vasp-util 0.0.0__tar.gz

vasp_util-0.0.0/LICENSE

@@ -0,0 +1,201 @@
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+   1. Definitions.
+
+      "License" shall mean the terms and conditions for use, reproduction,
+      and distribution as defined by Sections 1 through 9 of this document.
+
+      "Licensor" shall mean the copyright owner or entity authorized by
+      the copyright owner that is granting the License.
+
+      "Legal Entity" shall mean the union of the acting entity and all
+      other entities that control, are controlled by, or are under common
+      control with that entity. For the purposes of this definition,
+      "control" means (i) the power, direct or indirect, to cause the
+      direction or management of such entity, whether by contract or
+      otherwise, or (ii) ownership of fifty percent (50%) or more of the
+      outstanding shares, or (iii) beneficial ownership of such entity.
+
+      "You" (or "Your") shall mean an individual or Legal Entity
+      exercising permissions granted by this License.
+
+      "Source" form shall mean the preferred form for making modifications,
+      including but not limited to software source code, documentation
+      source, and configuration files.
+
+      "Object" form shall mean any form resulting from mechanical
+      transformation or translation of a Source form, including but
+      not limited to compiled object code, generated documentation,
+      and conversions to other media types.
+
+      "Work" shall mean the work of authorship, whether in Source or
+      Object form, made available under the License, as indicated by a
+      copyright notice that is included in or attached to the work
+      (an example is provided in the Appendix below).
+
+      "Derivative Works" shall mean any work, whether in Source or Object
+      form, that is based on (or derived from) the Work and for which the
+      editorial revisions, annotations, elaborations, or other modifications
+      represent, as a whole, an original work of authorship. For the purposes
+      of this License, Derivative Works shall not include works that remain
+      separable from, or merely link (or bind by name) to the interfaces of,
+      the Work and Derivative Works thereof.
+
+      "Contribution" shall mean any work of authorship, including
+      the original version of the Work and any modifications or additions
+      to that Work or Derivative Works thereof, that is intentionally
+      submitted to Licensor for inclusion in the Work by the copyright owner
+      or by an individual or Legal Entity authorized to submit on behalf of
+      the copyright owner. For the purposes of this definition, "submitted"
+      means any form of electronic, verbal, or written communication sent
+      to the Licensor or its representatives, including but not limited to
+      communication on electronic mailing lists, source code control systems,
+      and issue tracking systems that are managed by, or on behalf of, the
+      Licensor for the purpose of discussing and improving the Work, but
+      excluding communication that is conspicuously marked or otherwise
+      designated in writing by the copyright owner as "Not a Contribution."
+
+      "Contributor" shall mean Licensor and any individual or Legal Entity
+      on behalf of whom a Contribution has been received by Licensor and
+      subsequently incorporated within the Work.
+
+   2. Grant of Copyright License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      copyright license to reproduce, prepare Derivative Works of,
+      publicly display, publicly perform, sublicense, and distribute the
+      Work and such Derivative Works in Source or Object form.
+
+   3. Grant of Patent License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      (except as stated in this section) patent license to make, have made,
+      use, offer to sell, sell, import, and otherwise transfer the Work,
+      where such license applies only to those patent claims licensable
+      by such Contributor that are necessarily infringed by their
+      Contribution(s) alone or by combination of their Contribution(s)
+      with the Work to which such Contribution(s) was submitted. If You
+      institute patent litigation against any entity (including a
+      cross-claim or counterclaim in a lawsuit) alleging that the Work
+      or a Contribution incorporated within the Work constitutes direct
+      or contributory patent infringement, then any patent licenses
+      granted to You under this License for that Work shall terminate
+      as of the date such litigation is filed.
+
+   4. Redistribution. You may reproduce and distribute copies of the
+      Work or Derivative Works thereof in any medium, with or without
+      modifications, and in Source or Object form, provided that You
+      meet the following conditions:
+
+      (a) You must give any other recipients of the Work or
+          Derivative Works a copy of this License; and
+
+      (b) You must cause any modified files to carry prominent notices
+          stating that You changed the files; and
+
+      (c) You must retain, in the Source form of any Derivative Works
+          that You distribute, all copyright, patent, trademark, and
