<div dir="ltr"><div><div>Hi Nathan ,<br><br></div>Thanks, I need one last correction from you. my final goal is to get the Ejected_Mass. How can I get rid of this error?<br><br></div>Thanks in advance<br><div><br>import yt<br>import numpy as np<br><br>from yt import derived_field<br><br><br>@derived_field(name = "__mass_ejects")<br>def shock(field,data):<br> dm = data['cell_mass']<br> xv = data['velx']<br> yv = data['vely']<br> zv = data['velz']<br> grav_pot= data['gpot']<br>#define total energy<br> E_total=0.5*dm*(xv**2+yv**2+zv**2)+grav_pot*dm<br><br> return np.greater(E_total, 0)<br><br><br>ds = yt.load('~/super3d_hdf5_plt_cnt_0118')<br><br>ds.index<br>print ds.field_info["gas", "cell_mass"].get_source()<br>print ds.field_info["gas", "__mass_ejects"].get_source()<br><br>Ejected = data['cell_mass']*data['__mass_ejected']<br>--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------<br><div class="" style="padding:0px;display:flex;color:rgb(0,0,0);font-family:"Helvetica Neue",Helvetica,Arial,sans-serif;font-size:14px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:20px;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255)"><div class="" style="padding:0.4em;max-width:calc(100% - 14ex);text-align:left;color:rgb(0,0,0);line-height:1.21429em"><pre style="overflow:auto;font-family:monospace;font-size:inherit;display:block;padding:0px;margin:0px;line-height:inherit;word-wrap:break-word;color:black;border:0px none;border-radius:0px;white-space:pre-wrap;vertical-align:baseline;background-color:transparent"> def _cell_mass(field, data):
return data[ftype, "density"] * data["index", "cell_volume"]
@derived_field(name = "__mass_ejects")
def shock(field,data):
dm = data['cell_mass']
xv = data['velx']
yv = data['vely']
zv = data['velz']
grav_pot= data['gpot']
#define total energy
E_total=0.5*dm*(xv**2+yv**2+zv**2)+grav_pot*dm
return np.greater(E_total, 0)
</pre></div></div><div class="" style="padding:0px;display:flex;color:rgb(0,0,0);font-family:"Helvetica Neue",Helvetica,Arial,sans-serif;font-size:14px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:20px;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255)"><div class="" style="padding:0.4em;max-width:calc(100% - 14ex);text-align:left;color:rgb(0,0,0);line-height:1.21429em"><pre style="overflow:auto;font-family:monospace;font-size:inherit;display:block;padding:0px;margin:0px;line-height:inherit;word-wrap:break-word;color:black;border:0px none;border-radius:0px;white-space:pre-wrap;vertical-align:baseline;background-color:transparent"><span class="" style="color:darkred">---------------------------------------------------------------------------</span>
<span class="" style="color:darkred">NameError</span> Traceback (most recent call last)
<span class="" style="color:darkgreen"><ipython-input-5-bbb0b768fd76></span> in <span class="" style="color:steelblue"><module><span class="" style="color:darkblue">()</span>
<span class="" style="color:darkgreen"> 24</span> <span class="" style="color:darkgreen">print</span> ds<span class="" style="color:rgb(196,160,0)">.</span>field_info<span class="" style="color:rgb(196,160,0)">[</span><span class="" style="color:darkblue">"gas"</span><span class="" style="color:rgb(196,160,0)">,</span> <span class="" style="color:darkblue">"__mass_ejects"</span><span class="" style="color:rgb(196,160,0)">]</span><span class="" style="color:rgb(196,160,0)">.</span>get_source<span class="" style="color:rgb(196,160,0)">(</span><span class="" style="color:rgb(196,160,0)">)</span><span class="" style="color:rgb(196,160,0)"></span>
<span class="" style="color:darkgreen"> 25</span> <span class="" style="color:rgb(196,160,0)"></span>
<span class="" style="color:darkgreen">---> 26<span class="" style="color:rgb(196,160,0)"> </span>Ejected <span class="" style="color:rgb(196,160,0)">=</span> data<span class="" style="color:rgb(196,160,0)">[</span><span class="" style="color:darkblue">'cell_mass'</span><span class="" style="color:rgb(196,160,0)">]</span><span class="" style="color:rgb(196,160,0)">*</span>data<span class="" style="color:rgb(196,160,0)">[</span><span class="" style="color:darkblue">'__mass_ejected'</span><span class="" style="color:rgb(196,160,0)">]</span><span class="" style="color:rgb(196,160,0)"></span>
<span class="" style="color:darkred">NameError</span>: name 'data' is not defined
