<div dir="ltr"><div>Thanks a lot Manuel, that worked perfectly! This is all I really need John, but thank you for offering the workaround.<br><br></div>Cheers guys,<br>Corey<br></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Oct 3, 2014 at 12:56 PM, John ZuHone <span dir="ltr"><<a href="mailto:jzuhone@gmail.com" target="_blank">jzuhone@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="auto"><div>Corey,</div><div><br></div><div>Manuel's solution is probably the quickest for you, actually. </div><div><br></div><div>Thanks, Manuel!</div><div><br></div><div>If you need the particles to be actual fields in yt, we could still do that workaround.</div><span class=""><div><br></div><div>Best,</div><div><br></div><div>John<br><br><span style="font-size:13pt;background-color:rgba(255,255,255,0)">John ZuHone</span><br><div><span style="background-color:rgba(255,255,255,0)">Kavli Center for Astrophysics and Space Research<br>Massachusetts Institute of Technology<br><a>77 Massachusetts Ave.</a>, 37-582G<br><a>Cambridge, MA 02139</a><br>(w) <a href="tel:617-253-2354" target="_blank">617-253-2354</a><br>(m) <a href="tel:781-708-5004" target="_blank">781-708-5004</a><br><a href="mailto:jzuhone@space.mit.edu" target="_blank">jzuhone@space.mit.edu</a><br><a href="mailto:jzuhone@gmail.com" target="_blank">jzuhone@gmail.com</a><br><a href="http://www.jzuhone.com/" target="_blank">http://www.jzuhone.com</a></span><br style="font-family:UICTFontTextStyleBody"></div></div></span><div><div class="h5"><div><br>On Oct 3, 2014, at 12:37 PM, Manuel Zamora <<a href="mailto:mzamora06@gmail.com" target="_blank">mzamora06@gmail.com</a>> wrote:<br><br></div><blockquote type="cite"><div><div>Hi Corey,</div><div><br></div><div>This works for me: </div><div><br></div><div>%%%%%%%%%%%%%%%%%%%%%%%%</div><div><div style="margin:0px;font-size:13px;font-family:Menlo;color:rgb(213,59,211)">import<span style="color:#000000"> h5py</span></div><div style="margin:0px;font-size:13px;font-family:Menlo;min-height:15px"><br></div><div style="margin:0px;font-size:13px;font-family:Menlo;min-height:15px">...</div><div style="margin:0px;font-size:13px;font-family:Menlo;min-height:15px"><br></div><div style="margin:0px;font-size:13px;font-family:Menlo;color:rgb(195,55,32)"><span style="color:#000000">f = h5py.File(</span>"../r10f0/flows_hdf5_plt_cnt_0160"<span style="color:#000000">,</span>"r"<span style="color:#000000">)</span></div><div style="margin:0px;font-size:13px;font-family:Menlo">ParticleData = f[<span style="color:#c33720">'particle tracers'</span>]</div><div style="margin:0px;font-size:13px;font-family:Menlo">ppz = ParticleData[<span style="color:#c33720">"particle_z"</span>]</div><div style="margin:0px;font-size:13px;font-family:Menlo">ppy = ParticleData[<span style="color:#c33720">"particle_y"</span>]</div><div style="margin:0px;font-size:13px;font-family:Menlo">ppx = ParticleData[<span style="color:#c33720">"particle_x"</span>]</div><div style="margin:0px;font-size:13px;font-family:Menlo">ppm = ParticleData[<span style="color:#c33720">"particle_mass"</span>]</div><div style="margin:0px;font-size:13px;font-family:Menlo;color:rgb(195,55,32)"><span style="color:#000000">data = {</span>'particle_position_x'<span style="color:#000000">: ppx,</span></div><div style="margin:0px;font-size:13px;font-family:Menlo;color:rgb(195,55,32)"><span style="color:#000000"> </span>'particle_position_y'<span style="color:#000000">: ppy,</span></div><div style="margin:0px;font-size:13px;font-family:Menlo;color:rgb(195,55,32)"><span style="color:#000000"> </span>'particle_position_z'<span style="color:#000000">: ppz,</span></div><div style="margin:0px;font-size:13px;font-family:Menlo;color:rgb(195,55,32)"><span style="color:#000000"> </span>'particle_mass'<span style="color:#000000">: ppm}</span></div><div style="margin:0px;font-size:13px;font-family:Menlo">f.close()</div><div style="margin:0px;font-size:13px;font-family:Menlo"><span style="color:#ce7924">del</span> ParticleData</div><div style="margin:0px;font-size:13px;font-family:Menlo;color:rgb(206,121,36)">del<span style="color:#000000"> f</span></div><div style="margin:0px;font-size:13px;font-family:Menlo;min-height:15px"><br></div><div style="margin:0px;font-size:13px;font-family:Menlo;min-height:15px">...