gray-scott

This code has moved to pnorbert/adiosvm and will be maintained there

This is a 3D 7-point stencil code to simulate the following Gray-Scott reaction diffusion model:

u_t = Du * u_xx - u * v^2 + F * (1 - u)
v_t = Dv * v_xx + v * v^2 - (F + k) * v

How to build

Make sure MPI and ADIOS2 are installed.

$ cmake .
$ make

How to run

$ mpiexec -np 8 ./grayscott settings.json
========================================
grid:             64x64x64
steps:            3000
plotgap:          20
F:                0.02
k:                0.048
dt:               1
Du:               0.2
Dv:               0.1
noise:            0.01
output:           gray_scott.bp
adios_config:     adios2_config.xml
decomposition:    2x2x2
grid per process: 32x32x32
========================================
Writing step: 0
Writing step: 20
Writing step: 40
Writing step: 60
Writing step: 80
Writing step: 100
...

How to change the parameters

Edit settings.json to change the parameters for the simulation.

Key	Description
L	Size of global array (L x L x L cube)
Du	Diffusion coefficient of U
Dv	Diffusion coefficient of V
F	Feed rate of U
k	Kill rate of V
dt	Timestep
steps	Total number of steps to simulate
plotgap	Number of steps between output
noise	Amount of noise to inject
output	Output file/stream name
adios_config	ADIOS2 XML file name

Decomposition is automatically determined by MPI_Dims_create.