Topics

1

General Questions and Answers / Is there a way to get the value of hubbard U using the linear response approach

« on: December 30, 2022, 15:56 »

Dear all,

In ATK, one can use DFT+U method. However, the value of U is also very important. Is there a way or a tutorial for an ATK user to fix the value of U by using the linear response approach in DOI: 10.1103/PhysRevB.71.035105?

With best regards,

/Guang-Ping Zhang

2

General Questions and Answers / About the photocurrent calculated by QuantumATK

« on: July 27, 2021, 17:47 »

Dear ATK developers:

In the past days, I have looked into the photocurrent module in QuantumATK. As I understand,
(1) the photocurrent obtained by the photocurrent module is only the current induced by the photo illumination and it does not include that induced by the voltage between the source and drain.
(2) the transmission obtained from photonMediatedTransmission function is also the transmission induced by the photo illumination because I find the transmission is always zero for photon_energy = 0.0 eV.

Am I right?

(3) However, when I integrate the transmission obtained from photonMediatedTransmission function, the result is very different from the one obtained by Photocurrent module (from Photocurrent Report). Can you give some hints?

With best regards,

/Guang-Ping Zhang

3

General Questions and Answers / How to get the photon-mediated transmission for a two-probe junction

« on: June 15, 2021, 08:58 »

Dear ATK developers and users:

I want to know for a two-probe single-molecule junction, in the Class of Photocurrent,
(1) which region of the junction the photo illuminated on? That is, in the calculation, which region of the excitation is considered?
(2) Is the output photocurrent the current only induced by photon? That is, it does not include the current without photo illumination?
(3) How to get the photon-mediated transmission by using photonMediatedTransmission function? Can you give me an example?
(4) How to deal with the photocurrent calculations for a finite bias voltage applied on the junction? Specifically, how to set the energy lower and upper boundaries for the calculations with respect to a series of photons.

Thanks very much.

/Guang-Ping Zhang

4

General Questions and Answers / Some basic questions about photocurrent

« on: February 7, 2019, 04:50 »

Dear ATK developers:

Recently, I have dug on the function of photocurrent implemented in QuantumATK 2018.06. But, I have a few confusing questions about this function.

1) The manual gives the formula about how to calculate photocurrent,

I_{\alpha, \sigma} = \frac{e}{\hbar}\int \frac{dE}{2\pi}\sum_{k} T_\alpha(E, k, \sigma).

What are the lower and upper limits of the integral?

2) The obtained photocurrent from the above formula is just a photo induced current, which is a correction to the bias induced correction, Right? That is, the photocurrent does not contains the bias induced current.

3) How does the photocurrent flow, that is the flow direction, through a molecular junction, for zero bias and a finite bias?

4) On can only include the bias effect on photocurrent by using a *hdf5 file for a two probe junction converged under a bias?

Can you please kindly provide some more elementary tutorials or instructions or readings on photocurrent about, for example, the mechanism, etc.

With best regards,

/Guang-Ping Zhang

5

General Questions and Answers / Coupling strength between electrodes and the sandwiched molecule

« on: August 23, 2018, 06:57 »

Dear ATK staff and ATK users,

I want to quantitatively to describe the coupling strength between electrodes and the sandwiched molecule in a molecular junction. I have searched the forum and found this topic in 2016
https://quantumwise.com/forum/index.php?topic=4190.msg19127#msg19127

However, this topic did not give a explicit solution to this question.

I also tried to used "calculateSelfEnergy" function to get the self-energy from one electrode and then to get the energy level broadening. But I found, the self-energy and an specific energy is a matrix, which can not be used directly. Indeed, I want to use a scalar number.

Another way, as far as I know, is to used PDOS to get the broadening a specific energy, which is a scalar number.

I wonder, in ATK, is there a more convenient and reliable method to describe the coupling strength between electrodes and molecule in a molecular junction ?

With best regards,

/Guang-Ping Zhang

 

6

General Questions and Answers / How to calculated a bend two-probe system in ATK?

« on: May 13, 2018, 08:43 »

Dear ATK supporters,

I am wondering whether ATK can calculate a two-probe system with bend angle, like the one in the following article

 http://pubs.rsc.org/en/Content/ArticleLanding/2018/CP/C7CP08462E#!divAbstract

Thanks in advance.

/Guang-Ping Zhang

7

General Questions and Answers / How can I use a different number of valence electrons for a specific atom

« on: April 29, 2018, 10:15 »

Dear ATK supporters,

I now wonder how can I use a different number of valence electrons for a specific atom. To be specific, I want to use 4/5 valence electrons for nitrogen atom that uses the basis set and pseudopotential of a normal nitrogen (that is N+/N- atom). This trick will be a little different from charging this system, and it will localize this charge to the N+/N- atom. However, in ATK, I got the following WARNING and the code stops:

Exception: The number of electrons (4.000000) specified is not equal to the number of electrons in the pseudo-potential (5.000000).

