def anaget_emacro_and_becs(self, chneut=1, workdir=None, manager=None, verbose=0):
"""
Call anaddb to compute the macroscopic dielectric tensor and the Born effective charges.
Args:
chneut: Anaddb input variable. See official documentation.
manager: :class:`TaskManager` object. If None, the object is initialized from the configuration file
verbose: verbosity level. Set it to a value > 0 to get more information
Return:
emacro, becs
"""
inp = AnaddbInput(self.structure, anaddb_kwargs={"chneut": chneut})
task = AnaddbTask.temp_shell_task(inp, ddb_node=self.filepath, workdir=workdir, manager=manager)
if verbose:
print("ANADDB INPUT:\n", inp)
print("workdir:", task.workdir)
# Run the task here.
task.start_and_wait(autoparal=False)
report = task.get_event_report()
if not report.run_completed:
raise self.AnaddbError(task=task, report=report)
# Read data from the netcdf output file produced by anaddb.
with ETSF_Reader(os.path.join(task.workdir, "anaddb.nc")) as r:
structure = r.read_structure()
emacro = Tensor.from_cartesian_tensor(r.read_value("emacro_cart"), structure.lattice, space="r"),
becs = Becs(r.read_value("becs_cart"), structure, chneut=inp["chneut"], order="f")
return emacro, becs
def anaget_ifc(self,
ifcout=None,
asr=2,
chneut=1,
dipdip=1,
ngqpt=None,
workdir=None,
manager=None,
verbose=0,
anaddb_kwargs=None):
"""
Execute anaddb to compute the interatomic forces.
Args:
ifcout: Number of neighbouring atoms for which the ifc's will be output. If None all the atoms in the big box.
asr, chneut, dipdip: Anaddb input variable. See official documentation.
ngqpt: Number of divisions for the q-mesh in the DDB file. Auto-detected if None (default)
workdir: Working directory. If None, a temporary directory is created.
manager: :class:`TaskManager` object. If None, the object is initialized from the configuration file
verbose: verbosity level. Set it to a value > 0 to get more information
anaddb_kwargs: additional kwargs for anaddb
Returns:
:class:`InteratomicForceConstants` with the calculated ifc.
"""
if ngqpt is None: ngqpt = self.guessed_ngqpt
inp = AnaddbInput.ifc(self.structure,
ngqpt=ngqpt,
ifcout=ifcout,
q1shft=(0, 0, 0),
asr=asr,
chneut=chneut,
dipdip=dipdip,
anaddb_kwargs=anaddb_kwargs)
task = AnaddbTask.temp_shell_task(inp,
ddb_node=self.filepath,
workdir=workdir,
manager=manager)
if verbose:
print("ANADDB INPUT:\n", inp)
print("workdir:", task.workdir)
# Run the task here.
task.start_and_wait(autoparal=False)
report = task.get_event_report()
if not report.run_completed:
raise self.AnaddbError(task=task, report=report)
return InteratomicForceConstants.from_file(
os.path.join(task.workdir, 'anaddb.nc'))
def anaget_phbst_and_phdos_files(self, nqsmall=10, ndivsm=20, asr=2, chneut=1, dipdip=1, dos_method="tetra",
ngqpt=None, workdir=None, manager=None, verbose=0, lo_to_splitting=False):
"""
Execute anaddb to compute the phonon band structure and the phonon DOS
Args:
nqsmall: Defines the homogeneous q-mesh used for the DOS. Gives the number of divisions
used to sample the smallest lattice vector.
ndivsm: Number of division used for the smallest segment of the q-path
asr, chneut, dipdp: Anaddb input variable. See official documentation.
dos_method: Technique for DOS computation in Possible choices: "tetra", "gaussian" or "gaussian:0.001 eV".
In the later case, the value 0.001 eV is used as gaussian broadening
ngqpt: Number of divisions for the q-mesh in the DDB file. Auto-detected if None (default)
workdir: Working directory. If None, a temporary directory is created.
manager: :class:`TaskManager` object. If None, the object is initialized from the configuration file
verbose: verbosity level. Set it to a value > 0 to get more information
lo_to_splitting: if True calculation of the LO-TO splitting will be calculated and included in the
band structure
Returns:
:class:`PhbstFile` with the phonon band structure.
:class:`PhdosFile` with the the phonon DOS.
