VASP Tutorial @ UGent

Danny Vanpoucke
11-01-2010
 OUTLINE

• Goal of this tutorial

• What is VASP
• Lock and load: time to start working
1. Basics: Self Consistent Calculation
2. Relaxing a structure
3. DOS
4. Bands
5. Partial Charge Density
STM
• It’s all true ... For certain values of true
1. K-point convergence
2. Kinetic energy cutoff convergence
3. Volume-scans, external pressure,
Birch Murnaghan Equation of state
• Additional information

VASP Tutorial @ Ugent D.E.P.Vanpoucke

 Goal of this Tutorial

Provide some basic knowledge, to setup standard (minimal) VASP

calculations.

Give enough background knowledge to allow further self-education

on more specific details and specialized calculations.

Give some hints with regard to possible pitfalls of the VASP-program.

This tutorial will allow you to use the VASP program as a black-box
device. (Assume the program works, and those who wrote it had a clue
of what they were doing ;-) )

For detailed information on the inner workings of the program itself
(and the theory behind it) I refer to the literature, online sources,
textbooks and the source-code itself.

VASP Tutorial @ Ugent D.E.P.Vanpoucke

 What is VASP?

VASP is a package for performing ab-initio quantum-mechanical molecular

dynamics (MD) using pseudo-potentials and a plane wave basis set. Both
LDA and GGA potentials/functionals are available. This code can be used to
obtain electronic and structural properties of small atomic systems (roughly
up to 100-200 atoms).

1) Periodic boundary conditions

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

Ideal for Plane wave basis-sets

VASP Tutorial @ Ugent D.E.P.Vanpoucke

 What is VASP?

VASP is a package for performing ab-initio quantum-mechanical molecular

dynamics (MD) using pseudo-potentials and a plane wave basis set. Both
LDA and GGA potentials/functionals are available. This code can be used to
obtain electronic and structural properties of small atomic systems (roughly
up to 100-200 atoms).

1) Pseudo-potentials
2) Periodic boundary conditions
Good for bulk materials
To make
( = not solife
goodeasier with the systems
for isolated plane waves
i.e. molecules)

Different flavors:
Ideal for Plane LDA,
wave GGA, hybrid (> v5)
basis-sets

VASP Tutorial @ Ugent D.E.P.Vanpoucke

 What is VASP?

VASP is a package for performing ab-initio quantum-mechanical molecular

dynamics (MD) using pseudo-potentials and a plane wave basis set. Both
LDA and GGA potentials/functionals are available. This code can be used to
obtain electronic and structural properties of small atomic systems (roughly
up to 100-200 atoms).

1) Small
2)
3) Periodic
Pseudo-potentials
boundary conditions
systems
Good
100 for bulk
atoms materials
are already large systems.
To make
( = not solife
Relaxation oneasier
good 32for withcan
thetake
isolated
cores plane waves
systems i.e.(real
a week molecules)
time!).

Periodic Boundary conditions allow you to simulate

Different flavors:
Ideal for Plane LDA,
wave GGA, hybrid (> v5)
basis-sets
Bulk.

VASP Tutorial @ Ugent D.E.P.Vanpoucke

 Lock and Load

• Did you bring your own problem(atic system)?

2 – 5 atoms

structure data
* coordinates in real/direct space
* lattice parameter
* lattice-vectors

If not:
example system 1 example system 2
Ge-bulk C0-molecule
* 2-atoms, diamond lattice • 2-atoms , molecule
• Lattice parameter= 5.6575A • bond length: 1.128A
• a1=(0.5; 0.5; 0.0)
• a2=(0.0; 0.5; 0.5)
• a3=(0.5; 0;0; 0.5)
•
@1 (0.00, 0.00, 0.00) Ge
•
@2 (0.25, 0.25, 0.25) Ge

VASP Tutorial @ Ugent D.E.P.Vanpoucke

 Basics: Self Consistent Calculation I

VASP always needs minimum 4 files:

1) INCAR : contains all the settings of the program parameters

you wish to use. (energy cutoff, parallelism, smearing,...)

