scine_chemoton.gears.network_refinement.calculation_based_refinement¶
Classes
This gear allows the refinement of results from previous calculations that produced elementary steps. |
- class scine_chemoton.gears.network_refinement.calculation_based_refinement.CalculationBasedRefinement[source]¶
This gear allows the refinement of results from previous calculations that produced elementary steps. For instance, one could recalculate the single point energies for all structures in the elementary step or rerun the transition state optimization with a different electronic structure model.
- class Options[source]¶
See NetworkRefinement for options.
- aggregate_energy_window¶
- float
Energy window for the aggregate selection for single point refinement.
- caching_file_name¶
- str
The name of the file used to save the already considered calculation ids.
- calculation_model: db.Model¶
- db.Model
The model used for the loop over previous calculations. If just a place-holder is provided, the pre_refine_model is used.
- cycle_time: int¶
- int
The minimum number of seconds between two cycles of the Gear. Cycles are finished independently of this option, hence if a cycle takes longer than the cycle_time will effectively lead to longer cycle times and not cause multiple cycles of the same Gear.
- double_ended_job: db.Job¶
- db.Job (Scine::Database::Calculation::Job)
The Job used for searching for a transition state between two compounds. The default is: the ‘scine_react_double_ended’ order on a single core.
- double_ended_job_settings: utils.ValueCollection¶
- utils.ValueCollection
Additional settings for searching for a transition state between two compounds. Chemoton’s default NT settings without the NT and RCOpt parts by default.
- elementary_step_index_file_name¶
- str
The file name for the elementary step index.
- hessian_model: db.Model¶
- db.Model
A second electronic structure model along side the pre_refine_model. With this model, the free energy corrections are evaluated. If none is given, the pre_refine_model is used.
- model: db.Model¶
- db.Model
The model the Gear is working with.
- only_electronic_energies: bool¶
- bool
If true, free energies are approximated only by their electronic energy contribution.
- opt_job: db.Job¶
- db.Job (Scine::Database::Calculation::Job)
The Job used for optimizing all minima. The default is: the ‘scine_geometry_optimization’ order on a single core.
- opt_job_settings: utils.ValueCollection¶
- utils.ValueCollection
Additional settings for optimizing all minima. Chemoton’s default optimization settings by default.
- post_refine_model: db.Model¶
- db.Model (Scine::Database::Model)
The Model used for the refinement The default is: DFT
- reference_state: ReferenceState¶
- Optional[ReferenceState]
The reference state to calculate free energies with. If none is given, the reference state is deduced from the pre_refine model.
- refine_n_per_reaction¶
- int
The maximum number of elementary steps to refine for a given reaction.
- refinements: Dict[str, bool]¶
- Dict[str, bool]
A dictionary specifying the wanted refinement(s) ‘refine_single_points’: Calculate energies of all minima and transition states if they belong to a calculation that produced an elementary step with a barrier less than ‘max_barrier’. The job for the calculations can be selected with ‘options.sp_job’ and its settings with ‘options.sp_job_settings’. ‘refine_optimizations’: Perform optimizations of minima and transition states. The same maximum barrier condition applies as for ‘refine_single_points’. The job for the minima optimizations can be selected with ‘options.opt_job’ and its settings with ‘options.opt_job_settings’. The job for the transition state optimizations can be selected with ‘options.tsopt_job’ and its settings with ‘options.tsopt_job_settings’. ‘double_ended_refinement’: Perform double ended TS searches for compounds that are connected. The ‘max_barrier’ conditions applies as above. The job for this search can be selected with ‘options.double_ended_job’ and its settings with ‘options.double_ended_job_settings’. ‘double_ended_new_connections’: Perform double ended TS searches for compounds that might be connected. The job for this search can be selected with ‘options.double_ended_job’ and its settings with ‘options.double_ended_job_settings’. ‘refine_single_ended_search’: Perform single ended searches again with new model if they were already successful with another model. The ‘max_barrier’ conditions applies as above. The job for this search can be selected with ‘options.single_ended_job’ and its settings with ‘options.single_ended_job_settings’. ‘refine_structures_and_irc’: Reoptimize an elementary step that was found previously. The previous transition state is used as an initial guess. A complete IRC is performed. The ‘max_barrier’ conditions applies as above. The job for this search can be selected with ‘options.single_ended_step_refinement_job’ and its settings with ‘options.single_ended_step_refinement_settings’.
- single_ended_job: db.Job¶
- db.Job (Scine::Database::Calculation::Job)
The Job used for searching for redoing previously successful single ended searches. The default is: the ‘scine_react_complex_nt’ order on a single core. This job implies the approximation that the structures of the old model can be used for the single ended calculation with the new model.
- single_ended_job_settings: utils.ValueCollection¶
- utils.ValueCollection
Additional settings for single ended reaction search. Chemoton’s default NT job settings by default.
- single_ended_step_refinement_job: db.Job¶
- db.Job (Scine::Database::Calculation::Job)
The Job used for searching for refining previously successful single ended searches. The default is: the ‘scine_step_refinement’ order.
- single_ended_step_refinement_settings: utils.ValueCollection¶
- utils.ValueCollection
Additional settings for refining single ended reaction searches. Chemoton’s default NT settings without the NT and RCOpt part by default.
- sp_job: db.Job¶
- db.Job (Scine::Database::Calculation::Job)
The Job used for calculating new single point energies. The default is: the ‘scine_single_point’ order on a single core.
- sp_job_settings: utils.ValueCollection¶
- utils.ValueCollection
Additional settings for calculating new single point energies. Empty by default.
- transition_state_energy_window¶
- float
Energy window for the elementary step selection in kJ/mol for reaction based refinement (see reaction_based_loop).
- tsopt_job: db.Job¶
- db.Job (Scine::Database::Calculation::Job)
The Job used for optimizing all transition states. The default is: the ‘scine_ts_optimization’ order on a single core.
- tsopt_job_settings: utils.ValueCollection¶
- utils.ValueCollection
Additional settings for optimizing all transition states. Chemoton’s default optimization settings by default without the BFGS settings.
- elementary_step_filter: ElementaryStepFilter¶
- ElementaryStepFilter
The filter for the elementary step selection for refinement. By default max barrier of 262.5 kJ/mol and exclude all barrier-less.
- model_combination: Optional[ModelCombination]¶
- Optional[ModelCombination]
The electronic structure model combination combining the pre-refine model and the hessian model.
- reaction_disabling: ReactionDisabling¶
- ReactionDisabling
Reaction post-refinement-processing to disable them until the refinement is done.
- reaction_enabling: ReactionEnabling¶
- ReactionEnabling
If given, reactions/elementary steps already found with the refined model are enabled and not new calculations are created. This fakes the refinement and is useful for rapid testing of meta algorithms in the refinement.
- reaction_filter: ReactionFilter¶
- ReactionFilter
The filter for the reaction selection for refinement. By default max barrier of 262.5 kJ/mol, exclude all barrier-less, and only refine after all exploration calculations are done.
- reaction_validation: ReactionFilter¶
- Optional[ReactionFilter]
If reactions are enabled instead of refined (see option reaction_enabling), and this filter returns true, no further refinement calculations are done for the given reaction.
- result_enabling: EnableCalculationResults¶
- EnableCalculationResults
If this calculation result enabling policy is given, the result of an already existing calculation is enabled again (if disabled previously).
- step_disabling: StepDisabling¶
- StepDisabling
Elementary step post-refinement-processing to disable them until the refinement is done.