Author Topic: OVITO can't read my simulation output  (Read 50 times)

zmcdargh

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OVITO can't read my simulation output
« on: December 07, 2017, 11:33:10 PM »
I'm having trouble visualizing the output from some HOOMD-Blue simulations with Ovito. I keep finding the error "ERROR: GSD file I/O error: Number of elements in chunk 'particles/velocity' does not match expected value." This only happens when I try to view frames past the first frame. Also, the problem sometimes goes away on later frames, and sometimes returns again.

I'm not sure what this means, but I have a few guesses for what could be the source of the problem. Firstly, I have a few particles whose data is written to the output file, but that are not subject to the integrator. I thought this could lead to some strange properties, like maybe not having a defined velocity, but I've gotten other simulations with the same feature to work fine with Ovito.

I also thought it could have something to do with the fact that I'm creating and deleting particles throughout the simulation, but I've also gotten simulations with that feature to work with Ovito.

Is there some way I can get more information on what problem Ovito is having, to help me debug the problem?

Alexander Stukowski

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Re: OVITO can't read my simulation output
« Reply #1 on: December 08, 2017, 09:06:42 AM »
Hi,

The GSD/HOOMD file reader in OVITO is still a little rough around the edges and might not be prepared for all corner cases yet. To me that sounds like a bug in the GSD parsing routine, which needs to be sorted out.

I can try to do that. But first I need to understand where exactly the problem is. For that it would be very helpful if you send me one of the files that lead to the error as a test case. 

-Alex

zmcdargh

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Re: OVITO can't read my simulation output
« Reply #2 on: December 08, 2017, 03:59:18 PM »
Thanks a lot Alex. I've actually figured out the cause of the problem: it only occurs if I make a call to hoomd.run before a call to hoomd.dump.gsd. Would you still like an example of the code for which this occurs?

Alexander Stukowski

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Re: OVITO can't read my simulation output
« Reply #3 on: December 08, 2017, 04:04:26 PM »
I'm not a HOOMD user, so I cannot understand what your statement means. Does it mean that the problem is caused by HOOMD or your simulation control script? Or is there something we can change on the OVITO side to better deal which such data files? If the latter is the case, yes, please post an example file.

zmcdargh

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Re: OVITO can't read my simulation output
« Reply #4 on: December 08, 2017, 04:24:22 PM »
>I'm not a HOOMD user, so I cannot understand what your statement means. Does it mean that the problem is caused by HOOMD or your simulation control script? Or is there something we can change on the OVITO side to better deal which such data files?

Sorry about that. The problem was resolved by changing my hoomd script; since I'm new to MD simulations it's probably safe to say the error was on my end.