van der waals correction

[MaryamNazirfakhr]

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)!

[Anders Blom]

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.

[MaryamNazirfakhr]

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!

[Anders Blom]

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.

[MaryamNazirfakhr]

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?

[Jess Wellendorff]

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...

[MaryamNazirfakhr]

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