Fluctuating Hydrodynamics of Reaction-Diffusion Systems
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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

The executable codes are in the directory exec. Edit the makefile in
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.

1) The code used to perform structure factor analysis is not included in this