</div><div style="margin:0px;font-size:13px;font-family:Menlo;min-height:15px"><br></div><div style="margin:0px;font-size:13px;font-family:Menlo;min-height:15px">slc.annotate_marker([ppx,ppy,ppz], marker=<span style="color:rgb(195,55,32)">'o'</span>, plot_args={<span style="color:rgb(195,55,32)">'color'</span>: <span style="color:rgb(195,55,32)">'black'</span>,<span style="color:rgb(195,55,32)">'s'</span>:<span style="color:rgb(195,55,32)">10</span>})</div><div style="margin:0px;font-size:13px;font-family:Menlo;color:rgb(195,55,32)"><br></div></div><div>%%%%%%%%%%%%%%%%%%%%%%%% </div><div><br></div><div>I hope this helps :)</div><div>
<div style="color:rgb(0,0,0);font-family:Helvetica;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word"><div style="color:rgb(0,0,0);font-family:Helvetica;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word"><div>_</div><div>Manuel Zamora</div><div><br></div></div></div>
</div>
<br><div><div>On Oct 3, 2014, at 11:23 AM, <a href="mailto:yt-users-request@lists.spacepope.org" target="_blank">yt-users-request@lists.spacepope.org</a> wrote:</div><br><blockquote type="cite">Send yt-users mailing list submissions to<br><span style="white-space:pre-wrap"> </span><a href="mailto:yt-users@lists.spacepope.org" target="_blank">yt-users@lists.spacepope.org</a><br><br>To subscribe or unsubscribe via the World Wide Web, visit<br><span style="white-space:pre-wrap"> </span><a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>or, via email, send a message with subject or body 'help' to<br><span style="white-space:pre-wrap"> </span><a href="mailto:yt-users-request@lists.spacepope.org" target="_blank">yt-users-request@lists.spacepope.org</a><br><br>You can reach the person managing the list at<br><span style="white-space:pre-wrap"> </span><a href="mailto:yt-users-owner@lists.spacepope.org" target="_blank">yt-users-owner@lists.spacepope.org</a><br><br>When replying, please edit your Subject line so it is more specific<br>than "Re: Contents of yt-users digest..."<br><br><br>Today's Topics:<br><br> 1. Annotating particles in FLASH2.5 (C.S. Howard)<br> 2. Re: Annotating particles in FLASH2.5 (John ZuHone)<br> 3. Re: Annotating particles in FLASH2.5 (C.S. Howard)<br> 4. Re: Rockstar and RAMSES (DM only run). Rockstar appears to<br> run, but no halo information is written. (Ben Thompson)<br><br><br>----------------------------------------------------------------------<br><br>Message: 1<br>Date: Fri, 3 Oct 2014 12:14:08 -0400<br>From: "C.S. Howard" <<a href="mailto:howardcs@mcmaster.ca" target="_blank">howardcs@mcmaster.ca</a>><br>To: <a href="mailto:yt-users@lists.spacepope.org" target="_blank">yt-users@lists.spacepope.org</a><br>Subject: [yt-users] Annotating particles in FLASH2.5<br>Message-ID:<br><span style="white-space:pre-wrap"> </span><<a href="mailto:CADaEBaZ=LwWfN3TLaE2KTnC35vksfvmLwYiZeMnOoJ7BOyb_Og@mail.gmail.com" target="_blank">CADaEBaZ=LwWfN3TLaE2KTnC35vksfvmLwYiZeMnOoJ7BOyb_Og@mail.gmail.com</a>><br>Content-Type: text/plain; charset="utf-8"<br><br>Hi everyone,<br><br>I'm trying to draw sink particles on a slice plot using FLASH 2.5 data. I'm<br>using yt 3.0 with the commands:<br><br> pf = yt.load(pltfiles[k])<br> fig = plt.figure()<br> ax1 = fig.add_subplot(111)<br> axes = {'x':0, 'y':1, 'z':2}<br> slices = {'x':[0.0,0.5,0.5],\<br> 'y':[0.5,0.0,0.5],\<br> 'z':[0.5,0.5,0.5]}<br><br> slc = SlicePlot(pf, 'z', 'density', center = slices['z'],origin='domain')<br> slc.annotate_particles(1.0, p_size=15.0, col="Black")<br><br>but it doesn't work, giving me the following errors;<br><br>Traceback (most recent call last):<br> File "./sliceplots.py", line 42, in <module><br> slc.annotate_particles(1.0, p_size=15.0, col="Black")<br> File<br>"/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/visualization/plot_container.py",<br>line 70, in newfunc<br> args[0]._setup_plots()<br> File<br>"/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py",<br>line 862, in _setup_plots<br> self.run_callbacks(f)<br> File<br>"/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/visualization/plot_container.py",<br>line 315, in