flashFromTxt

Initialise a 2D FLASH radiation-hydrodynamics simulation from the output of a PIConGPU particle-in-cell simulation.

The workflow has two parts:

 PIConGPU openPMD output            openpmd2txt.py                 FLASH (Test_case)
 (H / e density, energy density) ──► text tables (dens, tele, ──► reads the tables once, broadcasts
                                     tion, x and y axes)          them and interpolates them onto
                                                                   every AMR block at initialisation

The opposite direction, from FLASH back to PIC, is covered by flash2openpmd:

 FLASH checkpoint / plot file       flash2openpmd.py               PIConGPU (or other PIC code)
 (dens, tele, tion, trad, ye)   ──► openPMD HDF5 meshes on a   ──► initial plasma profile
                                    uniform, optionally rotated
                                    2D grid (SI units)

Together they allow a PIC → FLASH → PIC chain, e.g. a short-pulse interaction in PIConGPU, its hydrodynamic expansion in FLASH, and a later PIC simulation on the expanded profile.

Folder	Content
openpmd2txt/	Python script that reads an openPMD series, converts it to FLASH units and writes the text tables. See openpmd2txt/README.md.
Test_case/	A FLASH 4 simulation directory (derived from LaserSlab) with a new sim_initGeom = "fromtxt" mode that reads and interpolates the tables. See Test_case/README.md.
flash2openpmd/	Python script that converts a 2D FLASH checkpoint into an openPMD file (dens, tele, tion, trad, ye) for initialising a PIC simulation, with optional density cutoff, boundary layer and rotation. See flash2openpmd/README.md, including its known limitations.
rosi/	Shell profile (FLASH_rome.sh, goes in ~), Makefile.h (goes in sites/Prototypes/Linux/) and an HDF5 + HYPRE install script for building and running FLASH 4.8 on the rosi cluster. See rosi/README.md.

Quick start

1. Make the tables from a PIConGPU run:

   cd openpmd2txt
   pip install -r requirements.txt
   python openpmd2txt.py -input_file /path/to/simData_%T.bp -output_name MyRun \
          -nx_flash 2400 -ny_flash 800 -smooth -debug
   # -> output/MyRun_{xfile,yfile,dens,tele,tion}.txt

2. Install the test case in your FLASH 4 tree, copy the tables into Test_case/input/, and set sim_inputFilenameRoot = "input/MyRun" in flash.par.

3. Build and run FLASH as usual (see Test_case/README.md for the setup line). On rosi, first install the profile and Makefile.h from rosi/.

4. Back to PIC (optional): convert a FLASH checkpoint to openPMD:

   cd flash2openpmd
   pip install -r requirements.txt
   python flash2openpmd.py -input_file /path/to/run/lasslab_hdf5_chk_0010 \
          -output_file profile_t10 -nx_pic 4800 -ny_pic 4800
   # -> output/profile_t10.h5

There is an example set of tables in Test_case/input/*.txt.gz. It is gzipped to keep the repository small, so decompress it before running:

gunzip -k Test_case/input/*.txt.gz

Licence note

The files in Test_case/ are modified FLASH source files. FLASH is distributed under its own user licence, so make sure anyone you share this repository with is a licensed FLASH user.