<div dir="ltr"><div dir="ltr">Hi Anthony,<div><br></div><div>This issue with Biermann-generated B-fields should be solved just by changing this line of your <b>example.par</b> file:</div><div><b><span style="background-color:rgb(255,255,255)"><font color="#ff0000">hy_useBiermann = .true.</font></span> ----> </b><font color="#0000ff">use_Biermann = .true.</font><b><br></b></div><div><br></div><div>Best,</div><div><br></div><div>Benjamin Khiar.</div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Le jeu. 28 mai 2020 à 15:11, Anthony Raymond <<a href="mailto:raymonda@fusion.gat.com">raymonda@fusion.gat.com</a>> a écrit :<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hello all,<br>
<br>
If I could resurrect this subject, I'm wondering if someone wouldn't mind guiding me in the right direction regarding a new issue which cropped up: despite activating the Biermann battery calculations and outputting the magnetic field outputs, the outputs are filled with zeros for all components over all time throughout the laserslab simulation.<br>
<br>
The .par file is attached to this email, and the setup command used was:<br>
<br>
./setup -auto magnetoHD/LaserSlab -2d +cylindrical -nxb=16 -nyb=16 +hdf5typeio species=cham,targ +mtmmmt +laser +mgd +usm3t mgd_meshgroups=6 -parfile=example.par<br>
<br>
This represents a simple series of modifications to the original LaserSlab example with the goal of calculating and outputting the magnetic field induced by non-parallel density and temperature gradients, for educational purposes. The LaserSlab directory was copied into the magnetoHD directory as well and run from that location, following advice from another FLASH user.<br>
<br>
It was my expectation to see an azimuthal magnetic field surrounding the laser/plasma interaction spot, but I suppose I'm missing something in setting up the simulation.<br>
<br>
Just curious if someone wouldn't mind pointing me in the right direction.<br>
<br>
Thanks and all the best,<br>
Tony<br>
<br>
<br>
<br>
----- Original Message -----<br>
> From: "shz133" <<a href="mailto:shz133@eng.ucsd.edu" target="_blank">shz133@eng.ucsd.edu</a> <mailto:<a href="mailto:shz133@eng.ucsd.edu" target="_blank">shz133@eng.ucsd.edu</a>>><br>
> To: "Anthony Raymond" <<a href="mailto:raymonda@fusion.gat.com" target="_blank">raymonda@fusion.gat.com</a> <mailto:<a href="mailto:raymonda@fusion.gat.com" target="_blank">raymonda@fusion.gat.com</a>>><br>
> Sent: Wednesday, May 27, 2020 1:06:18 PM<br>
> Subject: Re: [FLASH-USERS] How can I modify the LaserSlab example to calculate B fields?<br>
> <br>
> Hi Tony, <br>
> <br>
> Have you checked the chk file? Did you see magx, magy, magp? <br>
> <br>
> Shu<br>
> <br>
>> On May 27, 2020, at 12:39 PM, Anthony Raymond <<a href="mailto:raymonda@fusion.gat.com" target="_blank">raymonda@fusion.gat.com</a> <mailto:<a href="mailto:raymonda@fusion.gat.com" target="_blank">raymonda@fusion.gat.com</a>>> wrote:<br>
>> <br>
>> Thanks for the reply. I took your advice and copied my entire LaserSlab directory into the magnetoHD directory, then ran<br>
>> <br>
>> ./setup -auto magnetoHD/LaserSlab -2d +cylindrical -nxb=16 -nyb=16 +hdf5typeio species=cham,targ +mtmmmt +laser +mgd +usm3t mgd_meshgroups=6 -parfile=example.par<br>
>> <br>
>> then CD's into object, ran "make", then ran the simulation.<br>
>> <br>
>> However, when I run h5info in matlab on the first hdf5 file that is generated, I don't see any entries referencing the magnetic field.<br>
