<meta http-equiv="Content-Type" content="text/html; charset=utf-8"><div dir="ltr"><br><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Feb 17, 2015 at 12:12 PM, Britton Smith <span dir="ltr"><<a href="mailto:brittonsmith@gmail.com" target="_blank">brittonsmith@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="ltr">Hi Yuxiang,<div><br></div><div>Sorry for the late reply. I dropped the ball on this. Thank you very much for making the sample dataset available. I have download it and will use it when I start working on adding support for loading halos. I am pretty busy with other things at the moment, but will try to get to this as soon as I can.</div><div><br></div><div>As to your second question, I believe yt creates the ("gas", "density") field by depositing the PartType0 particles onto a mesh using cloud-in-cell deposit. The mesh itself is an octree.</div></div></blockquote><div><br></div><div>Not quite, it uses SPH smoothing on the gas particles. The kernel is evaluated on the centers of the cells in the octree mesh. </div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><span class="HOEnZb"><font color="#888888"><div></div><div>Britton</div></font></span></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Jan 29, 2015 at 1:34 AM, Yuxiang Qin <span dir="ltr"><<a href="mailto:yuxiangq@student.unimelb.edu.au" target="_blank">yuxiangq@student.unimelb.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Hi Britton,<div><br></div><div>I asked the data owner, he said it’s okay to provide a data for you. Here is the data:</div><div><div style="margin:0px;font-family:'Andale Mono';background-color:rgb(0,0,0)"><a href="https://www.dropbox.com/s/jc2gou0frajk9dw/NOSN_NOZCOOL_L010N0128_subhalos_103.tar?dl=0" target="_blank"><font color="#29f914">https://www.dropbox.com/s/jc2gou0frajk9dw</font><font color="#ffffff">/</font><font color="#29f914">NOSN_NOZCOOL_L010N0128_subhalos_103.tar?dl=0</font></a></div><div><br></div><div>It’s a OWLS format data (just like the sample data, owls_of_halos from yt website) with 10Mpc boxsize and 128^3 particles. </div><div><br></div><div>Besides, It would be great if I can involve in the development although I don’t think I am able to do it at this moment. But I will try :)</div><div><br></div><div>One more question, how does yt construct its mesh field e.g. the gas field data from the original PartType0 data? I think the former one is a mesh filed while the later one is particle filed, right? But in the snapshot data, e.g. the sample data, snapshot_033 from yt website, there are only PartType0, 1, 4 (gas, dm, star) data. So how does yt generate the gas field, e.g. (‘gas’,’density’)? </div><div><br></div><div>Cheers,</div><div>Yuxiang</div><div><div><div><br></div>
<br><div><blockquote type="cite"><div>On 28 Jan 2015, at 01:42, Britton Smith <<a href="mailto:brittonsmith@gmail.com" target="_blank">brittonsmith@gmail.com</a>> wrote:</div><br><div><div dir="ltr">Hi Yuxiang,<div><br></div><div>The issue is that the PartTypeN fields are not simply fields of one value per halo, but are values for the individual member particles of each halo. Loading these in is not supported yet, but it could be done.</div><div><br></div><div>Currently, there are two obstacles to implementing this. Firstly, I'm not entirely sure how to do it. There isn't a framework within yt for fields corresponding to the particles of a halo. I can see a couple ways this might be implemented, and I would greatly appreciate feedback from other devs on these:</div><div><br></div><div>1. Allow PartTypeN particles to be their own particle type and attempt to load them in similarly to the rest of the particles. This might be tricky because they live within the FOF and SUBFIND groups. Perhaps the particle type could be FOF/PartType0 and SUBFIND/PartType0, etc. Then, use the information given in the file to create a halo membership field which returns the ID of the halo each particle belongs to.</div><div><br></div><div>2. Create some sort of load_particles function that accepts a halo id and just grabs all particles for that halo and returns a data container. I'm not sure where this would hang off of, but maybe the OWLS_Subfind dataset object itself.