<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body style="overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;">Hi Jordi, <div><br></div><div>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. </div><div><br></div><div>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. </div><div><br></div><div>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. </div><div><br></div><div>Alternatively, we could reconstruct a FLASH3-like particle structure for you, but if you have a lot of files this may not be ideal. </div><div><br></div><div>Best,</div><div><br></div><div>John ZuHone<br id="lineBreakAtBeginningOfMessage"><div><br><blockquote type="cite"><div>On Aug 14, 2024, at 1:17 PM, Casanova, Jordi <jcasanova@regis.edu> wrote:</div><br class="Apple-interchange-newline"><div><meta charset="UTF-8"><div class="WordSection1" style="page: WordSection1; caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><div style="margin: 0cm; font-size: 11pt; font-family: Aptos, sans-serif;"><span style="font-size: 12pt;"><o:p> </o:p></span></div><div style="margin: 0cm; font-size: 11pt; font-family: Aptos, sans-serif;"><span style="font-size: 14pt; font-family: "Segoe UI", sans-serif; color: rgb(33, 37, 41); background: white;">Hello<span class="Apple-converted-space"> </span></span><span lang="ES" style="font-size: 14pt; font-family: "Segoe UI", sans-serif; color: rgb(33, 37, 41); background: white;">flash users</span><span style="font-size: 14pt; font-family: "Segoe UI", sans-serif; color: rgb(33, 37, 41); background: white;">!</span><span lang="ES" style="font-size: 14pt; font-family: "Segoe UI", sans-serif; color: rgb(33, 37, 41); background: white;"><o:p></o:p></span></div><div style="margin: 0cm; font-size: 11pt; font-family: Aptos, sans-serif;"><span lang="ES" style="font-size: 14pt; font-family: "Segoe UI", sans-serif; color: rgb(33, 37, 41); background: white;"><o:p> </o:p></span></div><div style="margin: 0cm; font-size: 11pt; font-family: Aptos, sans-serif;"><span style="font-size: 14pt; font-family: "Segoe UI", sans-serif; color: rgb(33, 37, 41); 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: 14pt; font-family: "Segoe UI", sans-serif; color: rgb(33, 37, 41); 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: 14pt; font-family: "Segoe UI", sans-serif; color: rgb(33, 37, 41); background: white;">am not able to load<span class="Apple-converted-space"> </span></span><span lang="EN-US" style="font-size: 14pt; font-family: "Segoe UI", sans-serif; color: rgb(33, 37, 41); background: white;">these FLASH2.5 files with yt</span><span style="font-size: 14pt; font-family: "Segoe UI", sans-serif; color: rgb(33, 37, 41); background: white;">.<span class="Apple-converted-space"> </span></span><span lang="EN-US" style="font-size: 14pt; font-family: "Segoe UI", sans-serif; color: rgb(33, 37, 41); background: white;">Below I am attaching the traceback with the error. Does anyone know what the problem might be? Thank you!<o:p></o:p></span></div><div style="margin: 0cm; font-size: 11pt; font-family: Aptos, sans-serif;"><span lang="EN-US" style="font-size: 14pt; font-family: "Segoe UI", sans-serif; color: rgb(33, 37, 41); background: white;"><o:p> </o:p></span></div><div style="margin: 0cm; font-size: 11pt; font-family: Aptos, sans-serif;"><span lang="EN-US" style="font-size: 14pt; font-family: "Segoe UI", sans-serif; color: rgb(33, 37, 41); background: white;"><o:p> </o:p></span></div><div style="margin: 0cm; font-size: 8.5pt; font-family: Menlo;"><span class="s1">yt : [INFO<span class="Apple-converted-space"> </span></span><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">] 2024-08-14 11:03:29,105 Particle file found: test_hdf5_chk_2396</span><o:p></o:p></div><div style="margin: 0cm; font-size: 8.5pt; font-family: Menlo;"><o:p> </o:p></div><div style="margin: 0cm; font-size: 8.5pt; font-family: Menlo;"><o:p> </o:p></div><div style="margin: 0cm; font-size: 8.5pt; font-family: Menlo;"><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">---------------------------------------------------------------------------</span><o:p></o:p></div><div style="margin: 0cm; font-size: 8.5pt; font-family: Menlo;"><o:p> </o:p></div><div style="margin: 0cm; font-size: 8.5pt; font-family: Menlo;"><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">TypeError<span class="Apple-converted-space"> </span></span><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">Traceback (most recent call last)</span><o:p></o:p></div><div style="margin: 0cm; font-size: 8.5pt; font-family: Menlo;"><o:p> </o:p></div><div style="margin: 0cm; font-size: 8.5pt; font-family: Menlo;"><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">Cell In[1], line 2</span><o:p></o:p></div><div style="margin: 0cm; font-size: 8.5pt; font-family: Menlo;"><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">1 import yt</span><o:p></o:p></div><div style="margin: 0cm; font-size: 8.5pt; font-family: Menlo;"><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">----> 2 ds=yt.load("/Users/novita/Desktop/test_hdf5_chk_2396")</span><o:p></o:p></div><div style="margin: 0cm; font-size: 8.5pt; font-family: Menlo;"><o:p> </o:p></div><div style="margin: 0cm; font-size: 8.5pt; font-family: Menlo;"><o:p> </o:p></div><div style="margin: 0cm; font-size: 8.5pt; font-family: Menlo;"><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">File ~/Library/Python/3.12/lib/python/site-packages/yt/_maintenance/deprecation.py:69, in future_positional_only.<locals>.outer.<locals>.inner(*args, **kwargs)</span><o:p></o:p></div><div style="margin: 0cm; font-size: 8.5pt; font-family: Menlo;"><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">60<span class="Apple-converted-space"> </span></span><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">value = kwargs[name]</span><o:p></o:p></div><div style="margin: 0cm; font-size: 8.5pt; font-family: Menlo;"><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">61<span class="Apple-converted-space"> </span></span><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">issue_deprecation_warning(</span><o:p></o:p></div><div style="margin: 0cm; font-size: 8.5pt; font-family: Menlo;"><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">62<span class="Apple-converted-space"> </span></span><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">f"Using the {name!r} argument as keyword (on position {no}) "</span><o:p></o:p></div><div style="margin: 0cm; font-size: 8.5pt; font-family: Menlo;"><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">63<span class="Apple-converted-space"> </span></span><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">"is deprecated. "</span><o:p></o:p></div><div style="margin: 0cm; font-size: 8.5pt; font-family: Menlo;"><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">(...)</span><o:p></o:p></div><div style="margin: 0cm; font-size: 8.5pt; font-family: Menlo;"><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">67<span class="Apple-converted-space"> </span></span><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">**depr_kwargs,</span><o:p></o:p></div><div style="margin: 0cm; font-size: 8.5pt; font-family: Menlo;"><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">68<span class="Apple-converted-space"> </span></span><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">)</span><o:p></o:p></div><div style="margin: 0cm; font-size: 8.5pt; font-family: Menlo;"><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">---> 69 return func(*args, **kwargs)</span><o:p></o:p></div><div style="margin: 0cm; font-size: 8.5pt; font-family: Menlo;"><o:p> </o:p></div><div style="margin: 0cm; font-size: 8.5pt; font-family: Menlo;"><o:p> </o:p></div><div style="margin: 0cm; font-size: 8.5pt; font-family: Menlo;"><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">File ~/Library/Python/3.12/lib/python/site-packages/yt/loaders.py:144, in load(fn, hint, *args, **kwargs)</span><o:p></o:p></div><div style="margin: 0cm; font-size: 8.5pt; font-family: Menlo;"><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">136<span class="Apple-converted-space"> </span></span><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">if missing := cls._missing_load_requirements():</span><o:p></o:p></div><div style="margin: 0cm; font-size: 8.5pt; font-family: Menlo;"><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">137<span class="Apple-converted-space"> </span></span><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">warnings.warn(</span><o:p></o:p></div><div style="margin: 0cm; font-size: 8.5pt; font-family: Menlo;"><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">138<span class="Apple-converted-space"> </span></span><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">f"This dataset appears to be of type {cls.