Based on the VASP wiki example in this link
Task: Do a volume relaxation as well as calculate the DOS and bandstructure for cubic diamond (cd) structure Si.
First, copy the example folder which contains some of the VASP input files and useful scripts
cp -r /software/sse/manual/vasp/training/ws2020/cd_Si .
cd cd_Si
and copy the latest POTCAR file for Si
cp /software/sse/manual/vasp/POTCARs/PBE/2015-09-21/Si/POTCAR .
POSCAR
cubic diamond Si
5.5
0.0 0.5 0.5
0.5 0.0 0.5
0.5 0.5 0.0
Si
2
Direct
-0.125 -0.125 -0.125
0.125 0.125 0.125
INCAR
System = diamond Si
ISTART = 0
ICHARG=2
ENCUT = 240
ISMEAR = 0
SIGMA = 0.1
KPOINTS
k-points
0
Monkhorst Pack
11 11 11
0 0 0
Here, investigate the total energy as a function of volume in a similar way as for the fcc Si example. There’s a job script which can be used “run-vol.sh”
#!/bin/bash
#SBATCH -A snic2020-13-76
#SBATCH -t 0:30:00
#SBATCH -n 4
#SBATCH -J vaspjob
module load VASP/6.1.0.28012020-nsc1-intel-2018a-eb
for i in 5.1 5.2 5.3 5.4 5.5 5.6 5.7 ; do
mkdir -p $i
cd $i
cp /software/sse/manual/vasp/POTCARs/PBE/2015-09-21/Si/POTCAR .
cp /software/sse/manual/vasp/training/ws2020/cd_Si/INCAR .
cp /software/sse/manual/vasp/training/ws2020/cd_Si/KPOINTS .
cat >POSCAR <<!
cubic diamond Si
$i
0.0 0.5 0.5
0.5 0.0 0.5
0.5 0.5 0.0
Si
2
Direct
-0.125 -0.125 -0.125
0.125 0.125 0.125
!
mpprun vasp_std
E=`awk '/F=/ {print $0}' OSZICAR` ; echo $i $E >>../SUMMARY.dia
cd ..
done
submit it with
sbatch run-vol.sh
after some short time, the folders 5.1 - 5.7 with the output should appear, the “slurm-JOBID.out” and a file “SUMMARY.dia”:
5.1 1 F= -.10233838E+02 E0= -.10233747E+02 d E =-.180914E-03
5.2 1 F= -.10528200E+02 E0= -.10528187E+02 d E =-.271766E-04
5.3 1 F= -.10713336E+02 E0= -.10713334E+02 d E =-.215112E-05
5.4 1 F= -.10806746E+02 E0= -.10806746E+02 d E =-.111754E-06
5.5 1 F= -.10823085E+02 E0= -.10823085E+02 d E =-.431458E-08
5.6 1 F= -.10775151E+02 E0= -.10775151E+02 d E =-.205580E-09
5.7 1 F= -.10673630E+02 E0= -.10673630E+02 d E =-.114038E-10
check it e.g. using gnuplot
gnuplot
and at the prompt type
plot "SUMMARY.dia" using ($1):($4) w lp
From the plot one can see that the equilibrium lattice constant is close to a = 5.5 Å.
As in the previous example compare with an equation of state method, first extract the volume and total energies by running
./get-vol-etot.sh
thereafter, use the ASE script “eqos.py”
python eqos.py
the output might look like
Equation of state:
-------------------
E0: -10.825495 eV
V0: 40.987525 A^3
B: 87.612808 GPa
using the Birch-Murnaghan EOS. Similar as before, we quickly compute the lattice constant a using python
python
and input at the “»>” prompt
(4*40.987525) ** (1./3.)
Calculate DOS in a new folder “dos”
mkdir dos
cp POSCAR INCAR KPOINTS POTCAR run.sh dos
cd dos
For a single step calculation, edit INCAR e.g. with gedit
or your text editor of choice, such that it looks like
System = diamond Si
ISTART = 0
ICHARG=2
ENCUT = 240
ISMEAR = -5
#SIGMA = 0.1
LORBIT = 11
thereafter submit the job
sbatch run.sh
After it finished, check that the output looks fine, e.g.
cat slurm*out
Now use p4vasp to check DOS, similar as was described for fcc Si DOS
p4v &
Return to the main example folder “cd_Si” and prepare for a bandstructure calculation
mkdir band
cp POSCAR INCAR KPOINTS POTCAR run.sh band
cd band
and edit INCAR such that it looks like
System = diamond Si
ISTART = 0
ICHARG=11
ENCUT = 240
ISMEAR = 0
SIGMA = 0.1
LORBIT = 11
assuring that CHGCAR
will be read (ICHARG=11) and same as for DOS, setting LORBIT=11. Submit the job with
sbatch run.sh
and wait for it to finish. Check that the output looks fine and once again use p4vasp, following the previous example of fcc Si bandstructure.
In addition, test to plot the orbital characters of the bands following the examples (see bottom figures) in the VASP wiki.
Test with other methods for EOS by editing the “eqos.py” script
Perform the volume relaxation in 1. with a higher ENCUT in INCAR
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