Mailman 3 May 2019 - yt-users

ISSUE ACCESSING 'PARTICLE_AGE' AFTER THE COMMIT 2259
by Vadlamani Samhitha May 14, 2019

May 14, 2019

Hi, Following the commit (https://github.com/yt-project/yt/pull/2259), I am unable to access the field 'particle_age' which I was able to do before. The list of fields I currently have for my RAMSES data is: > ('all', 'mesh_id') > > ('all', 'particle_angular_momentum') > > ('all', 'particle_angular_momentum_magnitude') > > ('all', 'particle_angular_momentum_x') > > ('all', 'particle_angular_momentum_y') > > ('all', 'particle_angular_momentum_z') > > ('all', 'particle_cylindrical_velocity_theta') > > ('all', 'particle_cylindrical_velocity_z') > > ('all', 'particle_extra_field_1') > > ('all', 'particle_extra_field_2') > > ('all', 'particle_extra_field_3') > > ('all', 'particle_extra_field_4') > > ('all', 'particle_extra_field_5') > > ('all', 'particle_identity') > > ('all', 'particle_index') > > ('all', 'particle_mass') > > ('all', 'particle_ones') > > ('all', 'particle_position') > > ('all', 'particle_position_cylindrical_radius') > > ('all', 'particle_position_cylindrical_theta') > > ('all', 'particle_position_cylindrical_z') > > ('all', 'particle_position_relative') > > ('all', 'particle_position_relative_x') > > ('all', 'particle_position_relative_y') > > ('all', 'particle_position_relative_z') > > ('all', 'particle_position_spherical_phi') > > ('all', 'particle_position_spherical_radius') > > ('all', 'particle_position_spherical_theta') > > ('all', 'particle_position_x') > > ('all', 'particle_position_y') > > ('all', 'particle_position_z') > > ('all', 'particle_radial_velocity') > > ('all', 'particle_radius') > > ('all', 'particle_refinement_level') > > ('all', 'particle_specific_angular_momentum') > > ('all', 'particle_specific_angular_momentum_x') > > ('all', 'particle_specific_angular_momentum_y') > > ('all', 'particle_specific_angular_momentum_z') > > ('all', 'particle_spherical_position_phi') > > ('all', 'particle_spherical_position_radius') > > ('all', 'particle_spherical_position_theta') > > ('all', 'particle_spherical_velocity_phi') > > ('all', 'particle_spherical_velocity_radius') > > ('all', 'particle_spherical_velocity_theta') > > ('all', 'particle_velocity') > > ('all', 'particle_velocity_cylindrical_radius') > > ('all', 'particle_velocity_cylindrical_theta') > > ('all', 'particle_velocity_cylindrical_z') > > ('all', 'particle_velocity_magnitude') > > ('all', 'particle_velocity_relative') > > ('all', 'particle_velocity_relative_x') > > ('all', 'particle_velocity_relative_y') > > ('all', 'particle_velocity_relative_z') > > ('all', 'particle_velocity_spherical_phi') > > ('all', 'particle_velocity_spherical_radius') > > ('all', 'particle_velocity_spherical_theta') > > ('all', 'particle_velocity_x') > > ('all', 'particle_velocity_y') > > ('all', 'particle_velocity_z') > > ('all', 'relative_particle_position') > > ('all', 'relative_particle_position_x') > > ('all', 'relative_particle_position_y') > > ('all', 'relative_particle_position_z') > > ('all', 'relative_particle_velocity') > > ('all', 'relative_particle_velocity_x') > > ('all', 'relative_particle_velocity_y') > > ('all', 'relative_particle_velocity_z') > I tried the 'extra_fields_x' but none of them match with the dimensions of time. Any help is appreciated and thanks.

3 5

Enzo gravitational fields
by Sam Patrick May 14, 2019

May 14, 2019

Hi all, I'm trying to find a way to access the gravitational field in an Enzo 2.5 simulation. I've tried creating a gradient field of ('gas', 'gravitational_potential') but I am unable to find this under the ds.derived_field_list either. Has anybody else been successful in extracting this information from an Enzo dataset? I'm currently running version 3.7.1 of Python and 3.5.0 of yt. Many thanks, Sam Patrick