run_callbacks<br> callback(cbw)<br> File<br>"/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/visualization/plot_modifications.py",<br>line 1055, in __call__<br> & ( reg[pt, field_y] >= y0 ) & ( reg[pt, field_y] <= y1 ) )<br> File<br>"/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",<br>line 233, in __getitem__<br> f = self._determine_fields([key])[0]<br> File<br>"/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",<br>line 486, in _determine_fields<br> finfo = self.ds._get_field_info(ftype, fname)<br> File<br>"/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/data_objects/static_output.py",<br>line 482, in _get_field_info<br> raise YTFieldNotFound((ftype, fname), self)<br>yt.utilities.exceptions.YTFieldNotFound: Could not find field '('all',<br>'particle_position_x')' in DensProfTurb_flattop_hdf5_plt_cnt_0200<br><br>Seems like its having trouble finding the particle information for<br>FLASH2.5. Any suggestions on where to go from here?<br><br>Thanks,<br>Corey<br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <<a href="http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20141003/b3ee5f2f/attachment-0001.htm" target="_blank">http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20141003/b3ee5f2f/attachment-0001.htm</a>><br><br>------------------------------<br><br>Message: 2<br>Date: Fri, 3 Oct 2014 12:18:49 -0400<br>From: John ZuHone <<a href="mailto:jzuhone@gmail.com" target="_blank">jzuhone@gmail.com</a>><br>To: Discussion of the yt analysis package<br><span style="white-space:pre-wrap"> </span><<a href="mailto:yt-users@lists.spacepope.org" target="_blank">yt-users@lists.spacepope.org</a>><br>Subject: Re: [yt-users] Annotating particles in FLASH2.5<br>Message-ID: <<a href="mailto:5851849E-3256-47D4-9FCA-45C02C3AA248@gmail.com" target="_blank">5851849E-3256-47D4-9FCA-45C02C3AA248@gmail.com</a>><br>Content-Type: text/plain; charset="us-ascii"<br><br>Hi Corey,<br><br>Unfortunately, we don't support FLASH 2.5 particle data, because it is in a different format from v. 3.0 and above.<br><br>If you like, I'd be happy to help figure out some kind of workaround.<br><br>Best,<br><br>John<br><br>John ZuHone<br>Kavli Center for Astrophysics and Space Research<br>Massachusetts Institute of Technology<br>77 Massachusetts Ave., 37-582G<br>Cambridge, MA 02139<br>(w) 617-253-2354<br>(m) 781-708-5004<br><a href="mailto:jzuhone@space.mit.edu" target="_blank">jzuhone@space.mit.edu</a><br><a href="mailto:jzuhone@gmail.com" target="_blank">jzuhone@gmail.com</a><br><a href="http://www.jzuhone.com" target="_blank">http://www.jzuhone.com</a><br><br><blockquote type="cite">On Oct 3, 2014, at 12:14 PM, C.S. Howard <<a href="mailto:howardcs@mcmaster.ca" target="_blank">howardcs@mcmaster.ca</a>> wrote:<br><br>Hi everyone,<br><br>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:<br><br> pf = yt.load(pltfiles[k])<br> fig = plt.figure()<br> ax1 = fig.add_subplot(111)<br> axes = {'x':0, 'y':1, 'z':2}<br> slices = {'x':[0.0,0.5,0.5],\<br> 'y':[0.5,0.0,0.5],\<br> 'z':[0.5,0.5,0.5]}<br><br> slc = SlicePlot(pf, 'z', 'density', center = slices['z'],origin='domain')<br> slc.annotate_particles(1.0, p_size=15.0, col="Black")<br><br>but it doesn't work, giving me the following errors; <br><br>Traceback (most recent call last):<br> File "./sliceplots.py", line 42, in <module><br> slc.annotate_particles(1.0, p_size=15.0, col="Black")<br> File "/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/visualization/plot_container.py", line 70, in newfunc<br> args[0]._setup_plots()<br> File "/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 862, in _setup_plots<br> self.run_callbacks(f)<br> File "/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/visualization/plot_container.py", line 315, in run_callbacks<br> callback(cbw)<br> File "/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/visualization/plot_modifications.py", line 1055, in __call__<br> & ( reg[pt, field_y] >= y0 ) & ( reg[pt, field_y] <= y1 ) )<br> File "/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 233, in __getitem__<br> f = self._determine_fields([key])[0]<br> File "/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 486, in _determine_fields<br> finfo = self.ds._get_field_info(ftype, fname)<br> 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<br> raise YTFieldNotFound((ftype, fname), self)<br>yt.utilities.exceptions.YTFieldNotFound: Could not find field '('all', 'particle_position_x')' in DensProfTurb_flattop_hdf5_plt_cnt_0200<br><br>Seems like its having trouble finding the particle information for FLASH2.5. Any suggestions on where to go from here?