def __init__(self,
directory=None,
name=None,
delta_strain=None,
strain=None,
bias=None,
supercell_matrix=None,
primitive_matrix=None,
distance=None,
lattice_tolerance=None,
force_tolerance=None,
pressure_target=None,
stress_tolerance=None,
max_increase=None,
max_iteration=None,
min_iteration=None,
is_cell_relaxed=False,
traverse=False):
TaskElement.__init__(self)
self._directory = directory
if not name:
self._name = directory
else:
self._name = name
self._task_type = "mode_gruneisen"
self._bias = bias
if delta_strain is None:
self._delta_strain = 0.001
else:
self._delta_strain = delta_strain
(self._delta_strain_minus,
self._delta_strain_orig,
self._delta_strain_plus) = self._get_delta_strains()
if strain is None:
self._strain = np.eye(3)
else:
self._strain = self._get_strain(strain)
self._supercell_matrix = supercell_matrix
self._primitive_matrix = primitive_matrix
self._distance = distance
self._lattice_tolerance = lattice_tolerance
self._pressure_target = pressure_target
self._stress_tolerance = stress_tolerance
self._force_tolerance = force_tolerance
self._max_increase = max_increase
self._max_iteration = max_iteration
self._min_iteration = min_iteration
self._traverse = traverse
self._is_cell_relaxed = is_cell_relaxed
self._stage = 0
self._tasks = None
self._cell = None
self._mode_gruneisen = None
self._all_tasks = None
def __init__(self,
directory=None,
name=None,
lattice_tolerance=None,
force_tolerance=None,
pressure_target=None,
stress_tolerance=None,
max_increase=None,
max_iteration=None,
traverse=False,
is_cell_relaxed=False):
TaskElement.__init__(self)
self._directory = directory
if not name:
self._name = directory
else:
self._name = name
self._task_type = "elastic_constants"
self._lattice_tolerance = lattice_tolerance
self._pressure_target = pressure_target
self._stress_tolerance = stress_tolerance
self._force_tolerance = force_tolerance
self._max_increase = max_increase
self._max_iteration = max_iteration
self._traverse = traverse
self._is_cell_relaxed = is_cell_relaxed
self._stage = 0
self._tasks = None
self._cell = None
self._ec_tasks = None
self._elastic_constants = None
def __init__(self,
directory=None,
name=None,
lattice_tolerance=None,
force_tolerance=None,
pressure_target=None,
stress_tolerance=None,
max_increase=None,
max_iteration=None,
traverse=False,
is_cell_relaxed=False):
TaskElement.__init__(self)
self._directory = directory
if not name:
self._name = directory
else:
self._name = name
self._task_type = "elastic_constants"
self._lattice_tolerance = lattice_tolerance
self._pressure_target = pressure_target
self._stress_tolerance = stress_tolerance
self._force_tolerance = force_tolerance
self._max_increase = max_increase
self._max_iteration = max_iteration
self._traverse = traverse
self._is_cell_relaxed = is_cell_relaxed
self._stage = 0
self._tasks = None
self._cell = None
self._ec_tasks = None
self._elastic_constants = None
def __init__(self,
directory=None,
name=None,
supercell_matrix=None,
primitive_matrix=None,
distance=None,
displace_plusminus='auto',
displace_diagonal=False,
lattice_tolerance=None,
force_tolerance=None,
pressure_target=None,
stress_tolerance=None,
max_increase=None,
max_iteration=None,
min_iteration=None,
is_cell_relaxed=False,
max_num_atoms=None,
stop_condition=None,
traverse=False):
TaskElement.__init__(self)
self._directory = directory
if not name:
self._name = directory
else:
self._name = name
self._task_type = "phonon"
self._supercell_matrix = supercell_matrix
if self._supercell_matrix is None:
self._primitive_matrix = np.eye(3, dtype='double')
else:
self._primitive_matrix = primitive_matrix
self._distance = distance
