NAME

       sc::MolecularCoor - The MolecularCoor abstract class describes the coordinate system used
       to describe a molecule.

SYNOPSIS

       #include <coor.h>

       Inherits sc::SavableState.

       Inherited by sc::CartMolecularCoor, and sc::IntMolecularCoor.

   Public Member Functions
       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.
       virtual void print (std::ostream &=ExEnv::out0()) const =0
           Print the coordinate.
       virtual void print_simples (std::ostream &=ExEnv::out0()) const =0
       virtual RefSCDimension dim ()=0
           Returns a smart reference to an SCDimension equal to the number of coordinates (be
           they Cartesian, internal, or whatever) that are being optimized.
       int to_cartesian (const RefSCVector &internal)
           Given a set of displaced internal coordinates, update the cartesian coordinates of the
           Molecule contained herein.
       virtual int to_cartesian (const Ref< Molecule > &mol, const RefSCVector &internal)=0
       virtual int to_internal (RefSCVector &internal)=0
           Fill in the vector ``internal'' with the current internal coordinates.
       virtual int to_cartesian (RefSCVector &cartesian, RefSCVector &internal)=0
           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)=0
           Convert the Cartesian coordinate gradients in cartesian'' to internal coordinates and
           copy these internal coordinate gradients tointernal''.
       virtual int to_cartesian (RefSymmSCMatrix &cartesian, RefSymmSCMatrix &internal)=0
           Convert the internal coordinate Hessian internal'' to Cartesian coordinates and copy
           the result tocartesian''.
       virtual int to_internal (RefSymmSCMatrix &internal, RefSymmSCMatrix &cartesian)=0
           Convert the Cartesian coordinate Hessian cartesian'' to internal coordinates and copy
           the result tointernal''.
       virtual void guess_hessian (RefSymmSCMatrix &hessian)=0
           Calculate an approximate hessian and place the result in ``hessian''.
       virtual RefSymmSCMatrix inverse_hessian (RefSymmSCMatrix &)=0
           Given an Hessian, return the inverse of that hessian.
       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 Attributes
       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)

       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 &)

Detailed Description

       The MolecularCoor abstract class describes the coordinate system used to describe a
       molecule.

       It is used to convert a molecule's cartesian coordinates to and from this coordinate
       system.

Constructor & Destructor Documentation

   sc::MolecularCoor::MolecularCoor (const Ref< KeyVal > &)
       The KeyVal constructor.

       molecule
           A Molecule object. There is no default.

       debug
           An integer which, if nonzero, will cause extra output.

       matrixkit
           A SCMatrixKit object. It is usually unnecessary to give this keyword.

       natom3
           An SCDimension object for the dimension of the vector of cartesian coordinates. It is
           usually unnecessary to give this keyword.

Member Function Documentation

   virtual Ref< NonlinearTransform > sc::MolecularCoor::change_coordinates () [virtual]
       When this is called, MoleculeCoor may select a new internal coordinate system and return a
       transform to it. The default action is to not change anything and return an
       IdentityTransform.

       Reimplemented in sc::SymmMolecularCoor.

   virtual RefSCDimension sc::MolecularCoor::dim () [pure virtual]
       Returns a smart reference to an SCDimension equal to the number of coordinates (be they
       Cartesian, internal, or whatever) that are being optimized.

       Implemented in sc::IntMolecularCoor, and sc::CartMolecularCoor.

   virtual void sc::MolecularCoor::guess_hessian (RefSymmSCMatrix & hessian) [pure virtual]
       Calculate an approximate hessian and place the result in ``hessian''.

       Implemented in sc::SymmMolecularCoor, sc::RedundMolecularCoor, and sc::CartMolecularCoor.

   virtual RefSymmSCMatrix sc::MolecularCoor::inverse_hessian (RefSymmSCMatrix &) [pure virtual]
       Given an Hessian, return the inverse of that hessian. For singular matrices this should
       return the generalized inverse.

       Implemented in sc::SymmMolecularCoor, sc::RedundMolecularCoor, and sc::CartMolecularCoor.

   virtual int sc::MolecularCoor::nconstrained () [virtual]
       Returns the number of constrained coordinates.

       Reimplemented in sc::IntMolecularCoor.

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

       Reimplemented from sc::DescribedClass.

       Implemented in sc::IntMolecularCoor, sc::SymmMolecularCoor, and sc::CartMolecularCoor.

   void sc::MolecularCoor::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.

       Reimplemented in sc::SymmMolecularCoor, and sc::RedundMolecularCoor.

   int sc::MolecularCoor::to_cartesian (const RefSCVector & internal)
       Given a set of displaced internal coordinates, update the cartesian coordinates of the
       Molecule contained herein. This function does not change the vector ``internal''.

   virtual int sc::MolecularCoor::to_cartesian (RefSCVector & cartesian, RefSCVector & internal)
       [pure 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.

       Implemented in sc::IntMolecularCoor, and sc::CartMolecularCoor.

   virtual int sc::MolecularCoor::to_cartesian (RefSymmSCMatrix & cartesian, RefSymmSCMatrix &
       internal) [pure virtual]
       Convert the internal coordinate Hessian internal'' to Cartesian coordinates and copy the
       result tocartesian''. Only the variable internal coordinate force constants are
       transformed.

       Implemented in sc::IntMolecularCoor, and sc::CartMolecularCoor.

   virtual int sc::MolecularCoor::to_internal (RefSCVector & internal) [pure virtual]
       Fill in the vector ``internal'' with the current internal coordinates. Note that this
       member will update the values of the variable internal coordinates.

       Implemented in sc::IntMolecularCoor, and sc::CartMolecularCoor.

   virtual int sc::MolecularCoor::to_internal (RefSCVector & internal, RefSCVector & cartesian)
       [pure 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.

       Implemented in sc::IntMolecularCoor, and sc::CartMolecularCoor.

   virtual int sc::MolecularCoor::to_internal (RefSymmSCMatrix & internal, RefSymmSCMatrix &
       cartesian) [pure virtual]
       Convert the Cartesian coordinate Hessian cartesian'' to internal coordinates and copy the
       result tointernal''. Only the variable internal coordinate force constants are calculated.

       Implemented in sc::IntMolecularCoor, and sc::CartMolecularCoor.

Author

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