+          attribution notices from the Source form of the Work,
+          excluding those notices that do not pertain to any part of
+          the Derivative Works; and
+
+      (d) If the Work includes a "NOTICE" text file as part of its
+          distribution, then any Derivative Works that You distribute must
+          include a readable copy of the attribution notices contained
+          within such NOTICE file, excluding those notices that do not
+          pertain to any part of the Derivative Works, in at least one
+          of the following places: within a NOTICE text file distributed
+          as part of the Derivative Works; within the Source form or
+          documentation, if provided along with the Derivative Works; or,
+          within a display generated by the Derivative Works, if and
+          wherever such third-party notices normally appear. The contents
+          of the NOTICE file are for informational purposes only and
+          do not modify the License. You may add Your own attribution
+          notices within Derivative Works that You distribute, alongside
+          or as an addendum to the NOTICE text from the Work, provided
+          that such additional attribution notices cannot be construed
+          as modifying the License.
+
+      You may add Your own copyright statement to Your modifications and
+      may provide additional or different license terms and conditions
+      for use, reproduction, or distribution of Your modifications, or
+      for any such Derivative Works as a whole, provided Your use,
+      reproduction, and distribution of the Work otherwise complies with
+      the conditions stated in this License.
+
+   5. Submission of Contributions. Unless You explicitly state otherwise,
+      any Contribution intentionally submitted for inclusion in the Work
+      by You to the Licensor shall be under the terms and conditions of
+      this License, without any additional terms or conditions.
+      Notwithstanding the above, nothing herein shall supersede or modify
+      the terms of any separate license agreement you may have executed
+      with Licensor regarding such Contributions.
+
+   6. Trademarks. This License does not grant permission to use the trade
+      names, trademarks, service marks, or product names of the Licensor,
+      except as required for reasonable and customary use in describing the
+      origin of the Work and reproducing the content of the NOTICE file.
+
+   7. Disclaimer of Warranty. Unless required by applicable law or
+      agreed to in writing, Licensor provides the Work (and each
+      Contributor provides its Contributions) on an "AS IS" BASIS,
+      WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+      implied, including, without limitation, any warranties or conditions
+      of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+      PARTICULAR PURPOSE. You are solely responsible for determining the
+      appropriateness of using or redistributing the Work and assume any
+      risks associated with Your exercise of permissions under this License.
+
+   8. Limitation of Liability. In no event and under no legal theory,
+      whether in tort (including negligence), contract, or otherwise,
+      unless required by applicable law (such as deliberate and grossly
+      negligent acts) or agreed to in writing, shall any Contributor be
+      liable to You for damages, including any direct, indirect, special,
+      incidental, or consequential damages of any character arising as a
+      result of this License or out of the use or inability to use the
+      Work (including but not limited to damages for loss of goodwill,
+      work stoppage, computer failure or malfunction, or any and all
+      other commercial damages or losses), even if such Contributor
+      has been advised of the possibility of such damages.
+
+   9. Accepting Warranty or Additional Liability. While redistributing
+      the Work or Derivative Works thereof, You may choose to offer,
+      and charge a fee for, acceptance of support, warranty, indemnity,
+      or other liability obligations and/or rights consistent with this
+      License. However, in accepting such obligations, You may act only
+      on Your own behalf and on Your sole responsibility, not on behalf
+      of any other Contributor, and only if You agree to indemnify,
+      defend, and hold each Contributor harmless for any liability
+      incurred by, or claims asserted against, such Contributor by reason
+      of your accepting any such warranty or additional liability.
+
+   END OF TERMS AND CONDITIONS
+
+   APPENDIX: How to apply the Apache License to your work.
+
+      To apply the Apache License to your work, attach the following
+      boilerplate notice, with the fields enclosed by brackets "[]"
+      replaced with your own identifying information. (Don't include
+      the brackets!)  The text should be enclosed in the appropriate
+      comment syntax for the file format. We also recommend that a
+      file or class name and description of purpose be included on the
+      same "printed page" as the copyright notice for easier
+      identification within third-party archives.
+
+   Copyright [yyyy] [name of copyright owner]
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.

