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

#include <simple.h>

Inheritance diagram for sc::SimpleCo:

[legend]

Collaboration diagram for sc::SimpleCo:

[legend]

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. More...

	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. More...

	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. More...

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. More...

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. More...

	IntCoor (const Ref< KeyVal > &)
	The KeyVal constructor. More...

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. More...

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. More...

virtual void	save_vbase_state (StateOut &)
	Save the virtual bases for the object. More...

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. More...

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. More...

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. More...

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. More...

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. More...

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

◆ SimpleCo()

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

◆ calc_intco()

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.

◆ equivalent()

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.

◆ save_data_state()

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.

The documentation for this class was generated from the following file:

simple.h

Public Member Functions

Protected Attributes