structuretoolkit 0.0.26__tar.gz → 0.0.28__tar.gz

{structuretoolkit-0.0.26/structuretoolkit.egg-info → structuretoolkit-0.0.28}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: structuretoolkit
-Version: 0.0.26
+Version: 0.0.28
 Summary: build, analyse and visualise atomistic structures for materials science
 Author-email: Jan Janssen <janssen@mpie.de>
 License: BSD 3-Clause License
@@ -51,32 +51,32 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: ase<=3.23.0,>=3.20.1
 Requires-Dist: numpy<=1.26.4,>=1.23.5
-Requires-Dist: scipy<=1.14.0,>=1.9.3
+Requires-Dist: scipy<=1.14.1,>=1.9.3
 Provides-Extra: dscribe
 Requires-Dist: dscribe==2.1.1; extra == "dscribe"
 Provides-Extra: grainboundary
 Requires-Dist: aimsgb<=1.1.1,>=1.0.2; extra == "grainboundary"
-Requires-Dist: pymatgen<=2024.6.10,>=2022.2.1; extra == "grainboundary"
+Requires-Dist: pymatgen<=2024.8.9,>=2022.2.1; extra == "grainboundary"
 Provides-Extra: pyscal
-Requires-Dist: pyscal2==2.10.18; extra == "pyscal"
+Requires-Dist: pyscal3<=3.2.7,>=3.2.5; extra == "pyscal"
 Provides-Extra: nglview
 Requires-Dist: nglview<=3.1.2,>=2.7.7; extra == "nglview"
 Provides-Extra: matplotlib
-Requires-Dist: matplotlib==3.8.4; extra == "matplotlib"
+Requires-Dist: matplotlib==3.9.2; extra == "matplotlib"
 Provides-Extra: plotly
-Requires-Dist: plotly<=5.22.0,>=4.14.3; extra == "plotly"
+Requires-Dist: plotly<=5.23.0,>=4.14.3; extra == "plotly"
 Provides-Extra: clusters
-Requires-Dist: scikit-learn==1.5.0; extra == "clusters"
+Requires-Dist: scikit-learn==1.5.1; extra == "clusters"
 Provides-Extra: symmetry
-Requires-Dist: spglib<=2.4.0,>=1.16.5; extra == "symmetry"
+Requires-Dist: spglib<=2.5.0,>=1.16.5; extra == "symmetry"
 Provides-Extra: surface
-Requires-Dist: spglib<=2.4.0,>=1.16.5; extra == "surface"
-Requires-Dist: pymatgen<=2024.6.10,>=2022.2.1; extra == "surface"
+Requires-Dist: spglib<=2.5.0,>=1.16.5; extra == "surface"
+Requires-Dist: pymatgen<=2024.8.9,>=2022.2.1; extra == "surface"
 Provides-Extra: phonopy
-Requires-Dist: phonopy<=2.24.3,>=2.16.2; extra == "phonopy"
-Requires-Dist: spglib<=2.4.0,>=1.16.5; extra == "phonopy"
+Requires-Dist: phonopy<=2.26.6,>=2.16.2; extra == "phonopy"
+Requires-Dist: spglib<=2.5.0,>=1.16.5; extra == "phonopy"
 Provides-Extra: pyxtal
-Requires-Dist: pyxtal<=0.6.7,>=0.5.5; extra == "pyxtal"
+Requires-Dist: pyxtal<=1.0.2,>=0.5.5; extra == "pyxtal"
 
 # structuretoolkit 
 

{structuretoolkit-0.0.26 → structuretoolkit-0.0.28}/pyproject.toml

@@ -26,7 +26,7 @@ classifiers = [
 dependencies = [
     "ase>=3.20.1,<=3.23.0",
     "numpy>=1.23.5,<=1.26.4",
-    "scipy>=1.9.3,<=1.14.0",
+    "scipy>=1.9.3,<=1.14.1",
 ]
 dynamic = ["version"]
 
@@ -39,23 +39,23 @@ Repository = "https://github.com/pyiron/structuretoolkit"
 dscribe = ["dscribe==2.1.1"]
 grainboundary = [
     "aimsgb>=1.0.2,<=1.1.1",
-    "pymatgen>=2022.2.1,<=2024.6.10",
+    "pymatgen>=2022.2.1,<=2024.8.9",
 ]
-pyscal = ["pyscal2==2.10.18"]
+pyscal = ["pyscal3>=3.2.5,<=3.2.7"]
 nglview = ["nglview>=2.7.7,<=3.1.2"]
-matplotlib = ["matplotlib==3.8.4"]
-plotly = ["plotly>=4.14.3,<=5.22.0"]
-clusters = ["scikit-learn==1.5.0"]
-symmetry = ["spglib>=1.16.5,<=2.4.0"]
+matplotlib = ["matplotlib==3.9.2"]
+plotly = ["plotly>=4.14.3,<=5.23.0"]
+clusters = ["scikit-learn==1.5.1"]
+symmetry = ["spglib>=1.16.5,<=2.5.0"]
 surface = [
-    "spglib>=1.16.5,<=2.4.0",
-    "pymatgen>=2022.2.1,<=2024.6.10",
+    "spglib>=1.16.5,<=2.5.0",
+    "pymatgen>=2022.2.1,<=2024.8.9",
 ]
 phonopy = [
-    "phonopy>=2.16.2,<=2.24.3",
-    "spglib>=1.16.5,<=2.4.0",
+    "phonopy>=2.16.2,<=2.26.6",
+    "spglib>=1.16.5,<=2.5.0",
 ]
-pyxtal = ["pyxtal>=0.5.5,<=0.6.7"]
+pyxtal = ["pyxtal>=0.5.5,<=1.0.2"]
 