>> <br>
>> I wonder if I'm still doing something incorrectly?<br>
>> <br>
>> Thanks and all the best,<br>
>> Tony<br>
>> <br>
>> <br>
>> ----- Original Message -----<br>
>> From: "Marissa B. P. Adams" <<a href="mailto:marissa@flash.uchicago.edu" target="_blank">marissa@flash.uchicago.edu</a> <mailto:<a href="mailto:marissa@flash.uchicago.edu" target="_blank">marissa@flash.uchicago.edu</a>><mailto:<a href="mailto:marissa@flash.uchicago.edu" target="_blank">marissa@flash.uchicago.edu</a> <mailto:<a href="mailto:marissa@flash.uchicago.edu" target="_blank">marissa@flash.uchicago.edu</a>>>><br>
>> To: "Anthony Raymond" <<a href="mailto:raymonda@fusion.gat.com" target="_blank">raymonda@fusion.gat.com</a> <mailto:<a href="mailto:raymonda@fusion.gat.com" target="_blank">raymonda@fusion.gat.com</a>> <mailto:<a href="mailto:raymonda@fusion.gat.com" target="_blank">raymonda@fusion.gat.com</a> <mailto:<a href="mailto:raymonda@fusion.gat.com" target="_blank">raymonda@fusion.gat.com</a>>>><br>
>> Cc: "flash-users" <<a href="mailto:flash-users@flash.uchicago.edu" target="_blank">flash-users@flash.uchicago.edu</a> <mailto:<a href="mailto:flash-users@flash.uchicago.edu" target="_blank">flash-users@flash.uchicago.edu</a>> <mailto:<a href="mailto:flash-users@flash.uchicago.edu" target="_blank">flash-users@flash.uchicago.edu</a> <mailto:<a href="mailto:flash-users@flash.uchicago.edu" target="_blank">flash-users@flash.uchicago.edu</a>>>><br>
>> Sent: Wednesday, May 27, 2020 11:34:51 AM<br>
>> Subject: Re: [FLASH-USERS] How can I modify the LaserSlab example to calculate B fields?<br>
>> <br>
>> Hi Anthony,<br>
>> <br>
>> ******First: Did you make a copy of the LaserSlab problem in magnetoHD ? See section 34.2 in the user manual for examples. Try that again but then do effectively the same setup script you did:<br>
>> <br>
>> ./setup -auto magnetoHD/LaserSlab -2d +cylindrical -nxb=16 -nyb=16 +hdf5typeio species=cham,targ +mtmmmt +laser +mgd +usm3t mgd_meshgroups=6 -parfile=example.par<br>
>> <br>
>>> On May 27, 2020, at 14:07, Anthony Raymond <<a href="mailto:raymonda@fusion.gat.com" target="_blank">raymonda@fusion.gat.com</a> <mailto:<a href="mailto:raymonda@fusion.gat.com" target="_blank">raymonda@fusion.gat.com</a>>> wrote:<br>
>>> <br>
>>> Hello all,<br>
>>> <br>
>>> Thank you in advance for the help!<br>
>>> <br>
>>> I am simply running the LaserSlab and want to keep track of the Biermann battery magnetic field induced by the laser-plasma interaction.<br>
>>> <br>
>>> Taking the advice in the manual, I added the following lines to the top of my example.par script:<br>
>>> <br>
>>> hy_useBiermann = .true.<br>
>>> hy_biermannSource = .true.<br>
>>> conserveAngField =.true.<br>
>>> shockDetect = .true.<br>
>>> <br>
>>> and added +usm3t to the setup script (removing +uhd3t):<br>
>>> <br>
>>> ./setup -auto LaserSlab -2d +cylindrical -nxb=16 -nyb=16 +hdf5typeio species=cham,targ +mtmmmt +laser +mgd +usm3t mgd_meshgroups=6 -parfile=example.par<br>
>>> <br>
>>> 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>
>>> <br>
>>> <br>
>>> plot_var_10 = "grbx"<br>
>>> plot_var_11 = "grby"<br>
>>> plot_var_12 = "grbz"<br>
>>> <br>
>> <br>
>> 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?<br>
>> <br>
>> I would recommend trying:<br>
>> <br>
>> plot_var_10 = “magx”<br>
>> plot_var_11 = “magy”<br>
>> plot_var_12 = “magz”<br>
>> <br>
