Clean up the structuretoolkit

structuretoolkit/analyse/neighbors.py

@@ -51,7 +51,7 @@ class Tree:
     def __init__(self, ref_structure):
         """
         Args:
-            ref_structure (pyiron_atomistics.atomistics.structure.atoms.Atoms): Reference
+            ref_structure (ase.atoms.Atoms): Reference
                 structure.
         """
         self._distances = None
@@ -399,7 +399,7 @@ def get_neighborhood(
 
         Returns:
 
-            pyiron.atomistics.structure.atoms.Tree: Neighbors instances with the neighbor indices,
+            structuretoolkit.analyse.neighbors.Tree: Neighbors instances with the neighbor indices,
                 distances and vectors
 
         """
@@ -799,8 +799,8 @@ def get_shell_matrix(
 
 
         Example:
-            from pyiron_atomistics import Project
-            structure = Project('.').create_structure('Fe', 'bcc', 2.83).repeat(2)
+            from ase.build import bulk
+            structure = bulk('Fe', 'bcc', 2.83).repeat(2)
             J = -0.1 # Ising parameter
             magmoms = 2*np.random.random((len(structure)), 3)-1 # Random magnetic moments between -1 and 1
             neigh = structure.get_neighbors(num_neighbors=8) # Iron first shell
@@ -1126,7 +1126,7 @@ def get_neighbors(
 
     Returns:
 
-        pyiron.atomistics.structure.atoms.Neighbors: Neighbors instances with the neighbor
+        structuretoolkit.analyse.neighbors.Neighbors: Neighbors instances with the neighbor
             indices, distances and vectors
 
     """
@@ -1218,7 +1218,7 @@ def get_neighborhood(
 
     Returns:
 
-        pyiron.atomistics.structure.atoms.Tree: Neighbors instances with the neighbor
+        structuretoolkit.analyse.neighbors.Tree: Neighbors instances with the neighbor
             indices, distances and vectors
 
     """

structuretoolkit/analyse/pyscal.py

@@ -43,7 +43,7 @@ def get_steinhardt_parameter_structure(
         numpy.ndarray: (number of q's, number of atoms) shaped array of q parameters
         numpy.ndarray: If `clustering=True`, an additional per-atom array of cluster ids is also returned
     """
-    sys = pyiron_to_pyscal_system(structure)
+    sys = ase_to_pyscal_system(structure)
     q = (4, 6) if q is None else q
 
     sys.find_neighbors(method=neighbor_method, cutoff=cutoff)
@@ -72,7 +72,7 @@ def analyse_centro_symmetry(structure, num_neighbors=12):
     Returns:
         csm (list) : list of centrosymmetry parameter
     """
-    sys = pyiron_to_pyscal_system(structure)
+    sys = ase_to_pyscal_system(structure)
     return np.array(sys.calculate_centrosymmetry(nmax=num_neighbors))
 
 
@@ -93,7 +93,7 @@ def analyse_diamond_structure(structure, mode="total", ovito_compatibility=False
     Returns:
         (depends on `mode`)
     """
-    sys = pyiron_to_pyscal_system(structure)
+    sys = ase_to_pyscal_system(structure)
     diamond_dict = sys.identify_diamond()
 
     ovito_identifiers = [
@@ -183,7 +183,7 @@ def analyse_cna_adaptive(structure, mode="total", ovito_compatibility=False):
     Use common neighbor analysis
 
     Args:
-        structure (pyiron_atomistics.structure.atoms.Atoms): The structure to analyze.
+        structure (ase.atoms.Atoms): The structure to analyze.
         mode ("total"/"numeric"/"str"): Controls the style and level
             of detail of the output.
             - total : return number of atoms belonging to each structure
@@ -195,7 +195,7 @@ def analyse_cna_adaptive(structure, mode="total", ovito_compatibility=False):
     Returns:
         (depends on `mode`)
     """
-    sys = pyiron_to_pyscal_system(structure)
+    sys = ase_to_pyscal_system(structure)
     if mode not in ["total", "numeric", "str"]:
         raise ValueError("Unsupported mode")
 
@@ -238,21 +238,21 @@ def analyse_voronoi_volume(structure):
     Calculate the Voronoi volume of atoms
 
     Args:
-        structure : (pyiron_atomistics.structure.atoms.Atoms): The structure to analyze.
+        structure : (ase.atoms.Atoms): The structure to analyze.
     """
-    sys = pyiron_to_pyscal_system(structure)
+    sys = ase_to_pyscal_system(structure)
     sys.find_neighbors(method="voronoi")
     structure = sys.atoms
     return np.array([atom.volume for atom in structure])
 
 
-def pyiron_to_pyscal_system(structure):
+def ase_to_pyscal_system(structure):
     """
     Converts atoms to ase atoms and than to a pyscal system.
     Also adds the pyscal publication.
 
     Args:
-        structure (pyiron atoms): Structure to convert.
+        structure (ase.atoms.Atoms): Structure to convert.
 
