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_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 from_ddb_list(cls, ddb_list, nqsmall=10, qppa=None, ndivsm=20, line_density=None, asr=2, chneut=1, dipdip=1,
dos_method="tetra", lo_to_splitting="automatic", ngqpt=None, qptbounds=None, anaddb_kwargs=None,
verbose=0, mpi_procs=1, workdir=None, manager=None):
"""
Execute anaddb to compute generate the object from a list of ddbs.
Args:
ddb_list: A list with the paths to the ddb_files at different volumes. There should be an odd number of
DDB files and the volume increment must be constant. The DDB files will be ordered according to the
volume of the unit cell and the middle one will be considered as the DDB at the relaxed volume.
nqsmall: Defines the homogeneous q-mesh used for the DOS. Gives the number of divisions
used to sample the smallest lattice vector. If 0, DOS is not computed and
(phbst, None) is returned.
qppa: Defines the homogeneous q-mesh used for the DOS in units of q-points per reciprocal atom.
Overrides nqsmall.
ndivsm: Number of division used for the smallest segment of the q-path.
line_density: Defines the a density of k-points per reciprocal atom to plot the phonon dispersion.
Overrides ndivsm.
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.
lo_to_splitting: Allowed values are [True, False, "automatic"]. Defaults to "automatic"
If True the LO-TO splitting will be calculated and the non_anal_directions
and the non_anal_phfreqs attributes will be addeded to the phonon band structure.
"automatic" activates LO-TO if the DDB file contains the dielectric tensor and Born effective charges.
ngqpt: Number of divisions for the q-mesh in the DDB file. Auto-detected if None (default).
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.
verbose: verbosity level. Set it to a value > 0 to get more information.
mpi_procs: Number of MPI processes to use.
workdir: Working directory. If None, a temporary directory is created.
manager: |TaskManager| object. If None, the object is initialized from the configuration file.
Returns:
A GrunsNcFile object.
"""
if len(ddb_list) % 2 != 1:
raise ValueError("An odd number of ddb file paths should be provided")
ddbs = [DdbFile(d) for d in ddb_list]
ddbs = sorted(ddbs, key=lambda d: d.structure.volume)
iv0 = int((len(ddbs) - 1) / 2)
ddb0 = ddbs[iv0]
# update list of paths with absolute paths in the correct order
ddb_list = [d.filepath for d in ddbs]
if ngqpt is None: ngqpt = ddb0.guessed_ngqpt
if lo_to_splitting == "automatic":
lo_to_splitting = ddb0.has_lo_to_data() and dipdip != 0
if lo_to_splitting and not ddb0.has_lo_to_data():
cprint("lo_to_splitting is True but Emacro and Becs are not available in DDB: %s" % ddb0.filepath, "yellow")
inp = AnaddbInput.phbands_and_dos(
ddb0.structure, ngqpt=ngqpt, ndivsm=ndivsm, nqsmall=nqsmall, qppa=qppa, line_density=line_density,
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)
inp["gruns_ddbs"] = ['"'+p+'"\n' for p in ddb_list]
inp["gruns_nddbs"] = len(ddb_list)
task = AnaddbTask.temp_shell_task(inp, ddb_node=ddb0.filepath, workdir=workdir, manager=manager, mpi_procs=mpi_procs)
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 ddb0.AnaddbError(task=task, report=report)
gruns = cls.from_file(os.path.join(task.workdir, "run.abo_GRUNS.nc"))
return gruns
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
def from_ddb_list(cls, ddb_list, nqsmall=10, qppa=None, ndivsm=20, line_density=None, asr=2, chneut=1, dipdip=1,
dos_method="tetra", lo_to_splitting="automatic", ngqpt=None, qptbounds=None, anaddb_kwargs=None,
verbose=0, mpi_procs=1, workdir=None, manager=None):
"""
Execute anaddb to compute generate the object from a list of ddbs.
Args:
ddb_list: A list with the paths to the ddb_files at different volumes. There should be an odd number of
DDB files and the volume increment must be constant. The DDB files will be ordered according to the
volume of the unit cell and the middle one will be considered as the DDB at the relaxed volume.
nqsmall: Defines the homogeneous q-mesh used for the DOS. Gives the number of divisions
used to sample the smallest lattice vector. If 0, DOS is not computed and
(phbst, None) is returned.
qppa: Defines the homogeneous q-mesh used for the DOS in units of q-points per reciprocal atom.
Overrides nqsmall.
ndivsm: Number of division used for the smallest segment of the q-path.
line_density: Defines the a density of k-points per reciprocal atom to plot the phonon dispersion.
Overrides ndivsm.
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.
lo_to_splitting: Allowed values are [True, False, "automatic"]. Defaults to "automatic"
If True the LO-TO splitting will be calculated and the non_anal_directions
and the non_anal_phfreqs attributes will be addeded to the phonon band structure.
"automatic" activates LO-TO if the DDB file contains the dielectric tensor and Born effective charges.
ngqpt: Number of divisions for the q-mesh in the DDB file. Auto-detected if None (default).
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.
verbose: verbosity level. Set it to a value > 0 to get more information.
mpi_procs: Number of MPI processes to use.
workdir: Working directory. If None, a temporary directory is created.
manager: |TaskManager| object. If None, the object is initialized from the configuration file.
Returns:
A GrunsNcFile object.
"""
if len(ddb_list) % 2 != 1:
raise ValueError("An odd number of ddb file paths should be provided")
ddbs = [DdbFile(d) for d in ddb_list]
ddbs = sorted(ddbs, key=lambda d: d.structure.volume)
iv0 = int((len(ddbs) - 1) / 2)
ddb0 = ddbs[iv0]
# update list of paths with absolute paths in the correct order
ddb_list = [d.filepath for d in ddbs]
if ngqpt is None: ngqpt = ddb0.guessed_ngqpt
if lo_to_splitting == "automatic":
lo_to_splitting = ddb0.has_lo_to_data() and dipdip != 0
if lo_to_splitting and not ddb0.has_lo_to_data():
cprint("lo_to_splitting is True but Emacro and Becs are not available in DDB: %s" % ddb0.filepath, "yellow")
inp = AnaddbInput.phbands_and_dos(
ddb0.structure, ngqpt=ngqpt, ndivsm=ndivsm, nqsmall=nqsmall, qppa=qppa, line_density=line_density,
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)
inp["gruns_ddbs"] = ['"'+p+'"\n' for p in ddb_list]
inp["gruns_nddbs"] = len(ddb_list)
task = AnaddbTask.temp_shell_task(inp, ddb_node=ddb0.filepath, workdir=workdir, manager=manager, mpi_procs=mpi_procs)
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 ddb0.AnaddbError(task=task, report=report)
gruns = cls.from_file(os.path.join(task.workdir, "run.abo_GRUNS.nc"))
return gruns