This repository provides a sample workflow for running quantum espresso calculations on nanoHUB.

To use this repository, first make an account at nanohub. This is a free account and will let you access hundreds of scientific tools, all hosted in a cloud environment.

To copy this workflow to your nanoHUB storage, you need to open a terminal in nanoHUB. You have two options on how to do this:

1. (recommended) open a jupyter notebook session with nanoHUB, and click on 'new terminal' from the top right

2. ssh into nanoHUB using ssh [email protected] with username as your nanoHUB account username, from your choice of terminal

From here, you can copy this workflow using git clone https://github.com/katnykiel/qe_workflow.git. This will put the workflow and pseudopotential files in your nanoHUB storage.

To run this from a command line, you first need to open a terminal in nanoHUB using one of the methods described above. Then, you can take the following steps:

1. Create your input file. An example input file is provided for the relaxation of a Ti3C2 MXene with O passivations, mxene_relax.in . These files can be edited from the command line using vi or the text editor of your choice. Documentation for the input files is provided on quantum-espresso.org. Copied below is the input file for a MXene relaxation:

&CONTROL
  calculation = 'vc-relax',
  outdir = './',
  pseudo_dir = './pseudo/pseudo_PAW/',
  tstress = .TRUE.,
/
&SYSTEM
  ecutwfc = 50,
  ibrav = 0,
  nat = 7,
  ntyp = 3,
/
&ELECTRONS
/
&IONS
/
&CELL
/
ATOMIC_SPECIES
  C  12.0107 C.upf
  O  15.9994 O.upf
  Ti  47.8670 Ti.upf
ATOMIC_POSITIONS (crystal)
  Ti       0.666667000   0.333333000   0.326623379
  Ti       0.333333000   0.666667000   0.673376621
  Ti      -0.000000000  -0.000000000   0.500000000
  C        0.333333000   0.666667000   0.418006988
  C        0.666667000   0.333333000   0.581993012
  O        0.333333000   0.666667000   0.261205357
  O        0.666667000   0.333333000   0.738794643
K_POINTS automatic
  3 3 3 0 0 0
CELL_PARAMETERS (angstrom)
   1.519306316  -2.631514017  -0.000000000
   1.519306316   2.631514017   0.000000000
  -0.000000000  -0.000000000  14.905657660

  

2. Run the simulation. We run the simulation using the following command, printing the output to the console as it is generated:

use espresso-6.2.1
pw.x -i mxene_relax.in > mxene_relax.out &
watch tail mxene_relax.out

This should take no more than 10 minutes.

To run this from a jupyter notebook, open qe_workflow.ipynb and run the cells.

This workflow demonstrates several additional features:

• how to submit jobs remotely to Purdue HPC clusters
• various helper functions to plot the convergence results and extract the outputs
• create new input files with pymatgen
• query for structures from Materials Project

Please raise any issues in the issues section of this repository.