Mailman 3 April 2019 - yt-users

mapping between grids
by Johann Higl April 16, 2019

April 16, 2019

Hi everyone, is there a yt native way to map between grids with different geometry? To be a bit more precise. I have a cartesian dataset (MAESTRO) and would like to map it onto a spherical grid to make some analysis easier. So far I tried to use the _find_field_values_at_points function to extract the necessary datapoints, which works fine for most fields, but fails as soon as the radius get involved. Somewhere in the process the point objects (or grid objects for the faster version in grid_geometry_handler) loose the information about the centre of my simulation, which messes up the radius calculation and all other fields that rely on that field parameter. Also, the set_field_parameter function does not seem to have any effect on the grid objects. To summarize: Is there an easier method to do what I'm trying to do and if not is there a way to get consistent radius calculations throughout the different data objects? Best Johann

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making a 3D grid box from Illustris simulations
by Vikram Khaire April 16, 2019

April 16, 2019

Dear yt users, I want to convert the default IllustrisTNG outputs into a mesh grid. I basically want to convert individual Voronoi cells into a 3 D coordinate grids and assign temperature density and velocities to each grid points. I am looking forward to using the yt 4.0 demeshening technique. Let me know if anybody has done something similar in the past or know how to do that. Thank you. -Vikram

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Stellar Age in GEAR/GIZMO
by SANTI ROCA FABREGA April 15, 2019

April 15, 2019

Dear yt users, I have been trying to get the correct Stellar Age in "Myr" from PartType1 (GEAR) and PartType4 (Gizmo) from "StarFormationTime" and "StellarFormationTime" fields, respectively. After several attempts I have not succeeded. Do anybody went through a similar problem? Is there an easy way to solve it? I know "StarFormationTime" and "StellarFormationTime" fields are supposed to be the scale factor time when stellar particle was created. Thank you a lot for your help. Best -- ---------------------------------------------------------------------------------- Santi Roca-Fabrega Office 233, Office Plaza Ciencias, 1 Departamento de Física de la Tierra y Astrofísica, Facultad de Ciencias Físicas, Universidad Complutense de Madrid, E-28040, Madrid, Spain Phone: +34 658310823 ----------------------------------------------------------------------------------

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Creating a regular grid using SPH kernel
by robin.kooistra＠ipmu.jp April 15, 2019

April 15, 2019

Hello, I apologize in advance for any ignorant questions. I am new to YT and am really struggling with this problem. I am trying to use YT (version 3.5.1) to grid my SPH simulation box to a regular grid with 1024^3 cells. The box itself has sides of 300 Mpc/h and the data consists of pre-loaded numpy arrays for positions (in Mpc/h), mass (in 10^10 Msun/h), density (in 10^10 Msun/h /(Mpc/h)^3 ), particle smoothing length (in Mpc/h) and an optical depth tau. How can I properly load this into a YT dataset and how can I then get YT to create the regular grid for the optical depth tau or the density with an SPH kernel, such as Wendland2? Also, is it possible to output the grids as an array that could then be saved to file or used with other scripts? To hopefully clarify what I am trying to do, below you can find the YT part of my current script. Thank you in advance for any help you could give. Robin Kooistra > import numpy as np > import yt .................... density, m, tau, smooth and pos are numpy arrays .................... >data = dict(particle_density = density, > particle_mass = m, > particle_tau = tau, > particle_smoothing_length = smooth, > particle_position_x = pos[:,0], > particle_position_y = pos[:,1], > particle_position_z = pos[:,2] > ) > > ds = yt.load_particles(data,bbox=n.array([[0.,300.],[0.,300.],[0.,300.]])) > > yt.fields.particle_fields.add_volume_weighted_smoothed_field(ptype='io', coord_name='particle_position', mass_name='particle_mass', smoothing_length_name='particle_smoothing_length', density_name='particle_density', smoothed_field='particle_tau',registry=ds.field_info, nneighbors=58,kernel_name='wendland2') > > ag = ds.arbitrary_grid(ds.domain_left_edge,ds.domain_right_edge,dims=[1024,1024,1024]) > mesh = ag['deposit','io_wendland2_smoothed_particle_tau']

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Increase label size in profile plot/ modify the interval numbering of x-axis and y-axis co-ordinates in slice plots/ adding box around annotate text in phase plots
by nirmit sakre April 15, 2019

April 15, 2019

Hi yt-users, I am facing few issues related to customizing the yt plots of my enzo-code based data. 1. How to change the size of labels in Profile plot. 2. How can we modify the interval numbering of x-axis and y-axis co-ordinates (selecting less numbers so that the axes are not crowded) in Slice plots/Projection plots. 3. How can we add box around the annotated text in Phase plots. Slice plot case is easy but Phase plot seems to be unhappy. I tried searching for right set of codes but was not successful. As a last resort, I am turning towards the yt community. If anybody can give the information it would save lot of my time.

