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Messages - berlin

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16
windows 7 64
every nc file you copied will have this err

17
this err only found in 2016.3, and 2016.1 works fine.

when I copied a nc file into the project folder, there will be noting for this nc file in LabFloor .   I can see it only until I re-opened the project.

18
The way to solve this problem temporarily is type some thing in the second line of *.xyz files.

Thx

19
This might happen if the "title" of the file (the second line in the file) is empty. It's not a big problem, what's supposed to happen is that a tooltip pops up, showing the title (which is empty anyway for your file).
So, a tiny bug which we can fix, but nothing for you to worry about.

Thank you very much!
I do believe this is not a big bug. That is why I post it here.
The only thing I need to worry is that make sure do not move mouse to that kind obj.
One time move to it, only get a err window. But too much time or times on those objects, my VNL will crash, and what I can only do then is to reboot VNL.

20
General Questions and Answers / [Bug] VNL LabFloor on *.xyz file
« on: September 8, 2016, 09:56 »
if in my Project folder has a *.xyz file, we can see is obj on LabFloor of VNL main page.
But when we move mouse to that obj, the fellowing err comes out:
Code
TypeError: invalid result from LabView.viewportEvent(), an integer is required

VNL 2015 does work fine,
Both 2016.0 and 2016.1 have this err.

21
OK, fine
Thanks anyway

22
Why cann't use Brenner potential to optimize lattice constraints?

When I am doing unitcell optimization with Brenner in ATK2016.0,  the atomics positions will change, but the lattice constraints not change at all.   (I have changed the  lattice constraints to try again, but not works)

However, when I only change (do not change any setings else) potential to others (such as Tersoff_C_2012 ), lattice constraints will be optimized and changed.

23
That is fine, thank you all very much!

24
Tersoff  does give results, but the Phonon Bandstructure from Tersoff  is not as good as Brenner, on the agreement to GGA/LDA plane wave DFT calculations or experiments for Graphene.

25
But why the Materials Studio or Gulp woks fine with Brenner ?  And their results have a good agreement with GGA/LDA plane wave DFT calculations.

26
when I am doing phonon band calculation for Graphene Nanoribbon by Brenner potential (ATK classical) in ATK2015.1, errors comes out:
Quote
Traceback (most recent call last):
  File "(3,3) Graphene Nanoribbon.py", line 46, in <module>
    bulk_configuration.update()
  File ".\zipdir\NL\CommonConcepts\Configurations\AtomicConfiguration.py", line 1072, in update
  File ".\zipdir\NL\Calculators\BrennerCalculator\BrennerCalculator.py", line 126, in _update
  File ".\build\lib\site-packages\ase\atoms.py", line 643, in get_potential_energy
asapserial3.AsapError: The height of the cell (2.461) must be larger than 4

What is wrong?

27
I got the method from the first url:
Quote
mode(mode_index, temperature): Return the vibrational mode with the specified mode_index. The eigenmode,v, is obtained from the eigenvectors,u, as v = u/sqrt(M)*s, where the scaling factor s = sqrt(kB*T)/omega gives the amplitude of a classical oscillator with frequency omega.

But the scaling factor is defined as
s = sqrt(kB*T)/omega
which may only make sense when kB*T >> omega,

For low tempture, any suggestion?

28
We can use "Vibration Visualizer" plugin to see the vibration eignvectors. But how to get or save numerical data of vibration eignvectors ?

What i can do now is to read the nc file, and  get some data from "VibrationalMode_gID00*_eigenvectors_real"  and "VibrationalMode_gID00*_eigenvectors_imag". However, I do not know the units of those data. It sames not be  Angstrom. And more, those have been divided by sqrt(mass_of_atom) or not?


29

Even those LCAO basis are real, as you mentioned, but the must be complex matrix.
 How to get a real DOS function based on that Eq. ?

30
errors of total energy calculation, which are intorduced from LCAO basis, may be several hundred meV. You'd better use vasp or other code based  on plane wave basis to calculate total energy!

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