Refactor

README.md

@@ -10,46 +10,54 @@ represent atomistic structures in python. The `structuretoolkit` is integrated i
 ## Disclaimer 
 The `structuretoolkit` is currently under development. 
 
-## Example 
+## Example
+
 ```python
 import structuretoolkit as stk
 from ase.build import bulk
 
 structure = bulk("Al", cubic=True)
-stk.analyse_cna_adaptive(structure)
+stk.analyse.get_adaptive_cna_descriptors(structure)
 stk.plot3d(structure)
 ```
 
 ## Features 
 ### Analysis
-* `get_neighbors`
-* `get_neighborhood`
-* `analyse_phonopy_equivalent_atoms`
-* `get_steinhardt_parameter_structure`
-* `analyse_centro_symmetry` 
-* `analyse_diamond_structure` 
-* `analyse_cna_adaptive` 
-* `analyse_voronoi_volume` 
-* `analyse_find_solids`
-* `get_mean_positions`
-* `get_average_of_unique_labels`
-* `get_interstitials`
-* `get_layers`
-* `get_voronoi_vertices`
-* `get_voronoi_neighbors`
-* `get_delaunay_neighbors`
-* `cluster_positions`
-* `get_strain`
+* `stk.analyse.get_neighbors()`
+* `stk.analyse.get_neighborhood()`
+* `stk.analyse.get_equivalent_atoms()`
+* `stk.analyse.get_steinhardt_parameters()`
+* `stk.analyse.get_centro_symmetry_descriptors()` 
+* `stk.analyse.get_diamond_structure_descriptors()` 
+* `stk.analyse.get_adaptive_cna_descriptors()` 
+* `stk.analyse.get_voronoi_volumes()` 
+* `stk.analyse.find_solids()`
+* `stk.analyse.get_mean_positions()`
+* `stk.analyse.get_average_of_unique_labels()`
+* `stk.analyse.get_interstitials()`
+* `stk.analyse.get_layers()`
+* `stk.analyse.get_voronoi_vertices()`
+* `stk.analyse.get_voronoi_neighbors()`
+* `stk.analyse.get_delaunay_neighbors()`
+* `stk.analyse.get_cluster_positions()`
+* `stk.analyse.get_strain()`
 
 ### Build
-* `grainboundary_build`
-* `grainboundary_info`
-* `get_sqs_structures`
-* `B2`
-* `C14`
-* `C15`
-* `C36`
-* `D03`
+* `stk.build.get_grainboundary_info()`
+* `stk.build.grainboundary()`
+* `stk.build.high_index_surface()`
+* `stk.build.get_high_index_surface_info()`
+* `stk.build.sqs_structures()`
+* `stk.build.B2()`
+* `stk.build.C14()`
+* `stk.build.C15()`
+* `stk.build.C36()`
+* `stk.build.D03()`
 
 ### Visualize 
-* `plot3d`
+* `stk.visualize.plot3d()`
+
+### Common 
+* `stk.common.ase_to_pymatgen()`
+* `stk.common.pymatgen_to_ase()`
+* `stk.common.ase_to_pyscal()`

setup.py

@@ -30,15 +30,20 @@
     keywords='pyiron',
     packages=find_packages(exclude=["*tests*", "*docs*", "*binder*", "*conda*", "*notebooks*", "*.ci_support*"]),
     install_requires=[
-        'aimsgb==0.1.1',
         'ase==3.22.1',
-        'matplotlib==3.7.0',
-        'numpy==1.24.2',
-        'phonopy==2.17.1',
-        'pymatgen==2022.11.7',
-        'scipy==1.10.0',
-        'scikit-learn==1.2.1',
-        'spglib==2.0.2',
+        'matplotlib==3.7.0',  # ase already requires matplotlib
+        'numpy==1.24.2',  # ase already requires numpy
+        'scipy==1.10.0',  # ase already requires scipy
     ],
+    extras_require={
+        "grainboundary": ['aimsgb==0.1.1', 'pymatgen==2022.11.7'],
+        "pyscal": ['pyscal2==2.10.20'],
+        "nglview": ['nglview==3.0.4'],
+        "plotly": ['plotly==5.14.1'],
+        "clusters": ['scikit-learn==1.2.1'],
+        "symmetry": ['spglib==2.0.2'],
+        "surface": ['spglib==2.0.2', 'pymatgen==2022.11.7'],
+        "phonopy": ['phonopy==2.17.1', 'spglib==2.0.2'],
+    },
     cmdclass=versioneer.get_cmdclass(),
 )

