[yt-users] cylindrical coordinates

Τρίτσης Άρης- Ευάγγελος tritsis at physics.uoc.gr
Mon May 12 05:39:08 PDT 2014


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
>>>> _______________________________________________
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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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> _______________________________________________
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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".
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