occ::mults::RigidBodyDynamics Class Reference

Rigid body molecular dynamics integrator. More...

#include <rigid_body_dynamics.h>

Classes
struct	Config
	Configuration for MD simulations. More...

Static Public Member Functions
static void	velocity_verlet_step (std::vector< RigidBodyState > &molecules, double dt)
	Perform one velocity Verlet integration step.
static void	compute_forces_torques (std::vector< RigidBodyState > &molecules)
	Compute forces and torques on all molecules (S-function engine)
static double	compute_forces_torques_cartesian (std::vector< RigidBodyState > &molecules)
	Compute forces and torques using Cartesian T-tensor engine.
static void	update_positions (std::vector< RigidBodyState > &molecules, double dt)
	Update positions using current velocities (half-step)
static void	update_velocities (std::vector< RigidBodyState > &molecules, double dt, bool first_half)
	Update velocities using forces (half-step)
static void	update_orientations_quaternion (std::vector< RigidBodyState > &molecules, double dt)
	Update orientations using quaternion integration.
static void	update_angular_velocities (std::vector< RigidBodyState > &molecules, double dt, bool first_half)
	Update angular velocities using torques (half-step)
static double	compute_kinetic_energy (const std::vector< RigidBodyState > &molecules)
	Compute total kinetic energy of system.
static double	compute_potential_energy (const std::vector< RigidBodyState > &molecules)
	Compute total potential energy of system (S-function engine)
static double	compute_potential_energy_cartesian (const std::vector< RigidBodyState > &molecules)
	Compute total potential energy using Cartesian engine.
static double	compute_total_energy (const std::vector< RigidBodyState > &molecules)
	Compute total energy (kinetic + potential)
static Vec3	compute_linear_momentum (const std::vector< RigidBodyState > &molecules)
	Compute total linear momentum of system.
static Vec3	compute_angular_momentum (const std::vector< RigidBodyState > &molecules)
	Compute total angular momentum of system.
static void	normalize_quaternions (std::vector< RigidBodyState > &molecules)
	Normalize all quaternions in the system.

Detailed Description

Rigid body molecular dynamics integrator.

This class implements the velocity Verlet algorithm for rigid body dynamics, integrating both translational and rotational equations of motion.

The quaternion-based formulation avoids gimbal lock and provides numerical stability for arbitrary rotations.

Member Function Documentation

compute_angular_momentum()

static Vec3 occ::mults::RigidBodyDynamics::compute_angular_momentum ( const std::vector< RigidBodyState > &  molecules )

static

Compute total angular momentum of system.

Parameters

molecules

Vector of rigid bodies

Returns

Total angular momentum vector (in space frame)

compute_forces_torques()

static void occ::mults::RigidBodyDynamics::compute_forces_torques ( std::vector< RigidBodyState > &  molecules )

static

Compute forces and torques on all molecules (S-function engine)

Calculates pairwise multipole interactions and updates force/torque on each molecule using the S-function/Euler-angle-based engine.

Parameters

molecules

Vector of rigid body states

compute_forces_torques_cartesian()

static double occ::mults::RigidBodyDynamics::compute_forces_torques_cartesian ( std::vector< RigidBodyState > &  molecules )

static

Compute forces and torques using Cartesian T-tensor engine.

Calculates pairwise multipole interactions using the Cartesian engine, which computes energy, forces, and torques in a single pass per pair. Supports multi-site molecules.

This is generally faster than compute_forces_torques() since:

• One call per pair (not two)
• No Euler angle conversion
• SIMD-batched T-tensor computation

Parameters

molecules

Vector of rigid body states

Returns

Total potential energy

compute_kinetic_energy()

static double occ::mults::RigidBodyDynamics::compute_kinetic_energy ( const std::vector< RigidBodyState > &  molecules )

static

Compute total kinetic energy of system.

Parameters

molecules

Vector of rigid bodies

Returns

Total kinetic energy (translational + rotational)

compute_linear_momentum()

static Vec3 occ::mults::RigidBodyDynamics::compute_linear_momentum ( const std::vector< RigidBodyState > &  molecules )

static

Compute total linear momentum of system.

Parameters

molecules

Vector of rigid bodies

Returns

Total linear momentum vector

compute_potential_energy()

static double occ::mults::RigidBodyDynamics::compute_potential_energy ( const std::vector< RigidBodyState > &  molecules )

static

Compute total potential energy of system (S-function engine)

Parameters

molecules

Vector of rigid bodies

Returns

Total potential energy (sum of all pairwise interactions)

compute_potential_energy_cartesian()

static double occ::mults::RigidBodyDynamics::compute_potential_energy_cartesian ( const std::vector< RigidBodyState > &  molecules )

static

Compute total potential energy using Cartesian engine.

Faster than compute_potential_energy() for multi-site molecules.

Parameters

molecules

Vector of rigid bodies

Returns

Total potential energy (sum of all pairwise interactions)

compute_total_energy()

static double occ::mults::RigidBodyDynamics::compute_total_energy ( const std::vector< RigidBodyState > &  molecules )

static

Compute total energy (kinetic + potential)

Parameters

molecules

Vector of rigid bodies

Returns

Total energy

normalize_quaternions()

static void occ::mults::RigidBodyDynamics::normalize_quaternions ( std::vector< RigidBodyState > &  molecules )

static

Normalize all quaternions in the system.

Call this periodically to prevent numerical drift from unit quaternion constraint.

Parameters

molecules

Vector of rigid bodies

update_angular_velocities()

static void occ::mults::RigidBodyDynamics::update_angular_velocities ( std::vector< RigidBodyState > &  molecules, double  dt, bool  first_half  )

static

Update angular velocities using torques (half-step)

Integrates Euler's equation in body frame: dL/dt = tau - omega x L

Parameters

molecules	Vector of rigid bodies
dt	Timestep
first_half	If true, do first half-step; if false, do second half-step

update_orientations_quaternion()

static void occ::mults::RigidBodyDynamics::update_orientations_quaternion ( std::vector< RigidBodyState > &  molecules, double  dt  )

static

Update orientations using quaternion integration.

Integrates quaternion using angular velocity in body frame: dq/dt = (1/2) * q * omega_quat

Parameters

molecules	Vector of rigid bodies
dt	Timestep

update_positions()

static void occ::mults::RigidBodyDynamics::update_positions ( std::vector< RigidBodyState > &  molecules, double  dt  )

static

Update positions using current velocities (half-step)

r(t+dt) = r(t) + v(t)*dt + (1/2)*a(t)*dt^2

Parameters

molecules	Vector of rigid bodies
dt	Timestep

update_velocities()

static void occ::mults::RigidBodyDynamics::update_velocities ( std::vector< RigidBodyState > &  molecules, double  dt, bool  first_half  )

static

Update velocities using forces (half-step)

v(t+dt) = v(t) + (1/2)*[a(t) + a(t+dt)]*dt

Parameters

molecules	Vector of rigid bodies
dt	Timestep
first_half	If true, do first half-step; if false, do second half-step

velocity_verlet_step()

static void occ::mults::RigidBodyDynamics::velocity_verlet_step ( std::vector< RigidBodyState > &  molecules, double  dt  )

static

Perform one velocity Verlet integration step.

This integrates both translational and rotational degrees of freedom using the velocity Verlet algorithm:

1. Update positions and orientations using current velocities
2. Compute new forces and torques
3. Update velocities using average of old and new forces/torques

Parameters

molecules	Vector of rigid body states to integrate
dt	Timestep in femtoseconds

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The documentation for this class was generated from the following file:

• /home/runner/work/occ/occ/include/occ/mults/rigid_body_dynamics.h