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.

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.

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.

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.

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 MPQC__NOEXCEPT
	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.

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

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

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.

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
	Return 1 if the object is managed. Otherwise return 0.

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 &)

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