[yt-users] cylindrical coordinates

Matthew Turk matthewturk at gmail.com
Mon May 12 04:34:05 PDT 2014


Hi Aris,

Hmm, this should work -- can you show me the results of your 1d
profile?  And, the output of "yt instinfo"?

-Matt

On Sat, May 10, 2014 at 2:50 PM, Τρίτσης Άρης- Ευάγγελος
<tritsis at physics.uoc.gr> wrote:
> On 2014-05-10 04:10, Suoqing JI wrote:
>>
>> Hi Aris,
>>
>> I assume you are dealing with FLASH 2-d cylindrical data. What do you
>> mean by saying you got wrong results? Have you used the correct
>> definition of cell volume (2 * pi * r * dr * dz for 2d cylindrical)
>> when you compute volume-weighted or cellmass-weighted quantities?
>>
>> Best wishes,
>>
>> --
>> Suoqing JI
>> Ph.D Student
>> Department of Physics
>> University of California, Santa Barbara
>> CA 93106, USA
>>
>> On May 9, 2014, at 10:11 AM, Τρίτσης Άρης-
>> Ευάγγελος <tritsis at physics.uoc.gr> wrote:
>>
>>> Hi Matt,
>>>
>>> Thanks a million for you immediate responses!! Since my main
>>> objective is to produce column density plots
>>> and then projection plots can you also tell me if such a feature is
>>> implemented for cylindrical coordinates?
>>> When I try to produce such plots with the ProjectionPlot and
>>> ProfilePlot routines I get wrong results. I
>>> have attached the plots I get from yt plus a dump from my model so
>>> you can check it if you like. Again I would really
>>> appreciate any help :).
>>>
>>>
>>
>> Aris<FlatCollIso_hdf5_plt_cnt_0157_Projection_theta_dens.png><FlatCollIso_hdf5_plt_cnt_0157_1d-Profile_r_density.png><FlatCollIso_hdf5_plt_cnt_0157>_______________________________________________
>>>
>>> yt-users mailing list
>>> yt-users at lists.spacepope.org
>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>
>>
>>> On 2014-05-09 19:04, Matthew Turk wrote:
>>> Hi Aris,
>>> Ah! I see the problem -- the off-axis slice plot probably isn't
>>> implemented. I'm sorry to say that might take a bit more work and
>>> won't be a readily added improvement; on-axis should work, however.
>>> -Matt
>>> On Fri, May 9, 2014 at 12:02 PM, Τρίτσης Άρης-
>>> Ευάγγελος
>>> <tritsis at physics.uoc.gr> wrote:
>>> On 2014-05-09 18:43, Matthew Turk wrote:
>>> Hi Aris,
>>> On Fri, May 9, 2014 at 9:21 AM, Τρίτσης Άρης-
>>> Ευάγγελος
>>> <tritsis at physics.uoc.gr> wrote:
>>> Hi yt users!
>>> I am new to yt and would like to ask if anyone has come across
>>> issues
>>> similar to mine.
>>> Is it possible to make slice,projection and 1D-profle plots in
>>> cylindrical
>>> coordinates in a Flash output file
>>> in any orientation and if not does anyone know when such a feature
>>> will
>>> be
>>> implemented to yt?
>>> Secondly, when I try to update all dependencies I get the following
>>> error:
>>> In terms of cylindrical coordinates, yt-3.0 ("bleeding edge" on the
>>> website) should fully support them. I'm not entirely sure I
>>> understand the question of orientation, though.
>>> /home/*/yt-x86_64/bin/python2.7: can't open file
>>> '/distribute_setup.py':
>>> [Errno 2] No such file or directory
>>> Ah, I think this might mean you are missing the libssl-dev
>>> dependencies? I'm not sure, though. Kacper?
>>> -Matt
>>> I would appreciate any help :)
>>> Aris
>>> _______________________________________________
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>>> _______________________________________________
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>>
>>  Hi Matt,
>> I do use the bleeding edge version which I installed from the
>> installation
>> script. However, when I try to produce an off axis slice plot I get
>> the
>> following:
>> YTCoordinateNotImplemented Traceback (most recent call last)
>> <ipython-input-67-440c2559450b> in <module>()
>> ----> 1 cut=OffAxisSlicePlot(pf, L, 'density', width=(25, 'pc'),
>> north_vector=north_vector)
>> /home/tritsis/yt-x86_64/src/yt-hg/yt/visualization/plot_window.pyc in
>> __init__(self, pf, normal, fields, center, width, axes_unit,
>> north_vector,
>> fontsize, field_parameters)
>>  1246 PWViewerMPL.__init__(self, cutting, bounds, fields=fields,
>>  1247 origin='center-window',periodic=False,
>> -> 1248 oblique=True, fontsize=fontsize)
>>  1249 if axes_unit is None:
>>  1250 axes_unit = get_axes_unit(width, pf)
>> /home/tritsis/yt-x86_64/src/yt-hg/yt/visualization/plot_window.pyc in
>> __init__(self, *args, **kwargs)
>>  675 if self._plot_type is None:
>>  676 self._plot_type = kwargs.pop("plot_type")
>> --> 677 PlotWindow.__init__(self, *args, **kwargs)
>>  678
>>  679 def _setup_origin(self):
