chemphase 0.1.0__tar.gz

chemphase-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2024 Phase Diagram Generator Team
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

chemphase-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: chemphase
+Version: 0.1.0
+Summary: 相图与化学势热图统一生成器 — 一键生成二元/三元成分相图、化学势热图，支持 Materials Project API 和本地 VASP 数据
+Author: Phase Diagram Generator Team
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/user/chemphase
+Project-URL: Repository, https://github.com/user/chemphase
+Project-URL: Issues, https://github.com/user/chemphase/issues
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Topic :: Scientific/Engineering :: Physics
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: pymatgen>=2023.0.0
+Requires-Dist: doped>=3.2.0
+Requires-Dist: matplotlib>=3.5.0
+Requires-Dist: numpy>=1.21.0
+Requires-Dist: scipy>=1.7.0
+Requires-Dist: plotly>=5.0.0
+Provides-Extra: dev
+Requires-Dist: pytest>=8.0; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Requires-Dist: ruff; extra == "dev"
+Dynamic: license-file
+
+# chemphase
+
+**相图与化学势热图统一生成器 v5.0**
+
+[![Python](https://img.shields.io/badge/Python-3.10%2B-blue)](https://python.org)
+[![License](https://img.shields.io/badge/License-MIT-green)](LICENSE)
+
+一键从 Materials Project API 或本地 VASP 计算结果生成高质量相图。
+
+## 功能
+
+- **API 模式**：从 Materials Project 数据库下载热力学数据
+- **本地模式**：读取本地 VASP 计算目录 (POSCAR + vasprun.xml/OUTCAR)
+- **混合模式**：本地数据 + API 补充
+- **二元成分相图**：ΔE vs 成分，含 Hull 连线、自动标签避让
+- **三元成分相图**：Gibbs 三角图 (Plotly 交互式)，含 Hull 三角剖分
+- **结构对比**：检测本地计算与 MP 数据库的晶体结构差异
+
+## 安装
+
+```bash
+pip install chemphase
+```
+
+## 快速开始
+
+### API 模式（默认）
+
+```bash
+# 使用默认元素 Cu-Ag-O-Se
+chemphase
+
+# 指定元素
+chemphase --elements Li O Co
+```
+
+### 本地 VASP 数据模式
+
+```bash
+chemphase --local /path/to/vasp/calculations --elements Cu Ag O Se
+```
+
+### 结构对比
+
+```bash
+chemphase --local /path/to/vasp/calculations --elements Cu Ag O Se --compare-structure
+```
+
+## 依赖
+
+- [pymatgen](https://pymatgen.org) — 材料分析库
+- [doped](https://github.com/SMTG-Bham/doped) — 缺陷计算工具
+- [matplotlib](https://matplotlib.org) — 二维绘图
+- [plotly](https://plotly.com) — 交互式三元图
+
+## API 密钥
+
+API 模式需要 Materials Project API 密钥。设置环境变量：
+
+```bash
+export MATERIALS_PROJECT_API_KEY=你的密钥
+```
+
+获取密钥：https://materialsproject.org/api
+
+## 命令行参数
+
+| 参数 | 说明 | 默认值 |
+|------|------|--------|
+| `--elements` | 元素列表 | `Cu Ag O Se` |
+| `--local` | 本地VASP目录 | — |
+| `--output` | 输出目录 | `phase_diagrams_output` |
+| `--eah` | E above hull 阈值 | `0.05` eV/atom |
+| `--compare-structure` | 启用结构对比 | `False` |
+| `--debug` | 调试模式 | `False` |
+
+## 许可证
+
+MIT License — 详见 [LICENSE](LICENSE)

