Messages

1

General Questions and Answers / Re: OptimizeDeviceConfiguration

« on: September 21, 2024, 19:17 »

Thank you for your interest in providing assistance with my study. I am currently facing a challenge regarding the optimization of the organic molecule situated between the gold electrodes.

The molecule's length is 12 angstroms. When using the OptimizeDeviceConfiguration block, I have observed that if I set the "optimization region length" above 10 angstroms, a break appears between the molecule and the electrode, as shown in the attached image (2a). I tested various settings between 10 and 30 angstroms, and consistently encountered this issue. However, when I set the "optimization region length" to exactly 10 angstroms, no break occurred, as illustrated in the attached image (2b).

I would appreciate any insights you might have regarding this behavior.

2

General Questions and Answers / Re: OptimizeDeviceConfiguration

« on: September 10, 2024, 17:45 »

I would like to thank you for your interest in providing assistance. However, my question is: Is 'the optimization region length' the same as 'the width of the optimization region'?

3

General Questions and Answers / Geometry Optimization of the two Probe System(organic molecule between 2 electro

« on: September 10, 2024, 17:09 »

I am having difficulty in performing a geometry optimization for a two-probe system. So I would like to have a sound methodology to properly perform a two-probe system geometry optimization, especially when studying the rectification properties of an organic molecule when placed between two gold electrodes.

4

General Questions and Answers / Geometry Optimization of the two-Probe System:

« on: August 24, 2024, 10:42 »

I have two gold electrodes with an organic molecule between them. The length of the organic molecule is 12 angstroms. When using the OptimizeDeviceConfiguration block to optimize the system, if I enter a value for the "optimization region length" higher than 10 angstroms, a break occurs between the molecule and the electrode as shown in the attached image(2a). I ran several tests with the "optimization region length" set between 10 and 30 angstroms, and in each case, a break occurred between the molecule and the electrode. However, when I set the "optimization region length" to 10 angstroms, no break occurred as shown in the attached image(2b).
I hope you can help me understand this part and explain more about what the "Optimization Region Length" refers to

5

General Questions and Answers / OptimizeDeviceConfiguration

« on: August 24, 2024, 10:37 »

I hope to find some help in understanding this part of the "OptimizeDeviceConfiguration" block mentioned in the QATK tutorials .So that I can do the geometric optimization of two-probe system.
Does the " the width of the optimization region " mentioned in the tutorial description refer to the " the optimization region length " mentioned in the illustration within the tutorial, as shown in the screenshot attached to the question for further clarification?
Here is the link to that section of the tutorials for further explanation.

https://docs.quantumatk.com/tutorials/optimize_device_configuration/optimize_device_configuration.html

6

General Questions and Answers / Geometry Optimization of the two electrode

« on: August 24, 2024, 10:28 »

Geometry Optimization of the two electrode before placing the molecule between them to form the two-Probe System:
In order to achieve the geometric optimization of the two-probe system, I first optimize the bulk gold "unit cell," then cleavage the two electrodes from the optimized bulk gold. After that, I place the molecule between the two electrodes and use the "OptimizeDeviceConfiguration block" to optimize the entire system.
 Is this method correct, and is optimizing the bulk gold sufficient, or is it necessary to optimize the two electrodes before placing the molecule between them? Also, how do I optimize the two electrodes before placing the molecule between them? I have searched extensively in the tutorials but did not find an answer.
I hope to find help in guiding to achieve this optimization

7

General Questions and Answers / Geometric optimization

« on: July 2, 2024, 10:18 »

Ask how to perform geometric optimization of a two-probe system (molecule between two gold electrodes) under a bias voltage from -4 to +4.

8

General Questions and Answers / Geometric optimization of the two-probe system?

« on: July 2, 2024, 09:57 »

I performed a geometric optimization on a single organic compound under a bias voltage from -4 to +4 using Gaussian 16W software. I now want to complete this study by placing this compound between two gold electrodes to form a two-probe system and studying it under the same bias voltages by using QuantumATK software.

I find that there are two main paths, but I don't know which one to follow:
Approach 1: Geometric optimization of the entire two-probe system (starting from scratch):
Begin by drawing the entire system from the beginning, which includes the organic compound and the two gold electrodes.
Perform a geometric optimization of the entire system (the compound between the electrodes) simultaneously.

Approach 2: Partial Geometric Optimization Using Existing Coordinates
Utilize the coordinates of the organic compound that was previously geometrically optimized using Gaussian 16W.
Introduce the two gold electrodes and optimize their positions relative to the fixed coordinates of the optimized compound.

Which of these two approaches is best?

9

General Questions and Answers / Relaxation of devices (optimize the geometry of a two-probe system)

« on: July 2, 2024, 09:24 »

I am a beginner in the ATK software
I'm trying to relax the device (optimize the geometry of the two-probe system). The two-probe system is the placement of a single organic molecule between two gold electrodes.
Is it better to perform the geometric optimization on the entire two-probe system (two electrodes + the central region), or to perform the optimization only on the central region?