Mailman 3 October 2014 - yt-users

Re: [yt-users] particle generator and update issues
by Elizabeth Tasker 14 Oct '14

14 Oct '14

Hi John, Thanks for looking into this! CICDeposit and CICSample are actually the opposite of each other—the first deposits particle quantities onto the mesh, the second interpolates mesh quantities onto the particles. I’m not sure why CICDeposit_3 wasn’t in your repo—I can import it over here. Ah! This was my mistake: I was searching for it in a python routine, but it lives in particle_deposit.c. Updating again has worked! I am now back on yt-3: tasker@schiehallion:~/yt-3/bin$ yt update yt : [INFO ] 2014-10-14 22:24:20,504 Loading plugins from /home/tasker/.yt/my_plugins.py yt module located at: /home/tasker/yt-new/src/yt-hg The current version and changeset for the code is: --- Version = 3.0.2 Changeset = a119d0a54bfe (stable) tip --- This installation CAN be automatically updated. So the only error is the is the "KeyError: ('io', 'particle_position_x’)” . Thanks! Elizabeth

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comoving length
by Junhwan Choi (최준환) 14 Oct '14

14 Oct '14

Hi yt user, I have very simple question. In older version of yt, there was comoving length unit such as mpccm. So that I can make visualization in following way: >pc = yt.ProjectionPlot(pf, "x", "Dark_Matter_Density", width = (4.0, 'mpccm'),center=cen_center) But, after I update the latest version, the plots made by this command give me very strange output. Instead, I use following command: pc = yt.ProjectionPlot(pf, "x", "Dark_Matter_Density", center=cen_center) It gives me correct output. Is "width = (4.0, 'mpccm')" keyword changed in new yt? Thank you in advance, Junhwan

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Syntax error in install_script.sh
by Aldo Alberto Batta Marquez 12 Oct '14

12 Oct '14

Hi all, I'm not yet in the mailing list but I was trying to install yt yesterday and got this message during installation: Installing yt install_script.sh: line 992: syntax error near unexpected token `fi' install_script.sh: line 992: ` fi' I looked at the install_script.sh and found there was a missing "then" in the script. I'll send the details in case you need to change the install_script. The problem is corrected by adding a then at line 990 replacing: ============================================================ if !( ( ${DEST_DIR}/bin/python2.7 -c "import readline" 2>&1 )>> ${LOG_FILE}) then if !( ( ${DEST_DIR}/bin/python2.7 -c "import gnureadline" 2>&1 )>> ${LOG_FILE}) echo "Installing pure-python readline" ( ${DEST_DIR}/bin/pip install gnureadline 2>&1 ) 1>> ${LOG_FILE} fi fi ============================================================ with: ============================================================ if !( ( ${DEST_DIR}/bin/python2.7 -c "import readline" 2>&1 )>> ${LOG_FILE}) then if !( ( ${DEST_DIR}/bin/python2.7 -c "import gnureadline" 2>&1 )>> ${LOG_FILE}) then echo "Installing pure-python readline" ( ${DEST_DIR}/bin/pip install gnureadline 2>&1 ) 1>> ${LOG_FILE} fi fi ============================================================ Bests Aldo Batta -- Aldo Alberto Batta Márquez Instituto de Astronomia Universidad Nacional Autonoma de Mexico (UNAM) http://www.astroscu.unam.mx

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Deprecation Woes
by Munier Azzam Salem 07 Oct '14

07 Oct '14

Hey Guys, A false sense of complacency / hubris led me to update my dev version of yt ... I thought "how much damage could this do?" ... well ... After updating 50 derived fields in my analysis scripts, I have learned a valuable life lesson. Well played yt. Well played. But I digress ... One of the deprecated usages I couldn't figure out how to fix involves pulling units from a pf object. Specifically I'd like to do this: pf.units['cm'] Alternatives I could live with: finding the length of a side of the simulation box in CGS, some way to convert between code and physical units, etc ... I'm working with enzo, if that matters. cheers, Munier -- Munier A. Salem // 845.489.6450

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How to stamp the vector scale on quiver plots?
by Manuel Zamora 07 Oct '14

07 Oct '14

Dear YT community, I'm using the annotate_velocity() and annotate_magnetic_field() routines for ‘quiver' plots, but I also want to stamp the scale of the vectors in the same plot. Could anyone point me to the respective documentation? Thanks a lot for your kind help! Cheers :) _ Manuel Zamora

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integrate a field along a direction
by Juan Camilo Ibanez Mejia 07 Oct '14

07 Oct '14

Dear yt users, I have a simulation from which I selected a region using: sph = data.sphere(center, (radius,"pc")) Now I want to integrate the density and velocity along the z axis and do some analysis on the projected field. like: I have some points in the projection I am interested in and I want to know the radial surface density profile or the divergence of the projected velocity. thanks in advance for your help, Juan _____________________________ Juan Camilo Ibañez Mejia Department of Astrophysics American Museum of Natural History +1-212-313-7435 jibanezmejia(a)amnh.org<mailto:jibanezmejia@amnh.org> _____________________________

