use updated API

pyiron_atomistics/atomistics/job/sqs.py

@@ -5,7 +5,7 @@
 import random
 import warnings
 import itertools
-from structuretoolkit import get_sqs_structures
+from structuretoolkit.build import sqs_structures
 from pyiron_atomistics.atomistics.job.atomistic import AtomisticGenericJob
 from pyiron_base import state, DataContainer, GenericParameters, ImportAlarm
 from pyiron_atomistics.atomistics.structure.atoms import Atoms, ase_to_pyiron
@@ -238,7 +238,7 @@ def _number_of_structures(self):
 
     # This function is executed
     def run_static(self):
-        structure_lst, decmp, iterations, cycle_time = get_sqs_structures(
+        structure_lst, decmp, iterations, cycle_time = sqs_structures(
             structure=self.structure,
             mole_fractions={k: v for k, v in self.input.mole_fractions.items()},
             weights=self.input.weights,

pyiron_atomistics/atomistics/structure/_visualize.py

@@ -3,7 +3,7 @@
 # Distributed under the terms of "New BSD License", see the LICENSE file.
 
 import numpy as np
-from structuretoolkit import plot3d
+from structuretoolkit.visualize import plot3d
 
 __author__ = "Joerg Neugebauer, Sudarsan Surendralal"
 __copyright__ = (

pyiron_atomistics/atomistics/structure/analyse.py

@@ -11,14 +11,14 @@
     analyse_voronoi_volume,
     analyse_find_solids,
 )
-from structuretoolkit import (
+from structuretoolkit.analyse import (
     get_strain,
     get_interstitials,
     get_layers,
     get_voronoi_vertices,
     get_voronoi_neighbors,
     get_delaunay_neighbors,
-    cluster_positions,
+    get_cluster_positions,
 )
 from pyiron_base import Deprecator
 
@@ -418,7 +418,7 @@ def cluster_positions(
             positions (numpy.ndarray): Mean positions
             label (numpy.ndarray): Labels of the positions (returned when `return_labels = True`)
         """
-        return cluster_positions(
+        return get_cluster_positions(
             structure=self._structure,
             positions=positions,
             eps=eps,

pyiron_atomistics/atomistics/structure/atoms.py

@@ -12,14 +12,14 @@
 import warnings
 import seekpath
 import importlib
-from structuretoolkit import (
+from structuretoolkit.analyse import (
     get_symmetry,
     get_neighbors,
     get_neighborhood,
-    center_coordinates_in_unit_cell,
     get_distances_array,
     find_mic,
 )
+from structuretoolkit.common import center_coordinates_in_unit_cell
 from pyiron_atomistics.atomistics.structure.atom import (
     Atom,
     ase_to_pyiron as ase_to_pyiron_atom,

pyiron_atomistics/atomistics/structure/factories/aimsgb.py

@@ -2,7 +2,7 @@
 # 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.
 
-from structuretoolkit import grainboundary_build, grainboundary_info
+from structuretoolkit.build import grainboundary, get_grainboundary_info
 from pyiron_atomistics.atomistics.structure.atoms import ase_to_pyiron
 
 __author__ = "Ujjal Saikia"
@@ -39,7 +39,7 @@ def info(axis, max_sigma):
         To construct the grain boundary select a GB plane and sigma value from the list and pass it to the
         GBBuilder.gb_build() function along with the rotational axis and initial bulk structure.
         """
-        return grainboundary_info(axis=axis, max_sigma=max_sigma)
+        return get_grainboundary_info(axis=axis, max_sigma=max_sigma)
 
     @staticmethod
     def build(
@@ -79,7 +79,7 @@ def build(
             :class:`.Atoms`: final grain boundary structure
         """
         return ase_to_pyiron(
-            grainboundary_build(
+            grainboundary(
                 axis=axis,
                 sigma=sigma,
                 plane=plane,

pyiron_atomistics/atomistics/structure/factories/compound.py

@@ -2,7 +2,7 @@
 # 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.
 
-from structuretoolkit import B2, C14, C15, C36, D03
+from structuretoolkit.build import B2, C14, C15, C36, D03
 from pyiron_atomistics.atomistics.structure.atoms import ase_to_pyiron
 
 __author__ = "Liam Huber"

pyiron_atomistics/atomistics/structure/factory.py

@@ -25,9 +25,9 @@
     surface as ase_surf,
 )
 import numpy as np
-from structuretoolkit import (
+from structuretoolkit.build import (
     high_index_surface,
-    high_index_surface_info,
+    get_high_index_surface_info,
 )
 from pyiron_atomistics.atomistics.structure.factories.ase import AseFactory
 from pyiron_atomistics.atomistics.structure.factories.atomsk import (
@@ -500,7 +500,7 @@ def high_index_surface_info(
             fin_kink_orientation: The kink orientation lying in the terrace
             fin_step_orientation: The step orientation lying in the terrace
         """
-        return high_index_surface_info(
+        return get_high_index_surface_info(
             element=element,
             crystal_structure=crystal_structure,
             lattice_constant=lattice_constant,

pyiron_atomistics/atomistics/structure/phonopy.py

@@ -29,7 +29,7 @@ def analyse_phonopy_equivalent_atoms(atoms, symprec=1e-5, angle_tolerance=-1.0):
 