2) KPOINTS : all the information with regard to your k-point set.

3) POSCAR : all the information with regard to the actual geometry

of your system.

4) POTCAR : the information regarding the potentials/functionals used

this one you get from a database

Let’s finally get started:

Make a folder with the name of your system. Inside this folder make a new folder
named: SelfConsistent.
VASP Tutorial @ Ugent D.E.P.Vanpoucke
 Basics: SC Calculation II
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.

This is a PAW potential for Ge

# electrons: 4 valence electrons for

this Ge potential, there also exists a
Ge potential including the d-
electrons in the valence shell
14e-
Type of exchange-functional:
CA=Ceperley-Alder  LDA

What if you have multiple/different kinds of

atoms in your system?
e.g. CO molecule
> cat POTCAR_C POTCAR_O >> POTCAR

VASP Tutorial @ Ugent D.E.P.Vanpoucke

 Basics: SC Calculation III
POSCAR-file
Ge-Bulk CO-molecule
Comment-tag

Scale factor
3 lattice vectors

Type and #atoms

Type coordinates: Direct or Cartesian

Comments
Positions of the atoms

Important: The order of the atom positions in the POSCAR file needs to be the
same as in the POTCAR file!

VASP Tutorial @ Ugent D.E.P.Vanpoucke

 Basics: SC Calculation IV
KPOINTS-file
Ge-Bulk CO-molecule

#K-points, 0
automatic grid

Type of automatic grid:

Monkhorst Packing
Gamma Centered (
hexagonal)

K-point grid + shift (second line)

Vacuum directions only need 1 k-point

molecule: 1,1,1 (=Gamma point only)
If your lattice-vectors have different length, then this needs to be reflected in the k-point
set (could give errors otherwise)
e.g. lattice vectors with lengths: a1=1, a2=2, a3=10

k-points: 6 3 1
VASP Tutorial @ Ugent D.E.P.Vanpoucke
 Basics: SC Calculation V
INCAR-file

More information and parameters can be found in the VASP manual.

VASP Tutorial @ Ugent D.E.P.Vanpoucke
 Basics: SC Calculation V
INCAR-file

More information and parameters can be found in the VASP manual.

VASP Tutorial @ Ugent D.E.P.Vanpoucke
 Basics: SC Calculation VI
Spoils of War

Parallel 4-cpu calculation

Our Bulk Ge system has only one type of
atoms: Ge, 2 atoms in our unit cell

Total ground-state energy

#Irreducible Brillouin zone K-points

(VASP scales ~linear with IBZKPT)

#bands (2e- per band)

Time per electronic step (LOOP)

and ionic step (LOOP+)
VASP Tutorial @ Ugent D.E.P.Vanpoucke
 Relaxation I: Setup
The structures we used for the SC calculations were not optimized.
To optimize them some parameters need to be changed.
 make a new folder : relax, and copy your 4 input files (INCAR, KPOINTS, POSCAR
and POTCAR) of the SC calculation.
INCAR
Modifications: POSCAR

Add the line

Selective dynamics

Indicate which atom

coordinates to update.

Modify atom positions ☺

KPOINTS

Reduce the k-point set to 11x11x11
for the Ge bulk system. Be careful using ISIF in combination with
vacuum systems: molecules, surfaces,…
VASP Tutorial @ Ugent D.E.P.Vanpoucke
 Relaxation II: Results
CO-molecule POSCAR

C-O bond length of 1.134998A

Not bad compared to the
experimental value of 1.128A

~0.6% larger

CONTCAR

The CONTCAR file is a

POSCAR file you can use to
continue either your relaxation
(if 100 ionic steps was not
enough) or start a SC
calculation. The CONTCAR file
is written at the end of each
ionic step.
(don’t forget to rename it
POSCAR is you want to use it)
VASP Tutorial @ Ugent D.E.P.Vanpoucke
 Relaxation III: Results

Only 12 ionic steps were needed

to relax to the final structure.

