VASP

2025 July 12, updated

In this tutorial, we try to use CrySPY in a PC cluster with a job scheduler system such as PBS. Here we employ VASP. The target system is Na8Cl8, 16 atoms.

Assumption

Here, we assume the following conditions:

CrySPY 1.2.0 or later in your PC cluster
CrySPY job command: qsub
CrySPY job filename: job_cryspy
executable file, vasp_std in your PC cluster

Input files

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

Download from Cryspy_utility/examples/vasp_Na8Cl8_RS
Copy from CrySPY utility that you installed

cd vasp_Na8Cl8_RS
tree

.
├── calc_in
│   ├── 1_INCAR
│   ├── 2_INCAR
│   ├── POTCAR_dummy
│   └── job_cryspy
└── cryspy.in

cryspy.in

cryspy.in is the input file of CrySPY.

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

[structure]
atype = Na Cl
nat = 8 8
mindist_1 = 2.5 1.5
mindist_2 = 1.5 2.5

[VASP]
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. You can name the following file whatever you want:

jobfile

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.

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

Info

See Input file > Kpoint for details of kppvol

The other input variables are discussed later.

calc_in directory

The job file and input files for VASP 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 Na8Cl8_CrySPY_ID
#$ -pe smp 20
####$ -q ibis1.q
####$ -q ibis2.q
####$ -q ibis3.q
####$ -q ibis4.q

# ---------- vasp
VASPROOT=/usr/local/vasp/vasp.6.4.2/bin
mpirun -np $NSLOTS $VASPROOT/vasp_std

Change VASPROOT to the appropriate path suitable for your environment. 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 VASP

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:

x_INCAR
INCAR_x
INCAR

If you use the same input for all stages, you can omit x_ or _x.

We are using nstage = 2, so we need 1_INCAR_1 and 2_INCAR. Here, 1_INCAR is set to fix the cell and relax only the ionic positions, while 2_INCAR is configured to fully relax both the cell and ionic positions.

1_INCAR

SYSTEM = NaCl
!!!LREAL = Auto
Algo = Fast
NSW = 40

LWAVE = .FALSE.
!LCHARG = .FALSE.

ISPIN =  1

ISMEAR = 0
SIGMA = 0.1

IBRION = 2
ISIF = 2

EDIFF = 1e-5
EDIFFG = -0.01

2_INCAR

SYSTEM = NaCl
!!LREAL = Auto
Algo = Fast
NSW = 200

ENCUT = 341

!!LWAVE = .FALSE.
!!LCHARG = .FALSE.


ISPIN =  1

ISMEAR = 0
SIGMA = 0.1

IBRION = 2
ISIF = 3

EDIFF = 1e-5
EDIFFG = -0.01

CrySPY automatically generates POSCAR and KPOINTS files. You have to prepare POTCAR file yourself. The POTCAR included in this example file is empty, so please be aware of that.

Warning

POTCAR in this example is empty. We cannot distribute it.

Running CrySPY

Go to Running CrySPY