<div dir="ltr">Hi, sorry I forgot to attach the figures. Here is it.</div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Jan 31, 2017 at 5:32 PM, Mu-Hung Chang <span dir="ltr"><<a href="mailto:mu-hung.chang@stonybrook.edu" target="_blank">mu-hung.chang@stonybrook.edu</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, I've encountered a problem when I tried to use yt to visualize simple 1D detonation simulation data generated by Castro. The figure I expected to get is a simple step function just as attachment "1d_detonation_expected.png". However, if I don't set a customized axis limit by hand, it will produce something weird at the origin, which can be seen in the attachment "1d_detonation_weird.png". Following is my simple script to make plots. I wonder where I did wrong thus make this happened. Thank you for answering.<div><br></div><div><p style="margin:0px;font-size:12px;line-height:normal;font-family:courier;color:rgb(185,28,255);background-color:rgb(223,219,195)"><span style="font-variant-ligatures:no-common-ligatures">import</span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(77,47,45)"> sys</span></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:courier;color:rgb(185,28,255);background-color:rgb(223,219,195)"><span style="font-variant-ligatures:no-common-ligatures">import</span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(77,47,45)"> yt</span></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:courier;color:rgb(77,47,45);background-color:rgb(223,219,195)"><span style="font-variant-ligatures:no-common-ligatures;color:rgb(185,28,255)">import</span><span style="font-variant-ligatures:no-common-ligatures"> yt.units </span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(185,28,255)">as</span><span style="font-variant-ligatures:no-common-ligatures"> u</span></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:courier;color:rgb(77,47,45);background-color:rgb(223,219,195);min-height:14px"><span style="font-variant-ligatures:no-common-ligatures"></span><br></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:courier;color:rgb(77,47,45);background-color:rgb(223,219,195)"><span style="font-variant-ligatures:no-common-ligatures;color:rgb(185,28,255)">def</span><span style="font-variant-ligatures:no-common-ligatures"> </span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(69,36,255)">doit</span><span style="font-variant-ligatures:no-common-ligatures">(plotfile):</span></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:courier;color:rgb(77,47,45);background-color:rgb(223,219,195)"><span style="font-variant-ligatures:no-common-ligatures">    </span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(183,101,10)">ds</span><span style="font-variant-ligatures:no-common-ligatures"> = yt.load(plotfile)</span></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:courier;color:rgb(18,141,141);background-color:rgb(223,219,195)"><span style="font-variant-ligatures:no-common-ligatures;color:rgb(77,47,45)">    </span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(183,101,10)">ds.periodicity</span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(77,47,45)"> = (</span><span style="font-variant-ligatures:no-common-ligatures">False</span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(77,47,45)">, </span><span style="font-variant-ligatures:no-common-ligatures">False</span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(77,47,45)">, </span><span style="font-variant-ligatures:no-common-ligatures">False</span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(77,47,45)">)</span></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:courier;color:rgb(77,47,45);background-color:rgb(223,219,195)"><span style="font-variant-ligatures:no-common-ligatures">    </span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(183,101,10)">ad</span><span style="font-variant-ligatures:no-common-ligatures"> = ds.all_data()</span></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:courier;color:rgb(77,47,45);background-color:rgb(223,219,195)"><span style="font-variant-ligatures:no-common-ligatures">    </span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(183,101,10)">plot</span><span style="font-variant-ligatures:no-common-ligatures"> = yt.ProfilePlot(ad, </span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(159,38,116)">"x"</span><span style="font-variant-ligatures:no-common-ligatures">, </span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(159,38,116)">"temperature"</span><span style="font-variant-ligatures:no-common-ligatures">)</span></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:courier;color:rgb(77,47,45);background-color:rgb(223,219,195)"><span style="font-variant-ligatures:no-common-ligatures">    plot.set_unit(</span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(159,38,116)">"temperature"</span><span style="font-variant-ligatures:no-common-ligatures">, </span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(159,38,116)">"K"</span><span style="font-variant-ligatures:no-common-ligatures">)</span></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:courier;color:rgb(77,47,45);background-color:rgb(223,219,195)"><span style="font-variant-ligatures:no-common-ligatures">    plot.set_unit(</span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(159,38,116)">"x"</span><span style="font-variant-ligatures:no-common-ligatures">, </span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(159,38,116)">"m"</span><span style="font-variant-ligatures:no-common-ligatures">)</span></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:courier;color:rgb(77,47,45);background-color:rgb(223,219,195)"><span style="font-variant-ligatures:no-common-ligatures">    plot.set_log(</span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(159,38,116)">'x'</span><span style="font-variant-ligatures:no-common-ligatures">, </span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(18,141,141)">False</span><span