def on_all_ok(self):
"""
This method is called once the `Work` is completed i.e. when all the tasks
have reached status S_OK. Here we get the forces from the output files, and
we call phonopy to compute the inter-atomic force constants.
"""
phonon = self.phonon
# Write POSCAR with initial unit cell.
structure = structure_from_atoms(phonon.get_primitive())
structure.to(filename=self.outdir.path_in("POSCAR"))
# Write yaml file with displacements.
supercell = phonon.get_supercell()
displacements = phonon.get_displacements()
#directions = phonon.get_displacement_directions()
file_IO.write_disp_yaml(displacements, supercell, # directions=directions,
filename=self.outdir.path_in('disp.yaml'))
# Extract forces from the main Abinit output files.
forces_filenames = [task.output_file.path for task in self.phonopy_tasks]
num_atoms = supercell.get_number_of_atoms()
force_sets = parse_set_of_forces(num_atoms, forces_filenames)
# Write FORCE_SETS file.
displacements = file_IO.parse_disp_yaml(filename=self.outdir.path_in('disp.yaml'))
num_atoms = displacements['natom']
for forces, disp in zip(force_sets, displacements['first_atoms']):
disp['forces'] = forces
file_IO.write_FORCE_SETS(displacements, filename=self.outdir.path_in('FORCE_SETS'))
# Write README and configuration files.
examples_url = "http://atztogo.github.io/phonopy/examples.html"
doctags_url = "http://atztogo.github.io/phonopy/setting-tags.html#setting-tags"
kptbounds = np.array([k.frac_coords for k in structure.hsym_kpoints])
path_coords = " ".join(str(rc) for rc in kptbounds.flat)
path_labels = " ".join(k.name for k in structure.hsym_kpoints)
ngqpt = structure.calc_ngkpt(nksmall=30)
with open(self.outdir.path_in("band.conf"), "wt") as fh:
fh.write("#" + doctags_url + "\n")
fh.write("DIM = %d %d %d\n" % tuple(self.scdims))
fh.write("BAND = %s\n" % path_coords)
fh.write("BAND_LABELS = %s\n" % path_labels)
fh.write("BAND_POINTS = 101\n")
fh.write("#BAND_CONNECTION = .TRUE.\n")
with open(self.outdir.path_in("dos.conf"), "wt") as fh:
fh.write("#" + doctags_url + "\n")
fh.write("DIM = %d %d %d\n" % tuple(self.scdims))
fh.write("MP = %d %d %d\n" % tuple(ngqpt))
fh.write("#GAMMA_CENTER = .TRUE.\n")
with open(self.outdir.path_in("band-dos.conf"), "wt") as fh:
fh.write("#" + doctags_url + "\n")
fh.write("DIM = %d %d %d\n" % tuple(self.scdims))
fh.write("BAND = %s\n" % path_coords)
fh.write("BAND_LABELS = %s\n" % path_labels)
fh.write("BAND_POINTS = 101\n")
fh.write("#BAND_CONNECTION = .TRUE.\n")
fh.write("MP = %d %d %d\n" % tuple(ngqpt))
fh.write("#GAMMA_CENTER = .TRUE.\n")
with open(self.outdir.path_in("README.md"), "wt") as fh:
fh.write("To plot bands, use:\n\tphonopy -p band.conf\n\n")
fh.write("To plot phonon dos, use:\n\tphonopy -p dos.conf\n\n")
fh.write("To plot bands and dos, use:\n\tphonopy -p band-dos.conf\n\n")
fh.write("See also:\n")
fh.write("\t" + examples_url + "\n")
fh.write("\t" + doctags_url + "\n")
if self.cpdata2dst:
self.outdir.copy_r(self.cpdata2dst)
return super(PhonopyWork, self).on_all_ok()
def on_all_ok(self):
"""
This method is called once the `Work` is completed i.e. when all the tasks
have reached status S_OK. Here we get the forces from the output files, and
we call phonopy to compute the inter-atomic force constants.
"""
phonon = self.phonon
# Write POSCAR with initial unit cell.
structure = structure_from_atoms(phonon.get_primitive())
structure.to(filename=self.outdir.path_in("POSCAR"))
# Write yaml file with displacements.
supercell = phonon.get_supercell()
displacements = phonon.get_displacements()
#directions = phonon.get_displacement_directions()
file_IO.write_disp_yaml(
displacements,
supercell, # directions=directions,
filename=self.outdir.path_in('disp.yaml'))
# Extract forces from the main Abinit output files.
forces_filenames = [
task.output_file.path for task in self.phonopy_tasks
]
num_atoms = supercell.get_number_of_atoms()
force_sets = parse_set_of_forces(num_atoms, forces_filenames)
# Write FORCE_SETS file.
displacements = file_IO.parse_disp_yaml(
filename=self.outdir.path_in('disp.yaml'))
num_atoms = displacements['natom']
for forces, disp in zip(force_sets, displacements['first_atoms']):
disp['forces'] = forces
file_IO.write_FORCE_SETS(displacements,
filename=self.outdir.path_in('FORCE_SETS'))
# Write README and configuration files.
examples_url = "http://atztogo.github.io/phonopy/examples.html"
doctags_url = "http://atztogo.github.io/phonopy/setting-tags.html#setting-tags"
kptbounds = np.array([k.frac_coords for k in structure.hsym_kpoints])
path_coords = " ".join(str(rc) for rc in kptbounds.flat)
path_labels = " ".join(k.name for k in structure.hsym_kpoints)
ngqpt = structure.calc_ngkpt(nksmall=30)
with open(self.outdir.path_in("band.conf"), "wt") as fh:
fh.write("#" + doctags_url + "\n")
fh.write("DIM = %d %d %d\n" % tuple(self.scdims))
fh.write("BAND = %s\n" % path_coords)
fh.write("BAND_LABELS = %s\n" % path_labels)
fh.write("BAND_POINTS = 101\n")
fh.write("#BAND_CONNECTION = .TRUE.\n")
with open(self.outdir.path_in("dos.conf"), "wt") as fh:
fh.write("#" + doctags_url + "\n")
fh.write("DIM = %d %d %d\n" % tuple(self.scdims))
fh.write("MP = %d %d %d\n" % tuple(ngqpt))
fh.write("#GAMMA_CENTER = .TRUE.\n")
with open(self.outdir.path_in("band-dos.conf"), "wt") as fh:
fh.write("#" + doctags_url + "\n")
fh.write("DIM = %d %d %d\n" % tuple(self.scdims))
fh.write("BAND = %s\n" % path_coords)
fh.write("BAND_LABELS = %s\n" % path_labels)
fh.write("BAND_POINTS = 101\n")
fh.write("#BAND_CONNECTION = .TRUE.\n")
fh.write("MP = %d %d %d\n" % tuple(ngqpt))
fh.write("#GAMMA_CENTER = .TRUE.\n")
with open(self.outdir.path_in("README.md"), "wt") as fh:
fh.write("To plot bands, use:\n\tphonopy -p band.conf\n\n")
fh.write("To plot phonon dos, use:\n\tphonopy -p dos.conf\n\n")
fh.write(
"To plot bands and dos, use:\n\tphonopy -p band-dos.conf\n\n")
fh.write("See also:\n")
fh.write("\t" + examples_url + "\n")
fh.write("\t" + doctags_url + "\n")
if self.cpdata2dst:
self.outdir.copy_r(self.cpdata2dst)
return super(PhonopyWork, self).on_all_ok()