The reaction diffusion solver solves the following system of N reaction diffusion equations:

\begin{align*} \frac{\partial c_1}{\partial t} = D \nabla^2c_1+kc_1+\text{secretion} + f_1(c_1,c_2,...,c_N, W) \\ \frac{\partial c_2}{\partial t} = D \nabla^2c_2+kc_2+\text{secretion} + f_2(c_1,c_2,...,c_N,W) \\ {\text ...} \\ \frac{\partial c_N}{\partial t} = D \nabla^2c_N+kC_N+\text{secretion} + f_N(c_1,c_2,...,c_N, W) \end{align*}

where W denotes cell type

Let’s consider a simple example of such system:

\begin{align*} \frac{\partial F}{\partial t} = 0.1 \nabla^2F - 0.1H \\ \frac{\partial H}{\partial t} = 0.0 \nabla^2H + 0.1F \end{align*}

It can be coded as follows:

<Steppable Type="ReactionDiffusionSolverFE">
  <DiffusionField Name="F">

  <DiffusionField Name="H">

Notice how we implement functions f from the general system of reaction diffusion equations. We simply use <AdditionalTerm> tag and there we type arithmetic expression involving field names (tags <FieldName>). In addition to this we may include in those expression word CellType. For example:


This means that function f will depend also on CellType . CellType holds the value of the type of the cell at particular location - x, y, z - of the lattice. The inclusion of the cell type might be useful if you want to use additional terms which may change depending of the cell type. Then all you have to do is to either use if statements inside <AdditionalTerm> or form equivalent mathematical expression using functions allowed by muParser:

For example, let’s assume that additional term for second equation is the following:

f_F = \begin{cases} 0.1F && \text{if CellType=1}\\ 0.51F && \text{otherwise} \end{cases}

In such a case additional term would be coded as follows:

<AdditionalTerm>CellType==1 ? 0.01*F : 0.15*F</AdditionalTerm>

Notice that we have used here, so called ternary operator which might be familiar to you from other programing languages such as C or C++ and is equivalent to`` if-then-els``e statement

The syntax of the ternary (aka if-then-else statement) is as follows:

condition ? expression if condition is true : expression if condition false


Important: If change the above expression to

we will get an XML parsing error. Why? This i because XML parser will think that <1 is the beginning of the new XML element. To fix this you could use two approaches:

1.Present your expression as CDATA

    CellType<1 ? 0.01*F : 0.15*F

In this case XML parser will correctly interpret the expression enclosed between <![CDATA[ and ]]> .

2. Replace XML using equivalent Python syntax - see ( in which case you would code the above XML element as the following Python statement:

DiffusionDataElmnt\_2.ElementCC3D('AdditionalTerm', {}, 'CellType<1 ? 0.01*F : 0.15*F')

The moral from this story is that if like to use muParser in the XML file make sure to use this general syntax:


One thing to remember is that computing time of the additional term depends on the level of complexity of this term. Thus, you might get some performance degradation for very complex expressions coded in muParser

Similarly as in the case of FlexibleDiffusionSolverFE we may use <AutoscaleDiffusion> tag tells CC3D to automatically rescale diffusion constant. See section FlexibleDiffusionSolver or the Appendix for more information.