structuretoolkit 0.0.18__tar.gz → 0.0.19__tar.gz

{structuretoolkit-0.0.18/structuretoolkit.egg-info → structuretoolkit-0.0.19}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: structuretoolkit
-Version: 0.0.18
+Version: 0.0.19
 Summary: build, analyse and visualise atomistic structures for materials science
 Author-email: Jan Janssen <janssen@mpie.de>
 License: BSD 3-Clause License
@@ -54,7 +54,7 @@ Requires-Dist: numpy<=1.26.3,>=1.23.5
 Requires-Dist: scipy<=1.12.0,>=1.9.3
 Provides-Extra: grainboundary
 Requires-Dist: aimsgb<=1.1.0,>=1.0.2; extra == "grainboundary"
-Requires-Dist: pymatgen<=2023.12.18,>=2022.2.1; extra == "grainboundary"
+Requires-Dist: pymatgen<=2024.1.27,>=2022.2.1; extra == "grainboundary"
 Provides-Extra: pyscal
 Requires-Dist: pyscal2==2.10.18; extra == "pyscal"
 Provides-Extra: nglview
@@ -66,15 +66,15 @@ Requires-Dist: plotly<=5.18.0,>=4.14.3; extra == "plotly"
 Provides-Extra: clusters
 Requires-Dist: scikit-learn==1.4.0; extra == "clusters"
 Provides-Extra: symmetry
-Requires-Dist: spglib<=2.2.0,>=1.16.5; extra == "symmetry"
+Requires-Dist: spglib<=2.3.0,>=1.16.5; extra == "symmetry"
 Provides-Extra: surface
-Requires-Dist: spglib<=2.2.0,>=1.16.5; extra == "surface"
-Requires-Dist: pymatgen<=2023.12.18,>=2022.2.1; extra == "surface"
+Requires-Dist: spglib<=2.3.0,>=1.16.5; extra == "surface"
+Requires-Dist: pymatgen<=2024.1.27,>=2022.2.1; extra == "surface"
 Provides-Extra: phonopy
 Requires-Dist: phonopy<=2.21.0,>=2.16.2; extra == "phonopy"
-Requires-Dist: spglib<=2.2.0,>=1.16.5; extra == "phonopy"
+Requires-Dist: spglib<=2.3.0,>=1.16.5; extra == "phonopy"
 Provides-Extra: pyxtal
-Requires-Dist: pyxtal<=0.6.1,>=0.5.5; extra == "pyxtal"
+Requires-Dist: pyxtal<=0.6.2,>=0.5.5; extra == "pyxtal"
 
 # structuretoolkit 
 

{structuretoolkit-0.0.18 → structuretoolkit-0.0.19}/pyproject.toml

@@ -38,23 +38,23 @@ Repository = "https://github.com/pyiron/structuretoolkit"
 [project.optional-dependencies]
 grainboundary = [
     "aimsgb>=1.0.2,<=1.1.0",
-    "pymatgen>=2022.2.1,<=2023.12.18",
+    "pymatgen>=2022.2.1,<=2024.1.27",
 ]
 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,<=2.2.0"]
+symmetry = ["spglib>=1.16.5,<=2.3.0"]
 surface = [
-    "spglib>=1.16.5,<=2.2.0",
-    "pymatgen>=2022.2.1,<=2023.12.18",
+    "spglib>=1.16.5,<=2.3.0",
+    "pymatgen>=2022.2.1,<=2024.1.27",
 ]
 phonopy = [
     "phonopy>=2.16.2,<=2.21.0",
-    "spglib>=1.16.5,<=2.2.0",
+    "spglib>=1.16.5,<=2.3.0",
 ]
-pyxtal = ["pyxtal>=0.5.5,<=0.6.1"]
+pyxtal = ["pyxtal>=0.5.5,<=0.6.2"]
 
 [tool.setuptools.packages.find]
 include = ["structuretoolkit*"]

