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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 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.  - inputs_BPM_2d is the Turing-like pattern formation example described in Section V.B in Ref.  - inputs_chemical_wave_3d is the spherical chemical wave propagation described in Section V.C in Ref.  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.