Spring School - National Chung Cheng University

Lecture Notes

Spring SchoolFirst-principles Computational

Material Research Advanced Level (2020)

Hands-on session 1

講師 : 中正大學物理系梁贊全教授

協助人員 : 林耿民博士、姚華凱研究生

P. 1

Exercise 1

1. Find the band structure, joint density of states, dielectric function, absorption constant and matrix element dispersion of Au, AuAl2 and Fe.

2. Find the effect of spin orbit interaction on the dielectric function of Au, AuAl2 and Fe

P. 2

How to start a VASP calculation1. Use the SSH to log in the Twnia at NCHC

ssh –X [email protected]

# -X is an option for using X11 forwarding when a GUI is required.

2. After the welcome messages appear and if there is no error message, you are in your home directory (folder), i.e., /home/username.

[u50tcl00@clogin1 ~]$ pwd

/home/u50tcl00

[u50tcl00@clogin1 ~]$ cp /work1/u50tcl00/vasp_school_summer/vasp_school.sh .

[u50tcl00@clogin1 ~]$ ./vasp_school.sh

# generate the following directories ~/bin_vasp_1, ~/input, ~/potential, and /work/username/result_VASPsummer_school

# copy your original ~/.bashrc to ~/bashrc.bk.201905 and add a few lines to the end of your original .bashrc

[u50tcl00@clogin1 ~]$ ll # The ‘ll’ is 'ls -l’. The words after ‘#’ is comments.

drwxr-xr-x 4 u500tcl00 u500tcl00 4096 4月 13 16:56 bin_vasp_1

drwxr-xr-x 5 u500tcl00 u500tcl00 4096 4月 16 16:03 input

drwxr-xr-x 4 u500tcl00 u500tcl00 4096 4月 13 16:29 potential

P. 3

u50tcl00> cdw

u50tcl00> mkdir work-vasp-summer

u50tcl00> cd work-vasp-summer

work-vasp-summer> mkdir.sh

work-vasp-summer> ls

1-Optics 2-Magnetism 3-Phonon 4-Molecularr-Dynamics 5-GW

work-vasp-summer> cd 1-Optics

1-Optics> mkdir Au-bulk

1-Optics> cd Au-bulk

Au-bulk> mkdir-optics.sh

Au-bulk> ls

0-scf 3-stress 5-band 6-optics 7-optics-so

mkdir 1-Optics

mkdir 2-Magnetism

mkdir 3-Molecularr-Dynamics

mkdir 4-Phonon

mkdir 5-GW

mkdir 0-scf

mkdir 3-stress

mkdir 5-band

mkdir 6-optics

mkdir 7-optics-so

mkdir.sh

mkdir-optics.sh

How to calculate Opitcal properties of Au-bulkP. 4

Au-bulk> cd 3-stress

3-stress> cp ~/vasp-pot/POTCAR.Au POTCAR

3-stress> cp ~/input/INCAR .

3-stress> cp ~/input/KPOINTS .

3-stress> cp ~/input/POSCAR .

3-stress> cp ~/input/job-vasp.jbf .

3-stress> vi KPOINTS ( INCAR, and POSCAR )

3-stress> qsub job-vasp.jbf

3-stress> myjob

Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time

8084522.srvc1 u50tcl00 ctest beta 194213 1 4 -- 00:30 R 00:00

System = fcc Au

ENCUT = 300

RWIGS = 1.503

ISIF = 3

IBRION = 2

NSW = 50

EIDFF = 0.00001

NGX = 18

NGY = 18

NGZ = 18

10x10x10

0

Monkhorst

10 10 10

0 0 0

Au-bulk FCC

4.21000

0.0 0.5 0.5

0.5 0.0 0.5

0.5 0.5 0.0

Au

1

Direct

0.0 0.0 0.0

INCAR

KPOINTS

POSCAR

P. 5


3-stress> vi OUTCAR

/externa pressure

external pressure = -160.21 kB Pullay stress = 0.00 kB

direct lattice vectors reciprocal lattice vectors

0.000000000 2.105000000 2.105000000 -0.237529691 0.237529691 0.237529691

2.105000000 0.000000000 2.105000000 0.237529691 -0.237529691 0.237529691

2.105000000 2.105000000 0.000000000 0.237529691 0.237529691 -0.237529691

………..



