<div dir="ltr"><div>Hi John & Nathan,<br><br></div><div>Yes, I'm having trouble using the time series analysis machinery with my FLASH simulations. I've checked that the plot files and particle files all have the same current_time variable, so there's no issue there. I'm using a development version of yt with a changeset ID of 5cf30893afdf. This changeset includes Nathan's changes supporting cut_region functionality for FLASH plot files. Here's what I see when I try to do a time series analysis:<br><br>###########################<br><br>In [9]: ts = yt.load("mysim_hdf5_plt_cnt_*",<br> particle_filename="mysim_hdf5_part_*")<br><br>In [10]: for ds in ts:<br> print ds.current_time<br> ....: <br>---------------------------------------------------------------------------<br>IOError Traceback (most recent call last)<br><ipython-input-10-fccd01bb5065> in <module>()<br>----> 1 for ds in ts:<br> 2 print ds.current_time<br> 3 <br><br>/home/emrys/yt/yt/data_objects/time_series.pyc in __iter__(self)<br> 179 for o in self._pre_outputs:<br> 180 if isinstance(o, string_types):<br>--> 181 ds = self._load(o, **self.kwargs)<br> 182 self._setup_function(ds)<br> 183 yield ds<br><br>/home/emrys/yt/yt/data_objects/time_series.pyc in _load(self, output_fn, **kwargs)<br> 396 elif self._mixed_dataset_types:<br> 397 return load(output_fn, **kwargs)<br>--> 398 ds = load(output_fn, **kwargs)<br> 399 self._dataset_cls = ds.__class__<br> 400 return ds<br><br>/home/emrys/yt/yt/convenience.pyc in load(*args, **kwargs)<br> 84 candidates = find_lowest_subclasses(candidates)<br> 85 if len(candidates) == 1:<br>---> 86 return candidates[0](*args, **kwargs)<br> 87 if len(candidates) == 0:<br> 88 if ytcfg.get("yt", "enzo_db") != '' \<br><br>/home/emrys/yt/yt/frontends/flash/data_structures.pyc in __init__(self, filename, dataset_type, storage_filename, particle_filename, units_override, unit_system)<br> 209 self._particle_handle = HDF5FileHandler(self.particle_filename)<br> 210 except:<br>--> 211 raise IOError(self.particle_filename)<br> 212 # Check if the particle file has the same time<br> 213 if self._particle_handle != self._handle:<br><br>IOError: mysim_hdf5_part_*<br><br></div><div>###########################<br><br></div><div>It looks to me like HDF5FileHandler() just does not like the wildcard. I've also tried, unsuccessfully, to feed a list of particle files to yt.load(). I thought perhaps that I should be using the DatasetSeries framework directly, but I'm not clear on how to pass in the list of particle files, as DatasetSeries does not understand the particle_filename keyword argument.<br></div><div><div><div class="gmail_extra"><br></div><div class="gmail_extra">Any ideas?<br><br></div><div class="gmail_extra">Thanks,<br></div><div class="gmail_extra">Jason<br><br></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Nov 30, 2016 at 1:57 PM, <span dir="ltr"><<a href="mailto:yt-users-request@lists.spacepope.org" target="_blank">yt-users-request@lists.spacepope.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Send yt-users mailing list submissions to<br>
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<br>Today's Topics:<br>
<br>
1. FLASH Time Series Analysis with Particle Files (Jason Galyardt)<br>
2. Re: FLASH Time Series Analysis with Particle Files<br>
(Nathan Goldbaum)<br>
3. Re: FLASH Time Series Analysis with Particle Files (John Zuhone)<br>
<br><br>---------- Forwarded message ----------<br>From: Jason Galyardt <<a href="mailto:jason.galyardt@gmail.com">jason.galyardt@gmail.com</a>><br>To: Discussion of the yt analysis package <<a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a>><br>Cc: <br>Date: Wed, 30 Nov 2016 10:16:44 -0500<br>Subject: [yt-users] FLASH Time Series Analysis with Particle Files<br><div dir="ltr"><div><div><div><div><div><div><div>Dear yt-users,<br><br></div>In May 2015, there was some traffic on this list concerning errors in time series analysis on FLASH simulations that include both plot files and particle files. Does anyone have an update on the status of this issue?<br><br></div><div>Thanks,<br></div><div>Jason<br><br>------<br></div><div>Jason Galyardt<br></div><div>University of Georgia<br><br></div></div></div></div></div></div></div>
<br><br>---------- Forwarded message ----------<br>From: Nathan Goldbaum <<a href="mailto:nathan12343@gmail.com">nathan12343@gmail.com</a>><br>To: Discussion of the yt analysis package <<a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a>><br>Cc: <br>Date: Wed, 30 Nov 2016 09:32:37 -0600<br>Subject: Re: [yt-users] FLASH Time Series Analysis with Particle Files<br><div dir="ltr">Hi Jason,<div><br></div><div>As far as I'm aware this should be working now. Are you having trouble?</div><div><br></div><div>-Nathan</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Nov 30, 2016 at 9:16 AM, Jason Galyardt <span dir="ltr"><<a href="mailto:jason.galyardt@gmail.com" target="_blank">jason.galyardt@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div><div><div><div><div><div><div>Dear yt-users,<br><br></div>In May 2015, there was some traffic on this list concerning errors in time series analysis on FLASH simulations that include both plot files and particle files. Does anyone have an update on the status of this issue?<br><br></div><div>Thanks,<br></div><div>Jason<br><br>------<br></div><div>Jason Galyardt<br></div><div>University of Georgia<br><br></div></div></div></div></div></div></div>
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<br><br>---------- Forwarded message ----------<br>From: John Zuhone <<a href="mailto:jzuhone@gmail.com">jzuhone@gmail.com</a>><br>To: Discussion of the yt analysis package <<a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a>><br>Cc: <br>Date: Wed, 30 Nov 2016 11:32:09 -0500<br>Subject: Re: [yt-users] FLASH Time Series Analysis with Particle Files<br><div style="overflow-wrap: break-word;">Yes, my understanding is that this is working, provided that your files have the same basename and the times of the files are the same. <div><br><div><blockquote type="cite"><div>On Nov 30, 2016, at 10:32 AM, Nathan Goldbaum <<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@gmail.com</a>> wrote:</div><br class="gmail-m_8949660079170970024Apple-interchange-newline"><div><div dir="ltr">Hi Jason,<div><br></div><div>As far as I'm aware this should be working now. Are you having trouble?</div><div><br></div><div>-Nathan</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Nov 30, 2016 at 9:16 AM, Jason Galyardt <span dir="ltr"><<a href="mailto:jason.galyardt@gmail.com" target="_blank">jason.galyardt@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div><div><div><div><div><div><div>Dear yt-users,<br><br></div>In May 2015, there was some traffic on this list concerning errors in time series analysis on FLASH simulations that include both plot files and particle files. Does anyone have an update on the status of this issue?<br><br></div><div>Thanks,<br></div><div>Jason<br><br>------<br></div><div>Jason Galyardt<br></div><div>University of Georgia<br><br></div></div></div></div></div></div></div>
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