Creating simulations¶
The Simulation type¶
In Jumos, simulations are first-class citizen, i.e. objects bound to variables.
The main type for simulations is MolecularDynamic, which can be constructed in
two ways:
-
MolecularDynamic(timestep)¶ Creates an empty molecular dynamic simulation using a Velocity-Verlet integrator with the specified timestep.
Without any thermostat or barostat, this performs a NVE integration of the system.
-
MolecularDynamic(::Integrator) Creates an empty simulation with the specified integrator.
Default algorithms¶
Default algorithms for molecular dynamic are presented in the following table:
| Simulation step | Default algorithms |
|---|---|
| Integration | Velocity-Verlet |
| Forces computation | Naive computation |
| Control | Wrap particles in the box |
| Check | All positions are defined |
| Compute | None |
| Output | None |