gotran.solver package¶

Submodules¶

gotran.solver.odesolver module¶

gotran.solver.odesolver.ODESolver(ode, method='scipy', **options)[source]¶

A generic ODE solver for solving problem of the types on the form,

\[\dot{y} = f(t,y), \quad y(t_0) = y_0.\]

Here one need to specific the backend which is either Scipy or Assimulo.

Arguments

ode : gotran.ODE or gotran.CellModel: The ode you want to solve in a gotran object
method : str: Solver method. Possible inputs are or ‘scipy’ (Default:’sundials’)
options : dict:: Options for the solver, see list_solver_options

exception gotran.solver.odesolver.ODESolverError[source]¶: Bases: Exception

class gotran.solver.odesolver.Solver(ode, **options)[source]¶

Bases: object

module¶

monitor(tsteps, results)[source]¶: Get monitored values

monitor_indices(*monitored)[source]¶

monitor_names¶

solve(*args, **kwargs)[source]¶: Solver ODE. See docs for the different solvers for solver specific arguments.

state_indices(*states)[source]¶

state_names¶

update_model_parameter()[source]¶: Update model parameters according to parameters in the cell model

gotran.solver.odesolver.check_method(method)[source]¶

gotran.solver.odesolver.generate_module(ode, monitored, **options)[source]¶: Generate a module to

gotran.solver.odesolver.timeout(timeout_seconds)[source]¶

gotran.solver.scipysolver module¶

class gotran.solver.scipysolver.ScipySolver(ode, **options)[source]¶

Bases: gotran.solver.odesolver.Solver

get_options()[source]¶

static list_solver_options()[source]¶

gotran.solver.sundialssolver module¶

To use install assimulo which is a python wrapper of the sundials solvers

conda install assimulo

class gotran.solver.sundialssolver.SundialsSolver(ode, method='cvode', **options)[source]¶

Bases: gotran.solver.odesolver.Solver

get_options()[source]¶: Get solver options for the current solver

static list_solver_options()[source]¶

problem¶

solver¶

exception gotran.solver.sundialssolver.SundialsNotInstalled[source]¶: Bases: Exception

gotran.solver.utils module¶

class gotran.solver.utils.suppress_stdout_stderr[source]¶