def read_cif(fileobj, index=-1):
if isinstance(fileobj, str):
fileobj = open(fileobj)
def search_key(fobj, key):
for line in fobj:
if key in line:
return line
return None
def get_key(fobj, key, pos=1):
line = search_key(fobj, key)
if line:
return float(line.split()[pos].split('(')[0])
return None
a = get_key(fileobj, '_cell_length_a')
b = get_key(fileobj, '_cell_length_b')
c = get_key(fileobj, '_cell_length_c')
alpha = pi * get_key(fileobj, '_cell_angle_alpha') / 180
beta = pi * get_key(fileobj, '_cell_angle_beta') / 180
gamma = pi * get_key(fileobj, '_cell_angle_gamma') / 180
va = a * np.array([1, 0, 0])
vb = b * np.array([cos(gamma), sin(gamma), 0])
cx = cos(beta)
cy = (cos(alpha) - cos(beta) * cos(gamma)) / sin(gamma)
cz = sqrt(1. - cx*cx - cy*cy)
vc = c * np.array([cx, cy, cz])
cell = np.array([va, vb, vc])
atoms = Atoms(cell=cell)
read = False
for line in fileobj:
if not read:
if '_atom_site_disorder_group' in line:
read = True
else:
word = line.split()
if len(word) < 5:
break
symbol = word[1]
pos = (float(word[2].split('(')[0]) * va +
float(word[3].split('(')[0]) * vb +
float(word[4].split('(')[0]) * vc )
atoms.append(Atom(symbol, pos))
return atoms
def read_I_info(fileobj, index=-1):
if isinstance(fileobj, str):
fileobj = open(fileobj)
lines = fileobj.readlines()
del lines[0]
finished = False
s = Atoms()
while not finished:
w = lines.pop(0).split()
if w[0].startswith('"'):
position = Bohr * np.array([float(w[3]), float(w[4]), float(w[5])])
s.append(Atom(w[0].replace('"', ''), position))
else:
finished = True
return s
def read_gpaw_text(fileobj, index=-1):
if isinstance(fileobj, str):
fileobj = open(fileobj)
def index_startswith(lines, string):
for i, line in enumerate(lines):
if line.startswith(string):
return i
raise ValueError
lines = fileobj.readlines()
images = []
while True:
try:
i = lines.index('Unit Cell:\n')
except ValueError:
pass
else:
cell = []
pbc = []
for line in lines[i + 3:i + 6]:
words = line.split()
if len(words) == 5: # old format
cell.append(float(words[2]))
pbc.append(words[1] == 'yes')
else: # new format with GUC
cell.append([float(word) for word in words[3:6]])
pbc.append(words[2] == 'yes')
try:
i = lines.index('Positions:\n')
except ValueError:
break
atoms = Atoms(cell=cell, pbc=pbc)
for line in lines[i + 1:]:
words = line.split()
if len(words) != 5:
break
n, symbol, x, y, z = words
symbol = symbol.split('.')[0]
atoms.append(Atom(symbol, [float(x), float(y), float(z)]))
lines = lines[i + 5:]
try:
i = lines.index('-------------------------\n')
except ValueError:
e = None
else:
line = lines[i + 9]
assert line.startswith('Zero Kelvin:')
e = float(line.split()[-1])
try:
ii = index_startswith(lines, 'Total Charge:')
except ValueError:
q = None
else:
q = float(lines[ii].split()[2])
try:
ii = lines.index('Forces in eV/Ang:\n')
except ValueError:
f = None
else:
f = []
for i in range(ii + 1, ii + 1 + len(atoms)):
try:
x, y, z = lines[i].split()[-3:]
f.append((float(x), float(y), float(z)))
except (ValueError, IndexError) as m:
raise IOError('Malformed GPAW log file: %s' % m)
if len(images) > 0 and e is None:
break
if e is not None or f is not None:
atoms.set_calculator(SinglePointCalculator(
e, f, None, None, atoms)) ### Fixme magmoms
if q is not None:
n = len(atoms)
atoms.set_charges([q / n] * n)
images.append(atoms)
lines = lines[i:]
if len(images) == 0:
raise IOError('Corrupted GPAW-text file!')
return images[index]