def do_phonons(strt=None, parameters=None, c_size=25):
"""
Setting up phonopy job using LAMMPS
Args:
strt: Structure object
parameters: LAMMPS input file parameters
c_size: cell-size
"""
p = get_phonopy_atoms(mat=strt)
bulk = p
dim1 = int((float(c_size) / float(max(abs(strt.lattice.matrix[0]))))) + 1
dim2 = int(float(c_size) / float(max(abs(strt.lattice.matrix[1])))) + 1
dim3 = int(float(c_size) / float(max(abs(strt.lattice.matrix[2])))) + 1
Poscar(strt).write_file("POSCAR")
tmp = strt.copy()
tmp.make_supercell([dim1, dim2, dim3])
Poscar(tmp).write_file("POSCAR-Super.vasp")
phonon = Phonopy(bulk, [[dim1, 0, 0], [0, dim2, 0], [0, 0, dim3]]) # ,
print("[Phonopy] Atomic displacements:")
disps = phonon.get_displacements()
for d in disps:
print("[Phonopy]", d[0], d[1:])
supercells = phonon.get_supercells_with_displacements()
# Force calculations by calculator
set_of_forces = []
disp = 0
for scell in supercells:
cell = Atoms(
symbols=scell.get_chemical_symbols(),
scaled_positions=scell.get_scaled_positions(),
cell=scell.get_cell(),
pbc=True,
)
disp = disp + 1
mat = Poscar(AseAtomsAdaptor().get_structure(cell))
mat.comment = str("disp-") + str(disp)
parameters["min"] = "skip"
parameters["control_file"] = "/users/knc6/in.phonon"
# a,b,forces=run_job(mat=mat,parameters={'min':'skip','pair_coeff': '/data/knc6/JARVIS-FF-NEW/ALLOY4/Mishin-Ni-Al-2009.eam.alloy', 'control_file': '/users/knc6/in.phonon', 'pair_style': 'eam/alloy', 'atom_style': 'charge'})
a, b, forces = run_job(mat=mat, parameters=parameters)
print("forces=", forces)
drift_force = forces.sum(axis=0)
print("drift forces=", drift_force)
print("[Phonopy] Drift force:", "%11.5f" * 3 % tuple(drift_force))
# Simple translational invariance
for force in forces:
force -= drift_force / forces.shape[0]
set_of_forces.append(forces)
phonon.produce_force_constants(forces=set_of_forces)
write_FORCE_CONSTANTS(phonon.get_force_constants(), filename="FORCE_CONSTANTS")
print()
print("[Phonopy] Phonon frequencies at Gamma:")
def get_displaced_structures(pmg_structure,
atom_disp=0.01,
supercell_matrix=None,
yaml_fname=None,
**kwargs):
r"""
Generate a set of symmetrically inequivalent displaced structures for
phonon calculations.
Args:
pmg_structure (Structure): A pymatgen structure object.
atom_disp (float): Atomic displacement. Default is 0.01 $\\AA$.
supercell_matrix (3x3 array): Scaling matrix for supercell.
yaml_fname (string): If not None, it represents the full path to
the outputting displacement yaml file, e.g. disp.yaml.
**kwargs: Parameters used in Phonopy.generate_displacement method.
Return:
A list of symmetrically inequivalent structures with displacements, in
which the first element is the perfect supercell structure.
"""
is_plusminus = kwargs.get("is_plusminus", "auto")
is_diagonal = kwargs.get("is_diagonal", True)
is_trigonal = kwargs.get("is_trigonal", False)
ph_structure = get_phonopy_structure(pmg_structure)
if supercell_matrix is None:
supercell_matrix = np.eye(3) * np.array((1, 1, 1))
phonon = Phonopy(unitcell=ph_structure, supercell_matrix=supercell_matrix)
phonon.generate_displacements(
distance=atom_disp,
is_plusminus=is_plusminus,
is_diagonal=is_diagonal,
is_trigonal=is_trigonal,
)
if yaml_fname is not None:
displacements = phonon.get_displacements()
write_disp_yaml(
displacements=displacements,
supercell=phonon.get_supercell(),
filename=yaml_fname,
)
# Supercell structures with displacement
disp_supercells = phonon.get_supercells_with_displacements()
# Perfect supercell structure
init_supercell = phonon.get_supercell()
# Structure list to be returned
structure_list = [get_pmg_structure(init_supercell)]
for c in disp_supercells:
if c is not None:
structure_list.append(get_pmg_structure(c))
return structure_list
def get_phonopy_displacements(phonon: phonopy.Phonopy):
""" Get displacements as arrays of ``phonopy_atom`` and ``[dx, dy, dz]`` (cartesian).
``phonopy_atom`` is the displaced atom index according to phonopy's supercell ordering convention.
Mind that this is different from ASE's convention. """
return tuple(
map(list,
zip(*[(i, xyz) for (i, *xyz) in phonon.get_displacements()])))
def do_phonons(strt=None,parameters=None):
p= get_phonopy_atoms(mat=strt)
bulk =p
c_size=parameters['phon_size']
dim1=int((float(c_size)/float( max(abs(strt.lattice.matrix[0])))))+1
dim2=int(float(c_size)/float( max(abs(strt.lattice.matrix[1]))))+1
dim3=int(float(c_size)/float( max(abs(strt.lattice.matrix[2]))))+1
Poscar(strt).write_file("POSCAR")
tmp=strt.copy()
tmp.make_supercell([dim1,dim2,dim3])
Poscar(tmp).write_file("POSCAR-Super.vasp")
print ('supercells',dim1,dim2,dim3)
phonon = Phonopy(bulk,[[dim1,0,0],[0,dim2,0],[0,0,dim3]])
print ("[Phonopy] Atomic displacements:")
disps = phonon.get_displacements()
for d in disps:
print ("[Phonopy]", d[0], d[1:])
supercells = phonon.get_supercells_with_displacements()
# Force calculations by calculator
set_of_forces = []
disp=0
for scell in supercells:
cell = Atoms(symbols=scell.get_chemical_symbols(),
scaled_positions=scell.get_scaled_positions(),
cell=scell.get_cell(),
pbc=True)
disp=disp+1
mat = Poscar(AseAtomsAdaptor().get_structure(cell))
mat.comment=str("disp-")+str(disp)
parameters['min']='skip'
parameters['control_file']= parameters['phonon_control_file'] #'/users/knc6/in.phonon'
#a,b,forces=run_job(mat=mat,parameters={'min':'skip','pair_coeff': '/data/knc6/JARVIS-FF-NEW/ALLOY4/Mishin-Ni-Al-2009.eam.alloy', 'control_file': '/users/knc6/in.phonon', 'pair_style': 'eam/alloy', 'atom_style': 'charge'})
a,b,forces=run_job(mat=mat,parameters=parameters)
#print "forces=",forces
drift_force = forces.sum(axis=0)
#print "drift forces=",drift_force
#print "[Phonopy] Drift force:", "%11.5f"*3 % tuple(drift_force)
# Simple translational invariance
for force in forces:
force -= drift_force / forces.shape[0]
set_of_forces.append(forces)
phonon.produce_force_constants(forces=set_of_forces)
write_FORCE_CONSTANTS(phonon.get_force_constants(),
filename="FORCE_CONSTANTS")
#print
#print "[Phonopy] Phonon frequencies at Gamma:"
for i, freq in enumerate(phonon.get_frequencies((0, 0, 0))):
print ("[Phonopy] %3d: %10.5f THz" % (i + 1, freq)) # THz
def get_displaced_structures(pmg_structure, atom_disp=0.01,
supercell_matrix=None, yaml_fname=None, **kwargs):
"""
Generate a set of symmetrically inequivalent displaced structures for
phonon calculations.
