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 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 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_
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. .IP "molecule" 1c 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.
RefSCDimension sc::MolecularCoor::dim_natom3 () [inline]
Returns a smart reference to an SCDimension equal to the number of
atoms in the molecule times 3.
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.
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.
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::IntMolecularCoor, and sc::CartMolecularCoor.
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::IntMolecularCoor, and sc::CartMolecularCoor.
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’’.
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::IntMolecularCoor, and sc::CartMolecularCoor.
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::IntMolecularCoor, and sc::CartMolecularCoor.
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::IntMolecularCoor, and sc::CartMolecularCoor.
Author
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