sc::molecularcoor(3)
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.
- 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
- 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.
- 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 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.
- 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 (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.
- 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.
- 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_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_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 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 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.
Author
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