def main(argv=[]):
args = getArgs(argv)
atoms = read(args.file, format=args.format) if args.format else read(args.file)
atoms = correct_z(atoms)
atoms = fix_layers(atoms, args.fix, args.n_layers)
kw = {'format': 'vasp', 'direct': True, 'vasp5': True, 'sort':True}
write('POSCAR' + args.pad, atoms, **kw)
def main(argv=None):
args = getArgs(argv)
atoms = read(args.file, format=args.f) if args.f else struct = read(args.file)
atoms = correct_z(atoms)
kw = {"format": args.format}
if args.format == 'vasp':
kw['sort'] = True
kw['vasp5'] = True
kw['direct'] = True
write(args.nam, atoms, **kw)
def main(argv=[]):
args = getArgs(argv)
# get slab
atoms = read(args.slab) if args.slab else slab(args)
# adjust cell
atoms = correct_z(atoms)
# set contraints
if args.fix:
atoms = fix_layers(atoms, args.fix, args.n_layers)
# write POSCAR
kw = {'format': 'vasp',
'sort': True,
'vasp5': True,
'direct': True}
nam = 'POSCAR' + args.pad
write(nam, atoms, **kw)
def get_args(args):
parser = argparse.ArgumentParser(
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('directories', nargs='*', default=[getcwd()],
help='path to directories with DOS files to read')
parser.add_argument('-n', nargs='+', default=[],
help='The index number of the atoms to be read')
parser.add_argument('-e', nargs='+', default=[],
help='Read info of atoms of selected elements')
parser.add_argument('-l', nargs='+', default=[], type=int,
help='Read info of atoms in selected layers')
parser.add_argument('--e-range', nargs=2, default=[None, ''],
type=float, dest='e_range',
help='Range of energies for DOS calculations')
parser.add_argument('--layers', type=int, default=4,
help='Number of layers in structure')
parser.add_argument('--dbc', '--d-band-center', action='store_true',
default=False, dest='dbc',
help='get d-band center')
parser.add_argument('-w', '--write', action='store_true', default=False,
help='write requested DOS data')
parser.add_argument('-p', '-g', '--graph', '--plot', nargs='*',
choices=['s', 'p', 'd', 'f', 'sum'], dest='plot',
help='plot DOS for the specified orbitals')
parser.add_argument('--name', default='DOSCAR',
help='name of DOSCAR file to read')
parser.add_argument('-v', action='count', default=0)
parser.add_argument('--test', action='store_true')
res = parser.parse_args(args.split()) if args else parser.parse_args()
if res.n:
res.n = set(parse_int_set(res.n))
if res.e_range[0]: res.e_range = [-1 * res.e_range[0], res.e_range[1]]
n = {}
for f in res.directories:
nams = listdir(f)
if res.name not in nams:
print "Omitting directory '{}': No '{}' found.".format(f, res.name)
res.directories.remove(f)
continue
indexes = res.n
if res.l or res.e:
for nam in ['CONTCAR', 'POSCAR', 'OUTCAR']:
if nam in nams: break
nam = path.join(f, nam)
# read structure
# TODO: read other formats?
atoms = read(nam, format='vasp')
indexes = res.n if res.n else set(xrange(1, len(atoms) + 1))
if res.e:
X_atoms = {a.index + 1 for a in atoms if a.symbol in res.e}
indexes.intersection_update(X_atoms)
if res.l:
# adjust cell
atoms = correct_z(atoms)
# set layer tag to atoms
atoms = tag_layers(atoms, res.layers)
# get atoms in layers of interest
atoms_in_layer = {a.index + 1 for a in atoms if a.tag in res.l}
indexes.intersection_update(atoms_in_layer)
if not indexes:
contraints = []
if res.n: contraints.append("n={}".format(res.n))
if res.l: contraints.append("l={}".format(res.l))
if res.e: contraints.append("e={}".format(res.e))
msg = "{}\n".format(f)
msg += " No atoms found within given constraints ("
msg += ', '.join(contraints)
msg += "), using all atoms."
if res.v:
print "{} atoms found with given constraints".format(len(indexes))
print indexes if indexes else " using all atoms"
n[f] = list(indexes)
res.n = n
if res.plot == []:
res.plot = ['s', 'p', 'd', 'sum']
return res
