Mailman 3 March 2017 - yt-dev

Issue #1330: save_as_dataset() function not work properly with cut_region() resutls (yt_analysis/yt)
by Weiguang Cui March 3, 2017

March 3, 2017

New issue 1330: save_as_dataset() function not work properly with cut_region() resutls https://bitbucket.org/yt_analysis/yt/issues/1330/save_as_dataset-function-n… Weiguang Cui: The ds.sphere() function results can be wrote without a problem: -------------------------------------------------------------------------------------- sp = ds.sphere("max", (0.5, 'Mpc')) In [6]: sp.save_as_dataset(fields=["temperature"]) yt : [INFO ] 2017-03-03 11:15:03,452 Saving field data to yt dataset: … [View More]

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Issue #1329: frb.data for OffAxisProjectionPlot giving back the exact same array for different fields (yt_analysis/yt)
by Christoph Federrath March 3, 2017

March 3, 2017

New issue 1329: frb.data for OffAxisProjectionPlot giving back the exact same array for different fields https://bitbucket.org/yt_analysis/yt/issues/1329/frbdata-for-offaxisproject… Christoph Federrath: Hi there, I have been trying to get off axis projections, but I've wanted to plot the projects with my own code, so have been using frb.data to retrieve the fields eg. weighted_proj = yt.OffAxisProjectionPlot(ds, L, ['velx', 'velz', 'magx', 'magz'], center=c, width=(x_width, 'AU'), depth=(… [View More]args.slice_thickness, 'AU'), weight_field='density') velx = weighted_proj.frb.data[('flash', 'velx')] velz = weighted_proj.frb.data[('flash', 'velz')] magx = weighted_proj.frb.data[('flash', 'magx')] magz = weighted_proj.frb.data[('flash', 'magz')] The output is all the same: (Pdb) velx ImageArray([[ 33142.74880205, 33142.74880205, 33142.74880205, ..., 33175.42774805, 33175.42774805, 33175.42774805], [ 33142.74880205, 33142.74880205, 33142.74880205, ..., 33175.42774805, 33175.42774805, 33175.42774805], [ 33142.74880205, 33142.74880205, 33142.74880205, ..., 33175.42774805, 33175.42774805, 33175.42774805], ..., [-33143.85074608, -33143.85074608, -33143.85074608, ..., -33172.57495914, -33172.57495914, -33172.57495914], [-33143.85074608, -33143.85074608, -33143.85074608, ..., -33172.57495914, -33172.57495914, -33172.57495914], [-33143.85074608, -33143.85074608, -33143.85074608, ..., -33172.57495914, -33172.57495914, -33172.57495914]]) code_length/code_time (Pdb) velz ImageArray([[ 33142.74880205, 33142.74880205, 33142.74880205, ..., 33175.42774805, 33175.42774805, 33175.42774805], [ 33142.74880205, 33142.74880205, 33142.74880205, ..., 33175.42774805, 33175.42774805, 33175.42774805], [ 33142.74880205, 33142.74880205, 33142.74880205, ..., 33175.42774805, 33175.42774805, 33175.42774805], ..., [-33143.85074608, -33143.85074608, -33143.85074608, ..., -33172.57495914, -33172.57495914, -33172.57495914], [-33143.85074608, -33143.85074608, -33143.85074608, ..., -33172.57495914, -33172.57495914, -33172.57495914], [-33143.85074608, -33143.85074608, -33143.85074608, ..., -33172.57495914, -33172.57495914, -33172.57495914]]) code_length/code_time (Pdb) magx ImageArray([[ 33142.74880205, 33142.74880205, 33142.74880205, ..., 33175.42774805, 33175.42774805, 33175.42774805], [ 33142.74880205, 33142.74880205, 33142.74880205, ..., 33175.42774805, 33175.42774805, 33175.42774805], [ 33142.74880205, 33142.74880205, 33142.74880205, ..., 33175.42774805, 33175.42774805, 33175.42774805], ..., [-33143.85074608, -33143.85074608, -33143.85074608, ..., -33172.57495914, -33172.57495914, -33172.57495914], [-33143.85074608, -33143.85074608, -33143.85074608, ..., -33172.57495914, -33172.57495914, -33172.57495914], [-33143.85074608, -33143.85074608, -33143.85074608, ..., -33172.57495914, -33172.57495914, -33172.57495914]]) code_magnetic (Pdb) magz ImageArray([[ 33142.74880205, 33142.74880205, 33142.74880205, ..., 33175.42774805, 33175.42774805, 33175.42774805], [ 33142.74880205, 33142.74880205, 33142.74880205, ..., 33175.42774805, 33175.42774805, 33175.42774805], [ 33142.74880205, 33142.74880205, 33142.74880205, ..., 33175.42774805, 33175.42774805, 33175.42774805], ..., [-33143.85074608, -33143.85074608, -33143.85074608, ..., -33172.57495914, -33172.57495914, -33172.57495914], [-33143.85074608, -33143.85074608, -33143.85074608, ..., -33172.57495914, -33172.57495914, -33172.57495914], [-33143.85074608, -33143.85074608, -33143.85074608, ..., -33172.57495914, -33172.57495914, -33172.57495914]]) code_magnetic I mean, it gives back the correct units, but the array values are all identical between the different fields. [View Less]

