def __init__(self, infile, radius):
gcell = GeneralIO.from_file(infile)
self.infile = infile
self.basefname = os.path.basename(infile)
self.mcell = ModifiedCell.from_gcell(gcell)
self.radius = radius
def __init__(self, infile, cenele, radius, ele, refined):
gcell = GeneralIO.from_file(infile)
self.infile = infile
self.basefname = os.path.basename(infile)
self.mcell = ModifiedCell.from_gcell(gcell)
self.clarifier = VerboseAtomRemoveClarifier(Specie(cenele), radius,
Specie(ele))
self.refined = refined
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)
def test_from_to_gcell(self):
gcell = GeneralCell(self.latt, self.pos, self.numbers)
modcell = ModifiedCell.from_gcell(gcell)
new_gcell = modcell.to_gcell()
self.assertTrue(np.allclose(new_gcell.positions, gcell.positions))