结构读入 | MOL2、PDB/ENT、PQR、GRO、XYZ、CIF/mmCIF、结构 JSON |
+| 连接性 | 显式键优先；无键结构按共价半径与价键上限自动建键 |
+| 拓扑 | 键、角、二面角、improper、1-4 pair，支持周期镜像 |
+| 原子类型 | GAFF 规则引擎；`gaff+uff` 自动回退；支持纯 UFF 与手动映射 |
+| 电荷 | 输入、MMFF94、AM1-BCC、RESP/RESP2、MK、CM5/raw-CM5、ADCH |
+| 量化 | 内置 pySCF：单点、PCM、Hessian、ESP，无外部量化程序依赖 |
+| 参数化 | 经典参数 + Hessian 投影；手动参数 JSON |
+| LAMMPS 输出 | `real` 单位、`atom_style full`、`.data` + `.in`，可选 moltemplate |
+| GROMACS 输出 | `.itp`、`.top`、`.gro`、`.mdp` |
+| 周期体系 | 镜像感知键合项；晶体必须显式提供电荷 |
+| 诊断 | 重要警告直接显示；完整披露写入 `<name>.lft/` |
+
+---
+
+## 安装
+
+要求 **Python 3.11+**。
+
+```bash
+python -m pip install --upgrade pip
+python -m pip install lammps-forcefield-tools
+```
+
+检查安装：
+
+```bash
+lft --version
+lft --help
+```
+
+从源码安装：
+
+```bash
+git clone https://github.com/tgraphite/LammpsForcefieldTools.git
+cd LammpsForcefieldTools
+python -m pip install .
+```
+
+开发/测试安装：
+
+```bash
+python -m pip install -e ".[test]"
+python -m pytest -q
+```
+
+安装包会自动拉取：`numpy`、`scipy`、`pyscf`、`dftd3`、`cclib`、`openbabel-wheel`、`PyYAML`。
+
+---
+
+## 快速开始
+
+仓库自带一个带电荷的水分子示例：
+
+```bash
+cd examples
+lft -f water.mol2
+```
+
+输出：
+
+```text
+water.data
+water.in
+```
+
+运行 LAMMPS：
+
+```bash
+lmp -in water.in
+```
+
+生成 GROMACS 输入：
+
+```bash
+lft -f water.mol2 --output gromacs
+# water.itp  water.top  water.gro  water.mdp
+```
+
+生成后立即做引擎输入烟测：
+
+```bash
+lft -f water.mol2 --engine-smoke
+```
+
+---
+
+## 模块
+
+程序按处理阶段组织，命令行会把各阶段自动串联：
+
+| 阶段 | Python 包 | 职责 |
+|---|---|---|
+| 结构 | `lft.io` | 读取常见分子/晶体格式，输出统一结构模型 |
+| 领域模型 | `lft.domain` | 原子、晶胞、拓扑项、参数、单位 |
+| 拓扑 | `lft.topology` | 建键、键合项枚举、周期镜像处理 |
+| 力场 | `lft.forcefields` | GAFF/UFF/manual 原子类型与非键参数 |
+| 电荷 | `lft.charges` | AM1-BCC、RESP、密度电荷、电荷文件 |
+| 量化 | `lft.qc` | pySCF 单点、PCM、Hessian、ESP |
+| 参数化 | `lft.parameterize` | 经典参数与 Hessian 投影 |
+| 后端 | `lft.backends` | LAMMPS 与 GROMACS 文件生成 |
+| 外部程序 | `lft.runners` | gmx、lmp、moltemplate、Packmol 受控调用 |
+| 校验 | `lft.validation` | 结构、电荷、能量与 ground truth 校验 |
+
+---
+
+## 通用参数
+
+| 参数 | 默认值 | 说明 |
+|---|---|---|
+| `-f`, `--structure` | 必填 | 输入结构文件 |
+| `-o`, `--output` | `lammps` | `lammps` 或 `gromacs` |
+| `--ff` | `gaff+uff` | `gaff`、`gaff+uff`、`uff`、`manual` |
+| `--charge` | 自动 | 电荷方法名或电荷文件路径 |
+| `--net-charge` | `0` | 分子形式电荷 |
+| `--mult`, `--multiplicity` | `1` | 自旋多重度 |
+| `--outdir` | 当前目录 | 产物目录 |
+| `--force` | 关闭 | 覆盖同名产物 |
+| `--debug` | 关闭 | 写出 `<name>.lft/debug.txt` 诊断包 |
