yt-users September 2013

yt-users@python.org

33 participants
42 discussions

Stars on volume rendering
by Elizabeth Harper-Clark 11 Dec '21

11 Dec '21

Hi all, Thanks for all your help over the last couple of days. One more question: - Can I plot particles on a volume rendered image? I have stars and I want to show where they are! Thanks, Libby -- Elizabeth Harper-Clark MA MSci PhD Candidate, Canadian Institute for Theoretical Astrophysics, UofT Sciences and Engineering Coordinator, Teaching Assistants' Training Program, UofT www.astro.utoronto.ca/~h-clark <http://www.astro.utoronto.ca/%7Eh-clark> h-clark(a)cita.utoronto.ca Astronomy office phone: +1-416-978-5759

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Variance in phase/profiles
by david collins 11 Apr '20

11 Apr '20

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.

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Light Cone Projection
by Pengfei Chen 01 Mar '14

01 Mar '14

Hi all, I downloaded the example script of light cone projectoin( http://yt-project.org/doc/cookbook/cosmological_analysis.html#light-cone-pr…) to my laptop and changed the Enzo simulation parameter file and redshifts. But when I ran it the following error occurred: File "light_cone_projection.py", line 19, in <module> find_outputs=False) File "/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/analysis_modules/cosmological_observation/light_cone/light_cone.py", line 158, in __init__ find_outputs=find_outputs) File "/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/analysis_modules/cosmological_observation/cosmology_splice.py", line 44, in __init__ find_outputs=find_outputs) File "/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/convenience.py", line 131, in simulation find_outputs=find_outputs) File "/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/frontends/enzo/simulation_handling.py", line 81, in __init__ find_outputs=find_outputs) File "/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/data_objects/time_series.py", line 343, in __init__ self._parse_parameter_file() File "/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/frontends/enzo/simulation_handling.py", line 273, in _parse_parameter_file param, vals = (i.strip() for i in line.split("=")) ValueError: need more than 1 value to unpack Does the parameters "near_redshift" and "far_redshift" in LightCone need to be the same with "CosmologyFinalRedshift" and "CosmologyInitialRedshift" in enzo parameter file? Does anyone know how to solve this? Thank you all! Pengfei

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Problems with fields
by Cameron Hummels 02 Oct '13

02 Oct '13

Hello fellow yt'ers: I'm having some issues with some fields that I don't think are behaving the way they should be in yt. I'm encountering a number of problems with a simple 2D enzo dataset (x and y), so I put together a notebook demonstrating my various issues. https://hub.yt-project.org/nb/727j2j To summarize the weirdness from the notebook: 1) The 'dx' field doesn't seem to be able to be displayed (i.e. when I try to slice it), whereas the 'dy' field is fine. 'dz' even exists, but it's just uniformly 0, as is expected from a 2D dataset. 2) When I try to produce a new field which is 2^GridLevel, I get weird results (ignored levels and more). 3-5) I get strange behavior when trying to make a new field combining GridLevel and 'dy', since GridLevel has twice as many indices as any of the spatial fields (in the z direction no less). This results in some odd behavior when I try to pair various subsets of GridLevel with 'dy'. Any clarification of these ideas is welcome. The docs and source haven't yet revealed what is going on here. Thanks! Cameron -- Cameron Hummels Postdoctoral Researcher Steward Observatory University of Arizona http://chummels.org

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reading Gadget-HDF5 format in yt-3.0
by Brendan Griffen 27 Sep '13

27 Sep '13

Hi, I noticed in the update log of yt-3.0 you can now read Gadget HDF5 format (for OWLS project), but it is possible for Rockstar to read the exact same formats? I have some HDF5 data and I'd like to run Rockstar on it through yt if it has this capability in 3.0. Are there any examples of carrying out such a process? Thanks. Thanks. Brendan

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new yt website, now with gallery!
by Britton Smith 27 Sep '13