<br><br>Thanks,<br>Corey <br>_______________________________________________<br>yt-users mailing list<br><a href="mailto:yt-users@lists.spacepope.org" target="_blank">yt-users@lists.spacepope.org</a><br><a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br></blockquote>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <<a href="http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20141003/a1f8ea8c/attachment-0001.htm" target="_blank">http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20141003/a1f8ea8c/attachment-0001.htm</a>><br><br>------------------------------<br><br>Message: 3<br>Date: Fri, 3 Oct 2014 12:22:02 -0400<br>From: "C.S. Howard" <<a href="mailto:howardcs@mcmaster.ca" target="_blank">howardcs@mcmaster.ca</a>><br>To: Discussion of the yt analysis package<br><span style="white-space:pre-wrap"> </span><<a href="mailto:yt-users@lists.spacepope.org" target="_blank">yt-users@lists.spacepope.org</a>><br>Subject: Re: [yt-users] Annotating particles in FLASH2.5<br>Message-ID:<br><span style="white-space:pre-wrap"> </span><<a href="mailto:CADaEBaapFJaCWnyWfS5s8NMp8KR7SQTf35-3BJEqWKutiCJY1A@mail.gmail.com" target="_blank">CADaEBaapFJaCWnyWfS5s8NMp8KR7SQTf35-3BJEqWKutiCJY1A@mail.gmail.com</a>><br>Content-Type: text/plain; charset="utf-8"<br><br>That would be awesome, as long as it isn't a huge headache. I'll be moving<br>to the newer versions of FLASH soon, but for now I'm stuck with version 2.5.<br><br>On Fri, Oct 3, 2014 at 12:18 PM, John ZuHone <<a href="mailto:jzuhone@gmail.com" target="_blank">jzuhone@gmail.com</a>> wrote:<br><br><blockquote type="cite">Hi Corey,<br><br>Unfortunately, we don't support FLASH 2.5 particle data, because it is in<br>a different format from v. 3.0 and above.<br><br>If you like, I'd be happy to help figure out some kind of workaround.<br><br>Best,<br><br>John<br><br>John ZuHone<br>Kavli Center for Astrophysics and Space Research<br>Massachusetts Institute of Technology<br>77 Massachusetts Ave., 37-582G<br>Cambridge, MA 02139<br>(w) 617-253-2354<br>(m) 781-708-5004<br><a href="mailto:jzuhone@space.mit.edu" target="_blank">jzuhone@space.mit.edu</a><br><a href="mailto:jzuhone@gmail.com" target="_blank">jzuhone@gmail.com</a><br><a href="http://www.jzuhone.com" target="_blank">http://www.jzuhone.com</a><br><br>On Oct 3, 2014, at 12:14 PM, C.S. Howard <<a href="mailto:howardcs@mcmaster.ca" target="_blank">howardcs@mcmaster.ca</a>> wrote:<br><br>Hi everyone,<br><br>I'm trying to draw sink particles on a slice plot using FLASH 2.5 data.<br>I'm using yt 3.0 with the commands:<br><br> pf = yt.load(pltfiles[k])<br> fig = plt.figure()<br> ax1 = fig.add_subplot(111)<br> axes = {'x':0, 'y':1, 'z':2}<br> slices = {'x':[0.0,0.5,0.5],\<br> 'y':[0.5,0.0,0.5],\<br> 'z':[0.5,0.5,0.5]}<br><br> slc = SlicePlot(pf, 'z', 'density', center = slices['z'],origin='domain')<br> slc.annotate_particles(1.0, p_size=15.0, col="Black")<br><br>but it doesn't work, giving me the following errors;<br><br>Traceback (most recent call last):<br> File "./sliceplots.py", line 42, in <module><br> slc.annotate_particles(1.0, p_size=15.0, col="Black")<br> File<br>"/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/visualization/plot_container.py",<br>line 70, in newfunc<br> args[0]._setup_plots()<br> File<br>"/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py",<br>line 862, in _setup_plots<br> self.run_callbacks(f)<br> File<br>"/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/visualization/plot_container.py",<br>line 315, in run_callbacks<br> callback(cbw)<br> File<br>"/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/visualization/plot_modifications.py",<br>line 1055, in __call__<br> & ( reg[pt, field_y] >= y0 ) & ( reg[pt, field_y] <= y1 ) )<br> File<br>"/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",<br>line 233, in __getitem__<br> f = self._determine_fields([key])[0]<br> File<br>"/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",<br>line 486, in _determine_fields<br> finfo = self.ds._get_field_info(ftype, fname)<br> File<br>"/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/data_objects/static_output.py",<br>line 482, in _get_field_info<br> raise YTFieldNotFound((ftype, fname), self)<br>yt.utilities.exceptions.YTFieldNotFound: Could not find field '('all',<br>'particle_position_x')' in DensProfTurb_flattop_hdf5_plt_cnt_0200<br><br>Seems like its having trouble finding the particle information for<br>FLASH2.5. Any suggestions on where to go from here?