def run(self):
import tempfile
working_path = os.getcwd()
self.mcell.perturb(self.radius)
gcell = self.mcell.to_gcell()
out = GeneralIO(gcell)
ofname = "{:}_PURB.vasp".format(self.basefname.split('.')[0])
print("PROCESSING: {:}".format(self.infile))
out.write_file(ofname)
def run(self):
# Create directory contain POSCARs
import random
import string
rd_suffix = ''.join(
random.choices(string.ascii_uppercase + string.digits, k=5))
working_path = os.getcwd()
out_dir = os.path.join(
working_path,
'STRUCTURES_{0:}_{1:}'.format(self.comment, rd_suffix))
if not os.path.exists(out_dir):
os.makedirs(out_dir)
else:
shutil.rmtree(out_dir)
os.makedirs(out_dir)
ogg = OccupyGenerator(self.cell)
if self.tr is not None:
tr = (Specie(self.tr[0]), self.tr[1])
applied_restriction = MinDistanceRestriction(tr)
for n1 in range(1, self.n - 1):
for n2 in range(1, self.n - n1):
g = ogg.gen_nodup_trinary_alloy(Specie(self.s1), n1,
Specie(self.s2), n2)
for n_count, c in enumerate(g):
if self.tr is not None:
condition = c.is_primitive(
) and applied_restriction.is_satisfied(c)
else:
condition = c.is_primitive()
if condition:
if self.refined:
c = c.get_refined_pcell()
out = GeneralIO(c)
f_suffix = ''.join(
random.choices(string.ascii_uppercase +
string.digits,
k=4))
ofname = "STRUCTURE_{:}_{:}.{:}".format(
c.comment, f_suffix, self.outmode)
lastpath = os.path.join(out_dir, ofname)
out.write_file(lastpath)
def concell(files, outmode, verbose):
from ababe.io.io import GeneralIO
import os
for infile in files:
basefname = os.path.basename(infile)
gcell = GeneralIO.from_file(infile)
pcell = gcell.get_refined_cell()
out = GeneralIO(pcell)
if outmode == 'stdio':
out.write_file(fname=None, fmt='vasp')
else:
if verbose: print("PROCESSING: {:}".format(infile))
ofname = "{:}_CONC.{:}".format(basefname.split('.')[0], outmode)
out.write_file(ofname)
def supcell(file, scale, outmode):
from ababe.io.io import GeneralIO
import os
import numpy as np
basefname = os.path.basename(file)
gcell = GeneralIO.from_file(file)
scale_matrix = np.diag(np.array(scale))
sc = gcell.supercell(scale_matrix)
out = GeneralIO(sc)
print("PROCESSING: {:}".format(file))
if outmode == 'stdio':
out.write_file(fname=None, fmt='vasp')
else:
ofname = "{:}_SUPC.{:}".format(basefname.split('.')[0], outmode)
out.write_file(ofname)
def run(self):
import tempfile
working_path = os.getcwd()
for infile in self.files:
basefname = os.path.basename(infile)
# read
gcell = GeneralIO.from_file(infile)
mcell = ModifiedCell.from_gcell(gcell)
new_mcell = self.clarifier.clarify(mcell)
gcell = new_mcell.to_gcell()
# todo: add feature- to convcell.
if self.refined:
gcell = gcell.get_refined_pcell()
out = GeneralIO(gcell)
ofname = "{:}_ACLR.vasp".format(basefname.split('.')[0])
print("PROCESSING: {:}".format(infile))
out.write_file(ofname)
def perturb(files, radius, outmode, verbose):
from ababe.io.io import GeneralIO
from ababe.stru.scaffold import ModifiedCell
from ababe.stru.element import Specie
import os
for infile in files:
basefname = os.path.basename(infile)
# read
gcell = GeneralIO.from_file(infile)
# process
mcell = ModifiedCell.from_gcell(gcell)
mcell.perturb(radius)
# write
out = GeneralIO(mcell.to_gcell())
if outmode == 'stdio':
out.write_file(fname=None, fmt='vasp')
else:
if verbose: print("PROCESSING: {:}".format(infile))
ofname = "{:}_PURB.{:}".format(basefname.split('.')[0], outmode)
out.write_file(ofname)