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Topics - Cyrille

Pages: [1] 2
1
General Questions and Answers / DFT+U + SOC
« on: July 12, 2019, 15:13 »
Dear QATK developers

I have a question concerning the use of QATK to perform DFT+U calculations including spin-orbit coupling since I am interested in the magnetic anisotropy (using the MAE study object) of a magnetic system that necessitate a +U treatment.
It seems from the vnl interface that it is not allowed. However I still tried by explictely defining the exchange correlation  in my python script (I alrady did that to perform DFT+U with VdW which is also in principle not allowed):

#----------------------------------------
# Exchange-Correlation
#----------------------------------------
exchange_correlation = ExchangeCorrelation(
  exchange=PerdewBurkeErnzerhofExchange,
  correlation=PerdewBurkeErnzerhofCorrelation,
  number_of_spins=4,
  hubbard_term=Dual,
  spin_orbit=True,
  )
exchange_correlation._setShortName("None")

However I get the following error message when the code start the calculation that includes SOC:
** Back Engine Exception : The SpinMatrix is NONCOLLINEAR, hence it can only be accessed with ALL_SPIN
** Location of Exception : spinmatrix.h:520

Is there a way to solve this issue?

best
Cyrille

ps: I am using 2019 version.

2
General Questions and Answers / density mesh cutoff
« on: December 11, 2017, 16:15 »
Dear atk experts

I have recently faced the following problem when working on MOF (metal-organic framework).
My system contains 3 metallic ions (Cobalt) which are strictly equivalent (when in "ideal" position: see image).  However during the scf loop the 3 atoms sometimes acquire different charges and magnetization which can in some cases have a rather drastic influence on the electronic structure.
I manage to "solve" this problem by increasing the density mesh cutoff (up to 150 Hartree).

Are there other possible options to solve this issue?

Cyrille

3
General Questions and Answers / DFT+U Anisotropic or SphericalSymmetric
« on: October 13, 2017, 15:53 »
Dear all

I have noticed a strange behaviour of the DFT+U with the "Anisotropic" option.
I am performing DFT+U calculation on a MOF (metal-organic framework) and when using the Anisotropic implementation the band structure looks totally weird while everything looks "nice" with the SphericalSymmetric implementation.
I have the feeling that there is something going wrong with Anisotropic implementation of DFT+U.

I have attached my python input.

Thanks in advance

Cyrille

4
General Questions and Answers / "unrealistic" relaxation of H2O molecules
« on: October 4, 2017, 09:26 »
Dear all

I am trying to relax a MOF (metal-organic framework) in presence of water molecules.
According to my colleagues chemist H2O should stay ontop (above and below) of the metallic atoms of the MOF.
However during the relaxation process with  ATK H2Omolecules  lays down on the MOF and starts forming H bonds with the Oxygens of the MOF.

Is there a reason for this behavior? Is there a way to cure this "problem"?


Thanks in advance

Cyrille

PS: here is a link towards my py and nc file
https://www.dropbox.com/sh/hjonz6hda1ocw5i/AADjfebjuHydbic8iovJIyBba?dl=0


5
General Questions and Answers / NEB calculation
« on: February 23, 2017, 09:16 »
Dear all

I have some difficulties regarding a NEB calculation.
I am investigating the configuration of a rather complex molecule.
I have first performed DFT+U+VdW calculations and found two possible conformations of the molecule that I call C1 and C2.
The energy of C2 is 0.3 eV lower  than C1 and I want to calculate the energy barrier between these two conformations.
I have therefore generated a NEB path and run the calculation.

First of all I get several warning messages:
1)  WARNING: The Grimme DFT-D2 correction is only intended for GGA.PBE and GGA.BLYP exchange-correlation functionals.
2)  WARNING: Reactant configuration is not optimized.
3)  WARNING: Product configuration is not optimized

For the first warning I know it is related to VdW and DFT+U

But what is the meaning of warning 2 and 3.

In addition at the end of the calculation I find that the energy of C2 is now higher  than the one of C1..
I do not understand how it is possible since these two configurations have been fully relaxed in my preliminary DFT calculation.

Thanks a lot in advance

Cyrille








6
General Questions and Answers / advice on basis set/pseudo for complex molecule
« on: February 3, 2017, 08:43 »
Dear all

I am having difficulties to model some complex molecules and I need your advice.
I have started using a small basis set (FHI SZP) to avoid too lengthy calculation.
However I realized by comparing with Quantum espresso that it was probably not sufficient.
I have switched to a much more complete basis set SG15 (medium) for all the atoms (C,H,B,N,Fe).
The calculation are becoming much heavier and I wonder if I could use SG15 only for the transition metal and keep smaller basis set for C,H,B and N.

