aiida-chemshell

AiiDA workflow plugin for the ChemShell chemical modelling software package

status stable

AiiDA >=2.6

General information

Install pip install aiida-chemshell

Source code https://github.com/stfc/aiida-chemshell

Documentation https://stfc.github.io/aiida-chemshell/

Contact "Dr. Benjamin T. Speake" <benjamin.speake@stfc.ac.uk>

Python import import aiida_chemshell

Latest version 0.1.13

Released 2026-06-25

Registry checks

All checks passed

Plugins provided

Calculations 2 Parsers 2 Workflows 2

Entry points

CalcJobs and calculation functions aiida.calculations

chemshell

class: aiida_chemshell.calculations.base:ChemShellCalculation

AiiDA calculation plugin wrapper for ChemShell calculations. Currently supports the following tasks: - Single point energy - Geometry optimisation

Input	Required	Valid types	Description
`structure`	true	`SinglefileData, StructureData`	The input structure for the ChemShell calculation either contained within an '.xyz', '.pun' or '.cjson' file or as a StructureData instance.
`calculation_parameters`	false	`Dict, NoneType`	A dictionary of parameters for the ChemShell Task object.
`code`	false	`AbstractCode, NoneType`	The `Code` to use for this job. This input is required, unless the `remote_folder` input is specified, which means an existing job is being imported and no code will actually be run.
`force_field_file`	false	`SinglefileData, NoneType`	A file containing the force field parameters for the ChemShell MM interface.
`metadata`	false
`mm_parameters`	false	`Dict, NoneType`	A dictionary of parameters for the ChemShell MM interface.
`monitors`	false	`Dict`	Add monitoring functions that can inspect output files while the job is running and decide to prematurely terminate the job.
`optimisation_parameters`	false	`Dict, NoneType`	A dictionary of parameters for the ChemShell geometry optimisation task. If this input is provided, a geometry optimisation task will be configured and added to this job.
`qm_parameters`	false	`Dict, NoneType`	A dictionary of parameters for to be passed to the Theory object for the ChemShell calculation.
`qmmm_parameters`	false	`Dict, NoneType`	A dictionary of parameters for the ChemShell QM/MM interface.
`remote_folder`	false	`RemoteData, NoneType`	Remote directory containing the results of an already completed calculation job without AiiDA. The inputs should be passed to the `CalcJob` as normal but instead of launching the actual job, the engine will recreate the input files and then proceed straight to the retrieve step where the files of this `RemoteData` will be retrieved as if it had been actually launched through AiiDA. If a parser is defined in the inputs, the results are parsed and attached as output nodes as usual.

Output	Required	Valid types	Description
`energy`	true	`Float`	The total energy of the system.
`remote_folder`	true	`RemoteData`	Input files necessary to run the process will be stored in this folder node.
`retrieved`	true	`FolderData`	Files that are retrieved by the daemon will be stored in this node. By default the stdout and stderr of the scheduler will be added, but one can add more by specifying them in `CalcInfo.retrieve_list`.
`gradients`	false	`ArrayData`	The gradients (and hessian) of the system if requested. The gradients are contained within an AiiDA ArrayData object with the key 'gradients'.
`optimisation_path`	false	`ArrayData`	Values calculated at each step of an optimisation based calculation.
`optimised_structure`	false	`SinglefileData`	The optimised structure of the given system, if a geometry optimisation task was configured and successfully completed. The structure is contained within a ChemShell '.pun' file.
`remote_stash`	false	`RemoteStashData`	Contents of the `stash.source_list` option are stored in this remote folder after job completion.
`trajectory_force`	false	`SinglefileData`	XYZ trajectory containing forces at each step of a geometry optimisation
`trajectory_path`	false	`SinglefileData`	XYZ trajectory file for the geometry optimisation
`vibrational_energies`	false	`Dict`	The calculated thermochemical properties of the system.
`vibrational_modes`	false	`ArrayData`	The calculated vibrational modes of the system.

Exit status	Message
1	The process has failed with an unspecified error.
2	The process failed with legacy failure mode.
10	The process returned an invalid output.
11	The process did not register a required output.
100	The process did not have the required `retrieved` output.
110	The job ran out of memory.
120	The job ran out of walltime.
131	The specified account is invalid.
140	The node running the job failed.
150	{message}
300	Error accessing the `output.log` ChemShell output file.
301	ChemShell calculation failed to compute a final energy for the given task.
302	ChemShell failed to produced the expected optimised structure file.
303	ChemShell calculation failed to produce the expected results file.
304	ChemShell calculation failed to compute the requested gradients or hessian for the given task.

chemshell.file_conversion.mlip_training

class: aiida_chemshell.calculations.file_conversion:CreateJanusTrainingInputsCalcJob

CalcJob to split an XYZ trajectory into individual ext XYZ files.

