def run(self):
import random
import string
# Create a dir contains suplat files
working_path = os.getcwd()
suplat_dir = os.path.join(working_path,
'SUPLAT_{:}'.format(self.comment))
if not os.path.exists(suplat_dir):
os.makedirs(suplat_dir)
else:
shutil.rmtree(suplat_dir)
os.makedirs(suplat_dir)
for hnf in self.hnfs:
rd_suffix = ''.join(random.choices(string.ascii_uppercase
+ string.digits, k=4))
sl_origin = hnf.to_general_cell()
sl = sl_origin.get_shaped_cell()
out = GeneralIO(sl)
ofname = "SUPLAT_{:}_{:}.{:}".format(self.v, rd_suffix, self.outmode)
lastpath = os.path.join(suplat_dir, ofname)
out.write_file(lastpath)
def setUp(self):
latt = np.array([[0., 0.5, 0.53333333333], [0.5, 0., 0.56666666667],
[0.5, 0.5, 0.]])
pos = np.array([[0., 0., 0.], [0.25, 0.25, 0.25]])
numbers = np.array([30, 16])
gcell = GeneralCell(latt, pos, numbers)
self.vasp_out = VaspOutput(gcell)
self.yaml_out = YamlOutput(gcell)
self.io_s = GeneralIO(gcell)
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)
g = ogg.gen_nodup_of_ele(self.ele, self.n, self.speckle)
# sym for getting degeneracy
sym_perm = self.cell.get_symmetry_permutation()
if self.tr is not None:
tr = (Specie(self.tr[0]), self.tr[1])
applied_restriction = MinDistanceRestriction(tr)
for n_count, c in enumerate(g):
if self.mpr:
if self.tr is not None:
condition = c.is_primitive(
) and applied_restriction.is_satisfied(c)
else:
condition = c.is_primitive()
else:
if self.tr is not None:
condition = applied_restriction.is_satisfied(c)
else:
condition = True
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_{:}_D{:}D_{:}.{:}".format(
c.comment, c.get_degeneracy(sym_perm), f_suffix,
self.outmode)
lastpath = os.path.join(out_dir, ofname)
out.write_file(lastpath)
def run(self):
# Create directory contain POSCARs
import random
import string
rd_suffix = ''.join(
random.choices(string.ascii_uppercase + string.digits, k=4))
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)
gg = ogg.all_speckle_gen_of_ele(self.nmax, self.ele, self.speckle)
if self.tr is not None:
tr = (Specie(self.tr[0]), self.tr[1])
applied_restriction = MinDistanceRestriction(tr)
for i, outer_gen in enumerate(gg):
# print("Processing: {0:3}s substitue {1:2d}...".format(speckle, i+1))
for n_count, c in enumerate(outer_gen):
if self.mpr:
if self.tr is not None:
condition = c.is_primitive(
) and applied_restriction.is_satisfied(c)
else:
condition = c.is_primitive()
else:
if self.tr is not None:
condition = applied_restriction.is_satisfied(c)
else:
condition = True
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 run(self):
import tempfile
working_path = os.getcwd()
new_mcell = self.clarifier.clarify(self.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(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 __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, comment, element, speckle, trs, refined,
outmode):
# read comment & zoom from setting file first
# if not exist, read from cmd args, then default
self.cell = GeneralIO.from_file(infile)
self.comment = comment or self.cell.comment
self.element = element
# Get number and index of target element
num = self.cell.numbers
if element is None:
tgt_ele = int(num[1])
else:
tgt_ele = Specie(element).Z
tgt_ele_index = np.where(num == tgt_ele)[0]
self.n = tgt_ele_index.size
self.s1, self.s2 = speckle
# self.ele for function all-speckle-gen-of-ele in run
self.ele = Specie.from_num(tgt_ele)
# if there no restriction given then no restriction
if trs != ():
self.tr = trs[0]
else:
self.tr = None
self.refined = refined
self.outmode = outmode
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 test_yaml_from_file(self):
filename = os.path.join(testdata_dir, "zns.yaml")
gcell = GeneralIO.from_file(filename)
expect_latt = np.array([[0., 2., 2.], [2., 0., 2.], [2., 2., 0.]])
