<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Anthony,<div class=""><br class=""></div><div class="">******First: Did you make a copy of the <i class="">LaserSlab</i> problem in <i class="">magnetoHD </i>? See section 34.2 in the user manual for examples. <span style="font-style: normal;" class="">Try that again but then do effectively the same setup script you did:</span></div><div class=""><br class=""></div><div class=""><font face="CMUTypewriter-Regular" color="#00fa00" style="background-color: rgb(0, 0, 0);" class="">./setup -auto magnetoHD/LaserSlab -2d +cylindrical -nxb=16 -nyb=16 +hdf5typeio species=cham,targ +mtmmmt +laser +mgd +usm3t mgd_meshgroups=6 -parfile=example.par</font><div><br class=""><blockquote type="cite" class=""><div class="">On May 27, 2020, at 14:07, Anthony Raymond <<a href="mailto:raymonda@fusion.gat.com" class="">raymonda@fusion.gat.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="">Hello all,<br class=""><br class="">Thank you in advance for the help!<br class=""><br class="">I am simply running the LaserSlab and want to keep track of the Biermann battery magnetic field induced by the laser-plasma interaction.<br class=""><br class="">Taking the advice in the manual, I added the following lines to the top of my example.par script:<br class=""><br class="">hy_useBiermann = .true.<br class="">hy_biermannSource = .true.<br class="">conserveAngField =.true.<br class="">shockDetect = .true.<br class=""><br class="">and added +usm3t to the setup script (removing +uhd3t):<br class=""><br class="">./setup -auto LaserSlab -2d +cylindrical -nxb=16 -nyb=16 +hdf5typeio species=cham,targ +mtmmmt +laser +mgd +usm3t mgd_meshgroups=6 -parfile=example.par<br class=""><br class="">At the bottom of the example.par file, I need to somehow tell FLASH to output the magnetic field components. From the manual, it seems like this should be done by adding:<br class=""><br class=""><br class="">plot_var_10 = "grbx"<br class="">plot_var_11 = "grby"<br class="">plot_var_12 = "grbz"<br class=""><br class=""></div></div></blockquote><div><br class=""></div><div>Continuing for purposes of caution for you…. I think this is true if you’re using the hybrid solver for a combo with PIC usage. Re: section 20.1.2.3. Is that what you want to use?</div><div><br class=""></div><div>I would recommend trying:</div><div><br class=""></div><div><font face="CMUTypewriter-Regular" class="">plot_var_10 <span class="Apple-tab-span" style="white-space: pre;"> </span>= “magx”</font></div><div><font face="CMUTypewriter-Regular" class="">plot_var_11<span class="Apple-tab-span" style="white-space:pre"> </span>= “magy”</font></div><div><font face="CMUTypewriter-Regular" class="">plot_var_12<span class="Apple-tab-span" style="white-space: pre;"> </span>= “magz”</font></div><br class="">instead if using the hybrid version of the code isn’t your original intent right now. You’ll probably want to assign those<font face="CMUTypewriter-Regular" class=""> gr*</font> variables in the <i class="">Config</i> file, as well as learn how to use that component of the code/learn what limitations it may have. I’ve never tried to use the hybrid stuff, so someone else may wanna chime in.</div><div><br class=""></div><div>You can also try looking at the “<font face="CMUTypewriter-Regular" class="">*chk*</font>” or checkpoint files. They store all of the UNK in there. They’re very large files though, so it is often suggested to not print so many. That means that both <font face="CMUTypewriter-Regular" class="">mag*</font> and <font face="CMUTypewriter-Regular" class="">gr*</font> should be stored in there (<font face="CMUTypewriter-Regular" class="">gr*</font> only if associated hybrid units/modules are also used).</div><div><br class=""><blockquote type="cite" class=""><div class=""><div class=""><br class="">I let the simulation run, and am trying to find the magnetic field data in the resulting hdf5 outputs. However, they don't appear to be in there. If I run in h5info(filename) in matlab, I find the datasets for density, temperature, etc., but no magnetic field info.