"""
if ngqpt is None: ngqpt = self.guessed_ngqpt
inp = AnaddbInput.phbands_and_dos(
self.structure, ngqpt=ngqpt, ndivsm=ndivsm, nqsmall=nqsmall, q1shft=(0,0,0), qptbounds=None,
asr=asr, chneut=chneut, dipdip=dipdip, dos_method=dos_method, lo_to_splitting=lo_to_splitting)
task = AnaddbTask.temp_shell_task(inp, ddb_node=self.filepath, workdir=workdir, manager=manager)
if verbose:
print("ANADDB INPUT:\n", inp)
print("workdir:", task.workdir)
# Run the task here.
task.start_and_wait(autoparal=False)
report = task.get_event_report()
if not report.run_completed:
raise self.AnaddbError(task=task, report=report)
phbst = task.open_phbst()
if lo_to_splitting:
with ETSF_Reader(os.path.join(task.workdir, "anaddb.nc")) as r:
directions = r.read_value("non_analytical_directions")
non_anal_phfreq = r.read_value("non_analytical_phonon_modes")
phbst.phbands.non_anal_directions = directions
phbst.phbands.non_anal_phfreqs = non_anal_phfreq
return phbst, task.open_phdos()
def anaget_emacro_and_becs(self,
chneut=1,
workdir=None,
manager=None,
verbose=0):
"""
Call anaddb to compute the macroscopic dielectric tensor and the Born effective charges.
Args:
chneut: Anaddb input variable. See official documentation.
manager: :class:`TaskManager` object. If None, the object is initialized from the configuration file
verbose: verbosity level. Set it to a value > 0 to get more information
Return:
emacro, becs
"""
inp = AnaddbInput(self.structure, anaddb_kwargs={"chneut": chneut})
task = AnaddbTask.temp_shell_task(inp,
ddb_node=self.filepath,
workdir=workdir,
manager=manager)
if verbose:
print("ANADDB INPUT:\n", inp)
print("workdir:", task.workdir)
# Run the task here.
task.start_and_wait(autoparal=False)
report = task.get_event_report()
if not report.run_completed:
raise self.AnaddbError(task=task, report=report)
# Read data from the netcdf output file produced by anaddb.
with ETSF_Reader(os.path.join(task.workdir, "anaddb.nc")) as r:
structure = r.read_structure()
emacro = Tensor.from_cartesian_tensor(r.read_value("emacro_cart"),
structure.lattice,
space="r"),
becs = Becs(r.read_value("becs_cart"),
structure,
chneut=inp["chneut"],
order="f")
return emacro, becs
def anaget_phmodes_at_qpoint(self, qpoint=None, asr=2, chneut=1, dipdip=1,
workdir=None, manager=None, verbose=0):
"""
Execute anaddb to compute phonon modes at the given q-point.
Args:
qpoint: Reduced coordinates of the qpoint where phonon modes are computed.
asr, chneut, dipdp: Anaddb input variable. See official documentation.
workdir: Working directory. If None, a temporary directory is created.
manager: :class:`TaskManager` object. If None, the object is initialized from the configuration file
verbose: verbosity level. Set it to a value > 0 to get more information
Return:
:class:`PhononBands` object.
"""
if qpoint is None:
qpoint = self.qpoints[0]
if len(self.qpoints) != 1:
raise ValueError("%s contains %s qpoints and the choice is ambiguous.\n"
"Please specify the qpoint." % (self, len(self.qpoints)))
# Check if qpoint is in the DDB.
try:
self.qindex(qpoint)
except:
raise ValueError("input qpoint %s not in ddb.qpoints:%s\n" % (qpoint, self.qpoints))
inp = AnaddbInput.modes_at_qpoint(self.structure, qpoint, asr=asr, chneut=chneut, dipdip=dipdip)
task = AnaddbTask.temp_shell_task(inp, ddb_node=self.filepath, workdir=workdir, manager=manager)
if verbose:
print("ANADDB INPUT:\n", inp)
print("workdir:", task.workdir)
# Run the task here
task.start_and_wait(autoparal=False)
report = task.get_event_report()
if not report.run_completed:
raise self.AnaddbError(task=task, report=report)
with task.open_phbst() as ncfile:
return ncfile.phbands
def anaget_phbst_and_phdos_files(self,
nqsmall=10,
ndivsm=20,
asr=2,
chneut=1,
dipdip=1,
dos_method="tetra",
ngqpt=None,
workdir=None,
manager=None,
verbose=0,
lo_to_splitting=False,
qptbounds=None,
anaddb_kwargs=None):
"""
Execute anaddb to compute the phonon band structure and the phonon DOS
Args:
nqsmall: Defines the homogeneous q-mesh used for the DOS. Gives the number of divisions
used to sample the smallest lattice vector.
ndivsm: Number of division used for the smallest segment of the q-path
asr, chneut, dipdip: Anaddb input variable. See official documentation.
dos_method: Technique for DOS computation in Possible choices: "tetra", "gaussian" or "gaussian:0.001 eV".
