diff --git a/planckton/sim.py b/planckton/sim.py index 42d7809..1e22d69 100644 --- a/planckton/sim.py +++ b/planckton/sim.py @@ -11,8 +11,7 @@ class Simulation: - """ - Convenience class for initializing and running a HOOMD simulation. + """Convenience class for initializing and running a HOOMD simulation. Parameters ---------- @@ -24,9 +23,9 @@ class Simulation: Scaling parameter for particle interaction strengths, used to simulate solvent tau : float, default 5.0 - Thermostat coupling period + Thermostat coupling period (in simulation time units) r_cut : float, default 2.5 - Cutoff radius for potentials + Cutoff radius for potentials (in simulation distance units) gsd_write : int, default 1e6 Period to write simulation snapshots to gsd file log_write : int, default 1e5 @@ -38,7 +37,7 @@ class Simulation: n_steps : int, default 1e3 Number of steps to run the simulation dt : float, default 0.0001 - Size of simulation timestep in simulation time units + Size of simulation timestep (in simulation time units) mode : str, default "gpu" Mode flag passed to hoomd.context.initialize. Options are "cpu" and "gpu".