 [tool.setuptools.packages.find]
 include = ["structuretoolkit*"]

{structuretoolkit-0.0.26 → structuretoolkit-0.0.28}/setup.py

@@ -1,8 +1,7 @@
-from setuptools import setup
-
 import versioneer
+from setuptools import setup
 
 setup(
     version=versioneer.get_version(),
     cmdclass=versioneer.get_cmdclass(),
-)
+)

{structuretoolkit-0.0.26 → structuretoolkit-0.0.28}/structuretoolkit/__init__.py

@@ -1,5 +1,3 @@
-from . import _version
-
 # Analyse
 from structuretoolkit.analyse import (
     find_mic,
@@ -25,6 +23,32 @@ from structuretoolkit.analyse import (
     get_voronoi_volumes,
 )
 
+# Analyse - for backwards compatibility
+from structuretoolkit.analyse import (
+    find_solids as analyse_find_solids,
+)
+from structuretoolkit.analyse import (
+    get_adaptive_cna_descriptors as analyse_cna_adaptive,
+)
+from structuretoolkit.analyse import (
+    get_centro_symmetry_descriptors as analyse_centro_symmetry,
+)
+from structuretoolkit.analyse import (
+    get_cluster_positions as cluster_positions,
+)
+from structuretoolkit.analyse import (
+    get_diamond_structure_descriptors as analyse_diamond_structure,
+)
+from structuretoolkit.analyse import (
+    get_equivalent_atoms as analyse_phonopy_equivalent_atoms,
+)
+from structuretoolkit.analyse import (
+    get_steinhardt_parameters as get_steinhardt_parameter_structure,
+)
+from structuretoolkit.analyse import (
+    get_voronoi_volumes as analyse_voronoi_volume,
+)
+
 # Build
 from structuretoolkit.build import (
     B2,
@@ -32,12 +56,26 @@ from structuretoolkit.build import (
     C15,
     C36,
     D03,
+    create_mesh,
     get_grainboundary_info,
     get_high_index_surface_info,
     grainboundary,
     high_index_surface,
     sqs_structures,
-    create_mesh,
+)
+
+# Build - for backwards compatibility
+from structuretoolkit.build import (
+    get_grainboundary_info as grainboundary_info,
+)
+from structuretoolkit.build import (
+    get_high_index_surface_info as high_index_surface_info,
+)
+from structuretoolkit.build import (
+    grainboundary as grainboundary_build,
+)
+from structuretoolkit.build import (
+    sqs_structures as get_sqs_structures,
 )
 
 # Common
@@ -47,35 +85,17 @@ from structuretoolkit.common import (
     ase_to_pymatgen,
     ase_to_pyscal,
     center_coordinates_in_unit_cell,
+    get_cell,
     get_extended_positions,
     get_vertical_length,
     get_wrapped_coordinates,
     pymatgen_to_ase,
     select_index,
-    get_cell,
 )
 
 # Visualize
 from structuretoolkit.visualize import plot3d
 
-# Analyse - for backwards compatibility
-from structuretoolkit.analyse import (
-    find_solids as analyse_find_solids,
-    get_adaptive_cna_descriptors as analyse_cna_adaptive,
-    get_centro_symmetry_descriptors as analyse_centro_symmetry,
-    get_cluster_positions as cluster_positions,
-    get_diamond_structure_descriptors as analyse_diamond_structure,
-    get_equivalent_atoms as analyse_phonopy_equivalent_atoms,
-    get_steinhardt_parameters as get_steinhardt_parameter_structure,
-    get_voronoi_volumes as analyse_voronoi_volume,
-)
-
-# Build - for backwards compatibility
-from structuretoolkit.build import (
-    get_grainboundary_info as grainboundary_info,
-    get_high_index_surface_info as high_index_surface_info,
-    grainboundary as grainboundary_build,
-    sqs_structures as get_sqs_structures,
-)
+from . import _version
 
 __version__ = _version.get_versions()["version"]

{structuretoolkit-0.0.26 → structuretoolkit-0.0.28}/structuretoolkit/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2024-06-25T10:24:48+0200",
+ "date": "2024-08-23T10:18:12+0200",
  "dirty": true,
  "error": null,
- "full-revisionid": "ad534b234cdbd638aeea242cefa4077059fd2ed8",
- "version": "0.0.26"
+ "full-revisionid": "654ff39333277ba99eda0c195167d3bc006f56b7",
+ "version": "0.0.28"
 }
 '''  # END VERSION_JSON
 