27 Sep '13

Hi everyone, Today we launched a completely redesigned yt website. It's still at yt-project.org, but with a completely new look. One of the brand new features is the yt Gallery (http://yt-project.org/gallery.html). The gallery is designed to show off examples of yt in the real world and to give new users an idea of all that's possible. We have a few really nice contributions up there now, but we want many more! If you have a figure made at least in part with yt that you're particularly proud from a paper, poster, talk, press release, or just something really cool, please consider submitting it to the gallery. To add something to the gallery, simply fork the yt website repository here: https://bitbucket.org/yt_analysis/website Then, add your image (400 pixels wide, preferably) to the directory img/gallery, add an entry to the gallery.html file, and submit a pull request. We will also accept embedded movies from vimeo or youtube. Make sure to add a caption with a brief explanation of the figure, what functionality you used to make it, and a citation if it appears in a publication. Also, make sure to add your figure to the top of the gallery page so it's easy to see what's new. We look forward to seeing what amazing things people have done! Britton

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Stars Particles
by Francia Riesco 27 Sep '13

27 Sep '13

Hi Everybody, I am trying to run this example from the cookbook from yt.mods import * from yt.analysis_modules.star_analysis.api import * pf = load("data0030") # Find all the haloes, and include star particles. haloes = HaloFinder(pf, dm_only=False) # Set up the spectrum builder. spec = SpectrumBuilder(pf, bcdir="/home/user/bc", model="salpeter") # Iterate over the haloes. for halo in haloes: # Get the pertinent arrays. ct = halo["creation_time"] sm = halo["ParticleMassMsun"] metal = halo["metallicity_fraction"] # Select just the stars. stars = (ct > 0) ct = ct[stars] sm = sm[stars] metal = metal[stars] # Calculate the spectrum. spec.calculate_spectrum(star_mass=sm, star_creation_time=ct, star_metallicity_fraction=metal) # Write out the SED using the default flux normalization. spec.write_out_SED(name="halo%05d.out" % halo.id) This is my code http://paste.yt-project.org/show/3885/ But I get this error: Link length is 0.001000 Filling in 3697686 particles Number of initial groups:6036 Number of groups:257 FOF CPU TIME: 10395.710700 secs Found [ -1 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257] unique groupings yt : [INFO ] 2013-09-25 15:15:27,721 Initializing HOP yt : [INFO ] 2013-09-25 15:15:27,721 Getting particle_position_x using ParticleIO yt : [INFO ] 2013-09-25 15:21:16,316 Getting particle_position_y using ParticleIO yt : [INFO ] 2013-09-25 15:25:36,923 Getting particle_position_z using ParticleIO yt : [INFO ] 2013-09-25 15:29:48,316 Getting ParticleMassMsun using ParticleIO Copying arrays for 47944939 particles Calling hop... 47944939 1.600e+02 nSmooth = 65 kd->nActive = 47944939 Building Tree... Finding Densities... Finding Densest Neighbors... Grouping... Merging Groups... Writing Output... All Done!Calling regroup... No minimum group size specified. Assuming 10 particles. ngroups = 262744 yt : [INFO ] 2013-09-25 15:52:17,649 Parsing outputs yt : [INFO ] 2013-09-25 15:52:24,347 Getting ParticleMassMsun using ParticleIO yt : [INFO ] 2013-09-25 15:57:00,506 Getting particle_position_x using ParticleIO yt : [INFO ] 2013-09-25 16:01:14,743 Getting particle_position_y using ParticleIO yt : [INFO ] 2013-09-25 16:06:14,673 Getting particle_position_z using ParticleIO Traceback (most recent call last): File "StarsParticleAnalysys.py", line 48, in <module> spec = SpectrumBuilder(data_source, bcdir="/astro/py/", model="salpeter") File "/astro/yt-dev/yt-x86_64/src/yt-hg/yt/analysis_modules/star_analysis/sfr_spectrum.py", line 278, in __init__ (100.0 * self._pf.hubble_constant), AttributeError: 'AMRRegion' object has no attribute 'hubble_constant' Any suggestion? Thanks a lot in Advance!

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--parallel not working for MPT?
by Semyeong Oh 26 Sep '13

26 Sep '13

Hi all, I want to divide ENZO simulation into certain regions, do some operation and save some files in parallel. I used parallel_objects for this. If I use openMPI and do $mpirun -np 6 python script.py --parallel it works fine. But if I use MPT(a variety of MPICH, I think) and run the exact same command, it ignores --parallel and just does things in serial. Is this expected? I'm new to parallel computation, and kind of stuck here. Thanks for your help. Best regards, Semyeong

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accessing colorbar directly
by Luigi Iapichino 26 Sep '13