2 1

Problem with unit when plotting profile(
by Eunjin Shin May 8, 2019

May 8, 2019

Hello all, I am making some profile plot for Gadget simualtion using yt (Version = 3.5.dev0 Changeset = ba2b2efe8962), but the resulting plot unit is mismatched with both yt-3 & 4.[The x-axis unit is extremly big 1e22kpc] I tested my script with Gadget example file (http://yt-project.org/data/GadgetDiskGalaxy.tar.gz), but that has same problem. The below is my script. import numpy import yt bb=100000 pf=yt.load('snapshot_200.hdf5' ,bounding_box=[[-bb,bb], [-bb, bb], [-bb,bb]]) figure_width=100 def _particle_position_cylindrical_z_abs(field, data): return numpy.abs(data[("PartType0", "particle_position_cylindrical_z")]) pf.add_field(("PartType0", "particle_position_cylindrical_z_abs"), function=_particle_position_cylindrical_z_abs, take_log=False, particle_type=True, units="kpc") v, cen = pf.h.find_max(("gas", "density")) sp = pf.sphere(cen, (0.5*figure_width, "kpc")) sp.set_field_parameter("normal", (0,0,1)) pf.field_info[("PartType0", "particle_position_cylindrical_z_abs")].take_log = False p = yt.ProfilePlot(sp, ("PartType0", "particle_position_cylindrical_z_abs"), ("PartType0", "density"), weight_field=None, n_bins=80, x_log=False, accumulation=False) p.set_unit(("PartType0", "density"), 'g/cm**3') p.set_unit(("PartType0", "particle_position_cylindrical_z_abs"), 'kpc') p.show() This is the resulting plot of the Gadget example file of yt, https://drive.google.com/file/d/1FGx2izfsnGrwP26SZ6JlfuIegz8eGVKo/view?usp=… Could I get some advice for this problem? Thank you in advance! Eun-jin

2 2

Projection data
by Edward Buie II May 8, 2019

May 8, 2019

Hello, hope you are doing well. I followed the steps to making a region and then making a projection of a field in this region. This step didn't give me an error, however when I tried to print this data, I get the following output, YTQuadTreeProj (ISM_hdf5_chk_0033): , axis=2, field=[('gas', 'ndens')], weight_field=('gas', 'ndens') but I expected it to print the values themselves. I was wondering how can I access this array and work with the data? -- Edward N. Buie II, *Ph.D. Candidate* Astrophysics School of Earth and Space Exploration (SESE) Arizona State University