structuretoolkit/__init__.py

@@ -1,42 +1,70 @@
 # Analyse
-from structuretoolkit.analyse.distance import get_distances_array, find_mic
-from structuretoolkit.analyse.neighbors import get_neighbors, get_neighborhood
-from structuretoolkit.analyse.phonopy import analyse_phonopy_equivalent_atoms
-from structuretoolkit.analyse.pyscal import (
-    get_steinhardt_parameter_structure,
-    analyse_centro_symmetry,
-    analyse_diamond_structure,
-    analyse_cna_adaptive,
-    analyse_voronoi_volume,
-    analyse_find_solids,
-)
-from structuretoolkit.analyse.spatial import (
+from structuretoolkit.analyse import (
+    get_distances_array,
+    find_mic,
+    get_neighbors,
+    get_neighborhood,
+    get_equivalent_atoms,
+    get_steinhardt_parameters,
+    get_centro_symmetry_descriptors,
+    get_diamond_structure_descriptors,
+    get_adaptive_cna_descriptors,
+    get_voronoi_volumes,
+    find_solids,
     get_mean_positions,
     get_average_of_unique_labels,
     get_interstitials,
     get_layers,
     get_voronoi_vertices,
     get_voronoi_neighbors,
     get_delaunay_neighbors,
-    cluster_positions,
+    get_cluster_positions,
+    get_strain,
+    get_symmetry,
+    # for backwards compatibility
+    get_cluster_positions as cluster_positions,
+    get_equivalent_atoms as analyse_phonopy_equivalent_atoms,
+    get_steinhardt_parameters as get_steinhardt_parameter_structure,
+    get_centro_symmetry_descriptors as analyse_centro_symmetry,
+    get_diamond_structure_descriptors as analyse_diamond_structure,
+    get_adaptive_cna_descriptors as analyse_cna_adaptive,
+    get_voronoi_volumes as analyse_voronoi_volume,
+    find_solids as analyse_find_solids,
 )
-from structuretoolkit.analyse.strain import get_strain
-from structuretoolkit.analyse.symmetry import get_symmetry
 
 # Build
-from structuretoolkit.build.aimsgb import grainboundary_build, grainboundary_info
-from structuretoolkit.build.compound import B2, C14, C15, C36, D03
-from structuretoolkit.build.sqs import get_sqs_structures
-from structuretoolkit.build.surface import high_index_surface, high_index_surface_info
+from structuretoolkit.build import (
+    grainboundary,
+    get_grainboundary_info,
+    B2,
+    C14,
+    C15,
+    C36,
+    D03,
+    sqs_structures,
+    high_index_surface,
+    get_high_index_surface_info,
+    # for backwards compatibility
+    grainboundary as grainboundary_build,
+    get_grainboundary_info as grainboundary_info,
+    sqs_structures as get_sqs_structures,
+    get_high_index_surface_info as high_index_surface_info,
+)
 
