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aiida-siesta

A plugin for Siesta's basic functionality within the AiiDA framework.

status stable AiiDA >=2.0.0,<3.0.0

General information

Install pip install aiida-siesta
Source code https://github.com/siesta-project/aiida_siesta_plugin/tree/master
Documentation https://aiida-siesta-plugin.readthedocs.io/
Contact Albero Garcia <albertog@icmab.es>"Victor M. Garcia-Suarez" <garciavictor@uniovi.es>Emanuele Bosoni <ebosoni@icmab.es>Vladimir Dikan <vdikan@icmab.es>Pol Febrer <pol.febrer@icn2.cat>
Python import import aiida_siesta
Latest version 2.0.0
Released 2022-07-17

Registry checks

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Plugins provided

Calculations 2 Parsers 2 Data 1 Workflows 13 Other 1

Entry points

CalcJobs and calculation functions aiida.calculations

  • siesta.siesta

    class: aiida_siesta.calculations.siesta:SiestaCalculation

    Siesta calculator class for AiiDA.

    InputRequiredValid typesDescription
    code true Code Input code
    parameters true Dict Input parameters
    structure true StructureData Input structure
    bandskpoints false KpointsData, NoneType Input kpoints for bands
    basis false Dict, NoneType Input basis
    ions false IonData Input ion file
    kpoints false KpointsData, NoneType Input kpoints
    lua false Script and files for the Lua engine
    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.
    optical false Dict, NoneType Specifications for optical properties
    parent_calc_folder false RemoteData, NoneType Parent folder
    pseudos false PsfData, PsmlData Input pseudo potentials
    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 Input settings
    OutputRequiredValid typesDescription
    output_parameters true Dict The calculation results
    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`.
    bands false BandsData Optional band structure
    forces_and_stress false ArrayData Optional forces and stress
    ion_files false IonData
    optical_eps2 false ArrayData Optional eps2 optical data
    output_structure false StructureData Optional relaxed structure
    remote_stash false RemoteStashData Contents of the `stash.source_list` option are stored in this remote folder after job completion.
    Exit statusMessage
    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}
    350 Statement "Job completed" not detected, unknown error
    448 Problems in the polarization of a basis element
    449 Split_norm parameter too small
    450 Calculation did not reach scf convergence!
    451 Calculation did not reach geometry convergence!
    452 Bands analysis was requested, but file is not present
    453 Failure while parsing the bands file
    454 Optical calculation requested, but file is not present

  • siesta.stm

    class: aiida_siesta.calculations.stm:STMCalculation

    Plugin for the "plstm" program in the Siesta distribution. The "plstm" program takes the .LDOS file and generates a plot file with a simulated STM image. It supports both the old "plstm" versions (inputs in a files) and the new ones (inputs in the command line). Spin options are supported only in recent "plstm" versions, therefore ignored otherwise.

    InputRequiredValid typesDescription
    code true Code Input code
    ldos_folder true RemoteData Parent folder
    mode true Str Allowed values are "constant-height" or "constant-current"
    value true Float Value of height in Ang or value of current in e/bohr**3
    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.
    settings false Dict, NoneType Input settings
    spin_option false Str Spin option follows plstm sintax: "q" no spin, "s" total spin, "x","y","z" the three spin components
    OutputRequiredValid typesDescription
    output_parameters true Dict For the moment only parser version and name of .STM file
    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`.
    stm_array true ArrayData The contour data for the STM image
    remote_stash false RemoteStashData Contents of the `stash.source_list` option are stored in this remote folder after job completion.
    Exit statusMessage
    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 retrieved folder data node could not be accessed.
    101 The retrieved folder does not contain a CH.STM file
    102 The .STM file can not be read
    102 The array containing the STM data can not be produced
    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

  • siesta.parser

    aiida_siesta.parsers.siesta:SiestaParser

  • siesta.stm

    aiida_siesta.parsers.stm:STMParser
WorkChains and work functions aiida.workflows

  • siesta.base

    class: aiida_siesta.workflows.base:SiestaBaseWorkChain

    Base Workchain to launch a total energy calculation via Siesta.

