[yt-users] Dark_Matter_Density Slice

Brian O'Shea bwoshea at gmail.com
Mon Mar 22 14:15:19 PDT 2010 

Also, you might want to change:

reg = pf.h.region([0.5, 0.5, 0.5], [0.4875, 0.0, 0.0], [5.125, 1.0, 1.0])

to:

reg = pf.h.region([0.5, 0.5, 0.5], [0.4875, 0.0, 0.0], [0.5125, 1.0, 1.0])

(note the change of 5.125 to 0.5125).  That's probably causing hilarity.

B

On Mon, Mar 22, 2010 at 4:57 PM, Matthew Turk <matthewturk at gmail.com> wrote:

> Hi Shankar,
>
> You're almost there!  :)
>
> Try:
>
> --
> from yt.mods import *
>
> fn = "RedshiftOutput0001"
> pf = load(fn) # load data
>
> reg = pf.h.region([0.5, 0.5, 0.5], [0.4875, 0.0, 0.0], [5.125, 1.0, 1.0])
> pc = PlotCollection(reg1,center=[0.5,0.5,0.5])
> p = pc.add_projection("Dark_Matter_Density", ax, source=reg)
> pc.save()
> --
>
> It's a bit subtle that data_source supplied to add_projection will do
> something different from source=.
>
> -Matt
>
>
> On Mon, Mar 22, 2010 at 1:55 PM, Agarwal, Shankar <sagarwal at ku.edu> wrote:
> > Hi,
> >
> > I need assistance on this.
> >
> > I tried taking a density projection of 1/40th (in code units) of the box
> thickness using the following code. But It gives me the projection of the
> entire box.
> >
> >
> > from yt.mods import *
> >
> > fn = "RedshiftOutput0001"
> > pf = load(fn) # load data
> >
> > reg = pf.h.region([0.5, 0.5, 0.5], [0.4875, 0.0, 0.0], [5.125, 1.0, 1.0])
> > pf.h.save_object(reg, "region")
> >
> > reg1 = pf.h.load_object("region")
> >
> > pc = PlotCollection(reg1,center=[0.5,0.5,0.5])
> >
> > for ax in range(1):
> >  p = pc.add_projection("Dark_Matter_Density", ax)
> > pc.save()
> >
> >
> > I will appreciate if somenone can tell me how may I take the projection
> of the AMR3dDATA object: reg1
> >
> >
> > Shankar
> >
> >
> > -----Original Message-----
> > From: yt-users-bounces at lists.spacepope.org on behalf of Matthew Turk
> > Sent: Mon 3/22/2010 1:46 PM
> > To: Discussion of the yt analysis package
> > Subject: Re: [yt-users] DM density field Slice
> >
> > Hi Shankar,
> >
> > Not sure I know what you mean by thick slice -- we're back on baryon
> > quantities, not on the particle rectangular prisms when using
> > Dark_Matter_Density -- but I think the answer is that it might end up
> > being more complicated than just replacing values.  IF you want to
> > project only a portion of the simulation, that can be done by
> > specifying a source argument to the projection routine, where the
> > source is any AMR3dData object -- like spheres, prisms, etc etc.
> > That's the only mechanism available for thick slicing; for slicing you
> > can also provide source arguments (I think ... you could at one
> > point!) but it will simply slice through that region, not do any
> > combinations.
> >
> > -Matt
> >
> > On Mon, Mar 22, 2010 at 11:39 AM, Agarwal, Shankar <sagarwal at ku.edu>
> wrote:
> >> Matt,
> >>
> >> That makes sense. So, for a thick slice, I will be able to find cells
> with non-zero density and fill the white spaces. Is it possible to specify
> the width in code units to the slice or projection routines?
> >>
> >> Shankar
> >>
> >>
> >> -----Original Message-----
> >> From: yt-users-bounces at lists.spacepope.org on behalf of Matthew Turk
> >> Sent: Mon 3/22/2010 1:07 PM
> >> To: Discussion of the yt analysis package
> >> Subject: Re: [yt-users] DM density field Slice
> >>
> >> Hi Shankar,
> >>
> >> This is something that Enzo actually does -- the Dark_Matter_Density
> >> is generated via the cic_deposit routines, which are cloud-in-cell
> >> interpolation.  Where no particles contribute, it gets marked as zero,
> >> which shows up as "bad values" in the log slice, and so it marks them
> >> as white.  Looks like everything in this image is working!
> >>
> >> -Matt
> >>
> >> On Mon, Mar 22, 2010 at 11:06 AM, Agarwal, Shankar <sagarwal at ku.edu>
