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:

property dos_energies

Returns:

property dos_total

Returns:

property dynamical_matrix

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]
property 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

validate_ready_to_run()[source]

Returns:

write_phonopy_force_constants(file_name='FORCE_CONSTANTS', cwd=None)[source]
Parameters

  • file_name –

  • cwd –

Returns:

class pyiron.atomistics.master.phonopy.PhonopyJobGenerator(master)[source]

Bases: pyiron_base.master.parallel.JobGenerator

static job_name(parameter)[source]

Return new job name from parameter object. The next child job created will have this name. Subclasses may override this to give custom job names.

Parameters

parameter (type) – current parameter object drawn from :attribute:`.parameter_list`.

Returns

job name for the next child job

Return type

str

modify_job(job, parameter)[source]

Modify next job with the parameter object. job is already the newly created job object cloned from the template job, so this function has to return the same instance, but may (and should) modify it.

Parameters
Returns

must be the given job

Return type

GenericJob

property parameter_list

Returns: (list)

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 –