rmc-dft 0.7.1__tar.gz

rmc_dft-0.7.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: rmc_dft
+Version: 0.7.1
+Summary: rmc_dft is a Python package for performing Reverse Monte Carlo modeling and ab initio molecular dynamics / relaxation using VASP code.
+Author: K.Kobayashi, Kengo NAKADA
+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
+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: author
+
+# rmc_vasp
+
+[![en](https://img.shields.io/badge/lang-en-red.svg)](https://github.com/shimane-dev/rmc_vasp/blob/main/README.md)
+[![ja](https://img.shields.io/badge/lang-ja-yellow.svg)](https://github.com/shimane-dev/rmc_vasp/blob/main/README.ja.md)
+
+"rmc_vasp" iteratively performs the ab initio molecular dynamics (MD)/ geometry optimization and the reverse monte carlo
+modeling (RMC).
+It is based on Structure Analysis Environment package (
+https://github.com/shimane-dev/sae.git ).
+
+## Requirements
+
+### VASP
+
+VASP need to be installed.
+(https://www.vasp.at/).
+Tested versions: 6.4.2, 5.3.5.
+
+#### Input files
+
+VASP input files.
+
+### RMC
+
+RMC POT need to be installed.
+(https://www.szfki.hu/~nphys/rmc++/opening.html).
+Tested version: 2023.1.
+
+#### Input files
+
+RMC POT input files especially experimental data.
+(Xray diffraction, Neutron diffraction and so on. )
+
+### Initial structure
+
+Density, number of atoms (system size).
+(Initial structure can be generated using Packmol. (https://m3g.github.io/packmol/). For random structure, set minimal
+interatomic distance to about 2Å, avoiding error.)
+
+## Install
+
+Download https://github.com/shimane-dev/rmc_vasp/ .
+Also, https://github.com/shimane-dev/x_logger .
+Install using pip:
+
+````
+$ pip install x_logger
+$ pip install rmc_vasp
+````
+
+## Using without installation
+
+Download https://github.com/shimane-dev/rmc_vasp/ .
+Also, https://github.com/shimane-dev/x_logger .
+Put "x_logger/" under "rmc_vasp/src/rmc_vasp/"
+
+## How to run
+
+Put input files in a folder (work??) and open python:
+
+````
+$ python3
+````
+
+then,
+
+````
+>>> import rmc_vasp
+````
+
+and,
+
+````
+>>> run()
+````
+
+### Beta version (Middle of August, 2025)
+
+We put input files at "rmc_vasp/src/rmc_vasp/" and run the code as follows:
+
+````
+$ python ./main.py
+````
+
+### Output
+
+The output files are placed in the log0, log1, log2, ... folders.
+The output files include the RMC POT input files, VASP input files, and ...
+aaa.chi : Chi value of RMC modeling. Agreement of S(Q) with experimental data or something else depending on the RMC
+input data.
+grep_E0_OSZICAR.txt : Energy

rmc_dft-0.7.1/README.md

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+# rmc_vasp
+
+[![en](https://img.shields.io/badge/lang-en-red.svg)](https://github.com/shimane-dev/rmc_vasp/blob/main/README.md)
+[![ja](https://img.shields.io/badge/lang-ja-yellow.svg)](https://github.com/shimane-dev/rmc_vasp/blob/main/README.ja.md)
+
+"rmc_vasp" iteratively performs the ab initio molecular dynamics (MD)/ geometry optimization and the reverse monte carlo
+modeling (RMC).
+It is based on Structure Analysis Environment package (
+https://github.com/shimane-dev/sae.git ).
+
+## Requirements
+
+### VASP
+
+VASP need to be installed.
+(https://www.vasp.at/).
+Tested versions: 6.4.2, 5.3.5.
+
+#### Input files
+
+VASP input files.
+
+### RMC
+
+RMC POT need to be installed.
+(https://www.szfki.hu/~nphys/rmc++/opening.html).
+Tested version: 2023.1.
+
+#### Input files
+
+RMC POT input files especially experimental data.
+(Xray diffraction, Neutron diffraction and so on. )
+
+### Initial structure
+
+Density, number of atoms (system size).
+(Initial structure can be generated using Packmol. (https://m3g.github.io/packmol/). For random structure, set minimal
+interatomic distance to about 2Å, avoiding error.)
+
+## Install
+
+Download https://github.com/shimane-dev/rmc_vasp/ .
+Also, https://github.com/shimane-dev/x_logger .
+Install using pip:
+
+````
+$ pip install x_logger
+$ pip install rmc_vasp
+````
+
+## Using without installation
+
+Download https://github.com/shimane-dev/rmc_vasp/ .
+Also, https://github.com/shimane-dev/x_logger .
+Put "x_logger/" under "rmc_vasp/src/rmc_vasp/"
+
+## How to run
+
+Put input files in a folder (work??) and open python:
+
+````
+$ python3
+````
+
+then,
+
+````
+>>> import rmc_vasp
+````
+
+and,
+
+````
+>>> run()
+````
+
+### Beta version (Middle of August, 2025)
+
+We put input files at "rmc_vasp/src/rmc_vasp/" and run the code as follows:
+
+````
+$ python ./main.py
+````
+
+### Output
+
+The output files are placed in the log0, log1, log2, ... folders.
+The output files include the RMC POT input files, VASP input files, and ...
+aaa.chi : Chi value of RMC modeling. Agreement of S(Q) with experimental data or something else depending on the RMC
+input data.
+grep_E0_OSZICAR.txt : Energy

