Fast Efficient Reaction Network (FERN) Solver

Student Code - Research Code Only! Not Software!

NOTE - This code was written primarily by students. It is of poor quality and should not be used for anything more than basic research. An effort is underway to rewrite it as part of Fire.

Prerequisites

You will need git and cmake to build FERN.

Checkout and build

From a shell, execute the following commands:

git clone --recursive https://github.com/jayjaybillings/fern
mkdir fern-build
cd fern-build
cmake ../fern -DCMAKE_BUILD_TYPE=Debug -G"Eclipse CDT4 - Unix Makefiles" -DCMAKE_ECLIPSE_VERSION=4.5
make

Build flags, such as -Wall, can be set by prepending the CXX_FLAGS variable to the cmake command as such

CXX_FLAGS='-Wall' cmake ../fern -DCMAKE_BUILD_TYPE=Debug -G"Eclipse CDT4 - Unix Makefiles" -DCMAKE_ECLIPSE_VERSION=4.5

Optimization flags should be handled by setting -DCMAKE_BUILD_TYPE=Release instead of Debug. Likewise, an optimized build with debug information can be acheived by setting -DCMAKE_BUILD_TYPE=RelWithDebugInfo.

Running FERN

You can run FERN from any directory and it only requires one of its INI files to run. So, assuming you are in the build directory and using one of the test files in the data directory, you would run

./fern-exec ../fern/data/alpha.ini

Updating Submodules

FERN uses the Fire Framework for various utilities. This is included as a git submodule, which can be updated by running the the following from the FERN source directory

bash ./tools/updateSubModules.sh

FERN always checks out the latest release version of the submodule from the repository, so it should not be necessary to update it. However, the utility should be used as required.

Questions

Questions can be directed to me at billingsjj ornl gov.