import ase
from ase.io import *
import smact.builder as build
import smact.surface as surface
PbZrO = build.cubic_perovskite(['Pb', 'Zr', 'O'])
S100 = surface.cut100(PbZrO)
S110 = surface.cut110(PbZrO)
S111 = surface.cut111(PbZrO)
write('100.cif', S100)
write('110.cif', S110)
write('111.cif', S111)
write('Bulk.cif', PbZrO)
def pretty_print_atoms(atoms, linewrap=15):
entries = [
"{0:5.3f} {1:5.3f} {2:5.3f} {symbol}".format(*position, symbol=symbol)
for position, symbol in zip(atoms.get_positions(), atoms.get_chemical_symbols())
]
for output_i in range(linewrap):
line = ""
for i, entry in enumerate(entries):
if output_i == i % linewrap:
line = line + entry + "\t"
print line
# Build the input
smact_lattice, test_case = builder.cubic_perovskite(["Ba", "Ti", "O"], repetitions=[2, 2, 2])
hlinewidth = 68
print ("-" * hlinewidth)
print "Original coordinates: "
pretty_print_atoms(test_case)
print ("-" * hlinewidth)
# Do the single substitution first, it is trivial as all Ba
# sites are equivalent we will choose the first Ba
subs_site = [0.0, 0.0, 0.0]
single_substitution = distort.make_substitution(test_case, subs_site, "Sr")
print "Single: "
pretty_print_atoms(single_substitution)
entries = [
"{0:5.3f} {1:5.3f} {2:5.3f} {symbol}".format(*position, symbol=symbol)
for position, symbol in zip(atoms.get_positions(),
atoms.get_chemical_symbols())
]
for output_i in range(linewrap):
line = ''
for i, entry in enumerate(entries):
if (output_i == i % linewrap):
line = line + entry + '\t'
print line
# Build the input
smact_lattice, test_case = builder.cubic_perovskite(['Ba', 'Ti', 'O'],
repetitions=[2, 2, 2])
hlinewidth = 68
print('-' * hlinewidth)
print "Original coordinates: "
pretty_print_atoms(test_case)
print('-' * hlinewidth)
# Do the single substitution first, it is trivial as all Ba
# sites are equivalent we will choose the first Ba
subs_site = [0.0, 0.0, 0.0]
single_substitution = distort.make_substitution(test_case, subs_site, "Sr")
print "Single: "
pretty_print_atoms(single_substitution)
# Example script of using distorter, generate all possible (symmetry inequivalent) subsitiutions of Sr on Ba # sites; single and double substitutions. import ase import smact.builder as builder import smact.distorter as distort import numpy as np import ase.io as io # Build the input test_case = builder.cubic_perovskite(['Ba','Ti','O'],repetitions=[2,2,2]) print "------------------------------" print "Original coordinates: ", test_case print "------------------------------" # Do the single substitution first, it is trivial as all Ba sites are equivalent we will choose the first Ba subs_site = [0.0, 0.0, 0.0] # Fractional coordinates of the site to substitute single_substitution = distort.make_substitution(test_case,subs_site,"Sr") print "Single: ", single_substitution #Build a sub-lattice you wish to disorder [test case do the Ba sub-lattice] sub_lattice = distort.build_sub_lattice(single_substitution,"Ba") # Enumerate the inequivalent sites inequivalent_sites = distort.get_inequivalent_sites(sub_lattice,single_substitution)