0.000000000 2.030995533 2.030995533 -0.246184687 0.246184687 0.246184687

2.030995533 -0.000000000 2.030995533 0.246184687 -0.246184687 0.246184687

2.030995533 2.030995533 -0.000000000 0.246184687 0.246184687 -0.246184687

a = 4.06 0A

P. 6

3-stress> cd ../0-scf

0-scf>cp ../3-stress/POSCAR .

0-scf>cp ../3-stress/POTCAR .

0-scf>cp ../3-stress/INCAR .

0-scf>cp ../3-stress/KPOINTS .

0-scf> cp ../3-stress/job-vasp.jbf .

0-scf> vi POSCAR ( and INCAR )

0-scf> qsub job-vasp.jbf

System = fcc Au

ENCUT = 230

RWIGS = 1.503

# ISIF = 3

IBRION = 2

# NSW = 50

NGX = 18

NGY = 18

NGZ = 18

EIDFF = 0.00001

Au-bulk FCC

4.06100

0.0 0.5 0.5

0.5 0.0 0.5

0.5 0.5 0.0

Au

1

Direct

0.0 0.0 0.0

P. 7

0-scf> cd ../5-band

5-band> cp ../0-scf/POSCAR .

5-band> cp ../0-scf/POTCAR .

5-band> cp ../0-scf/INCAR .

5-band> cp ../0-scf/CHGCAR .

5-band> cp ~/input/KPOINTS-fcc KPOINTS

5-band> cp ../0-scf/job-vasp.jbf .

5-band> vi INCAR

5-band> qsub job-vasp.jbf

K-points along high symmetry lines for FCC

20

Line-mode

cart

0.5 1.0 0.0

0.5 0.5 0.5

0.5 0.5 0.5

0.0 0.0 0.0

0.0 0.0 0.0

0.0 1.0 0.0

0.0 1.0 0.0

0.5 1.0 0.0

0.5 1.0 0.0

0.75 0.75 0.0

System = fcc Au

ENCUT = 230

RWIGS = 1.503

# ISIF = 3

IBRION = 2

# NSW = 50

NGX = 18

NGY = 18

NGZ = 18

EIDFF = 0.00001

ICHARG = 11

LCHARG = .FALSE.

LOPTICS=.TRUE.

NBANDS=20

NPAR = 1

P. 8

fermi=`grep E-fermi ../0-scf/OUTCAR | tail -1 | awk '{print $3}'`

cat > inp <<!

1

-20 10

$fermi

1

1

1

!

band-procar-new.x < inp

cp band-p.dat band-s.dat

cat > inp <<!

1

-20 10

$fermi

1

2

1

!


cp band-p.dat band-p.dat

cat > inp <<!

1

-20 10

$fermi

1

3

1

!


cp band-p.dat band-d.dat

5-band> band-procar.sh

5-band> ls band*

band-d.dat band-p.dat band-s.dat

band-procar.sh

P. 9

5-band> xmgrace &

1

2

Import band-s.dat , band-p.dat and band-d.dat

3

P.10

1

2

3

P.11

P.12

5-band> cd ../6-optics

6-optics> cp ../0-scf/POSCAR .

6-optics> cp ../0-scf/POTCAR .

6-optics > cp ../0-scf/INCAR .

6-optics > cp ../0-scf/CHGCAR .

6-optics > cp ../0-scf/KPOINTS .

6-optics > cp ../0-scf/job-vasp.jbf .

6-optics > vi INCAR and KPOINTS

6-optics > qsub job-vasp.jbf

…………………….

