yt-users December 2009

yt-users@python.org

10 participants
9 discussions

Re: [yt-users] Analyzing DM-only data
by Eric Hallman 22 Dec '09

22 Dec '09

Ok, I am not 100% sure what is going on, I've only tried this a few times with dm_only, but I have noticed not too many other people are around, so I will tell you what I know. There are some quirky things with dm_only, for instance: if you start with from yt.mods import * pf = EnzoStaticOutput("datasetname",data_style="enzo_packed_3d") (or pf = load(...)) the behavior of creating plot collections, reading field lists is different than if you use from yt.lagos import * pf = EnzoStaticOutput("datasetname",data_style="enzo_packed_3d") In the first case, if you type print pf.h.field_list it fails in the second case, it works. Unclear why. You can project quantities, or take slices, but not for all the particle quantities as they are (as near as I can tell). Some of the derived quantites (e.g. particle_density_pyx) can be projected without a problem, once you import raven. Though I am not the expert on the particle quantities, I seem to remember that you can only take slices/ projections with grid quantities. Anyway, I would start with loading up the data by importing lagos first, loading the dataset, then check your field list and derived field list for what you want to make slices of. There is some more documentation on the enzotools site on how to manage particle data etc. Hopefully someone else can help with the real answers here at some point. Sorry I couldn't help more. On Dec 22, 2009, at 12:52 PM, kcai(a)pa.uky.edu wrote: > Hi Eric, > > Quoting Eric Hallman <Eric.Hallman(a)colorado.edu>: > >> Kai, >> I am getting a completely different error than you are, but I also >> fail at the same step. Which version of yt are you using? >> > I think it is yt-1.5, but I'm not 100% sure. I used the installation > script. > >> I will see if I can get this figured out. >> >> > Thank you for this! > Kai > > >> On Dec 22, 2009, at 11:58 AM, kcai(a)pa.uky.edu wrote: >> >>> Eric, >>> No, 'Dark_Matter_Density' does not work, either... >>> -> similar error: >>> >>> In [5]: pc.add_slice('Dark_Matter_Density', 0) >>> Exception AttributeError: "EnzoHierarchy instance has no >>> attribute '_data_file'" in <bound method EnzoHierarchy.__del__ >>> of <yt.lagos.HierarchyType.EnzoHierarchy instance at >>> 0x2aa1cfbcf8>> ignored >>> --------------------------------------------------------------------------- >>> KeyError Traceback (most recent >>> call last) >>> >>> /share/home/kca223/src/yt-1.5/scripts/iyt in <module>() >>> ----> 1 >>> 2 >>> 3 >>> 4 >>> 5 >>> >>> /share/home/kca223/src/yt-1.5/yt/raven/PlotCollection.pyc in >>> add_slice(self, *args, **kwargs) >>> 180 *fig_size* in (height_inches, width_inches) >>> 181 """ >>> --> 182 return self.__add_slice(PlotTypes.SlicePlot, >>> *args, **kwargs) >>> 183 >>> 184 def add_slice_interpolated(self, *args, **kwargs): >>> >>> /share/home/kca223/src/yt-1.5/yt/raven/PlotCollection.pyc in >>> __add_slice(self, ptype, field, axis, coord, center, >>> use_colorbar, figure, axes, fig_size, periodic, data_source, >>> **kwargs) >>> 204 coord = center[axis] >>> 205 if data_source is None: >>> --> 206 data_source = self.pf.hierarchy.slice(axis, >>> coord, field, center, **kwargs) >>> 207 p = self._add_plot(ptype(data_source, field, >>> use_colorbar=use_colorbar, >>> 208 axes=axes, figure=figure, >>> >>> /share/home/kca223/src/yt-1.5/yt/lagos/OutputTypes.pyc in >>> _get_hierarchy(self) >>> 144 if self._hierarchy_class == None: >>> 145 raise RuntimeError("You should not >>> instantiate StaticOutput.") >>> --> 146 self.