vaspparser 0.0.1__tar.gz

vaspparser-0.0.1/LICENSE

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+BSD 3-Clause License
+
+Copyright (c) 2021, Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name of the copyright holder nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

vaspparser-0.0.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: vaspparser
+Version: 0.0.1
+Summary: Parser for the Vienna Ab initio Simulation Package (VASP)
+Project-URL: Homepage, https://pyiron.org
+Project-URL: Documentation, https://vaspparser.readthedocs.io
+Project-URL: Repository, https://github.com/pyiron/vaspparser
+Author-email: Jan Janssen <janssen@mpie.de>
+License: BSD 3-Clause License
+        
+        Copyright (c) 2021, Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department
+        All rights reserved.
+        
+        Redistribution and use in source and binary forms, with or without
+        modification, are permitted provided that the following conditions are met:
+        
+        * Redistributions of source code must retain the above copyright notice, this
+          list of conditions and the following disclaimer.
+        
+        * Redistributions in binary form must reproduce the above copyright notice,
+          this list of conditions and the following disclaimer in the documentation
+          and/or other materials provided with the distribution.
+        
+        * Neither the name of the copyright holder nor the names of its
+          contributors may be used to endorse or promote products derived from
+          this software without specific prior written permission.
+        
+        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+        IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+        FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+        DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+        SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+        CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+        OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+        OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+License-File: LICENSE
+Keywords: pyiron
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Scientific/Engineering :: Physics
+Requires-Python: <3.15,>=3.9
+Requires-Dist: ase<=3.27.0,>=3.23.0
+Requires-Dist: defusedxml<=0.7.1,>=0.7.0
+Requires-Dist: numpy<=2.4.2,>=1.26.0
+Requires-Dist: pandas<=3.0.0,>=2.0.3
+Requires-Dist: scipy<=1.17.0,>=1.11.1
+Provides-Extra: plot
+Requires-Dist: matplotlib==3.10.8; extra == 'plot'
+Description-Content-Type: text/markdown
+
+# vaspparser
+
+[![Pipeline](https://github.com/pyiron/vaspparser/actions/workflows/pipeline.yml/badge.svg)](https://github.com/pyiron/vaspparser/actions/workflows/pipeline.yml)
+[![codecov](https://codecov.io/gh/pyiron/vaspparser/graph/badge.svg?token=PWWLjnbDJz)](https://codecov.io/gh/pyiron/vaspparser)
+
+Parser for the Vienna Ab initio Simulation Package (VASP)
+
+## Installation 
+Via pip
+```
+pip install vaspparser
+```
+
+Via conda
+```
+conda install -c conda-forge vaspparser
+```
+
+## Usage
+Parse an directory with VASP output files 
+```python
+from vaspparser.vasp.output import parse_vasp_output
+
+output_dict = parse_vasp_output(working_directory="path/to/calculation")
+```

vaspparser-0.0.1/README.md

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+# vaspparser
+
+[![Pipeline](https://github.com/pyiron/vaspparser/actions/workflows/pipeline.yml/badge.svg)](https://github.com/pyiron/vaspparser/actions/workflows/pipeline.yml)
+[![codecov](https://codecov.io/gh/pyiron/vaspparser/graph/badge.svg?token=PWWLjnbDJz)](https://codecov.io/gh/pyiron/vaspparser)
+
+Parser for the Vienna Ab initio Simulation Package (VASP)
+
+## Installation 
+Via pip
+```
+pip install vaspparser
+```
+
+Via conda
+```
+conda install -c conda-forge vaspparser
+```
+
+## Usage
+Parse an directory with VASP output files 
+```python
+from vaspparser.vasp.output import parse_vasp_output
+
+output_dict = parse_vasp_output(working_directory="path/to/calculation")
+```

