sc_SetIntCoor man page

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.

Additional Inherited Members

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 $0 leq i < n$, 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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Info

Fri May 6 2016 Version 2.3.1 MPQC