Molecular dynamics integrator for rotational motion. More...

#include "rotation.hpp"
#include <utils/Vector.hpp>
#include <utils/mask.hpp>
#include <cassert>
#include <cmath>

Include dependency graph for rotation.cpp:

Go to the source code of this file.

Functions
static void	define_Qdd (Particle const &p, Utils::Quaternion< double > &Qd, Utils::Quaternion< double > &Qdd, Utils::Vector3d &S, Utils::Vector3d &Wd)
	Calculate the derivatives of the quaternion and angular acceleration for a given particle.

void	propagate_omega_quat_particle (Particle &p, double time_step)
	See [31].

void	convert_torque_propagate_omega (Particle &p, double time_step)

void	convert_initial_torques (const ParticleRange &particles)
	Convert torques to the body-fixed frame before the integration loop.

Detailed Description

Molecular dynamics integrator for rotational motion.

A velocity Verlet algorithm using quaternions is implemented to tackle rotational motion. See [27] for the method and [3] for the quaternion components indexing used here. A random torque and a friction term are added to provide the constant NVT conditions. Due to this feature all particles are treated as 3D objects with 3 translational and 3 rotational degrees of freedom if ROTATION is compiled in.

Definition in file rotation.cpp.

Function Documentation

◆ convert_initial_torques()

void convert_initial_torques ( const ParticleRange & particles )

Convert torques to the body-fixed frame before the integration loop.

Definition at line 188 of file rotation.cpp.

References convert_torque_to_body_frame_apply_fix().

Referenced by System::System::integrate().

◆ convert_torque_propagate_omega()

void convert_torque_propagate_omega	(	Particle &	p,
		double	time_step
	)

Definition at line 159 of file rotation.cpp.

References Particle::can_rotate(), convert_torque_to_body_frame_apply_fix(), Particle::omega(), Particle::rinertia(), and Particle::torque().

Referenced by velocity_verlet_rotator_2().

◆ define_Qdd()

static void define_Qdd	(	Particle const &	p,
		Utils::Quaternion< double > &	Qd,
		Utils::Quaternion< double > &	Qdd,
		Utils::Vector3d &	S,
		Utils::Vector3d &	Wd
	)

static

Calculate the derivatives of the quaternion and angular acceleration for a given particle.

See [39]. Please note that ESPResSo uses scalar-first notation for quaternions, while [39] uses scalar-last notation.

Parameters

[in]	p	Particle
[out]	Qd	First derivative of the particle quaternion
[out]	Qdd	Second derivative of the particle quaternion
[out]	S	Function of `Qd` and `Qdd`, used to evaluate the Lagrange parameter lambda
[out]	Wd	Angular acceleration of the particle

Definition at line 56 of file rotation.cpp.

References Particle::can_rotate_around(), Utils::Quaternion< T >::norm2(), Particle::omega(), Particle::quat(), Particle::rinertia(), and Particle::torque().

Referenced by propagate_omega_quat_particle().

◆ propagate_omega_quat_particle()

void propagate_omega_quat_particle	(	Particle &	p,
		double	time_step
	)

See [31].

Propagate angular velocities and update quaternions on a particle.

Please note that ESPResSo uses scalar-first notation for quaternions, while [31] uses scalar-last notation.

For very high angular velocities (e.g. if the product of time_step with the largest component of p.omega() is superior to ~2.0) and for time_step superior or equal to unity, the calculation might fail.

Todo:: implement for fixed_coord_flag

Definition at line 125 of file rotation.cpp.

References Particle::can_rotate(), define_Qdd(), Utils::Quaternion< T >::identity(), Utils::mask(), Particle::omega(), Particle::quat(), and Particle::rotation().