>> /home/tritsis/yt-x86_64/src/yt-hg/yt/visualization/plot_window.pyc in
>> __init__(self, data_source, bounds, buff_size, antialias, periodic,
>> origin,
>> oblique, window_size, fields, fontsize, aspect, setup)
>>  300 self.fields = fields
>>  301 super(PlotWindow, self).__init__(data_source, window_size,
>> fontsize)
>> --> 302 self._set_window(bounds) # this automatically updates the
>> data and plot
>>  303 self.origin = origin
>>  304 if self.data_source.center is not None and oblique == False:
>> /home/tritsis/yt-x86_64/src/yt-hg/yt/visualization/plot_container.pyc
>> in
>> newfunc(*args, **kwargs)
>>  29 args[0]._plot_valid = False
>>  30 if hasattr(args[0], '_recreate_frb'):
>> ---> 31 args[0]._recreate_frb()
>>  32 if args[0]._initfinished:
>>  33 args[0]._setup_plots()
>> /home/tritsis/yt-x86_64/src/yt-hg/yt/visualization/plot_window.pyc in
>> _recreate_frb(self)
>>  349 periodic=self._periodic)
>>  350 if old_fields is None:
>> --> 351 self.frb._get_data_source_fields()
>>  352 else:
>>  353 for key, unit in zip(old_fields, old_units):
>> /home/tritsis/yt-x86_64/src/yt-hg/yt/visualization/fixed_resolution.pyc
>> in
>> _get_data_source_fields(self)
>>  140 for f in fields:
>>  141 if f not in exclude and f[0] not in
>> self.data_source.pf.particle_types:
>> --> 142 self[f]
>>  143
>>  144
>> /home/tritsis/yt-x86_64/src/yt-hg/yt/visualization/fixed_resolution.pyc
>> in
>> __getitem__(self, item)
>>  370 def __getitem__(self, item):
>>  371 if item in self.data: return self.data[item]
>> --> 372 indices = np.argsort(self.data_source['dx'])[::-1]
>>  373 bounds = []
>>  374 for b in self.bounds:
>> /home/tritsis/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc
>> in
>> __getitem__(self, key)
>>  210 return self.field_data[f]
>>  211 else:
>> --> 212 self.get_data(f)
>>  213 # fi.units is the unit expression string. We depend on the
>> registry
>>  214 # hanging off the dataset to define this unit object.
>> /home/tritsis/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc
>> in
>> get_data(self, fields)
>>  619
>>  620 fields_to_generate += gen_fluids + gen_particles
>> --> 621 self._generate_fields(fields_to_generate)
>>  622
>>  623 def _generate_fields(self, fields_to_generate):
>> /home/tritsis/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc
>> in
>> _generate_fields(self, fields_to_generate)
>>  636 fi = self.pf._get_field_info(*field)
>>  637 try:
>> --> 638 fd = self._generate_field(field)
>>  639 if type(fd) == np.ndarray:
>>  640 fd = self.pf.arr(fd, fi.units)
>> /home/tritsis/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc
>> in
>> _generate_field(self, field)
>>  247 tr = self._generate_particle_field(field)
>>  248 else:
>> --> 249 tr = self._generate_fluid_field(field)
>>  250 if tr is None:
>>  251 raise YTCouldNotGenerateField(field, self.pf)
>> /home/tritsis/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc
>> in
>> _generate_fluid_field(self, field)
>>  267 rv = self._generate_spatial_fluid(field,
>> ngt_exception.ghost_zones)
>>  268 else:
>> --> 269 rv = finfo(gen_obj)
>>  270 return rv
>>  271
>> /home/tritsis/yt-x86_64/src/yt-hg/yt/fields/derived_field.pyc in
>> __call__(self, data)
>>  176 "for %s" % (self.name,))
>>  177 with self.unit_registry(data):
>> --> 178 dd = self._function(self, data)
>>  179 for field_name in data.keys():
>>  180 if field_name not in original_fields:
>> /home/tritsis/yt-x86_64/src/yt-hg/yt/geometry/coordinate_handler.pyc
>> in
>> _unknown_coord(field, data)
>>  31
>>  32 def _unknown_coord(field, data):
>> ---> 33 raise YTCoordinateNotImplemented
>>  34
>>  35 def _get_coord_fields(axi, units = "code_length"):
>> YTCoordinateNotImplemented: This coordinate is not implemented for
>> this
>> geometry type
>> Plus I checked and I have all libssl-dev dependencies. Thanks again.
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>>
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>
>
>
> Hi Suoqing,
>
> You assume correctly :). I do not yet have the need to compute
> volume-weighted or cellmass-weighted quantities.
> What I want to do instead is more like ray tracing through the AMR so I can
> get column densities. However when I try to do something like that with the
> '1D profile plot' of yt I get discontinuities which makes no sense. Plus,
> when I try to produce Projection Plots you can see that the results are
> wrong just from the shape(I have an oblate). You can check the attachments
> of my previous mail.
>
> Regards,
>
> Aris
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