+| `-V`, `--version` | — | 显示版本 |
+| `-h`, `--help` | — | 显示帮助 |
+
+### 电荷自动选择
+
+未指定 `--charge` 时：
+
+1. 结构自带电荷 → 直接使用；
+2. 非周期且 ≤100 原子 → `resp`；
+3. 非周期且 >100 原子 → `am1-bcc`；
+4. 周期结构 → 必须显式提供电荷，否则报错。
+
+`--charge` 也可以直接给文件路径：
+
+```bash
+lft -f molecule.xyz --charge charges.txt
+lft -f crystal.pdb --charge charges.txt --ff uff
+```
+
+### 高级参数
+
+以下参数默认值通常正确，完整说明见[使用手册](docs/MANUAL.md)：
+
+`--parameter-mode`、`--qc`、`--qc-backend`、`--hessian-file`、`--hessian-method`、`--manual-file`、`--no-qc`、`--engine-smoke`、`--moltemplate`。
+
+---
+
+## 输入与输出
+
+### 输入格式
+
+| 后缀 | 连接性 | 周期性 |
+|---|---|---|
+| `.mol2` | `@<TRIPOS>BOND`（推荐） | `@<TRIPOS>CRYSIN` |
+| `.pdb`、`.ent`、`.pqr` | `CONECT` 或距离推断 | `CRYST1` |
+| `.gro` | 距离推断 | box 行 |
+| `.xyz` | 距离推断 | 注释行晶格（可选） |
+| `.cif`、`.mmcif` | 距离推断 | 晶胞参数 |
+| `.json` | 文件内 `bonds` | 文件内 `cell` |
+
+### 输出文件
+
+LAMMPS（默认）：
+
+```text
+<name>.data   坐标、拓扑、原子类型与系数
+<name>.in     units / pair_style / bond_style / 运行设置
+```
+
+GROMACS：
+
+```text
+<name>.itp    原子、键、角、二面角、1-4 pair
+<name>.top    力场默认项与系统定义
+<name>.gro    坐标
+<name>.mdp    最小运行参数
+```
+
+按需出现：
+
+```text
+<name>.lft/notes.txt          警告与参数来源披露
+<name>.lft/image_map.json     周期图镜像映射
+<name>.lft/debug.txt          --debug 诊断
+<name>.lft/normalized_ir.json --debug 规范化结构
+```
+
+---
+
+## 配置
+
+可选全局配置文件 `lft.config`，格式为 `key = value`：
+
+```ini
+output = lammps
+ff = gaff+uff
+charge = resp
+qc = b3lyp-d3bj/def2-svp
+gmx = /usr/local/gromacs/bin/gmx
+lmp = /opt/lammps/bin/lmp
+```
+
+查找顺序：`$LFT_CONFIG` → 安装根目录 → Python 包目录。优先级：**命令行 > 配置文件 > 内置默认**。
+
+常用环境变量：
+
+| 变量 | 作用 |
+|---|---|
+| `LFT_CONFIG` | 配置文件路径 |
+| `LFT_GMX` | GROMACS 可执行文件 |
+| `LFT_LMP` | LAMMPS 可执行文件 |
+| `LFT_OBABEL` | OpenBabel 可执行文件 |
+| `LFT_AM1BCC_OPTIMIZE` | AM1-BCC 几何优化：`yes`/`no`/`auto` |
+| `LFT_ATOMTYPE_EXTERNAL` | 用外部 `atomtype` 做对照 |
+
+---
+
+## 文档
+
+| 文档 | 内容 |
+|---|---|
+| [使用手册](docs/MANUAL.md) | 安装、完整 CLI、电荷、周期、产物、排错 |
+| [模块现状](docs/PROJECT_STATUS.md) | 模块成熟度、能力矩阵、验证结果与已知边界 |
+| [更新日志](docs/CHANGELOG.md) | 版本变更 |
+
+---
+
+## 已知限制
+
+- 经典键合参数库尚不完整；未命中项使用确定性通用值，并在 `notes.txt` 中标注。
+- UFF/共轭二面角当前使用占位参数，定量工作前应核对或用 `--manual-file` 覆盖。
+- AM1-BCC 默认不做几何优化，电荷依赖输入构象。
+- 周期体系只接受显式电荷，不做 ESP/密度电荷拟合。
+- LAMMPS 输出固定 10 Å 直接截断，未启用 PPPM/PME。
+- 不提供构象搜索、体系组装、MD 采样或力场重优化。
+
+---
+
+## 许可证
+
+GNU General Public License v2.0，见 [LICENSE](LICENSE)。