This page introduces basic usage of APNS implemented presently.

This page is not well-formatted yet

ABACUS Pseudopot-Nao Square

Example `input.json`


{

    // some global settings placed here

    "global": {

        "test_mode": "pseudopotential",           // "pseudopotential" or "numerical_orbital"

        "software": "ABACUS",                     // "ABACUS" or "qespresso"

        "work_dir": "./",                         // the working directory

        "pseudo_dir": "./module_pseudo/download", // always fixed, pseudopotential now is 

                                                  // designed to distribute along with the code

        "orbital_dir": "./module_nao/download",   // will be the directory to store numerical orbital files

        "save_log": true                          // will dump json

    },

    "calculation": {

        "basis_type": "pw",     // "pw" or "lcao". "pw" is supported by both ABACUS and qespresso, 

                                // "lcao" is only supported by ABACUS

        "functionals": ["PBE"], // enumerate! xc functional

        "ecutwfc": [100],       // enumerate! ecutwfc that will impose for all systems

        ...                     // other keywords

    },

    "systems": ["Er2O3"],       // enumerate! system name, will be used to find CIF via Materials Project API.

                                // or specify not symmetrized CIF file path in structures list

    "extensive": {

        "characteristic_lengths": [] // for isolated system such as dimer,..., is bond length. For crystal, it is scale factor of cell

        "nkpoints_in_line": 10,      // number of kpoints in each segment of kpath. Default is 0, for isolated system, autoset to -1.

                                     // 0 is interpreted as MP sampling, a positive number will generate a kpath instead of mesh

    },

    "materials_project": {

        "api_key": "xxx",       // your Materials Project API

        "n_structures": 1,      // number of structures want to download, for each system or specify a list for systems

        "theoretical": false,   // always keep false to get only experimentally observed structures

        "most_stable": true     // get the most stable structure

    },

    // psedupotential section supports two ways input, the first is list, the second is dict.

    // For a list, the specified kinds, versions and appendices will be used for all elements in

    // all systems. For a dict, must specify kinds, versions and appendices for each element.

    "pseudopotentials": {

        "kinds": ["sg15", "pd"],   // supports "sg15", "pd" or "dojo" presently, also "all" for all available norm-conserving pseudopotentials stored locally

        "versions": ["10", "04"],  // support version selection of pseudopotentials, also "all" for all available versions

        "appendices": [""]         // support appendix selection of pseudopotentials, also "all" for all available appendices

    },

    // similarly for numerical orbitals, BUT NOT IMPLEMENTED YET

    "numerical_orbitals": {

        "types": ["DZP"],

        "rcuts": [7, 8, 9, 10],

        "appendices": [""]

    }

}

Full input keywords list

This document provides a full list of keywords for ABACUS Pseudopot-Nao Square. The keywords are divided into several sections, each section is for a specific purpose. The keywords are listed in alphabetical order within each section.

`global` section

`test_mode`

Description: mode to test, can be pseudopotential or numerical_orbital. For pseudopotential mode, if software specified as ABACUS, then basis_type pw will be automatically set, if software specified as qespresso, nothing would happen. pseudopotential test mode will only test the pseudopotential, and numerical_orbital mode need user specify information of pseudopotential and numerical orbitals both.
Type: string
Default: pseudopotential

`software`

Description: software to test, can be ABACUS or qespresso. If software specified as ABACUS, then basis_type pw will be automatically set, if software specified as qespresso, nothing would happen.
Type: string
Default: ABACUS

`work_dir`

Description: working directory, all the files will be generated in this directory.
Type: string
Default: ./

`pseudo_dir`

Description: directory to store pseudopotential files.
Type: string
Default: ./module_pseudo/resources/

`orbital_dir`

Description: directory to store numerical orbital files.
Type: string
Default: ./module_nao/resources/

`save_log`

Description: whether to save log (json)
Type: bool
Default: True

`calculation` section

This section actually supports any number of keywords that specified list values, which indicate values in list are needed to enumerate and cross-test. Therefore to add additional keywords, specify value as usual. To let program do crosstest on this keyword with all possible values, give this keyword a list of possible values. Keyword should have identical name with that in input script. There are discrepancies between ABACUS and qespresso, so use with care.

