structuretoolkit 0.0.13__tar.gz → 0.0.14__tar.gz

structuretoolkit-0.0.14/MANIFEST.in

@@ -0,0 +1 @@
+include LICENSE

{structuretoolkit-0.0.13/structuretoolkit.egg-info → structuretoolkit-0.0.14}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: structuretoolkit
-Version: 0.0.13
+Version: 0.0.14
 Summary: build, analyse and visualise atomistic structures for materials science
 Author-email: Jan Janssen <janssen@mpie.de>
 License: BSD 3-Clause License

{structuretoolkit-0.0.13 → structuretoolkit-0.0.14}/pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = ["ase", "matplotlib", "numpy", "setuptools", "scipy"]
+requires = ["ase", "matplotlib", "numpy", "setuptools", "scipy", "versioneer[toml]==0.29"]
 build-backend = "setuptools.build_meta"
 
 [project]
@@ -56,8 +56,8 @@ phonopy = [
 ]
 pyxtal = ["pyxtal>=0.5.5,<=0.6.1"]
 
-[tool.setuptools]
-packages = ["structuretoolkit"]
+[tool.setuptools.packages.find]
+include = ["structuretoolkit*"]
 
 [tool.setuptools.dynamic]
 version = {attr = "structuretoolkit.__version__"}

structuretoolkit-0.0.14/setup.py

@@ -0,0 +1,8 @@
+from setuptools import setup
+
+import versioneer
+
+setup(
+    version=versioneer.get_version(),
+    cmdclass=versioneer.get_cmdclass(),
+)

structuretoolkit-0.0.14/structuretoolkit/_version.py

@@ -0,0 +1,21 @@
+
+# This file was generated by 'versioneer.py' (0.29) 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": "2023-11-26T23:00:57+0100",
+ "dirty": true,
+ "error": null,
+ "full-revisionid": "985776e9464b45fc318cddad01f767eb3a308f2f",
+ "version": "0.0.14"
+}
+'''  # END VERSION_JSON
+
+
+def get_versions():
+    return json.loads(version_json)

