The CartMolecularCoor class implements Cartesian coordinates in a way suitable for use in geometry optimizations. More...

#include <chemistry/molecule/coor.h>

Inheritance diagram for sc::CartMolecularCoor:

Public Member Functions
	CartMolecularCoor (Ref< Molecule > &mol)

	CartMolecularCoor (StateIn &)

	CartMolecularCoor (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.

virtual RefSCDimension	dim ()
	These implement the virtual functions inherited from MolecularCoor.

virtual int	to_cartesian (const Ref< Molecule > &, const RefSCVector &internal)

virtual int	to_internal (RefSCVector &internal)
	Fill in the vector `‘internal’' with the current internal coordinates.

virtual int	to_cartesian (RefSCVector &cartesian, RefSCVector &internal)
	Convert the internal coordinate gradients in `internal'' to Cartesian coordinates and copy these Cartesian coordinate gradients to`cartesian''.

virtual int	to_internal (RefSCVector &internal, RefSCVector &cartesian)
	Convert the Cartesian coordinate gradients in `cartesian'' to internal coordinates and copy these internal coordinate gradients to`internal''.

virtual int	to_cartesian (RefSymmSCMatrix &cart, RefSymmSCMatrix &internal)
	Convert the internal coordinate Hessian `internal'' to Cartesian coordinates and copy the result to`cartesian''.

virtual int	to_internal (RefSymmSCMatrix &internal, RefSymmSCMatrix &cart)
	Convert the Cartesian coordinate Hessian `cartesian'' to internal coordinates and copy the result to`internal''.

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

virtual void	print_simples (std::ostream &=ExEnv::out0()) const

void	guess_hessian (RefSymmSCMatrix &hessian)

RefSymmSCMatrix	inverse_hessian (RefSymmSCMatrix &)
	Calculate an approximate hessian and place the result in `‘hessian’'.

Public Member Functions inherited from sc::MolecularCoor
	MolecularCoor (Ref< Molecule > &)

	MolecularCoor (StateIn &)

	MolecularCoor (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.

RefSCDimension	dim_natom3 ()
	Returns a smart reference to an SCDimension equal to the number of atoms in the molecule times 3.

Ref< Molecule >	molecule () const
	Returns the molecule.

int	to_cartesian (const RefSCVector &internal)
	Given a set of displaced internal coordinates, update the cartesian coordinates of the Molecule contained herein.

virtual int	nconstrained ()
	Returns the number of constrained coordinates.

virtual Ref< NonlinearTransform >	change_coordinates ()
	When this is called, MoleculeCoor may select a new internal coordinate system and return a transform to it.

Ref< SCMatrixKit >	matrixkit () const

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.

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.

Protected Member Functions
virtual void	init ()
	Initializes the dimensions.

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 &)

Protected Attributes
RefSCDimension	dim_

Protected Attributes inherited from sc::MolecularCoor
Ref< Molecule >	molecule_

RefSCDimension	dnatom3_

Ref< SCMatrixKit >	matrixkit_

int	debug_

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)

Detailed Description

The CartMolecularCoor class implements Cartesian coordinates in a way suitable for use in geometry optimizations.

CartMolecularCoor is a SavableState has StateIn and KeyVal constructors. CartMolecularCoor is derived from MolecularCoor.

Member Function Documentation

◆ dim()

virtual RefSCDimension sc::CartMolecularCoor::dim ( )

virtual

These implement the virtual functions inherited from MolecularCoor.

Implements sc::MolecularCoor.

◆ inverse_hessian()

RefSymmSCMatrix sc::CartMolecularCoor::inverse_hessian ( RefSymmSCMatrix & )

virtual

Calculate an approximate hessian and place the result in `‘hessian’'.

*‍/ virtual void guess_hessian(RefSymmSCMatrix&hessian) = 0;

/** Given an Hessian, return the inverse of that hessian. For singular matrices this should return the generalized inverse.

Implements sc::MolecularCoor.

◆ print()

virtual void sc::CartMolecularCoor::print ( std::ostream & = ExEnv::out0() ) const

virtual

Print the coordinate.

Implements sc::MolecularCoor.

◆ print_simples()

virtual void sc::CartMolecularCoor::print_simples ( std::ostream & = ExEnv::out0() ) const

virtual

Implements sc::MolecularCoor.

◆ save_data_state()

void sc::CartMolecularCoor::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.

◆ to_cartesian() [1/3]

virtual int sc::CartMolecularCoor::to_cartesian	(	const Ref< Molecule > &	,
		const RefSCVector &	internal )

virtual

Implements sc::MolecularCoor.

◆ to_cartesian() [2/3]

virtual int sc::CartMolecularCoor::to_cartesian	(	RefSCVector &	cartesian,
		RefSCVector &	internal )

virtual

Convert the internal coordinate gradients in internal'' to Cartesian coordinates and copy these Cartesian coordinate gradients tocartesian''.

Only the variable internal coordinate gradients are transformed.

Implements sc::MolecularCoor.

◆ to_cartesian() [3/3]

virtual int sc::CartMolecularCoor::to_cartesian	(	RefSymmSCMatrix &	cartesian,
		RefSymmSCMatrix &	internal )

virtual

Convert the internal coordinate Hessian internal'' to Cartesian coordinates and copy the result tocartesian''.

Only the variable internal coordinate force constants are transformed.

Implements sc::MolecularCoor.

◆ to_internal() [1/3]

virtual int sc::CartMolecularCoor::to_internal ( RefSCVector & internal )

virtual

Fill in the vector `‘internal’' with the current internal coordinates.

Note that this member will update the values of the variable internal coordinates.

Implements sc::MolecularCoor.

◆ to_internal() [2/3]

virtual int sc::CartMolecularCoor::to_internal	(	RefSCVector &	internal,
		RefSCVector &	cartesian )

virtual

Convert the Cartesian coordinate gradients in cartesian'' to internal coordinates and copy these internal coordinate gradients tointernal''.

Only the variable internal coordinate gradients are calculated.

Implements sc::MolecularCoor.

◆ to_internal() [3/3]

virtual int sc::CartMolecularCoor::to_internal	(	RefSymmSCMatrix &	internal,
		RefSymmSCMatrix &	cartesian )

virtual

Convert the Cartesian coordinate Hessian cartesian'' to internal coordinates and copy the result tointernal''.

Only the variable internal coordinate force constants are calculated.

Implements sc::MolecularCoor.

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

src/lib/chemistry/molecule/coor.h

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ dim()

◆ inverse_hessian()

◆ print()

◆ print_simples()

◆ save_data_state()

◆ to_cartesian() [1/3]

◆ to_cartesian() [2/3]

◆ to_cartesian() [3/3]

◆ to_internal() [1/3]

◆ to_internal() [2/3]

◆ to_internal() [3/3]