vasp_util-0.0.0/PKG-INFO

@@ -0,0 +1,56 @@
+Metadata-Version: 2.4
+Name: vasp-util
+Version: 0.0.0
+Summary: rmc_dft is a Python package for performing Reverse Monte Carlo modeling and ab initio molecular dynamics / relaxation using VASP code.
+Author-email: Kengo NAKADA <kengo.nakada@email.com>, Kentaro Kobayashi <kobayashi@mat.shimane-u.ac.jp>
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: xlogger-py
+Requires-Dist: packmol-util
+Requires-Dist: rmc-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
+Dynamic: license-file
+
+# vasp_util
+
+[![en](https://img.shields.io/badge/lang-en-red.svg)](https://github.com/ohara-lab-su/vasp_util/blob/main/README.md)
+[![ja](https://img.shields.io/badge/lang-ja-yellow.svg)](https://github.com/ohara-lab-su/vasp_util/blob/main/README.ja.md)
+
+Yet another tool for making VASP easier to use, among the countless tools already out there.
+
+This library was originally part of the [RMC-DFT](https://github.com/ohara-lab-su/rmc_dft/) package. It brings together VASP-related utilities that were used internally there and makes them available as a standalone library.
+
+In many cases, pymatgen or ASE may be more convenient. Still, there are plenty of situations where having my own tools works better for me, so here I am, building another one.
+
+## Background
+
+Around 2010–2015, I developed [sae](https://github.com/ohara-lab-su/sae), a fairly comprehensive collection of tools for crystal structures, including VASP-related functionality. Much of the VASP know-how I accumulated back then forms the basis of my current tools.
+
+However, as I kept adding features, sae grew rather large. Combined with my limited understanding of Python at the time, this led to various design problems.
+
+Meanwhile, pymatgen and ASE had become remarkably useful. As a result, sae gradually lost much of its reason for existing and ended up sitting on the shelf for years.
+
+Even so, whenever I developed new tools involving VASP, I often found myself wishing I had something like sae—especially when I simply wanted to manipulate structures described in POSCAR files.
+
+I worked around this by implementing similar functionality separately in each tool, but that eventually left me with nearly identical code scattered across multiple projects.
+
+Redesigning sae from scratch would have been a substantial undertaking. Instead, I started small, creating a minimal set of classes for handling VASP-related operations within RMC-DFT.
+
+Those classes have now been extracted into a standalone package, `vasp_util`, so they can be reused more easily in other projects.
+
+In the end, this may look much like other libraries already available. Nevertheless, I hope to gradually consolidate the functionality I have repeatedly implemented across my various tools into this package.

vasp_util-0.0.0/README.md

@@ -0,0 +1,28 @@
+# vasp_util
+
+[![en](https://img.shields.io/badge/lang-en-red.svg)](https://github.com/ohara-lab-su/vasp_util/blob/main/README.md)
+[![ja](https://img.shields.io/badge/lang-ja-yellow.svg)](https://github.com/ohara-lab-su/vasp_util/blob/main/README.ja.md)
+
+Yet another tool for making VASP easier to use, among the countless tools already out there.
+
+This library was originally part of the [RMC-DFT](https://github.com/ohara-lab-su/rmc_dft/) package. It brings together VASP-related utilities that were used internally there and makes them available as a standalone library.
+
+In many cases, pymatgen or ASE may be more convenient. Still, there are plenty of situations where having my own tools works better for me, so here I am, building another one.
+
+## Background
+
+Around 2010–2015, I developed [sae](https://github.com/ohara-lab-su/sae), a fairly comprehensive collection of tools for crystal structures, including VASP-related functionality. Much of the VASP know-how I accumulated back then forms the basis of my current tools.
+
+However, as I kept adding features, sae grew rather large. Combined with my limited understanding of Python at the time, this led to various design problems.
+
+Meanwhile, pymatgen and ASE had become remarkably useful. As a result, sae gradually lost much of its reason for existing and ended up sitting on the shelf for years.
+
+Even so, whenever I developed new tools involving VASP, I often found myself wishing I had something like sae—especially when I simply wanted to manipulate structures described in POSCAR files.
+
+I worked around this by implementing similar functionality separately in each tool, but that eventually left me with nearly identical code scattered across multiple projects.
+
+Redesigning sae from scratch would have been a substantial undertaking. Instead, I started small, creating a minimal set of classes for handling VASP-related operations within RMC-DFT.
+
+Those classes have now been extracted into a standalone package, `vasp_util`, so they can be reused more easily in other projects.
+
+In the end, this may look much like other libraries already available. Nevertheless, I hope to gradually consolidate the functionality I have repeatedly implemented across my various tools into this package.

