pyiron.thermodynamics.sxphonons module

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

Bases: pyiron.base.job.generic.GenericJob

child_id_lst
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]
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(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
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
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]