Wolfram Language package to stochastically simulate chemical reaction networks.
Includes Gillespie's Direct SSA and Dr. Soloveichik's Bounded Tau Leaping algorithms.
Dependent on Dr. Soloveichik's CRNSimulator package.
Note: requires Wolfram Mathematica version 12.
Installation instructions: Drop StoChemSim.wl, CRNSimulator.m, and the "StoChemSimSequential" directory in the Mathematica Applications directory. This will allow the package to be loaded using "<<StoChemSim`" in Mathematica.
The Mathematica Applications directory can be opened with "SystemOpen@FileNameJoin[{$UserBaseDirectory, "Applications"}]" in Mathematica.
Demo notebooks can be found in the WolframNotebooks directory.
Step 1: Ensure that TARGET_CUDA is set to OFF and then build with CMake.
Step 2: Run the executable. The command line arguments should be entered in the following order: executable name, input file path, output file path, tEnd, flag(s).
Example: ./stochemsim_direct ./inputs/large_crn.txt ./output.txt 0 -fo
Note: Information on how to format input files can be found in InputFileDocumentation.txt.
Step 1: Download Boost version 1.75.0 and install it. Ensure that Boost's root is on your system's PATH variable.
Step 2: Download CUDA v11.2 and install it. Ensure that CUDA's root directory is given as CUDA_PATH in your system variables.
Step 3: Ensure that TARGET_CUDA is set to ON and then build with CMake.
Troubleshooting: You may be missing CMake configuration files for Thrust and CUB. If CMake throws an error because of this, you can find the necessary files in StoChemSimParallel/external.
Ahad Ahmed
Tarek Allam
Isaac Lee
Jackson Lightfoot
Seth Sehon
Vidur Sinha
David Soloveichik
Zhecheng Wang