[yt-users] cylindrical coordinates

Τρίτσης Άρης- Ευάγγελος tritsis at physics.uoc.gr
Sat May 10 11:50:45 PDT 2014


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>_______________________________________________
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> 
>> 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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>  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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