SimBiology.CompileOptions
Compile options for SimBiology models
Description
This object defines the compile options for simulating SimBiology models. For instance, you can specify whether to perform unit conversion for the model before simulation. Compile options are checked during compile time.
Creation
This object is a property of a Configset
object. Use dot notation or get
or set
to access and modify this object from a
configset
object.
Properties
DefaultSpeciesDimension
— Dimension of species name in expression
'concentration'
(default) | 'substance'
Dimension of species name in expression, specified as
'concentration'
or 'substance'
.
This property specifies how SimBiology® interprets species names in expressions (namely reaction rate, rule, or
event expressions). The valid property values are substance
or
concentration
. If you specify
InitialAmountUnits
, SimBiology interprets species names appearing in expressions as concentration or
substance amount according to the units specified, regardless of the value in
DefaultSpeciesDimension
. Thus, if
DefaultSpeciesDimension
is concentration
and you
specify species units as molecule
, SimBiology interprets species names in expressions as substance
.
This interpretation applies even when DimensionalAnalysis
is
off.
You can find DefaultSpeciesDimension
in the CompileOptions
property.
When you set DefaultSpeciesDimension
to
substance
, if you do not specify units, SimBiology interprets species names appearing in expressions as substance amounts,
and does not scale by compartment capacity. To include a species concentration in an
expression, divide by the appropriate compartment capacity in the expression. To specify
compartment capacity in an expression enter the compartment name.
When you set DefaultSpeciesDimension
to
concentration
, SimBiology interprets species names appearing in expressions as concentrations, and
scales by compartment capacity in the expressions. To include a species amount in an
expression, multiply by the species name by the appropriate compartment name in the
expression.
For information on dimensional analysis for reaction rates, see How Reaction Rates Are Evaluated.
Data Types: char
| string
DimensionalAnalysis
— Flag to perform dimensional analysis on SimBiology model
true
or 1 (default) | false
or 0
Flag to perform dimensional analysis on a SimBiology model, specified as a numeric
or logical 1 (true
) or 0 (false
).
The DimensionalAnalysis
property specifies whether to perform
dimensional analysis on the model before simulation. When
DimensionalAnalysis
is set to true
, SimBiology
checks whether the physical quantities of the units involved in reactions and rules,
match and are applicable.
For example, consider a reaction a + b —> c
. Using mass
action kinetics, the reaction rate is defined as a*b*k
, where
k
is the rate constant of the reaction. If you specify that initial
amounts of a
and b
are 0.01M and 0.005M
respectively, then units of k
are 1/(M*second)
. If
you specify k
with another equivalent unit definition, for example,
1/[(moles/liter)*second]
, DimensionalAnalysis
checks whether the physical quantities match. If the physical quantities do not match,
you see an error and the model is not simulated.
Unit conversion requires dimensional analysis. If
DimensionalAnalysis
is off, and you turn
UnitConversion
on, then DimensionalAnalysis
is
turned on automatically. If UnitConversion
is on and you turn off
DimensionalAnalysis
, then UnitConversion
is
turned off automatically.
If you have MATLAB® function calls in your model, dimensional analysis ignores any expressions containing function calls and generates a warning.
Warning
This property will be removed in a future release. Use
UnitConversion
instead.
Data Types: double
| logical
Type
— Object type
'compileoptions'
(default)
This property is read-only.
Object type, specified as 'compileoptions'
. When you create a
SimBiology object, the value of Type
is automatically
defined.
Data Types: char
UnitConversion
— Flag to perform unit conversion
false
or 0 (default) | true
or 1
Flag to perform unit conversion for a SimBiology model before simulation, specified
as numeric or logical 1 (true
) or 0
(false
).
When UnitConversion
is set to true
, SimBiology
converts the matching physical quantities to one consistent unit system in order to
resolve them. This conversion is in preparation for correct simulation, but species
amounts are returned in the user-specified units.
For example, consider a reaction a + b —> c
. Using mass
action kinetics the reaction rate is defined as a*b*k
where
k
is the rate constant of the reaction. If you specify that initial
amounts of a
and b
are 0.01M and 0.005M
respectively, then units of k
are 1/(M*second)
. If
you specify k
with another equivalent unit definition, for example,
1/((molecules/liter)*second)
, UnitConversion
occurs after DimensionalAnalysis
.
Unit conversion requires dimensional analysis. If
DimensionalAnalysis
is off, and you turn
UnitConversion
on, then DimensionalAnalysis
is
turned on automatically. If UnitConversion
is on and you turn off
DimensionalAnalysis
, then UnitConversion
is
turned off automatically.
If UnitConversion
fails, then you see an error when you
simulate.
If UnitConversion
is set to false
, the
simulation uses the given object values.
Note
SimBiology uses units including empty units in association with DimensionalAnalysis and UnitConversion features.
When
DimensionalAnalysis
andUnitConversion
are bothfalse
, units are not used. However, SimBiology still performs a minimum level of dimensional analysis to decide whether a reaction rate is in dimensions of amount/time or concentration/time.When
DimensionalAnalysis
istrue
andUnitConversion
isfalse
, units (if not empty) must have consistent dimensions so that SimBiology can perform dimensional analysis. However, the units are not converted.When
UnitConversion
is set totrue
(which requiresDimensionalAnalysis
to betrue
), SimBiology performs a dimensional analysis and converts everything to consistent units. Hence, you must specify consistent units, and no units can be empty. If you have a dimensionless parameter, you must still set its unit todimensionless
.SimBiology allows exponentiation of any dimensionless quantity to any dimensionless power. For example, you can write the following expression if both
x
anda
are dimensionless:(x + 3)^(a + 0.5)
Tip
If you have a custom function and UnitConversion is on, follow the recommendation below.
Non-dimensionalize the parameters that are passed to the function if they are not already dimensionless.
Suppose you have a custom function defined as
y = f(t)
wheret
is the time in hour andy
is the concentration of a species in mole/liter. When you use this function in your model to define a repeated assignment rule for instance, define it as:s1 = f(time/t0)*s0
, wheretime
is the simulation time,t0
is a parameter defined as 1.0 hour,s0
is a parameter defined as 1.0 mole/liter, ands1
is the concentration of a species in mole/liter. Note thattime
ands1
do not have to be in the same units ast0
ands0
, but they must be dimensionally consistent. For example, thetime
ands1
units can be set to minute and picomole/liter, respectively.
Data Types: double
| logical
Examples
Enable Unit Conversion for SimBiology Model
Create a model.
m1 = sbiomodel("m1");
Get the configset
object from the model.
cs = getconfigset(m1);
Get the CompileOptions
object from the configset
object.
copt = cs.CompileOptions;
Turn on unit conversion.
copt.UnitConversion = true;
Version History
Introduced in R2006bR2023a: DimensionalAnalysis
will be removed
The DimensionalAnalysis
property will be removed in a future
release. Use UnitConversion
instead.
See Also
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