-# Other
-from structuretoolkit.helper import (
+# Visualize
+from structuretoolkit.visualize import plot3d
+
+# Common
+from structuretoolkit.common import (
+    ase_to_pymatgen,
+    pymatgen_to_ase,
+    ase_to_pyscal,
     get_atomic_numbers,
     get_extended_positions,
     get_vertical_length,
     get_wrapped_coordinates,
     select_index,
     center_coordinates_in_unit_cell,
     apply_strain,
+    SymmetryError,
 )
-from structuretoolkit.visualize import plot3d

structuretoolkit/analyse/__init__.py

@@ -0,0 +1,48 @@
+from structuretoolkit.analyse.distance import get_distances_array, find_mic
+from structuretoolkit.analyse.neighbors import get_neighbors, get_neighborhood
+from structuretoolkit.analyse.phonopy import get_equivalent_atoms
+from structuretoolkit.analyse.pyscal import (
+    get_steinhardt_parameters,
+    get_centro_symmetry_descriptors,
+    get_diamond_structure_descriptors,
+    get_adaptive_cna_descriptors,
+    get_voronoi_volumes,
+    find_solids,
+    ase_to_pyscal,
+)
+from structuretoolkit.analyse.spatial import (
+    get_mean_positions,
+    get_average_of_unique_labels,
+    get_interstitials,
+    get_layers,
+    get_voronoi_vertices,
+    get_voronoi_neighbors,
+    get_delaunay_neighbors,
+    get_cluster_positions,
+)
+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 (ase.atoms.Atoms): Atomistic Structure object
+        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 get_symmetry
+
+    return get_symmetry(
+        structure=structure,
+        use_magmoms=use_magmoms,
+        use_elements=use_elements,
+        symprec=symprec,
+        angle_tolerance=angle_tolerance,
+    )

structuretoolkit/analyse/neighbors.py

@@ -3,15 +3,17 @@
 # Distributed under the terms of "New BSD License", see the LICENSE file.
 
 import numpy as np
-from sklearn.cluster import AgglomerativeClustering
 from scipy.sparse import coo_matrix
 from scipy.special import gamma
 from scipy.spatial.transform import Rotation
 from scipy.special import sph_harm
 from scipy.spatial import cKDTree
 import warnings
 import itertools
-from structuretoolkit.helper import get_extended_positions, get_average_of_unique_labels
+from structuretoolkit.common.helper import (
+    get_extended_positions,
+    get_average_of_unique_labels,
+)
 
 __author__ = "Joerg Neugebauer, Sam Waseda"
 __copyright__ = (
@@ -905,6 +907,8 @@ def cluster_by_vecs(
                 `euclidean` is accepted.
 
         """
+        from sklearn.cluster import AgglomerativeClustering
+
         if distance_threshold is None and n_clusters is None:
             distance_threshold = np.min(self.filled.distances)
         dr = self.flattened.vecs
@@ -952,6 +956,8 @@ def cluster_by_distances(
                 obtained from the clustered vectors is used for the distance clustering. Otherwise
                 neigh.distances is used.
         """
+        from sklearn.cluster import AgglomerativeClustering
+
         if distance_threshold is None:
             distance_threshold = 0.1 * np.min(self.flattened.distances)
         dr = self.flattened.distances

structuretoolkit/analyse/phonopy.py

@@ -3,8 +3,6 @@
 # Distributed under the terms of "New BSD License", see the LICENSE file.
 
 import numpy as np
-from phonopy.structure.atoms import PhonopyAtoms
-import spglib as spg
 
 __author__ = "Osamu Waseda"
 __copyright__ = (
@@ -18,7 +16,7 @@
 __date__ = "Sep 1, 2018"
 
 
-def analyse_phonopy_equivalent_atoms(structure, symprec=1e-5, angle_tolerance=-1.0):
+def get_equivalent_atoms(structure, symprec=1e-5, angle_tolerance=-1.0):
     """
     Args: (read phonopy.structure.spglib for more details)
         symprec:
@@ -29,6 +27,9 @@ def analyse_phonopy_equivalent_atoms(structure, symprec=1e-5, angle_tolerance=-1
                 is used to judge symmetry.
 
     """
+    import spglib as spg
+    from phonopy.structure.atoms import PhonopyAtoms
+
     positions = structure.get_scaled_positions()
     cell = structure.cell
     types = structure.get_chemical_symbols()