Part 3: Initial and finial image of step 2

Since this is the second step of the reaction where the product of the previous step reacts with another molecule of ethylene, the initial state need to reflect this.
Accordingly, the final state is different. Now it has a hydrocarbon chain of 4 carbons attached to the surface.

Creating the initial state calculation

1. Create a directory "step2" under your lab4 directory.
2. Inside your step2 directory, create a directory "ini".
3. Go to the "ini" directory, copy over the INCAR, KPOINTS CONTCAR (or POSCAR) and slurm_fri.sub from your /lab4/step1/fin/.
4. Edit the POSCAR with ag POSCAR .
   
   Add another ethylene molecule to the surface close to the C that is bonded to the surface.

   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.

5. Sort the elements in the POSCAR with the script sortpos.py .
6. 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 step2 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 C₂ group up and put slightly higher to the surface than the new coming ethylene molecule. Move the molecules closer so that the two carbons that we want a new bond to form between is close to each other. You may also move the hydrogens of the new carbon so that the new carbon has 4 bonds distributed in a tetrahedral geometry.
4. Modify the .sub file accordingly and keep running this job until it's converged. Cross your fingers and wish that this will optimize to your desired product. If the bond formation is not what you desired, change the relative positions of your molecule/atoms and try again.