    InputRequiredValid typesDescription
    code true Code Input code
    options true Dict
    parameters true Dict Input parameters
    structure true StructureData Input structure
    bandskpoints false KpointsData, NoneType Input kpoints for bands
    basis false Dict, NoneType Input basis
    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.
    ions false IonData Input ion file
    kpoints false KpointsData, NoneType Input kpoints
    lua false Script and files for the Lua engine
    max_iterations false Int Maximum number of iterations the work chain will restart the process to finish successfully.
    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.
    optical false Dict, NoneType Specifications for optical properties
    parent_calc_folder false RemoteData, NoneType Parent folder
    pseudo_family false Str, NoneType
    pseudos false PsfData, PsmlData Input pseudo potentials
    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 Input settings
    OutputRequiredValid typesDescription
    output_parameters true Dict The calculation results
    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`.
    bands false BandsData Optional band structure
    forces_and_stress false ArrayData Optional forces and stress
    ion_files false IonData
    optical_eps2 false ArrayData Optional eps2 optical data
    output_structure false StructureData Optional relaxed structure
    remote_stash false RemoteStashData Contents of the `stash.source_list` option are stored in this remote folder after job completion.
    Exit statusMessage
    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.
    401 The maximum number of iterations was exceeded.
    402 The process failed for an unknown reason, twice in a row.
    403 Basis polarization problem.
    404 Error in the parsing of bands

  • siesta.eos

    class: aiida_siesta.workflows.eos:EqOfStateFixedCellShape

    WorkChain to calculate the equation of state of a solid. The cell shape is fixed, only the volume is rescaled. In particular the volumes considered are 7 equidistant volumes around a starting volume. The starting volume is an optional input of the WorkChain (called volume_per_atom). If not specified, the input structure volume is used with no modifications. All the SiestaBaseWorkChain inputs are other inputs of the workchain. This WorkChain also tries to perform a Birch_Murnaghan fit on the calculatad E(V) data.

    InputRequiredValid typesDescription
    code true Code Input code
    options true Dict
    parameters true Dict Input parameters
    structure true StructureData Input structure
    bandskpoints false KpointsData, NoneType Input kpoints for bands
    basis false Dict, NoneType Input basis
    batch_size false Int The maximum number of simulations that should run at the same time. You can set this to a very large number to make sure that all simulations run in one single batch if you want.
    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.
    ions false IonData Input ion file
    iterate_mode false Str Indicates the way the parameters should be iterated. Currently allowed values are: - 'zip': zips all the parameters together (all parameters should have the same number of values!) - 'product': performs a cartesian product of the parameters. That is, all possible combinations of parameters and values are explored.
    kpoints false KpointsData, NoneType Input kpoints
    lua false Script and files for the Lua engine
    max_iterations false Int Maximum number of iterations the work chain will restart the process to finish successfully.
    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.
    optical false Dict, NoneType Specifications for optical properties
    parent_calc_folder false RemoteData, NoneType Parent folder
    pseudo_family false Str, NoneType
    pseudos false PsfData, PsmlData Input pseudo potentials
    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.
    scales false Factors by which the structure should be scaled.
    settings false Dict, NoneType Input settings
    volume_per_atom false Float, NoneType Volume per atom around which to perform the EqOfState
    OutputRequiredValid typesDescription
    results_dict true Dict Containing the calculated E(V) data and, if the fit is sucessfull, the resulting fit parameters
    equilibrium_structure false StructureData Equilibrium volume structure. Returned only if the fit is succesfull
    Exit statusMessage
    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.

  • siesta.bandgap

    class: aiida_siesta.workflows.bandgap:BandgapWorkChain

    Workchain to obtain the bands and bandgap of a structure through Siesta. If "bandskpoints" are set in inputs, it behaves like `SiestaBaseWorkChain` adding just the bandgap calculation at the end. If no bandskpoints was specified, the bands are computed anyway on a kpoints path automatically assigned using seekpath and the input (output) structure of the single-point (relaxation/md) calculation.

    InputRequiredValid typesDescription
    code true Code Input code
    options true Dict
    parameters true Dict Input parameters
    structure true StructureData Input structure
    bandskpoints false KpointsData, NoneType Input kpoints for bands
    basis false Dict, NoneType Input basis
    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.
    ions false IonData Input ion file
    kpoints false KpointsData, NoneType Input kpoints
    lua false Script and files for the Lua engine
    max_iterations false Int Maximum number of iterations the work chain will restart the process to finish successfully.
    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.
    optical false Dict, NoneType Specifications for optical properties
    parent_calc_folder false RemoteData, NoneType Parent folder
    pseudo_family false Str, NoneType
    pseudos false PsfData, PsmlData Input pseudo potentials
    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.
    seekpath_dict false Dict dictionary of seekpath parameters that are pased to `get_explicit_kpoints_path`
    settings false Dict, NoneType Input settings
    OutputRequiredValid typesDescription
    output_parameters true Dict The calculation results
    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`.
    band_gap_info false Dict
    bands false BandsData Optional band structure
    forces_and_stress false ArrayData Optional forces and stress
    ion_files false IonData
    optical_eps2 false ArrayData Optional eps2 optical data
    output_structure false StructureData Optional relaxed structure
    remote_stash false RemoteStashData Contents of the `stash.source_list` option are stored in this remote folder after job completion.
    Exit statusMessage
    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.
    200 The main SiestaBaseWorkChain failed
    201 The SiestaBaseWorkChain to obtain the bands failed

