Density Functional Theory Calculation of CO on Ni(111)

Once the ni_111_co.car file containing the structural coordinates for the unit cell of carbon monoxide on Ni(111) copy the template.input file to the same working directory and rename it ni_111_co.input. Since the structure you created was not correct you will want to perform a geometry optimization. In this case, we will use effective core potentials (ECP) to make the calculation less expensive. To do this use vi editor to change the "pseudopotential keyword".

#Pseudopotential none

Pseudopotential ecp

#Pseudopotential vpsr

We will also fix the positions of the Ni atoms and optimize only the CO. To do this find the Opt_Fixed keyword. In vi you can search for a word using the backslash. So you would type "/Opt_Fixed". Change the commenting by removing the number sign "#". Then list the atoms that are to be fixed. In the car file the CO atoms are the first four atoms and atoms number 5 - 22 are Ni. The input file should have the following appearance.

# (i4,2x,a3)

Opt_Fixed

5 XYZ

6 XYZ

7 XYZ

8 XYZ

9 XYZ

10 XYZ

11 XYZ

12 XYZ

13 XYZ

14 XYZ

15 XYZ

16 XYZ

17 XYZ

18 XYZ

19 XYZ

20 XYZ

21 XYZ

22 XYZ

Once the car and input files are ready you can create a job file and submit the job.

Examining the output

When the job has completed the car file contains the updated (optimized coordinates). Use the Molecule/Get command to read in the optimized structure file. If you want to see the trajectory taken as the CO changed its position you can examine the archive file (ni_111_co_hist.arc).

The CO atoms are nearly perpendicular to the surface in the geometry optimized structure as shown in the figure below.

Now to place the fragment in a periodic coordinate system use the Assembly/Cell command. The dimensions will be automatically read from the PBC line of the car file. In this case you will not want to check the Center in Cell box. Once you Execute this command you will see the box defining the periodic boundaries in a white outline on the black background. To see multiple copies of this unit cell you will want to use the Assembly/Cell_Display menu. Check the Border_and_Pack option since x is the normal to the Ni(111) surface you will want to have 0 in the A dimension and 1 in the B and C dimension in the menu box. When you select Execute the periodicity will be evident as shown in the Figure below.

To create images that show the structure for display you may use the Molecule/Render command. The types of rendering are:

Ball_and_Stick

Stick

CPK

Shown below is the Ball_and_Stick option for the structure.

Also shown is the CPK rendering.

You may also change the background color. To do this, use the Session/Environment menu and select Background. You can click on the white box in the Background menu and the background will be changed once you Execute the command. You may also rotate the structure (using the right mouse button) so that the disposition of the CO molecules in a (3x3)R30^o lattice is evident.

At this stage you may perform further analysis. There are many possible studies that can be carried out. A few possibilities are listed below.

1. Binding energy of CO on the Ni(111) surface.

2. Vibrational frequency of bound CO compared to free CO.

3. Comparison with other diatomic molecules.