[FLASH-USERS] How can I modify the LaserSlab example to calculate B fields?

Wed May 27 16:26:07 EDT 2020

Ah, thanks for the help everyone.

So the problem is that I was using:

plot_var_8           = "grbx"
plot_var_9           = "grby"
plot_var_10          = "grbz"

But the correct variable names to enter were:

plot_var_8           = "magx"
plot_var_9           = "magy"
plot_var_10          = "magz"

Doing this results in the expected output. Please consider this issue resolved.

All the best,
Tony

----- Original Message -----
From: "shz133" <shz133 at eng.ucsd.edu>
To: "Anthony Raymond" <raymonda at fusion.gat.com>
Sent: Wednesday, May 27, 2020 1:06:18 PM
Subject: Re: [FLASH-USERS] How can I modify the LaserSlab example to calculate B fields?

Hi Tony, 

Have you checked the chk file? Did you see magx, magy, magp? 

Shu

> On May 27, 2020, at 12:39 PM, Anthony Raymond <raymonda at fusion.gat.com> wrote:
> 
> Thanks for the reply. I took your advice and copied my entire LaserSlab directory into the magnetoHD directory, then ran
> 
> ./setup -auto magnetoHD/LaserSlab -2d +cylindrical -nxb=16 -nyb=16 +hdf5typeio species=cham,targ +mtmmmt +laser +mgd +usm3t mgd_meshgroups=6 -parfile=example.par
> 
> then CD's into object, ran "make", then ran the simulation.
> 
> 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.
> 
> I wonder if I'm still doing something incorrectly?
> 
> Thanks and all the best,
> Tony
> 
> 
> ----- Original Message -----
> From: "Marissa B. P. Adams" <marissa at flash.uchicago.edu <mailto:marissa at flash.uchicago.edu>>
> To: "Anthony Raymond" <raymonda at fusion.gat.com <mailto:raymonda at fusion.gat.com>>
> Cc: "flash-users" <flash-users at flash.uchicago.edu <mailto:flash-users at flash.uchicago.edu>>
> Sent: Wednesday, May 27, 2020 11:34:51 AM
> Subject: Re: [FLASH-USERS] How can I modify the LaserSlab example to calculate B fields?
> 
> Hi Anthony,
> 
> ******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:
> 
> ./setup -auto magnetoHD/LaserSlab -2d +cylindrical -nxb=16 -nyb=16 +hdf5typeio species=cham,targ +mtmmmt +laser +mgd +usm3t mgd_meshgroups=6 -parfile=example.par
> 
>> On May 27, 2020, at 14:07, Anthony Raymond <raymonda at fusion.gat.com> wrote:
>> 
>> Hello all,
>> 
>> Thank you in advance for the help!
>> 
>> I am simply running the LaserSlab and want to keep track of the Biermann battery magnetic field induced by the laser-plasma interaction.
>> 
>> Taking the advice in the manual, I added the following lines to the top of my example.par script:
>> 
>> hy_useBiermann = .true.
>> hy_biermannSource = .true.
>> conserveAngField =.true.
>> shockDetect = .true.
>> 
>> and added +usm3t to the setup script (removing +uhd3t):
>> 
>> ./setup -auto LaserSlab -2d +cylindrical -nxb=16 -nyb=16 +hdf5typeio species=cham,targ +mtmmmt +laser +mgd +usm3t mgd_meshgroups=6 -parfile=example.par
>> 
>> 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:
>> 
>> 
>> plot_var_10          = "grbx"
>> plot_var_11          = "grby"
>> plot_var_12          = "grbz"
>> 
> 
> 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?
> 
> I would recommend trying:
> 
> plot_var_10 	= “magx”
> plot_var_11	= “magy”
> plot_var_12	= “magz”
> 
> 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.
> 
> 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).
> 
>> 
>> 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.
>> 
>> Could someone please suggest what I might be doing incorrectly?
>> 
>> I've attached the par file that I used to this email.
> 
> 
> 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).
> 
> .
> .
> .
> ### Checkpoint Options  ###
> checkpointFileIntervalTime = 1.0
> checkpointFileIntervalStep = 1000
> 
> ### Plot Options ###
> plotFileNumber       = 0
> plotFileIntervalStep = 100
> plotFileIntervalTime = 0.01e-09
> .
> .
> .
> tmax           = 2.0e-09
> 
> 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. 
> 
>> 
>> Thanks and all the best,
>> Tony
>> <example.par>
> 
> 
> With washed hands,
> Marissa
> 
> 
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