[yt-users] Loading RAMSES Data into yt.

k.grisdale at surrey.ac.uk k.grisdale at surrey.ac.uk
Thu Oct 31 02:16:47 PDT 2013 

Hi Matt 

Your instructions are very clear. I have used these and now have yt producing slices and projection with correct units. Now I just need to figure out why my data looks odd.

Thanks for  help

Kearn

On 30 Oct 2013, at 19:08, Matthew Turk <matthewturk at gmail.com> wrote:

> 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
>>>>>>>>> 
>>>>>>>>> _______________________________________________
>>>>>>>>> yt-users mailing list
>>>>>>>>> yt-users at lists.spacepope.org
>>>>>>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>>>>> _______________________________________________
>>>>>>>> yt-users mailing list
>>>>>>>> yt-users at lists.spacepope.org
>>>>>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>>>> 
>>>>>>> 
>>>>>>> _______________________________________________
>>>>>>> yt-users mailing list
>>>>>>> yt-users at lists.spacepope.org
>>>>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>>> _______________________________________________
>>>>>> yt-users mailing list
>>>>>> yt-users at lists.spacepope.org
>>>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>>> 
>>>>> 
>>>>> _______________________________________________
>>>>> yt-users mailing list
>>>>> yt-users at lists.spacepope.org
>>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>> _______________________________________________
>>>> yt-users mailing list
>>>> yt-users at lists.spacepope.org
>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>> 
>>> 
>>> 
>>> _______________________________________________
>>> yt-users mailing list
>>> yt-users at lists.spacepope.org
>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> _______________________________________________
> yt-users mailing list
> yt-users at lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>

More information about the yt-users mailing list