<div dir="ltr"><div><div>Hello,<br></div><div><br>I have modified the yt files as given in the pull request. I get the following error code:<br><br>Traceback (most recent call last):<br> File "dev.py", line 9, in <module><br> import yt<br> File "/home/alankar/anaconda3/lib/python3.6/site-packages/yt/__init__.py", line 133, in <module><br> frontends = _frontend_container()<br> File "/home/alankar/anaconda3/lib/python3.6/site-packages/yt/frontends/api.py", line 52, in __init__<br> setattr(self, frontend, importlib.import_module(_mod))<br> File "/home/alankar/anaconda3/lib/python3.6/importlib/__init__.py", line 126, in import_module<br> return _bootstrap._gcd_import(name[level:], package, level)<br> File "/home/alankar/anaconda3/lib/python3.6/site-packages/yt/frontends/eagle/api.py", line 17, in <module><br> from .data_structures import \<br> File "/home/alankar/anaconda3/lib/python3.6/site-packages/yt/frontends/eagle/data_structures.py", line 21, in <module><br> from yt.frontends.gadget.data_structures import \<br> File "/home/alankar/anaconda3/lib/python3.6/site-packages/yt/frontends/gadget/data_structures.py", line 28, in <module><br> from yt.frontends.sph.data_structures import \<br>ImportError: cannot import name 'SPHDataset'<br><br></div>The following is my code:<br>import yt<br>ds = yt.load("snapshot_068.0")<br><br></div>Alankar Dutta<br></div><div class="gmail_extra"><br><div class="gmail_quote">On Sat, Mar 4, 2017 at 3:13 PM, Alankar Dutta <span dir="ltr"><<a href="mailto:dutta.alankar@gmail.com" target="_blank">dutta.alankar@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">Oh I missed telling that the full dataset is around 950 GB<br></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">On Sat, Mar 4, 2017 at 1:02 PM, Alankar Dutta <span dir="ltr"><<a href="mailto:dutta.alankar@gmail.com" target="_blank">dutta.alankar@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"><div><div>Hello,<br><br>This is only one part of the multipart snapshot of the simulation. I am sending you the header information from the snapshot file:<br><br><pre style="box-sizing:border-box;overflow:auto;font-family:monospace;font-size:14px;display:block;padding:0px;margin:0px;line-height:inherit;word-break:break-all;color:rgb(0,0,0);background-color:rgb(255,255,255);border-width:0px;border-style:none;border-color:-moz-use-text-color;border-radius:0px;white-space:pre-wrap;vertical-align:baseline;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:left;text-indent:0px;text-transform:none;word-spacing:0px">{'O0': 0.27500000000000002,
'Ol': 0.72499999999999998,
'boxsize': 100000.0,
'flag_age': 1,
'flag_cooling': 1,
'flag_delaytime': 0,
'flag_fb': 1,
'flag_fh2': 0,
'flag_metals': 1,
'flag_potential': 3,
'flag_sfr': 1,
'flag_tmax': 0,
'h': 0.70199999999999996,
'massTable': array([ 0. , 0.00110449, 0. , 0. , 0. , 0. ]),
'nbndry': 76247,
'nbulge': 0,
'ndisk': 0,
'ndm': 1459617792,
'nfiles': 1024,
'ngas': 1343721867,
'npartThisFile': array([10045237, 10239661, 0, 0, 451148, 67], dtype=uint32),
'npartTotal': array([1343721867, 1459617792, 0, 0, 503500456,
76247], dtype=uint32),
'npartTotalHW': array([1, 1, 0, 0, 0, 0], dtype=uint32),
'nstar': 503500456,
'redshift': 1.0000000010567627,
'rhocrit': 2.707660428120944e-29,
'time': 0.49999999973580939}</pre><br><br></div>I extracted this information using a different python program.<span class="m_7426300707668143112HOEnZb"><font color="#888888"><br><br></font></span></div><span class="m_7426300707668143112HOEnZb"><font color="#888888">Alankar Dutta<br></font></span></div><div class="m_7426300707668143112HOEnZb"><div class="m_7426300707668143112h5"><div class="gmail_extra"><br><div class="gmail_quote">On Sat, Mar 4, 2017 at 12:45 PM, Nathan Goldbaum <span dir="ltr"><<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@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"><br><div class="gmail_extra"><br><div class="gmail_quote"><span>On Sat, Mar 4, 2017 at 12:25 AM, Nathan Goldbaum <span dir="ltr"><<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><br><div class="gmail_extra"><br><div class="gmail_quote"><span class="m_7426300707668143112m_2054906823403235472m_-7680578832292161778gmail-">On Sat, Mar 4, 2017 at 12:13 AM, Alankar Dutta <span dir="ltr"><<a href="mailto:dutta.alankar@gmail.com" target="_blank">dutta.alankar@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="auto">Hello,<div dir="auto"><br></div><div dir="auto">Modifying the GADGET simulation isn't possible the moment because it has already been developed by someone else who has a paper published on this simulation and I want to use that simulation snapshots to make mock xray map from it.</div></div></blockquote><div><br></div></span><div>I'm talking about modifying yt, not Gadget.<div><br></div><div>Is the file you attached to your other e-mail just a single file in a multi-file dataset? How large is the full dataset? Do you not have a way to produce a full dataset in this output format that's not prohibitively large?