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

Thu May 28 09:14:29 EDT 2020

Thanks Shu. Glad it worked out Tony. I recommend that you familiarize yourself with the information in Chapter 3 (just for good measure) and (especially) Chapter 9 of the user manual as understanding Flash’s file I/O and outputs were crucial to solving the issue.

> On May 27, 2020, at 16:26, Anthony Raymond <raymonda at fusion.gat.com> wrote:
> 
> 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 <mailto:shz133 at eng.ucsd.edu>>
> To: "Anthony Raymond" <raymonda at fusion.gat.com <mailto: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 <mailto: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><mailto: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> <mailto: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> <mailto: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 <mailto: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
>> 
>> 
>> %———————————————————%
>> Marissa B. P. Adams
>> (she/her/hers)
>> Phd Candidate, University of Rochester
>> E-mail: madams at pas.rochester.edu <mailto:madams at pas.rochester.edu> <mailto:madams at pas.rochester.edu <mailto:madams at pas.rochester.edu>> <mailto:madams at pas.rochester.edu <mailto:madams at pas.rochester.edu> <mailto:madams at pas.rochester.edu <mailto:madams at pas.rochester.edu>>>
>> Website: https://www.pas.rochester.edu/~madams <https://www.pas.rochester.edu/~madams><https://www.pas.rochester.edu/~madams <https://www.pas.rochester.edu/~madams>> <http://www.pas.rochester.edu/~madams <http://www.pas.rochester.edu/~madams><http://www.pas.rochester.edu/~madams <http://www.pas.rochester.edu/~madams>>>
>> Twitter: https://urldefense.proofpoint.com/v2/url?u=https-3A__twitter.com_mbpadams&d=DwIFaQ&c=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU&r=wlIj2Wk5AYR_utqRRqN2OpI1nykd7sy-UZesSWABUiw&m=4SbFFgmGwlfZ3yJpty90gcWi9WiPDLZz7cm3TubTmNI&s=1yRBceFQO7Kd83QTCxOTU1syoCW6CVkLb-COJaDM24Y&e= <https://urldefense.proofpoint.com/v2/url?u=https-3A__twitter.com_mbpadams&d=DwIFaQ&c=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU&r=wlIj2Wk5AYR_utqRRqN2OpI1nykd7sy-UZesSWABUiw&m=4SbFFgmGwlfZ3yJpty90gcWi9WiPDLZz7cm3TubTmNI&s=1yRBceFQO7Kd83QTCxOTU1syoCW6CVkLb-COJaDM24Y&e=>  <https://urldefense.proofpoint.com/v2/url?u=https-3A__twitter.com_mbpadams&d=DwIFaQ&c=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU&r=wlIj2Wk5AYR_utqRRqN2OpI1nykd7sy-UZesSWABUiw&m=4SbFFgmGwlfZ3yJpty90gcWi9WiPDLZz7cm3TubTmNI&s=1yRBceFQO7Kd83QTCxOTU1syoCW6CVkLb-COJaDM24Y&e= <https://urldefense.proofpoint.com/v2/url?u=https-3A__twitter.com_mbpadams&d=DwIFaQ&c=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU&r=wlIj2Wk5AYR_utqRRqN2OpI1nykd7sy-UZesSWABUiw&m=4SbFFgmGwlfZ3yJpty90gcWi9WiPDLZz7cm3TubTmNI&s=1yRBceFQO7Kd83QTCxOTU1syoCW6CVkLb-COJaDM24Y&e=> > <https://urldefense.proofpoint.com/v2/url?u=https-3A__twitter.com_mbpadams&d=DwIFaQ&c=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU&r=wlIj2Wk5AYR_utqRRqN2OpI1nykd7sy-UZesSWABUiw&m=4SbFFgmGwlfZ3yJpty90gcWi9WiPDLZz7cm3TubTmNI&s=1yRBceFQO7Kd83QTCxOTU1syoCW6CVkLb-COJaDM24Y&e= <https://urldefense.proofpoint.com/v2/url?u=https-3A__twitter.com_mbpadams&d=DwIFaQ&c=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU&r=wlIj2Wk5AYR_utqRRqN2OpI1nykd7sy-UZesSWABUiw&m=4SbFFgmGwlfZ3yJpty90gcWi9WiPDLZz7cm3TubTmNI&s=1yRBceFQO7Kd83QTCxOTU1syoCW6CVkLb-COJaDM24Y&e=>  <https://urldefense.proofpoint.com/v2/url?u=https-3A__twitter.com_mbpadams&d=DwIFaQ&c=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU&r=wlIj2Wk5AYR_utqRRqN2OpI1nykd7sy-UZesSWABUiw&m=4SbFFgmGwlfZ3yJpty90gcWi9WiPDLZz7cm3TubTmNI&s=1yRBceFQO7Kd83QTCxOTU1syoCW6CVkLb-COJaDM24Y&e= <https://urldefense.proofpoint.com/v2/url?u=https-3A__twitter.com_mbpadams&d=DwIFaQ&c=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU&r=wlIj2Wk5AYR_utqRRqN2OpI1nykd7sy-UZesSWABUiw&m=4SbFFgmGwlfZ3yJpty90gcWi9WiPDLZz7cm3TubTmNI&s=1yRBceFQO7Kd83QTCxOTU1syoCW6CVkLb-COJaDM24Y&e=> >>
>> Current Location:
>> My 400 sq. ft. apartment
>> 371 Bausch and Lomb Hall
>> University of Rochester
>> Rochester, NY 14627

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://flash.rochester.edu/pipermail/flash-users/attachments/20200528/f0651d2d/attachment-0001.htm>