vaspparser-0.0.1/pyproject.toml

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+[build-system]
+requires = ["ase", "defusedxml", "matplotlib", "numpy", "pandas", "scipy", "hatchling==1.28.0", "hatch-vcs==0.5.0"]
+build-backend = "hatchling.build"
+
+[project]
+name = "vaspparser"
+description = "Parser for the Vienna Ab initio Simulation Package (VASP)"
+authors = [
+    { name = "Jan Janssen", email = "janssen@mpie.de" },
+]
+readme = "README.md"
+license = { file = "LICENSE" }
+keywords = ["pyiron"]
+requires-python = ">=3.9, <3.15"
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Topic :: Scientific/Engineering :: Physics",
+    "License :: OSI Approved :: BSD License",
+    "Intended Audience :: Science/Research",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
+]
+dependencies = [
+    "ase>=3.23.0,<=3.27.0",
+    "defusedxml>=0.7.0,<=0.7.1",
+    "numpy>=1.26.0,<=2.4.2",
+    "pandas>=2.0.3,<=3.0.0",
+    "scipy>=1.11.1,<=1.17.0",
+]
+dynamic = ["version"]
+
+[project.urls]
+Homepage = "https://pyiron.org"
+Documentation = "https://vaspparser.readthedocs.io"
+Repository = "https://github.com/pyiron/vaspparser"
+
+[project.optional-dependencies]
+plot = [
+    "matplotlib==3.10.8"
+]
+
+[tool.hatch.build]
+include = [
+    "src/vaspparser"
+]
+
+[tool.hatch.build.hooks.vcs]
+version-file = "src/vaspparser/_version.py"
+
+[tool.hatch.build.targets.sdist]
+include = [
+    "src/vaspparser"
+]
+
+[tool.hatch.build.targets.wheel]
+packages = [
+    "src/vaspparser"
+]
+
+[tool.hatch.version]
+source = "vcs"
+path = "src/vaspparser/_version.py"
+
+[tool.coverage.run]
+source = ["vaspparser"]
+command_line = "-m unittest discover tests"

vaspparser-0.0.1/src/vaspparser/__init__.py

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+import vaspparser._version
+
+__version__ = vaspparser._version.__version__

vaspparser-0.0.1/src/vaspparser/_version.py

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+# file generated by setuptools-scm
+# don't change, don't track in version control
+
+__all__ = [
+    "__version__",
+    "__version_tuple__",
+    "version",
+    "version_tuple",
+    "__commit_id__",
+    "commit_id",
+]
+
+TYPE_CHECKING = False
+if TYPE_CHECKING:
+    from typing import Tuple
+    from typing import Union
+
+    VERSION_TUPLE = Tuple[Union[int, str], ...]
+    COMMIT_ID = Union[str, None]
+else:
+    VERSION_TUPLE = object
+    COMMIT_ID = object
+
+version: str
+__version__: str
+__version_tuple__: VERSION_TUPLE
+version_tuple: VERSION_TUPLE
+commit_id: COMMIT_ID
+__commit_id__: COMMIT_ID
+
+__version__ = version = '0.0.1'
+__version_tuple__ = version_tuple = (0, 0, 1)
+
+__commit_id__ = commit_id = None