Position 2nd atom

at the end of each
Force eV/A
ionic step
VASP Tutorial @ Ugent D.E.P.Vanpoucke
 More advanced: Density of States (DOS) I

Both DOS and band-structure calculations are 2-step calculations.

1. Do a SC calculation to get a ready converged charge density
2. Do a Non-self consistent Calculation with high K-point density,
using the charge density obtained in the SC calculation.

Make a new directory: DOS and copy POSCAR, POTCAR, INCAR, KPOINTS and
CHGCAR to this folder from your SC calculation.

The files CHGCAR, POTCAR and POSCAR remain unchanged for the DOS
calculation. However, to get a good DOS we would like a denser k-point grid than
the one we used up to now. (Charge density and effective potential converge
rapidly wrt. k-points, so we can use a “small” k-point set to get the charge density)

Increase your k-point set in the file KPOINTS to e.g. 41x41x41

(btw this is also the maximum that VASP can handle)

VASP Tutorial @ Ugent D.E.P.Vanpoucke

 More advanced: DOS II

The only file left to modify is the INCAR file. Set ICHARG=1+10=11

1: read the CHGCAR from
our SC calc.

10: keep the Charge density
fixed during the calculation.
(only wave function update)

Increase convergence criterion

slightly

To get a good PDOS, you do

not want the spheres of the
atoms to overlap
chance to
see states from atom A in the
PDOS of atom B

Optional.
These allow you to specify the
part of the DOS you are
interested in, and the resolution
you wish to have.
VASP Tutorial @ Ugent D.E.P.Vanpoucke
 More advanced: DOS III: Results Ge Bulk

ICHARG=11, CHGCAR was read from

the SC calc.

Is this a good value?

Yes: Packing factor for diamond is
(Pi*sqrt(3)/16=~34.0087%)

Spreading in s, p, and d states per ion

VASP Tutorial @ Ugent D.E.P.Vanpoucke

 More advanced: DOS IV: Results

Ge Bulk DOS

CO DOS

Be very careful with the

smearing width!

 Check the PROCAR

VASP Tutorial @ Ugent D.E.P.Vanpoucke

 More advanced: DOS V: Results CO molecule
Be very careful with the
smearing width!

 Check the PROCAR file

for more information on the
nature of the spikes

VASP Tutorial @ Ugent D.E.P.Vanpoucke

 More advanced: DOS V: Results CO molecule
Be very careful with the
smearing width!

 Check the PROCAR file

for more information on the
nature of the spikes

Band 1: O-s
Band 2: C+O s  σ?
Band 3,4,5: C+O pπ?

VASP Tutorial @ Ugent D.E.P.Vanpoucke

 More advanced: BANDS I

Similar as to the DOS calculation, a band-structure calculation consists of

two parts:
1. Do a SC calculation to get a ready converged charge density
2. Do a Non-self consistent Calculation with high K-point density
along lines of high symmetry, using the charge density obtained in
the SC calculation.

Make a new directory: bands and copy POSCAR, POTCAR, INCAR, KPOINTS and
CHGCAR to this folder from your SC calculation.

The files CHGCAR, POTCAR and POSCAR remain unchanged for the band-
structure calculation. Since we only use K-points along lines of high symmetry, a
SC calculation is out of the question.
all k-points need to be treated
independently.

VASP Tutorial @ Ugent D.E.P.Vanpoucke

 More advanced: BANDS II
For band-structures we use k-points along certain lines

In this calculation we will use 25 k-points per line segment

2 line segments: L
Γ and Γ
X

Total: 50 Irreducible K-points in our calculation

Do a non-SC calculation
Since the k-points form lines, it is
impossible to make tetrahedra, so a
different integration scheme is necessary.