<br class=""><br class="">Could someone please suggest what I might be doing incorrectly?<br class=""><br class="">I've attached the par file that I used to this email.<br class=""></div></div></blockquote><div><br class=""></div><div><br class=""></div><div>Correct me if I am wrong but from the looks of your <i class="">example.par </i>you may not printing any checkpoint files (sorry it is very hot and I don’t have AC so my brain is fried, almost literally).</div><div><br class=""></div><div><font face="CMUTypewriter-Regular" class="">.</font></div><div><font face="CMUTypewriter-Regular" class="">.</font></div><div><font face="CMUTypewriter-Regular" class="">.</font></div><div><div><font face="CMUTypewriter-Regular" class="">### Checkpoint Options ###</font></div><div><font face="CMUTypewriter-Regular" class="">checkpointFileIntervalTime = 1.0</font></div><div><font face="CMUTypewriter-Regular" class="">checkpointFileIntervalStep = 1000</font></div><div><font face="CMUTypewriter-Regular" class=""><br class=""></font></div><div><font face="CMUTypewriter-Regular" class="">### Plot Options ###</font></div><div><font face="CMUTypewriter-Regular" class="">plotFileNumber = 0</font></div><div><font face="CMUTypewriter-Regular" class="">plotFileIntervalStep = 100</font></div><div><font face="CMUTypewriter-Regular" class="">plotFileIntervalTime = 0.01e-09</font></div><div><font face="CMUTypewriter-Regular" class="">.</font></div><div><font face="CMUTypewriter-Regular" class="">.</font></div><div><font face="CMUTypewriter-Regular" class="">.</font></div><div><font face="CMUTypewriter-Regular" class="">tmax = 2.0e-09</font></div></div><div><br class=""></div><div>How many time steps did the simulation take? Did it make it to a checkpoint? You can look at the UNK variables that are being used using h5ls or VisIt. </div><br class=""><blockquote type="cite" class=""><div class=""><div class=""><br class="">Thanks and all the best,<br class="">Tony<br class=""><span id="cid:C1FADD0A-661B-4E81-AB06-ACA43CEBBB34@home"><example.par></span></div></div></blockquote><br class=""></div><div><br class=""></div><div><div><div class="">With washed hands,</div><div class="">Marissa</div></div><div><font face="monospace" size="1" color="#000000" class=""><br class=""></font></div><div><font face="monospace" size="1" color="#000000" class=""><br class=""></font></div><div><font face="monospace" size="1" color="#000000" class="">%———————————————————%</font><div class=""><font face="monospace" size="1" color="#000000" class="">Marissa B. P. Adams</font></div><div class=""><font face="monospace" size="1" color="#000000" class="">(she/her/hers)</font></div><div class=""><font face="monospace" size="1" color="#000000" class="">Phd Candidate, University of Rochester</font></div><div class=""><b class="" style="font-family: monospace; font-size: x-small;">E-mail:</b><span class="" style="font-family: monospace; font-size: x-small;"> <a href="mailto:madams@pas.rochester.edu" target="_blank" class="">madams@pas.rochester.edu</a></span><br class=""></div><div class=""><font face="monospace" size="1" color="#000000" class=""><b class="">Website:</b> <a href="http://www.pas.rochester.edu/~madams" target="_blank" class="">https://www.pas.rochester.edu/~madams</a></font></div><div class=""><font face="monospace" color="#000000" size="1" class=""><b class="">Twitter:</b> <a href="https://twitter.com/mbpadams" target="_blank" class="">https://twitter.com/mbpadams</a></font></div><div class=""><font color="#000000" face="monospace" size="1" class=""><b class="">Current Location:</b></font></div><div class=""><font color="#000000" face="monospace" size="1" class="">My 400 sq. ft. apartment</font></div><div class=""><font color="#000000" face="monospace" size="1" class=""><strike class="">371 Bausch and Lomb Hall</strike></font></div><div class=""><font color="#000000" face="monospace" size="1" class=""><strike class="">University of Rochester</strike></font></div><div class=""><font color="#000000" face="monospace" size="1" class=""><strike class="">Rochester, NY 14627</strike></font></div></div></div><br class=""></div></body></html>