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yt 3.0.2 release
by Nathan Goldbaum 03 Oct '14

03 Oct '14

Hi all, We've just released yt 3.0.2. This is a regularly scheduled bugfix release that includes all of the fixes that have been submitted as pull requests in the past month. See this page for a full listing of merged pull requests: https://bitbucket.org/yt_analysis/yt/pull-requests?displaystatus=merged We urge all users to update as soon as is convenient. If you built yt using the install script, you can update with the following shell command: $ yt update If you installed using pip, you can do: $ pip install -U yt Finally, if you installed using conda, you can do: $ conda update yt Note that it might take a day or two for the conda package to be updated. As always, if you have any questions, concerns, or run into any trouble updating please don't hesitate to send a message to the mailing list or stop by our IRC channel. Hope you all have a relaxing weekend, Nathan Goldbaum

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Re: [yt-users] yt-users Digest, Vol 80, Issue 7
by Manuel Zamora 03 Oct '14

03 Oct '14

Hi Corey, This works for me: %%%%%%%%%%%%%%%%%%%%%%%% import h5py ... f = h5py.File("../r10f0/flows_hdf5_plt_cnt_0160","r") ParticleData = f['particle tracers'] ppz = ParticleData["particle_z"] ppy = ParticleData["particle_y"] ppx = ParticleData["particle_x"] ppm = ParticleData["particle_mass"] data = {'particle_position_x': ppx, 'particle_position_y': ppy, 'particle_position_z': ppz, 'particle_mass': ppm} f.close() del ParticleData del f ... slc.annotate_marker([ppx,ppy,ppz], marker='o', plot_args={'color': 'black','s':10}) %%%%%%%%%%%%%%%%%%%%%%%% I hope this helps :) _ Manuel Zamora On Oct 3, 2014, at 11:23 AM, yt-users-request(a)lists.spacepope.org wrote: > Send yt-users mailing list submissions to > yt-users(a)lists.spacepope.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > or, via email, send a message with subject or body 'help' to > yt-users-request(a)lists.spacepope.org > > You can reach the person managing the list at > yt-users-owner(a)lists.spacepope.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of yt-users digest..." > > > Today's Topics: > > 1. Annotating particles in FLASH2.5 (C.S. Howard) > 2. Re: Annotating particles in FLASH2.5 (John ZuHone) > 3. Re: Annotating particles in FLASH2.5 (C.S. Howard) > 4. Re: Rockstar and RAMSES (DM only run). Rockstar appears to > run, but no halo information is written. (Ben Thompson) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 3 Oct 2014 12:14:08 -0400 > From: "C.S. Howard" <howardcs(a)mcmaster.ca> > To: yt-users(a)lists.spacepope.org > Subject: [yt-users] Annotating particles in FLASH2.5 > Message-ID: > <CADaEBaZ=LwWfN3TLaE2KTnC35vksfvmLwYiZeMnOoJ7BOyb_Og(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi everyone, > > I'm trying to draw sink particles on a slice plot using FLASH 2.5 data. I'm > using yt 3.0 with the commands: > > pf = yt.load(pltfiles[k]) > fig = plt.figure() > ax1 = fig.add_subplot(111) > axes = {'x':0, 'y':1, 'z':2} > slices = {'x':[0.0,0.5,0.5],\ > 'y':[0.5,0.0,0.5],\ > 'z':[0.5,0.5,0.5]} > > slc = SlicePlot(pf, 'z', 'density', center = slices['z'],origin='domain') > slc.annotate_particles(1.0, p_size=15.0, col="Black") > > but it doesn't work, giving me the following errors; > > Traceback (most recent call last): > File "./sliceplots.py", line 42, in <module> > slc.annotate_particles(1.0, p_size=15.0, col="Black") > File > "/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/visualization/plot_container.py", > line 70, in newfunc > args[0]._setup_plots() > File > "/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", > line 862, in _setup_plots > self.run_callbacks(f) > File > "/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/visualization/plot_container.py", > line 315, in run_callbacks > callback(cbw) > File > "/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/visualization/plot_modifications.py", > line 1055, in __call__ > & ( reg[pt, field_y] >= y0 ) & ( reg[pt, field_y] <= y1 ) ) > File > "/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", > line 233, in __getitem__ > f = self._determine_fields([key])[0] > File > "/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", > line 486, in _determine_fields > finfo = self.ds._get_field_info(ftype, fname) > File > "/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/data_objects/static_output.py", > line 482, in _get_field_info > raise