def crystal(file='fort.34'):
""" Reads CRYSTAL's external format. """
from numpy import array, abs, zeros, any, dot
from numpy.linalg import inv
from ..crystal import which_site
from ..misc import RelativePath
from ..error import IOError
from ..periodic_table import find as find_specie
from . import Structure
if isinstance(file, str):
if file.find('\n') == -1:
with open(RelativePath(file).path, 'r') as file: return crystal(file)
else: file = file.splitlines().__iter__()
# read first line
try: line = file.next()
except StopIteration: raise IOError('Premature end of stream.')
else: dimensionality, centering, type = [int(u) for u in line.split()[:3]]
# read cell
try: cell = array( [file.next().split()[:3] for i in xrange(3)],
dtype='float64' ).T
except StopIteration: raise IOError('Premature end of stream.')
result = Structure( cell=cell, centering=centering,
dimensionality=dimensionality, type=type, scale=1e0 )
# read symmetry operators
result.spacegroup = []
try: N = int(file.next())
except StopIteration: raise IOError('Premature end of stream.')
for i in xrange(N):
try: op = array( [file.next().split()[:3] for j in xrange(4)],
dtype='float64' )
except StopIteration: raise IOError('Premature end of stream.')
else: op[:3] = op[:3].copy().T
result.spacegroup.append(op)
result.spacegroup = array(result.spacegroup)
# read atoms.
try: N = int(file.next())
except StopIteration: raise IOError('Premature end of stream.')
for i in xrange(N):
try: line = file.next().split()
except StopIteration: raise IOError('Premature end of stream.')
else: type, pos = int(line[0]), array(line[1:4], dtype='float64')
if type < 100: type = find_specie(atomic_number=type).symbol
result.add_atom(pos=pos, type=type, asymmetric=True)
# Adds symmetrically equivalent structures.
identity = zeros((4, 3), dtype='float64')
for i in xrange(3): identity[i, i] == 1
symops = [u for u in result.spacegroup if any(abs(u - identity) > 1e-8)]
invcell = inv(result.cell)
for atom in [u for u in result]:
for op in symops:
pos = dot(op[:3], atom.pos) + op[3]
if which_site(pos, result, invcell=invcell) == -1:
result.add_atom(pos=pos, type=atom.type, asymmetric=False)
return result
def crystal(file='fort.34'):
""" Reads CRYSTAL's external format. """
from six import next
from numpy import array, abs, zeros, any, dot
from numpy.linalg import inv
from ..crystal import which_site
from ..misc import RelativePath
from .. import error
from ..periodic_table import find as find_specie
from . import Structure
if isinstance(file, str):
if file.find('\n') == -1:
with open(RelativePath(file).path, 'r') as file:
return crystal(file)
else:
file = file.splitlines().__iter__()
# read first line
try:
line = next(file)
except StopIteration:
raise error.IOError('Premature end of stream.')
else:
dimensionality, centering, type = [int(u) for u in line.split()[:3]]
# read cell
try:
cell = array([next(file).split()[:3] for i in range(3)],
dtype='float64').T
except StopIteration:
raise error.IOError('Premature end of stream.')
result = Structure(cell=cell, centering=centering,
dimensionality=dimensionality, type=type, scale=1e0)
# read symmetry operators
result.spacegroup = []
try:
N = int(next(file))
except StopIteration:
raise error.IOError('Premature end of stream.')
for i in range(N):
try:
op = array([next(file).split()[:3] for j in range(4)],
dtype='float64')
except StopIteration:
raise error.IOError('Premature end of stream.')
else:
op[:3] = op[:3].copy().T
result.spacegroup.append(op)
result.spacegroup = array(result.spacegroup)
# read atoms.
try:
N = int(next(file))
except StopIteration:
raise error.IOError('Premature end of stream.')
for i in range(N):
try:
line = next(file).split()
except StopIteration:
raise error.IOError('Premature end of stream.')
else:
type, pos = int(line[0]), array(line[1:4], dtype='float64')
if type < 100:
type = find_specie(atomic_number=type).symbol
result.add_atom(pos=pos, type=type, asymmetric=True)
# Adds symmetrically equivalent structures.
identity = zeros((4, 3), dtype='float64')
for i in range(3):
identity[i, i] == 1
symops = [u for u in result.spacegroup if any(abs(u - identity) > 1e-8)]
invcell = inv(result.cell)
for atom in [u for u in result]:
for op in symops:
pos = dot(op[:3], atom.pos) + op[3]
if which_site(pos, result, invcell=invcell) == -1:
result.add_atom(pos=pos, type=atom.type, asymmetric=False)
return result
