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<p class="MsoNormal"><span lang="ES" style="font-size:14.0pt">Hi John,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="ES" style="font-size:14.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:14.0pt">Thank you for your response. I don’t need particle data in these files, so I am guessing that ignoring them might be a good solution. Do you have any guess on how to do that?<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:14.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:14.0pt">Best regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:14.0pt">Jordi<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><b><span style="color:black">From:
</span></b><span style="color:black">John Zuhone <jzuhone@gmail.com><br>
<b>Date: </b>Wednesday, 14 August 2024, 18:26<br>
<b>To: </b>Casanova, Jordi <jcasanova@regis.edu><br>
<b>Cc: </b>flash-users@flash.rochester.edu <flash-users@flash.rochester.edu><br>
<b>Subject: </b>Re: [FLASH-USERS] Loading FLASH2.5 files problem with yt<o:p></o:p></span></p>
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<p class="MsoNormal">Another option is that if you do not care at all about the particle data in this or other files we could find a way to ignore them.<o:p></o:p></p>
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<o:p></o:p></p>
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<p class="MsoNormal">On Aug 14, 2024, at 1:23<span style="font-family:"Arial",sans-serif"> </span>PM, John Zuhone <jzuhone@gmail.com> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Hi Jordi, <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">The problem here is that the particle structure in the HDF5 file for versions of FLASH less than 3 is very different than versions >= 3. <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">The structure in FLASH3 and later is much simpler, it’s a simple 2D real array of number of particles x number of particle attributes. But in FLASH2 it’s a compound data structure. We never got around to supporting that in yt. <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">You could file an issue on the yt Github page with this error message and with the description I gave here so we don’t forget, not sure when we’d get a chance to address it. If we did address it, we’d need a copy of the file so that we
could formulate the fix and test it. <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Alternatively, we could reconstruct a FLASH3-like particle structure for you, but if you have a lot of files this may not be ideal. <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Best,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">John ZuHone<o:p></o:p></p>
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<p class="MsoNormal"><br>
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<o:p></o:p></p>
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<p class="MsoNormal">On Aug 14, 2024, at 1:17<span style="font-family:"Arial",sans-serif"> </span>PM, Casanova, Jordi <jcasanova@regis.edu> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"> <span style="font-size:11.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:14.0pt;font-family:"Segoe UI",sans-serif;color:#212529;background:white">Hello<span class="apple-converted-space"> </span></span><span lang="ES" style="font-size:14.0pt;font-family:"Segoe UI",sans-serif;color:#212529;background:white">flash
users</span><span style="font-size:14.0pt;font-family:"Segoe UI",sans-serif;color:#212529;background:white">!</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="ES" style="font-size:14.0pt;font-family:"Segoe UI",sans-serif;color:#212529;background:white"> </span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:14.0pt;font-family:"Segoe UI",sans-serif;color:#212529;background:white">I am using yt to analyze simulations performed with the latest version of FLASH4.7, and everything works fine. However, I<span class="apple-converted-space"> </span></span><span lang="EN-US" style="font-size:14.0pt;font-family:"Segoe UI",sans-serif;color:#212529;background:white">would
like to check out some old files performed with FLASH2.5. I<span class="apple-converted-space"> </span></span><span style="font-size:14.0pt;font-family:"Segoe UI",sans-serif;color:#212529;background:white">am not able to load<span class="apple-converted-space"> </span></span><span lang="EN-US" style="font-size:14.0pt;font-family:"Segoe UI",sans-serif;color:#212529;background:white">these
FLASH2.5 files with yt</span><span style="font-size:14.0pt;font-family:"Segoe UI",sans-serif;color:#212529;background:white">.<span class="apple-converted-space"> </span></span><span lang="EN-US" style="font-size:14.0pt;font-family:"Segoe UI",sans-serif;color:#212529;background:white">Below
I am attaching the traceback with the error. Does anyone know what the problem might be? Thank you!</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:14.0pt;font-family:"Segoe UI",sans-serif;color:#212529;background:white"> </span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:14.0pt;font-family:"Segoe UI",sans-serif;color:#212529;background:white"> </span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">yt : [INFO</span></span><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo"> </span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">]
2024-08-14 11:03:29,105 Particle file found: test_hdf5_chk_2396</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo"> </span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">---------------------------------------------------------------------------</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo"> </span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">TypeError</span></span><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo">
</span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">Traceback (most recent call last)</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo"> </span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">Cell In[1], line 2</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo"> </span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">1 import yt</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo"> </span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">----> 2 ds=yt.load("/Users/novita/Desktop/test_hdf5_chk_2396")</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo"> </span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">File ~/Library/Python/3.12/lib/python/site-packages/yt/_maintenance/<a href="https://linkprotect.cudasvc.com/url?a=https%3a%2f%2fdeprecation.py%3a69&c=E,1,-Z3illELaXQsiVLZDYTF6eFoa3B-L9NyvEP8nHMDhZ_5LeErt7dMUq9e2zUmdKjuFaj0XI7WmY7cum3HZw0F9B3jpOvcFwmwJSP2umH01R45GnyD&typo=1&ancr_add=1">deprecation.py:69</a>,
in future_positional_only.<locals>.outer.<locals>.inner(*args, **kwargs)</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo"> </span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">60</span></span><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo">
