alframework.tools.molecules_class module

class MoleculesObject(atoms, moleculeid)

Bases: object

Class to create molecule objects

append_atoms(new_atoms)

Append atoms to the existing atomic system.

Args:

new_atoms (ase.Atoms): ase.Atoms object to append to the current system.

check_convergence()

True if converged, False otherwise, and None if no QM calculation was performed yet

check_stored_results()

Checks if there is any QM result stored

get_atoms()

Get the ase.Atoms object

get_metadata()

Get metadata

get_moleculeid()

Get the moleculeid of the system

get_results()

Get the QM results

get_system_signature()

Returns the system signature as a string.

Returns:

(str): String representing the system cell and the atoms types and coordinates.

#TODO: Compute system moments of inertia and rotate the system so that the highest order moment points along

the x-axis, midde moment point along y-axis and last moment points along z-axis.

set_converged_flag(convergence_flag)

Set the convergence flag.

Args:

convergence_flag (bool): Bool indicating whether the calculation converged or not.

store_results(results, replace=True)

Stores the QM results

Args:

results (dict): Dictionary containing the results of the QM calculations that we wish to store replace (bool): If True completely update self.qm_results including values of common keys, but if False only

the keys in ‘results’ that doesn’t exist in self.qm_results are added.

update_atoms(new_atoms)

Update the atoms attribute

This is necessary because when running MLMD we may find a new configuration of the system that the NNs disagree. Thus, we want to store this configuration to run QM. When we update to None it means that there was no configuration during the MLMD in which the ensemble of NNs disagreed.

Args:

new_atoms (ase.Atoms): Atoms object representing the new configuration or system.

update_metadata(new_metadata, replace=True)

Updates the object metadata

Args:

new_metadata (dict): New metadata to be added. replace (bool): If True completely update self.metadata including values of common keys, but if False only

the keys in ‘new_metadata’ that doesn’t exist in self.metadata are added.

compare_chemical_composition(system1, system2)

Check if two MoleculesObject instances have the same chemical composition

Args:

system1 (MoleculesObject): First object to be compared. system2 (MoleculesObject): Second object to be compared.

Returns:

(bool): True if the two systems have the same chemical composition.