</div></div></div></div></div></blockquote><div><br></div></span><div>I've opened a pull request that allows me to do IO on the data you attached: <a href="https://bitbucket.org/yt_analysis/yt/pull-requests/2537" target="_blank">https://bitbucket.or<wbr>g/yt_analysis/yt/pull-requests<wbr>/2537</a></div><div><br></div><div>This allows me to read your data in, getting sensible values for e.g. position. I suspect we're not using the correct field specification because I see this warning:</div><div><br></div><div>yt : [WARNING ] 2017-03-04 01:06:09,109 Your Gadget-2 file may have extra columns or different precision! (1814947576 file vs 1486279952 computed)<br></div><div><br></div><div>yt supports a number of field specifications out of the box, see:</div><div><br></div><div><a href="https://bitbucket.org/yt_analysis/yt/src/3eca2ae80ab14a48b643d3055d7d3c0933fa77ae/yt/frontends/gadget/definitions.py?at=yt&fileviewer=file-view-default#definitions.py-50" target="_blank">https://bitbucket.org/yt_analy<wbr>sis/yt/src/3eca2ae80ab14a48b64<wbr>3d3055d7d3c0933fa77ae/yt/front<wbr>ends/gadget/definitions.py?at=<wbr>yt&fileviewer=file-view-defaul<wbr>t#definitions.py-50</a><br></div><div><br></div><div>Do you happen to know which fields are in your output file?</div><div><div class="m_7426300707668143112m_2054906823403235472h5"><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div class="gmail_extra"><div class="gmail_quote"><div><div class="m_7426300707668143112m_2054906823403235472m_-7680578832292161778gmail-h5"><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="auto"><div dir="auto"><span class="m_7426300707668143112m_2054906823403235472m_-7680578832292161778gmail-m_-4150620841045583989gmail-HOEnZb"><font color="#888888"><br><br><div dir="auto">Alankar Dutta</div></font></span></div></div><div class="m_7426300707668143112m_2054906823403235472m_-7680578832292161778gmail-m_-4150620841045583989gmail-HOEnZb"><div class="m_7426300707668143112m_2054906823403235472m_-7680578832292161778gmail-m_-4150620841045583989gmail-h5"><div class="gmail_extra"><br><div class="gmail_quote">On Mar 4, 2017 11:38 AM, "Nathan Goldbaum" <<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@gmail.com</a>> wrote:<br type="attribution"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">I think the most straightforward thing to do here is to fix the Gadget frontend so it properly reads in gadget binary data with positions written in double precision.<div><br></div><div>Is there any chance you can generate a smallish test dataset in your Gadget output format that we can use for debugging purposes? With that available it should be straightforward to add support. You can share the dataset using the yt curldrop (<a href="https://docs.hub.yt/services.html#curldrop" target="_blank">https://docs.hub.yt/services.<wbr>html#curldrop</a>) or a cloud filesharing service like dropbox or google drive.</div><div><br></div><div>Unfortunately there isn't a way to load SPH data without a full-fledged frontend right now.</div><div><br></div><div>We do have a load_particles function which allows creating a dataset from particle data loaded as numpy arrays, but it's currently not possible to use it to load SPH data. </div><div><br></div><div>I'm currently actively working on improving support for SPH data in yt and adding the ability to load SPH data with load_particles is one of the things I've added in that branch of the code. Hopefully this work will be stabilized sometime in the next few months.<br></div><div><br></div><div><br></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Mar 3, 2017 at 11:45 PM, Alankar Dutta <span dir="ltr"><<a href="mailto:dutta.alankar@gmail.com" target="_blank">dutta.alankar@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div><div><div><div>Hello yt-community,<br><br>I am a beginner on yt. I have an array of data which I have read from a Gadget simulation snapshot. It is not directly supported by yt at present (I have ensured this by already discussing this issue in the community before). The array has position,velocity, density, mass, internal energy and smoothing length information on the gas particles. Now how can I use this to make the slice plots or other useful visualizations?<span class="m_7426300707668143112m_2054906823403235472m_-7680578832292161778gmail-m_-4150620841045583989gmail-m_5927581532522955128m_-3416413581748429304m_-832106199985279372HOEnZb"><font color="#888888"><br><br></font></span></div><span class="m_7426300707668143112m_2054906823403235472m_-7680578832292161778gmail-m_-4150620841045583989gmail-m_5927581532522955128m_-3416413581748429304m_-832106199985279372HOEnZb"><font color="#888888">Alankar Dutta,<br></font></span></div><span class="m_7426300707668143112m_2054906823403235472m_-7680578832292161778gmail-m_-4150620841045583989gmail-m_5927581532522955128m_-3416413581748429304m_-832106199985279372HOEnZb"><font color="#888888">Third year Undergraduate,<br></font></span></div><span class="m_7426300707668143112m_2054906823403235472m_-7680578832292161778gmail-m_-4150620841045583989gmail-m_5927581532522955128m_-3416413581748429304m_-832106199985279372HOEnZb"><font color="#888888">Physics Department,<br></font></span></div><span class="m_7426300707668143112m_2054906823403235472m_-7680578832292161778gmail-m_-4150620841045583989gmail-m_5927581532522955128m_-3416413581748429304m_-832106199985279372HOEnZb"><font color="#888888">Presidency University, India<br></font></span></div>
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