2 1

Re: OVERPLOTTING PARTICLE PROJECTION MAP ON DENSITY PROJECTION MAP
by Corentin CADIOU May 4, 2019

May 4, 2019

Hey, Indeed, the previous version was actually able to read these files — even if invalid. The code should have never worked in the first place if it wanted to be compliant with the binary format RAMSES uses. I think that the easiest fix is to use a version of yt prior to commit #016c7e04bdf443d16b0431369be364dbb152e4ed (https://github.com/yt-project/yt/commit/016c7e04bdf443d16b0431369be364dbb15…). The latest release that do /not/ include this commit is yt 3.4.1. If you installed yt using git, you can easily switch to yt 3.4.1 by running in the folder that contains yt |git checkout yt-3.4.1 pip install . | If installed via conda, simpy run |conda install -c conda-forge yt=3.4.1|. Cheers, Corentin On 03/05/2019 15.33, Vadlamani Samhitha wrote: > I see. Thank you. But I’m pretty positive I didn’t face this issue > with the version I had before ( 3.4.0 ) as I was able to get the > required plots. It’s just that when I upgraded and trying to do the > same plots that I face this issue and I am unable get back to the > older version now. Is there a possibility that outputs could have been > corrupted during the upgrade somehow? > > On Fri, 3 May 2019 at 3:25 PM, Corentin CADIOU <contact(a)cphyc.me > <mailto:contact@cphyc.me>> wrote: > > Hi, > > The issue is that your amr file does not contain any value for the > field ‘mass_sph’. In fact, yt should /not/ haver never been able > to read it because the structure is somehow broken. > > Here’s what I get from your file (as read by yt) > > |ncpu [4, 30, 4] ndim [4, 3, 4] nx [12, 3, 3, 3, 12] nlevelmax [4, > 11, 4] ngridmax [4, 2000000, 4] nboundary [4, 6, 4] ngrid_current > [4, 8722, 4] boxlen [8, 2000.0, 8] nout [12, 1, 1, 2, 12] tout [8, > 50000.0, 8] aout [8, 1.100000023841858, 8] t [8, 0.0, 8] dtold > [88, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 88] > dtnew [88, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, > 88] nstep [8, 0, 0, 8] stat [24, 0.0, 0.0, 0.0, 24] cosm [56, 1.0, > 0.0, 0.0, 0.0, 1.0, 10.0, 0.0, 56] timing [40, 1.0, 0.0, 1.0, 0.0, > 0.0, 40] mass_sph [0, 2.801034444074e-311, 0] | > > The first and last item of each list are the length of each record > (in bytes). For example the first record that contains ncpu has a > length of 4 bytes and contains the value 30 (ncpu=30). However, > the last record (mass_sph) has a length of 0 even though one even > though it is not empty. I am not sure how that could happen, but > it’s definitely on RAMSES side. The last line should read > |mass_sph [8, 2.801034444074e-311, 8]|. > > I have to think about how that could be fixed. > > On 03/05/2019 14.56, Vadlamani Samhitha wrote: > >> Hi, >> >> If it's only one of the air files, I'm attaching it below. Let me >> know if you would need the entire output folder too. Thank you. >> >> On Fri, May 3, 2019 at 2:52 PM Corentin CADIOU <contact(a)cphyc.me >> <mailto:contact@cphyc.me>> wrote: >> >> Hey Vadlamani, >> >> This looks like a bug to me. Could you share one of your file >> |amr_xxxxx.out00001|? It looks like yt has troubles reading >> the headers. >> >> This can either be due to a backward incompatible change on >> yt side (which would be a bug) or maybe your file became >> corrupted at some point. >> >> Cheers, >> Corentin >> >> On 02/05/2019 18.03, Vadlamani Samhitha wrote: >> >>> Hi, >>> >>> I was able to upgrade to the latest version and still have >>> an issue with annotating particles on density map. I'm >>> getting the following error: >>> >>> Traceback (most recent call last): >>> >>> File "density.py", line 47, in <module> >>> >>> plot = yt.ProjectionPlot(ds, 'z', 'density', width=(800, >>> "kpc"), center="c") >>> >>> File >>> "/home/samvad/yt-conda/lib/python3.7/site-packages/yt/visualization/plot_window.py", >>> line 1464, in __init__ >>> >>> validate_mesh_fields(test_data_source, fields) >>> >>> File >>> "/home/samvad/yt-conda/lib/python3.7/site-packages/yt/visualization/plot_window.py", >>> line 132, in validate_mesh_fields >>> >>> canonical_fields = data_source._determine_fields(fields) >>> >>> File >>> "/home/samvad/yt-conda/lib/python3.7/site-packages/yt/data_objects/data_containers.py", >>> line 1165, in _determine_fields >>> >>> finfo = self.ds._get_field_info("unknown", fname) >>> >>> File >>> "/home/samvad/yt-conda/lib/python3.7/site-packages/yt/data_objects/static_output.py", >>> line 756, in _get_field_info >>> >>> self.index >>> >>> File >>> "/home/samvad/yt-conda/lib/python3.7/site-packages/yt/data_objects/static_output.py", >>> line 509, in index >>> >>> self, dataset_type=self.dataset_type) >>> >>> File >>> "/home/samvad/yt-conda/lib/python3.7/site-packages/yt/frontends/ramses/data_structures.py", >>> line 236, in __init__ >>> >>> super(RAMSESIndex, self).