structuretoolkit-0.0.14/structuretoolkit/analyse/__init__.py

@@ -0,0 +1,250 @@
+import numpy as np
+
+from structuretoolkit.analyse.distance import find_mic, get_distances_array
+from structuretoolkit.analyse.neighbors import get_neighborhood, get_neighbors
+from structuretoolkit.analyse.phonopy import get_equivalent_atoms
+from structuretoolkit.analyse.pyscal import (
+    find_solids,
+    get_adaptive_cna_descriptors,
+    get_centro_symmetry_descriptors,
+    get_diamond_structure_descriptors,
+    get_steinhardt_parameters,
+    get_voronoi_volumes,
+)
+from structuretoolkit.analyse.spatial import (
+    get_average_of_unique_labels,
+    get_cluster_positions,
+    get_delaunay_neighbors,
+    get_interstitials,
+    get_layers,
+    get_mean_positions,
+    get_voronoi_neighbors,
+    get_voronoi_vertices,
+)
+from structuretoolkit.analyse.strain import get_strain
+
+
+def get_symmetry(
+    structure, use_magmoms=False, use_elements=True, symprec=1e-5, angle_tolerance=-1.0
+):
+    """
+
+    Args:
+        structure (Atoms): The structure to analyse.
+        use_magmoms (bool): Whether to consider magnetic moments (cf.
+        get_initial_magnetic_moments())
+        use_elements (bool): If False, chemical elements will be ignored
+        symprec (float): Symmetry search precision
+        angle_tolerance (float): Angle search tolerance
+
+    Returns:
+        symmetry (:class:`structuretoolkit.analyse.symmetry.Symmetry`): Symmetry class
+
+
+    """
+    from structuretoolkit.analyse.symmetry import Symmetry
+
+    return Symmetry(
+        structure=structure,
+        use_magmoms=use_magmoms,
+        use_elements=use_elements,
+        symprec=symprec,
+        angle_tolerance=angle_tolerance,
+    )
+
+
+def symmetrize_vectors(
+    structure,
+    vectors,
+    use_magmoms=False,
+    use_elements=True,
+    symprec=1e-5,
+    angle_tolerance=-1.0,
+):
+    """
+    Symmetrization of natom x 3 vectors according to box symmetries
+
+    Args:
+        structure (Atoms): The structure to analyse.
+        vectors (ndarray/list): natom x 3 array to symmetrize
+        use_magmoms (bool): Whether to consider magnetic moments (cf.
+        get_initial_magnetic_moments())
+        use_elements (bool): If False, chemical elements will be ignored
+        symprec (float): Symmetry search precision
+        angle_tolerance (float): Angle search tolerance
+
+    Returns:
+        (np.ndarray) symmetrized vectors
+    """
+    from structuretoolkit.analyse.symmetry import Symmetry
+
+    return Symmetry(
+        structure=structure,
+        use_magmoms=use_magmoms,
+        use_elements=use_elements,
+        symprec=symprec,
+        angle_tolerance=angle_tolerance,
+    ).symmetrize_vectors(vectors=vectors)
+
+
+def group_points_by_symmetry(
+    structure,
+    points,
+    use_magmoms=False,
+    use_elements=True,
+    symprec=1e-5,
+    angle_tolerance=-1.0,
+):
+    """
+    This function classifies the points into groups according to the box symmetry given by
+    spglib.
+
+    Args:
+        structure (Atoms): The structure to analyse.
+        points: (np.array/list) nx3 array which contains positions
+        use_magmoms (bool): Whether to consider magnetic moments (cf.
+        get_initial_magnetic_moments())
+        use_elements (bool): If False, chemical elements will be ignored
+        symprec (float): Symmetry search precision
+        angle_tolerance (float): Angle search tolerance
+
+    Returns: list of arrays containing geometrically equivalent positions
+
+    It is possible that the original points are not found in the returned list, as the
+    positions outsie the box will be projected back to the box.
+    """
+    from structuretoolkit.analyse.symmetry import Symmetry
+
+    return Symmetry(
+        structure=structure,
+        use_magmoms=use_magmoms,
+        use_elements=use_elements,
+        symprec=symprec,
+        angle_tolerance=angle_tolerance,
+    ).get_arg_equivalent_sites(points)
+
+
+def get_equivalent_points(
+    structure,
+    points,
+    use_magmoms=False,
+    use_elements=True,
+    symprec=1e-5,
+    angle_tolerance=-1.0,
+):
+    """
+
+    Args:
+        structure (Atoms): The structure to analyse.
+        points (list/ndarray): 3d vector
+        use_magmoms (bool): Whether to consider magnetic moments (cf.
+        get_initial_magnetic_moments())
+        use_elements (bool): If False, chemical elements will be ignored
+        symprec (float): Symmetry search precision
+        angle_tolerance (float): Angle search tolerance
+
+    Returns:
+        (ndarray): array of equivalent points with respect to box symmetries
+    """
+    from structuretoolkit.analyse.symmetry import Symmetry
+
+    return Symmetry(
+        structure=structure,
+        use_magmoms=use_magmoms,
+        use_elements=use_elements,
+        symprec=symprec,
+        angle_tolerance=angle_tolerance,
+    ).get_arg_equivalent_sites(points)
+
+
+def get_symmetry_dataset(structure, symprec=1e-5, angle_tolerance=-1.0):
+    """
+
+    Args:
+        structure (Atoms): The structure to analyse.
+        symprec (float): Symmetry search precision
+        angle_tolerance (float): Angle search tolerance
+
+    Returns:
+
+    https://atztogo.github.io/spglib/python-spglib.html
+    """
+    from structuretoolkit.analyse.symmetry import Symmetry
+
+    return Symmetry(
+        structure=structure,
+        symprec=symprec,
+        angle_tolerance=angle_tolerance,
+    ).info
+
+
+def get_spacegroup(structure, symprec=1e-5, angle_tolerance=-1.0):
+    """
+
+    Args:
+        structure (Atoms): The structure to analyse.
+        symprec (float): Symmetry search precision
+        angle_tolerance (float): Angle search tolerance
+
+    Returns:
+
+    https://atztogo.github.io/spglib/python-spglib.html
+    """
+    from structuretoolkit.analyse.symmetry import Symmetry
+
+    return Symmetry(
+        structure=structure,
+        symprec=symprec,
+        angle_tolerance=angle_tolerance,
+    ).spacegroup
+
+
+def get_primitive_cell(structure, symprec=1e-5, angle_tolerance=-1.0):
+    """
+
+    Args:
+        structure (Atoms): The structure to analyse.
+        symprec (float): Symmetry search precision
+        angle_tolerance (float): Angle search tolerance
+
+    Returns:
+
+    """
+    from structuretoolkit.analyse.symmetry import Symmetry
+
+    return Symmetry(
+        structure=structure,
+        symprec=symprec,
+        angle_tolerance=angle_tolerance,
+    ).get_primitive_cell(standardize=False)
+
+
+def get_ir_reciprocal_mesh(
+    structure,
+    mesh,
+    is_shift=np.zeros(3, dtype="intc"),
+    is_time_reversal=True,
+    symprec=1e-5,
+):
+    """
+
+    Args:
+        structure (Atoms): The structure to analyse.
+        mesh:
+        is_shift:
+        is_time_reversal:
+        symprec (float): Symmetry search precision
+
+    Returns:
+
+    """
+    from structuretoolkit.analyse.symmetry import Symmetry
+
+    return Symmetry(
+        structure=structure,
+        symprec=symprec,
+    ).get_ir_reciprocal_mesh(
+        mesh=mesh,
+        is_shift=is_shift,
+        is_time_reversal=is_time_reversal,
+    )

structuretoolkit-0.0.14/structuretoolkit/analyse/distance.py

@@ -0,0 +1,59 @@
+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)