The protocols system


In order to submit SiestaCalculations, the user needs to manually select all the inputs, being careful to pass the correct specifications to perform the calculation (as explained in the corresponding section). The package aiida_siesta provides also a set of pre-selected inputs to run a SiestaCalculations, and the WorkChains distributed in the package, supporting the tasks of the relaxation of a structure and the calculations of bands. In other words, the user can obtain a builder of the SiestaCalculation that is ready to be submitted. This builder, in fact, is pre-filled with inputs selected according to the structure under investigation and very few options specified by the user. The lengthy inputs selection is substitute by:

inp_gen = SiestaCalculation.inputs_generator()
builder = inp_gen.get_filled_builder(structure, calc_engines, protocol)

The list of options to obtain the builder is presented here, however the main feature is the use of protocols. A protocol groups operational parameters for a Siesta calculation and it is meant to offer a set of inputs with the desired balance of accuracy and efficiency. At the moment only one protocol is shipped in the package, it is called standard_psml. More on it is presented in the next to next subsection. It is important to note that the implemented protocols are not, for the moment, input parameters that are guaranteed to perform in any situation. They are only based on reasonable assumptions and few tests. However, in the package it is also implemented a system that allows users to create their own protocols, as clarified here. Finally, it must be remembered that the builder produced according to a protocol and few other options is fully modifiable before submission, leaving full flexibility to the user. We expect in the future to have more and more “know how” and improve the reliability and richness of the available protocols.

We focus here on the description of the use of protocols for the SiestaCalculation, but the same system is available for all the WorkChains distributed in this package. A small paragraph in the documentation of each WorkChain will explain the details of the usage of protocols for that particular WorkChain.

Supported Siesta versions

The protocol system, at the moment, requires a version of siesta with support for psml pseudopotential. At least the MaX-1.0 release of Siesta, which can be found in the development platform (, meets this requirement. For more up to date info on compatibility, please check the wiki.

Available protocols

With the word protocol we mean a series of suggested inputs for AiiDA CalJobs/WorkChains that allow users to more easily automatize their workflows. These inputs reflects a certain set of operational parameters for a Siesta calculation. The choice of the inputs of a DFT simulation should be carefully tested for any new system. Therefore the use of protocols, in place of a careful and tested choice of inputs, it is always somehow limiting. It can be, however, considered a good starting point. This is the very beginning of the development and, for the moment, only one very basic protocol is implemented. A description of its variables is now reported. Each protocol contain a section with global variables and an atomic_heuristics dictionary, a dictionary intended to encode the peculiarities of particular elements.

  • standard_psml

    The full list of variables for this protocol are collected in the protocol_registry.yaml file, located in aiida_siesta/utils.

    • global variables

      Pseudopotential ONCVPSPv0.4 (norm-conserving) of Pseudo Dojo in psml format, scalar relativistic, PBE and with standard accuracy (download available from the PseudoDojo web site). Basis set apply globally, with size DZP and energy-shift of 50 meV. The mesh-cutoff is 200 Ry, electronic-temp 25 meV, and a kpoint mesh with distance 0.1 are implemented. Concerning the trashold for convergence, we implement 1.e-4 tolerance for the density matrix, 0.04 ev/ang for forces and 0.1 GPa for stress. Few more global variables are related to mixing options: scf-mixer-history is set to 5, and scf-mixer-weight is 0.1. As only the Max-1.0 version of Siesta is supported, the default mixer is Pulay and the quantity mixed is the Hamiltonian.

    • atomic_heuristics

      The element “Ag” requires a bigger mesh-cutoff because mesh-cutoff = 200 Ry was leading to a “Failure to converge standard eigenproblem” error for the “Ag” elemental crystal. Custom basis for “Ca”,”Sr”,”Ba” are necessary because the automatic generation results in a too-large radius for the “s” orbitals. The “Hg” custom basis introduces an increment of all radii of 5% compared to the automatic generated orbitals and adds a Z orbital for the “p” channel, while removing polarization. The elements “Li”, “Be”, “Mg”, Na”, “Fe”, “Mn”, “Sb” require a bigger mesh-cutoff because mesh-cutoff = 200 Ry resulted in a discontinuous equation of state.