__hierarchy = >>> self._hierarchy_class(self, data_style=self.data_style) >>> 147 return self.__hierarchy >>> 148 >>> >>> /share/home/kca223/src/yt-1.5/yt/lagos/HierarchyType.pyc in >>> __init__(self, pf, data_style) >>> 689 break >>> 690 self.__guess_data_style(pf["TopGridRank"], >>> testGrid, testGridID) >>> --> 691 self._setup_data_queue() >>> 692 # For some reason, r8 seems to want Float64 >>> 693 if pf.has_key("CompilerPrecision") \ >>> >>> /share/home/kca223/src/yt-1.5/yt/lagos/HierarchyType.pyc in >>> _setup_data_queue(self) >>> 137 >>> 138 def _setup_data_queue(self): >>> --> 139 self.queue = _data_style_funcs[self.data_style][5]() >>> 140 >>> 141 def _setup_grid_corners(self): >>> >>> KeyError: 'enzo_packed_3d' >>> >>> I think it is I did not set the "data_style" right... >>> >>> Thanks, >>> Kai >>> >>> >>> Quoting Eric Hallman <Eric.Hallman(a)colorado.edu>: >>> >>>> , >>>> I think the solution is that dark matter only runs do not have the >>>> field "Density", but only dark matter density is defined as a >>>> field. >>>> Density is a baryon field. >>>> >>>> >>>> On Dec 22, 2009, at 9:18 AM, kcai(a)pa.uky.edu wrote: >>>> >>>>> Sorry - forgot to change the subject of last email... >>>>> >>>>> Quoting kcai(a)pa.uky.edu: >>>>> >>>>>> Hi Matt, >>>>>> Last night I was browsing the archives of the yt-users list, and >>>>>> came across this thread of emails: >>>>>> >>>>>> [yt-users] corrupt enzo restart file? >>>>>> Matthew Turk matthewturk at gmail.com >>>>>> Thu Nov 12 09:30:36 PST 2009 >>>>>> >>>>>> Hi Stephen, >>>>>> >>>>>> A problem with the way yt opens up dark matter only simulations >>>>>> is >>>>>> that the data_style has to be specified. This would be, for >>>>>> running >>>>>> on trunk, done with the parameter: >>>>>> >>>>>> data_style="enzo_packed_3d" >>>>>> >>>>>> to the StaticOutput initialization. Britton Smith has done >>>>>> some work >>>>>> recently on improving this, so he might be able to chime in >>>>>> with more >>>>>> info. >>>>>> >>>>>> -Matt >>>>>> >>>>>> On Thu, Nov 12, 2009 at 9:27 AM, Stephen Skory <stephenskory at >>>>>> yahoo.com> wrote: >>>>>>> Hi all, >>>>>>> >>>>>>> I am getting this error <http://paste.enzotools.org/show/257/ >>>>>>> > when I attempt to instantiate the grid hierarchy. >>>>>> ...... >>>>>> >>>>>> >>>>>> I am encountering the same "TypeError" when I tried to analyze >>>>>> a DM- only run. >>>>>> But I use iyt (the interactive yt) - how do I add the >>>>>> data_style then? I tried >>>>>> with >>>>>> >>>>>> pf = load("RD0000/RD0000", data_style="enzo_packed_3d") >>>>>> and then >>>>>> In [3]: pc = PlotCollection(pf, center=[0.5,0.5,0.5]) >>>>>> yt INFO 2009-12-22 00:01:13,536 Created plot >>>>>> collection >>>>>> with default plot-center = [0.5, 0.5, 0.5] >>>>>> >>>>>> But when I tried to plot a slice, I got: >>>>>> In [4]: pc.add_slice("Density", 0) >>>>>> --------------------------------------------------------------------------- >>>>>> KeyError Traceback (most >>>>>> recent call last) >>>>>> >>>>>> /share/home/kca223/src/yt-1.5/scripts/iyt in <module>() >>>>>> ----> 1 >>>>>> 2 >>>>>> 3 >>>>>> 4 >>>>>> 5 >>>>>> >>>>>> /share/home/kca223/src/yt-1.5/yt/raven/PlotCollection.pyc in >>>>>> add_slice(self, *args, **kwargs) >>>>>> 180 *fig_size* in (height_inches, width_inches) >>>>>> 181 """ >>>>>> --> 182 return self.__add_slice(PlotTypes.SlicePlot, >>>>>> *args, **kwargs) >>>>>> 183 >>>>>> 184 def add_slice_interpolated(self, *args, **kwargs): >>>>>> >>>>>> /share/home/kca223/src/yt-1.5/yt/raven/PlotCollection.pyc in >>>>>> __add_slice(self, ptype, field, axis, coord, center, >>>>>> use_colorbar, >>>>>> figure, axes, fig_size, periodic, data_source, **kwargs) >>>>>> 204 coord = center[axis] >>>>>> 205 if data_source is None: >>>>>> --> 206 data_source = >>>>>> self.pf.hierarchy.slice(axis, coord, >>>>>> field, center, **kwargs) >>>>>> 207 p = self._add_plot(ptype(data_source, field, >>>>>> use_colorbar=use_colorbar, >>>>>> 208 axes=axes, figure=figure, >>>>>> >>>>>> /share/home/kca223/src/yt-1.5/yt/lagos/OutputTypes.pyc in >>>>>> _get_hierarchy(self) >>>>>> 144 if self._hierarchy_class == None: >>>>>> 145 raise RuntimeError("You should not >>>>>> instantiate >>>>>> StaticOutput.") >>>>>> --> 146 self.__hierarchy = >>>>>> self._hierarchy_class(self, >>>>>> data_style=self.data_style) >>>>>> 147 return self.__hierarchy >>>>>> 148 >>>>>> >>>>>> /share/home/kca223/src/yt-1.5/yt/lagos/HierarchyType.pyc in >>>>>> __init__(self, pf, data_style) >>>>>> 689 break >>>>>> 690 self.__guess_data_style(pf["TopGridRank"], testGrid, >>>>>> testGridID) >>>>>> --> 691 self._setup_data_queue() >>>>>> 692 # For some reason, r8 seems to want Float64 >>>>>> 693 if pf.has_key("CompilerPrecision") \ >>>>>> >>>>>> /share/home/kca223/src/yt-1.5/yt/lagos/HierarchyType.pyc in >>>>>> _setup_data_queue(self) >>>>>> 137 >>>>>> 138 def _setup_data_queue(self): >>>>>> --> 139 self.queue = _data_style_funcs[self.data_style] >>>>>> [5] () >>>>>> 140 >>>>>> 141 def _setup_grid_corners(self): >>>>>> >>>>>> KeyError: 'enzo_packed_3d' >>>>>> >>>>>> Thanks a lot! >>>>>> Kai >>>>>> >>>>> >>>>>> This message was sent using IMP, the Internet Messaging Program. >>>>> >>>>> >>>>> >>>>> ---------------------------------------------------------------- >>>>> This message was sent using IMP, the Internet Messaging Program. >>>>> >>>>> _______________________________________________ >>>>> yt-users mailing list >>>>> yt-users(a)lists.spacepope.org >>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>>> >>>> Dr. Eric J. Hallman >>>> NSF Astronomy and Astrophysics Postdoctoral Fellow >>>> Center for Astrophysics and Space Astronomy >>>> University of Colorado at Boulder >>>> hallman (at) casa.colorado.edu >>>> Phone: (312) 725-4626 >>>> http://solo.colorado.edu/~hallman/ >>> > > > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. Dr. Eric J. Hallman NSF Astronomy and Astrophysics Postdoctoral Fellow Center for Astrophysics and Space Astronomy University of Colorado at Boulder hallman (at) casa.colorado.edu Phone: (312) 725-4626 http://solo.colorado.edu/~hallman/

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Re: [yt-users] [Enzo-users-l] Compiling Enzo on TACC Ranger
by kcai＠pa.uky.edu 22 Dec '09

22 Dec '09

Hi Matt, Last night I was browsing the archives of the yt-users list, and came across this thread of emails: [yt-users] corrupt enzo restart file? Matthew Turk matthewturk at gmail.com Thu Nov 12 09:30:36 PST 2009 Hi Stephen, A problem with the way yt opens up dark matter only simulations is that the data_style has to be specified. This would be, for running on trunk, done with the parameter: data_style="enzo_packed_3d" to the StaticOutput initialization. Britton Smith has done some work recently on improving this, so he might be able to chime in with more info. -Matt On Thu, Nov 12, 2009 at 9:27 AM, Stephen Skory <stephenskory at yahoo.com> wrote: > Hi all, > > I am getting this error <http://paste.enzotools.org/show/257/> when > I attempt to instantiate the grid hierarchy. ...... I am encountering the same "TypeError" when I tried to analyze a DM-only run. But I use iyt (the interactive yt) - how do I add the data_style then? I tried with pf = load("RD0000/RD0000", data_style="enzo_packed_3d") and then In [3]: pc = PlotCollection(pf, center=[0.5,0.5,0.5]) yt INFO 2009-12-22 00:01:13,536 Created plot collection with default plot-center = [0.5, 0.5, 0.5] But when I tried to plot a slice, I got: In [4]: pc.add_slice("Density", 0) --------------------------------------------------------------------------- KeyError Traceback (most recent call last) /share/home/kca223/src/yt-1.5/scripts/iyt in <module>() ----> 1 2 3 4 5 /share/home/kca223/src/yt-1.5/yt/raven/PlotCollection.pyc in add_slice(self, *args, **kwargs) 180 *fig_size* in (height_inches, width_inches) 181 """ --> 182 return self.__add_slice(PlotTypes.SlicePlot, *args, **kwargs) 183 184 def add_slice_interpolated(self, *args, **kwargs): /share/home/kca223/src/yt-1.5/yt/raven/PlotCollection.pyc in __add_slice(self, ptype, field, axis, coord, center, use_colorbar, figure, axes, fig_size, periodic, data_source, **kwargs) 204 coord = center[axis] 205 if data_source is None: --> 206 data_source = self.pf.hierarchy.slice(axis, coord, field, center, **kwargs) 207 p = self._add_plot(ptype(data_source, field, use_colorbar=use_colorbar, 208 axes=axes, figure=figure, /share/home/kca223/src/yt-1.5/yt/lagos/OutputTypes.pyc in _get_hierarchy(self) 144 if self._hierarchy_class == None: 145 raise RuntimeError("You should not instantiate StaticOutput.") --> 146 self.__hierarchy = self._hierarchy_class(self, data_style=self.data_style) 147 return self.__hierarchy 148 /share/home/kca223/src/yt-1.5/yt/lagos/HierarchyType.pyc in __init__(self, pf, data_style) 689 break 690 self.__guess_data_style(pf["TopGridRank"], testGrid, testGridID) --> 691 self._setup_data_queue() 692 # For some reason, r8 seems to want Float64 693 if pf.has_key("CompilerPrecision") \ /share/home/kca223/src/yt-1.5/yt/lagos/HierarchyType.pyc in _setup_data_queue(self) 137 138 def _setup_data_queue(self): --> 139 self.queue = _data_style_funcs[self.data_style][5]() 140 141 def _setup_grid_corners(self): KeyError: 'enzo_packed_3d' Thanks a lot! Kai ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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r_min in HaloProfiler
by Agarwal, Shankar 09 Dec '09

09 Dec '09

Hi, While running HaloProfiler, I am seeing this... P001 yt.lagos ERROR 2009-12-08 15:53:22,403 Skipping halo with r_max / r_min = 1.885682. I looked at yt/extensions/HaloProfiler.py... r_min = 2 * self.pf.h.get_smallest_dx() * self.pf['mpc'] if (halo['r_max'] / r_min < PROFILE_RADIUS_THRESHOLD): mylog.error("Skipping halo with r_max / r_min = %f." % (halo['r_max']/r_min)) r_max would be the distance to the furthest particle in the halo as found by HaloFinder. But what is r_min ? And what is the basis for skipping this halo ? shankar

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HaloFinder- parallel is slower?
by Agarwal, Shankar 07 Dec '09

07 Dec '09

Hi, I ran yt's HaloFinder routine on 1 processor, and then on 8 processors. Both give identical output : 40,000 halos starting from 512^3 particles. 1 processor : took 1 hour 45 minutes. 8 processors : took 2 hours. My script is hop_yt.py.... from yt.mods import * fn = "RedshiftOutput0002" pf = load(fn) halos = HaloFinder(pf,40,padding=0.02) halos.write_out("HopAnalysis.out") commands I used.... mpirun -np 1 python hop_yt.py --parallel mpirun -np 8 python hop_yt.py --parallel Any idea why 8 cpus would take longer ? shankar

2 1

running halo_profiler.py using mpi4py
by Agarwal, Shankar 07 Dec '09

07 Dec '09

Hi, I have about 40,000 halos (using Hop_Finder). And I want to run Halo_profiler on it. Since the number of halos is so large, I would like to use... mpirun -np <cpus> halo_profiler.py --parallel Steele-purdue has 8cpus per node. The 8 cpus have shared memory. But the nodes do not share memory. I want to know would I be better off using just 8 cpus (on 1 node) or should I use more nodes, considering I have 40,000 halos. regards shankar

2 1

mpi4py on Steele
by Agarwal, Shankar 06 Dec '09

06 Dec '09

Hi, I am trying to build/install mpi4py on Steele. I have downloaded mpi4py-1.1.0. The modules I have are... [agarwa23@tg-steele mpi4py-1.1.0]$ module list Currently Loaded Modulefiles: 1) intel64/11.1.038 2) mpich-intel64/11.1.038 3) java/1.6.0_14 4) mpich2-intel64/11.1.038 5) hdf5-1.8.3/intel-parallel I am getting warnings while building... [agarwa23@tg-steele mpi4py-1.1.0]$ python setup.py build running build running build_py creating build creating build/lib.linux-x86_64-2.6 creating build/lib.linux-x86_64-2.6/mpi4py copying src/rc.py -> build/lib.linux-x86_64-2.6/mpi4py copying src/__init__.py -> build/lib.linux-x86_64-2.6/mpi4py creating build/lib.linux-x86_64-2.6/mpi4py/include creating build/lib.linux-x86_64-2.6/mpi4py/include/mpi4py copying src/include/mpi4py/mpi4py.h -> build/lib.linux-x86_64-2.6/mpi4py/include/mpi4py copying src/include/mpi4py/mpi4py.MPI.h -> build/lib.linux-x86_64-2.6/mpi4py/include/mpi4py copying src/include/mpi4py/mpi4py.MPI_api.h -> build/lib.linux-x86_64-2.6/mpi4py/include/mpi4py copying src/include/mpi4py/MPI.pxd -> build/lib.linux-x86_64-2.6/mpi4py/include/mpi4py copying src/include/mpi4py/mpi_c.pxd -> build/lib.linux-x86_64-2.6/mpi4py/include/mpi4py copying src/include/mpi4py/__init__.pyx -> build/lib.linux-x86_64-2.6/mpi4py/include/mpi4py copying src/include/mpi4py/mpi.pxi -> build/lib.linux-x86_64-2.6/mpi4py/include/mpi4py copying src/include/mpi4py/mpi4py.i -> build/lib.linux-x86_64-2.6/mpi4py/include/mpi4py running build_ext MPI C compiler: /apps/rhel5/mpich2-1.1.1p1/64/nemesis-intel-11.1.038/bin/mpicc MPI C++ compiler: /apps/rhel5/mpich2-1.1.1p1/64/nemesis-intel-11.1.038/bin/mpicxx MPI linker: /apps/rhel5/mpich2-1.1.1p1/64/nemesis-intel-11.1.038/bin/mpicc building 'mpi4py.MPI' extension creating build/temp.linux-x86_64-2.6 creating build/temp.linux-x86_64-2.6/src /apps/rhel5/mpich2-1.1.1p1/64/nemesis-intel-11.1.038/bin/mpicc -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/ba01/u118/agarwa23/enzo1/src/yt/doc/yt-x86_64/include/python2.6 -c src/MPI.c -o build/temp.linux-x86_64-2.6/src/MPI.o src/mpi4py.MPI.c(80664): remark #111: statement is unreachable return (signed short)__Pyx_PyInt_AsSignedLong(x); ^ src/mpi4py.MPI.c(80679): remark #111: statement is unreachable return (signed int)__Pyx_PyInt_AsSignedLong(x); ^ src/mpi4py.MPI.c(153): remark #593: variable "__pyx_skip_dispatch" was set but never used static int __pyx_skip_dispatch = 0; ^ src/mpi4py.MPI.c(986): remark #593: variable "__pyx_v_6mpi4py_3MPI_inited_atimport" was set but never used static int __pyx_v_6mpi4py_3MPI_inited_atimport; ^ These warnings are only a chunk of a whole lot of warnings I get. Help needed shankar KU Cosmology

