Running Calculations

Running Calculations#

Introduction#

This guide demonstrates how to use aiida-atomistic structures in computational workflows, particularly with Quantum ESPRESSO through the aiida-quantumespresso plugin. We’ll cover the basic PwBaseWorkChain for a generic self-consistent field (SCF) calculation.

Prerequisites#

Ensure you have the necessary packages installed:

pip install aiida-pseudo # for now: `atomistic` branch from https://github.com/mikibonacci/aiida-pseudo.git
pip install aiida-quantumespresso # for now: `atomistic ` branch from https://github.com/mikibonacci/aiida-quantumespresso.git

And configure your Quantum ESPRESSO code:

verdi code list  # Check existing codes
verdi code create core.code.installed  # Create new code if needed

Finally, install pseudos, if not already done:

aiida-pseudo install sssp # install the default SSSP/1.3/PBE/efficiency family

Basic SCF WorkChain#

from aiida import orm, load_profile
from aiida.engine import run_get_node

from aiida_quantumespresso.workflows.pw.base import PwBaseWorkChain
from aiida_atomistic import StructureData

from ase.build import bulk

load_profile()

# Create silicon structure
si_atoms = bulk('Si', 'diamond', a=5.43)
structure = StructureData.from_ase(si_atoms, detect_kinds=True)

print(f"Created structure: {structure.properties.formula}")
print(f"Cell volume: {structure.properties.cell_volume:.2f} Angstrom^3")
print(f"Kinds: {structure.kinds}")

Output:

Created structure: Si2
Cell volume: 40.03 Angstrom^3
Kinds: [Kind(symbol='Si', position=None, mass=28.085, charge=None, magmom=None, magnetization=None, weight=None, kind_name='Si0', positions=array([[0.    , 0.    , 0.    ],1.3575, 1.3575, 1.3575]]), site_indices=[0, 1])]

As you can see, we detected kinds (from the ASE atom tags) and we have them defined in our StructureData. This is needed as Quantum ESPRESSO works with kinds.

Then, we can initialise the WorkChain instance and run the calculation:

builder = PwBaseWorkChain.get_builder_from_protocol(
    code=orm.load_code("pw-qe-7.4@localhost"),
    structure=structure,
    protocol="moderate",
    overrides={
        "pseudo_family": "SSSP/1.3/PBE/efficiency",
    }
)

run = run_get_node(builder)

Output:

09/08/2025 05:21:51 PM <79134> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [13671|PwBaseWorkChain|run_process]: launching PwCalculation<13676> iteration #1
09/08/2025 05:22:11 PM <79134> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [13671|PwBaseWorkChain|results]: work chain completed after 1 iterations
09/08/2025 05:22:11 PM <79134> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [13671|PwBaseWorkChain|on_terminated]: remote folders will not be cleaned

Adding tot_charge in our input#

Here below we show a simple example on how to add(remove) charge to the system, and run again the calculation. We basically load the Atoms object using the StructureDataMutable, we add charge and we resubmit:

structure = StructureDataMutable.from_ase(si_atoms, detect_kinds=True)
structure.set_tot_charge(1.0)

builder = PwBaseWorkChain.get_builder_from_protocol(
    code=orm.load_code("pw-qe-7.4@localhost"),
    structure=StructureData.from_mutable(structure),
    protocol="moderate",
    overrides={
        "pseudo_family": "SSSP/1.3/PBE/efficiency",
    }
)

run = run_get_node(builder)

Output:

09/08/2025 05:35:10 PM <88111> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [13688|PwBaseWorkChain|run_process]: launching PwCalculation<13693> iteration #1
09/08/2025 05:35:29 PM <88111> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [13688|PwBaseWorkChain|results]: work chain completed after 1 iterations
09/08/2025 05:35:29 PM <88111> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [13688|PwBaseWorkChain|on_terminated]: remote folders will not be cleaned

Next Steps#

You now have the tools to run sophisticated calculations with aiida-atomistic! Explore the API documentation for more advanced features.

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