FAQ

Time scales

“How can I specify time scales?” Specifying time scales is important, especially in multiscale models in which dynamics occur at multiple temporal scales. In Morpheus, we distinguish three time scales:

Neighborhoods

“How are neighborhoods defined?” Types of Neighborhoods Types of neighborhood are used: Space → Lattice → Neighborhood: This is the default Neighborhood for the lattice. It ist used by the NeighborhoodReporter and fallback for all other Neighborhood definitions.

Equation vs. Rule vs. Function

“What is the difference between an Equation, a Rule and a Function ?” Both are algebraic expressions, however: An Equation is an equality relation the simulator is expected to keep throughout simulation time.

3D visualization

“How can I visualize 3D simulations?” To visualize 3D simulations, Morpheus can create z-slice plots via GnuPlotter or write TIFF images stacks and VTK files. These files can be rendered with external software, such as Fiji or Paraview.

Execution modes

“What is the meaning of ‘local’, ‘interactive’ and ‘remote’ job queues?” Simulations can be executed in different job queues for different tasks. local and interactive jobs are started in a local job queue that is handled by Morpheus itself.

Checkpointing

“How can I store simulation snapshots?” Storing snapshots of the simulation state during execution is called checkpointing. This allows the user to e.g.: restore a simulation, continue a simulation under different conditions, use the end-state of a simulation as initial condition of a new simulation, Enable checkpointing.

Parallelization

“How are jobs parallelized?” Number of threads: Used to set the number of OpenMP threads (in-job parallelization). Concurrent jobs: Number of jobs executed in parallel (between-job parallelization).

Gnuplot path

“Where can I configure the Gnuplot path?” By default, Morpheus uses the first Gnuplot executable it can find in the PATH environmental variable. Optionally, you can overrule this path.