Introduction to VASP 4 - GIST2).pdf · Introduction to VASP 4.6 ... cycle to calculate the...
Transcript of 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.
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
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.
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
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.
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
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.
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
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.
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
EDIFFG = break condition for the ionic
relaxation loop
Default : EDIFF*10
EDIFFG Tag
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
NSW = number of ionic steps
Default : 0
NSW defines the number of ionic steps.
NSW Tag
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
ISIF = 0|1|2|3|4|5|6
Default
if IBRION=0 (MD) 0
else 2
ISIF Tag
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.
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)