[yt-users] Loading RAMSES Data into yt.

Wed Oct 30 12:08:34 PDT 2013

Hi Kearn,

Sorry, that was a hasty reply!  Here's an example, for a dataset that
only has five fields:

pf = load("output_00010/info_00010.txt", fields = ["Density",
"x-velocity", "y-velocity", "z-velocity", "Pressure"])

If you have 7 or more fields (i.e., MHD?) you will have to add them on
to the end of the list.  The default list is:

["Density", "x-velocity", "y-velocity", "z-velocity", "Pressure", "Metallicity"]

Hope that helps -- let me know if it's not clear!

-Matt

On Wed, Oct 30, 2013 at 3:02 PM, Matthew Turk <matthewturk at gmail.com> wrote:
> Yup, this looks like a field count issue.  It looks like you've got
> n_fields != 6 -- you can specify this by supplying fields = [ ... ]
> (where ... ius the list of fields) to your load() command.
>
> On Wed, Oct 30, 2013 at 2:58 PM,  <k.grisdale at surrey.ac.uk> wrote:
>> Hi Matt,
>>
>> I updated yt and it now lets me input the data into yt. However when I try to plot a slice I get this error:
>>
>>>>> slc = SlicePlot(pf, 'z', 'Density').save()
>> You are running with the wrong number of fields.
>> Please specify these in the load command.
>> We are looking for 6 fields.
>> The last set of field sizes was: [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 16, 16, 16, 16, 16, 16]
>> Traceback (most recent call last):
>>   File "<stdin>", line 1, in <module>
>>   File "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 2148, in SlicePlot
>>     return AxisAlignedSlicePlot(pf, normal, fields, *args, **kwargs)
>>   File "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 1320, in __init__
>>     slc.get_data(fields)
>>   File "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 531, in get_data
>>     fluids, self, self._current_chunk)
>>   File "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/geometry/geometry_handler.py", line 520, in _read_fluid_fields
>>     chunk_size)
>>   File "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/frontends/ramses/io.py", line 41, in _read_fluid_selection
>>     rv = subset.fill(content, fields, selector)
>>   File "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/frontends/ramses/data_structures.py", line 304, in fill
>>     for level, offset in enumerate(self.domain.hydro_offset):
>>   File "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/frontends/ramses/data_structures.py", line 102, in hydro_offset
>>     hvals = fpu.read_attrs(f, header, "=")
>>   File "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/utilities/fortran_utils.py", line 74, in read_attrs
>>     assert(s1 == s2)
>> AssertionError.
>>
>> Is this related or a different problem?
>>
>> Thanks
>>
>> Kearn
>> On 30 Oct 2013, at 17:41, Matthew Turk <matthewturk at gmail.com> wrote:
>>
>>> Hi Kearn,
>>>
>>> Not a dumb question at all!  You should be able to run this command:
>>>
>>> cd $YT_DEST/src/yt-hg
>>> hg pull -r tip http://bitbucket.org/yt_analysis/yt-3.0
>>> hg up -C yt-3.0
>>>
>>> We do have a "yt update" command but I want to make sure it does
>>> precisely this, so it'd be best if you ran it.
>>>
>>> -Matt
>>>
>>> On Wed, Oct 30, 2013 at 1:37 PM,  <k.grisdale at surrey.ac.uk> wrote:
>>>> This is probably a dumb question but how do I update yt?
>>>>
>>>> Thanks
>>>> Kearn
>>>>
>>>>> On 30 Oct 2013, at 17:35, "Matthew Turk" <matthewturk at gmail.com> wrote:
>>>>>
>>>>> Hi Kearn,
>>>>>
>>>>> Did you update yt?  If so, it should have given at least a better error message.
>>>>>
>>>>> cd $YT_DEST/src/yt-hg
>>>>> hg pull -r tip http://bitbucket.org/yt_analysis/yt-3.0
>>>>> hg up -C yt-3.0
>>>>>
>>>>>
>>>>> -Matt
>>>>>
>>>>>> On Wed, Oct 30, 2013 at 1:29 PM,  <k.grisdale at surrey.ac.uk> wrote:
>>>>>> Hi,
>>>>>>
>>>>>> I completed a new run in RAMSES using the new version of the code and go the same results again.
>>>>>>
>>>>>>>>> from yt.mods import *
>>>>>>>>> pf =  load("output_00001/info_00001.txt") Traceback (most recent call last):
>>>>>> File "<stdin>", line 1, in <module>
>>>>>> File "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/convenience.py", line 76, in load
>>>>>>   if c._is_valid(*args, **kwargs): candidates.append(n)
>>>>>> File "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/frontends/art/data_structures.py", line 427, in _is_valid
>>>>>>   amr_header_vals = read_attrs(fh, amr_header_struct, '>')
>>>>>> File "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/utilities/fortran_utils.py", line 62, in read_attrs
>>>>>>   vals = list(struct.unpack(net_format, f.read(size)))
>>>>>> struct.error: unpack requires a string argument of length 892
>>>>>>
>>>>>> Is there anything else I can try?
>>>>>>
>>>>>> Thanks
>>>>>>
>>>>>> Kearn
>>>>>>> On 30 Oct 2013, at 17:02, Matthew Turk <matthewturk at gmail.com> wrote:
>>>>>>>
>>>>>>> Hi Kearn,
>>>>>>>
>>>>>>> I think Romain's suggestion is likely going to fix the issue, but I
>>>>>>> also just pushed a change that will show the error differently and in
>>>>>>> a more informative way.  ("hg pull
>>>>>>> http://bitbucket.org/yt_analysis/yt-3.0 && hg up" in your yt-hg
>>>>>>> directory will fix it.)
>>>>>>>
>>>>>>> -Matt
>>>>>>>
>>>>>>>> On Wed, Oct 30, 2013 at 12:39 PM,  <k.grisdale at surrey.ac.uk> wrote:
>>>>>>>> Hi,
>>>>>>>>
>>>>>>>> I have been trying to load RAMSES data into yt 2.5. Orginaly it was loading
>>>>>>>> in but the graphs I was able to produce didn’t make sense.  So I tried to
>>>>>>>> change to yt3 using the commands
>>>>>>>>
>>>>>>>> cd $YT_DEST/src/yt-hg/
>>>>>>>> hg pull http://bitbucket.org/yt_analysis/yt-3.0
>>>>>>>> hg up -C yt-3.0
>>>>>>>> python2.7 setup.py build_ext -i -f
>>>>>>>>
>>>>>>>> The commands appear to have worked. But when I try to use yt to load in
>>>>>>>> RAMSES data I now get this error:
>>>>>>>>
>>>>>>>>
>>>>>>>> Traceback (most recent call last): File
>>>>>>>> "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/gui/reason/basic_repl.py",
>>>>>>>> line 81, in execute exec code in self.locals File "", line 1, in File
>>>>>>>> "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/convenience.py", line 76, in
>>>>>>>> load if c._is_valid(*args, **kwargs): candidates.append(n) File
>>>>>>>> "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/frontends/art/data_structures.py",
>>>>>>>> line 427, in _is_valid amr_header_vals = read_attrs(fh, amr_header_struct,
>>>>>>>> '>') File
>>>>>>>> "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/utilities/fortran_utils.py",
>>>>>>>> line 62, in read_attrs vals = list(struct.unpack(net_format, f.read(size)))
>>>>>>>> error: unpack requires a string argument of length 892
>>>>>>>>
>>>>>>>>
>>>>>>>> Any idea what I need to do?
>>>>>>>>
>>>>>>>> Thanks
>>>>>>>>
>>>>>>>> Kearn
>>>>>>>>
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