Args:
pmg_structure (Structure): A pymatgen structure object.
atom_disp (float): Atomic displacement. Default is 0.01 $\\AA$.
supercell_matrix (3x3 array): Scaling matrix for supercell.
yaml_fname (string): If not None, it represents the full path to
the outputting displacement yaml file, e.g. disp.yaml.
**kwargs: Parameters used in Phonopy.generate_displacement method.
Return:
A list of symmetrically inequivalent structures with displacements, in
which the first element is the perfect supercell structure.
"""
is_plusminus = kwargs.get("is_plusminus", "auto")
is_diagonal = kwargs.get("is_diagonal", True)
is_trigonal = kwargs.get("is_trigonal", False)
ph_structure = get_phonopy_structure(pmg_structure)
if supercell_matrix is None:
supercell_matrix = np.eye(3) * np.array((1, 1, 1))
phonon = Phonopy(unitcell=ph_structure, supercell_matrix=supercell_matrix)
phonon.generate_displacements(distance=atom_disp,
is_plusminus=is_plusminus,
is_diagonal=is_diagonal,
is_trigonal=is_trigonal)
if yaml_fname is not None:
displacements = phonon.get_displacements()
directions = phonon.get_displacement_directions()
write_disp_yaml(displacements=displacements,
supercell=phonon.get_supercell(),
directions=directions, filename=yaml_fname)
# Supercell structures with displacement
disp_supercells = phonon.get_supercells_with_displacements()
# Perfect supercell structure
init_supercell = phonon.get_supercell()
# Structure list to be returned
structure_list = [get_pmg_structure(init_supercell)]
for c in disp_supercells:
if c is not None:
structure_list.append(get_pmg_structure(c))
return structure_list
def phonopy_pre_process(cell, config_type, supercell_matrix=None):
smat = [[3, 0, 0], [0, 3, 0], [0, 0, 3]]
phonon = Phonopy(cell, smat)
phonon.generate_displacements(distance=0.16) #0.02
print("[Phonopy] Atomic displacements:")
disps = phonon.get_displacements()
for d in disps:
print("[Phonopy] %d %s" % (d[0], d[1:]))
return phonon
def build_phonon(self, atoms = None,
supercell_matrix = None,
primitive_matrix = None,
distance = None):
if atoms is None:
atoms = self.atoms
phonon = Phonopy(atoms,
supercell_matrix,
primitive_matrix = primitive_matrix)
phonon.generate_displacements(distance = distance)
self.log("[Phonopy] Atomic displacements:")
disps = phonon.get_displacements()
for d in disps:
self.log("[Phonopy] %d %s" % (d[0], d[1:]))
self.phonon = phonon
def phonopy_pre_process(cell, disp, config_type, supercell_matrix=None):
if config_type == "al":
print config_type
smat = [[2, 0, 0], [0, 2, 0], [0, 0, 2]]
else:
smat = [[3, 0, 0], [0, 3, 0], [0, 0, 3]]
phonon = Phonopy(cell, smat)
phonon.generate_displacements(distance=disp)
print("[Phonopy] Atomic displacements:")
disps = phonon.get_displacements()
for d in disps:
print("[Phonopy] %d %s" % (d[0], d[1:]))
return phonon
def phonopy_pre_process(cell, supercell_matrix=None):
if supercell_matrix is None:
smat = [[2,0,0], [0,2,0], [0,0,2]],
else:
smat = supercell_matrix
phonon = Phonopy(cell,
smat,
primitive_matrix=[[0, 0.5, 0.5],
[0.5, 0, 0.5],
[0.5, 0.5, 0]])
phonon.generate_displacements(distance=0.03)
print("[Phonopy] Atomic displacements:")
disps = phonon.get_displacements()
for d in disps:
print("[Phonopy] %d %s" % (d[0], d[1:]))
return phonon
def _get_phononobject_phonopy(self,
structure,
potential,
smat,
save_parameters,
path,
displacement_distance=0.01):
cell = get_phonopy_structure(structure)
phonon = Phonopy(cell,
smat,
primitive_matrix=[[1.0, 0.0, 0.0], [0.0, 1, 0.0],
[0., 0., 1.0]],
factor=VaspToTHz)
# displacements
phonon.generate_displacements(distance=displacement_distance)
print("[Phonopy] Atomic displacements:")
disps = phonon.get_displacements()
for d in disps:
print("[Phonopy] %d %s" % (d[0], d[1:]))
supercells = phonon.get_supercells_with_displacements()
# Force calculations by calculator
set_of_forces = []
for scell in supercells:
cell = Atoms(symbols=scell.get_chemical_symbols(),
scaled_positions=scell.get_scaled_positions(),
cell=scell.get_cell(),
pbc=True)
cell.set_calculator(potential)
# this part is adapted from: https://web.archive.org/web/20200610084959/https://github.com/phonopy/phonopy/blob/develop/example/ase/8Si-phonon.py
# Copyright by Atsushi Togo
forces = cell.get_forces()
drift_force = forces.sum(axis=0)
print(
("[Phonopy] Drift force:" + "%11.5f" * 3) % tuple(drift_force))
for force in forces:
force -= drift_force / forces.shape[0]
set_of_forces.append(forces)
phonon.produce_force_constants(forces=set_of_forces)
if save_parameters:
phonon.save(path)
return phonon
class PhononBase(TaskElement):
"""PhononBase class
This is an interface to phonopy.
"""
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 get_phonon(self):
return self._phonon
def get_cell(self):
if self._is_cell_relaxed:
return self._cell
else:
return self._phonon_tasks[0].get_cell()
def get_energy(self):
"""Return energies at geometry optimization steps"""
return self._energy
def set_status(self):
done = True
terminate = False
for task in self._tasks:
done &= task.done()
if task.get_status() == "terminate":
terminate = True
if done:
if terminate:
self._status = "terminate"
else:
self._status = "next"
self._write_yaml()
def begin(self):
if not self._job:
print "set_job has to be executed."