vasp_util-0.0.0/pyproject.toml

@@ -0,0 +1,54 @@
+[build-system]
+requires = ["setuptools>=71.0", "coloredlogs"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "vasp-util"
+version = "0.0.0"
+
+description = "rmc_dft is a Python package for performing Reverse Monte Carlo modeling and ab initio molecular dynamics / relaxation using VASP code."
+authors = [
+    { name = "Kengo NAKADA", email = "kengo.nakada@email.com" },
+    { name = "Kentaro Kobayashi", email = "kobayashi@mat.shimane-u.ac.jp" }
+]
+readme = "README.md"
+# requires-python = ">=3.8"
+requires-python = ">=3.10"
+dependencies = [
+    # my-modules
+    #"x_logger",
+    "xlogger-py",
+    "packmol-util",
+    "rmc-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"

vasp_util-0.0.0/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

vasp_util-0.0.0/src/vasp_util/__init__.py

@@ -0,0 +1,17 @@
+"""
+K.NAKADA, kengo.nakada@gmail.com
+"""
+
+from vasp_util.vasp import Vasp
+from vasp_util.vasp_incar import VaspIncar
+from vasp_util.vasp_kpoints import VaspKpoints
+from vasp_util.vasp_potcar import VaspPotcarBuilder
+from vasp_util.vasp_log import VaspLog
+from vasp_util.vasp_outcar import VaspOutcar
+
+from vasp_util.vasp_poscar import VaspPoscar
+from vasp_util.vasp_poscar_analyzer import VaspPoscarAnalyzer
+
+# from .vasp import Vasp
+# from .collect_result import VaspLog
+# from . import util

vasp_util-0.0.0/src/vasp_util/config.py

@@ -0,0 +1,102 @@
+"""
+K.NAKADA, kengo.nakada@gmail.com (1st, 3rd varsion)
+K.KOBAYASHI (2nd version)
+"""
+
+from typing import Any, Dict, List, Optional, Union, Tuple, Callable, Sequence
+import yaml
+import os
+
+from x_logger import XLogger
+
+
+class Config:
+
+    # VASP parameter mirror
+    vasp_incar_tags: Dict[str, Any] = {}
+    vasp_kpoints_mode: Optional[str] = None
+    vasp_kpoints_grid: Optional[Tuple[int, int, int]] = None
+    vasp_kpoints_shift: Optional[Tuple[int, int, int]] = None
+    vasp_kpoints_comment: Optional[str] = None
+
+    # ------- DFT (VASP) --------
+    dft_code: str = "Vasp"
+    dft_log_dir: str = "vasp_log"
+    vasp_name: str = "aaa"  # aaa.vasp
+    run_mode: str = "local"
+
+    #
+    # VASP  path
+    #
+    # dft_bin = f"/home/hpc/vasp/bin/vasp-gamma"
+    # dft_bin = f"/home/k/Downloads/vasp.6.4.2/bin/vasp_gam"
+    # dft_bin = "/home/hpc/vasp/bin/vasp"
+    dft_bin: Optional[str] = f"vasp_gam"
+
+    num_procs: Optional[int] = 1
+
+    mpi_cmd: Optional[str] = "mpirun"
+    # mpi = f"mpirun -np {num_procs} {os.path.expanduser('/home/hpc/vasp/bin/vasp')}"
+
+    mpi_flag: Optional[str] = "-np"
+
+    dft_omp_num_threads: Optional[int] = None
+
+    # default job_name
+    job_cmd: Optional[str] = "qsub job_hpcs2024_node2.sh"
+
+    # 自動セーブ
+    auto_write: bool = True
+
+    def __init__(
+        self,
+        yaml_path: Optional[str] = None,
+        *,
+        logger: Optional[XLogger] = XLogger(),
+    ):
+        """
+
+        Args:
+            yaml_path (str):
+            logger (XLogger):
+        """
+        self._logger = logger
+
+        # インスタンスで使いたいときだけ、ここで個別設定
+        if yaml_path:
+            self._load_yaml(yaml_path)
+
+    @classmethod
+    def load_yaml(cls, yaml_path=None):
+        if yaml_path is None:
+            yaml_path = os.environ.get("RMC_DFT_CONFIG_YAML")
+            if yaml_path is None:
+                return
+        # with open(yaml_path, "r") as f:
+        with open(yaml_path, "r", encoding="utf-8") as f:
+            data = yaml.safe_load(f)
+        for k, v in data.items():
+            if hasattr(cls, k):
+                setattr(cls, k, v)
+            else:
+                print("NO SUCH VAR:", k)
+
+    def _load_yaml(self, yaml_path=None):
+        # インスタンス用：インスタンスdictにのみ上書き
+        self._logger.info(f"load_yaml: {yaml_path}")
+        if yaml_path is None:
+            yaml_path = os.environ.get("RMC_DFT_CONFIG_YAML")
+            if yaml_path is None:
+                return
+        yaml_path = os.path.abspath(yaml_path)
+        self._logger.info(f"abspath: {yaml_path}")
+        with open(yaml_path, "r") as f:
+            data = yaml.safe_load(f)
+        for k, v in data.items():
+            setattr(self, k, v)
+
+
+if __name__ == "__main__":
+    config = Config("config.yml")
+    print(config.num_procs)
+    print(type(config.num_procs))

