Quantum Espresso (QE)

If you want your jobs to run faster in the queue

#SBATCH -A mendoza_q

#SBATCH --exclude=amr-163,amr-178,amr-179

this should submit to our queue, exclude your buyin nodes and flip the jobs to run in the general partition, avoiding incurring cpu.

Usage of QE at the ICER ( New Cluster )

Submission Script, Parallel version (hpcc)

For a job script example running Quantum Espresso for single-point or optimization in parallel, you can use the following script:

submit.slurm

#!/bin/bash --login

#SBATCH --ntasks=16

#SBATCH -N 2

#SBATCH --cpus-per-task=1

#SBATCH --mem-per-cpu=3G

#SBATCH --time=05:00:00

#SBATCH -A general

#SBATCH --job-name QE_parallel

export JOB=QE_parallel

export DIR=$SLURM_SUBMIT_DIR

module load QuantumESPRESSO/6.2

srun pw.x < $DIR/${JOB}.in > $DIR/${JOB}.out

This command is for submitting the .slurm file you just create

>> sbatch submit.slurm

These command lines are for showing job information and resource usages.

>> scontrol show job $SLURM_JOB_ID

>> js -j $SLURM_JOB_ID

Besides the memory and the walltime request, you can also change the number of tasks and number of nodes in the first and second #SBATCH lines, respectively. If you want to run on the mendoza partition, change general-long to mendoza_q. Make sure to change the job name according to your input file, i.e. replace both instances of "QE_parallel" for the name of the .in file that you want to run.

E.g. if you use the example below for graphene, you would substitute "QE_parallel" by "graphene."

If you want to submit to general, but not incur cpu hours

If you want to submit to general, but not incur cpu hours, as what happens when they don't go through the buyin, they can try submitting with the following options in their submit scripts:

#SBATCH -A mendoza_q

#SBATCH --exclude=amr-163,amr-178,amr-179

this should submit to your queue, exclude your buyin nodes and flip the jobs to run in the general partition, avoiding incurring cpu.

QE INPUT

Geometry Optimization

Running a Quantum Espresso input file for structure optimization requires entering the appropriate keywords in agreement with the manual.

Geometry Optimization Example: Graphene

The following is an example of a Quantum Espresso input file for a geometry optimization calculation of a unit cell of graphene. Extra keywords were added so they can help extending the input to different structures. The keywords used in each section are commented for a quick view of their meaning:

graphene.in

&control

       calculation='vc-relax'        ! total geometry optimization, for atom only use 'relax'

       title='graphene'       

       prefix='graphene'             ! output file name

       outdir='./'                   ! output file directory, set to working directory

       pseudo_dir = './'             ! potential file directory, set to working directory

       verbosity='high'              ! additional information will be displayed in output file

       restart_mode='from_scratch'   

       nstep=1000                    ! number of optimization steps, set to 0 for a 'dry run'

       iprint=1                      ! display band energies at every step, 0 for convergence only

       tprnfor=.true.                ! calculate forces, default true if 'relax'

       tstress=.true.                ! calculate stress, default true if 'vc-relax'

       forc_conv_thr=1.0d-4          ! convergence energy threshold for total energy in a.u., default is 1d-4

       etot_conv_thr=1.0d-3          ! convergence forces threshold for ionic minimization, default is 1d-3

/

&system

   ibrav     = 4,                     ! bravais lattice, see manual for details

   celldm(1) = 4.0,                   ! cell parameters in bohr

   celldm(3) = 2.0,

   nat  = 4,                          ! number of atoms inside unit cell

   ntyp = 1,                          ! type of atoms

   ecutwfc = 40.0 ,                   ! kinetic energy cutoff in Ry for wavefunctions,

   ecutrho = 400.0 ,                  ! kinetic energy cutoff in Ry for charge density and potential, depends on pseudopotential for norm-conserving 4*ecutwfc, ultrasoft 8 to 12*ecutwfc

   input_DFT = 'PBE' ,                ! functional

   ! occupations = 'smearing' ,       ! for options, see manual

   ! degauss = 1.0d-4 ,

   ! smearing = 'gaussian' ,          

/

&electrons

   electron_maxstep = 100,            ! max number of iterations in a SCF step

   conv_thr = 1.0d-8 ,                ! convergence threshold for selfconsistency, default is 1d-6

   mixing_mode = 'plain' ,            ! default plain, see manual for other options

   mixing_beta = 0.3d0 ,              ! mixing factor for self-consistency, default is 0.7

/

&ions

   ion_dynamics='bfgs'                ! type of ionic dynamics, may differ per type of calculation, see manual for more details

   upscale=20.0,                      ! max reduction factor for conv_thr, default is 100

/

&cell

   press_conv_thr  = 0.5D0,           ! convergence threshold on the pressure for variable cell in Kbar

   press = 0.D0,                      ! target pressure in a variable-cell run (md or relaxation)

   cell_dynamics = 'bfgs',            ! type of ionic dynamics, may differ per type of calculation, see manual for more details

   ! cell_dofree     = '2Dxy'         ! which parameters of the cell should be moved

   cell_factor = 2.0D0                ! used in construction of pseudopotential tables usually 2 for variable-cell calculations, 1 otherwise, see manual

/

ATOMIC_SPECIES                                ! geometry input, there are many different ways other than the method shown below, see manual for detailed explanations

       C    12.011 c_pbe_v1.2.uspp.F.UPF      ! pseudopotential files for the present elements can be obtained at: https://www.physics.rutgers.edu/gbrv/

ATOMIC_POSITIONS crystal

    C    0.000000    0.000000    0.250000

    C    0.000000    0.000000    0.750000

    C    0.333333    0.666666    0.250000

    C    0.666666    0.333333    0.750000

K_POINTS automatic

12 12 2 0 0 0

Manual link for detailed information about keywords: https://www.quantum-espresso.org/Doc/INPUT_PW.html

For additional information you can also use: https://www.quantum-espresso.org/Doc/user_guide_PDF/pw_user_guide.pdf

About Units

For a.u. units, remember that this could mean atomic units of energy, force or length:

https://en.wikipedia.org/wiki/Hartree_atomic_units#Units

E.g. 

Atomic unit of  | Name    | Other equivalents 

energy          | hartree | 27.211386245988(53) eV

force           |         | 51.421 eV·Å−1

length          | bohr    | 0.529177210903(80) Å