In the later case, the value 0.001 eV is used as gaussian broadening
ngqpt: Number of divisions for the q-mesh in the DDB file. Auto-detected if None (default)
workdir: Working directory. If None, a temporary directory is created.
manager: :class:`TaskManager` object. If None, the object is initialized from the configuration file
verbose: verbosity level. Set it to a value > 0 to get more information
lo_to_splitting: if True the LO-TO splitting will be calculated and included in the band structure
qptbounds: Boundaries of the path. If None, the path is generated from an internal database
depending on the input structure.
anaddb_kwargs: additional kwargs for anaddb
Returns:
:class:`PhbstFile` with the phonon band structure.
:class:`PhdosFile` with the the phonon DOS.
"""
if ngqpt is None: ngqpt = self.guessed_ngqpt
inp = AnaddbInput.phbands_and_dos(self.structure,
ngqpt=ngqpt,
ndivsm=ndivsm,
nqsmall=nqsmall,
q1shft=(0, 0, 0),
qptbounds=qptbounds,
asr=asr,
chneut=chneut,
dipdip=dipdip,
dos_method=dos_method,
lo_to_splitting=lo_to_splitting,
anaddb_kwargs=anaddb_kwargs)
task = AnaddbTask.temp_shell_task(inp,
ddb_node=self.filepath,
workdir=workdir,
manager=manager)
if verbose:
print("ANADDB INPUT:\n", inp)
print("workdir:", task.workdir)
# Run the task here.
task.start_and_wait(autoparal=False)
report = task.get_event_report()
if not report.run_completed:
raise self.AnaddbError(task=task, report=report)
phbst = task.open_phbst()
if lo_to_splitting:
phbst.phbands.read_non_anal_from_file(
os.path.join(task.workdir, "anaddb.nc"))
return phbst, task.open_phdos()
def anaget_phmodes_at_qpoint(self,
qpoint=None,
asr=2,
chneut=1,
dipdip=1,
workdir=None,
manager=None,
verbose=0,
lo_to_splitting=False,
directions=None,
anaddb_kwargs=None):
"""
Execute anaddb to compute phonon modes at the given q-point.
Args:
qpoint: Reduced coordinates of the qpoint where phonon modes are computed.
asr, chneut, dipdp: Anaddb input variable. See official documentation.
workdir: Working directory. If None, a temporary directory is created.
manager: :class:`TaskManager` object. If None, the object is initialized from the configuration file
verbose: verbosity level. Set it to a value > 0 to get more information
lo_to_splitting: if True the LO-TO splitting will be calculated if qpoint==Gamma and the non_anal_directions
non_anal_phfreqs attributes will be added to the returned object
directions: list of 3D directions along which the LO-TO splitting will be calculated. If None the three
cartesian direction will be used
anaddb_kwargs: additional kwargs for anaddb
Return:
:class:`PhononBands` object.
"""
if qpoint is None:
qpoint = self.qpoints[0]
if len(self.qpoints) != 1:
raise ValueError(
"%s contains %s qpoints and the choice is ambiguous.\n"
"Please specify the qpoint." % (self, len(self.qpoints)))
# Check if qpoint is in the DDB.
try:
self.qindex(qpoint)
except:
raise ValueError("input qpoint %s not in ddb.qpoints:%s\n" %
(qpoint, self.qpoints))
inp = AnaddbInput.modes_at_qpoint(self.structure,
qpoint,
asr=asr,
chneut=chneut,
dipdip=dipdip,
lo_to_splitting=lo_to_splitting,
directions=directions,
anaddb_kwargs=anaddb_kwargs)
task = AnaddbTask.temp_shell_task(inp,
ddb_node=self.filepath,
workdir=workdir,
manager=manager)
if verbose:
print("ANADDB INPUT:\n", inp)
print("workdir:", task.workdir)
# Run the task here
task.start_and_wait(autoparal=False)
report = task.get_event_report()
if not report.run_completed:
raise self.AnaddbError(task=task, report=report)
with task.open_phbst() as ncfile:
if lo_to_splitting and np.allclose(qpoint, [0, 0, 0]):
ncfile.phbands.read_non_anal_from_file(
os.path.join(task.workdir, "anaddb.nc"))
return ncfile.phbands
