structuretoolkit 0.0.1__tar.gz

structuretoolkit-0.0.1/LICENSE

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+BSD 3-Clause License
+
+Copyright (c) 2018, 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.

structuretoolkit-0.0.1/MANIFEST.in

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+include versioneer.py
+include structuretoolkit/_version.py
+include LICENSE

structuretoolkit-0.0.1/PKG-INFO

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+Metadata-Version: 2.1
+Name: structuretoolkit
+Version: 0.0.1
+Summary: structuretoolkit - to analyse, build and visualise atomistic structures.
+Home-page: https://github.com/pyiron/structuretoolkit
+Author: Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department
+Author-email: janssen@mpie.de
+License: BSD
+Keywords: pyiron
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Topic :: Scientific/Engineering :: Physics
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+License-File: LICENSE
+
+http://pyiron.org

structuretoolkit-0.0.1/README.md

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+# structuretoolkit 
+Originally developed as part of the `pyiron_atomistics` module the `structuretoolkit` was release as standalone library
+for analysing, building and visualising atomistic structures. Internally it uses the `ase.atoms.Atoms` class to 
+represent atomistic structures in python. The `structuretoolkit` is integrated inside `pyiron_atomistics`.
+
+## Disclaimer 
+The `structuretoolkit` is currently under development. 
+
+## Example 
+```python
+import structuretoolkit as stk
+from ase.build import bulk
+
+structure = bulk("Al", cubic=True)
+stk.analyse_cna_adaptive(structure)
+stk.plot3d(structure)
+```
+
+## Features 
+### Analysis
+* `get_neighbors`
+* `get_neighborhood`
+* `analyse_phonopy_equivalent_atoms`
+* `get_steinhardt_parameter_structure`
+* `analyse_centro_symmetry` 
+* `analyse_diamond_structure` 
+* `analyse_cna_adaptive` 
+* `analyse_voronoi_volume` 
+* `analyse_find_solids`
+* `get_mean_positions`
+* `get_average_of_unique_labels`
+* `get_interstitials`
+* `get_layers`
+* `get_voronoi_vertices`
+* `get_voronoi_neighbors`
+* `get_delaunay_neighbors`
+* `cluster_positions`
+* `get_strain`
+
+### Build
+* `grainboundary_build`
+* `grainboundary_info`
+* `get_sqs_structures`
+* `B2`
+* `C14`
+* `C15`
+* `C36`
+* `D03`
+
+### Visualize 
+* `plot3d`

structuretoolkit-0.0.1/setup.cfg

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+[versioneer]
+VCS = git
+style = pep440-pre
+versionfile_source = structuretoolkit/_version.py
+tag_prefix = structuretoolkit-
+parentdir_prefix = structuretoolkit
+
+[egg_info]
+tag_build = 
+tag_date = 0
+

structuretoolkit-0.0.1/setup.py

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+"""
+Setuptools based setup module
+"""
+from setuptools import setup, find_packages
+import versioneer
+
+setup(
+    name='structuretoolkit',
+    version=versioneer.get_version(),
+    description='structuretoolkit - to analyse, build and visualise atomistic structures.',
+    long_description='http://pyiron.org',
+
+    url='https://github.com/pyiron/structuretoolkit',
+    author='Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department',
+    author_email='janssen@mpie.de',
+    license='BSD',
+
+    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 :: 3.8',
+        'Programming Language :: Python :: 3.9',
+        'Programming Language :: Python :: 3.10',
+        'Programming Language :: Python :: 3.11'
+    ],
+
+    keywords='pyiron',
+    packages=find_packages(exclude=["*tests*", "*docs*", "*binder*", "*conda*", "*notebooks*", "*.ci_support*"]),
+    install_requires=[
+        'aimsgb>=0.1.1',
+        'ase>=3.22.1',
+        'matplotlib>=3.7.0',
+        'numpy>=1.24.2',
+        'phonopy>=2.17.1',
+        'pymatgen>=2022.11.7',
+        'scipy>=1.10.0',
+        'scikit-learn>=1.2.1',
+        'spglib>=2.0.2',
+    ],
+    cmdclass=versioneer.get_cmdclass(),
+)