<br><br>Thanks,<br>Corey<br><br>_______________________________________________<br>yt-users mailing list<br><a href="mailto:yt-users@lists.spacepope.org" target="_blank">yt-users@lists.spacepope.org</a><br><a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br><br><br>_______________________________________________<br>yt-users mailing list<br><a href="mailto:yt-users@lists.spacepope.org" target="_blank">yt-users@lists.spacepope.org</a><br><a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br><br><br></blockquote>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <<a href="http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20141003/445c0f5f/attachment-0001.htm" target="_blank">http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20141003/445c0f5f/attachment-0001.htm</a>><br><br>------------------------------<br><br>Message: 4<br>Date: Fri, 3 Oct 2014 17:22:59 +0100<br>From: Ben Thompson <<a href="mailto:bthompson2090@gmail.com" target="_blank">bthompson2090@gmail.com</a>><br>To: Discussion of the yt analysis package<br><span style="white-space:pre-wrap"> </span><<a href="mailto:yt-users@lists.spacepope.org" target="_blank">yt-users@lists.spacepope.org</a>><br>Subject: Re: [yt-users] Rockstar and RAMSES (DM only run). Rockstar<br><span style="white-space:pre-wrap"> </span>appears to run, but no halo information is written.<br>Message-ID:<br><span style="white-space:pre-wrap"> </span><<a href="mailto:CAFO9rXeHkwzeLCLg8vuKQ66JgVu3j0LziYXPH7uOzPgQhNO_OA@mail.gmail.com" target="_blank">CAFO9rXeHkwzeLCLg8vuKQ66JgVu3j0LziYXPH7uOzPgQhNO_OA@mail.gmail.com</a>><br>Content-Type: text/plain; charset="utf-8"<br><br>Hello.<br><br>My simulation runs to z=0. Only with 10 timesteps though (purely a test<br>run). It identifies no halos in halos_0 (expected with it being the first<br>snapshot) and halos_9 (the final snapshot).. All files are the same size<br>too with no data.<br><br>My code is (with the filters taken out... it's a dark matter only one<br>anyway)<br><br><br>from mpi4py import MPI<br>import yt, sys, os<br>yt.enable_parallelism()<br>from yt.config import ytcfg<br>from yt.analysis_modules.halo_finding.rockstar.api import \<br> RockstarHaloFinder<br>from yt.data_objects.particle_filters import \<br> particle_filter<br>from yt.data_objects.time_series import DatasetSeries<br>import numpy as np<br><br>ncpu = MPI.COMM_WORLD.Get_size()<br>ytcfg.set('yt', '__global_parallel_size', str(ncpu))<br><br>outputs = np.arange(1, 11)<br>dirs = []<br>#Add the datasets<br>for ioutput in outputs:<br> ds = yt.load('../output_%05d/info_%05d.txt'%(ioutput, ioutput))<br> dirs.append(ds)<br><br>es = DatasetSeries(dirs)<br>readers = int(ncpu/4.)<br>writers = ncpu - readers - 1<br>rh = RockstarHaloFinder(es, num_readers=readers, num_writers=writers)<br>rh.run()<br><br><br>Ben<br><br><br>On Fri, Oct 3, 2014 at 5:09 PM, Cameron Hummels <<a href="mailto:chummels@gmail.com" target="_blank">chummels@gmail.com</a>> wrote:<br><br><blockquote type="cite">Hi Ben,<br><br>No, you don't need to have halos in the first timestep. Rockstar will<br>find the halos when they exist, so if you run it on all of the outputs and<br>you get to a later redshift then 5 or so, rockstar will start to identify<br>halos. Does your simulation run to z=0? If so, just look at the output<br>file associated with that redshift and see if it identifies any halos. It<br>doesn't matter your starting redshift.<br><br>Cameron<br><br>On Fri, Oct 3, 2014 at 9:02 AM, Ben Thompson <<a href="mailto:bthompson2090@gmail.com" target="_blank">bthompson2090@gmail.com</a>><br>wrote:<br><br><blockquote type="cite">Hi Cameron.