structuretoolkit 0.0.22__tar.gz → 0.0.23__tar.gz

{structuretoolkit-0.0.22/structuretoolkit.egg-info → structuretoolkit-0.0.23}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: structuretoolkit
-Version: 0.0.22
+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
@@ -42,41 +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<=1.13.0,>=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<=1.1.1,>=1.0.2; extra == "grainboundary"
-Requires-Dist: pymatgen<=2024.3.1,>=2022.2.1; 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<=3.1.2,>=2.7.7; extra == "nglview"
 Provides-Extra: matplotlib
-Requires-Dist: matplotlib==3.8.3; extra == "matplotlib"
+Requires-Dist: matplotlib==3.8.4; extra == "matplotlib"
 Provides-Extra: plotly
-Requires-Dist: plotly<=5.19.0,>=4.14.3; extra == "plotly"
+Requires-Dist: plotly<=5.22.0,>=4.14.3; extra == "plotly"
 Provides-Extra: clusters
-Requires-Dist: scikit-learn==1.4.1.post1; 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<=2024.3.1,>=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<=2.22.1,>=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-0.0.22 → 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,<=1.13.0",
+    "scipy>=1.9.3,<=1.13.1",
 ]
 dynamic = ["version"]
 
@@ -39,23 +39,23 @@ Repository = "https://github.com/pyiron/structuretoolkit"
 dscribe = ["dscribe==2.1.0"]
 grainboundary = [
     "aimsgb>=1.0.2,<=1.1.1",
-    "pymatgen>=2022.2.1,<=2024.3.1",
+    "pymatgen>=2022.2.1,<=2024.5.1",
 ]
 pyscal = ["pyscal2==2.10.18"]
 nglview = ["nglview>=2.7.7,<=3.1.2"]
-matplotlib = ["matplotlib==3.8.3"]
-plotly = ["plotly>=4.14.3,<=5.19.0"]
-clusters = ["scikit-learn==1.4.1.post1"]
-symmetry = ["spglib>=1.16.5,<=2.3.1"]
+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,<=2024.3.1",
+    "spglib>=1.16.5,<=2.4.0",
+    "pymatgen>=2022.2.1,<=2024.5.1",
 ]
 phonopy = [
-    "phonopy>=2.16.2,<=2.22.1",
-    "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-0.0.22 → 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-0.0.22 → structuretoolkit-0.0.23}/structuretoolkit/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2024-04-08T11:30:30-0500",
+ "date": "2024-05-23T11:34:35-0500",
  "dirty": true,
  "error": null,
- "full-revisionid": "cbb00e1ec4efc047fa4f1c31dfd34110952b834c",
- "version": "0.0.22"
+ "full-revisionid": "d365999a6d980c073a9aad91304db97456d42200",
+ "version": "0.0.23"
 }
 '''  # END VERSION_JSON
 

{structuretoolkit-0.0.22 → structuretoolkit-0.0.23}/structuretoolkit/build/__init__.py

@@ -8,4 +8,5 @@ from structuretoolkit.build.sqs import sqs_structures
 from structuretoolkit.build.surface import (
     high_index_surface,
     get_high_index_surface_info
-)
+)
+from structuretoolkit.build.mesh import create_mesh

