[yt-users] updated examples for 3.0 volume rendering

Michael Zingale michael.zingale at stonybrook.edu
Fri Mar 28 17:03:12 PDT 2014 

ok, one issue for Maestro is that there are 2 temperatures.  For low Mach
flows, you don't need an energy equation formally, but we carry one in
Maestro anyway.  So you can get the temperature with or without the energy
(enthalpy actually).  So it would be nice if we could specify which of the
temperature fields we want to use with yt (they are named "tfromp" and
"tfromh").


On Fri, Mar 28, 2014 at 8:00 PM, Matthew Turk <matthewturk at gmail.com> wrote:

> On Fri, Mar 28, 2014 at 7:59 PM, Michael Zingale
> <michael.zingale at stonybrook.edu> wrote:
> > Thanks.  I see in there
> >
> > def _temperature(field,data):
> >     mu = data.get_field_parameter("mu")
> >     return ( (data.pf.gamma-1.0) * mu * mh *
> >              data["thermal_energy"] / (kboltz * data["density"]) )
> >
> > is it the case that yt will assume a gamma-law gas?
>
> Only if temperature isn't defined -- the field system is set up now to
> be able to dynamically swap these in and out, so we definitely should.
>
> -Matt
>
> >
> >
> > On Fri, Mar 28, 2014 at 7:53 PM, Nathan Goldbaum <nathan12343 at gmail.com>
> > wrote:
> >>
> >>
> >>
> >> On Fri, Mar 28, 2014 at 4:52 PM, Michael Zingale
> >> <michael.zingale at stonybrook.edu> wrote:
> >>>
> >>> ok, final update -- I am able to do a basic volume rendering, but I
> need
> >>> to set
> >>>
> >>> no_ghost=True
> >>>
> >>> if this is False, then there is a units error in sanitize_units_add.
> >>> Perhaps when the ghost-cells are added, that is done as a normal
> ndarray and
> >>> not a YTarray?
> >>>
> >>> Similar issues arise if I try to draw_coordinate_vectors()
> >>>
> >>>
> >>
> >> Can you report these issues on our bug tracker?  A test script that
> fails
> >> for you would be especially helpful.
> >>
> >>>
> >>>
> >>> On Fri, Mar 28, 2014 at 7:26 PM, Michael Zingale
> >>> <michael.zingale at stonybrook.edu> wrote:
> >>>>
> >>>> I made a bit more progress here, but I get an error in
> >>>>
> >>>> amr_kdtree/amr_kdtree.py
> >>>>
> >>>> in line 257, it does
> >>>>
> >>>>         dds = grid.dds.ndarray_view()
> >>>>
> >>>> but grid.dds is already an ndarray, so this should be
> >>>>
> >>>>         dds = grid.dds
> >>>>
> >>>> still not through the cam.snapshot() part of my script, but I got
> >>>> everything up to there working.
> >>>>
> >>>>
> >>>>
> >>>> On Fri, Mar 28, 2014 at 4:23 PM, Michael Zingale
> >>>> <michael.zingale at stonybrook.edu> wrote:
> >>>>>
> >>>>> On Fri, Mar 28, 2014 at 3:37 PM, Nathan Goldbaum
> >>>>> <nathan12343 at gmail.com> wrote:
> >>>>>>
> >>>>>> Hi Mike,
> >>>>>>
> >>>>>> You've hit a bunch of big changes we've been making recently.  If
> you
> >>>>>> want to get back to the version of yt before we merged these big
> changes in,
> >>>>>> you'll need to update to the 'development' bookmark.  Right now
> you're on
> >>>>>> the 'experimental' bookmark.
> >>>>>>
> >>>>>
> >>>>> Oh... lucky me.
> >>>>>
> >>>>>>
> >>>>>>
> >>>>>> On Fri, Mar 28, 2014 at 12:10 PM, Michael Zingale
> >>>>>> <michael.zingale at stonybrook.edu> wrote:
> >>>>>>>
> >>>>>>> Is there any updated examples for using the yt 3.0 volume
> rendering?
> >>>>>>>
> >>>>>>> For instance, looking at this:
> >>>>>>>
> >>>>>>>
> >>>>>>>
> http://yt-project.org/docs/dev/cookbook/simple_plots.html#simple-volume-rendering
> >>>>>>
> >>>>>>
> >>>>>> We haven't finished updating the docs yet.  In-development docs
> >>>>>> (including some out-of-date information that we need to update) are
> >>>>>> available here: http://yt-project.org/docs/dev-3.0/
> >>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> The field name is no longer simply "Density", but now, for my
> data, I
> >>>>>>> need to use a tuple like:
> >>>>>>>
> >>>>>>> field =  ('boxlib', 'magvel')
> >>>>>>
> >>>>>>
> >>>>>> We no longer have a 'Density' field, since this introduces
> ambiguities
> >>>>>> for Enzo data and to create a consistent naming scheme for fields.
>  The new
> >>>>>> name is 'density'. See:
> >>>>>> http://ytep.readthedocs.org/en/latest/YTEPs/YTEP-0003.html
> >>>>>
> >>>>>
> >>>>> thanks for the list.  Maestro has it's own fun with variables (two
> >>>>> definitions for temperature, several pressures, etc., magvel above
> is not
> >>>>> simply the vector magnitude of x_vel, y_vel, z_vel, etc), so I'll pay
> >>>>> attention to these definitions.
> >>>>>
> >>>>>
> >>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> And then when I look at the extrema, I no longer take the [0]
> index,
> >>>>>>> as that just gives the min, but instead if I look at:
> >>>>>>>
> >>>>>>
> >>>>>> That true, we've simplified the derived quantity API somewhat.  This
> >>>>>> fixes a long-standing issue at the cost of breaking some old user
> scripts.
> >>>>>> As you can see we are planning to break backward compatibility
> somewhat for
> >>>>>> the final yt 3.0 release.
> >>>>>>
> >>>>>>>
> >>>>>>> dd.quantities["Extrema"](field)
> >>>>>>>
> >>>>>>> I get:
> >>>>>>>
> >>>>>>> (124.858613718 dimensionless, 18061918.0546 dimensionless)
> >>>>>>
> >>>>>>
> >>>>>>>
> >>>>>>> (not sure why they are dimensionless, but that's a different
> >>>>>>> problem).
> >>>>>>>
> >>>>>>
> >>>>>> If you do
> >>>>>>
> >>>>>> type(dd.quantities["Extrema"](field)[0])
> >>>>>>
> >>>>>> you will see that it is a new type, YTQuantity, which is a new class
> >>>>>> we've defined to handle units for scalar data.  YTArray does the
> same thing
> >>>>>> for array data.  More detail here:
> >>>>>> http://yt-project.org/docs/dev-3.0/analyzing/units/index.html
> >>>>>>
> >>>>>> These are 'dimensionless' because the boxlib frontend does not know
> >>>>>> what the appropriate units are for the 'magvel' field.  It may be
> the case
> >>>>>> that we could modify the frontend to detect the units
> >>>>>>
> >>>>>>>
> >>>>>>> Finally, if I try to make a transfer function, like:
> >>>>>>>
> >>>>>>> tf = ColorTransferFunction((mi, ma))
> >>>>>>>
> >>>>>>> I get:
> >>>>>>>
> >>>>>>> NameError: name 'ColorTransferFunction' is not defined
> >>>>>>
> >>>>>>
> >>>>>> I think this was an oversight on Matt's part.  Thanks for the
> report!
> >>>>>> For now you should be able to import ColorTransferFunction from
> >>>>>> yt.visualization.volume_rendering.api, but this should be fixed
> soon.
> >>>>>>
> >>>>>> The reason this happened is that we've changed the way imports work
> in
> >>>>>> the top-level yt namespace in the interest of yt behaving more like
> a
> >>>>>> 'normal' scientific python package.  More detail is available here:
> >>>>>>
> >>>>>> http://ytep.readthedocs.org/en/latest/YTEPs/YTEP-0019.html
> >>>>>>
> >>>>>> as well as in the following pull request:
> >>>>>>
> >>>>>>
> https://bitbucket.org/yt_analysis/yt/pull-request/729/ytep-0019/diff
> >>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> I just synced up with the development version today.
> >>>>>>>
> >>>>>>> Mike
> >>>>>>>
> >>>>>>>
> >>>>>>
> >>>>>> We're working hard to update the docs and get the code into shape to
> >>>>>> release.  If you're ok with dealing with not having fully
> up-to-date docs,
> >>>>>> we'd really appreciate you trying out the changes to the code,
> letting us
> >>>>>> know what you think, and reporting any bugs you find.
> >>>>>>
> >>>>>
> >>>>> yeah, I'm happy to keep playing with this version if it helps.  The
> >>>>> reason I updated today is because Matt told me that he had
> incorporated the
> >>>>> Maestro field info that I sent him.
> >>>>>
> >>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> --
> >>>>>>> Michael Zingale
> >>>>>>> Associate Professor
> >>>>>>>
> >>>>>>> Dept. of Physics & Astronomy * Stony Brook University * Stony
> Brook,
> >>>>>>> NY 11794-3800
> >>>>>>> phone:  631-632-8225
> >>>>>>> e-mail: Michael.Zingale at stonybrook.edu
> >>>>>>> web: http://www.astro.sunysb.edu/mzingale
> >>>>>>>
> >>>>>>> _______________________________________________
> >>>>>>> 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
> >>>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>> --
> >>>>> Michael Zingale
> >>>>> Associate Professor
> >>>>>
> >>>>> Dept. of Physics & Astronomy * Stony Brook University * Stony Brook,
> NY
> >>>>> 11794-3800
> >>>>> phone:  631-632-8225
> >>>>> e-mail: Michael.Zingale at stonybrook.edu
> >>>>> web: http://www.astro.sunysb.edu/mzingale
> >>>>
> >>>>
> >>>>
> >>>>
> >>>> --
> >>>> Michael Zingale
> >>>> Associate Professor
> >>>>
> >>>> Dept. of Physics & Astronomy * Stony Brook University * Stony Brook,
> NY
> >>>> 11794-3800
> >>>> phone:  631-632-8225
> >>>> e-mail: Michael.Zingale at stonybrook.edu
> >>>> web: http://www.astro.sunysb.edu/mzingale
> >>>
> >>>
> >>>
> >>>
> >>> --
> >>> Michael Zingale
> >>> Associate Professor
> >>>
> >>> Dept. of Physics & Astronomy * Stony Brook University * Stony Brook, NY
> >>> 11794-3800
> >>> phone:  631-632-8225
> >>> e-mail: Michael.Zingale at stonybrook.edu
> >>> web: http://www.astro.sunysb.edu/mzingale
> >>>
> >>> _______________________________________________
> >>> 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
> >>
> >
> >
> >
> > --
> > Michael Zingale
> > Associate Professor
> >
> > Dept. of Physics & Astronomy * Stony Brook University * Stony Brook, NY
> > 11794-3800
> > phone:  631-632-8225
> > e-mail: Michael.Zingale at stonybrook.edu
> > web: http://www.astro.sunysb.edu/mzingale
> >
> > _______________________________________________
> > 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
>



-- 
Michael Zingale
Associate Professor

Dept. of Physics & Astronomy * Stony Brook University * Stony Brook, NY
11794-3800
*phone*:  631-632-8225
*e-mail*: Michael.Zingale at stonybrook.edu
*web*: http://www.astro.sunysb.edu/mzingale
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20140328/e7210b5d/attachment.htm>

More information about the yt-users mailing list