Part 1: Initial and finial image of step 1

In this part you will create two calculations: the initial state and the final state.
The initial state is the reactant state. In this case you have an activated surface and a molecule of ethylene close to the surface.

Creating the initial state calculation

1. Create a directory "step1" under your lab4 directory.
2. Inside your step1 directory, create a directory "ini".
3. Go to the "ini" directory, copy over the INCAR, KPOINTS and slurm_fri.sub from your /lab3/Slab/Slab111.
4. Copy over your converged structure of your Au(111) slab. If you did not run vfin.pl on your last run, the converged geometry should be your CONTCAR. Otherwise, it should be the POSCAR. If you copied over the CONTCAR, rename it POSCAR.
5. Edit the POSCAR with ag POSCAR .
   
   Add an H to a hollow site on the surface, and an ethylene molecule near by, such as on top of another Au atom next to the hollow site where the H is.

   Refer to lab 3 where calculated binding energies for how to use ase gui to add molecules and groups.
   Note that ase gui allows you to add the molecule C₂H₄.

6. Sort the elements in the POSCAR with the script sortpos.py .
7. Obtain the POTCAR with the script sogetsoftpbe.py and edit the slurm_fri.sub file accordingly. Keep running the job until the structure is optimized.

Creating the final state calculation

1. Go to your step1 directory and create the "fin" directory.
2. Go to the "fin" dicrectory. Copy over the INCAR, KPOINTS, POTCAR, slurm_fri.sub from your "ini" directory. If your ini is converged, you can copy over the CONTCAR. If not, the POSCAR will do.
3. Move the H that was on the surface to under one of the C. Keep at least 0.5 Å distance from C and the surface Au.
4. Modify the .sub file accordingly and keep running this job until it's converged.