structuretoolkit-0.0.23/structuretoolkit/build/mesh.py

@@ -0,0 +1,53 @@
+from __future__ import annotations
+
+import numpy as np
+import warnings
+import typing
+from structuretoolkit.common.helper import get_cell
+
+
+class MeshInputError(ValueError):
+    """ Raised when mesh input format is wrong """
+
+
+def create_mesh(
+    cell: typing.Union["ase.atoms.Atoms", np.ndarray, list, float],
+    n_mesh: typing.Union[int, list[int, int, int]] = 10,
+    density: typing.Optional[float] = None,
+    endpoint: bool = False
+):
+    """
+    Create a mesh based on a structure cell
+
+    Args:
+        cell (ase.atoms.Atoms|np.ndarray|list|float): ASE Atoms or cell
+        n_mesh (int): Number of grid points in each direction. If one number
+            is given, it will be repeated in every direction (i.e. n_mesh = 3
+            is the same as n_mesh = [3, 3, 3])
+        density (float): Density of grid points. Ignored when n_mesh is not
+            None
+        endpoint (bool): Whether both the edges get separate points or not.
+            cf. endpoint in numpy.linspace
+
+    Returns:
+        (3, n, n, n)-array: mesh
+    """
+    cell = get_cell(cell)
+    if n_mesh is None:
+        if density is None:
+            raise MeshInputError("either n_mesh or density must be specified")
+        n_mesh = np.rint(np.linalg.norm(cell, axis=-1) / density).astype(int)
+    elif density is not None:
+        raise MeshInputError(
+            "You cannot set n_mesh at density at the same time. Set one of"
+            " them to None"
+        )
+    n_mesh = np.atleast_1d(n_mesh).astype(int)
+    if len(n_mesh) == 1:
+        n_mesh = np.repeat(n_mesh, 3)
+    elif len(n_mesh) != 3:
+        raise MeshInputError("n_mesh must be a 3-dim vector")
+    linspace = [np.linspace(0, 1, nn, endpoint=endpoint) for nn in n_mesh]
+    x_mesh = np.meshgrid(*linspace, indexing='ij')
+    return np.einsum("ixyz,ij->jxyz", x_mesh, cell)
+

{structuretoolkit-0.0.22 → structuretoolkit-0.0.23}/structuretoolkit/common/__init__.py

@@ -6,6 +6,7 @@ from structuretoolkit.common.helper import (
     get_vertical_length,
     get_wrapped_coordinates,
     select_index,
+    get_cell,
 )
 from structuretoolkit.common.pymatgen import (
     ase_to_pymatgen,

{structuretoolkit-0.0.22 → structuretoolkit-0.0.23}/structuretoolkit/common/helper.py

@@ -2,7 +2,7 @@ import numpy as np
 from ase.atoms import Atoms
 from ase.data import atomic_numbers
 from scipy.sparse import coo_matrix
-from typing import Optional
+from typing import Optional, Union
 
 
 def get_extended_positions(
@@ -226,3 +226,36 @@ def apply_strain(
     structure_copy.set_cell(cell, scale_atoms=True)
     if return_box:
         return structure_copy
+
+
+def get_cell(cell: Union[Atoms, list, tuple, np.ndarray, float]):
+    """
+    Get cell of an ase structure, or convert a float or a (3,)-array into a
+    orthogonal cell.
+
+    Args:
+        cell (Atoms|ndarray|list|float|tuple): Cell
+
+    Returns:
+        (3, 3)-array: Cell
+    """
+    if isinstance(cell, Atoms):
+        return cell.cell
+    # Convert float into (3,)-array. No effect if it is (3,3)-array or
+    # (3,)-array. Raises error if the shape is not correct
+    try:
+        cell = cell * np.ones(3)
+    except ValueError:
+        raise ValueError(
+            f"Invalid cell type or shape: {type(cell).__name__}, {np.shape(cell)}"
+        )
+
+    if np.shape(cell) == (3, 3):
+        return cell
+    # Convert (3,)-array into (3,3)-array. Raises error if the shape is wrong
+    try:
+        return cell * np.eye(3)
+    except ValueError:
+        raise ValueError(
+            f"Invalid cell type or shape: {type(cell).__name__}, {np.shape(cell)}"
+        )

{structuretoolkit-0.0.22 → structuretoolkit-0.0.23}/structuretoolkit/visualize.py

@@ -9,6 +9,8 @@ import numpy as np
 from typing import Optional
 from scipy.interpolate import interp1d
 
