MeanSquareDisplacement¶
Overview¶
The Mean Square Displacement (MSD) analysis calculates the average squared displacement of particles over time, providing insights into diffusion and mobility.
Constructor¶
MeanSquareDisplacement(system, particles, ...)¶
Creates a new analysis instance.
Parameters:
- system (System): The molecular system to analyze
- particles (List[Particle]): List of particles to include in analysis
Methods¶
compute()¶
Performs the analysis calculation.
is_computed() → bool¶
Returns whether the analysis has been computed.
msd_values() → List[float]¶
Returns the calculated MSD values.
lag_times() → List[float]¶
Returns the lag times for MSD calculation.
Usage Example¶
import smolsat
# Create trajectory and system
trajectory = smolsat.create_example_trajectory(num_particles=100, num_frames=1000)
system = smolsat.System(trajectory, periodic_boundaries=True)
# Select particles for analysis
particles = [trajectory.particle(i) for i in range(50)]
# Create and run analysis
analysis = smolsat.MeanSquareDisplacement(system, particles)
analysis.compute()
# Get results
msd_values = analysis.msd_values()
lag_times = analysis.lag_times()