`basis_type`

Description: basis type, can be pw or lcao. software ABACUS supports both pw and lcao, software qespresso only supports pw.
Type: string
Default: pw

`functionals`

Description: DFT functionals to test, specified as list.
Type: list
Default: ['PBE']

`ecutwfc`

Description: kinetic energy cutoffs for wavefunctions, in Rydberg, specified as list, but instead this keyword can be set via ABACUSTEST application, see https://labs.dp.tech/projects/abacustest/
Type: list
Default: [100]

`systems` section

This section should be organized in the following way:


{
    "systems": ["Yb2O3", "Er", "TiO2"]
}

Elements will be recognized from this section, then `pseudopotentials` and `numerical_orbitals` section will search available files for these elements. For analysis task, this section will have more options, e.g.:


{
    "systems": {
        "Yb2O3": {
            "band_gap": 5.0,
            "lattice_constant": 10.0,
        },
        "Er": {
            "band_gap": 5.0,
            "lattice_constant": 10.0,
        },
    }
}

`extensive` section

`characteristic_lengths`

Description: characteristic length, for cell, it is deformation ratio of lattice, for isolated system, it is the bond length
Type: list
Default: [0.00]

`nkpoints_in_line`

Description: number of kpoints in each segment of kpath. Default is 0, for isolated system, autoset to -1. 0 is interpreted as MP sampling, a positive number will generate a kpath instead of mesh
Type: int
Default: 0

`materials_project` section

`api_key`

Description: Materials Project Application Program Interface (API) Key. Get your API key following tutorial in https://docs.materialsproject.org/downloading-data/using-the-api
Type: string

This keyword is compulsory for running APNS test suite generation, no default value is given. If not specified, will raise error

`n_structures`

Description: For each system specified, how many structures are needed. If a list is given, then the length of the list should be the same as the length of systems section. If an integar is given, then will use the same number for all systems.
Type: int or list
Default: 1

`theoretical`

Description: Whether to get theoretical structures. If True, then will get theoretical structures, if False, then will only get experimental structures.
Type: boolean
Default: False

`most_stable`

Description: If only get structures which are marked as is_stable in Materials Project. If True, then will only get the most stable structure, if False, then will get all structures. The is_stable here sometimes means the most stable, some sub-stable structures will be filtered out, like TiO2 anatase.
Type: boolean
Default: False

`pseudopotentials` section

`kinds`

Description: kinds of pseudopotentials to test (sg15, pd, rrkjus or something other), specified as list. If contents are not organized element-by-element, then will use the same pseudopotential for all elements. all can also be given, then all kinds of pseudopotentials will be included in test suite, use with caution.
Type: list or dict
Default: [""]

`versions`

Description: versions of pseudopotentials to test, specified as list. If contents are not organized element-by-element, then will use the same version for all elements. all can also be given, then all versions of pseudopotentials will be included in test suite, use with caution.
Type: list or dict
Default: [""]

`appendices`

Description: appendices of pseudopotentials to test, specified as list. If contents are not organized element-by-element, then will use the same appendix for all elements. all can also be given, then all appendices of pseudopotentials will be included in test suite, use with caution.
Type: list or dict
Default: [""]

`numerical_orbitals` section

`types`

Description: types of numerical orbitals to test (DZP or TZDP, conventionally), specified as list. If contents are not organized element-by-element, then will use the same type for all elements.
Type: list or dict
Default: [""]

`rcuts`

Description: cutoff radii of numerical orbitals to test, specified as list. If contents are not organized element-by-element, then will use the same cutoff radius for all elements.
Type: list or dict
Default: [""]

`appendices`

Description: appendices of numerical orbitals to test, specified as list. If contents are not organized element-by-element, then will use the same appendix for all elements.
Type: list or dict
Default: [""]

ABACUS Pseudopot-Nao Square

Example input.json

Full input keywords list

global section

test_mode

software

work_dir

pseudo_dir

orbital_dir

save_log

calculation section

basis_type

functionals

ecutwfc

systems section

extensive section

characteristic_lengths

nkpoints_in_line

materials_project section

api_key

n_structures

theoretical

most_stable

pseudopotentials section

kinds

versions

appendices

numerical_orbitals section

types

rcuts

appendices

Example `input.json`

`global` section

`test_mode`

`software`

`work_dir`

`pseudo_dir`

`orbital_dir`

`save_log`

`calculation` section

`basis_type`

`functionals`

`ecutwfc`

`systems` section

`extensive` section

`characteristic_lengths`

`nkpoints_in_line`

`materials_project` section

`api_key`

`n_structures`

`theoretical`

`most_stable`

`pseudopotentials` section

`kinds`

`versions`

`appendices`

`numerical_orbitals` section

`types`

`rcuts`

`appendices`