The SetIntCoor class describes a set of internal coordinates. More...

#include <chemistry/molecule/coor.h>

Inheritance diagram for sc::SetIntCoor:

Public Member Functions
	SetIntCoor (StateIn &)

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

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...

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. More...

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.

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 MPQC__NOEXCEPT
	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.

virtual void	print (std::ostream &=ExEnv::out0()) const
	Print the object.

Ref< DescribedClass >	ref ()
	Return this object wrapped up in a Ref smart pointer. More...

Public Member Functions inherited from sc::RefCount
size_t	identifier () const
	Return the unique identifier for this object that can be compared for different objects of different types. More...

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...

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 &)

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

◆ SetIntCoor()

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

◆ guess_hessian()

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.

◆ save_data_state()

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.

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

src/lib/chemistry/molecule/coor.h