NAME

       sc::SymmMolecularCoor - 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_

   Additional Inherited Members

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.

       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,
           $ppa_2$, 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

   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.

       Reimplemented from sc::IntMolecularCoor.

Author

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