The PROCAR file is always useful to

have if you are interested in the
character of your bands (cf. CO DOS)

VASP Tutorial @ Ugent D.E.P.Vanpoucke

 More advanced: BANDS III: Result
The energy values for all bands at each k-
point can be found in the EIGENVAL-file 
this can be used to generate a band-
structure (as seen on the left)

K-point

bands

VASP Tutorial @ Ugent D.E.P.Vanpoucke

 More advanced: Partial Charge Density
STM
Between molecules and bulk we find surfaces. These systems can also be studied
with VASP. Periodic boundary conditions make sure your system extends infinitely in
both x and y direction. In the z-direction we will have copies of the same slab (just
like we had for the molecule), and a vacuum region thick enough to negate
interaction needs to be added. As a consequence you should not try to perform cell-
optimizations, in which you allow the volume to change (your vacuum will implode).

How do you set up a slab calculation?

1 Make a POSCAR and POTCAR file just as before
 try to center your slab around a zero-plane
 watch out for the symmetry (sometimes 1extra layer might halve
the number of IBZKPTS)
 fix layers that should represent bulk
2 Make a KPOINTS file with 1 k-point in the direction perpendicular to the
surface (e.g. 8x8x1, for a slab in the xy-plane)
3 Setup an INCAR file just as before
Next to DOS and band-structure calculations you can also do a Partial Charge Density
calculation. The results of such a calculation could then be used to simulate STM
images.
VASP Tutorial @ Ugent D.E.P.Vanpoucke
 More advanced: Partial Charge Density
STM II
A Partial Charge Density calculation is the shortest calculation you can run, it doesn’t
even perform a single electronic step.
You need:
WAVECAR-file (LWAVE=.TRUE.  INCAR SC calc.)
Keep everything the same as for your SC calculation only modify the INCAR file like this:
(use a new folder, if something goes wrong or your want to do multiple runs you can simply copy the WAVECAR file again)

This tells VASP to just read the

WAVECAR files and then start writing
the PARCHG files

How the Partial charge needs to

be generated

VASP tend to generate a new random

WAVECAR at every possible chance.
So be very careful and mind the
#bands, #CPU,…
VASP Tutorial @ Ugent D.E.P.Vanpoucke
 More advanced: Partial Charge Density
STM III
VASP will now generate files called PARCHG, which have the same formatting as a
normal CHGCAR file…in combination with some programming you can now generate
STM images of your surface under study.

VASP Tutorial @ Ugent D.E.P.Vanpoucke

 It’s all true … for certain values of true.
Of course you wish your calculations to reflect reality to perfection, however, infinite
precision and numerical never fit in the same sentence in the absence of a negation.

1) ENCUT: energy cutoff for the kinetic energy (any contribution above
is assumed negligible (and hoped zero))
2) (finite) k-point grids
continuous functions are approximated by
points on a discrete grid. This grid is then made as coarse as possible
to reduce the number of points to evaluate (while trying to maintain as
much accuracy as possible)
3) Functionals: each flavor will give you quantitatively different results
(qualitative results can also differ (e.g.: CO-adsorption site on
Pt(111)) ), and their value can only be assessed by comparison to
reality. (e.g.: Metallic Ge bulk)
4) Convergence criteria

Convergence tests are needed (for each new system)

VASP Tutorial @ Ugent D.E.P.Vanpoucke

 It’s all true … k-points and ENCUT
First time VASP usage, first time study new study:
The ground-state energy of a system is connected to both K-points and kinetic
energy cutoff
spend some CPU-time on a 2D grid (k-points-ENCUT), to get a
feel for the behavior of VASP

VASP Tutorial @ Ugent D.E.P.Vanpoucke

 It’s all true … k-points and ENCUT
First time VASP usage, first time study new study:
The ground-state energy of a system is connected to both K-points and kinetic
energy cutoff
spend some CPU-time on a 2D grid (k-points-ENCUT), to get a
feel for the behavior of VASP

VASP Tutorial @ Ugent D.E.P.Vanpoucke

 It’s all true … k-points and ENCUT
First time VASP usage, first time study new study:
The ground-state energy of a system is connected to both K-points and kinetic
energy cutoff
spend some CPU-time on a 2D grid (k-points-ENCUT), to get a
feel for the behavior of VASP

