Inheritance diagram for OpenMD::ApproximateModel:

Public Member Functions
	ApproximateModel ()
	References:

virtual void	setShape (Shape *shape)

virtual HydroProp *	calcHydroProps (RealType viscosity)

virtual std::size_t	assignElements ()=0

virtual void	checkElement (std::size_t i)=0

virtual void	writeElements (std::ostream &os)=0

virtual Mat3x3d	interactionTensor (std::size_t i, std::size_t j, RealType viscosity)=0

virtual RealType	volumeCorrection ()

Public Member Functions inherited from OpenMD::HydrodynamicsModel
virtual void	init ()

void	writeHydroProps (HydroProp *hp, RealType temperature, std::ostream &os)

Protected Attributes
std::vector< HydrodynamicsElement >	elements_

Protected Attributes inherited from OpenMD::HydrodynamicsModel
Shape *	shape_

Detailed Description

Definition at line 67 of file ApproximateModel.hpp.

Constructor & Destructor Documentation

◆ ApproximateModel()

OpenMD::ApproximateModel::ApproximateModel ( )

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 ApproximateModel.cpp.

Member Function Documentation

◆ calcHydroProps()

HydroProp * OpenMD::ApproximateModel::calcHydroProps ( RealType viscosity )

virtual

Reimplemented from OpenMD::HydrodynamicsModel.

Definition at line 107 of file ApproximateModel.cpp.

◆ setShape()

void OpenMD::ApproximateModel::setShape ( Shape * shape )

virtual

Reimplemented from OpenMD::HydrodynamicsModel.

Definition at line 99 of file ApproximateModel.cpp.

◆ volumeCorrection()

virtual RealType OpenMD::ApproximateModel::volumeCorrection ( )

inlinevirtual

Definition at line 80 of file ApproximateModel.hpp.

◆ writeElements()

virtual void OpenMD::ApproximateModel::writeElements ( std::ostream & os )

pure virtual

Implements OpenMD::HydrodynamicsModel.

Member Data Documentation

◆ elements_

std::vector<HydrodynamicsElement> OpenMD::ApproximateModel::elements_

protected

Definition at line 83 of file ApproximateModel.hpp.

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

hydrodynamics/ApproximateModel.hpp
hydrodynamics/ApproximateModel.cpp

Public Member Functions

Protected Attributes