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]
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)[source]

Bases: pyiron.base.master.parallel.JobGenerator

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

Returns: (list)

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

Bases: pyiron.atomistics.master.phonopy.PhonopyJob

Parameters
  • project

  • job_name

class pyiron.atomistics.master.phonopy.PhonopyMaster2(project, job_name)[source]

Bases: pyiron.atomistics.master.phonopy.PhonopyJob

Parameters
  • project

  • job_name

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