Introduction to VASP 4 - GIST2).pdf · Introduction to VASP 4.6 ... cycle to calculate the...

Introduction to VASP 4.6

Gwangju Institute of Science and Technology (GIST) Super Computing & Collaboration ENvironment Technlogy Center (SCENT)

Course contents

• Overview: What is VASP

• Lesson 1: Preparing input file

• Lesson 2: Running VASP

• Lesson 3: Viewing outputs and visualization

Each lesson includes hand-on excises.

Overview: What is VASP

• Vienna Ab-initio Simulation Package

• VASP is a complex package for performing ab-initio quantum-mechanical molecular dynamics (MD) simulations using pseudopotentials or the projector-augmented wave method and a plane wave basis set.

• Both LDA and GGA potentials/functionals are available.

• Hybrid functional (B3LYP, HSE06 ….) are available (only 5.2 version)

• Uses the PAW method or ultra-soft pseudopotentials

• Execution time scales like N3 for some parts of the code, where N is the number of valence electrons in the system.

• VASP uses a rather “traditional" and “old fashioned" self-consistency cycle to calculate the electronic ground state.

Overview: What is VASP

1. Periodic boundary condition

Good for bulk materials

(= not so good for isolated systems i.e. molecules)

Ideal for Plane wave basis-sets

2. Pseudo-potentials

To make life easier with the plane waves

Different flavors: LDA, GGA, hybrid

Preparing input file

• INCAR

– contains all the settings of the program parameters you wish to use. (energy cutoff, parallelism, smearing,...)

• KPOINTS

– all the information with regard to your k-point set.

• POSCAR

– all the information with regard to the actual geometry of your system.

• POTCAR

– the information regarding the potentials/functionals used this one you get from a database

hand-on excises

• Connect to the GIST supercomputer (kigi)

$ ssh kigi-lg01 connect to the kigi

$ mkdir test1 making the directory

$ cd test1 change the directory

Basic rules for making input files

All file name should be capitalized.

INCAR, KPOINTS, POTCAR, and POSCAR

Tab is not allowed (only space is allowed)

POSCAR

Si

1

5.4307 0 0

0 5.4307 0

0 0 5.4307

8

Direct

0.00000 0.00000 0.00000

0.00000 0.50000 0.50000

0.50000 0.00000 0.50000

0.50000 0.50000 0.00000

0.75000 0.25000 0.75000

0.25000 0.25000 0.25000

0.25000 0.75000 0.75000

0.75000 0.75000 0.25000

Types of coordinates

Direct: Fractional coordinate

Cartesian: Cartesian coordinate

Lattice vector of x, y, and z-direction

# of aomts

Comment line

Coordinates

hand-on excises

• Making a POSCAR file

$ vi POSCAR POSCAR name should be capitalized

In the vi editor, press “i” insert mode

Press “esc” key on your keyboard

:wq save and quit

INCAR SYSTEM = Si

Parallelization:

NPAR = 2

LPLAEN = .TRUE.

Startparameter for this run:

NWRITE = 2

PREC = high

ISTART = 0

ICHARG = 2

ISPIN = 2

ENCUT = 550

Electronic Relaxation 1

EDIFF = 0.1E-04 ! stopping-criterion for ELM

LREAL = .FALSE. ! real-space projection

LWAVE = .TRUE.

LCHARG = .TRUE.

Ionic relaxation

EDIFFG = 0.1E-03 !stopping-criterion for IOM

NSW = 200 ! number of steps for IOM

IBRION = 2 !ionic relax: 0-MD 1-quasi-New 2-CG

ISIF = 3

NWRITE Tag

f+l first and last ionic step

f first ionic step

I each ionic step

E each electronic step

X when applicable

INCAR SYSTEM = Si

Parallelization:

NPAR = 2

LPLAEN = .TRUE.


NWRITE = 2

PREC = high

ISTART = 0

ICHARG = 2

ISPIN = 2

ENCUT = 550




LWAVE = .TRUE.

LCHARG = .TRUE.

Ionic relaxation




ISIF = 3

ISTART Tag

ISTART = 0|1|2

Default:

If WAVECAR exist 1

Else 0

This flag determines whether to read

the file WAVECAR or not.

INCAR SYSTEM = Si

Parallelization:

NPAR = 2

LPLAEN = .TRUE.


NWRITE = 2

PREC = high

ISTART = 0

ICHARG = 2

ISPIN = 2

ENCUT = 550




LWAVE = .TRUE.

LCHARG = .TRUE.

Ionic relaxation




ISIF = 3

ICHARG Tag

ICHARG = 0|1|2

Default:

if ISTART=0 2

Else 0

This tag determines how to construct

the 'initial' charge density.

INCAR SYSTEM = Si

Parallelization:

NPAR = 2

LPLAEN = .TRUE.


NWRITE = 2

PREC = high

ISTART = 0

ICHARG = 2

ISPIN = 2

ENCUT = 550




LWAVE = .TRUE.

LCHARG = .TRUE.