rmc_dft-0.7.1/pyproject.toml

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+[build-system]
+requires = ["setuptools>=71.0", "coloredlogs"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "rmc_dft"
+version = "0.7.1"
+
+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"

rmc_dft-0.7.1/setup.cfg

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

rmc_dft-0.7.1/setup.py

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+#!/usr/bin/env python
+"""
+python 3.6 環境のための setup.py
+"""
+
+__author__ = "K.Kobayashi, Kengo NAKADA"
+__maintainer__ = "Kengo NAKADA"
+__credits__ = ["Kengo NAKADA"]
+__email__ = "kengo.nakada@gmail.com"
+# __email__ = "kengo.nakada@spring8.or.jp"
+# __copyright__ = "Copyright 2014-2018 Kengo NAKADA"
+__license__ = "Apache2"
+__status__ = "alpha"
+
+from setuptools import setup, find_packages
+import glob
+import re
+import os
+import shutil
+
+# --- クリーン処理 ---
+for path in ["build", "dist"]:
+    if os.path.exists(path):
+        shutil.rmtree(path)
+
+for name in os.listdir("."):
+    if name.endswith(".egg-info"):
+        shutil.rmtree(name)
+
+
+# version = __version__
+# from StructureAnalysisEnvironment import __version__
+def read_version_from_toml() -> str:
+    with open("pyproject.toml", encoding="utf-8") as f:
+        for line in f:
+            if line.strip().startswith("version"):
+                m = re.search(r'version\s*=\s*["\']([^"\']+)["\']', line)
+                if m:
+                    return m.group(1)
+    raise RuntimeError("version not found in pyproject.toml")
+
+
+__version__ = read_version_from_toml()
+long_description = "RMC_DFT"
+description = "RMC_DFT"
+
+# パッケージ指定
+# packages = find_packages(exclude=["StructureAnalysisEnvironment.bin"])
+packages = find_packages("src")
+package_dir = {"": "src"}
+
+setup(
+    name="rmc_dft",
+    # packages=find_packages(),
+    packages=packages,
+    package_dir=package_dir,
+    #       package_dir  = {'':'StructureAnalysisEnvironment'},
+    #       include_package_data=True,
+    #       package_data = { '': ['LICENSE.txt', 'README.md']},
+    # package_data=package_data,
+    # data_files=[(package_src_dir, files)],
+    # scripts=__script__,
+    version=__version__,
+    description=description,
+    long_description=long_description,
+    author=__author__,
+    #       author_email = ['kengo.nakada@gmail.com','kengo.nakada@spring8.or.jp'],
+    #       author_email = 'kengo.nakada@gmail.com',
+    # author_email='kengo.nakada@spring8.or.jp',
+    author_email=__email__,
+    license=__license__,
+    # python 3.11 などと違う環境にする
+    install_requires=[
+        "dataclasses",
+        "coloredlogs",
+        "colorlog",
+        # python 3.6 だと test を入れない
+        "pytest; python_version > '3.7'",
+        "pytest-asyncio; python_version > '3.7'",
+        "pyyaml",
+        "toml",
+        # "grpcio",
+        "nest_asyncio",
+        # わざわざ python 3.6 環境(setup.py)だと入れない
+        "sphinx; python_version > '3.7'",
+        "myst-parser; python_version > '3.7'",
+        "sphinx-autobuild; python_version > '3.7'",
+        "sphinx-rtd-theme; python_version > '3.7'",
+        "sphinxcontrib-napoleon; python_version > '3.7'",
+        "linkify-it-py; python_version > '3.7'",  # for sphinx
+    ],
+    #
+    #       platforms = ['linux','OSX','Window'],
+    #       classifiers = [
+    #           'Programming Language :: Python :: 2.7',
+    #           'Intended Audience :: Science/Research',
+    #           'License :: OSI Approved :: MIT License'
+    #           ]
+)

