Messages

1

General Questions and Answers / Re: Bias direction for different electrodes

« on: October 9, 2024, 11:00 »

What confuses me a bit when you say that is that when I calculate the current from the transmission spectrums I can only reproduce the IV curve when I have the bias window from -0.5 to 0.5. In the transmission analyzer the left electrode is at 0 and the right is then moved from -1 to 1. So I would assume, based on what you say, that the bias window that is integrated in the code would be e.g. at one point from 0 to 1.  Is this how I should understand it?

2

General Questions and Answers / Re: Bias direction for different electrodes

« on: October 2, 2024, 10:27 »

Okay thanks.

Let's say I am looking at the transmission via the IVCharacteristics. The current there is (just to give a number) 1.4*10**-5 at 1V.

To get this current (1.4*10**-5)  at 1V the code would then have the bias window in the transmission spectrum from -0.5 to 0.5 - is the correct?  Or, would the code have the bias window from 0 to  -1V?

I ask about this because I am using the transmissionspectrum to investigate what happens when do an IV sweep - but to do so I need to be sure how the current is integrated from the transmission spectrum.

3

General Questions and Answers / Re: Bias direction for different electrodes

« on: September 30, 2024, 14:53 »

It actually might just be that it is difficult to undetstand how the bias window opens up.
In the older versions of ATK I understand it opened up symmetrically (so 1V, the bias window would be from -0.5 to 0.5. Is this the same case for the newer versions? (2022 + ) Or is the bias window now from  0V to eg. 1V and -1V to 0V ?

this is not stated anywhere clear in the tutorials. In the transmission where the fermi level of the electrodes are shown it seems like the window is from 0 to -1V (or +1V) depending on the bias. 

4

General Questions and Answers / Re: Bias direction for different electrodes

« on: September 17, 2024, 09:11 »

Yes of course. As you can see it is a rectifying molecule I am looking at. The Right electrode is Au and the left is Al. I have no gate (0V) and the transmission is at chosen at -0.5V.  In the transmission spectrum the fermi level of the left electrode is 0 and the right is 0.5.  So as I understand uL < uR indicating that the current should be positive not negative.

I observe a behavior in the transmission changing with the bias that I am investigating together with other properties, so it is important for me to be sure of the direction of the current (and electrons).

As you suggested I tried changing the source electrode to be the right instead of the left electrode. That flipped everything around (more current negative than positive).

So basically I "just" need to be sure of the direction of the current.

It seems that it does not open the bias window up symmetrically, is that also correct? Is this a feature of two different electrodes ? As i recall in the older version it opens up symmetrically, but that could also just be a choice of two Au electrodes…

5

General Questions and Answers / Re: Bias direction for different electrodes

« on: September 16, 2024, 13:18 »

Thank you for your help.

Just to be sure, how should I then understand the fermi levels of the left/right electrode when I have the left electrode as the source (since this does not follow the convention in the tutorials). I cannot find the electrode potentials anywhere only the current and the fermi levels. Is it correct to take the direction of the bias based only on the current I>0 or I<0, and then ignoring the fermi levels? So when I have +0.5V then  VL > VR and I ignore that the fermi levels do not follow this?

6

General Questions and Answers / Re: Bias direction for different electrodes

« on: September 13, 2024, 10:38 »

Thank you, I can see that when I do as you say it follow the convention.

I am working with a rectifying molecule, so it matters which electrode I choose as the source. So the question is whether I can "trust" the transmissions and IV curve (is the transmission spectrum at e.g. -0.5V correct or is this actually 0.5V) when I use the left electrode as the source when it does not follow the convention? Or can I do something different so it works? 

7

General Questions and Answers / Re: Bias direction for different electrodes

« on: September 11, 2024, 09:09 »

Is it that you might have a mistake in the transmission analyzer?

In the transmission spectrum shown in the transmission analyzer, via the iv characteristic, it is written as the fermi level (right) and fermi level (left). Should this instead be the electrode potential? If this is the case the current seems to be correct, if not the current is opposite of what the iv characteristic shows, if you follow the note in my post above.

8

General Questions and Answers / Bias direction for different electrodes

« on: August 27, 2024, 09:29 »

Hi,

I have tried looking through the forum but I couldn't find an answer to my question.
I am investigating the difference between a molecular junction with two Au electrodes and a molecular junction with Au and Al.

