def _set_stage1(self, cell):
prim_cell = get_primitive(cell, tolerance=self._symmetry_tolerance)
sym_dataset = get_symmetry_dataset(prim_cell)
self._space_group_type = sym_dataset['international_standard']
spg_number = sym_dataset['number']
if (spg_number >= 143 and
spg_number <= 194 and
not self._space_group_type[0] == 'R'): # Hexagonal lattice
self._supercell_dimensions = [[3, 3, 2], [2, 2, 2]]
else: # Other cases
self._supercell_dimensions = [[2, 2, 2]]
# Long cell axis is not multiplied.
for dimension in self._supercell_dimensions:
for i, length in enumerate(
get_lattice_parameters(prim_cell.get_lattice())):
if length * dimension[i] > 20:
dimension[i] = 1
self._tasks = []
for i, dimension in enumerate(self._supercell_dimensions):
task = self._get_phonon_task(prim_cell,
np.diag(dimension),
"phonon-%d" % (i + 1))
self._phre_tasks.append(task)
self._tasks.append(task)
def begin(self):
if not self._job:
print "set_job has to be executed."
raise
self._overwrite_settings()
self._status = "stage 1"
if self._impose_symmetry:
prim_cell = get_primitive(self._cell,
tolerance=self._symmetry_tolerance)
self._space_group = get_symmetry_dataset(prim_cell)
task = self._get_next_task(prim_cell)
else:
if self._find_symmetry:
self._space_group = get_symmetry_dataset(
self._cell,
self._symmetry_tolerance)
task = self._get_next_task(self._cell)
if self._space_group:
self._comment = self._space_group['international_standard']
self._so_tasks = [task]
self._tasks = [task]
self._write_yaml()
def next(self):
if self._status == "terminate":
self._stress = None
self._forces = None
self._energy = None
self._next_cell = None
else:
task = self._tasks[0]
self._next_cell = task.get_current_cell()
stress = task.get_stress()
forces = task.get_forces()
energy = task.get_energy()
if not stress == None:
self._stress = stress
if not forces == None:
self._forces = forces
if not energy == None:
self._energy = energy
if self._status == "terminate" and self._traverse == "restart":
self._traverse = False
if self._stage > 2:
self._stage -= 2
task = self._so_tasks.pop()
task = self._so_tasks.pop()
self._next_cell = task.get_cell()
else:
self._so_tasks = []
self._stage = 0
self._next_cell = self._cell
self._status = "next"
if self._next_cell:
if self._impose_symmetry:
self._next_cell = get_primitive(self._next_cell, tolerance=self._symmetry_tolerance)
self._space_group = get_symmetry_dataset(self._next_cell)
else:
if self._find_symmetry:
self._space_group = get_symmetry_dataset(self._next_cell, tolerance=self._symmetry_tolerance)
if self._space_group:
self._comment = self._space_group["international_standard"]
if self._status == "done":
if self._stage < self._min_iteration:
self._status = "next"
if self._status == "next":
if self._stage == self._max_iteration:
self._status = "max_iteration"
else:
self._set_next_task()
self._write_yaml()
if "stage" in self._status:
return self._tasks
else:
self._tasks = []
raise StopIteration
def _set_stage1(self, cell):
prim_cell = get_primitive(cell, tolerance=self._symmetry_tolerance)
sym_dataset = get_symmetry_dataset(prim_cell)
self._space_group_type = sym_dataset['international_standard']
spg_number = sym_dataset['number']
if (spg_number >= 143 and spg_number <= 194
and not self._space_group_type[0] == 'R'): # Hexagonal lattice
self._supercell_dimensions = [[3, 3, 2], [2, 2, 2]]
else: # Other cases
self._supercell_dimensions = [[2, 2, 2]]
# Long cell axis is not multiplied.
for dimension in self._supercell_dimensions:
for i, length in enumerate(
get_lattice_parameters(prim_cell.get_lattice())):
if length * dimension[i] > 20:
dimension[i] = 1
self._tasks = []
for i, dimension in enumerate(self._supercell_dimensions):
task = self._get_phonon_task(prim_cell, np.diag(dimension),
"phonon-%d" % (i + 1))
self._phre_tasks.append(task)
self._tasks.append(task)
def next(self):
if self._status == "terminate":
self._stress = None
self._forces = None
self._energy = None
self._next_cell = None
else:
task = self._tasks[0]
self._next_cell = task.get_current_cell()
stress = task.get_stress()
forces = task.get_forces()
energy = task.get_energy()
if not stress == None:
self._stress = stress
if not forces == None:
self._forces = forces
if not energy == None:
self._energy = energy
if "terminate" in self._status and self._traverse == "restart":
self._traverse = False
if self._stage > 2:
self._stage -= 2
task = self._so_tasks.pop()
task = self._so_tasks.pop()
self._next_cell = task.get_cell()
else:
self._so_tasks = []
self._stage = 0
self._next_cell = self._cell
self._status = "next"
if self._next_cell:
if self._impose_symmetry:
self._next_cell = get_primitive(
self._next_cell,
tolerance=self._symmetry_tolerance)
self._space_group = get_symmetry_dataset(self._next_cell)
else:
if self._find_symmetry:
self._space_group = get_symmetry_dataset(
self._next_cell,
tolerance=self._symmetry_tolerance)
if self._space_group:
self._comment = self._space_group['international_standard']
if self._status == "done":
if self._stage < self._min_iteration:
self._status = "next"
if self._status == "next":
if self._stage == self._max_iteration:
self._status = "max_iteration"
else:
self._set_next_task()
self._write_yaml()
if "stage" in self._status:
return self._tasks
else:
self._tasks = []
raise StopIteration