self._displace_plusminus = displace_plusminus
self._displace_diagonal = displace_diagonal
self._lattice_tolerance = lattice_tolerance
self._pressure_target = pressure_target
self._stress_tolerance = stress_tolerance
self._force_tolerance = force_tolerance
self._max_increase = max_increase
self._max_iteration = max_iteration
self._min_iteration = min_iteration
self._is_cell_relaxed = is_cell_relaxed
self._max_num_atoms = max_num_atoms
self._stop_condition = stop_condition
self._traverse = traverse
self._stage = 0
self._tasks = []
self._energy = None
self._space_group = None
self._cell = None
self._phonon = None # Phonopy object
self._all_tasks = None # Phonopy object
self._try_collect_forces = True
def __init__(self,
directory=None,
name=None,
ancestral_cells={},
tid_parent=None,
distance=None,
lattice_tolerance=None,
force_tolerance=None,
pressure_target=None,
stress_tolerance=None,
max_increase=None,
max_iteration=None,
min_iteration=None,
symmetry_tolerance=None,
cutoff_eigenvalue=None,
max_displacement=None,
num_sampling_points=None,
traverse=False):
TaskElement.__init__(self)
self._directory = directory
if not name:
self._name = directory
else:
self._name = name
self._ancestral_cells = ancestral_cells
self._tid_parent = tid_parent
self._task_type = "phonon_relax_element"
self._distance = distance
self._lattice_tolerance = lattice_tolerance
self._pressure_target = pressure_target
self._stress_tolerance = stress_tolerance
self._force_tolerance = force_tolerance
self._max_increase = max_increase
self._max_iteration = max_iteration
self._min_iteration = min_iteration
self._symmetry_tolerance = symmetry_tolerance
self._cutoff_eigenvalue = cutoff_eigenvalue
self._max_displacement = max_displacement
self._num_sampling_points = num_sampling_points
self._traverse = traverse
self._tasks = []
self._phre = []
self._stage = 0
self._supercell_dimention = None
self._space_group_type = None
self._energy = None
# self._imaginary_modes:
# (cell with modulation,
# q-point,
# Im(frequency),
# Index of q-point in the mesh sampling,
# Band index,
# Number of degeneracy)
self._imaginary_modes = []
def __init__(self,
directory=None,
name=None,
ancestral_cells={},
tid_parent=None,
distance=None,
lattice_tolerance=None,
force_tolerance=None,
pressure_target=None,
stress_tolerance=None,
max_increase=None,
max_iteration=None,
min_iteration=None,
symmetry_tolerance=None,
cutoff_eigenvalue=None,
max_displacement=None,
num_sampling_points=None,
traverse=False):
TaskElement.__init__(self)
self._directory = directory
if not name:
self._name = directory
else:
self._name = name
self._ancestral_cells = ancestral_cells
self._tid_parent = tid_parent
self._task_type = "phonon_relax_element"
self._distance = distance
self._lattice_tolerance = lattice_tolerance
self._pressure_target = pressure_target
self._stress_tolerance = stress_tolerance
self._force_tolerance = force_tolerance
self._max_increase = max_increase
self._max_iteration = max_iteration
self._min_iteration = min_iteration
self._symmetry_tolerance = symmetry_tolerance
self._cutoff_eigenvalue = cutoff_eigenvalue
self._max_displacement = max_displacement
self._num_sampling_points = num_sampling_points
self._traverse = traverse
self._tasks = []
self._phre = []
self._stage = 0
self._supercell_dimention = None
self._space_group_type = None
self._energy = None
# self._imaginary_modes:
# (cell with modulation,
# q-point,
# Im(frequency),
# Index of q-point in the mesh sampling,
# Band index,
# Number of degeneracy)
self._imaginary_modes = []
def __init__(self,
directory=None,
name=None,
ancestral_cells={},
distance=None,
lattice_tolerance=None,
force_tolerance=None,
