structuretoolkit 0.0.21__tar.gz → 0.0.23__tar.gz

{structuretoolkit-0.0.21/structuretoolkit.egg-info → structuretoolkit-0.0.23}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: structuretoolkit
-Version: 0.0.21
+Version: 0.0.23
 Summary: build, analyse and visualise atomistic structures for materials science
 Author-email: Jan Janssen <janssen@mpie.de>
 License: BSD 3-Clause License
@@ -42,39 +42,41 @@ 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
-Requires-Python: >=3.8
+Classifier: Programming Language :: Python :: 3.12
+Requires-Python: <3.13,>=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: ase<=3.22.1,>=3.20.1
 Requires-Dist: numpy<=1.26.4,>=1.23.5
-Requires-Dist: scipy<=1.12.0,>=1.9.3
+Requires-Dist: scipy<=1.13.1,>=1.9.3
+Provides-Extra: dscribe
+Requires-Dist: dscribe==2.1.0; extra == "dscribe"
 Provides-Extra: grainboundary
-Requires-Dist: aimsgb<=1.1.0,>=1.0.2; extra == "grainboundary"
-Requires-Dist: pymatgen<=2024.2.8,>=2022.2.1; extra == "grainboundary"
+Requires-Dist: aimsgb<=1.1.1,>=1.0.2; extra == "grainboundary"
+Requires-Dist: pymatgen<=2024.5.1,>=2022.2.1; extra == "grainboundary"
 Provides-Extra: pyscal
 Requires-Dist: pyscal2==2.10.18; extra == "pyscal"
 Provides-Extra: nglview
-Requires-Dist: nglview<=3.1.1,>=2.7.7; extra == "nglview"
+Requires-Dist: nglview<=3.1.2,>=2.7.7; extra == "nglview"
 Provides-Extra: matplotlib
-Requires-Dist: matplotlib==3.8.2; extra == "matplotlib"
+Requires-Dist: matplotlib==3.8.4; extra == "matplotlib"
 Provides-Extra: plotly
-Requires-Dist: plotly<=5.18.0,>=4.14.3; extra == "plotly"
+Requires-Dist: plotly<=5.22.0,>=4.14.3; extra == "plotly"
 Provides-Extra: clusters
-Requires-Dist: scikit-learn==1.4.0; extra == "clusters"
+Requires-Dist: scikit-learn==1.5.0; extra == "clusters"
 Provides-Extra: symmetry
-Requires-Dist: spglib<=2.3.1,>=1.16.5; extra == "symmetry"
+Requires-Dist: spglib<=2.4.0,>=1.16.5; extra == "symmetry"
 Provides-Extra: surface
-Requires-Dist: spglib<=2.3.1,>=1.16.5; extra == "surface"
-Requires-Dist: pymatgen<=2024.2.8,>=2022.2.1; extra == "surface"
+Requires-Dist: spglib<=2.4.0,>=1.16.5; extra == "surface"
+Requires-Dist: pymatgen<=2024.5.1,>=2022.2.1; extra == "surface"
 Provides-Extra: phonopy
-Requires-Dist: phonopy<=2.21.0,>=2.16.2; extra == "phonopy"
-Requires-Dist: spglib<=2.3.1,>=1.16.5; extra == "phonopy"
+Requires-Dist: phonopy<=2.23.1,>=2.16.2; extra == "phonopy"
+Requires-Dist: spglib<=2.4.0,>=1.16.5; extra == "phonopy"
 Provides-Extra: pyxtal
-Requires-Dist: pyxtal<=0.6.2,>=0.5.5; extra == "pyxtal"
+Requires-Dist: pyxtal<=0.6.6,>=0.5.5; extra == "pyxtal"
 
 # structuretoolkit 
 

{structuretoolkit-0.0.21 → structuretoolkit-0.0.23}/pyproject.toml

@@ -11,22 +11,22 @@ authors = [
 readme = "README.md"
 license = { file = "LICENSE" }
 keywords = ["pyiron"]
-requires-python = ">=3.8"
+requires-python = ">=3.9, <3.13"
 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",
+    "Programming Language :: Python :: 3.12",
 ]
 dependencies = [
     "ase>=3.20.1,<=3.22.1",
     "numpy>=1.23.5,<=1.26.4",
-    "scipy>=1.9.3,<=1.12.0",
+    "scipy>=1.9.3,<=1.13.1",
 ]
 dynamic = ["version"]
 
@@ -36,25 +36,26 @@ Documentation = "https://github.com/pyiron/structuretoolkit"
 Repository = "https://github.com/pyiron/structuretoolkit"
 
