atoms.cellvec[0][1] = atoms.cellvec[0][1] * bohr2ang
atoms.cellvec[0][2] = atoms.cellvec[0][2] * bohr2ang
atoms.cellvec[1][0] = atoms.cellvec[1][0] * bohr2ang
atoms.cellvec[1][1] = atoms.cellvec[1][1] * bohr2ang
atoms.cellvec[1][2] = atoms.cellvec[1][2] * bohr2ang
atoms.cellvec[2][0] = atoms.cellvec[2][0] * bohr2ang
atoms.cellvec[2][1] = atoms.cellvec[2][1] * bohr2ang
atoms.cellvec[2][2] = atoms.cellvec[2][2] * bohr2ang
for iat in range(atoms.nat):
atoms.rat[iat][0] = atoms.rat[iat][0] * bohr2ang
atoms.rat[iat][1] = atoms.rat[iat][1] * bohr2ang
atoms.rat[iat][2] = atoms.rat[iat][2] * bohr2ang
if len(atoms_all) == 1:
if not atoms_all[0].boundcond == "free":
atoms_all[0].cellvec, atoms_all[0].rat = latvec2dproj(
atoms_all[0].cellvec, atoms_all[0].rat, atoms_all[0].nat)
ascii_write(atoms_all[0], args.fn_out)
else:
print(
"\nATTENTION: The are more than one configuration in YAML file. The given name for the output is ignored!"
)
prefix = input(
"Please provide a prefix to generate files enumeratedly: [Default=tt]")
if prefix == "": prefix = "tt"
nconf = 0
for atoms in atoms_all:
nconf += 1
fnout = "%s%5.5d.ascii" % (prefix, nconf)
if not atoms.boundcond == "free":
atoms.cellvec, atoms.rat = latvec2dproj(atoms.cellvec, atoms.rat,
atoms.nat)
help="Name of the input file in yaml format")
parser.add_argument('dkpt',
action='store',
type=float,
help="Density of k-points")
args = parser.parse_args()
bohr2ang = 0.52917720859
ang2bohr = 1.0 / 0.52917720859
atoms_all = read_yaml(args.fn_inp)
iconf = 0
for atoms in atoms_all:
iconf += 1
#rotation
atoms.cellvec, atoms.rat = latvec2dproj(atoms.cellvec, atoms.rat,
atoms.nat)
if atoms.units_length_io == "angstrom":
ax = atoms.cellvec[0][0] * ang2bohr
bx = atoms.cellvec[1][0] * ang2bohr
by = atoms.cellvec[1][1] * ang2bohr
cx = atoms.cellvec[2][0] * ang2bohr
cy = atoms.cellvec[2][1] * ang2bohr
cz = atoms.cellvec[2][2] * ang2bohr
else:
ax = atoms.cellvec[0][0]
bx = atoms.cellvec[1][0]
by = atoms.cellvec[1][1]
cx = atoms.cellvec[2][0]
cy = atoms.cellvec[2][1]
cz = atoms.cellvec[2][2]
pi = math.acos(-1.0)