<br><br>So it is dependent as of what timestep I start my run at? I start my run<br>(i.e there needs to be halos in the snapshot that you start with)? This is<br>the first time I have used Rockstar before (figured that since the package<br>is there, for free, I should use it) I have DM only runs that start at z=50<br>(of which I am not expecting to find halos there, as part of the loading<br>script I loop over all the snapshots)<br><br>This is what I have<br><br>cat halos_0.0.ascii<br>#id num_p mvir mbound_vir rvir vmax rvmax vrms x y z vx vy vz Jx Jy Jz E<br>Spin PosUncertainty VelUncertainty bulk_vx bulk_vy bulk_vz BulkVelUnc<br>n_core m200b m200c m500c m2500c Xoff Voff spin_bullock b_to_a c_to_a A[x]<br>A[y] A[z] b_to_a(500c) c_to_a(500c) A[x](500c) A[y](500c) A[z](500c) Rs<br>Rs_Klypin T/|U| M_pe_Behroozi M_pe_Diemer idx i_so i_ph num_cp mmetric<br>#a = 0.019608<br>#Bounds: (0.000000, 0.000000, 0.000000) - (99.816002, 99.816002,<br>19.807144)<br>#Om = 0.300000; Ol = 0.700000; h = 0.700000<br>#FOF linking length: 0.280000<br>#Unbound Threshold: 0.500000; FOF Refinement Threshold: 0.700000<br>#Particle mass: 2.87164e+10 Msun/h<br>#Box size: 99.816005 Mpc/h<br>#Total particles processed: 419422<br>#Force resolution assumed: 0.780498 Mpc/h<br>#Units: Masses in Msun / h<br>#Units: Positions in Mpc / h (comoving)<br>#Units: Velocities in km / s (physical, peculiar)<br>#Units: Halo Distances, Lengths, and Radii in kpc / h (comoving)<br>#Units: Angular Momenta in (Msun/h) * (Mpc/h) * km/s (physical)<br>#Units: Spins are dimensionless<br>#Units: Total energy in (Msun/h)*(km/s)^2 (physical)<br>#Note: idx, i_so, and i_ph are internal debugging quantities<br>#Np is an internal debugging quantity.<br>#Rockstar Version: 0.99.9-RC3<br><br>(yt-x86_64)[bthompson1@leopard rockstar_halos]$ cat halos_9.0.ascii<br>#id num_p mvir mbound_vir rvir vmax rvmax vrms x y z vx vy vz Jx Jy Jz E<br>Spin PosUncertainty VelUncertainty bulk_vx bulk_vy bulk_vz BulkVelUnc<br>n_core m200b m200c m500c m2500c Xoff Voff spin_bullock b_to_a c_to_a A[x]<br>A[y] A[z] b_to_a(500c) c_to_a(500c) A[x](500c) A[y](500c) A[z](500c) Rs<br>Rs_Klypin T/|U| M_pe_Behroozi M_pe_Diemer idx i_so i_ph num_cp mmetric<br>#a = 1.000879<br>#Bounds: (0.000000, 0.000000, 0.000000) - (99.816002, 99.816002,<br>19.667080)<br>#Om = 0.300000; Ol = 0.700000; h = 0.700000<br>#FOF linking length: 0.280000<br>#Unbound Threshold: 0.500000; FOF Refinement Threshold: 0.700000<br>#Particle mass: 2.87164e+10 Msun/h<br>#Box size: 99.816005 Mpc/h<br>#Total particles processed: 419437<br>#Force resolution assumed: 0.779813 Mpc/h<br>#Units: Masses in Msun / h<br>#Units: Positions in Mpc / h (comoving)<br>#Units: Velocities in km / s (physical, peculiar)<br>#Units: Halo Distances, Lengths, and Radii in kpc / h (comoving)<br>#Units: Angular Momenta in (Msun/h) * (Mpc/h) * km/s (physical)<br>#Units: Spins are dimensionless<br>#Units: Total energy in (Msun/h)*(km/s)^2 (physical)<br>#Note: idx, i_so, and i_ph are internal debugging quantities<br>#Np is an internal debugging quantity.<br>#Rockstar Version: 0.99.9-RC3<br><br>Both exactly the same pretty much.<br><br>If it is because I am starting at an early timestep, then I will cut out<br>the earlier ones from the initial setup.<br><br>Thanks.<br><br>Ben,<br><br>On Fri, Oct 3, 2014 at 4:55 PM, Cameron Hummels <<a href="mailto:chummels@gmail.com" target="_blank">chummels@gmail.com</a>><br>wrote:<br><br><blockquote type="cite">Hi Ben,<br><br>Oftentimes, rockstar cannot find any halos for the first few snapshots<br>of a cosmology DM-only sim because things have not collapsed enough. In<br>that case, you'll get files like this:<br><br>$ % cat halos_0.0.ascii<br>#id num_p mvir mbound_vir rvir vmax rvmax vrms x y z vx vy vz Jx Jy Jz E<br>Spin PosUncertainty VelUncertainty bulk_vx bulk_vy bulk_vz BulkVelUnc<br>n_core m200b m200c m500c m2500c Xoff Voff spin_bullock b_to_a c_to_a A[x]<br>A[y] A[z] b_to_a(500c) c_to_a(500c) A[x](500c) A[y](500c) A[z](500c) Rs<br>Rs_Klypin T/|U| M_pe_Behroozi M_pe_Diemer idx i_so i_ph num_cp mmetric<br>#a = 0.009901<br>#Bounds: (0.000000, 0.000000, 0.000000) - (40.000000, 40.000000,<br>3.099222)<br>#Om = 0.282000; Ol = 