26 Sep '13

Dear all, I am in the process of moving most of my visualisation scripts from PlotCollection to the PlotWindow interface. One feature that now I am not able to find is the capability of customising the tick values in the colorbar of a plot. Inspired by the example script found in http://yt-project.org/docs/2.5/cookbook/simple_plots.html#accessing-and-mod… , I was thinking about interacting with a matplotlib object directly, but I am not able to find a suitable one. Could you please suggest me a workaround for this issue? Thanks in advance, Luigi -- --------------------------------------------------------------- Luigi Iapichino Universität Heidelberg, Zentrum für Astronomie Institut für Theoretische Astrophysik Philosophenweg 12, D-69120 Heidelberg, Germany Tel: +49 6221 548983, Fax: +49 6221 544221 e-mail: luigi(a)uni-heidelberg.de URL: http://www.ita.uni-heidelberg.de/~luigi/

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Overplotting equipotential contours from total potential
by trobolo dinni 25 Sep '13

25 Sep '13

Dear yt users, I am running a binary star simulation with enzo, and in my box there is a star made up of a gas envelope and a particle as core, and a secondary star represented by a single particle (no gas). I would like to plot the equipotential surfaces of the system on a slice plot, hence, since the default Grav_Potential field does not include the particles potential, I created a custom made field as follows: * def _Total_Grav_Potential(field,data): * * #G in cgs* * grav_const_cgs = 6.674e-8* * * * #data for gas* * gas_grav_potential_cgs = data['Grav_Potential'] * (length_unit1/time_unit1)**2.0 #in units of velocity^2* * gas_position_x_cgs = data['x'] * length_unit1* * gas_position_y_cgs = data['y'] * length_unit1* * gas_position_z_cgs = data['z'] * length_unit1* * * * #initialize the array for the total grav potential to the gas grav potential* * total_grav_potential_cgs = gas_grav_potential_cgs* * * * #loops on the particles* * for i in range(len(data['ParticleMassMsun'])):* * * * #data of the current particle* * current_particle_mass_cgs= data['ParticleMassMsun'][i] * mass_unit* * current_particle_position_x_cgs = data['particle_position_x'][i] * length_unit1* * current_particle_position_y_cgs = data['particle_position_y'][i] * length_unit1* * current_particle_position_z_cgs = data['particle_position_z'][i] * length_unit1* * * * #computes the array of grav potential for the current particle* * current_particle_grav_potential_cgs = -(grav_const_cgs * current_particle_mass_cgs)/(((gas_position_x_cgs - current_particle_position_x_cgs)**2.0 + (gas_position_y_cgs - current_particle_position_y_cgs)**2.0 + (gas_position_z_cgs - current_particle_position_z_cgs)**2.0)**0.5)* * * * #adds the current particle potential to the total potential* * total_grav_potential_cgs = total_grav_potential_cgs + current_particle_grav_potential_cgs* * * * return total_grav_potential_cgs* * #adds the field to the available yt fields* * add_field("Total_Grav_Potential", function=_Total_Grav_Potential, take_log=True ,units=r"\rm{erg}/\rm{g}")* * * where the length unit and time unit variables have the function to convert my quantities in cgs. If I then call my "Total_Grav_Potential" field, I get reasonable values, but when I try to inspect the shape of the equipotential surfaces on the xy-plane by plotting the following: * sp = SlicePlot(pf, 'z', "Density", width = 1.0)* * sp.annotate_velocity(factor=16, normalize=True)* * sp.annotate_contour('Total_Grav_Potential',clim=(max_total_pot,min_total_pot)) * * sp.annotate_particles(1.0, p_size=50.0, marker='o', col='black')* * sp.annotate_text((0.7,1.05), "time = "+str(pf.current_time)+"yr") * * sp.save(plot_dir+"density_slice_z_"+str(index)+".png")* nothing happens, and the plot does not show any additional contour; while if I do the same with the default "Grav_Potential" field, the gas equipotential contours get plotted without problems. I also tried to play with the "annotate_contour" options "ncont", "factor" and "clim" to refine my plot but the result is always the same. Additionally, if I do not set the "clim" option the following error shows up: *ValueError: zero-size array to minimum.reduce without identity* * * I would like to ask if my custom definition of the Total_Grav_Potential field is correct from a yt coding point of view and if I should modify it (or if there is any improvement I can do). Also, I would like to ask if you have any idea of what could be the problem with the plotting. Thanks for the help, Roberto

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yt-users September 2013