Computational Lab 2

Calculation of reference atoms and molecules.

Click here to go back to Lab 2

Pt reference

In this lab you will use an isolated Pt atom in vacuum as the reference state for the element Pt.
You need to calculate the total energy of this atom.
The directory containing all files you need is /home/fri/lab_files_2022/lab2/pt1. Copy it over to your ~/lab2.
Change the jobname in your sub file for this calculation and submit the job.
Refer to your Pt32 calculation for detailed steps.

Pd reference

To get the energy of a single palladium atom, you need to simulate an isolated Pd atom in vacuum.
Here is how to create that calculation:

Copy the /home/fri/lab_files_2022/lab2/pt1 into your ~/lab2 but rename the directory at the destination as pd1

Use the command cp -r /home/fri/lab_files_2022/lab2/pt1 ~/lab2/pd1 will create a directory in your ~/lab2 called "pd1" containing all files in the original pt1 directory.

With vim, edit the POSCAR and change element in line 1 (potentially also line 6) from Pt to Pd.
Once the POSCAR is correct, use this script to acquire a new correct POTCAR. /home/wc5879/kingRaychardsArsenal/sogetsoftpbe.py .
Edit the sub file to have the correct reflective job name, then submit this job.

O₂ reference

The reference energy for O atoms will be 0.5 O₂ energy. Therefore, you need to create a calculation to obtain the total energy for O₂.
Follow the same procedure in Pd1 section to create the o2 directory in your ~/lab2.

Edit the POSCAR with vim to replace element Pt with O, and change the number of atoms and write the position for the new atom so that the new atom is about 1.5 Å away from the existing atom.

In line 6 or 7, change 1 to 2. After the line "Direct" or "Cartesian", add line "0.75 0.75 0.75" if Direct, "4.5 4.5 4.5" if Cartesian.

Then get the correct POTCAR with sogetsoftpbe.py, change job name and submit the job.