qn-util 0.0.0__tar.gz

qn_util-0.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: qn-util
+Version: 0.0.0
+Summary: Qn network Tools
+Author-email: Kengo NAKADA <kengo.nakada@email.com>
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+Requires-Dist: xlogger-py
+Requires-Dist: packmol-util
+Requires-Dist: pymatgen
+Requires-Dist: dataclasses
+Requires-Dist: coloredlogs
+Requires-Dist: colorlog
+Requires-Dist: pytest
+Requires-Dist: pytest-asyncio
+Requires-Dist: pyyaml
+Requires-Dist: toml
+Requires-Dist: nest_asyncio
+Requires-Dist: sphinx
+Requires-Dist: myst-parser
+Requires-Dist: sphinx-autobuild
+Requires-Dist: sphinx-rtd-theme
+Requires-Dist: sphinxcontrib-napoleon
+Requires-Dist: linkify-it-py
+
+# Qn-Util — Qn Network Analysis and RMC Constraint Generation
+
+[![en](https://img.shields.io/badge/lang-en-red.svg)](https://github.com/ohara-lab-su/qn_util/blob/main/README.md)
+[![ja](https://img.shields.io/badge/lang-ja-yellow.svg)](https://github.com/ohara-lab-su/qn_util/blob/main/README.ja.md)
+
+[![GitHub](https://img.shields.io/badge/GitHub-ohara--lab--su%2Fqn_util-181717?logo=github)](https://github.com/ohara-lab-su/qn_util/)
+[![GitHub Pages](https://img.shields.io/badge/GitHub%20Pages-Documentation-222222?logo=githubpages&logoColor=white)](https://ohara-lab-su.github.io/qn_util/ja/)
+[![Ohara Lab](https://img.shields.io/badge/Ohara%20Lab-Home-4B5563?logo=homeassistant&logoColor=white)](https://ohara-lab-su.github.io/index.ja.html)
+
+Qn-Util is a Python library for constructing and analyzing Qn networks and generating constraint files for RMC_POT, using VASP POSCAR/CONTCAR structures and JSON configuration files as input. It outputs Qn distributions, network connectivity information, and analysis reports.
+
+The library is primarily intended for generating RMC_POT constraint files and is used for research and study purposes.
+
+## Main Components
+
+- `VaspStructure`: Reads POSCAR files and calculates distances and angles under periodic boundary conditions.
+- `QnNetworkAnalysis`: Builds networks from JSON configurations, counts Qn species, and outputs connectivity information and analysis results.
+- `RmcConstraintWriter`: Generates FNC=3 constraint files, unit definitions, and network topology files for RMC_POT.
+- `QnNetworkBuilder`: A facade that preserves existing calling conventions and provides combined access to analysis and output functions.
+- `ConfigError`: An exception for configuration and input validation errors.
+
+## Input and Output
+
+Inputs are structural files in POSCAR/CONTCAR format and JSON configuration files. Outputs include `*_qn.csv`, `*_network_bonds.csv`, `*_report.txt`, `*_rmc_fnc3.fnc`, and `*_rmc_unit.top`. See the tutorials for required configuration parameters and the meaning of the constraints.
+
+## Python API Example
+
+```python
+from qn_util.qn_network_builder import QnNetworkBuilder
+
+builder = QnNetworkBuilder.from_poscar("POSCAR", "qn_config.json")
+print(builder.get_qn_counts())
+builder.write_analysis("sample")
+builder.write_all("sample")
+```
+
+`write_all` generates analysis results and RMC input files. See `scripts/` for concrete configuration examples.
+
+## Installation
+
+```bash
+pip install qn-util
+```
+
+## Installing Example Scripts
+
+After installing the package, run the following command in your working directory to copy the files bundled under `scripts/` (Python scripts and `qn_config.json`) into the current directory.
+
+```bash
+qn_util install
+```
+
+If files with the same names already exist, the command exits with an error without overwriting them. Specify `--force` only when you want to overwrite existing files.
+
+```bash
+qn_util install --force
+```
+
+## Documentation
+
+The tutorials cover Qn networks, FNC, topology, JSON configuration, and future development. The API Reference is generated from source docstrings.
+
+[日本語](https://ohara-lab-su.github.io/qn_util/ja/) / [English](https://ohara-lab-su.github.io/qn_util/en/)

