yt-users January 2018

yt-users@python.org

21 participants
25 discussions

BLANK TEMPERATURE PROJECTION PLOT
by Vadlamani Samhitha 28 Jan '18

28 Jan '18

Hi, I'm trying to obtain a projection plot of temperature for RAMSES data using: *plot = yt.ProjectionPlot(ds, "z", "temperature", weight_field=None)* However, I get a blank plot as attached in the picture below. Could someone help me figure out what could have gone wrong?

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Unable to locate the YT 2.6(Legacy (2.x)) installation script
by Reju Sam John 26 Jan '18

26 Jan '18

Dear all, The link http://hg.yt-project.org/yt/raw/stable/doc/install_script.sh for installing yt 2.6 on the page http://yt-project.org/docs/2.6/installing.html is not working. Could you please provide the likeinstall_script.sh of the yt 2.6(Legacy (2.x)) -- Reju Sam John

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error while installing yt 3.4 in Ubuntu 16.04
by Reju Sam John 26 Jan '18

26 Jan '18

Dear all, I am getting the following error while installing yt 3.4 in Ubuntu 16.04. # # To activate this environment, use: # > source activate py27 # # To deactivate an active environment, use: # > source deactivate # EXECUTING: ln -s /home/john/yt_3_4/yt-conda/envs/py27/bin/hg /home/john/yt_3_4/yt-conda/bin EXECUTING: /home/john/yt_3_4/yt-conda/bin/git clone https://github.com/yt-project/yt_conda /home/john/yt_3_4/yt-conda/src/yt_conda Cloning into '/home/john/yt_3_4/yt-conda/src/yt_conda'... https://github-production-release-asset-2e65be.s3.amazonaws.com/6946079/0ee… : 2018-01-26 05:01:29 ERROR 403: Forbidden. Also, I am attaching the installation script which I used. What could be the reason for the error ? Thank you -- Reju Sam John

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Plotting Streamlines
by sushil.sush19us＠gmail.com 26 Jan '18

26 Jan '18

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Plotting streamlines
by Sushilkumar 26 Jan '18

26 Jan '18

Dear yt: I am plotting streamlines using yt and I want to make it look "nicer". Something like the outward moving wave has different color scheme. I am not sure how to play around with color scheme. Any suggestions? Link to the movie and script is below Thanks in advance https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc -- *SK2* *"**Claiming that something can move faster than light is a good conversation-stopper in physics. People edge away from you in cocktail parties; friends never return phone calls. You just don’t mess with Albert Einstein.**"*

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HDF5 problem on lustre file systems
by Philipp Girichidis 26 Jan '18

26 Jan '18

Dear YT users, I ran into a problem with hdf5 on lustre file systems after a recent update (check file system with df -Tvh). The binaries h5ls, h5dump etc were not able to load files, neither yt/python via the python interface. I found out that hdf5 version 1.10 has problems with (at leat our) lustre file system downgrading hdf to version 1.8.18 $> conda install hdf5=1.8.18 solved the hdf5 problem and brought up the recursion problem that Travis Thieme reported earlier. $> conda install numpy=1.13.3 did the job for me! Cheers, Philipp

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RecursionError: maximum recursion depth exceeded when using SlicePlot
by Travis Thieme 25 Jan '18

