organize repo

README.md

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+# perovskites-oct-distortions
+Collection of python functions useful to manipulate the structures of hybrid organic/inorganic perovskites.
+Main directory contains:
+- `rotations.py` : functions to apply random rotations to the organic molecules occupiying the A site in your perovskite. Useful to break symmetries, avoid the polar parallel arrangement (if your cation has a dipole moment, e.g. formamdinium)
+- folder `octahedral_distortions`: hosts the file `oct_distortions.py`. This contains the function `get_tilting_angles`, which calculates the average of the Pb-I-Pb angles in your structure. Values close to 180º indicate small tilting while angles deviating from 180º point towards significant tilting of the octahedra.

license

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+MIT License
+
+Copyright (c) 2022 Laboratory of Computational Chemistry and Biochemistry - EPFL
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

rotations.py

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+# Funtions to rotate the molecules in the A cation position, useful to avoid all molecules being parallel 
+import random
+from copy import deepcopy
+from pymatgen.core.structure import Structure   
+import numpy as np 
+
+def get_center_of_mass(
+    structure: Structure,
+    sites_indexes: list
+    ) -> np.array:
+    """
+    Calculates center of mass for sites specified as sites_indexes 
+    """
+    center = np.zeros(3)
+    total_weight= 0
+    for index in sites_indexes:
+        site = structure[index]
+        wt = site.species.weight
+        center += site.coords * wt
+        total_weight += wt
+    return center/ total_weight
+
+def get_a_cation_sites(
+    struct: Structure,
+    a_cation_center_species: str='C',
+    radius_cutoff: float = 3.5, # in Angstroms
+) -> list:
+    """
+    Get the indices of the A cation sites in the structure.
+    Args:
+        struct (Structure): structure
+        a_cation_center_species (str, optional): Species of the A cation center. Defaults to 'C'.
+        radius_cutoff (float, optional): Radius cutoff for finding the neighbours of the A cation center. \
+            Defaults to 3.5 Angstroms.
+    """
+    # Get the central atom of all A cations, by default Carbon (e.g, A_cation = formamidinium)
+    carbon_sites = [(index, site) for index, site in enumerate(struct) if site.species_string == a_cation_center_species]
+    fa_molecules = []
+    count = 0
+    for index, carbon in carbon_sites:
+        # Get the indices of all atoms bonded to the central atom
+        neighbors = struct.get_neighbors(carbon, r= radius_cutoff)
+        print([site.species_string for site in neighbors]) # Make sure we're getting the right atoms
+        fa_molecules.append([index,])
+        fa_molecules[count] += ([site.index for site in neighbors])
+        count += 1
+    # assert all elements in list have the same length
+    assert len(set([len(molecule) for molecule in fa_molecules])) == 1
+    return fa_molecules
+
+def rotate_a_cation(
+    struct: Structure,
+    fa_molecules: list,
+    maximum_angle: int = 180, # in degrees
+    rotation_axis: list=[0,1,0],
+):
+    """ 
+    Rotates A cation molecules by random angles chosen between -maximum_angle and +maximum_angle.
+
+    Args:
+        struct (Structure): structure
+        fa_molecules (list): list of lists with the indices of the sites for each molecule (e.g. [[0,1,2,3], [4,5,6,7]])
+        maximum_angle (int, optional): Random angles will be chosen between [-maximum_angle, +maximum_angle] Defaults to 180 degrees.
+        rotation_axis (list, optional): Vector to rotate around. \
+            For formamidinium, the vector defined between the two Nitrogens (for FA). Defaults to [0,1,0].
+    Returns:
+        Structure: structure with A cation molecules rotated 
+    """
+    struct_rotated = deepcopy(struct)
+    # Need to perturb structure to break symmetries. \
+    # Otherwise, it breaks some of the FA molecules when rotating (does weird shit with the H bonded to the C)
+    struct_rotated.perturb(distance = 0.000001)
+    for sites in fa_molecules:
+        angle = random.randrange(-maximum_angle, maximum_angle)
+        #print(f"Rotating by {angle} degrees")
+        center_of_mass = get_center_of_mass(struct_rotated, sites)
+        struct_rotated.rotate_sites(
+            indices = sites, 
+            theta = angle * np.pi / 180,
+            axis = rotation_axis,
+            anchor = center_of_mass, # struct_rotated[sites[0]].coords,
+            to_unit_cell = False,
+            )
+    return struct_rotated