def write_input(self, atoms, properties=None, system_changes=None):
FileIOCalculator.write_input(self, atoms, properties,
system_changes)
struct = crys.atoms2struct(atoms)
self.cell = common.str_arr(struct.cell)
self.kpoints = pwscf.kpoints_str_pwin(kpts2mp(atoms, self.kpts))
if isinstance(self.pp, types.StringType):
pseudos = ["%s.%s" %(sym, self.pp) for sym in struct.symbols_unique]
else:
assert len(self.pp) == struct.ntypat
pseudos = []
for sym in struct.symbols_unique:
for ppi in self.pp:
if ppi.startswith(sym):
pseudos.append(ppi)
break
assert len(pseudos) == struct.ntypat
self.atspec = pwscf.atspec_str(symbols=struct.symbols_unique,
masses=struct.mass_unique,
pseudos=pseudos)
self.atpos = pwscf.atpos_str(symbols=struct.symbols,
coords=struct.coords_frac)
self.natoms = struct.natoms
self.ntyp = struct.ntypat
if self.backup:
for fn in [self.infile, self.outfile]:
if os.path.exists(fn):
common.backup(fn)
common.file_write(self.infile, self.fill_infile_templ())
def write_input(self, atoms, properties=None, system_changes=None):
FileIOCalculator.write_input(self, atoms, properties, system_changes)
struct = crys.atoms2struct(atoms)
self.cell = common.str_arr(struct.cell)
self.kpoints = pwscf.kpoints_str_pwin(kpts2mp(atoms, self.kpts))
if isinstance(self.pp, bytes):
pseudos = [
"%s.%s" % (sym, self.pp) for sym in struct.symbols_unique
]
else:
assert len(self.pp) == struct.ntypat
pseudos = []
for sym in struct.symbols_unique:
for ppi in self.pp:
if ppi.startswith(sym):
pseudos.append(ppi)
break
assert len(pseudos) == struct.ntypat
self.atspec = pwscf.atspec_str(symbols=struct.symbols_unique,
masses=struct.mass_unique,
pseudos=pseudos)
self.atpos = pwscf.atpos_str(symbols=struct.symbols,
coords=struct.coords_frac)
self.natoms = struct.natoms
self.ntyp = struct.ntypat
if self.backup:
for fn in [self.infile, self.outfile]:
if os.path.exists(fn):
common.backup(fn)
common.file_write(self.infile, self.fill_infile_templ())
from pwtools.constants import Bohr, Angstrom
def indent(txt, num=4):
"""Indent text block by `num` white spaces."""
space = " "*num
return '\n'.join(space + line for line in txt.splitlines())
# All lengths in Bohr
struct = io.read_cif(sys.argv[1], units={'length': Angstrom/Bohr})
rcell = crys.recip_cell(struct.cell)
norms = np.sqrt((rcell**2.0).sum(axis=1))
bar = '-'*78
mass_unique = [atomic_data.pt[sym]['mass'] for sym in struct.symbols_unique]
atspec = pwscf.atspec_str(struct.symbols_unique,
mass_unique,
[sym + '.UPF' for sym in struct.symbols_unique])
celldm = crys.cc2celldm(struct.cryst_const)
atpos_frac = pwscf.atpos_str(struct.symbols, struct.coords_frac)
print("""\
Notes
-----
The .cif file is assumed to contain NO symmetry information:
_symmetry_space_group_name_H-M 'P 1'
_symmetry_Int_Tables_number 1
loop_
_symmetry_equiv_pos_as_xyz
x,y,z
Only a,b,c,alpha,beta,gamma and the fractional coords as found in the file are
used.
from pwtools.constants import Bohr, Angstrom
def indent(txt, num=4):
"""Indent text block by `num` white spaces."""
space = " " * num
return '\n'.join(space + line for line in txt.splitlines())
# All lengths in Bohr
struct = io.read_cif(sys.argv[1], units={'length': Angstrom / Bohr})
rcell = crys.recip_cell(struct.cell)
norms = np.sqrt((rcell**2.0).sum(axis=1))
bar = '-' * 78
mass_unique = [atomic_data.pt[sym]['mass'] for sym in struct.symbols_unique]
atspec = pwscf.atspec_str(struct.symbols_unique, mass_unique,
[sym + '.UPF' for sym in struct.symbols_unique])
celldm = crys.cc2celldm(struct.cryst_const)
atpos_frac = pwscf.atpos_str(struct.symbols, struct.coords_frac)
print("""\
Notes
-----
The .cif file is assumed to contain NO symmetry information:
_symmetry_space_group_name_H-M 'P 1'
_symmetry_Int_Tables_number 1
loop_
_symmetry_equiv_pos_as_xyz
x,y,z
Only a,b,c,alpha,beta,gamma and the fractional coords as found in the file are
used.