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Version: v1.0.0

Mathematical Expressions

Mathematical expressions are permitted on different sections of the Parameter Tree. Such expressions may contain typical math operations such as +, -, *, ^, sin, tan, etc. The complete list of possibilities is found here. That is, the muParser built in operators.

Furthermore, we provide extra variables/functions that may be included on the math expressions.

Variables

Context-Independent

The following list of variables are unconditionally available when defining expressions:

VariableDescription
tTime
xFirst dimension in the cartesian coordinate system
ySecond dimension in the cartesian coordinate system
zThird dimension in the cartesian coordinate system (only in 3D)
dimDimension of the euclidean space
piApproximation to the number π

Context-Dependent

Additionally, there are other variables that are conditionally available to define the expression. These variables depend on the context of its definition. An example of it is the reaction expressions within a compartment. If the section [model.nucleus.reaction] defines expressions u, v, and w, then, they all will be available to each other. E.g.

[model.nucleus.reaction]
u = u*v*w
v = u*v*w
w = u*v*w

Functions

Context-Dependent

There are also functions that may be conditionally available depending on the context. In such case, the function will have a custom name and fixed number of arguments and will be available for use on the mathematical expression.

Currently we only provide these for defining TIFF input images as 2D functions for initial conditions (See Input Data section).