+from structuretoolkit.common.helper import get_cell
+
 __author__ = "Joerg Neugebauer, Sudarsan Surendralal"
 __copyright__ = (
     "Copyright 2021, Max-Planck-Institut für Eisenforschung GmbH - "
@@ -165,6 +167,16 @@ def _get_box_skeleton(cell: np.ndarray):
     return all_lines @ cell
 
 
+def _draw_box_plotly(fig, structure, px, go):
+    cell = get_cell(structure)
+    data = fig.data
+    for lines in _get_box_skeleton(cell):
+        fig = px.line_3d(**{xx: vv for xx, vv in zip(["x", "y", "z"], lines.T)})
+        fig.update_traces(line_color="#000000")
+        data = fig.data + data
+    return go.Figure(data=data)
+
+
 def _plot3d_plotly(
     structure: Atoms,
     show_cell: bool = True,
@@ -223,12 +235,7 @@ def _plot3d_plotly(
         ),
     )
     if show_cell:
-        data = fig.data
-        for lines in _get_box_skeleton(structure.cell):
-            fig = px.line_3d(**{xx: vv for xx, vv in zip(["x", "y", "z"], lines.T)})
-            fig.update_traces(line_color="#000000")
-            data = fig.data + data
-        fig = go.Figure(data=data)
+        fig = _draw_box_plotly(fig, structure, px, go)
     fig.layout.scene.camera.projection.type = camera
     rot = _get_orientation(view_plane).T
     rot[0, :] *= distance_from_camera * 1.25

{structuretoolkit-0.0.22 → structuretoolkit-0.0.23/structuretoolkit.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: structuretoolkit
-Version: 0.0.22
+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
@@ -42,41 +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<=1.13.0,>=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<=1.1.1,>=1.0.2; extra == "grainboundary"
-Requires-Dist: pymatgen<=2024.3.1,>=2022.2.1; 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<=3.1.2,>=2.7.7; extra == "nglview"
 Provides-Extra: matplotlib
-Requires-Dist: matplotlib==3.8.3; extra == "matplotlib"
+Requires-Dist: matplotlib==3.8.4; extra == "matplotlib"
 Provides-Extra: plotly
-Requires-Dist: plotly<=5.19.0,>=4.14.3; extra == "plotly"
+Requires-Dist: plotly<=5.22.0,>=4.14.3; extra == "plotly"
 Provides-Extra: clusters
-Requires-Dist: scikit-learn==1.4.1.post1; 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<=2024.3.1,>=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<=2.22.1,>=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-0.0.22 → structuretoolkit-0.0.23}/structuretoolkit.egg-info/SOURCES.txt

@@ -24,6 +24,7 @@ structuretoolkit/analyse/symmetry.py
 structuretoolkit/build/__init__.py
 structuretoolkit/build/aimsgb.py
 structuretoolkit/build/compound.py
+structuretoolkit/build/mesh.py
 structuretoolkit/build/random.py
 structuretoolkit/build/sqs.py
 structuretoolkit/build/surface.py
@@ -37,7 +38,9 @@ tests/test_aimsgb.py
 tests/test_analyse.py
 tests/test_compound.py
 tests/test_dscribe.py
+tests/test_helpers.py
 tests/test_high_index_surface.py
+tests/test_mesh.py
 tests/test_neighbors.py
 tests/test_pymatgen.py
 tests/test_pyscal.py

structuretoolkit-0.0.23/structuretoolkit.egg-info/requires.txt

@@ -0,0 +1,39 @@
+ase<=3.22.1,>=3.20.1
+numpy<=1.26.4,>=1.23.5
+scipy<=1.13.1,>=1.9.3
+
+[clusters]
+scikit-learn==1.5.0
+
+[dscribe]
+dscribe==2.1.0
+
+[grainboundary]
+aimsgb<=1.1.1,>=1.0.2
+pymatgen<=2024.5.1,>=2022.2.1
+
+[matplotlib]
+matplotlib==3.8.4
+
+[nglview]
+nglview<=3.1.2,>=2.7.7
+
+[phonopy]
+phonopy<=2.23.1,>=2.16.2
+spglib<=2.4.0,>=1.16.5
+
+[plotly]
+plotly<=5.22.0,>=4.14.3
+
+[pyscal]
+pyscal2==2.10.18
+
+[pyxtal]
+pyxtal<=0.6.6,>=0.5.5
+
+[surface]
+spglib<=2.4.0,>=1.16.5
+pymatgen<=2024.5.1,>=2022.2.1
+
+[symmetry]
+spglib<=2.4.0,>=1.16.5