     Returns:
         Pyscal system: See the pyscal documentation.
@@ -296,7 +296,7 @@ def analyse_find_solids(
         int: number of solids,
         pyscal system: pyscal system when return_sys=True
     """
-    sys = pyiron_to_pyscal_system(structure)
+    sys = ase_to_pyscal_system(structure)
     sys.find_neighbors(method=neighbor_method, cutoff=cutoff)
     sys.find_solids(
         bonds=bonds,

structuretoolkit/analyse/spatial.py

@@ -185,7 +185,7 @@ def neigh(self):
         Neighborhood information of each interstitial candidate and their surrounding atoms. E.g.
         `class.neigh.distances[0][0]` gives the distance from the first interstitial candidate to
         its nearest neighboring atoms. The functionalities of `neigh` follow those of
-        `pyiron_atomistics.structure.atoms.neighbors`.
+        `structuretoolkit.analyse.neighbors`.
         """
         if self._neigh is None:
             self._neigh = get_neighborhood(
@@ -578,7 +578,7 @@ def cluster_positions(
     Example I:
 
     ```
-    analyse = Analyze(some_pyiron_structure)
+    analyse = Analyze(some_ase_structure)
     positions = analyse.cluster_points(eps=2)
     ```
 
@@ -589,7 +589,7 @@ def cluster_positions(
     Example II:
 
     ```
-    analyse = Analyze(some_pyiron_structure)
+    analyse = Analyze(some_ase_structure)
     print(analyse.cluster_positions([3*[0.], 3*[1.]], eps=3))
     ```
 

structuretoolkit/analyse/strain.py

@@ -29,9 +29,9 @@ def __init__(
         """
 
         Args:
-            structure (pyiron_atomistics.atomistics.structure.Atoms): Structure to calculate the
+            structure (ase.atoms.Atoms): Structure to calculate the
                 strain values.
-            ref_structure (pyiron_atomistics.atomistics.structure.Atoms): Reference bulk structure
+            ref_structure (ase.atoms.Atoms): Reference bulk structure
                 (against which the strain is calculated)
             num_neighbors (int): Number of neighbors to take into account to calculate the local
                 frame. If not specified, it is estimated based on cna analysis (only available if

structuretoolkit/analyse/symmetry.py

@@ -50,7 +50,7 @@ def __init__(
     ):
         """
         Args:
-            structure (:class:`pyiron.atomistics.structure.atoms.Atoms`): reference Atom structure.
+            structure (:class:`ase.atoms.Atoms`): reference Atom structure.
             use_magmoms (bool): Whether to consider magnetic moments (cf.
             get_initial_magnetic_moments())
             use_elements (bool): If False, chemical elements will be ignored
@@ -334,7 +334,7 @@ def get_primitive_cell(
             use_elements (bool): If False, chemical elements will be ignored
 
         Returns:
-            (pyiron_atomistics.atomistics.structure.atoms.Atoms): Primitive cell
+            (ase.atoms.Atoms): Primitive cell
 
         Example (assume `basis` is a primitive cell):
 
@@ -391,7 +391,7 @@ def get_symmetry(
         angle_tolerance (float): Angle search tolerance
 
     Returns:
-        symmetry (:class:`pyiron.atomistics.structure.symmetry.Symmetry`): Symmetry class
+        symmetry (:class:`structuretoolkit.analyse.symmetry.Symmetry`): Symmetry class
 
 
     """

structuretoolkit/build/aimsgb.py

@@ -58,7 +58,7 @@ def grainboundary_build(
         axis : Rotational axis for the GB you want to construct (for example, axis=[1,0,0])
         sigma (int) : The sigma value of the GB you want to construct (for example, sigma=5)
         plane: The grain boundary plane of the GB you want to construct (for example, plane=[2,1,0])
-        initial_struct : Initial bulk structure from which you want to construct the GB (a pyiron
+        initial_struct : Initial bulk structure from which you want to construct the GB (a ase
                         structure object).
         delete_layer : To delete layers of the GB. For example, delete_layer='1b0t1b0t'. The first
                        4 characters is for first grain and the other 4 is for second grain. b means

structuretoolkit/build/surface.py

@@ -134,7 +134,7 @@ def high_index_surface(
         vacuum (float): Thickness of vacuum on the top of the slab. default:10
 
     Returns:
-        slab: pyiron_atomistics.atomistics.structure.atoms.Atoms instance Required surface
+        slab: ase.atoms.Atoms instance Required surface
     """
     basis = bulk(
         name=element,

structuretoolkit/helper.py

@@ -167,7 +167,7 @@ def center_coordinates_in_unit_cell(structure, origin=0, eps=1e-4):
         eps (float): Tolerance to detect atoms at cell edges
 
     Returns:
-        :class:`pyiron_atomistics.atomistics.structure.atoms.Atoms`: reference to this structure
+        :class:`ase.atoms.Atoms`: reference to this structure
     """
     if any(structure.pbc):
         structure.set_scaled_positions(