Merge remote-tracking branch 'origin/main' into primitive

.ci_support/environment.yml

@@ -17,4 +17,4 @@ dependencies:
 - scipy =1.11.2
 - spglib =2.0.2
 - sqsgenerator =0.2
-- pyxtal =0.5.9
+- pyxtal =0.6.0

setup.py

@@ -44,7 +44,7 @@
         "symmetry": ['spglib==2.0.2'],
         "surface": ['spglib==2.0.2', 'pymatgen==2023.8.10'],
         "phonopy": ['phonopy==2.20.0', 'spglib==2.0.2'],
-        "pyxtal": ['pyxtal==0.5.9']
+        "pyxtal": ['pyxtal==0.6.0']
     },
     cmdclass=versioneer.get_cmdclass(),
 )

structuretoolkit/analyse/__init__.py

@@ -1,3 +1,5 @@
+import numpy as np
+
 from structuretoolkit.analyse.distance import find_mic, get_distances_array
 from structuretoolkit.analyse.neighbors import get_neighborhood, get_neighbors
 from structuretoolkit.analyse.phonopy import get_equivalent_atoms
@@ -26,22 +28,223 @@ 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())
+        structure (Atoms): The structure to analyse.
+        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 Symmetry
+
+    return Symmetry(
+        structure=structure,
+        use_magmoms=use_magmoms,
+        use_elements=use_elements,
+        symprec=symprec,
+        angle_tolerance=angle_tolerance,
+    )
+
+
+def symmetrize_vectors(
+    structure,
+    vectors,
+    use_magmoms=False,
+    use_elements=True,
+    symprec=1e-5,
+    angle_tolerance=-1.0,
+):
+    """
+    Symmetrization of natom x 3 vectors according to box symmetries
+
+    Args:
+        structure (Atoms): The structure to analyse.
+        vectors (ndarray/list): natom x 3 array to symmetrize
+        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:
+        (np.ndarray) symmetrized vectors
+    """
+    from structuretoolkit.analyse.symmetry import Symmetry
+
+    return Symmetry(
+        structure=structure,
+        use_magmoms=use_magmoms,
+        use_elements=use_elements,
+        symprec=symprec,
+        angle_tolerance=angle_tolerance,
+    ).symmetrize_vectors(vectors=vectors)
+
+
+def group_points_by_symmetry(
+    structure,
+    points,
+    use_magmoms=False,
+    use_elements=True,
+    symprec=1e-5,
+    angle_tolerance=-1.0,
+):
+    """
+    This function classifies the points into groups according to the box symmetry given by
+    spglib.
+
+    Args:
+        structure (Atoms): The structure to analyse.
+        points: (np.array/list) nx3 array which contains positions
+        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: list of arrays containing geometrically equivalent positions
+
+    It is possible that the original points are not found in the returned list, as the
+    positions outsie the box will be projected back to the box.
+    """
+    from structuretoolkit.analyse.symmetry import Symmetry
+
+    return Symmetry(
+        structure=structure,
+        use_magmoms=use_magmoms,
+        use_elements=use_elements,
+        symprec=symprec,
+        angle_tolerance=angle_tolerance,
+    ).get_arg_equivalent_sites(points)
+
+
+def get_equivalent_points(
+    structure,
+    points,
+    use_magmoms=False,
+    use_elements=True,
+    symprec=1e-5,
+    angle_tolerance=-1.0,
+):
+    """
+
+    Args:
+        structure (Atoms): The structure to analyse.
+        points (list/ndarray): 3d vector
+        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:
+        (ndarray): array of equivalent points with respect to box symmetries
     """
-    from structuretoolkit.analyse.symmetry import get_symmetry
+    from structuretoolkit.analyse.symmetry import Symmetry
 