vasp_util-0.0.0/src/vasp_util/util/__init__.py

@@ -0,0 +1,22 @@
+from rmc_dft.vasp.util.poscar2cfg import (
+    vasp2cfg,
+    poscar2cfg,
+    contcar2cfg,
+    convert_to_cfg,
+)
+
+from rmc_dft.vasp.util.cell_geometry import (
+    _lattice,
+    cell_volume,
+    cartesian_to_direct,
+    wrap_direct,
+    wrap_cartesian,
+    minimum_image_vector,
+    periodic_distance,
+)
+
+from rmc_dft.vasp.util.copy_contcar_to_vasp import copy_contcar_to_vasp
+from rmc_dft.vasp.util.copy_vasp_to_poscar import copy_vasp_to_poscar
+from rmc_dft.vasp.util.ensure_vasp5_format import ensure_vasp5_format
+from rmc_dft.vasp.util.xdatcar2poscar import xdatcar2poscar
+from rmc_dft.vasp.util.make_potcar import VaspPotcarBuilder

vasp_util-0.0.0/src/vasp_util/util/cell_geometry.py

@@ -0,0 +1,130 @@
+"""周期結晶セルの汎用幾何操作。格子ベクトルは3x3行列の行に格納する。
+
+POSCARの読み込みは既存の rmc_dft.vasp.vasp_poscar.VaspPoscar を使用する。
+本モジュールはファイル入出力やRMC/ænet固有の構造生成を行わない。
+最短画像は整数格子シフトを列挙して直交座標ノルムで判定する。
+"""
+
+from itertools import product
+from typing import List, Dict, Optional, Tuple
+import numpy as np
+
+
+def _lattice(
+    cell: np.ndarray,
+) -> np.ndarray:
+    """格子行列を検査し、float64の3x3行列として返す。"""
+    lattice = np.asarray(cell, dtype=float)
+    if lattice.shape != (3, 3):
+        raise ValueError("cell must be a 3x3 matrix")
+    if abs(float(np.linalg.det(lattice))) < 1.0e-12:
+        raise ValueError("cell is singular")
+    return lattice
+
+
+def cell_volume(
+    cell: np.ndarray,
+) -> float:
+    """周期セルの体積を返す（格子がÅならų）。"""
+    return abs(float(np.linalg.det(_lattice(cell))))
+
+
+def direct_to_cartesian(
+    coords: np.ndarray,
+    cell: np.ndarray,
+) -> np.ndarray:
+    """分率座標 (...,3) を直交座標へ変換する。"""
+    return np.asarray(coords, dtype=float) @ _lattice(cell)
+
+
+def cartesian_to_direct(
+    coords: np.ndarray,
+    cell: np.ndarray,
+) -> np.ndarray:
+    """直交座標 (...,3) を分率座標へ変換する。"""
+    return np.asarray(coords, dtype=float) @ np.linalg.inv(_lattice(cell))
+
+
+def wrap_direct(
+    coords: np.ndarray,
+) -> np.ndarray:
+    """分率座標を [0,1) に折り返す。入力は変更しない。"""
+    return np.mod(np.asarray(coords, dtype=float), 1.0)
+
+
+def wrap_cartesian(
+    coords: np.ndarray,
+    cell: np.ndarray,
+) -> np.ndarray:
+    """直交座標を周期セル内に折り返す。"""
+    return direct_to_cartesian(wrap_direct(cartesian_to_direct(coords, cell)), cell)
+
+
+def minimum_image_vector(
+    a: np.ndarray,
+    b: np.ndarray,
+    cell: np.ndarray,
+    search_radius: int = 1,
+) -> np.ndarray:
+    """aからbへの最短周期変位（直交座標、Å）を返す。
+
+    分率差を最近整数で中心化した後、[-search_radius,+search_radius]^3
+    の画像を探索する。強く歪んだセルでは探索範囲の拡大が必要。
+    """
+    if search_radius < 0:
+        raise ValueError("search_radius must be nonnegative")
