README

Fluctuating Hydrodynamics of Reaction-Diffusion Systems
Authors: Andy J. Nonaka, Changho Kim (CCSE, Lawrence Berkeley Laboratory) and
         Aleksandar Donev (Courant Institute, NYU)
Last updated: April 14st, 2017

These codes use the BoxLib framework to develop a fluctuating hydrodynamics
code for simulating stochastic reaction-diffusion systems. Rather than using a
Langevin description based on Gaussian white noise, reactions are treated in an
equivalent manner to the reaction-diffusion master equation description.

Details can be found in the paper (see doc/FHD_ReactDiff.pdf):
1. "Stochastic Simulation of Reaction-Diffusion Systems: A Fluctuating-
    Hydrodynamics Approach", 
    C. Kim, A.J. Nonaka, J.B. Bell, A.L. Garcia, A. Donev,
    J. Chem. Phys. 146, 124110 (2017) [ArXiv: 1612.07238].

To compile the code, you need to also download the Fortran BoxLib library from
https://github.com/BoxLib-Codes/BoxLib

The executable codes are in the directory exec. Edit the makefile in
exec/test/GNUMakefile
and then do "make" to build the code.

Example input files are provided in the directory exec:
- inputs_Schlogl_1d is the steady state Schlogl model example described in 
   Section V.A in Ref. [1]
- inputs_BPM_2d is the Turing-like pattern formation example described in
   Section V.B in Ref. [1]
- inputs_chemical_wave_3d is the spherical chemical wave propagation described
   in Section V.C in Ref. [1]

You can run these examples by providing the input filename after the executable,
for example:
./main.Linux.gfortran.mpi.exe inputs_Schlogl_1d
mpiexec -n 4 ./main.Linux.gfortran.mpi.exe inputs_BPM_2d

For the visulazation of results (BPM_2d and chemical_wave_3d), see Section
"Visualization Using VisIt" in BoxLib User's Guide.

Caveats: 
1) The code used to perform structure factor analysis is not included in this 
    distribution.