Messages

1

General Questions and Answers / Kinetic Energy Distribution and Extraction of coordinates of Trapped Hydrogen

« on: May 17, 2018, 07:37 »

Hello Everyone,
I bombarded the hydrogen atom on the tungsten substrate with fixed energy 100eV. I was wondering how to do following post processing things.
1. How to find kinetic energy distribution of  Trapped hydrogens (ONLY) in Tungsten?
2. How to extract the final coordinates of trapped hydrogen atoms?
The attached file is the input file for the simulation, and it gives the coordinates of trapped hydrogen, however I want to extract the coordinates of trapped hydrogen from ".nc " file. which is the output file of simulation.

Any help will be really appreciated.
Thanks,
Ashok

2

General Questions and Answers / Re: Size of Helium Cluster

« on: April 6, 2018, 02:38 »

Hello Petr,
Actually, I am trying to see the size of helium bubbles formed inside the  tungsten matrix on different temperature .
After you send the output file in builder, How can we measure the diameter of the clusters? Is there any more easy way to count the total number of atoms in each cluster? Thank you for your time, and consideration.
Regards,
Ashok

3

General Questions and Answers / Re: Size of Helium Cluster

« on: April 2, 2018, 23:10 »

Thank you for the response, but I am talking about after your simulation done (i.e output file). Is there any convenient way to count the number of atoms in each cluster and the radius of each cluster in your output file? Thanks for your time and consideration.
Regards,
Ashok

4

General Questions and Answers / Size of Helium Cluster

« on: March 31, 2018, 20:32 »

Dear Sir\Madam,
I am running the simulation regarding helium cluster formation in Tungsten matrix at different temperature.
Is it possible to determine the size of cluster and the number of atoms in a single cluster? Thanks for your time and consideration.
Best Regards,
Ashok

5

General Questions and Answers / Re: Error Message

« on: March 14, 2018, 17:54 »

Thank you Ulrik.
Actually I already did the method you described in your email. To see more detail about the deposition, I did the simulation with only 2 Hydrogen atom on reservoir, I ran the simulation making 100 deposition interval with only 1 log interval, making 200 md steps. What I observed in this situation, on next deposition it reuse the same Hydrogen that it already used for the first deposition, not the new hydrogen atom. So, Is there anyway to fix this issue?
I tried to attach my potential file, but its size more than 400KB. This is the link where I found potential for Tungsten, Hydrogen, and Helium interaction.
https://www.ctcms.nist.gov/potentials/W.html, I used these potential files: potential-WHHe-EAM1.eam.alloy , potential-WHHe-EAM2.eam.alloy

Regards,
Ashok
,

6

General Questions and Answers / Re: Error Message

« on: March 12, 2018, 23:43 »

Thank you for the response.
But if I run that simulation for large number of atoms let say 108 Hydrogen atoms on reservoir, with making  total MD step around 500000, log interval of around 100, hydrogen atom deposition interval around 100. Then I still found the trapping of some number of Hydrogen atoms. How does that possible if thickness of the tungsten is not thick enough?

Another question for you, Is there any way to study how much percentage of hydrogen atom get trapped inside the tungsten? Currently, I am running simulation to see the trapping of Hydrogen in Tungsten matrix, but my hydrogen atom gets reused after they reflected back from tungsten matrix, which I don't want. Is there any way to make reflected hydrogen not get reused up, make them freeze at reservoir, and next deposition start with the new hydrogen atom, so that I can count how many number of atoms get trapped and how many atoms reflected from tungsten matrix among given number of hydrogen?
Thank you in advance.
Regards,
Ashok

7

General Questions and Answers / Re: Error Message

« on: March 10, 2018, 01:15 »

Hello,
Thanks for the response. I think, I fixed the problem.
However, I have another issue. I tried to see the trapping of hydrogen atom in tungsten matrix. For this, I bombarded hydrogen atom, with K.E around 100eV,  on tungsten matrix at 2000K. During my simulation, I found that hydrogen atom get transmitted through bottom layer of tungsten, although I made reservoir fixed. Is this because of thin bottom layer of tungsten matrix? The attached is my input file. My software version is 2016.4.
Thanks,
Ashok

8

General Questions and Answers / Error Message

« on: February 28, 2018, 18:34 »

Hello,

I am getting this kind of error while  doing my simulation of Hydrogen Bombardment on Tungsten Matrix.
I don't why I am getting this error.  The attached file is the description of error.

Thanks,
Ashok

9

General Questions and Answers / Re: About Tracking the coordinates of each atom

« on: January 27, 2018, 05:15 »

Thank you for the help
Ashok

10

General Questions and Answers / Re: About Tracking the coordinates of each atom

« on: January 24, 2018, 17:50 »

Hi,
I tried to run the code that you provided to me but it keeps saying 
"Traceback (most recent call last):
  File "Test1.py", line 76, in <module>
    elements=trajectory[image].elements()
TypeError: 'MDTrajectory' object does not support indexing.
 
I am wondering it is because of the version of the quantumwise that I used. I am using Quantumwise 2016.4, because I know hdf5 format works for the latest version of quantumwise.
Thanks,
Ashok

11

General Questions and Answers / Re: About Tracking the coordinates of each atom

« on: January 23, 2018, 22:21 »

Thanks for the help

12

General Questions and Answers / Re: About Tracking the coordinates of each atom

« on: January 23, 2018, 04:33 »

Thank you for the information.
What about the mixture of atoms, for example: we have a cluster of atoms like Hydrogen, Helium and Tungsten. if I want to find the coordinates of hydrogen atoms only in the cluster, is it possible to do that? I am asking these questions because I am looking for the trajectory that hydrogen follow throughout simulation.
Thanks,
Ashok

13

General Questions and Answers / About Tracking the coordinates of each atom

« on: January 18, 2018, 22:05 »

Hi There,
I am trying to get each coordinates of the atom for each time interval in molecular dynamics. How can I get these information?
Thanks,
Ashok

14

General Questions and Answers / Re: Thin film deposition of Sn on CdTe

« on: November 6, 2017, 07:44 »

Thank you for the reply.  So it means that the potential that I choose is not compatible with my simulation.
Thank you !

15

General Questions and Answers / Re: Thin film deposition of Sn on CdTe

« on: November 6, 2017, 02:36 »

Dear Sir\Madam,
I am trying to deposit Sn on Corundum substrate, and was able to make a bombardment of Sn on Corundum. On analyzing my output file through movie tool, the result was completely different than what I supposed to get. The Sn atoms which I bombardment on Corundum substrate are not completely attached with the substrate. I mean there are barely three to four atoms stick with the substrate, and remaining atoms are reflected back from the substrate. When I ran the example that quantumwise provided on there tutorial for thin film deposition, all of the Si atoms are deposited on the substrate. I don't know what's wrong with my input file. I would really appreciate if you guys help me to figure out this problem on my script file. The file which I attached along with this email is my input file.
Respectfully,
Ashok Gurung