QE

2024 April 24, updated

In this tutorial, we try to use CrySPY in a machine with a job scheduler system such as PBS. Here we employ QUANTUM ESPRESSO. (QE). The target system is Si 8 atoms.

Assumption

Here, we assume the following conditions:

CrySPY job command: qsub
CrySPY job filename: job_cryspy
QE executable file: /usr/local/qe-6.5/bin/pw.x
QE input filename: pwscf.in
QE output filename: pwscf.out

Input files

Move to your working directory, and copy input example files by one of the following methods.

Download from cryspy_utility/examples/qe_Si8_RS
Copy from CrySPY utility that you installed
(only version 0.10.3 or earlier) cp -r ~/CrySPY_root/CrySPY-0.9.0/example/v0.9.0/QE_Si8_RS .

cd QE_RS_Si8
tree

.
├── calc_in
│   ├── job_cryspy
│   ├── pwscf.in_1
│   └── pwscf.in_2
└── cryspy.in

cryspy.in

cryspy.in is the input file of CrySPY.

[basic]
algo = RS
calc_code = QE
tot_struc = 5
nstage = 2
njob = 2
jobcmd = qsub
jobfile = job_cryspy

[structure]
natot = 8
atype = Si
nat = 8

[QE]
qe_infile = pwscf.in
qe_outfile = pwscf.out
kppvol =  40  80

[option]

In [basic] section, jobcmd = qsub can be changed in accordance with your environment. CrySPY runs qsub job_cryspy as a background job internally in this setting.

We adopt a stage-based system for structure optimization calculations. Here, we use nstage = 2. For example, users can configure the following settings. In the first stage, only the ionic positions are relaxed, fixing the cell shape, with low k-point grid density. Next, the ionic positions and cell shape are fully relaxed with high accuracy in the second stage.

[QE] section is required when you use QE. You have to specify k-point grid density (Å^-3) for each stage in kppvol.

Info

See Input file > Kpoint for details of kppvol

You can name the following files whatever you want:

jobfile
qe_infile
qe_outfile

The other input variables are discussed later.

calc_in directory

The job file and input files for QE are prepared in this directory.

Job file

The name of the job file must match the value of jobfile in cryspy.in. The example of job file (here, job_cryspy) is shown below.

#!/bin/sh
#$ -cwd
#$ -V -S /bin/bash
####$ -V -S /bin/zsh
#$ -N Si8_CrySPY_ID
#$ -pe smp 20
####$ -q ibis1.q
####$ -q ibis2.q

mpirun -np $NSLOTS /path/to/pw.x < pwscf.in > pwscf.out


if [ -e "CRASH" ]; then
    sed -i -e '3 s/^.*$/skip/' stat_job
    exit 1
fi

sed -i -e '3 s/^.*$/done/' stat_job

Change /path/to/pw.x to the appropriate path suitable for your environment. You can specify the input (pwscf.in) and output (pwscf.out) file names, but they must match the values of qe_infile and qe_outfile in cryspy.in.

The job file is written in the same way as the one you usually use except for the last line. You must add sed -i -e '3 s/^.*$/done/' stat_job at the end of the file in CrySPY.

Note

sed -i -e '3 s/^.*$/done/' stat_job is required at the end of the job file.

Tip

In the job file of CrySPY, the string “CrySPY_ID” is automatically replaced with the structure ID. When you use a job scheduler such as PBS and SLURM, it is useful to set the structure ID to the job name. For example, in the PBS system, #PBS -N Si_CrySPY_ID in ID 10 is replaced with #PBS -N Si_10. Note that starting with a number will result in an error. You should add a prefix like Si_.

Input for QE

Input files based on the number of stages (nstage in cryspy.in) are required. Name the input file(s) with a suffix _x. Here x means the stage number.

We are using nstage = 2, so we need pwscf.in_1 and pwscf.in_2. Here, pwscf.in_1 is set to fix the cell and relax only the ionic positions, while pwscf.in_2 is configured to fully relax both the cell and ionic positions.

pwscf.in_1

 &control
    title = 'Si8'
    calculation = 'relax'
    nstep = 100
    restart_mode = 'from_scratch',
    pseudo_dir = '/usr/local/pslibrary.1.0.0/pbe/PSEUDOPOTENTIALS/'
    outdir='./out.d/'
 /

 &system
    ibrav = 0
    nat = 8
    ntyp = 1
    ecutwfc = 44.0
    occupations = 'smearing'
    degauss = 0.01
 /

 &electrons
 /

 &ions
 /

 &cell
 /

ATOMIC_SPECIES
  Si  28.086  Si.pbe-n-kjpaw_psl.1.0.0.UPF

pwscf.in_2

 &control
    title = 'Si8'
    calculation = 'vc-relax'
    nstep = 200
    restart_mode = 'from_scratch',
    pseudo_dir = '/usr/local/pslibrary.1.0.0/pbe/PSEUDOPOTENTIALS/'
    outdir='./out.d/'
 /

 &system
    ibrav = 0
    nat = 8
    ntyp = 1
    ecutwfc = 44.0
    occupations = 'smearing'
    degauss = 0.01
 /

 &electrons
 /

 &ions
 /

 &cell
 /

ATOMIC_SPECIES
  Si  28.086  Si.pbe-n-kjpaw_psl.1.0.0.UPF

Change pseudo_dir to your suitable directory. Inputs for structure data and k-point such as ATOMIC_POSITIONS and K_POINTS are automatically appended by CrySPY with pymatgen. Users do not have to prepare them in pwscf.in_x.

Running CrySPY

Go to Running CrySPY