-    return get_symmetry(
+    return Symmetry(
         structure=structure,
         use_magmoms=use_magmoms,
         use_elements=use_elements,
         symprec=symprec,
         angle_tolerance=angle_tolerance,
+    ).get_arg_equivalent_sites(points)
+
+
+def get_symmetry_dataset(structure, symprec=1e-5, angle_tolerance=-1.0):
+    """
+
+    Args:
+        structure (Atoms): The structure to analyse.
+        symprec (float): Symmetry search precision
+        angle_tolerance (float): Angle search tolerance
+
+    Returns:
+
+    https://atztogo.github.io/spglib/python-spglib.html
+    """
+    from structuretoolkit.analyse.symmetry import Symmetry
+
+    return Symmetry(
+        structure=structure,
+        symprec=symprec,
+        angle_tolerance=angle_tolerance,
+    ).info
+
+
+def get_spacegroup(structure, symprec=1e-5, angle_tolerance=-1.0):
+    """
+
+    Args:
+        structure (Atoms): The structure to analyse.
+        symprec (float): Symmetry search precision
+        angle_tolerance (float): Angle search tolerance
+
+    Returns:
+
+    https://atztogo.github.io/spglib/python-spglib.html
+    """
+    from structuretoolkit.analyse.symmetry import Symmetry
+
+    return Symmetry(
+        structure=structure,
+        symprec=symprec,
+        angle_tolerance=angle_tolerance,
+    ).spacegroup
+
+
+def get_primitive_cell(structure, symprec=1e-5, angle_tolerance=-1.0):
+    """
+
+    Args:
+        structure (Atoms): The structure to analyse.
+        symprec (float): Symmetry search precision
+        angle_tolerance (float): Angle search tolerance
+
+    Returns:
+
+    """
+    from structuretoolkit.analyse.symmetry import Symmetry
+
+    return Symmetry(
+        structure=structure,
+        symprec=symprec,
+        angle_tolerance=angle_tolerance,
+    ).get_primitive_cell(standardize=False)
+
+
+def get_ir_reciprocal_mesh(
+    structure,
+    mesh,
+    is_shift=np.zeros(3, dtype="intc"),
+    is_time_reversal=True,
+    symprec=1e-5,
+):
+    """
+
+    Args:
+        structure (Atoms): The structure to analyse.
+        mesh:
+        is_shift:
+        is_time_reversal:
+        symprec (float): Symmetry search precision
+
+    Returns:
+
+    """
+    from structuretoolkit.analyse.symmetry import Symmetry
+
+    return Symmetry(
+        structure=structure,
+        symprec=symprec,
+    ).get_ir_reciprocal_mesh(
+        mesh=mesh,
+        is_shift=is_shift,
+        is_time_reversal=is_time_reversal,
     )

structuretoolkit/analyse/symmetry.py

@@ -383,29 +383,3 @@ def get_ir_reciprocal_mesh(
         if mesh is None:
             raise SymmetryError(spglib.spglib.spglib_error.message)
         return mesh
-
-
-def get_symmetry(
-    structure, use_magmoms=False, use_elements=True, symprec=1e-5, angle_tolerance=-1.0
-):
-    """
-
-    Args:
-        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
-
-
-    """
-    return Symmetry(
-        structure=structure,
-        use_magmoms=use_magmoms,
-        use_elements=use_elements,
-        symprec=symprec,
-        angle_tolerance=angle_tolerance,
-    )

structuretoolkit/common/__init__.py

@@ -13,3 +13,4 @@
     pymatgen_to_ase,
 )
 from structuretoolkit.common.pyscal import ase_to_pyscal
+from structuretoolkit.common.phonopy import phonopy_to_atoms, atoms_to_phonopy

structuretoolkit/common/phonopy.py

@@ -0,0 +1,36 @@
+def phonopy_to_atoms(ph_atoms):
+    """
+    Convert Phonopy Atoms to ASE-like Atoms
+    Args:
+        ph_atoms: Phonopy Atoms object
+
+    Returns: ASE-like Atoms object
+
+    """
+    from ase.atoms import Atoms
+
+    return Atoms(
+        symbols=list(ph_atoms.get_chemical_symbols()),
+        positions=list(ph_atoms.get_positions()),
+        cell=list(ph_atoms.get_cell()),
+        pbc=True,
+    )
+
+
+def atoms_to_phonopy(atom):
+    """
+    Convert ASE-like Atoms to Phonopy Atoms
+    Args:
+        atom: ASE-like Atoms
+
+    Returns:
+        Phonopy Atoms
+
+    """
+    from phonopy.structure.atoms import PhonopyAtoms
+
+    return PhonopyAtoms(
+        symbols=list(atom.get_chemical_symbols()),
+        scaled_positions=list(atom.get_scaled_positions()),
+        cell=list(atom.get_cell()),
+    )