def strout2poscar(src='str.out'):
"""
str.outをposcarの記述に変換し, Poscar objをreturn
"""
with open(src, 'r') as rfile:
lines = rfile.readlines()
latt_tmp = [[float(x) for x in y.split()] for y in lines[0:3]]
trans = [[float(x) for x in y.split()] for y in lines[3:6]]
sites_tmp = [[float(x) for x in y.split()[0:3]] for y in lines[6:]]
elements = [x.split()[3].split('+')[0].split('-')[0] for x in lines[6:]]
num_atoms = [elements.count(e)
for e in sorted(set(elements), key=elements.index)]
latt = np.dot(np.array(trans), np.array(latt_tmp))
sites = np.dot(np.array(sites_tmp), np.array(latt_tmp))
posc_str = "posc_orig\n"
posc_str += "1.00\n"
posc_str += "\n".join([" ".join([str(f) for f in l]) for l in latt])
posc_str += "\n"
posc_str += " ".join(sorted(set(elements), key=elements.index)) + "\n"
posc_str += " ".join([str(d) for d in num_atoms]) + "\n"
posc_str += "Cartesian\n"
posc_str += "\n".join([" ".join([str(f) for f in s]) for s in sites])
return Poscar.from_string(posc_str)
def _parse_structure(self, structure_schema):
data = structure_schema['data']
format = structure_schema['format']
if format == 'cif':
structure = (CifParser.from_string(data)).get_structures()[0]
elif format == 'POSCAR':
structure = (Poscar.from_string(data)).structure
return structure
def _parse_structure(self, structure_schema):
data = structure_schema['data']
format = structure_schema['format']
if format == 'cif':
# cif lattice can be weird non standard shape
structure = (CifParser.from_string(data)).get_structures()[0]
lattice = pmg.Lattice.from_parameters(*structure.lattice.abc, *structure.lattice.angles)
structure = pmg.Structure(lattice, structure.species, structure.frac_coords, coords_are_cartesian=False)
elif format == 'POSCAR':
structure = (Poscar.from_string(data)).structure
return structure
def poscar_scale(poscar_in, poscar_out, scale):
with open(poscar_in, 'r') as fin:
lines = list(fin)
if 'D' == lines[7][0] or 'd' == lines[7][0]:
lines = poscar_scale_direct(lines, scale)
elif 'C' == lines[7][0] or 'c' == lines[7][0]:
lines = poscar_scale_cartesian(lines, scale)
else:
raise RuntimeError("Unknow poscar style at line 7: %s" % lines[7])
poscar = Poscar.from_string("".join(lines))
with open(poscar_out, 'w') as fout:
fout.write(poscar.get_string(direct=False))
def _parse_structure(self, structure_schema):
data = structure_schema['data']
format = structure_schema['format']
if format == 'cif':
# cif lattice can be weird non standard shape
structure = (CifParser.from_string(data)).get_structures()[0]
lattice = pmg.Lattice.from_parameters(*structure.lattice.abc,
*structure.lattice.angles)
structure = pmg.Structure(lattice,
structure.species,
structure.frac_coords,
coords_are_cartesian=False)
elif format == 'POSCAR':
structure = (Poscar.from_string(data)).structure
return structure
def get_structure(f):
name = f.name
content = f.read()
content = content.decode("utf-8")
if "POSCAR" in name or "CONTCAR" in name:
s = Poscar.from_string(content, False).structure
elif ".cif" in name.lower():
parser = CifParser.from_string(content)
s = parser.get_structures(False)[0]
elif ".cssr" in name.lower():
cssr = Cssr.from_string(content)
s = cssr.structure
elif ".mson" in name.lower():
s = json.loads(content, cls=MontyDecoder)
if type(s) != Structure:
raise IOError("File does not contain a valid serialized "
"structure")
else:
raise ValueError(name + " is an invalid file format. Only "
"POSCAR, CIF, CSSR and MSON (Materials "
"Project JSON) are supported right now.")
return name, s
return np.array([[xx, 0, 0], [yx, yy, 0], [zx, zy, zz]])
def lammps_friendly(structure):
orig_lattice = structure.lattice.matrix
lmp_lattice = lammps_lattice(orig_lattice)
fracs = structure.frac_coords
return Structure(lmp_lattice, structure.species, fracs)
input = sys.argv[1]
import lzma, json
with lzma.open(os.path.join(input, 'structure.vasp.xz'), 'rt') as f:
structure = Poscar.from_string(f.read()).structure
with lzma.open(os.path.join(input, 'layers.json.xz'), 'rt') as f:
layers = json.load(f)
num_types = max(layers) + 1
structure = lammps_friendly(structure)
carts = structure.cart_coords
lattice = structure.lattice.matrix
species = structure.species
print()
print()
print(f'{len(carts)} atoms')
print()
print(f'{num_types} atom types')
print()
from featurebox.data.impot_element_table import element_table
name_and_abbr = element_table.iloc[[0, 1], :]
element_table = element_table.iloc[2:, :]
elemen = element_table[[
'electronegativity(martynov&batsanov)', 'electron number'
]]
dict_all = []
for i in tqdm(list_name):
try:
a = json.read_json(i, orient='index', typ='series')
cif_str = a["Structure_rlx"]
del a["Structure_rlx"]
POSCAR = Poscar.from_string(cif_str)
ele_den = POSCAR.structure.composition.total_electrons / POSCAR.structure.volume
composition_mp = POSCAR.structure.composition
ncom = POSCAR.structure.composition.to_data_dict[
'unit_cell_composition'].values()
sym_amt = composition_mp.get_el_amt_dict()
syms = sorted(sym_amt.keys(), key=lambda sym: get_el_sp(sym).X)
formula = {s: formula_double_format(sym_amt[s], False) for s in syms}
departElementProPFeature = DepartElementFeaturizer(
elem_data=elemen,
n_composition=len(ncom),
n_jobs=1,
return_type='df')
def lammps_friendly(structure):
orig_lattice = structure.lattice.matrix
lmp_lattice = lammps_lattice(orig_lattice)
fracs = structure.frac_coords
return Structure(lmp_lattice, structure.species, fracs)
input = sys.argv[1]
if input.endswith('.xz'):
import lzma
with lzma.open(input, 'rt') as f:
poscar_str = f.read()
else:
with open(input, 'rt') as f:
poscar_str = f.read()
structure = Poscar.from_string(poscar_str).structure
structure = lammps_friendly(structure)
carts = structure.cart_coords
lattice = structure.lattice.matrix
species = structure.species
print()
print()
print(f'{len(carts)} atoms')
print()
print(f'2 atom types')
print()
print(f'0.0 {lattice[0][0]} xlo xhi')
print(f'0.0 {lattice[1][1]} ylo yhi')
print(f'0.0 {lattice[2][2]} zlo zhi')
print(f'{lattice[1][0]} {lattice[2][0]} {lattice[2][1]} xy xz yz')
print()