</div><div><br></div><div>The second obstacle is that at this time we don't have any sample data that contains these types of particles. Yuxiang, if are able to provide us with a sample dataset that contains all of the complexity of the one you're working with but in a much smaller size (no more than a few GB), that would be a great help. Additionally, if you're interested in spear-heading this development yourself, we would gladly provide you with assistance and feedback.</div><div><br></div><div>Other devs, what sounds like the best way to implement this feature?</div><div><br></div><div>Finally, in the future, it would be better to start a new thread for a different question. I completely missed this question because I thought it was part of a discussion that others had well in hand.</div><div><br></div><div>Britton</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Jan 26, 2015 at 11:33 PM, Yuxiang Qin <span dir="ltr"><<a href="mailto:yuxiangq@student.unimelb.edu.au" target="_blank">yuxiangq@student.unimelb.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Hi guys,<div><br></div><div>Can I continue my question? still about loading in gadget/owls data...</div><div><br></div><div>When I try to load subhalo files, it cannot load in FOF/PartTypeN data. Neither ds.field_list and ds.derived_field_list shows those PartTypeN fields. They only contains ‘SF’, ’NSF’ and ‘Star’ fields. So Is there any way that I can load in those PartTypeN fields?</div><div><br></div><div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">[yqin@gstar001 subhalos_103]$ h5ls subhalo_103.0.hdf5 </div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">Constants Group</div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">FOF Group</div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">Header Group</div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">Parameters Group</div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">SUBFIND Group</div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">Units Group</div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">[yqin@gstar001 subhalos_103]$ h5ls subhalo_103.0.hdf5/FOF</div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">CenterOfMass Dataset {1920}</div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">CenterOfMassVelocity Dataset {1920}</div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">Mass Dataset {640}</div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">MassType Dataset {3840}</div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">NSF Group</div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">PartType0 Group</div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">PartType1 Group</div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">PartType4 Group</div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">SF Group</div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">StarFormationRate Dataset {640}</div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">Stars Group</div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">[yqin@gstar001 subhalos_103]$ h5ls subhalo_103.0.hdf5/FOF/PartType0</div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">AExpMaximumTemperature Dataset {15607}</div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">Coordinates Dataset {46821}</div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">Density Dataset {15607}</div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">ElementAbundance Group</div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">IronFromSNIa Dataset {15607}</div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">Length Dataset {530}</div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">Mass Dataset {15607}</div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">MaximumTemperature Dataset {15607}</div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">Metallicity Dataset {15607}</div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">MetallicityWeightedRedshift Dataset {15607}</div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">Offset Dataset {530}</div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">OnEquationOfState Dataset {15607}</div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">ParticleIDs Dataset {15607}</div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">SUB_Length Dataset {410}</div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">SUB_Offset Dataset {410}</div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">SmoothedMetallicity Dataset {15607}</div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">SmoothingLength Dataset {15607}</div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">StarFormationRate Dataset {15607}</div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">Temperature Dataset {15607}</div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">Velocity Dataset {46821}</div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">WindFlag Dataset {15607}</div></div><div><br></div><div>Cheers,</div><div>Yuxiang</div><div><div><div><div>
