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

Thu May 28 17:39:08 EDT 2020

Hi Anthony,

This issue with Biermann-generated B-fields should be solved just by
changing this line of your *example.par* file:
*hy_useBiermann = .true.  ---->    *use_Biermann = .true.

Best,

Benjamin Khiar.

Le jeu. 28 mai 2020 à 15:11, Anthony Raymond <raymonda at fusion.gat.com> a
écrit :

> Hello all,
>
> 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.
>
> The .par file is attached to this email, and the setup command used was:
>
> ./setup -auto magnetoHD/LaserSlab -2d +cylindrical -nxb=16 -nyb=16
> +hdf5typeio species=cham,targ +mtmmmt +laser +mgd +usm3t mgd_meshgroups=6
> -parfile=example.par
>
> 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.
>
> 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.
>
> Just curious if someone wouldn't mind pointing me in the right direction.
>
> Thanks and 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=
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> <
> 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
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