> wrote:
> >>> Hi Matt,
> >>>
> >>> I just plotted a slice of Dark_Matter_Density. It looks ok except that
> there are some white patches (the density legend is VIBGYOR)
> >>>
> >>> http://drop.io/Dark_Matter_Density#
> >>>
> >>>
> >>> It looks like those white patches are regions from where the density
> data was not read. Any thoughts?
> >>>
> >>>
> >>> Shankar
> >>>
> >>> -----Original Message-----
> >>> From: yt-users-bounces at lists.spacepope.org on behalf of Matthew Turk
> >>> Sent: Mon 3/22/2010 11:58 AM
> >>> To: Discussion of the yt analysis package
> >>> Subject: Re: [yt-users] DM particles or baryon density field ?
> >>>
> >>> Yup, you're right.
> >>>
> >>> On Mon, Mar 22, 2010 at 9:57 AM, Agarwal, Shankar <sagarwal at ku.edu>
> wrote:
> >>>> Yes, "Dark_Matter_Density field projections and slices" is what I
> meant. I will try replacing "Density" with "Dark_Matter_Density".
> >>>>
> >>>>
> >>>> Also, let me know if I am right...
> >>>>
> >>>> p = pc.add_projection("Density", 0)    ------- This is baryon density
> field.
> >>>>
> >>>> p.modify["nparticles"](1.0)            ------- But this is DM
> particles (since there is no baryon particles dataset ?).
> >>>>
> >>>>
> >>>> Shankar
> >>>>
> >>>>
> >>>>
> >>>>
> >>>> -----Original Message-----
> >>>> From: yt-users-bounces at lists.spacepope.org on behalf of Matthew Turk
> >>>> Sent: Mon 3/22/2010 11:32 AM
> >>>> To: Discussion of the yt analysis package
> >>>> Subject: Re: [yt-users] DM particles or baryon density field ?
> >>>>
> >>>> Hi Shankar,
> >>>>
> >>>> I guess the question is sort of ill-defined.  Dark matter is
> >>>> discretized as particles; the idea of projecting dark matter is not
> >>>> the same as projecting a field quantity.  The same goes for plotting
> >>>> slices.
> >>>>
> >>>> However, you can make dark matter plots.  You cna use the
> >>>> "add_particles" method on the PlotCollection, which accepts an axis
> >>>> and a width -- what it does is plot all the particles within that
> >>>> rectangular prism.  This can be mocked up as a projection by setting
> >>>> the width equal to the domain width along that axis.
> >>>>
> >>>> You can also try using "Dark_Matter_Density", which might be easier to
> >>>> visualize, as a projection or a slice.
> >>>>
> >>>> If you run into any problems with the particle plot, let us know --
> >>>> it's not as well-used as the other plots, so there might be subtle
> >>>> bugs.  :)
> >>>>
> >>>> -Matt
> >>>>
> >>>> On Mon, Mar 22, 2010 at 9:27 AM, Agarwal, Shankar <sagarwal at ku.edu>
> wrote:
> >>>>> Hi,
> >>>>>
> >>>>> The projection, slice, velocity and overplot particles routines: They
> read the DM particles or gas ?
> >>>>>
> >>>>> Looking at the density legend, it looks like this is baryon density
> field.
> >>>>>
> >>>>> Is there a provision to plot projection and slice for DM ?
> >>>>>
> >>>>>
> >>>>> Also, I get this error when overplotting particles...
> >>>>>
> >>>>> yt         INFO       2010-03-22 12:17:44,051 Created plot collection
> with default plot-center = [0.5, 0.5, 0.5]
> >>>>> yt         INFO       2010-03-22 12:17:44,144 Getting the binary
> hierarchy
> >>>>> yt         INFO       2010-03-22 12:17:44,153 Finished with binary
> hierarchy reading
> >>>>> yt         INFO       2010-03-22 12:17:46,108 Added slice of Density
> at x = 0.5 with 'center' = [0.5, 0.5, 0.5]
> >>>>> Traceback (most recent call last):
> >>>>>  File "slice.py", line 42, in <module>
> >>>>>    p.modify["nparticles"](0.005)
> >>>>>  File
> "/autohome/u118/agarwa23/yt-x86_64/src/yt-1.6/yt/raven/PlotTypes.py", line
> 52, in __getitem__
> >>>>>    raise KeyError(item)
> >>>>> KeyError: 'nparticles'
> >>>>>
> >>>>>
> >>>>>
> >>>>> Shankar
> >>>>> _______________________________________________
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