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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: [legend]Collaboration diagram for sc::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::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. 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_ 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 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. 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. 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. 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. 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. 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. 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. The documentation for this class was generated from the following file: coor.h