sc_MolecularCoor3

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.

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.

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::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 tocartesian''. Only the variable internal coordinate force constants are transformed.

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.

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 (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::IntMolecularCoor, and sc::CartMolecularCoor.