pystospa
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.
Installation
Easy way
pip install pystospa
Hard way
After cloning the following repository
git clone https://github.com/BartoszBartmanski/StoSpa2.git --recursive
do the following
cd StoSpa2
python setup.py install
This way of installing pystospa assumes the following packages are installed are met
- scikit-build
- setuptools
- wheel
- cmake
Example
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])
v.add_reaction(r)
s = ss.Simulator([v])
s.run("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.
v.add_reaction(r)
And finally, we pass the voxel objects, contained in a list, to a simulator object
s = ss.Simulator([v])
s.run("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.
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