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MolecularCoor Class Reference

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

#include <coor.h>

Inheritance diagram for MolecularCoor

[legend]Collaboration diagram for MolecularCoor:

[legend]List of all members.

Public Methods
	MolecularCoor (Ref< Molecule > &)
	MolecularCoor (StateIn &)
	MolecularCoor (const Ref< KeyVal > &)
	The KeyVal constructor. More...
virtual	~MolecularCoor ()
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::out()) const=0
	Print the coordinate.
virtual void	print_simples (std::ostream &=ExEnv::out()) 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
Protected Attributes
Ref<Molecule>	molecule_
RefSCDimension	dnatom3_
Ref<SCMatrixKit>	matrixkit_
int	debug_

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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.

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Constructor & Destructor Documentation

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.

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Member Function Documentation

Ref< NonlinearTransform > 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 SymmMolecularCoor.

RefSymmSCMatrix MolecularCoor::inverse_hessian ( RefSymmSCMatrix & ) [pure virtual]

Given an Hessian, return the inverse of that hessian. For singular matrices this should return the generalized inverse. Reimplemented in SymmMolecularCoor, RedundMolecularCoor, and CartMolecularCoor.

void MolecularCoor::save_data_state ( StateOut & s ) [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 SavableState. Reimplemented in IntMolecularCoor, SymmMolecularCoor, RedundMolecularCoor, and CartMolecularCoor.

int MolecularCoor::to_cartesian ( RefSymmSCMatrix & cart, 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. Reimplemented in IntMolecularCoor, and CartMolecularCoor.

int 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. Reimplemented in IntMolecularCoor, and CartMolecularCoor.

int 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''.

int MolecularCoor::to_internal ( RefSymmSCMatrix & internal, RefSymmSCMatrix & cart ) [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. Reimplemented in IntMolecularCoor, and CartMolecularCoor.

int 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. Reimplemented in IntMolecularCoor, and CartMolecularCoor.

int 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. Reimplemented in IntMolecularCoor, and CartMolecularCoor.

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

• coor.h

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