pystospa 2.0.17

A python binding of C++ package for stochastic simulations of spatially extended systems

StoSpa2

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A C++ software package for stochastic simulations of spatially extended systems. Code-base has been completely refactored since the previous version of StoSpa. Python bindings have also been included.

Requirements

Necessary:

• C++ compiler (GCC, clang)
• Cmake (>= 3.5)
• Make (or ninja)

Optional:

• Pybind11 - to build pystospa (python binding of StoSpa2)
• Python (>=3.5)
• Boost - if boost branch of StoSpa2 is used
• Doxygen - to build C++ documentation
• Sphinx - to build python documentation

Installation

After cloning this repository using

git clone https://github.com/BartoszBartmanski/StoSpa2.git --recursive

compile the package with

cd StoSpa2
mkdir build
cmake ../
make all

Example

Included in the src directory is a cpp file example.cpp where we run a simple simulation of diffusion on a one-dimensional domain [0, 10] discretised into 10 voxels.

First, we include the main header from StoSpa2 and we start the main function that will contain the code for the simulation.

#include "simulator.hpp"

using namespace StoSpa2;

int main() {

Within the main function we first define a lambda function for the propensity function of a diffusion reaction.

auto diffusion = [](const std::vector<unsigned>& mols, const double& area) { return mols[0]; };

Then, we create an array of voxels, each of size 1, with 10000 molecules in the leftmost one, as shown below.

std::vector<Voxel> vs = std::vector<Voxel>(9, Voxel({0}, 1.0));
vs.insert(vs.begin(), Voxel({10000}, 1.0));

We add diffusion reactions to all the voxels

for (unsigned i=0; i<vs.size()-1; i++) {
    vs[i].add_reaction(Reaction(1.0, diffusion, {-1}, i+1));
    vs[i+1].add_reaction(Reaction(1.0, diffusion, {-1}, i));
}

and finally, we create a simulator instance and run the simulation.

Simulator sim(vs);
sim.run("example.dat", 0.01, 1000);
}

The resulting simulation output: