Visualization is disabled by default due to performance reasons, but enabling it is very easy. BioDynaMo can be configured through its own configuration file: bdm.toml. Visualization is just one of the many configuration options. Let's take a look at how to set it. We shall continue using the hello_world example from the previous exercise.

Create the configuration file

In your simulation directory hello_world create a new file called bdm.toml. You can do this from the command line with the following command:

touch bdm.toml

Export visualization files

One way to enable visualization is to export a visualization file every time step (or every N time steps). In the bdm.toml file add the following lines:

[visualization]
export = true
export_interval = 1

	[[visualize_sim_object]]
	name = "Cell"

This will export a visualization file every time step. You can set the frequency by setting the export_interval. Make sure that you run a good number of steps so that the cells have time to divide. Set it to around 2000 for the hello_world example. You can do this in src/hello_world.h in the Simulate(time_steps) function. Run your simulation with biodynamo run.

Now we need to open ParaView:

Warning

Make sure you start ParaView from the project directory. Otherwise, ParaView might not find the exported files.


paraview

Select "File->Load State" as shown below:

ParaView Load State

Navigate to your simulation output directory and select the pvsm file.

ParaView Select *.pvsm

In the next window keep the default (Use File Names From State) and click OK.

ParaView Load State Data