</span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">value = kwargs[name]</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo"> </span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">61</span></span><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo">
</span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">issue_deprecation_warning(</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo"> </span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">62</span></span><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo">
</span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">f"Using the {name!r} argument as keyword (on position {no}) "</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo"> </span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">63</span></span><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo">
</span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">"is deprecated. "</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo"> </span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">(...)</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo"> </span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">67</span></span><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo">
</span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">**depr_kwargs,</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo"> </span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">68</span></span><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo">
</span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">)</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo"> </span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">---> 69 return func(*args, **kwargs)</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo"> </span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">File ~/Library/Python/3.12/lib/python/site-packages/yt/<a href="https://linkprotect.cudasvc.com/url?a=https%3a%2f%2floaders.py%3a144&c=E,1,rZ00vrsk9zhqLaP5AYsakqkhNPYNof6PazciT12owMNo--I47XXBAm2UCEyyFjdZpViLuBxMwvjozDQybzKGr4YphL_BpasuaBYbk6BsvxZExZdkjprm&typo=1&ancr_add=1">loaders.py:144</a>,
in load(fn, hint, *args, **kwargs)</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo"> </span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">136</span></span><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo">
</span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">if missing := cls._missing_load_requirements():</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo"> </span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">137</span></span><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo">
</span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">warnings.warn(</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo"> </span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">138</span></span><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo">
</span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">f"This dataset appears to be of type {cls.__name__}, "</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo"> </span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">139</span></span><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo">
</span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">"but the following requirements are currently missing: "</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo"> </span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">(...)</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo"> </span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">142</span></span><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo">
</span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">stacklevel=3,</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo"> </span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">143</span></span><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo">
</span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">)</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo"> </span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">--> 144</span></span><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo">
</span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">return cls(fn, *args, **kwargs)</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo"> </span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">146 if len(candidates) > 1:</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo"> </span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">147</span></span><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo">
</span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">raise YTAmbiguousDataType(_input_fn, candidates)</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo"> </span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">File ~/Library/Python/3.12/lib/python/site-packages/yt/frontends/flash/<a href="https://linkprotect.cudasvc.com/url?a=https%3a%2f%2fdata_structures.py%3a206&c=E,1,D00Ro1fV0bYQ58DvnC8nKGC5-TLDWU_dzuGsAdsbJAhs5Vy-nwNh9k9AUebww8i1GZH-Z4jsQOkIYTMHZ_9c7CecxeUxVewsU57nlx_bUI0c0o74wwWOpT95GfhI&typo=1&ancr_add=1">data_structures.py:206</a>,
in FLASHDataset.__init__(self, filename, dataset_type, storage_filename, particle_filename, units_override, unit_system, default_species_fields)</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo"> </span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">204 # Check if the particle file has the same time</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo"> </span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">205 if self._particle_handle != self._handle:</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo"> </span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">--> 206</span></span><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo">
</span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">part_time = self._particle_handle.handle.get("real scalars")[0][1]</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo"> </span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">207</span></span><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo">
</span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">plot_time = self._handle.handle.get("real scalars")[0][1]</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo"> </span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">208</span></span><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo">
</span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">if not np.isclose(part_time, plot_time):</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo"> </span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">TypeError: 'NoneType' object is not subscriptable</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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