__init__(ds, dataset_type) >>> >>> File >>> "/home/samvad/yt-conda/lib/python3.7/site-packages/yt/geometry/geometry_handler.py", >>> line 50, in __init__ >>> >>> self._setup_geometry() >>> >>> File >>> "/home/samvad/yt-conda/lib/python3.7/site-packages/yt/geometry/oct_geometry_handler.py", >>> line 25, in _setup_geometry >>> >>> self._initialize_oct_handler() >>> >>> File >>> "/home/samvad/yt-conda/lib/python3.7/site-packages/yt/frontends/ramses/data_structures.py", >>> line 245, in _initialize_oct_handler >>> >>> for i in cpu_list] >>> >>> File >>> "/home/samvad/yt-conda/lib/python3.7/site-packages/yt/frontends/ramses/data_structures.py", >>> line 245, in <listcomp> >>> >>> for i in cpu_list] >>> >>> File >>> "/home/samvad/yt-conda/lib/python3.7/site-packages/yt/frontends/ramses/data_structures.py", >>> line 82, in __init__ >>> >>> self._read_amr_header() >>> >>> File >>> "/home/samvad/yt-conda/lib/python3.7/site-packages/yt/frontends/ramses/data_structures.py", >>> line 141, in _read_amr_header >>> >>> hvals.update(f.read_attrs(header)) >>> >>> File "yt/utilities/cython_fortran_utils.pyx", line 223, in >>> yt.utilities.cython_fortran_utils.FortranFile.read_attrs >>> >>> IndexError: index 0 is out of bounds for axis 0 with size 0 >>> >>> >>> >>> >>> On Tue, Apr 30, 2019 at 4:39 AM Vadlamani Samhitha >>> <vadlamani.samhitha(a)gmail.com >>> <mailto:vadlamani.samhitha@gmail.com>> wrote: >>> >>> Downgraded to initial version, but the 'Index error' >>> still persists. Did a conda installation from scratch >>> too. Reported it as a bug. >>> >>> On Mon, Apr 29, 2019 at 6:00 PM Nathan Goldbaum >>> <nathan12343(a)gmail.com <mailto:nathan12343@gmail.com>> >>> wrote: >>> >>> Hmm, I'm not sure, perhaps try uninstalling pyembree? >>> >>> You can also try creating a new conda environment >>> from scratch. >>> >>> On Mon, Apr 29, 2019 at 10:56 AM Vadlamani Samhitha >>> <vadlamani.samhitha(a)gmail.com >>> <mailto:vadlamani.samhitha@gmail.com>> wrote: >>> >>> Thanks again, sorry but looks like I've messed >>> up the installation. The installation wasn't >>> right and I don't get the issue. >>> >>> Upon doing yt --help I get: >>> >>> Traceback (most recent call last): >>> >>> File "/home/samvad/yt-conda/bin/yt", line >>> 4, in <module> >>> >>> import yt.utilities.command_line >>> >>> File >>> "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/__init__.py", >>> line 102, in <module> >>> >>> from yt.visualization.api import \ >>> >>> File >>> "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/api.py", >>> line 22, in <module> >>> >>> from .particle_plots import \ >>> >>> File >>> "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/particle_plots.py", >>> line 18, in <module> >>> >>> from yt.visualization.fixed_resolution >>> import \ >>> >>> File >>> "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/fixed_resolution.py", >>> line 23, in <module> >>> >>> from .volume_rendering.api import >>> off_axis_projection >>> >>> File >>> "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/volume_rendering/api.py", >>> line 23, in <module> >>> >>> from .camera import Camera >>> >>> File >>> "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/volume_rendering/camera.py", >>> line 21, in <module> >>> >>> from .utils import data_source_or_all >>> >>> File >>> "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/volume_rendering/utils.py", >>> line 11, in <module> >>> >>> from yt.utilities.lib import mesh_traversal >>> >>> File "rtcore_scene.pxd", line 61, in init >>> yt.utilities.lib.mesh_traversal >>> >>> ValueError: >>> pyembree.rtcore_scene.EmbreeScene has the >>> wrong size, try recompiling. Expected 32, got 24 >>> >>> -bash-4.2$ yt version >>> >>> Traceback (most recent call last): >>> >>> File "/home/samvad/yt-conda/bin/yt", line >>> 4, in <module> >>> >>> import yt.utilities.command_line >>> >>> File >>> "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/__init__.py", >>> line 102, in <module> >>> >>> from yt.visualization.api import \ >>> >>> File >>> "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/api.py", >>> line 22, in <module> >>> >>> from .particle_plots import \ >>> >>> File >>> "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/particle_plots.py", >>> line 18, in <module> >>> >>> from yt.visualization.fixed_resolution >>> import \ >>> >>> File >>> "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/fixed_resolution.py", >>> line 23, in <module> >>> >>> from .volume_rendering.api import >>> off_axis_projection >>> >>> File >>> "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/volume_rendering/api.py", >>> line 23, in <module> >>> >>> from .camera import