6-optics > ls

System = Au fcc

# PREC = high

RWIGS = 1.503

# ISIF = 3

# IBRION = 2

EIDFF = 0.00001

ICHARG = 11

LCHARG = .FALSE.

LOPTICS=.TRUE.

NBANDS = 20

NPAR = 1

20x20x20

0

Monkhorst

20 20 20

0 0 0

P.13

CHG MME OSZICAR WAVECAR CHGCAR IBZKPT MME2 OUTCAR

STRUC WAVEDER CONTCAR OPTIC POSCAR XDATCAR DOSCAR INCAR

POTCAR vasprun.xml EIGENVAL KPOINTS PCDAT PROCAR

frequency dependent IMAGINARY DIELECTRIC FUNCTION (independent particle, no ……..

E(ev) X Y Z XY YZ ZX

--------------------------------------------------------------------------------------

0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000

0.198937 0.031729 0.031729 0.031729 0.000000 0.000000 -0.000000

0.397874 0.066434 0.066434 0.066434 0.000000 0.000000 -0.000000

………………………………………….

39.190636 0.002417 0.002417 0.002417 -0.000000 0.000000 -0.000000

39.389573 0.002367 0.002367 0.002367 -0.000000 0.000000 -0.000000

39.588510 0.002319 0.002319 0.002319 -0.000000 0.000000 -0.000000

frequency dependent REAL DIELECTRIC FUNCTION (independent particle, no local field effects)

E(ev) X Y Z XY YZ ZX

--------------------------------------------------------------------------------------

0.000000 9.386833 9.386833 9.386833 0.000000 0.000000 -0.000000

0.198937 9.417927 9.417927 9.417927 0.000000 0.000000 -0.000000

0.397874 9.513975 9.513975 9.513975 0.000000 0.000000 -0.000000

P.14

OUTCAR

<dielectricfunction>

<imag>

<array>

<dimension dim="1">gridpoints</dimension>

<field>energy</field>

<field>xx</field>

<field>yy</field>

<field>zz</field>

<field>xy</field>

<field>yz</field>

<field>zx</field>

<set>

<r> 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 </r>

<r> 0.0199 0.0031 0.0031 0.0031 0.0000 0.0000 -0.0000 </r>

…………………………………………

<r> 39.7676 0.0023 0.0023 0.0023 -0.0000 0.0000 -0.0000 </r>

</set>

</array>

</imag>

vasprun.xml

P.15

6-optics> plotoptics2.sh

awk 'BEGIN{i=1} /imag/,\

/\/imag/ \

{a[i]=$2 ; b[i]=$3 ; i=i+1} \

END{for (j=12;j<i-3;j++) print a[j],b[j]}' vasprun.xml > imag.dat

awk 'BEGIN{i=1} /real/,\

/\/real/ \

{a[i]=$2 ; b[i]=$3 ; i=i+1} \

END{for (j=12;j<i-3;j++) print a[j],b[j]}' vasprun.xml > real.dat

…….

plotoptics2.sh

6-optics > xmgrace imag.dat real.dat &

P.16

P.17

mkdir optics

cp MME optics/$1.mme

cp MME2 optics/$1.mme2

cp STRUC optics/$1.strucin

cp PROCAR optics/$1.procar

fermi=`grep E-fermi OUTCAR | tail -1 | awk '{print $3}'`

cd optics

cat > opticpack.def <<!

$1

!

cat > $1.opticin << !

