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 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::CartMolecularCoor, sc::RedundMolecularCoor, and 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::CartMolecularCoor,    sc::RedundMolecularCoor,    sc::SymmMolecularCoor,   and
       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_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::CartMolecularCoor, and 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
       tocartesian''. Only the variable internal coordinate force constants are transformed.

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

   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
       tointernal''. Only the variable internal coordinate force constants are calculated.

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

Author

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Version 2.3.1                                    Sun Oct 4 2020                             sc::MolecularCoor(3)