https://github.com/sheepforce/reaction-diffusion-simulation

Simulation of diffusion-reaction network systems by numerical methods
https://github.com/sheepforce/reaction-diffusion-simulation

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Simulation of diffusion-reaction network systems by numerical methods

• Host: GitHub
• URL: https://github.com/sheepforce/reaction-diffusion-simulation
• Owner: sheepforce
• License: gpl-3.0
• Created: 2016-01-22T21:25:25.000Z (over 10 years ago)
• Default Branch: master
• Last Pushed: 2016-09-08T08:58:11.000Z (almost 10 years ago)
• Last Synced: 2025-03-03T16:26:48.758Z (over 1 year ago)
• Language: FORTRAN
• Size: 20.4 MB
• Stars: 0
• Watchers: 2
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# Reaction-Diffusion-Simulation

Simulating a chemical system in a 3-dimensional circular pipe. Laminar flow, reaction kinetics and diffusion are taken into account. The numerical routines are implemented in Fortran90. For preparation of the input a Python program is used, which offers a graphical interface. Output can be visualized by Gnuplot, which requires awk and sed to process the output.

Parallelization is rudimentary implemented with OpenMP and optionally and experimentally using MPI.

## Dependencies

* gfortran

* make

* Python2

* Qt 4 (optional but higly recommended)

* Gnuplot (optional but highly recommended)

	* awk

	* sed

* OpenMPI (optional)

On Debian you can install those packages with:

> \# aptitude install gfortran make python libpython-dev qt4-default libqt4-dev gnuplot gawk sed openmpi-bin libopenmpi-dev

## Build

A Makefile for use with gfortran on Unix-Systems is provided. Its head looks like this. 

    ############################

    ## CONFIGURATION OPTIIONS ##

    ############################

    #

    # Installation prefix

    PREFIX		= /usr/local

    

    # Fortran compiler, must support Fortran90, others will propably work too but were not tested

    FC			= gfortran			# gfortran from the gnu compiler collection, RECOMMENDED

    #FC			= mpif90			# OpenMPI mpif90 if you want to build with MPI Support, EXPERIMENTAL

    

    # Fortran compiler flags

    FFLAGS		=  -fopenmp			# enables OpenMP SMP parallelization, RECOMMENDED

    FFLAGS		+= -cpp				# use C preprocessor directives, NECESSARY

    FFLAGS		+= -O3				# highest optimization level. -O2 is also fine, RECOMMENDED

    FFLAGS		+= -march=native		# optimize for cpu architecture, OPTIONAL

    FFLAGS		+= -mtune=native		# optimize for cpu architecture, OPTIONAL

    FFLAGS		+= -ffast-math			# optimize math, OPTIONAL

    FFLAGS		+= -mfpmath=sse			# optimize math, OPTIONAL

    

    # Parallelization

    #FPPOPTIONS		= -DopenMPI			# preprocessor directives, enables MPI, disbales OpenMP, EXPERIMENTAL

Edit the prefix if you want a different path for the installation. Comment out

    FC		= gfortran

and uncomment 

    FC		= mpif90

    FPPOPTIONS 	= -DopenMPI

if you would like  to use OpenMPI instead of OpenMP.

You can now enter

> make all && make install

# How to prepare an input