Re: [yt-users] Dark_Matter_Density Slice

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 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

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Hi,

I need assistance on this.

I tried taking a density projection of 1/40th (in code units) of the box

On Mon, Mar 22, 2010 at 1:55 PM, Agarwal, Shankar wrote: thickness using the following code. But It gives me the projection of the entire box.

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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@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

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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

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Shankar

-----Original Message----- From: yt-users-bounces@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

wrote:

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Hi Matt,

I just plotted a slice of Dark_Matter_Density. It looks ok except that

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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@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

wrote:

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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

wrote: the width in code units to the slice or projection routines? there are some white patches (the density legend is VIBGYOR) particles (since there is no baryon particles dataset ?).

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Shankar

-----Original Message----- From: yt-users-bounces@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

wrote:

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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'

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