[yt-users] FLASH Time Series Analysis with Particle Files
Jason Galyardt
jason.galyardt at gmail.com
Wed Nov 30 11:47:06 PST 2016
Hi John & Nathan,
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:
###########################
In [9]: ts = yt.load("mysim_hdf5_plt_cnt_*",
particle_filename="mysim_hdf5_part_*")
In [10]: for ds in ts:
print ds.current_time
....:
---------------------------------------------------------------------------
IOError Traceback (most recent call last)
<ipython-input-10-fccd01bb5065> in <module>()
----> 1 for ds in ts:
2 print ds.current_time
3
/home/emrys/yt/yt/data_objects/time_series.pyc in __iter__(self)
179 for o in self._pre_outputs:
180 if isinstance(o, string_types):
--> 181 ds = self._load(o, **self.kwargs)
182 self._setup_function(ds)
183 yield ds
/home/emrys/yt/yt/data_objects/time_series.pyc in _load(self, output_fn,
**kwargs)
396 elif self._mixed_dataset_types:
397 return load(output_fn, **kwargs)
--> 398 ds = load(output_fn, **kwargs)
399 self._dataset_cls = ds.__class__
400 return ds
/home/emrys/yt/yt/convenience.pyc in load(*args, **kwargs)
84 candidates = find_lowest_subclasses(candidates)
85 if len(candidates) == 1:
---> 86 return candidates[0](*args, **kwargs)
87 if len(candidates) == 0:
88 if ytcfg.get("yt", "enzo_db") != '' \
/home/emrys/yt/yt/frontends/flash/data_structures.pyc in __init__(self,
filename, dataset_type, storage_filename, particle_filename,
units_override, unit_system)
209 self._particle_handle =
HDF5FileHandler(self.particle_filename)
210 except:
--> 211 raise IOError(self.particle_filename)
212 # Check if the particle file has the same time
213 if self._particle_handle != self._handle:
IOError: mysim_hdf5_part_*
###########################
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.
Any ideas?
Thanks,
Jason
On Wed, Nov 30, 2016 at 1:57 PM, <yt-users-request at lists.spacepope.org>
wrote:
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> Today's Topics:
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> 1. FLASH Time Series Analysis with Particle Files (Jason Galyardt)
> 2. Re: FLASH Time Series Analysis with Particle Files
> (Nathan Goldbaum)
> 3. Re: FLASH Time Series Analysis with Particle Files (John Zuhone)
>
>
> ---------- Forwarded message ----------
> From: Jason Galyardt <jason.galyardt at gmail.com>
> To: Discussion of the yt analysis package <yt-users at lists.spacepope.org>
> Cc:
> Date: Wed, 30 Nov 2016 10:16:44 -0500
> Subject: [yt-users] FLASH Time Series Analysis with Particle Files
> Dear yt-users,
>
> 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?
>
> Thanks,
> Jason
>
> ------
> Jason Galyardt
> University of Georgia
>
>
>
> ---------- Forwarded message ----------
> From: Nathan Goldbaum <nathan12343 at gmail.com>
> To: Discussion of the yt analysis package <yt-users at lists.spacepope.org>
> Cc:
> Date: Wed, 30 Nov 2016 09:32:37 -0600
> Subject: Re: [yt-users] FLASH Time Series Analysis with Particle Files
> Hi Jason,
>
> As far as I'm aware this should be working now. Are you having trouble?
>
> -Nathan
>
> On Wed, Nov 30, 2016 at 9:16 AM, Jason Galyardt <jason.galyardt at gmail.com>
> wrote:
>
>> Dear yt-users,
>>
>> 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?
>>
>> Thanks,
>> Jason
>>
>> ------
>> Jason Galyardt
>> University of Georgia
>>
>>
>> _______________________________________________
>> yt-users mailing list
>> yt-users at lists.spacepope.org
>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>
>>
>
>
> ---------- Forwarded message ----------
> From: John Zuhone <jzuhone at gmail.com>
> To: Discussion of the yt analysis package <yt-users at lists.spacepope.org>
> Cc:
> Date: Wed, 30 Nov 2016 11:32:09 -0500
> Subject: Re: [yt-users] FLASH Time Series Analysis with Particle Files
> 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.
>
> On Nov 30, 2016, at 10:32 AM, Nathan Goldbaum <nathan12343 at gmail.com>
> wrote:
>
> Hi Jason,
>
> As far as I'm aware this should be working now. Are you having trouble?
>
> -Nathan
>
> On Wed, Nov 30, 2016 at 9:16 AM, Jason Galyardt <jason.galyardt at gmail.com>
> wrote:
>
>> Dear yt-users,
>>
>> 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?
>>
>> Thanks,
>> Jason
>>
>> ------
>> Jason Galyardt
>> University of Georgia
>>
>>
>> _______________________________________________
>> yt-users mailing list
>> yt-users at lists.spacepope.org
>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>
>>
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