<div dir="ltr">Hi Malia :<div><br></div><div> Ok, good -- without nuclear burning, there are a few major checks to focus on. I'd be certain to read in your zeroeth checkpoint file and inspect the composition very closely in a tool like yt to ensure everything is initialized properly. Once you have confirmed the t = 0 data is valid, I would be concerned about the hydrodynamic stability, which you can test by lowering the CFL number. </div><div> </div><div> Best wishes,</div><div><br></div><div> Bob</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, May 4, 2017 at 2:24 PM, Malia Jenks <span dir="ltr"><<a href="mailto:rikku.hotaru@gmail.com" target="_blank">rikku.hotaru@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><div>I am not using nuclear burning for the simulation. I do call physics/sourceTerms/Burn/<wbr>BurnMain/nuclearBurn and Simulation/<wbr>SimulationComposition in my Config file to get the species information from the burn unit but I have useBurn set to false. I use the same mass fractions for all points on my initial grid, so all the abar and zbar values should be the same. I am not sure that the error isn't appearing in the t=0 data. I know it is after successfully reading in my data file and then I get the following outputs before the error message: <br><br> iteration, no. not moved = 0 9<br> iteration, no. not moved = 1 2<br> iteration, no. not moved = 2 0<br> refined: total leaf blocks = 64<br> refined: total blocks = 80<br> [amr_morton_process]: Initializing surr_blks using standard orrery implementati<br> on<br></div> <br></div>Thanks<span class="HOEnZb"><font color="#888888"><br><br></font></span></div><span class="HOEnZb"><font color="#888888">Malia <br></font></span></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">On Thu, May 4, 2017 at 5:04 AM, Robert Fisher <span dir="ltr"><<a href="mailto:rfisher1@umassd.edu" target="_blank">rfisher1@umassd.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 Malia :<div><br></div><div> When you say the initial EOS data, I presume you mean that you've verified the t = 0 data to be good. Helmholtz is fairly robust on good data, so I suspect if you inspected the data passed to Helmholtz during this call, you will find it to be already corrupted. </div><div><br></div><div> To add to Dean's comment, in my experience as well, when the code dies in Helmholtz, it is usually the symptom and not the underlying disease. The 'bad' data which manifests itself in this way is usually symptomatic of a more fundamental problem elsewhere in the code. For instance, you may be encountering a numerical instability in the hydrodynamics, or the nuclear burning, but because these modules do not trap NaNs or Infs, they will happily propagate to Helmholtz, where an exception is thrown. You will need to root out the underlying cause, because the NaNs and Infs will progressively corrupt the simulation.</div><div><br></div><div> Are you using nuclear burning in this simulation?</div><div><br></div><div> Best wishes,</div><div><br></div><div> Bob</div></div><div class="gmail_extra"><div><div class="m_-259847273043547222h5"><br><div class="gmail_quote">On Wed, May 3, 2017 at 5:02 PM, Jenks, Malia T. <span dir="ltr"><<a href="mailto:mjenks@ou.edu" target="_blank">mjenks@ou.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">
<div id="m_-259847273043547222m_-4672114048322732035m_1881886895311193561divtagdefaultwrapper" style="font-size:12pt;color:#000000;font-family:Calibri,Arial,Helvetica,sans-serif" dir="ltr">
<p></p>
<div>
<div>
<div>
<div>I am getting the following error from the helmholtz eos about negative pressure:<br>
<br>
[eos_helm] Negative total pressure.<br>
values: dens,temp: 2.321442471007820E-004 1549.01220000000 <br>
<br>
values: abar,zbar: Infinity NaN <br>
<br>
coulomb coupling parameter Gamma: NaN <br>
<br>
Prad 1.45198E-02 Pion 0.00000E+00 Pele NaN Pcoul 0.00000E+00 <br>
<br>
Ptot NaN df_d 8.31451E+21 <wbr>
<br>
<br>
<br>
</div>
I know that the initial mass fraction supplied to the eos is correct. The initial call of the eos sets abar and zbar correctly. I am not sure what is causing them to error. I also don't know why I am getting a NaN for the electron Pressure. Could anyone help
point me to what is going wrong and how I can solve it?<br>
<br>
</div>
Thanks,<br>
</div>
<br>
Malia Jenks</div>
<br>
<p></p>
</div>
</div>
</blockquote></div><br><br clear="all"><div><br></div></div></div><span class="m_-259847273043547222HOEnZb"><font color="#888888">-- <br><div class="m_-259847273043547222m_-4672114048322732035gmail_signature" data-smartmail="gmail_signature"><div dir="ltr">Dr. Robert Fisher<br>Associate Professor / Graduate Program Director<br>University of Massachusetts/Dartmouth<br>Department of Physics<br>285 Old Westport Road<br>North Dartmouth, Massachusetts 02747<br><a href="mailto:robert.fisher@umassd.edu" target="_blank">robert.fisher@umassd.edu</a><br><a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__www.novastella.org&d=DwMFaQ&c=qKdtBuuu6dQK9MsRUVJ2DPXW6oayO8fu4TfEHS8sGNk&r=nUT1oi3cRbKdsMTgT8_PUA&m=IsU8-Q_7pskVm8mOGqAylHzx3sb3Wi_WleaKUvuYnhg&s=n3YrwE4TWfK7mKn_s3nlTXXvpfQUJIOx-9P9XNvgwN0&e=" target="_blank">http://www.novastella.org</a></div></div>
</font></span></div>
</blockquote></div><br></div>
</div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr">Dr. Robert Fisher<br>Associate Professor / Graduate Program Director<br>University of Massachusetts/Dartmouth<br>Department of Physics<br>285 Old Westport Road<br>North Dartmouth, Massachusetts 02747<br><a href="mailto:robert.fisher@umassd.edu" target="_blank">robert.fisher@umassd.edu</a><br><a href="http://www.novastella.org" target="_blank">http://www.novastella.org</a></div></div>
</div>