Messages

16

General Questions and Answers / Re: ProjectionList

« on: November 7, 2016, 14:47 »

OK thanks Daniele.
It will be very useful for electronic structure analysis.

Cyrille

17

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

18

General Questions and Answers / Re: typing problem within vnl

« on: October 19, 2016, 14:54 »

I already tried that but I get the following error when using coma instead of point:

Traceback (most recent call last):
  File "C:\Program Files (x86)\QuantumWise\VNL-ATK-2016.2\Lib\site-packages\AddOns\BuilderCore\PanelPlugins\TranslatePlugin.py", line 172, in applyClicked
    translation = _computeTranslation(configuration, self.translation(), fractional)
  File "C:\Program Files (x86)\QuantumWise\VNL-ATK-2016.2\Lib\site-packages\AddOns\BuilderCore\PanelPlugins\TranslatePlugin.py", line 221, in _computeTranslation
    translation = gui_translation*Angstrom
  File ".\zipdir\NL\CommonConcepts\PhysicalQuantity.py", line 2001, in __mul__
NLValueError: Multiplying the unit Ang with "[None, 0.0, 0.0]" of type <type 'list'> failed.

19

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

20

General Questions and Answers / Re: atomic relaxation problem

« on: October 7, 2016, 15:34 »

Yes I was quite happy to manage getting 0.05eV/A after several restarts because the relaxation took longer than expected..
I am even more happy since I got the result I was looking for since several months!
Maybe I should not try to change the basis set: I could deteriorate the agreement with experimental results:-)

Cyrille

21

General Questions and Answers / Re: atomic relaxation problem

« on: October 7, 2016, 13:57 »

Thanks a lot for these advices.

I have started with a SZP basis set since it is cheaper for a first run but I realized it was almost impossible to get below 0.05eV/A. I do not see that particular atoms are more difficult than other but I admit that these are complex systems (so called spin-crossover)
Then I was planning to improve the calculation with a better basis set: DZP or SG15.
Maybe SG15 are harder and I need finer meshes?

Cyrille

22

General Questions and Answers / Re: atomic relaxation problem

« on: October 7, 2016, 10:38 »

Thanks Petr

Unfortunately the spin polarization is crucial in these molecules where atomic structure is intimately related to the magnetism. So I cannot do what you propose. I admit that this is a rather delicate system.

I was more thinking of using another relaxation scheme or tuning the parameters of the algorithm. Or maybe using a finer mesh..

Cyrille

23

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

24

General Questions and Answers / Re: non magnetic device in LSDA

« on: September 2, 2016, 14:43 »

Here is my input script.

Cyrille

25

General Questions and Answers / Re: non magnetic device in LSDA

« on: September 2, 2016, 10:11 »

In fact this a general problem that I already encountered.
My system is an atomic contact. I know it is magnetic but I want to do a non-magnetic calculation within LSDA.
The standard DFT calculation remain non magnetic but as soon as the NEGF cycle start it seems that a "small magnetic kick" is given to the system that switches magnetic.

Cyrille

26

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

27

General Questions and Answers / Re: spin density + atomic structure

« on: September 1, 2016, 09:38 »

Great thanks, that's too easy:-)

Cyrille

28

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

29

General Questions and Answers / Re: adding a fragment that is not in the predefined one

« on: June 16, 2016, 09:31 »

Great! I need to improve my chemistry:-)

Cyrille

30

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