Camera >>> >>> File >>> "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/volume_rendering/camera.py", >>> line 21, in <module> >>> >>> from .utils import data_source_or_all >>> >>> File >>> "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/volume_rendering/utils.py", >>> line 11, in <module> >>> >>> from yt.utilities.lib import mesh_traversal >>> >>> File "rtcore_scene.pxd", line 61, in init >>> yt.utilities.lib.mesh_traversal >>> >>> ValueError: >>> pyembree.rtcore_scene.EmbreeScene has the >>> wrong size, try recompiling. Expected 32, got 24 >>> >>> -bash-4.20.9169398134926968nbsp; >>> >>> >>> >>> On Mon, Apr 29, 2019 at 5:30 PM Nathan Goldbaum >>> <nathan12343(a)gmail.com >>> <mailto:nathan12343@gmail.com>> wrote: >>> >>> Sure, you can use conda to install any >>> version of any package. Just specify the >>> version when you install: >>> >>> conda install -c conda-forge yt=3.4.1 >>> >>> On Mon, Apr 29, 2019 at 10:27 AM Vadlamani >>> Samhitha <vadlamani.samhitha(a)gmail.com >>> <mailto:vadlamani.samhitha@gmail.com>> wrote: >>> >>> Will do, but is it possible to revert to >>> the old version for now since none of my >>> scripts are working with the latest >>> version? A fresh installation of 3.4.0? >>> >>> On Mon, Apr 29, 2019 at 3:25 PM Nathan >>> Goldbaum <nathan12343(a)gmail.com >>> <mailto:nathan12343@gmail.com>> wrote: >>> >>> Hmm, not sure what’s happening >>> there, you might need to report this >>> as a bug on yt’s github, if you can >>> please include a data file and >>> script that triggers this error. >>> >>> On Mon, Apr 29, 2019 at 8:00 AM >>> Vadlamani Samhitha >>> <vadlamani.samhitha(a)gmail.com >>> <mailto:vadlamani.samhitha@gmail.com>> >>> wrote: >>> >>> Thank you, have done the upgrade >>> but the following error is >>> popping up: >>> >>> Traceback (most recent call >>> last): >>> >>> File "density.py", line >>> 43, in <module> >>> >>> >>> ds.add_field(name=("gas", >>> "density_threshold"), >>> function=density_threshold, >>> units="H/cm**3") >>> >>> File >>> "/home/samvad/yt-conda/lib/python3.7/site-packages/yt/data_objects/static_output.py", >>> line 1227, in add_field >>> >>> self.index >>> >>> File >>> "/home/samvad/yt-conda/lib/python3.7/site-packages/yt/data_objects/static_output.py", >>> line 509, in index >>> >>> self, >>> dataset_type=self.dataset_type) >>> >>> File >>> "/home/samvad/yt-conda/lib/python3.7/site-packages/yt/frontends/ramses/data_structures.py", >>> line 236, in __init__ >>> >>> super(RAMSESIndex, >>> self).__init__(ds, dataset_type) >>> >>> File >>> "/home/samvad/yt-conda/lib/python3.7/site-packages/yt/geometry/geometry_handler.py", >>> line 50, in __init__ >>> >>> self._setup_geometry() >>> >>> File >>> "/home/samvad/yt-conda/lib/python3.7/site-packages/yt/geometry/oct_geometry_handler.py", >>> line 25, in _setup_geometry >>> >>> >>> self._initialize_oct_handler() >>> >>> File >>> "/home/samvad/yt-conda/lib/python3.7/site-packages/yt/frontends/ramses/data_structures.py", >>> line 245, in >>> _initialize_oct_handler >>> >>> for i in cpu_list] >>> >>> File >>> "/home/samvad/yt-conda/lib/python3.7/site-packages/yt/frontends/ramses/data_structures.py", >>> line 245, in <listcomp> >>> >>> for i in cpu_list] >>> >>> File >>> "/home/samvad/yt-conda/lib/python3.7/site-packages/yt/frontends/ramses/data_structures.py", >>> line 82, in __init__ >>> >>> self._read_amr_header() >>> >>> File >>> "/home/samvad/yt-conda/lib/python3.7/site-packages/yt/frontends/ramses/data_structures.py", >>> line 141, in _read_amr_header >>> >>> >>> hvals.update(f.read_attrs(header)) >>> >>> File >>> "yt/utilities/cython_fortran_utils.pyx", >>> line 223, in >>> yt.utilities.cython_fortran_utils.FortranFile.read_attrs >>> >>> IndexError: index 0 is out >>> of bounds for axis 0 with size 0 >>> >>> >>> On Mon, Apr 29, 2019 at 1:51 PM >>> Nathan Goldbaum >>> <nathan12343(a)gmail.com >>> <mailto:nathan12343@gmail.com>> >>> wrote: >>> >>> Yes, use conda-forge: >>> >>> conda update -c conda-forge yt >>> >>> On Mon, Apr 29, 2019 at 6:32 >>> AM Vadlamani Samhitha >>> <vadlamani.samhitha(a)gmail.com >>> <mailto:vadlamani.samhitha@gmail.com>> >>> wrote: >>> >>> I installed yt from >>> conda so, yt update is >>> only being done to 3.4.1 >>> version with 'yt conda >>> update' and with this my >>> scripts are throwing >>> assertion errors. Is >>> there a way I could do a >>> conda update to the >>> latest version specifically? >>> >>> On Mon, Apr 29, 2019 at >>> 1:05 PM Nathan Goldbaum >>> <nathan12343(a)gmail.com >>> <mailto:nathan12343@gmail.com>> >>> wrote: >>> >>> The latest stable >>> release is 3.5.1, >>> please try updating >>> your yt installation. >>> >>> On Mon, Apr 29, 2019 >>> at 5:58 AM Vadlamani >>> Samhitha >>> <vadlamani.samhitha(a)gmail.com >>> <mailto:vadlamani.samhitha@gmail.com>> >>> wrote: >>> >>> 3.4.0 >>> >>> On Mon, Apr 29, >>> 2019 at 12:52 PM >>> Nathan Goldbaum >>> <nathan12343(a)gmail.com >>> <mailto:nathan12343@gmail.com>> >>> wrote: >>> >>> What yt >>> version are >>> you using? >>> >>> On Mon, Apr >>> 29, 2019 at >>> 5:34 AM >>> Vadlamani >>> Samhitha >>> <vadlamani.samhitha(a)gmail.com >>> <mailto:vadlamani.samhitha@gmail.com>> >>> wrote: >>> >>> Hi, I >>> did try >>> that as >>> well, >>> but >>> doing so >>> gives >>> 'unexpected >>> keyword' >>> error. >>> >>> Traceback >>> (most >>> recent >>> call >>> last): >>> >>> >>> File >>> "density.py", >>> line >>> 57, >>> in >>> <module> >>> >>> >>> plot.save(fil) >>> >>> >>> File >>> "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/plot_container.py", >>> line >>> 94, >>> in >>> newfunc >>> >>> >>> args[0]._setup_plots() >>> >>> >>> File >>> "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/plot_window.py", >>> line >>> 948, >>> in >>> _setup_plots >>> >>> >>> self.run_callbacks() >>> >>> >>> File >>> "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/plot_window.py", >>> line >>> 997, >>> in >>> run_callbacks >>> >>> >>> callback >>> = >>> CallbackMaker(*args[1:], >>> **kwargs) >>> >>> TypeError: >>> __init__() >>> got >>> an >>> unexpected >>> keyword >>> argument >>> 'data_source' >>> >>> >>> >>> >>> On Mon, >>> Apr 29, >>> 2019 at >>> 12:18 PM >>> Wise, >>> John H >>> <jwise(a)physics.gatech.edu >>> <mailto:jwise@physics.gatech.edu>> >>> wrote: >>> >>> Hi, >>> >>> Because >>> there >>> are >>> many >>> optional >>> arguments >>> to >>> annotate_particles, >>> you >>> have >>> to >>> specify >>> that >>> dd >>> is >>> the >>> data_source. >>> Try >>> >>> plot.annotate_particles(1.0, >>> data_source=dd) >>> >>> John >>> >>> On >>> 4/27/2019 >>> 15:46, >>> Vadlamani >>> Samhitha >>> wrote: >>> > Hi, >>> > >>> > I >>> am >>> trying >>> to >>> overlap >>> two >>> different >>> projection >>> plots >>> (particles >>> and >>> > >>> density) >>> with >>> two >>> different >>> color >>> bars. >>> However, >>> I >>> couldn't >>> figure >>> out a >>> > >>> way >>> to >>> do >>> that >>> but >>> found >>> over >>> plotting >>> particles >>> over >>> fluids. >>> > >>> > >>> So, >>> I >>> have >>> RAMSES >>> data >>> which >>> can't >>> distinguish >>> between >>> dark >>> matter >>> and >>> > >>> stars >>> through >>> particle >>> types >>> but >>> only >>> with >>> mass >>> cut_off. >>> So I >>> create >>> a >>> > >>> filter >>> for >>> the >>> particles >>> accordingly >>> and >>> supply >>> it >>> as >>> the >>> 'data_source' >>> >>> > >>> argument >>> in >>> 'annotate_particles'. >>> So, >>> I do >>> the >>> following: >>> > >>> > >>> defstars(pfilter, >>> data): >>> > >>> > >>> # >>> age >>> = >>> (data.ds.current_time >>> - >>> data[pfilter.filtered_type, >>> > >>> "particle_birth_time"]).in_units('Myr') >>> > >>> > >>> >>> >>> >>> stars_only >>> = >>> data[pfilter.filtered_type, >>> > >>> "particle_mass"].in_units('Msun') >>> > >>> > >>> filter= >>> (stars_only<4e6) >>> > >>> > >>> returnfilter >>> > >>> > >>> yt.add_particle_filter("stars", >>> function=stars, >>> filtered_type='io', >>> > >>> requires=["particle_mass"]) >>> > >>> > >>> > >>> ini=1 >>> > >>> > >>> fin=2 >>> > >>> > >>> forx >>> inrange(ini, >>> fin): >>> > >>> > >>> filename="/lunarc/nobackup/users/samvad/SQ-8-5/output/output_%0*d/info_%0*d.txt" >>> >>> > >>> % >>> (5,x,5,x) >>> > >>> > >>> >>> >>> ds >>> = >>> yt.load(filename) >>> > >>> > >>> >>> >>> >>> ds.define_unit("H", >>> (1.674*10**(-24), >>> "g")) >>> > >>> > >>> defdensity_threshold(field, >>> data): >>> > >>> > >>> >>> >>> >>> >>> >>> dens=data["gas", >>> "density"].in_units('H/cm**3') >>> > >>> > >>> >>> >>> >>> >>> >>> dens[dens >>> < 0] = 0 >>> > >>> > >>> returndens >>> > >>> > >>> >>> >>> >>> ds.add_field(name=("gas", >>> "density_threshold"), >>> > >>> function=density_threshold, >>> units="H/cm**3") >>> > >>> > >>> >>> >>> >>> ad=ds.all_data() >>> > >>> > >>> >>> >>> >>> denst=ad["gas", >>> "density_threshold"].in_units('H/cm**3') >>> > >>> > >>> #plot >>> = >>> yt.SlicePlot(ds, >>> 'z', >>> 'density_threshold', >>> width=(400, >>> "kpc")) >>> > >>> > >>> >>> >>> >>> plot >>> = >>> yt.ProjectionPlot(ds, >>> 'z', >>> 'density', >>> > >>> weight_field='density', >>> width=(800, >>> "kpc"), >>> center="c") >>> > >>> > >>> >>> >>> >>> ds.add_particle_filter('stars') >>> > >>> > >>> >>> >>> >>> dd=ds.all_data() >>> > >>> > >>> >>> >>> >>> plot.annotate_particles(1.0, >>> dd) >>> > >>> > >>> >>> >>> >>> plot.set_cmap(field='density', >>> cmap='Blues') >>> > >>> > >>> >>> >>> >>> plot.set_unit(("gas", >>> "density"), >>> "H/cm**3") >>> > >>> > >>> >>> >>> >>> plot.set_zlim(("gas", >>> "density"), >>> 