pyiron_base.jobs.flex.executablecontainer module

class pyiron_base.jobs.flex.executablecontainer.ExecutableContainerJob(project, job_name)

Bases: TemplateJob

The ExecutableContainerJob is designed to wrap any kind of external executable into a pyiron job object by providing a write_input(input_dict, working_directory) and a collect_output(working_directory) function.

Example:

>>> import os
>>>
>>> def write_input(input_dict, working_directory="."):
>>>     with open(os.path.join(working_directory, "input_file"), "w") as f:
>>>         f.write(str(input_dict["energy"]))
>>>
>>>
>>> def collect_output(working_directory="."):
>>>     with open(os.path.join(working_directory, "output_file"), "r") as f:
>>>         return {"energy": float(f.readline())}
>>>
>>>
>>> from pyiron_base import Project
>>> pr = Project("test")
>>> pr.create_job_class(
>>>     class_name="CatJob",
>>>     write_input_funct=write_input,
>>>     collect_output_funct=collect_output,
>>>     default_input_dict={"energy": 1.0},
>>>     executable_str="cat input_file > output_file",
>>> )
>>> job = pr.create.job.CatJob(job_name="job_test")
>>> job.input["energy"] = 2.0
>>> job.run()
>>> print(job.output)
DataContainer({'energy': 2.0})
collect_output()

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_dict(job_dict)
run_static()

The run static function is called by run to execute the simulation.

set_job_type(executable_str, write_input_funct=None, collect_output_funct=None, default_input_dict=None)

Set the pre-defined write_input() and collect_output() function plus a dictionary of default inputs and an executable string.

Parameters:

  • executable_str (str) – Call to an external executable

  • write_input_funct (callable) – The write input function write_input(input_dict, working_directory)

  • collect_output_funct (callable) – The collect output function collect_output(working_directory)

  • default_input_dict (dict/None) – Default input for the newly created job class

Returns:

Function which requires a project and a job_name as input and returns a job object

Return type:

callable

to_dict()
write_input()

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