[yt-users] cylindrical coordinates
Suoqing JI
suoqing at physics.ucsb.edu
Fri May 9 18:10:39 PDT 2014
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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> 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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>>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>> _______________________________________________
>>>> yt-users mailing list
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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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