Provided by: libsc-doc_2.3.1-22build2_all 
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 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.
Public Member Functions inherited from sc::IntCoor
IntCoor (StateIn &)
IntCoor (const IntCoor &)
IntCoor (const char *label=0)
This constructor takes a string containing a label for the internal coordinate.
IntCoor (const Ref< KeyVal > &)
The KeyVal constructor.
virtual const char * label () const
Returns the string containing the label for the internal coordinate.
virtual double value () const
Returns the value of the coordinate in atomic units or radians.
virtual void set_value (double)
Sets the value of the coordinate in atomic units or radians.
virtual double preferred_value () const
Returns the value of the coordinate in more familiar units.
virtual const char * ctype () const =0
Returns a string representation of the type of coordinate this is.
virtual void print (std::ostream &o=ExEnv::out0()) const
Print information about the coordinate.
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.
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.
Protected Attributes
int natoms_
int * atoms
Protected Attributes inherited from sc::IntCoor
char * label_
double value_
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 &)
Static Protected Attributes inherited from sc::IntCoor
static double bohr_conv
static double radian_conv
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
void sc::SimpleCo::bmat (const Ref< Molecule > &, RefSCVector & bmat, double coef = 1.0)
[virtual]
Fill in a row of the B matrix.
Implements sc::IntCoor.
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.
double sc::SimpleCo::force_constant (Ref< Molecule > &) [virtual]
Returns an approximate force constant (a la Almlof).
Implements sc::IntCoor.
void sc::SimpleCo::print_details (const Ref< Molecule > &, std::ostream & = ExEnv::out0())
const [virtual]
Print the coordinate.
Reimplemented from 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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