0.718000; h = 0.697000<br>#FOF linking length: 0.280000<br>#Unbound Threshold: 0.500000; FOF Refinement Threshold: 0.700000<br>#Particle mass: 2.98630e+08 Msun/h<br>#Box size: 40.000000 Mpc/h<br>#Total particles processed: 1290100<br>#Force resolution assumed: 0.15625 Mpc/h<br>#Units: Masses in Msun / h<br>#Units: Positions in Mpc / h (comoving)<br>#Units: Velocities in km / s (physical, peculiar)<br>#Units: Halo Distances, Lengths, and Radii in kpc / h (comoving)<br>#Units: Angular Momenta in (Msun/h) * (Mpc/h) * km/s (physical)<br>#Units: Spins are dimensionless<br>#Units: Total energy in (Msun/h)*(km/s)^2 (physical)<br>#Note: idx, i_so, and i_ph are internal debugging quantities<br>#Np is an internal debugging quantity.<br>#Rockstar Version: 0.99.9-RC3<br><br><br>Is this what you're seeing or are your files truly empty? If you're<br>seeing this, you may just need to run Rockstar on data files that are more<br>evolved in time, so as to allow for more non-linear collapse of the halos.<br>For my DM-only runs, depending on the mass resolution that I use, I may not<br>start to see halos until after z=10 to z=5, with the first outputs all<br>looking like the stuff above: empty.<br><br>Cameron<br><br>On Fri, Oct 3, 2014 at 8:46 AM, Ben Thompson <<a href="mailto:bthompson2090@gmail.com" target="_blank">bthompson2090@gmail.com</a>><br>wrote:<br><br><blockquote type="cite">P.S sorry if I sent the same email twice.. this is the actual email...<br>accidental press send before I sent the email out.<br><br>Hello everyone.<br><br>I am currently using YT to run rockstar on my simulation.<br><br>I have been following the instructions which are around and about and<br>have managed to write a script to run rockstar via MPI<br><br>readers = int(ncpu/4.)<br>#Reserve one cpu for the server<br>writers = ncpu - readers - 1<br>print 'Running rockstar with %i writers and %i readers'%(writers,<br>readers)<br>rh = RockstarHaloFinder(es, num_readers=readers, num_writers=writers,<br> particle_type="dark_matter", dm_only=True)<br>rh.run()<br><br>using a particle filter on the datasets<br><br>@yt.particle_filter("dark_matter", requires=[('particle_mass')])<br>def dark_matter(pfilter, data):<br> if ('all', 'particle_age') in data.ds.field_list:<br> return data[("all", "particle_age")] == 0.0<br> else:<br> arr = np.zeros(len(data['particle_mass']))<br> return arr == 0.0<br><br>def setup_ds(ds):<br> #Return only dark matter particles, and assert that the filter<br>holds<br> print 'Here'<br> assert(ds.add_particle_filter("dark_matter"))<br><br><br>It seems to run fine.... e.g<br><br><br>[ 111s] Sending projection requests...<br>[ 112s] Transferring particles to writers...<br>[ 116s] Analyzing for FoF groups...<br>[ 116s] Transferring boundary particles between writers...<br>[ 117s] Linking boundary particles...<br>[ 117s] Analyzing for halos / subhalos...<br>[ 119s] Loading merger tree information...<br>[ 120s] Constructing merger tree...<br>[ 121s] [Success] Done with snapshot 7.<br>[ 121s] Reading 6 blocks for snapshot 8...<br>P001 yt : [INFO ] 2014-10-03 16:19:28,101 Loading field plugins.<br>P002 yt : [INFO ] 2014-10-03 16:19:28,101 Loading field plugins.<br>P001 yt : [INFO ] 2014-10-03 16:19:28,101 Loaded angular_momentum<br>(8 new fields)<br>P001 yt : [INFO ] 2014-10-03 16:19:28,101 Loaded astro (14 new<br>fields)<br>P001 yt : [INFO ] 2014-10-03 16:19:28,102 Loaded cosmology (20 new<br>fields)<br>P001 yt : [INFO ] 2014-10-03 16:19:28,102 Loaded fluid (56 new<br>fields)<br>P001 yt : [INFO ] 2014-10-03 16:19:28,103 Loaded fluid_vector (88<br>new fields)<br>P001 yt : [INFO ] 2014-10-03 16:19:28,103 Loaded geometric (102 new<br>fields)<br>P001 yt : [INFO ] 2014-10-03 16:19:28,103 Loaded local (102 new<br>fields)<br>P001 yt : [INFO ] 2014-10-03 16:19:28,104 Loaded magnetic_field<br>(108 new fields)<br>P001 yt : [INFO ] 2014-10-03 16:19:28,104 Loaded species (108 new<br>fields)<br>P006 yt : [INFO ] 2014-10-03 16:19:28,127 Loading field plugins.<br>P005 yt : [INFO ] 2014-10-03 16:19:28,128 Loading field plugins.<br>P003 yt : [INFO ] 2014-10-03 16:19:28,128 Loading field plugins.<br>P004 yt : [INFO ] 2014-10-03 16:19:28,135 Loading field plugins.<br>[ 129s] Sending projection requests...