[FLASH-USERS] Plotting particle positions

[Joshua Wall]

Thanks everyone for the assistance. I'm currently working my way through
some of the suggestions, hopefully coming to a solution that works with my
current setup. I'll check back in with the group if I'm still stuck after a
few days of hashing through it.


Joshua Wall

Doctoral Candidate
Department of Physics
Drexel University

On Tue, Nov 18, 2014 at 1:43 PM, John ZuHone <jzuhone at space.mit.edu> wrote:

> This was my original message to Joshua, but I wasn’t able to get it
> through to FLASH-USERS until today. I’m including it for posterity.
>
> Hi Joshua,
>
> First, based on what you posted from the Config and flash.par, you should
> have the particles inside the checkpoint files and the particle files. The
> reason you’re having trouble finding the particles in the files is because
> the way they are stored is not quite as obvious as is the case with the
> grid-based variables.
>
> The particle data is stored in a HDF5 dataset called “tracer particles” at
> the top level of the HDF5 file. It is a two-dimensional array of
> double-precision floats in the shape of (number_of_particles,
> number_of_particle_attributes). The order of the attributes along that
> second axis can be found in the top-level dataset “particle names” in the
> same file.
>
> Because things are laid out in this way, I would recommend trying to look
> at the particle data in yt, as it knows a bit more about the structure of
> FLASH files than VisIt does.
>
> To load up a checkpoint file in yt, you can do it like this (these
> instructions are assuming yt version 3.0 or higher):
>
> import yt
>
> ds = yt.load(“name_of_my_checkpoint_file”)
>
> Or, if you have a particle file that was dumped at the same time as a plot
> file, then you can do it this way:
>
> ds = yt.load(“name_of_my_plotfile”,
> particle_filename=“name_of_my_particle_file”)
>
> Then, you can look at the raw particle positions from the entire dataset
> by doing this:
>
> dd = ds.all_data()
> print dd[“particle_position_x”]
> print dd[“particle_position_y”]
> print dd[“particle_position_z”]
>
> or the velocities:
>
> print dd[“particle_velocity_x”]
> print dd[“particle_velocity_y”]
> print dd[“particle_velocity_z”]
>
> If you want to plot the positions, you can plot them over a slice of a
> grid variable such as “dens” like this:
>
> slc = yt.SlicePlot(ds, “z”, “dens”) # Sliced along the “z” axis through
> the center of the domain
> slc.annotate_particles(width) # for this you should replace width with the
> width of the slab you want
> slc.save()
>
> which will write a plot to disk.
>
> For more information, check out the yt docs: http://yt-project.org/doc
>
> Any other questions, don’t hesitate to write back.
>
> Best,
>
> John Z
>
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