The MolecularCoor abstract class describes the coordinate system used to describe a molecule. More...

#include <chemistry/molecule/coor.h>

Inheritance diagram for sc::MolecularCoor:

Public Member Functions
	MolecularCoor (Ref< Molecule > &)

	MolecularCoor (StateIn &)

	MolecularCoor (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...

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.

virtual void	print (std::ostream &=ExEnv::out0()) const =0
	Print the coordinate.

virtual void	print_simples (std::ostream &=ExEnv::out0()) const =0

virtual RefSCDimension	dim ()=0
	Returns a smart reference to an SCDimension equal to the number of coordinates (be they Cartesian, internal, or whatever) that are being optimized.

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

virtual int	to_cartesian (const Ref< Molecule > &mol, const RefSCVector &internal)=0

virtual int	to_internal (RefSCVector &internal)=0
	Fill in the vector `‘internal’' with the current internal coordinates. More...

virtual int	to_cartesian (RefSCVector &cartesian, RefSCVector &internal)=0
	Convert the internal coordinate gradients in `‘internal’' to Cartesian coordinates and copy these Cartesian coordinate gradients to `‘cartesian’'. More...

virtual int	to_internal (RefSCVector &internal, RefSCVector &cartesian)=0
	Convert the Cartesian coordinate gradients in `‘cartesian’' to internal coordinates and copy these internal coordinate gradients to `‘internal’'. More...

virtual int	to_cartesian (RefSymmSCMatrix &cartesian, RefSymmSCMatrix &internal)=0
	Convert the internal coordinate Hessian `internal'' to Cartesian coordinates and copy the result to`cartesian''. More...

virtual int	to_internal (RefSymmSCMatrix &internal, RefSymmSCMatrix &cartesian)=0
	Convert the Cartesian coordinate Hessian `cartesian'' to internal coordinates and copy the result to`internal''. More...

virtual void	guess_hessian (RefSymmSCMatrix &hessian)=0
	Calculate an approximate hessian and place the result in `‘hessian’'.

virtual RefSymmSCMatrix	inverse_hessian (RefSymmSCMatrix &)=0
	Given an Hessian, return the inverse of that hessian. More...

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. More...

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. 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.

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...

Protected Attributes
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. 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 MolecularCoor abstract class describes the coordinate system used to describe a molecule.

It is used to convert a molecule's cartesian coordinates to and from this coordinate system.

Constructor & Destructor Documentation

◆ MolecularCoor()

sc::MolecularCoor::MolecularCoor ( const Ref< KeyVal > & )

The KeyVal constructor.

molecule

A Molecule object. There is no default.

debug

An integer which, if nonzero, will cause extra output.

matrixkit

A SCMatrixKit object. It is usually unnecessary to give this keyword.

natom3

An SCDimension object for the dimension of the vector of cartesian coordinates. It is usually unnecessary to give this keyword.

Member Function Documentation

◆ change_coordinates()

virtual Ref<NonlinearTransform> sc::MolecularCoor::change_coordinates ( )

virtual

When this is called, MoleculeCoor may select a new internal coordinate system and return a transform to it.

The default action is to not change anything and return an IdentityTransform.

Reimplemented in sc::SymmMolecularCoor.

◆ inverse_hessian()

virtual RefSymmSCMatrix sc::MolecularCoor::inverse_hessian ( RefSymmSCMatrix & )

pure virtual

Given an Hessian, return the inverse of that hessian.

For singular matrices this should return the generalized inverse.

Implemented in sc::CartMolecularCoor, sc::RedundMolecularCoor, and sc::SymmMolecularCoor.

◆ save_data_state()

void sc::MolecularCoor::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.

Reimplemented in sc::CartMolecularCoor, sc::RedundMolecularCoor, sc::SymmMolecularCoor, and sc::IntMolecularCoor.

◆ to_cartesian() [1/3]

int sc::MolecularCoor::to_cartesian ( const RefSCVector & internal )

Given a set of displaced internal coordinates, update the cartesian coordinates of the Molecule contained herein.

This function does not change the vector `‘internal’'.

◆ to_cartesian() [2/3]

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

pure virtual

Convert the internal coordinate gradients in `‘internal’' to Cartesian coordinates and copy these Cartesian coordinate gradients to `‘cartesian’'.

Only the variable internal coordinate gradients are transformed.

Implemented in sc::CartMolecularCoor, and sc::IntMolecularCoor.

◆ to_cartesian() [3/3]

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

pure virtual

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

Only the variable internal coordinate force constants are transformed.

Implemented in sc::CartMolecularCoor, and sc::IntMolecularCoor.

◆ to_internal() [1/3]

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

pure virtual

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

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

Implemented in sc::CartMolecularCoor, and sc::IntMolecularCoor.

◆ to_internal() [2/3]

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

pure virtual

Convert the Cartesian coordinate gradients in `‘cartesian’' to internal coordinates and copy these internal coordinate gradients to `‘internal’'.

Only the variable internal coordinate gradients are calculated.

Implemented in sc::CartMolecularCoor, and sc::IntMolecularCoor.

◆ to_internal() [3/3]

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

pure virtual

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

Only the variable internal coordinate force constants are calculated.

Implemented in sc::CartMolecularCoor, and sc::IntMolecularCoor.

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

src/lib/chemistry/molecule/coor.h

Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ MolecularCoor()

Member Function Documentation

◆ change_coordinates()

◆ inverse_hessian()

◆ 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]