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Useful libraries are simple to understand for use in your own project.

This library is as simple as it gets and should serve as a simple stepping stone for other Gillespie codes in C++.

Hopefully, because it's entirely C++, it will beat out some other Python variants out there.

• Simple STL +C++ 17 standard.
• Gillespie algorithm.
• Tau leaping, with adaptive tau step as inCao 2006.

• Clone the repo.
• mkdir build && cd build
• cmake ..
• make && make install

The default install location is/usr/local/lib.

It requiresstd==c++17 to work with the filesystem for i/o.The namespace isgilsp.

Here is a simple snippet for the reactonA -> 0 (note: bimolecular and higher order reactionsare also supported). It is in theexample directory.

#include <iostream>#include <vector>#include <gilsp>using namespace gilsp;using namespace std;int main() {    // Random seed    srand (time(NULL));    // Make the reaction A->0 with rate 3    Rxn rxn = Rxn("rxn", 3.0, {"A"}, {});    // Initial counts of particles    Counts counts = Counts();    counts.set_count("A", 100);    // Run    Gillespie g;    vector<Rxn> rxn_list({rxn});    double dt_st_every = 0.1;    double t_max = 100.0;    CountsHist counts_hist = g.run(rxn_list, counts, dt_st_every, t_max);    // Print it    counts_hist.print();    // Write it    counts_hist.write_all_count_hist("../data");    return 0;}