rr::SimulateOptions Struct Reference

#include <rrRoadRunnerOptions.h>

Public Types
enum	Options { RESET_MODEL = (0x1 << 0), STRUCTURED_RESULT = (0x1 << 1) }
enum	Integrator
enum	IntegratorFlags { STIFF = (0x1 << 0) }

Public Member Functions
	SimulateOptions ()
	SimulateOptions (const std::string &sbmlSettingFilePath)

Public Attributes
uint32_t	flags
Integrator	integrator
uint32_t	integratorFlags
int	steps
double	start
double	duration
double	absolute
double	relative
std::vector< std::string >	variables
std::vector< std::string >	amounts
std::vector< std::string >	concentrations

Static Public Attributes
static const double	MIN_RELATIVE = 1.e-5
static const double	MIN_ABSOLUTE = 1.e-10

Detailed Description

RoadRunner simulation options.

This is the full set of options that determines how RoadRunner performs a simulation of an sbml model.

This is a superset of the values stored in a sbml test suite settings file, the documentation of the fields which correspond to an sbml test suite settings was taken from http://sbml.org

Member Enumeration Documentation

enum rr::SimulateOptions::Integrator

the list of ODE solvers RoadRunner currently supports.

enum rr::SimulateOptions::IntegratorFlags

Enumerator
STIFF	Is the model a stiff system? setting this to stiff causes RoadRunner to load a stiff solver which could potentially be extremly slow

enum rr::SimulateOptions::Options

Enumerator
RESET_MODEL	reset the model to the initial state.
STRUCTURED_RESULT	Simulate should return a raw result matrix without adding any column names.

Constructor & Destructor Documentation

rr::SimulateOptions::SimulateOptions

(

)

init with default options.

rr::SimulateOptions::SimulateOptions

(

const std::string &

sbmlSettingFilePath

)

Set the default flags, but the fields start, duration, absolute, relative, variables, amounts and concentrations are loaded from an sbml test suite settings file.

Member Data Documentation

double rr::SimulateOptions::absolute

A number representing the absolute difference permitted.

std::vector<std::string> rr::SimulateOptions::amounts

A list of the variable whose output in the results file is in amount (not concentration) units. This list of variables must be a subset of the names listed in variables.

std::vector<std::string> rr::SimulateOptions::concentrations

A list of the variable whose output in the results file is in concentration (not amount) units. This list of variables must be a subset of the names listed in variables.

double rr::SimulateOptions::duration

The duration of the simulation run, in the model's units of time.

uint32_t rr::SimulateOptions::flags

a bitmask of the options specified in the Options enumeration.

Integrator rr::SimulateOptions::integrator

which integrator to use

uint32_t rr::SimulateOptions::integratorFlags

Set of options to use when configuring the integrator. This is a bitfield composed of options from the IntegratorOpt enum.

const double rr::SimulateOptions::MIN_ABSOLUTE = 1.e-10

static

The minumum absolute error that the CVODE integrator supports in order to to pass the sbml test suite using the default integtator.

If a test suite config file is loaded, and the relative error is higher than MIN_ABSOLUTE, it will be lowered to MIN_ABSOLUTE.

const double rr::SimulateOptions::MIN_RELATIVE = 1.e-5

static

The minumum relative error that the CVODE integrator supports in order to to pass the sbml test suite using the default integtator.

If a test suite config file is loaded, and the relative error is higher than MIN_RELATIVE, it will be lowered to MIN_RELATIVE.

double rr::SimulateOptions::relative

A float-point number representing the relative difference permitted. Defaults 0.0001

double rr::SimulateOptions::start

The start time of the simulation time-series data. Often this is 0, but not necessarily.

int rr::SimulateOptions::steps

The number of steps at which the output is sampled. The samples are evenly spaced. When a simulation system calculates the data points to record, it will typically divide the duration by the number of time steps. Thus, for X steps, the output will have X+1 data rows.

std::vector<std::string> rr::SimulateOptions::variables

The variables (in addition to time) whose values will be saved in the result. These are SBML model id's. Order is significant, as this determines the order of the columns in the result matrix.

Important: if a symbol in this list refers to a species in the model, then that symbol will also be listed in either the amount or concentration lists below.

NOTE:If a listed variable has two underscores in it ('__'), that variable is actually present only in a submodel of the main model, from the Hierarchical Model Composition package, in the format submodelID__variableID. If the model is flattened, the variable will appear automatically.

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The documentation for this struct was generated from the following files:

• rrRoadRunnerOptions.h
• rrRoadRunnerOptions.cpp