scine_puffin.jobs.turbomole_bond_orders¶
Classes
A job generating Wiberg bond orders and derived data for a single structure. |
- class scine_puffin.jobs.turbomole_bond_orders.TurbomoleBondOrders[source]¶
A job generating Wiberg bond orders and derived data for a single structure.
- Order Name
turbomole_bond_orders
- Optional Settings
Optional settings are read from the
settings
field, which is part of anyCalculation
stored in a SCINE Database. Possible settings for this job are:All settings that are recognized by the turbomole_single_point job.
- Required Packages
SCINE: Database (present by default)
SCINE: Utils (present by default)
The Turbomole program has to be available
- Generated Data
If successful the following data will be generated and added to the database:
- Properties
The
bond_orders
and theelectronic_energy
associated with the structure.
- archive(archive: str) None ¶
Archives all files existent in the job’s directory into tarball named with the job’s ID. The tarball is then moved to the given destination.
- Parameters:
- archivestr
The path to move the resulting tarball to.
- capture_raw_output() Tuple[str, str] ¶
Tries to capture the raw output of the calculation context and save it in the raw_output field of the configured calculation. This should never throw.
Notes
Requires run configuration
- classmethod check_configuration(instance: T) typing_extensions.TypeGuard[T] ¶
- static check_duplicate_property(structure: db.Structure, properties: db.Collection, property_name: str, model: db.Model) db.ID | bool ¶
Checks for a property that is an exact match for the one queried here. Exact match meaning that key and model both are matches.
- Parameters:
- propertiesdb.Collection (Scine::Database::Collection)
The collection housing all properties.
- property_namestr
The name (key) of the queried property, e.g.
electronic_energy
.- modeldb.Model (Scine::Database::Model)
The model used in the calculation that resulted in this property.
- structuredb.Structure (Scine::Database::Structure)
The structure to be checked in. The structure has to be linked to its collection.
- Returns:
- IDdb.ID (Scine::Database::ID)
Returns
False
if there is no existing property like the one queried or the ID of the first duplicate.
- config: Configuration¶
- configure_run(manager: db.Manager, calculation: db.Calculation, config: Configuration) None ¶
Configures a job for a given Calculation to do tasks in the run function
- Parameters:
- managerdb.Manager (Scine::Database::Manager)
The manager of the database holding all collections
- calculationdb.Calculation (Scine::Database::Calculation)
The calculation to be performed
- configConfiguration
The configuration of the Puffin doing the job
- failed_file() str ¶
Returns the path to the file indicating a failed calculation, None if job has not been prepared
- get_bond_orders(natoms: int) ndarray [source]¶
Read Wiberg bond orders from file generated by the ‘proper’ postprocessing tool
- postprocess_calculation_context() bool ¶
Postprocesses a calculation context, pushing all errors and comments.
- Returns:
- True if the job succeeded, False otherwise.
- prepare(job_dir: str, id: db.ID) None ¶
Prepares the actual job. This function has to be implemented by any job that shall be added to Puffins job portfolio.
- Parameters:
- job_dirstr
The path to the directory in which all jobs are executed.
- iddb.ID (Scine::Database::ID)
The calculation that triggered the execution of this job.
- prepare_calculation(structure: db.Structure, calculation_settings: utils.ValueCollection, model: db.Model, job: db.Job) None ¶
- run(manager: db.Manager, calculation: db.Calculation, config: Configuration) bool [source]¶
See Job.run()
- store_property(properties: db.Collection, property_name: str, property_type: str, data: Any, model: db.Model, calculation: db.Calculation, structure: db.Structure, replace: bool = True) db.Property | None ¶
Adds a single property into the database, connecting it with a given structure and calculation (it’s results section) and also
- Parameters:
- propertiesdb.Collection (Scine::Database::Collection)
The collection housing all properties.
- property_namestr
The name (key) of the new property, e.g.
electronic_energy
.- property_typestr
The type of property to be added, e.g.
NumberProperty
.- dataAny (According to ‘property_type’)
The data to be stored in the property, the type of this object is dependent on the type of property requested. A
NumberProperty
will require afloat
, aVectorProperty
will require aList[float]
, etc.- modeldb.Model (Scine::Database::Model)
The model used in the calculation that resulted in this property.
- calculationdb.Calculation (Scine::Database::Calculation)
The calculation that resulted in this property. The calculation has to be linked to its collection.
- structuredb.Structure (Scine::Database::Structure)
The structure for which the property is to be added. The properties field of the structure will receive an additional entry, or have an entry replaced, based on the options given to this function. The structure has to be linked to its collection.
- replacebool
If true, replaces an existing property (identical name and model) with the new one. This option is true by default. If false, doesnothing in the previous case, and returns
None
- Returns:
- propertyDerived of db.Property (Scine::Database::Property)
The property, a derived class of db.Property, linked to the properties’ collection, or
None
if no property was generated due to duplication.
- success_file() str ¶
Returns the path to the file indicating a successful calculation, empty string if job has not been prepared