raise
self._overwrite_settings()
if self._is_cell_relaxed:
self._phonon_tasks = [None]
self._set_stage1()
else:
self._set_stage0()
def end(self):
pass
def done(self):
return ("terminate" in self._status or
"done" in self._status or
"next" in self._status)
def next(self):
if self._stage == 0:
if "next" in self._status:
self._energy = self._tasks[0].get_energy()
self._comment = "%s\\n%f" % (
self._tasks[0].get_space_group()['international_standard'],
self._energy)
self._set_stage1()
return self._tasks
elif "terminate" in self._status and self._traverse == "restart":
self._traverse = False
self._set_stage0()
return self._tasks
else:
raise StopIteration
else: # task 1..n: displaced supercells
if "next" in self._status:
self._status = "done"
forces = []
for task in self._phonon_tasks[1:]:
forces.append(task.get_properties()['forces'][-1])
self._write_FORCE_SETS(forces)
self._phonon.set_post_process(self._primitive_matrix,
forces,
force_constants_decimals=14)
self._tasks = []
raise StopIteration
elif "terminate" in self._status and self._traverse == "restart":
self._traverse = False
disp_terminated = []
for i, task in enumerate(self._tasks):
if task.get_status() == "terminate":
disp_terminated.append(i)
tasks = self._get_displacement_tasks()[1:]
self._tasks = []
for i in disp_terminated:
self._tasks.append(tasks[i])
self._phonon_tasks[i + 1] = tasks[i]
self._status = "displacements"
return self._tasks
else:
raise StopIteration
def _set_stage0(self):
self._status = "equilibrium"
task = self._get_equilibrium_task()
self._phonon_tasks = [task]
self._tasks = [task]
def _set_stage1(self):
self._stage = 1
self._status = "displacements"
self._set_phonon()
self._tasks = self._get_displacement_tasks()[1:]
self._phonon_tasks += self._tasks
def _set_phonon(self):
cell = self.get_cell()
phonopy_cell = Atoms(
cell=cell.get_lattice().T,
scaled_positions=cell.get_points().T,
symbols=cell.get_symbols())
self._phonon = Phonopy(phonopy_cell,
self._supercell_matrix,
is_auto_displacements=False)
self._phonon.generate_displacements(distance=self._distance,
is_diagonal=False)
supercell = self._phonon.get_supercell()
displacements = self._phonon.get_displacements()
write_poscar(cell, "POSCAR-unitcell")
write_disp_yaml(displacements, supercell)
def _write_FORCE_SETS(self, forces):
displacements = [[x[0], x[1:4]]
for x in self._phonon.get_displacements()]
natom = self._phonon.get_supercell().get_number_of_atoms()
write_FORCE_SETS("FORCE_SETS",
natom,
displacements,
forces,
verbose=False)
def _write_yaml(self):
w = open("%s.yaml" % self._directory, 'w')
if self._phonon_tasks[0]:
if self._lattice_tolerance is not None:
w.write("lattice_tolerance: %f\n" % self._lattice_tolerance)
if self._stress_tolerance is not None:
w.write("stress_tolerance: %f\n" % self._stress_tolerance)
w.write("pressure_target: %f\n" % self._pressure_target)
w.write("force_tolerance: %f\n" % self._force_tolerance)
w.write("max_increase: %f\n" % self._max_increase)
w.write("max_iteration: %d\n" % self._max_iteration)
w.write("min_iteration: %d\n" % self._min_iteration)
w.write("supercell_matrix:\n")
for row in self._supercell_matrix:
w.write("- [ %3d, %3d, %3d ]\n" % tuple(row))
w.write("primitive_matrix:\n")
for row in self._primitive_matrix:
w.write("- [ %6.3f, %6.3f, %6.3f ]\n" % tuple(row))
w.write("distance: %f\n" % self._distance)
w.write("iteration: %d\n" % self._phonon_tasks[0].get_stage())
if self._energy:
w.write("electric_total_energy: %20.10f\n" % self._energy)
w.write("status: %s\n" % self._status)
w.write("tasks:\n")
for task in self._phonon_tasks:
if task and task.get_status():
w.write("- name: %s\n" % task.get_name())
w.write(" status: %s\n" % task.get_status())
w.close()
class PhononBase(TaskElement, PhononYaml):
"""PhononBase class
This is an interface to phonopy.
"""
def __init__(self,
directory=None,
name=None,
supercell_matrix=None,
primitive_matrix=None,
nac=False,
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,
symmetry_tolerance=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._nac = nac
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._symmetry_tolerance = symmetry_tolerance
self._traverse = traverse
self._stage = 0
self._tasks = []
self._energy = None
self._born = None
self._epsilon = None
self._space_group = None
self._cell = None
self._phonon = None # Phonopy object
self._all_tasks = None
self._try_collect_forces = True
def get_phonon(self):
return self._phonon
def get_cell(self):
if self._is_cell_relaxed:
return self._cell
else:
return self._all_tasks[0].get_cell()
def get_energy(self):
"""Return energies at geometry optimization steps"""
return self._energy
def get_space_group(self):
return self._space_group
def set_status(self):
if self._stage == 0:
task = self._tasks[0]
if task.done():
self._space_group = task.get_space_group()
status = task.get_status()
if status == "done":
if not self._evaluate_stop_condition():
self._status = "next"
else:
self._status = status
else:
done = True
terminate = False
for i, task in enumerate(self._tasks):
done &= task.done()
if (task.get_status() == "terminate" or
task.get_status() == "max_iteration"):
terminate = True
if done:
if terminate:
self._status = "terminate"
else:
self._status = "next"
self._write_yaml()
def begin(self):
if not self._job:
print("set_job has to be executed.")
raise RuntimeError
if self._is_cell_relaxed:
self._all_tasks = [None]
self._set_stage1()
else:
self._set_stage0()
def done(self):
return (self._status == "terminate" or
self._status == "done" or
self._status == "max_iteration" or
self._status == "low_symmetry" or
self._status == "force_collection_failure" or
self._status == "next")
def __next__(self):
return self.next()
def next(self):
if self._stage == 0:
if self._status == "next":
self._energy = self._tasks[0].get_energy()
num_atom = len(self._tasks[0].get_cell().get_symbols())
self._comment = self._space_group['international']
self._comment += "\\n%f/%d" % (self._energy, num_atom)
self._set_stage1()
return self._tasks
elif (self._status == "terminate" and self._traverse == "restart"):
self._traverse = False
self._set_stage0()
return self._tasks
elif self._stage == 1: # task 1..n: displaced supercells
if self._status == "next":
if self._collect_forces():
if self._nac:
self._set_stage2()
return self._tasks
else:
self._status = "done"
else:
if self._try_collect_forces:
self._status = "displacements"
self._log += ("Collection of forces failed. "
"Try once more.\n")
self._try_collect_forces = False
raise StopIteration
else:
self._status = "force_collection_failure"
elif self._status == "terminate" and self._traverse == "restart":
self._traverse = False
disp_terminated = []
for i, task in enumerate(self._tasks):
if task.get_status() == "terminate":
disp_terminated.append(i)
tasks = self._get_displacement_tasks()
self._tasks = []
for i in disp_terminated:
self._tasks.append(tasks[i])
self._all_tasks[i + 1] = tasks[i]
self._status = "displacements"
return self._tasks
elif self._stage == 2:
if self._status == "next":
self._status = "done"
self._set_born_and_epsilon()
elif self._status == "terminate" and self._traverse == "restart":
self._traverse = False
self._all_tasks.pop()
self._set_stage2()
else:
pass
self._tasks = []
self._write_yaml()
raise StopIteration
def _set_stage0(self):
self._status = "equilibrium"
task = self._get_equilibrium_task()
self._all_tasks = [task]
self._tasks = [task]
def _set_stage1(self):
self._stage = 1
self._status = "displacements"
self._set_phonon()
self._tasks = self._get_displacement_tasks()
self._all_tasks += self._tasks
def _set_stage2(self):
self._stage = 2
self._status = "nac"
if self._nac == "relax":
nac_task = self._get_nac_task(is_cell_relaxed=False)
else:
nac_task = self._get_nac_task()
self._tasks = [nac_task]
self._all_tasks += self._tasks
def _collect_forces(self):
forces = []
for task in self._tasks:
forces.append(task.get_properties()['forces'][-1])
if self._phonon.produce_force_constants(forces=forces):
write_FORCE_SETS(self._phonon.get_displacement_dataset())
return True
else:
# This can be due to delay of writting file to file system.
return False
def _set_born_and_epsilon(self):
nac_task = self._tasks[0]
born = nac_task.get_born_effective_charge()
epsilon = nac_task.get_dielectric_constant()
indep_atoms = self._phonon.get_symmetry().get_independent_atoms()
supercell = self._phonon.get_supercell()
s2u = supercell.get_supercell_to_unitcell_map()
u2u = supercell.get_unitcell_to_unitcell_map()
indep_atoms_u = [u2u[i] for i in s2u[indep_atoms]]
if born is not None and epsilon is not None:
self._born = born
self._epsilon = epsilon
header = "# epsilon and Z* of atoms "
header += ' '.join(["%d" % (n + 1) for n in indep_atoms_u])
lines = [header]
lines.append(("%13.8f" * 9) % tuple(epsilon.flatten()))
for z in born[indep_atoms_u]:
lines.append(("%13.8f" * 9) % tuple(z.flatten()))
with open("BORN", 'w') as w:
w.write('\n'.join(lines))
def _evaluate_stop_condition(self):
if self._stop_condition:
if "symmetry_operations" in self._stop_condition:
num_ops = len(self._space_group['rotations'])
if (num_ops <
self._stop_condition['symmetry_operations']):
self._status = "low_symmetry"
return True
return False
def _set_phonon(self):
if self._supercell_matrix is None:
cell = sort_cell_by_symbols(
get_crystallographic_cell(self.get_cell()))
self._supercell_matrix = estimate_supercell_matrix(
cell,
max_num_atoms=self._max_num_atoms)
else:
cell = self.get_cell()
phonopy_cell = cell2atoms(cell)
self._phonon = Phonopy(phonopy_cell,
self._supercell_matrix,
primitive_matrix=self._primitive_matrix,
dynamical_matrix_decimals=14,
force_constants_decimals=14,
symprec=self._symmetry_tolerance)
self._phonon.generate_displacements(
distance=self._distance,
is_plusminus=self._displace_plusminus,
is_diagonal=self._displace_diagonal)
supercell = self._phonon.get_supercell()
displacements = self._phonon.get_displacements()
write_poscar(cell, filename="POSCAR-unitcell")
write_poscar_yaml(cell, filename="POSCAR-unitcell.yaml")
write_disp_yaml(displacements, supercell)
def get_yaml_lines(self):
lines = TaskElement.get_yaml_lines(self)
if self._is_cell_relaxed:
cell = self._cell
else:
cell = self.get_cell()
lines += self._get_phonon_yaml_lines(cell)
if self._all_tasks[0] is not None:
if self._energy:
lines.append("electric_total_energy: %20.10f" % self._energy)
return lines
class PhononBase(TaskElement):
"""PhononBase class
This is an interface to phonopy.
"""
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,
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
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._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._phonon_tasks = None # Phonopy object
def get_phonon(self):
return self._phonon
def get_cell(self):
if self._is_cell_relaxed:
return self._cell
else:
return self._phonon_tasks[0].get_cell()
def get_energy(self):
"""Return energies at geometry optimization steps"""
return self._energy
def get_space_group(self):
return self._space_group
def set_status(self):
if self._stage == 0:
task = self._tasks[0]
if task.done():
self._space_group = task.get_space_group()
status = task.get_status()
if status == "done":
if not self._evaluate_stop_condition():
self._status = "next"
else:
self._status = status
else:
done = True
terminate = True
for task in self._tasks:
done &= task.done()
terminate &= (task.get_status() == "terminate")
if done:
if terminate:
self._status = "terminate"
else:
self._status = "next"
self._write_yaml()
def begin(self):
if not self._job:
print "set_job has to be executed."
raise
self._overwrite_settings()
if self._is_cell_relaxed:
self._phonon_tasks = [None]
self._set_stage1()
else:
self._set_stage0()
def done(self):
return (self._status == "terminate" or
self._status == "done" or
self._status == "max_iteration" or
self._status == "low_symmetry" or
self._status == "next")
def next(self):
if self._stage == 0:
if self._status == "next":
self._energy = self._tasks[0].get_energy()
num_atom = len(self._tasks[0].get_cell().get_symbols())
self._comment = self._space_group['international_standard']
self._comment += "\\n%f/%d" % (self._energy, num_atom)
self._set_stage1()
return self._tasks
elif (self._status == "terminate" and self._traverse == "restart"):
self._traverse = False
self._set_stage0()
return self._tasks
else: # task 1..n: displaced supercells
if self._status == "next":
self._status = "done"
forces = []
for task in self._tasks:
forces.append(task.get_properties()['forces'][-1])
self._phonon.produce_force_constants(forces)
write_FORCE_SETS(self._phonon.get_displacement_dataset())
self._tasks = []
elif self._status == "terminate" and self._traverse == "restart":
self._traverse = False
disp_terminated = []
for i, task in enumerate(self._tasks):
if task.get_status() == "terminate":
disp_terminated.append(i)
tasks = self._get_displacement_tasks()
self._tasks = []
for i in disp_terminated:
self._tasks.append(tasks[i])
self._phonon_tasks[i + 1] = tasks[i]
self._status = "displacements"
return self._tasks
self._write_yaml()
raise StopIteration
def _set_stage0(self):
self._status = "equilibrium"
task = self._get_equilibrium_task()
self._phonon_tasks = [task]
self._tasks = [task]
def _set_stage1(self):
self._stage = 1
self._status = "displacements"
self._set_phonon()
self._tasks = self._get_displacement_tasks()
self._phonon_tasks += self._tasks
def _evaluate_stop_condition(self):
if self._stop_condition:
if "symmetry_operations" in self._stop_condition:
num_ops = len(self._space_group['rotations'])
if (num_ops <
self._stop_condition['symmetry_operations']):
self._status = "low_symmetry"
return True
return False
def _set_phonon(self):
cell = self.get_cell()
phonopy_cell = cell2atoms(cell)
self._phonon = Phonopy(phonopy_cell,
self._supercell_matrix,
primitive_matrix=self._primitive_matrix,
is_auto_displacements=False,
dynamical_matrix_decimals=14,
force_constants_decimals=14)
self._phonon.generate_displacements(
distance=self._distance,
is_plusminus=self._displace_plusminus,
is_diagonal=self._displace_diagonal)
supercell = self._phonon.get_supercell()
displacements = self._phonon.get_displacements()
write_poscar(cell, "POSCAR-unitcell")
write_disp_yaml(displacements, supercell)
def _write_yaml(self):
w = open("%s.yaml" % self._directory, 'w')
w.write("supercell_matrix:\n")
for row in self._supercell_matrix:
w.write("- [ %3d, %3d, %3d ]\n" % tuple(row))
w.write("primitive_matrix:\n")
for row in self._primitive_matrix:
w.write("- [ %6.3f, %6.3f, %6.3f ]\n" % tuple(row))
w.write("distance: %f\n" % self._distance)
if self._phonon_tasks[0]:
if self._lattice_tolerance is not None:
w.write("lattice_tolerance: %f\n" % self._lattice_tolerance)
if self._stress_tolerance is not None:
w.write("stress_tolerance: %f\n" % self._stress_tolerance)
w.write("pressure_target: %f\n" % self._pressure_target)
w.write("force_tolerance: %f\n" % self._force_tolerance)
if self._max_increase is None:
w.write("max_increase: unset\n")
else:
w.write("max_increase: %f\n" % self._max_increase)
w.write("max_iteration: %d\n" % self._max_iteration)
w.write("min_iteration: %d\n" % self._min_iteration)
w.write("iteration: %d\n" % self._phonon_tasks[0].get_stage())
if self._energy:
w.write("electric_total_energy: %20.10f\n" % self._energy)
w.write("status: %s\n" % self._status)
w.write("tasks:\n")
for task in self._phonon_tasks:
if task and task.get_status():
w.write("- name: %s\n" % task.get_name())
w.write(" status: %s\n" % task.get_status())
w.close()
class PhononFC3Base(TaskElement):
"""PhononFC3Base class
This is an interface to anharmonic phonopy.