rmc_dft-0.7.1/src/rmc_dft/__init__.py

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+"""
+K.NAKADA, kengo.nakada@gmail.com
+"""
+
+from rmc_dft.rmc_dft import RmcDft
+
+from rmc_dft.vasp.vasp import Vasp
+from rmc_dft.vasp.vasp_log import VaspLog
+from rmc_dft.vasp.vasp_incar import VaspIncar
+from rmc_dft.vasp.vasp_kpoints import VaspKpoints
+from rmc_dft.vasp.vasp_potcar import VaspPotcarBuilder
+from rmc_dft.vasp.vasp_outcar import VaspOutcar
+
+from rmc_dft.vasp.vasp_poscar import VaspPoscar
+from rmc_dft.vasp.vasp_poscar_analyzer import VaspPoscarAnalyzer
+
+from rmc_dft.rmc_pot.rmc_pot import RmcPot
+from rmc_dft.rmc_pot.rmc_pot_log import RmcPotLog
+from rmc_dft.rmc_pot.rmc_pot_dat import RmcPotDat
+from rmc_dft.rmc_pot.rmc_pot_fit import RmcPotFit
+from rmc_dft.rmc_pot.rmc_pot_hst import RmcPotHst
+from rmc_dft.rmc_pot.rmc_pot_ppcf import RmcPotPpcf
+
+# from rmc_dft.packmol.packmol import Packmol
+# from rmc_dft.packmol.packmol_inp import PackmolInp
+
+from rmc_dft.config import Config
+
+from rmc_dft.util import poscar2cfg
+from rmc_dft.util import ensure_vasp5_format
+from rmc_dft.util import check_rmc_and_vasp
+from rmc_dft.util import find_next_log_index
+from rmc_dft.util import next_log_dir_name
+from rmc_dft.util import logs_exist
+
+
+# from .vasp.vasp import Vasp
+# from .vasp.collect_result import VaspLog
+# from .rmc.rmc_pot import RmcPot
+# from .rmc.collect_result import RmcPotLog

rmc_dft-0.7.1/src/rmc_dft/config.py

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+"""
+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:
+    max_rmc_dft_loop: int = 10
+
+    N_tot: int = 400  # セルサイズ(原子数)
+    # mass_density_g_cm3: float = 7.35  # 質量密度
+    mass_density_g_cm3: float = 7.3336  # 質量密度
+    # number_density_A3: float = 0.0915 # 数密度
+    number_density_A3: float = 0.09119  # 数密度
+    # element_info: Union[str, Sequence[str]] = "label.txt"
+    element_info: Union[str, Sequence[str]] = ["Fe", "Si", "B"]
+    # ratios: Sequence[int] = [80, 9, 11]
+    ratios: Sequence[int] = [82, 4, 14]
+
+    # RMC parameter mirror
+    rmc_comment: Optional[str] = None
+    rmc_cutoffs: Optional[Sequence[float]] = None
+    rmc_max_moves: Optional[Sequence[float]] = None
+    rmc_r_spacing: Optional[float] = None
+    rmc_moveout_option: Optional[bool] = None
+    rmc_time_and_save: Optional[Tuple[float, int]] = None
+    rmc_data_flags: Optional[Sequence[int]] = None
+    rmc_exp_range: Optional[Tuple[int, int]] = None
+    rmc_sigma_factor: Optional[float] = None
+    rmc_num_atoms_per_move: Optional[int] = None
+
+    # 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
+
+    # ---------- RMC -----------
+    rmc_code: str = "RmcPot"
+    rmc_log_dir: str = "rmc_log"
+    cfg_name: str = "aaa"  # aaa.cfg
+    rmc_exp_filename: str = "ascast.xsq"
+
+    # ------- DFT (VASP) --------
+    dft_code: str = "Vasp"
+    dft_log_dir: str = "vasp_log"
+    vasp_name: str = "aaa"  # aaa.vasp
+    run_mode: str = "local"
+
+    #
+    # RMCPOT path
+    #
+    # rmc_bin = "/home/k/Downloads/Source_RMC_POT_lin_2023.1/rmcp.exe"
+    # rmc_bin = "/usr/local/src/RMCPOT/rmcp.exe"
+    rmc_bin: str = "rmcp.exe"
+
+    #
+    # 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"
+
+    rmc_omp_num_threads: Optional[int] = None
+    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))