pyiron.thermodynamics.sxphonons module

class pyiron.thermodynamics.sxphonons.SxDynMat(project, job_name)[source]

Bases: pyiron_base.job.generic.GenericJob

property child_id_lst
property child_lst
collect_logfiles()[source]

Collect the log files of the external executable and store the information in the HDF5 file. This method has to be implemented in the individual hamiltonians.

collect_output()[source]

Collect the output files of the external executable and store the information in the HDF5 file. This method has to be implemented in the individual hamiltonians.

get_hesse_matrix()[source]
static matrix_to_str(matrix)[source]

Function to convert an numpy matrix to an Sphinx input compatible matrix.

Parameters

matrix (numpy.d2type) – the matrix to be converted

Returns

the matrix representation in the Sphinx input.

Return type

str

static vector_to_str(vector)[source]

Function to convert an numpy vector to an Sphinx input compatible vector.

Parameters

vector (numpy.d2type) – the vector to be converted

Returns

the vector representation in the Sphinx input.

Return type

str

write_input()[source]

Write the input files for the external executable. This method has to be implemented in the individual hamiltonians.

write_sxdynmat(file_name='sxdynmat.sx', cwd=None)[source]
class pyiron.thermodynamics.sxphonons.SxHarmPotTst(project, job_name)[source]

Bases: pyiron.atomistics.job.atomistic.AtomisticGenericJob

collect_output()[source]

Collect the output files of the external executable and store the information in the HDF5 file. This method has to be implemented in the individual hamiltonians.

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

Restore the ExampleJob object in the HDF5 File

Parameters

  • hdf (ProjectHDFio) – HDF5 group object - optional

  • group_name (str) – HDF5 subgroup name - optional

get_hesse_matrix()[source]
property md_job
set_input_to_read_only()[source]

This function enforces read-only mode for the input classes, but it has to be implement in the individual classes.

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

Store the ExampleJob object in the HDF5 File

Parameters

  • hdf (ProjectHDFio) – HDF5 group object - optional

  • group_name (str) – HDF5 subgroup name - optional

validate_ready_to_run()[source]

Returns:

write_harmpot(cwd, file_name='harmpot.sx')[source]
write_input()[source]

Write the input files for the external executable. This method has to be implemented in the individual hamiltonians.

write_structure(cwd, file_name='structure_wrapper.sx')[source]
class pyiron.thermodynamics.sxphonons.SxPhonons(project, job_name)[source]

Bases: pyiron.atomistics.master.parallel.AtomisticParallelMaster

collect_output()[source]

Returns:

get_hesse_matrix()[source]
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.

class pyiron.thermodynamics.sxphonons.SxPhononsJobGenerator(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)

class pyiron.thermodynamics.sxphonons.SxUniqDispl(project, job_name)[source]

Bases: pyiron.atomistics.job.atomistic.AtomisticGenericJob

collect_output()[source]

Collect the output files of the external executable and store the information in the HDF5 file. This method has to be implemented in the individual hamiltonians.

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

Restore the ExampleJob object in the HDF5 File

Parameters

  • hdf (ProjectHDFio) – HDF5 group object - optional

  • group_name (str) – HDF5 subgroup name - optional

property id_pyi_to_spx
property id_spx_to_pyi
list_structures()[source]
set_input_to_read_only()[source]

This function enforces read-only mode for the input classes, but it has to be implement in the individual classes.

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

Store the ExampleJob object in the HDF5 File

Parameters

  • hdf (ProjectHDFio) – HDF5 group object - optional

  • group_name (str) – HDF5 subgroup name - optional

write_input()[source]

Write the input files for the external executable. This method has to be implemented in the individual hamiltonians.

write_structure(cwd, file_name='structure_wrapper.sx')[source]