Messages

16

General Questions and Answers / Re: Density of states

« on: July 20, 2009, 05:31 »

Hi,

Thanks for your reply. However, the tutorial writes: "The method used for the DOS calculation is the tetrahedron method, suitable for real
3D crystal. The provided script is, as the name indicates, not suitable for 1D or 2D systems like nanotubes or graphene."

We need to calculate the DOS of CNT, a 1-D structure.

Also, the tutorial has an example:

Code

from ATK.KohnSham import *
from bulk_dos import *
# Specify checkpoint file here!
scf = restoreSelfConsistentCalculation('c:/vnl/au.nc')
dos = calculateDensityOfStates(scf, -5*eV, 5*eV, 100, accuracy=4)
dos.plot('c:/vnl/au_dos.png')

From this I understand that the DOS can be extracted from scf included in *.nc files.

Cheers,
Serhan

17

General Questions and Answers / Density of states

« on: July 19, 2009, 21:10 »

I'd like to ask how can we calculate the density of states and plot it for carbon nanotubes in ATK? We have *.nc files of the simulations of various metallic CNTs (two-probe simulations). How can we extract DOS from these *.nc files?

Cheers,
Serhan

18

Scripts, Tutorials and Applications / Re: Exporting electron density etc to XYZ file for plotting in other software

« on: July 16, 2009, 07:27 »

Thank you very much for your answers. I could do it now.

Cheers,
Serhan

19

Scripts, Tutorials and Applications / Re: Exporting electron density etc to XYZ file for plotting in other software

« on: July 14, 2009, 21:06 »

Hi all,

I'm trying to export electron density to file using the script given in this thread. I need to extract electron densities of lots of .nc files.

If the exportED.py is like this

Code

scf=restoreSelfConsistenCalculation('/home/master/atk/1.nc')
electron_density=calculateElectronDensity(scf)
from export3d import *
export3D(electron_density)

And I execute this file as

/home/master/atk/atk /home/master/atk/exportED.py > /home/master/atk/electronDensity1.dat &

then, a file named electrondensity1.dat is successfully created in the directory. The code is excellent. However, I have dozens of .nc files of which the electron densities are to be extracted as:

1.nc -> electronDensity1.dat
2.nc -> electronDensity2.dat
.
.
.

etc. How can I achieve this as a batch mode instead of executing

/home/master/atk/atk /home/master/atk/exportED.py > /home/master/atk/electronDensity1.dat & (when 1.nc is pointed in exportED.py)
/home/master/atk/atk /home/master/atk/exportED.py > /home/master/atk/electronDensity2.dat & (when 2.nc is pointed in exportED.py)
.
.

etc. Any help is greatly appreciated  

Cheers,
Serhan

20

General Questions and Answers / Re: some question about the voltage profiles

« on: July 11, 2009, 12:00 »

Thank you for your answers. I'll try the DensityMatrix constaint

Cheers
Serhan

21

General Questions and Answers / Re: some question about the voltage profiles

« on: July 10, 2009, 05:00 »

Hi,

Thank you for the answer. However:

In other words, what is the driving force for the electron motion in CNT at the above situation?

Assume a car on a way that is frictionless. Do we need to continuously apply force to move it, or do we give a force (velocity) at the beginning and it continues to move? It is obvious that electron motion is the not the same as a macro car but, the equations are similar in the example.

The conductivity of a conductor is an intrinsic physical quantity, but voltage drop inside conductor is not.

I agree with this statement. The formula I gave is in the first chapter of Datta's book and in his lecture noted as given as movies. The formula (4q^2/h) is the conductance of a ballistic conductor, it is not conductivity, i.e. we do not need to regard the length, diameter, etc. of CNT in order to calculate the net conductance. It is caused from the effort needed to insert an electron into a ballistic channel as I understand from Datta: http://nanohub.org/resources/1831 . Also, this fundamental resistance is modelled as near the contacts of ballistic CNTs in the literature, e.g.: http://ieeexplore.ieee.org/xpls/abs_all.jsp?tp=&arnumber=1159214&isnumber=25976 .

My doubts on this subject remains 

Again thanks for the answer 

Cheers,
Serhan

22

General Questions and Answers / Re: some question about the voltage profiles

« on: July 9, 2009, 21:17 »

Hi,

I've calculated the voltage drop profile of a (6,6) metallic CNT and it is attached to this message. I applied a 0.1V bias voltage and it is clearly seen on the figure. The voltage gradually decreases from 0.1V to zero. It's ok. However, I have a question: In theory, the electron motion is ballistic in these short CNTs, the voltage drop must not occur in the ballistic transport since the scattering is negligible I think. But in the figure, the voltage drops continuously. Is here a conflict? The question is identical to this: There is a fundemamental minimum resistance of (4q^2/h) in a CNT plus an additional resistance caused from scattering effects. Where does this fundamental resistance is? Is it spread along the whole CNT?

