MolecularDynamics

MolecularDynamics #

It performs a normal molecular dynamics simulation.

It takes one system and one forcefield to run the simulation.

Example #

[simulator]
type          = "MolecularDynamics"
boundary_type = "PeriodicCuboid"
precision     = "double"
parallelism   = "OpenMP" # optional
seed          = 12345
delta_t       = 0.1
total_step    = 50_000
save_step     = 100
integrator.type = "VelocityVerlet"

Input Reference #

  • type: String
    • To use MolecularDynamicsSimulator, set "MolecularDynamics".
  • boundary_type: String
    • Type of the boundary condition. The size will be specified in [[systems]].
    • "Unlimited": No boundary condition will applied.
    • "Periodic": Periodic boundary condition will be applied. The shape is recutangular box.
  • precision: String
    • Precision of floating point number used in the simulation.
    • "float": 32bit floating point number.
    • "double": 64bit floating point number.
  • parallelism: String (Optional. By default, "sequencial".)
    • "OpenMP": OpenMP implementation will be used.
    • "sequencial": Simulation runs on single core.
  • seed: Integer
    • Random number generator will be initialized by this value.
  • delta_t: Floating
    • Time step of the simulation. The unit depends on the unit system defined in [units]
  • total_step: Integer
    • Total time step of the simulation.
  • save_step: Integer
    • The state of the system will be saved at this interval.
  • integrator: Table