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<p>Dear John,</p>
<p>Thank you very much for your help.</p>
<p>Best,</p>
<p>Ariadna</p>
<br>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>De:</b> yt-users <yt-users-bounces@lists.spacepope.org> en nombre de John ZuHone <jzuhone@gmail.com><br>
<b>Enviado:</b> lunes, 2 de mayo de 2016 10:47 p. m.<br>
<b>Para:</b> Discussion of the yt analysis package<br>
<b>Asunto:</b> Re: [yt-users] FLASH particle trajectories</font>
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<div>Hi Ariadna,
<div class=""><br class="">
</div>
<div class="">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:</div>
<div class=""><br class="">
</div>
<div class=""><a href="https://bitbucket.org/yt_analysis/yt/pull-requests/2153/try-to-guess-and-load-particle-file-for/" class="" id="LPlnk889140">https://bitbucket.org/yt_analysis/yt/pull-requests/2153/try-to-guess-and-load-particle-file-for/</a></div>
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<a id="LPImageAnchor_14622473451570.09451985079795122" href="https://bitbucket.org/yt_analysis/yt/pull-requests/2153/try-to-guess-and-load-particle-file-for/" target="_blank" style="display: table-cell; text-align: center;"><img aria-label="Imagen de vista previa con vínculo seleccionado. Pulse dos veces para abrir el vínculo." style="display: inline-block; margin-left: auto; margin-right: auto; max-width: 250px; max-height: 250px; height: 35px; width: 35px; border-width: 0px; vertical-align: bottom;" width="35" height="35" src="https://bitbucket.org/yt_analysis/yt/avatar/xxxlarge/?ts=1462235122"></a></div>
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<a id="LPUrlAnchor_14622473451590.8638233221136034" href="https://bitbucket.org/yt_analysis/yt/pull-requests/2153/try-to-guess-and-load-particle-file-for/" target="_blank" style="text-decoration: none;">Try to guess and load particle file for FLASH dataset.
Closes #1179</a></div>
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bitbucket.org</div>
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### * Try to guess and load particle file for FLASH dataset ### Assuming the loaded file is a plot file with "plt_cnt" in the filename, we can replace the "plt_cnt" by "part" to get the particle filename. ### * Check if the particle file has the same time as
the plot file ### Based on the suggestions by @joshuawall in issue [#1179](https://bitbucket.org/yt_analysis/yt/issues/1179/)</div>
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<div class=""><a href="https://bitbucket.org/yt_analysis/yt/pull-requests/2157/flashparticledataset/" class="" title="https://bitbucket.org/yt_analysis/yt/pull-requests/2157/flashparticledataset/
Cmd+Haga clic o pulse para seguir el vínculo">https://bitbucket.org/yt_analysis/yt/pull-requests/2157/flashparticledataset/</a></div>
<div class=""><br class="">
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<div class="">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.</div>
<div class=""><br class="">
</div>
<div class="">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.</div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class=""><br class="">
</div>
<div class="">John </div>
<div class=""><br class="">
<div>
<blockquote type="cite" class="">
<div class="">On May 2, 2016, at 7:33 PM, Ariadna Murguia <<a href="mailto:doggies012@hotmail.com" class="">doggies012@hotmail.com</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
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<div class="" style="margin-top:0px; margin-bottom:0px">Dear John,</div>
<div class="" style="margin-top:0px; margin-bottom:0px">If I did have the plot files (which I can make), do I just load them with the correspondent particle file?</div>
<div class="" style="margin-top:0px; margin-bottom:0px">I'm also implementing the load_particles, and I think it is a great and helpful idea.</div>
<div class="" style="margin-top:0px; margin-bottom:0px">Thank you very much,</div>
<div class="" style="margin-top:0px; margin-bottom:0px">Ariadna</div>
<p class="" style="margin-top:0px; margin-bottom:0px"></p>
<br class="">
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<div id="divRplyFwdMsg" dir="ltr" class=""><font face="Calibri, sans-serif" class="" style="font-size:11pt"><b class="">De:</b><span class="Apple-converted-space"> </span>yt-users <<a href="mailto:yt-users-bounces@lists.spacepope.org" class="">yt-users-bounces@lists.spacepope.org</a>>