Regards,
Serhan

23

Scripts, Tutorials and Applications / Re: Script for creating nanotubes

« on: May 5, 2009, 20:44 »

Thank you very much,

Cheers,
Serhan

24

Scripts, Tutorials and Applications / Re: Script for creating nanotubes

« on: May 5, 2009, 05:26 »

Thanks again 

OK, the voltage drops in the padding layers (as you've shown it as LP ans RP). However, the drop also occurs in L and P, is it right?

Cheers,
Serhan

25

Scripts, Tutorials and Applications / Re: Script for creating nanotubes

« on: May 4, 2009, 17:55 »

Hi,

I've made a (6,6) CNT with the script provided in this thread. I've plotted its voltage drop along z-direction. Attached is this Figure. However, I'm surprised that a voltage drop also occurs in the electrodes (the first and last 0.9nm correspond to the electrodes). Is this true? Does ATK take the voltage drop in the electrodes into account? Or am I missing something?

Cheers,
Serhan

26

Scripts, Tutorials and Applications / Re: Exporting electron density etc to XYZ file for plotting in other software

« on: April 30, 2009, 21:56 »

Thank you very much.

Cheers,
Serhan

27

Scripts, Tutorials and Applications / Re: Exporting electron density etc to XYZ file for plotting in other software

« on: April 30, 2009, 07:14 »

Hi Nordland,

The new_export3D exports the coordinates as this sort (if z=[z0,z4], x=[x0, x4], y=[y0, y4] and p is the physical quantity to be extracted):

Code

z0  x0  y0  p000
z1  x0  y0  p100
z2  x0  y0  p200
z3  x0  y0  p300
z4  x0  y0  p400
z0  x1  y0  p010
z1  x1  y0  p110
z2  x1  y0  p210
z3  x1  y0  p310
z4  x1  y0  p410
....................
....................
z3  x4  y4  p344
z4  x4  y4  p444

However, I need to export it as sorted in the z-axis coordinate such as:

Code

z0  x0  y0  p000
z0  x1  y0  p010
z0  x2  y0  p020
z0  x3  y0  p030
z0  x4  y0  p040
z0  x0  y1  p001
z0  x1  y1  p011
z0  x2  y1  p021
z0  x3  y1  p031
z0  x4  y1  p041
....................
....................
z0  x3  y4  p034
z0  x4  y4  p044
z1  x0  y0  p100
z1  x1  y0  p110
....................
....................
z4  x4  y3  p443
z4  x4  y4  p444

I could not success modifying the new_export3D.py to write in this sort. Could you please help?

Cheers,
Serhan

28

General Questions and Answers / Re: can VNL calculate the variation of the current as a function of voltage?

« on: April 28, 2009, 06:36 »

Code

for voltage in numpy.arange(4.5, 5.01, 0.1):
	two_probe_method = TwoProbeMethod(
	    electrode_parameters = (left_electrode_parameters,right_electrode_parameters),
	    exchange_correlation_type = exchange_correlation_type,
	    iteration_mixing_parameters = iteration_mixing_parameters,
	    electron_density_parameters = electron_density_parameters,
	    basis_set_parameters = basis_set_parameters,
	    iteration_control_parameters = iteration_control_parameters,
	    energy_contour_integral_parameters = energy_contour_integral_parameters,
	    two_center_integral_parameters = two_center_integral_parameters,
	    electrode_voltages = (voltage, 0)*Volt,
	    algorithm_parameters = two_probe_algorithm_parameters
	)

	if processIsMaster(): nlPrint(voltage)
	import datetime
	
	if processIsMaster(): print "Calculation started:", datetime.datetime.now().replace(microsecond=0)

	runtime_parameters = runtimeParameters(
    	verbosity_level = 1,
    	checkpoint_filename = '/home/master/sweep/%.1fV.nc' % voltage
	)

	# Perform self-consistent field calculation
	scf = executeSelfConsistentCalculation(
    	twoprobe_configuration,
    	two_probe_method,
    	runtime_parameters = runtime_parameters,
	initial_calculation=scf
	)

This works...

Cheers,
Serhan

29

General Questions and Answers / Re: Choice of basis

« on: April 27, 2009, 04:13 »

Thanks Anders for adding.

In fact, I faced the memory problem as I have written in other threads. A (6,6) nanotube as two-probe with 4 electrode repetitions and 20 central repetitions gave badalloc error. I have not tried to use 6 MPIs in 6 PC yet. I think this will also solve the problem without going to change the basis.

Cheers,
Serhan

30

Future Releases / Re: Usage of graphics card for future ATK technology

« on: April 26, 2009, 18:21 »

We're looking for the realization of plans.

Cheers,
Serhan