aiida_aimall.workchains.input

Base input workchain

Module Contents

Classes

BaseInputWorkChain

A workchain to generate and validate inputs.

class aiida_aimall.workchains.input.BaseInputWorkChain(inputs: dict | None = None, logger: logging.Logger | None = None, runner: aiida.engine.runners.Runner | None = None, enable_persistence: bool = True)

Bases: aiida.engine.WorkChain

A workchain to generate and validate inputs.

Provided an .xyz file as SinglefileData, molecule StructureData, or SMILES of the molecule validates that only one is provided. Then, prepares the input into a format for future GaussianCalculations.

structure

StructureData of molecule to run

Type:

aiida.orm.StructureData

smiles

smiles string of molecule

Type:

aiida.orm.Str

xyz_file

file data of an xyz file

Type:

aiida.orm.SinglefileData

Note

This is a base class that is used by other WorkChains

(aiida_aimall.workchains.subparam.SubstituentParameterWorkChain(), and aiida_aimall.workchains.qc_programs.GaussianToAIMWorkChain())

classmethod define(spec)

Define the specification of the process, including its inputs, outputs and known exit codes.

A metadata input namespace is defined, with optional ports that are not stored in the database.

is_xyz_input()

Validates if xyz_file was provided as input

is_smiles_input()

Validates if smiles was provided as input

is_structure_input()

Validates if structure was provided as input

validate_input()

Check that only one of smiles, structure, or xyz_file was input

create_structure_from_xyz()

Convert the xyzfile to StructureData. Calls aiida_aimall.workchains.calcfunctions.xyzfile_to_StructureData()

structure_in_context()

Store the input structure in context, to make consistent with the results of xyz_file or SMILES input.

get_molecule_inputs_step()

Given list of substituents and previously done smiles, get input. Calls aiida_aimall.workchains.calcfunctions.get_molecule_str_from_smiles()

string_to_StructureData()

Convert an xyz string of molecule geometry to StructureData. Calls aiida_aimall.workchains.calcfunctions.generate_structure_data()