YTFieldNotFound((ftype, fname), self) > yt.utilities.exceptions.YTFieldNotFound: Could not find field '('all', > 'particle_position_x')' in DensProfTurb_flattop_hdf5_plt_cnt_0200 > > Seems like its having trouble finding the particle information for > FLASH2.5. Any suggestions on where to go from here? > > Thanks, > Corey > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201…> > > ------------------------------ > > Message: 2 > Date: Fri, 3 Oct 2014 12:18:49 -0400 > From: John ZuHone <jzuhone(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] Annotating particles in FLASH2.5 > Message-ID: <5851849E-3256-47D4-9FCA-45C02C3AA248(a)gmail.com> > Content-Type: text/plain; charset="us-ascii" > > Hi Corey, > > Unfortunately, we don't support FLASH 2.5 particle data, because it is in a different format from v. 3.0 and above. > > If you like, I'd be happy to help figure out some kind of workaround. > > Best, > > John > > John ZuHone > Kavli Center for Astrophysics and Space Research > Massachusetts Institute of Technology > 77 Massachusetts Ave., 37-582G > Cambridge, MA 02139 > (w) 617-253-2354 > (m) 781-708-5004 > jzuhone(a)space.mit.edu > jzuhone(a)gmail.com > http://www.jzuhone.com > >> On Oct 3, 2014, at 12:14 PM, C.S. Howard <howardcs(a)mcmaster.ca> wrote: >> >> Hi everyone, >> >> I'm trying to draw sink particles on a slice plot using FLASH 2.5 data. I'm using yt 3.0 with the commands: >> >> pf = yt.load(pltfiles[k]) >> fig = plt.figure() >> ax1 = fig.add_subplot(111) >> axes = {'x':0, 'y':1, 'z':2} >> slices = {'x':[0.0,0.5,0.5],\ >> 'y':[0.5,0.0,0.5],\ >> 'z':[0.5,0.5,0.5]} >> >> slc = SlicePlot(pf, 'z', 'density', center = slices['z'],origin='domain') >> slc.annotate_particles(1.0, p_size=15.0, col="Black") >> >> but it doesn't work, giving me the following errors; >> >> Traceback (most recent call last): >> File "./sliceplots.py", line 42, in <module> >> slc.annotate_particles(1.0, p_size=15.0, col="Black") >> File "/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/visualization/plot_container.py", line 70, in newfunc >> args[0]._setup_plots() >> File "/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 862, in _setup_plots >> self.run_callbacks(f) >> File "/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/visualization/plot_container.py", line 315, in run_callbacks >> callback(cbw) >> File "/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/visualization/plot_modifications.py", line 1055, in __call__ >> & ( reg[pt, field_y] >= y0 ) & ( reg[pt, field_y] <= y1 ) ) >> File "/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 233, in __getitem__ >> f = self._determine_fields([key])[0] >> File "/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 486, in _determine_fields >> finfo = self.ds._get_field_info(ftype, fname) >> File "/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/data_objects/static_output.py", line 482, in _get_field_info >> raise YTFieldNotFound((ftype, fname), self) >> yt.utilities.exceptions.YTFieldNotFound: Could not find field '('all', 'particle_position_x')' in DensProfTurb_flattop_hdf5_plt_cnt_0200 >> >> Seems like its having trouble finding the particle information for FLASH2.5. Any suggestions on where to go from here? >> >> Thanks, >> Corey >> _______________________________________________ >> yt-users mailing list >> yt-users(a)lists.spacepope.org >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201…> > > ------------------------------ > > Message: 3 > Date: Fri, 3 Oct 2014 12:22:02 -0400 > From: "C.S. Howard" <howardcs(a)mcmaster.ca> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] Annotating particles in FLASH2.5 > Message-ID: > <CADaEBaapFJaCWnyWfS5s8NMp8KR7SQTf35-3BJEqWKutiCJY1A(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > That would be awesome, as long as it isn't a huge headache. I'll be moving > to the newer versions of FLASH soon, but for now I'm stuck with version 2.5. > > On Fri, Oct 3, 2014 at 12:18 PM, John ZuHone <jzuhone(a)gmail.com> wrote: > >> Hi Corey, >> >> Unfortunately, we don't support FLASH 2.5 particle data, because it is in >> a different format from v. 3.0 and above. >> >> If you like, I'd be happy to help figure out some kind of workaround. >> >> Best, >> >> John >> >> John ZuHone >> Kavli Center for Astrophysics and Space Research >> Massachusetts Institute of Technology >> 77 Massachusetts Ave., 37-582G >> Cambridge, MA 02139 >> (w) 617-253-2354 >> (m) 781-708-5004 >> jzuhone(a)space.mit.edu >> jzuhone(a)gmail.com >> http://www.jzuhone.com >> >> On Oct 3, 2014, at 12:14 PM, C.S. Howard <howardcs(a)mcmaster.ca> wrote: >> >> Hi everyone, >> >> I'm trying to draw sink particles on a slice plot using FLASH 2.5 data. >> I'm using yt 3.0 with the commands: >> >> pf = yt.load(pltfiles[k]) >> fig = plt.figure() >> ax1 = fig.add_subplot(111) >> axes = {'x':0, 'y':1, 'z':2} >> slices = {'x':[0.0,0.5,0.5],\ >> 'y':[0.5,0.0,0.5],\ >> 'z':[0.5,0.5,0.5]} >> >> slc = SlicePlot(pf, 'z', 'density', center = slices['z'],origin='domain') >> slc.annotate_particles(1.0, p_size=15.0, col="Black") >> >> but it doesn't work, giving me the following errors; >> >> Traceback (most recent call last): >> File "./sliceplots.py", line 42, in <module> >> slc.annotate_particles(1.0, p_size=15.0, col="Black") >> File >> "/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/visualization/plot_container.py", >> line 70, in newfunc >> args[0]._setup_plots() >> File >> "/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", >> line 862, in _setup_plots >> self.run_callbacks(f) >> File >> "/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/visualization/plot_container.py", >> line 315, in run_callbacks >> callback(cbw) >> File >> "/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/visualization/plot_modifications.py", >> line 1055, in __call__ >> & ( reg[pt, field_y] >= y0 ) & ( reg[pt, field_y] <= y1 ) ) >> File >> "/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", >> line 233, in __getitem__ >> f = self._determine_fields([key])[0] >> File >> "/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", >> line 486, in _determine_fields >> finfo = self.ds._get_field_info(ftype, fname) >> File >> "/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/data_objects/static_output.py", >> line 482, in _get_field_info >> raise YTFieldNotFound((ftype, fname), self) >> yt.utilities.exceptions.YTFieldNotFound: Could not find field '('all', >> 'particle_position_x')' in DensProfTurb_flattop_hdf5_plt_cnt_0200 >> >> Seems like its having trouble finding the particle information for >> FLASH2.5. Any suggestions on where to go from here? >> >> Thanks, >> Corey >> >> _______________________________________________ >> yt-users mailing list >> yt-users(a)lists.spacepope.org >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> >> >> _______________________________________________ >> yt-users mailing list >> yt-users(a)lists.spacepope.org >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> >> > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201…> > > ------------------------------ > > Message: 4 > Date: Fri, 3 Oct 2014 17:22:59 +0100 > From: Ben Thompson <bthompson2090(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] Rockstar and RAMSES (DM only run). Rockstar > appears to run, but no halo information is written. > Message-ID: > <CAFO9rXeHkwzeLCLg8vuKQ66JgVu3j0LziYXPH7uOzPgQhNO_OA(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hello. > > My simulation runs to z=0. Only with 10 timesteps though (purely a test > run). It identifies no halos in halos_0 (expected with it being the first > snapshot) and halos_9 (the final snapshot).. All files are the same size > too with no data. > > My code is (with the filters taken out... it's a dark matter only one > anyway) > > > from mpi4py import MPI > import yt, sys, os > yt.enable_parallelism() > from yt.config import ytcfg > from yt.analysis_modules.halo_finding.rockstar.api import \ > RockstarHaloFinder > from yt.data_objects.particle_filters import \ > particle_filter > from yt.data_objects.time_series import DatasetSeries > import numpy as np > > ncpu = MPI.COMM_WORLD.Get_size() > ytcfg.set('yt', '__global_parallel_size', str(ncpu)) > > outputs = np.arange(1, 11) > dirs = [] > #Add the datasets > for ioutput in outputs: > ds = yt.load('../output_%05d/info_%05d.txt'%(ioutput, ioutput)) > dirs.append(ds) > > es = DatasetSeries(dirs) > readers = int(ncpu/4.) > writers = ncpu - readers - 1 > rh = RockstarHaloFinder(es, num_readers=readers, num_writers=writers) > rh.run() > > > Ben > > > On Fri, Oct 3, 2014 at 5:09 PM, Cameron Hummels <chummels(a)gmail.com> wrote: > >> Hi Ben, >> >> No, you don't need to have halos in the first timestep. Rockstar will >> find the halos when they exist, so if you run it on all of the outputs and >> you get to a later redshift then 5 or so, rockstar will start to identify >> halos. Does your simulation run to z=0? If so, just look at the output >> file associated with that redshift and see if