Dear yt users,
I have a problem when trying to make a SlicePlot along the y-axis of any
data, for any field. yt just hangs and no plot is created. For the x-
and z-axes everything works fine, and a ProjectionPlot along the y-axis
is also not a problem.
I have tried updating yt and installing the current development version,
but to no avail.
Any help is much appreciated!
Best regards,
Caroline
Hi yt user,
I have run a DM only cosmological simulation.
And, I would like to make usual Projection/Slice plots for DM
properties (density/ velocity).
Is there any way yt compute the dark matter properties and make
Projection/Slice plots.
In addition, when I make a Projection/Slice plots for inner ## kpc, it
turns out the length is a physical unit.
Is there any yt commend set width of plots as comoving length scale?
The comoving length scale could be useful when I make time series
Projection/Slice plots for a given region.
Thank you in advance,
Junhwan
--
--------------------------------------------------------------
Jun-Hwan Choi, Ph.D.
Department of Physics and Astronomy, University of Kentucky
Tel: (859) 897-6737 Fax: (859) 323-2846
Email: jhchoi(a)pa.uky.edu URL: http://www.pa.uky.edu/~jhchoi
--------------------------------------------------------------
Hi, all--
When I make a plot window, the axes are centered on the window center and
go from \pm 0.5. Is it possible to have those aligned with the thing I
plotted?
For instance, i have a region
reg = pf.h.region(Center,Left,Right)
proj = pf.h.proj( 0, 'Density', source=reg)
I'd like the center of the axes to be on Center, rather than 0. How do I
do that?
Thanks,
d.
--
Sent from my computer.
Hello Everybody,
I am writing you because I am using ProjectionPlot with annotate_marker
& annotate_point and I want them come in white. Right now, the
annotate_marker x is coming in blue and annotate_point in black. Do you
know how can changes them both to come in color white.
Thank in Advance
p = ProjectionPlot(pf,2,'Density','max',(100,'kpc'))
p.annotate_marker((0.402647,0.471724,0.461609),'x')
p.annotate_point((0.402862,0.472019,0.461895), "c1")
p.save('sliceplot')
Best Regards
Hi, all--
I have a dumb projection question.
Why is it that when I do a projection, the minimum pdx is smaller than the
minimum cell width in my simulation?
>>> pf.h.get_smallest_dx()
0.0001220703125
>>> 1./pf.h.get_smallest_dx()
8192.0
Additionally, the sum of the areas is not what I expect. I expect
>>> proj=pf.h.proj(0,'Density')
>>> (proj['pdx']*proj['pdy']).sum()
0.25
I get 0.25, instead of 1 (consistent with the above, if all the widths are
down by a factor of 2.)
I assumed that proj['pdx'] is the width of the zone of the projection,
which I naievely expect to be the smallest cell width along any line of
sight.
Could one of you good people fill in what I'm misunderstanding?
Thanks a ton!
d.
Hi all,
About a week ago, I issued a pull request to update the dependencies that get built by the install script:
https://bitbucket.org/yt_analysis/yt/pull-request/475/updating-the-dependen…
This pull request was accepted today.
If you are running the development version of yt built using the install script, you can upgrade the dependencies by doing running the yt updater at the command line:
$ yt update --all
If you are running yt 2.5.1 or an earlier stable release, you will be able to update your dependencies when the next stable yt release happens on or around May 1st.
As you can see reading over the discussion regarding the pull request, there was some concern about possible breakages due to these updates. If, after updating, you run into any broken functionality or odd issues, please let us know either by mailing the yt-users list or by reporting an issue on yt's bug tracker (https://bitbucket.org/yt_analysis/yt/issues/new).
Hopefully with periodic updates to yt's dependencies like this, we will be able to make bugfixes and new features available to users who run yt installations based on the install script in a painless, automated manner.
Happy computing,
Nathan Goldbaum
Hi all,
I'm not sure what list to send this to since it is about inline yt in
enzo, but I will try it here. I'm trying to do some simple inline tasks
for a non-cosmology problem (one that is not currently in the enzo-dev
repo). I'm trying to do some slices; I eventually want to do some 1-d
profiles and derived quantities.