Input	Required	Valid types	Description
`atom_energies`	true	`Dict`	The isolated atomic energies for the training set.
`energies`	true	`ArrayData`	The calculated dft energy of each step in the data series in a.u.
`force`	true	`SinglefileData`	An XYZ trajectory file containing the forces at each step.
`path`	true	`SinglefileData`	An XYZ trajectory file containing the positions of each step.
`code`	false	`AbstractCode, NoneType`	The `Code` to use for this job. This input is required, unless the `remote_folder` input is specified, which means an existing job is being imported and no code will actually be run.
`filename`	false	`Str, NoneType`	The name to give the directory of output files.
`metadata`	false
`monitors`	false	`Dict`	Add monitoring functions that can inspect output files while the job is running and decide to prematurely terminate the job.
`remote_folder`	false	`RemoteData, NoneType`	Remote directory containing the results of an already completed calculation job without AiiDA. The inputs should be passed to the `CalcJob` as normal but instead of launching the actual job, the engine will recreate the input files and then proceed straight to the retrieve step where the files of this `RemoteData` will be retrieved as if it had been actually launched through AiiDA. If a parser is defined in the inputs, the results are parsed and attached as output nodes as usual.

Output	Required	Valid types	Description
`remote_folder`	true	`RemoteData`	Input files necessary to run the process will be stored in this folder node.
`retrieved`	true	`FolderData`	Files that are retrieved by the daemon will be stored in this node. By default the stdout and stderr of the scheduler will be added, but one can add more by specifying them in `CalcInfo.retrieve_list`.
`test_input`	true	`SinglefileData`	The testing data set in extended XYZ format.
`training_input`	true	`SinglefileData`	The main training data set in extended XYZ format.
`validation_input`	true	`SinglefileData`	The validation data set in extended XYZ format.
`remote_stash`	false	`RemoteStashData`	Contents of the `stash.source_list` option are stored in this remote folder after job completion.

Exit status	Message
1	The process has failed with an unspecified error.
2	The process failed with legacy failure mode.
10	The process returned an invalid output.
11	The process did not register a required output.
100	The process did not have the required `retrieved` output.
110	The job ran out of memory.
120	The job ran out of walltime.
131	The specified account is invalid.
140	The node running the job failed.
150	{message}
300	No trajectory files have been produced.

CalcJob parsers aiida.parsers

chemshell
aiida_chemshell.parsers.base:ChemShellParser
chemshell.file_conversion.mlip_training
aiida_chemshell.parsers.file_conversion:CreateJanusTrainingInputsParser

WorkChains and work functions aiida.workflows

chemshell.atomic_energies

class: aiida_chemshell.workflows.isolated_atoms:IsolatedAtomicEnergiesWorkChain

AiiDA workflow for extracting isolated atomic energies from a given structure.

Input	Required	Valid types	Description
`structure`	true	`SinglefileData, StructureData`	The input structure for the ChemShell calculation either contained within an '.xyz', '.pun' or '.cjson' file or as a StructureData instance.
`code`	false	`AbstractCode, NoneType`	The `Code` to use for this job. This input is required, unless the `remote_folder` input is specified, which means an existing job is being imported and no code will actually be run.
`metadata`	false
`qm_parameters`	false	`Dict, NoneType`	A dictionary of parameters for to be passed to the Theory object for the ChemShell calculation.

Output	Required	Valid types	Description
`atom_energies`	false	`Dict`	The individual isolated atomic energies for every unique atom type in the given system.

Exit status	Message
1	The process has failed with an unspecified error.
2	The process failed with legacy failure mode.
10	The process returned an invalid output.
11	The process did not register a required output.

chemshell.opt

class: aiida_chemshell.workflows.optimisation:GeometryOptimisationWorkChain

Geometry optimisation calculation with extended optional calculation options.

Input	Required	Valid types	Description
`chemsh`	true	`Data`
`metadata`	false
`vibrational_analysis`	false	`Bool, NoneType`	Calculate vibrational modes of resulting structure. (default=True)

Output	Required	Valid types	Description
`final_energy`	true	`Float`	The final energy for the optimised structure.
`optimised_structure`	true	`SinglefileData`	The final optimised geometry of the given structure.
`vibrational_energies`	false	`Dict`	The calculated thermochemical properties of the optimised structure
`vibrational_modes`	false	`ArrayData`	The calculated vibrational modes for the optimised structure.

Exit status	Message
1	The process has failed with an unspecified error.
2	The process failed with legacy failure mode.
10	The process returned an invalid output.
11	The process did not register a required output.