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SymmMolecularCoor Class Reference

The SymmMolecularCoor class derives from IntMolecularCoor. More...

#include <coor.h>

Inheritance diagram for SymmMolecularCoor

[legend]Collaboration diagram for SymmMolecularCoor:

[legend]List of all members.

Public Methods
	SymmMolecularCoor (Ref< Molecule > &mol)
	SymmMolecularCoor (StateIn &)
	SymmMolecularCoor (const Ref< KeyVal > &)
	The KeyVal constructor. More...
virtual	~SymmMolecularCoor ()
void	save_data_state (StateOut &)
	Save the base classes (with save_data_state) and the members in the same order that the StateIn CTOR initializes them. More...
void	form_coordinates (int keep_variable=0)
	Actually form the variable and constant internal coordinates from simple internal coordinates.
void	guess_hessian (RefSymmSCMatrix &hessian)
	Form the approximate hessian.
RefSymmSCMatrix	inverse_hessian (RefSymmSCMatrix &)
	Invert the hessian.
Ref<NonlinearTransform>	change_coordinates ()
	This overrides MoleculeCoor's change_coordinates and might transform to a new set of coordinates.
void	print (std::ostream &=ExEnv::out()) const
	Print the coordinate.
Protected Methods
void	init ()
	This is called by the constructors of classes derived from IntMolecularCoor. More...
Protected Attributes
int	change_coordinates_
int	transform_hessian_
double	max_kappa2_

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Detailed Description

The SymmMolecularCoor class derives from IntMolecularCoor.

It provides a unique set of totally symmetric internal coordinates. Giving an MolecularEnergy object a coor is usually the best way to optimize a molecular structure. However, for some classes of molecules SymmMolecularCoor doesn't work very well. For example, enediyne can cause problems. In these cases, cartesian coordinates (obtained by not giving the MolecularEnergy object the coor keyword) might be better or you can manually specify the coordinates that the SymmMolecularCoor object uses with the variable keyword (see the IntMolecularCoor class description).

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Constructor & Destructor Documentation

SymmMolecularCoor::SymmMolecularCoor ( const Ref< KeyVal > & )

The KeyVal constructor. change_coordinates If true, the quality of the internal coordinates will be checked periodically and if they are beginning to become linearly dependent a new set of internal coordinates will be computed. The default is false. max_kappa2 A measure of the quality of the internal coordinates. Values of the 2-norm condition, , larger than max_kappa2 are considered linearly dependent. The default is 10.0. transform_hessian If true, the hessian will be transformed every time the internal coordinates are formed. The default is true.

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Member Function Documentation

void SymmMolecularCoor::init ( ) [protected, virtual]

This is called by the constructors of classes derived from IntMolecularCoor. It initialized the lists of simple internal coordinates, and then calls the form_coordinates() member. Reimplemented from IntMolecularCoor.

void SymmMolecularCoor::save_data_state ( StateOut & s ) [virtual]

Save the base classes (with save_data_state) and the members in the same order that the StateIn CTOR initializes them. This must be implemented by the derived class if the class has data. Reimplemented from IntMolecularCoor.

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

• coor.h

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