vaspparser-0.0.1/src/vaspparser/dft/bader.py

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+# coding: utf-8
+# Copyright (c) Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department
+# Distributed under the terms of "New BSD License", see the LICENSE file.
+
+import os
+import subprocess
+
+import numpy as np
+
+from vaspparser.vasp.volumetric_data import VaspVolumetricData
+
+__author__ = "Sudarsan Surendralal"
+__copyright__ = (
+    "Copyright 2021, Max-Planck-Institut für Eisenforschung GmbH - "
+    "Computational Materials Design (CM) Department"
+)
+__version__ = "1.0"
+__maintainer__ = "Sudarsan Surendralal"
+__email__ = "surendralal@mpie.de"
+__status__ = "production"
+__date__ = "May 1, 2021"
+
+
+class Bader:
+    """
+    Module to apply the Bader charge partitioning scheme to finished DFT jobs. This module is interfaced with the
+    `Bader code`_ from the Greame Henkelmann group.
+
+    .. _Bader code: http://theory.cm.utexas.edu/henkelman/code/bader
+    """
+
+    def __init__(self, structure, working_directory):
+        """
+        Initialize the Bader module
+
+        Args:
+            job (pyiron_atomistics.dft.job.generic.GenericDFTJob): A DFT job instance (finished/converged job)
+        """
+        self._working_directory = working_directory
+        self._structure = structure
+
+    def _create_cube_files(self):
+        """
+        Create CUBE format files of the total and valce charges to be used by the Bader program
+        """
+        cd_val, cd_total = get_valence_and_total_charge_density(
+            working_directory=self._working_directory
+        )
+        cd_val.write_cube_file(
+            filename=os.path.join(self._working_directory, "valence_charge.CUBE")
+        )
+        cd_total.write_cube_file(
+            filename=os.path.join(self._working_directory, "total_charge.CUBE")
+        )
+
+    def compute_bader_charges(self, extra_arguments=None):
+        """
+        Run Bader analysis on the output from the DFT job
+
+        Args:
+            extra_arguments (str): Extra arguments to the Bader program
+
+        Returns:
+            tuple: Charges and volumes as numpy arrays
+
+        """
+        self._create_cube_files()
+        error_code = call_bader(
+            foldername=self._working_directory, extra_arguments=extra_arguments
+        )
+        if error_code > 0:
+            self._remove_cube_files()
+            raise ValueError("Invoking Bader charge analysis failed!")
+        self._remove_cube_files()
+        return self._parse_charge_vol()
+
+    def _remove_cube_files(self):
+        """
+        Delete created CUBE files
+        """
+        os.remove(os.path.join(self._working_directory, "valence_charge.CUBE"))
+        os.remove(os.path.join(self._working_directory, "total_charge.CUBE"))
+
+    def _parse_charge_vol(self):
+        """
+        Parse Bader charges and volumes
+
+        Returns:
+            tuple: charges and volumes
+
+        """
+        filename = os.path.join(self._working_directory, "ACF.dat")
+        return parse_charge_vol_file(structure=self._structure, filename=filename)
+
+
+def call_bader(foldername, extra_arguments=None):
+    """
+    Call the Bader program inside a given folder
+
+    Args:
+        foldername (str): Folder path
+        extra_arguments (str): Extra arguments to the Bader program
+
+    Returns:
+        int: Result from the subprocess call (>0 if an error occurs)
+
+    """
+    if extra_arguments is None:
+        extra_arguments = ""
+    cmd = "bader valence_charge.CUBE -ref total_charge.CUBE {0}".format(extra_arguments)
+    return subprocess.call(cmd, shell=True, cwd=foldername)
+
+
+def parse_charge_vol_file(structure, filename="ACF.dat"):
+    """
+    Parse charges and volumes from the output file
+
+    Args:
+        structure (pyiron_atomistics.atomistics.structure.atoms.Atoms): The snapshot to be analyzed
+        filename (str): Filename of the output file
+
+    Returns:
+        tuple: charges and volumes
+
+    """
+    with open(filename, errors="ignore") as f:
+        lines = f.readlines()
+        charges = np.genfromtxt(lines[2:], max_rows=len(structure))[:, 4]
+        volumes = np.genfromtxt(lines[2:], max_rows=len(structure))[:, 6]
+    return charges, volumes
+
+
+def get_valence_and_total_charge_density(working_directory):
+    """
+    Gives the valence and total charge densities
+
+    Returns:
+        tuple: The required charge densities
+    """
+    cd_core = VaspVolumetricData()
+    cd_total = VaspVolumetricData()
+    cd_val = VaspVolumetricData()
+    if os.path.isfile(working_directory + "/AECCAR0"):
+        cd_core.from_file(working_directory + "/AECCAR0")
+        cd_val.from_file(working_directory + "/AECCAR2")
+        cd_val.atoms = cd_val.atoms
+        cd_total.total_data = cd_core.total_data + cd_val.total_data
+        cd_total.atoms = cd_val.atoms
+    return cd_val, cd_total