sc::MolecularCoor Class Reference

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

#include <coor.h>

Inheritance diagram for sc::MolecularCoor:

Collaboration diagram for sc::MolecularCoor:

Public Member Functions
	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.
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.
virtual int	to_cartesian (RefSCVector &cartesian, RefSCVector &internal)=0
	Given a set of displaced internal coordinates, update the cartesian coordinates of the Molecule contained herein.
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''.
virtual int	to_cartesian (RefSymmSCMatrix &cartesian, RefSymmSCMatrix &internal)=0
	Convert the internal coordinate Hessian internal'' to Cartesian coordinates and copy the result to cartesian''.
virtual int	to_internal (RefSymmSCMatrix &internal, RefSymmSCMatrix &cartesian)=0
	Convert the Cartesian coordinate Hessian cartesian'' to internal coordinates and copy the result to internal''.
virtual RefSymmSCMatrix	inverse_hessian (RefSymmSCMatrix &)=0
	Calculate an approximate hessian and place the result in ``hessian''.
*Returns the number of constrained virtual coordinates int	nconstrained ()
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 throw ()
	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.
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.
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.

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.
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 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.

dim()

virtual RefSCDimension sc::MolecularCoor::dim ( )

pure virtual

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

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

inverse_hessian()

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

pure 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.

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

print()

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

pure virtual

Print the coordinate.

Reimplemented from sc::DescribedClass.

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

References sc::ExEnv::out0().

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::RedundMolecularCoor, and sc::SymmMolecularCoor.

to_cartesian() [1/2]

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

pure virtual

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

This function does not change the vector ``internal''. */ int to_cartesian(const RefSCVector&internal); virtual int to_cartesian(const Ref<Molecule>&mol, const RefSCVector&internal) = 0;

/** Fill in the vector ``internal'' with the current internal coordinates. Note that this member will update the values of the variable internal coordinates. */ virtual int to_internal(RefSCVector&internal) = 0;

/** 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() [2/2]

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 to cartesian''.

Only the variable internal coordinate force constants are transformed.

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

to_internal() [1/2]

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() [2/2]

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 to internal''.

Only the variable internal coordinate force constants are calculated.

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

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

• coor.h