25 Jan '18

Hello everyone, I’m a new user of yt and I’ve been encountering a problem when trying to make a SlicePlot of some ALMA data I have been working with. I’m also not sure what the best way to format these emails are, but I’ll include as mush detail as I can. Basically, when using SlicePlot, I get this error —> RecursionError: maximum recursion depth exceeded Here’s some info about what I’m using: - Python version: 3.6.4 - yt version: 3.3.5 - jupyter version: 4.4.0 My four lines of code are: import yt ds = yt.load(‘data.fits', nan_mask=0.0, z_axis_decomp=True) slc = yt.SlicePlot(ds, "z", ["Intensity"], origin="native") slc.show() And I get the following error: --------------------------------------------------------------------------- RecursionError Traceback (most recent call last) <ipython-input-9-46c5ac6a89f9> in <module>() ----> 1 slc = yt.SlicePlot(ds, "z", ["Intensity"], origin="native") 2 slc.show() ~/miniconda3/envs/astro36/lib/python3.6/site-packages/yt/visualization/plot_window.py in SlicePlot(ds, normal, fields, axis, *args, **kwargs) 1911 del kwargs['north_vector'] 1912 -> 1913 return AxisAlignedSlicePlot(ds, normal, fields, *args, **kwargs) ~/miniconda3/envs/astro36/lib/python3.6/site-packages/yt/visualization/plot_window.py in __init__(self, ds, axis, fields, center, width, axes_unit, origin, fontsize, field_parameters, window_size, aspect, data_source) 1265 PWViewerMPL.__init__(self, slc, bounds, origin=origin, 1266 fontsize=fontsize, fields=fields, -> 1267 window_size=window_size, aspect=aspect) 1268 if axes_unit is None: 1269 axes_unit = get_axes_unit(width, ds) ~/miniconda3/envs/astro36/lib/python3.6/site-packages/yt/visualization/plot_window.py in __init__(self, *args, **kwargs) 636 self._plot_type = kwargs.pop("plot_type") 637 self._splat_color = kwargs.pop("splat_color", None) --> 638 PlotWindow.__init__(self, *args, **kwargs) 639 640 def _setup_origin(self): ~/miniconda3/envs/astro36/lib/python3.6/site-packages/yt/visualization/plot_window.py in __init__(self, data_source, bounds, buff_size, antialias, periodic, origin, oblique, window_size, fields, fontsize, aspect, setup) 215 self._field_transform[field] = linear_transform 216 self.setup_callbacks() --> 217 self._setup_plots() 218 219 def _initialize_dataset(self, ts): ~/miniconda3/envs/astro36/lib/python3.6/site-packages/yt/visualization/plot_window.py in _setup_plots(self) 705 return 706 if not self._data_valid: --> 707 self._recreate_frb() 708 self._data_valid = True 709 self._colorbar_valid = True ~/miniconda3/envs/astro36/lib/python3.6/site-packages/yt/visualization/plot_window.py in _recreate_frb(self) 276 # At this point the frb has the valid bounds, size, aliasing, etc. 277 if old_fields is None: --> 278 self._frb._get_data_source_fields() 279 else: 280 # Restore the old fields ~/miniconda3/envs/astro36/lib/python3.6/site-packages/yt/visualization/fixed_resolution.py in _get_data_source_fields(self) 160 for f in fields: 161 if f not in exclude and f[0] not in self.data_source.ds.particle_types: --> 162 self[f] 163 164 def _is_ion( self, fname ): ~/miniconda3/envs/astro36/lib/python3.6/site-packages/yt/visualization/fixed_resolution.py in __getitem__(self, item) 147 # self._period, int(self.periodic) 148 ia = ImageArray(buff, input_units=self.data_source[item].units, --> 149 info=self._get_info(item)) 150 self.data[item] = ia 151 return self.data[item] ~/miniconda3/envs/astro36/lib/python3.6/site-packages/yt/visualization/fixed_resolution.py in _get_info(self, item) 198 ftype, fname = field = self.data_source._determine_fields(item)[0] 199 finfo = self.data_source.ds._get_field_info(*field) --> 200 info['data_source'] = self.data_source.__str__() 201 info['axis'] = self.data_source.axis 202 info['field'] = str(item) ~/miniconda3/envs/astro36/lib/python3.6/site-packages/yt/data_objects/data_containers.py in __repr__(self) 943 for i in self._con_args: 944 try: --> 945 s += ", %s=%s" % (i, getattr(self, i).in_base(unit_system=self.ds.unit_system)) 946 except AttributeError: 947 s += ", %s=%s" % (i, getattr(self, i)) ~/miniconda3/envs/astro36/lib/python3.6/site-packages/yt/units/yt_array.py in __str__(self) 453 454 """ --> 455 return super(YTArray, self).__str__()+' '+self.units.__str__() 456 457 # ~/miniconda3/envs/astro36/lib/python3.6/site-packages/numpy/core/arrayprint.py in array_str(a, max_line_width, precision, suppress_small) 1398 # in quotes. So we return the str of the scalar value. 1399 if a.shape == (): -> 1400 return str(a[()]) 1401 1402 return array2string(a, max_line_width, precision, suppress_small, ' ', "") ... last 2 frames repeated, from the frame below ... ~/miniconda3/envs/astro36/lib/python3.6/site-packages/yt/units/yt_array.py in __str__(self) 453 454 """ --> 455 return super(YTArray, self).__str__()+' '+self.units.__str__() 456 457 # RecursionError: maximum recursion depth exceeded I’m following the tutorial on the yt website called FITS Radio Cubes in yt (http://yt-project.org/doc/cookbook/fits_radio_cubes.html <http://yt-project.org/doc/cookbook/fits_radio_cubes.html>). I’ve tried uninstalling yt and reinstalling. I should add that I was able to make the plot before with no problems, it was only after I updated my python packages I started to receive this error. Any help is appreciated. Thank you. Best Regards, Travis Thieme Graduate Student Institute of Astronomy National Tsing Hua University

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Velocity Unit in Reading EAGLE
by Stephanie Ho 24 Jan '18

24 Jan '18

Hi all, I am concerned about the velocity unit when yt reads EAGLE simulation. To convert the on-disk peculiar velocity (call this raw_velocity) to a physical velocity [cm/s]: physical velocity [cm/s] = raw_velocity * sqrt(a) * 1e5 When I specify: ad['PartType0','Velocity'].in_units('km/s') The output says it is in km/s, so I would expect this is the physical velocity. However, the output actually does not multiply the raw_velocity by sqrt(a) Looking at the source code (and its comments), I am not sure if this is intentional, or is this sqrt(a) accidentally missed out. https://github.com/yt-project/yt/blob/master/yt/frontends/gadget/data_struc… Line 490-499 A possibly relevant discussion (several years ago) with Gadget using yt (this is now fixed): https://bitbucket.org/yt_analysis/yt/pull-requests/1710/gadget-cosmology-si… So, does yt intentionally not to multiply the velocity unit by sqrt(a) factor, or is the factor accidentally missed out? This could be confusing for relative new users like myself. Apologize if this is well known for experts. Thanks, Stephanie

