def _read_lattice(self, line):
"""Read the lattice vectors"""
line = self.file_descriptor.readline()
line = self.file_descriptor.readline()
x = float(line.split()[0])
y = float(line.split()[1])
z = float(line.split()[2])
avector = [x, y, z]
line = self.file_descriptor.readline()
x = float(line.split()[0])
y = float(line.split()[1])
z = float(line.split()[2])
bvector = [x, y, z]
line = self.file_descriptor.readline()
x = float(line.split()[0])
y = float(line.split()[1])
z = float(line.split()[2])
cvector = [x, y, z]
cell = UnitCell(avector, bvector, cvector)
self.unit_cells.append(cell)
self.volume = cell.volume
self.ncells = len(self.unit_cells)
# Convert fractional coordinates to cartesians
if len(self._cartesian_coordinates) == 0:
if len(self._fractional_coordinates) == 0:
print("Error no coordinates fraction or cartesian found")
exit()
for atom_frac in self._fractional_coordinates:
atom_cart = cell.convert_abc_to_xyz(atom_frac)
self.cartesian_coordinates.append(atom_cart)
# end for
# end if
self.unit_cells[-1].set_fractional_coordinates(self._fractional_coordinates)
self.unit_cells[-1].set_element_names(self._atom_types)
def _read_crystal_axes(self, line):
linea = self.file_descriptor.readline().split()
avector = [float(f) * self._alat / angs2bohr for f in linea[3:6]]
linea = self.file_descriptor.readline().split()
bvector = [float(f) * self._alat / angs2bohr for f in linea[3:6]]
linea = self.file_descriptor.readline().split()
cvector = [float(f) * self._alat / angs2bohr for f in linea[3:6]]
self.unit_cells.append(UnitCell(avector, bvector, cvector))
self.ncells = len(self.unit_cells)
self.volume = self.unit_cells[-1].volume
return
def _read_lattice_vectors(self, line):
linea = self.file_descriptor.readline().split()
avector = [float(f) * self._alat / angs2bohr for f in linea[0:3]]
linea = self.file_descriptor.readline().split()
bvector = [float(f) * self._alat / angs2bohr for f in linea[0:3]]
linea = self.file_descriptor.readline().split()
cvector = [float(f) * self._alat / angs2bohr for f in linea[0:3]]
self.unit_cells.append(UnitCell(avector, bvector, cvector))
self.ncells = len(self.unit_cells)
self.volume = self.unit_cells[-1].volume
self._read_masses()
return
def _read_lattice_vectors(self, line):
self.volume = float(line.split()[4])
line = self.file_descriptor.readline()
line = self.file_descriptor.readline()
avector = [
float(line.split()[0]),
float(line.split()[1]),
float(line.split()[2])
]
line = self.file_descriptor.readline()
bvector = [
float(line.split()[0]),
float(line.split()[1]),
float(line.split()[2])
]
line = self.file_descriptor.readline()
cvector = [
float(line.split()[0]),
float(line.split()[1]),
float(line.split()[2])
]
cell = UnitCell(avector, bvector, cvector)
if self.ncells > 0:
cell.set_fractional_coordinates(
self.unit_cells[-1].fractional_coordinates)
cell.set_element_names(self.species_list)
self.unit_cells.append(cell)
self.ncells = len(self.unit_cells)
return
def _read_lattice_vectors(self, line):
linea = line.split()
avector = [float(linea[1]), float(linea[2]), float(linea[3])]
linea = self.file_descriptor.readline().split()
bvector = [float(linea[0]), float(linea[1]), float(linea[2])]
linea = self.file_descriptor.readline().split()
cvector = [float(linea[0]), float(linea[1]), float(linea[2])]
avector = [f * self._acell[0] for f in avector]
bvector = [f * self._acell[1] for f in bvector]
cvector = [f * self._acell[2] for f in cvector]
self.unit_cells.append(UnitCell(avector, bvector, cvector))
self.ncells = len(self.unit_cells)
self.volume = self.unit_cells[-1].volume
return
def _read_lattice_vectors(self, line):
line = self.file_descriptor.readline()