{structuretoolkit-0.0.18 → structuretoolkit-0.0.19}/structuretoolkit/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2024-01-22T09:34:21+0100",
+ "date": "2024-02-09T08:34:00+0100",
  "dirty": true,
  "error": null,
- "full-revisionid": "b27285c3dda8921aa6c6e0b85a3f0be5838b2732",
- "version": "0.0.18"
+ "full-revisionid": "e6f880b960f6aaa479844d7a76533353225d21a1",
+ "version": "0.0.19"
 }
 '''  # END VERSION_JSON
 

{structuretoolkit-0.0.18 → structuretoolkit-0.0.19}/structuretoolkit/analyse/strain.py

@@ -6,7 +6,6 @@ from structuretoolkit.analyse.pyscal import get_adaptive_cna_descriptors
 
 
 class Strain:
-
     """
     Calculate local strain of each atom following the Lagrangian strain tensor:
 

{structuretoolkit-0.0.18 → structuretoolkit-0.0.19}/structuretoolkit/analyse/symmetry.py

@@ -24,7 +24,6 @@ __date__ = "Sep 1, 2017"
 
 
 class Symmetry(dict):
-
     """
 
     Return a class for operations related to box symmetries. Main attributes:

{structuretoolkit-0.0.18 → structuretoolkit-0.0.19}/structuretoolkit/visualize.py

@@ -41,6 +41,7 @@ def plot3d(
     view_plane=np.array([0, 0, 1]),
     distance_from_camera=1.0,
     opacity=1.0,
+    height=None,
 ):
     """
     Plot3d relies on NGLView or plotly to visualize atomic structures. Here, we construct a string in the "protein database"
@@ -82,6 +83,8 @@ def plot3d(
             call. (Default is np.array([0, 0, 1]), which is view normal to the x-y plane.)
         distance_from_camera (float): Distance of the camera from the structure. Higher = farther away.
             (Default is 14, which also seems to be the NGLView default value.)
+        height (int/float/None): height of the plot area in pixel (only
+            available in plotly) Default: 600
 
         Possible NGLView color schemes:
           " ", "picking", "random", "uniform", "atomindex", "residueindex",
@@ -96,6 +99,8 @@ def plot3d(
         * The colour interpretation of some hex codes is weird, e.g. 'green'.
     """
     if mode == "NGLview":
+        if height is not None:
+            warnings.warn("`height` is not implemented in NGLview", SyntaxWarning)
         return _plot3d(
             structure=structure,
             show_cell=show_cell,
@@ -120,6 +125,7 @@ def plot3d(
     elif mode == "plotly":
         return _plot3d_plotly(
             structure=structure,
+            show_cell=show_cell,
             camera=camera,
             particle_size=particle_size,
             select_atoms=select_atoms,
@@ -127,8 +133,11 @@ def plot3d(
             view_plane=view_plane,
             distance_from_camera=distance_from_camera,
             opacity=opacity,
+            height=height,
         )
     elif mode == "ase":
+        if height is not None:
+            warnings.warn("`height` is not implemented in ase", SyntaxWarning)
         return _plot3d_ase(
             structure=structure,
             show_cell=show_cell,
@@ -143,8 +152,20 @@ def plot3d(
         raise ValueError("plot method not recognized")
 
 
+def _get_box_skeleton(cell):
+    lines_dz = np.stack(np.meshgrid(*3 * [[0, 1]], indexing="ij"), axis=-1)
+    # eight corners of a unit cube, paired as four z-axis lines
+
+    all_lines = np.reshape(
+        [np.roll(lines_dz, i, axis=-1) for i in range(3)], (-1, 2, 3)
+    )
+    # All 12 two-point lines on the unit square
+    return all_lines @ cell
+
+
 def _plot3d_plotly(
     structure,
+    show_cell=True,
     scalar_field=None,
     select_atoms=None,
     particle_size=1.0,
@@ -152,6 +173,7 @@ def _plot3d_plotly(
     view_plane=np.array([1, 1, 1]),
     distance_from_camera=1,
     opacity=1,
+    height=None,
 ):
     """
     Make a 3D plot of the atomic structure.
@@ -170,6 +192,7 @@ def _plot3d_plotly(
         distance_from_camera (float): Distance of the camera from the structure. Higher = farther away.
             (Default is 14, which also seems to be the NGLView default value.)
         opacity (float): opacity
+        height (int/float/None): height of the plot area in pixel. Default: 600
 
