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.
Here, we assume the following conditions:
~/CrySPY_root/CrySPY-0.9.0/cryspy.pyqsubjob_cryspy/usr/local/qe-6.5/bin/pw.xpwscf.inpwscf.outMove to your working directory, and copy input example files.
$ 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 is the input file of CrySPY.
[basic]
algo = RS
calc_code = QE
tot_struc = 5
nstage = 2
njob = 1
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 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.
You can name the following files whatever you want:
jobfileqe_infileqe_outfileThe other input variables are discussed later.
The job file and input files for QE are prepared in this directory.
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 8
####$ -q ibis1.q
####$ -q ibis2.q
mpirun -np $NSLOTS pw.x -nk 4 -nb 2 < pwscf.in > pwscf.out
if [ -e "CRASH" ]; then
exit 1
fi
sed -i -e '3 s/^.*$/done/' stat_job
Change pw.x to 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/^.*$/done/' stat_job at the end of the file in CrySPY.
sed -i -e '3 s/^.*$/done/' stat_job is required at the end of the job file.
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 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.
For example, users can configure the following settings.
In the first stage, only the ionic positions are relaxed, fixing the cell shape.
Next, the ionic positions and cell shape are fully relaxed in the second stage.
pwscf.in_1 is listed below.
&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
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.
Go to Running CrySPY