two probe with atk-vnl

[sweta]

Hello quantumwise

I have two questions:

1. Whether ATK have the facility to merge two fig (for example transmission spectra) in one fig?

2. How to calculate anchoring group and electrode distance exactly.

For example if we take sulfur anchoring group and adsorption height= 1.7 but the problem is that after optimization of two probe geometry its absorption height changes than how we can caculate the optimized adsorption height exactly.

Thank you!

[Anders Blom]

1. Not in the GUI currently, but you can always write a script for it. See e.g. http://quantumwise.com/forum/index.php?topic=1822

2. I don't understand what you mean. The way to find the distance is to run an optimization, as you say did. And if you do, of course the absorption height will change, that's the whole point. So now you have found the optimized height, it's in the result of the optimization.

[sweta]

1. I think your suggested script is for calculating only one transmission spectra but i want to merge two or three spectra in one fig.

2. I just want to calculate the adsorption height after optimizing the geometry.

[Anders Blom]

1. Yes, sure, so you would read in more than one NC file (or perhaps the spectra are in the same file, but the same approach applies) and then you add the plot, i.e. do P.plot several times.

2. So, just load the optimized geometry into the Viewer or Builder, put the mouse over the atoms (or open Coordinate Tools>Coordinate List) and inspect the coordinates.

[sweta]

Following script doesn't calculate the transmission spectra of two nc file in same plot.
how i will modify it to do the same

t = nlread('analysis.nc', TransmissionSpectrum)[0]
t = nlread('analysis1.nc', TransmissionSpectrum)[0]
import pylab as P 
P.plot(t.evaluate(),t.energies() )
P.plot(t.evaluate(),t.energies() )
P.xlabel("Transmission T(E)") 
P.ylabel("Energy / eV") 
P.savefig('transmission2.png', dpi=120)

[Anders Blom]

Call the variables t1 and t2 instead of t, the second line overwrites t as defined on the first line

[Anders Blom]

Or, you can always export the transmission spectrum and other data from VNL by right-clicking the plot and choose Export. Then you can plot in Excel, GNUPlot, IDL, or whatever you prefer.

[sweta]

thank you! it works well if spectra are in different nc file.

can you tell me what modifications i should do in the above script if two spectra in same file (for example transmission spectra at different voltages) and i want to merge it

[Anders Blom]

In that case use

Code: python

import pylab as P 
all = nlread('analysis.nc', TransmissionSpectrum)
for t in all:
    P.plot(t.evaluate(),t.energies())
P.xlabel("Transmission T(E)") 
P.ylabel("Energy / eV") 
P.savefig('transmission3.png', dpi=120)

Note the indentation of the "plot" line.

[sweta]

Thanks Dr. Blom!

Your suggested script works for all transmission spectra in same .nc file.

If we want to merge only some specific spectra in same .nc file (for example gID002, gID004 only) what changes i should do in the above script?

[Anders Blom]

Code: python

import pylab as P
ids = ['gID002', 'gID004']
for id in ids:
    t = nlread('analysis.nc', object_id=id)[0]
    P.plot(t.evaluate(),t.energies())  
P.xlabel("Transmission T(E)")   
P.ylabel("Energy / eV")   
P.savefig('transmission4.png', dpi=120)

Tip: learn Python - it will help you a lot

[sweta]

Thanks Dr. Blom!

Is this possible to show bias window through the above process? How i can do this

[Anders Blom]

Easy

Code: python

P.plot([0,6],[0,6], 'b-')
P.plot([0,6],[0,-6], 'b-')

where perhaps the range 0 to 6 V is a bit much, but that's easy to adjust.

[sweta]

import pylab as P
P.plot([0,1],[0,1], 'b-') 
P.plot([0,1],[0,-1], 'b-')
ids = ['gID002', 'gID004'] 
for id in ids: 
    t = nlread('analysis.nc', object_id=id)[0] 
    P.plot(t.evaluate(),t.energies())   
P.xlabel("Transmission T(E)")     
P.ylabel("Energy / eV")     
P.savefig('transmission4.png', dpi=120)

It does not show the bias window like attached fig

[Anders Blom]

That can be done with some pylab coding, but if the bias is different for the different transmission spectra it doesn't really make sense.