Running a Simulation
To simulate the spatial model, click on the “Simulate” tab, specify the simulation time and desired interval between images, then click “Simulate”.
The default simulation type is DUNE, a high-quality FEM solver, which solves the PDE on the triangular meshed approximation of the geometry.
The other alternative is Pixel, a simple FTCS solver, which solves the PDE on the grid formed by the pixels of the geometry image.
The simulation type can be chosen by clicking on Tools->Set simulation type.
The resulting average species concentrations are plotted as a function of time. A snapshot of the spatial distribution is shown on the left, and the slider below the plot can be used to change the time that is being displayed.
Note
The solvers have various parameters which can be customized via the Advanced->Simulation options menu.
Below the time series of the averaged species concentrations, you see three buttons, on the right of the time slider: - Slice image…: This opens a new window in which you can choose a line through the geometry and plot the distribution of species along that line. In 3D, this represents a slice through the currently selected z-plane. You can choose vertical or horizontal slices, or draw a line yourself by holding the left mouse buton and dragging it over the image on the left side. - Export: This opens a new dialog in which you can select various things to export from the simulation and save them on disk. You can export the entire simulation as a series of images (one for each time point), the averaged time series as a csv file, or you can export single time points to use as model initial conditions or to an image file to initialize the model from later on. - Display options: This button opens a dialog in which the displayed plots can be customized to show only selected species, which is especially useful for analyzing complex systems with many species.
An example of a simple spatial simulation.