aiida-pyscf

AiiDA plugin for the Python-based Simulations of Chemistry Framework (PySCF).

status alpha

AiiDA >=2.5,<3.0

General information

Install pip install aiida-pyscf

Documentation No documentation provided by the package author.

Python import import aiida_pyscf

Latest version 0.5.1

Released 2024-01-03

All checks passed

Calculations 1 Parsers 1 Workflows 1

CalcJobs and calculation functions aiida.calculations

pyscf.base

class: aiida_pyscf.calculations.base:PyscfCalculation

``CalcJob`` plugin for PySCF.

Input	Required	Valid types	Description
`code`	true	`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.
`structure`	true	`StructureData`	Input structure with molecular structure definition.
`checkpoint`	false	`SinglefileData, NoneType`	Checkpoint of a previously completed calculation that failed to converge.
`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.
`parameters`	false	`Dict, NoneType`	Input parameters used to render the PySCF script template.
`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`.
`checkpoint`	false	`SinglefileData`	The checkpoint file in case the calculation did not converge. Can be used as an input for a restart.
`cubegen`	false
`fcidump`	false	`SinglefileData`	Computed fcidump files.
`hessian`	false	`ArrayData`	The computed Hessian.
`model`	false	`PickledData`	The model in serialized form. Can be deserialized and used without having to run the kernel again.
`parameters`	false	`Dict`	Various computed properties parsed from the `FILENAME_RESULTS` output file.
`remote_stash`	false	`RemoteStashData`	Contents of the `stash.source_list` option are stored in this remote folder after job completion.
`structure`	false	`StructureData`	The optimized structure if the input parameters contained the `optimizer` key.
`trajectory`	false	`TrajectoryData`	The geometry optimization trajectory if the input parameters contained the `optimizer` key.

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}
302	The stdout output file was not retrieved.
303	The results JSON file was not retrieved.
410	The electronic minimization cycle did not reach self-consistency.
500	The ionic minimization cycle did not converge for the given thresholds.

CalcJob parsers aiida.parsers

WorkChains and work functions aiida.workflows

pyscf.base

class: aiida_pyscf.workflows.base:PyscfBaseWorkChain

Workchain to run a pyscf calculation with automated error handling and restarts.

Input	Required	Valid types	Description
`pyscf`	true	`Data`
`clean_workdir`	false	`Bool`	If `True`, work directories of all called calculation jobs will be cleaned at the end of execution.
`handler_overrides`	false	`Dict, NoneType`	Mapping where keys are process handler names and the values are a dictionary, where each dictionary can define the ``enabled`` and ``priority`` key, which can be used to toggle the values set on the original process handler declaration.
`max_iterations`	false	`Int`	Maximum number of iterations the work chain will restart the process to finish successfully.
`metadata`	false

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`.
`checkpoint`	false	`SinglefileData`	The checkpoint file in case the calculation did not converge. Can be used as an input for a restart.
`cubegen`	false
`fcidump`	false	`SinglefileData`	Computed fcidump files.
`hessian`	false	`ArrayData`	The computed Hessian.
`model`	false	`PickledData`	The model in serialized form. Can be deserialized and used without having to run the kernel again.
`parameters`	false	`Dict`	Various computed properties parsed from the `FILENAME_RESULTS` output file.
`remote_stash`	false	`RemoteStashData`	Contents of the `stash.source_list` option are stored in this remote folder after job completion.
`structure`	false	`StructureData`	The optimized structure if the input parameters contained the `optimizer` key.
`trajectory`	false	`TrajectoryData`	The geometry optimization trajectory if the input parameters contained the `optimizer` key.

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.
300	The calculation failed with an unrecoverable error.
301	The sub process excepted.
302	The sub process was killed.
310	The calculation failed and did not retrieve a checkpoint file from which can be restarted.
401	The maximum number of iterations was exceeded.
402	The process failed for an unknown reason, twice in a row.