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<p class="MsoNormal"><span style="font-size:11.0pt">Thank you for the suggestion. I’ve started a new sim with your fix, and it has gotten rid of the issues with the heat exchange, the logs no longer complain about bad EION/TION or EELE/TELE. However, I do
still get the message that there are “Negative internal energies in 3T update” and that it is “Falling back to using internal energy ratios instead of pressure ratios”.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;mso-ligatures:standardcontextual">Paul Campbell<o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> Hansen, Eddie <ehansen@pas.rochester.edu>
<br>
<b>Sent:</b> Friday, November 8, 2024 11:34 AM<br>
<b>To:</b> Paul Campbell <Paul.Campbell@zap.energy>; Sutcliffe, Graeme <sutcliffe2@llnl.gov><br>
<b>Cc:</b> flash-users@flash.rochester.edu<br>
<b>Subject:</b> Re: [External Sender] [FLASH-USERS] [External Sender] Negative Internal Energies in the 2D, AMR, Z-Pinch problem<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Hi Paul,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Since your errors seem to be coming from Heatexchange, the issue might be with the equilibration time.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">For v4.8, we removed some redundant code and started using the subroutine PlasmaState_ieEquilTime. This routine calls PlasmaState_tau to get the electron-ion collision time and then rescales it to get the
equilibration time. The problem is that we had implemented a floor on the average ionization state zbar inside PlasmaState_tau; this is useful for transport coefficients to avoid tau blowing up for small zbar. However, we should allow tau to be large for low
zbar for the equilibration time. <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">We’re going to fix this in 4.8.1, but in the meantime, you can edit PlasmaState_ieEquilTime.F90. Remove the call to PlsmaState_tau and add:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">tau = (3.*sqrt(pls_mele)*(pls_boltz*tele)**1.5) / &
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> (4.*sqrt(2.*PI) * ll * pls_qele**4 * zbar**2 * nion)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Can’t guarantee this will solve your issue, but it’s worth a try.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black">--</span><span style="font-size:10.0pt;font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;color:#181A1B">Eddie Hansen</span><span style="font-size:10.0pt;font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;color:#181A1B">Applications Group Leader<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;color:#181A1B">Flash Center for Computational Science</span><span style="font-size:10.0pt;font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><b><span style="color:black">From:
</span></b><span style="color:black">flash-users <<a href="mailto:flash-users-bounces@flash.rochester.edu">flash-users-bounces@flash.rochester.edu</a>> on behalf of Paul Campbell <<a href="mailto:Paul.Campbell@zap.energy">Paul.Campbell@zap.energy</a>><br>
<b>Date: </b>Tuesday, November 5, 2024 at 7:37 PM<br>
<b>To: </b>Sutcliffe, Graeme <<a href="mailto:sutcliffe2@llnl.gov">sutcliffe2@llnl.gov</a>><br>
<b>Cc: </b><a href="mailto:flash-users@flash.rochester.edu">flash-users@flash.rochester.edu</a> <<a href="mailto:flash-users@flash.rochester.edu">flash-users@flash.rochester.edu</a>><br>
<b>Subject: </b>Re: [FLASH-USERS] [External Sender] Negative Internal Energies in the 2D, AMR, Z-Pinch problem<o:p></o:p></span></p>
</div>
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<p class="MsoNormal"><span style="font-size:11.0pt">Thanks for the advice, I’ve resubmitted a job with the extra parameters you’ve suggested. So far the log files are still complaining about Negative internal energy but I will let it run over night and see
how far it gets. I should have included in my first email that I’m using version 4.8 (although for your suggestion I don’t think the difference in version matters). For reference this is what the warning from the log files look like:<br>
<br>
“</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">[ 11-04-2024 13:44:58.918 ] [Heatexchange] Warning: Negative internal energy detected</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">[ 11-04-2024 13:44:58.920 ] [Heatexchange] Correcting for this...</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">[ 11-04-2024 13:44:58.922 ] [Heatexchange] OLD EION/TION: 7.292804E+10 5.244171E+03</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">[ 11-04-2024 13:44:58.923 ] [Heatexchange] OLD EELE/TELE: 5.715019E+08 7.379651E+03</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">[ 11-04-2024 13:44:58.925 ] [Heatexchange] BAD EION/TION: 7.721564E+10 5.546998E+03</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">[ 11-04-2024 13:44:58.926 ] [Heatexchange] BAD EELE/TELE: -3.716098E+09 5.546998E+03</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">[ 11-04-2024 13:44:58.927 ] [Heatexchange] CORRECTED EION: 7.721564E+10</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">[ 11-04-2024 13:44:58.929 ] [Heatexchange] CORRECTED EELE: 2.116656E+08</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">[ 11-04-2024 13:44:58.930 ] [Heatexchange] FINAL EION: 7.329861E+10</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">[ 11-04-2024 13:44:58.931 ] [Heatexchange] FINAL EELE: 2.009281E+08</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">[ 11-04-2024 13:44:58.932 ] </span>
