QE

2025 July 18, 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
│   ├── 1_pwscf.in
│   └── 2_pwscf.in
└── 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]
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

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. Starting from version 1.4.2, CrySPY automatically appends the following line to the end of the job file. (See also: Features > Job file auto-rewriting)

# ---------- CrySPY
sed -i -e '3s/^sub.*/done/' stat_job
Note

For versions older than 1.4.2, the last line of the job file must be written as sed -i -e '3s/^sub.*/done/' stat_job. If you use a job file with this sed command in version 1.4.2 or later, it will simply be executed twice, which does not cause any problems.
The meaning of the above sed command is to change the part starting with “sub” in the third line of the file stat_job to “done”.

Tip

(Detail: Features > Job file auto-rewriting)
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 corresponding to the number of stages (nstage in cryspy.in) are required. Prepare the input file names by adding x_ as a prefix or _x as a suffix, where x is the stage number.

CrySPY searches for input files in the following order of priority:

  1. x_pwscf.in
  2. pwscf.in_x
  3. pwscf.in

We are using nstage = 2, so we need 1_pwscf.in and 2_pwscf.in. Here, 1_pwscf.in is set to fix the cell and relax only the ionic positions, while 2_pwscf.in is configured to fully relax both the cell and ionic positions.

1_pwscf.in

 &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

1_pwscf.in

 &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 x_pwscf.in.

Running CrySPY

Go to Running CrySPY