NAME
sc::SimpleCo -
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 ith 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 its value.
virtual double calc_intco (Molecule &, double *=0, double=1)=0
Calculate the value of the coordinate based on whats 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 > &) [virtual]
Tests to see if two coordinates are equivalent to each other. This is
false if the atoms don’t match.
Implements sc::IntCoor.
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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