aiida-codtools

The Official AiiDA plugin for the cod-tools package.

status stable

AiiDA >=2.1,<3.0

General information

Install pip install aiida-codtools

Source code https://github.com/aiidateam/aiida-codtools

Documentation https://aiida-codtools.readthedocs.io/

Contact The AiiDA team <developers@aiida.net>

Python import import aiida_codtools

Latest version 3.1.0

Released 2023-02-02

Registry checks

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Plugins provided

Calculations 9 Parsers 6 Workflows 1 Console scripts 1

Entry points

CalcJobs and calculation functions aiida.calculations

codtools.cif_base

Generic `CalcJob` implementation that can easily be extended to work with any of the `cod-tools` scripts.

Input	Required	Valid types	Description
`cif`	true	`CifData`	The CIF to be processed.
`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.
`parameters`	false	`Dict, NoneType`	Command line parameters.
`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`.
`messages`	false	`Dict`	Warning and error messages returned by script.
`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	Neither the output for the error file could be read from the retrieved folder.
311	The output file could not be read from the retrieved folder.
312	The error file could not be read from the retrieved folder.
313	The output file is empty.
320	Invalid command line option passed.
400	The output file could not be parsed.
410	The output file could not be parsed into a CifData object.

codtools.cif_cell_contents

class: aiida_codtools.calculations.cif_cell_contents:CifCellContentsCalculation

CalcJob plugin for the `cif_cell_contents` script of the `cod-tools` package.

Input	Required	Valid types	Description
`cif`	true	`CifData`	The CIF to be processed.
`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.
`parameters`	false	`Dict, NoneType`	Command line parameters.
`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
`formulae`	true	`Dict`	A dictionary of formulae present in the CIF.
`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`.
`messages`	false	`Dict`	Warning and error messages returned by script.
`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	Neither the output for the error file could be read from the retrieved folder.
311	The output file could not be read from the retrieved folder.
312	The error file could not be read from the retrieved folder.
313	The output file is empty.
320	Invalid command line option passed.
400	The output file could not be parsed.
410	The output file could not be parsed into a CifData object.

codtools.cif_cod_check

CalcJob plugin for the `cif_cod_check` script of the `cod-tools` package.

Input	Required	Valid types	Description
`cif`	true	`CifData`	The CIF to be processed.
`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.
`parameters`	false	`Dict, NoneType`	Command line parameters.
`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
`messages`	true	`Dict`	Warning and error messages returned by the script.
`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}
300	Neither the output for the error file could be read from the retrieved folder.
311	The output file could not be read from the retrieved folder.
312	The error file could not be read from the retrieved folder.
313	The output file is empty.
320	Invalid command line option passed.
400	The output file could not be parsed.
410	The output file could not be parsed into a CifData object.

codtools.cif_cod_deposit

CalcJob plugin for the `cif_cod_deposit` script of the `cod-tools` package.

Input	Required	Valid types	Description
`cif`	true	`CifData`	The CIF to be processed.
`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.
`parameters`	false	`Dict, NoneType`	Command line parameters.
`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`.
`messages`	false	`Dict`	Warning and error messages returned by script.
`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	Neither the output for the error file could be read from the retrieved folder.
300	The deposition failed for unknown reasons.
310	The deposition failed because the input was invalid.
311	The output file could not be read from the retrieved folder.
312	The error file could not be read from the retrieved folder.
313	The output file is empty.
320	Invalid command line option passed.
400	The output file could not be parsed.
410	The output file could not be parsed into a CifData object.
410	The deposition failed because one or more CIFs already exist in the COD.
420	The structure is unchanged and so deposition is unnecessary.

codtools.cif_cod_numbers

CalcJob plugin for the `cif_cod_numbers` script of the `cod-tools` package.

Input	Required	Valid types	Description
`cif`	true	`CifData`	The CIF to be processed.
`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.
`parameters`	false	`Dict, NoneType`	Command line parameters.
`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
`numbers`	true	`Dict`	Mapping of COD IDs found with their formula and count.
`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`.
`messages`	false	`Dict`	Warning and error messages returned by script.
`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	Neither the output for the error file could be read from the retrieved folder.
311	The output file could not be read from the retrieved folder.
312	The error file could not be read from the retrieved folder.
313	The output file is empty.
320	Invalid command line option passed.
400	The output file could not be parsed.
410	The output file could not be parsed into a CifData object.

codtools.cif_filter

CalcJob plugin for the `cif_filter` script of the `cod-tools` package.

Input	Required	Valid types	Description
`cif`	true	`CifData`	The CIF to be processed.
`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.
`parameters`	false	`Dict, NoneType`	Command line parameters.
`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
`cif`	true	`CifData`	The CIF produced by the script.
`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`.
`messages`	false	`Dict`	Warning and error messages returned by script.
`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	Neither the output for the error file could be read from the retrieved folder.
311	The output file could not be read from the retrieved folder.
312	The error file could not be read from the retrieved folder.
313	The output file is empty.
320	Invalid command line option passed.
400	The output file could not be parsed.
410	The output file could not be parsed into a CifData object.

codtools.cif_select

CalcJob plugin for the `cif_select` script of the `cod-tools` package.

