OpenMD::RPYMobility Class Reference

Public Member Functions
	RPYMobility (const std::vector< RealType > &radii, RealType viscosity)
bool	update (const std::vector< Vector3d > &positions)
	(Re)build M, R = M^{-1}, and S = chol(R) from current bead positions. Positions must be the unwrapped intramolecular coordinates. Returns false if R is not positive definite (Cholesky hit a non-positive pivot).
std::vector< Vector3d >	effectiveAmbient (const std::vector< Vector3d > &positions, const std::vector< Vector3d > &ambient, const Mat3x3d &E) const
	vinf_eff_i = ambient_i + sum{j!=i} mu_td_ij : E (E symmetric traceless)
std::vector< Vector3d >	dragForce (const std::vector< Vector3d > &vEff, const std::vector< Vector3d > &vel) const
	Hydrodynamic drag: f_i = sum_j R_ij ( vEff_j - vel_j ).
std::vector< Vector3d >	randomForce (const std::vector< RealType > &Z, RealType kT, RealType dt) const
	FDT random force: sqrt(2 kT / dt) * S * Z, with Z a 3N vector of independent standard normal draws (row 3i+a is bead i, component a).
std::size_t	size () const
bool	isPositiveDefinite () const
const DynamicRectMatrix< RealType > &	mobility () const
const DynamicRectMatrix< RealType > &	resistance () const
const DynamicRectMatrix< RealType > &	cholesky () const

Detailed Description

Definition at line 71 of file RPYMobility.hpp.

Constructor & Destructor Documentation

RPYMobility()

OpenMD::RPYMobility::RPYMobility	(	const std::vector< RealType > &	radii,
		RealType	viscosity )

Definition at line 51 of file RPYMobility.cpp.

Member Function Documentation

cholesky()

const DynamicRectMatrix< RealType > & OpenMD::RPYMobility::cholesky ( ) const

inline

Definition at line 98 of file RPYMobility.hpp.

dragForce()

std::vector< Vector3d > OpenMD::RPYMobility::dragForce	(	const std::vector< Vector3d > &	vEff,
		const std::vector< Vector3d > &	vel ) const

Hydrodynamic drag: f_i = sum_j R_ij ( vEff_j - vel_j ).

Definition at line 115 of file RPYMobility.cpp.

References dragForce().

Referenced by dragForce().

effectiveAmbient()

std::vector< Vector3d > OpenMD::RPYMobility::effectiveAmbient	(	const std::vector< Vector3d > &	positions,
		const std::vector< Vector3d > &	ambient,
		const Mat3x3d &	E ) const

vinf_eff_i = ambient_i + sum{j!=i} mu_td_ij : E (E symmetric traceless)

Definition at line 101 of file RPYMobility.cpp.

References effectiveAmbient().

Referenced by effectiveAmbient().

isPositiveDefinite()

bool OpenMD::RPYMobility::isPositiveDefinite ( ) const

inline

Definition at line 95 of file RPYMobility.hpp.

mobility()

const DynamicRectMatrix< RealType > & OpenMD::RPYMobility::mobility ( ) const

inline

Definition at line 96 of file RPYMobility.hpp.

randomForce()

std::vector< Vector3d > OpenMD::RPYMobility::randomForce	(	const std::vector< RealType > &	Z,
		RealType	kT,
		RealType	dt ) const

FDT random force: sqrt(2 kT / dt) * S * Z, with Z a 3N vector of independent standard normal draws (row 3i+a is bead i, component a).

Definition at line 136 of file RPYMobility.cpp.

References randomForce().

Referenced by randomForce().

resistance()

const DynamicRectMatrix< RealType > & OpenMD::RPYMobility::resistance ( ) const

inline

Definition at line 97 of file RPYMobility.hpp.

size()

std::size_t OpenMD::RPYMobility::size ( ) const

inline

Definition at line 94 of file RPYMobility.hpp.

update()

bool OpenMD::RPYMobility::update

(

const std::vector< Vector3d > &

positions

)

(Re)build M, R = M^{-1}, and S = chol(R) from current bead positions. Positions must be the unwrapped intramolecular coordinates. Returns false if R is not positive definite (Cholesky hit a non-positive pivot).

Definition at line 60 of file RPYMobility.cpp.

References OpenMD::invertMatrix(), and update().

Referenced by update().

---

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

• hydrodynamics/RPYMobility.hpp
• hydrodynamics/RPYMobility.cpp