QuantumATK Forum
QuantumATK => General Questions and Answers => Topic started by: GJK on July 15, 2014, 19:46
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Hi,
Kindly provide the script for calculating the formation energy of GNR either doped or adsorbed with a biomolecule???
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This kind of request is over the normal support. Please stop asking such request. Alternatively, you may post the exact problem you have met.
1). Since one does a scientific research of computational simulation, the preparing input file for the simulation by himself is one of the regular jobs for him.
2). The estimation of formation energy for your system is quite simple. The formation energy can be estimated in the following way:
step 1: perform the geometry optimization and the total energy calculation for the perfect GNR (i.e., no doping or adsorption of a biomolecule) and extract the value of the corresponding total energy.
step 2: perform the geometry optimization and the total energy calculation for isolated biomolecule and extract the value of the corresponding total energy.
step 3 perform the geometry optimization and the total energy calculation for the whole system of biomoelcule doped or adsorbed GNR and extract the value of the corresponding total energy.
step 4: formation energy = total energy obtained in step 3 - total energy obtained in step 2 - total energy obtained in step 1
Note: the size (i.e., length and width) of GNR in steps 1 and 3 should be same, and the k-point grid size are also same.
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Dear zh,
Thanks for the reply.But the equation which you provided is the formula for binding energy(which includes all terms of total energy).
But in the litreature survey which I have gone through they are calculating the total energy of isolated carbon atom in GNR and the isolated dopant and including their total energy in the formula.
One more already Dr.Nordland and Dr.Blom have provided the scripts for atomization energy(which is the energy required for breaking the bonds in the atoms).Thats why I requested for formation energy script which indicates structural stability of the system.
Waiting for the interaction.
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Dear zh,
Thanks for the reply.But the equation which you provided is the formula for binding energy(which includes all terms of total energy).
This is more meaningful to assert the stability of the adsorbed (doped) biomolecule on GNRs.
Even for the formation of a pure GNRs, you can use the total energy per atom of a perfect graphene as a reference, rather than the total energy of a C atom. If the edges of GNR is hydrogenated, the total energy per atom of of a H2 molecule is used as a reference for H element.
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No matter your definition and preferred approach for obtaining the result, all in all it's just a combination of total energies. If you understand the formula you want to compute, each term is a total energy of some system - just compute those and insert in the formula. No special script needed - or it's easy to make on your own.
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Thanks Dr.Anders