pressure_target=None,
stress_tolerance=None,
max_increase=None,
max_iteration=None,
min_iteration=None,
symmetry_tolerance=None,
restrict_offspring=False,
max_offspring=None,
cutoff_eigenvalue=None,
max_displacement=None,
num_sampling_points=None,
stop_condition=None,
traverse=False):
TaskElement.__init__(self)
self._directory = directory
if not name:
self._name = directory
else:
self._name = name
self._ancestral_cells = ancestral_cells
self._task_type = "phonon_relax"
self._distance = distance
self._lattice_tolerance = lattice_tolerance
self._pressure_target = pressure_target
self._stress_tolerance = stress_tolerance
self._force_tolerance = force_tolerance
self._max_increase = max_increase
self._max_iteration = max_iteration
self._min_iteration = min_iteration
self._symmetry_tolerance = symmetry_tolerance
self._restrict_offspring = restrict_offspring
self._max_offspring = max_offspring
self._cutoff_eigenvalue = cutoff_eigenvalue
if max_displacement:
self._max_displacement = max_displacement
else:
self._max_displacement = symmetry_tolerance * MAX_DISPLACEMENT_RATIO
self._num_sampling_points = num_sampling_points
self._stop_condition = stop_condition
self._traverse = traverse
self._phr_tasks = []
self._tasks = []
self._stage = 0
self._energy = None
def __init__(self,
directory=None,
name=None,
ancestral_cells={},
distance=None,
lattice_tolerance=None,
force_tolerance=None,
pressure_target=None,
stress_tolerance=None,
max_increase=None,
max_iteration=None,
min_iteration=None,
symmetry_tolerance=None,
restrict_offspring=False,
max_offspring=None,
cutoff_eigenvalue=None,
max_displacement=None,
num_sampling_points=None,
traverse=False):
TaskElement.__init__(self)
self._directory = directory
if not name:
self._name = directory
else:
self._name = name
self._ancestral_cells = ancestral_cells
self._task_type = "phonon_relax"
self._distance = distance
self._lattice_tolerance = lattice_tolerance
self._pressure_target = pressure_target
self._stress_tolerance = stress_tolerance
self._force_tolerance = force_tolerance
self._max_increase = max_increase
self._max_iteration = max_iteration
self._min_iteration = min_iteration
self._symmetry_tolerance = symmetry_tolerance
self._restrict_offspring = restrict_offspring
self._max_offspring = max_offspring
self._cutoff_eigenvalue = cutoff_eigenvalue
if max_displacement:
self._max_displacement = max_displacement
else:
self._max_displacement = symmetry_tolerance * MAX_DISPLACEMENT_RATIO
self._num_sampling_points = num_sampling_points
self._traverse = traverse
self._phr_tasks = []
self._tasks = []
self._stage = 0
self._energy = None
def __init__(self, directory=None, name=None, traverse=False):
TaskElement.__init__(self)
self._directory = directory
if not name:
self._name = directory
else:
self._name = name
self._tasks = [] # Means singular task
self._traverse = traverse
self._cell = None
def __init__(self,
directory=None,
name=None,
supercell_matrix=None,
primitive_matrix=None,
distance=None,
is_diagonal=True,
check_imaginary=True,
cutoff_frequency=None,
lattice_tolerance=None,
force_tolerance=None,
pressure_target=None,
stress_tolerance=None,
max_increase=None,
max_iteration=None,
min_iteration=None,
is_cell_relaxed=False,
traverse=False):
TaskElement.__init__(self)
self._directory = directory
if not name:
self._name = directory
else:
self._name = name
self._task_type = "anharmonic_phonon"
self._supercell_matrix = supercell_matrix
self._primitive_matrix = primitive_matrix
self._distance = distance
self._is_diagonal = is_diagonal
self._check_imaginary = check_imaginary
self._cutoff_frequency = cutoff_frequency # determine imaginary freq.