  • siesta.stm

    class: aiida_siesta.workflows.stm:SiestaSTMWorkChain

    STM Workchain. This workchain runs a DFT calculation with siesta, calculates the local density of states in an energy window specified by the user (stored in a .LDOS file) and post-process it in order to produce simulated STM images.

    InputRequiredValid typesDescription
    code true Code Input code
    emax true Float Higher boundary energy (in eV respect to Ef) for LDOS calculation
    emin true Float Lower boundary energy (in eV respect to Ef) for LDOS calculation
    options true Dict
    parameters true Dict Input parameters
    stm_code true Code STM plstm code
    stm_mode true Str Allowed values are "constant-height" or "constant-current"
    stm_spin true Str Allowed values are "none", "collinear" or "non-collinear"
    stm_value true Float Value of height in Ang or value of current in e/bohr**3
    structure true StructureData Input structure
    bandskpoints false KpointsData, NoneType Input kpoints for bands
    basis false Dict, NoneType Input basis
    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.
    ions false IonData Input ion file
    kpoints false KpointsData, NoneType Input kpoints
    lua false Script and files for the Lua engine
    max_iterations false Int Maximum number of iterations the work chain will restart the process to finish successfully.
    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.
    optical false Dict, NoneType Specifications for optical properties
    parent_calc_folder false RemoteData, NoneType Parent folder
    pseudo_family false Str, NoneType
    pseudos false PsfData, PsmlData Input pseudo potentials
    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 Input settings
    stm_options false Dict, NoneType STM plstm code resources and options
    OutputRequiredValid typesDescription
    stm_array true ArrayData
    output_structure false StructureData
    Exit statusMessage
    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.
    200 The main SiestaBaseWorkChain failed
    201 The SiestaBaseWorkChain to obtain the .LDOS file failed
    202 The STM post-process failed

  • siesta.baseneb

    class: aiida_siesta.workflows.neb_base:SiestaBaseNEBWorkChain

    Workchain to run a NEB MEP optimization starting from a guessed path. In theory, such task can be accomplished using directly the SiestaCalculation and passing the guessed path as xyz files in lua.input_files input (see `examples/plugins/siesta/example_neb.py`). Here, instead, the guessed path must be specified as a set of structures in a `TrajectoryData` object. The structures in `TrajectoryData` are then transformed in xyz files and placed in a directory that is the passed to lua.input_files when the SiestaCalculation is called. This better preserves the provenance. Moreover allows cleaner use of ghost (often necessaries) Finally, we have a dedicated output containing all the NEB quantities. This workchain can also become the place where to deal with possible errors due to the lua features.

    InputRequiredValid typesDescription
    code true Code Input code
    neb_script true SinglefileData Lua script for NEB engine
    options true Dict Options
    parameters true Dict Input parameters
    starting_path true TrajectoryData Starting Path
    bandskpoints false KpointsData, NoneType Input kpoints for bands
    basis false Dict, NoneType Input basis
    ions false IonData Input ion file
    kpoints false KpointsData, NoneType Input kpoints
    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.
    optical false Dict, NoneType Specifications for optical properties
    parent_calc_folder false RemoteData, NoneType Parent folder
    pseudos false PsfData, PsmlData Input pseudo potentials
    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 Input settings
    spring_constant false Float
    OutputRequiredValid typesDescription
    neb_output_package true TrajectoryData
    Exit statusMessage
    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.
    201 The NEB calculation failed
    202 The .xyz files or the NEB.results file could not be retrieved

  • siesta.epsilon

    class: aiida_siesta.workflows.epsilon:EpsilonWorkChain

    Workchain to obtain the electronic contribution to the static dielectric constant using Siesta.

