Geometry optimization (Geopt)

The Geopt allows to find the relaxed structure that minimizes the forces of a given input system.

class mybigdft.workflows.geopt.Geopt(base_job, method='SQNM', forcemax=1e-06, frac_fluct=0.0, betax=1, ncount_cluster_x=200, **kwargs)[source]

Bases: mybigdft.workflows.workflow.AbstractWorkflow

This class allows to relax the input geometry of a given system in order to find the structure that minimizes the forces. It is meant to ease the creation of this type of calculation by automatically setting the main input parameters under the “geopt” key.

The base job has a given set of input parameters, and default values for the main parameters of the “geopt” key are automatically updated. The extra arguments of the “geopt” input parameters key can also be passed as keyword arguments.

Parameters

  • base_job (Job) – Base job for which a geometry optimization procedure is desired.

  • method (str) – Name of the minimization method.

  • forcemax (float) – Convergence criterion.

  • frac_fluct (float) – Convergence criterion.

  • betax (float) – Step size.

  • ncount_cluster_x (int) – Maximum number of force evaluations to be used.

  • kwargs – Other valid input parameters under the “geopt” key.

property final_posinp
Returns

Final posinp of the geometry optimization procedure.

Return type

Posinp

post_proc()[source]

Read the final posinp from a file.

property is_completed
Returns

True if all the post-processing attributes are no longer set to their default value.

Return type

bool

property logfiles
Returns

A dictionary of all the logfiles of the workflow, with the name of the associated job as key.

Return type

dict

property queue
Returns

All the jobs of the workflow.

Return type

list

run(nmpi=1, nomp=1, force_run=False, dry_run=False, restart_if_incomplete=False, timeout=None)

Run all the calculations if the post-processing was not already performed.

Warning

If force_run or dry_run is set to True, then any previous value of the post-processing attributes is deleted and set back to their default value, so that the post-processing is not considered as being performed.

Parameters

  • nmpi (int) – Number of MPI tasks.

  • nomp (int) – Number of OpenMP tasks.

  • force_run (bool) – If True, the calculations are run even though a logfile already exists.

  • dry_run (bool) – If True, the input files are written on disk, but the bigdft-tool command is run instead of the bigdft one.

  • restart_if_incomplete (bool) – If True, the job is restarted if the existing logfile is incomplete.

  • timeout (float or int or None) – Number of minutes after which each job must be stopped.

Warns

UserWarning – If the post-processing was already completed.