md.Simulator

class md.Simulator(*args: Any, **kwargs: Any)[source]

Main driver of the molecular dynamics simulation. Uses an integrator to propagate the molecular system defined in the system class according to the forces yielded by a provided calculator.

In addition, hooks can be applied at five different stages of each simulation step:

  • Start of the simulation (e.g. for initializing thermostat)

  • Before first integrator half step (e.g. thermostat)

  • After computation of the forces and before main integrator step (e.g.

for accelerated MD)

  • After second integrator half step (e.g. thermostat, output routines)

  • At the end of the simulation (e.g. general wrap up of file writes, etc.)

This routine has a state dict which can be used to restart a previous simulation.

Parameters:

  • system (schnetpack.md.System) – Instance of the system class defined in molecular_dynamics.system holding the structures, masses, atom type, momenta, forces and properties of all molecules and their replicas

  • integrator (schnetpack.md.Integrator) – Integrator for propagating the molecular dynamics simulation, defined in schnetpack.md.integrators

  • calculator (schnetpack.md.calculator) – Calculator class used to compute molecular forces for propagation and (if requested) various other properties.

  • simulator_hooks (list(object)) – List of different hooks to be applied during simulations. Examples would be file loggers and thermostat.

  • step (int) – Index of the initial simulation step.

  • restart (bool) – Indicates, whether the simulation is restarted. E.g. if set to True, the simulator tries to continue logging in the previously created dataset. (default=False) This is set automatically by the restart_simulation function. Enabling it without the function currently only makes sense if independent simulations should be written to the same file.

  • progress (bool) – show progress bar during simulation. Can be deactivated e.g. for cluster runs.