chemphase-0.1.0/README.md

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+# chemphase
+
+**相图与化学势热图统一生成器 v5.0**
+
+[![Python](https://img.shields.io/badge/Python-3.10%2B-blue)](https://python.org)
+[![License](https://img.shields.io/badge/License-MIT-green)](LICENSE)
+
+一键从 Materials Project API 或本地 VASP 计算结果生成高质量相图。
+
+## 功能
+
+- **API 模式**：从 Materials Project 数据库下载热力学数据
+- **本地模式**：读取本地 VASP 计算目录 (POSCAR + vasprun.xml/OUTCAR)
+- **混合模式**：本地数据 + API 补充
+- **二元成分相图**：ΔE vs 成分，含 Hull 连线、自动标签避让
+- **三元成分相图**：Gibbs 三角图 (Plotly 交互式)，含 Hull 三角剖分
+- **结构对比**：检测本地计算与 MP 数据库的晶体结构差异
+
+## 安装
+
+```bash
+pip install chemphase
+```
+
+## 快速开始
+
+### API 模式（默认）
+
+```bash
+# 使用默认元素 Cu-Ag-O-Se
+chemphase
+
+# 指定元素
+chemphase --elements Li O Co
+```
+
+### 本地 VASP 数据模式
+
+```bash
+chemphase --local /path/to/vasp/calculations --elements Cu Ag O Se
+```
+
+### 结构对比
+
+```bash
+chemphase --local /path/to/vasp/calculations --elements Cu Ag O Se --compare-structure
+```
+
+## 依赖
+
+- [pymatgen](https://pymatgen.org) — 材料分析库
+- [doped](https://github.com/SMTG-Bham/doped) — 缺陷计算工具
+- [matplotlib](https://matplotlib.org) — 二维绘图
+- [plotly](https://plotly.com) — 交互式三元图
+
+## API 密钥
+
+API 模式需要 Materials Project API 密钥。设置环境变量：
+
+```bash
+export MATERIALS_PROJECT_API_KEY=你的密钥
+```
+
+获取密钥：https://materialsproject.org/api
+
+## 命令行参数
+
+| 参数 | 说明 | 默认值 |
+|------|------|--------|
+| `--elements` | 元素列表 | `Cu Ag O Se` |
+| `--local` | 本地VASP目录 | — |
+| `--output` | 输出目录 | `phase_diagrams_output` |
+| `--eah` | E above hull 阈值 | `0.05` eV/atom |
+| `--compare-structure` | 启用结构对比 | `False` |
+| `--debug` | 调试模式 | `False` |
+
+## 许可证
+
+MIT License — 详见 [LICENSE](LICENSE)

chemphase-0.1.0/pyproject.toml

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+[build-system]
+requires = ["setuptools>=68.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "chemphase"
+version = "0.1.0"
+description = "相图与化学势热图统一生成器 — 一键生成二元/三元成分相图、化学势热图，支持 Materials Project API 和本地 VASP 数据"
+authors = [
+    {name = "Phase Diagram Generator Team"}
+]
+readme = "README.md"
+license = "MIT"
+license-files = ["LICENSE"]
+requires-python = ">=3.10"
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Intended Audience :: Science/Research",
+    "Operating System :: OS Independent",
+    "Topic :: Scientific/Engineering :: Physics",
+    "Topic :: Scientific/Engineering :: Chemistry",
+]
+
+dependencies = [
+    "pymatgen>=2023.0.0",
+    "doped>=3.2.0",
+    "matplotlib>=3.5.0",
+    "numpy>=1.21.0",
+    "scipy>=1.7.0",
+    "plotly>=5.0.0",
+]
+
+[project.optional-dependencies]
+dev = [
+    "pytest>=8.0",
+    "pytest-cov",
+    "ruff",
+]
+
+[project.scripts]
+chemphase = "chemphase.cli:main"
+
+[project.urls]
+Homepage = "https://github.com/user/chemphase"
+Repository = "https://github.com/user/chemphase"
+Issues = "https://github.com/user/chemphase/issues"
+
+[tool.setuptools.packages.find]
+where = ["src"]
+exclude = ["tests*", "docs*"]
+
+[tool.setuptools.package-data]
+"chemphase" = ["py.typed"]
+
+[tool.ruff]
+line-length = 100
+lint.select = ["E", "F", "I", "N", "W", "UP", "B", "SIM"]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+pythonpath = ["src"]

chemphase-0.1.0/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

chemphase-0.1.0/src/chemphase/__init__.py

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+"""chemphase — 相图与化学势热图生成器
+
+一键从 Materials Project API 或本地 VASP 计算结果生成：
+- 二元/三元成分相图（含 Hull 连线、标签自动避让）
+- 化学势热图
+- 结构对比报告
+"""
+
+__version__ = "0.1.0"
+
+
+def __getattr__(name):
+    """惰性导入：仅在实际使用子模块时才导入"""
+    if name == "PhaseDiagramConfig":
+        from chemphase.core import PhaseDiagramConfig
+        return PhaseDiagramConfig
+    if name == "generate_binary_composition_diagram":
+        from chemphase.diagrams import generate_binary_composition_diagram
+        return generate_binary_composition_diagram
+    if name == "generate_ternary_composition_diagram":
+        from chemphase.diagrams import generate_ternary_composition_diagram
+        return generate_ternary_composition_diagram
+    if name == "main":
+        from chemphase.cli import main
+        return main
+    raise AttributeError(f"module 'chemphase' has no attribute '{name}'")
+
+
+__all__ = [
+    "__version__",
+    "PhaseDiagramConfig",
+    "generate_binary_composition_diagram",
+    "generate_ternary_composition_diagram",
+    "main",
+]