Ionic relaxation




ISIF = 3

ENCUT = Ecut

default taken from POTCAR-file

Cutoff energy for plane wave basis set

in eV. All plane-waves with a kinetic-

energy smaller than Ecut are included

in the basis set: i.e.

ENCUT Tag

INCAR SYSTEM = Si

Parallelization:

NPAR = 2

LPLAEN = .TRUE.


NWRITE = 2

PREC = high

ISTART = 0

ICHARG = 2

ISPIN = 2

ENCUT = 550




LWAVE = .TRUE.

LCHARG = .TRUE.

Ionic relaxation




ISIF = 3

EDIFF = allowed error in total energy

Default : 10-4

Specifies the global break condition for the

electronic SC-loop. The relaxation of the

electronic degrees of freedom will be stopped if

the total (free) energy change and the band

structure energy change ('change of

eigenvalues’) between two steps are both

smaller than EDIFF. For EDIFF=0, NELM

electronic SC-steps will always be performed.

EDIFF Tag

INCAR SYSTEM = Si

Parallelization:

NPAR = 2

LPLAEN = .TRUE.


NWRITE = 2

PREC = high

ISTART = 0

ICHARG = 2

ISPIN = 2

ENCUT = 550




LWAVE = .TRUE.

LCHARG = .TRUE.

Ionic relaxation




ISIF = 3

EDIFFG = break condition for the ionic

relaxation loop

Default : EDIFF*10

EDIFFG Tag

INCAR SYSTEM = Si

Parallelization:

NPAR = 2

LPLAEN = .TRUE.


NWRITE = 2

PREC = high

ISTART = 0

ICHARG = 2

ISPIN = 2

ENCUT = 550




LWAVE = .TRUE.

LCHARG = .TRUE.

Ionic relaxation




ISIF = 3

NSW = number of ionic steps

Default : 0

NSW defines the number of ionic steps.

NSW Tag

INCAR SYSTEM = Si

Parallelization:

NPAR = 2

LPLAEN = .TRUE.


NWRITE = 2

PREC = high

ISTART = 0

ICHARG = 2

ISPIN = 2

ENCUT = 550




LWAVE = .TRUE.

LCHARG = .TRUE.

Ionic relaxation




ISIF = 3

ISIF = 0|1|2|3|4|5|6

Default

if IBRION=0 (MD) 0

else 2

ISIF Tag

KPOINTS

K-Points

0

Monkhorst Pack

6 6 6

0 0 0

Automatic mesh

POTCAR file

VASP provides potential files for all

chemical elements. Each of these files is

called POTCAR, and VASP only recognizes

a file named POTCAR as potential file.

Type of exchange-functional:

PE = Perdew-Burke-Ernzerhof (PBE) GGA

CA = Ceperley-Alder LDA

# of electrons:

4 valence electrons for this Si potential,

there also exists a Si potential including the

d-electrons in the valence shell 14e-

Q.) What if you have multiple/different kinds of atoms in your

system?

e.g. CO molecule

> cat POTCAR_C POTCAR_O >> POTCAR

Running VASP on PLSI supercomputer

$ llsubmit vasp_kigi.cmd # submit the job

$ llcancel job_id # cancel the job

$ llq # job status

$ llstatus # system status

OUTPUT Files

• CHG, CHGCAR Charge density data

• CONTCAR Calculated Lattice constant and atomic coordinates

• DOSCAR Density of States data

• OSZICAR Information about convergence speed and

about the current step

• WAVECAR All wavefunction data

• OUTCAR All information from the calculations

Parallel 10-cpu calculation

Our bulk Si system has only one

type of atoms: Si 8 atoms in our

unit cell

Total ground state energy

Visualization

Freeware Support for Windows, Mac, and Linux

You can download this website http://www.geocities.jp/kmo_mma/crystal/en/vesta.html

VESTA: a three-dimensional visualization system for electronic and structural analysis

K. Momma and F. Izumi (2008): J. Appl. Crystallogr., 41, 653-658.

http://www.geocities.jp/kmo_mma/crystal/en/vesta.html



http://dx.doi.org/10.1107/S0021889808012016

http://dx.doi.org/10.1107/S0021889808012016

http://dx.doi.org/10.1107/S0021889808012016

http://dx.doi.org/10.1107/S0021889808012016

http://dx.doi.org/10.1107/S0021889808012016

References

• P. Hohenberg and W. Kohn, Physical Review 136 (1964).

• W. Kohn and L. J. Sham, Physical Review 137 (1965).

• H. J. Monkhorst and J. D. Pack, Physical Review B 13, 5188 (1976).

• P. E. Blöchl, Physical Review B 50, 17953 (1994).

• G. Kresse and J. Furthmüller, Physical Review B - Condensed Matter and Materials Physics

54, 11169 (1996).

• J. P. Perdew, K. Burke, and M. Ernzerhof, Physical Review Letters 77, 3865 (1996).

• J. P. Perdew, K. Burke, and M. Ernzerhof, Physical Review Letters 78, 1396 (1997).

• VASP Manual (http://scent.gist.ac.kr)

• VESTA Manual (http://scent.gist.ac.kr)

http://scent.gist.ac.kr/

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