[yt-users] Not able to read 2D BoxLib files
Mani Chandra
mc0710 at gmail.com
Wed Jul 24 09:49:29 PDT 2013
Hi Chris,
I am just using the default output that BoxLib has, so I guess its pretty
standard. Attached is a Header file from one of my plt files.
Cheers,
Mani
On Wed, Jul 24, 2013 at 10:58 AM, Chris Malone <chris.m.malone at gmail.com>wrote:
> Hi Mani,
>
> The pull request mentioned by the others is your best bet. That being
> said, I don't think any of the BoxLib frontend has been written for
> two-dimensional datasets, yet. It would be a useful addition. Our groups'
> current MO of getting Matplotlib-like plots of 2d BoxLib data is cumbersome
> and uses some fortran code that interfaces with the BoxLib underlying data
> formats, wrapped in f2py calls to get the data into numpy arrays.
>
> I too have been bandwidth-limited lately, but hopefully I can get back to
> working out the issue to which Matt alluded.
>
> For completeness, is there anything in particular outside of the standard
> Header file (or job_info, if that exists) that is needed to visualize or
> make sense of your dataset?
>
> Chris
>
>
> On Wed, Jul 24, 2013 at 8:03 AM, Matthew Turk <matthewturk at gmail.com>wrote:
>
>> Hi Mani,
>>
>> Nathan and Andrew's suggestions are about right -- the boxlib frontend
>> rewrite is definitely going to be the best way to do this, as I think
>> it's much more generic than the current fragmented state. I've been
>> bandwidth limited on that front, but if you look in the main PR you'll
>> see the outstanding issues. I think the last one that was presenting
>> a problem was the issue of varying refinement factors between levels,
>> but I think Chris Malone and I have figured that out. I hope to be
>> able to implement it soon, but I'm going to be on vacation for a few
>> weeks starting Friday and so I won't be able to look at it during that
>> time.
>>
>> Best,
>>
>> Matt
>>
>> On Tue, Jul 23, 2013 at 10:41 PM, Mani Chandra <mc0710 at gmail.com> wrote:
>> > Thanks Nathan! That looks like a good place to start.
>> >
>> >
>> > On Wed, Jul 24, 2013 at 12:29 AM, Nathan Goldbaum <
>> nathan12343 at gmail.com>
>> > wrote:
>> >>
>> >> Hi Mani,
>> >>
>> >> Take a look at this pull request from Matt:
>> >>
>> https://bitbucket.org/yt_analysis/yt/pull-request/501/consolidation-of-boxlib-frontends
>> >>
>> >> I suspect it will be a lot easier to write a frontend using this new
>> >> framework. I think there are still a few minor issues to work out
>> (that's
>> >> why it's not in the codebase yet) but it should be a good place to
>> start.
>> >>
>> >> Andrew and Matt should have more information about this.
>> >>
>> >> -Nathan
>> >>
>> >>
>> >> On Tue, Jul 23, 2013 at 10:27 PM, Mani Chandra <mc0710 at gmail.com>
>> wrote:
>> >>>
>> >>> Hi Andrew,
>> >>>
>> >>> This is a code which I'm writing now using the BoxLib framework, so
>> it is
>> >>> not exactly any of Nyx, Castro, Maestro or Orion. But I thought that
>> since
>> >>> they all use BoxLib, I could simply use any of those frontends
>> (although
>> >>> those frontends require a lot of parameters specific to those codes,
>> which I
>> >>> just commented out).
>> >>>
>> >>> So I guess I'll have to write a frontend then.
>> >>>
>> >>> Thanks,
>> >>> Mani
>> >>>
>> >>>
>> >>> On Wed, Jul 24, 2013 at 12:21 AM, Andrew Myers <atmyers2 at gmail.com>
>> >>> wrote:
>> >>>>
>> >>>> Hi Mani,
>> >>>>
>> >>>> To my knowledge, no one has ever used yt with 2D Orion data. I'm not
>> >>>> sure if any of the other BoxLib codes support 2D. I think the reason
>> the
>> >>>> Orion code is getting called is because yt can tell your dataset uses
>> >>>> BoxLib, but not that it belongs to any of the other BoxLib-based
>> codes (Nyx,
>> >>>> Castro, or Maestro), so it falls back to Orion.
>> >>>>
>> >>>> What simulation code generated this dataset? If it's not one of Nyx,
>> >>>> Castro, Maestro, or Orion, then you'll probably need to write a new
>> frontend
>> >>>> for your data.
>> >>>>
>> >>>> -Andrew Myers
>> >>>>
>> >>>> On Tue, Jul 23, 2013 at 7:50 PM, Mani Chandra <mc0710 at gmail.com>
>> wrote:
>> >>>>>
>> >>>>> Hi Everyone,
>> >>>>>
>> >>>>> I'm trying to load a 2D BoxLib file into yt. It looks like it is
>> using
>> >>>>> the same code as the Orion frontend and it fails with the following
>> error:
>> >>>>>
>> >>>>>
>> >>>>>
>> /home/mc/Downloads/yt/yt-x86_64/src/yt-hg/yt/data_objects/static_output.pyc
>> >>>>> in hierarchy(self)
>> >>>>> 191 raise RuntimeError("You should not
>> instantiate
>> >>>>> StaticOutput.")
>> >>>>> 192 self._instantiated_hierarchy =
>> >>>>> self._hierarchy_class(
>> >>>>> --> 193 self, data_style=self.data_style)
>> >>>>> 194 return self._instantiated_hierarchy
>> >>>>> 195 h = hierarchy # alias
>> >>>>>
>> >>>>>
>> >>>>>
>> /home/mc/Downloads/yt/yt-x86_64/src/yt-hg/yt/frontends/orion/data_structures.py
>> >>>>> in __init__(self, pf, data_style)
>> >>>>> 119 self.data_style = data_style
>> >>>>> 120
>> >>>>> --> 121
>> >>>>>
>> self.readGlobalHeader(header_filename,self.parameter_file.paranoid_read) #
>> >>>>> also sets up the grid objects
>> >>>>> 122 self.__cache_endianness(self.levels[-1].grids[-1])
>> >>>>> 123 AMRHierarchy.__init__(self,pf, self.data_style)
>> >>>>>
>> >>>>>
>> >>>>>
>> /home/mc/Downloads/yt/yt-x86_64/src/yt-hg/yt/frontends/orion/data_structures.py
>> >>>>> in readGlobalHeader(self, filename, paranoid_read)
>> >>>>> 194 self.dimension =
>> >>>>> int(self.__global_header_lines[counter])
>> >>>>> 195 if self.dimension != 3:
>> >>>>> --> 196 raise RunTimeError("Orion must be in 3D to use
>> >>>>> yt.")
>> >>>>> 197 counter += 1
>> >>>>> 198 self.Time =
>> float(self.__global_header_lines[counter])
>> >>>>>
>> >>>>> Has anyone managed to load 2D Orion files into yt?
>> >>>>>
>> >>>>> Thanks,
>> >>>>> Mani
>> >>>>>
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