NAME

       sc::SetIntCoor - The SetIntCoor class describes a set of internal coordinates.

SYNOPSIS

       #include <coor.h>

       Inherits sc::SavableState.

   Public Member Functions
       SetIntCoor (StateIn &)
       SetIntCoor (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 add (const Ref< IntCoor > &)
           Adds an internal coordinate to the set.
       void add (const Ref< SetIntCoor > &)
           Adds all the elements of another set to this one.
       void pop ()
           Removes the last coordinate from this set.
       void clear ()
           Removes all coordinates from the set.
       int n () const
           Returns the number of coordinates in the set.
       Ref< IntCoor > coor (int i) const
           Returns a reference to the i'th coordinate in the set.
       virtual void fd_bmat (const Ref< Molecule > &, RefSCMatrix &)
           Compute the B matrix by finite displacements.
       virtual void bmat (const Ref< Molecule > &, RefSCMatrix &)
           Compute the B matrix the old-fashioned way.
       virtual void guess_hessian (Ref< Molecule > &, RefSymmSCMatrix &)
           Create an approximate Hessian for this set of coordinates.
       virtual void print_details (const Ref< Molecule > &, std::ostream &=ExEnv::out0()) const
           Print the coordinates in the set.
       virtual void update_values (const Ref< Molecule > &)
           Recalculate the values of the internal coordinates in the set.
       virtual void values_to_vector (const RefSCVector &)
           Copy the values of the internal coordinates to a vector.

       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.
       virtual void print (std::ostream &=ExEnv::out0()) const
           Print the object.

       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::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 SetIntCoor class describes a set of internal coordinates.

       It can automatically generate these coordinates using a integral coordinate generator
       object (see the IntCoorGen class) or the internal coordinates can be explicity given.

       The following is a sample ParsedKeyVal input for a SetIntCoor object.

         setintcoor<SetIntCoor>: [
           <SumIntCoor>: (
             coor: [
               <StreSimpleCo>:( atoms = [ 1 2 ] )
               <StreSimpleCo>:( atoms = [ 2 3 ] )
               ]
             coef = [ 1.0 1.0 ]
             )
           <BendSimpleCo>:( atoms = [ 1 2 3 ] )
         ]

Constructor & Destructor Documentation

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

       generator
           A IntCoorGen object that will be used to generate the internal coordinates.

       i   A sequence of integer keywords, all $i$ for $0  i < n$, can be assigned to IntCoor
           objects.

Member Function Documentation

   virtual void sc::SetIntCoor::guess_hessian (Ref< Molecule > &, RefSymmSCMatrix &) [virtual]
       Create an approximate Hessian for this set of coordinates. This Hessian is a symmetric
       matrix whose i'th diagonal is the force constant for the i'th coordinate in the set.

   void sc::SetIntCoor::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.

Author

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