self._lattice_tolerance = lattice_tolerance
self._pressure_target = pressure_target
self._stress_tolerance = stress_tolerance
self._force_tolerance = force_tolerance
self._max_increase = max_increase
self._max_iteration = max_iteration
self._min_iteration = min_iteration
self._traverse = traverse
self._is_cell_relaxed = is_cell_relaxed
self._stage = 0
self._tasks = []
self._energy = None
self._cell = None
self._phonon = None # Phonopy object
self._phonon_fc3 = None # Phono3py object
self._phonon_fc3_tasks = None
def __init__(
self,
directory="structure_optimization",
name=None,
lattice_tolerance=None,
force_tolerance=None,
pressure_target=None,
stress_tolerance=None,
max_increase=None,
max_iteration=None,
min_iteration=None,
find_symmetry=True,
impose_symmetry=False,
symmetry_tolerance=None,
traverse=False,
):
TaskElement.__init__(self)
self._directory = directory
if not name:
self._name = directory
else:
self._name = name
self._task_type = "structure_optimization"
self._lattice_tolerance = lattice_tolerance
self._pressure_target = pressure_target
self._stress_tolerance = stress_tolerance
self._force_tolerance = force_tolerance
self._max_increase = max_increase
self._max_iteration = max_iteration
self._min_iteration = min_iteration
self._find_symmetry = find_symmetry
self._impose_symmetry = impose_symmetry
self._symmetry_tolerance = symmetry_tolerance
self._traverse = traverse
self._stage = 1
self._tasks = None
self._cell = None
self._next_cell = None
self._so_tasks = None
self._stress = None
self._forces = None
self._energy = None
self._space_group = None
def __init__(self,
directory=None,
name=None,
traverse=False):
TaskElement.__init__(self)
self._directory = directory
if not name:
self._name = directory
else:
self._name = name
self._tasks = [] # Means singular task
self._traverse = traverse
self._cell = None
def __init__(self,
directory="structure_optimization",
name=None,
lattice_tolerance=None,
force_tolerance=None,
pressure_target=None,
stress_tolerance=None,
max_increase=None,
max_iteration=None,
min_iteration=None,
find_symmetry=True,
impose_symmetry=False,
symmetry_tolerance=None,
traverse=False):
TaskElement.__init__(self)
self._directory = directory
if not name:
self._name = directory
else:
self._name = name
self._task_type = "structure_optimization"
self._lattice_tolerance = lattice_tolerance
self._pressure_target = pressure_target
self._stress_tolerance = stress_tolerance
self._force_tolerance = force_tolerance
self._max_increase = max_increase
self._max_iteration = max_iteration
self._min_iteration = min_iteration
self._find_symmetry = find_symmetry
self._impose_symmetry = impose_symmetry
self._symmetry_tolerance = symmetry_tolerance
self._traverse = traverse
self._stage = 1
self._tasks = None
self._cell = None
self._next_cell = None
self._so_tasks = None
self._stress = None
self._forces = None
self._energy = None
self._space_group = None
def __init__(self,
directory=None,
name=None,
supercell_matrix=None,
primitive_matrix=None,
distance=None,
lattice_tolerance=None,
force_tolerance=None,
pressure_target=None,
stress_tolerance=None,
max_increase=None,
max_iteration=None,
min_iteration=None,
traverse=False,
is_cell_relaxed=False):
TaskElement.__init__(self)
self._directory = directory
if not name:
self._name = directory
else:
self._name = name
self._task_type = "phonon"
self._supercell_matrix = supercell_matrix
self._primitive_matrix = primitive_matrix
self._distance = distance
self._lattice_tolerance = lattice_tolerance
self._pressure_target = pressure_target
self._stress_tolerance = stress_tolerance
self._force_tolerance = force_tolerance
self._max_increase = max_increase
self._max_iteration = max_iteration
self._min_iteration = min_iteration
self._traverse = traverse
self._is_cell_relaxed = is_cell_relaxed