     Returns:
         (plotly.express): The NGLView widget itself, which can be operated on further or viewed as-is.
@@ -177,6 +200,7 @@ def _plot3d_plotly(
     """
     try:
         import plotly.express as px
+        import plotly.graph_objects as go
     except ModuleNotFoundError:
         raise ModuleNotFoundError("plotly not installed - use plot3d instead")
     if select_atoms is None:
@@ -196,6 +220,13 @@ def _plot3d_plotly(
             scale=particle_size / (0.1 * structure.get_volume() ** (1 / 3)),
         ),
     )
+    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.layout.scene.camera.projection.type = camera
     rot = _get_orientation(view_plane).T
     rot[0, :] *= distance_from_camera * 1.25
@@ -206,6 +237,10 @@ def _plot3d_plotly(
     fig.update_layout(scene_camera=angle)
     fig.update_traces(marker=dict(line=dict(width=0.1, color="DarkSlateGrey")))
     fig.update_scenes(aspectmode="data")
+    if height is None:
+        height = 600
+    fig.update_layout(autosize=True, height=height)
+    fig.update_layout(legend={"itemsizing": "constant"})
     return fig
 
 

{structuretoolkit-0.0.18 → structuretoolkit-0.0.19/structuretoolkit.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: structuretoolkit
-Version: 0.0.18
+Version: 0.0.19
 Summary: build, analyse and visualise atomistic structures for materials science
 Author-email: Jan Janssen <janssen@mpie.de>
 License: BSD 3-Clause License
@@ -54,7 +54,7 @@ Requires-Dist: numpy<=1.26.3,>=1.23.5
 Requires-Dist: scipy<=1.12.0,>=1.9.3
 Provides-Extra: grainboundary
 Requires-Dist: aimsgb<=1.1.0,>=1.0.2; extra == "grainboundary"
-Requires-Dist: pymatgen<=2023.12.18,>=2022.2.1; extra == "grainboundary"
+Requires-Dist: pymatgen<=2024.1.27,>=2022.2.1; extra == "grainboundary"
 Provides-Extra: pyscal
 Requires-Dist: pyscal2==2.10.18; extra == "pyscal"
 Provides-Extra: nglview
@@ -66,15 +66,15 @@ Requires-Dist: plotly<=5.18.0,>=4.14.3; extra == "plotly"
 Provides-Extra: clusters
 Requires-Dist: scikit-learn==1.4.0; extra == "clusters"
 Provides-Extra: symmetry
-Requires-Dist: spglib<=2.2.0,>=1.16.5; extra == "symmetry"
+Requires-Dist: spglib<=2.3.0,>=1.16.5; extra == "symmetry"
 Provides-Extra: surface
-Requires-Dist: spglib<=2.2.0,>=1.16.5; extra == "surface"
-Requires-Dist: pymatgen<=2023.12.18,>=2022.2.1; extra == "surface"
+Requires-Dist: spglib<=2.3.0,>=1.16.5; extra == "surface"
+Requires-Dist: pymatgen<=2024.1.27,>=2022.2.1; extra == "surface"
 Provides-Extra: phonopy
 Requires-Dist: phonopy<=2.21.0,>=2.16.2; extra == "phonopy"
-Requires-Dist: spglib<=2.2.0,>=1.16.5; extra == "phonopy"
+Requires-Dist: spglib<=2.3.0,>=1.16.5; extra == "phonopy"
 Provides-Extra: pyxtal
-Requires-Dist: pyxtal<=0.6.1,>=0.5.5; extra == "pyxtal"
+Requires-Dist: pyxtal<=0.6.2,>=0.5.5; extra == "pyxtal"
 
