Rajasekarakumar Vadapoo

S.No: 401-03-9023
Electronic Structure Theory HW# : 3
Oxygen Molecule- Using VASP

AIM:

To calculate the equilibrium distance between the oxygen atoms in the oxygen molecule
by the following ways:

1) Manual change of the inter -atomic distance

2) Using the atomic structure relaxation.

INTRODUCATION:

In this calculation we use oxygen molecule to find out the magnetic moment and
minimum energy in different environments. We used VASP-code for this calculation.

1) To find out the interatomic distance manually, we used three different parameters:
a. symmetry on with spin off
b. Symmetry off with spin off
c. Symmetry off with spin on
2) To use the atomic structure relaxation, we have used six different parameters:
a. Both atoms have 3 degrees of freedom and relaxed with spin on
b. Both atoms have 3 degrees of freedom and relaxed with spin off and then a
static run with spin on
c. Single atom fixed with another has 3 degrees of freedom
d. Single atom fixed with another has 2 degrees of freedom
e. Single atom fixed with another has degree of freedom only in c-direction
f. Single atom fixed with another has degree of freedom only in a-direction

CALCULATIONS:

INPUT files:

Since we want to calculate the details for

oxygen molecule, we have made a unit cell with sufficient
vacuum around it, so that the interaction between each
molecule would be negligible. We have used a unit cell
with a single oxygen atom with a = b = 13 A0 and c = 14

Figure 1. Unit cell contains oxygen atom

A0 as shown in fig.1. and the corresponding POSCAR files are as shown below.

1) POSCAR:
O

1.000000

13.000000 0.000000 0.000000

0.000000 13.000000 0.000000

0.000000 0.000000 14.000000

Direct

0.500000 0.500000 0.447143

0.500000 0.500000 0.552857

For atomic structure calculation to have no translation of the centre of mass we have
used the following POSCAR with different atomic directions fixes as the cases comes.

1.000000

13.000000 0.000000 0.000000

0.000000 13.000000 0.000000

0.000000 0.000000 14.000000

Selective dynamics

Cartesian

0.500000 0.500000 0.447143 F F F

0.500000 0.500000 0.552857 T T T

~
2) KPOINTS:

We have used only one K-pt ( Gamma Pt.), since the unit cell is really big in the real
space which makes the reciprocal state very small. The k-pt file used in the calculation as
follows:

automatic k mesh

0
g
111
0.0 0.0 0.0
3) POTCAR:
POTCAR files would be the same since we have only oxygen for all the calculations.

4) INPUT:

We have used two different input files.

a) For manual change of atomic distance we used the following input file
System = oxygen
ISYM = 0
ISMEAR =0

LPLANE=.FALSE.
NPAR=4 number of nodes to use
LSCALU=.FALSE. do you have SCALAPACK
NSIM=1 nodes grouping for efficiency
• We have used the flag ISYM= 0 for the symmetric off calculations and left to
the default value for the symmetric on calculations. For the spin calculation
addition of the above details we have included another flag ISPIN= 2
b) For Automatic atomic structure calculations we have used the following input file:
System = oxygen
ISMEAR =0
ISYM = 0
LPLANE=.FALSE.
NPAR=4 number of nodes to use
LSCALU=.FALSE. do you have SCALAPACK
NSIM=1 nodes grouping for efficiency
NSW = 400 number of steps for IOM
 IBRION = 2 ionic relax: 0-MD 1-quasi-New 2-CG
ISIF = 2 stress and relaxation
IWAVPR = 11 prediction: 0-non 1-charg 2-wave 3-comb
ISYM = 0 0-nonsym 1-usesym 2-fastsym
ISPIN= 2
• We have used the default value for ISPIN for the calculations without spin

RESULTS AND DISCUSSION:

40 symmetryon-spin off
1) Manual change of interatomic symmetryoff-spin off
distance: symmetry off-spinon
30
We have done the
calculation to find out the Energy (eV) 20
equilibrium distance for the
oxygen molecule manually in 3 10

different ways and the results

0
are as shown in figure.2. The
corresponding details are -10
shown in table.1.
0.6 0.8 1.0 1.2 1.4 1.6 1.8 2.0 2.2 2.4 2.6

Inter atomic distance (A0 )

Figure.2. Energy Vs Inter atomic distance

Type Symmetry on -spin Symmetry off- spin off Symmetry off –spin
on
Off

Emin -8.82469 -8.82475 -9.8636

Inter atomic 1.26 1.26 1.12

distance for min
Energy

Table.1. Minimam Energy position for manually

changed interatomic distances.
 From fig.2, we infer that there is no difference between the symmetry on-spin off &
symmetry off-spin off calculations both gave the minimum energy at around -8.824 eV @
interatomic distance of 1.26 A0. Among the three related calculations the one with symmetry off-
spin on calculations gave a low energy than all which
4 symmetry off-spin on
is -9.8636 @1.12 interatomic distance. And this is the
3 most stable one.
magnetization (Bohr magneton)

2
1 Fig.3. shows the magnetization of the
0 symmetry off – spin on case for different atomic
-1
distance. All other cases spin is off, so the
-2
magnetization is zero. Fig.3 shows some anomaly of
-3
-4
magnetization at two different inter atomic distances
0.6 0.8 1.0 1.2 1.4 1.6 1.8 2.0 2.2 and for all other it gave the value of 2 Bohr magnetron.
atomic distance (Ao)

Figure.3. magnetization Vs Inter atomic

distance

2) Atomic structure relaxation:

The atomic structure relaxation with fixing the degrees of freedom of atoms is shown in
table.2. Among all the cases of calculations carried out the one which allowed to have 3 degrees
of freedom for both the atoms in the oxygen molecule is the most stable one with the Emin @ -
9.863440 eV and all other cases are less stable but the one with single atom fixed and the other

Properti Both atoms Both atoms Single Single atom Single atom Single atom
es have 3 have 3 degrees atom fixed fixed with fixed and the fixed and the
degrees of of freedom with another has other has other has
freedom relaxed another 2 degrees of freedom of freedom of
with spin without spin has 3 freedom motion only in motion only in
on then static run degres of c-direction a-direction
with spin on freedom

Emin -9.863440 -9.862970 -9.859520 -9.859520 -9.859520 3865.811354

(eV)

Magneti 2 2 2 2 2 3.9994
zation

Table. 2. Atomic structure relaxation with fixing the degrees

of freedom of atoms
has the degree of freedom only in a- direction shown highly unstable with the energy of
3865.811354 eV. In the case of magnetization all the cases have the value of 2 Bohr magneton
except the highly unstable one has a value of 3.9994 Bohr magneton.

CONCLUSION:

We have successfully carried out the ab-initio calculations of oxygen molecule with
VASP-code to find the Energy minimal position mainly by two different ways manually and by
atomic structure relaxation. The results show that for the oxygen molecule the calculations with
spin and without spin gives different energy minimal positions. The one with spin gives the most
stable one. The manually calculated with spin on and symmetry off has the almost same energy
(-9.863 eV) with the one in the atomic structure calculation carried out on the case where both
the atoms have complete degrees of freedom which are the most stable ones. In the case of
magnetic properties all the calculations done by atomic structure calculations have the
magnetization of 2 Bohr magneton except the most unstable one having the value of 3.9994
Bohr magneton.