Mailman 3 November 2013 - yt-users

Yt-3.0 Ray Casting Progress bar
by Alex Bogert 30 Nov '13

30 Nov '13

Hi Guys, The ray casting progress bar is growing the white space in the ipython notebook when I have it inside of a for loop. I think this is because the progress bar is always being drawn on a new line after each iteration. Alex

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Segmentation Fault Analyzing Gasoline (TIPSY) data with yt-3.0
by Samantha Benincasa 29 Nov '13

29 Nov '13

Hello, I have been trying to analyze a TIPSY dataset using the new features in yt-3.0. I am unable to do any analysis without getting a segmentation fault. Following the python notebook example for Gasoline, I read in the data using the command: ds = TipsyStaticOutput('test.00001',parameter_file='test.param') When I try to construct a plot collection, I am given the following error: YTDomainOverflow: Particle bounds [ 1.25443703e-02 -5.12246704e+02 -5.46726685e+02] and [ 1.25443703e-02 5.65781677e+02 4.61335541e+02] exceed domain bounds [-0.5 -0.5 -0.5] and [ 0.5 0.5 0.5] If I instead try to manually set the domain bounds in the TipsyStaticOutput command, ds = TipsyStaticOutput('test.00001',parameter_file='test.param',domain_left_edge=[-57,-57,-57],domain_right_edge=[57,57,57]) This gets rid of the domain boundary errors but I still receive a segmentation fault when I try to create the PlotCollection. I am just trying to read the data in so I can make slices/projections in temperature and density. Thank you in advance for the help, Samantha

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Problem with covering_grid
by Wolfram Schmidt 29 Nov '13

29 Nov '13

Hi, I want to read in the root-grid data from AMR output produce by Nyx. The following piece of code used to work a while ago and something similar can be found in the recipes: n_levels = 0 pf =load(path) left=na.amin(pf.h.grid_left_edge,axis=0) right=na.amax(pf.h.grid_right_edge,axis=0) resolution = 2**n_levels*pf.domain_dimensions print n_levels, left, right, resolution cg = pf.h.covering_grid(n_levels, left_edge=left, right_edge=right, dims=resolution) With the current stable yt version, however, I get the following error: 0 [ 0. 0. 0.] [ 2.46880000e+25 1.23440000e+25 1.23440000e+25] [256, 128, 128] Traceback (most recent call last): File "/usr/users/wschmid2/scripts/radial_profile.py", line 71, in <module> cg = pf.h.covering_grid(n_levels, left_edge=left, right_edge=right, dims=resolution) File "/home/uni05/wschmid2/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 3706, in __init__ rdx[np.where(dims - 2 * num_ghost_zones <= 1)] = 1 # issue 602 TypeError: list indices must be integers, not tuple Since the output in the first line produced by the print statement shows that all parameters are perfectly ok, I don't understant what's the problem. Can anyone help? Cheers, Wolfram

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more gadget visualization
by Desika Narayanan 27 Nov '13

27 Nov '13

Hey Team YT, I have a couple of (I think super-easy) questions: a. How do you paste a script to the yt pastebin? I've done it successfully once before, but can't for the life of me figure out how I did it. b. Relatedly, there's a (like 10 line) script appended below where I projection plot gas densities from a Gadget simulation. I'd like to be able to do the following: b.i - I'd like to be able to project other fields. For example, if I look at pf.h.field_list, I get that for particle type 0, the fields: ('PartType0', 'Masses'), ('PartType0', 'Metallicity') exist. However, if I try to project: >p = ProjectionPlot(pf,'z',(("deposit", "PartType0_metallicity"))) (instead of the successful density line below), I get the error : >YTFieldNotFound: Could not find field '('deposit', 'PartType0_metallicity')' in snapshot_006. b.ii. Assuming the parts from b.i are possible, is it then possible to multiply two fields together in the projection (say, I wanted metal mass and wanted to multiply the particle masses by the particle metallicities). Similarly, is it possible to multiply a field by a constant for the particle deposition into a projection plot? Thanks, Desika ------------------------- from yt.mods import * snap = "/Users/desika/powderday/grid_data/snapshot_006.hdf5" bbox = [[-220.0, 220.0], [-220.0, 220.0], [-220.0, 220.0]] unit_base = {'UnitLength_in_cm' : 3.08568e+21, 'UnitMass_in_g' : 1.989e+43, 'UnitVelocity_in_cm_per_s' : 100000} pf = load(snap,unit_base = unit_base,bounding_box=bbox) pf.h p = ProjectionPlot(pf,'z',(("deposit", "PartType0_density"))) p.set_width(200,'kpc') p.save()

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Fwd: [Anaconda Support] yt available on 64-bit Linux and Mac
by Nathan Goldbaum 27 Nov '13