Doing so I ran into a definition problem of the forward/reverse current and the chemical potential for the Au-Al junction. It seems that  in this case the Au (left) is kept at 0 and Al(right) is changed.

A forward bias is defined as VL > VR (that being the voltage of the left electrode is higher than of the right)
in the same line the chemical potential is like this: uL < uR.
When I look at the uL given in the transmission spectra (as I understand is the fermi level of the left electrode) at postive 1V I get that uL = 0 and uR = -1.  But this would be uL > uR - so actually reverse bias?

In general I get:
positive 1V: uL=0 , uR = -1
negative 1V: uL=0, uR = +1

I am a little confused here, could you help clarify this for me?

I have attached the note from the tutorial that I tried using to understand this.

Thanks in advance.

9

Scripts, Tutorials and Applications / Re: 1D projector sum, average and line

« on: July 31, 2024, 11:55 »

Thank you for clarifying 

10

Scripts, Tutorials and Applications / 1D projector sum, average and line

« on: June 13, 2024, 09:38 »

Hi,

I am using the 1D projector in quantumATK to visualise different things. In that regard I got confused reading the forum as well as the tutorial as to how I should understand the different projections.

In this tutorial (https://docs.quantumatk.com/tutorials/atk_transport_calculations/atk_transport_calculations.html) it is written as "With this tool you can project a potential or density along a certain direction, integrated or averaged over the two directions perpendicular to it. "

But in this post (https://forum.quantumatk.com/index.php?topic=9735.msg32591#msg32591) from 2022,  it is not an integral " It's not an integral over the perpendicular direction, just a sum or average."

So my question is, how do you calculate/how should I understand, the sum, average and line in the 1D plot? 

Thanks in advance,

Louise

11

General Questions and Answers / Re: Orbital coefficients

« on: May 13, 2024, 08:38 »

Wonderful thank you!  - you had a great idea 10 years ago 

Just to be sure, the script "only" needs the configuration and the energy state of the molecule I am interested in? and then I can choose which atoms I want to project on? where you have e.g. 0, can I then have a list or do I need to have a line for each atom in the molecule?

12

General Questions and Answers / Re: Orbital coefficients

« on: May 7, 2024, 10:53 »

Thank you for getting back to me. :-)
Say we have a C-O molecule. I define the orbital coefficient as how much the atomic orbitals of C is contributing to the molecular orbital(MO) - at e.g. the HOMO of the molecule. This I wanted to use to compare the HOMO of the molecule at different electric fields.

I also tried to use the 1D projector to compare the MOs(eigenstates), but got a bit suspicious about the unit (psi Å^-1.5).  Maybe you can clarify this?

I hope this makes sense.

13

General Questions and Answers / Orbital coefficients

« on: May 2, 2024, 13:14 »

Hi,

Is it possible somehow to get the orbital coefficients out when calculating the eigenstates of a molecule?

I cannot find anywhere in the documentation that mentions this, so it might be that you call it something else.

thank you in advance,

Louise

14

General Questions and Answers / Dipole moment calculation

« on: August 29, 2022, 13:25 »

Hi,
I am trying to understand how to calculate the dipole moment of a molecule (or a junction).

I have used the two exact script that you put on the manuel for the electron density. https://docs.quantumatk.com/manual/Types/ElectronDensity/ElectronDensity.html   nh3_density.py and nh3_density_multipoles.py

Everything is running, my problem is the results.  I get the result shown below. I am aware that the dipole is a vector and that the length of the vector should be the dipole moment. But both the unit and the size of the dipole moment does not make sense. Could you help me understand how this works?
Why is it Bohr**4*e when the unit is e*bohr? (for the dipole)
And when I convert the length of the vector to Debye (1 Debye = 0.39 e*bohr) the dipole moment is no where near comparable with results from e.g. Gaussain. 

Thanks in advance.

----------------------------------------- output from nh3_density_multipoles.py ---------------------------------------------------
center of mass (bohr)  =  [ 10.56827806   9.91727343   9.60194572] Bohr
monopole   (e)         =  8.00000122768 Bohr**3*e
dipole     (e*bohr)    =  [-9.02093396e-16 -2.84059249e-14 -1.58800480e-14] Bohr**4*e
quadropole (e*bohr**2) =  [[ 1.88237189e+01 -8.12198595e-06 -1.01224738e-05]
 [-8.12198595e-06  1.88237184e+01  7.58701761e-05]
 [-1.01224738e-05  7.58701761e-05  1.61672803e+01]] Bohr**5*e