[yt-users] units of cic mesh output from covering_grid

[Nathan Goldbaum]

Hi Brendan,

Not sure exactly what's happening.  In general it's difficult to remotely
debug something like this without a simple test case that one of us can run
locally.  Can you perhaps make a test that illustrates the issue using one
of the datasets on yt-project.org/data?


On Tue, Jul 1, 2014 at 3:05 PM, Brendan Griffen <brendan.f.griffen at gmail.com
> wrote:

> I have made a mesh using covering_grid:
>
> pf = load(basepath+ext+'.0.hdf5', unit_base = unit_base, bounding_box =
> bbox)
>
> unit_base = {'UnitLength_in_cm'         : 3.08568e+21,
>              'UnitMass_in_g'            :   1.989e+43,
>              'UnitVelocity_in_cm_per_s' :      100000}
>
>
FWIW, you shouldn't need to set the units or the bbox by hand, yt can read
this data from the hdf5 file.


> In [3]: bbox
>
> Out[3]:
>
> array([[   0.,  100.],
>
>        [   0.,  100.],
>
>        [   0.,  100.]])
>
> ndim = 512
>
> level = int(math.log(ndim,2))
>
> cg = pf.covering_grid(level=level, left_edge=[0,0,0],dims=[ndim,ndim,ndim])
>
> arr = cg['deposit', 'all_cic']
>
> When I do arr.mean() etc. I get the output:
>
>  --> Doing dimension: 512
>
>         == Mass density ==
>
>    --- Max:  2.367e-13 [g/cm^-3]
>
>    --- Min:  0.000e+00 [g/cm^-3]
>
>    --- Mean: 1.764e-21 [g/cm^-3]
>
>         == Number density ==
>
>    --- Max:  1.158e+11 [cm^-3]
>
>    --- Min:  0.000e+00 [cm^-3]
>
>    --- Mean: 8.630e+02 [cm^-3]
>
> Written out mesh:
> /bigbang/data/bgriffen/c2ray/cicfiles/parent/512/density/z0.000.dat
>
> I thought it returns the mesh in g/cm^3. Compared to just using the
> particles number, box width and particle mass I get (mass & number density):
>
> orig_mass =
> (head.massarr[1]*10**10*head.nall[1]/head.hubble)/(head.boxwidth/head.hubble)**3
>
> # just total_mass/total_volume where "head" => header info of HDF5 gadget
> snapshot
>
> In [29]: orig_mass*MsolMpc3_to_gcm3
>
> Out[29]: 2.701e-30
>
> In [30]: orig_mass*MsolMpc3_to_gcm3*coeff
>
> Out[30]: 1.321e-06
>
> These seem reasonable but the values back from yt don't. Can anyone
> confirm the yt units of the mesh returned? Does it take care of hubble
> parameter as read from block? Though this would only account for some minor
> discrepancy - it is orders of magnitude off at this stage.
>
> Thanks.
>
> Brendan
>
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