A python binding of C++ package for stochastic simulations of spatially extended systems
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.
pip install pystospa
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
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(, 1.0) r = ss.Reaction(1.0, lambda x, y : x, [-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(, 1.0) r = ss.Reaction(1.0, lambda x, y : x, [-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]) 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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