<o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> [ 11-04-2024 13:44:58.933 ] [Heatexchange] Note: Further warnings suppressed</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">[ 11-04-2024 16:00:05.980 ] Species 1: Lookup for T > Tmax(table): 35 times,first for (3.1052449E+08,1.0000000E+16),highest T was 2.3375415E+10</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">...... (lots of look ups for the 3 species here) …….</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">[ 11-04-2024 16:27:26.386 ] [hy_uhd_ragelike] Negative internal energies in 3T update</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">[ 11-04-2024 16:27:26.387 ] Falling back to using internal energy ratios instead of pressure ratios</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">“</span><o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Paul Campbell</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
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<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> Sutcliffe, Graeme <<a href="mailto:sutcliffe2@llnl.gov">sutcliffe2@llnl.gov</a>>
<br>
<b>Sent:</b> Tuesday, November 5, 2024 1:56 PM<br>
<b>To:</b> Paul Campbell <<a href="mailto:Paul.Campbell@zap.energy">Paul.Campbell@zap.energy</a>><br>
<b>Cc:</b> <a href="mailto:flash-users@flash.rochester.edu">flash-users@flash.rochester.edu</a><br>
<b>Subject:</b> Re: [External Sender] [FLASH-USERS] Negative Internal Energies in the 2D, AMR, Z-Pinch problem</span><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"><span style="color:black">Hi Paul,</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="color:black"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="color:black">You can try the following par file options if you haven't already, which helped me to get some laserslab runs working back in FLASH4.7 (adjust accordingly if you're not doing a 3T sim):</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="color:black">dr_usePOSdefComputeDt = .true.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="color:black">dr_posdefdtfactor = 0.1</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="color:black">dr_numPosdefVars = 3</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="color:black">dr_posdefVar_1 = "eele"</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="color:black">dr_posdefVar_2 = "eion"</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="color:black">dr_posdefVar_3 = "erad"</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="color:black"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="color:black">The dr_posdefdtfactor of 0.1 might be a bit aggressive (i.e. too small), I haven't played with it. </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="color:black"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="color:black">Graeme</span><o:p></o:p></p>
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<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black"> flash-users <<a href="mailto:flash-users-bounces@flash.rochester.edu">flash-users-bounces@flash.rochester.edu</a>>
on behalf of Paul Campbell <<a href="mailto:Paul.Campbell@zap.energy">Paul.Campbell@zap.energy</a>><br>
<b>Sent:</b> Tuesday, November 5, 2024 1:37 PM<br>
<b>To:</b> <a href="mailto:flash-users@flash.rochester.edu">flash-users@flash.rochester.edu</a> <<a href="mailto:flash-users@flash.rochester.edu">flash-users@flash.rochester.edu</a>><br>
<b>Subject:</b> [FLASH-USERS] Negative Internal Energies in the 2D, AMR, Z-Pinch problem</span>
<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="xmsonormal">Hello,<o:p></o:p></p>
<p class="xmsonormal"> <o:p></o:p></p>
<p class="xmsonormal">I am attempting to get the 2D Z-pinch problem working with AMR but have been unable to get the sim to run without crashing . From the logs, I appear to be running into many negative internal energy warnings. It looks like both the electron
and ion temperatures/energies need to be continuously corrected. To try and address this issue, I have tried refining on density, electron, and ion temperatures but the warnings persist. In terms of the AMR settings, I am using a 32x32 grid with 4x4 cells,
a lrefine_max=4, and I have left the refinement cutoffs and filters unchanged from default. My questions are:<o:p></o:p></p>
<p class="xmsonormal"> <o:p></o:p></p>
<ol style="margin-top:0in" start="1" type="1">
<li class="xmsolistparagraph" style="margin-left:0in;mso-list:l0 level1 lfo3">Is this an issue with the AMR settings, would a finer grid fix this problem?<o:p></o:p></li><li class="xmsolistparagraph" style="margin-left:0in;mso-list:l0 level1 lfo3">Should I be refining on different parameters?<o:p></o:p></li><li class="xmsolistparagraph" style="margin-left:0in;mso-list:l0 level1 lfo3">Is this an issue with a non-AMR setting?<o:p></o:p></li></ol>
<p class="xmsonormal"> <o:p></o:p></p>
<p class="xmsonormal" style="margin-bottom:12.0pt"><span style="font-family:"Calibri",sans-serif">Paul Campbell</span><o:p></o:p></p>
<p class="xmsonormal"> <o:p></o:p></p>
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