<br><div><blockquote type="cite"><div>On 24 Jan 2015, at 22:38, Yuxiang Qin <<a href="mailto:yuxiangq@student.unimelb.edu.au" target="_blank">yuxiangq@student.unimelb.edu.au</a>> wrote:</div><br><div><div style="word-wrap:break-word">I figure it. Thanks for fix this bug :)<div><br></div><div>Yuxiang<br><div><blockquote type="cite"><div>On 24 Jan 2015, at 17:39, Nathan Goldbaum <<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@gmail.com</a>> wrote:</div><br><div>I opened a PR for this: <br><br><a href="https://bitbucket.org/yt_analysis/yt/pull-request/1424/use-the-correct-filename-template-for/diff" target="_blank">https://bitbucket.org/yt_analysis/yt/pull-request/1424/use-the-correct-filename-template-for/diff</a><br><div class="gmail_quote">On Fri, Jan 23, 2015 at 10:35 PM Gabriel Altay <<a href="mailto:gabriel.altay@gmail.com" target="_blank">gabriel.altay@gmail.com</a>> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">We could definitely do that. When I first worked on the OWLS front end I considered only the actual OWLS snapshots which all have at least 8 files in their output. It think it would be a minor change but glancing through the code base, I see that someone has gone to the trouble of organizing the frontend folder. That is awesome!, but I can't immediately see where the file name construction is happening. </div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Jan 23, 2015 at 9:47 PM, Yuxiang Qin <span dir="ltr"><<a href="mailto:yuxiangq@student.unimelb.edu.au" target="_blank">yuxiangq@student.unimelb.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Hi Nathan,<div><br></div><div>That’s exactly what I would suggest :)</div><div><br></div><div>Cheers,</div><div>Yuxiang<div><div><br><div>
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<br><div><blockquote type="cite"><div>On 24 Jan 2015, at 14:44, Nathan Goldbaum <<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@gmail.com</a>> wrote:</div><br><div>Perhaps we should adjust the OWLS frontend to allow for datasets that fit in a single file? I believe when Gabe originally wrote the frontend he assumed that the dataset would be split into multiple files.<br><div class="gmail_quote">On Fri, Jan 23, 2015 at 7:43 PM Yuxiang Qin <<a href="mailto:yuxiangq@student.unimelb.edu.au" target="_blank">yuxiangq@student.unimelb.edu.au</a>> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Hi Matthew,<div><br></div><div>Thanks! Your method works. Actually, I think it’s because this simulation doesn’t have too many particles (Box size is 10Mpc, particle number is 128^3), so it doesn’t require too many processes to run the simulation, then the number of output files is only one. </div><div><br></div><div>Cheers,</div><div>Yuxiang</div></div><div style="word-wrap:break-word"><div><br><div>
<div style="letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word"><div><br></div></div></div><div><blockquote type="cite"><div>On 24 Jan 2015, at 14:28, Matthew Turk <<a href="mailto:matthewturk@gmail.com" target="_blank">matthewturk@gmail.com</a>> wrote:</div><br><div><div dir="ltr">Hi Yuxiang,<div><br></div><div>yt chooses the template for the filenames based on the value in NumFiles for vanilla Gadget; it doesn't add a zero if NumFiles == 1. Looking over the code, it looks like this behavior is not hte same if it thinks it's an EAGLE simulation or an OWLS simulation.</div><div><br></div><div>I believe that if you do this:</div><div><br></div><div>ds = yt.load( ...</div><div>ds.filename_template = ds.parameter_filename</div><div><br></div><div>it will force the behavior you're looking for. But, I don't know why for OWLS and EAGLE we don't make the same assumption about file naming convention.</div><div><br></div><div>-Matt</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Jan 23, 2015 at 8:38 PM, Yuxiang Qin <span dir="ltr"><<a href="mailto:yuxiangq@student.unimelb.edu.au" target="_blank">yuxiangq@student.unimelb.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Hi Guys,<div><br></div><div>I understand those warnings are not big problems and I think I decide to just ignore them at this moment.