self._stage = 0
self._tasks = []
self._energy = None
self._cell = None
self._phonon = None # Phonopy object
def __init__(self,
directory=None,
name=None,
supercell_matrix=None,
primitive_matrix=None,
distance=None,
lattice_tolerance=None,
force_tolerance=None,
pressure_target=None,
stress_tolerance=None,
max_increase=None,
max_iteration=None,
min_iteration=None,
traverse=False,
is_cell_relaxed=False):
TaskElement.__init__(self)
self._directory = directory
if not name:
self._name = directory
else:
self._name = name
self._task_type = "phonon"
self._supercell_matrix = supercell_matrix
self._primitive_matrix = primitive_matrix
self._distance = distance
self._lattice_tolerance = lattice_tolerance
self._pressure_target = pressure_target
self._stress_tolerance = stress_tolerance
self._force_tolerance = force_tolerance
self._max_increase = max_increase
self._max_iteration = max_iteration
self._min_iteration = min_iteration
self._traverse = traverse
self._is_cell_relaxed = is_cell_relaxed
self._stage = 0
self._tasks = []
self._energy = None
self._cell = None
self._phonon = None # Phonopy object
def __init__(self,
directory=None,
name=None,
strains=None,
lattice_tolerance=None,
force_tolerance=None,
pressure_target=None,
stress_tolerance=None,
max_increase=None,
max_iteration=None,
min_iteration=None,
is_cell_relaxed=False,
traverse=False):
TaskElement.__init__(self)
self._directory = directory
if not name:
self._name = directory
else:
self._name = name
self._task_type = "bulk_modulus"
self._strains = strains
self._lattice_tolerance = lattice_tolerance
self._pressure_target = pressure_target
self._stress_tolerance = stress_tolerance
self._force_tolerance = force_tolerance
self._max_increase = max_increase
self._max_iteration = max_iteration
self._min_iteration = min_iteration
self._traverse = traverse
self._is_cell_relaxed = is_cell_relaxed
self._stage = 0
self._tasks = None
self._cell = None
self._bulk_modulus = None
self._all_tasks = None
self._eos = None # Energy function of V, only for strains mode
def __init__(self,
directory=None,
name=None,
is_partial_dos=False,
lattice_tolerance=None,
force_tolerance=None,
pressure_target=None,
stress_tolerance=None,
max_increase=None,
max_iteration=None,
min_iteration=None,
is_cell_relaxed=False,
traverse=False):
TaskElement.__init__(self)
self._directory = directory
if not name:
self._name = directory
else:
self._name = name
self._task_type = "density_of_states"
self._is_partial_dos = is_partial_dos
self._lattice_tolerance = lattice_tolerance
self._pressure_target = pressure_target
self._stress_tolerance = stress_tolerance
self._force_tolerance = force_tolerance
self._max_increase = max_increase
self._max_iteration = max_iteration
self._min_iteration = min_iteration
self._traverse = traverse
self._is_cell_relaxed = is_cell_relaxed
self._stage = 0
self._tasks = None
self._cell = None
self._density_of_states = None
self._dos_tasks = None
def __init__(self,
directory=None,
name=None,
strains=None,
sampling_mesh=None,
is_gamma_center=False,
t_step=None,
t_max=None,
t_min=None,
supercell_matrix=None,
primitive_matrix=None,
nac=False,
distance=None,
lattice_tolerance=None,
force_tolerance=None,
pressure_target=None,
stress_tolerance=None,
max_increase=None,
max_iteration=None,
min_iteration=None,
is_cell_relaxed=False,
max_num_atoms=None,
first_phonon_index=None,
traverse=False):
TaskElement.__init__(self)
self._directory = directory
if not name:
self._name = directory
else:
self._name = name
self._task_type = "quasiharmonic_phonon"
self._strains = strains
if self._strains is None:
self._estimate_strain = True
else:
self._estimate_strain = False
self._sampling_mesh = sampling_mesh
self._is_gamma_center = is_gamma_center
if t_step is None:
self._t_step = 2
else:
self._t_step = t_step
