SimBiology.Configset
Solver settings information for model simulation
Description
A SimBiology.Configset object, also known as the configuration
set object, contains the options that the solver uses during simulation of a SimBiology® model.
Use dot notation to query the object properties or change properties that are not
read-only. You can also use the get and set commands.
The configuration set object contains the following options for you to choose:
Type of solver
Stop time for the simulation
Solver error tolerances, and for ode solvers — the maximum time step the solver should take
Whether to perform sensitivity analysis during simulation
Whether to perform dimensional analysis and unit conversion during simulation
Species and parameter input factors for sensitivity analysis
A SimBiology model can contain multiple configsets with one being active at any given time.
The active SimBiology.Configset object contains the settings that are used
during the simulation. Use the method setactiveconfigset to define the active configset. Use the method getconfigset to return a list of configset objects contained by
a model. Use the method addconfigset to add a new
configset to a model.
Creation
Use addconfigset (model) to create and add a
configset object to a SimBiology model. Use getconfigset (model) to get an existing configset object from a
model.
Properties
Object Functions
Examples
Set the maximum number of logs that triggers a simulation to stop.
Create a model object named cell and save it in a variable named modelObj.
modelObj = sbiomodel('cell');Retrieve the configuration set from modelObj and save it in a variable named configsetObj.
configsetObj = getconfigset(modelObj);
Configure the simulation stop criteria by setting the MaximumNumberOfLogs property to 50. Leave the StopTime and MaximumWallClock properties at their default values of 10 seconds and Inf, respectively.
set(configsetObj, 'MaximumNumberOfLogs', 50)View the properties of configsetObj.
get(configsetObj)
Active: 1
CompileOptions: [1×1 SimBiology.CompileOptions]
Name: 'default'
Notes: ''
RuntimeOptions: [1×1 SimBiology.RuntimeOptions]
SensitivityAnalysisOptions: [1×1 SimBiology.SensitivityAnalysisOptions]
SolverOptions: [1×1 SimBiology.ODESolverOptions]
SolverType: 'ode15s'
StopTime: 10
MaximumNumberOfLogs: 50
MaximumWallClock: Inf
TimeUnits: 'second'
AmountUnits: '<automatic>'
MassUnits: '<automatic>'
Type: 'configset'
When you simulate modelObj, the simulation stops when 50 logs are created or when the simulation time reaches 10 seconds, whichever comes first.
Set the maximum wall clock time (in seconds) that triggers a simulation to stop.
Create a model object named cell and save it in a variable named modelObj.
modelObj = sbiomodel('cell');Retrieve the configuration set from modelObj and save it in a variable named configsetObj.
configsetObj = getconfigset(modelObj);
Configure the simulation stop criteria by setting the MaximumWallClock property to 20 seconds. Leave the StopTime and MaximumNumberOfLogs properties at their default values of 10 seconds and Inf, respectively.
set(configsetObj, 'MaximumWallClock', 20)View the properties of configsetObj.
get(configsetObj)
Active: 1
CompileOptions: [1×1 SimBiology.CompileOptions]
Name: 'default'
Notes: ''
RuntimeOptions: [1×1 SimBiology.RuntimeOptions]
SensitivityAnalysisOptions: [1×1 SimBiology.SensitivityAnalysisOptions]
SolverOptions: [1×1 SimBiology.ODESolverOptions]
SolverType: 'ode15s'
StopTime: 10
MaximumNumberOfLogs: Inf
MaximumWallClock: 20
TimeUnits: 'second'
AmountUnits: '<automatic>'
MassUnits: '<automatic>'
Type: 'configset'
When you simulate modelObj, the simulation stops when the simulation time reaches 10 seconds or the wall clock time reaches 20 seconds, whichever comes first.
Load the Lotka-Volterra model.
sbioloadproject lotka;Get the configset object of the lotka model m1.
configset = getconfigset(m1);
Display the list of species whose data are logged by default during the simulation.
configset.RuntimeOptions.StatesToLog
ans = SimBiology Species Array Index: Compartment: Name: Value: Units: 1 unnamed x 1 2 unnamed y1 900 3 unnamed y2 900 4 unnamed z 0
Suppose you want to log just species y1 and y2 data. You can specify their names as a cell array of strings and set it to StatesToLog property.
configset.RuntimeOptions.StatesToLog = {'y1','y2'};Confirm the setting.
configset.RuntimeOptions.StatesToLog
ans = SimBiology Species Array Index: Compartment: Name: Value: Units: 1 unnamed y1 900 2 unnamed y2 900
Alternatively, you can specify an array of species objects (instead of strings) to StatesToLog property.
y1 = m1.Species(2); y2 = m1.Species(3); configset.RuntimeOptions.StatesToLog = [y1, y2];
Simulate and plot the results. Notice that simulation results of only y1 and y2 are plotted.
sbioplot(sbiosimulate(m1));
To reset to the default list, set StatesToLog to a string 'all', which means all species objects, all nonconstant compartment objects and all nonconstant parameter objects are logged by default. A nonconstant compartment or parameter means that its Constant property is set to false.
configset.RuntimeOptions.StatesToLog = 'all';Simulate again. Notice all the species data are plotted.
sbioplot(sbiosimulate(m1));
Do not specify 'all' as a cell string such as {'all'}. If so, SimBiology interprets it as a species named all.
