rotation.hpp File Reference

This file contains all subroutines required to process rotational motion. More...

#include "config/config.hpp"
#include "Particle.hpp"
#include "ParticleRange.hpp"
#include <utils/Vector.hpp>
#include <utils/mask.hpp>
#include <utils/math/quaternion.hpp>
#include <utils/matrix.hpp>
#include <utils/quaternion.hpp>
#include <cassert>
#include <cmath>
#include <limits>
#include <utility>

Include dependency graph for rotation.hpp:

This graph shows which files directly or indirectly include this file:

Go to the source code of this file.

Functions
void	propagate_omega_quat_particle (Particle &p, double time_step)
	Propagate angular velocities and update quaternions on a particle.
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.
Utils::Vector3d	convert_vector_body_to_space (const Particle &p, const Utils::Vector3d &vec)
Utils::Vector3d	convert_vector_space_to_body (const Particle &p, const Utils::Vector3d &v)
template<class T >
auto	convert_body_to_space (const Utils::Quaternion< double > &quat, const Utils::Matrix< T, 3, 3 > &A)
	Transform matrix from body- to space-fixed frame.
template<class T >
auto	convert_body_to_space (const Particle &p, const Utils::Matrix< T, 3, 3 > &A)
	Transform matrix from body- to space-fixed frame.
std::pair< Utils::Quaternion< double >, double >	convert_dip_to_quat (const Utils::Vector3d &dip)
	convert a dipole moment to quaternions and dipolar strength
Utils::Quaternion< double >	local_rotate_particle_body (Particle const &p, const Utils::Vector3d &axis_body_frame, const double phi)
	Rotate the particle p around the body-frame defined NORMALIZED axis aBodyFrame by amount phi.
void	local_rotate_particle (Particle &p, const Utils::Vector3d &axis_space_frame, const double phi)
	Rotate the particle p around the NORMALIZED axis aSpaceFrame by amount phi.
void	convert_torque_to_body_frame_apply_fix (Particle &p)

Detailed Description

This file contains all subroutines required to process rotational motion.

Definition in file rotation.hpp.

Function Documentation

convert_body_to_space() [1/2]

template<class T >

auto convert_body_to_space	(	const Particle &	p,
		const Utils::Matrix< T, 3, 3 > &	A
	)

Transform matrix from body- to space-fixed frame.

Template Parameters

T	Scalar type

Parameters

p	Particle transforming from.
A	Matrix representation in body-fixed coordinates.

Returns

Matrix representation in space-fixed coordinates.

Definition at line 100 of file rotation.hpp.

References convert_body_to_space(), and Particle::quat().

convert_body_to_space() [2/2]

template<class T >

auto convert_body_to_space	(	const Utils::Quaternion< double > &	quat,
		const Utils::Matrix< T, 3, 3 > &	A
	)

Transform matrix from body- to space-fixed frame.

Given a linear map represented by \( A \in \mathbb{R}^{3 \times 3}\) in the body-fixed frame, this returns the matrix \( A \in \mathbb{R}^{3 \times 3}\) representing the map in the space-fixed frame. They are related by the map between the space-fixed and body-fixed frame \(O\) like

\[ A' = O A O^T. \]

Template Parameters

T	Scalar type

Parameters

quat	quaternion to transform from, i.e. the rotation that transforms space- to body-fixed frame.
A	Matrix representation in body-fixed coordinates.

Returns

Matrix representation in space-fixed coordinates.

Definition at line 86 of file rotation.hpp.

References Utils::Matrix< T, Rows, Cols >::transposed().

Referenced by convert_body_to_space(), and Thermostat::handle_particle_anisotropy().

convert_dip_to_quat()

std::pair< Utils::Quaternion< double >, double > convert_dip_to_quat ( const Utils::Vector3d &  dip )

inline

convert a dipole moment to quaternions and dipolar strength

Definition at line 108 of file rotation.hpp.

References Utils::convert_director_to_quaternion(), and Utils::Vector< T, N >::norm().

Referenced by ScriptInterface::Particles::ParticleHandle::ParticleHandle().

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().

convert_torque_to_body_frame_apply_fix()

void convert_torque_to_body_frame_apply_fix ( Particle &  p )

inline

Definition at line 143 of file rotation.hpp.

References convert_vector_space_to_body(), Particle::rotation(), and Particle::torque().

Referenced by brownian_dynamics_rotator(), convert_initial_torques(), and convert_torque_propagate_omega().

convert_vector_body_to_space()

Utils::Vector3d convert_vector_body_to_space ( const Particle &  p, const Utils::Vector3d &  vec  )

inline

Definition at line 57 of file rotation.hpp.

References Particle::quat().

Referenced by ParticleObservables::traits< Particle >::angular_velocity(), bd_drag(), bd_drag_vel(), bd_random_walk(), ScriptInterface::Particles::ParticleHandle::do_call_method(), ScriptInterface::Particles::ParticleHandle::ParticleHandle(), System::System::thermostat_force_init(), and velocity().

convert_vector_space_to_body()

Utils::Vector3d convert_vector_space_to_body ( const Particle &  p, const Utils::Vector3d &  v  )

inline

Definition at line 61 of file rotation.hpp.

References Particle::quat().

Referenced by bd_drag(), bd_drag_vel(), convert_torque_to_body_frame_apply_fix(), ScriptInterface::Particles::ParticleHandle::do_call_method(), local_rotate_particle(), ScriptInterface::Particles::ParticleHandle::ParticleHandle(), and ParticleObservables::traits< Particle >::velocity_body().

local_rotate_particle()

void local_rotate_particle ( Particle &  p, const Utils::Vector3d &  axis_space_frame, const double  phi  )

inline

Rotate the particle p around the NORMALIZED axis aSpaceFrame by amount phi.

Definition at line 133 of file rotation.hpp.

References convert_vector_space_to_body(), local_rotate_particle_body(), and Particle::quat().

Referenced by ScriptInterface::Particles::ParticleHandle::do_call_method(), ScriptInterface::System::rotate_system(), steepest_descent_step(), and stokesian_dynamics_step_1().

local_rotate_particle_body()

Utils::Quaternion< double > local_rotate_particle_body ( Particle const &  p, const Utils::Vector3d &  axis_body_frame, const double  phi  )

inline

Rotate the particle p around the body-frame defined NORMALIZED axis aBodyFrame by amount phi.

Definition at line 119 of file rotation.hpp.

References Particle::can_rotate(), Particle::quat(), and Particle::rotation().

Referenced by bd_drag_rot(), bd_random_walk_rot(), and local_rotate_particle().

propagate_omega_quat_particle()

void propagate_omega_quat_particle	(	Particle &	p,
		double	time_step
	)

Propagate angular velocities and update quaternions on a particle.

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().

Referenced by velocity_verlet_rotator_1().