1, 2 # intra, mme

0.05 # drude_damping

1, $fermi, 1, 1, 0, 0 # ival,ef,imetal,ispin,iso,itr

0,60,0.02,0.2,20 # emin,erange,de,sigma,nbcal0

1 # isci

0.0 # eshift

!

cp-optics.sh

P.18

6-optics> cp-optics.sh Au

6-optics> cd optics

6-optics> ls

Au.mme Au.mme2 Au.opticin Au.procar Au.strucin opticpack.def

optics> optics-2018.x

optics> ls

Au.alpha1 Au.eels_intra Au.epsim_inter Au.epsre_inter

Au.mme Au.opticout Au.refrare Au.strucin

Au.eels Au.epsabs Au.epsim_intra Au.epsre_intra

Au.mme2 Au.procar Au.sigim Au.wplas

Au.eels_inter Au.epsim Au.epsre Au.jdos

Au.opticin Au.refraim Au.sigre opticpack.def

optics> xmgrace &

P.19

Au-bulk dielectric constant

P.20

6-optics> cd ../7-optics-so

7-optics-so> cp ../6-optics/ IN* .

7-optics-so> cp ../6-optics/ PO* .

7-optics-so> cp ../6-optics/ KP* .

7-optics-so> cp ../6-optics/ CHGCAR .

7-optics-so> cp ../6-optics/job-vasp.jbf .

7-optics-so> vi INCAR

7-optics-so> qsub job-vasp.jbf

System = Au fcc

RWIGS = 1.503

IBRION = 2

EIDFF = 0.00001

ICHARG = 11

LCHARG = .FALSE.

LOPTICS=.TRUE.

NBANDS=20

NPAR = 1

MAGMOM = 0 0 0.00001

LSORBIT = .TRUE.

SAXIS=0 0 1

EMIN = 0

EMAX = 30

NEDOS = 2000

P.21

7-optics-so> cp-optics.sh

optics> cd optics

optics> vi Au.opticin


1,2 # intra, mme


1,5.8833,1,1,1,0 # ival,ef,imetal,ispin,iso,itr


1 # isci

0.0 # eshift

Au.opticin

P.22

Spin-orbit interaction effect on dielectric constant

P.23

optics> cd ../../5-band

5-band> cp-optics-band.sh Au

5-band> cd optics-band

optics-band> vi Au.opticin

optics-band> optics-mme.x

optics-band> optics-mme.sh

1,2 # intra, mme




1 # isci

0.0 # eshift

0.2 # scale

3 5 # ntrans interval

3 6 # noc(j), nunoc(j) , j=1,ntrans



Au.opticin

P.24

mkdir optics-band

cp MME optics-band/$1.mme

cp MME2 optics-band/$1.mme2

cp STRUC optics-band/$1.strucin

cp PROCAR optics-band/$1.procar

fermi=`grep E-fermi ../0-scf/OUTCAR | tail -1 | awk '{print $3}'`

cd optics-band

cat > opticpack.def <<!

$1

!

cat >$1.opticin <<!

1,2 # intra, mme


1,$fermi,1,1,0,0 # ival,ef,imetal,ispin,iso,itr


1 # isci

0.0 # eshift

0.2 # scale





!

cp-optics-band.shP.25

# optics-mme.x

mv fort.1101 mmex-01.dat

mv fort.1201 mmey-01.dat

mv fort.1301 mmez-01.dat

mv fort.101 eij-x-01.dat

mv fort.201 eij-y-01.dat

mv fort.301 eij-z-01.dat

mv fort.601 band-ij-01.dat















optics-mme.shP.26

optics-band> xmgrace -free &

1

2

3

4

P.27

1

2 3

4

5

P.28

1

P.29

2

1

3

P.30

1

2

P.31

2

1

P.32

1

\xe\B\sij\N (eV)

2

P.33

1

2

3

P.34

1

2

P.35

P.36

u50tcl00> cdw

work-vasp-summer> cd 1-Optics

1-Optics> mkdir AuAl2

1-Optics> cd AuAl2

AuAl2> mkdir-optics.sh

AuAl2> ls

0-scf 3-stress 5-band 6-optics 7-optics-so

AuAl2> cd 3-stress

3-stress> cp ~/vasp-pot/POTCAR.AuAl POTCAR

3-stress> cp ~/input/INCAR .

3-stress> cp ~/input/KPOINTS .