</div><div><br></div><div>I still have the problem loading only one file.</div><div><br></div><div>Here is a example. In directory ’snapshot_103’, I just have one file, snap_103.hdf5</div><div><br></div><div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">[yqin@gstar001 snapshot_103]$ ls</div><div style="margin:0px;font-family:'Andale Mono';color:rgb(51,196,38);background-color:rgb(0,0,0)">snap_103.hdf5</div></div><div><br></div><div>Then we I try to use this file, yt gives me this:</div><div><br></div><div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0);min-height:14px"><span style="color:rgb(52,189,38)">In [2]: </span>fname='../../Smaug/REF_L010N0128/data/snapshot_103/snap_103.hdf5' </div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0);min-height:14px"> <br></div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)"><span style="color:#34bd26">In [3]: </span>ds=yt.load(fname) </div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">yt : [INFO ] 2015-01-24 13:19:41,119 Parameters: current_time = 3.7953673 </div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">7148e+16 s </div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">yt : [INFO ] 2015-01-24 13:19:41,119 Parameters: domain_dimensions = [2 2 2] </div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">yt : [INFO ] 2015-01-24 13:19:41,119 Parameters: domain_left_edge = [ 0. 0. </div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)"> 0.] </div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">yt : [INFO ] 2015-01-24 13:19:41,120 Parameters: domain_right_edge = [ 10. 10 </div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">. 10.] </div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">yt : [INFO ] 2015-01-24 13:19:41,120 Parameters: cosmological_simulation = 1 </div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">yt : [INFO ] 2015-01-24 13:19:41,120 Parameters: current_redshift = 5.0000024 </div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">yt : [INFO ] 2015-01-24 13:19:41,121 Parameters: omega_lambda = 0.725 </div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">yt : [INFO ] 2015-01-24 13:19:41,121 Parameters: omega_matter = 0.275 </div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">yt : [INFO ] 2015-01-24 13:19:41,121 Parameters: hubble_constant = 0.702 </div></div><div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)"><span style="color:#34bd26"><br></span></div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)"><span style="color:#34bd26">In [4]: </span>ds.field_list </div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">ERROR OPENING /lustre/projects/p071_swin/Smaug/REF_L010N0128/data/snapshot_103/snap_103.0. </div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">hdf5 </div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">FILENAME DOES NOT EXIST </div><div style="margin:0px;font-family:'Andale Mono';color:rgb(195,55,32);background-color:rgb(0,0,0)">---------------------------------------------------------------------------<span style="color:#29f914"> </span></div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)"><span style="color:#c33720">IOError</span> Traceback (most recent call last) </div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)"><span style="color:#34bd26"><ipython-input-4-c4d73f2b23ef></span> in <span style="color:#34bbc7"><module></span><span style="color:#5330e1">()</span> </div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)"><span style="color:#34bd26">----> 1</span><span style="color:#afad24"> </span>ds<span style="color:#afad24">.</span>field_list </div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0);min-height:14px"> <br></div></div><div><br></div><div>Loading file is fine but using the information has a bug here. I think the problem is yt would automatically add a '.0’ in the filename and try to load from snapshot_103.0.hdf5 to snapshot_103.MAX_NUMBER.hdf5.</div><div><br></div><div>And Gabriel, when I said making a symbol link. I mean:</div><div><br></div><div>Firstly, I create a link named snap_103.0.hdf5 to snap_103.hdf5, so that when yt automatically add a ‘.0’ in the filename, it would visit the real file since I create the link. It’s just a trick. I can also rename my file snap_103.hdf5 to snap_103.0.hdf5.