    This choice of parameters have been tested on crystal elements up to the element “Rn” and compared with the reference equation of state of the DeltaTest project, resulting on an average delta value of 7.1 meV. The parameters of this protocol for noble gasses do not result in an a minimum of the equation of state. Because Van der Waals forces are not included in the calculation, the result is not surprising. We warn users to use with care this protocol for noble gasses. It is important to stress that the present protocol has not been conceived to produce good results for the Delta test; the basis sets are mostly automatic and the choice of mesh-cutoff / kpoints-mesh is farely loose. The average value for the delta (7.1 meV) is just an indication that the parameters’ choice gives reasonable results for elemental crystals. We are working on a more accurate (and expensive) protocol that will provide much better values of delta. New tests and checks on the standard_psml protocol will be added in the aiida-siesta wiki.

The management of the pseudos is, at the moment, very fragile. It imposes that the user loads a pseudo_family with the correct name that is hard-coded for the each protocol. This name is ‘nc-sr-04_pbe_standard_psml’ for the standard_psml protocol. Therefore a user, before using protocol, needs to download the correct pseudos and load them (see next section) with the correct name. —This last part will change soon, replaced with a proper setup-profile script —-

How to use protocols

In this section we explain how to obtain a pre-filled builder according to a protocol and an input structure, that is ready to be submitted (or modified and then submitted).

First of all, the scalar relativistic “standard” pseudo set from PseudoDojo must be installed as aiida family pseudo family:

aiida-pseudo install pseudo-dojo -v 0.4 -x PBE -r SR -p standard -f psml

Once this first step is done, the pre-filled builder can be accessed through the method inputs_generator of the SiestaCalculation (and of any other workchain). For example:

from aiida_siesta.calculations.siesta import SiestaCalculation
inp_gen = SiestaCalculation.inputs_generator()
builder = inp_gen.get_filled_builder(structure, calc_engines, protocol)
#here user can modify builder befor submission.

The arguments of get_filled_builder of the input generator are explained here:

  • structure, class StructureData, Mandatory

    A structure. See the plugin documentation for more details.

  • calc_engine, python dict, Mandatory

    A dictionary containing the specifications of the code to run and the computational resources. An example:

    calc_engines = {
        'siesta': {
            'code': codename,
            'options': {
                    'resources': {'num_machines': 1, "num_mpiprocs_per_machine": 1},
                    'max_wallclock_seconds': 360,
                    'queue_name': 'DevQ',
                    'withmpi': True,
                    'account': "tcphy113c"

    The dictionary must present siesta as upper level key of the dictionary. This might seem unnecessary, but will become fundamental for the use of protocols in more complicated WorkChain, involving not only the siesta plugin, but also, for instance, the stm plugin. The structure of calc_engines for each WorkChain of the package will be specified in the WorkChain documentation.

  • protocol, python str, Mandatory

    The protocol name, selected among the available ones, as explained in the previous section.

  • bands_path_generator, python str, Optional

    The presence of this parameter triggers the calculation of bands. Two are the available value to pass as bands_path_generator: “seekpath” or “legacy”. They set the way the path in k-space is produced. This path is used to display the bands. While “seekpath” modify the structure running the calculation on an equivalent “conventional” cell, “legacy” doesn’t and preserves the input structure. However the “legacy” method is known to have bugs for certain structure cells.

  • relaxation_type, python str, Optional

    The presence of this parameter triggers the possibility to relax the structure. The specifications of the relaxation_type are “atoms_only”, “variable_cell” or “constant_volume”, that should be self expalnatory. For the moment only the CG relaxation algorithm is implemented (in the future more will be added).

  • spin, python str, Optional

    The presence of this parameter triggers the spin options. The specifications of the spin are the one of modern version of Siesta, they are “polarized”, “non-collinear” and “spin-orbit”. If no spin option is defined, the calculation will not be spin polarized.

An example of the use is in aiida_siesta/examples/plugins/siesta/

The method get_filled_builder is definitely the most important tool offered by the inputs_generator, however through the inputs_generator other methods can be accessed to explore the various options of the protocol system. For instance, there is a method listing all the available protocols, the available relaxation types and so on.

