In Situ Python Analysis: Plummer - hyschive/gamer-fork GitHub Wiki

This test problem Plummer demonstrates the in situ Python analysis feature in GAMER.

1. Install the required packages for this demo.

• libyt and yt_libyt: the in situ analysis library and its yt frontend.

• yt: the core analysis tool.
• FFTW: needed in this test problem.
• HDF5: this is optional since we are not going to output any data.

2. Generate Makefile with the following options:

   --gravity=true --particle=true --passive=2 --mpi=true --fftw=FFTW2 --libyt=true --libyt_interactive=true

   Also please set the paths FFTW_PATH, MPI_PATH, and LIBYT_PATH in configuration file.

3. Compile the code in the src folder.

   make clean
   make -j 4

   ...
   ...
Compiling GAMER --> Successful!

4. Create a working directory in the bin folder and copy the GAMER executable and Plummer test problem files.

   mkdir Plummer                                       # create a folder for this test
   cd Plummer
   cp -r ../../example/test_problem/Hydro/Plummer/* .  # copy test problem settings
   cp ../../src/gamer .                                # copy GAMER executable

5. In Input__Parameter, set OPT__OUTPUT_TOTAL to 0 since we don't need to dump data to disk in this demo. (If you want to make GAMER dump data snapshots, enable SUPPORT_HDF5 and set HDF5_PATH in Makefile. Keep OPT__OUTPUT_TOTAL to 1.)

   # data dump
   OPT__OUTPUT_TOTAL       0     # output the simulation snapshot: (0=off, 1=HDF5, 2=C-binary) [1]
   

6. In Input__TestProb, set Plummer_Collision to 1 for simulating colliding Plummer clouds.

   Plummer_Collision       1     # (0/1)--> single Plummer cloud/two colliding Plummer clouds
   Plummer_AddColor        1     # assign different colors to different clouds (must turn on Plummer_Collision
                                 # and set NCOMP_PASSIVE_USER to 2 in the Makefile) [0]
   

7. Create a LIBYT_STOP file. This demo assumes libyt is in interactive mode. It will only enter interactive Python prompt if errors occur while running Python codes or it detects the file LIBYT_STOP.

   touch LIBYT_STOP

8. Run GAMER.

   OMPI_MCA_osc=sm,pt2pt mpirun -np 4 ./gamer

9. Results from the inline script.

Inline script inline_script.py:

import yt_libyt
import yt

yt.enable_parallelism()

def yt_inline():
    # Get data
    ds = yt_libyt.libytDataset()

    # Do ProjectionPlot to field Cloud0.
    sz = yt.ProjectionPlot(ds, 'z', ('gamer', 'Cloud0'), center='c')

    # Do ParticlePlot
    par = yt.ParticlePlot(ds, 'particle_position_x', 'particle_position_y', 'particle_mass', center='c')

    if yt.is_root():
        sz.save()
        par.save()

def yt_inline_inputArg( fields ):
    pass

Projection of field Cloud01 along the z-axis:

Particle plot using particle position x and y as axes with particle mass mapped to a colorbar:

10. Since we have run libyt in interactive mode, the program should now pause and wait for user input.

=====================================================================
  Inline Function                              Status         Run
---------------------------------------------------------------------
  * yt_inline                                  success         V
  * yt_inline_inputArg                         success         V
=====================================================================
>>>

11. You can explore interactive prompt or simply press Ctrl + C to shut down the process.