chemphase-0.1.0/src/chemphase/__main__.py

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+"""chemphase 命令行入口
+
+支持 python -m chemphase 调用
+"""
+
+from chemphase.cli import main
+
+if __name__ == "__main__":
+    main()

chemphase-0.1.0/src/chemphase/cli.py

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+"""命令行接口 (CLI)
+
+安装后通过终端命令 `chemphase` 或 `python -m chemphase` 调用
+"""
+
+import sys
+import argparse
+from pathlib import Path
+from itertools import combinations
+
+from chemphase.core import (
+    PhaseDiagramConfig, validate_elements, ensure_api_key,
+    scan_local_phases, build_local_entries, structure_comparison_report,
+    get_entries_from_mp, get_system_name, get_all_element_combinations,
+    print_banner, DEFAULT_ELEMENTS,
+)
+from chemphase.diagrams import (
+    generate_binary_composition_diagram,
+    generate_ternary_composition_diagram,
+)
+
+
+def run_local_mode(config: PhaseDiagramConfig, elements, output_root: str):
+    """本地数据模式：读取 VASP 计算结果生成相图"""
+    print(f"\n扫描本地目录: {config.local_dir}")
+    local_phases = scan_local_phases(config.local_dir, elements, config.eah_threshold)
+    print(f"找到 {len(local_phases)} 个相关相")
+
+    if not local_phases:
+        print("没有找到有效的相数据")
+        return
+
+    # 结构对比
+    if config.compare_structure:
+        print("\n" + "=" * 60)
+        print("  结构对比分析")
+        print("=" * 60)
+        report = structure_comparison_report(local_phases, config)
+        print(f"  总共对比: {report['total_compared']}")
+        print(f"  结构匹配: {report['matching']}")
+        print(f"  结构不同: {report['different']}")
+        print(f"  MP未收录: {report['not_found_in_mp']}")
+
+        import json
+        report_file = Path(output_root) / "structure_comparison_report.json"
+        report_file.parent.mkdir(parents=True, exist_ok=True)
+        with open(report_file, 'w') as f:
+            json.dump(report, f, indent=2, sort_keys=True)
+        print(f"  报告已保存: {report_file}")
+
+    entries = build_local_entries(local_phases)
+    print(f"\n构建了 {len(entries)} 个PhaseDiagramEntry")
+
+    output_dir = Path(output_root)
+    output_dir.mkdir(parents=True, exist_ok=True)
+
+    binary_combos = list(combinations(elements, 2))
+    ternary_combos = list(combinations(elements, 3))
+
+    # 二元相图
+    print("\n" + "=" * 60)
+    print("  生成二元相图")
+    print("=" * 60)
+    binary_dir = output_dir / "binary"
+    binary_dir.mkdir(parents=True, exist_ok=True)
+    for e1, e2 in binary_combos:
+        sub_entries = [e for e in entries if set(e.composition.as_dict().keys()) <= {e1, e2}]
+        if len(sub_entries) >= 2:
+            generate_binary_composition_diagram(sub_entries, (e1, e2), binary_dir, "本地数据")
+
+    # 三元相图
+    print("\n" + "=" * 60)
+    print("  生成三元相图")
+    print("=" * 60)
+    ternary_dir = output_dir / "ternary"
+    ternary_dir.mkdir(parents=True, exist_ok=True)
+    for e1, e2, e3 in ternary_combos:
+        sub_entries = [e for e in entries if set(e.composition.as_dict().keys()) <= {e1, e2, e3}]
+        if len(sub_entries) >= 3:
+            generate_ternary_composition_diagram(sub_entries, (e1, e2, e3), ternary_dir, "本地数据")
+
+    print("\n" + "=" * 60)
+    print("  本地数据模式完成")
+    print("=" * 60)
+    print(f"输出目录: {output_dir}")
+
+
+def run_api_mode(config: PhaseDiagramConfig, elements, output_root: str):
+    """API 下载模式：从 Materials Project 下载数据生成相图"""
+    print(f"\n从Materials Project下载 {get_system_name(elements)} 体系数据")
+
+    output_dir = Path(output_root)
+    output_dir.mkdir(parents=True, exist_ok=True)
+
+    binary_combos = list(combinations(elements, 2))
+    ternary_combos = list(combinations(elements, 3))
+
+    # 二元相图
+    print("\n" + "=" * 60)
