sc::SetIntCoor(3) Library Functions Manual sc::SetIntCoor(3)

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

#include <coor.h>

Inherits sc::SavableState.


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.

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 &)

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 ] )
  ]

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 assigned to IntCoor objects.

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.

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.

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