Computational Lab 2
Calculation of reference atoms and molecules.
Click here to go back to Lab 2 To better show case how we can calculate reaction energies and its limitations (things you should keep in mind while designing your calculations), we are going to do the following exercises:
You will need to create, under your ~/lab2 directory, the following directories: c, co2, h2, h2o, cl2, hcl.
E_reaction = E_CO2 - E_c - E_O2
E_reaction = E_H2O - 1/2 * E_O2 - E_H2
E_reaction = E_HCl - 1/2 * E_H2 - E_Cl2
In a box with each lattice vectors having a length of 10 Angstroms, create and optimize the following: a single C atom, a carbon dioxide molecule, a hydrogen gas molecule, a water molecule, a chlorine gas molecule and a hydrogen chloride molecule. Remember that you already have the oxygen gas molecule as this point. Use the energies of these molecule to calculate the following:
You can create these directories by copying your pt1 and rename it into these directories.
Then, you will need to edit the POSCARs to change the element type, number of atoms, and add or edit atomic positions when necessary.
As a rule of thumb, don't put two atoms closer than 1 Å apart.
It's recommended that you change the box size in POSCAR to 10 on x,y, and z directions.
Make sure that you have one line of positions for each atom. I recommend putting one atom at the center of the box (5,5,5) and arrange other atoms accordingly.
As an initial guess for the relaxation calculation, ues known bondlength of these molecules. You can google "HCl bond length" to see how far your Cl atom should be from your H atom.
Reaction energy for a single carbon atom to react with a oxygen molecule, forming a carbon dioxide molecule.
Reaction energy for forming a single water molecule from hydrogen and oxygen gas molecules.
Reaction energy for forming a single hydrogen chloride molecule from hydrogen and chlorine gas molecules.