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I calculate the surface energy of Pt3Ni(001) using the formula as

Surf. Energy = E(total free energy from OSZICAR) - N(pt)*chem.Pot.(Pt) - N(Ni)*chem.Pot.(Ni)

I calculated chemical potential of Pt and Ni from the FCC bulk free energy divided by 4 (No. of Atoms)

When I calculated the surface energy with different termination. I found the surface energy positive. If i don't consider the negative value of chemical potential it will be negative.

Am I in correct way? How can I find the stable surface termination. If i care the sign of chemical potential, Pt-Pt surface termination is more stable with positive minimum energy if I don't care sign Pt-Ni termination is stable.

Please note that the surface energy is the change in Gibbs free energy per change in area. So first of all it should be divided by the area of your surfaces.

Then you really should look at what you are calculating. You are comparing the surface system with respect to the reference states which also build your Pt3Ni bulk system (since you have assumed the Pt3Ni-bulk is in equilibrium with the reference states). This means that if the surface energy is negative the bulk system would be less stable and decompose into just surfaces since it would be more energy favorable. So since the bulk system is stable (materials don't just decompose spontaneously) the surface energy should be positive!

The surface termination for a planar surface will be the surface with the lowest surface energy since this will be most energetically favorable. Then if you start to have e.g. nanoparticles and want to find the equilibrium shape then you will weight the total surface area into account too. Then you should read a bit of Wulff contructions and related literature.