Mailman 3 July 2011 - yt-users

derived field and TotalQuantity from two sources possible?
by gso＠physics.ucsd.edu 19 Jul '11

19 Jul '11

Hi, I was wondering if it is possible to specify two different sources of input to create a derived field. Currently with a single source, I have a derived field defined as: def _HII_HFraction(field, data): return data["HII_Density"]/(data["HI_Density"]+data["HII_Density"]) add_field("HII_HFraction", function=_HII_HFraction, units=r"\frac{\rho_{HII}}{\rho_H}") And I can access the total quantity in parallel pf=load(file) dd = pf.h.all_data() dd.quantities["TotalQuantity"]("HII_HFraction")[0] But I'm dealing with pf1=load(file1) pf2=load(file2) pf1 has the HI_Density field data and pf2 has the HII_Density field data. Is there a way to create a derived field and use TotalQuantity to operate on the data in parallel? From G.S. PS. I guess my alternative is to glue the two HDF5 files into one, but want to avoid it if possible.

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new fields in output
by Elizabeth Tasker 17 Jul '11

17 Jul '11

Hi, I've added PotentialField to the data that gets outputted. I'd like to read this into yt, but how does this work when yt won't be expecting PotentialField to be one of the data sets? Elizabeth

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Erroneous values from 'TotalQuantity' derived quantity
by Anthony Harness 14 Jul '11

14 Jul '11

I am trying to use the derived quantity, 'TotalQuantity', to count the number of cells included in my cut_region as follows: cut = dd.cut_region(["grid['x'] > 0.5"]) #Example cut numberCells = cut.quantities['TotalQuantity']('Ones')[0] #Totals a 'one' for each cell, which gives the total number of cells being used This works fine when I have plenty of cells to split up between 84 processors (or when there are exactly zero cells in the cut), but when there is a small number of cells in the cut (<~300), I get erroneous (way too large) random values like 1.e18 or -4.2e17. I know there are cells in the cut because I don't get a 'nan' when I calculate a 'WeightedAverageQuantity' value. I have tried to use "cut['Density'].size" to get the number of cells, but I get killed by the OOM Killer. My original data set has 1024^3 cells and I am running on Kraken with 84 processors. Thanks, Anthony

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functions within functions
by Elizabeth Tasker 14 Jul '11

14 Jul '11

Hi, I'm not sure where this is actually a yt question or a python one... I'm trying to create a slice of a new field that consists of the PotentialField (in the raw Enzo output) minus the background value, created by the profile tool. I have two functions that I created to do this: def _DiskRadius(field, data): ..... return dradius add_field("DiskRadius", function=_DiskRadius) That returns the value of the radius in the disk plane and def _SubtractBackgroundPotential(field, data): ..... profile = BinnedProfile1D(source, 128, "DiskRadius", 0.0, 16.0) ..... add_field("SubtractBackgroundPotential", function=_SubtractBackgroundPotential) which uses the first function to create a profile as a function of disk radius. then I have: p = pc.add_slice("SubtractBackgroundPotential", 2) Except that yt fails inside def _SubtractBackgroundPotential(field, data) because it can't find DiskRadius: ---> 23 profile = BinnedProfile1D(source, 128, "DiskRadius", 0.0, 16.0) Could anyone tell me how to get function 2 recognizing function 1? Thank you, Elizabeth

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rendering FLASH 2D simulations
by Florian Bürzle 11 Jul '11

11 Jul '11

Hi! While I'm at asking stupid questions - probably I missed it in the documentation (if so, I apologize), but is it possible to make rendered plots from FLASH 2D simulations? Thanks! Florian

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ImportError: No module named amr_utils
by Florian Bürzle 11 Jul '11