__name__}, "</span><o:p></o:p></div><div style="margin: 0cm; font-size: 8.5pt; font-family: Menlo;"><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">139<span class="Apple-converted-space"> </span></span><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">"but the following requirements are currently missing: "</span><o:p></o:p></div><div style="margin: 0cm; font-size: 8.5pt; font-family: Menlo;"><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">(...)</span><o:p></o:p></div><div style="margin: 0cm; font-size: 8.5pt; font-family: Menlo;"><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">142<span class="Apple-converted-space"> </span></span><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">stacklevel=3,</span><o:p></o:p></div><div style="margin: 0cm; font-size: 8.5pt; font-family: Menlo;"><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">143<span class="Apple-converted-space"> </span></span><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">)</span><o:p></o:p></div><div style="margin: 0cm; font-size: 8.5pt; font-family: Menlo;"><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">--> 144<span class="Apple-converted-space"> </span></span><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">return cls(fn, *args, **kwargs)</span><o:p></o:p></div><div style="margin: 0cm; font-size: 8.5pt; font-family: Menlo;"><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">146 if len(candidates) > 1:</span><o:p></o:p></div><div style="margin: 0cm; font-size: 8.5pt; font-family: Menlo;"><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">147<span class="Apple-converted-space"> </span></span><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">raise YTAmbiguousDataType(_input_fn, candidates)</span><o:p></o:p></div><div style="margin: 0cm; font-size: 8.5pt; font-family: Menlo;"><o:p> </o:p></div><div style="margin: 0cm; font-size: 8.5pt; font-family: Menlo;"><o:p> </o:p></div><div style="margin: 0cm; font-size: 8.5pt; font-family: Menlo;"><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">File ~/Library/Python/3.12/lib/python/site-packages/yt/frontends/flash/data_structures.py:206, in FLASHDataset.__init__(self, filename, dataset_type, storage_filename, particle_filename, units_override, unit_system, default_species_fields)</span><o:p></o:p></div><div style="margin: 0cm; font-size: 8.5pt; font-family: Menlo;"><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">204 # Check if the particle file has the same time</span><o:p></o:p></div><div style="margin: 0cm; font-size: 8.5pt; font-family: Menlo;"><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">205 if self._particle_handle != self._handle:</span><o:p></o:p></div><div style="margin: 0cm; font-size: 8.5pt; font-family: Menlo;"><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">--> 206<span class="Apple-converted-space"> </span></span><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">part_time = self._particle_handle.handle.get("real scalars")[0][1]</span><o:p></o:p></div><div style="margin: 0cm; font-size: 8.5pt; font-family: Menlo;"><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">207<span class="Apple-converted-space"> </span></span><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">plot_time = self._handle.handle.get("real scalars")[0][1]</span><o:p></o:p></div><div style="margin: 0cm; font-size: 8.5pt; font-family: Menlo;"><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">208<span class="Apple-converted-space"> </span></span><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">if not np.isclose(part_time, plot_time):</span><o:p></o:p></div><div style="margin: 0cm; font-size: 8.5pt; font-family: Menlo;"><o:p> </o:p></div><div style="margin: 0cm; font-size: 8.5pt; font-family: Menlo;"><o:p> </o:p></div><div style="margin: 0cm; font-size: 8.5pt; font-family: Menlo;"><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">TypeError: 'NoneType' object is not subscriptable</span><span lang="ES"><o:p></o:p></span></div></div><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;">_______________________________________________</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;">flash-users mailing list</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;">https://flash.rochester.edu/mailman/listinfo/flash-users</a></div></blockquote></div><br></div></body></html>