aiida_chemshell.calculations.base module¶

Core ChemShell calculations module.

class aiida_chemshell.calculations.base.ChemShellCalculation(*args: Any, **kwargs: Any)¶

Bases: CalcJob

AiiDA calculation plugin wrapper for ChemShell calculations.

Currently supports the following tasks:

Single point energy
Geometry optimisation

FILE_DLFIND = '_dl_find.cjson'¶

FILE_RESULTS = 'result.json'¶

FILE_SCRIPT = 'chemshell_input.py'¶

FILE_STDOUT = 'output.log'¶

FILE_TMP_STRUCTURE = 'input_structure.xyz'¶

FILE_TMP_STRUCTURE2 = 'input_structure_2.xyz'¶

FILE_TRJFRC = 'path_force.xyz'¶

FILE_TRJPTH = 'path.xyz'¶

chemsh_script_generator() → str¶

Generate the input script for a ChemShell calculation.

Returns:: script – A string containing the ChemShell input script for the calculation.
Return type:: str

classmethod default_process_label(node) → str¶

AiiDA Process label definition (Class Method).

Defines the process label to be associated with the created ProcessNode stored in the AiiDA database.

Returns:: The process label based on what inputs have been provided.
Return type:: str

classmethod define(spec: CalcJobProcessSpec) → None¶

Define the inputs, outputs and metadata of the ChemShell calculation.

Parameters:: spec (CalcJobProcessSpec) – The AiiDA Process specification object for the job.

classmethod get_mm_theory_key(theory: ChemShellMMTheory) → str¶

Get the key for the MM theory interface in ChemShell.

Parameters:: theory (ChemShellMMTheory) – The MM theory interface to get the key for.
Returns:: The ChemShell class key for the MM theory interface.
Return type:: str

classmethod get_qm_theory_key(theory: ChemShellQMTheory) → str¶

Get the key for the QM theory interface in ChemShell.

Parameters:: theory (ChemShellQMTheory) – The MM theory interface to get the key for.
Returns:: The ChemShell class key for the QM theory interface.
Return type:: str

classmethod get_valid_calculation_parameter_keys() → tuple[str]¶

Return the valid parameter keys for the ChemShell Single Point calculation.

Returns:: A tuple of valid parameter keys for the ChemShell calculation.
Return type:: tuple[str]

classmethod get_valid_mm_parameter_keys(theory: str = '') → dict[slice(<class 'str'>, <class 'type'>, None)]¶

Return a tuple of valid parameter keys for the ChemShell MM interface.

Returns:: validKeys – A tuple of valid MM parameter keys for the ChemShell calculation.
Return type:: dict[str: type]

classmethod get_valid_optimisation_parameter_keys() → tuple[str]¶

Return the valid parameter keys for a ChemShell geometry optimisation task.

Returns:: A tuple of valid optimisation parameter keys for the ChemShell calculation.
Return type:: tuple[str]

classmethod get_valid_qm_parameter_keys() → dict¶

Return a tuple of valid parameter keys for the ChemShell calculation.

Returns:: validKeys – A tuple of valid Theory parameter keys for the ChemShell calculation.
Return type:: dict[str: type]

prepare_for_submission(folder: Folder) → CalcInfo¶

Prepare the ChemShell calculation for submission.

Params¶

folderFolder: An aiida.common.folders.Folder specifying the temporary working directory for the calculation.

returns:: calcInfo – An aiida.common.CalcInfo instance.
rtype:: CalcInfo

classmethod validate_calculation_parameters(value: Dict | None, _) → str | None¶

Validate the ChemShell Single Point calculation input parameters.

Parameters:: value (Dict | None) – A dictionary of parameters for the ChemShell calculation. If None, no validation is performed.
Returns:: Returns None if the parameters are valid, otherwise returns an error message string.
Return type:: str | None

classmethod validate_inputs_namespace(value: Dict, namespace: PortNamespace) → str | None¶: Perform additional validation checks on the total inputs namespace.

classmethod validate_mm_parameters(value: Dict | None, _) → str | None¶

Validate the MM interface parameter inputs to the ChemShell calculation.

Parameters:: value (Dict | None) – A dictionary of parameters for the ChemShell calculation. If None, no validation is performed.
Returns:: Returns None if the parameters are valid, otherwise returns an error message string.
Return type:: str | None

classmethod validate_optimisation_parameters(value: Dict | None, _) → str | None¶

Validate the ChemShell optimisation input parameters.

Parameters:: value (Dict | None) – A dictionary of parameters for the ChemShell geometry optimisation task. If None, no validation is performed.
Returns:: Returns None if the parameters are valid, otherwise returns an error message string.
Return type:: str | None

classmethod validate_qm_parameters(value: Dict | None, _) → str | None¶

Validate the Theory object parameters to be passed to the ChemShell calculation.

Parameters:: value (Dict | None) – A dictionary of parameters for the ChemShell calculation. If None, no validation is performed.
Returns:: Returns None if the parameters are valid, otherwise returns an error message string.
Return type:: str | None

classmethod validate_structure_file(value: SinglefileData | StructureData | None, _) → str | None¶

Validate the ChemShell input structure file.

Parameters:: value (SinglefileData | StructureData | None) – The input structure to validate. This can be either a file containing the structure or an AiiDA StructureData object. If None, no validation is performed.
Returns:: Returns None if no error is found otherwise returns an error message
Return type:: str | None