scine_chemoton.gears.network_refinement.reaction_based_refinement

Classes

ReactionBasedRefinement()

This class allows the refinement of elementary steps (or the associated energies and structures).

class scine_chemoton.gears.network_refinement.reaction_based_refinement.ReactionBasedRefinement[source]

This class allows the refinement of elementary steps (or the associated energies and structures). The elementary steps are selected based on their reaction. For instance one can calculate the single point energies of the 10 lowest transition states and structures on the lhs/rhs of the reaction with a different electronic structure method.

The reactions and steps may be filtered through elementary step and reaction filters.

class Options

The options for the NetworkRefinement Gear.

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: 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: 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: 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: 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: 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: 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: ValueCollection
utils.ValueCollection

Additional settings for optimizing all minima. Chemoton’s default optimization settings by default.

post_refine_model: 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: 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: ValueCollection
utils.ValueCollection

Additional settings for single ended reaction search. Chemoton’s default NT job settings by default.

single_ended_step_refinement_job: 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: 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: 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: 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: 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: ValueCollection
utils.ValueCollection

Additional settings for optimizing all transition states. Chemoton’s default optimization settings by default without the BFGS settings.

unset_collections()

Duplicate name to HoldCollections method to be triggered in pickling process, so infinite _parent loops are avoided.

Return type:

None

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.

initialize_collections(manager)
Return type:

None

model_combination: Optional[ModelCombination]
Optional[ModelCombination]

The electronic structure model combination combining the pre-refine model and the hessian model.

property name: str
options: Options
static possible_attributes()
Return type:

List[str]

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.

stop()
Return type:

None

property stop_at_next_break_point: bool
unset_collections()
Return type:

None