man sc::SymmMolecularCoor (3): The SymmMolecularCoor class derives from IntMolecularCoor.

SYNOPSIS

#include <coor.h>

Inherits sc::IntMolecularCoor.

Public Member Functions

SymmMolecularCoor (Ref< Molecule > &mol)

SymmMolecularCoor (StateIn &)

SymmMolecularCoor (const Ref< KeyVal > &)
The KeyVal constructor.
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.
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::out0()) const
Print the coordinate.

Protected Member Functions

void init ()
This is called by the constructors of classes derived from IntMolecularCoor.

Protected Attributes

int change_coordinates_

int transform_hessian_

double max_kappa2_

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).

Constructor & Destructor Documentation

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

The KeyVal constructor. .IP "change_coordinates" 1c 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, $ppa_2$, 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.

Member Function Documentation

Ref<NonlinearTransform> sc::SymmMolecularCoor::change_coordinates () [virtual]

This overrides MoleculeCoor's change_coordinates and might transform to a new set of coordinates.

Reimplemented from sc::MolecularCoor.

void sc::SymmMolecularCoor::form_coordinates (int keep_variable = 0) [virtual]

Actually form the variable and constant internal coordinates from simple internal coordinates.

Implements sc::IntMolecularCoor.

void sc::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 sc::IntMolecularCoor.

void sc::SymmMolecularCoor::save_data_state (StateOut &) [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.