[FLASH-USERS] Output files

Tue May 19 00:34:18 EDT 2020

Hi, 

thank you all, now it works! 

Best, 

Petr 

On 2020-05-18 18:12, Ryan Farber wrote:

> Just a quick follow up on Marissa's terrific explanation which briefly mentioned handling HDF5 outputs using VisIt, IDL, python, etc: I personally recommend the python package yt. It makes processing FLASH simulations as easy as 
> 
> 1) import yt 
> 2) ds = yt.load("YOUR_HDF5_FILE") 
> 3) ad = ds.all_data() # or subset of data if you prefer, many options available 
> https://yt-project.org/
> 
> Best,
> 
> -------- 
> Ryan 
> 
> On Mon, May 18, 2020 at 9:16 AM Marissa B. P. Adams <marissa at flash.uchicago.edu> wrote: 
> If you would like output information for each time step, you can use the routine Simulation_adjustEvolution.F90. 
> 
> If you open any old Simulation_adjustEvolution.F90 from an object directory you will find that it is effectively empty. The routine takes in the number of blocks as an integer, the block list, current cycle number, time step, and current simulation time. From that you can tell that the purpose of this routine is to acquire or change block information for each time step, hence its name.  
> 
> Assuming your routine is empty, you may want to do the following: 
> 
> 1. Loop through the number of blocks. 
> 2. Call Grid_getBlkIndexLimits, Grid_getCellCoords, Grid_getBlkPtr, and Grid_getDeltas. Some of these are crucial (Grid_getBlkIndexLimits, Grid_getBlkPtr) if you want to a access the blkPtr, or, as Ryan said, the UNK. The other routines are helpful if you would like to a access the coordinates and their differences, in the case that you may want to preform an integration. If you want to get the coordinates make sure you allocate, initialize the arrays, and then deallocate after the step (3) series of loops. 
> 3. Then you will want to loop over all three block limits for each i, j,k direction.

> 4. After this third step you can then assign your UNK to variables and preform calculations that may be grid based, or require special calculations.

> 5. Don't forget to close the four essential loops, and deallocate allocated arrays, etc.

You can find examples of what I have just described in various parts of
the code. I tried to provide the "shape" of the code, which can be
helpful, in the formatting. If you want to create new UNK variables make
sure you follow the appropriate procedure to do so... edit the
configuration file, initialize it, etc. You can then access it in
whatever routine. 

Around this whole operation you could then preform the standard methods
of file I/O or whatever you please, or within it. Whether it is a ._dat_
file or a ._txt_ file, whatever you want. 

If you're looking to access _all_ block to cell information for each UNK
though I would really recommend just sticking to HDF5, using VisIt, IDL,
or python's associated libraries.... Honestly the idea of any other
format gives me nightmares for post processing purposes... and ASCII
file for each output dump would probably eat your storage alive.  

I know that Flash also has chombo capabilities but I am pretty certain
that part of the code is not maintained well. 

%--------------------------------------% 
Marissa B. P. Adams 
(she/her/hers) 
Phd Candidate, University of Rochester 
E-MAIL: madams at pas.rochester.edu 
WEBSITE: https://www.pas.rochester.edu/~madams [1] 
TWITTER: https://twitter.com/mbpadams 
CURRENT LOCATION: 
My 400 sq. ft studio apartment 
371 Bausch and Lomb Hall 
University of Rochester 
Rochester, NY 14627 

> On May 17, 2020, at 18:43, Ryan Farber <rjfarber at umich.edu> wrote: 
> 
> Hi Petr, 
> 
> While I have not modified the dat file before, note that it should be easy to write to stdout. 
> For example, if you're debugging and want to know the minimum and maximum density before your code crashes you can do 
> ========== 
> !! some flash file 
> use physicaldata, ONLY : unk 
> use Driver_data, ONLY : dr_globalMe ! or you can use pt_globalMe if you're in a Particle file and want to stay modular for example 
> 
> if (dr_globalMe == MASTER_PE) then 
> write(*,*) "max dens: ", maxval(unk(DENS_VAR,:,:,:,:)) ! unk has indices to variables, i, j, k, blocks 
> write(*,*) "min dens: ", minval(unk(DENS_VAR,:,:,:,:)) 
> endif 
> ========= 
> Note that it's probably safer (especially for getting the minimum values, I don't remember if the above will just yield zero) to loop over list of blocks to find the maximum, minimum. Or do an MPI_ALLREDUCE. Many options :) 
> 
> Best,
> 
> -------- 
> Ryan 
> 
> On Sun, May 17, 2020 at 2:04 AM petrk <petrk at physics.muni.cz> wrote: 
> 
>> Hello users, 
>> 
>> Is there any possibility to write output data (for example for some particular quantities - density, pressure, etc.) explicitly to the ordinary .dat file and not to hdf? 
>> 
>> Thanks a lot, 
>> 
>> Petr

Links:
------
[1] http://www.pas.rochester.edu/~madams
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