OpenMD  2.5
Molecular Dynamics in the Open
OpenMD::HydroProp Class Reference

#include "hydrodynamics/HydroProp.hpp"

Public Member Functions

 HydroProp ()
 HydroProp (Vector3d cor, Mat6x6d Xi, Mat6x6d D)
 HydroProp (const std::string &frictionLine)
 ~HydroProp ()
void complete ()
void setCOR (Vector3d cor)
void setXi (Mat6x6d Xi)
void setD (Mat6x6d D)
void setName (std::string name)
Vector3d getCOR ()
Mat3x3d getXitt ()
Mat3x3d getXitr ()
Mat3x3d getXirt ()
Mat3x3d getXirr ()
Mat6x6d getS ()
Mat6x6d getD ()
Mat6x6d getXi ()
std::string getName ()

Private Attributes

std::string name_
Vector3d cor_
Mat6x6d Xi_
Mat6x6d D_
Mat3x3d Xitt_
Mat3x3d Xirt_
Mat3x3d Xitr_
Mat3x3d Xirr_
Mat6x6d S_
bool hasCOR
bool hasXi

Detailed Description

Container for information about the hydrodynamic behavior of objects undergoing Langevin dynamics.

the units for the center of resistance (a location) are in Angstroms
the units of Xi, the resistance tensor are: Xitt (Translation-translation) : kcal fs mol^-1 Angstroms^-2 Xirt (Rotation-translation) : kcal fs mol^-1 Angstroms^-1 radians^-1 Xitr (Translation-rotation) : kcal fs mol^-1 Angstroms^-1 radians^-1 Xirr (Rotation-rotation) : kcal fs mol^-1 radians^-2
the units of D, the diffusion tensor are: Dtt (Translation-translation) : Angstroms^2 fs^-1 Drt (Rotation-translation) : Angstroms fs^-1 Dtr (Translation-rotation) : Angstroms fs^-1 Drr (Rotation-rotation) : fs^-1
after setting the value of Xi manually, the complete() function should be called to perform the Cholesky Decomposition.

Definition at line 70 of file HydroProp.hpp.

Constructor & Destructor Documentation

◆ HydroProp() [1/3]

OpenMD::HydroProp::HydroProp ( )

Definition at line 49 of file HydroProp.cpp.

◆ HydroProp() [2/3]

OpenMD::HydroProp::HydroProp ( Vector3d  cor,
Mat6x6d  Xi,
Mat6x6d  D 

Definition at line 52 of file HydroProp.cpp.

◆ HydroProp() [3/3]

◆ ~HydroProp()

OpenMD::HydroProp::~HydroProp ( )

Definition at line 76 of file HydroProp.hpp.

References complete().

Member Function Documentation

◆ complete()

void OpenMD::HydroProp::complete ( )

◆ getCOR()

Vector3d OpenMD::HydroProp::getCOR ( )

Definition at line 83 of file HydroProp.hpp.

References cor_.

Referenced by OpenMD::HydrodynamicsModel::writeHydroProps().

◆ getD()

Mat6x6d OpenMD::HydroProp::getD ( )

Definition at line 89 of file HydroProp.hpp.

References D_.

Referenced by OpenMD::HydrodynamicsModel::writeHydroProps().

◆ getName()

std::string OpenMD::HydroProp::getName ( )

Definition at line 91 of file HydroProp.hpp.

References name_.

Referenced by OpenMD::LDForceManager::parseFrictionFile().

◆ getS()

Mat6x6d OpenMD::HydroProp::getS ( )

Definition at line 88 of file HydroProp.hpp.

References S_.

◆ getXi()

Mat6x6d OpenMD::HydroProp::getXi ( )

Definition at line 90 of file HydroProp.hpp.

References Xi_.

Referenced by OpenMD::HydrodynamicsModel::writeHydroProps().

◆ getXirr()

Mat3x3d OpenMD::HydroProp::getXirr ( )

Definition at line 87 of file HydroProp.hpp.

References Xirr_.

◆ getXirt()

Mat3x3d OpenMD::HydroProp::getXirt ( )

Definition at line 86 of file HydroProp.hpp.

References Xirt_.

◆ getXitr()

Mat3x3d OpenMD::HydroProp::getXitr ( )

Definition at line 85 of file HydroProp.hpp.

References Xitr_.

◆ getXitt()

Mat3x3d OpenMD::HydroProp::getXitt ( )

Definition at line 84 of file HydroProp.hpp.

References Xitt_.

◆ setCOR()

void OpenMD::HydroProp::setCOR ( Vector3d  cor)

◆ setD()

void OpenMD::HydroProp::setD ( Mat6x6d  D)

◆ setName()

void OpenMD::HydroProp::setName ( std::string  name)

Definition at line 81 of file HydroProp.hpp.

References name_.

◆ setXi()

void OpenMD::HydroProp::setXi ( Mat6x6d  Xi)

Member Data Documentation

◆ cor_

Vector3d OpenMD::HydroProp::cor_

Definition at line 96 of file HydroProp.hpp.

Referenced by getCOR(), HydroProp(), and setCOR().

◆ D_

Mat6x6d OpenMD::HydroProp::D_

Definition at line 98 of file HydroProp.hpp.

Referenced by getD(), and setD().

◆ hasCOR

bool OpenMD::HydroProp::hasCOR

Definition at line 104 of file HydroProp.hpp.

Referenced by HydroProp(), and setCOR().

◆ hasXi

bool OpenMD::HydroProp::hasXi

Definition at line 105 of file HydroProp.hpp.

Referenced by complete(), HydroProp(), and setXi().

◆ name_

std::string OpenMD::HydroProp::name_

Definition at line 95 of file HydroProp.hpp.

Referenced by getName(), HydroProp(), and setName().

◆ S_

Mat6x6d OpenMD::HydroProp::S_

Definition at line 103 of file HydroProp.hpp.

Referenced by complete(), getS(), and HydroProp().

◆ Xi_

Mat6x6d OpenMD::HydroProp::Xi_

Definition at line 97 of file HydroProp.hpp.

Referenced by complete(), getXi(), HydroProp(), and setXi().

◆ Xirr_

Mat3x3d OpenMD::HydroProp::Xirr_

Definition at line 102 of file HydroProp.hpp.

Referenced by complete(), getXirr(), and HydroProp().

◆ Xirt_

Mat3x3d OpenMD::HydroProp::Xirt_

Definition at line 100 of file HydroProp.hpp.

Referenced by complete(), getXirt(), and HydroProp().

◆ Xitr_

Mat3x3d OpenMD::HydroProp::Xitr_

Definition at line 101 of file HydroProp.hpp.

Referenced by complete(), getXitr(), and HydroProp().

◆ Xitt_

Mat3x3d OpenMD::HydroProp::Xitt_

Definition at line 99 of file HydroProp.hpp.

Referenced by complete(), getXitt(), and HydroProp().

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