Author Topic: GSD File Format Type Issues  (Read 2485 times)

bvansade

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GSD File Format Type Issues
« on: January 20, 2017, 09:08:46 PM »
Hi!

I'm trying to switch over to OVITO being my main visualization tool. I'm working with HOOMD-Blue, so the recent(ish) addition of a GSD file reader is really great. However I have an issue when trying to visualize simulations with more than one particle type. For the first frame, things look ok, but all subsequent frames have all particles as type 0. Am I missing something simple, or is this a bug with the way OVITO interprets the static fields of the GSD format?

Thanks

Alexander Stukowski

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Re: GSD File Format Type Issues
« Reply #1 on: January 27, 2017, 09:09:59 AM »
Hi,
I just want to leave a short notice here that I am currently traveling and I will look into this issue as soon as possible.
In the meantime: If you have a small example GSD file to demonstrate/reproduce this issue, it would be great.

bvansade

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Re: GSD File Format Type Issues
« Reply #2 on: January 27, 2017, 08:33:14 PM »
Hi,
Thanks for the reply. I've attached a small gsd file that shows what I'm referring to. On the first frame I can use expression select to pick type index 0, or 1. On subsequent frames, expression selecting for type index 1 gets me no particles. I see this using version 2.8.1

Alexander Stukowski

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Re: GSD File Format Type Issues
« Reply #3 on: January 29, 2017, 02:22:30 PM »
I have fixed the loading of GSD files now. Please check out the newest development version available here.

Loading of GSD files with static data like the particle types was not correctly implemented, mainly because I didn't have appropriate test data available. Thanks for providing a file. Let me know if you notice any remaining problems with the new program version.

bvansade

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Re: GSD File Format Type Issues
« Reply #4 on: February 01, 2017, 06:46:08 PM »
Thanks. The dev version is interpreting the types like I want. I'll let you know if I find anything else. Also, if you ever want to test gsd/hoomd related features I can always supply you with files

ehsan

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Re: GSD File Format Type Issues
« Reply #5 on: February 22, 2017, 06:53:01 PM »
Hi,

Nice job for implementing the GSD reader and also fixing the bug that bvansade mentioned.

However, there is another issue that I would like to point out. If you add a new particle to you system during the simulation (and dump new frames to the gsd file), ovito doesn't show it! Do you have any idea what is the origin of the problem?

Thanks

Alexander Stukowski

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Re: GSD File Format Type Issues
« Reply #6 on: February 23, 2017, 07:19:38 AM »
Maybe the GSD file reader still isn't fully confirming to the standard in this regard.

I couldn't test the aspect of changing particle numbers so far, because we don't use hoomd in our group (yet). Thus, a test file would be super helpful, maybe you have one for me. Thanks.