[yt-users] cylindrical coordinates

Matthew Turk matthewturk at gmail.com
Mon May 12 06:49:52 PDT 2014


Hi Aris,

So, the "R" reported is the cell center.  Can you try plotting the "t"
that you get out of the data, if you're doing a ray tracing?  And,
what's your script look like?

-Matt

On Mon, May 12, 2014 at 8:39 AM, Τρίτσης Άρης- Ευάγγελος
<tritsis at physics.uoc.gr> wrote:
> On 2014-05-12 14:34, Matthew Turk wrote:
>>
>> 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
>>>>> _______________________________________________
>>>>> 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
>>>>
>>>>
>>>>  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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>>>>
>>>>
>>>> _______________________________________________
>>>> yt-users mailing list
>>>> yt-users at lists.spacepope.org
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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
>>> _______________________________________________
>>> 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
>
>
> Hi Matt,
>
> I have attached the results from the 1D profile plot as you requested. The
> yt instinfo is:
>
> yt module located at:
>     /home/tritsis/yt-x86_64/src/yt-hg
> The supplemental repositories are located at:
>     /home/tritsis/yt-x86_64/src/yt-supplemental
>
> The current version and changeset for the code is:
>
> ---
> Version = 3.0-dev
> Changeset = a14a150c7c81
> ---
>
> This installation CAN be automatically updated.
> yt dependencies were last updated on
> Mon May  5 12:03:34 EEST 2014
>
> To update all dependencies, run "yt update --all".
> _______________________________________________
> yt-users mailing list
> yt-users at lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>



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