"""
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 get_phonon(self):
return self._phonon
def get_phonon_fc3(self):
for i, task in enumerate(self._phonon_fc3_tasks[1:]):
forces_fc3.append(task.get_properties()['forces'][-1])
disp_dataset = self._phonon_fc3.get_displacement_dataset()
self._phonon_fc3.produce_fc3(forces_fc3)
return self._phonon_fc3
def get_cell(self):
if self._is_cell_relaxed:
return self._cell
else:
return self._phonon_fc3_tasks[0].get_cell()
def get_energy(self):
"""Return energies at geometry optimization steps"""
return self._energy
def set_status(self):
if self._stage == 0:
task = self._tasks[0]
if task.done():
status = task.get_status()
if status == "done":
self._status = "next"
else:
self._status = status
else:
done = True
terminate = False
for i, task in enumerate(self._tasks):
done &= task.done()
terminate |= (task.get_status() == "terminate")
if done:
if terminate:
self._status = "terminate"
else:
self._status = "next"
self._write_yaml()
def begin(self):
if not self._job:
print("set_job has to be executed.")
raise RuntimeError
if self._is_cell_relaxed:
self._phonon_fc3_tasks = [None]
self._set_stage1()
else:
self._set_stage0()
def end(self):
pass
def done(self):
return (self._status == "terminate" or
self._status == "done" or
self._status == "max_iteration" or
self._status == "next" or
self._status == "imaginary_mode")
def __next__(self):
return self.next()
def next(self):
if self._stage == 0:
if "next" in self._status:
self._energy = self._tasks[0].get_energy()
self._comment = "%s\\n%f" % (
self._tasks[0].get_space_group()['international'],
self._energy)
self._set_stage1()
return self._tasks
elif "terminate" in self._status and self._traverse == "restart":
self._traverse = False
self._set_stage0()
return self._tasks
else:
raise StopIteration
elif self._stage == 1:
if "next" in self._status:
disp_dataset = self._phonon_fc3.get_displacement_dataset()
for disp1, task in zip(disp_dataset['first_atoms'], self._tasks):
disp1['forces'] = task.get_properties()['forces'][-1]
write_FORCE_SETS(disp_dataset)
self._phonon.set_displacement_dataset(disp_dataset)
self._phonon.produce_force_constants(
calculate_full_force_constants=False)
if self._exist_imaginary_mode():
self._status = "imaginary_mode"
self._write_yaml()
self._tasks = []
raise StopIteration
else:
self._set_stage2()
return self._tasks
elif "terminate" in self._status and self._traverse == "restart":
self._reset_stage1()
return self._tasks
else:
raise StopIteration
elif self._stage == 2:
if "next" in self._status:
self._status = "done"
forces_fc3 = []
for i, task in enumerate(self._phonon_fc3_tasks[1:]):
forces_fc3.append(task.get_properties()['forces'][-1])
disp_dataset = self._phonon_fc3.get_displacement_dataset()
write_FORCES_FC3(disp_dataset, forces_fc3)
self._tasks = []
raise StopIteration
elif "terminate" in self._status and self._traverse == "restart":
self._reset_stage2()
return self._tasks
else:
raise StopIteration
else: # stage2
pass
def _set_stage0(self):
self._status = "equilibrium"
task = self._get_equilibrium_task()
self._phonon_fc3_tasks = [task]
self._tasks = [task]
def _set_stage1(self):
self._set_phonon_fc3()
if self._check_imaginary:
self._stage = 1
self._status = "fc2_displacements"
disp_dataset = self._phonon_fc3.get_displacement_dataset()
self._tasks = self._get_displacement_tasks(
stop=len(disp_dataset['first_atoms']))
self._phonon_fc3_tasks += self._tasks
else:
self._set_stage2()
def _reset_stage1(self):
self._traverse = False
disp_terminated = []
for i, task in enumerate(self._tasks):
if task.get_status() == "terminate":
disp_terminated.append(i)
disp_dataset = self._phonon_fc3.get_displacement_dataset()
tasks = self._get_displacement_tasks(
stop=len(disp_dataset['first_atoms']))
self._tasks = []
for i in disp_terminated:
self._tasks.append(tasks[i])
self._phonon_fc3_tasks[i + 1] = tasks[i]
self._status = "fc2_displacements"
def _set_stage2(self):
self._stage = 2
self._status = "fc3_displacements"
if self._check_imaginary:
disp_dataset = self._phonon_fc3.get_displacement_dataset()
start_index = len(disp_dataset['first_atoms'])
else:
start_index = 0
self._tasks = self._get_displacement_tasks(start=start_index)
self._phonon_fc3_tasks += self._tasks
def _reset_stage2(self):
self._traverse = False
disp_terminated = []
for i, task in enumerate(self._tasks):
if task.get_status() == "terminate":
disp_terminated.append(i)
if self._check_imaginary:
disp_dataset = self._phonon_fc3.get_displacement_dataset()
start_index = len(disp_dataset['first_atoms'])
else:
start_index = 0
tasks = self._get_displacement_tasks(start=start_index)
self._tasks = []
for i in disp_terminated:
self._tasks.append(tasks[i])
self._phonon_fc3_tasks[i + 1 + start_index] = tasks[i]
self._status = "fc3_displacements"
def _set_phonon_fc3(self):
cell = self.get_cell()
phonopy_cell = cell2atoms(cell)
self._phonon = Phonopy(phonopy_cell,
self._supercell_matrix,
primitive_matrix=self._primitive_matrix,
dynamical_matrix_decimals=14,
force_constants_decimals=14)
self._phonon_fc3 = Phono3py(phonopy_cell,
self._supercell_matrix,
primitive_matrix=self._primitive_matrix)
self._phonon_fc3.generate_displacements(distance=self._distance,
is_diagonal=self._is_diagonal)
supercell = self._phonon_fc3.get_supercell()
disp_dataset = self._phonon_fc3.get_displacement_dataset()
self._phonon.set_displacement_dataset(disp_dataset)
write_poscar(cell, "POSCAR-unitcell")
write_disp_yaml(self._phonon.get_displacements(),
supercell,
directions=self._phonon.get_displacement_directions())
write_disp_fc3_yaml(disp_dataset, supercell)
def _exist_imaginary_mode(self):
if self._primitive_matrix is None:
pmat = np.eye(3)
else:
pmat = self._primitive_matrix
exact_point_matrix = np.dot(np.linalg.inv(self._supercell_matrix),
pmat).T
max_integer = np.rint(np.amax(np.abs(np.linalg.inv(exact_point_matrix))))
q_points = []
for i in np.arange(-max_integer, max_integer + 1):
for j in np.arange(-max_integer, max_integer + 1):
for k in np.arange(-max_integer, max_integer + 1):
q = np.dot(exact_point_matrix, [i, j, k])
if (-1 < q).all() and (q < 1).all():
q_points.append(q)
self._phonon.set_qpoints_phonon(q_points)
frequencies = self._phonon.get_qpoints_phonon()[0]
if (frequencies < self._cutoff_frequency).any():
self._log = "Stop at phonon calculation due to imaginary modes"
return True
else:
return False
def _write_yaml(self):
w = open("%s.yaml" % self._directory, 'w')
if self._lattice_tolerance is not None:
w.write("lattice_tolerance: %f\n" % self._lattice_tolerance)
if self._stress_tolerance is not None:
w.write("stress_tolerance: %f\n" % self._stress_tolerance)
w.write("pressure_target: %f\n" % self._pressure_target)
w.write("force_tolerance: %f\n" % self._force_tolerance)
if self._max_increase is None:
w.write("max_increase: unset\n")
else:
w.write("max_increase: %f\n" % self._max_increase)
w.write("max_iteration: %d\n" % self._max_iteration)
w.write("min_iteration: %d\n" % self._min_iteration)
w.write("supercell_matrix:\n")
for row in self._supercell_matrix:
w.write("- [ %3d, %3d, %3d ]\n" % tuple(row))
if self._primitive_matrix is not None:
w.write("primitive_matrix:\n")
for row in self._primitive_matrix:
w.write("- [ %6.3f, %6.3f, %6.3f ]\n" % tuple(row))
w.write("distance: %f\n" % self._distance)
if self._phonon_fc3_tasks[0] is not None:
w.write("iteration: %d\n" % self._phonon_fc3_tasks[0].get_stage())
if self._energy:
w.write("electric_total_energy: %20.10f\n" % self._energy)
w.write("status: %s\n" % self._status)
w.write("tasks:\n")
for task in self._phonon_fc3_tasks:
if task and task.get_status():
w.write("- name: %s\n" % task.get_name())
w.write(" status: %s\n" % task.get_status())
w.close()
def phonopy_run(phonon, single=True, filename='FORCE_SETS'):
"""Run the phonon calculations, using PhonoPy.
The force constants are then stored in the Phonon ASE object.
input:
phonon: ASE Phonon object with Atoms and Calculator
single: when True, the forces are computed only for a single step, and then
exit. This allows to split the loop in independent iterations. When
calling again the 'run' method, already computed steps are ignored,
missing steps are completed, until no more are needed. When set to
False, all steps are done in a row.
output:
True when a calculation step was performed, False otherwise or no more is needed.
nb_of_iterations: the number of steps remaining
"""
from phonopy import Phonopy
from phonopy.structure.atoms import Atoms as PAtoms
from phonopy.structure.atoms import PhonopyAtoms
import phonopy.file_IO as file_IO
# we first look if an existing phonon pickle exists. This is the case if we
# are running with iterative calls while return value is True. The first call
# will then create the objects, which are subsequently updated until False.
# Set calculator if provided
# assert phonon.calc is not None, "Provide calculator in Phonon __init__ method"
# Atoms in the supercell -- repeated in the lattice vector directions
# beginning with the last
supercell = phonon.atoms * phonon.N_c
# create a PhonopyAtoms object
cell = PhonopyAtoms(phonon.atoms.get_chemical_symbols(),
positions=phonon.atoms.get_positions(),
cell=phonon.atoms.get_cell(),
magmoms=None)
# is there an existing PhonoPy calculation ?
# using factor=6.46541380e-2=VaspToeV
if os.path.exists('FORCE_SETS'):
phonpy = Phonopy(cell,
numpy.diag(phonon.N_c),
primitive_matrix=None,
dynamical_matrix_decimals=None,
force_constants_decimals=None,
symprec=1e-05,
is_symmetry=True,
use_lapack_solver=False,
log_level=1)
force_sets = file_IO.parse_FORCE_SETS(filename='FORCE_SETS')
phonpy.set_displacement_dataset(force_sets)
# inactivate magmoms in supercell as some calculators do not provide that
phonpy._supercell.magmoms = None
phonpy.produce_force_constants(calculate_full_force_constants=False)
else:
# create a PhonoPy Phonon object.
phonpy = Phonopy(cell, numpy.diag(phonon.N_c))
# generate displacements (minimal set)
phonpy.generate_displacements(distance=0.01)
# iterative call for all displacements
set_of_forces, flag, nb_of_iterations = phonopy_run_calculate(
phonon, phonpy, supercell, single)
if flag is True:
return nb_of_iterations # some more work is required
sys.stdout.write('[ASE/Phonopy] Computing force constants\n')
# use symmetry to derive forces in equivalent displacements
phonpy.produce_force_constants(forces=set_of_forces)
# generate disp.yaml and FORCE_SETS (for later use)
displacements = phonpy.get_displacements()
directions = phonpy.get_displacement_directions()
file_IO.write_disp_yaml(displacements,
phonpy.get_supercell(),
directions=directions)
file_IO.write_FORCE_SETS(phonpy.get_displacement_dataset())
# store as additional data in atoms 'info'
phonon.atoms.info["phonopy"] = phonpy
# save the PhonoPy object
fid = opencew("phonopy.pkl")
if fid is not None and rank == 0:
print("[ASE/Phonopy] Writing %s" % "phonopy.pkl")
pickle.dump(phonpy, fid, protocol=2)
fid.close()
# transfer results to the ASE phonon object
# Number of atoms (primitive cell)
natoms = len(phonon.indices)
# Number of unit cells (supercell)
N = numpy.prod(phonon.N_c)
# Phonopy: force_constants size is [N*natoms,N*natoms,3,3]
# Phi[i,j,a,b] with [i,j = atom in supercell] and [a,b=xyz]
force_constants = phonpy.get_force_constants()
# the atoms [i] which are moved are in the first cell of the supercell, i.e.Ni=0
# the forces are then stored for all atoms [Nj,j] as [3,3] matrices
# we compute the sum on all supercells, which all contain n atoms.
C_N = numpy.zeros((N, 3 * natoms, 3 * natoms), dtype=complex)
Ni = 0
for Nj in range(N):
for ni in range(natoms):
Nni = ni
for nj in range(natoms):
# compute Nn indices
Nnj = Nj * natoms + nj
# get fc 3x3 matrix
C_N[Nj, (3 * ni):(3 * ni + 3),
(3 * nj):(3 * nj + 3)] += force_constants[Nni][Nnj]
# convert to ASE storage
# ASE: phonon.C_N size is be [N, 3*natoms, 3*natoms]
# Phi[i,j] = Phi[j,i]
phonon.C_N = C_N
# fill dynamical matrix (mass prefactor)
phonon.D_N = phonon.C_N.copy()
# Add mass prefactor
m_a = phonon.atoms.get_masses()
phonon.m_inv_x = numpy.repeat(m_a[phonon.indices]**-0.5, 3)
M_inv = numpy.outer(phonon.m_inv_x, phonon.m_inv_x)
for D in phonon.D_N:
D *= M_inv
return 0 # nothing left to do
def phonons(self,
atoms=None,
lammps_cmd="",
enforce_c_size=15.0,
parameters={}):
"""Make Phonon calculation setup."""
from phonopy import Phonopy
from phonopy.file_IO import (
# parse_FORCE_CONSTANTS,
write_FORCE_CONSTANTS, )
bulk = atoms.phonopy_converter()
dim = get_supercell_dims(atoms, enforce_c_size=enforce_c_size)
atoms = atoms.make_supercell([dim[0], dim[1], dim[2]])
Poscar(atoms).write_file("POSCAR")
atoms = atoms.make_supercell_matrix([dim[0], dim[1], dim[2]])
Poscar(atoms).write_file("POSCAR-Super.vasp")
phonon = Phonopy(bulk,
[[dim[0], 0, 0], [0, dim[1], 0], [0, 0, dim[2]]])
print("[Phonopy] Atomic displacements1:", bulk)
print("[Phonopy] Atomic displacements2:", phonon, dim[0], dim[1],
dim[2])
phonon.generate_displacements(distance=0.03)
disps = phonon.get_displacements()
print("[Phonopy] Atomic displacements3:", disps)
for d in disps:
print("[Phonopy]", d[0], d[1:])
supercells = phonon.get_supercells_with_displacements()
# Force calculations by calculator
set_of_forces = []
disp = 0
from ase import Atoms as AseAtoms
for scell in supercells:
ase_atoms = AseAtoms(
symbols=scell.get_chemical_symbols(),
scaled_positions=scell.get_scaled_positions(),
cell=scell.get_cell(),
pbc=True,
)
j_atoms = ase_to_atoms(ase_atoms)
disp = disp + 1
parameters["control_file"] = "run0.mod"
a, b, forces = LammpsJob(
atoms=j_atoms,
lammps_cmd=lammps_cmd,
parameters=parameters,
jobname="disp-" + str(disp),
).runjob()
print("forces=", forces)
drift_force = forces.sum(axis=0)
print("drift forces=", drift_force)
# Simple translational invariance
for force in forces:
force -= drift_force / forces.shape[0]
set_of_forces.append(forces)
phonon.produce_force_constants(forces=set_of_forces)
write_FORCE_CONSTANTS(phonon.get_force_constants(),
filename="FORCE_CONSTANTS")
print()
print("[Phonopy] Phonon frequencies at Gamma:")
def calculate_phonon(atoms,
calc,
ndim=np.eye(3),
primitive_matrix=np.eye(3),
distance=0.01,
factor=VaspToTHz,
is_symmetry=True,
symprec=1e-5,
func=None,
**func_args):
"""
"""
if 'magmoms' in atoms.arrays:
is_mag = True
else:
is_mag = False
# 1. get displacements and supercells
atoms.set_calculator(calc)
# bulk = PhonopyAtoms(atoms=atoms)
if is_mag:
bulk = PhonopyAtoms(
symbols=atoms.get_chemical_symbols(),
scaled_positions=atoms.get_scaled_positions(),
cell=atoms.get_cell(),
magmoms=atoms.arrays['magmoms'],
)
else:
bulk = PhonopyAtoms(symbols=atoms.get_chemical_symbols(),
scaled_positions=atoms.get_scaled_positions(),
cell=atoms.get_cell())
phonon = Phonopy(bulk,
ndim,
primitive_matrix=primitive_matrix,
factor=factor,
symprec=symprec)
phonon.generate_displacements(distance=distance)
disps = phonon.get_displacements()
for d in disps:
print("[phonopy] %d %s" % (d[0], d[1:]))
supercell0 = phonon.get_supercell()
supercells = phonon.get_supercells_with_displacements()
write_supercells_with_displacements(supercell0, supercells)
write_disp_yaml(disps, supercell0)
