QuantumATK Forum

QuantumATK => General Questions and Answers => Topic started by: ashokgrg19 on March 31, 2018, 20:32

Title: Size of Helium Cluster
Post by: ashokgrg19 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

Title: Re: Size of Helium Cluster
Post by: Petr Khomyakov on March 31, 2018, 23:40

In the Builder, there is a measure tool that can be used to measure separation distances between atoms. The number of atoms is given in the Coordinate Tools -> Coordinate List.

Title: Re: Size of Helium Cluster
Post by: ashokgrg19 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

Title: Re: Size of Helium Cluster
Post by: Petr Khomyakov on April 3, 2018, 09:53

You can still drag and drop your outputted structure from the LabFloor to the Stash in the Builder and do all the measurement of the cluster size and number of atoms. Actually, it would be easier to understand what exactly you are trying to do and what your system of study looks like if you would post the python script and hdf5 file with your outputted structure. 

You may also consider using the MD analyzer that allows analyzing structural properties, e.g., radial distribution function and coordination numbers for given a atom type(s) and maximum atom-atom separation distance.   

You can certainly do this type of analysis through python scripting in QuantumATK, see https://docs.quantumwise.com/manuals/Python.html and https://docs.quantumwise.com/manuals/NLRefMan.html, and https://docs.quantumwise.com/manuals/Types/BulkConfiguration/BulkConfiguration.html (I assumed that you are using bulk configuration for these calculations).

Title: Re: Size of Helium Cluster
Post by: ashokgrg19 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

Title: Re: Size of Helium Cluster
Post by: Petr Khomyakov on April 6, 2018, 09:57

I think the only way to really do it is by writing an analysis script in python, see the links I posted previously.