[yt-users] Dark_Matter_Density Slice
Agarwal, Shankar
sagarwal at ku.edu
Mon Mar 22 13:55:01 PDT 2010
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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