I also need to perform DFT+U with VdW (as discussed yesterday).

Let me also add that the python file attached to my message correspond to an isolated molecule but I want to perform calculation for organized layers with a super-cell containing 3 molecules and test many configurations! Therefore I should find the optimal solution in terms of precision/speed.

Thanks a lot for your help.

Cyrille


7
General Questions and Answers / DFT+U with VdW
« on: February 2, 2017, 11:35 »
Dear all

I have noticed that VdW is disabled in DFT+U calculations. Is there a particular reason for this "limitation"?
I am presently doing calculations on molecular layers where DFT+U must be taken into account to describe properly the magnetic properties but the inter- and intra-molecular interaction probably needs to also include VdW.
What do you propose?

thanks in advance

Cyrille

8
General Questions and Answers / ProjectionList
« on: November 4, 2016, 12:58 »
Dear all

I would like to perform a LDOS analysis.
I am using a python script to extract the LDOS projected on "d" orbitals of a given atom.

dos.gaussianSpectrum(energies=energies,
                                spin=Spin.Down,
            broadening = 0.01*eV,
                                projection_list = ProjectionList(atoms=[1], angular_momenta=[2]))

However I would also like to decompose the DOS over the different d orbitals: xy, xz etc...
Is there a way to do this?

Cyrille

9
General Questions and Answers / typing problem within vnl
« on: October 19, 2016, 14:18 »
Dear all

I am facing a typing problem within vnl.
When I want to write a number with a "point" such as 8.5 I cannot write the point.
This is quite annoying when for example I want to make a transformation (such as translation etc..) I can only use integers..

I precise that I am using vnl under windows 7 and a French keyboard (azerty).

Any idea to solve this problem?

thanks in advance

Cyrille

10
General Questions and Answers / atomic relaxation problem
« on: October 3, 2016, 16:04 »
Dear all

I am trying to relax a molecular network but the optimization process is extremely long and the forces keep oscillating. Even though the total energy is slightly going down it takes ages to reach a local minimum.

I have attached the python script to my email. The system is indeed rather complex but I am quite sure there are ways to tweak the parameters to accelerate the convergence.

thanks in advance

Cyrille

11
General Questions and Answers / non magnetic device in LSDA
« on: September 2, 2016, 09:06 »
Dear all

I am facing the following problem: I want to perform a two terminal device calculation of a non magnetic system but with LSDA and starting with a zero magnetization. I know it seems weird since I could just do a LDA (non polarized)  but I have something else in mind:-)
The funny thing is that in the standard DFT cycles (leads and central part) the system remain non-magnetic but suddenly when entering the NEGF cycle the system acquires a magnetic moment as if the NEGF was not starting from the previous DFT.

Could you tell me why is it so?

thanks in advance

Cyrille

12
General Questions and Answers / spin density + atomic structure
« on: August 31, 2016, 14:37 »
Dear all

I want to plot the spin density superimposed with the atomic structure.
Is there a way to do this?
I can only manage to represent separately the atomic structure and the spin density but I could not find a way to show the position of the atoms on the spin density.

Thanks in advance

Cyrille

13
General Questions and Answers / adding a fragment that is not in the predefined one
« on: June 15, 2016, 09:13 »
Dear all

I am dealing with a molecular network and my favorite chemist colleague told me that to stabilize my network I should add some water molecules.
I recently discovered the vnl tool for adding atoms and predefined fragment but unfortunately I did not find the water molecule.
Is there a way to include H2O among the predefined fragments?

thanks in advance

Cyrille

14
General Questions and Answers / fermi level problem
« on: May 12, 2016, 13:16 »
Dear all

I am performing calculations on a structurally very simple but magnetically very complicated system: FeCr in B2 structure.
B2 structure is just based on bcc structure but Fe is sitting at the corner of the cube and Cr at the centre (or vice versa:-) so it is simple cubic.
Since I realized that FHI pseudo/basis was doing a very bad job (in fact totally wrong) I am using HGH pseudo (Tier0)
Now the magnetization of the system is very reasonable (in agreement with other DFT results) but when I plot the band structure I am convinced that the Fermi level is not at the right position.
Indeed the band structure looks very reasonable but the Fermi level (zero of energy) is clearly too high.
I wonder if someone has experienced this type of problem.

I have attached my input and log file..

Thanks in advance

Cyrille

15
General Questions and Answers / ProjectionList and angularMomenta..
« on: February 26, 2016, 10:58 »
Dear all

I wanted to write a script to calculate the density of states that is not only decomposed in term of anglular momenta (l=0,1,2) but also in terms of magnetic number m or more precisely in real harmonics px,py,pz (same for d..).
Is there an easy way to extract to do that?

thanks in advance

Cyrille

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