Author Topic: Combine Particle Set Modifier issue.  (Read 495 times)

Shamail

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Combine Particle Set Modifier issue.
« on: February 19, 2018, 06:48:44 PM »
Hi,

First of all many thanks for this excellent visualization tool.

I have some issues with Combine Particle Set modifier. The issue is that the modifier is itself changing the the labels of the atoms in the second particle set. Does anyone know what's wrong with it? Or maybe I'm doing something wrong.

The second set is from the same Crystal system with same orientation and it is exactly the other half of the set with just some atoms at specific atomic positions are replaced by another atom.

Thanks.

Alexander Stukowski

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Re: Combine Particle Set Modifier issue.
« Reply #1 on: February 19, 2018, 10:31:34 PM »
Hi,
I don't understand what you mean with the "labels of the atoms". Do you mean the atom types, the atom IDs, or some other property? Please clarify.
Thanks.

If you mean the atom IDs, please note the following statement from the user manual:

Quote
The IDs of particles loaded from the second file are newly assigned by the modifier to ensure that they do not conflict with the existing particle IDs in the current dataset.

This is to ensure the uniqueness of the particle IDs.

-Alex

Shamail

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Re: Combine Particle Set Modifier issue.
« Reply #2 on: February 20, 2018, 02:18:57 PM »
Thanks for your reply Alex.

Yes, I meant IDs of atoms. In my case, the first set contains the layered structure of Li, Ni and O and the second contains Ni and O only with just Ni is occupying the Li positions.  The crystal structure and the orientations are same but in the second set the modifier changes O to Li and Ni remains same. It should have changed Ni also but it is only changing O.

Thanks

Alexander Stukowski

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Re: Combine Particle Set Modifier issue.
« Reply #3 on: February 20, 2018, 03:03:31 PM »
Can you please post the data files with the two atom sets? I would like to reproduce the problem that you are facing. Right now, I still don't understand what you are doing and what is happening. On one hand you write that atom IDs are not correct, on the other hand you talk about chemical types not being as expected. Note that, in Ovito, all particles have two different properties: "Particle Type" and "Particle Identifier", which have nothing to do with each other. The first property describes the chemical type of an atom while the second property is a numeric identifier, which is unique throughout a system. The particle type determines the display color of particles, while the particle identifier is a non-visual property, which is used by Ovito behind the scenes to track particles over time.

My suspicion is that there might be problem with the particle types. Note that Ovito encodes the chemical types using numbers, e.g. Li=1, Ni=2, O=3. if this mapping differs in the two input files, a problem may arise when the datasets are merged into one.
« Last Edit: February 20, 2018, 03:06:14 PM by Alexander Stukowski »

Shamail

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Re: Combine Particle Set Modifier issue.
« Reply #4 on: February 21, 2018, 12:55:23 PM »
Sorry, for the confusion. Yes, the problem is actually with the Particle type, that is their chemical identity is being changed. I have attached the files.

Thanks

Alexander Stukowski

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Re: Combine Particle Set Modifier issue.
« Reply #5 on: February 22, 2018, 10:01:03 AM »
Thanks for sending the data files. Now it became clear what the issue is.

It turned out that the 'Combine particle sets' modifier in the current Ovito version is still too dumb to combine datasets with different atom types. I worked on the modifier code yesterday to make it smarter. Please download the latest development version of Ovito (3.0.0-dev123), which is able to merge datasets correctly that do not have the same set of particle types:

http://ovito.org/index.php/download

Let me know if you still experience any problems.

-Alex

Shamail

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Re: Combine Particle Set Modifier issue.
« Reply #6 on: February 22, 2018, 11:25:17 AM »
Thanks, Alex. Now it is working flawlessly.   :D

Big Thanks.