OpenMD::BeadModel Class Reference

References: More...

#include <BeadModel.hpp>

Inheritance diagram for OpenMD::BeadModel:

Public Member Functions
	BeadModel ()
	References:
virtual std::size_t	assignElements ()=0
virtual void	checkElement (std::size_t i)
virtual void	writeElements (std::ostream &os)
virtual Mat3x3d	interactionTensor (const std::size_t i, const std::size_t j, const RealType viscosity)
virtual RealType	volumeCorrection ()
Public Member Functions inherited from OpenMD::ApproximateModel
	ApproximateModel ()
	References:
virtual void	setShape (Shape *shape)
virtual HydroProp *	calcHydroProps (RealType viscosity)
Public Member Functions inherited from OpenMD::HydrodynamicsModel
virtual void	init ()
void	writeHydroProps (HydroProp *hp, RealType temperature, std::ostream &os)

Protected Attributes
RealType	volumeOverlap_
Protected Attributes inherited from OpenMD::ApproximateModel
std::vector< HydrodynamicsElement >	elements_
Protected Attributes inherited from OpenMD::HydrodynamicsModel
Shape *	shape_

Detailed Description

References:

For overlapping beads and overlapping volume:

Beatriz Carrasco and Jose Garcia de la Torre and Peter Zipper; "Calculation of hydrodynamic properties of macromolecular bead models with overlapping spheres", Eur Biophys J (1999) 28: 510-515

For overlapping volume between two spherical beads: http://mathworld.wolfram.com/Sphere-SphereIntersection.html

For non-overlapping and overlapping translation-translation mobility tensors:

Zuk, P. J., E. Wajnryb, K. A. Mizerski, and P. Szymczak; “Rotne–Prager–Yamakawa Approximation for Different-Sized Particles in Application to Macromolecular Bead Models.”, Journal of Fluid Mechanics, 741 (2014)

For distinctions between centers of resistance and diffusion: Steven Harvey and Jose Garcia de la Torre; "Coordinate Systems for Modeling the Hydrodynamic Resistance and Diffusion Coefficients of Irregularly Shaped Rigid Macromolecules", Macromolecules 1980 13 (4), 960-964

Definition at line 87 of file BeadModel.hpp.

Constructor & Destructor Documentation

BeadModel()

OpenMD::BeadModel::BeadModel

(

)

References:

For the General Hydro Framework: Beatriz Carrasco and Jose Gracia de la Torre; "Hydrodynamic Properties of Rigid Particles: Comparison of Different Modeling and Computational Procedures", Biophysical Journal, 75(6), 3044, 1999

Xiuquan Sun, Teng Lin, and J. Daniel Gezelter; "Langevin dynamics for rigid bodies of arbitrary shape", J. Chem. Phys. 128, 234107 (2008)

For overlapping beads and overlapping volume:

Beatriz Carrasco and Jose Garcia de la Torre and Peter Zipper; "Calculation of hydrodynamic properties of macromolecular bead models with overlapping spheres", Eur Biophys J (1999) 28: 510-515

For overlapping volume between two spherical beads: http://mathworld.wolfram.com/Sphere-SphereIntersection.html

For non-overlapping and overlapping translation-translation mobility tensors:

Zuk, P. J., E. Wajnryb, K. A. Mizerski, and P. Szymczak; “Rotne–Prager–Yamakawa Approximation for Different-Sized Particles in Application to Macromolecular Bead Models.”, Journal of Fluid Mechanics, 741 (2014)

For distinctions between centers of resistance and diffusion: Steven Harvey and Jose Garcia de la Torre; "Coordinate Systems for Modeling the Hydrodynamic Resistance and Diffusion Coefficients of Irregularly Shaped Rigid Macromolecules", Macromolecules 1980 13 (4), 960-964

Definition at line 95 of file BeadModel.cpp.

Member Function Documentation

assignElements()

virtual std::size_t OpenMD::BeadModel::assignElements ( )

pure virtual

Implements OpenMD::ApproximateModel.

checkElement()

void OpenMD::BeadModel::checkElement ( std::size_t i )

virtual

Implements OpenMD::ApproximateModel.

Definition at line 97 of file BeadModel.cpp.

interactionTensor()

Mat3x3d OpenMD::BeadModel::interactionTensor ( const std::size_t i, const std::size_t j, const RealType viscosity )

virtual

Implements OpenMD::ApproximateModel.

Definition at line 136 of file BeadModel.cpp.

volumeCorrection()

RealType OpenMD::BeadModel::volumeCorrection ( )

virtual

Reimplemented from OpenMD::ApproximateModel.

Definition at line 114 of file BeadModel.cpp.

writeElements()

void OpenMD::BeadModel::writeElements ( std::ostream & os )

virtual

Implements OpenMD::ApproximateModel.

Definition at line 126 of file BeadModel.cpp.

Member Data Documentation

volumeOverlap_

RealType OpenMD::BeadModel::volumeOverlap_

protected

Definition at line 100 of file BeadModel.hpp.

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

• hydrodynamics/BeadModel.hpp
• hydrodynamics/BeadModel.cpp