def get_irred_perts(self,
ngkpt=None,
shiftk=None,
kptopt=None,
qpoint=None,
workdir=None,
manager=None):
"""
This function, computes the list of irreducible perturbations for DFPT.
It should be called with an input file that contains all the mandatory variables required by ABINIT.
Args:
ngkpt: Number of divisions for the k-mesh (default None i.e. use ngkpt from self)
shiftk: Shiftks (default None i.e. use shiftk from self)
qpoint: qpoint in reduced coordinates. Used to shift the k-mesh (default None i.e no shift)
workdir: Working directory of the fake task used to compute the ibz. Use None for temporary dir.
manager: :class:`TaskManager` of the task. If None, the manager is initialized from the config file.
Returns:
List of dictionaries with the Abinit variables defining the irreducible perturbation
Example:
[{'idir': 1, 'ipert': 1, 'qpt': [0.25, 0.0, 0.0]},
{'idir': 2, 'ipert': 1, 'qpt': [0.25, 0.0, 0.0]}]
.. warning::
Multiple datasets are ignored. Only the list of k-points for dataset 1 are returned.
"""
if self.ndtset != 1:
raise RuntimeError(
"get_irred_perts cannot be used if the input contains more than one dataset"
)
warnings.warn("get_irred_perts is still under development.")
# Avoid modifications in self.
inp = self.split_datasets()[0].deepcopy()
# Use the magic value paral_rf = -1 to get the list of irreducible perturbations for this q-point.
d = dict(
paral_rf=-1,
rfatpol=[1, len(inp.structure)], # Set of atoms to displace.
rfdir=[1, 1, 1], # Along this set of reduced coordinate axis.
)
inp.set_vars(d)
# Build a Task to run Abinit in a shell subprocess
task = AbinitTask.temp_shell_task(inp,
workdir=workdir,
manager=manager)
task.start_and_wait(autoparal=False)
# Parse the file to get the perturbations.
try:
return yaml_read_irred_perts(task.log_file.path)
except Exception as exc:
# Try to understand if it's a problem with the Abinit input.
report = task.get_event_report()
if report.errors: raise self.Error(str(report))
raise exc
def get_ibz(self, ngkpt=None, shiftk=None, kptopt=None, qpoint=None, workdir=None, manager=None):
"""
This function, computes the list of points in the IBZ and the corresponding weights.
It should be called with an input file that contains all the mandatory variables required by ABINIT.
Args:
ngkpt: Number of divisions for the k-mesh (default None i.e. use ngkpt from self)
shiftk: Shiftks (default None i.e. use shiftk from self)
qpoint: qpoint in reduced coordinates. Used to shift the k-mesh (default None i.e no shift)
workdir: Working directory of the fake task used to compute the ibz. Use None for temporary dir.
manager: :class:`TaskManager` of the task. If None, the manager is initialized from the config file.
Returns:
`namedtuple` with attributes:
points: `ndarray` with points in the IBZ in reduced coordinates.
weights: `ndarray` with weights of the points.
.. warning::
Multiple datasets are ignored. Only the list of k-points for dataset 1 are returned.
"""
if self.ndtset != 1:
raise RuntimeError("get_ibz cannot be used if the input contains more than one dataset")
# Avoid modifications in self.
inp = self.split_datasets()[0].deepcopy()
# The magic value that makes ABINIT print the ibz and then stop.
inp.prtkpt = -2
if ngkpt is not None: inp.ngkpt = ngkpt
if shiftk is not None:
inp.shiftk = np.reshape(shiftk, (-1,3))
inp.nshiftk = len(inp.shiftk)
if kptopt is not None:
inp.kptopt = kptopt
if qpoint is not None:
inp.qptn, inp.nqpt = qpoint, 1
# Build a Task to run Abinit in a shell subprocess
task = AbinitTask.temp_shell_task(inp, workdir=workdir, manager=manager)
task.start_and_wait(autoparal=False)
# Read the list of k-points from the netcdf file.
try:
with NetcdfReader(os.path.join(task.workdir, "kpts.nc")) as r:
ibz = collections.namedtuple("ibz", "points weights")
return ibz(points=r.read_value("reduced_coordinates_of_kpoints"),
weights=r.read_value("kpoint_weights"))
except Exception as exc:
# Try to understand if it's a problem with the Abinit input.
report = task.get_event_report()
if report.errors: raise self.Error(str(report))
raise exc
def get_irred_perts(self, ngkpt=None, shiftk=None, kptopt=None, qpoint=None, workdir=None, manager=None):
"""
This function, computes the list of irreducible perturbations for DFPT.
It should be called with an input file that contains all the mandatory variables required by ABINIT.
Args:
ngkpt: Number of divisions for the k-mesh (default None i.e. use ngkpt from self)
shiftk: Shiftks (default None i.e. use shiftk from self)
qpoint: qpoint in reduced coordinates. Used to shift the k-mesh (default None i.e no shift)
workdir: Working directory of the fake task used to compute the ibz. Use None for temporary dir.
manager: :class:`TaskManager` of the task. If None, the manager is initialized from the config file.