it identifies any halos. It >> doesn't matter your starting redshift. >> >> Cameron >> >> On Fri, Oct 3, 2014 at 9:02 AM, Ben Thompson <bthompson2090(a)gmail.com> >> wrote: >> >>> Hi Cameron. >>> >>> So it is dependent as of what timestep I start my run at? I start my run >>> (i.e there needs to be halos in the snapshot that you start with)? This is >>> the first time I have used Rockstar before (figured that since the package >>> is there, for free, I should use it) I have DM only runs that start at z=50 >>> (of which I am not expecting to find halos there, as part of the loading >>> script I loop over all the snapshots) >>> >>> This is what I have >>> >>> cat halos_0.0.ascii >>> #id num_p mvir mbound_vir rvir vmax rvmax vrms x y z vx vy vz Jx Jy Jz E >>> Spin PosUncertainty VelUncertainty bulk_vx bulk_vy bulk_vz BulkVelUnc >>> n_core m200b m200c m500c m2500c Xoff Voff spin_bullock b_to_a c_to_a A[x] >>> A[y] A[z] b_to_a(500c) c_to_a(500c) A[x](500c) A[y](500c) A[z](500c) Rs >>> Rs_Klypin T/|U| M_pe_Behroozi M_pe_Diemer idx i_so i_ph num_cp mmetric >>> #a = 0.019608 >>> #Bounds: (0.000000, 0.000000, 0.000000) - (99.816002, 99.816002, >>> 19.807144) >>> #Om = 0.300000; Ol = 0.700000; h = 0.700000 >>> #FOF linking length: 0.280000 >>> #Unbound Threshold: 0.500000; FOF Refinement Threshold: 0.700000 >>> #Particle mass: 2.87164e+10 Msun/h >>> #Box size: 99.816005 Mpc/h >>> #Total particles processed: 419422 >>> #Force resolution assumed: 0.780498 Mpc/h >>> #Units: Masses in Msun / h >>> #Units: Positions in Mpc / h (comoving) >>> #Units: Velocities in km / s (physical, peculiar) >>> #Units: Halo Distances, Lengths, and Radii in kpc / h (comoving) >>> #Units: Angular Momenta in (Msun/h) * (Mpc/h) * km/s (physical) >>> #Units: Spins are dimensionless >>> #Units: Total energy in (Msun/h)*(km/s)^2 (physical) >>> #Note: idx, i_so, and i_ph are internal debugging quantities >>> #Np is an internal debugging quantity. >>> #Rockstar Version: 0.99.9-RC3 >>> >>> (yt-x86_64)[bthompson1@leopard rockstar_halos]$ cat halos_9.0.ascii >>> #id num_p mvir mbound_vir rvir vmax rvmax vrms x y z vx vy vz Jx Jy Jz E >>> Spin PosUncertainty VelUncertainty bulk_vx bulk_vy bulk_vz BulkVelUnc >>> n_core m200b m200c m500c m2500c Xoff Voff spin_bullock b_to_a c_to_a A[x] >>> A[y] A[z] b_to_a(500c) c_to_a(500c) A[x](500c) A[y](500c) A[z](500c) Rs >>> Rs_Klypin T/|U| M_pe_Behroozi M_pe_Diemer idx i_so i_ph num_cp mmetric >>> #a = 1.000879 >>> #Bounds: (0.000000, 0.000000, 0.000000) - (99.816002, 99.816002, >>> 19.667080) >>> #Om = 0.300000; Ol = 0.700000; h = 0.700000 >>> #FOF linking length: 0.280000 >>> #Unbound Threshold: 0.500000; FOF Refinement Threshold: 0.700000 >>> #Particle mass: 2.87164e+10 Msun/h >>> #Box size: 99.816005 Mpc/h >>> #Total particles processed: 419437 >>> #Force resolution assumed: 0.779813 Mpc/h >>> #Units: Masses in Msun / h >>> #Units: Positions in Mpc / h (comoving) >>> #Units: Velocities in km / s (physical, peculiar) >>> #Units: Halo Distances, Lengths, and Radii in kpc / h (comoving) >>> #Units: Angular Momenta in (Msun/h) * (Mpc/h) * km/s (physical) >>> #Units: Spins are dimensionless >>> #Units: Total energy in (Msun/h)*(km/s)^2 (physical) >>> #Note: idx, i_so, and i_ph are internal debugging quantities >>> #Np is an internal debugging quantity. >>> #Rockstar Version: 0.99.9-RC3 >>> >>> Both exactly the same pretty much. >>> >>> If it is because I am starting at an early timestep, then I will cut out >>> the earlier ones from the initial setup. >>> >>> Thanks. >>> >>> Ben, >>> >>> On Fri, Oct 3, 2014 at 4:55 PM, Cameron Hummels <chummels(a)gmail.com> >>> wrote: >>> >>>> Hi Ben, >>>> >>>> Oftentimes, rockstar cannot find any halos for the first few snapshots >>>> of a cosmology DM-only sim because things have not collapsed enough. In >>>> that case, you'll get files like this: >>>> >>>> $ % cat halos_0.0.ascii >>>> #id num_p mvir mbound_vir rvir vmax rvmax vrms x y z vx vy vz Jx Jy Jz E >>>> Spin PosUncertainty VelUncertainty bulk_vx bulk_vy bulk_vz BulkVelUnc >>>> n_core m200b m200c m500c m2500c Xoff Voff spin_bullock b_to_a c_to_a A[x] >>>> A[y] A[z] b_to_a(500c) c_to_a(500c) A[x](500c) A[y](500c) A[z](500c) Rs >>>> Rs_Klypin T/|U| M_pe_Behroozi M_pe_Diemer idx i_so i_ph num_cp mmetric >>>> #a = 0.009901 >>>> #Bounds: (0.000000, 0.000000, 0.000000) - (40.000000, 40.000000, >>>> 3.099222) >>>> #Om = 0.282000; Ol = 0.718000; h = 0.697000 >>>> #FOF linking length: 0.280000 >>>> #Unbound Threshold: 0.500000; FOF Refinement Threshold: 