Author Topic: MOLECULAR ARRANGEMENT CHARACTERIZATION  (Read 66 times)

akhoursh

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MOLECULAR ARRANGEMENT CHARACTERIZATION
« on: August 16, 2019, 10:30:09 PM »
Dear Ovito users,

I have a molecular system, and the molecules are placed in an HCP arrangement ( i.e. consider an FCC system that at each atomic site there exist a molecule rather than an atom ). Is there anyway to monitor this molecular arrangement in OVITO similar to what we usually do with CNA or PTD in case of atomic arrangement ? I tried with CNA and PTD. But, it shows 100% others as expected. Any comment would be appreciated.
Thanks,
Al

Alexander Stukowski

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Re: MOLECULAR ARRANGEMENT CHARACTERIZATION
« Reply #1 on: August 16, 2019, 11:13:27 PM »
Dear Al,

What do you think yourself would be an appropriate strategy to apply here? Replace each molecule with a virtual atom positioned in its center of mass and then run the CNA or PTM analysis on these virtual atoms?

This would probably require some Python coding. A simpler strategy would be to pick one particular (physical) atom out of each molecule and run the structure analysis on these selected atoms. But this wouldn't be as precise as the center-of-mass approach, I guess.

-Alex

akhoursh

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Re: MOLECULAR ARRANGEMENT CHARACTERIZATION
« Reply #2 on: August 17, 2019, 12:09:40 AM »
Hi Alex,

Thanks for the reply. Actually, I thought of the CM as well. But, I hoped there was something quicker. Also, the second method does not work since I have a random distribution of the direction of central axes of each molecule. 
Regards,
Al