NAME

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

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 tocartesian''.
       virtual int to_internal (RefSCVector &internal, RefSCVector &cartesian)
           Convert the Cartesian coordinate gradients in cartesian'' to internal coordinates and
           copy these internal coordinate gradients tointernal''.
       virtual int to_cartesian (RefSymmSCMatrix &cart, RefSymmSCMatrix &internal)
           Convert the internal coordinate Hessian internal'' to Cartesian coordinates and copy
           the result tocartesian''.
       virtual int to_internal (RefSymmSCMatrix &internal, RefSymmSCMatrix &cart)
           Convert the Cartesian coordinate Hessian cartesian'' to internal coordinates and copy
           the result tointernal''.
       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.

       Public Member Functions inherited from sc::MolecularCoor
       MolecularCoor (Ref< Molecule > &)
       MolecularCoor (StateIn &)
       MolecularCoor (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.
       RefSCDimension dim_natom3 ()
           Returns a smart reference to an SCDimension equal to the number of atoms in the
           molecule times 3.
       Ref< Molecule > molecule () const
           Returns the molecule.
       int to_cartesian (const RefSCVector &internal)
           Given a set of displaced internal coordinates, update the cartesian coordinates of the
           Molecule contained herein.
       virtual int nconstrained ()
           Returns the number of constrained coordinates.
       virtual Ref< NonlinearTransform > change_coordinates ()
           When this is called, MoleculeCoor may select a new internal coordinate system and
           return a transform to it.
       Ref< SCMatrixKit > matrixkit () const

       Public Member Functions inherited from sc::SavableState
       SavableState & operator= (const SavableState &)
       void save_state (StateOut &)
           Save the state of the object as specified by the StateOut object.
       void save_object_state (StateOut &)
           This can be used for saving state when the exact type of the object is known for both
           the save and the restore.
       virtual void save_vbase_state (StateOut &)
           Save the virtual bases for the object.

       Public Member Functions inherited from sc::DescribedClass
       DescribedClass (const DescribedClass &)
       DescribedClass & operator= (const DescribedClass &)
       ClassDesc * class_desc () const  throw ()
           This returns the unique pointer to the ClassDesc corresponding to the given type_info
           object.
       const char * class_name () const
           Return the name of the object's exact type.
       int class_version () const
           Return the version of the class.

       Public Member Functions inherited from sc::RefCount
       int lock_ptr () const
           Lock this object.
       int unlock_ptr () const
           Unlock this object.
       void use_locks (bool inVal)
           start and stop using locks on this object
       refcount_t nreference () const
           Return the reference count.
       refcount_t reference ()
           Increment the reference count and return the new count.
       refcount_t dereference ()
           Decrement the reference count and return the new count.
       int managed () const
       void unmanage ()
           Turn off the reference counting mechanism for this object.
       int managed () const
           Return 1 if the object is managed. Otherwise return 0.

       Public Member Functions inherited from sc::Identity
       Identifier identifier ()
           Return the Identifier for this argument.

   Protected Member Functions
       virtual void init ()
           Initializes the dimensions.

       Protected Member Functions inherited from sc::SavableState
       SavableState (const SavableState &)
       SavableState (StateIn &)
           Each derived class StateIn CTOR handles the restore corresponding to calling
           save_object_state, save_vbase_state, and save_data_state listed above.

       Protected Member Functions inherited from sc::RefCount
       RefCount (const RefCount &)
       RefCount & operator= (const RefCount &)

   Protected Attributes
       RefSCDimension dim_

       Protected Attributes inherited from sc::MolecularCoor
       Ref< Molecule > molecule_
       RefSCDimension dnatom3_
       Ref< SCMatrixKit > matrixkit_
       int debug_

   Additional Inherited Members
       Static Public Member Functions inherited from sc::SavableState
       static void save_state (SavableState *s, StateOut &)
       static SavableState * restore_state (StateIn &si)
           Restores objects saved with save_state.
       static SavableState * key_restore_state (StateIn &si, const char *keyword)
           Like restore_state, but keyword is used to override values while restoring.
       static SavableState * dir_restore_state (StateIn &si, const char *objectname, const char
           *keyword=0)

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

   virtual RefSCDimension sc::CartMolecularCoor::dim () [virtual]
       These implement the virtual functions inherited from MolecularCoor.

       Implements sc::MolecularCoor.

   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.

   virtual void sc::CartMolecularCoor::print (std::ostream & = ExEnv::out0()) const [virtual]
       Print the coordinate.

       Implements sc::MolecularCoor.

   virtual void sc::CartMolecularCoor::print_simples (std::ostream & = ExEnv::out0()) const
       [virtual]
       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::SavableState.

   virtual int sc::CartMolecularCoor::to_cartesian (const Ref< Molecule > &, const RefSCVector &
       internal) [virtual]
       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 tocartesian''. Only the variable internal coordinate
       gradients are transformed.

       Implements 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 tocartesian''. Only the variable internal coordinate force constants are
       transformed.

       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.

   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 tointernal''. Only the variable internal coordinate
       gradients are calculated.

       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 tointernal''. Only the variable internal coordinate force constants are calculated.

       Implements sc::MolecularCoor.

Author

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