qn_util-0.0.0/README.md

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+# Qn-Util — Qn Network Analysis and RMC Constraint Generation
+
+[![en](https://img.shields.io/badge/lang-en-red.svg)](https://github.com/ohara-lab-su/qn_util/blob/main/README.md)
+[![ja](https://img.shields.io/badge/lang-ja-yellow.svg)](https://github.com/ohara-lab-su/qn_util/blob/main/README.ja.md)
+
+[![GitHub](https://img.shields.io/badge/GitHub-ohara--lab--su%2Fqn_util-181717?logo=github)](https://github.com/ohara-lab-su/qn_util/)
+[![GitHub Pages](https://img.shields.io/badge/GitHub%20Pages-Documentation-222222?logo=githubpages&logoColor=white)](https://ohara-lab-su.github.io/qn_util/ja/)
+[![Ohara Lab](https://img.shields.io/badge/Ohara%20Lab-Home-4B5563?logo=homeassistant&logoColor=white)](https://ohara-lab-su.github.io/index.ja.html)
+
+Qn-Util is a Python library for constructing and analyzing Qn networks and generating constraint files for RMC_POT, using VASP POSCAR/CONTCAR structures and JSON configuration files as input. It outputs Qn distributions, network connectivity information, and analysis reports.
+
+The library is primarily intended for generating RMC_POT constraint files and is used for research and study purposes.
+
+## Main Components
+
+- `VaspStructure`: Reads POSCAR files and calculates distances and angles under periodic boundary conditions.
+- `QnNetworkAnalysis`: Builds networks from JSON configurations, counts Qn species, and outputs connectivity information and analysis results.
+- `RmcConstraintWriter`: Generates FNC=3 constraint files, unit definitions, and network topology files for RMC_POT.
+- `QnNetworkBuilder`: A facade that preserves existing calling conventions and provides combined access to analysis and output functions.
+- `ConfigError`: An exception for configuration and input validation errors.
+
+## Input and Output
+
+Inputs are structural files in POSCAR/CONTCAR format and JSON configuration files. Outputs include `*_qn.csv`, `*_network_bonds.csv`, `*_report.txt`, `*_rmc_fnc3.fnc`, and `*_rmc_unit.top`. See the tutorials for required configuration parameters and the meaning of the constraints.
+
+## Python API Example
+
+```python
+from qn_util.qn_network_builder import QnNetworkBuilder
+
+builder = QnNetworkBuilder.from_poscar("POSCAR", "qn_config.json")
+print(builder.get_qn_counts())
+builder.write_analysis("sample")
+builder.write_all("sample")
+```
+
+`write_all` generates analysis results and RMC input files. See `scripts/` for concrete configuration examples.
+
+## Installation
+
+```bash
+pip install qn-util
+```
+
+## Installing Example Scripts
+
+After installing the package, run the following command in your working directory to copy the files bundled under `scripts/` (Python scripts and `qn_config.json`) into the current directory.
+
+```bash
+qn_util install
+```
+
+If files with the same names already exist, the command exits with an error without overwriting them. Specify `--force` only when you want to overwrite existing files.
+
+```bash
+qn_util install --force
+```
+
+## Documentation
+
+The tutorials cover Qn networks, FNC, topology, JSON configuration, and future development. The API Reference is generated from source docstrings.
+
+[日本語](https://ohara-lab-su.github.io/qn_util/ja/) / [English](https://ohara-lab-su.github.io/qn_util/en/)

