def test_AnaDdbAbinitTask(self):
ana_inp = AnaddbInput.phbands_and_dos(self.si_structure,
ngqpt=[4, 4, 4],
nqsmall=10)
task = abinit_tasks.AnaDdbAbinitTask(ana_inp)
task.to_dict()
self.assertFwSerializable(task)
def abinp_anaph(options):
"""Build Anaddb input file for the computation of phonon bands DOS."""
ddb = DdbFile(options.filepath)
nqsmall = 10
inp = AnaddbInput.phbands_and_dos(ddb.structure, ddb.guessed_ngqpt, nqsmall, ndivsm=20, q1shft=(0, 0, 0),
qptbounds=None, asr=2, chneut=0, dipdip=1, dos_method="tetra", lo_to_splitting=False,
anaddb_args=None, anaddb_kwargs=None)
return finalize(inp, options)
def abinp_anaph(options):
"""Build Anaddb input file for the computation of phonon bands DOS."""
ddb = DdbFile(options.filepath)
nqsmall = 10
inp = AnaddbInput.phbands_and_dos(ddb.structure, ddb.guessed_ngqpt, nqsmall, ndivsm=20, q1shft=(0, 0, 0),
qptbounds=None, asr=2, chneut=0, dipdip=1, dos_method="tetra", lo_to_splitting=False,
anaddb_args=None, anaddb_kwargs=None)
return finalize(inp, options)
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_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):
"""
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
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)
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 task.open_phbst(), task.open_phdos()
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 add_phonon_works_and_build(self):
"""
Get relaxed structures from the tasks, build Phonons works with new structures.
Add works to the flow and build new directories.
"""
ddb_paths, struct_middle, middle_idx = [], None, None
relaxed_structs = []
for i, task in enumerate(self.relax_tasks):
relaxed_structure = task.get_final_structure()
relaxed_structs.append(relaxed_structure)
if i == len(self.relax_tasks) // 2:
middle_idx, struct_middle = i, relaxed_structure
# work to compute phonons with new structure.
gsinp_vol = self.gs_inp.new_with_structure(relaxed_structure)
work = PhononWork.from_scf_input(gsinp_vol, self.ngqpt, is_ngqpt=True, tolerance=self.tolerance,
with_becs=self.with_becs, ddk_tolerance=self.ddk_tolerance)
# Add it to the flow.
self.flow.register_work(work)
ddb_paths.append(work.outdir.path_in("out_DDB"))
# Write Anaddb input file to compute Gruneisen parameters in flow.outdata.
from abipy.abio.inputs import AnaddbInput
anaddb_inp = AnaddbInput.phbands_and_dos(struct_middle, self.ngqpt, nqsmall=20, ndivsm=20,
chneut=1 if self.with_becs else 0,
dipdip=1 if self.with_becs else 0,
lo_to_splitting=self.with_becs,
comment="Anaddb input file for Grunesein parameters")
# Add DDB files for Gruns
anaddb_inp["gruns_nddbs"] = len(ddb_paths)
anaddb_inp["gruns_ddbs"] = "\n" + "\n".join('"%s"' % p for p in ddb_paths)
in_path = self.flow.outdir.path_in("anaddb_gruns.in")
anaddb_inp.write(in_path)
files_file = []
app = files_file.append
app(in_path) # 1) Path of the input file
app(self.flow.outdir.path_in("anaddb_gruns.out")) # 2) Path of the output file
app(ddb_paths[middle_idx]) # 3) Input derivative database (not used if Gruns)
for i in range(4):
app("FOOBAR")
with open(self.flow.outdir.path_in("anaddb_gruns.files"), "wt") as fh:
fh.write("\n".join(files_file))
#with_ebands = False
#if with_ebands:
# bands_work = Work(manager=self.manager)
# for i, structure in enumerate(relaxed_structs):
# nscf_inp = self.gs_inp.new_with_structure(structure)
# nscf_inp.pop_tolerances()
# nscf_inp.set_kpath(ndivsm, kptbounds=None, iscf=-2)
# nscf_inp["tolwfr"] = 1e-18
# work.register_nscf_task(nscf_inp, deps={self.relax_tasks[i]: "DEN"})
# # Add it to the flow.
# self.flow.register_work(work)
# Allocate new works and update the pickle database.
self.flow.allocate()
self.flow.build_and_pickle_dump()
def test_AnaDdbAbinitTask(self):
ana_inp = AnaddbInput.phbands_and_dos(self.si_structure, ngqpt=[4,4,4], nqsmall=10)
task = abinit_tasks.AnaDdbAbinitTask(ana_inp)
task.to_dict()
self.assertFwSerializable(task)
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
