Some questions about "MolecularEnergySpectrum"

[Roc]

Dear everyone,

In the topic about"Calculating molecular properties" of the VNL manuscript, the results "The Kohn-Sham eigenvalue spectrum" of water molecular is that:

Energy eigenvalues for water (in eV)

-----------------------------------------
  LDA             GGA             diff
-----------------------------------------
-24.243         -24.376           0.133
-12.470         -12.442          -0.028
 -8.187          -8.129          -0.058
 -6.140          -5.988          -0.152
  1.811           1.977          -0.166
  4.195           4.342          -0.147
 11.994          12.330          -0.336

The manuscript says：the energy level of -6.140 eV is the HOMO ，the energy level of 1.811 eV  is the LUMO,

when I caculate the "Fermi energy" and "MolecularEnergySpectrum" of my single molecular, the result is that:

Fermi energy
-3.70010920918 eV
# -----------------------------------------------------------------------------
# Energy Spectrum
# -----------------------------------------------------------------------------
# Energy (eV)
        -6.54
        -6.50
        -6.38
        -6.38
        -6.05
        -3.93
        -3.39
        -3.39
        -3.32
        -2.41
        -2.41
        -2.29
        -1.34
        -1.19
        -1.19
        -0.94
         1.93
         1.94
         2.63
         4.63
what't the  HOMO and LUMO energy of the molecular, -3.93 and -3.39? or -0.94 and 1.93?

Thanks!

[Nordland]

The MolecularEnergySpectrum is adjusted according to the fermi level, so for the molecular energy spectrum energies
the fermi level is 0 eV. So the correct answer is -0.94 and 1.93.

[Roc]

Thanks, Nordland

[nori]

According to the ATK manual, "The energy zero-level for the molecular spectrum is chosen at the vacuum level (so not the Fermi level) ".
(See The ATK manual top/index/calculateMolecularEnergySpectrum)
If you want to know the HOMO and the LUMO level, you should look at the total number of electron or the output of "calculateEigenstateOccupations" in the system.

I show the example, which is the calculation for DTB(see attached).
The total number of electron is 42, so the 20th level( = -4.4699eV) is HOMO and the 21st level( = -1.1254eV) is LUMO.
And the Fermi energy is -2.2612eV, that is between HOMO and LUMO.

[renren123123]

the HOMO and the LUMO level of molecule is judged by its EigenstateOccupations!

[Roc]

Oh, Thank everyone for the discussion!  ,

However, for the two-probe system, when I caculated "Projected Hamiltonian energy spectrum ", I got the results as follows,

# Energy Spectrum
# -----------------------------------------------------------------------------
# Energy (eV)
      ............
        -4.09
        -4.02
        -3.86
        -3.48
        -3.48
        -3.25
        -3.18
        -2.53
        -0.34
        -0.33
         0.35
         0.59
         0.59
         0.84
         1.87

Is here different from the above? The Fermi level is 0eV? The HOMO is -0.33eV, LUMO is 0.35eV? Are all these right?
I am confused with "the single molecular EnergySpectrum" and "two-probe Projected Hamiltonian energy spectrum " , the Fermi level,HOMO and LUMO. Who can explain it .
 
Thanks!

[Nordland]

According to the ATK manual, "The energy zero-level for the molecular spectrum is chosen at the vacuum level (so not the Fermi level) ".
(See The ATK manual top/index/calculateMolecularEnergySpectrum)
If you want to know the HOMO and the LUMO level, you should look at the total number of electron or the output of "calculateEigenstateOccupations" in the system.

I was wrong and you are right The molecular energies are simply the eigenvalues of the hamiltonian.

[Roc]

Thanks!

Regards!

[Nordland]

Okay I tryed to investigate this a little.

For the molecular energy spectrum, the fermi level has to be calculated independently
in order to identify the HOMO-LUMO ( if you are not into counting electrons manually, as nori suggests)
The zero point of the spectrum is the vacuum level ( just as nori said. )

For Twoprobe Projected Hamiltonian energy spectrum, the fermi level is taken from the electrodes,
and the Projected Hamiltonian Energy Spectrum is then shifted such that the zero point of this spectrum
is the fermi-energy of the electrode.
Therefore you can identify the HOMO as the last negative energy and the LUMO as the first positive energy.

[Roc]

Thank you!

[Hasan Sahin]

I want to prepare a script that calculates the eigenstateoccupations and writes them as a list...
And, I used the example from manual ( http://quantumwise.com/documents/manuals/ATK-2008.10/ref.calculateeigenstateoccupations.html ) but I couldnt. Script is attached.

My script does not work and ATK does not give any error message. Can you help to prepare an eigenstate occupation calculator for a spin polarized molecular system...

[Nordland]

I have modified your script slightly, and it was a minor detail in the import statements.

I changed from ATK.MPI import * to from ATK.KohnSham import *

[zhangguangping]

I have modified your script slightly, and it was a minor detail in the import statements.

I changed from ATK.MPI import * to from ATK.KohnSham import *

Does this script valid for the MPSH of a two probe system?i.e. can it output the occupation for MPSH spectrum?

[zh]

This script can be used only for a molecule system.

[zhangguangping]

This script can be used only for a molecule system.

Thanks zh.
And can you give me some advice on this question?
http://quantumwise.com/forum/index.php?topic=815.0
Thanks in advance.