VASP Tutorial @ Ugent D.E.P.Vanpoucke

 It’s all true … optimizing your lattice
Although you might get a nice, high precision value for the lattice parameters of your
system from experiment, this will probably not be the energy minimum for your
calculation. Even more, the lattice parameters vary from functional to functional (and
also depend on the accuracy of your k-pointset!).
There are several ways to obtain the optimum lattice parameters
1) Lazy: just use the experimental value and ignore the above, or get if from a
colleague working on the same system and same setup.
2) Quick (and sometimes dirty): a volume scan

do a set of SC calculations with varying scale factor (line 2 in POSCAR)
and find the minimum ground-state energy. Ideally at this point also the
external pressure given by VASP should become zero.
 Works good for Ge
If you have more than one internal parameter (e.g. lattice vectors with different length) or the
external pressure and the minimum energy don’t coincide (i.e. they differ a lot) then you will need
something more complex.
3) Fit to an equation of state: Do a set of fixed volume relaxations and fit these to the
Equation of state of your choice.

advantage: no problem handling multiple internal parameters

disadvantage: expensive compared to (2) + need to implement a fitting
algorithm.
VASP Tutorial @ Ugent D.E.P.Vanpoucke
 Optimizing your lattice… Birch-Murnaghan ES
OPTION 3: Loop (set of Volumes)
Step 1: Fixed Volume relaxation
(ISIF=4, LCHARG=.TRUE.)
Step 2: Second fixed Volume relaxation
(continuation)
(ISIF=4, ICHARG=1, LCHARG=.TRUE.)
Step 3: SC calculation
(ICHARG=1, no ISIF parameter)
End Loop
Fit Volume-Energy to Equation of State

The two relaxations in sequence are due to the effect the change in cell-shape
has on the energy cutoff region (G-vectors).

Possible equation of state: Birch-Murnaghan Equation of state

 gives the Bulk modulus as a bonus.

VASP Tutorial @ Ugent D.E.P.Vanpoucke

 VASP-speed
In the examples of this tutorial, the systems were small and it was possible to run a
calculation on a single CPU within a few minutes. However, for a reasonable
system of 100 atoms (you get there quickly) a relaxation can easily take half a
week on 32 CPU’s …or even more.

VASP also exists in a parallel version

Next to a good parallel compilation, you might be able to speed up
calculations by
• clever sequences of calculations (e.g. do a relaxation in multiple
steps with increasing accuracy)
• use the CHGCAR and WAVECAR from a previous calculation to
reduce the length of the first new ionic step. (can be a factor of 3)
• optimize some parallelization parameters in the INCAR file for your
specific system(-size): NPAR, LPLANE, NSIM (can give a global
speedup of 20%)

Although such checks can be expensive at first, you can gain a lot in
future calculations.

VASP Tutorial @ Ugent D.E.P.Vanpoucke

 Additional Information
• VASP manual: http://cms.mpi.univie.ac.at/vasp/vasp/vasp.html
(make sure you have the latest newest version, older versions are still available online,
but might contain ‘wrong’ information w.r.t. the function of INCAR-parameters of your
VASP version (cf. NPAR))

• Official VASP Tutorials: http://cms.mpi.univie.ac.at/vasp-

workshop/slides/documentation.htm

• VASP forum: http://cms.mpi.univie.ac.at/vasp-forum/forum.php

(if you have special questions, and time to wait for an answer…and for the site to load)

• VESTA: http://www.geocities.jp/kmo_mma/crystal/en/vesta.html
((free) program (OPENGL + C++) to visualize crystal structures, CHGCARS, etc… short
learning curve, export in images in most used formats (Win, Linux, Mac))

• P4Vasp: http://cms.mpi.univie.ac.at/odubay/p4vasp_site/news.php
(a second visualization program (python+??), specifically aimed at VASP…however I
would urge you to try VESTA ;))

• Hive STM-plotter: http://users.ugent.be/~devpouck/

(if you are interested in generating STM images from your VASP data, this program
(Delphi=pascal+GUI) will do the trick. Export images as bmp)
VASP Tutorial @ Ugent D.E.P.Vanpoucke
VASP Tutorial @ Ugent D.E.P.Vanpoucke