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

Thu May 28 17:40:53 EDT 2020

This shouldn't resolve the issue, but you have 'shockDetect' defined twice
in your par file. The 2nd instance is set to false, so shock detection is
likely turned off. This would cause the Biermann source to be calculated
everywhere, including at shocks, which would potentially lead to
erroneously large values.

Could you also attach your log file so we can at least verify that the run
is using the correct setup, units, and runtime parameters?

On Thu, May 28, 2020 at 3:11 PM Anthony Raymond <raymonda at fusion.gat.com>
wrote:

> 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=
> <
> 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

-- 
Eddie Hansen, PhD
Postdoctoral Associate
University of Rochester
607-341-6126 | Flash Center
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