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Messages - MaryamNazirfakhr

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1
General Questions and Answers / Re: proper basis sets of extended Huckel, for hexagonal BN-C nanoribbons
« on: December 28, 2015, 19:37 »
Dears

I have attached 3 pictures ( structure and Huckel basis set ) here, could you please take a look at them and tell me if i'm doing right or not?!

Thanks

2
General Questions and Answers / proper basis sets of extended Huckel, for hexagonal BN-C nanoribbons
« on: December 12, 2015, 23:17 »
Hello   :)

I would like to know that ,what are the proper basis sets of extended Huckel, for hexagonal BN-C nanoribbons?

Regards

3
General Questions and Answers / Re: van der waals correction
« on: December 9, 2015, 22:43 »
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

4
General Questions and Answers / Re: van der waals correction
« on: December 9, 2015, 07:43 »
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?

5
General Questions and Answers / Re: van der waals correction
« on: December 9, 2015, 00:57 »
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!

6
General Questions and Answers / Re: van der waals correction
« on: December 8, 2015, 22:06 »
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)!

7
General Questions and Answers / Re: van der waals correction
« on: December 6, 2015, 22:30 »
I have attached the files for you.
Thanks

8
General Questions and Answers / Re: van der waals correction
« on: December 4, 2015, 22:56 »
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

9
General Questions and Answers / Re: van der waals correction
« on: December 3, 2015, 11:20 »
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

10
General Questions and Answers / Re: van der waals correction
« on: December 2, 2015, 20:12 »
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!


11
General Questions and Answers / Re: van der waals correction
« on: December 1, 2015, 22:36 »
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

12
General Questions and Answers / Re: van der waals correction
« on: December 1, 2015, 11:23 »
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



13
General Questions and Answers / van der waals correction
« on: November 30, 2015, 10:14 »
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

14
General Questions and Answers / Re: optimization of bilayer ZGNR (DFT & DFTB)
« on: November 23, 2015, 22:39 »
I use DFT.

Calculator:
cut-off : 150Ryd
k-point sampling : 5,5,5
Tolerance : 0.0001
max step : 500

OptimizeGeometry:
default

Thanks

15
General Questions and Answers / ZGNR-BNNR structure and optimization
« on: November 23, 2015, 22:30 »
Hello

I use ATK2013. I'm trying to build a unitcell of a 8ZGNR-4BNNR hybrid nanoribbon.
1. Once I used the "merge" tool, in order to merge 8ZGNR and 4BNNR, and then I optimized the whole 8ZGNR-4BNNR unitcell.
2. I created a 12ZGNR, then I changed 2 dimer lines of C atoms to B and N atoms (4BNNR), finally I optimized the whole   8ZGNR-4BNNR unitcell.

I have 3 questions:
1. I would like to know that which one of the mentioned methods is  more recommended?
2. what is the lattice constant for a ZGNR-BNNR structure? (when i used the first method, the lattice constant was 2.505, and by the second method it was 2.46. )
3. I use DFT for optimization. I set cut-off and k-point sampling to 150Ryd and 5,5,5 respectively. the optimization setting is the defeult setting. is it correct? what is your recommendation for the setting of scripter?

Thank you

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