27 Nov '13

It looks like yt 2.6 is now available on Anaconda! Thanks very much to Ilan Schnell at Continuum analytics for setting this up. ---------- Forwarded message ---------- From: Ilan Schnell <ilan(a)continuum.io> Date: Wed, Nov 27, 2013 at 1:05 AM Subject: [Anaconda Support] yt available on 64-bit Linux and Mac To: Anaconda <anaconda(a)continuum.io> Since there has been some discussion about how to build yt (in particular for the Mac), I've spend some time building it and making it available: $ conda install yt will give you the latest yt 2.6. Note that the above will only work if you're on either 64-bit Linux or 64-bit Mac. - Ilan -- Anaconda Community Support Group Brought to you by Continuum Analytics --- You received this message because you are subscribed to the Google Groups "Anaconda - Public" group. To unsubscribe from this group and stop receiving emails from it, send an email to anaconda+unsubscribe(a)continuum.io. To post to this group, send email to anaconda(a)continuum.io. Visit this group at http://groups.google.com/a/continuum.io/group/anaconda/.

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RFC: RAMSES field aliases in yt-3.0
by Matthew Turk 26 Nov '13

26 Nov '13

Hi all, especially RAMSES users, I'm setting up aliases to make it easier to load RAMSES datasets that have different field configurations. Right now, to specify a different set of fields, you have to do: pf = load( ... , fields = [ "Density", "x-velocity", ...]) I am going to change this to add on different field configurations that can be specified with just a string. For instance: pf = load(..., fields = "standard_five") I'm wondering what the different configurations are. I have these two: standard_five: Density, x-velocity, y-velocity, z-velocity, Pressure standard_six: Density, x-velocity, y-velocity, z-velocity, Pressure, Metallicity But for MHD and RHD, what are the additional fields that should be added, and in what order? And are there other common configurations that should be aliased? If we can come up with a set of aliases that match most use cases, that'd work quite well. I'm going to issue a PR for this shortly, and hopefully it will make everybody's life a bit easier. -Matt

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Problem in accessing ramses data
by Junhwan Choi (최준환) 25 Nov '13

25 Nov '13

Hi yt user, Here I try to make some plots with centering to the densest cell using following script: ===================== from yt.mods import * ds = load("/lustre/widow2/proj/ast031/test11_rhd_fesc=0.05/output_00048/info_00048.txt", fields = ["Density","x-velocity", "y-velocity", "z-velocity","Pressure","Metallicity","HI"]) center = ds.h.find_max("Density")[1] pw = ProjectionPlot(ds, "x", "Density", weight_field="Density", center=center) pw.zoom(1.01) pw.save("allviewGas") pw = ProjectionPlot(ds, "y", "Density", weight_field="Density", center=center) pw.zoom(1.01) pw.save("allviewGas") pw = ProjectionPlot(ds, "z", "Density" , weight_field="Density", center=center) pw.zoom(1.01) pw.save("allviewGas") ===================== and, I got the following error message File "VisFrame.py", line 4, in <module> den_center = ds.h.find_max("Density")[1] File "/autofs/na3_home1/jhchoi/common/src/yt-hg/yt/geometry/oct_geometry_handler.py", line 59, in find_max mv, pos = self.find_max_cell_location(field, finest_levels) File "/autofs/na3_home1/jhchoi/common/src/yt-hg/yt/geometry/oct_geometry_handler.py", line 69, in find_max_cell_location source.quantities["MaxLocation"](field) File "/autofs/na3_home1/jhchoi/common/src/yt-hg/yt/data_objects/derived_quantities.py", line 79, in __call__ return self.c_func(self._data_source, *retvals) File "/autofs/na3_home1/jhchoi/common/src/yt-hg/yt/data_objects/derived_quantities.py", line 666, in _combMaxLocation i = np.argmax(args[0]) # ma is arg[0] File "/ccs/home/jhchoi/common/lib/python2.7/site-packages/numpy/core/fromnumeric.py", line 738, in argmax return argmax(axis) ValueError: attempt to get argmax of an empty sequence In order to check whether the simulation Density output is messed up, I replace "center = ds.h.find_max("Density")[1]" to "center=[0,0,0]", then I am able to make Density projection. This test suggest that the Density output in the simulation is alright, but the "ds.h.find_max("Density")[1]" has problem. Does anyone know how to resolve it? Thank you in advance, Junhwan

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How to access fields from a previous level?
by Reju Sam John 25 Nov '13

25 Nov '13

Dear all, I am analyzing a particular level "RD0040/RedshiftOutput0040". If I want to load a field from previous level ie. from "RD0039/RedshiftOutput0039", what is the method? I want to calculate data["Temperature"] / data["Temperature"], where first one is from RD0040/RedshiftOutput0040" and second one is from "RD0039/RedshiftOutput0039". Please suggest a method. -- Reju Sam John

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Error in reading the hydrodynamics dataset in Ramses
by Junhwan Choi (최준환) 25 Nov '13

