def _read_cif_block(cb):
s = strx.Structure()
s.cell = latparams_to_basis(_get_lattice_parameters(cb))
sym_ops = _get_sym_ops(cb)
ox_data = _get_oxidation_state_data(cb)
for atom in cb.GetLoop('_atom_site_label'):
na = _get_atom(atom)
if ox_data:
na.ox = ox_data.get(atom._atom_site_type_symbol, None)
for rot, trans in zip(*sym_ops):
coord = np.dot(rot, na.coord) + trans
coord = wrap(coord)
a = na.copy()
a.coord = coord
s.add_atom(a, tol=1e-1)
s.composition = comp.Composition.get(s.comp)
## meta data
s.r_val = float(cb.get('_refine_ls_R_factor_all', 0.0))
s.temperature = _get_value(cb.get('_cell_measurement_temperature', 0.0))
s.pressure = _get_value(cb.get('_cell_measurement_pressure', 0.0))
if cb.get('_chemical_name_structure_type'):
s.prototype = strx.Prototype.get(cb.get('_chemical_name_structure_type'))
try:
s.reported_composition = strx.Composition.get(
parse_comp(cb.get('_chemical_formula_sum')))
except:
pass
s.input_format = 'cif'
s.natoms = len(s)
s.get_volume()
return s
def read(poscar, species=None):
"""
Read a POSCAR format file.
Reads VASP 4.x and 5.x format POSCAR files.
Keyword Arguments:
`species`:
If the file is 4.x format and the title line doesn't indicate what
species are present, you must supply them (in the correct order)
with the `species` keyword.
Raises:
POSCARError: If species data is not available.
Examples::
>>> io.poscar.read(INSTALL_PATH+'/io/files/POSCAR_FCC')
"""
# Initialize the structure output
struct = st.Structure()
# Read in the title block, and system sell
if isinstance(poscar, StringIO.StringIO):
poscar = poscar
else:
poscar = open(poscar, 'r')
title = poscar.readline().strip()
scale = float(poscar.readline().strip())
s = float(scale)
cell = [[float(v) for v in poscar.readline().split()],
[float(v) for v in poscar.readline().split()],
[float(v) for v in poscar.readline().split()]]
cell = np.array(cell)
if s > 0:
struct.cell = cell * s
else:
struct.cell = cell
struct.volume = -1 * s
# Determine whether POSCAR is in VASP 5 format
# VASP 5 has the elements listed after the
# the cell parameters
vasp5 = False
_species = poscar.readline().strip().split()
try:
float(_species[0])
except:
vasp5 = True
counts = [int(v) for v in poscar.readline().split()]
# If the format is not VASP 5, the elements should
# have been listed in the title
if not vasp5:
counts = map(int, _species)
if not species:
_species = title.strip().split()
for s in _species:
if not s in qmpy.elements.keys():
msg = 'In VASP4.x format, title line MUST be species present'
raise POSCARError
else:
_species = species
species = _species
# Prepare a list of numbers of atom types
atom_types = []
for n, e in zip(counts, species):
atom_types += [e] * n
# Determine whether coordinates are in direct or cartesian
direct = False
style = poscar.readline()
if style[0].lower() == 's':
# The POSCAR contains selective dynamics info
style = poscar.readline()
if style[0] in ['D', 'd']:
direct = True
# Read in the atom coordinates
struct.natoms = sum(counts)
struct.ntypes = len(counts)
atoms = []
inv = np.linalg.inv(cell).T
for i in range(struct.natoms):
atom = st.Atom()
atom.element_id = atom_types[i]
if direct:
atom.coord = [float(v) for v in poscar.readline().split()[0:3]]
else:
cart = [float(v) for v in poscar.readline().split()[0:3]]
atom.coord = np.dot(inv, cart)
struct.add_atom(atom)
struct.get_volume()
struct.set_composition()
return struct
def read(poscar, species=None):
"""
Read a POSCAR format file.
Reads VASP 4.x and 5.x format POSCAR files.
Keyword Arguments:
`species`:
If the file is 4.x format and the title line doesn't indicate what
species are present, you must supply them (in the correct order)
with the `species` keyword.
Raises:
POSCARError: If species data is not available.
Examples::
>>> io.poscar.read(INSTALL_PATH+'/io/files/POSCAR_FCC')
"""
struct = st.Structure()
poscar = open(poscar, 'r')
title = poscar.readline().strip()
scale = float(poscar.readline().strip())
s = float(scale)
cell = [[float(v) for v in poscar.readline().split()],
[float(v) for v in poscar.readline().split()],
[float(v) for v in poscar.readline().split()]]
cell = np.array(cell)
if s > 0:
struct.cell = cell * s
else:
struct.cell = cell
struct.volume = -1 * s
vasp5 = False
_species = poscar.readline().strip().split()
try:
float(_species[0])
except:
vasp5 = True
counts = [int(v) for v in poscar.readline().split()]
if not vasp5:
counts = map(int, _species)
if not species:
_species = title.strip().split()
for s in _species:
if not s in qmpy.elements.keys():
msg = 'In VASP4.x format, title line MUST be species present'
raise POSCARError
else:
_species = species
species = _species
atom_types = []
for n, e in zip(counts, species):
atom_types += [e] * n
style = poscar.readline()
direct = False
if style[0] in ['D', 'd']:
direct = True
struct.natoms = sum(counts)
struct.ntypes = len(counts)
atoms = []
inv = np.linalg.inv(cell).T
for i in range(struct.natoms):
atom = st.Atom()
atom.element_id = atom_types[i]
if direct:
atom.coord = [float(v) for v in poscar.readline().split()[0:3]]
else:
cart = [float(v) for v in poscar.readline().split()[0:3]]
atom.coord = np.dot(inv, cart)
struct.add_atom(atom)
struct.get_volume()
struct.set_composition()
return struct