aiida-gaussian

AiiDA plugin for the Gaussian quantum chemistry software.

status stable

AiiDA >=2.0.0,<3.0.0

General information

Install pip install aiida-gaussian

Source code https://github.com/nanotech-empa/aiida-gaussian

Documentation No documentation provided by the package author.

Author(s) Kristjan Eimre, Pezhman Zarabadi-Poor, Aliaksandr Yakutovich

Python import import aiida_gaussian

Latest version 2.2.0

Released 2024-09-25

Registry checks

All checks passed

Plugins provided

Calculations 3 Parsers 3 Workflows 2

Entry points

CalcJobs and calculation functions aiida.calculations

gaussian

AiiDA calculation plugin wrapping Gaussian Template: parameters = Dict(dict={ 'link0_parameters': { '%chk':'aiida.chk', '%mem': '1024MB', '%nprocshared': '2', }, 'functional':'PBE1PBE', 'basis_set':'6-31g', 'charge': 0, 'multiplicity': 1, 'route_parameters': { 'scf': {'cdiis': None} 'nosymm': None, 'opt': 'tight', }, })

Input	Required	Valid types	Description
`parameters`	true	`Dict`	Input parameters
`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
`monitors`	false	`Dict`	Add monitoring functions that can inspect output files while the job is running and decide to prematurely terminate the job.
`parent_calc_folder`	false	`RemoteData, NoneType`	the folder of a completed gaussian calculation
`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.
`settings`	false	`Dict, NoneType`	additional input parameters
`structure`	false	`StructureData, NoneType`	Input structure; will be converted to pymatgen object

Output	Required	Valid types	Description
`output_parameters`	true	`Dict`	The result parameters of the calculation
`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`.
`energy_ev`	false	`Float`	Final energy in electronvolts
`output_structure`	false	`StructureData`	Final optimized structure, if available
`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.
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}
200	The retrieved folder data node could not be accessed.
210	The retrieved folder did not contain the output file.
211	The retrieved output log could not be read.
220	The output file could not be parsed.
301	The SCF did not converge and the calculation was terminated.
302	The calculation was terminated due to a logic error in ASyTop.
303	The calculation was terminated due to an inaccurate quadrature in CalDSu.
390	The calculation was terminated due to an error.
391	The log did not contain 'Normal termination' (probably out of time).

gaussian.cubegen

Plugin to run the cubegen utility Example: parameters = { "homo-5": { "kind": "AMO=16", "npts": -2, }, "spin": { "kind": "Spin=SCF", "npts": 0, }, } Each key corresponds to one produced cube. key specifies the name of the output node In case of "npts": -1, you have to use the stencil file input: IFlag X0 Y0 Z0 # Output unit number and initial point. N1 X1 Y1 Z1 # Number of points and step-size in the X-direction. N2 X2 Y2 Z2 # Number of points and step-size in the Y-direction. N3 X3 Y3 Z3 # Number of points and step-size in the Z-direction. See more details at https://gaussian.com/cubegen/

Input	Required	Valid types	Description
`parameters`	true	`Dict`	dictionary containing entries for cubes to be printed.
`parent_calc_folder`	true	`RemoteData`	the folder of a containing the .fchk
`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.
`gauss_memdef`	false	`Int, NoneType`	Set the GAUSS_MEMDEF env variable to set the max memory in MB.
`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.
`retrieve_cubes`	false	`Bool, NoneType`	should the cubes be retrieved?
`stencil`	false	`SinglefileData, NoneType`	In case of npts=-1, use this cube specification.

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`.
`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.
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	The retrieved folder could not be accessed.
301	The retrieved temporary folder could not be accessed.

gaussian.formchk

Very simple plugin to run the formchk utility

Input	Required	Valid types	Description
`parent_calc_folder`	true	`RemoteData`	the folder of a containing the .chk
`chk_name`	false	`Str, NoneType`	name of the checkpoint file
`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
`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.
`retrieve_fchk`	false	`Bool, NoneType`	retrieve the fchk file

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`.
`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}

CalcJob parsers aiida.parsers

gaussian.advanced
aiida_gaussian.parsers.gaussian:GaussianAdvancedParser
gaussian.base
aiida_gaussian.parsers.gaussian:GaussianBaseParser
gaussian.cubegen_base
aiida_gaussian.parsers.cubegen:CubegenBaseParser

WorkChains and work functions aiida.workflows

gaussian.base

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

Input	Required	Valid types	Description
`gaussian`	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

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.
301	The sub process excepted.
302	The sub process was killed.
350	The calculation failed with an unrecoverable SCF convergence error.
399	The calculation failed with an unrecoverable error.
401	The maximum number of iterations was exceeded.
402	The process failed for an unknown reason, twice in a row.

gaussian.cubes

No description available

Input	Required	Valid types	Description
`cubegen_code`	true	`Code`
`formchk_code`	true	`Code`
`gaussian_calc_folder`	true	`RemoteData`	The gaussian calculation output folder.
`gaussian_output_params`	true	`Dict`	The gaussian calculation output parameters.
`cubegen_parser_name`	false	`str`
`cubegen_parser_params`	false	`Dict, NoneType`	Additional parameters to cubegen parser.
`dx`	false	`Float, NoneType`	Cube file spacing [ang].
`edge_space`	false	`Float, NoneType`	Extra cube space in addition to molecule bounding box [ang].
`generate_density`	false	`Bool, NoneType`	Generate density cube.
`generate_spin_density`	false	`Bool, NoneType`	Generate spin density cube (if applicable).
`metadata`	false
`natural_orbitals`	false	`Bool, NoneType`	The cube files are natural orbitals.
`orbital_index_ref`	false	`Str, NoneType`	Reference index, possible choices: 'half_num_el', 'abs'.
`orbital_indexes`	false	`List, NoneType`	Indexes of the orbital cubes to generate.
`retrieve_cubes`	false	`Bool, NoneType`	should the cubes be retrieved?

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.
302	Input options are invalid.
390	One or more steps of the work chain failed.