11 Jul '11

Hi! I've tried to get the hg version of yt working on my Mac Book Pro (OS X 10.6.8) using EPD Python 7.1., however unsuccessfully. I chose the development version hg up -C yt and performed the installation by using 'python setup.py install', and everything seemed to work fine (I captured the screen output in install_log.txt, attached). However, trying to import yt.mods gives the following error: Enthought Python Distribution -- www.enthought.com Version: 7.1-1 (32-bit) Python 2.7.2 |EPD 7.1-1 (32-bit)| (default, Jul 3 2011, 15:40:35) [GCC 4.0.1 (Apple Inc. build 5493)] on darwin Type "packages", "demo" or "enthought" for more information. >>> from yt.mods import * Traceback (most recent call last): File "<stdin>", line 1, in <module> File "yt/mods.py", line 45, in <module> from yt.data_objects.api import \ File "yt/data_objects/api.py", line 34, in <module> from hierarchy import \ File "yt/data_objects/hierarchy.py", line 39, in <module> from yt.utilities.io_handler import io_registry File "yt/utilities/io_handler.py", line 28, in <module> import yt.utilities.amr_utils as au ImportError: No module named amr_utils Many thanks in advance for your help! Best regards Florian

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disk Profiles
by Elizabeth Tasker 11 Jul '11

11 Jul '11

Hi all, I'm trying to create a profile object of the density in my disk as a function of radius. I don't actually want to plot it; I just need to grab an average to use as a background value elsewhere. I think I've almost got it: source = pf.h. disk((16,16,16), (0,0,1), 12, 15.6e-3/pf['kpc']) profile = BinnedProfile1D(source, 128, "RadiusCode", 0.5, 12.0) profile.add_fields("CellMass", weight="CellVolume") print profile["CellMass"] I just have a couple of questions: 1. Is there a way to print out the radial bins being used? i.e. the value at the centre of each bin? 2. RadiusCode is going to be the 3d radius, is that true? I can create my own variable for the in-disk radius, but is there a quantity already in yt for that to use with the disk profile? Thank you~ Elizabeth

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Re: [yt-users] disk Profiles
by Elizabeth Tasker 11 Jul '11

11 Jul '11

In a fit of impatience born of being in the wrong time zone, can I wave this at people again? :) On 2011-07-09, at 6:23 PM, Elizabeth Tasker wrote: > Hi all, > > I'm trying to create a profile object of the density in my disk as a function of radius. I don't actually want to plot it; I just need to grab an average to use as a background value elsewhere. > > I think I've almost got it: > > source = pf.h. disk((16,16,16), (0,0,1), 12, 15.6e-3/pf['kpc']) > profile = BinnedProfile1D(source, 128, "RadiusCode", 0.5, 12.0) > profile.add_fields("CellMass", weight="CellVolume") > print profile["CellMass"] > > I just have a couple of questions: > > 1. Is there a way to print out the radial bins being used? i.e. the value at the centre of each bin? > > 2. RadiusCode is going to be the 3d radius, is that true? I can create my own variable for the in-disk radius, but is there a quantity already in yt for that to use with the disk profile? > > Thank you~ > > Elizabeth > > > _______________________________________________ > yt-users mailing list > yt-users(a)lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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changing the name of saved files
by Elizabeth Tasker 08 Jul '11

08 Jul '11

Hi, I'd like to create a bunch of slices of the same field, but with different options (width, modifiers etc). Is it possible to change the file name yt saves the plots under so: GT_BTAccel_256AMR4_PeHeat_sf5_SNe_0301_Slice_z_PotentialField.png Doesn't get over-written with each one? Thanks you~ Elizabeth

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Phase plot question
by david collins 07 Jul '11

07 Jul '11

Hi -- I have a dumb question about the contents of the _data member of a BinnedProfile2D. I feel like I may have asked this question before, but I didn't see it in my archive, sorry if this is a dumb one. Why is the size of the Z array the same as Xbins \cross Ybins? For instance, I asked for 512 bins in both X and Y between X1,X2 and Y1,Y2. This gives me 513 bins in the Xbins array, as I expect (same for Y). But the Z array is also 513x513. My assumption has been that in Zarrray[I,J] is the value of Zvalue with Xbins[I] < Xvalue < Xbins[I+1], but that should give me 512 bins for the Z array. What's the extra bin for? Thanks, d. -- Sent from my computer.

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