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

DEFAULT_INPUT_TAGS = {'calculation_parameters': ('ChemShell Calculation Parameters', 'Base parameters for the ChemShell Task object.'), 'force_field_file': ('ChemShell Force Field File', 'Force field parameters for the ChemShell MM interface.'), 'mm_parameters': ('ChemShell MM Parameters', 'Parameters for the ChemShell MM interface.'), 'optimisation_parameters': ('ChemShell Optimisation Parameters', 'Parameters for the ChemShell geometry optimisation task.'), 'qm_parameters': ('ChemShell QM Parameters', 'Parameters for the ChemShell QM Theory object.'), 'qmmm_parameters': ('ChemShell QM/MM Parameters', 'Parameters for the ChemShell QM/MM interface.'), 'structure': ('Input Chemical Structure', 'The input structure for the ChemShell calculation.'), 'structure2': ('Secondary Input Structure', 'The additional (final) input structure for the ChemShell calculation.'), 'structure_index': ('Structure Input Index', 'Index used to select a structure from a multi-structure input.')}

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'

apply_default_input_tags() → None

Apply default labels and descriptions to the calculation input nodes.

Iterates over the provided input nodes and, for any node defined in DEFAULT_INPUT_TAGS that does not already have a label or description set, assigns the corresponding default value. Existing labels and descriptions are left untouched.

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.

Parameters:

node (ProcessNode) – The process (or its ProcessNode) whose inputs are inspected to build the label.

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, 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, str]

classmethod get_valid_mm_parameter_keys(theory: str = '') → dict[str, type]

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

Parameters:

theory (str) – The MM theory whose valid parameter keys should be returned (e.g. ‘DL_POLY’). Defaults to an empty string.

Returns:

A mapping of valid MM parameter keys to their expected value types 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 dictionary of valid parameter keys for the ChemShell calculation.

Returns:

A mapping of valid Theory parameter keys to their expected value types for the ChemShell calculation.

Return type:

dict[str, type]

prepare_for_submission(folder: Folder) → CalcInfo

Prepare the ChemShell calculation for submission.

Parameters:

folder (Folder) – An aiida.common.folders.Folder specifying the temporary working directory for the calculation.

Returns:

calcInfo – An aiida.common.CalcInfo instance.

Return type:

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