Hands-on session on VASP

2012$PLSI$summery$school$for$HPC,$UNIST$

Hands-on session on VASP Nodo Lee Molecular Modeling Laboratory (MML) School of Materials Science and Engineering (MSE) Gwangju Institute of Science and Technology (GIST) 1

Course contents •  Overview: What is VASP •  Lesson 1: Preparing input files

- Inorganic Crystal Structure Database (ICSD) - Build the crystal structure using VESTA •  Lesson 2: Running VASP on KIGI •  Lesson 3: Viewing outputs and visualization

Each lesson includes hand-on excises. 2

Preparing input file •  INCAR –  contains all the settings of the program parameters you wish to use. (energy cutoff, parallelism, convergence criteria, 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

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Hands-on excises (Linux basic) •  Connect to the GIST supercomputer (KIGI) using PLSI portal software •  Visit PLSI Portal (http://portal.plsi.or.kr)

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h"p://portal.plsi.or.kr$

Downloads the PORTAL software for your platform

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1. Extract the files from archive (*.zip) 2. Execute the file - plsi.exe (Windows) - plsi (Mac)

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Sign in - Enter your account information

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Select “원격 시스템”

Click the right mouse button and click the “터미널 실행(A)”

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Connected to PLSI login node with SSH terminal

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Basic rules for making input files All file name should be capitalized. INCAR, KPOINTS, POTCAR, and POSCAR

In those files, Tab is not allowed (only space is allowed)

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POSCAR Si 1 5.4307 0 0 8 Direct 0.00000 0.00000 0.50000 0.50000 0.75000 0.25000 0.25000 0.75000

Comment line 0 5.4307 0

0 0 5.4307

Lattice vector of x, y, and z-direction # of aomts

0.00000 0.50000 0.00000 0.50000 0.25000 0.25000 0.75000 0.75000

0.00000 0.50000 0.50000 0.00000 0.75000 0.25000 0.75000 0.25000

Types of coordinates Direct: Fractional coordinate Cartesian: Cartesian coordinate Coordinates

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POSCAR Si 5.4307 1 0 0 8 Direct 0.00000 0.00000 0.50000 0.50000 0.75000 0.25000 0.25000 0.75000

Comment line 0 1 0

0 0 1

Lattice vector of x, y, and z-direction # of aomts

0.00000 0.50000 0.00000 0.50000 0.25000 0.25000 0.75000 0.75000

0.00000 0.50000 0.50000 0.00000 0.75000 0.25000 0.75000 0.25000

Types of coordinates Direct: Fractional coordinate Cartesian: Cartesian coordinate Coordinates

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Visualization

Freeware

Support for Windows, Mac, and Linux

You can download this website

http://jp-minerals.org/vesta/en/download.html VESTA: a three-dimensional visualization system for electronic and structural analysis Drawings produced by VESTA may be used in any publications provided that its use is explicitly acknowledged. A suitable reference for VESTA is K. Momma and F. Izumi, "VESTA 3 for three-dimensional visualization of crystal, volumetric and morphology data," J. Appl. Crystallogr., 44, 1272-1276 (2011). 13

Enter the element count

Select elements

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Build a crystal structure with VESTA •  Click the File ! “New structure” (Ctrl + N) in the menu

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Unit cell TAB

Structure parameters TAB

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Hands-on excises (Vi editor) •  Making a POSCAR file

vi POSCAR

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! POSCAR name should be capitalized

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In the vi editor, press “ ”

! insert mode

esc” key on your keyboard

Press “ :wq

! save and quit

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INCAR SYSTEM = Si

NWRITE Tag

Parallelization: NPAR = 2 LPLAEN = .TRUE. Startparameter for this run: NWRITE = 2 PREC = high ISTART = 0 ICHARG = 2 ISPIN = 1 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

f+l f I E X

first and last ionic step first ionic step each ionic step each electronic step when applicable 22

INCAR ISTART Tag

SYSTEM = Si Parallelization: NPAR = 2 LPLAEN = .TRUE. Startparameter for this run: NWRITE = 2 PREC = high ISTART = 0 ICHARG = 2 ISPIN = 1 ENCUT = 550 Electronic Relaxation 1 EDIFF = 0.1E-04 ! stopping-criterion for ELM LREAL = .FALSE. ! real-space projection LWAVE = .TRUE. LCHARG = .TRUE.

ISTART = 0|1|2 Default: If WAVECAR exist 1 Else 0 This flag determines whether to read the file WAVECAR or not.

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 23

INCAR ICHARG Tag


ICHARG = 0|1|2 Default: if ISTART=0 Else

2 0

This tag determines how to construct the 'initial' charge density.


INCAR ENCUT Tag


ENCUT = Ecut default taken from POTCAR-file Cutoff energy for plane wave basis set in eV. All plane-waves with a kineticenergy smaller than Ecut are included in the basis set: i.e.


INCAR EDIFF Tag


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 struc ture energy change ('change of eigenvalues’) between two steps are both smaller than EDIFF. For EDIFF=0, NELM electronic SC-steps will always be performed.


INCAR EDIFFG Tag

SYSTEM = Si Parallelization: NPAR = 2 LPLAEN = .TRUE. Startparameter for this run: NWRITE = 2 PREC = high ISTART = 0 ICHARG = 2 ISPIN = 1 ENCUT = 550

EDIFFG = break condition for the ionic relaxation loop Default : EDIFF*10

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 27

INCAR NSW Tag

SYSTEM = Si Parallelization: NPAR = 2 LPLAEN = .TRUE. Startparameter for this run: NWRITE = 2 PREC = high ISTART = 0 ICHARG = 2 ISPIN = 1 ENCUT = 550

NSW = number of ionic steps Default : 0 NSW defines the number of ionic steps.


INCAR ISIF Tag

SYSTEM = Si Parallelization: NPAR = 2 LPLAEN = .TRUE.

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

Startparameter for this run: NWRITE = 2 PREC = high ISTART = 0 ICHARG = 2 ISPIN = 1 ENCUT = 550

Default if IBRION=0 (MD) else

0 2


VASP Manual for INCAR tags

.. .. .

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KPOINTS K-Points 0 Monkhorst Pack 6 6 6 0 0 0

Automa2c4mesh4

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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. # of electrons: 4 valence electrons for this Si potential,

Type of exchange-functional: PE = Perdew-Burke-Ernzerhof (PBE) ! GGA CA = Ceperley-Alder ! LDA Q.) What if you have multiple/different kinds of atoms in your system? e.g. SiO2 system? > cat POTCAR_Si POTCAR_O >> POTCAR

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Running VASP on PLSI supercomputer $ $ $ $

llsubmit vasp_kigi.cmd llcancel job_id llq llstatus

# submit the job # cancel the job # job status # system status

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OUTPUT Files • 

CHG, CHGCAR

Charge density data

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CONTCAR

Calculated Lattice constant and atomic coordinates

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DOSCAR

Density of States data

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OSZICAR

Information about convergence speed and about the current step

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WAVECAR

All wavefunction binary file

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OUTCAR

All information from the calculations

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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

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Visualization

Freeware

Support for Windows, Mac, and Linux

You can download this website

http://jp-minerals.org/vesta/en/download.html VESTA: a three-dimensional visualization system for electronic and structural analysis Drawings produced by VESTA may be used in any publications provided that its use is explicitly acknowledged. A suitable reference for VESTA is K. Momma and F. Izumi, "VESTA 3 for three-dimensional visualization of crystal, volumetric and morphology data," J. Appl. Crystallogr., 44, 1272-1276 (2011). 36

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)

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Thank you very much

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This is the end of the slides

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