QuantumATK Forum
QuantumATK => General Questions and Answers => Topic started by: MaryamNazirfakhr on November 30, 2015, 10:14
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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
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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.
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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
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Change "include_three_body_term" to False. The script works fine as it is, but including the 3-body terms makes it extremely slow.
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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
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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.
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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!
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I do not understand the question. What sort of parameters? What is matsci?
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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
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Looks like the DFTB CP2K Slater-Koster basis set is the only one available for systems containing B, N, C, and H.
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... 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.
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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 " !!! :o
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
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Please upload the Python script. Much easier to help that way.
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I have attached the files for you.
Thanks
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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 :)
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thank you very much
I have used your recommended scripter for optimization, but an error appears (as you can see in http://8pic.ir/images/59quqyrfa1w2gyll8e3f.png) and simulation stops! There is a comment at the end of the log file: "Back Engine Exception : Diagonalization error, overlap matrix not positive definite. This may be caused by atoms that are too close to each other or situated in equivalent positions, or a too low value of interaction_max_range. Check the configuration, basis set and/or try to increase the interaction_max_range."
I have incresed the "interaction max range" up to 100 Ang , but still this error appears! What's wrong with it? What should I do? :'( should I change the lattice parameters or the initial interlayer distance?
The project file is here for you (to see the bilayer structure, if needed)!
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Very simple, you have 2 atoms on top of each other, everywhere in the structure. Look at the error message, and pick the first and easiest option to troubleshoot - use the "Close neighbors" tools in the Builder to find atoms that are close to each other.
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unfortunatly online troubleshoot does not work!!
Could you please explain a little more about "close neighbors"? It deletes some of the atoms, so the structure will be destroyed!
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1. Post Python scripts, not project.ini, it's difficult to get the structure out of there.
2. At least in the structure you called "Billayer 12-BNNR , before opt", all or almost all atoms are duplicated, so that will of course not work. Yes the tool will delete some atoms - those that are on top of each other. This will not destroy the structure, it will fix it.
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I have attached the scripter for you.
I have optimized the single layer BNNR unit cell with LDA, and then created the bilayer unitccell with merge tool. finally I ran the bilayer unitcell optimization with recommended D3 scriper. till now there is no warning!
but in the attached scripter the single layers are opemized with GGA. and when i I run the bilayer unitcell optimization with recommended D3 scriper, that error appear. what's wrong?
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You should read such errors closely. Often they actually tell you exactly what the problem is:
** Back Engine Exception : Diagonalization error, overlap matrix not positive definite. This may be caused by atoms that are too close to each other or situated in equivalent positions, or a too low value of interaction_max_range. Check the configuration, basis set and/or try to increase the interaction_max_range.
** Location of Exception : eigensolutions.cpp:2091
In this case, you have somehow managed to overlay 3 duplicates of the structure, so in all atomic positions you have three identical atoms. That's the problem causing the error. You should only have 14x2=28 atoms in the cell, but you have 84...
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Thanks for your patience dear! :)
I have tested your recommended D3 scripter by optimizing a bilayer 12-ZGNR unitcell (http://8pic.ir/images/xhj6q24la202bjxwsu6x.png).
For "OptimizeGeometry" I have also used this settings => force=0.05 , stress=0.05, method=LBFGS , constrain: unchecked just Z.
As you can see the result of optimization in "http://8pic.ir/images/gein7f25if6nr29g4t1f.png", layers are somehow bended! Is that correct?
I would like to repeat this simulation for BNNR. Since this type of simulations (DFT+D3) take too much time, I would like to be sure about the settings and checking for my probable mistakes ;)
One more question! Is it possible to use D2 instead of D3?
Regards