0.700000 >>>> #Particle mass: 2.98630e+08 Msun/h >>>> #Box size: 40.000000 Mpc/h >>>> #Total particles processed: 1290100 >>>> #Force resolution assumed: 0.15625 Mpc/h >>>> #Units: Masses in Msun / h >>>> #Units: Positions in Mpc / h (comoving) >>>> #Units: Velocities in km / s (physical, peculiar) >>>> #Units: Halo Distances, Lengths, and Radii in kpc / h (comoving) >>>> #Units: Angular Momenta in (Msun/h) * (Mpc/h) * km/s (physical) >>>> #Units: Spins are dimensionless >>>> #Units: Total energy in (Msun/h)*(km/s)^2 (physical) >>>> #Note: idx, i_so, and i_ph are internal debugging quantities >>>> #Np is an internal debugging quantity. >>>> #Rockstar Version: 0.99.9-RC3 >>>> >>>> >>>> Is this what you're seeing or are your files truly empty? If you're >>>> seeing this, you may just need to run Rockstar on data files that are more >>>> evolved in time, so as to allow for more non-linear collapse of the halos. >>>> For my DM-only runs, depending on the mass resolution that I use, I may not >>>> start to see halos until after z=10 to z=5, with the first outputs all >>>> looking like the stuff above: empty. >>>> >>>> Cameron >>>> >>>> On Fri, Oct 3, 2014 at 8:46 AM, Ben Thompson <bthompson2090(a)gmail.com> >>>> wrote: >>>> >>>>> P.S sorry if I sent the same email twice.. this is the actual email... >>>>> accidental press send before I sent the email out. >>>>> >>>>> Hello everyone. >>>>> >>>>> I am currently using YT to run rockstar on my simulation. >>>>> >>>>> I have been following the instructions which are around and about and >>>>> have managed to write a script to run rockstar via MPI >>>>> >>>>> readers = int(ncpu/4.) >>>>> #Reserve one cpu for the server >>>>> writers = ncpu - readers - 1 >>>>> print 'Running rockstar with %i writers and %i readers'%(writers, >>>>> readers) >>>>> rh = RockstarHaloFinder(es, num_readers=readers, num_writers=writers, >>>>> particle_type="dark_matter", dm_only=True) >>>>> rh.run() >>>>> >>>>> using a particle filter on the datasets >>>>> >>>>> @yt.particle_filter("dark_matter", requires=[('particle_mass')]) >>>>> def dark_matter(pfilter, data): >>>>> if ('all', 'particle_age') in data.ds.field_list: >>>>> return data[("all", "particle_age")] == 0.0 >>>>> else: >>>>> arr = np.zeros(len(data['particle_mass'])) >>>>> return arr == 0.0 >>>>> >>>>> def setup_ds(ds): >>>>> #Return only dark matter particles, and assert that the filter >>>>> holds >>>>> print 'Here' >>>>> assert(ds.add_particle_filter("dark_matter")) >>>>> >>>>> >>>>> It seems to run fine.... e.g >>>>> >>>>> >>>>> [ 111s] Sending projection requests... >>>>> [ 112s] Transferring particles to writers... >>>>> [ 116s] Analyzing for FoF groups... >>>>> [ 116s] Transferring boundary particles between writers... >>>>> [ 117s] Linking boundary particles... >>>>> [ 117s] Analyzing for halos / subhalos... >>>>> [ 119s] Loading merger tree information... >>>>> [ 120s] Constructing merger tree... >>>>> [ 121s] [Success] Done with snapshot 7. >>>>> [ 121s] Reading 6 blocks for snapshot 8... >>>>> P001 yt : [INFO ] 2014-10-03 16:19:28,101 Loading field plugins. >>>>> P002 yt : [INFO ] 2014-10-03 16:19:28,101 Loading field plugins. >>>>> P001 yt : [INFO ] 2014-10-03 16:19:28,101 Loaded angular_momentum >>>>> (8 new fields) >>>>> P001 yt : [INFO ] 2014-10-03 16:19:28,101 Loaded astro (14 new >>>>> fields) >>>>> P001 yt : [INFO ] 2014-10-03 16:19:28,102 Loaded cosmology (20 new >>>>> fields) >>>>> P001 yt : [INFO ] 2014-10-03 16:19:28,102 Loaded fluid (56 new >>>>> fields) >>>>> P001 yt : [INFO ] 2014-10-03 16:19:28,103 Loaded fluid_vector (88 >>>>> new fields) >>>>> P001 yt : [INFO ] 2014-10-03 16:19:28,103 Loaded geometric (102 new >>>>> fields) >>>>> P001 yt : [INFO ] 2014-10-03 16:19:28,103 Loaded local (102 new >>>>> fields) >>>>> P001 yt : [INFO ] 2014-10-03 16:19:28,104 Loaded magnetic_field >>>>> (108 new fields) >>>>> P001 yt : [INFO ] 2014-10-03 16:19:28,104 Loaded species (108 new >>>>> fields) >>>>> P006 yt : [INFO ] 2014-10-03 16:19:28,127 Loading field plugins. >>>>> P005 yt : [INFO ] 2014-10-03 16:19:28,128 Loading field plugins. >>>>> P003 yt : [INFO ] 2014-10-03 16:19:28,128 Loading field plugins. >>>>> P004 yt : [INFO ] 2014-10-03 16:19:28,135 Loading field plugins. >>>>> [ 129s] Sending projection requests... >>>>> [ 130s] Transferring particles to writers... >>>>> [ 132s] Analyzing for FoF groups... >>>>> [ 133s] Transferring boundary particles between writers... >>>>> [ 133s] Linking boundary particles... >>>>> [ 134s] Analyzing