1e-4, >>> 1e-1) >>> > >>> > >>> plot.annotate_timestamp() >>> > >>> > >>> >>> >>> fil="density_%0*d.png" >>> % (5,x) >>> > >>> > >>> >>> >>> >>> plot.save(fil) >>> > >>> > >>> > >>> But >>> ending >>> up >>> with >>> the >>> error: >>> > >>> > >>> Traceback >>> (most >>> recent >>> call >>> last): >>> > >>> > >>> File >>> > >>> "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/plot_window.py", >>> >>> > >>> line >>> 999, >>> in >>> run_callbacks >>> > >>> > >>> >>> callback(cbw) >>> > >>> > >>> File >>> > >>> "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/plot_modifications.py", >>> >>> > >>> line >>> 53, >>> in >>> _check_geometry >>> > >>> > >>> >>> return >>> func(self, >>> plot) >>> > >>> > >>> File >>> > >>> "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/plot_modifications.py", >>> >>> > >>> line >>> 1563, >>> in >>> __call__ >>> > >>> > >>> >>> s=self.p_size, >>> c=self.color,alpha=self.alpha) >>> > >>> > >>> File >>> > >>> "/home/samvad/yt-conda/lib/python3.6/site-packages/matplotlib/__init__.py", >>> >>> > >>> line >>> 1717, >>> in inner >>> > >>> > >>> >>> return >>> func(ax, >>> *args, >>> **kwargs) >>> > >>> > >>> File >>> > >>> "/home/samvad/yt-conda/lib/python3.6/site-packages/matplotlib/axes/_axes.py", >>> >>> > >>> line >>> 4032, >>> in >>> scatter >>> > >>> > >>> >>> alpha=alpha >>> > >>> > >>> File >>> > >>> "/home/samvad/yt-conda/lib/python3.6/site-packages/matplotlib/collections.py", >>> >>> > >>> line >>> 880, >>> in >>> __init__ >>> > >>> > >>> >>> self.set_sizes(sizes) >>> > >>> > >>> File >>> > >>> "/home/samvad/yt-conda/lib/python3.6/site-packages/matplotlib/collections.py", >>> >>> > >>> line >>> 853, >>> in >>> set_sizes >>> > >>> > >>> >>> scale >>> = >>> np.sqrt(self._sizes) >>> * >>> dpi >>> / >>> 72.0 >>> * >>> self._factor >>> > >>> > >>> AttributeError: >>> 'YTRegion' >>> object >>> has >>> no >>> attribute >>> 'sqrt' >>> > >>> > >>> > >>> During >>> handling >>> of >>> the >>> above >>> exception, >>> another >>> exception >>> occurred: >>> > >>> > >>> > >>> Traceback >>> (most >>> recent >>> call >>> last): >>> > >>> > >>> File >>> "density.py", >>> line >>> 57, >>> in >>> <module> >>> > >>> > >>> >>> plot.save(fil) >>> > >>> > >>> File >>> > >>> "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/plot_container.py", >>> >>> > >>> line >>> 94, >>> in >>> newfunc >>> > >>> > >>> >>> args[0]._setup_plots() >>> > >>> > >>> File >>> > >>> "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/plot_window.py", >>> >>> > >>> line >>> 948, >>> in >>> _setup_plots >>> > >>> > >>> >>> self.run_callbacks() >>> > >>> > >>> File >>> > >>> "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/plot_window.py", >>> >>> > >>> line >>> 1005, >>> in >>> run_callbacks >>> > >>> > >>> >>> sys.exc_info()[2]) >>> > >>> > >>> File >>> "/home/samvad/yt-conda/lib/python3.6/site-packages/six.py", >>> line >>> > >>> 692, >>> in >>> reraise >>> > >>> > >>> >>> raise >>> value.with_traceback(tb) >>> > >>> > >>> File >>> > >>> "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/plot_window.py", >>> >>> > >>> line >>> 999, >>> in >>> run_callbacks >>> > >>> > >>> >>> callback(cbw) >>> > >>> > >>> File >>> > >>> "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/plot_modifications.py", >>> >>> > >>> line >>> 53, >>> in >>> _check_geometry >>> > >>> > >>> >>> return >>> func(self, >>> plot) >>> > >>> > >>> File >>> > >>> "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/plot_modifications.py", >>> >>> > >>> line >>> 1563, >>> in >>> __call__ >>> > >>> > >>> >>> s=self.p_size, >>> c=self.color,alpha=self.alpha) >>> > >>> > >>> File >>> > >>> "/home/samvad/yt-conda/lib/python3.6/site-packages/matplotlib/__init__.py", >>> >>> > >>> line >>> 1717, >>> in inner >>> > >>> > >>> >>> return >>> func(ax, >>> *args, >>> **kwargs) >>> > >>> > >>> File >>> > >>> "/home/samvad/yt-conda/lib/python3.6/site-packages/matplotlib/axes/_axes.py", >>> >>> > >>> line >>> 4032, >>> in >>> scatter >>> > >>> > >>> >>> alpha=alpha >>> > >>> > >>> File >>> > >>> "/home/samvad/yt-conda/lib/python3.6/site-packages/matplotlib/collections.py", >>> >>> > >>> line >>> 880, >>> in >>> __init__ >>> > >>> > >>> >>> self.set_sizes(sizes) >>> > >>> > >>> File >>> > >>> "/home/samvad/yt-conda/lib/python3.6/site-packages/matplotlib/collections.py", >>> >>> > >>> line >>> 853, >>> in >>> set_sizes >>> > >>> > >>> >>> scale >>> = >>> np.sqrt(self._sizes) >>> * >>> dpi >>> / >>> 72.0 >>> * >>> self._factor >>> > >>> > >>> yt.utilities.exceptions.YTPlotCallbackError: >>> annotate_particles >>> > >>> callback >>> failed >>> with >>> the >>> following >>> error: >>> 'YTRegion' >>> object >>> has no >>> > >>> attribute >>> 'sqrt' >>> > >>> > I >>> don't >>> seem to >>>