</div><div><br></div><div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">[yqin@gstar001 snapshot_103]$ ln -s snap_103.hdf5 snap_103.0.hdf5 </div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">[yqin@gstar001 snapshot_103]$ ls</div><div style="margin:0px;font-family:'Andale Mono';color:rgb(30,253,255);background-color:rgb(0,0,0)">snap_103.0.hdf5<span style="color:#29f914"> </span><span style="color:#33c426">snap_103.hdf5</span></div></div><div><span style="color:#33c426"><br></span></div><div>Then when I do this in yt:</div><div><br></div><div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)"><span style="color:#34bd26">In [5]: </span>ds.field_list </div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">yt : [INFO ] 2015-01-24 13:30:47,423 Allocating for 4.194e+06 particles </div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">yt : [INFO ] 2015-01-24 13:30:48,233 Identified 3.000e+05 octs </div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">yt : [WARNING ] 2015-01-24 13:30:48,366 Field ('deposit', 'PartType4_smoothed_O_fraction') alre</div><span><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">ady exists. To override use force_override=True. </div></span><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">yt : [WARNING ] 2015-01-24 13:30:48,367 Field ('deposit', 'PartType4_smoothed_Mg_fraction') alr</div><span><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">eady exists. To override use force_override=True. </div></span><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">yt : [WARNING ] 2015-01-24 13:30:48,367 Field ('deposit', 'PartType4_smoothed_C_fraction') alre</div><span><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">ady exists. To override use force_override=True. </div></span></div><div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">yt : [WARNING ] 2015-01-24 13:30:48,962 Field ('gas', 'Fe_mass') already exists. To override us</div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">e force_override=True. </div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)"><br></div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">BLA…BLA…BLA…</div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">A LOT OF WARNINGS</div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)"> </div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">yt : [INFO ] 2015-01-24 13:30:55,017 Loading field plugins. </div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">yt : [INFO ] 2015-01-24 13:30:55,019 Loaded angular_momentum (8 new fields) </div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">yt : [INFO ] 2015-01-24 13:30:55,019 Loaded astro (15 new fields) </div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">yt : [INFO ] 2015-01-24 13:30:55,020 Loaded cosmology (22 new fields) </div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">yt : [WARNING ] 2015-01-24 13:30:55,021 Field ('gas', 'metallicity') already exists. To overrid</div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">e use force_override=True. </div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">yt : [INFO ] 2015-01-24 13:30:55,021 Loaded fluid (63 new fields) </div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">yt : [INFO ] 2015-01-24 13:30:55,023 Loaded fluid_vector (95 new fields) </div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">yt : [INFO ] 2015-01-24 13:30:55,024 Loaded geometric (111 new fields) </div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">yt : [INFO ] 2015-01-24 13:30:55,024 Loaded local (111 new fields) </div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">yt : [INFO ] 2015-01-24 13:30:55,025 Loaded magnetic_field (119 new fields) </div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">yt : [INFO ] 2015-01-24 13:30:55,026 Loaded my_plugins (119 new fields) </div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">yt : [INFO ] 2015-01-24 13:30:55,027 Loaded species (121 new fields) </div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)"><span style="color:#c33720">Out[5]: </span> </div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)">[('PartType0', 'Coordinates'), </div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)"> ('PartType0', 'Density'), </div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)"> ('PartType0', 'Carbon'), </div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)"> ('PartType0', 'Helium'), </div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)"> ('PartType0', 'Hydrogen'), </div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)"> ('PartType0', 'Iron'), </div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)"> ('PartType0', 'Magnesium'), </div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)"> ('PartType0', 'Neon'), </div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)"> ('PartType0', 'Nitrogen'), </div><div style="margin:0px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)"> ('PartType0', 'Oxygen'), </div></div><div><br></div><div>Also yt still reports those warnings, but it actually succeeds reading the file.