# 2. calculated forces.
set_of_forces = []
for iscell, scell in enumerate(supercells):
cell = Atoms(symbols=scell.get_chemical_symbols(),
scaled_positions=scell.get_scaled_positions(),
cell=scell.get_cell(),
pbc=True)
if is_mag:
cell.set_initial_magnetic_moments(
atoms.get_initial_magnetic_moments())
cell.set_calculator(calc)
dir_name = "PHON_CELL%s" % iscell
cur_dir = os.getcwd()
if not os.path.exists(dir_name):
os.mkdir(dir_name)
os.chdir(dir_name)
forces = cell.get_forces()
#print "[Phonopy] Forces: %s" % forces
# Do something other than calculating the forces with func.
# func: func(atoms, calc, func_args)
if func is not None:
func(cell, calc, **func_args)
os.chdir(cur_dir)
drift_force = forces.sum(axis=0)
#print "[Phonopy] Drift force:", "%11.5f" * 3 % tuple(drift_force)
# Simple translational invariance
for force in forces:
force -= drift_force / forces.shape[0]
set_of_forces.append(forces)
# Phonopy post-process
phonon.produce_force_constants(forces=set_of_forces)
force_constants = phonon.get_force_constants()
write_FORCE_CONSTANTS(force_constants, filename='FORCE_CONSTANTS')
print('')
print("[Phonopy] Phonon frequencies at Gamma:")
for i, freq in enumerate(phonon.get_frequencies((0, 0, 0))):
print("[Phonopy] %3d: %10.5f THz" % (i + 1, freq)) # THz
print("[Phonopy] %3d: %10.5f cm-1" % (i + 1, freq * 33.35)) #cm-1
return phonon
def calculate_phonon(atoms,
calc=None,
forces_set_file=None,
ndim=np.eye(3),
primitive_matrix=np.eye(3),
distance=0.01,
factor=VaspToTHz,
is_plusminus='auto',
is_symmetry=True,
symprec=1e-5,
func=None,
prepare_initial_wavecar=False,
skip=None,
restart=True,
parallel=True,
sc_mag=None,
**func_args):
"""
"""
if 'magmoms' in atoms.arrays or 'initial_magmoms' in atoms.arrays:
is_mag = True
else:
is_mag = False
print("is_mag: ", is_mag)
# 1. get displacements and supercells
if calc is not None:
atoms.set_calculator(calc)
# bulk = PhonopyAtoms(atoms=atoms)
if is_mag:
bulk = PhonopyAtoms(
symbols=atoms.get_chemical_symbols(),
scaled_positions=atoms.get_scaled_positions(),
cell=atoms.get_cell(),
magmoms=atoms.arrays['initial_magmoms'],
)
else:
bulk = PhonopyAtoms(symbols=atoms.get_chemical_symbols(),
scaled_positions=atoms.get_scaled_positions(),
cell=atoms.get_cell())
phonon = Phonopy(bulk,
ndim,
primitive_matrix=primitive_matrix,
factor=factor,
symprec=symprec)
phonon.generate_displacements(distance=distance, is_plusminus=is_plusminus)
disps = phonon.get_displacements()
for d in disps:
print(("[phonopy] %d %s" % (d[0], d[1:])))
supercell0 = phonon.get_supercell()
supercells = phonon.get_supercells_with_displacements()
#write_supercells_with_displacements(supercell0, supercells)
write_disp_yaml(disps, supercell0)
# 2. calculated forces.
if forces_set_file is not None:
symmetry = phonon.get_symmetry()
set_of_forces = parse_FORCE_SETS(
is_translational_invariance=False,
filename=forces_set_file) # ['first_atoms']
# set_of_forces=np.array(set_of_forces)
#set_of_forces=[np.asarray(f) for f in set_of_forces]
phonon.set_displacement_dataset(set_of_forces)
phonon.produce_force_constants()
else:
# initialize set of forces
if restart and os.path.exists('forces_set.pickle'):
try:
with open("forces_set.pickle", 'rb') as myfile:
set_of_forces = pickle.load(myfile)
iskip = len(set_of_forces) - 1
except:
set_of_forces = []
iskip = -1
else:
set_of_forces = []
iskip = -1
if prepare_initial_wavecar and skip is None:
scell = supercell0
cell = Atoms(symbols=scell.get_chemical_symbols(),
scaled_positions=scell.get_scaled_positions(),
cell=scell.get_cell(),
pbc=True)
if is_mag:
cell.set_initial_magnetic_moments(sc_mag)
write('Supercell.cif', cell)
mcalc = copy.deepcopy(calc)
mcalc.set(lwave=True, lcharg=True)
cell.set_calculator(mcalc)
dir_name = "SUPERCELL0"
cur_dir = os.getcwd()
if not os.path.exists(dir_name):
os.mkdir(dir_name)
os.chdir(dir_name)
mcalc.scf_calculation(cell)
os.chdir(cur_dir)
def calc_force(iscell):
scell = supercells[iscell]
cell = Atoms(symbols=scell.get_chemical_symbols(),
scaled_positions=scell.get_scaled_positions(),
cell=scell.get_cell(),
pbc=True)
if is_mag:
cell.set_initial_magnetic_moments(sc_mag)
cell.set_calculator(copy.deepcopy(calc))
dir_name = "PHON_CELL%s" % iscell
cur_dir = os.getcwd()
if not os.path.exists(dir_name):
os.mkdir(dir_name)
if prepare_initial_wavecar:
os.system('ln -s %s %s' %
(os.path.abspath("SUPERCELL0/WAVECAR"),
os.path.join(dir_name, 'WAVECAR')))
os.chdir(dir_name)
forces = cell.get_forces()
print("[Phonopy] Forces: %s" % forces)
