pyiron.testing.randomatomistic module

class pyiron.testing.randomatomistic.AtomisticExampleJob(project, job_name)[source]

Bases: pyiron.testing.randomatomistic.ExampleJob, pyiron.atomistics.job.interactive.GenericInteractive

ExampleJob generating a list of random numbers to simulate energy fluctuations.

Parameters

  • project (ProjectHDFio) – ProjectHDFio instance which points to the HDF5 file the job is stored in

  • job_name (str) – name of the job, which has to be unique within the project

.. attribute:: job_name

name of the job, which has to be unique within the project

.. attribute:: status
execution status of the job, can be one of the following [initialized, appended, created, submitted, running,

aborted, collect, suspended, refresh, busy, finished]

.. attribute:: job_id

unique id to identify the job in the pyiron database

.. attribute:: parent_id

job id of the predecessor job - the job which was executed before the current one in the current job series

.. attribute:: master_id

job id of the master job - a meta job which groups a series of jobs, which are executed either in parallel or in serial.

.. attribute:: child_ids

list of child job ids - only meta jobs have child jobs - jobs which list the meta job as their master

.. attribute:: project

Project instance the jobs is located in

.. attribute:: project_hdf5

ProjectHDFio instance which points to the HDF5 file the job is stored in

.. attribute:: job_info_str

short string to describe the job by it is job_name and job ID - mainly used for logging

.. attribute:: working_directory

working directory of the job is executed in - outside the HDF5 file

.. attribute:: path

path to the job as a combination of absolute file system path and path within the HDF5 file.

.. attribute:: version

Version of the hamiltonian, which is also the version of the executable unless a custom executable is used.

.. attribute:: executable

Executable used to run the job - usually the path to an external executable.

.. attribute:: library_activated

For job types which offer a Python library pyiron can use the python library instead of an external executable.

.. attribute:: server

Server object to handle the execution environment for the job.

.. attribute:: queue_id

the ID returned from the queuing system - it is most likely not the same as the job ID.

.. attribute:: logger

logger object to monitor the external execution and internal pyiron warnings.

.. attribute:: restart_file_list

list of files which are used to restart the calculation from these files.

.. attribute:: job_type
Job type object with all the available job types: [‘ExampleJob’, ‘SerialMaster’, ‘ParallelMaster’, ‘ScriptJob’,

‘ListMaster’]

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_structure(iteration_step=- 1, wrap_atoms=True)[source]

Gets the structure from a given iteration step of the simulation (MD/ionic relaxation). For static calculations there is only one ionic iteration step :param iteration_step: Step for which the structure is requested :type iteration_step: int

Returns

atomistics.structure.atoms.Atoms object

run_if_interactive()[source]

Run the job as Python library and store the result in the HDF5 File.

Returns

job ID

Return type

int

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.

property structure

Returns:

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

class pyiron.testing.randomatomistic.ExampleInput(input_file_name=None)[source]

Bases: pyiron.base.generic.parameters.GenericParameters

Input class for the ExampleJob based on the GenericParameters class.

Parameters

input_file_name (str) – Name of the input file - optional

load_default()[source]

Loading the default settings for the input file.

class pyiron.testing.randomatomistic.ExampleJob(project, job_name)[source]

Bases: pyiron.base.job.generic.GenericJob

ExampleJob generating a list of random numbers to simulate energy fluctuations.

Parameters

  • project (ProjectHDFio) – ProjectHDFio instance which points to the HDF5 file the job is stored in

  • job_name (str) – name of the job, which has to be unique within the project

.. attribute:: job_name

name of the job, which has to be unique within the project

.. attribute:: status
execution status of the job, can be one of the following [initialized, appended, created, submitted, running,

aborted, collect, suspended, refresh, busy, finished]

.. attribute:: job_id

unique id to identify the job in the pyiron database

.. attribute:: parent_id

job id of the predecessor job - the job which was executed before the current one in the current job series

.. attribute:: master_id

job id of the master job - a meta job which groups a series of jobs, which are executed either in parallel or in serial.

.. attribute:: child_ids

list of child job ids - only meta jobs have child jobs - jobs which list the meta job as their master

.. attribute:: project

Project instance the jobs is located in

.. attribute:: project_hdf5

ProjectHDFio instance which points to the HDF5 file the job is stored in

.. attribute:: job_info_str

short string to describe the job by it is job_name and job ID - mainly used for logging

.. attribute:: working_directory

working directory of the job is executed in - outside the HDF5 file

.. attribute:: path

path to the job as a combination of absolute file system path and path within the HDF5 file.

.. attribute:: version

Version of the hamiltonian, which is also the version of the executable unless a custom executable is used.

.. attribute:: executable

Executable used to run the job - usually the path to an external executable.

.. attribute:: library_activated

For job types which offer a Python library pyiron can use the python library instead of an external executable.

.. attribute:: server

Server object to handle the execution environment for the job.

.. attribute:: queue_id

the ID returned from the queuing system - it is most likely not the same as the job ID.

.. attribute:: logger

logger object to monitor the external execution and internal pyiron warnings.

.. attribute:: restart_file_list

list of files which are used to restart the calculation from these files.

.. attribute:: job_type
Job type object with all the available job types: [‘ExampleJob’, ‘SerialMaster’, ‘ParallelMaster’, ‘ScriptJob’,

‘ListMaster’]

collect_logfiles()[source]

Collect the errors from the info.log file and store them in the HDF5 file

collect_output()[source]

Parse the output files of the example job and store the results in the HDF5 File.

collect_output_log(file_name='output.log')[source]

general purpose routine to extract output from logfile

Parameters

file_name (str) – output.log - optional

collect_warnings()[source]

Collect the warnings if any were written to the info.log file and store them in the HDF5 file

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

interactive_close()[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. After the interactive execution, the job can be closed using the interactive_close function.

run_if_interactive()[source]

Run the job as Python library and store the result in the HDF5 File.

Returns

job ID

Return type

int

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]

Call routines that generate the codespecifc input files