Messages

16

General Questions and Answers / Re: Slater-Koster method for charge transfer calculations

« on: January 14, 2021, 13:12 »

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!

17

General Questions and Answers / Re: Slater-Koster method for charge transfer calculations

« on: January 13, 2021, 09:44 »

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.

18

General Questions and Answers / Re: Slater-Koster method for charge transfer calculations

« on: January 12, 2021, 16:44 »

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.

19

General Questions and Answers / Re: Slater-Koster method for charge transfer calculations

« on: January 12, 2021, 16:09 »

Thank you very much for your responses.

If I want to benchmark it against DFT, what DFT parameters and predefined functions are suitable for doing it? LDA, GGA, MGGA, and PBE , ...?

Yes I assigned the dielectric constant and unselected "No SCF". I have attached my script. please find the attachment.

Thank you very much.

20

General Questions and Answers / Slater-Koster method for charge transfer calculations

« on: January 12, 2021, 10:25 »

Dear QuantumATK staff,

I am using the semi-empirical method, particularly the Slater-Koster method (dftb.org parameters) to calculate the interactions between a ZnO surface with a molecule (look at the attached pic). I am calculating the charge transfer, HOMO-LUMO, binding energy and so on. I have two important and almost independent questions and I will be so grateful if you can help me:

FIRST QUESTION- Is the Slater-Koster method reliable for these calculations? I know that each method has its approximations but I want to know that generally, the Slater-Koster method (dftb.org parameters) performs correctly in calculating the parameters I am calculating or I must use for example Huckel method or even DFT?

The SECOND QUESTION- I would like to investigate the impacts of implicit solvent on my calculations. I mean I want my molecule to be in a solvent above the slab surface and not in a vacuum. I read the tutorial and I know that in the DFTB method I can change the dielectric constant in the poisson solver and in this way the solvent will be considered. I choose Multigrid solver and leave the boundary conditions for A and B periodic and choose Neumann and Dirichlet for C left and right respectively and 80 for dielectric constant. However, I never can see any differences between with-solvent and without-solvent calculations in any way and it seems to me that no solvent is considered at all. What could be the reason?

I am looking forward to your help. Thanks.

21

General Questions and Answers / Re: HOMO-LUMO of a slab+molecule system

« on: January 8, 2021, 13:05 »

Thank you very much
Would you mind responding to my next questions about isovalue and Salter-Koster method please?
Thank you for your patience 

22

General Questions and Answers / Re: HOMO-LUMO of a slab+molecule system

« on: January 8, 2021, 09:22 »

Anyone to answer my questions please?

23

General Questions and Answers / Re: HOMO-LUMO of a slab+molecule system

« on: January 7, 2021, 13:46 »

Sorry an another important question. I am using SemiEmprical (Slater-Koster, dftb.org option) for calculating MullikenPopulation, charge transfer, HOMO-LUMO and binding energy for my system. Is it okay or I have to use Extended Huckel option? Thank you very much.

24

General Questions and Answers / Re: HOMO-LUMO of a slab+molecule system

« on: January 7, 2021, 11:24 »

Thank you very much for your valuable responses. May I ask some other questions?
I used MolecularEnergySpectrum and since it also represents the orbital occupations I could find HOMO and LUMO orbitals. Then I used Eigenstate and plotted HOMO and LUMO. I attached the output file.
- HOMO is 388 and LUMO is 389, am I right?
- My next question is about choosing the suitable isovalue when I want to plot HOMO and LUMO. For different isovalues I will get a totally different plots. How can I make a relevant choice of isovalue for visualizing HOMO and LUMO orbitals?
Thank you for your responses.

25

General Questions and Answers / Re: HOMO-LUMO of a slab+molecule system

« on: January 5, 2021, 12:49 »

Thank you very much.
And what about charge transfer? How I can calculate the charge transfer between the absorbed molecule and the slab?
Thanks alot.

26

General Questions and Answers / Re: HOMO-LUMO of a slab+molecule system

« on: December 17, 2020, 14:26 »

Thank you very much for your response.
Considering this that I am using the slab method (the structure I attached to the first message) and I am interested in calculating the homo-lumo and visualizing them, would you please guide me how to do that?
Best regards,
Hadi

27

General Questions and Answers / Re: HOMO-LUMO of a slab+molecule system

« on: December 16, 2020, 16:52 »

Dear mlee,

Thank you very much for your response. I am going to  investigate adsorption energy, binding energy, homo-lumo and charge transfer.
You mentioned two methods. Would you please elaborate on them?
You wrote "In the slab model, you can analyze the BandStructure, DensityOfStates, or MolecularEnergySpectrum related to homo and lumo energy." slab (the structure I sent you in my former message) is periodic from two sides, isnt it? is it possible to calculate HOMO-LUMO for a periodic structure in ATK?
You also wrote me "In the molecular model, cluster model is commonly used to analyze the homo-lumo energy or adsorption energy. You need to assume the cluster as a surface." May I ask you explain me how I can do it? I have no idea what you mean by cluster? How can I make it?
Generally, if I want to investigate the interactions of a molecule with the surface of a crystal in ATK for calculating some parameters like adsorption energy, binding energy, homo-lumo and charge transfer, how would you recommend me to set the structure? making a slab and putting the molecule above it was the only idea I could come up with. What is the best option in your opinion? The cluster? would you elaborate on it please?
Sorry for asking many questions? Thank you for your help.

Best regards,
Hadi

28

General Questions and Answers / Re: HOMO-LUMO of a slab+molecule system

« on: December 16, 2020, 15:31 »

Dear all,
I am in an urgent situation. Would you please help me? Thanks
Best regards,
Hadi

29

General Questions and Answers / HOMO-LUMO of a slab+molecule system

« on: December 16, 2020, 11:30 »

Dear QuantumATK family,

I am trying to investigate the interactions between a molecule with ZnO surface. To do this I use a ZnO crystal and use the "cleave surface" and make a normal slab of ZnO with a vacuum on the top of the surface and relax it. Then I put the relaxed molecule on the vicinity of the surface and optimize the system and observe the trajectory to see what . You can see the system attached to this message.

Now I want to calculate the HOMO-LUMO of the whole system (ZnO +absorbed molecule). I read all the posts about HOMO-LUMO in the forum and I know that HOMO-LUMO are defined for a non-periodic isolated system but I think my system is periodic in A and B direction. I used "change the configuration to molecule" to eliminate the periodicity of the slab but when I try to relax it the whole structure of the ZnO will be changed (see the second attached pic). Do you have any idea how I can build up a system so I can investigate the interactions of a molecule with ZnO surface and also see the homo-lumo in the whole system?

Thank you in advance

30

General Questions and Answers / Re: QM/MM simulations

« on: November 27, 2020, 13:37 »

Thank you very much for the useful link