NAME

sc::MolecularCoor - The MolecularCoor abstract class describes the coordinate system used to describe a molecule.

SYNOPSIS

#include <coor.h>

Inherits sc::SavableState.

Inherited by sc::CartMolecularCoor, and sc::IntMolecularCoor.

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. int to_cartesian (const RefSCVector &internal)
Given a set of displaced internal coordinates, update the cartesian coordinates of the Molecule contained herein. 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. 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''. 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 tocartesian''. virtual int to_internal (RefSymmSCMatrix &internal, RefSymmSCMatrix &cartesian)=0
Convert the Cartesian coordinate Hessian cartesian'' to internal coordinates and copy the result tointernal''. 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. 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

Protected Attributes

Ref< Molecule > molecule_
RefSCDimension dnatom3_
Ref< SCMatrixKit > matrixkit_
int debug_

Additional Inherited Members

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

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

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.

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::IntMolecularCoor, and sc::CartMolecularCoor.

virtual void sc::MolecularCoor::guess_hessian (RefSymmSCMatrix & hessian) [pure virtual]

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

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

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

virtual int sc::MolecularCoor::nconstrained () [virtual]

Returns the number of constrained coordinates.

Reimplemented in sc::IntMolecularCoor.

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

Print the coordinate.

Reimplemented from sc::DescribedClass.

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

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

Author

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