SYNOPSIS

#include <coor.h>

Inherits sc::MolecularCoor.

Public Member Functions

CartMolecularCoor (Ref< Molecule > &mol)

CartMolecularCoor (StateIn &)

CartMolecularCoor (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.
virtual RefSCDimension dim ()
These implement the virtual functions inherited from MolecularCoor.
virtual int to_cartesian (const Ref< Molecule > &, const RefSCVector &internal)

virtual int to_internal (RefSCVector &internal)
Fill in the vector ``internal'' with the current internal coordinates.
virtual int to_cartesian (RefSCVector &cartesian, RefSCVector &internal)
Convert the internal coordinate gradients in ``internal'' to Cartesian coordinates and copy these Cartesian coordinate gradients to ``cartesian''.
virtual int to_internal (RefSCVector &internal, RefSCVector &cartesian)
Convert the Cartesian coordinate gradients in ``cartesian'' to internal coordinates and copy these internal coordinate gradients to ``internal''.
virtual int to_cartesian (RefSymmSCMatrix &cart, RefSymmSCMatrix &internal)
Convert the internal coordinate Hessian ``internal'' to Cartesian coordinates and copy the result to ``cartesian''.
virtual int to_internal (RefSymmSCMatrix &internal, RefSymmSCMatrix &cart)
Convert the Cartesian coordinate Hessian ``cartesian'' to internal coordinates and copy the result to ``internal''.
virtual void print (std::ostream &=ExEnv::out0()) const
Print the coordinate.
virtual void print_simples (std::ostream &=ExEnv::out0()) const

void guess_hessian (RefSymmSCMatrix &hessian)
Calculate an approximate hessian and place the result in ``hessian''.
RefSymmSCMatrix inverse_hessian (RefSymmSCMatrix &)
Given an Hessian, return the inverse of that hessian.

Protected Member Functions

virtual void init ()
Initializes the dimensions.

Protected Attributes

RefSCDimension dim_

Detailed Description

The CartMolecularCoor class implements Cartesian coordinates in a way suitable for use in geometry optimizations.

CartMolecularCoor is a SavableState has StateIn and KeyVal constructors. CartMolecularCoor is derived from MolecularCoor.

Member Function Documentation

void sc::CartMolecularCoor::guess_hessian (RefSymmSCMatrix & hessian) [virtual]

Calculate an approximate hessian and place the result in ``hessian''.

Implements sc::MolecularCoor.

RefSymmSCMatrix sc::CartMolecularCoor::inverse_hessian (RefSymmSCMatrix &) [virtual]

Given an Hessian, return the inverse of that hessian. For singular matrices this should return the generalized inverse.

Implements sc::MolecularCoor.

void sc::CartMolecularCoor::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.

Reimplemented from sc::MolecularCoor.

virtual int sc::CartMolecularCoor::to_cartesian (RefSymmSCMatrix & cartesian, RefSymmSCMatrix & internal) [virtual]

Convert the internal coordinate Hessian ``internal'' to Cartesian coordinates and copy the result to ``cartesian''. Only the variable internal coordinate force constants are transformed.

Implements sc::MolecularCoor.

virtual int sc::CartMolecularCoor::to_cartesian (RefSCVector & cartesian, RefSCVector & internal) [virtual]

Convert the internal coordinate gradients in ``internal'' to Cartesian coordinates and copy these Cartesian coordinate gradients to ``cartesian''. Only the variable internal coordinate gradients are transformed.

Implements sc::MolecularCoor.

virtual int sc::CartMolecularCoor::to_internal (RefSymmSCMatrix & internal, RefSymmSCMatrix & cartesian) [virtual]

Convert the Cartesian coordinate Hessian ``cartesian'' to internal coordinates and copy the result to ``internal''. Only the variable internal coordinate force constants are calculated.

Implements sc::MolecularCoor.

virtual int sc::CartMolecularCoor::to_internal (RefSCVector & internal, RefSCVector & cartesian) [virtual]

Convert the Cartesian coordinate gradients in ``cartesian'' to internal coordinates and copy these internal coordinate gradients to ``internal''. Only the variable internal coordinate gradients are calculated.

Implements sc::MolecularCoor.

virtual int sc::CartMolecularCoor::to_internal (RefSCVector & internal) [virtual]

Fill in the vector ``internal'' with the current internal coordinates. Note that this member will update the values of the variable internal coordinates.

Implements sc::MolecularCoor.

Author

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