Author Topic: total number of particle displacement from its lattice  (Read 208 times)

zahid

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total number of particle displacement from its lattice
« on: April 29, 2019, 05:10:01 AM »
Dear Sir

I want to calculate the total number of particle displacement from a cutoff distance of 0.75 angstroms with respect to frame or times. Can you tell me which modification will help me with it?

Constanze Kalcher

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Re: total number of particle displacement from its lattice
« Reply #1 on: April 29, 2019, 11:52:22 AM »
Dear zahid,

just so I understand correctly: You would like to count how many atoms have displacement vectors larger than 0.75 Å with respect to your reference state?
Then you would first add a Displacement vector modifier to your pipeline and load the reference state of your choice.
You will see that each particle now has a particle property "Displacement Magnitude" which is the length of the corresponding displacement vector.
In a next step, you can insert an Expression selection modifier at the top of your pipeline and create a selection based on the displacement, e.g.
Code: [Select]
DisplacementMagnitude > 0.75 . You will then see the number of selected atoms below the Expression editor field. It will also appear as Global Attribute under "SelectExpression.num_selected". That means you can export that
information (even the time-series) as a text-file using the built-in file-export function.

-Constanze

zahid

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Re: total number of particle displacement from its lattice
« Reply #2 on: May 23, 2019, 04:07:22 AM »
thank you very much.

zahid

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Re: total number of particle displacement from its lattice
« Reply #3 on: June 29, 2019, 01:49:39 AM »
Dear Sir,
I have tried whatever you have said and it works well but I am doing simulation for nanoparticles and consider the open boundary condition. For this reason, my system loss few particles during the simulation. For this reason, I always get the error "Cannot perform calculation. Numbers of particles in reference configuration and current configuration do not match."

Can you suggest me about it?

Constanze Kalcher

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Re: total number of particle displacement from its lattice
« Reply #4 on: July 03, 2019, 02:58:12 PM »
Dear zahid,

in that case you cannot use the Displacement vector modifier, since the positions of every atom in the current and reference position will be compared.

-Constanze

zahid

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Re: total number of particle displacement from its lattice
« Reply #5 on: July 03, 2019, 11:05:02 PM »
thank you.