25 Nov '13

Hi yt users, I try to make a basic visualization for the Ramses simulation using following script: ========================== from yt.mods import * ds = load("/lustre/widow2/proj/ast031/test11_rhd_fesc=0.05/output_00048/info_00048.txt") center = [0.5, 0.5, 0.5] pw = ProjectionPlot(ds, "x", ("deposit", "all_density")) pw.zoom(1.01) pw.save("allview") pw = ProjectionPlot(ds, "x", "Density") pw.zoom(1.01) pw.save("allviewGas") ============================ It WORKS for the particle projection (for allview) but it does not work for gas projection. When the yt try to deal with gas dataset, I got the following error message and the script crash. You are running with the wrong number of fields. Please specify these in the load command. We are looking for 6 fields. The last set of field sizes was: [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] Traceback (most recent call last): File "DenVis_DM_Gas.py", line 10, in <module> pw = ProjectionPlot(ds, "x", ("gas", "Density")) File "/autofs/na3_home1/jhchoi/common/src/yt-hg/yt/visualization/plot_window.py", line 1441, in __init__ field_parameters = field_parameters) File "/autofs/na3_home1/jhchoi/common/src/yt-hg/yt/data_objects/construction_data_containers.py", line 234, in __init__ self.get_data(field) File "/autofs/na3_home1/jhchoi/common/src/yt-hg/yt/data_objects/construction_data_containers.py", line 278, in get_data chunk_fields, "io")): File "/autofs/na3_home1/jhchoi/common/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 434, in parallel_objects for obj_id, obj in oiter: File "/autofs/na3_home1/jhchoi/common/src/yt-hg/yt/data_objects/data_containers.py", line 453, in chunks self.get_data(fields) File "/autofs/na3_home1/jhchoi/common/src/yt-hg/yt/data_objects/data_containers.py", line 531, in get_data fluids, self, self._current_chunk) File "/autofs/na3_home1/jhchoi/common/src/yt-hg/yt/geometry/geometry_handler.py", line 520, in _read_fluid_fields chunk_size) File "/autofs/na3_home1/jhchoi/common/src/yt-hg/yt/frontends/ramses/io.py", line 41, in _read_fluid_selection rv = subset.fill(content, fields, selector) File "/autofs/na3_home1/jhchoi/common/src/yt-hg/yt/frontends/ramses/data_structures.py", line 304, in fill for level, offset in enumerate(self.domain.hydro_offset): File "/autofs/na3_home1/jhchoi/common/src/yt-hg/yt/frontends/ramses/data_structures.py", line 102, in hydro_offset hvals = fpu.read_attrs(f, header, "=") File "/autofs/na3_home1/jhchoi/common/src/yt-hg/yt/utilities/fortran_utils.py", line 74, in read_attrs assert(s1 == s2) AssertionError I do not understand what is the problem since it is such a basic visualization. Since I am new for Ramses data, I may take a simple mistake. Can anyone explain what the error message means and how to resolve the problem? Thank you in advance, Junhwan

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Install script doesn't copy progressbar
by Sam Geen 25 Nov '13

25 Nov '13

Hi, I noticed that in the latest version of the install script from yt 3.0 obtained via "hg clone https://bitbucket.org/yt_analysis/yt-3.0" (in the past hour) seems to have a bug; when I tried it, it didn't copy yt/extern/progressbar to the install location; when running "from yt.mods import *", it brings up an error. Copying the folder by hand to the extern folder at the install location appears to fix the problem. Error text: --- In [1]: import yt.mods --------------------------------------------------------------------------- ImportError Traceback (most recent call last) <ipython-input-1-fcd62da66eec> in <module>() ----> 1 import yt.mods /usr/local/lib/python2.7/dist-packages/yt-3.0dev-py2.7-linux-x86_64.egg/yt/mods.py in <module>() 33 # See http://lists.spacepope.org/pipermail/yt-dev-spacepope.org/2011-December/ 34 # 001727.html ---> 35 import yt.startup_tasks as __startup_tasks 36 unparsed_args = __startup_tasks.unparsed_args 37 /usr/local/lib/python2.7/dist-packages/yt-3.0dev-py2.7-linux-x86_64.egg/yt/startup_tasks.py in <module>() 20 21 from yt.config import ytcfg ---> 22 from yt.funcs import * 23 24 exe_name = os.path.basename(sys.executable) /usr/local/lib/python2.7/dist-packages/yt-3.0dev-py2.7-linux-x86_64.egg/yt/funcs.py in <module>() 25 from yt.utilities.logger import ytLogger as mylog 26 from yt.utilities.definitions import inv_axis_names, axis_names, x_dict, y_dict ---> 27 import yt.extern.progressbar as pb 28 import yt.utilities.rpdb as rpdb 29 from collections import defaultdict ImportError: No module named progressbar > /usr/local/lib/python2.7/dist-packages/yt-3.0dev-py2.7-linux-x86_64.egg/yt/funcs.py(27)<module>() 26 from yt.utilities.definitions import inv_axis_names, axis_names, x_dict, y_dict ---> 27 import yt.extern.progressbar as pb 28 import yt.utilities.rpdb as rpdb --- Cheers, Sam

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