| sc::MolecularCoor(3) | MPQC | sc::MolecularCoor(3) |
sc::MolecularCoor - The MolecularCoor abstract class describes the coordinate system used to describe a molecule.
#include <coor.h>
Inherits sc::SavableState.
Inherited by sc::CartMolecularCoor, and sc::IntMolecularCoor.
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
Ref< Molecule > molecule_
RefSCDimension dnatom3_
Ref< SCMatrixKit > matrixkit_
int debug_
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.
The KeyVal constructor.
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.
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.
Calculate an approximate hessian and place the result in ``hessian''.
Implemented in sc::SymmMolecularCoor, sc::RedundMolecularCoor, and sc::CartMolecularCoor.
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.
Returns the number of constrained coordinates.
Reimplemented in sc::IntMolecularCoor.
Print the coordinate.
Reimplemented from sc::DescribedClass.
Implemented in sc::IntMolecularCoor, sc::SymmMolecularCoor, and sc::CartMolecularCoor.
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.
Given a set of displaced internal coordinates, update the cartesian coordinates of the Molecule contained herein. This function does not change the vector ``internal''.
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.
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.
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.
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.
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.
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| Fri Dec 2 2022 | Version 2.3.1 |