def process_structure(s: Structure):
# kill off any lone carbons or those with only 1 bond
from pyputil.structure.bonds import calculate_bond_list
n_bonds = np.array([len(b) for b in calculate_bond_list(s)])
s.remove_sites(np.where(n_bonds <= 1)[0])
# add hydrogen atoms on the edges
add_hydrogen(s, cutoff=1.05, dist=DEFAULT_CH_DIST / DEFAULT_CC_DIST)
# scale coordinates to bond distance
s.lattice = Lattice(matrix=s.lattice.matrix * bond_dist)
return s
#
# Maintainer: Wei Xie
# Last updated: 2014-02-07
##############################################################
import sys, getopt, os
import shutil
import matplotlib.pyplot as plt
import numpy as np
import scipy as sp
from pymatgen import Lattice, Structure
from pymatgen.io.smartio import read_structure, write_structure
stdX = read_structure("POSCAR_std")
prmX = read_structure("POSCAR_prm")
stdL = Structure.lattice(stdX)
prmL = Structure.lattice(stdX)
def finite_size_scale(standard, ssize, primordial, fsize, psize=[1,1,1]):
"""Function to perform finite size scaling for defect structure relaxation
Inputs:
standard = POSCAR file of structure containing defect
ssize = Supercell size of structure with defect (list of size 3)
primordial = POSCAR file of structure for basic unit of perfect cell
psize = Supercell size of structure for padding. Default = [1,1,1] (list of size 3)
fsize = Desired supercell size of final structure (list of size 3)
Outputs:
POSCAR file of structure containing defect and padding"""
#
# Maintainer: Wei Xie
# Last updated: 2014-02-07
##############################################################
import sys, getopt, os
import shutil
import matplotlib.pyplot as plt
import numpy as np
import scipy as sp
from pymatgen import Lattice, Structure
from pymatgen.io.smartio import read_structure, write_structure
stdX = read_structure("POSCAR_std")
prmX = read_structure("POSCAR_prm")
stdL = Structure.lattice(stdX)
prmL = Structure.lattice(stdX)
def finite_size_scale(standard, ssize, primordial, fsize, psize=[1, 1, 1]):
"""Function to perform finite size scaling for defect structure relaxation
Inputs:
standard = POSCAR file of structure containing defect
ssize = Supercell size of structure with defect (list of size 3)
primordial = POSCAR file of structure for basic unit of perfect cell
psize = Supercell size of structure for padding. Default = [1,1,1] (list of size 3)
fsize = Desired supercell size of final structure (list of size 3)
Outputs:
POSCAR file of structure containing defect and padding"""
# Check if the input sizes work out with the desired final size
