cation_utilities.py

__all__ = ['count_rings','add_cation']

from ase import Atoms
from ase.io import write
import os
import numpy as np

def count_rings(paths):
    Class = []
    for p in paths:
        Class.append(int(len(p)/2))

    paths = [x for _,x in sorted(zip(Class,paths),reverse=True)]
    Class.sort(reverse=True)

    class_count = []
    for i in range(len(Class)):
        if i == 0:
            class_count.append(1)
        else:
            counter = 1
            for j in range(i):
                if Class[i]==Class[j]:
                    counter+=1
            class_count.append(counter)

    return Class, class_count, paths

def add_cation(atoms,large_atoms,radii,index,symbol,paths,included_rings,class_count,path=None,bvect=None):
    traj= []
    locations = []
    for i in range(len(paths)):
        p = paths[i]
        if len(p) in included_rings:
            trans = atoms[index].position - large_atoms[index].position
            positions = large_atoms[p].positions
            co = sum(positions)/len(positions)
            co +=trans
            vector = co-atoms[index].position
            vector = np.array(vector)
            vhat = vector/np.linalg.norm(vector)

            if bvect:
                bond_length = bvect
            else:
                bond_length = radii[symbol]+2/radii[symbol]

            new_p = [atoms[index].position +bond_length*vhat]

            adsorbate = Atoms(symbol)
            adsorbate.set_positions(new_p)
            c_atoms = atoms+adsorbate
            c_atoms.wrap()
            traj+=[c_atoms]
            locations.append('{1}MR'.format(path,str(int(len(p)/2))))
            # write POSCAR for each structure

            if path:
                os.makedirs('{0}/D-{1}MR-{2}'.format(path,str(int(len(p)/2)),str(class_count[i])),exist_ok=True)

                write('{0}/D-{1}MR-{2}/POSCAR'.format(path,str(int(len(p)/2)),str(class_count[i])),c_atoms, sort = True)
    return traj, locations