Skip to main content

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

Project description


Build Status Documentation Status

A Python binding of a C++ software package for stochastic simulations of spatially extended systems, StoSpa2. Code-base has been completely refactored since the previous version of StoSpa. Python bindings have also been included.


Easy way

pip install pystospaboost

Hard way

After cloning the following repository

git clone --recursive

do the following

cd StoSpa2
python install

This way of installing pystospa assumes the following packages are installed are met

  • scikit-build
  • setuptools
  • wheel
  • cmake
  • boost


Let's consider the following chemical reaction

A \rightarrow \emptyset

happening at rate k. The python code for this simulation is as follows

import pystospa as ss

v = ss.Voxel([100], 1.0)
r = ss.Reaction(1.0, lambda x, y : x[0], [-1])

s = ss.Simulator([v])"example.dat", 0.01, 500)

After importing pystospa, we create the voxel and reaction objects with

v = ss.Voxel([100], 1.0)
r = ss.Reaction(1.0, lambda x, y : x[0], [-1])

and then we add the reaction object to the voxel object.


And finally, we pass the voxel objects, contained in a list, to a simulator object

s = ss.Simulator([v])"example.dat", 0.01, 500)

and we invoke the run function of the Simulator class, to run a stochastic simulation saving the state every 0.01 seconds for 500 steps.

Project details

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for pystospaboost, version 2.0.30
Filename, size File type Python version Upload date Hashes
Filename, size pystospaboost-2.0.30.tar.gz (720.0 kB) File type Source Python version None Upload date Hashes View

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring DigiCert DigiCert EV certificate Facebook / Instagram Facebook / Instagram PSF Sponsor Fastly Fastly CDN Google Google Object Storage and Download Analytics Pingdom Pingdom Monitoring Salesforce Salesforce PSF Sponsor Sentry Sentry Error logging StatusPage StatusPage Status page