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Covering Grid Array Order
by Rick Wagner 02 Dec '09

02 Dec '09

Hi, I'm looking at the fixed resolution extraction example, and I'm wondering: what ordering (row or column) will the final will have? Thanks, Rick http://yt.enzotools.org/doc/cookbook/recipes.html#extract-fixed- resolution-data

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Hop vs HaloProfiler
by Agarwal, Shankar 02 Dec '09

02 Dec '09

Hi, I am a little confused as to how to use hop_circles. I tried this but it fails... from yt.mods import * fn = "RedshiftOutput0002" pf = load(fn) halos = HaloFinder(pf) halos.modify["hop_circles"](self, hop_output, max_number=None, annotate=False, min_size=20, max_size=10000000, font_size=8, print_halo_size=False, print_halo_mass=False, width=None) halos.write_out("HopAnalysis.out") Also, I tried HaloProfiler using http://yt.enzotools.org/doc/cookbook/recipes.html#cookbook-run-halo-profiler. It generated the radial_profiles/ directory with Halo_xxxx_profile.dat files. I am printing here the first few lines from Halo_0000_profile.dat... # ActualOverdensity CellVolume Density RadiusMpc Temperature TotalMassMsun myweight 2.796608e+03 9.422900e+72 1.407563e-27 1.086579e+00 4.551426e+07 3.320010e+13 3.334302e+12 1.587191e+03 1.884580e+73 3.247510e-28 1.121908e+00 3.392715e+07 3.768487e+13 7.692859e+11 1.213350e+03 3.298015e+73 8.512354e-28 1.158386e+00 3.176131e+07 5.041525e+13 2.016447e+12 9.092253e+02 5.182595e+73 7.672296e-28 1.196051e+00 3.692482e+07 5.936658e+13 1.817450e+12 Is Halo_0000_profile.dat related to the first Halo listed in HopAnalysis.out file ? What is # ? What is the meaning of ActualOverdensity ? And units ? What is the meaning of CellVolume? And units ? What is Density referring to ? And units ? What is mywieght ? I also got the projection/ directory. But I got errors... yt.lagos INFO 2009-11-24 16:57:52,561 Writing filtered halo list to /usr/rmt_share/scratch95/a/agarwa23/0eV/512/box200/sim1/RD0002/FilteredQuantities.out. yt INFO 2009-11-24 16:57:53,873 Created plot collection with default plot-center = [0.5, 0.5, 0.5] yt.lagos INFO 2009-11-24 16:57:53,873 Projecting halo 0000 in region: [0.154949, 0.130009, 0.810277] to [0.183709, 0.158769, 0.839037]. yt INFO 2009-11-24 16:57:53,875 Generating overlap masks for level 0 Reading and masking grids 100% ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Time: 00:00:00 yt INFO 2009-11-24 16:57:53,875 Finished calculating overlap. Projecting level 0 / 0 100% ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Time: 00:00:01 Combining level 0 / 0 100% ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Time: 00:00:00 yt INFO 2009-11-24 16:57:55,640 Level 0 done: 256 final yt INFO 2009-11-24 16:57:55,896 Generating overlap masks for level 0 Reading and masking grids 100% ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Time: 00:00:00 yt INFO 2009-11-24 16:57:55,896 Finished calculating overlap. Projecting level 0 / 0 100% ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Time: 00:00:01 