van der waals correction

[MaryamNazirfakhr]

hello

i'm trying to optimize "billayer Boron nitride (BN) nanoribbon" and "billayer Boron nitride-Carbon (BNC) nanoribbons ". I need to use PBE+vdW approach. but i don't have enough information about the parameters of "van der waals" icon in ATK2015.

1.could you please help me by some explanation or a tutorial?
2. What is your recommendation for better and faster optimization of such a structure?

one more question. I run the simulation, and then i click on log icon which is below the menu bar in job mannager in order to see the code running. when the log page opens, sometimes the log page is blank during the simulaton. sometimes I can see the code running but it suddenly stops (of course just the code in log page and not the simulation itself).could you please tell me that how can i fix this problem?

Thanks a lot

[Jess Wellendorff]

If by "PBE+vdW" you mean the Grimme DFT-D3 method with PBE, you should not need to specify any parameters manually. ATK will do this for you.

[MaryamNazirfakhr]

Dear Jess Wellendorff!

I have attached the project, scripter and log file for you.

1. As you see I have used (GGA) + (PBE) + (DFT-D3 for van der Waals correction). Using this setting, the simulation does not proceed well and the code in log page stops running (at the point which you can see in the attached note pad file)! This happens just when I use DFT-D3! Could you please tell me that what is the problem and how can I fix it? i use is a core i7 system, and the RAM is 4GB. Moreover, it seems that the simulation is so time consuming... is there any trick to reduce it?

2. Is matsci (slater-DFTB) sutable for calculating the transport properties of BNC?

3. For calculating the transport properties of billayer BNC, What are the suitable Huckel basis set?

4. For calculating the interllayer distance shall we optimize just the billayer unitcell, or the total billayer structure?

Thank you

[Anders Blom]

Change  "include_three_body_term" to False. The script works fine as it is, but including the 3-body terms makes it extremely slow.

[MaryamNazirfakhr]

Dear Mr. Blom!

I have unchecked the "include three body term" in DFT-D3, but still the log file stops at the aformentioned point! please provide me a solution.

thank you

[Jess Wellendorff]

No, the calculation does not stop even though the log file "stands still". What is happening is that ATK evaluates the forces on all atoms, and this simply takes a while with the DFT-D3. Be patient, and the calculation runs ok, provided that the three-body term is switched off.

[MaryamNazirfakhr]

Is there any other parameter to work with Boron, Nitrogen, Carbon and Hydrogen (or BNC nanorribon)? We have used matsci, but the simulation does not go well and it's hard to converge. Is there any other choise?

Thanks for your kind help and support!

[Jess Wellendorff]

I do not understand the question. What sort of parameters? What is matsci?

[MaryamNazirfakhr]

Dear Jess!

I mean the "Slater-Koster parameter set". like DFTB(matsci), DFTB(cp2k), bassani ch sp3d5s*, vogl.ch sp3[Vogl et al ...], ... .
I would like to know that is there any suitable "Slater-Koster parameter set" for BNC nanoribbon? I mean for B, Ni, H and C atoms? I extremely need it

Thank you

[Jess Wellendorff]

Looks like the DFTB CP2K Slater-Koster basis set is the only one available for systems containing B, N, C, and H.

[Anders Blom]

... and as far as I recall it gives very bad results. I think that for general material combinations like this, unless you are lucky to find some semiempirical model in the literature, DFT is the only way to go. It's kind of why we use DFT in the first place, to handle such situations. Unless your system is very large, I don't think DFT will be significantly slower than (self-consistent) DFTB.

[MaryamNazirfakhr]

Dear all!

I have optimized the unitcell of a billayer zigzag 12-BNNR (as you see in " http://8pic.ir/images/k1m9crzy2r6f7r3iz5i8.png ") by the following setting.:

calculator setting:  DFT    /    cut-off: 450 eV   /    k-point: 8,8,1    /    Exchange-correlation: GGA,PBE    /    van der Waals correction: Grimme DFT-D2    /   max step:700     /   Tolerance: ^-04    /   others as default.
OptimizeGeometry setting: force tolerance 0.05   /   stress tolerance 0.05    /   optimizer method: LBFGS   /    Generally all as default except that I have unchecked the "constrain cell" just in z direction.

The result of this optimization is " http://8pic.ir/images/t2ulmqjvmnnx0fnwbfxw.png "    /  " http://8pic.ir/images/upjveqrlo7oeih08om3v.png "  !!!
Could you please tell me that which part of the setting is wrong? What should I do in order to obtain the desired optimized geometry?

Further more, I'm going to run the same simulation with (van der Waals correction: Grimme DFT-D3) + unchecking "include three body term". If the problem in not the correction method, please tell me the problem, so i stop this simulation. My time is so so limited and I extremely need your generosity.

Thank you

[Jess Wellendorff]

Please upload the Python script. Much easier to help that way.

[MaryamNazirfakhr]

I have attached the files for you.
Thanks

[Jess Wellendorff]

I see a few serious mistake in your scripts:
- you use a 8x8x1 k-point grid, but your bilayer structure is supposed to periodic along the C-direction and non-periodic along A and B. So that k-point grid makes no sense. Try using 1x1x9 instead.
- your density mesh cut-off of 450 eV (16 Hartree) is way to small. Remove that line to use the default 75 Hartree instead.
- You have increased the maximum number of SCF steps to 700. You should never expect to use that many SCF steps. In general, especially for simple systems such as this one, problems with SCF convergence usually indicate problems with the way the calculation is set up.

I have attached an updated version of your DFT-D3 script. Please have a look at it