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GETTING BACK TO YT 3.4.0
by Vadlamani Samhitha May 3, 2019

May 3, 2019

Hi, I was initially having yt version 3.4.0 that worked well with my RAMSES data, however when I upgraded to 3.5.1 even the basic scripts would throw error (Index error). So, I tried downgrading to 3.4.0, but yt only gets downgraded to 3.4.1 even with which my scripts are not working. Why is that I am unable to get back to 3.4.0 and is there a way I could solve this issue? Thank you

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OVERPLOTTING PARTICLE PROJECTION MAP ON DENSITY PROJECTION MAP
by Vadlamani Samhitha May 2, 2019

May 2, 2019

Hi, I am trying to overlap two different projection plots (particles and density) with two different color bars. However, I couldn't figure out a way to do that but found over plotting particles over fluids. So, I have RAMSES data which can't distinguish between dark matter and stars through particle types but only with mass cut_off. So I create a filter for the particles accordingly and supply it as the 'data_source' argument in 'annotate_particles'. So, I do the following: > def stars(pfilter, data): > > # age = (data.ds.current_time - data[pfilter.filtered_type, > "particle_birth_time"]).in_units('Myr') > > stars_only = data[pfilter.filtered_type, "particle_mass" > ].in_units('Msun') > > filter = (stars_only<4e6) > > return filter > > yt.add_particle_filter("stars", function=stars, filtered_type='io', > requires=["particle_mass"]) > > > ini=1 > > fin=2 > > for x in range(ini, fin): > > filename="/lunarc/nobackup/users/samvad/SQ-8-5/output/output_%0*d/info_%0* > d.txt" % (5,x,5,x) > > ds = yt.load(filename) > > ds.define_unit("H", (1.674*10**(-24), "g")) > > def density_threshold(field, data): > > dens=data["gas", "density"].in_units('H/cm**3') > > dens[dens < 0] = 0 > > return dens > > ds.add_field(name=("gas", "density_threshold"), > function=density_threshold, units="H/cm**3") > > ad=ds.all_data() > > denst=ad["gas", "density_threshold"].in_units('H/cm**3') > > #plot = yt.SlicePlot(ds, 'z', 'density_threshold', width=(400, "kpc")) > > plot = yt.ProjectionPlot(ds, 'z', 'density', weight_field= > 'density', width=(800, "kpc"), center="c") > > ds.add_particle_filter('stars') > > dd=ds.all_data() > > plot.annotate_particles(1.0, dd) > > plot.set_cmap(field='density', cmap='Blues') > > plot.set_unit(("gas", "density"), "H/cm**3") > > plot.set_zlim(("gas", "density"), 1e-4, 1e-1) > plot.annotate_timestamp() fil="density_%0*d.png" % (5,x) > > plot.save(fil) > But ending up with the error: Traceback (most recent call last): File "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/plot_window.py", line 999, in run_callbacks callback(cbw) File "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/plot_modifications.py", line 53, in _check_geometry return func(self, plot) File "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/plot_modifications.py", line 1563, in __call__ s=self.p_size, c=self.color,alpha=self.alpha) File "/home/samvad/yt-conda/lib/python3.6/site-packages/matplotlib/__init__.py", line 1717, in inner return func(ax, *args, **kwargs) File "/home/samvad/yt-conda/lib/python3.6/site-packages/matplotlib/axes/_axes.py", line 4032, in scatter alpha=alpha File "/home/samvad/yt-conda/lib/python3.6/site-packages/matplotlib/collections.py", line 880, in __init__ self.set_sizes(sizes) File "/home/samvad/yt-conda/lib/python3.6/site-packages/matplotlib/collections.py", line 853, in set_sizes scale = np.sqrt(self._sizes) * dpi / 72.0 * self._factor AttributeError: 'YTRegion' object has no attribute 'sqrt' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "density.py", line 57, in <module> plot.save(fil) File "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/plot_container.py", line 94, in newfunc args[0]._setup_plots() File "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/plot_window.py", line 948, in _setup_plots self.run_callbacks() File "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/plot_window.py", line 1005, in run_callbacks sys.exc_info()[2]) File "/home/samvad/yt-conda/lib/python3.6/site-packages/six.py", line 692, in reraise raise value.with_traceback(tb) File "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/plot_window.py", line 999, in run_callbacks callback(cbw) File "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/plot_modifications.py", line 53, in _check_geometry return func(self, plot) File "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/visualization/plot_modifications.py", line 1563, in __call__ s=self.p_size, c=self.color,alpha=self.alpha) File "/home/samvad/yt-conda/lib/python3.6/site-packages/matplotlib/__init__.py", line 1717, in inner return func(ax, *args, **kwargs) File "/home/samvad/yt-conda/lib/python3.6/site-packages/matplotlib/axes/_axes.py", line 4032, in scatter alpha=alpha File "/home/samvad/yt-conda/lib/python3.6/site-packages/matplotlib/collections.py", line 880, in __init__ self.set_sizes(sizes) File "/home/samvad/yt-conda/lib/python3.6/site-packages/matplotlib/collections.py", line 853, in set_sizes scale = np.sqrt(self._sizes) * dpi / 72.0 * self._factor > yt.utilities.exceptions.YTPlotCallbackError: annotate_particles callback > failed with the following error: 'YTRegion' object has no attribute 'sqrt' > I don't seem to understand the issue here. Is there a workaround to get particle plot over density plot in a simpler way? Thank you.

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