</div><div><br></div><div>So my question is can yt load file non-recursively. For example, can I say, ds=yt.load(fname, recursively==False), so that I don’t need to create the symbol links every time.</div><div><br></div><div>Again, thanks for helping me, guys :)</div><div><br></div><div>Cheers,</div><div>Yuxiang</div><div><div><div><br></div><div><div><blockquote type="cite"><div>On 24 Jan 2015, at 04:40, Gabriel Altay <<a href="mailto:gabriel.altay@gmail.com" target="_blank">gabriel.altay@gmail.com</a>> wrote:</div><br><div><div dir="ltr">Yuxiang, are you trying to read a single file still? Are you making symlinks between files? Can you explain in more detail?</div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Jan 22, 2015 at 9:16 PM, Yuxiang Qin <span dir="ltr"><<a href="mailto:yuxiang.l.qin@gmail.com" target="_blank">yuxiang.l.qin@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 style="word-wrap:break-word">Hi Desika,<div><br></div><div>I tried to reinstall yt by the script but I failed. So I reinstall it from source (hg clone). It still gives me those Warning… </div><span><font color="#888888"><div><br></div><div><br></div></font></span><div><span><font color="#888888">Yuxiang</font></span><div><div><br><div><blockquote type="cite"><div>On 23 Jan 2015, at 02:56, Desika Narayanan <<a href="mailto:dnarayan@haverford.edu" target="_blank">dnarayan@haverford.edu</a>> wrote:</div><br><div><div dir="ltr">Hi Yuxiang,<div><br></div><div>Are you running anaconda python?</div><div><br>One thing I've noticed this morning for the first time is that when I run yt installed via anaconda on gadget data sets (albeit not owls) I get similar warnings - i.e.:</div><div><p>yt : [WARNING ] 2015-01-22 10:44:54,090 Field ('deposit', 'PartType0_smoothed_Ne_fraction') already exists. To override use force_override=True.</p><p>whereas I didn't' receive them when running yt installed via the install script (and using the python that ships with yt). Not a solution, just another symptom.</p><p>-d</p></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Jan 21, 2015 at 7:06 PM, Yuxiang Qin <span dir="ltr"><<a href="mailto:yuxiangq@student.unimelb.edu.au" target="_blank">yuxiangq@student.unimelb.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Hi Andrew,<div><br></div><div>I had a look of those files and I think I get what you mean. By the way, about my second question, ‘cannot load in PartTypeN fields’, I think probably it’s because there is no definition of those fields in yt’s source code.</div><div><br></div><div>Cheers,</div><div>Yuxiang<div><div><br>
<br><div><blockquote type="cite"><div>On 22 Jan 2015, at 10:42, Andrew Myers <<a href="mailto:atmyers2@gmail.com" target="_blank">atmyers2@gmail.com</a>> wrote:</div><br><div><div dir="ltr">Hi <span style="font-size:13px">Yuxiang,</span><div><span style="font-size:13px"><br></span></div><div>There is a standard list of fields that yt automatically defines whenever you load an OWLS dataset (you can see the list in yt/frontends/owls/fields.py). You don't need to explicitly define any new fields yourself for this to happen - this all takes place under the hood. I think that the code that does this is adding all the fields twice for some reason. This is something that needs to get fixed in the OWLS frontend in yt's source code, not anything you are doing in your scripts. </div><div><br></div><div>-Andrew</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Jan 21, 2015 at 3:30 PM, Yuxiang Qin <span dir="ltr"><<a href="mailto:yuxiangq@student.unimelb.edu.au" target="_blank">yuxiangq@student.unimelb.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Hi,<div><br></div><div>Thanks for your help.</div><div><br></div><div>Nathan, I am using OWLS, a Gadget format data.</div><div><br></div><div>Andrew, what do you mean by ‘add a field that has already been defined’? I am not defining a new field. Does it mean there is already a new field in my data? If so, why yt says it’s a new field since it’s already there? I am kind of confused about it.</div><div><br></div><div>Cheers,</div><div>Yuxiang<div><div><br>
