Diagnostics tool: diag

Post-processing tool for GKV binary output

What is diag?

One difficulty of users may read GKV binary output which are decomposed by MPI. Post-processing program diag helps to read GKV binary output of a desired quantity at a desired time step. Since the read quantity is constructed as a global variable, e.g., phi(-nx:nx,0:global ny,-global nz:global nz-1) (not a local variable decomposed by MPI, phi_local(-nx:nx,0:ny,-nz:nz-1)), users do not need to be conscious of MPI parallelization of GKV. The main program diag_main.f90 calls each diagnostics module out_******.f90, which should be encapsulated so as to avoid interference and misuse. Reading GKV binary file is done by calling diag_rb module in each diagnostics module. Although there are some diagnostics modules implemented, users can design a new diagnostics module by themselves.

How to use diag

Expanding source codes of diag:

• diag/
  • README.md
  • Makefile
  • go.diag (Batch script)
  • backup/ (Makefile and go.diag in some environments)
  • plot_gn/ (Sample plot files for gnuplot)
  • plot_ipynb/ (Sample plot files for python)
  • src
    • diag_header.f90 (Module for setting grid resolutions and MPI processes in GKV)
    • diag_main.f90 (Main program calling each diagnostics module)
    • diag_rb.f90 (Module for reading GKV binary output)
    • diag_******.f90 (Module for other settings)
    • ...
    • out_******.f90 (Module for each diagnostics)
    • ...

How to use diag is in the following steps:

1. Setting parameters in diag/src/diag_header.f90

   %%% DIAG parameters %%%
   integer, parameter :: snum = 1 ! begining of simulation runs
   integer, parameter :: enum = 1 ! end of simulation runs
   !%%%%%%%%%%%%%%%% ! Set run numbers covering diagnosed time range.
   
   !%%% GKV parameters %%%
   integer, parameter :: nxw = 2, nyw = 8
   integer, parameter :: nx = 0, global ny = 5 ! 2/3 de-aliasing rule
   integer, parameter :: global nz = 64, global nv = 24, global nm = 15
   integer, parameter :: nzb = 3, & ! the number of ghost grids in z
                         nvb = 3 ! the number of ghost grids in v and m
   
   integer, parameter :: nprocw = 1, nprocz = 4, nprocv = 2, nprocm = 2, nprocs = 2
   !%%%%%%%%%%%%%%%% ! These should be same as gkvp_header.f90.
   

2. Calling diagnostics modules in diag/src/diag_main.f90

3. Setting the output directory of GKV, DIR, in go.diag

4. Compile & Execution

5. Output data is dumped in $DIR/post/