Mailman 3 April 2013 - yt-users

cut region vs. projection?
by David Collins April 24, 2013

April 24, 2013

Hi, all-- Can I hand a cut_region to a projection? I want to make a bunch of projections based on parameters, and don't want to have to instantiate 47 different fields. I'm hoping something like region = pf.h.all_data().cut_region('grid["Density"] > 0.1 and grid["Density"] < 0.2') proj = pf.h.proj(0,"Density",region=cut_region) or something like that. Is that possible? I'm poking around the help and source, but no method immediately popped out at me. Thanks, d.

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cannot find some particle fields
by Jean-Claude Passy April 24, 2013

April 24, 2013

Hi all, sorry, I have a pretty dumb question. I have a non-cosmological simulation with only 1 particle. I can get the particle_mass field, but yt throws the following error when I try to grab particle_index: --------------------------------------------------------------------------------------------------------------------------------- In [1]: pf = load('CE0001') yt : [INFO ] 2013-04-24 00:32:02,190 Parameters: current_time = 0.00149998503444 yt : [INFO ] 2013-04-24 00:32:02,190 Parameters: domain_dimensions = [32 32 32] yt : [INFO ] 2013-04-24 00:32:02,190 Parameters: domain_left_edge = [ 0. 0. 0.] yt : [INFO ] 2013-04-24 00:32:02,190 Parameters: domain_right_edge = [ 1. 1. 1.] yt : [INFO ] 2013-04-24 00:32:02,191 Parameters: cosmological_simulation = 0.0 In [2]: region = pf.h.region([0.5, 0.5, 0.5], [0.0, 0.0, 0.0], [1.0, 1.0, 1.0]) yt : [INFO ] 2013-04-24 00:32:05,802 Getting the binary hierarchy yt : [INFO ] 2013-04-24 00:32:05,805 Finished with binary hierarchy reading In [3]: region['particle_mass'] yt : [INFO ] 2013-04-24 00:32:12,685 Getting particle_mass using ParticleIO Out[3]: array([ 6585896.1408]) In [4]: region['particle_index'] --------------------------------------------------------------------------- KeyError Traceback (most recent call last) /Users/jcpassy/Work/yt-x86_64/src/yt-hg/scripts/iyt in <module>() ----> 1 region['particle_index'] /Users/jcpassy/Work/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in __getitem__(self, key) 328 if key not in self.fields: 329 self.fields.append(key) --> 330 self.get_data(key) 331 return self.field_data[key] 332 /Users/jcpassy/Work/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in get_data(self, fields, in_grids, force_particle_read) 2614 pass 2615 if field not in self.hierarchy.field_list and not in_grids: -> 2616 if self._generate_field(field): 2617 continue # True means we already assigned it 2618 mylog.info("Getting field %s from %s", field, len(self._grids)) /Users/jcpassy/Work/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _generate_field(self, field) 361 return True 362 else: # Can't find the field, try as it might --> 363 raise KeyError(field) 364 365 def _generate_field_in_grids(self, field, num_ghost_zones=0): KeyError: 'particle_index' --------------------------------------------------------------------------------------------------------------------------------- However, the field is there: --------------------------------------------------------------------------------------------------------------------------------- [ 0:30:13] Obiwan:$ h5ls CE0001.cpu0000/Grid00000004 Dark_Matter_Density Dataset {52, 52, 52} Density Dataset {52, 52, 52} TotalEnergy Dataset {52, 52, 52} particle_index Dataset {1} particle_mass Dataset {1} particle_position_x Dataset {1} particle_position_y Dataset {1} particle_position_z Dataset {1} particle_type Dataset {1} particle_velocity_x Dataset {1} particle_velocity_y Dataset {1} particle_velocity_z Dataset {1} x-velocity Dataset {52, 52, 52} y-velocity Dataset {52, 52, 52} z-velocity Dataset {52, 52, 52} [ 0:30:13] Obiwan:$ h5ls -d CE0001.cpu0000/Grid00000004/particle_index particle_index Dataset {1} Data: (0) 0 --------------------------------------------------------------------------------------------------------------------------------- Am I missing something obvious? Thanks a lot for you help, JC

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SlicePlot y-axis problem
by Caroline Van Borm April 23, 2013

April 23, 2013

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

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DM visualization question
by Jun-Hwan Choi April 22, 2013

April 22, 2013

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 --------------------------------------------------------------

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plot window axes
by david collins April 16, 2013

April 16, 2013

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.

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ProjectionPlot, annotate_marker & annotate_point
by Francia Riesco April 15, 2013

April 15, 2013

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

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Projection Question
by david collins April 12, 2013

April 12, 2013

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.

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Updates for yt dependencies
by Nathan Goldbaum April 12, 2013

April 12, 2013

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

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inline yt in parallel
by Christine Simpson April 12, 2013

April 12, 2013

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

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gcc compiler option problem during install
by Drummond Fielding April 11, 2013

April 11, 2013

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

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