<br><div><blockquote type="cite"><div>On 22 Jan 2015, at 09:43, Nathan Goldbaum <<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@gmail.com</a>> wrote:</div><br><div><div dir="ltr">Hi Yuxiang,<div><br></div><div>What simulation code produced these files? Judging by the naming, I'd have to guess some flavor of gadget, but it's not clear based on your e-mail.</div><div><br></div><div>-Nathan</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Jan 20, 2015 at 4:29 PM, Yuxiang Qin <span dir="ltr"><<a href="mailto:yuxiangq@student.unimelb.edu.au" target="_blank">yuxiangq@student.unimelb.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word"><span style="font-size:14px">Dear yt-users,</span><div><span style="font-size:14px"><br></span></div><div><span style="font-size:14px">I have a tiny question about loading files.</span></div><div><span style="font-size:14px"><br></span></div><div><span style="font-size:14px">I understand when yt load files, it will load all the files in the directory. For example: if I do </span><span style="font-size:14px;background-color:rgb(0,0,0)"><font color="#29f914" face="Andale Mono">ds=yt.load('snap_103.0.hdf5’)</font></span><span style="font-size:14px">, then </span><span style="font-size:14px;color:rgb(41,249,20);font-family:'Andale Mono';background-color:rgb(0,0,0)">ds.field_list</span><span style="font-size:14px"> , yt would open all the files:</span></div><div><span style="font-size:14px"><br></span></div><div><div style="margin:0px;font-family:'Andale Mono';color:rgb(51,196,38);background-color:rgb(0,0,0)"><span style="font-size:14px">snap_103.0.hdf5<span style="color:#29f914">* </span>snap_103.16.hdf5<span style="color:#29f914">* </span>snap_103.22.hdf5<span style="color:#29f914">* </span>snap_103.29.hdf5<span style="color:#29f914">* </span>snap_103.6.hdf5<span style="color:#29f914">*</span></span></div><div style="margin:0px;font-family:'Andale Mono';color:rgb(51,196,38);background-color:rgb(0,0,0)"><span style="font-size:14px">snap_103.10.hdf5<span style="color:#29f914">* </span>snap_103.17.hdf5<span style="color:#29f914">* </span>snap_103.23.hdf5<span style="color:#29f914">* </span>snap_103.2.hdf5<span style="color:#29f914">* </span>snap_103.7.hdf5<span style="color:#29f914">*</span></span></div><div style="margin:0px;font-family:'Andale Mono';color:rgb(51,196,38);background-color:rgb(0,0,0)"><span style="font-size:14px">snap_103.11.hdf5<span style="color:#29f914">* </span>snap_103.18.hdf5<span style="color:#29f914">* </span>snap_103.24.hdf5<span style="color:#29f914">* </span>snap_103.30.hdf5<span style="color:#29f914">* </span>snap_103.8.hdf5<span style="color:#29f914">*</span></span></div><div style="margin:0px;font-family:'Andale Mono';color:rgb(51,196,38);background-color:rgb(0,0,0)"><span style="font-size:14px">snap_103.12.hdf5<span style="color:#29f914">* </span>snap_103.19.hdf5<span style="color:#29f914">* </span>snap_103.25.hdf5<span style="color:#29f914">* </span>snap_103.31.hdf5<span style="color:#29f914">* </span>snap_103.9.hdf5<span style="color:#29f914">*</span></span></div><div style="margin:0px;font-family:'Andale Mono';color:rgb(51,196,38);background-color:rgb(0,0,0)"><span style="font-size:14px">snap_103.13.hdf5<span style="color:#29f914">* </span>snap_103.1.hdf5<span style="color:#29f914">* </span>snap_103.26.hdf5<span style="color:#29f914">* </span>snap_103.3.hdf5<span style="color:#29f914">* </span></span></div><div style="margin:0px;font-family:'Andale Mono';color:rgb(51,196,38);background-color:rgb(0,0,0)"><span style="font-size:14px">snap_103.14.hdf5<span style="color:#29f914">* </span>snap_103.20.hdf5<span style="color:#29f914">* </span>snap_103.27.hdf5<span style="color:#29f914">* </span>snap_103.4.hdf5<span style="color:#29f914">* </span></span></div><div style="margin:0px;font-family:'Andale Mono';color:rgb(51,196,38);background-color:rgb(0,0,0)"><span style="font-size:14px">snap_103.15.hdf5<span style="color:#29f914">* </span>snap_103.21.hdf5<span style="color:#29f914">* </span>snap_103.28.hdf5<span style="color:#29f914">* </span>snap_103.5.hdf5<span style="color:#29f914">* </span></span></div></div><div><span style="font-size:14px"> <br></span><div>
