VASP

2024 April 24

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.

cd vasp_Na8Cl8_RS
tree

.
├── calc_in
│   ├── INCAR_1
│   ├── INCAR_2
│   ├── POTCAR
│   ├── POTCAR_is_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]
natot = 16
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

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

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.

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 VASP

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 INCAR_1 and INCAR_2. Here, INCAR_1 is set to fix the cell and relax only the ionic positions, while INCAR_2 is configured to fully relax both the cell and ionic positions.

INCAR_1

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

INCAR_2

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