</span></span></pre></div></div><br class=""><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Feb 8, 2016 at 11:18 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">Hi Tazkera,<div><br></div><div>It works if I do this:</div><div><br></div><div><a href="http://paste.yt-project.org/show/6233/" target="_blank">http://paste.yt-project.org/show/6233/</a></div><div><br></div><div>The issue with your example is that your derived field definition either returns 1 or 0, when instead it should return an array with the same shape as E_total.</div><span class="HOEnZb"><font color="#888888"><div><br></div></font></span><div><span class="HOEnZb"><font color="#888888">-Nathan</font></span><div><div class="h5"><br><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Feb 8, 2016 at 9:49 PM, tazkera haque <span dir="ltr"><<a href="mailto:h.tazkera@gmail.com" target="_blank">h.tazkera@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr"><span style="font-size:12.8px">I am trying to derive a new field here and will test it with one of the scripts first. but I am getting error when I am checking if that field has been added already. please take a look at the errors for me.</span><br><div><span style="font-size:12.8px"><br></span></div><div><div><span style="font-size:12.8px">import yt</span></div><div><span style="font-size:12.8px"><br></span></div><div><span style="font-size:12.8px">from yt import derived_field</span></div><div><span style="font-size:12.8px"><br></span></div><div><span style="font-size:12.8px"><br></span></div><div><span style="font-size:12.8px">@derived_field(name = "__mass_ejects")</span></div><div><span style="font-size:12.8px">def shock(field,data):</span></div><div><span style="font-size:12.8px"> dm = data['cell_mass']</span></div><div><span style="font-size:12.8px"> xv = data['velx']</span></div><div><span style="font-size:12.8px"> yv = data['vely']</span></div><div><span style="font-size:12.8px"> zv = data['velz']</span></div><div><span style="font-size:12.8px"> grav_pot= data['gpot']</span></div><div><span style="font-size:12.8px">#define total energy</span></div><div><span style="font-size:12.8px"> E_total=0.5*dm*(xv**2+yv**2+zv**2)+grav_pot*dm</span></div><div><span style="font-size:12.8px"> </span></div><div><span style="font-size:12.8px"> </span></div><div><span style="font-size:12.8px"> if E_total >0:</span></div><div><span style="font-size:12.8px"> return 0</span></div><div><span style="font-size:12.8px"> else :</span></div><div><span style="font-size:12.8px"> return 1</span></div></div><div><span style="font-size:12.8px"><div>ds.index</div><div>print ds.field_info["gas", "cell_mass"].get_source()</div><div>print ds.field_info["gas", "__mass_ejects"].get_source()</div><div><br></div><div>------------------------------------------------------------------------------------------------------------------------------------------------------------------------</div><div><div style="padding:0px;display:flex;color:rgb(0,0,0);font-family:'Helvetica Neue',Helvetica,Arial,sans-serif;font-size:14px;line-height:20px"><div style="padding:0.4em;max-width:calc(100% - 14ex);line-height:1.21429em"><pre style="overflow:auto;font-size:inherit;padding:0px;margin-top:0px;margin-bottom:0px;line-height:inherit;word-wrap:break-word;border:0px;border-radius:0px;white-space:pre-wrap;vertical-align:baseline;background-color:transparent"> def _cell_mass(field, data):
return data[ftype, "density"] * data["index", "cell_volume"]
</pre></div></div><div style="padding:0px;display:flex;color:rgb(0,0,0);font-family:'Helvetica Neue',Helvetica,Arial,sans-serif;font-size:14px;line-height:20px"><div style="min-width:14ex;padding:0px 0.4em;margin:0px;font-family:monospace;text-align:right;line-height:1.21429em"></div><div style="padding:0.4em;max-width:calc(100% - 14ex);line-height:1.21429em"><pre style="overflow:auto;font-size:inherit;padding:0px;margin-top:0px;margin-bottom:0px;line-height:inherit;word-wrap:break-word;border:0px;border-radius:0px;white-space:pre-wrap;vertical-align:baseline;background-color:transparent"><span style="color:darkred">---------------------------------------------------------------------------</span>
<span style="color:darkred">KeyError</span> Traceback (most recent call last)
<span style="color:darkgreen"><ipython-input-29-bfb3007289ba></span> in <span style="color:steelblue"><module><span style="color:darkblue">()</span>
<span style="color:darkgreen"> 1</span> ds<span style="color:rgb(196,160,0)">.</span>index<span style="color:rgb(196,160,0)"></span>
<span style="color:darkgreen"> 2</span> <span style="color:darkgreen">print</span> ds<span style="color:rgb(196,160,0)">.</span>field_info<span style="color:rgb(196,160,0)">[</span><span style="color:darkblue">"gas"</span><span style="color:rgb(196,160,0)">,</span> <span style="color:darkblue">"cell_mass"</span><span style="color:rgb(196,160,0)">]</span><span style="color:rgb(196,160,0)">.</span>get_source<span style="color:rgb(196,160,0)">(</span><span style="color:rgb(196,160,0)">)</span><span style="color:rgb(196,160,0)"></span>
<span style="color:darkgreen">----> 3<span style="color:rgb(196,160,0)"> <span style="color:darkgreen">print</span> ds<span>.</span>field_info<span>[</span><span style="color:darkblue">"gas"</span><span>,</span> <span style="color:darkblue">"__mass_ejects"</span><span>]</span><span>.</span>get_source<span>(</span><span>)</span><span></span>
<span style="color:darkgreen">/home/trina/anaconda2/lib/python2.7/site-packages/yt/fields/field_info_container.pyc</span> in <span style="color:steelblue">__missing__<span style="color:darkblue">(self, key)</span>