style="font-variant-ligatures:no-common-ligatures">)</span></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:courier;color:rgb(77,47,45);background-color:rgb(223,219,195)"><span style="font-variant-ligatures:no-common-ligatures">    plot.set_xlim(1e-20, 450.0)</span></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:courier;color:rgb(77,47,45);background-color:rgb(223,219,195)"><span style="font-variant-ligatures:no-common-ligatures">    </span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(183,101,10)">pid</span><span style="font-variant-ligatures:no-common-ligatures"> = plotfile.split(</span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(159,38,116)">"plt"</span><span style="font-variant-ligatures:no-common-ligatures">)[1]</span></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:courier;color:rgb(159,38,116);background-color:rgb(223,219,195)"><span style="font-variant-ligatures:no-common-ligatures;color:rgb(77,47,45)">    plot.save(</span><span style="font-variant-ligatures:no-common-ligatures">"1d_detonation_{}.<wbr>png"</span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(77,47,45)">.</span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(107,107,148)">format</span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(77,47,45)">(pid))</span></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:courier;color:rgb(77,47,45);background-color:rgb(223,219,195);min-height:14px"><span style="font-variant-ligatures:no-common-ligatures"></span><br></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:courier;color:rgb(159,38,116);background-color:rgb(223,219,195)"><span style="font-variant-ligatures:no-common-ligatures;color:rgb(185,28,255)">if</span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(77,47,45)"> </span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(107,107,148)">__name__</span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(77,47,45)"> == </span><span style="font-variant-ligatures:no-common-ligatures">"__main__"</span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(77,47,45)">:</span></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:courier;color:rgb(77,47,45);background-color:rgb(223,219,195);min-height:14px"><span style="font-variant-ligatures:no-common-ligatures"></span><br></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:courier;color:rgb(195,35,15);background-color:rgb(223,219,195)"><span style="font-variant-ligatures:no-common-ligatures;color:rgb(77,47,45)">    </span><span style="font-variant-ligatures:no-common-ligatures"># Choose a field                                                                                                                                                                                      </span></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:courier;color:rgb(183,101,10);background-color:rgb(223,219,195)"><span style="font-variant-ligatures:no-common-ligatures;color:rgb(77,47,45)">    </span><span style="font-variant-ligatures:no-common-ligatures">plotfile</span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(77,47,45)"> = </span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(159,38,116)">""</span></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:courier;color:rgb(77,47,45);background-color:rgb(223,219,195)"><span style="font-variant-ligatures:no-common-ligatures">    </span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(185,28,255)">try</span><span style="font-variant-ligatures:no-common-ligatures">:</span></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:courier;color:rgb(77,47,45);background-color:rgb(223,219,195)"><span style="font-variant-ligatures:no-common-ligatures">        </span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(183,101,10)">plotfile</span><span style="font-variant-ligatures:no-common-ligatures"> = sys.argv[1]</span></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:courier;color:rgb(185,28,255);background-color:rgb(223,219,195)"><span style="font-variant-ligatures:no-common-ligatures;color:rgb(77,47,45)">    </span><span style="font-variant-ligatures:no-common-ligatures">except</span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(77,47,45)">:</span></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:courier;color:rgb(159,38,116);background-color:rgb(223,219,195)"><span style="font-variant-ligatures:no-common-ligatures;color:rgb(77,47,45)">        sys.</span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(18,141,141)">exit</span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(77,47,45)">(</span><span style="font-variant-ligatures:no-common-ligatures">"ERROR: no plotfile specified"</span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(77,47,45)">)</span></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:courier;color:rgb(77,47,45);background-color:rgb(223,219,195)"><span style="font-variant-ligatures:no-common-ligatures">    </span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(185,28,255)">for</span><span style="font-variant-ligatures:no-common-ligatures"> plt </span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(185,28,255)">in</span><span style="font-variant-ligatures:no-common-ligatures"> sys.argv[1:]:</span></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:courier;color:rgb(77,47,45);background-color:rgb(223,219,195)"><span style="font-variant-ligatures:no-common-ligatures">        </span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(183,101,10)">plotfile</span><span style="font-variant-ligatures:no-common-ligatures"> = plt</span></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:courier;color:rgb(77,47,45);background-color:rgb(223,219,195)"><span style="font-variant-ligatures:no-common-ligatures">        doit(plotfile)</span></p></div><div><br></div><div>Best, </div><span class="HOEnZb"><font color="#888888"><div>Mu-Hung</div></font></span></div>
</blockquote></div><br></div>