sc_MolecularCoor man page

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 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::CartMolecularCoor, and sc::IntMolecularCoor.

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::CartMolecularCoor, sc::RedundMolecularCoor, and 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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Info

Fri May 6 2016 Version 2.3.1 MPQC