<span style="color:darkgreen"> 285</span> <span style="color:darkgreen">def</span> __missing__<span style="color:rgb(196,160,0)">(</span>self<span style="color:rgb(196,160,0)">,</span> key<span style="color:rgb(196,160,0)">)</span><span style="color:rgb(196,160,0)">:</span><span style="color:rgb(196,160,0)"></span>
<span style="color:darkgreen"> 286</span> <span style="color:darkgreen">if</span> self<span style="color:rgb(196,160,0)">.</span>fallback <span style="color:darkgreen">is</span> None<span style="color:rgb(196,160,0)">:</span><span style="color:rgb(196,160,0)"></span>
<span style="color:darkgreen">--> 287<span style="color:rgb(196,160,0)"> <span style="color:darkgreen">raise</span> KeyError<span>(</span><span style="color:darkblue">"No field named %s"</span> <span>%</span> <span>(</span>key<span>,</span><span>)</span><span>)</span><span></span>
<span style="color:darkgreen"> 288</span> <span style="color:darkgreen">return</span> self<span>.</span>fallback<span>[</span>key<span>]</span><span></span>
<span style="color:darkgreen"> 289</span> <span></span>
<span style="color:darkred">KeyError</span>: "No field named ('gas', '__mass_ejects')"</span></span></span></span></span></span></pre></div></div></div><div><br></div></span></div><div><span style="font-size:12.8px"><br></span></div></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Feb 8, 2016 at 11:18 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-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr">This error happens when yt can't find a field for a given dataset. In this case it's looking for a field named 'absReynoldsStress'. It reports it with the funny spelling "('all', 'absReynoldsStrss')" because it's guessing that it's a particle field.<div><br></div><div>Since that isn't a field in your FLASH dataset (unless you've modified FLASH to output such a field), and it's not defined as a derived field in that script or in yt itself, yt isn't able to generate it.</div><div><br></div><div>Do you have an 'absReynoldsStress' derived field defined somewhere else?</div><span><font color="#888888"><div><br></div><div>-Nathan</div></font></span></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">On Sun, Feb 7, 2016 at 9:53 PM, tazkera haque <span dir="ltr"><<a href="mailto:h.tazkera@gmail.com" target="_blank">h.tazkera@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr">Hi, can anyone please check my script and the corresponding error? <br></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">On Sun, Feb 7, 2016 at 1:29 PM, tazkera haque <span dir="ltr"><<a href="mailto:h.tazkera@gmail.com" target="_blank">h.tazkera@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr">thanks very much everyone. solves my problem.</div><div><div><div class="gmail_extra"><br><div class="gmail_quote">On Sun, Feb 7, 2016 at 11:15 AM, Kacper Kowalik <span dir="ltr"><<a href="mailto:xarthisius.kk@gmail.com" target="_blank">xarthisius.kk@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><span>On 02/06/2016 09:03 PM, tazkera haque wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
Hi , thanks very much for the helps. but I happen to get the errors still<br>
though I did the exact same things as suggested. I am attaching the summary<br>
and error.<br>
</blockquote>
<br></span>
Hi Tazkera,<br>
<br>
clean.sh unfortunately doesn't remove cythonized modules (.c files). You can either manually remove the offending file (yt/geometry/grid_container.c) or use hg purge. In order to do the latter you'll need to add the following to $HOME/.hgrc:<br>
<br>
[extensions]<br>
hgext.purge =<br>
<br>
Then try:<br>
<br>
$ cd /work/03858/thaque56/sw/yt-3.1/yt-x86_64/src/yt-hg/<br>
$ hg purge --all<br>
$ python setup.py build_ext -i # (or python setup.py develop)<br>
<br>
Cheers,<br>
Kacper<div><div><br>
<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
On Sat, Feb 6, 2016 at 9:05 PM, Nathan Goldbaum <<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@gmail.com</a>><br>
wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
It looks like yt's C extensions need to be recompiled. Can you activate<br>
the yt environment and do the following:<br>
<br>
$ cd /work/03858/thaque56/sw/yt-3.1/yt-x86_64/src/yt-hg/<br>
$ bash ./clean.sh<br>
$ hg pull<br>
$ hg update<br>
$ python setup.py develop<br>
<br>
If that doesn't work, can you reply with the output of "hg summary", as<br>
well as the error that you see?<br>
<br>
Hope that helps,<br>
<br>
Nathan<br>
<br>
On Sat, Feb 6, 2016 at 7:25 PM, tazkera haque <<a href="mailto:h.tazkera@gmail.com" target="_blank">h.tazkera@gmail.com</a>> wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
Hi , I am trying to run a python file with yt packages on STAMPEDE. and<br>
getting some errors each time. I think the error is due to some<br>
installation error of yt at first place. can you please look at both my<br>
code and error and send me the solutions to solve the problem. both the<br>
files are attached for your convenience.<br>
<br>
regards<br>
Tazkera<br>
<br>
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