+    print("  生成二元相图")
+    print("=" * 60)
+    binary_dir = output_dir / "binary"
+    binary_dir.mkdir(parents=True, exist_ok=True)
+    for e1, e2 in binary_combos:
+        try:
+            entries = get_entries_from_mp(config, [e1, e2])
+            if len(entries) >= 2:
+                from pymatgen.analysis.phase_diagram import PDEntry
+                pd_entries = [PDEntry(composition=e.composition, energy=e.energy, name=e.name)
+                             for e in entries]
+                generate_binary_composition_diagram(pd_entries, (e1, e2), binary_dir, "MP数据")
+        except Exception as e:
+            print(f"    - {e1}-{e2}: {e}")
+
+    # 三元相图
+    print("\n" + "=" * 60)
+    print("  生成三元相图")
+    print("=" * 60)
+    ternary_dir = output_dir / "ternary"
+    ternary_dir.mkdir(parents=True, exist_ok=True)
+    for e1, e2, e3 in ternary_combos:
+        try:
+            entries = get_entries_from_mp(config, [e1, e2, e3])
+            if len(entries) >= 3:
+                from pymatgen.analysis.phase_diagram import PDEntry
+                pd_entries = [PDEntry(composition=e.composition, energy=e.energy, name=e.name)
+                             for e in entries]
+                generate_ternary_composition_diagram(pd_entries, (e1, e2, e3), ternary_dir, "MP数据")
+        except Exception as e:
+            print(f"    - {e1}-{e2}-{e3}: {e}")
+
+    print("\n" + "=" * 60)
+    print("  API模式完成")
+    print("=" * 60)
+    print(f"输出目录: {output_dir}")
+
+
+def main():
+    """主入口函数"""
+    parser = argparse.ArgumentParser(
+        prog="chemphase",
+        description="相图与化学势热图统一生成器 v5.0",
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+        epilog="""
+使用示例:
+  # API模式 - 下载CuAgOSe数据（默认）
+  chemphase
+
+  # 指定API模式的元素
+  chemphase --elements Li O Co
+
+  # 本地模式 - 读取VASP计算结果
+  chemphase --local /path/to/calculations --elements Cu Ag O Se
+
+  # 混合模式 - 本地数据为主
+  chemphase --local /path/to/data --elements Cu Ag O Se
+
+  # 启用结构对比
+  chemphase --local /path/to/data --elements Cu Ag O Se --compare-structure
+        """
+    )
+    parser.add_argument('--local', type=str, help='本地VASP计算结果目录')
+    parser.add_argument('--elements', nargs='+', help='目标元素列表（如 Cu Ag O Se）')
+    parser.add_argument('--output', default='phase_diagrams_output', help='输出目录 (默认: phase_diagrams_output)')
+    parser.add_argument('--eah', type=float, default=0.05, help='Energy above hull 阈值 (默认: 0.05 eV/atom)')
+    parser.add_argument('--compare-structure', action='store_true', help='启用本地结构 vs MP数据库对比')
+    parser.add_argument('--debug', action='store_true', help='调试模式')
+
+    args = parser.parse_args()
+
+    print_banner()
+
+    config = PhaseDiagramConfig(
+        eah_threshold=args.eah,
+        output_root=args.output,
+        local_dir=Path(args.local) if args.local else None,
+        compare_structure=args.compare_structure,
+        debug=args.debug
+    )
+
+    if args.local:
+        if not args.elements:
+            print("错误: 本地模式需要指定 --elements")
+            sys.exit(1)
+        ok, valid, errors = validate_elements(args.elements)
+        if not ok:
+            print("错误: " + ", ".join(errors))
+            sys.exit(1)
+        run_local_mode(config, valid, args.output)
+    else:
+        ensure_api_key(config)
+        elements = args.elements if args.elements else DEFAULT_ELEMENTS
+        ok, valid, errors = validate_elements(elements)
+        if not ok:
+            print("错误: " + ", ".join(errors))
+            sys.exit(1)
+        run_api_mode(config, valid, args.output)
+
+    print("\n" + "=" * 60)
+    print("  执行完成")
+    print("=" * 60)
+
+
+if __name__ == "__main__":
+    main()