if t_max is None:
self._t_max = 1500
else:
self._t_max = t_max
if t_min is None:
self._t_min = 0
else:
self._t_min = t_min
self._supercell_matrix = supercell_matrix
self._primitive_matrix = primitive_matrix
self._nac = nac
self._distance = distance
self._lattice_tolerance = lattice_tolerance
self._pressure_target = pressure_target
self._stress_tolerance = stress_tolerance
self._force_tolerance = force_tolerance
self._max_increase = max_increase
self._max_iteration = max_iteration
self._min_iteration = min_iteration
self._traverse = traverse
self._is_cell_relaxed = is_cell_relaxed
self._max_num_atoms = max_num_atoms
self._first_phonon_index = first_phonon_index
self._stage = 0
self._tasks = None
self._cell = None
self._all_tasks = None
self._imaginary_ratio = None
self._grid_spacing = 200
def __init__(
self,
directory=None,
name=None,
strains=None,
sampling_mesh=None,
t_step=None,
t_max=None,
t_min=None,
supercell_matrix=None,
primitive_matrix=None,
distance=None,
lattice_tolerance=None,
force_tolerance=None,
pressure_target=None,
stress_tolerance=None,
max_increase=None,
max_iteration=None,
min_iteration=None,
is_cell_relaxed=False,
traverse=False,
):
TaskElement.__init__(self)
self._directory = directory
if not name:
self._name = directory
else:
self._name = name
self._task_type = "quasiharmonic_phonon"
self._lattices = [np.eye(3)]
for strain in strains:
if isinstance(strain, int) or isinstance(strain, float):
self._lattices.append((1 + strain) ** (1.0 / 3) * np.eye(3))
else:
self._lattices.append(np.eye(3) + np.array(strain))
self._sampling_mesh = sampling_mesh
if t_step is None:
self._t_step = 10
else:
self._t_step = t_step
if t_max is None:
self._t_max = 1500
else:
self._t_max = t_max
if t_min is None:
self._t_min = 0
else:
self._t_min = t_min
self._supercell_matrix = supercell_matrix
self._primitive_matrix = primitive_matrix
self._distance = distance
self._lattice_tolerance = lattice_tolerance
self._pressure_target = pressure_target
self._stress_tolerance = stress_tolerance
self._force_tolerance = force_tolerance
self._max_increase = max_increase
self._max_iteration = max_iteration
self._min_iteration = min_iteration
self._traverse = traverse
self._is_cell_relaxed = is_cell_relaxed
self._stage = 0
self._tasks = None
self._cell = None
self._qh_tasks = None
def __init__(self,
directory=None,
name=None,
strains=None,
sampling_mesh=None,
t_step=None,
t_max=None,
t_min=None,
supercell_matrix=None,
primitive_matrix=None,
distance=None,
lattice_tolerance=None,
force_tolerance=None,
pressure_target=None,
stress_tolerance=None,
max_increase=None,
max_iteration=None,
min_iteration=None,
traverse=False,
is_cell_relaxed=False):
TaskElement.__init__(self)
self._directory = directory
if not name:
self._name = directory
else:
self._name = name
self._task_type = "quasiharmonic_phonon"
self._lattices = [np.eye(3)]
for strain in strains:
if isinstance(strain, int) or isinstance(strain, float):
self._lattices.append((1 + strain)**(1.0 / 3) * np.eye(3))
else:
self._lattices.append(np.eye(3) + np.array(strain))
self._sampling_mesh = sampling_mesh
if t_step is None:
self._t_step = 10
else:
self._t_step = t_step
if t_max is None:
self._t_max = 1500
else:
self._t_max = t_max
if t_min is None:
self._t_min = 0
else:
self._t_min = t_min
self._supercell_matrix = supercell_matrix
self._primitive_matrix = primitive_matrix
self._distance = distance
self._lattice_tolerance = lattice_tolerance
self._pressure_target = pressure_target
self._stress_tolerance = stress_tolerance
self._force_tolerance = force_tolerance
self._max_increase = max_increase
self._max_iteration = max_iteration
self._min_iteration = min_iteration
self._traverse = traverse
self._is_cell_relaxed = is_cell_relaxed
self._stage = 0
self._tasks = None
self._cell = None
self._qh_tasks = None