I have a script that works on one processor (with MPI on), but when I
try to use more than one processor I get odd results. The slices I get
appear to contain only part of the simulation domain (so there is stuff
in part of the image and the rest is blank) and I get key errors from
some processors saying they can't find the Density field. The error is
pasted below. I'm guessing something about parallel yt is not working
correctly? I should also mention that this run does not use AMR. My yt
script is also pasted below, along with the enzo parameter file (which
is a little jumbled, sorry).
The yt version I'm using is the current one (I checked out the install
script today). I did have to comment out the following line in
yt-x86_64-shared/src/yt-hg/yt/frontends/enzo/data_structures.py:
#self.periodicity =
ensure_tuple(self.parameters["LeftFaceBoundaryCondition"] == 3)
The enzo version I'm using is the tip of the enzo-dev-mom fork which
diverged from enzo-dev after changeset e01ad22. I glanced through the
accepted pull requests, but nothing jumped out at me as being a
solution.
Any ideas would be appreciated.
Thanks
Christine
Error:
yt : [INFO ] 2013-04-02 16:00:50,454 Parameters: current_time
= 4.81533679704e-05
yt : [INFO ] 2013-04-02 16:00:50,454 Parameters: domain_dimensions
= [98 98 98]
yt : [INFO ] 2013-04-02 16:00:50,455 Parameters: current_time
= 4.81533679704e-05
yt : [INFO ] 2013-04-02 16:00:50,455 Parameters: domain_left_edge
= [ 0. 0. 0.]
yt : [INFO ] 2013-04-02 16:00:50,455 Parameters: domain_dimensions
= [98 98 98]
yt : [INFO ] 2013-04-02 16:00:50,455 Parameters: current_time
= 4.81533679704e-05
yt : [INFO ] 2013-04-02 16:00:50,455 Parameters: domain_right_edge
= [ 1. 1. 1.]
yt : [INFO ] 2013-04-02 16:00:50,455 Parameters: domain_left_edge
= [ 0. 0. 0.]
yt : [INFO ] 2013-04-02 16:00:50,455 Parameters:
cosmological_simulation = 0.0
yt : [INFO ] 2013-04-02 16:00:50,455 Parameters: domain_dimensions
= [98 98 98]
yt : [INFO ] 2013-04-02 16:00:50,455 Parameters: domain_right_edge
= [ 1. 1. 1.]
yt : [INFO ] 2013-04-02 16:00:50,456 Parameters:
cosmological_simulation = 0.0
yt : [INFO ] 2013-04-02 16:00:50,456 Parameters: domain_left_edge
= [ 0. 0. 0.]
yt : [INFO ] 2013-04-02 16:00:50,456 Parameters: domain_right_edge
= [ 1. 1. 1.]
yt : [INFO ] 2013-04-02 16:00:50,456 Parameters: current_time
= 4.81533679704e-05
yt : [INFO ] 2013-04-02 16:00:50,456 Parameters:
cosmological_simulation = 0.0
yt : [INFO ] 2013-04-02 16:00:50,456 Parameters: domain_dimensions
= [98 98 98]
yt : [INFO ] 2013-04-02 16:00:50,457 Parameters: current_time
= 4.81533679704e-05
yt : [INFO ] 2013-04-02 16:00:50,456 Parameters: domain_left_edge
= [ 0. 0. 0.]
yt : [INFO ] 2013-04-02 16:00:50,457 Parameters: domain_dimensions
= [98 98 98]
yt : [INFO ] 2013-04-02 16:00:50,457 Parameters: domain_right_edge
= [ 1. 1. 1.]
yt : [INFO ] 2013-04-02 16:00:50,457 Parameters:
cosmological_simulation = 0.0
yt : [INFO ] 2013-04-02 16:00:50,457 Parameters: domain_left_edge
= [ 0. 0. 0.]
yt : [INFO ] 2013-04-02 16:00:50,457 Parameters: current_time
= 4.81533679704e-05
yt : [INFO ] 2013-04-02 16:00:50,457 Parameters: domain_right_edge
= [ 1. 1. 1.]