{structuretoolkit-0.0.26 → structuretoolkit-0.0.28}/structuretoolkit/analyse/distance.py

@@ -1,6 +1,7 @@
 from typing import Optional
-from ase.atoms import Atoms
+
 import numpy as np
+from ase.atoms import Atoms
 
 
 def get_distances_array(
@@ -9,7 +10,7 @@ def get_distances_array(
     p2: Optional[np.ndarray] = None,
     mic: bool = True,
     vectors: bool = False,
-):
+) -> np.ndarray:
     """
     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
@@ -18,13 +19,14 @@ def get_distances_array(
     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
+        structure (ase.atoms.Atoms): The structure object
+        p1 (numpy.ndarray/list, optional): Nx3 array of positions. Defaults to None.
+        p2 (numpy.ndarray/list, optional): Nx3 array of positions. Defaults to None.
+        mic (bool, optional): Minimum image convention. Defaults to True.
+        vectors (bool, optional): Return vectors instead of distances. Defaults to False.
+
     Returns:
         numpy.ndarray: NxN if vector=False and NxNx3 if vector=True
-
     """
     if p1 is None and p2 is not None:
         p1 = p2
@@ -47,16 +49,18 @@ def get_distances_array(
     return find_mic(structure=structure, v=diff_relative, vectors=vectors)
 
 
-def find_mic(structure: Atoms, v: np.ndarray, vectors: bool = True):
+def find_mic(structure: Atoms, v: np.ndarray, vectors: bool = True) -> np.ndarray:
     """
     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
+        structure (ase.atoms.Atoms): The structure object
+        v (numpy.ndarray/list): 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
+    Returns:
+        numpy.ndarray: 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)

structuretoolkit-0.0.28/structuretoolkit/analyse/dscribe.py

@@ -0,0 +1,75 @@
+from typing import Optional
+
+import numpy as np
+from ase.atoms import Atoms
+
+
+def soap_descriptor_per_atom(
+    structure: Atoms,
+    r_cut: Optional[float] = None,
+    n_max: Optional[int] = None,
+    l_max: Optional[int] = None,
+    sigma: Optional[float] = 1.0,
+    rbf: str = "gto",
+    weighting: Optional[np.ndarray] = None,
+    average: str = "off",
+    compression: dict = {"mode": "off", "species_weighting": None},
+    species: Optional[list] = None,
+    periodic: bool = True,
+    sparse: bool = False,
+    dtype: str = "float64",
+    centers: Optional[np.ndarray] = None,
+    n_jobs: int = 1,
+    only_physical_cores: bool = False,
+    verbose: bool = False,
+) -> np.ndarray:
+    """
+    Calculates the SOAP descriptor for each atom in the given structure.
+
+    Args:
+        structure (ase.atoms.Atoms): The atomic structure.
+        r_cut (float, optional): The cutoff radius. Defaults to None.
+        n_max (int, optional): The maximum number of radial basis functions. Defaults to None.
+        l_max (int, optional): The maximum degree of spherical harmonics. Defaults to None.
+        sigma (float, optional): The width parameter for the Gaussian-type orbital. Defaults to 1.0.
+        rbf (str, optional): The radial basis function. Defaults to "gto".
+        weighting (np.ndarray, optional): The weighting coefficients for the radial basis functions. Defaults to None.
+        average (str, optional): The type of averaging. Defaults to "off".
+        compression (dict, optional): The compression settings. Defaults to {"mode": "off", "species_weighting": None}.
+        species (list, optional): The list of chemical symbols. Defaults to None.
+        periodic (bool, optional): Whether the system is periodic. Defaults to True.
+        sparse (bool, optional): Whether to use sparse matrices. Defaults to False.
+        dtype (str, optional): The data type of the output. Defaults to "float64".
+        centers (np.ndarray, optional): The centers for the descriptor calculation. Defaults to None.
+        n_jobs (int, optional): The number of parallel jobs. Defaults to 1.
+        only_physical_cores (bool, optional): Whether to use only physical cores. Defaults to False.
+        verbose (bool, optional): Whether to print verbose output. Defaults to False.
+
+    Returns:
+        np.ndarray: The SOAP descriptor for each atom.
+    """
+    from dscribe.descriptors import SOAP
+
+    if species is None:
+        species = list(set(structure.get_chemical_symbols()))
+    periodic_soap = SOAP(
+        r_cut=r_cut,
+        n_max=n_max,
+        l_max=l_max,
+        sigma=sigma,
+        rbf=rbf,
+        weighting=weighting,
+        average=average,
+        compression=compression,
+        species=species,
+        periodic=periodic,
+        sparse=sparse,
+        dtype=dtype,
+    )
+    return periodic_soap.create(
+        system=structure,
+        centers=centers,
+        n_jobs=n_jobs,
+        only_physical_cores=only_physical_cores,
+        verbose=verbose,
+    )