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Messages - Daniele Stradi

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211
General Questions and Answers / Re: MD with electric field
« on: October 19, 2016, 09:15 »
Which kind of MD? Classical or Quantum (DFT, Tight-Binding)? For the latter, there is no technical limitation about running dynamics including an E-field.

213
General Questions and Answers / Re: BAND gap of Cu2O Bulk
« on: October 10, 2016, 13:17 »
There was already a lengthy discussion on this in the Forum. Check:
http://quantumwise.com/forum/index.php?topic=4111.msg18783#msg18783

214
General Questions and Answers / Re: Building grain boundaries
« on: October 10, 2016, 12:57 »
Also, if you want to simulate one single grain boundary such as those shown here:
https://staff.aist.go.jp/h.ogawa/GBstudio/gallery/indexE.html

you can simply use the Surface (Cleave) and Interface Builders plugins. Here it is shown how to generate a simple grain boundary in the context of a thermal conductance calculation, see section "Preparing the grain boundary":
http://docs.quantumwise.com/tutorials/interfacial_thermal_conductance/interfacial_thermal_conductance.html?highlight=thermal%20conductance

Regards,
Daniele.

215
General Questions and Answers / Re: atomic relaxation problem
« on: October 8, 2016, 09:55 »
I agree with Anders, sometimes it is worth thinking in terms of "time to solution"  :)

216
General Questions and Answers / Re: atomic relaxation problem
« on: October 7, 2016, 15:38 »
Convergence with local basis set is not systematic, so it does not necessarily means that you will get a better result by making the basis larger and larger.

Daniele

217
General Questions and Answers / Re: atomic relaxation problem
« on: October 7, 2016, 15:13 »
I would say that for a system such as this one getting to 0.05 eV/Ang with SZP is quite good :)

SG15 basis set should be converged with 100 Ha cutoff, so your 150 cutoff should be sufficient. In few days we will have on docs.quantumwise.com the tables with the delta tests (https://molmod.ugent.be/deltacodesdft) for all the ATK basis sets online to help you choose basis set and potentials.

Daniele

218
General Questions and Answers / Re: atomic relaxation problem
« on: October 7, 2016, 11:28 »
Hi Cyrille,

I addition to the comments by Ulrik and Petr:

1) Where are the maximum forces located? Are they on the core of the molecular network, or on the hydrogen atoms? Hydrogen atoms can be quite painful to relax, because their movement leads only to tiny changes on the potential energy surface, but you have a lot of H atoms in your structure.

2) You are using the PBE functional, which - by personal experience - gives rather flat minima for H-bonded potential energy surfaces, or more in general surfaces involving H atoms.

3) you are using a SZP basis set for all atoms, which might also results in a poor description of the potential energy surface, if the minimum in the potential energy surface turns out to be rather flat.

My suggestion is that in the spirit of quantum-chemistry calculations, you perform the optimization stepwise: first a rough (0.05 eV - 0.025 eV/Ang) optimization with SZP basis set, then a more accurate (0.01 eV/Ang) optimization using a SZP or better an SG15 basis set (Medium or High). Notice that SG15 basis sets are more long ranged than FHI basis sets, so they might work better for system with rather flat potential energy surfaces.

Cheers,
Daniele.

219
Hello,

to have a clearer answer, you should provide additional details such as an input script with the system you are studying.

Daniele

220
I think the most likely thing is that you ran out of memory, your system is quite big and you are using a very outdated version of ATK.

221
General Questions and Answers / Re: K-poit selection
« on: October 3, 2016, 09:29 »
I repeated the calculations using 30 and 40 k-points in the Z direction for non-spin polarized system. I have taken exactly the same geometry (it is not the same in the two python scripts you provided), and all the parameters have been kept the same apart from the k-points sampling.

I have attached the input and bandstructure/dos of the two systems. Notice that the dos and bandstructure are calculated with the same precision in both calculations, because this is just a post-scf analysis.

As you can see, the dos and the bandstructure look exactly the same, independently on the k-point sampling used. This strongly suggest that the weird behavior you observed including spin-polarization is due to the fact that the magnetic ground state of the system is quite complex - e.g. anti-ferromagnetic coupling, which is tricky to describe in DFT.

As Petr suggested, you should run the convergence tests without spin polarization. You should especially check two things:

- You should also make sure to lower the threshold for the SCF energy tolerance to e.g. 10-6 Ha or lower.
- You should converge the total energy to 1 meV or lower.

These points are important because for complex magnetic systems, different magnetic solutions may actually differ in energy by just few millielectronvolts.

Good Luck.


222
In your python input the thresholds are set to:

max_forces=0.05*eV/Ang,
max_stress=0.05*eV/Ang**3,

The calculated forces and stresses in the log file are:

Max force = 0.0465979 eV/Ang
Max stress =  0.003555 eV/Ang**3

Both are lower than max_forces and max_stress. To start seeing some relaxation, you should set in your python script something like:

max_forces=0.025*eV/Ang,
max_stress=0.0025*eV/Ang**3,

223
General Questions and Answers / Re: K-poit selection
« on: October 2, 2016, 23:52 »
Hi,

may I ask you what happens if you try to perform the same DOS vs. k-points analysis but for the non-spin-polarized system (even without relaxing)?

Your results may indicate that the system has a complex energy landscape, with several different magnetic configuration very close in energy. The energy differences might be so tiny that their relative order changes if the k-point sampling is changed.

Daniele

224
Where is the error? The max. force in your system is lower than the threshold. Same for the stress. Lower the threshold and you will see that the system will start to optimize its geometry.

225
General Questions and Answers / Re: Visualize vdW forces
« on: September 30, 2016, 14:08 »
What suggested by Anders will give you exactly what you want: E(D2) = E(DFT+D2) - E(DFT). The same is valid for the forces. Of course it will be functional dependent.

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