Calculation of the Binding Energy of
CO on Ni(111)
Using the CO structure on Ni(111) we can
generate a series of structures with different distances between adsorbate
layer (CO) and the surface. You may use
the computer program fragcell to do this.
The program fragcell prompts the user for the total number of atoms
(here it is 22) and the number of adsorbate atoms (here it is 4). It also asks how many displacements are
requested and what the starting distance and increment are. Good results can be achieved for 40
displacements with a starting distance of 1.2 Å and increments of 0.1 Å.
Fragcell also requested a four letter root name. The structure files generated by the program
will have the form.
root
where the number starts at 1 and increases to
the maximum requested number of files.
If you examine a few the files they have
appearance shown below.
Figure 1. Separation distance of the adsorbate
layer is 1.2 Å.
Figure 2. Separation distance of the adsorbate
layer is 4.2 Å.
Figure 3. Separation distance of the adsorbate
layer is 10 Å.
We can use the
structure in Figure 3 as a reference energy for an adlayer that is not
interacting with the surface. You will
want to run fragcell a second time a create one file with a separation distance
of 10 Å for this purpose.
Now you are ready to
submit the files. You will need an input
file for each of the car files. Rather
than copying each of the files and preparing each of the 40 or more files for
submission you can run a script that is automatically created by fragcell. The script has the name root.job. To activate the script type:
Ø
chmod +x root.job
with the root name that you have given to the
files. You will need one input
file. It should have the name
root1.input (again with the root name that you have given to the files). To obtain this file copy the ni_111_co.input
file.
Ø
cp ni_111_co.input root1.input
You will want to edit the root1.input and change
the job type. For the current analysis
you will want to calculate single point energies (Calculation type:
energy). These jobs will run much more
quickly since you are not optimizing at this stage, but only determining the
energy of each modified structure.
The root.job file will also create the job
files.
You may want to submit the job files as one
batch job to save typing the submit command 40 or more times.
Analysis of the Output
Once the outmol files have been created you can
run the program pesgen or pesgen_thermal to extract the binding energies from
each of the files.
pesgen – extracts energies from outmol files in
units of kcal/mol when the Fermi option is used for Occupation. The program
pesgen will generate a file root.kcal that contains the energy in kcal/mol for
each structure.
pesgen_thermal – extracts the energies from
outmol files in units of kJ/mol when the Thermal option is used for Occupation. The program automatically corrects for the
finite temperature used in the Thermal calculation. The program pesgen_thermal
will generate a file root.kj that contains the energy in kJ/mol for each
structure.
The output files can be plotted in Excel or any
convenient plotting program. The
calculated potential energy surface using the GGA functional and GGA basis set
is shown in the Figure below.
Figure 4. Calculated potential energy surface
for CO on a Ni(111) surface.