Re: [yt-users] Analyzing DM-only data
by Eric Hallman
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/
8 years, 11 months
Re: [yt-users] [Enzo-users-l] Compiling Enzo on TACC Ranger
by kcai＠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.
8 years, 11 months
r_min in HaloProfiler
by Agarwal, Shankar
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
9 years
HaloFinder- parallel is slower?
by Agarwal, Shankar
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
9 years
running halo_profiler.py using mpi4py
by Agarwal, Shankar
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
9 years
mpi4py on Steele
by Agarwal, Shankar
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
9 years
Hop vs HaloProfiler
by Agarwal, Shankar
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
9 years
limits of the colorbar
by Agarwal, Shankar
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
9 years