<div style="text-align:start;text-indent:0px;word-wrap:break-word"><div style="letter-spacing:normal;text-transform:none;white-space:normal;word-spacing:0px"><span style="font-size:14px"><span style="font-family:Helvetica,Arial,sans-serif;background-color:rgb(255,255,255)">However, if our data only has one file :</span><span style="color:rgb(51,196,38);font-family:'Andale Mono';background-color:rgb(0,0,0)">snap_103.hdf5</span><span style="font-family:'Andale Mono';background-color:rgb(0,0,0);color:rgb(41,249,20)">*</span><span style="font-family:Helvetica,Arial,sans-serif;background-color:rgb(255,255,255)">, then if I do </span><span style="background-color:rgb(0,0,0)"><font color="#29f914" face="Andale Mono">ds=yt.load('snap_103.hdf5’)</font></span>, then <span style="color:rgb(41,249,20);font-family:'Andale Mono';background-color:rgb(0,0,0)">ds.field_list</span>, yt would still try to open all the files from <span style="color:rgb(51,196,38);font-family:'Andale Mono';background-color:rgb(0,0,0)">snap_103.0.hdf5</span>, however there is no <span style="color:rgb(51,196,38);font-family:'Andale Mono';background-color:rgb(0,0,0)">snap_103.0.hdf5</span>. It would report error: </span></div><div style="letter-spacing:normal;text-transform:none;white-space:normal;word-spacing:0px"><span style="font-size:14px"><br></span></div><div style="color:rgb(41,249,20);letter-spacing:normal;text-transform:none;white-space:normal;word-spacing:0px;margin:0px;font-family:'Andale Mono';background-color:rgb(0,0,0);min-height:14px"><span style="font-size:14px"><span style="color:rgb(195,55,32)">IOError</span>: Unable to open file (Unable to open file: name = '/lustre/projects/p071_swin/yqin/smaug/ref_eff_l010n0128/data/snapshot_102/snap_102.0.hdf5', errno = 2, error message = 'no such file or directory', flags = 0, o_flags = 0) <span></span></span></div><div style="letter-spacing:normal;text-transform:none;white-space:normal;word-spacing:0px"><span style="font-family:Helvetica,Arial,sans-serif;background-color:rgb(255,255,255);font-size:14px"><br></span></div><div><font face="Helvetica, Arial, sans-serif"><span style="background-color:rgb(255,255,255);font-size:14px">Is there an argument saying I don’t want to do loading recursively? I can make a link named </span></font><span style="color:rgb(51,196,38);font-family:'Andale Mono';font-size:14px;background-color:rgb(0,0,0)">snap_103.0.hdf5</span><span style="font-family:Helvetica,Arial,sans-serif;font-size:14px;background-color:rgb(255,255,255)"> to </span><span style="color:rgb(51,196,38);font-family:'Andale Mono';font-size:14px;background-color:rgb(0,0,0)">snap_103.hdf5</span><span style="background-color:rgb(255,255,255)"><font face="Helvetica, Arial, sans-serif"><span style="font-size:14px">. But it’s kind of inconvenient.</span></font></span></div><div><font face="Helvetica, Arial, sans-serif"><span style="background-color:rgb(255,255,255)"><span style="font-size:14px"><br></span></span></font></div><div><font face="Helvetica, Arial, sans-serif"><span style="background-color:rgb(255,255,255)"><span style="font-size:14px">Cheers,</span></span></font></div><div style="letter-spacing:normal;text-transform:none;white-space:normal;word-spacing:0px"><span style="font-size:14px"><span style="font-family:Helvetica,Arial,sans-serif;background-color:rgb(255,255,255)">--</span></span></div><div style="letter-spacing:normal;text-transform:none;white-space:normal;word-spacing:0px"><span style="font-size:14px"><span style="font-family:Helvetica,Arial,sans-serif;background-color:rgb(255,255,255)">Yuxiang Qin</span></span></div><div style="letter-spacing:normal;text-transform:none;white-space:normal;word-spacing:0px"><span style="font-size:14px"><span style="background-color:rgb(255,255,255)"><font face="Helvetica, Arial, sans-serif">PhD Student</font><br style="font-family:Helvetica,Arial,sans-serif"></span><span style="font-family:Helvetica,Arial,sans-serif;background-color:rgb(255,255,255)">School of Physics</span><br style="font-family:Helvetica,Arial,sans-serif"><span style="font-family:Helvetica,Arial,sans-serif;background-color:rgb(255,255,255)">The University of Melbourne</span><br style="font-family:Helvetica,Arial,sans-serif"><span style="font-family:Helvetica,Arial,sans-serif;background-color:rgb(255,255,255)">VIC, Australia, 3010</span></span><br style="font-family:Helvetica,Arial,sans-serif;font-size:15px"></div></div>
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