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reporting a bug
by Vikram Khaire April 12, 2019

April 12, 2019

I don't know where to report bugs. I am new to yt. I was testing a few things with trident. I tried an example from https://trident.readthedocs.io/en/latest/generated/trident.make_onezone_dat… The code breaks at some line in yt/yt/frontend/ytdata/io.py I think this block needs small change from dx to x in two places. if ptype == "grid": dx = f["grid"]["dx"][()].min() dx = self.ds.quan( dx, parse_h5_attr(f["grid"]["dx"], "units")).to("code_length") as: if ptype == "grid": dx = f["grid"]["x"][()].min() dx = self.ds.quan( dx, parse_h5_attr(f["grid"]["x"], "units")).to("code_length")

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Re: Finding two-point correlation function
by Salome Mtchedlidze April 11, 2019

April 11, 2019

As for halo mass function I found this: https://yt-project.org/doc/reference/api/yt.analysis_modules.halo_mass_func… <https://yt-project.org/doc/reference/api/yt.analysis_modules.halo_mass_func…> Which I think does same as the script in the link, I provided above; However, here the comment : This module has been deprecated as it no longer functions correctly and is unmaintained. The code has been moved to the yt attic <https://github.com/yt-project/yt_attic>. If you’d like to take it over, please do! does not appear anymore. So I assume that this can be used for finding halo mass function, cannot it?

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Changing font size and colorbar ticks for eps_writer
by Mihir Kulkarni April 3, 2019

April 3, 2019

Hello, I am trying to make eps figures using yt and have some trouble fine-tuning them. I want to create a multiplot with 3 density projections at different snapshots. I create the projection plots as follows. prj = yt.ProjectionPlot(ds, 'x', 'density', center='m', width=(20,'pc')) prj.set_font({'size':40}) prj.set_zlim('density',4e-3,3) I then create a multiplot using eps_writer as follows: import yt.visualization.eps_writer as eps eps_fig = eps.multiplot_yt(3,1,[prj10, prj60, prj110], savefig='yt',bare_axes=False, yt_nocbar=False, margins=(0.5,0.5), cb_flags=[0,0,1]) This creates a multiplot with nrow=1, ncol=3 as I expect. However, the font size in saved eps figure is back to normal and not very large as I want. Also, the ticks on the colorbar are in float format instead of exponential format. (Showing 0.01, 0.02, 0.5 etc. instead of 10^{-2}, 10^{-1} etc.) Could you please help me with this - increasing the overall font size and changing colorbar ticks format with eps_writer? Thanks, Mihir Kulkarni

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Finding two-point correlation function
by Salome Mtchedlidze April 3, 2019

April 3, 2019

Hello again, I am doing ENZO magnetized simulations and want to get two point correlation function for the magnetic field and density. I found this: https://yt-project.org/doc/analyzing/analysis_modules/two_point_functions.h… I am not sure if it is the good way to use it, since the note says: "This module has been deprecated as it is unmaintained". I have the same question for finding cumulative mass function (if I can use this): http://yt-project.org/doc/analyzing/analysis_modules/halo_mass_function.html Could you please advise if there are any other sample scripts for finding two point correlation functions?

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Changing font size and colorbar ticks for eps_writer
by Mihir Kulkarni April 2, 2019

April 2, 2019

Hello, I am trying to make eps figures using yt and have some trouble fine-tuning them. I want to create a multiplot with 3 density projections at different snapshots. I create the projection plots as follows. prj = yt.ProjectionPlot(ds, 'x', 'density', center='m', width=(20,'pc')) prj.set_font({'size':40}) prj.set_zlim('density',4e-3,3) I then create a multiplot using eps_writer as follows: import yt.visualization.eps_writer as eps eps_fig = eps.multiplot_yt(3,1,[prj10, prj60, prj110], savefig='yt',bare_axes=False, yt_nocbar=False, margins=(0.5,0.5), cb_flags=[0,0,1]) This creates a multiplot with nrow=1, ncol=3 as I expect. However, the font size in saved eps figure is back to normal and not very large as I want. Also, the ticks on the colorbar are in float format instead of exponential format. (Showing 0.01, 0.02, 0.5 etc. instead of 10^{-2}, 10^{-1} etc.) Could you please help me with this - increasing the overall font size and changing colorbar ticks format with eps_writer? Thanks, Mihir Kulkarni

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