Thus far, we have established a general framework for a molecular dynamics simulation, a suitable system of units, and mechanisms for propagating the system forward in time. However, there remains the inevitable task of assigning initial conditions.
When a configuration is loaded from a file, it takes as its initial conditions the final conditions of the saved configuration. If the Gear algorithm is selected, these initial conditions include position and its derivatives up to fifth order. If the velocity-Verlet algorithm is selected, the initial conditions include position, velocity, and acceleration.
TrapApp also provides several methods for customized initialization of positions and velocities of the ions.