structuretoolkit-0.0.23/tests/test_helpers.py

@@ -0,0 +1,28 @@
+# 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 unittest
+import numpy as np
+from ase.build import bulk
+import structuretoolkit as stk
+
+
+class TestHelpers(unittest.TestCase):
+    def test_get_cell(self):
+        self.assertEqual((3 * np.eye(3)).tolist(), stk.get_cell(3).tolist())
+        self.assertEqual(
+            ([1, 2, 3] * np.eye(3)).tolist(), stk.get_cell([1, 2, 3]).tolist()
+        )
+        atoms = bulk("Fe")
+        self.assertEqual(
+            atoms.cell.tolist(), stk.get_cell(atoms).tolist()
+        )
+        with self.assertRaises(ValueError):
+            stk.get_cell(np.arange(4))
+        with self.assertRaises(ValueError):
+            stk.get_cell(np.ones((4, 3)))
+
+
+if __name__ == "__main__":
+    unittest.main()

structuretoolkit-0.0.23/tests/test_mesh.py

@@ -0,0 +1,31 @@
+# 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 unittest
+from ase.build import bulk
+import structuretoolkit as stk
+
+
+class TestMesh(unittest.TestCase):
+    def test_mesh(self):
+        structure = bulk("Al", cubic=True)
+        self.assertEqual(stk.create_mesh(structure, n_mesh=4).shape, (3, 4, 4, 4))
+        with self.assertRaises(stk.build.mesh.MeshInputError):
+            stk.create_mesh(structure, n_mesh=None, density=None)
+        with self.assertRaises(stk.build.mesh.MeshInputError):
+            stk.create_mesh(
+                structure, n_mesh=10, density=structure.cell[0, 0] / 4
+            )
+        self.assertEqual(
+            stk.create_mesh(
+                structure, n_mesh=None, density=structure.cell[0, 0] / 4
+            ).shape,
+            (3, 4, 4, 4),
+        )
+        with self.assertRaises(stk.build.mesh.MeshInputError):
+            _ = stk.create_mesh(structure, n_mesh=[1, 2, 3, 4])
+
+
+if __name__ == "__main__":
+    unittest.main()

structuretoolkit-0.0.22/structuretoolkit.egg-info/requires.txt

@@ -1,39 +0,0 @@
-ase<=3.22.1,>=3.20.1
-numpy<=1.26.4,>=1.23.5
-scipy<=1.13.0,>=1.9.3
-
-[clusters]
-scikit-learn==1.4.1.post1
-
-[dscribe]
-dscribe==2.1.0
-
-[grainboundary]
-aimsgb<=1.1.1,>=1.0.2
-pymatgen<=2024.3.1,>=2022.2.1
-
-[matplotlib]
-matplotlib==3.8.3
-
-[nglview]
-nglview<=3.1.2,>=2.7.7
-
-[phonopy]
-phonopy<=2.22.1,>=2.16.2
-spglib<=2.3.1,>=1.16.5
-
-[plotly]
-plotly<=5.19.0,>=4.14.3
-
-[pyscal]
-pyscal2==2.10.18
-
-[pyxtal]
-pyxtal<=0.6.2,>=0.5.5
-
-[surface]
-spglib<=2.3.1,>=1.16.5
-pymatgen<=2024.3.1,>=2022.2.1
-
-[symmetry]
-spglib<=2.3.1,>=1.16.5