for halos / subhalos... >>>>> [ 137s] Loading merger tree information... >>>>> [ 138s] Constructing merger tree... >>>>> [ 139s] [Success] Done with snapshot 8. >>>>> [ 139s] Reading 6 blocks for snapshot 9... >>>>> [ 143s] Sending projection requests... >>>>> [ 144s] Transferring particles to writers... >>>>> [ 146s] Analyzing for FoF groups... >>>>> [ 147s] Transferring boundary particles between writers... >>>>> [ 147s] Linking boundary particles... >>>>> [ 148s] Analyzing for halos / subhalos... >>>>> [ 150s] Loading merger tree information... >>>>> [ 151s] Constructing merger tree... >>>>> [ 152s] Constructing merger tree... >>>>> [ 153s] [Success] Done with snapshot 9. >>>>> [ 153s] [Finished] >>>>> >>>>> generates the outputs >>>>> >>>>> >>>>> halos_0.0.ascii halos_1.14.bin halos_2.4.ascii >>>>> halos_3.9.bin halos_5.14.ascii halos_6.3.bin halos_7.9.ascii >>>>> halos_9.13.bin >>>>> halos_0.0.bin halos_1.15.ascii halos_2.4.bin >>>>> halos_4.0.ascii halos_5.14.bin halos_6.4.ascii halos_7.9.bin >>>>> halos_9.14.ascii >>>>> halos_0.10.ascii halos_1.15.bin halos_2.5.ascii >>>>> halos_4.0.bin halos_5.15.ascii halos_6.4.bin halos_8.0.ascii >>>>> halos_9.14.bin >>>>> halos_0.10.bin halos_1.16.ascii halos_2.5.bin >>>>> halos_4.10.ascii halos_5.15.bin halos_6.5.ascii halos_8.0.bin >>>>> halos_9.15.ascii >>>>> halos_0.11.ascii halos_1.16.bin halos_2.6.ascii >>>>> halos_4.10.bin halos_5.16.ascii halos_6.5.bin halos_8.10.ascii >>>>> halos_9.15.bin >>>>> >>>>> >>>>> but they are all empty.... yet within profiling, it seems to imply that >>>>> there were some particles submitted to be analised >>>>> >>>>> >>>>> [Prof] S0,C0 0s: 10191 fofs, 123365 particles, 0s for conf. >>>>> [Prof] S0,C0: 0p,0h,0w; wt:0s; rcv:0s,0s; snd:0s; wk:0s; idl:1s >>>>> [Prof] S1,C0 0s: 10377 fofs, 123363 particles, 0s for conf. >>>>> [Prof] S1,C0: 1814p,73h,1w; wt:1s; rcv:0s,0s; snd:0s; wk:0s; idl:1s >>>>> [Prof] S2,C0 0s: 9843 fofs, 123353 particles, 0s for conf. >>>>> [Prof] S2,C0: 5115p,139h,1w; wt:1s; rcv:0s,0s; snd:0s; wk:0s; idl:1s >>>>> [Prof] S3,C0 0s: 9616 fofs, 123359 particles, 0s for conf. >>>>> [Prof] S3,C0: 9637p,221h,1w; wt:1s; rcv:0s,0s; snd:0s; wk:0s; idl:1s >>>>> [Prof] S4,C0 1s: 9256 fofs, 123367 particles, 0s for conf. >>>>> [Prof] S4,C0: 14849p,314h,1w; wt:0s; rcv:0s,1s; snd:0s; wk:0s; idl:0s >>>>> [Prof] S5,C0 0s: 9233 fofs, 123361 particles, 0s for conf. >>>>> [Prof] S5,C0: 17771p,369h,1w; wt:0s; rcv:0s,0s; snd:1s; wk:0s; idl:0s >>>>> [Prof] S6,C0 0s: 8964 fofs, 123365 particles, 0s for conf. >>>>> [Prof] S6,C0: 19888p,388h,1w; wt:0s; rcv:0s,1s; snd:0s; wk:0s; idl:0s >>>>> [Prof] S7,C0 0s: 8996 fofs, 123356 particles, 0s for conf. >>>>> [Prof] S7,C0: 22352p,426h,1w; wt:0s; rcv:0s,1s; snd:0s; wk:0s; idl:1s >>>>> [Prof] S8,C0 0s: 8801 fofs, 123361 particles, 0s for conf. >>>>> [Prof] S8,C0: 22553p,441h,1w; wt:0s; rcv:0s,1s; snd:0s; wk:0s; idl:1s >>>>> [Prof] S9,C0 1s: 8806 fofs, 123361 particles, 0s for conf. >>>>> [Prof] S9,C0: 22685p,440h,1w; wt:0s; rcv:0s,1s; snd:0s; wk:0s; idl:1s >>>>> >>>>> >>>>> Is there anything I should consider looking at to debug this problem? >>>>> Any suggestions of what to look at? >>>>> >>>>> Thanks >>>>> >>>>> Ben >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> yt-users mailing list >>>>> yt-users(a)lists.spacepope.org >>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>>>> >>>>> >>>> >>>> >>>> -- >>>> Cameron Hummels >>>> Postdoctoral Researcher >>>> Steward Observatory >>>> University of Arizona >>>> http://chummels.org >>>> >>>> _______________________________________________ >>>> yt-users mailing list >>>> yt-users(a)lists.spacepope.org >>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>>> >>>> >>> >>> _______________________________________________ >>> yt-users mailing list >>> yt-users(a)lists.spacepope.org >>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>> >>> >> >> >> -- >> Cameron Hummels >> Postdoctoral Researcher >> Steward Observatory >> University of Arizona >> http://chummels.org >> >> _______________________________________________ >> yt-users mailing list >> yt-users(a)lists.spacepope.org >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> >> > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201…> > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > yt-users mailing list > yt-users(a)lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > ------------------------------ > > End of yt-users Digest, Vol 80, Issue 7 > ***************************************

