diff --git a/docs/source/user/py/tutorials/ChemicalBistables.rst b/docs/source/user/py/tutorials/ChemicalBistables.rst index 6ac360cb3b67e38a77ed7c33bd017e23615951c2..b4a449ab9595cd052c2443472d3de1857b2ab32a 100644 --- a/docs/source/user/py/tutorials/ChemicalBistables.rst +++ b/docs/source/user/py/tutorials/ChemicalBistables.rst @@ -21,9 +21,18 @@ In chemical bistable models that use solvers, there are optional arguments that python filename.py [gsl | gssa | ee] -Where ``gsl`` is Gnu Scientific Library's deterministic solver, ``gssa`` stands for Gillespie stochastic simulation algorithm, and ``ee`` is the exponential euler algorithm. +Where: -All the following examples can be run with either of the three solvers, which in some cases produces a different outcome. However, simply running the file without the optional argument will by default use the ``gsl`` solver. These ``gsl`` outputs are the ones shown below. + - gsl: This is the Runge-Kutta-Fehlberg implementation from the GNU Scientific Library (GSL). It is a fifth order variable timestep explicit method. Works well for most reaction systems except if they have very stiff reactions. + - gssl: Optimized Gillespie stochastic systems algorithm, custom implementation. This uses variable timesteps internally. Note that it slows down with increasing numbers of molecules in each pool. It also slows down, but not so badly, if the number of reactions goes up. + - Exponential Euler:This methods computes the solution of partial and ordinary differential equations. + +All the following examples can be run with either of the three solvers, each of which has different advantages and disadvantages and each of which might produce a slightly different outcome. + +Simply running the file without the optional argument will by default use the ``gsl`` solver. These ``gsl`` outputs are the ones shown below. + +| +| Simple Bistables ================ diff --git a/docs/source/user/py/tutorials/ChemicalOscillators.rst b/docs/source/user/py/tutorials/ChemicalOscillators.rst index c356ab6aabcd389356d929c5db7c9d2e1af0f290..2fb8c5abeb5a6a679bc3f54d39ea73e94ed025d8 100644 --- a/docs/source/user/py/tutorials/ChemicalOscillators.rst +++ b/docs/source/user/py/tutorials/ChemicalOscillators.rst @@ -23,9 +23,15 @@ In chemical models that use solvers, there are optional arguments that allow you python filename.py [gsl | gssa | ee] -Where ``gsl`` is Gnu Scientific Library's deterministic solver, ``gssa`` stands for Gillespie stochastic simulation algorithm, and ``ee`` is the exponential euler algorithm. +Where: -All the following examples can be run with either of the three solvers, which in some cases produces a different outcome. However, simply running the file without the optional argument will by default use the ``gsl`` solver. These ``gsl`` outputs are the ones shown below. + - gsl: This is the Runge-Kutta-Fehlberg implementation from the GNU Scientific Library (GSL). It is a fifth order variable timestep explicit method. Works well for most reaction systems except if they have very stiff reactions. + - gssl: Optimized Gillespie stochastic systems algorithm, custom implementation. This uses variable timesteps internally. Note that it slows down with increasing numbers of molecules in each pool. It also slows down, but not so badly, if the number of reactions goes up. + - Exponential Euler:This methods computes the solution of partial and ordinary differential equations. + +All the following examples can be run with either of the three solvers, each of which has different advantages and disadvantages and each of which might produce a slightly different outcome. + +Simply running the file without the optional argument will by default use the ``gsl`` solver. These ``gsl`` outputs are the ones shown below. | |