fcc Si DOS

Based on the VASP wiki example in this link

Task: Calculation of the density of states (DOS) for fcc Si.

System-specific instructions

Select instructions for the system you are using:

Instructions for use on the NAISS cluster Tetralith (NSC)

A DOS calculation is typically done in two steps:
(1) a self consistent, static, converged calculation and
(2) a non-self consistent calculation, using the charge density (CHGCAR) from the first with a denser k-mesh

Note that

  • This approach saves computational time, in particular for large systems

  • DOS is only meaningful for static (no structural relaxation) calculations

First, copy the example folder which contains some of the VASP input files and useful scripts

cp -r /software/sse2/tetralith_el9/manual/vasp/training/ws2024/fcc_Si_DOS .
cd fcc_Si_DOS

also copy the latest POTCAR file for Si

cp /software/sse2/tetralith_el9/manual/vasp/POTCARs/PBE/2024-03-19/Si/POTCAR .

Input files

POSCAR

fcc Si
 3.9
 0.5 0.5 0.0
 0.0 0.5 0.5
 0.5 0.0 0.5
Si
   1
cartesian
0 0 0

INCAR

System = fcc Si

#ICHARG = 11   # read charge file
ENCUT = 240
ISMEAR = -5 
LORBIT = 11

  • ICHARG=11, VASP will do a non-self consistent calculation for a fixed charged density read from CHGCAR

  • For DOS we want to use the tetrahedron method + Blöchl corrections for how to treat partial occupancies of bands, controlled by setting ISMEAR=-5

  • LORBIT gives output to PROOUT or PROCAR files, also see RWIGS

  • With LORBIT set, partial charge densities are found in OUTCAR

KPOINTS

k-points
 0
Monkhorst Pack
 21 21 21
 0  0  0

  • We keep an odd number of k-points in each direction for MP k-mesh -> Gamma centered mesh, also needed for the tetrahedron method

1a. Calculation from scratch

We can either start completely from scratch, or use the results from the previous example “fcc Si”. For the latter, go to the next section 1b further below.

Since this is a small system, calculation will be fast independent of the procedure.

From scratch, set up the folder “dos” with all the input files (use * or INCAR POSCAR KPOINTS POTCAR plotdos.sh run.sh)

mkdir dos
mv * dos
cd dos

submit the calculation

sbatch run.sh

and wait for it to finish. Any interesting messages in slurm-JOBID.out or the output?

cat slurm*.out

1b. Calculation from using previous example

If you did the calculations from scratch in 1a, you can skip this section.

First, create a folder and move the input files for the static self consistent calculation

mkdir dos
mv INCAR POSCAR KPOINTS POTCAR plotdos.sh run.sh dos
cd dos

Now, copy the charge density file CHGCAR from a calculation in the previous example, checking that the path is correct

cp ../../fcc_Si/3.9/CHGCAR .

Now, edit INCAR (with e.g. vior use your favourite editor)

vi INCAR

such that it looks like

System = fcc Si

ICHARG = 11
ENCUT = 240
ISMEAR = -5 #tetrahedron
LORBIT = 11

submit the calculation

sbatch run.sh

and wait for it to finish. Any interesting messages in slurm-JOBID.out or output?

cat slurm*.out

2. Check the result

To quickly check the resulting DOS, you can use the small script “plotdos.sh” provided with the example, it looks like

#!/bin/bash

awk 'BEGIN{i=1} /dos>/,\
                /\/dos>/ \
                 {a[i]=$2 ; b[i]=$3 ; i=i+1} \
     END{for (j=12;j<i-5;j++) print a[j],b[j]}' vasprun.xml > dos.dat

ef=`awk '/efermi/ {print $3}' vasprun.xml`

cat >plotfile <<EOF
# set term postscript enhanced eps colour lw 2 "Helvetica" 20
# set output "optics.eps"
plot "dos.dat" using (\$1-$ef):(\$2) w lp
EOF

gnuplot -persist plotfile

run it with

./plotdos.sh

it produces the two files “dos.dat” and “plotfile”, it also automatically starts gnuplot (Tetralith) or produces an image “optics.png” (LEONARDO).

For more advanced functionalities and lots of different options, one can instead use p4vasp (Tetralith) or py4vasp (Tetralith, local computer)

Here, an example is made on how to use p4vasp

module load p4vasp/0.3.30-nsc1
p4v &

this will open the GUI of p4vasp in your ThinLinc session. If you started p4vasp outside the folder, you’ll need to load the vasprun.xmloutput file by selecting File > Load system > step to correct folder and select vasprun.xml > press “Ok”.

To check the DOS, in the upper menu select “Electronic” and click “DOS + bands”.

When the DOS window is shown, you can e.g. select to export the DOS data by clicking “Graph” in the menu bar, selecting the raw data (.dat) option. It’s also possible to directly export for use with XmGrace(.agr).

Extra tasks

  • Compare DOS for s, p and d states using p4vasp (select “Electronic” > “Local DOS + bands control”) or by using py4vasp, e.g.:

    import py4vasp
mycalc = py4vasp.Calculation.from_path("/path/to/your/calculation/folder/here")
mycalc.dos.plot("s,p,d")

  • Anything interesting about the fcc Si system considering the DOS?

  • Compare total DOS for using a denser k-mesh (KPOINTS), ENCUT = 1.5 x ENMAX (grep ENMAX POTCAR) and PREC=Accurate (INCAR), any difference?

  • Tetralith: Test to export DOS as a file “dos.agr” and open using XmGrace

    module load grace/5.1.25-hpc1-intel-2023a-eb
xmgrace dos.agr &