 # structuretoolkit 
 

{structuretoolkit-0.0.18 → structuretoolkit-0.0.19}/structuretoolkit.egg-info/requires.txt

@@ -7,7 +7,7 @@ scikit-learn==1.4.0
 
 [grainboundary]
 aimsgb<=1.1.0,>=1.0.2
-pymatgen<=2023.12.18,>=2022.2.1
+pymatgen<=2024.1.27,>=2022.2.1
 
 [matplotlib]
 matplotlib==3.8.2
@@ -17,7 +17,7 @@ nglview<=3.1.1,>=2.7.7
 
 [phonopy]
 phonopy<=2.21.0,>=2.16.2
-spglib<=2.2.0,>=1.16.5
+spglib<=2.3.0,>=1.16.5
 
 [plotly]
 plotly<=5.18.0,>=4.14.3
@@ -26,11 +26,11 @@ plotly<=5.18.0,>=4.14.3
 pyscal2==2.10.18
 
 [pyxtal]
-pyxtal<=0.6.1,>=0.5.5
+pyxtal<=0.6.2,>=0.5.5
 
 [surface]
-spglib<=2.2.0,>=1.16.5
-pymatgen<=2023.12.18,>=2022.2.1
+spglib<=2.3.0,>=1.16.5
+pymatgen<=2024.1.27,>=2022.2.1
 
 [symmetry]
-spglib<=2.2.0,>=1.16.5
+spglib<=2.3.0,>=1.16.5

structuretoolkit-0.0.19/tests/test_visualize.py

@@ -0,0 +1,45 @@
+# 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 structuretoolkit.visualize import _get_flattened_orientation, _get_box_skeleton
+
+
+class TestAtoms(unittest.TestCase):
+    @classmethod
+    def tearDownClass(cls):
+        pass
+
+    @classmethod
+    def setUpClass(cls):
+        pass
+
+    def test_get_flattened_orientation(self):
+        R = np.random.random(9).reshape(-1, 3)
+        R = np.array(_get_flattened_orientation(R, 1)).reshape(4, 4)
+        self.assertAlmostEqual(np.linalg.det(R), 1)
+
+    def test_get_frame(self):
+        frame = _get_box_skeleton(np.eye(3))
+        self.assertLessEqual(
+            np.unique(frame.reshape(-1, 6), axis=0, return_counts=True)[1].max(),
+            1
+        )
+        dx, counts = np.unique(
+            np.diff(frame, axis=-2).squeeze().astype(int), axis=0, return_counts=True
+        )
+        self.assertEqual(
+            dx.ptp(), 1, msg="Frames not drawn along the nearest edges"
+        )
+        msg = (
+            "There must be four lines along each direction"
+            + " (4 x [1, 0, 0], 4 x [0, 1, 0] and 4 x [0, 0, 1])"
+        )
+        self.assertEqual(counts.min(), 4, msg=msg)
+        self.assertEqual(counts.max(), 4, msg=msg)
+
+
+if __name__ == "__main__":
+    unittest.main()

structuretoolkit-0.0.18/tests/test_visualize.py

@@ -1,26 +0,0 @@
-# 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 structuretoolkit.visualize import _get_flattened_orientation
-
-
-class TestAtoms(unittest.TestCase):
-    @classmethod
-    def tearDownClass(cls):
-        pass
-
-    @classmethod
-    def setUpClass(cls):
-        pass
-
-    def test_get_flattened_orientation(self):
-        R = np.random.random(9).reshape(-1, 3)
-        R = np.array(_get_flattened_orientation(R, 1)).reshape(4, 4)
-        self.assertAlmostEqual(np.linalg.det(R), 1)
-
-
-if __name__ == "__main__":
-    unittest.main()