yt-users October 2018

yt-users@python.org

14 participants
25 discussions

by david collins

Hi, Everybody! Does anyone out there have a technique for getting the variance out of a profile object? A profile object is good at getting <X> vs. B, I'd then like to get < (X - <X>)^2 > vs B. Matt and I had spittballed the possibility some time ago, but I was wondering if anyone out there had successfully done it. Thanks, d. -- Sent from my computer.

5 months, 2 weeks

3-D Mass power spectra

by 梁家豪

Dear yt Can current yt calculate 3-D Mass power spectra? I checked the website but I didn't find any information. I think calculating 3-D Mass power spectra is a very useful for cosmological simulations. So I guess maybe yt supports this function now....? Thanks in advance

1 year, 3 months

ACCESSING GAS FILEDS THROUGH ARBITRARY_GRID

by Vadlamani Samhitha

Hi, I am using arbitrary_grid to access my data without flattening: > dd=ds.arbitrary_grid(left_edge=[(com_x_1.value-30), (com_y_1.value-30), > (com_z_1.value-30)]*kpc, right_edge=[(com_x_1.value+30), (com_y_1.value+30), > (com_z_1.value+30)]*kpc, dims=[128, 128, 128]) > and as I attempt to get the gas fields for this object, > print(dd['gas', 'velocity_x']) > but end up getting the error: (which isn't the case for deposit fields) yt.units.unit_registry.UnitParseError: Code units have not been defined. > Try creating the array or quantity using ds.arr or ds.quan instead. If I'm thinking right, is it because the arbitrary_grid is only applied to the particles. In that case, is there any equivalent for gas fields where I can access my 3D data for the gas as it is , without flattening? Thanks

1 year, 10 months

Re: using young stars to calculate the angular momentum vector

by Nathan Goldbaum

Hi Sam, This is a new feature in yt 3.5.0, you’ll need to update to be able to use it. Let us know if you have questions about updating. Nathan On Tue, Oct 30, 2018 at 2:16 PM Samantha M Benincasa < smbenincasa(a)ucdavis.edu> wrote: > Hi everyone, > > I'm trying to get a halo into a face-on and side-on configuration using > sp.quantities.angular_momentum_vector. > > Is there a way to do this calculation with only the young stars in the > sphere? The docs suggest that angular_momentum_vector will take a > "particle_type" keyword, but my version does not recognize this. > > Cheers, > Sam > _______________________________________________ > yt-users mailing list -- yt-users(a)python.org > To unsubscribe send an email to yt-users-leave(a)python.org >

1 year, 10 months

using young stars to calculate the angular momentum vector

by Samantha M Benincasa

Hi everyone, I'm trying to get a halo into a face-on and side-on configuration using sp.quantities.angular_momentum_vector. Is there a way to do this calculation with only the young stars in the sphere? The docs suggest that angular_momentum_vector will take a "particle_type" keyword, but my version does not recognize this. Cheers, Sam

1 year, 11 months

ACCESSING DATA AS IT IS

by Vadlamani Samhitha

Hi, I would like to access data from Ramses as it is because I would want to divide my selected region into subgrids and compute some quantity locally in those subgrids. However, using all_data or ds.r would rearrange the information as it flattens the data (please correct me if I got this wrong). Is there a way in yt, where I can simply access the 3D data as it is and divide into subcubes? Thank you.

1 year, 11 months

Postdoc in Comp. Astro. at MSU

by Sean M. Couch

Hi yt-users, We have an open postdoctoral research associate position in computational astrophysics/supernova theory at Michigan State. More info and application portal here: http://careers.msu.edu/cw/en-us/job/500160/research-associatefixed-term. Please pass along to anyone you think might be interested. Apologies if you receive this announcement multiple times. Thanks! Sean ---------------------------------------------------------------------------------------------------------- Sean M. Couch, Ph.D. Assistant Professor Department of Physics and Astronomy Department of Computational Mathematics, Science, and Engineering National Superconducting Cyclotron Laboratory/Facility for Rare Isotope Beams Michigan State University 567 Wilson Rd, 3250 BPS East Lansing, MI 48824 (517) 884-5035 —— couch(a)pa.msu.edu<mailto:couch@pa.msu.edu> —— www.pa.msu.edu/~couch<http://www.pa.msu.edu/~couch>

1 year, 11 months

BUILT-IN VELOCITY DISPERSION COMPUTATION

by Vadlamani Samhitha

Hi, I am still a bit new to yt and am trying to compute local velocity dispersions of the gas in my simulation by dividing the entire volume into ‘n’ number of sub grids. Does yt offer any functionality that could perform this in a simple fashion? (I looked up the documentation and couldn’t find any such function). Thank you.

