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Polyhedra Visualization

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Greetings,

Firstly, I love the software and have been changing most of my code outputs from VMD to Ovito as it handles changing atom trajectory files and 5th, 6th etc column data (with a continuous spectrum) colouring so much better.

I'm querying about the possibility of putting in a 'Polyhedra' visualization feature.

For course grained simulations and even visualization of multi-element glasses for example, this can be handy.  For my work developing a course grained MD code (https://research.csiro.au/mmm/snap/), I currently output the centre of mass and orientation to POVRAY and with a model in POVRAY, make the animation.  It's a long and painful process.   I almost managed to get a much faster solution in VMD using their 'Polyhedra' feature but it didn't allow for atom selection and the nanoparticles would get rendered joined together as their atoms came within their defining cutoff.  Labelling the atoms in the nanoparticles as different elements should of been a logical way out of this but this was never implemented in VMD (I tried mailing a few years back).

The surface mesh feature might even be able to do it possibly if it can be kept separate to each nanoparticle.

Ovito is a much more MD friendly code to use and if that visualization was in there, that would be great.  I understand that this might not be a simple undertaking but thought I'd put it out there as food for thought.

Appreciate your work.

 

 

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Hi George,

Thank you for the positive feedback on Ovito.

Can you please specify a bit more precisely what you mean with a 'Polyhedra visualization feature'? Does each polyhedron represent an individual particle? Or do the polyhedra connect neighboring particles in the sense of 'coordination polyhedra'?

Note that Ovito already supports visualization of particles with user-defined shapes. I added this capability just a few weeks ago to the development version of Ovito 3.0.0. It allows you to set the shape of a particle type to be any geometry loaded from an STL, OBJ or VTK file. See the attached screenshot. Maybe this is already the program feature you have been asking for.

-Alex

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Thank you for the prompt feedback.

The implementation of the STL, OBJ and VTK files should be ideal along with the orientation input information.  I'll let you know how it goes.

UPDATE:  Might of found an issue.  When I try to import an XYZ file for the dev 3.0 version, the particle properties drop down menu is missing.  If I start typing in the property, its auto-completes it but I'm sure a drop down menu should exist there.

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Appreciate the original tip.

Using .obj files for the vertex models along with the quaternion orientation works great for visualizing nanoparticles.

 

 

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Nice! This looks great.

George,

Thanks for pointing out the UI issue related to the drop-down boxes in the file column table. This issue should be fixed in the latest dev build 475 of Ovito.

-Alex

Quote from Alexander Stukowski on September 2, 2019, 8:53 pm

George,

Thanks for pointing out the UI issue related to the drop-down boxes in the file column table. This issue should be fixed in the latest dev build 475 of Ovito.

-Alex

Hi Alex,

I'm working from 3.0.0-dev507 and have found something with the object visualization.

When I load in an XYZ movie (only 10 frames for testing) and I 'Load shape...', it works just fine for a single frame.

However if I move the slider over to the next frame, the object information is lost immediately (including if I move it back to the first frame where I loaded it) and I have to Load Shape again.

I would be good if Ovito retained that loaded shape information over all the frames.

Thanks!

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Hi George,

Thanks for making me aware of this. It's indeed a small bug that slipped into the program recently when I extended the GSD file reader to directly load particle mesh shapes from an input file. I fixed the bug and made sure now that manually assigned shapes are not lust during animation frame reloads.

An updated build of OVITO should be available in 1-2 hours.

-Alex

Thanks!  Works great!  The points are overlayed points of force intereaction on the surfaces.

Just curious if there is a way to colour individual facets in an .OBJ file I'm reading in for my representation?

 

 

 

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Hi,

This looks cool.

No, all mesh color information from the .OBJ file is currently overwritten by the per-particle or per-type color information. I'll see if I can add a user option that gives precedence to the mesh color information.

In your video, note that you can turn off the rendering of the simulation cell(s). This makes sense in particular if the cell is automatically computed as a bounding box of the particle coordinates loaded from an XYZ file.

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