[FLASH-USERS] output files: Getting started guide?

[Matthew Turk]

Hi David,

I'd be happy to provide some more guidance on this.  We have a set of
documentation, some tutorials and videos, but it's entirely possible they
aren't tuned to your use case.  We could correspond off-list, and I can use
that to update the yt docs or even prepare videos/tutorials.  I think it's
probably out of scope for the FLASH-USERS mailing list to go through it,
but I could report back once we've worked through it and come up with the
results.

For starters, however, getting the data back in an array of coordinates of
cell centers is straightforward:

ds = yt.load( filename )
ds.r[:]["x"]

and also the same for "y" and "z".  There are vertex arrays too, which I
believe are "x_vertex", "y_vertex" and "z_vertex".  It's appropriately
changed for r, theta, phi as well.

-Matt

On Fri, Oct 6, 2023 at 11:12 AM Blackman David <david.blackman at eli-beams.eu>
wrote:

> Actually to add to the previous question, is there any simple
> documentation on how to process these files? The flash documentation
> doesn't provide a particularly straightforward answer. The yt-project is a
> reasonable choice. I am planning to run a large quantity of flash
> simulations coupled with PIC simulations. For this purpose I would need to
> write some sort of automated script to generate a cartesian or cylindrical
> grid. The yt-project seems like a good place to start, but a simple
> understanding of how to reconstructed the flash grid into an array of
> co-ordinates of vertices would be helpful.
> ------------------------------
> *From:* flash-users <flash-users-bounces at flash.rochester.edu> on behalf
> of Leland Ellison <lee at pacificfusion.energy>
> *Sent:* 06 October 2023 17:42
> *To:* Ryan Farber <rjfarber at umich.edu>
> *Cc:* flash-users at flash.rochester.edu <flash-users at flash.rochester.edu>
> *Subject:* Re: [FLASH-USERS] output files: Getting started guide?
>
> Another good option for visualizing FLASH output is VisIt:
> https://visit-dav.github.io/visit-website/index.html
>
> One hiccup you might encounter is an error when attempting to open FLASH
> files using the default VisIt settings. You can remedy this with either:
> (i) In the Open File menu, look for the  "Open file as type" box and
> choose: FLASH (If this fails, try restarting VisIt. Once the above error
> happens it seems to perpetually fail even if you specify the file type.)
> (ii) If you're launching VisIt from the command line, add the
> argument: -assume_format FLASH
>
> Best,
> Lee
>
> On Fri, Oct 6, 2023 at 6:27 AM Ryan Farber <rjfarber at umich.edu> wrote:
>
> Hi Joe,
>
> 8x8 refers to the number of cells per block.
> The 53 probably refers to the number of blocks.
> Additional details might be in the FLASH user guide.
>
> I'd recommend just using yt. yt is for analysis as well as visualization.
>
> Best,
> --------
> Ryan
>
>
> On Thu, Oct 5, 2023 at 8:05 PM Joe Frisch <joseffrisch at google.com> wrote:
>
> Just getting started with FLASH just got the sedov code (with the default
> parameters) to run, trying to understand the output files.  For example
> there is a hdf5 output file sedov_hdf5_plt_cnt_0000
>
> That contains grid data in 'coordinates"  which has 53 x,y,z locations
>
> There is also "pres' (presumably pressure) , 'temp"
> (presumably temperature)  and desdata.
>
> Those objects are 4-dimensional:   [53,1,8,8]
> where is that defined / described?
> The 53 presumably maps onto the 53 plot coordinates.  But 8X8??  Those
> seem to be either initial or final state, but not in a pattern I can
> decypher
>
> Is the plot file format , or more specifically the fields in the plot file
> defined somewhere?
>
> Maybe this is the wrong approach and I should just use yt?   does yt
> provide access to all the data for analysis or is it just a plotting tool?
>
>
>
>
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