Running Quantum ESPRESSO

Quantum ESPRESSO is a group of codes that is used to compute the microscopic properties of materials and molecules at the atomic levels using density functional theory. The core codes of Quantum ESPRESSO are parallelizable and require large amounts of memory making them the perfect candidates for high performance computing. This article is written to understanding the nuances of using Quantum ESPRESSO on Pinnacles and MERCED. To follow a tutorial on Quantum ESPRESSO, follow one of the links on this page.

Job Script for Bilayer MoS₂

Below is an example job script and input file for running pw.x on bilayer MoS₂. Refer to the Quantum ESPRESSO documentation for details on pw.x input parameters.

SLURM Batch Script Tutorial

• Node and Task Allocation: Use --nodes=1 and --ntasks-per-node=24 to utilize 24 cores on a single node.
  • This can be extended to any number of nodes and cores for scalability of the experiment.
• Exclusive Access: Use --exclusive to reserve the entire node.
  • Avoid if using fewer than the node's full core count.
• Memory Allocation: Set --mem=0 to access all node memory, or specify a value (e.g., --mem=5G) if not using the entire node. Quantum ESPRESSO outputs memory requirements (e.g., "Estimated total dynamical RAM > 3.25 GB") in test runs.
• Load the default Quantum ESPRESSO module version (quantum-espresso/7.2-gcc-openblas) with:

module load quantum-espresso

• To view all versions of Quantum ESPRESSO available use:

module avail quantum-espresso

The next set of lines link the pseudopotential files to the current working directory, ./. In this scheme, the directory ${HOME}/PPs has been created by the user and pseudopotential files (.upf) have been stored into it. Those lines are linked to ./ and are then read by ESPRESSO in the line pseudo_dir='./'. They are then ascribed to the atom under the ATOMIC_SPECIES card.

The job script then sets the variable nCores to be the total number of cores expected to be used, and runs pw.x in parallel using mpirun. It takes the file moS2.scf.in as input and saves it (along with errors &>) to the file moS2.scf.out. The -nk 12 option to pw.x is one of the parallelization levels employed by ESPRESSO--specifically the "pools" option that parallelizes across 12 groups of k-points.

Quantom Expresso Job Script

#!/usr/bin/env bash
#SBATCH --job-name=QE_EXAMPLE
#SBATCH --partition=test
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=20
#SBATCH --time=00:30:00
#SBATCH --mem=0
#SBATCH --output=qe_test%j.qlog

module load openmpi/4.1.1-gcc-8.4.1
module load quantum-espresso/7.2-gcc-openblas

nCores=${SLURM_NTASKS}
mpirun -n $nCores pw.x  < moS2.scf.in &> moS2.scf.out
# mpirun -n $nCores pw.x -nk 12  < moS2.scf.in &> moS2.scf.out 
# If setting the pools properly in the input files for parallelism

Example of `pw.x` input

&CONTROL
    calculation = 'scf'
    pseudo_dir  = './'
    outdir       = './'
    prefix = 'moS2'
    tprnfor = .true.
    tstress = .true.
    etot_conv_thr = 1.0D-8
    forc_conv_thr = 1.0D-5
/

&SYSTEM
    ibrav       = 0,
    ecutwfc     = 60,
    nat         = 6,
    ntyp        = 2,
/

&ELECTRONS
    conv_thr         =  1.00000e-10
/

K_POINTS {automatic}
6 6 1 1 1 0

ATOMIC_SPECIES
Mo     95.94000  Mo_ONCV_PBE-1.0.upf
S      32.06600  Sc_ONCV_PBE-1.0.oncvpsp.upf

CELL_PARAMETERS (angstrom)
   3.190560000   0.000000000   0.000000000
  -1.595280000   2.763110000   0.000000000
   0.000000000   0.000000000  25.000000000

ATOMIC_POSITIONS (angstrom)
S        1.595280002   0.920977084   1.539433305
Mo       3.190559998   1.842097452   3.098045063
S        1.595280002   0.920977074   4.656657474
S        3.19056   1.842132926   7.735684114
Mo       1.59528   0.921012548   9.294296525
S        3.19056   1.842132916  10.852908283

warning

Quantum ESPRESSO Requires the upf files to be loaded before running the experiment.

The upf files can be downloaded from SSSP page

Here are the input files neccessary to run this tutorial.

`moS2.scf.in` Input

&CONTROL
    calculation   = 'scf',
    restart_mode  = 'from_scratch',
    pseudo_dir    = './',
    prefix        = 'MoS2',
    outdir        = './',
    nstep         = 100,
/

&SYSTEM
    ibrav         = 4,
    a             = 3.16000e+00,
    c             = 2.00000e+01,
    nat           = 3,
    ntyp          = 2,
    ecutwfc       = 60,
    occupations   = 'fixed',
    smearing      = 'gauss',
    vdw_corr      = 'DFT-D',
/

&ELECTRONS
    conv_thr      = 1.0d-9,
/

ATOMIC_SPECIES
    Mo     95.94000  Mo_ONCV_PBE-1.0.upf
    S      32.06600  Sc_ONCV_PBE-1.0.oncvpsp.upf

ATOMIC_POSITIONS (angstrom)
    S        0.002804304   0.001613133   8.429890591
    S        0.002804304   0.001613133  11.570109409
    Mo       1.582007393   0.913365735  10.000000000

K_POINTS automatic
    51 51 1 0 0 0

`Sc_ONCV_PBE-1.0.oncvpsp.upf` Input

The contents of the file is long, please download Sc_ONCV_PBE-1.0.oncvpsp.upf from the SSSP page