[yt-users] FLASH particle trajectories

[John ZuHone]

Hi Ariadna,

I’ve since remembered that we can’t do particle trajectories when we load them with the plotfiles, but we have two open pull requests that will resolve this problem:

https://bitbucket.org/yt_analysis/yt/pull-requests/2153/try-to-guess-and-load-particle-file-for/

https://bitbucket.org/yt_analysis/yt/pull-requests/2157/flashparticledataset/

The first resolves it by making sure we can grab the particle files with plot files, and the second resolves it by giving support within yt to FLASH particle files without the need for the plotfiles at all.

Once these are merged into the codebase, we’ll have better options for working with FLASH particle files for the particle trajectories analysis module. In the meantime, I would suggest continuing with load_particles and letting us know if you have trouble.

Best,

John 

> On May 2, 2016, at 7:33 PM, Ariadna Murguia <doggies012 at hotmail.com> wrote:
> 
> Dear John,
> If I did have the plot files (which I can make), do I just load them with the correspondent particle file?
> I'm also implementing the load_particles, and I think it is a great and helpful idea.
> Thank you very much,
> Ariadna
> 
> 
> De: yt-users <yt-users-bounces at lists.spacepope.org <mailto:yt-users-bounces at lists.spacepope.org>> en nombre de John Zuhone <jzuhone at gmail.com <mailto:jzuhone at gmail.com>>
> Enviado: lunes, 2 de mayo de 2016 11:58 a. m.
> Para: Discussion of the yt analysis package
> Asunto: Re: [yt-users] FLASH particle trajectories
>  
> Hi Ariadna,
> 
> The issue with this is that FLASH particle files do not carry the grid information with them, so yt cannot figure out where they should go on the grid (this is why checkpoint files work, because the particles and the grid metadata are in the same file) There are two solutions here:
> 
> 1. Does your simulation have a plot file written at the same time as every particle file? In that case we have ways of using the grid information from the plot file. 
> 
> 2. Alternatively, we can use yt’s “load_particles” functionality to load the particle fields into memory and then run the trajectory that way:
> 
> http://yt-project.org/docs/dev/examining/generic_particle_data.html?highlight=load_particles <http://yt-project.org/docs/dev/examining/generic_particle_data.html?highlight=load_particles>
> 
> Let us know if you have plot files at the same time as particle files, or if you need to use option 2, and we can provide some assistance. 
> 
> Best,
> 
> John
> 
>> On Apr 27, 2016, at 7:37 PM, Ariadna Murguia <doggies012 at hotmail.com <mailto:doggies012 at hotmail.com>> wrote:
>> 
>> Dear Nathan,
>> First, thank you very much for your help.
>> Here is an example of a checkpoint file and its correspondent particle file. I tried using Particle trajectories only on the particle file, but I get an error that yt cannot load the file (although it was provided). 
>> I'm trying to load it with particles instead (reading the positions and velocity with h5py), and trying to add all of the derived fields to an all_data() array. It works fine for most fields, but it is giving me an error for ('index', 'grid_indices'), ('index', 'grid_level')  and ('index', 'x'). Do you have any idea how to get around it?
>> Thank you very much,
>> Ariadna
>> 
>> 
>> De: yt-users <yt-users-bounces at lists.spacepope.org <mailto:yt-users-bounces at lists.spacepope.org>> en nombre de Nathan Goldbaum <nathan12343 at gmail.com <mailto:nathan12343 at gmail.com>>
>> Enviado: miércoles, 27 de abril de 2016 11:41 a. m.
>> Para: Discussion of the yt analysis package
>> Asunto: Re: [yt-users] FLASH particle trajectories
>>  
>> Yes, I think that should work. I don't have any datasets that look like yours to check with though.
>> 
>> On Tue, Apr 26, 2016 at 6:12 PM, Ariadna Murguia <doggies012 at hotmail.com <mailto:doggies012 at hotmail.com>> wrote:
>> Dear yt-users,
>> I'm trying to plot some particle trajectories taken from a FLASH simulation that has particle files. The number of particle files is greater than the checkpoint files. I was wondering if I could use a similar recipe to the yt documentation for particle trajectories but loading data from the particle files instead of using the checkpoints so I have more trajectory points.
>> Thank you very much!
>> Ariadna
>> 
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