Messages

1

General Questions and Answers / Poisson Ratio nanotube

« on: December 28, 2020, 17:00 »

Hi.

I am trying to extract the plot such as stress vs strain, radius change vs strain, and energy vs strain for a nanotube that is strained in z (length) direction. I combined the python codes found in the forum and the code in the tutorial which is attached. As you see the nanotube is under 1.0 (no strain), 1.01 (1 percent strain), and 1.02 (2 percent strain). I was wondering how I can save/print the total energy of each strained structure after optimization and plot it against strain?
Furthermore, I would like to save/print the radius change (final radius-initial/initial) of the 3 strained structures versus strain in order to find the poison ratio.
Can someone please help me modify the code?
One last question, what is the correct command for finding the distance between two atoms (for example carbon #5 and carbon #10).

2

General Questions and Answers / GGA-PAW Memory error

« on: October 16, 2020, 03:31 »

Hi dear ATK

I am trying to use GGA-PAW-DFT-D3 for optimizing Mxene structure (python file was attached). I am aware that running PAW would reduce performance and increase accuracy. However, in my case after almost 2 days  my job was stopped due to "MemoryError: Unable to allocate the required storage. This is probably caused by insufficient available memory." (please see the end of attached log file for the rest of the error message)

In the log file (attached) the "Memory estimate for plane-wave quantities per process" is 3.70 GB!
 
The server that I use is equipped with 2 Intel Xeon Gold 6148 CPU and 384 GB RAM. In submission settings I used Multiprocesss parallel and chose 26 for number of processors (please see attached log file)

I was wondering if you could help me with a way to complete the job in a faster and more efficient way or reduce the memory usage...

3

General Questions and Answers / Re: DFT band gap underestimation

« on: July 27, 2015, 21:37 »

Thanks Sir

 I employed MGGA for the calculation. I determined c parameter ( 0.917)  by calculating the band gap of bulk silicon ( about 1.13 eV). [ I have no idea why this value is different from tutorial (( http://www.quantumwise.com/documents/tutorials/latest/NanowireDevice/index.html/chap.nanowirebulk.html#sect2.nanowirebulk.job.cvalue )) where c is 1.0364!! and gives a band gap of 1.58 eV for Si bulk based on my calculations]

Then, I used both parameters to calculate ASiNR band gap with large vacuum regions. But, the results show that the bang gap does not change significantly:

--- ( Eg for 4ASiNR using MGGA = 1.004 eV) when c=0.917
--- ( Eg for 4ASiNR using MGGA = 1.02 eV) when c=1.0364

while ( Eg for 4ASiNR using GGA = 0.957 eV)

Enclosed to this message you can find the python files. Due to the file uploading restrictions, only python files are attached. Can you please help me with that?

4

General Questions and Answers / DFT band gap underestimation

« on: July 27, 2015, 05:31 »

Hello everyone,

The well-known band gap underestimation in LDA and GGA-PBE calculations is confirmed. I am trying to get accurate band gap for ASiNRs and AGNRs. As you may know, using GW or HSE03 can give a derivation of 20-30% compared to LDA and GGA. But there is not this opportunity to calculate band gap using these methods by ATK. I tried MGGA and got a more accurate band gap for the structures compared to LDA and GGA ( no significant changes). Is there a way to get an accurate band gap (in good agreement with experiments) using ATK?

Thanks in Advance 

5

General Questions and Answers / Re: Edge Functionalization of Graphene Nanoribbons

« on: April 28, 2015, 17:51 »

Dear Martinez,

Thanks for your quick response. I will try the Move Tool.

Just a point, I expected, unlike flat edges of hydrogenated graphene, halogens cause armchair edges to form out of plane distorted ripples due to steric repulsion. But, with simply changing hydrogen atoms to for example F atom, I got a completely flat structure!
I used: DFT method, Exchange correlation: LDA-PZ, basis-set: Double Zeta P, k-point: 1*1*12
 max Force: 0.005 ev/A, max stress: 0.05 ev/A3, without applying constraints.

Do I need to bring atoms close together in order to overlapping of their electron clouds?

   

6

General Questions and Answers / Edge Functionalization of Graphene Nanoribbons

« on: April 27, 2015, 19:48 »

Hello All,

I want to investigate F-, Br- , and Cl-, terminated graphene nanoribbons. As you may know ,and also you can find in the following references, the most stable geometry for halogen – terminated graphene nanoribbons has rippled in the edges. My question is that in ATK if one wants to consider all configurations (planar or edge rippled with all possibilities in order to find the most stable configuration, I mean, in a unit cell, one edge up and one edge down….), how should we apply ripples to edges of the nanoribbons before optimization step? I want to know how I can get their results using ATK?

I would really appreciate it if one could shed some light on this question.


- First-principles study of edge-modified armchair graphene nanoribbons:

http://scitation.aip.org/content/aip/journal/jap/113/18/10.1063/1.4804657

- Ripple edge engineering of graphene nanoribbons:

http://journals.aps.org/prb/abstract/10.1103/PhysRevB.84.134110