pyiron_contrib.atomistics.interactive.mixer module

class pyiron_contrib.atomistics.interactive.mixer.Input(input_file_name=None, table_name='input')[source]

Bases: GenericParameters

class to control the generic input for a Mixer calculation.

Parameters

input_file_name (str) – name of the input file
table_name (str) – name of the GenericParameters table

load_default()[source]: Loads the default file content

class pyiron_contrib.atomistics.interactive.mixer.Mixer(project, job_name)[source]

Bases: InteractiveWrapper

Mixing forces of two atomistic interpreters, e.g. a LAMMPS or VASP job

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

input

handles the input

Type: pyiron_base.GenericParameters

ref_job_0

First atomistic interpreter

Type: pyiron.atomistics.job.atomistic.AtomisticGenericJob

ref_job_1

Second atomistic interpreter

Type: pyiron.atomistics.job.atomistic.AtomisticGenericJob

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

Restore the Mixer from an HDF5 file

Parameters

hdf (ProjectHDFio) – HDF5 group object - optional
group_name (str) – HDF5 subgroup name - optional

interactive_close()[source]: Internal helper function to close the interactive interface.

interactive_initialize_interface()[source]: Internal helper function to initialize the interactive interface

interactive_store_in_cache(key, value)[source]

Helper function to store the output in the cache - storing the same information in both reference jobs

Parameters

key (str) – Key in cache
value (list/float/int) – value to store

property ref_job

Compatibility function - it is recommended to use ref_job_0 instead

Returns: Reference Job
Return type: pyiron.atomistics.job.atomistic.AtomisticGenericJob

property ref_job_0

First Quantum engine to mix forces

Returns: Reference Job
Return type: pyiron.atomistics.job.atomistic.AtomisticGenericJob

property ref_job_1

Second Quantum engine to mix forces

Returns: Reference Job
Return type: pyiron.atomistics.job.atomistic.AtomisticGenericJob

run_if_interactive()[source]: The interactive run function calls run on both quantum engines - both interactive and non-interactive jobs are supported.

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

Atomistic Structure - returns structure of first reference job

Returns: Atomistic crystal structure
Return type: pyiron.atomistics.structure.atoms.Atoms

write_input()[source]: No input is written for the Mixer class

class pyiron_contrib.atomistics.interactive.mixer.MixingOutput(job)[source]

Bases: ReferenceJobOutput

property energy_pot

Combined potential energy

Returns: potential energy
Return type: list

property energy_tot

Combined total energy

Returns: total energy
Return type: list

property forces

Combined forces

Returns: forces
Return type: list

property pressures

Combined pressure

Returns: pressure
Return type: list

property temperature

Combined temperature

Returns: temperature
Return type: list