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**Questions and Answers / Re: ±isovalue option meaning in visualizing molecular orbitals**

« **on:**February 25, 2021, 14:28 »

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Dear all,

When I visualize molecular orbitals (for example HOMO or LUMO), when I tick the ±isovalue option, the orbitals will be shown with two colors red and blue. What do these colors mean? what is the difference between blue and red regions?

Thanks

When I visualize molecular orbitals (for example HOMO or LUMO), when I tick the ±isovalue option, the orbitals will be shown with two colors red and blue. What do these colors mean? what is the difference between blue and red regions?

Thanks

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Anyone to help me please?

I think the problem is the number of electrons. The number of electrons for the solo slab is 1080 and for the solo molecule is 58, but for the whole structure is 1138.4 !!!

Thanks

I think the problem is the number of electrons. The number of electrons for the solo slab is 1080 and for the solo molecule is 58, but for the whole structure is 1138.4 !!!

Thanks

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Dear all,

How can I determine HOMO-LUMO for this structure? there are some partial occupations in some orbitals! the script and the molecular energy spectrum have been attached.

562 -1.457714e+00 2.000000e+00

563 -1.396535e+00 2.000000e+00

564 -2.405055e-01 1.999818e+00

565 -7.608169e-02 1.899860e+00

566 2.848218e-02 4.988281e-01

567 3.148024e-01 1.029389e-05

568 3.187673e-01 8.830246e-06

569 3.190502e-01 8.734142e-06

570 5.065160e-01 6.193482e-09

571 5.070444e-01 6.068169e-09

Thanks

Best regards,

How can I determine HOMO-LUMO for this structure? there are some partial occupations in some orbitals! the script and the molecular energy spectrum have been attached.

562 -1.457714e+00 2.000000e+00

563 -1.396535e+00 2.000000e+00

564 -2.405055e-01 1.999818e+00

565 -7.608169e-02 1.899860e+00

566 2.848218e-02 4.988281e-01

567 3.148024e-01 1.029389e-05

568 3.187673e-01 8.830246e-06

569 3.190502e-01 8.734142e-06

570 5.065160e-01 6.193482e-09

571 5.070444e-01 6.068169e-09

Thanks

Best regards,

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I checked several papers and all of them use plane wave, but as far as I know, U correction is not possible for the plane wave method in ATK. What do you suggest me to do? thanks.

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Thank you very much for your response. How should I do that? I mean how can I make a good guess for the beginning? I am totally blind for starting with what quantities of U and for what orbitals

Thanks

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Dear ATK staff,

I am trying to calculate the ZnO bandstructure by using the GGA PBE + U method as it has been done in this paper: Ferromagnetism properties of Er-doped ZnO:a GGA +Ustudy (https://doi.org/10.1039/C6RA17921E)

I changed the lattice parameters to a=3.32 and c=5.34 which are the optimized numbers in the paper and selected 7 eV and 10.5 eV as U for oxygen and zinc atoms. Everything is similar to the ones in the paper but I can not calculate the bandstructure and the bandgap is 0 for my calculations. I attached the script and the log and the result. Would you please help me solve this problem?

Thanks.

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Okay, thanks alot.

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Hi all,

Is there any way to export images from "viewer" in any vector format?

Thanks.

Hadi

Is there any way to export images from "viewer" in any vector format?

Thanks.

Hadi

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The problem has been solved. The 0001 ZnO surface is not stable and needs some modifications to become stable. Just to share what I found out: if anyone is interested in more info, he/she may take a look at the following paper:

http://dx.doi.org/10.1016/j.susc.2012.09.004

Thanks,

Hadi

http://dx.doi.org/10.1016/j.susc.2012.09.004

Thanks,

Hadi

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Thank you very much for your response. I will do so. Sorry, I asked a new question titled "Asking for help; I can not relax a ZnO slab". Would you mind checking it to help me, please? It has been a week I am trying to solve that problem. Thank you for being supportive

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Dear all,

I am trying to relax ZnO (10-10),(11-20), and (0001) slabs by using the semiempirical method, Slater-Koster. For (10-10) and (11-20) the calculations are fast and the surfaces are stable and in a good form and everything is reasonable. However, for the (0001) slab, I tried several slabs with different sizes and boundary conditions but the calculations will converge in a very long time (2-3 days!!!) while the surface finally collapses or deforms. I attached the script and a pic. Would you please guide me on what the problem could be and what the solution is? I have been struggling with this for one week, trying any solution I assumed may work

Thanks.

Hadi

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Thank you very much. I can not see it, so I will do it manually.

Have you checked my script as well? I have no idea why the dielectric constant has no impact on the optimization trajectory. I change it from 1 to 50 but when I check the optimization trajectories the identical things happen. I hoped to see some changes when I change the dielectric constant since I am implementing the molecule in implicit solvent!

Have you checked my script as well? I have no idea why the dielectric constant has no impact on the optimization trajectory. I change it from 1 to 50 but when I check the optimization trajectories the identical things happen. I hoped to see some changes when I change the dielectric constant since I am implementing the molecule in implicit solvent!

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Sorry, would you mind telling me where in GUI I can consider BSSE correction?! I am using version P-2019.03.

And would you please guide me on the script I sent you?

Thank you very much for being so supportive.

And would you please guide me on the script I sent you?

Thank you very much for being so supportive.

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Thank you again for your response.

I am using ATK version P-2019.03. In the link you sent me I can see "The DFT-D dispersion corrections" and "BSSE and the counterpoise correction". The first one is accessible in GUI as DFT-D2 and DFT-D3 but how about the second one? I can not see anything about it and the tutorial says it should be added manually! would you please guide me a bit more? Thanks for your patience.

I am using ATK version P-2019.03. In the link you sent me I can see "The DFT-D dispersion corrections" and "BSSE and the counterpoise correction". The first one is accessible in GUI as DFT-D2 and DFT-D3 but how about the second one? I can not see anything about it and the tutorial says it should be added manually! would you please guide me a bit more? Thanks for your patience.