Module lumol::sim::md

Molecular dynamics related algorithms.

Each class of algorithms is represented by a trait, and each single method is a struct implementing said trait.

The main entry point is the MolecularDynamics struct, implementing the Propagator trait.

Integrator

The core of molecular dynamics simulation happens in an Integrator. The implemented integrators are the following:

• Verlet: simple Verlet integrator;
• VelocityVerlet: simple velocity-Verlet integrator;
• LeapFrog: Leap-Frog integrator;
• BerendsenBarostat: isotropic Berendsen barostat coupled to a velocity-Verlet integrator;
• AnisoBerendsenBarostat anisotropic Berendsen barostat coupled to a velocity-Verlet integrator

Themostats

Thermostat are algorihtms used to fix the temperature during a simulation. The following implementation are available:

• RescaleThermostat: basic themostat rescaling the velocities of all atoms. This is highly unphysical but can be usefull for equilibration;
• CSVRThermostat: Canonical Sampling through Velocities Rescaling is a well-behaved thermostating algorithm generating the expected canonical ensemble distribution of states.
• BerendsenThermostat: berendsen or weak-coupling thermostat;

Control

Control algorihtms group any algorithm modifying the system to enforce some type of invariant.

• RemoveTranslation: remove the global translational momentum of a system;
• RemoveRotation: remove the global rotational momentum of a system;
• Rewrap: wrap all atoms from a system inside the unit cell;

Structs

AnisoBerendsenBarostat	Anisotropic Berendsen barostat integrator based on velocity-Verlet.
BerendsenBarostat	Berendsen barostat integrator based on velocity-Verlet.
BerendsenThermostat	Berendsen (or weak coupling) thermostat.
CSVRThermostat	A thermostat using the Canonical Sampling Through Velocities Rescaling algorithm.
LeapFrog	Leap-frog integrator.
MolecularDynamics	Molecular Dynamics propagator for the simulation.
RemoveRotation	Remove global rotation from the system
RemoveTranslation	Remove global translation from the system
RescaleThermostat	Velocity rescaling thermostat.
Rewrap	Rewrap all molecules' centers of mass to lie within the unit cell.
VelocityVerlet	Velocity-Verlet integrator.
Verlet	Verlet integrator.

Traits

Control	Trait for controlling some parameters in a system during a simulation.
Integrator	The Integrator trait define integrator interface for molecular dynamics. An integrator is an algorithm responsible for propagating the equations of motion in the system.
Thermostat	Trait for thermostat algorithms some parameters in a system during a simulation.