structuretoolkit-0.0.1/structuretoolkit/__init__.py

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+# Analyse
+from structuretoolkit.analyse.distance import get_distances_array, find_mic
+from structuretoolkit.analyse.neighbors import get_neighbors, get_neighborhood
+from structuretoolkit.analyse.phonopy import analyse_phonopy_equivalent_atoms
+from structuretoolkit.analyse.pyscal import (
+    get_steinhardt_parameter_structure,
+    analyse_centro_symmetry,
+    analyse_diamond_structure,
+    analyse_cna_adaptive,
+    analyse_voronoi_volume,
+    analyse_find_solids,
+)
+from structuretoolkit.analyse.spatial import (
+    get_mean_positions,
+    get_average_of_unique_labels,
+    get_interstitials,
+    get_layers,
+    get_voronoi_vertices,
+    get_voronoi_neighbors,
+    get_delaunay_neighbors,
+    cluster_positions,
+)
+from structuretoolkit.analyse.strain import get_strain
+from structuretoolkit.analyse.symmetry import get_symmetry
+
+# Build
+from structuretoolkit.build.aimsgb import grainboundary_build, grainboundary_info
+from structuretoolkit.build.compound import B2, C14, C15, C36, D03
+from structuretoolkit.build.sqs import get_sqs_structures
+from structuretoolkit.build.surface import high_index_surface, high_index_surface_info
+
+# Other
+from structuretoolkit.helper import (
+    get_atomic_numbers,
+    get_extended_positions,
+    get_vertical_length,
+    get_wrapped_coordinates,
+    select_index,
+    center_coordinates_in_unit_cell,
+    apply_strain,
+)
+from structuretoolkit.visualize import plot3d

structuretoolkit-0.0.1/structuretoolkit/_version.py

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+
+# This file was generated by 'versioneer.py' (0.18) from
+# revision-control system data, or from the parent directory name of an
+# unpacked source archive. Distribution tarballs contain a pre-generated copy
+# of this file.
+
+import json
+
+version_json = '''
+{
+ "date": "2023-03-27T17:01:19-0600",
+ "dirty": true,
+ "error": null,
+ "full-revisionid": "02120876560fcd96d15bf7f7c77b8120151fbbbe",
+ "version": "0.0.1"
+}
+'''  # END VERSION_JSON
+
+
+def get_versions():
+    return json.loads(version_json)

structuretoolkit-0.0.1/structuretoolkit/analyse/distance.py

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+import numpy as np
+
+
+def get_distances_array(structure, p1=None, p2=None, mic=True, vectors=False):
+    """
+    Return distance matrix of every position in p1 with every position in
+    p2. If p2 is not set, it is assumed that distances between all
+    positions in p1 are desired. p2 will be set to p1 in this case. If both
+    p1 and p2 are not set, the distances between all atoms in the box are
+    returned.
+
+    Args:
+        p1 (numpy.ndarray/list): Nx3 array of positions
+        p2 (numpy.ndarray/list): Nx3 array of positions
+        mic (bool): minimum image convention
+        vectors (bool): return vectors instead of distances
+    Returns:
+        numpy.ndarray: NxN if vector=False and NxNx3 if vector=True
+
+    """
+    if p1 is None and p2 is not None:
+        p1 = p2
+        p2 = None
+    if p1 is None:
+        p1 = structure.positions
+    if p2 is None:
+        p2 = structure.positions
+    p1 = np.asarray(p1)
+    p2 = np.asarray(p2)
+    diff_relative = (
+        p2.reshape(-1, 3)[np.newaxis, :, :] - p1.reshape(-1, 3)[:, np.newaxis, :]
+    )
+    diff_relative = diff_relative.reshape(p1.shape[:-1] + p2.shape[:-1] + (3,))
+    if not mic:
+        if vectors:
+            return diff_relative
+        else:
+            return np.linalg.norm(diff_relative, axis=-1)
+    return find_mic(structure=structure, v=diff_relative, vectors=vectors)
+
+
+def find_mic(structure, v, vectors=True):
+    """
+    Find vectors following minimum image convention (mic). In principle this
+    function does the same as ase.geometry.find_mic
+
+    Args:
+        v (list/numpy.ndarray): 3d vector or a list/array of 3d vectors
+        vectors (bool): Whether to return vectors (distances are returned if False)
+
+    Returns: numpy.ndarray of the same shape as input with mic
+    """
+    if any(structure.pbc):
+        v = np.einsum("ji,...j->...i", np.linalg.inv(structure.cell), v)
+        v[..., structure.pbc] -= np.rint(v)[..., structure.pbc]
+        v = np.einsum("ji,...j->...i", structure.cell, v)
+    if vectors:
+        return np.asarray(v)
+    return np.linalg.norm(v, axis=-1)