please execute the cell below before starting the tutorial by selecting the cell and pressing Ctrl+Enter

%load_ext autoreload
%autoreload 2
from aiida import load_profile
load_profile()

from aiida.orm import Dict, load_node, load_code
from aiida.engine import submit
# First we will import a prepared dataset for this tutorial with some structures and simulations
# If this was already executed, it will add nothing to the database
!verdi archive import ~/4.AiiDA-FLEUR/files/fleur_tutorial_data.aiida

Fleur calculations

DISCLAIMER: In real life work, one will probably not execute inpgen or even fleur calculation like we show you below, but one rather runs directly higher workflows/workchains, which is part of the 6th Notebook. This is for demonstration purposes and to familiarize yourself with aiida and concepts of the plugin

A Fleur calculation is represented by a FleurCalculation class in AiiDA.

Generally one needs only two inputs for a Fleur calculation: an inp.xml file and initial charge density. As you already know, there is a FleurinpData class representing an inp.xml file. Therefore, there is a FleurinpData object in the inputs.

No class represents charge density in AiiDA-Fleur and one can not pass it explicitly into a FleurCalculation. However, it can be done specifying RemoteData node that represents a calculation folder of a previous FLEUR calculation. If a RemoteData input is given, the calculation automatically finds its charge density (and inp.xml in some cases) and uses it as an input. This will be explained more in next sub-section.

Inputs of the Fleur calculation

name type description required
code Code Fleur code yes
fleurinpdata FleurinpData Object representing inp.xml no
parent_folder RemoteData Remote folder of another calculation no
settings Dict special settings no
metadata.options Dict computational resources yes

code is a Code object representing Fleur code stored in the database; it is the only required input (except metadata.options). However, it is not enough to specify the code only: one must provide one of supported input configurations:

  • code + fleurinpdata : start a calculation from scratch using given inp.xml
  • code + parent_folder : start a calculation using inp.xml and charge density from the previous calculation
  • code + fleurinpdata + parent_folder : start a calculation using inp.xml from given FleurinpData and charge density from the previous calculation

In this tutorial we are going to use code + fleurinpdata configuration only.

settings is used to modify a list of files to be copied to/from/between calculation folders and to append command options to the executable. We will not cover this in the tutorial.

Fleur code submission

Inputs preparation

First of all, we need to import FleurCalculation class.

from aiida_fleur.calculation.fleur import FleurCalculation

or use the CalculationFactory:

from aiida.plugins import CalculationFactory
FleurCalculation = CalculationFactory('fleur.fleur')

and prepare input nodes. Configured and ready-to-use Fleur code nodes are already stored in your database (verdi code list -A). Now you can load them per label, pk, or uuid:

fleur_code = load_code('fleur@localhost')

We are going to use a FleurinpData that you created in tutorial 4. Please, remind a PK of a Fe monolayer structure and load in via the same command:

# you need to modify this - please remind the PK of previously created FleurinpData 
fleurinpdata = load_node(PK_IRON_FLEURINPDATA)

We also need to define computational options. We use a parallel Fleur version and thus set 'withmpi' to True and submit two MPI processes:

options = {'resources' : {"num_machines": 1, "num_mpiprocs_per_machine" : 1},
           'queue_name' : '',
           'withmpi' : True,
           'max_wallclock_seconds' : 600}

Assembling inputs in a single dictionary

Similarly to FleurinpgenCalculation, we will use get_builder() method to assemble all the inputs:

inputs = FleurCalculation.get_builder()
inputs.code = fleur_code
inputs.fleurinpdata = fleurinpdata
inputs.metadata.options = options

Job submission

Looks the same as for FluerinpgenCalculation (and any other AiiDA calculation):

fleur_process = submit(inputs)
print('The PK of submitted job is {}'.format(fleur_process.pk))

Results analysis

After FLEUR code is submitted, you can check the status of all submitted processes for last 24 hours:

!verdi process list -a -p 1

You can also check the status of inpgen calculation directly. Try running next cell and examine the output:

# you need to modify this - insert the FleurCalculation PK:
!verdi process status FLEUR_CALC_PK

Wait till the process status becomes 'Finished'. Then, let us explore the output nodes. FleurCalculation generates three output nodes:

name type comment
output_parameters Dict contains parsed out.xml
remote_folder FolderData represents calculation folder
retrieved FolderData represents retrieved folder

To extract their PKs, run:

# you need to modify this - insert the FleurCalculation PK:
!verdi process show FLEUR_CALC_PK

The other way to access the output nodes is to find them in fleur_calc_node.outputs:

# you need to modify this - insert the FleurCalculation PK:
fleur_calc_node = load_node(FLEUR_CALC_PK)
output_parameters = fleur_calc_node.outputs.output_parameters
print('PK of the output parameters is {}'.format(output_parameters.pk))

The output_parameters dictionary contains parsed out.xml file. To print its content, run:

output_parameters.get_dict()

or

#you need to modify it - replace OUTPUT_PARAM_PK
!verdi data dict show OUTPUT_PARAM_PK

Analysing output dictionary, can you tell what is the band gap and total energy of the ground state?

Scripting tasks

1. Run a Fleur calculation for the Si (remote_folder input configuration)

Create a script and run it in the terminal, passing to FleurCalculation code + fleurinpdata + remote_folder. Use remote_folder and fleurinpdata of the calculation in this tutorial. Modify fleurinpdata: change the number of iterations to 30 and mixing parameter alpha to 0.02.

Answer the questions:

  1. What files were copied to the calculation folder?
  2. How did the total energy change?
  3. How did the band gap change?
  4. How did the walltime change?