     """
     state.publications.add(publication())
-    return stk.analyse_phonopy_equivalent_atoms(
+    return stk.analyse.get_equivalent_atoms(
         structure=atoms, symprec=symprec, angle_tolerance=angle_tolerance
     )
 

pyiron_atomistics/atomistics/structure/pyscal.py

@@ -6,7 +6,6 @@
 import structuretoolkit as stk
 from pyiron_base import state
 import pyiron_atomistics.atomistics.structure.atoms
-import pyscal.core as pc
 from pyiron_base import Deprecator
 
 deprecate = Deprecator()
@@ -52,7 +51,7 @@ def get_steinhardt_parameter_structure(
     if clustering == False:
         n_clusters = None
     state.publications.add(publication())
-    return stk.get_steinhardt_parameter_structure(
+    return stk.analyse.get_steinhardt_parameters(
         structure=structure,
         neighbor_method=neighbor_method,
         cutoff=cutoff,
@@ -74,7 +73,7 @@ def analyse_centro_symmetry(structure, num_neighbors=12):
         csm (list) : list of centrosymmetry parameter
     """
     state.publications.add(publication())
-    return stk.analyse_centro_symmetry(structure=structure, num_neighbors=num_neighbors)
+    return stk.analyse.get_centro_symmetry_descriptors(structure=structure, num_neighbors=num_neighbors)
 
 
 def analyse_diamond_structure(structure, mode="total", ovito_compatibility=False):
@@ -95,7 +94,7 @@ def analyse_diamond_structure(structure, mode="total", ovito_compatibility=False
         (depends on `mode`)
     """
     state.publications.add(publication())
-    return stk.analyse_diamond_structure(
+    return stk.analyse.get_diamond_structure_descriptors(
         structure=structure, mode=mode, ovito_compatibility=ovito_compatibility
     )
 
@@ -118,7 +117,7 @@ def analyse_cna_adaptive(structure, mode="total", ovito_compatibility=False):
         (depends on `mode`)
     """
     state.publications.add(publication())
-    return stk.analyse_cna_adaptive(
+    return stk.analyse.get_adaptive_cna_descriptors(
         structure=structure, mode=mode, ovito_compatibility=ovito_compatibility
     )
 
@@ -131,7 +130,7 @@ def analyse_voronoi_volume(structure):
         structure : (pyiron_atomistics.structure.atoms.Atoms): The structure to analyze.
     """
     state.publications.add(publication())
-    return stk.analyse_voronoi_volume(structure=structure)
+    return stk.analyse.get_voronoi_volumes(structure=structure)
 
 
 def pyiron_to_pyscal_system(structure):
@@ -146,12 +145,7 @@ def pyiron_to_pyscal_system(structure):
         Pyscal system: See the pyscal documentation.
     """
     state.publications.add(publication())
-    sys = pc.System()
-    sys.read_inputfile(
-        pyiron_atomistics.atomistics.structure.atoms.pyiron_to_ase(structure),
-        format="ase",
-    )
-    return sys
+    return stk.common.ase_to_pyscal(pyiron_atomistics.atomistics.structure.atoms.pyiron_to_ase(structure))
 
 
 def analyse_find_solids(
@@ -186,8 +180,8 @@ def analyse_find_solids(
         pyscal system: pyscal system when return_sys=True
     """
     state.publications.add(publication())
-    return stk.analyse_find_solids(
-        atoms=structure,
+    return stk.analyse.find_solids(
+        structure=structure,
         neighbor_method=neighbor_method,
         cutoff=cutoff,
         bonds=bonds,

pyiron_atomistics/atomistics/structure/structurestorage.py

@@ -15,7 +15,7 @@
 from pyiron_base import FlattenedStorage, ImportAlarm
 from pyiron_atomistics.atomistics.structure.atom import Atom
 from pyiron_atomistics.atomistics.structure.atoms import Atoms
-from structuretoolkit.analyse.symmetry import SymmetryError
+from structuretoolkit.common.error import SymmetryError
 from pyiron_atomistics.atomistics.structure.neighbors import NeighborsTrajectory
 import pyiron_atomistics.atomistics.structure.has_structure as pa_has_structure
 

tests/atomistics/structure/test_symmetry.py

@@ -5,7 +5,7 @@
 import unittest
 import numpy as np
 from pyiron_atomistics.atomistics.structure.atoms import Atoms
-from structuretoolkit.analyse.symmetry import SymmetryError
+from structuretoolkit.common.error import SymmetryError
 from pyiron_atomistics.atomistics.structure.factory import StructureFactory