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Annotating particles in FLASH2.5
by C.S. Howard 03 Oct '14

03 Oct '14

Hi everyone, I'm trying to draw sink particles on a slice plot using FLASH 2.5 data. I'm using yt 3.0 with the commands: pf = yt.load(pltfiles[k]) fig = plt.figure() ax1 = fig.add_subplot(111) axes = {'x':0, 'y':1, 'z':2} slices = {'x':[0.0,0.5,0.5],\ 'y':[0.5,0.0,0.5],\ 'z':[0.5,0.5,0.5]} slc = SlicePlot(pf, 'z', 'density', center = slices['z'],origin='domain') slc.annotate_particles(1.0, p_size=15.0, col="Black") but it doesn't work, giving me the following errors; Traceback (most recent call last): File "./sliceplots.py", line 42, in <module> slc.annotate_particles(1.0, p_size=15.0, col="Black") File "/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/visualization/plot_container.py", line 70, in newfunc args[0]._setup_plots() File "/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 862, in _setup_plots self.run_callbacks(f) File "/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/visualization/plot_container.py", line 315, in run_callbacks callback(cbw) File "/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/visualization/plot_modifications.py", line 1055, in __call__ & ( reg[pt, field_y] >= y0 ) & ( reg[pt, field_y] <= y1 ) ) File "/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 233, in __getitem__ f = self._determine_fields([key])[0] File "/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 486, in _determine_fields finfo = self.ds._get_field_info(ftype, fname) File "/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/data_objects/static_output.py", line 482, in _get_field_info raise YTFieldNotFound((ftype, fname), self) yt.utilities.exceptions.YTFieldNotFound: Could not find field '('all', 'particle_position_x')' in DensProfTurb_flattop_hdf5_plt_cnt_0200 Seems like its having trouble finding the particle information for FLASH2.5. Any suggestions on where to go from here? Thanks, Corey

2 4

Rockstar and RAMSES (DM only run). Rockstar appears to run, but no halo information is written.
by Ben Thompson 03 Oct '14

03 Oct '14

Hello everyone. I am currently using YT to run rockstar on my simulation. I have been following the instructions which are around and about and have managed to write a script to run rockstar via MPI readers = int(ncpu/4.) #Reserve one cpu for the server writers = ncpu - readers - 1 print 'Running rockstar with %i writers and %i readers'%(writers, readers) rh = RockstarHaloFinder(es, num_readers=readers, num_writers=writers, particle_type="dark_matter", dm_only=True) rh.run() using a particle filter on the datasets @yt.particle_filter("dark_matter", requires=[('particle_mass')]) def dark_matter(pfilter, data): if ('all', 'particle_age') in data.ds.field_list: return data[("all", "particle_age")] == 0.0 else: arr = np.zeros(len(data['particle_mass'])) return arr == 0.0 def setup_ds(ds): #Return only dark matter particles, and assert that the filter holds print 'Here' assert(ds.add_particle_filter("dark_matter")) It seems to run fine.... e.g

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