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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 and codes installed, which you can verify by following the corresponding installation guide.

Compatible AiiDA and other plugins version with aiida-atomistic

For now, please install these versions of the following packages:

  • aiida-core: dev/atomistic branch from https://github.com/mikibonacci/aiida-core.git
  • aiida-pseudo: dev/atomistic branch from https://github.com/mikibonacci/aiida-pseudo.git
  • aiida-quantumespresso: dev/atomistic branch from https://github.com/mikibonacci/aiida-quantumespresso.git

You can install all of them by running pip install .[run].

If not already done, remember to install the sssp pseudopotentials:

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

Preparing and submitting a basic PwBaseWorkChain

If you are new to the PwBaseWorkChain, please follow the corresponding tutorial.

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)

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

Output: 

Created structure: Si2
Cell volume: 40.03 Angstrom^3
Kinds: ['Si', 'Si']

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 only 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 calculation

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 StructureBuilder, we add charge and we resubmit:

structure = StructureBuilder.from_ase(si_atoms)
structure.set_tot_charge(1.0)

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

run = run_get_node(builder)

Output: 

11/04/2025 05:48:46 PM <42782> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [13784|PwBaseWorkChain|run_process]: launching PwCalculation<13789> iteration #1
11/04/2025 05:49:09 PM <42782> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [13784|PwBaseWorkChain|results]: work chain completed after 1 iterations
11/04/2025 05:49:10 PM <42782> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [13784|PwBaseWorkChain|on_terminated]: remote folders will not be cleaned

You can verify that the tot_charge was indeed set in the input file of the pw.x calculation:

verdi calcjob inputcat 13789 | grep tot_charge

Output: 

tot_charge =   1.0000000000d+00

Full explanation on how to set all the properties and automatically detect kinds, is contained in the How to sections.