smrfeld / gillespie-cpp

Simple as it gets Gillespie library in C++, as a stepping stone for your own Gillespie codes

A simple Gillespie library for C++

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.

Features

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

Installing

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

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

It requires std==c++17 to work with the filesystem for i/o. The namespace is gilsp.

Example

Here is a simple snippet for the reacton A -> 0 (note: bimolecular and higher order reactions are also supported). It is in the example 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;
}