aiida_chemshell package

Submodules

aiida_chemshell.calculations module

Core ChemShell calculations module.

class aiida_chemshell.calculations.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.pun'

FILE_RESULTS = 'result.json'

FILE_SCRIPT = 'chemshell_input.py'

FILE_STDOUT = 'output.log'

FILE_TMP_STRUCTURE = 'input_structure.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 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_paramater_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_paramater_keys() → dict[slice(<class 'str'>, <class 'type'>, None)]

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_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

aiida_chemshell.parsers module

Defines the calculation parsers for the ChemShell AiiDA plugin.

class aiida_chemshell.parsers.ChemShellParser(node: CalcJobNode)

Bases: Parser

AiiDA parser plugin for ChemShell calculations.

parse(**kwargs)

Parse the output of a ChemShell calculation.

aiida_chemshell.utils module

Utility functions for the aiida-chemshell AiiDA plugin.

class aiida_chemshell.utils.ChemShellMMTheory(*values)

Bases: Enum

Enum for the ChemShell MM theory interfaces.

DL_POLY = 2

GULP = 3

NAMD = 4

NONE = 1

class aiida_chemshell.utils.ChemShellQMTheory(*values)

Bases: Enum

Enum fr the ChemShell theory interfaces.

CASTEP = 2

CP2K = 3

DFTBP = 4

FHI_AIMS = 5

GAMESS_UK = 6

GAUSSIAN = 7

LSDALTON = 8

MNDO = 9

MOLPRO = 10

NONE = 1

NWCHEM = 11

ORCA = 12

PYSCF = 13

TURBOMOLE = 14

aiida_chemshell.utils.chemsh_punch_to_structure_data(data: str) → StructureData

Create a AiiDA StructureData object from a ChemShell punch file.

Module contents

ChemShell AiiDA plugin.