Tutorial

In this tutorial, we will introduce how to use my plugins for accelerating the computational research.

My plugins hzdplugins have the following module structures:

  • aiidaplugins

    • submit module: for submitting the computational jobs

    • io module: for managing the contents on remote server

    • info module: for getting information from structures

  • structure

    • build module: for building the structure that we want to calculate.

So in the following tutorial, I will show a very simple script that can calculate the OH adsorption on Pt(111) surface.

First you need to setup your Aiida environment, for how to do that I have uploaded 2 articles:

# import the important functions
%aiida # start the basic aiida environment
from hzdplugins.structure.build import bulkFromString, millerSurfaces, adsorptionSites, visualizeSlab, addAdsorbates, setFixedCoords
from hzdplugins.aiidaplugins.info import getStructure
from hzdplugins.aiidaplugins.submit import qePwOriginalSubmit
from aiida.orm import Int, List, Dict, Str, Bool, Float, Data

# creating the Pt_bulk
Pt_bulk = bulkFromString(bulkStr = Str('Pt'), crystal_structure=Str('fcc'), a = Float(3.98), cubic=Bool(True), supercell = List(list=[1, 1, 1]))

# creating the slab
slab_list = millerSurfaces(bulk = Pt_bulk, miller_index = List(list=[1, 1, 1]), layers = Int(4), vacuum = Int(8))
slab_list = slab_list.get_list()
surface = load_node(slab_list[0])

# find adsorption sites
adsorption_sites = adsorptionSites(slab = surface)
adsorption_sites = adsorption_sites.get_dict()

# create adsorption configuration
adsSiteDictionary = {
    'OH': [adsorption_sites['ontop'][0]]
}

# create slab with the surface and adsorbates
surfSlabWithAds = addAdsorbates(slab = surface,
                                adsSiteDictionary=Dict(dict=adsSiteDictionary))

# assign fixed_coords (or selective dynamics in VASP term)
fixed_coords = setFixedCoords(slab=surfSlabWithAds, height=14)

# settings for the pw.x calculation
settings_dict = {
'fixed_coords': fixed_coords,
'cmdline': ['-nk', '4'],
'additional_retrieve_list': ['aiida.out']
}

# start the pw.x original calculation (no previous calculations are needed)
results = {}
results, uuid_new = qePwOriginalSubmit(
    results = results,
    codename = 'pw.x-6.6-juwels@juwels-mac',
    structure = surfSlabWithAds,
    kpoints = [[4, 4, 1]],
    pseudo_family = 'sssp-precision',
    pseudo_dict = {},
    metadata = {
        'label': 'Pt111-OH',
        'description': 'test whether my package is good.'
    },
    add_parameters = {
        'SYSTEM': {
            'input_dft': 'PBESOL'
        },
        'ELECTRONS': {
            'mixing_mode': 'local-TF',
            'mixing_beta': 0.3,
            'mixing_ndim': 10
        }
    },
    del_parameters = {},
    cluster_options = {},
    settings_dict = settings_dict
)

# then you can check the results by using
# node = load_node(uuid=uuid_new)