+    lattice = _lattice(cell)
+    delta = cartesian_to_direct(
+        np.asarray(b, dtype=float) - np.asarray(a, dtype=float), lattice
+    )
+    if delta.shape != (3,):
+        raise ValueError("a and b must be 3-vectors")
+    delta = delta - np.round(delta)
+    best = None
+    best_squared = float("inf")
+    for shift in product(range(-search_radius, search_radius + 1), repeat=3):
+        vec = (delta + np.asarray(shift, dtype=float)) @ lattice
+        squared = float(vec @ vec)
+        if squared < best_squared:
+            best = vec
+            best_squared = squared
+    if best is None:
+        raise RuntimeError("周期画像の探索に失敗しました")
+    return best
+
+
+def periodic_distance(
+    a: np.ndarray,
+    b: np.ndarray,
+    cell: np.ndarray,
+    search_radius: int = 1,
+) -> float:
+    """2点の周期最短距離（Å）。"""
+    return float(np.linalg.norm(minimum_image_vector(a, b, cell, search_radius)))
+
+
+def check_pair_distances(
+    symbols: List[str],
+    positions: np.ndarray,
+    cell: np.ndarray,
+    minimums: Dict[str, float],
+    fallback: Optional[float] = None,
+) -> Tuple[bool, float]:
+    """周期距離に基づき、全原子対の下限距離を検証する。"""
+    shortest = float("inf")
+    for i in range(len(symbols)):
+        for j in range(i + 1, len(symbols)):
+            key = "-".join(sorted((symbols[i], symbols[j])))
+            if key in minimums:
+                threshold = minimums[key]
+            elif fallback is not None:
+                threshold = fallback
+            else:
+                raise ValueError(f"距離閾値が未設定です: {key}")
+            distance = periodic_distance(positions[i], positions[j], cell)
+            shortest = min(shortest, distance)
+            if not np.isfinite(distance):
+                return False, shortest
+            if distance < threshold:
+                return False, shortest
+    return True, shortest

vasp_util-0.0.0/src/vasp_util/util/copy_contcar_to_vasp.py

@@ -0,0 +1,37 @@
+#!/usr/bin/env python
+"""
+K.NAKADA, kengo.nakada@gmail.com
+"""
+
+from typing import Any, Dict, List, Optional, Union, Tuple, Callable, Sequence
+
+import shutil
+from pathlib import Path
+from x_logger import XLogger
+
+
+def copy_contcar_to_vasp(
+    vasp_name: str,
+    logger: Optional[XLogger] = XLogger(),
+) -> bool:
+    """
+    CONTCAR ファイルを {name}.vasp にコピーする
+
+    Args:
+        vasp_name (str): 出力ファイル名（拡張子なし）
+        logger (XLogger):
+
+    Returns:
+        bool:
+
+    """
+    src = Path("CONTCAR")
+    dst = Path(f"{vasp_name}.vasp")
+
+    if not src.exists():
+        logger.error("Error: CONTCAR ファイルが見つかりません。")
+        return False
+
+    shutil.copyfile(src, dst)
+    logger.info(f"{src} --> {dst} にコピーしました")
+    return True