Returns:
List of dictionaries with the Abinit variables defining the irreducible perturbation
Example:
[{'idir': 1, 'ipert': 1, 'qpt': [0.25, 0.0, 0.0]},
{'idir': 2, 'ipert': 1, 'qpt': [0.25, 0.0, 0.0]}]
.. warning::
Multiple datasets are ignored. Only the list of k-points for dataset 1 are returned.
"""
if self.ndtset != 1:
raise RuntimeError("get_irred_perts cannot be used if the input contains more than one dataset")
warnings.warn("get_irred_perts is still under development.")
# Avoid modifications in self.
inp = self.split_datasets()[0].deepcopy()
# Use the magic value paral_rf = -1 to get the list of irreducible perturbations for this q-point.
d = dict(
paral_rf=-1,
rfatpol=[1, len(inp.structure)], # Set of atoms to displace.
rfdir=[1, 1, 1], # Along this set of reduced coordinate axis.
)
inp.set_vars(d)
# Build a Task to run Abinit in a shell subprocess
task = AbinitTask.temp_shell_task(inp, workdir=workdir, manager=manager)
task.start_and_wait(autoparal=False)
# Parse the file to get the perturbations.
try:
return yaml_read_irred_perts(task.log_file.path)
except Exception as exc:
# Try to understand if it's a problem with the Abinit input.
report = task.get_event_report()
if report.errors: raise self.Error(str(report))
raise exc
def validate(self):
"""
Run ABINIT in dry mode to validate the input file.
Return:
`namedtuple` with the following attributes:
retcode: Return code. 0 if OK.
log_file: log file of the Abinit run, use log_file.read() to access its content.
stderr_file: stderr file of the Abinit run. use stderr_file.read() to access its content.
Raises:
`RuntimeError` if executable is not in $PATH.
"""
task = AbinitTask.temp_shell_task(inp=self)
retcode = task.start_and_wait(autoparal=False, exec_args=["--dry-run"])
return dict2namedtuple(retcode=retcode, log_file=task.log_file, stderr_file=task.stderr_file)
def validate(self):
"""
Run ABINIT in dry mode to validate the input file.
Return:
`namedtuple` with the following attributes:
retcode: Return code. 0 if OK.
log_file: log file of the Abinit run, use log_file.read() to access its content.
stderr_file: stderr file of the Abinit run. use stderr_file.read() to access its content.
Raises:
`RuntimeError` if executable is not in $PATH.
"""
task = AbinitTask.temp_shell_task(inp=self)
retcode = task.start_and_wait(autoparal=False, exec_args=["--dry-run"])
return dict2namedtuple(retcode=retcode,
log_file=task.log_file,
stderr_file=task.stderr_file)
def get_ibz(self,
ngkpt=None,
shiftk=None,
kptopt=None,
qpoint=None,
workdir=None,
manager=None):
"""
This function, computes the list of points in the IBZ and the corresponding weights.
It should be called with an input file that contains all the mandatory variables required by ABINIT.
Args:
ngkpt: Number of divisions for the k-mesh (default None i.e. use ngkpt from self)
shiftk: Shiftks (default None i.e. use shiftk from self)
qpoint: qpoint in reduced coordinates. Used to shift the k-mesh (default None i.e no shift)
workdir: Working directory of the fake task used to compute the ibz. Use None for temporary dir.
manager: :class:`TaskManager` of the task. If None, the manager is initialized from the config file.
Returns:
`namedtuple` with attributes:
points: `ndarray` with points in the IBZ in reduced coordinates.
weights: `ndarray` with weights of the points.
.. warning::
Multiple datasets are ignored. Only the list of k-points for dataset 1 are returned.
"""
if self.ndtset != 1:
raise RuntimeError(
"get_ibz cannot be used if the input contains more than one dataset"
)
# Avoid modifications in self.
inp = self.split_datasets()[0].deepcopy()
# The magic value that makes ABINIT print the ibz and then stop.
inp.prtkpt = -2
if ngkpt is not None: inp.ngkpt = ngkpt
if shiftk is not None:
inp.shiftk = np.reshape(shiftk, (-1, 3))
inp.nshiftk = len(inp.shiftk)
if kptopt is not None:
inp.kptopt = kptopt
if qpoint is not None:
inp.qptn, inp.nqpt = qpoint, 1
# Build a Task to run Abinit in a shell subprocess
task = AbinitTask.temp_shell_task(inp,
workdir=workdir,
manager=manager)
task.start_and_wait(autoparal=False)
# Read the list of k-points from the netcdf file.
try:
with NetcdfReader(os.path.join(task.workdir, "kpts.nc")) as r:
ibz = collections.namedtuple("ibz", "points weights")
return ibz(
points=r.read_value("reduced_coordinates_of_kpoints"),
weights=r.read_value("kpoint_weights"))
except Exception as exc:
# Try to understand if it's a problem with the Abinit input.
report = task.get_event_report()
if report.errors: raise self.Error(str(report))
raise exc