1 year, 11 months

Error while deriving vorticity field

by Prateek Gupta

Dear yt-users I am creating a derived field for new_vorticity_magnitude. But when I take the SlicePlot of this derived field I am getting the following error: ############################################### slc = yt.SlicePlot(ds, 'z', "Vorticity_mag", center= center_old , width = (4,'Mpccm/h')) File "/home/dumbo/yt/yt/visualization/plot_window.py", line 1953, in SlicePlot return AxisAlignedSlicePlot(ds, normal, fields, *args, **kwargs) File "/home/dumbo/yt/yt/visualization/plot_window.py", line 1266, in __init__ slc.get_data(fields) File "/home/dumbo/yt/yt/data_objects/data_containers.py", line 1336, in get_data self._generate_fields(fields_to_generate) File "/home/dumbo/yt/yt/data_objects/data_containers.py", line 1356, in _generate_fields fd = self._generate_field(field) File "/home/dumbo/yt/yt/data_objects/data_containers.py", line 318, in _generate_field tr = self._generate_fluid_field(field) File "/home/dumbo/yt/yt/data_objects/data_containers.py", line 338, in _generate_fluid_field rv = finfo(gen_obj) File "/home/dumbo/yt/yt/fields/derived_field.py", line 237, in __call__ dd = self._function(self, data) File "vorticity_test.py", line 63, in _newvorticity_x_ f = (data[ftype, "zVel"][sl_center,sl_right,sl_center] - data[ftype, "zVel"][sl_center,sl_left,sl_center]) / (div_fac*just_one(data["index", "dy"])) File "/home/dumbo/yt/yt/units/yt_array.py", line 1036, in __getitem__ ret = super(YTArray, self).__getitem__(item) IndexError: too many indices for array ############################################### The current version of yt is: --- Version = 3.5.dev0 Changeset = 0cb7ad5befb2 --- Please let me know, why I am getting this error? Best regards -Prateek

1 year, 11 months

ISSUE WITH PLOTTING MULTIPLE PROFILES WITH RAMSES DATA

by Vadlamani Samhitha

Hi, I am trying to get multiple profile plots of density pdf for ramses data and I encounter the following error: > /home/samvad/yt-conda/lib/python3.6/site-packages/h5py/__init__.py:36: > 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 > > Traceback (most recent call last): > > File "pdf.py", line 8, in <module> > > sim = yt.simulation(filename, "Ramses") > > File > "/home/samvad/yt-conda/lib/python3.6/site-packages/yt/convenience.py", line > 112, in simulation > > raise YTSimulationNotIdentified(simulation_type) > > yt.utilities.exceptions.YTSimulationNotIdentified: Simulation time-series > type ramses not defined. > and the following is the code I am using to do so: > import yt > > from yt.units import kpc > > import matplotlib.pyplot as plt > > import numpy as np > > import yt.visualization.eps_writer as eps > filename="/lunarc/nobackup/users/samvad/BIG-12-new/output/" > sim = yt.simulation(filename, "Ramses") > sim.get_time_series(time=[0,50,100,150,200,250,300]) > profiles=[] > labels=[] > plot_specs=[] > for ds in sim: > ds.define_unit("hpc", (1.674*10**(-24), "g/cm**3")) > ad=ds.all_data() > dens=ad.cut_region(["obj['density'].in_units('hpc') > 0"]) > profiles.append(yt.create_profile(dens, "density", "cell_mass", > weight_field=None, fractional=True)) > labels.append("time=%.2f" % ds.current_time.in_units('Myr')) > plot_specs.append(dict(linewidth=2, alpha=0.7)) > plot = yt.ProfilePlot.from_profiles(profiles, labels=labels, > plot_specs=plot_specs) > plot.set_log("density", True) > plot.set_unit("density", "hpc") > plot.set_xlim(1e-7, 1e7) plot.save(name='density-pdf', suffix='eps') could someone please let me know how I can get the simulation_type for ramses? Thanks.

1 year, 11 months

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yt-users October 2018