yt : [INFO ] 2013-04-02 16:00:50,457 Parameters: domain_dimensions
= [98 98 98]
yt : [INFO ] 2013-04-02 16:00:50,457 Parameters:
cosmological_simulation = 0.0
yt : [INFO ] 2013-04-02 16:00:50,457 Parameters: domain_left_edge
= [ 0. 0. 0.]
yt : [INFO ] 2013-04-02 16:00:50,458 Parameters: domain_right_edge
= [ 1. 1. 1.]
yt : [INFO ] 2013-04-02 16:00:50,458 Parameters:
cosmological_simulation = 0.0
yt : [INFO ] 2013-04-02 16:00:50,459 Gathering a field list (this
may take a moment.)
yt : [INFO ] 2013-04-02 16:00:50,459 Gathering a field list (this
may take a moment.)
yt : [INFO ] 2013-04-02 16:00:50,460 Gathering a field list (this
may take a moment.)
Traceback (most recent call last):
File "<string>", line 1, in <module>
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "./user_script.py", line 19, in main
File "./user_script.py", line 19, in main
pc = PlotCollection(pf)
File
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/visualization/plot_collection.py", line 120, in __init__
pc = PlotCollection(pf)
v,self.c = pf.h.find_max("Density") # @todo: ensure no caching
File
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/object_finding_mixin.py", line 61, in find_max
File
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/visualization/plot_collection.py", line 120, in __init__
mg, mc, mv, pos = self.find_max_cell_location(field, finest_levels)
File
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/object_finding_mixin.py", line 74, in find_max_cell_location
v,self.c = pf.h.find_max("Density") # @todo: ensure no caching
File
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/object_finding_mixin.py", line 61, in find_max
source.quantities["MaxLocation"]( field, lazy_reader=True)
File
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/derived_quantities.py", line 92, in __call__
mg, mc, mv, pos = self.find_max_cell_location(field, finest_levels)
File
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/object_finding_mixin.py", line 74, in find_max_cell_location
return self._call_func_lazy(args, kwargs)
File
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/derived_quantities.py", line 99, in _call_func_lazy
source.quantities["MaxLocation"]( field, lazy_reader=True)
File
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/derived_quantities.py", line 92, in __call__
rv = self.func(GridChildMaskWrapper(g, self._data_source), *args,
**kwargs)
File
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/derived_quantities.py", line 669, in _MaxLocation
return self._call_func_lazy(args, kwargs)
File
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/derived_quantities.py", line 99, in _call_func_lazy
rv = self.func(GridChildMaskWrapper(g, self._data_source), *args,
**kwargs)
File
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/derived_quantities.py", line 669, in _MaxLocation
if data[field].size > 0:
File
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/derived_quantities.py", line 60, in __getitem__
if data[field].size > 0:
File
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/derived_quantities.py", line 60, in __getitem__
data = self.data_source._get_data_from_grid(self.grid, item)
File
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/data_containers.py", line 95, in save_state
data = self.data_source._get_data_from_grid(self.grid, item)
File
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/data_containers.py", line 95, in save_state
tr = func(self, grid, field, *args, **kwargs)
File
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/data_containers.py", line 2645, in _get_data_from_grid
tr = func(self, grid, field, *args, **kwargs)
File
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/data_containers.py", line 2645, in _get_data_from_grid
tr = grid[field]
File
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/grid_patch.py", line 157, in __getitem__