Input	Required	Valid types	Description
`cif`	true	`CifData`	The CIF to be processed.
`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.
`parameters`	false	`Dict, NoneType`	Command line parameters.
`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
`cif`	true	`CifData`	The CIF produced by the script.
`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`.
`messages`	false	`Dict`	Warning and error messages returned by script.
`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	Neither the output for the error file could be read from the retrieved folder.
311	The output file could not be read from the retrieved folder.
312	The error file could not be read from the retrieved folder.
313	The output file is empty.
320	Invalid command line option passed.
400	The output file could not be parsed.
410	The output file could not be parsed into a CifData object.

codtools.cif_split_primitive

class: aiida_codtools.calculations.cif_split_primitive:CifSplitPrimitiveCalculation

CalcJob plugin for the `cif_split_primitive` script of the `cod-tools` package.

Input	Required	Valid types	Description
`cif`	true	`CifData`	The CIF to be processed.
`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.
`parameters`	false	`Dict, NoneType`	Command line parameters.
`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
`cifs`	true	`CifData`	The CIFs produced by the script.
`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`.
`messages`	false	`Dict`	Warning and error messages returned by script.
`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	Neither the output for the error file could be read from the retrieved folder.
311	The output file could not be read from the retrieved folder.
312	The error file could not be read from the retrieved folder.
313	The output file is empty.
320	Invalid command line option passed.
400	The output file could not be parsed.
410	The output file could not be parsed into a CifData object.

codtools.primitive_structure_from_cif

class: aiida_codtools.calculations.functions.primitive_structure_from_cif:primitive_structure_from_cif

Attempt to parse the given `CifData` and create a `StructureData` from it. First the raw CIF file is parsed with the given `parse_engine`. The resulting `StructureData` is then passed through SeeKpath to try and get the primitive cell. If that is successful, important structural parameters as determined by SeeKpath will be set as extras on the structure node which is then returned as output. :param cif: the `CifData` node :param parse_engine: the parsing engine, supported libraries 'ase' and 'pymatgen' :param symprec: a `Float` node with symmetry precision for determining primitive cell in SeeKpath :param site_tolerance: a `Float` node with the fractional coordinate distance tolerance for finding overlapping sites. This will only be used if the parse_engine is pymatgen :return: the primitive `StructureData` as determined by SeeKpath

Input	Required	Valid types	Description
`cif`	true	`Data`	the `CifData` node
`parse_engine`	true	`Data`	the parsing engine, supported libraries 'ase' and 'pymatgen'
`site_tolerance`	true	`Data`	a `Float` node with the fractional coordinate distance tolerance for finding overlapping sites. This will only be used if the parse_engine is pymatgen
`symprec`	true	`Data`	a `Float` node with symmetry precision for determining primitive cell in SeeKpath
`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.

CalcJob parsers aiida.parsers

codtools.cif_base
aiida_codtools.parsers.cif_base:CifBaseParser
codtools.cif_cell_contents
aiida_codtools.parsers.cif_cell_contents:CifCellContentsParser
codtools.cif_cod_check
aiida_codtools.parsers.cif_cod_check:CifCodCheckParser
codtools.cif_cod_deposit
aiida_codtools.parsers.cif_cod_deposit:CifCodDepositParser
codtools.cif_cod_numbers
aiida_codtools.parsers.cif_cod_numbers:CifCodNumbersParser
codtools.cif_split_primitive
aiida_codtools.parsers.cif_split_primitive:CifSplitPrimitiveParser

WorkChains and work functions aiida.workflows

codtools.cif_clean

WorkChain to clean a `CifData` node using the `cif_filter` and `cif_select` scripts of `cod-tools`. It will first run `cif_filter` to correct syntax errors, followed by `cif_select` which will canonicalize the tags. If a group is passed for the `group_structure` input, the atomic structure library defined by the `engine` input will be used to parse the final cleaned `CifData` to construct a `StructureData` object, which will then be passed to the `SeeKpath` library to analyze it and return the primitive structure

Input	Required	Valid types	Description
`cif`	true	`CifData`	The CifData node that is to be cleaned.
`cif_filter`	true	`Data`
`cif_select`	true	`Data`
`group_cif`	false	`Group, NoneType`	An optional Group to which the final cleaned CifData node will be added.
`group_structure`	false	`Group, NoneType`	An optional Group to which the final reduced StructureData node will be added.
`metadata`	false
`parse_engine`	false	`Str`	The atomic structure engine to parse the cif and create the structure.
`site_tolerance`	false	`Float`	The fractional coordinate distance tolerance for finding overlapping sites (pymatgen only).
`symprec`	false	`Float`	The symmetry precision used by SeeKpath for crystal symmetry refinement.

Output	Required	Valid types	Description
`cif`	true	`CifData`	The cleaned CifData node.
`structure`	false	`StructureData`	The primitive cell structure created with SeeKpath from the cleaned CifData.

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.
401	The CifFilterCalculation step failed.
402	The CifSelectCalculation step failed.
410	The cleaned CifData contains sites with unknown species.
411	The cleaned CifData defines no atomic sites.
412	The cleaned CifData defines sites with attached hydrogens with incomplete positional data.
413	The cleaned CifData defines sites with invalid atomic occupancies.
414	Failed to parse a StructureData from the cleaned CifData.
420	SeeKpath failed to determine the primitive structure.
421	SeeKpath detected inconsistent symmetry operations.

Console scripts console_scripts

aiida-codtools
aiida_codtools.cli:cmd_root