Formation energy-optimization method -reg

[GJK]

Hi,
Formation energy=Ef = (Et1+E2)-(Et2+E1)

where Et2 is the total energy of perfect GNR,
Et1 is the total energy of GNR with substitutional nitrogen atoms,
E1 and E2 are the energies of single free nitrogen and carbon atom,respectively.
This is the formula for substitutional impurity(USING NITROGEN)

Here are my queries?? Kindly help-Since ATK have three optimization tool-Bulk Device and Molecule

So there are three physical parameters for which the total energy is to be found.
What optimization method?-Bulk mtd (or) Molecule mtd for the three parameters I should follow for the total energy calculation?
1.   GNR
2.   GNR with impurity atoms or molecule
3.   Impurity atom (or) impurity molecule

I am eagerly waiting sir.
Thanks in advance

[Anders Blom]

If the system is a molecule you should treat it as a molecule. However, if the simulation is carried out correctly, meaning you have enough vacuum in the bulk version of the molecule (inscribed in a big box) the results should not be very different at all.

[GJK]

If the system is a molecule you should treat it as a molecule. However, if the simulation is carried out correctly, meaning you have enough vacuum in the bulk version of the molecule (inscribed in a big box) the results should not be very different at all.

Hi Mr.Anders Blom,

Can you specify the minimum vacuum requirements for the molecule optimized in bulk for total energy analysis.

Thanks in advance.

[Anders Blom]

The minimum would be a box such that there are no basis set overlaps between repeated images, but in addition one will always need some vacuum padding also to reduce the long-range electrostatic interactions. Therefore, the best approach is to treat a molecule as a molecule.

[GJK]

The minimum would be a box such that there are no basis set overlaps between repeated images, but in addition one will always need some vacuum padding also to reduce the long-range electrostatic interactions. Therefore, the best approach is to treat a molecule as a molecule.

Hi Mr.Anders Thanks.But I have a doubt

Does calculating the formation energy by doing optimization of Bulk(graphene,graphene and functional group) and Molecule(functional group) affect the result Kindly clarify.

Any ways I will check the result for total energy for the functional group molecule and let you know the results for both Bulk and Molecule optimization.

[GJK]

The minimum would be a box such that there are no basis set overlaps between repeated images, but in addition one will always need some vacuum padding also to reduce the long-range electrostatic interactions. Therefore, the best approach is to treat a molecule as a molecule.

Hi Mr.Anders Thanks.But I have a doubt

Does calculating the formation energy by doing optimization of Bulk(graphene,graphene and functional group) and Molecule(functional group) affect the result Kindly clarify.

Any ways I will check the result for total energy for the functional group molecule and let you know the results for both Bulk and Molecule optimization.

Dear Mr.Anders,

I have calculated the total energy for the bulk and molecule configuration as you said I didt' get much change,provided my vacuum padding should have been good enough.Thanks for your guidance.I have posted my queries below???

These are the values I got---
Molecule optimized in bulk config-           -2717.84430 eV
Molecule optimized in molecule config-    -2717.77142 eV

But the formula which I mentioned for formation energy is for doping(with a substitutional atom).

In my system I am using Graphene and a molecule to check for the binding/interaction energy,charge transfer density(Mulliken population-correct???) ,polarisability and formation energy.

Kindly help me how to calculate the following in my study??
1. formation energy (in the reference paper S.S. Yu, W.T. Zheng, Q.B. Wen, Q. Jiang, Carbon 46 (2008) 537–543.) was calculated for Ni doping,where they estimate the total energy of carbon and nitrogen separately for calculating the formation energy.But my system has molecule with different atoms.So confused how to calculate formation energy in my study??? Should I optimize my molecule itself and subtract the total energy or what should I do???

 2.charge transer,polarisability(from the results of polarisation).How to calculate alpha(polarisability) from the Pi,Pe,Pt values which I got???

3.Then the charge transfer or withdrawal from the Mulliken Population.I got   values for Mulliken Population but could not predict anything due to lack of formulas or knowledge.

4.There is no vander Waal's interaction in my system.It's purely the bonding of the molecule on graphene.So should I calculate the BSSE and counterpoise correction which is for two systems separated by a distance.If then help me for scripts and incorporation of the scripts ate the right place.

Your  assistance will be helpful to me.

Regards
Jananikumar