line = self.file_descriptor.readline()
avector = [float(line.split()[0]), float(line.split()[1]), float(line.split()[2])]
line = self.file_descriptor.readline()
bvector = [float(line.split()[0]), float(line.split()[1]), float(line.split()[2])]
line = self.file_descriptor.readline()
cvector = [float(line.split()[0]), float(line.split()[1]), float(line.split()[2])]
self.unit_cells.append(UnitCell(avector, bvector, cvector))
self.ncells = len(self.unit_cells)
self.volume = self.unit_cells[-1].volume
# The fractional coordinates are specified before the lattice vectors
self.unit_cells[-1].set_fractional_coordinates(self._fractional_coordinates)
self.unit_cells[-1].set_element_names(self.species_list)
return
def _read_lattice_vectors(self, line):
scalar = float(line.split()[1])
line = self.file_descriptor.readline()
avector = [
scalar * float(line.split()[0]), scalar * float(line.split()[1]),
scalar * float(line.split()[2])
]
line = self.file_descriptor.readline()
bvector = [
scalar * float(line.split()[0]), scalar * float(line.split()[1]),
scalar * float(line.split()[2])
]
line = self.file_descriptor.readline()
cvector = [
scalar * float(line.split()[0]), scalar * float(line.split()[1]),
scalar * float(line.split()[2])
]
cell = UnitCell(avector, bvector, cvector)
self.unit_cells.append(cell)
self.ncells = len(self.unit_cells)
self.volume = cell.volume
return
def _read_cellcontents(self, line):
line = self._read_till_phrase(re.compile(' *Real Lattice'))
line = self.file_descriptor.readline()
avector = [
float(line.split()[0]),
float(line.split()[1]),
float(line.split()[2])
]
line = self.file_descriptor.readline()
bvector = [
float(line.split()[0]),
float(line.split()[1]),
float(line.split()[2])
]
line = self.file_descriptor.readline()
cvector = [
float(line.split()[0]),
float(line.split()[1]),
float(line.split()[2])
]
self.unit_cells.append(UnitCell(avector, bvector, cvector))
self.ncells = len(self.unit_cells)
line = self._read_till_phrase(re.compile(' *Current cell volume'))
self.volume = float(line.split()[4])
if self.nions == 0:
line = self._read_till_phrase(
re.compile(' *Total number of ions in cell'))
if len(self.unit_cells) == 1:
self.nions = int(line.split()[7])
line = self.file_descriptor.readline()
self.nspecies = int(line.split()[7])
line = self.file_descriptor.readline()
line = self.file_descriptor.readline()
line = self.file_descriptor.readline()
line = self.file_descriptor.readline()
line = self.file_descriptor.readline()
line = self.file_descriptor.readline()
# end if self.nions
else:
# Not all Unit Cell output is the same in Castep 17
line = self._read_till_phrase(
re.compile(' *xxxxxxxxxxxxxxxxxxxxxxxxxxxx'))
line = self.file_descriptor.readline()
line = self.file_descriptor.readline()
line = self.file_descriptor.readline()
# end of else
fractional_coordinates = []
# ions_per_type is a dictionary here and is local
ions_per_type = {}
self.atom_type_list = []
self.species = []
species_list = []
for i in range(self.nions):
line = self.file_descriptor.readline()
atom_type = line.split()[1].capitalize()
species_list.append(atom_type)
if atom_type not in ions_per_type:
self.species.append(atom_type)
ions_per_type[atom_type] = 0
self.atom_type_list.append(self.species.index(atom_type))
ions_per_type[atom_type] += 1
atom_frac = [float(f) for f in line.split()[3:6]]
fractional_coordinates.append(atom_frac)
# At some point we should store the fractional coordinates
for species in self.species:
n = ions_per_type[species]
# self.ions_per_type is a list
self.ions_per_type.append(n)
self.unit_cells[-1].set_fractional_coordinates(fractional_coordinates)
self.unit_cells[-1].set_element_names(species_list)
return