NAME

       sc::RedundMolecularCoor - The RedundMolecularCoor class provides a redundant set of simple
       internal coordinates.

SYNOPSIS

       #include <coor.h>

       Inherits sc::IntMolecularCoor.

   Public Member Functions
       RedundMolecularCoor (Ref< Molecule > &mol)
       RedundMolecularCoor (StateIn &)
       RedundMolecularCoor (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 the simple internal
           coordinates.
       void guess_hessian (RefSymmSCMatrix &hessian)
           Form the approximate hessian.
       RefSymmSCMatrix inverse_hessian (RefSymmSCMatrix &)
           Invert the hessian.

       Public Member Functions inherited from sc::IntMolecularCoor
       IntMolecularCoor (StateIn &)
       IntMolecularCoor (Ref< Molecule > &mol)
       IntMolecularCoor (const Ref< KeyVal > &)
           The KeyVal constructor.
       virtual int all_to_cartesian (const Ref< Molecule > &, RefSCVector &internal)
           Like to_cartesians(), except all internal coordinates are considered, not just the
           variable ones.
       virtual int all_to_internal (const Ref< Molecule > &, RefSCVector &internal)
           Like to_internal(), except all internal coordinates are considered, not just the
           variable ones.
       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
       virtual void print_variable (std::ostream &=ExEnv::out0()) const
       virtual void print_constant (std::ostream &=ExEnv::out0()) const
       int nconstrained ()
           Returns the number of constrained coordinates.

       Public Member Functions inherited from sc::MolecularCoor
       MolecularCoor (Ref< Molecule > &)
       MolecularCoor (StateIn &)
       MolecularCoor (const Ref< KeyVal > &)
           The KeyVal constructor.
       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 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.

   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::IntMolecularCoor
       void form_K_matrix (RefSCDimension &dredundant, RefSCDimension &dfixed, RefSCMatrix &K,
           int *&is_totally_symmetric)
       virtual void init ()
           This is called by the constructors of classes derived from IntMolecularCoor.
       virtual void new_coords ()
           Allocates memory for the SetIntCoor's used to store the simple and internal
           coordinates.
       virtual void read_keyval (const Ref< KeyVal > &)
           Reads the KeyVal input.

       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 inherited from sc::IntMolecularCoor
       Ref< IntCoorGen > generator_
       RefSCDimension dim_
       RefSCDimension dvc_
       Ref< SetIntCoor > variable_
       Ref< SetIntCoor > constant_
       Ref< SetIntCoor > fixed_
       Ref< SetIntCoor > watched_
       Ref< IntCoor > followed_
       Ref< SetIntCoor > bonds_
       Ref< SetIntCoor > bends_
       Ref< SetIntCoor > tors_
       Ref< SetIntCoor > outs_
       Ref< SetIntCoor > extras_
       Ref< SetIntCoor > all_
       int update_bmat_
       int only_totally_symmetric_
       double symmetry_tolerance_
       double simple_tolerance_
       double coordinate_tolerance_
       double cartesian_tolerance_
       double scale_bonds_
       double scale_bends_
       double scale_tors_
       double scale_outs_
       int nextra_bonds_
       int * extra_bonds_
       int given_fixed_values_
       int decouple_bonds_
       int decouple_bends_
       int max_update_steps_
       double max_update_disp_
       int form_print_simples_
       int form_print_variable_
       int form_print_constant_
       int form_print_molecule_

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

Detailed Description

       The RedundMolecularCoor class provides a redundant set of simple internal coordinates.

Member Function Documentation

   void sc::RedundMolecularCoor::form_coordinates (int keep_variable = 0) [virtual]
       Actually form the variable and constant internal coordinates from the simple internal
       coordinates.

       Implements sc::IntMolecularCoor.

   void sc::RedundMolecularCoor::guess_hessian (RefSymmSCMatrix & hessian) [virtual]
       Form the approximate hessian.

       Implements sc::MolecularCoor.

   RefSymmSCMatrix sc::RedundMolecularCoor::inverse_hessian (RefSymmSCMatrix &) [virtual]
       Invert the hessian.

       Implements sc::MolecularCoor.

   void sc::RedundMolecularCoor::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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