However, I can do this in SIESTA code, and get an expected result, where the N+ atom has 3.941 valence electrons while N- has 5.513 valence electrons).

In some calculation, it is necessary to calculate a charged system, where the net charge spatially localized on a specific atom. So, how can I do such calculations in ATK?

With best regards,

/Guang-Ping Zhang

8

General Questions and Answers / How to remove all the basis set for a specific atom in a calculation

« on: November 28, 2017, 11:08 »

Dear ATK developer,

Here, I want to remove the basis set for a atom while just using it potential, which is on the opposite to the ghost atom. Is there a way to achieve it in ATK-2015.1?

Thanks very much.

With best regards,

/Guang-Ping Zhang

9

General Questions and Answers / Can not understand the results by using ghost atom

« on: November 27, 2017, 06:00 »

Dear ATK developer and ATK user,

I use ATK to investigate the distance between graphene and the Cu(111) surface. In the calculation, there are five layers of Cu(111) with the leftmost three layers fixed and the two surface layers optimzed.  During the optimization, the graphene is also relaxed. I used GGA functional and a SZP basis set for Cu atoms/DZP for C atoms. The result shows that the distance between graphene and the surface is only 2.4 Angstrom, which is much smaller to that of 3.5 Angstrom reported by other studies. So, I used a layer of ghost atom to do the optimization again, where the ghost atom layer is also optimized. The optimized positions of ghost atoms are very close to the surface layer. In this way, I would expect a very similar distance between graphene and the surface. However, the optimized distance is 3.38 Angstrom, which is close to the ones in literatures. How to understand it?

With best regards,

Guang-Ping Zhang

10

General Questions and Answers / Can not find the "search" button in docs

« on: November 26, 2017, 15:31 »

Dear ATK team,

Before, I can find the "search" function on the page of https://docs.quantumwise.com so that I can quick find some relevant links in the docs section by some keys words. However, it disappear now. Is there a plan to active this function again?

With best regards,

Guang-Ping Zhang

11

Future Releases / Reordering for coordinate list

« on: April 12, 2017, 08:27 »

Dear developer,

I find the reorder function in coordinate list only order one of the components, but the other two components are out of order (in version 2015.1). However, sometimes, the ordering of the other two components maybe also useful. Therefore, a function that can set a primary order component, a second one and the third one is proposed in the feature version.

With best regards,

/Guangping Zhang

12

General Questions and Answers / tolerance object of the iteration control

« on: October 19, 2016, 06:48 »

Dear all,

I am now wondering what is the toerance object of the interation control in two-probe system calculation. Say, I set 0.0001 Hartree in Tolerance, then I see when the dE of the self-consistent cyc reach 0.0001, then the convergence is achieved. What is dE? Is it the difference of the max difference between an element of the Hamiltonian or the total energy? I guess it is the former from the manual (http://www.quantumwise.com/documents/manuals/latest/ReferenceManual/index.html/ref.iterationcontrolparameters.html), but I am not sure.

With best regards,

Guangping Zhang

13

General Questions and Answers / Possible bug in VNL

« on: April 30, 2016, 16:26 »

Dear QW stuff,

I find a possible bug in VNL.
VNL:  2015.1.5b36b25
Platform:  windows 10 x64
Description: When you set the parameters in “New Calculator” of the "Script Generator",  the "Density mesh cut-off" can not be changed under the card "Basic device", it always go back to the default value 75 Hartree when you come back to this “Basic device” card, until you set the value in the card "Numerical accuracy parameters". That is to say,  the "Density mesh cut-off" can not use the value set in the card "Basic device", and only use the value set in the card "Numerical accuracy parameters".

With best regards,

Guangping

14

General Questions and Answers / Tutorial of Inelastic electron tunneling spectrum

« on: April 29, 2016, 15:15 »

Dear all,

Is there a detail tutorial for Inelastic electron tunneling spectrum (IETS)? I saw this can be realized in InelasticTransmissionSpectrum Class. However, I did not find a detailed tutorial of how to use it:
(1) how to set the dynamical region when calculate the phonon.
(2) how to inspect the vibrational mode after the phonon calculation.
(3) how to calculate the IETS based on the above data.

With best regards,

/Guangping

Moderator edit: Confusing spelling mistake in subject corrected.

15

General Questions and Answers / part of MPSH orbital outside the unit cell

« on: April 28, 2016, 18:35 »

Dear all,

When I plot the MPSH orbital of a junction, I found the MPSH orbital is split into two part because some part are outside the unit cell as seen in the attachment. How to solve this by no construct a new junction and rerun the job?

And how to show the configuration of the two probe in the MPSH orbital? I did not find the option. I have used nlsave to save the configuration into the nc file before the MPSH orbitals are save into this nc file.

With best regards,

/Guangping