sc::SimpleCo(3) The SimpleCo abstract class describes a simple internal coordinate of a molecule.

SYNOPSIS


#include <simple.h>

Inherits sc::IntCoor.

Inherited by sc::BendSimpleCo, sc::LinIPSimpleCo, sc::LinOPSimpleCo, sc::OutSimpleCo, sc::ScaledTorsSimpleCo, sc::StreSimpleCo, and sc::TorsSimpleCo.

Public Member Functions


SimpleCo (int, const char *=0)
This constructor takes an integer argument which is the number of atoms needed to describe the coordinate.
SimpleCo (const Ref< KeyVal > &, int natom)
The KeyVal constructor requires the number of atoms.
int natoms () const
Returns the number of atoms in the coordinate.
int operator[] (int i) const
Returns the index of the i'th atom in the coordinate.
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.
SimpleCo (StateIn &)

virtual int operator== (SimpleCo &)

int operator!= (SimpleCo &u)

double force_constant (Ref< Molecule > &)
Returns an approximate force constant (a la Almlof).
void update_value (const Ref< Molecule > &)
Recalculates the value of the coordinate based on the geometry in the Molecule.
void bmat (const Ref< Molecule > &, RefSCVector &bmat, double coef=1.0)
Fill in a row of the B matrix.
virtual double calc_force_con (Molecule &)=0
Calculates an approximate force constant and returns it's value.
virtual double calc_intco (Molecule &, double *=0, double=1)=0
Calculate the value of the coordinate based on what's in Molecule.
void print_details (const Ref< Molecule > &, std::ostream &=ExEnv::out0()) const
Print the coordinate.
int equivalent (Ref< IntCoor > &)
Tests to see if two coordinates are equivalent to each other.

Protected Attributes


int natoms_

int * atoms

Detailed Description

The SimpleCo abstract class describes a simple internal coordinate of a molecule.

The number atoms involved can be 2, 3 or 4 and is determined by the specialization of SimpleCo.

There are three ways to specify the atoms involved in the internal coordinate. The first way is a shorthand notation, just a vector of a label followed by the atom numbers (starting at 1) is given. For example, a stretch between two atoms, 1 and 2, is given, in the ParsedKeyVal format, as 

  stretch<StreSimpleCo>: [ R12 1 2 ]

The other two ways to specify the atoms are more general. With them, it is possible to give parameters for the IntCoor base class (and thus give the value of the coordinate). In the first of these input formats, a vector associated with the keyword atoms gives the atom numbers. The following specification for stretch is equivalent to that above: 

  stretch<StreSimpleCo>:( label = R12 atoms = [ 1 2 ] )

In the second, a vector, atom_labels, is given along with a Molecule object. The atom labels are looked up in the Molecule object to find the atom numbers. The following specification for stretch is equivalent to those above: 

  molecule<Molecule>: (
    { atom_labels atoms   geometry      } = {
          H1         H   [ 1.0 0.0 0.0 ]
          H2         H   [-1.0 0.0 0.0 ] } )
  stretch<StreSimpleCo>:( label = R12
                          atom_labels = [ H1 H2 ]
                          molecule = $:molecule )


 

Constructor & Destructor Documentation

sc::SimpleCo::SimpleCo (int, const char * = 0)

This constructor takes an integer argument which is the number of atoms needed to describe the coordinate. A second optional char* argument is a label for the coordinate. This argument is passed on to the IntCoor constructor.

Member Function Documentation

virtual double sc::SimpleCo::calc_intco (Molecule &, double * = 0, double = 1) [pure virtual]

Calculate the value of the coordinate based on what's in Molecule. If given a double*, fill in that part of the B matrix. If the bmatrix is to be calculated, the third argument gives the coefficient.

int sc::SimpleCo::equivalent (Ref< IntCoor > &)

Tests to see if two coordinates are equivalent to each other. This is false if the atoms don't match.

void sc::SimpleCo::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::IntCoor.

void sc::SimpleCo::update_value (const Ref< Molecule > &) [virtual]

Recalculates the value of the coordinate based on the geometry in the Molecule.

Implements sc::IntCoor.

Author

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