How to create my protocols

The protocol system allows also to create customized protocol. To this end, a file similar to aiida_siesta/utils/protocol_registry.yaml must be created, listing the custom protocols. Then the path of this file must be added to the environment variable AIIDA_SIESTA_PROTOCOLS. This will be sufficient to let aiida-siesta recognize the protocols. The file containing the customized protocols must have the same structure of protocol_registry.yaml. An example:

  description: 'My description'
    xc-functional: "GGA"
    xc-authors: "PBE"
    mesh-cutoff: '200 Ry'
    write-mulliken-pop: 1
    scf-dm-tolerance: 1.e-4
    md-max-force-tol: '0.04 eV/ang'
    md-max-stress-tol: '0.1 GPa'
    pao-energy-shift: '50 meV'
    pao-basis-size: 'DZP'
  pseudo_family: 'nc-sr-04_pbe_standard_psml'
    distance: 0.1
    offset: [0., 0., 0.]
        mesh-cutoff: '250 Ry'
        polarization: 'non-perturbative'
        pao-block: "Li 3 \n  ... "
        split-tail-norm: True

The protocol name should be the outer entry of the indentation. For each protocol, some keyword are mandatory. They are description, parameters, basis and pseudo_family. The pseudo_family must contain the name of a family (Psml or Psf family) that has been already uploaded in the database. The number of elements covered by your pseudo family will limit the materials you can simulate with your protocol. The parameters and basis entries are transformed into dictionaries and passed to AiiDA after possible modifications due to atom heuristics or spin/relax additions. For this reason, the syntax (lower case and ‘-’ between words) must be respected in full.

Two optional keywords are relax_additions and spin_additions. This two entries are not meant to host the siesta keywords that activate the relaxation or spin options, but possible additions/modifications to the parameters entry, to apply in case of relaxation or spin. When the use of protocols is called and the relax/spin options are requested (see here), the system will automatically take care of introducing the correct siesta keyword (MD.TypeOfRun, MD.VariableCell, spin etc.) that are indispensable to run the task. However, it might happen that a user desires a more loose scf-dm-tolerance for the task of the relaxation or a different scf-mixer-weight when the spin is active. The relax_additions and spin_additions keywords have been created exactly for this purpose. Please be carefull that (except for the mesh-cutoff) if a keyword in spin_additions or relax_additions is already present in parameters, its value in parameters will overriden. In other words, values in spin_additions or relax_additions have priority compared to the one in parameters. Moreover relax_additions has priority respect to spin_additions. For the mesh-cutoff the situation is different, because the biggest value will always be considered, no metter where it is specified. Another optional entry is kpoints, where a distance and an offset only can be specified. The system will take care to create a uniform mesh for the structure under investigation with a density that correspond to a distance (in 1/Angstrom) between adjacent kpoints equal to dinstance.

The final allowed (optional) keyword is atomic_heuristics. In it, two only sub-keys are allowed: parameters and basis. In parameters, only a ‘mesh-cutoff’ can be specified. This mesh-cutoff applies globally and only if it is the biggest one among the all mesh-cutoff that apply. This system is meant to signal elements that requires a bigger ‘mesh-cutoff’ than normal. For basis, we allow ‘split-tail-norm’, ‘polarization’, ‘size’ and ‘pao-block’. The ‘size’ and’ polarization’ introduce a block reporting the change of pao size and polarization schema only for the element under definition. The ‘pao-block’ allows to specify an explicit “block Pao-basis” for the element. The ‘split-tail-norm’ instead activate in siesta the key ‘pao-split-tail-norm’, that applies globally.

We conclude this subsection with few more notes to keep in mind. First, the units mut be specified for each siesta keyword that require units and they must be consisten throughout the protocol. This means that it is not possible to define ‘mesh-cutoff’ in Ry in parameters, but in eV in the atomic_heuristics. Second, it is up to the creator to remember to introcude the correct ‘xc-functional’ and ‘xc-authors’ keywords in the protocol that matches the same exchange-correlation functional of the pseudos in the pseudo family. This also means that we do not support pseudos presenting different exchange-correlation functionals in the same family. Third, we impose a description for each protocol because in the description the creator must underline the limitations of the protocol. For instance, the case when a certain protocol do not support spin-orbit as the pseudos are not relativistics. The schema we presented here is certanly not perfect and it is far to cover all the possible situations, however it must be remembered that any user has always the chance to modify the inputs (builder) before submission.