Combining level 0 / 0 100% ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Time: 00:00:00 yt INFO 2009-11-24 16:57:57,381 Level 0 done: 256 final yt INFO 2009-11-24 16:57:57,527 Generating overlap masks for level 0 Reading and masking grids 100% ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Time: 00:00:00 yt INFO 2009-11-24 16:57:57,527 Finished calculating overlap. Traceback (most recent call last): | ETA: --:--:-- File "run_halo_profiler.py", line 37, in <module> halo_list='filtered',axes=[0,1,2]) File "/autohome/u118/agarwa23/enzo1/src/yt/yt/extensions/HaloProfiler.py", line 474, in make_projections serialize=False, **kwargs) File "/autohome/u118/agarwa23/enzo1/src/yt/yt/raven/PlotCollection.py", line 262, in add_projection return self._add_projection(PlotTypes.ProjectionPlot, *args, **kwargs) File "/autohome/u118/agarwa23/enzo1/src/yt/yt/raven/PlotCollection.py", line 285, in _add_projection center=center, **kwargs) File "/autohome/u118/agarwa23/enzo1/src/yt/yt/lagos/BaseDataTypes.py", line 951, in __init__ self._refresh_data() File "/autohome/u118/agarwa23/enzo1/src/yt/yt/lagos/BaseDataTypes.py", line 190, in _refresh_data self.get_data() File "/autohome/u118/agarwa23/enzo1/src/yt/yt/lagos/BaseDataTypes.py", line 1137, in get_data my_coords, my_dx, my_fields = self.__project_level(level, fields) File "/autohome/u118/agarwa23/enzo1/src/yt/yt/lagos/BaseDataTypes.py", line 1029, in __project_level g_coords, g_fields = self._project_grid(grid, fields, zero_out) File "/autohome/u118/agarwa23/enzo1/src/yt/yt/lagos/BaseDataTypes.py", line 1182, in _project_grid for field in fields] File "/autohome/u118/agarwa23/enzo1/src/yt/yt/lagos/BaseDataTypes.py", line 40, in save_state tr = func(self, grid, field) File "/autohome/u118/agarwa23/enzo1/src/yt/yt/lagos/BaseDataTypes.py", line 1222, in _get_data_from_grid return grid[field] * bad_points File "/autohome/u118/agarwa23/enzo1/src/yt/yt/lagos/BaseDataTypes.py", line 199, in __getitem__ self.get_data(key) File "/autohome/u118/agarwa23/enzo1/src/yt/yt/lagos/BaseGridType.py", line 96, in get_data self._generate_field(field) File "/autohome/u118/agarwa23/enzo1/src/yt/yt/lagos/BaseGridType.py", line 54, in _generate_field self.pf.field_info[field].check_available(self) File "/autohome/u118/agarwa23/enzo1/src/yt/yt/lagos/FieldInfoContainer.py", line 244, in check_available validator(data) File "/autohome/u118/agarwa23/enzo1/src/yt/yt/lagos/FieldInfoContainer.py", line 337, in __call__ raise NeedsDataField(doesnt_have) yt.lagos.FieldInfoContainer.NeedsDataField: (['Metal_Density']) shankar

5 12

limits of the colorbar
by Agarwal, Shankar 02 Dec '09

02 Dec '09

Hi, I tried to set the limits of the colorbar using set_zlim as below... fn = "RedshiftOutput0002" pf = load(fn) pc = PlotCollection(pf,center=[0.5,0.5,0.5]) p = pc.add_slice("Density", 0) p.set_zlim(1e-31, 1e-30) pc.save() But I keep getting a plot with colorbar ranging between (1e-31,1e-28). I can't see what I am missing. shankar

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yt-users December 2009