# Do something other than calculating the forces with func.
# func: func(atoms, calc, func_args)
if func is not None:
func(cell, calc, **func_args)
os.chdir(cur_dir)
drift_force = forces.sum(axis=0)
print("[Phonopy] Drift force:", "%11.5f" * 3 % tuple(drift_force))
# Simple translational invariance
for force in forces:
force -= drift_force / forces.shape[0]
return forces
if parallel:
p = Pool()
set_of_forces = p.map(calc_force,
list(range(iskip, len(supercells))))
else:
for iscell, scell in enumerate(supercells):
if iscell > iskip:
fs = calc_force(iscell)
set_of_forces.append(fs)
with open("forces_set.pickle", 'wb') as myfile:
pickle.dump(set_of_forces, myfile)
phonon.produce_force_constants(forces=np.array(set_of_forces))
force_constants = phonon.get_force_constants()
write_FORCE_CONSTANTS(force_constants, filename='FORCE_CONSTANTS')
#print("[Phonopy] Phonon frequencies at Gamma:")
# for i, freq in enumerate(phonon.get_frequencies((0, 0, 0))):
# print(("[Phonopy] %3d: %10.5f THz" % (i + 1, freq))) # THz
# print(("[Phonopy] %3d: %10.5f cm-1" % (i + 1, freq * 33.35))) #cm-1
with open('phonon.pickle', 'wb') as myfile:
pickle.dump(phonon, myfile)
phonon.save(settings={'force_constants': True})
return phonon
(0.75, 0.25, 0.75),
(0.75, 0.75, 0.25)] )
bulk.set_cell(np.diag((a, a, a)))
calc = GPAW(mode=PW(300),
kpts={'size': (4, 4, 4)},
symmetry={'symmorphic': False})
phonon = Phonopy(bulk,
[[1,0,0],[0,1,0],[0,0,1]],
primitive_matrix=[[0, 0.5, 0.5],
[0.5, 0, 0.5],
[0.5, 0.5, 0]],
distance=0.01)
print "[Phonopy] Atomic displacements:"
disps = phonon.get_displacements()
for d in disps:
print "[Phonopy]", d[0], d[1:]
supercells = phonon.get_supercells_with_displacements()
# Force calculations by calculator
set_of_forces = []
for scell in supercells:
cell = Atoms(symbols=scell.get_chemical_symbols(),
scaled_positions=scell.get_scaled_positions(),
cell=scell.get_cell(),
pbc=True)
cell.set_calculator(calc)
forces = cell.get_forces()
drift_force = forces.sum(axis=0)
print "[Phonopy] Drift force:", "%11.5f"*3 % tuple(drift_force)
scaled_positions=[(0, 0, 0), (0, 0.5, 0.5), (0.5, 0, 0.5),
(0.5, 0.5, 0), (0.25, 0.25, 0.25),
(0.25, 0.75, 0.75), (0.75, 0.25, 0.75),
(0.75, 0.75, 0.25)])
bulk.set_cell(np.diag((a, a, a)))
calc = GPAW(mode=PW(300),
kpts={'size': (4, 4, 4)},
symmetry={'symmorphic': False})
phonon = Phonopy(bulk, [[1, 0, 0], [0, 1, 0], [0, 0, 1]],
primitive_matrix=[[0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5,
0]],
distance=0.01)
print "[Phonopy] Atomic displacements:"
disps = phonon.get_displacements()
for d in disps:
print "[Phonopy]", d[0], d[1:]
supercells = phonon.get_supercells_with_displacements()
# Force calculations by calculator
set_of_forces = []
for scell in supercells:
cell = Atoms(symbols=scell.get_chemical_symbols(),
scaled_positions=scell.get_scaled_positions(),
cell=scell.get_cell(),
pbc=True)
cell.set_calculator(calc)
forces = cell.get_forces()
drift_force = forces.sum(axis=0)
print "[Phonopy] Drift force:", "%11.5f" * 3 % tuple(drift_force)
class PhononBase(TaskElement):
"""PhononBase class
This is an interface to phonopy.
"""
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 get_phonon(self):
return self._phonon
def get_cell(self):
if self._is_cell_relaxed:
return self._cell
else:
return self._phonon_tasks[0].get_cell()
def get_energy(self):
"""Return energies at geometry optimization steps"""
return self._energy
def set_status(self):
done = True
terminate = False
for task in self._tasks:
done &= task.done()
if task.get_status() == "terminate":
terminate = True
if done:
if terminate:
self._status = "terminate"
else:
self._status = "next"
self._write_yaml()
def begin(self):
if not self._job:
print "set_job has to be executed."
raise
self._overwrite_settings()
if self._is_cell_relaxed:
self._phonon_tasks = [None]
self._set_stage1()
else:
self._set_stage0()
def end(self):
pass
def done(self):
return ("terminate" in self._status or "done" in self._status
or "next" in self._status)
def next(self):
if self._stage == 0:
if "next" in self._status:
self._energy = self._tasks[0].get_energy()
self._comment = "%s\\n%f" % (self._tasks[0].get_space_group(
)['international_standard'], self._energy)
self._set_stage1()
return self._tasks
elif "terminate" in self._status and self._traverse == "restart":
self._traverse = False
self._set_stage0()
return self._tasks
else:
raise StopIteration
else: # task 1..n: displaced supercells
if "next" in self._status:
self._status = "done"
forces = []
for task in self._phonon_tasks[1:]:
forces.append(task.get_properties()['forces'][-1])
self._write_FORCE_SETS(forces)
self._phonon.set_post_process(self._primitive_matrix,
forces,
force_constants_decimals=14)
self._tasks = []
raise StopIteration
elif "terminate" in self._status and self._traverse == "restart":
self._traverse = False
disp_terminated = []
for i, task in enumerate(self._tasks):
if task.get_status() == "terminate":
disp_terminated.append(i)
tasks = self._get_displacement_tasks()[1:]
self._tasks = []
for i in disp_terminated:
self._tasks.append(tasks[i])
self._phonon_tasks[i + 1] = tasks[i]
self._status = "displacements"
return self._tasks
else:
raise StopIteration
def _set_stage0(self):
self._status = "equilibrium"
task = self._get_equilibrium_task()
self._phonon_tasks = [task]
self._tasks = [task]
def _set_stage1(self):
self._stage = 1
self._status = "displacements"
self._set_phonon()
self._tasks = self._get_displacement_tasks()[1:]
self._phonon_tasks += self._tasks
def _set_phonon(self):
cell = self.get_cell()
phonopy_cell = Atoms(cell=cell.get_lattice().T,
scaled_positions=cell.get_points().T,
symbols=cell.get_symbols())
self._phonon = Phonopy(phonopy_cell,
self._supercell_matrix,
is_auto_displacements=False)
self._phonon.generate_displacements(distance=self._distance,
is_diagonal=False)
supercell = self._phonon.get_supercell()
displacements = self._phonon.get_displacements()
write_poscar(cell, "POSCAR-unitcell")
write_disp_yaml(displacements, supercell)
def _write_FORCE_SETS(self, forces):
displacements = [[x[0], x[1:4]]
for x in self._phonon.get_displacements()]
natom = self._phonon.get_supercell().get_number_of_atoms()
write_FORCE_SETS("FORCE_SETS",
natom,
displacements,
forces,
verbose=False)
def _write_yaml(self):
w = open("%s.yaml" % self._directory, 'w')
if self._phonon_tasks[0]:
if self._lattice_tolerance is not None:
w.write("lattice_tolerance: %f\n" % self._lattice_tolerance)
if self._stress_tolerance is not None:
w.write("stress_tolerance: %f\n" % self._stress_tolerance)
w.write("pressure_target: %f\n" % self._pressure_target)
w.write("force_tolerance: %f\n" % self._force_tolerance)
w.write("max_increase: %f\n" % self._max_increase)
w.write("max_iteration: %d\n" % self._max_iteration)
w.write("min_iteration: %d\n" % self._min_iteration)
w.write("supercell_matrix:\n")
for row in self._supercell_matrix:
w.write("- [ %3d, %3d, %3d ]\n" % tuple(row))
w.write("primitive_matrix:\n")
for row in self._primitive_matrix:
w.write("- [ %6.3f, %6.3f, %6.3f ]\n" % tuple(row))
w.write("distance: %f\n" % self._distance)
w.write("iteration: %d\n" % self._phonon_tasks[0].get_stage())
if self._energy:
w.write("electric_total_energy: %20.10f\n" % self._energy)
w.write("status: %s\n" % self._status)
w.write("tasks:\n")
for task in self._phonon_tasks:
if task and task.get_status():
w.write("- name: %s\n" % task.get_name())
w.write(" status: %s\n" % task.get_status())
w.close()