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Issue #1328: "Too many files" error when trying to create ExodusII simulation (yt_analysis/yt)
by Alexander Lindsay March 2, 2017

March 2, 2017

New issue 1328: "Too many files" error when trying to create ExodusII simulation https://bitbucket.org/yt_analysis/yt/issues/1328/too-many-files-error-when-… Alexander Lindsay: We have a user who has a large transient simulation broken up into several exodus files because of adaptive mesh refinement. In general in these AMR simulations, it is unknown which file will contain a certain time point. One can determine the file using a script like the following: ``` sim = yt.simulation("… [View More]

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Issue #1327: Covering Grid is not working (yt_analysis/yt)
by Yi-Hao Chen March 2, 2017

March 2, 2017

New issue 1327: Covering Grid is not working https://bitbucket.org/yt_analysis/yt/issues/1327/covering-grid-is-not-worki… Yi-Hao Chen: Using the sample data and example script in the documentation, it seems that covering_grid is not working under the "tip" version of the code. It works under the "stable" branch. ``` #!python In [1]: import yt In [2]: ds = yt.load('Enzo_64/DD0043/data0043') yt : [INFO ] 2017-03-02 13:01:44,769 Parameters: current_time = 645.817072369 yt : … [View More][INFO ] 2017-03-02 13:01:44,769 Parameters: domain_dimensions = [64 64 64] yt : [INFO ] 2017-03-02 13:01:44,770 Parameters: domain_left_edge = [ 0. 0. 0.] yt : [INFO ] 2017-03-02 13:01:44,770 Parameters: domain_right_edge = [ 1. 1. 1.] yt : [INFO ] 2017-03-02 13:01:44,771 Parameters: cosmological_simulation = 1 yt : [INFO ] 2017-03-02 13:01:44,771 Parameters: current_redshift = 0.00139308806408 yt : [INFO ] 2017-03-02 13:01:44,771 Parameters: omega_lambda = 0.7 yt : [INFO ] 2017-03-02 13:01:44,771 Parameters: omega_matter = 0.3 yt : [INFO ] 2017-03-02 13:01:44,771 Parameters: hubble_constant = 0.71 In [3]: all_data_level_0 = ds.covering_grid(level=0, left_edge=[0,0.0,0.0],dims=[64, 64, 64]) In [4]: print(all_data_level_0['density'].shape) Parsing Hierarchy : 100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 752/752 [00:00<00:00, 5132.73it/s] yt : [INFO ] 2017-03-02 13:02:05,512 Gathering a field list (this may take a moment.) --------------------------------------------------------------------------- TypeError Traceback (most recent call last) <ipython-input-4-4b159ea40f36> in <module>() ----> 1 print(all_data_level_0['density'].shape) /home/ychen/src/yt_yihaochen/yt/data_objects/data_containers.pyc in __getitem__(self, key) 279 return self.field_data[f] 280 else: --> 281 self.get_data(f) 282 # fi.units is the unit expression string. We depend on the registry 283 # hanging off the dataset to define this unit object. /home/ychen/src/yt_yihaochen/yt/data_objects/construction_data_containers.pyc in get_data(self, fields) 629 raise 630 if len(part) > 0: self._fill_particles(part) --> 631 if len(fill) > 0: self._fill_fields(fill) 632 for a, f in sorted(alias.items()): 633 self[a] = f(self) /home/ychen/src/yt_yihaochen/yt/data_objects/construction_data_containers.pyc in _fill_fields(self, fields) 677 fill_region(input_fields, output_fields, self.level, 678 self.global_startindex, chunk.icoords, chunk.ires, --> 679 domain_dims, refine_by) 680 for name, v in zip(fields, output_fields): 681 fi = self.ds._get_field_info(*name) /home/ychen/src/yt_yihaochen/yt/utilities/lib/misc_utilities.pyx in yt.utilities.lib.misc_utilities.fill_region (yt/utilities/lib/misc_utilities.c:16208)() 796 if i < 0 or i >= ofield.shape[0]: continue 797 for oj in range(3): --> 798 j = nj + (oj - 1) 799 if j < 0 or j >= ofield.shape[1]: continue 800 for ok in range(3): TypeError: only length-1 arrays can be converted to Python scalars ``` [View Less]

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New YTEP needs review: major changes for SPH data
by Nathan Goldbaum March 1, 2017

March 1, 2017

Hi all, I've just opened a pull request for a new YTEP: https://bitbucket.org/yt_analysis/ytep/pull-requests/67/ This describes a big piece of work that several community members have been collaborating on for the past year or two. I've personally been involved over the past six months in an effort to get this into a state where it can be included in yt. The goal is to improve the scaling, performance, and ease of use of yt when working with particle data (including and especially SPH … [View More]

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