Script for calculating the atomization energies of molecule.

[Nordland]

Hey everyone.

I just wanted to share with you a script that I made for calculating the atomization energy of molecules using NanoLanguage.
You can use the script either by copying the code directly into your own program or
 you can also just download the script and store it along your other scripts and use it by writing:

from AtomizationEnergy import *
E = calculateAtomizationEnergy(molecule, method, verbosity)

Please feel free to use and share!

[Nordland]

I did a calculation of the atomization energy of a Hydrogen molecule (H2).
I got the following values for the atomization energy of the molecule using default parameters.

LDA.PZ = 4.79218961857 eV
GGA.PBE = 4.47776121909 eV
GGA.revPBE = 4.50626999466 eV

According to Blaha et al, the all-electron calculation gives 4.54 eV.
Futhermore I found this experimental value to be 4.7 eV, so I think it is quite close.

I have attached the script to perform the calculation.

[Nordland]

For the methane case using default parameters I found the following:

LDA.PZ = 20.622076671 eV
GGA.PBE = 18.9564183782 eV
GGA.revPBE = 18.7426438569 eV

The experimental value is 18.16 eV and Bhala et al gets it to be 18.21 eV.
Again the error is only around 3-4%, however it is clear that you must use the revPBE functional in order to get good atomization energies as the error for LDA is in the order of 20%!

Please feel free to post your own atomization energy calculations!

[Nordland]

I also did it for a calculation for Acetylene (C2H2) and compare the values to Blaha et al.

LDA.PZ     =  20.2639146361 eV
GGA.PBE    =  18.5128556649 eV
GGA.revPBE =  18.2398891734 eV

The all-electron calculation gives 17.9944 and reports a 17.5608 for the experimental value.

[rahulprajesh]

Its a nice script sir ,
                            Is there any way to calculate the particular bond's energy in a molecule like what if we want to calculate for example c-h  bond energy in Methane Molecule how can we do that.
                            thanks Sir

[zh]

First, please refer to here to understand the definition of "bond energy": http://en.wikipedia.org/wiki/Bond_energy.

Second, from the definition of "bond energy", one may estimate it according to the following procedure:
Here, the bond energy of C-H in methane as an example.
1) optimize the geometry of methane molecule and the calculate the total energy;
2) calculate the total energy of a carbon atom;
3) calculate the total energy of a hydrogen atom;
4) following the definition of bond energy (see the above http link), do the numerical manipulation.

[rahulprajesh]

dear Sir, I've proceeded in the same way as you indicated...
         and used the DZP(Basis Set) With GGA.pbe.
                    But Still  My result is far away from experimental values like I laso tried to calculate c-h bond dissociation energy for c-h bond in c2h6 ..and got a value = 6.5195 eV (experimatal is=4.40625eV)
i dont know where is the problem and why its not working. help me ?

[zh]

The following parameters could affect the accuracy of calculation results:
i) basis set;
ii) mesh cutoff;
iii) exchange-correlation functional; Note that for the total energy calculation of single atom, one had better perform the spin-polarized calculation;
iv) "padding_factor" in poissonEquationParameters();

In additional, DFT calculations are carried out at 0 K and the zero-point energy of molecule is neglected, but the experimental value for bond energy may be measured at finite temperature.  These may also lead to the difference between the DFT and experimental values for bond energy.

[rahulprajesh]

I think Sir if we Can Use Formation Energy instead of Total energy it will serve My purpose because change in enthalpy of a reaction uses:: (sum of Formation energies of Products - sum of formation energies of reactants)..Now the problem is how to calculate the formation energy???

[zh]

What is the definition of "Formation energy" in your mind? If you understand it clearly, it can be obtained from the calculated total energy without taking into account the T*S term (i.e. entropy due to the phonon and temperature contributions).

[Anders Blom]

An updated version of these scripts for ATK 13.8 (and in fact 12.8 and probably also 11.x) is available at http://quantumwise.com/forum/index.php?topic=2588.msg12300#msg12300

[GJK]

First, please refer to here to understand the definition of "bond energy": http://en.wikipedia.org/wiki/Bond_energy.

Second, from the definition of "bond energy", one may estimate it according to the following procedure:
Here, the bond energy of C-H in methane as an example.
1) optimize the geometry of methane molecule and the calculate the total energy;
2) calculate the total energy of a carbon atom;
3) calculate the total energy of a hydrogen atom;
4) following the definition of bond energy (see the above http link), do the numerical manipulation.

Hi,

Dear sir, can u tell the formula for calculating Bond energy.Because in the link it is given as Bond length/bond distance.

[kstokbro]

According to the link, bond energy is the energy required to break all bonds in a molecule.

For the Bond-strength, you devide by distance