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ASSERTION ERROR ACCESSING RAMSES FIELDS
by Vadlamani Samhitha 22 Jan '18

22 Jan '18

Hi, I am working on data from ramses and I have the following output files from my simulations: amr grav hydro part and info.txt However, when I try to make projection plots, I am obtaining the error: FutureWarning: Conversion of the second argument of issubdtype from `float` > to `np.floating` is deprecated. In future, it will be treated as > `np.float64 == np.dtype(float).type`. > > from ._conv import register_converters as _register_converters > > yt : [INFO ] 2018-01-19 16:31:46,982 Parameters: current_time > = 0.254337758876396 > > yt : [INFO ] 2018-01-19 16:31:46,982 Parameters: domain_dimensions > = [32 32 32] > > yt : [INFO ] 2018-01-19 16:31:46,983 Parameters: domain_left_edge > = [0. 0. 0.] > > yt : [INFO ] 2018-01-19 16:31:46,983 Parameters: domain_right_edge > = [1. 1. 1.] > > yt : [INFO ] 2018-01-19 16:31:46,983 Parameters: > cosmological_simulation = 0 > > Traceback (most recent call last): > > File "pyt.py", line 11, in <module> > > p = yt.ProjectionPlot(ds, "x", "density") > > File > "/Users/xxxx/Documents/yt-conda/lib/python3.6/site-packages/yt/visualization/plot_window.py", > line 1441, in __init__ > > validate_mesh_fields(test_data_source, fields) > > File > "/Users/xxxx/Documents/yt-conda/lib/python3.6/site-packages/yt/visualization/plot_window.py", > line 132, in validate_mesh_fields > > canonical_fields = data_source._determine_fields(fields) > > File > "/Users/xxxx/Documents/yt-conda/lib/python3.6/site-packages/yt/data_objects/data_containers.py", > line 1127, in _determine_fields > > finfo = self.ds._get_field_info("unknown", fname) > > File > "/Users/xxxx/Documents/yt-conda/lib/python3.6/site-packages/yt/data_objects/static_output.py", > line 711, in _get_field_info > > self.index > > File > "/Users/xxxx/Documents/yt-conda/lib/python3.6/site-packages/yt/data_objects/static_output.py", > line 504, in index > > self, dataset_type=self.dataset_type) > > File > "/Users/xxxx/Documents/yt-conda/lib/python3.6/site-packages/yt/frontends/ramses/data_structures.py", > line 357, in __init__ > > super(RAMSESIndex, self).__init__(ds, dataset_type) > > File > "/Users/xxxx/Documents/yt-conda/lib/python3.6/site-packages/yt/geometry/geometry_handler.py", > line 50, in __init__ > > self._setup_geometry() > > File > "/Users/xxxx/Documents/yt-conda/lib/python3.6/site-packages/yt/geometry/oct_geometry_handler.py", > line 25, in _setup_geometry > > self._initialize_oct_handler() > > File > "/Users/xxxx/Documents/yt-conda/lib/python3.6/site-packages/yt/frontends/ramses/data_structures.py", > line 361, in _initialize_oct_handler > > for i in range(self.dataset['ncpu'])] > > File > "/Users/xxxx/Documents/yt-conda/lib/python3.6/site-packages/yt/frontends/ramses/data_structures.py", > line 361, in <listcomp> > > for i in range(self.dataset['ncpu'])] > > File > "/Users/xxxx/Documents/yt-conda/lib/python3.6/site-packages/yt/frontends/ramses/data_structures.py", > line 67, in __init__ > > self._read_amr_header() > > File > "/Users/xxxx/Documents/yt-conda/lib/python3.6/site-packages/yt/frontends/ramses/data_structures.py", > line 191, in _read_amr_header > > hvals.update(fpu.read_attrs(f, header)) > > File > "/Users/samhitha/Documents/yt-conda/lib/python3.6/site-packages/yt/utilities/fortran_utils.py", > line 86, in read_attrs > > assert(s1 == s2) > > AssertionError > I tried specifying the fields externally using: ds = > yt.load("/Users/xxxx/SIM001/output_00002/info_00002.txt",fields=["density", > "velocity_x", "velocity_y", "velocity_z", "thermal_pressure", "var6", > "var7"]) > p = yt.ProjectionPlot(ds, "x", "density") PS: Rebooting the system didn't work in my case. Any help is greatly appreciated.

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New mailing list addresses
by Matthew Turk 18 Jan '18

18 Jan '18

Hi folks, The new mailing lists should be active! I'm working to forward and migrate fully off the old ones, but for now all messages to those have been disabled. From now on, the email addresses to use are: yt-users(a)python.org yt-dev(a)python.org The archives are accessible at: https://mail.python.org/mm3/archives/list/yt-users@python.org/ https://mail.python.org/mm3/archives/list/yt-dev@python.org/ Updates to the website and documentation are forthcoming. -Matt

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yt-users January 2018