    InputRequiredValid typesDescription
    code true Code Input code
    optical true Dict, NoneType Specifications for optical properties
    options true Dict
    parameters true Dict Input parameters
    structure true StructureData Input structure
    bandskpoints false KpointsData, NoneType Input kpoints for bands
    basis false Dict, NoneType Input basis
    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.
    ions false IonData Input ion file
    kpoints false KpointsData, NoneType Input kpoints
    lua false Script and files for the Lua engine
    max_iterations false Int Maximum number of iterations the work chain will restart the process to finish successfully.
    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 Parent folder
    pseudo_family false Str, NoneType
    pseudos false PsfData, PsmlData Input pseudo potentials
    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 Input settings
    OutputRequiredValid typesDescription
    output_parameters true Dict The calculation results
    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`.
    bands false BandsData Optional band structure
    epsilon false Float Low-frequency dielectric constant
    forces_and_stress false ArrayData Optional forces and stress
    ion_files false IonData
    optical_eps2 false ArrayData Optional eps2 optical data
    output_structure false StructureData Optional relaxed structure
    remote_stash false RemoteStashData Contents of the `stash.source_list` option are stored in this remote folder after job completion.
    Exit statusMessage
    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.
    401 The maximum number of iterations was exceeded.
    402 The process failed for an unknown reason, twice in a row.
    403 Basis polarization problem.
    404 Error in the parsing of bands

  • siesta.iterator

    class: aiida_siesta.workflows.iterate:SiestaIterator

    Iterator for the SietaBaseWorkChain. The iterator is extended to iterate over any Siesta keyword. WARNING: if a keyword not recognized by Siesta is used in `iterate_over`, the iterator will not complain. It will just add the keyword to the parameters dict and run the calculation!

    InputRequiredValid typesDescription
    iterate_over true Dict A dictionary where each key is the name of a parameter we want to iterate over (str) and each value is a list with all the values to iterate over for that parameter. Each value in the list can be either a node (unstored or stored) or a simple python object (str, float, int, bool). Note that each subclass might parse this keys and values differently, so you should know how they do it.
    bandskpoints false KpointsData, NoneType Input kpoints for bands
    basis false Dict, NoneType Input basis
    batch_size false Int The maximum number of simulations that should run at the same time. You can set this to a very large number to make sure that all simulations run in one single batch if you want.
    clean_workdir false Bool If `True`, work directories of all called calculation jobs will be cleaned at the end of execution.
    code false Code Input code
    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.
    ions false IonData Input ion file
    iterate_mode false Str Indicates the way the parameters should be iterated. Currently allowed values are: - 'zip': zips all the parameters together (all parameters should have the same number of values!) - 'product': performs a cartesian product of the parameters. That is, all possible combinations of parameters and values are explored.
    kpoints false KpointsData, NoneType Input kpoints
    lua false Script and files for the Lua engine
    max_iterations false Int Maximum number of iterations the work chain will restart the process to finish successfully.
    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.
    optical false Dict, NoneType Specifications for optical properties
    options false Dict
    parameters false Dict Input parameters
    parent_calc_folder false RemoteData, NoneType Parent folder
    pseudo_family false Str, NoneType
    pseudos false PsfData, PsmlData Input pseudo potentials
    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 Input settings
    structure false StructureData Input structure
    Exit statusMessage
    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.

  • siesta.converger

    class: aiida_siesta.workflows.converge:SiestaConverger

    Only connects the two parent classes.

    InputRequiredValid typesDescription
    iterate_over true Dict A dictionary where each key is the name of a parameter we want to iterate over (str) and each value is a list with all the values to iterate over for that parameter. Each value in the list can be either a node (unstored or stored) or a simple python object (str, float, int, bool). Note that each subclass might parse this keys and values differently, so you should know how they do it.
    bandskpoints false KpointsData, NoneType Input kpoints for bands
    basis false Dict, NoneType Input basis
    batch_size false Int The maximum number of simulations that should run at the same time. You can set this to a very large number to make sure that all simulations run in one single batch if you want.
    clean_workdir false Bool If `True`, work directories of all called calculation jobs will be cleaned at the end of execution.
    code false Code Input code
    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.
    ions false IonData Input ion file
    iterate_mode false Str Indicates the way the parameters should be iterated. Currently allowed values are: - 'zip': zips all the parameters together (all parameters should have the same number of values!) - 'product': performs a cartesian product of the parameters. That is, all possible combinations of parameters and values are explored.
    kpoints false KpointsData, NoneType Input kpoints
    lua false Script and files for the Lua engine
    max_iterations false Int Maximum number of iterations the work chain will restart the process to finish successfully.
    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.
    optical false Dict, NoneType Specifications for optical properties
    options false Dict
    parameters false Dict Input parameters
    parent_calc_folder false RemoteData, NoneType Parent folder
    pseudo_family false Str, NoneType
    pseudos false PsfData, PsmlData Input pseudo potentials
    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 Input settings
    structure false StructureData Input structure
    target false Str, NoneType The parameter that you want to track.
    threshold false Int, Float The maximum difference between two consecutive steps to consider that convergence is reached
    OutputRequiredValid typesDescription
    converged true Whether the target has converged
    converged_parameters false The values for the parameters that was enough to achieve convergence. If converged is not achieved, it won't be returned
    converged_target_value false The value of the target with convergence reached.
    Exit statusMessage
    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.