tr = grid[field]
File
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/grid_patch.py", line 157, in __getitem__
self.get_data(key)
File
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/grid_patch.py", line 200, in get_data
self.get_data(key)
File
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/grid_patch.py", line 200, in get_data
self._generate_field(field)
File
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/grid_patch.py", line 147, in _generate_field
self._generate_field(field)
File
"/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/data_objects/grid_patch.py", line 147, in _generate_field
raise exceptions.KeyError(field)
KeyError: raise exceptions.KeyError(field)
'Density'
KeyError: 'Density'
yt : [INFO ] 2013-04-02 16:00:50,892 Max Value is 1.00000e-24 at
0.0051020408163265 0.0051020408163265 0.0051020408163265 in grid
EnzoGrid_0001 at level 0 (0, 0, 0)
yt : [INFO ] 2013-04-02 16:00:50,892 Created plot collection with
default plot-center = [0.0051020408163265302, 0.0051020408163265302,
0.0051020408163265302]
yt : [INFO ] 2013-04-02 16:00:51,222 Added slice of Density at y =
0.00510204081633 with 'center' = [0.0051020408163265302,
0.0051020408163265302, 0.0051020408163265302]
yt : [INFO ] 2013-04-02 16:00:52,250 Saved
cycle00000001_Slice_y_Density.png
['z-velocity', 'Temperature', 'GasEnergy', 'Density', 'TotalEnergy',
'x-velocity', 'y-velocity']
python script:
from yt.mods import *
def main():
pf = EnzoStaticOutputInMemory()
pc = PlotCollection(pf)
pc.add_slice("Density",1)
pc.save()
print pf.h.field_list
enzo parameter file:
#
# AMR PROBLEM DEFINITION FILE: TestStarParticle
#
PythonTopGridSkip = 1
CellFlaggingMethod = 0
PPMDiffusionParameter = 0
PPMSteepeningParameter = 0
DensityUnits = 1.0e-24
LengthUnits = 3.01802501047e+20
#RadiativeCooling = 1
StarParticleFeedback = 2
RefineBy = 2
CourantSafetyNumber = 0.4
OutputCoolingTime = 1
dtDataDump = 0.1
TopGridDimensions = 98 98 98
TestStarParticleEnergy = 0.00104392468495
MaximumRefinementLevel = 0
Initialdt = 4.81533668755e-05
TestStarParticleDensity = 1.0
ProblemType = 90
PPMFlatteningParameter = 0
StopTime = 0.3
TopGridRank = 3
StarFeedbackKineticFraction = 1.0
StaticHierarchy = 1
Gamma = 1.66667
StarMassEjectionFraction = 0.25
TimeUnits = 3.15e13
TestStarParticleStarMass = 100.0
StarEnergyToThermalFeedback = 5.59e-6
HydroMethod = 0
DualEnergyFormalism = 1
#CycleSkipDataDump = 1
OutputTemperature = 1
Hello all,
I am having a some what weird issue while trying to run the latest version of the install script. This is the error I am getting:
creating build/temp.macosx-10.4-x86_64-2.7/numpy/core/blasdot
compile options: '-DNO_ATLAS_INFO=3 -Inumpy/core/blasdot -Inumpy/core/include -Ibuild/src.macosx-10.4-x86_64-2.7/numpy/core/include/numpy -Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/Users/Drummond/Cal/Research/Software/YT/yt-x86_64/include/python2.7 -Ibuild/src.macosx-10.4-x86_64-2.7/numpy/core/src/multiarray -Ibuild/src.macosx-10.4-x86_64-2.7/numpy/core/src/umath -c'
extra options: '-faltivec -I/System/Library/Frameworks/vecLib.framework/Headers'
gcc: numpy/core/blasdot/_dotblas.c
gcc.exec: error: unrecognized command line option ‘-faltivec’
gcc.exec: error: unrecognized command line option ‘-faltivec’
error: Command "gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -DNO_ATLAS_INFO=3 -Inumpy/core/blasdot -Inumpy/core/include -Ibuild/src.macosx-10.4-x86_64-2.7/numpy/core/include/numpy -Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/Users/Drummond/Cal/Research/Software/YT/yt-x86_64/include/python2.7 -Ibuild/src.macosx-10.4-x86_64-2.7/numpy/core/src/multiarray -Ibuild/src.macosx-10.4-x86_64-2.7/numpy/core/src/umath -c numpy/core/blasdot/_dotblas.c -o build/temp.macosx-10.4-x86_64-2.7/numpy/core/blasdot/_dotblas.o -faltivec -I/System/Library/Frameworks/vecLib.framework/Headers" failed with exit status 1
Any thoughts?
Thanks
Drummond
