def read_sc(self, *args, **kwargs):
""" Returns `SuperCell` object from the FDF file """
f, lc = self._read('LatticeConstant')
s = float(lc.split()[1])
if 'ang' in lc.lower():
pass
elif 'bohr' in lc.lower():
s *= Bohr2Ang
# Read in cell
cell = np.empty([3, 3], np.float64)
f, lc = self._read_block('LatticeVectors')
if f:
for i in range(3):
cell[i, :] = [float(k) for k in lc[i].split()[:3]]
else:
f, lc = self._read_block('LatticeParameters')
if f:
tmp = [float(k) for k in lc[0].split()[:6]]
cell = SuperCell.tocell(*tmp)
if not f:
# the fdf file contains neither the latticevectors or parameters
raise SileError(
'Could not find Vectors or Parameters block in file')
cell *= s
return SuperCell(cell)
def read_sc(self, *args, **kwargs):
""" Returns `SuperCell` object from the FDF file """
f, lc = self._read('LatticeConstant')
s = float(lc.split()[1])
if 'ang' in lc.lower():
pass
elif 'bohr' in lc.lower():
s *= Bohr2Ang
# Read in cell
cell = np.empty([3, 3], np.float64)
f, lc = self._read_block('LatticeVectors')
if f:
for i in range(3):
cell[i, :] = [float(k) for k in lc[i].split()[:3]]
else:
f, lc = self._read_block('LatticeParameters')
if f:
tmp = [float(k) for k in lc[0].split()[:6]]
cell = SuperCell.tocell(*tmp)
if not f:
# the fdf file contains neither the latticevectors or parameters
raise SileError(
'Could not find Vectors or Parameters block in file')
cell *= s
return SuperCell(cell)
def _r_supercell_fdf(self, *args, **kwargs):
""" Returns `SuperCell` object from the FDF file """
s = self.get('LatticeConstant', unit='Ang')
if s is None:
raise SileError('Could not find LatticeConstant in file')
# Read in cell
cell = np.empty([3, 3], np.float64)
lc = self.get('LatticeVectors')
if lc:
for i in range(3):
cell[i, :] = [float(k) for k in lc[i].split()[:3]]
else:
lc = self.get('LatticeParameters')
if lc:
tmp = [float(k) for k in lc[0].split()[:6]]
cell = SuperCell.tocell(*tmp)
if lc is None:
# the fdf file contains neither the latticevectors or parameters
raise SileError(
'Could not find LatticeVectors or LatticeParameters block in file'
)
cell *= s
# When reading from the fdf, the warning should be suppressed
with warnings.catch_warnings():
warnings.simplefilter("ignore")
nsc = self.read_supercell_nsc()
return SuperCell(cell, nsc=nsc)
def read_supercell(self):
""" Read supercell from the contained file """
f, line = self._step_record('CRYST1')
if not f:
raise SileError(str(self) + ' does not contain a CRYST1 record.')
a = float(line[6:15])
b = float(line[15:24])
c = float(line[24:33])
alpha = float(line[33:40])
beta = float(line[40:47])
gamma = float(line[47:54])
cell = SuperCell.tocell([a, b, c, alpha, beta, gamma])
f, line = self._step_record('SCALE1')
if f:
cell[0, :] = float(line[11:20]), float(line[21:30]), float(line[31:40])
f, line = self._step_record('SCALE2')
if not f:
raise SileError(str(self) + ' found SCALE1 but not SCALE2!')
cell[1, :] = float(line[11:20]), float(line[21:30]), float(line[31:40])
f, line = self._step_record('SCALE3')
if not f:
raise SileError(str(self) + ' found SCALE1 but not SCALE3!')
cell[2, :] = float(line[11:20]), float(line[21:30]), float(line[31:40])
origo = np.zeros(3)
for i in range(3):
f, line = self._step_record('ORIGX{}'.format(i + 1))
if f:
origo[i] = float(line[45:55])
return SuperCell(cell, origo=origo)