  • siesta.sequential_converger

    class: aiida_siesta.workflows.converge:SiestaSequentialConverger

    An iterator of convergers.

    InputRequiredValid typesDescription
    converger_inputs true Data
    iterate_over true List A dictionary where each key is the name of a parameter we want to iterate over (str) and each value is a list with all the values to iterate over for that parameter. Each value in the list can be either a node (unstored or stored) or a simple python object (str, float, int, bool). Note that each subclass might parse this keys and values differently, so you should know how they do it.
    batch_size false Int The maximum number of simulations that should run at the same time. You can set this to a very large number to make sure that all simulations run in one single batch if you want.
    iterate_mode false Str Indicates the way the parameters should be iterated. Currently allowed values are: - 'zip': zips all the parameters together (all parameters should have the same number of values!) - 'product': performs a cartesian product of the parameters. That is, all possible combinations of parameters and values are explored.
    metadata false
    OutputRequiredValid typesDescription
    converged_parameters true The values for the parameters that was enough to achieve convergence. If convergence is not achieved, it will be an empty dictionary
    converged_target_value false The value of the target with convergence reached.
    unconverged_parameters false The list of unconverged parameters.
    Exit statusMessage
    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.

  • siesta.forbasisopt

    class: aiida_siesta.workflows._for_optimization:ForBasisOptWorkChain

    Wrapper of SiestaBaseWorkChain. Class wrapping the SiestaBaseWorkChain with the scope of assigning the variables of the optimization process to the right input of the SiestaBaseWorkChain.

    InputRequiredValid typesDescription
    lower_bounds true List
    out_name true Str
    siesta_base true Data
    the_names true List
    the_values true List
    upper_bounds true List
    metadata false
    OutputRequiredValid typesDescription
    ene true Float
    Exit statusMessage
    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.

  • siesta.simplex_basis

    class: aiida_siesta.workflows.simplex_basis:SimplexBasisOptimization

    Workchain running a simple NelderMead optimization (simplex) varing variables defined in the basis dictionaries.

    InputRequiredValid typesDescription
    siesta_base true Data
    simplex true
    metadata false
    OutputRequiredValid typesDescription
    last_simplex true List
    optimal_process_output true Output value of the optimal evaluation process.
    optimal_process_uuid true UUID of the optimal evaluation process.
    optimal_process_input false Input value of the optimal evaluation process.
    Exit statusMessage
    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.
    200 The OptimizationWorkChain did not finished

  • siesta.two_step_basis_opt

    class: aiida_siesta.workflows.two_steps_optimization:TwoStepsBasisOpt

    Optimization that is more similar to the simplex code in the siesta utils. The optimization has two levels, a "marcrostep" that consists in the restart of a simplex with gradual reduction of the dimention of the initial simplex.

    InputRequiredValid typesDescription
    macrostep true
    siesta_base true Data
    simplex true
    metadata false
    OutputRequiredValid typesDescription
    last_simplex true List
    optimal_process_output true Output value of the optimal evaluation process.
    optimal_process_uuid true UUID of the optimal evaluation process.
    optimal_process_input false Input value of the optimal evaluation process.
    Exit statusMessage
    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.

  • siesta.basis_optimization

    class: aiida_siesta.workflows.basis_optimization:BasisOptimizationWorkChain

    WorkChain for basis optimization.

    InputRequiredValid typesDescription
    optimization_schema true
    siesta_base true Data
    simplex true
    add_orbital false Dict, NoneType
    basis_sizes false List
    metadata false
    sizes_monitored_quantity false Str
    OutputRequiredValid typesDescription
    optimal_basis_block true Dict
    Exit statusMessage
    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.
    200 The SiestaIterator running pao sizes failed
    201 The basis optimization failed, probably not sufficient steps
    202 The basis optimization failed, probably not sufficient steps
Data node types aiida.data

  • siesta.ion

    aiida_siesta.data.ion:IonData
aiida.tools.data.orbitals aiida.tools.data.orbitals

  • siesta.atomic_orbital

    aiida_siesta.data.atomic_orbitals:SislAtomicOrbital