Commit 2724c169 authored by Mathieu Hemery's avatar Mathieu Hemery
Browse files

Merge branch 'develop' of gitlab.inria.fr:lifeware/biocham into develop

parents 69fc268b 7b339ccc
......@@ -27,11 +27,12 @@
:- doc('
Biocham v4 uses the GNU Scientific Library (GSL \\url{http://www.gnu.org/software/gsl/}) to perform numerical simulations.
Biocham v5 uses its own implementation of the Rosenbrock implicit method \\texttt{rsbk} for numerical simulations.
This method is well suited to stiff systems and is the default one.
Biocham v5 is also interfaced to the GNU Scientific Library (GSL \\url{http://www.gnu.org/software/gsl/}) to perform numerical simulations.
The page
\\url{http://www.gnu.org/software/gsl/manual/html_node/Stepping-Functions.html#Stepping-Functions}
gives a detailed description of the numerical integration methods and options listed below.
The implicit method \\texttt{bsimp} for stiff systems is the default one.
').
:- doc(' The ODE simulation of a Biocham model proceeds by creating an ODE system if there is none, and deleting it after the simulation.
......@@ -41,6 +42,8 @@ It is worth noting that if there is an ODE system already present (e.g. created
:- grammar(method).
method(rsbk).
:- grammar_doc('\\emphright{\\emph{Default method}. Rosenbrock method.}').
% Note: a list of GSL supported methods is given in gsl:gsl_methods/1
method(rk2).
......@@ -68,7 +71,7 @@ method(rk4imp).
:- grammar_doc('\\emphright{Implicit Gaussian 4th order Runge-Kutta. Error estimation is carried out by the step doubling method.}').
method(bsimp).
:- grammar_doc('\\emphright{\\emph{Default method}. Implicit Bulirsch-Stoer method of Bader and Deuflhard. The method is generally suitable for stiff problems.}').
:- grammar_doc('Implicit Bulirsch-Stoer method of Bader and Deuflhard. The method is generally suitable for stiff problems.}').
method(msadams).
:- grammar_doc('\\emphright{A variable-coefficient linear multistep Adams method in Nordsieck form. This stepper uses explicit Adams-Bashforth (predictor) and implicit Adams-Moulton (corrector) methods in P(EC)^m functional iteration mode. Method order varies dynamically between 1 and 12.}').
......@@ -98,8 +101,7 @@ method(bn).
:- grammar_doc('\\emphright{Random Boolean net simulation run. All transitions are
equiprobable.}').
method(rsbk).
:- grammar_doc('\\emphright{Rosenbrock method.}').
:- grammar(time).
......@@ -119,7 +121,7 @@ filter(no_filter).
filter(only_extrema).
:- grammar_doc('\\emphright{Only keeps the points that are an extremum for some variable.}').
:- initial(option(method: bsimp)).
:- initial(option(method: bsimp)). % rsbk)). % msbdf too slow
:- initial(option(error_epsilon_absolute: 1e-6)).
:- initial(option(error_epsilon_relative: 1e-6)).
:- initial(option(initial_step_size: 1e-6)).
......
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