Computational Lab 2
Calculation of reference atoms and molecules.
Click here to go back to Lab 2 While changing the core elements of a particle has a relatively mild change on the reactivity (binding energy) of the particle, changing the surface element has a dramatic effect on the reactivity of the particle. Afterall, an Au particle is different from a Zn particle.Here you will create a new (potentially core-shell) nanoparticle, get its energy, then bind an oxygen to it and calculate the O-bonded particle energy.
Create a new O-bonded particle
Copy the "ptO/" (or "ptpdO" if you want to swap two elements) directory to your ~/lab2 directory and re-name the directory to what ever element you want.
For example, if you want to create a Au particle with ptO, you will copy the pt directory over and rename it as auO with: cp /home/fri/lab_files_2022/lab2/ptO ~/lab2/auO
If you are creating a new core shell, for example, with Ir@Ag, you will copy pdpto directory over and rename it irago with: cp /home/fri/lab_files_2022/lab2/pdptO ~/lab2/iragO
Once you change the elements, you must then get the corresponding POTCAR with /home/wc5879/kingRaychardsArsenal/sogetsoftpbe.py
Then, you can change the job name and submit the job. Depending on what element you choose, your relaxation job may take many runs but the energy of each run should be consistently getting smaller.
Create your reference particle
To calculate the oxygen bindin energy, you need to have the reference for oxygen (you already have) and the reference for your new particle. Copy over the directory without O to your ~/lab2 directory.
If you created a pure metal particle with oxygen, you need pt38. If you created a core-shell, you need pdpt
Change the job name and submit your job. You may need to run this relaxation multiple times depending on what element you choose.