 [project.optional-dependencies]
+dscribe = ["dscribe==2.1.0"]
 grainboundary = [
-    "aimsgb>=1.0.2,<=1.1.0",
-    "pymatgen>=2022.2.1,<=2024.2.8",
+    "aimsgb>=1.0.2,<=1.1.1",
+    "pymatgen>=2022.2.1,<=2024.5.1",
 ]
 pyscal = ["pyscal2==2.10.18"]
-nglview = ["nglview>=2.7.7,<=3.1.1"]
-matplotlib = ["matplotlib==3.8.2"]
-plotly = ["plotly>=4.14.3,<=5.18.0"]
-clusters = ["scikit-learn==1.4.0"]
-symmetry = ["spglib>=1.16.5,<=2.3.1"]
+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"]
 surface = [
-    "spglib>=1.16.5,<=2.3.1",
-    "pymatgen>=2022.2.1,<=2024.2.8",
+    "spglib>=1.16.5,<=2.4.0",
+    "pymatgen>=2022.2.1,<=2024.5.1",
 ]
 phonopy = [
-    "phonopy>=2.16.2,<=2.21.0",
-    "spglib>=1.16.5,<=2.3.1",
+    "phonopy>=2.16.2,<=2.23.1",
+    "spglib>=1.16.5,<=2.4.0",
 ]
-pyxtal = ["pyxtal>=0.5.5,<=0.6.2"]
+pyxtal = ["pyxtal>=0.5.5,<=0.6.6"]
 
 [tool.setuptools.packages.find]
 include = ["structuretoolkit*"]

{structuretoolkit-0.0.21 → structuretoolkit-0.0.23}/structuretoolkit/__init__.py

@@ -37,6 +37,7 @@ from structuretoolkit.build import (
     grainboundary,
     high_index_surface,
     sqs_structures,
+    create_mesh,
 )
 
 # Common
@@ -51,6 +52,7 @@ from structuretoolkit.common import (
     get_wrapped_coordinates,
     pymatgen_to_ase,
     select_index,
+    get_cell,
 )
 
 # Visualize

{structuretoolkit-0.0.21 → structuretoolkit-0.0.23}/structuretoolkit/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2024-02-12T08:28:49+0100",
+ "date": "2024-05-23T11:34:35-0500",
  "dirty": true,
  "error": null,
- "full-revisionid": "a6c09d88b2024ef8ca8a64c3249e94d55355b251",
- "version": "0.0.21"
+ "full-revisionid": "d365999a6d980c073a9aad91304db97456d42200",
+ "version": "0.0.23"
 }
 '''  # END VERSION_JSON
 

{structuretoolkit-0.0.21 → structuretoolkit-0.0.23}/structuretoolkit/analyse/__init__.py

@@ -1,6 +1,7 @@
 import numpy as np
 
 from structuretoolkit.analyse.distance import find_mic, get_distances_array
+from structuretoolkit.analyse.dscribe import soap_descriptor_per_atom
 from structuretoolkit.analyse.neighbors import get_neighborhood, get_neighbors
 from structuretoolkit.analyse.phonopy import get_equivalent_atoms
 from structuretoolkit.analyse.pyscal import (
@@ -22,6 +23,11 @@ from structuretoolkit.analyse.spatial import (
     get_voronoi_vertices,
 )
 from structuretoolkit.analyse.strain import get_strain
+from structuretoolkit.analyse.snap import (
+    get_snap_descriptor_names,
+    get_snap_descriptors_per_atom,
+    get_snap_descriptor_derivatives,
+)
 
 
 def get_symmetry(

{structuretoolkit-0.0.21 → structuretoolkit-0.0.23}/structuretoolkit/analyse/distance.py

@@ -1,7 +1,15 @@
+from typing import Optional
+from ase.atoms import Atoms
 import numpy as np
 
 
-def get_distances_array(structure, p1=None, p2=None, mic=True, vectors=False):
+def get_distances_array(
+    structure: Atoms,
+    p1: Optional[np.ndarray] = None,
+    p2: Optional[np.ndarray] = None,
+    mic: bool = True,
+    vectors: bool = 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
@@ -39,7 +47,7 @@ def get_distances_array(structure, p1=None, p2=None, mic=True, vectors=False):
     return find_mic(structure=structure, v=diff_relative, vectors=vectors)
 
 
-def find_mic(structure, v, vectors=True):
+def find_mic(structure: Atoms, v: np.ndarray, vectors: bool = True):
     """
     Find vectors following minimum image convention (mic). In principle this
     function does the same as ase.geometry.find_mic

structuretoolkit-0.0.23/structuretoolkit/analyse/dscribe.py

@@ -0,0 +1,49 @@
+import numpy as np
+from ase.atoms import Atoms
+from typing import Optional
+
+
+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:
+    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,
+    )