expect_positions = np.array([[0., 0., 0.], [0.25, 0.25, 0.25]])
expect_numbers = np.array([30, 16])
self.assertTrue(np.allclose(gcell.lattice, expect_latt))
self.assertTrue(np.allclose(gcell.positions, expect_positions))
self.assertTrue(np.allclose(gcell.numbers, expect_numbers))
def pspg(files, sym, verbose):
from ababe.io.io import GeneralIO
import os
for infile in files:
basefname = os.path.basename(infile)
# read
gcell = GeneralIO.from_file(infile)
# print spacegroup
print(gcell.get_spacegroup(sym))
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 test_vasp_from_file(self):
filename = os.path.join(testdata_dir, "POSCAR_")
gcell = GeneralIO.from_file(filename)
expect_latt = np.array([[2.8284, 0.0000, 0.0000],
[0.0000, 2.8284, 0.0000],
[0.0000, 0.0000, 12.0000]])
expect_positions = np.array([[0., 0., 0.666667], [0., 0.5, 0.250000],
[0., 0.5, 0.583333], [0., 0.5, 0.916667],
[0.5, 0., 0.083333], [0.5, 0., 0.416667],
[0.5, 0., 0.750000], [0.5, 0.5,
0.833333]])
expect_numbers = [30, 16, 16, 16, 16, 16, 16, 30]
self.assertTrue(np.allclose(gcell.lattice, expect_latt))
self.assertTrue(np.allclose(gcell.positions, expect_positions))
self.assertTrue(np.allclose(gcell.numbers, expect_numbers))
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 pcell(input, outmode):
from ababe.io.io import GeneralIO
import os
infile = click.format_filename(input)
basefname = os.path.basename(infile)
gcell = GeneralIO.from_file(infile)
pcell = gcell.get_refined_pcell()
out = GeneralIO(pcell)
if outmode == 'stdio':
out.write_file(fname=None, fmt='vasp')
else:
print("PROCESSING: {:}".format(infile))
ofname = "{:}_PRIMC.{:}".format(basefname.split('.')[0], outmode)
out.write_file(ofname)
def __init__(self, infile, comment, volumn, ld, outmode):
self.ucell = GeneralIO.from_file(infile)
# check whether input a unit cell
if not self.ucell.is_primitive():
raise ValueError('Lattice in setting file are not primitive.\n'
'You can reinput OR get the primitive lattice\n'
'by using runati pcell <file>\n')
self.v = volumn
self.comment = comment or "default"
self.outmode = outmode
if ld:
LatticeGen = SuperLatticeGenerator2D
else:
LatticeGen = SuperLatticeGenerator
self.hnfs = LatticeGen.hnfs_from_n(self.ucell, self.v)
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 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)
class TestGeneralIO(unittest.TestCase):
def setUp(self):
latt = np.array([[0., 0.5, 0.53333333333], [0.5, 0., 0.56666666667],
[0.5, 0.5, 0.]])
pos = np.array([[0., 0., 0.], [0.25, 0.25, 0.25]])
numbers = np.array([30, 16])
gcell = GeneralCell(latt, pos, numbers)
self.vasp_out = VaspOutput(gcell)
self.yaml_out = YamlOutput(gcell)
self.io_s = GeneralIO(gcell)
def test_vasp_from_file(self):
filename = os.path.join(testdata_dir, "POSCAR_")
gcell = GeneralIO.from_file(filename)
expect_latt = np.array([[2.8284, 0.0000, 0.0000],
[0.0000, 2.8284, 0.0000],
[0.0000, 0.0000, 12.0000]])
expect_positions = np.array([[0., 0., 0.666667], [0., 0.5, 0.250000],
[0., 0.5, 0.583333], [0., 0.5, 0.916667],
[0.5, 0., 0.083333], [0.5, 0., 0.416667],
[0.5, 0., 0.750000], [0.5, 0.5,
0.833333]])
expect_numbers = [30, 16, 16, 16, 16, 16, 16, 30]
self.assertTrue(np.allclose(gcell.lattice, expect_latt))
self.assertTrue(np.allclose(gcell.positions, expect_positions))
self.assertTrue(np.allclose(gcell.numbers, expect_numbers))
def test_yaml_from_file(self):
filename = os.path.join(testdata_dir, "zns.yaml")
gcell = GeneralIO.from_file(filename)
expect_latt = np.array([[0., 2., 2.], [2., 0., 2.], [2., 2., 0.]])
expect_positions = np.array([[0., 0., 0.], [0.25, 0.25, 0.25]])
expect_numbers = np.array([30, 16])
self.assertTrue(np.allclose(gcell.lattice, expect_latt))
self.assertTrue(np.allclose(gcell.positions, expect_positions))
self.assertTrue(np.allclose(gcell.numbers, expect_numbers))
def test_vasp_write_file(self):
##################################################
# vasp POSCAR write test
##################################################
tmp_file = os.path.join(testdata_dir, "testing.vasp")
self.io_s.write_file(tmp_file)
with open(tmp_file, 'r') as testing_file:
data = testing_file.read()
self.assertEqual(data, str(self.vasp_out))
os.remove(tmp_file)
#################
tmp_file = os.path.join(testdata_dir, "POSCAR______")
self.io_s.write_file(tmp_file)
with open(tmp_file, 'r') as testing_file:
data = testing_file.read()
self.assertEqual(data, str(self.vasp_out))
os.remove(tmp_file)
###################
tmp_file = os.path.join(testdata_dir, "i_have_noname")
self.io_s.write_file(tmp_file, fmt='vasp')
with open(tmp_file, 'r') as testing_file:
data = testing_file.read()
self.assertEqual(data, str(self.vasp_out))
os.remove(tmp_file)
def test_yaml_write_file(self):
##################################################
# yaml write test
##################################################
tmp_file = os.path.join(testdata_dir, "testing.yaml")
self.io_s.write_file(tmp_file)
with open(tmp_file, 'r') as testing_file:
data = testing_file.read()
self.assertEqual(data, str(self.yaml_out))
os.remove(tmp_file)
########################3
tmp_file = os.path.join(testdata_dir, "testing")
self.io_s.write_file(tmp_file, fmt='yaml')
with open(tmp_file, 'r') as testing_file:
data = testing_file.read()
self.assertEqual(data, str(self.yaml_out))
os.remove(tmp_file)
def test_noname_write_file(self):
self.io_s.write_file(fmt="vasp")
pass