scine_puffin.jobs.templates.kinetic_modeling_jobs¶

Classes

KineticModelingJob()

Abstract base class for the RMS kinetic modeling and KiNetX kinetic modeling jobs.

class scine_puffin.jobs.templates.kinetic_modeling_jobs.KineticModelingJob[source]¶

Abstract base class for the RMS kinetic modeling and KiNetX kinetic modeling jobs.

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.

clear() → None¶: Clears the directory in which the job was run.

complete_job() → None¶: Saves the executing Puffin, changes status to db.Status.COMPLETE.

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

fail_job() → None¶: Saves the executing Puffin, changes status to db.Status.FAILED.

failed_file() → str¶: Returns the path to the file indicating a failed calculation, None if job has not been prepared

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.

abstract static required_programs() → List[str]¶

This function has to be implemented by any job that shall be added to Puffins job portfolio.

Returns:

requirementsList[str]: A list of names of programs/packages that are required for the execution of the job.

abstract run(manager: db.Manager, calculation: db.Calculation, config: Configuration) → bool¶

Runs the actual job. This function has to be implemented by any job that shall be added to Puffins job portfolio.

Parameters:

managerdb.Manager (Scine::Database::Manager): The manager/database to work on/with.
calculationdb.Calculation (Scine::Database::Calculation): The calculation that triggered the execution of this job.
configscine_puffin.config.Configuration: The configuration of Puffin.

stderr_path: str = 'stderr'¶

stdout_path: str = 'stdout'¶

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 a float, a VectorProperty will require a List[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

verify_connection() → None¶

Verifies the connection to the database. Returns only if a connection is established, if it is not, the function will attempt to generate a connection every 10 seconds, indefinitely.

Notes

Requires run configuration

work_dir: str¶