en nombre de John Zuhone <<a href="mailto:jzuhone@gmail.com" class="">jzuhone@gmail.com</a>><br class="">
<b class="">Enviado:</b><span class="Apple-converted-space"> </span>lunes, 2 de mayo de 2016 11:58 a. m.<br class="">
<b class="">Para:</b><span class="Apple-converted-space"> </span>Discussion of the yt analysis package<br class="">
<b class="">Asunto:</b><span class="Apple-converted-space"> </span>Re: [yt-users] FLASH particle trajectories</font>
<div class=""> </div>
</div>
<div class="">Hi Ariadna,
<div class=""><br class="">
</div>
<div class="">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:</div>
<div class=""><br class="">
</div>
<div class="">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. </div>
<div class=""><br class="">
</div>
<div class="">2. Alternatively, we can use yt’s “load_particles” functionality to load the particle fields into memory and then run the trajectory that way:</div>
<div class=""><br class="">
</div>
<div class=""><a href="http://yt-project.org/docs/dev/examining/generic_particle_data.html?highlight=load_particles" class="" id="LPlnk798285">http://yt-project.org/docs/dev/examining/generic_particle_data.html?highlight=load_particles</a></div>
<div class=""><br class="">
</div>
<div class="">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. </div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class=""><br class="">
</div>
<div class="">John</div>
<div class=""><br class="">
<div class="">
<blockquote type="cite" class="">
<div class="">On Apr 27, 2016, at 7:37 PM, Ariadna Murguia <<a href="mailto:doggies012@hotmail.com" class="">doggies012@hotmail.com</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div id="divtagdefaultwrapper" class="" style="font-style:normal; font-weight:normal; letter-spacing:normal; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; word-spacing:0px; font-size:12pt; background-color:rgb(255,255,255); font-family:Calibri,Arial,Helvetica,sans-serif">
<div class="" style="margin-top:0px; margin-bottom:0px">Dear Nathan,</div>
<div class="" style="margin-top:0px; margin-bottom:0px">First, thank you very much for your help.</div>
<div class="" style="font-family:Calibri,Arial,Helvetica,sans-serif">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). </div>
<div class="" style="font-family:Calibri,Arial,Helvetica,sans-serif">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?</div>
<div class="" style="font-family:Calibri,Arial,Helvetica,sans-serif">Thank you very much,</div>
<div class="" style="font-family:Calibri,Arial,Helvetica,sans-serif">Ariadna</div>
<br class="">
<br class="">
<div class="">
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<div id="divRplyFwdMsg" dir="ltr" class=""><font face="Calibri, sans-serif" class="" style="font-size:11pt"><b class="">De:</b><span class="Apple-converted-space"> </span>yt-users <<a href="mailto:yt-users-bounces@lists.spacepope.org" class="">yt-users-bounces@lists.spacepope.org</a>>
en nombre de Nathan Goldbaum <<a href="mailto:nathan12343@gmail.com" class="">nathan12343@gmail.com</a>><br class="">
<b class="">Enviado:</b><span class="Apple-converted-space"> </span>miércoles, 27 de abril de 2016 11:41 a. m.<br class="">
<b class="">Para:</b><span class="Apple-converted-space"> </span>Discussion of the yt analysis package<br class="">
<b class="">Asunto:</b><span class="Apple-converted-space"> </span>Re: [yt-users] FLASH particle trajectories</font>
<div class=""> </div>
</div>
<div class="">
<div dir="ltr" class="">Yes, I think that should work. I don't have any datasets that look like yours to check with though.</div>
<div class="gmail_extra"><br class="">
<div class="gmail_quote">On Tue, Apr 26, 2016 at 6:12 PM, Ariadna Murguia<span class="Apple-converted-space"> </span><span dir="ltr" class=""><<a href="mailto:doggies012@hotmail.com" target="_blank" class="">doggies012@hotmail.com</a>></span><span class="Apple-converted-space"> </span>wrote:<br class="">
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<div class="" style="margin-top:0px; margin-bottom:0px">Dear yt-users,</div>
<div class="" style="margin-top:0px; margin-bottom:0px">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.</div>
<div class="" style="margin-top:0px; margin-bottom:0px">Thank you very much!</div>
<span class="HOEnZb"><font color="#888888" class="">
<div class="" style="margin-top:0px; margin-bottom:0px">Ariadna</div>
</font></span></div>
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