qn_util-0.0.0/pyproject.toml

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+[build-system]
+requires = ["setuptools>=71.0","coloredlogs"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "qn-util"
+version = "0.0.0"
+
+description = "Qn network Tools"
+authors = [
+    { name="Kengo NAKADA", email="kengo.nakada@email.com" },
+]
+readme = "README.md"
+# requires-python = ">=3.8"
+requires-python = ">=3.10"
+dependencies = [
+    # my-modules
+    # "x_logger",
+    "xlogger-py",
+    "packmol-util" ,
+    # fnc
+    "pymatgen",
+    # basic
+    "dataclasses",
+    "coloredlogs",
+    "colorlog",
+    "pytest",
+    "pytest-asyncio",
+    "pyyaml",
+    "toml",
+    # "grpcio",
+    "nest_asyncio",
+    # pages
+    "sphinx",
+    "myst-parser",
+    "sphinx-autobuild",
+    "sphinx-rtd-theme",
+    "sphinxcontrib-napoleon",
+    "linkify-it-py"
+]
+
+[tool.pytest.ini_options]
+pythonpath = ["src"]
+
+# ここでpytestのiniと同じようにオプションが書ける
+# 例えばテストマーク、フィルタ、カバレッジなども追記可能
+
+[tool.black]
+line-length = 88
+
+[tool.isort]
+profile = "black"

qn_util-0.0.0/setup.cfg

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

qn_util-0.0.0/src/qn_util/__init__.py

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+# from rmc_dft.rmc_pot.qn.config_error import ConfigError
+# from rmc_dft.rmc_pot.qn.qn_network_analysis import QnNetworkAnalysis
+# from rmc_dft.rmc_pot.qn.qn_network_builder import QnNetworkBuilder
+# from rmc_dft.rmc_pot.qn.rmc_constraint_writer import RmcConstraintWriter
+# from rmc_dft.rmc_pot.qn.vasp_structure import VaspStructure
+
+from qn.config_error import ConfigError
+from qn.qn_network_analysis import QnNetworkAnalysis
+from qn.qn_network_builder import QnNetworkBuilder
+from qn.rmc_constraint_writer import RmcConstraintWriter
+from qn.vasp_structure import VaspStructure

qn_util-0.0.0/src/qn_util/config_error.py

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+"""
+K.NAKADA, kengo.nakada@gmail.com
+"""
+
+class ConfigError(Exception):
+    """
+    設定ファイルまたは入力構造が不正な場合の例外。
+
+    JSON 設定の必須キー不足、POSCAR の形式不整合、未知の constraint source など、
+    ユーザー入力に起因するエラーをこの例外にまとめる。
+    """

qn_util-0.0.0/src/qn_util/install.py

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+"""qn_util に付属するサンプルスクリプトを作業ディレクトリへ配置する。"""
+
+import argparse
+import shutil
+from importlib.resources import files
+from pathlib import Path
+
+
+def install(force: bool = False, destination: Path | None = None) -> list[Path]:
+    """同梱 scripts の全ファイルを指定先（既定はカレント）へコピーする。"""
+    target = Path.cwd() if destination is None else Path(destination)
+    source = files("qn_util").joinpath("scripts")
+    if not source.is_dir():
+        raise FileNotFoundError("パッケージ内に scripts がありません。配布設定を確認してください。")
+    items = list(source.iterdir())
+    conflicts = [target / item.name for item in items if (target / item.name).exists()]
+    if conflicts and not force:
+        names = ", ".join(str(x) for x in conflicts)
+        raise FileExistsError(f"同名ファイルが存在します: {names}（上書きには --force を指定）")
+    copied = []
+    for item in items:
+        dst = target / item.name
+        if item.is_dir():
+            shutil.copytree(str(item), dst, dirs_exist_ok=force)
+        else:
+            with item.open("rb") as src, dst.open("wb") as out:
+                shutil.copyfileobj(src, out)
+        copied.append(dst)
+    return copied
+
+
+def main() -> None:
+    """qn_util コマンドのエントリーポイント。"""
+    parser = argparse.ArgumentParser(prog="qn_util")
+    sub = parser.add_subparsers(dest="command", required=True)
+    cmd = sub.add_parser("install", help="付属スクリプトをカレントディレクトリへコピー")
+    cmd.add_argument("--force", action="store_true", help="同名ファイルを上書き")
+    args = parser.parse_args()
+    if args.command == "install":
+        try:
+            copied = install(force=args.force)
+        except (FileExistsError, FileNotFoundError) as exc:
+            parser.exit(1, f"エラー: {exc}\n")
+        for path in copied:
+            print(f"コピー: {path}")
+
+
+if __name__ == "__main__":
+    main()