pyiron.atomistics.master.phonopy module

class pyiron.atomistics.master.phonopy.PhonopyJob(project, job_name)[source]

Bases: pyiron.atomistics.master.parallel.AtomisticParallelMaster

Parameters:
  • project
  • job_name
collect_output()[source]

Returns:

dos_energies

type: Returns

dos_total

type: Returns

dynamical_matrix

type: Returns

dynamical_matrix_at_q(q)[source]
Parameters:q

Returns:

from_hdf(hdf=None, group_name=None)[source]

Restore the PhonopyJob from an HDF5 file

Parameters:
  • hdf (ProjectHDFio) – HDF5 group object - optional
  • group_name (str) – HDF5 subgroup name - optional
get_hesse_matrix()[source]

Returns:

get_thermal_properties(t_min=1, t_max=1500, t_step=50, temperatures=None)[source]
Parameters:
  • t_min
  • t_max
  • t_step
  • temperatures

Returns:

list_structures()[source]
phonopy_pickling_disabled
plot_dos(ax=None, *args, **qwargs)[source]
Parameters:
  • *args
  • ax
  • **qwargs

Returns:

run_if_interactive()[source]

For jobs which executables are available as Python library, those can also be executed with a library call instead of calling an external executable. This is usually faster than a single core python job.

run_static()[source]

The run_static function is executed within the GenericJob class and depending on the run_mode of the Parallelmaster and its child jobs a more specific run function is selected.

to_hdf(hdf=None, group_name=None)[source]

Store the PhonopyJob in an HDF5 file

Parameters:
  • hdf (ProjectHDFio) – HDF5 group object - optional
  • group_name (str) – HDF5 subgroup name - optional
write_phonopy_force_constants(file_name='FORCE_CONSTANTS', cwd=None)[source]
Parameters:
  • file_name
  • cwd

Returns:

class pyiron.atomistics.master.phonopy.PhonopyJobGenerator(job, no_job_checks=False)[source]

Bases: pyiron.base.master.parallel.JobGenerator

static job_name(parameter)[source]
modify_job(job, parameter)[source]
parameter_list

(list)

Type:Returns
pyiron.atomistics.master.phonopy.atoms_to_phonopy(atom)[source]

Convert ASE-like Atoms to Phonopy Atoms :param atom: ASE-like Atoms

Returns:Phonopy Atoms
pyiron.atomistics.master.phonopy.phonopy_to_atoms(ph_atoms)[source]

Convert Phonopy Atoms to ASE-like Atoms :param ph_atoms: Phonopy Atoms object

Returns: ASE-like Atoms object

class pyiron.atomistics.master.phonopy.thermal(temps, fe, entropy, cv)[source]

Bases: object

Parameters:
  • temps
  • fe
  • entropy
  • cv