3-stress> cp ~/input/POSCAR .

3-stress> cp ~/input/job-vasp.jbf .

mkdir 0-scf

mkdir 3-stress

mkdir 5-band

mkdir 6-optics

mkdir 7-optics-so

mkdir-optics.sh

How to calculate Opitcal properties of AuAl2

P.37

3-stress> vi KPOINTS ( INCAR, and POSCAR )


System=AuAl2

ENCUT = 320

ISIF=3

IBRION=2

NSW=100

EDIFF=0.000001

RWIGS=1.503 1.402

10x10x10

0

Monkhorst

10 10 10

0 0 0

AuAl2

5.990000

0.000000 0.500000 0.500000

0.500000 0.000000 0.500000

0.500000 0.500000 0.000000

1 2

Direct

0.000000 0.000000 0.000000

0.250000 0.250000 0.250000

-0.250000 -0.250000 -0.250000

INCAR KPOINTS POSCAR

P.38

3-stress> vi OUTCAR

/externa pressure


…….


0.000000000 2.995000000 2.995000000 -0.166944908 0.166944908 0.166944908

2.995000000 0.000000000 2.995000000 0.166944908 -0.166944908 0.166944908

2.995000000 2.995000000 0.000000000 0.166944908 0.166944908 -0.166944908

…………………………………..


……………………………

0.000000000 2.977486227 2.977486227 -0.167926889 0.167926889 0.167926889

2.977486227 0.000000000 2.977486227 0.167926889 -0.167926889 0.167926889

2.977486227 2.977486227 0.000000000 0.167926889 0.167926889 -0.167926889

a = 5.955 0A

P.39

3-stress> cd ../0-scf

0-scf>cp ../3-stress/POSCAR .

0-scf>cp ../3-stress/POTCAR .

0-scf>cp ../3-stress/INCAR .

0-scf>cp ../3-stress/KPOINTS .

0-scf> cp ../3-stress/job-vasp.jbf .

0-scf> vi POSCAR ( and INCAR )

0-scf> qsub job-vasp.jbf

System=AuAl2

ENCUT = 250

RWIGS=1.503 1.402

AuAl2

5.955000

0.000000 0.500000 0.500000

0.500000 0.000000 0.500000

0.500000 0.500000 0.000000

1 2

Direct

0.000000 0.000000 0.000000

0.250000 0.250000 0.250000

0.750000 0.750000 0.750000

INCAR

POSCAR

P.40

0-scf> cd ../5-band

5-band> cp ../0-scf/POSCAR .

5-band> cp ../0-scf/POTCAR .

5-band> cp ../0-scf/INCAR .

5-band> cp ../0-scf/CHGCAR .

5-band> cp ~/input/KPOINTS-fcc KPOINTS

5-band> cp ../0-scf/job-vasp.jbf .

5-band> vi INCAR

5-band> qsub job-vasp.jbf

5-band> band-all.sh

5-band> ls band-atom-*

band-atom-2-p.dat band-atom-2-s.dat band-atom-2-d.dat

band-atom-1-p.dat band-atom-1-s.dat band-atom-1-d.dat

System=AuAl2

ENCUT = 250

ICHARG=11

LCHARG=.FALSE.

RWIGS=1.503 1.402

NBANDS=30

LOPTICS=.TRUE.

NPAR=1

P.41

INCAR

#!/bin/bash

scale=2

fermi=`grep fermi OUTCAR | tail -1 | awk '{ print $3 }' `

for atom in 1 2

do

for L in s p d

do

if [ "$L" == 's' ] ; then

orbit=1

elif [ "$L" == 'p' ] ; then

orbit=2

else

orbit=3

fi

cat > tmp << !

1

-20,20

$fermi

$atom

$orbit

$scale

!

band-procar-1.sh atom-$atom-$L tmp

rm tmp

done

done

band-all.sh

P.42

band-procar-new.x < $2

mv band-p.dat band-$1.dat

band-procar-1.sh

AuAl2-band.agr

P.43

5-band> cd ../6-optics

6-optics> cp ../0-scf/POSCAR .