<br>[ 130s] Transferring particles to writers...<br>[ 132s] Analyzing for FoF groups...<br>[ 133s] Transferring boundary particles between writers...<br>[ 133s] Linking boundary particles...<br>[ 134s] Analyzing for halos / subhalos...<br>[ 137s] Loading merger tree information...<br>[ 138s] Constructing merger tree...<br>[ 139s] [Success] Done with snapshot 8.<br>[ 139s] Reading 6 blocks for snapshot 9...<br>[ 143s] Sending projection requests...<br>[ 144s] Transferring particles to writers...<br>[ 146s] Analyzing for FoF groups...<br>[ 147s] Transferring boundary particles between writers...<br>[ 147s] Linking boundary particles...<br>[ 148s] Analyzing for halos / subhalos...<br>[ 150s] Loading merger tree information...<br>[ 151s] Constructing merger tree...<br>[ 152s] Constructing merger tree...<br>[ 153s] [Success] Done with snapshot 9.<br>[ 153s] [Finished]<br><br>generates the outputs<br><br><br>halos_0.0.ascii halos_1.14.bin halos_2.4.ascii<br>halos_3.9.bin halos_5.14.ascii halos_6.3.bin halos_7.9.ascii<br>halos_9.13.bin<br>halos_0.0.bin halos_1.15.ascii halos_2.4.bin<br>halos_4.0.ascii halos_5.14.bin halos_6.4.ascii halos_7.9.bin<br>halos_9.14.ascii<br>halos_0.10.ascii halos_1.15.bin halos_2.5.ascii<br>halos_4.0.bin halos_5.15.ascii halos_6.4.bin halos_8.0.ascii<br>halos_9.14.bin<br>halos_0.10.bin halos_1.16.ascii halos_2.5.bin<br>halos_4.10.ascii halos_5.15.bin halos_6.5.ascii halos_8.0.bin<br>halos_9.15.ascii<br>halos_0.11.ascii halos_1.16.bin halos_2.6.ascii<br>halos_4.10.bin halos_5.16.ascii halos_6.5.bin halos_8.10.ascii<br>halos_9.15.bin<br><br><br>but they are all empty.... yet within profiling, it seems to imply that<br>there were some particles submitted to be analised<br><br><br>[Prof] S0,C0 0s: 10191 fofs, 123365 particles, 0s for conf.<br>[Prof] S0,C0: 0p,0h,0w; wt:0s; rcv:0s,0s; snd:0s; wk:0s; idl:1s<br>[Prof] S1,C0 0s: 10377 fofs, 123363 particles, 0s for conf.<br>[Prof] S1,C0: 1814p,73h,1w; wt:1s; rcv:0s,0s; snd:0s; wk:0s; idl:1s<br>[Prof] S2,C0 0s: 9843 fofs, 123353 particles, 0s for conf.<br>[Prof] S2,C0: 5115p,139h,1w; wt:1s; rcv:0s,0s; snd:0s; wk:0s; idl:1s<br>[Prof] S3,C0 0s: 9616 fofs, 123359 particles, 0s for conf.<br>[Prof] S3,C0: 9637p,221h,1w; wt:1s; rcv:0s,0s; snd:0s; wk:0s; idl:1s<br>[Prof] S4,C0 1s: 9256 fofs, 123367 particles, 0s for conf.<br>[Prof] S4,C0: 14849p,314h,1w; wt:0s; rcv:0s,1s; snd:0s; wk:0s; idl:0s<br>[Prof] S5,C0 0s: 9233 fofs, 123361 particles, 0s for conf.<br>[Prof] S5,C0: 17771p,369h,1w; wt:0s; rcv:0s,0s; snd:1s; wk:0s; idl:0s<br>[Prof] S6,C0 0s: 8964 fofs, 123365 particles, 0s for conf.<br>[Prof] S6,C0: 19888p,388h,1w; wt:0s; rcv:0s,1s; snd:0s; wk:0s; idl:0s<br>[Prof] S7,C0 0s: 8996 fofs, 123356 particles, 0s for conf.<br>[Prof] S7,C0: 22352p,426h,1w; wt:0s; rcv:0s,1s; snd:0s; wk:0s; idl:1s<br>[Prof] S8,C0 0s: 8801 fofs, 123361 particles, 0s for conf.<br>[Prof] S8,C0: 22553p,441h,1w; wt:0s; rcv:0s,1s; snd:0s; wk:0s; idl:1s<br>[Prof] S9,C0 1s: 8806 fofs, 123361 particles, 0s for conf.<br>[Prof] S9,C0: 22685p,440h,1w; wt:0s; rcv:0s,1s; snd:0s; wk:0s; idl:1s<br><br><br>Is there anything I should consider looking at to debug this problem?<br>Any suggestions of what to look at?<br><br>Thanks<br><br>Ben<br><br><br><br><br><br>_______________________________________________<br>yt-users mailing list<br><a href="mailto:yt-users@lists.spacepope.org" target="_blank">yt-users@lists.spacepope.org</a><br><a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br><br><br></blockquote><br><br>--<br>Cameron Hummels<br>Postdoctoral Researcher<br>Steward Observatory<br>University of Arizona<br><a href="http://chummels.org" target="_blank">http://chummels.org</a><br><br>_______________________________________________<br>yt-users mailing list<br><a href="mailto:yt-users@lists.spacepope.org" target="_blank">yt-users@lists.spacepope.org</a><br><a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br><br><br></blockquote><br>_______________________________________________<br>yt-users mailing list<br><a href="mailto:yt-users@lists.spacepope.org" target="_blank">yt-users@lists.spacepope.org</a><br><a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" 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