aiida-flexpart

AiiDA plugin for the FLEXPART code (simulation of atmospheric transport processes).

status alpha

AiiDA >=1.6.5,<3.0.0

General information

Install pip install git+https://github.com/aiidaplugins/aiida-flexpart

Source code https://github.com/aiidaplugins/aiida-flexpart

Documentation No documentation provided by the package author.

Python import import aiida_flexpart

Latest version 0.2.1

Registry checks

W010: Entry point 'netcdf.data' does not start with prefix 'flexpart.'

W010: Entry point 'collect.sensitivities' does not start with prefix 'flexpart.'

W010: Entry point 'inversion.calc' does not start with prefix 'flexpart.'

W010: Entry point 'collect.sensitivities' does not start with prefix 'flexpart.'

W010: Entry point 'inversion.calc' does not start with prefix 'flexpart.'

W010: Entry point 'inspect.workflow' does not start with prefix 'flexpart.'

W010: Entry point 'inversion.workflow' does not start with prefix 'flexpart.'

Click any code (W001, E001…) to jump to troubleshooting instructions .

Plugins provided

Calculations 5 Parsers 5 Data 1 Workflows 4

Entry points

Data node types aiida.data

netcdf.data
aiida_flexpart.data.nc_data:NetCdfData

CalcJobs and calculation functions aiida.calculations

flexpart.cosmo

AiiDA calculation plugin wrapping the FLEXPART executable.

Input	Required	Valid types	Description
`meteo_path`	true	`List`	Path to the folder containing the meteorological input data.
`model_settings`	true
`outgrid`	true	`Dict`	Input file for the Lagrangian particle dispersion model FLEXPART.
`species`	true	`RemoteData`
`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.
`land_use`	false	`RemoteData`	#TODO
`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.
`outgrid_nest`	false	`Dict, NoneType`	Input file for the Lagrangian particle dispersion model FLEXPART. Nested output grid.
`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`.
`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	Calculation did not produce all expected output files.

flexpart.ifs

AiiDA calculation plugin wrapping the FLEXPART IFS executable.

Input	Required	Valid types	Description
`meteo_path`	true	`List`	Path to the folder containing the meteorological input data.
`model_settings`	true
`outgrid`	true	`Dict`	Input file for the Lagrangian particle dispersion model FLEXPART.
`species`	true	`RemoteData`
`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.
`land_use`	false	`RemoteData`	#TODO
`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.
`outgrid_nest`	false	`Dict, NoneType`	Input file for the Lagrangian particle dispersion model FLEXPART. Nested output grid.
`parent_calc_folder`	false	`RemoteData, NoneType`	Working directory of a previously ran calculation to restart from.
`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`.
`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	Calculation did not produce all expected output files.

flexpart.post

AiiDA calculation plugin for post processing.

Input	Required	Valid types	Description
`input_dir`	true	`RemoteData`	main FLEXPART output dir
`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.
`input_offline_dir`	false	`RemoteData, NoneType`	offline-nested FLEXPART output dir
`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`.
`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	Calculation did not produce all expected output files.

collect.sensitivities

class: aiida_flexpart.calculations.collect_sens:CollectSensitivitiesCalculation

AiiDA calculation plugin for the collection of sensitivities. The main input are the stashed Netcdf files for the previous FLEXPART calculations.

Input	Required	Valid types	Description
`model`	true	`str`
`outgrid`	true	`str`
`outgrid_n`	true	`bool`
`remote`	true	`RemoteStashFolderData`
`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.
`name`	false	`str, NoneType`
`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`.
`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	Calculation did not produce all expected output files.

inversion.calc

No description available

Input	Required	Valid types	Description
`chunk`	true	`Str`	Options are 'year' and 'month'. Default is 'year'
`chunk_w`	true	`Str`	Width of the individual inversion chunk. These can be wider than the chunking itself to allow for running average fluxes., Possible values are 'year' and '3year' for 'chunk.by=year' and, 'month' and '3month' for 'chunk.by=month'. Default is 'year'
`end_date`	true	`Str`	End date (yyyy-mm-dd)
`inv_params`	true	`Dict`	File containing inversion settings, either as R source file or yaml
`observations`	true	`NetCdfData`	Dictionary of observations as NetCDF objects
`remotes`	true	`NetCdfData`	Dictionary of sensitivities as NetCDF objects
`start_date`	true	`Str`	Start date (yyyy-mm-dd)
`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.

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

flexpart.cosmo
aiida_flexpart.parsers.flexpart_cosmo:FlexpartCosmoParser
flexpart.ifs
aiida_flexpart.parsers.flexpart_ifs:FlexpartIfsParser
flexpart.post
aiida_flexpart.parsers.flexpart_post:FlexpartPostParser
collect.sensitivities
aiida_flexpart.parsers.collect_sens:CollectSensParser
inversion.calc
aiida_flexpart.parsers.inversion:InvesrionParser

WorkChains and work functions aiida.workflows

flexpart.multi_dates
aiida_flexpart.workflows.multi_dates_workflow:FlexpartMultipleDatesWorkflow
flexpart.multi_workflow
aiida_flexpart.workflows.parent_workflow:ParentWorkflow
inspect.workflow
aiida_flexpart.workflows.inspect:InspectWorkflow
inversion.workflow
aiida_flexpart.workflows.inversion_workflow:InversionWorkflow