>> instead if using the hybrid version of the code isn’t your original intent right now. You’ll probably want to assign those gr* variables in the Config 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.<br>
>> <br>
>> You can also try looking at the “*chk*” 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 mag* and gr* should be stored in there (gr* only if associated hybrid units/modules are also used).<br>
>> <br>
>>> <br>
>>> 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>
>>> <br>
>>> Could someone please suggest what I might be doing incorrectly?<br>
>>> <br>
>>> I've attached the par file that I used to this email.<br>
>> <br>
>> <br>
>> Correct me if I am wrong but from the looks of your example.par 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).<br>
>> <br>
>> .<br>
>> .<br>
>> .<br>
>> ### Checkpoint Options ###<br>
>> checkpointFileIntervalTime = 1.0<br>
>> checkpointFileIntervalStep = 1000<br>
>> <br>
>> ### Plot Options ###<br>
>> plotFileNumber = 0<br>
>> plotFileIntervalStep = 100<br>
>> plotFileIntervalTime = 0.01e-09<br>
>> .<br>
>> .<br>
>> .<br>
>> tmax = 2.0e-09<br>
>> <br>
>> 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. <br>
>> <br>
>>> <br>
>>> Thanks and all the best,<br>
>>> Tony<br>
>>> <example.par><br>
>> <br>
>> <br>
>> With washed hands,<br>
>> Marissa<br>
>> <br>
>> <br>
>> %———————————————————%<br>
>> Marissa B. P. Adams<br>
>> (she/her/hers)<br>
>> Phd Candidate, University of Rochester<br>
>> E-mail: <a href="mailto:madams@pas.rochester.edu" target="_blank">madams@pas.rochester.edu</a> <mailto:<a href="mailto:madams@pas.rochester.edu" target="_blank">madams@pas.rochester.edu</a>> <mailto:<a href="mailto:madams@pas.rochester.edu" target="_blank">madams@pas.rochester.edu</a> <mailto:<a href="mailto:madams@pas.rochester.edu" target="_blank">madams@pas.rochester.edu</a>>> <mailto:<a href="mailto:madams@pas.rochester.edu" target="_blank">madams@pas.rochester.edu</a> <mailto:<a href="mailto:madams@pas.rochester.edu" target="_blank">madams@pas.rochester.edu</a>> <mailto:<a href="mailto:madams@pas.rochester.edu" target="_blank">madams@pas.rochester.edu</a> <mailto:<a href="mailto:madams@pas.rochester.edu" target="_blank">madams@pas.rochester.edu</a>>>><br>
>> Website: <a href="https://www.pas.rochester.edu/~madams" rel="noreferrer" target="_blank">https://www.pas.rochester.edu/~madams</a> <<a href="https://www.pas.rochester.edu/~madams" rel="noreferrer" target="_blank">https://www.pas.rochester.edu/~madams</a>><<a href="https://www.pas.rochester.edu/~madams" rel="noreferrer" target="_blank">https://www.pas.rochester.edu/~madams</a> <<a href="https://www.pas.rochester.edu/~madams" rel="noreferrer" target="_blank">https://www.pas.rochester.edu/~madams</a>>> <<a href="http://www.pas.rochester.edu/~madams" rel="noreferrer" target="_blank">http://www.pas.rochester.edu/~madams</a> <<a href="http://www.pas.rochester.edu/~madams" rel="noreferrer" target="_blank">http://www.pas.rochester.edu/~madams</a>><<a href="http://www.pas.rochester.edu/~madams" rel="noreferrer" target="_blank">http://www.pas.rochester.edu/~madams</a> <<a href="http://www.pas.rochester.edu/~madams" rel="noreferrer" target="_blank">http://www.pas.rochester.edu/~madams</a>>>><br>
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>> Current Location:<br>
>> My 400 sq. ft. apartment<br>
>> 371 Bausch and Lomb Hall<br>
>> University of Rochester<br>
>> Rochester, NY 14627</blockquote></div></div>