[yt-users] Flux Across Surfaces

[Melinda Soares-Furtado]

I figured out the problem, Matt. It was due to the fact that I was setting
the sphere radius equal to the surface radius -- the trilinear
interpolation was impacted by this. When I simply increased the sphere
radius to a value larger than the surface radius, the flux calculation
worked perfectly.

I noticed this when I used the code below to plot the generated surface and
saw that there were large regions that were empty. The flux was not being
computed in these regions and, as a result, the total flux was lower than
what I had expected.

****code to generate a plot of the generated
surface************************************
colors = apply_colormap(np.log10(surf["Temperature"]), cmap_name="hot")
#cmap_name="jet", "algae", "hot", "gist_stern", "RdBu","kamae"

fig = plt.figure(figsize=(10, 10), dpi=150)
ax = fig.gca(projection='3d')
p3dc = Poly3DCollection(surf.triangles, linewidth=0.0)
p3dc.set_facecolors(colors[0,:,:]/255.)
ax.add_collection(p3dc)
ax.auto_scale_xyz(surf.vertices[0,:], surf.vertices[1,:],
surf.vertices[2,:])
ax.set_aspect(1.0)
plt.savefig("%s_Surface.png" % pf)


Also, I realized what you meant by the surface area of a sphere! ;)

Regards,
Melinda Soares-Furtado



On Wed, Jul 30, 2014 at 2:59 PM, Matthew Turk <matthewturk at gmail.com> wrote:

> Hi Melinda,
>
> (As a quick note, we have test coverage for a few cases like this, but
> non-spherical.  The rest of my email assumes that the flux calculation
> is working as desired, but I can also attempt to set up a simple
> problem to demonstrate this from first principles, which I will put on
> my todo list.)
>
> I can think of a few things that might be going on.  The first is that
> the flux is typically computed using tri-linear interpolation, as well
> as a dot product.  This will interpolate to the barycenter of the
> triangles found through the marching cubes algorithm the velocity and
> density.  Increasing the refinement will increase this value, but
> we're still both approximating the sphere surface as a set of
> triangles, as well as taking the interpolated velocities and
> multiplying them by the area.  So the weak points:
>
>  * Interpolation
>  * Dot product of interpolated values
>  * Approximating surface
>
> One possible thing to try would be to examine the flux of "ones"
> across the surface, where the fluxing field is defined radially
> outward.  This would then give the total surface area.  So, we'd
> create three new derived fields:
>
> @derived_field(name="rad_x_vec")
> def rad_x_vec(field, data):
>     center = data.get_field_parameter("center")
>     return data["x"] - center[0]
>
> @derived_field(name="rad_y_vec")
> def rad_y_vec(field, data):
>     center = data.get_field_parameter("center")
>     return data["y"] - center[1]
>
> @derived_field(name="rad_z_vec")
> def rad_z_vec(field, data):
>     center = data.get_field_parameter("center")
>     return data["z"] - center[2]
>
> Then you can use "rad_x_vec", "rad_y_vec", "rad_z_vec" as the vector
> fields, which should point radially outward, and the "ones" field as
> the fluxing field.  This should return to you the total surface area,
> which you can then compare against 4/3 pi r**3, and see the total
> difference between the two.  That will at least indicate how different
> they are, and provide a semblance of a normalization?
>
> -Matt
>
> On Mon, Jul 28, 2014 at 5:13 PM, Melinda Soares-Furtado
> <msoares.physics at gmail.com> wrote:
> > I have used yt to determine the flux calculation for a region
> surrounding a
> > single star with a given mass loss rate. This region is right outside the
> > stellar radius (see attached). Comparing the flux calculation to the
> known
> > mass loss rate, I see that not all of the mass is accounted for and,
> what's
> > more, improved refinement of the simulation enhances this percentage,
> > however it is still below 70%. I need to calculate the flux for a region
> > surrounding a large group of stars, so simply increasing the refinement
> is
> > really not an option. Any suggestions as to how I can use yt for my flux
> > diagnostics in a manner that is more accurate?
> >
> > Best,
> > Melinda
> >
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