Add seekpath get_path() function

.ci_support/environment.yml

@@ -15,5 +15,6 @@ dependencies:
 - pyscal =2.10.18
 - scikit-learn =1.3.0
 - scipy =1.11.3
+- seekpath =2.1.0
 - spglib =2.0.2
 - sqsgenerator =0.3

setup.py

@@ -44,7 +44,8 @@
         "symmetry": ['spglib==2.1.0'],
         "surface": ['spglib==2.1.0', 'pymatgen==2023.9.10'],
         "phonopy": ['phonopy==2.20.0', 'spglib==2.1.0'],
-        "pyxtal": ['pyxtal==0.6.0']
+        "pyxtal": ['pyxtal==0.6.0'],
+        "seekpath": ['seekpath==2.1.0'],
     },
     cmdclass=versioneer.get_cmdclass(),
 )

structuretoolkit/analyse/__init__.py

@@ -1,6 +1,7 @@
 import numpy as np
 
 from structuretoolkit.analyse.distance import find_mic, get_distances_array
+from structuretoolkit.analyse.line import create_line_mode_structure
 from structuretoolkit.analyse.neighbors import get_neighborhood, get_neighbors
 from structuretoolkit.analyse.phonopy import get_equivalent_atoms
 from structuretoolkit.analyse.pyscal import (

structuretoolkit/analyse/line.py

@@ -0,0 +1,55 @@
+from ase.atoms import Atoms
+
+
+def create_line_mode_structure(
+    structure,
+    with_time_reversal=True,
+    recipe="hpkot",
+    threshold=1e-07,
+    symprec=1e-05,
+    angle_tolerance=-1.0,
+):
+    """
+    Uses 'seekpath' to create a new structure with high symmetry points and path for band structure calculations.
+
+    Args:
+        with_time_reversal (bool): if False, and the group has no inversion symmetry,
+            additional lines are returned as described in the HPKOT paper.
+        recipe (str): choose the reference publication that defines the special points and paths.
+            Currently, only 'hpkot' is implemented.
+        threshold (float): the threshold to use to verify if we are in and edge case
+            (e.g., a tetragonal cell, but a==c). For instance, in the tI lattice, if abs(a-c) < threshold,
+            a EdgeCaseWarning is issued. Note that depending on the bravais lattice,
+            the meaning of the threshold is different (angle, length, …)
+        symprec (float): the symmetry precision used internally by SPGLIB
+        angle_tolerance (float): the angle_tolerance used internally by SPGLIB
+
+    Returns:
+        pyiron.atomistics.structure.atoms.Atoms: new structure
+    """
+    import seekpath
+
+    input_structure = (structure.cell, structure.get_scaled_positions(), self.indices)
+    sp_dict = seekpath.get_path(
+        structure=input_structure,
+        with_time_reversal=with_time_reversal,
+        recipe=recipe,
+        threshold=threshold,
+        symprec=symprec,
+        angle_tolerance=angle_tolerance,
+    )
+
+    original_element_list = structure.get_chemical_symbols()
+    element_list = [original_element_list[l] for l in sp_dict["primitive_types"]]
+    positions = sp_dict["primitive_positions"]
+    pbc = structure.pbc
+    cell = sp_dict["primitive_lattice"]
+
+    struc_new = Atoms(
+        elements=element_list, scaled_positions=positions, pbc=pbc, cell=cell
+    )
+
+    struc_new._set_high_symmetry_points(sp_dict["point_coords"])
+    struc_new._set_high_symmetry_path({"full": sp_dict["path"]})
+
+    return struc_new