6-optics> cp ../0-scf/POTCAR .

6-optics > cp ../0-scf/INCAR .

6-optics > cp ../0-scf/CHGCAR .

6-optics > cp ../0-scf/KPOINTS .

6-optics > cp ../0-scf/job-vasp.jbf .

6-optics > vi INCAR and KPOINTS

6-optics > qsub job-vasp.jbf

…………………….

6-optics > cp-optics.sh AuAl2

6-optics > cd optics

optics> vi AuAl2.strucin

opitcs> optics-2018.x

System=AuAl2

ENCUT = 250

RWIGS=1.503 1.402

NPAR=1

ISMEAR=0

LOPTICS=.TRUE.

NBANDS=30

20x20x20

0

Monkhorst

20 20 20

0 0 0

P.44

1,2 # intra, mme




1 # isci

0.0 # eshift

AuAl2.strucin

optics> ls

AuAl2.alpha1 AuAl2.epsabs AuAl2.epsre AuAl2.mme AuAl2.procar AuAl2.sigre AuAl2.eels AuAl2.epsim AuAl2.epsre_inter AuAl2.mme2 AuAl2.refraim AuAl2.strucin AuAl2.eels_inter AuAl2.epsim_inter AuAl2.epsre_intra AuAl2.opticin AuAl2.refrare AuAl2.wplas AuAl2.eels_intra AuAl2.epsim_intra AuAl2.jdos AuAl2.opticout AuAl2.sigim opticpack.def

optics> xmgrace &

P.45

AuAl2 dielectric constant

6-optics> cd ../7-optics-so

7-optics-so> cp ../6-optics/ IN* .

7-optics-so> cp ../6-optics/ PO* .

7-optics-so> cp ../6-optics/ KP* .

7-optics-so> cp ../6-optics/ CHGCAR .

7-optics-so> cp ../6-optics/job-vasp.jbf .

7-optics-so> vi INCAR

7-optics-so> qsub job-vasp.jbf

System = Au fcc

RWIGS = 1.503

IBRION = 2

EIDFF = 0.00001

ICHARG = 11

LCHARG = .FALSE.

LOPTICS=.TRUE.

NBANDS=20

NPAR = 1

MAGMOM = 0 0 0.00001

LSORBIT = .TRUE.

SAXIS=0 0 1

EMIN = 0

EMAX = 30

NEDOS = 2000

P.46

7-optics-so> cp-optics.sh AuAl2

optics> cd optics

optics> vi AuAl2.opticin


1,2 # intra, mme




1 # isci

0.0 # eshift

AuAl2.opticin

P.47

Spin-orbit interaction effect on dielectric constant

P.48

AuAl2 dielectric constant

optics> cd ../../5-band

5-band> cp-optics-band.sh AuAl2

5-band> cd optics-band

optics-band> vi AuAl2.opticin

optics-band> optics-mme.x

optics-band> optics-mme.sh

1,2 # intra, mme




1 # isci

0.0 # eshift

0.2 # scale





AuAl2.opticin

P.49

P.50

Fe-bulk

P.51

Fe-bulkP.52

Fe-bulk

P.53

Au-bulk

P.54

Au-bulk

P.55

IBZ of fcc lattice

Al

AppendixP.56

P.57

P.58

optics-vasp-modify

linear_optics.F main.F optics.F symmetry.F

linear_optics_orig.F main_orig.F optics_orig.F symmetry_orig.F

readme

cd ~/bin_vasp_1/optics-vasp-modify

please replace main.F, optics.F and symmetry.F

in the vasp.5.3.5 code with the corresponding subroutines

provided here. You can see the modifications I made

by comparing xxx.F and xxx_orig.F.

Documents

Spring School - National Chung Cheng University