scine_chemoton.gears.compound¶
Classes
This Gear updates all relevant Structures stored in the database with bond orders and graph representations. |
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This Gear updates all relevant Structures stored in the database with frequencies, bond orders and graph representations. |
- class scine_chemoton.gears.compound.BasicAggregateHousekeeping[source]¶
This Gear updates all relevant Structures stored in the database with bond orders and graph representations. This data is then used to sort each Structure into existing Compounds/Flasks or to create a new Compound/Flask if no appropriate one exists.
Notes
Checks for all ‘user_optimized’, ‘minimum_optimized’, and ‘complex_optimized’ Structures that do not have an Aggregate assigned. The Gear then generates bond orders and molecular graphs (‘masm_cbor_graph’, and ‘masm_decision_list’) if they are not yet present. Using the molecular graphs the Structures are then sorted into Compounds/Flasks.
- Attributes:
- optionsBasicAggregateHousekeeping.Options
The options for the BasicAggregateHousekeeping Gear.
- class Options[source]¶
The options for the BasicAggregateHousekeeping Gear.
-
aggregate_enabling:
AggregateEnabling¶ - AggregateEnabling
If a structure is added to an aggregate, the analysis of the corresponding aggregate is enabled according to this policy.
-
bond_order_job:
Job¶ - db.Job (Scine::Database::Calculation::Job)
The Job used for the bond order calculations. The default is: the ‘scine_bond_orders’ order on a single core.
-
bond_order_settings:
ValueCollection¶ - utils.ValueCollection
Additional settings passed to the bond order calculations. Empty by default.
-
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.
-
exclude_misguided_conformer_optimizations:
bool¶ - bool
If true, no additional aggregate is created if the structure was generated only by geometry optimization. The default policy does nothing.
-
graph_job:
Job¶ - db.Job (Scine::Database::Calculation::Job)
The Job used for the graph calculations. The default is: the ‘graph’ order on a single core.
-
graph_settings:
ValueCollection¶ - Dict[str, str]
Additional settings passed to the graph calculations. Empty by default.
-
model:
Model¶ - db.Model
The model the Gear is working with.
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aggregate_enabling:
- class scine_chemoton.gears.compound.ThermoAggregateHousekeeping[source]¶
This Gear updates all relevant Structures stored in the database with frequencies, bond orders and graph representations. This data is then used to sort each Structure into existing Compounds/Flasks or to create a new Compound/Flask if no appropriate one exists. To be sorted into an Aggregate, a Structure must have no imaginary frequencies above the given absolute frequency threshold. Otherwise, a validation job is setup or, if this has been attempted already, the exploration and analysis of this Structure are disabled.
Notes
Checks for all ‘user_optimized’, ‘minimum_optimized’, and ‘complex_optimized’ Structures that do not have an Aggregate assigned and are enabled for analysis. The Gear then generates bond orders and molecular graphs (‘masm_cbor_graph’, and ‘masm_decision_list’) if they are not yet present. Using the molecular graphs, the Structures are then sorted into Compounds/Flasks.
- Attributes:
- optionsThermoAggregateHousekeeping.Options
The options for the ThermoAggregateHousekeeping Gear.
- class Options[source]¶
The options for the ThermoAggregateHouseKeeping Gear.
-
aggregate_enabling:
AggregateEnabling¶ - AggregateEnabling
If a structure is added to an aggregate, the analysis of the corresponding aggregate is enabled according to this policy.
-
bond_order_job:
Job¶ - db.Job (Scine::Database::Calculation::Job)
The Job used for the bond order calculations. The default is: the ‘scine_bond_orders’ order on a single core.
-
bond_order_settings:
ValueCollection¶ - utils.ValueCollection
Additional settings passed to the bond order calculations. Empty by default.
-
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.
-
exclude_misguided_conformer_optimizations:
bool¶ - bool
If true, no additional aggregate is created if the structure was generated only by geometry optimization. The default policy does nothing.
-
graph_job:
Job¶ - db.Job (Scine::Database::Calculation::Job)
The Job used for the graph calculations. The default is: the ‘graph’ order on a single core.
-
graph_settings:
ValueCollection¶ - Dict[str, str]
Additional settings passed to the graph calculations. Empty by default.
-
model:
Model¶ - db.Model
The model the Gear is working with.
-
structure_model:
Model¶ - Optional[db.Model]
Validation calculations are only started for structures with the given model.
- unset_collections()¶
Duplicate name to HoldCollections method to be triggered in pickling process, so infinite _parent loops are avoided.
- Return type:
-
validation_job:
Job¶ - db.Job
The Job used for the geometry validation calculations. The default is: the ‘scine_geometry_validation’ order on a single core.
-
validation_settings:
ValueCollection¶ - utils.ValueCollection
Additional settings passed to the geometry validation order calculation. Empty by default.
-
aggregate_enabling: