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sc::SymmMolecularCoor Class Reference The SymmMolecularCoor class derives from IntMolecularCoor. More... #include <coor.h> Inheritance diagram for sc::SymmMolecularCoor: [legend]Collaboration diagram for sc::SymmMolecularCoor: [legend]List of all members. Public Methods   SymmMolecularCoor (Ref< Molecule > &mol)   SymmMolecularCoor (StateIn &)   SymmMolecularCoor (const Ref< KeyVal > &)   The KeyVal constructor. More... virtual  ~SymmMolecularCoor () 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... void  form_coordinates (int keep_variable=0)   Actually form the variable and constant internal coordinates from simple internal coordinates. void  guess_hessian (RefSymmSCMatrix &hessian)   Form the approximate hessian. RefSymmSCMatrix  inverse_hessian (RefSymmSCMatrix &)   Invert the hessian. Ref< NonlinearTransform >  change_coordinates ()   This overrides MoleculeCoor's change_coordinates and might transform to a new set of coordinates. void  print (std::ostream &=ExEnv::out0()) const   Print the coordinate. Protected Methods void  init ()   This is called by the constructors of classes derived from IntMolecularCoor. More... Protected Attributes int  change_coordinates_ int  transform_hessian_ double  max_kappa2_ Detailed Description The SymmMolecularCoor class derives from IntMolecularCoor. It provides a unique set of totally symmetric internal coordinates. Giving an MolecularEnergy object a coor is usually the best way to optimize a molecular structure. However, for some classes of molecules SymmMolecularCoor doesn't work very well. For example, enediyne can cause problems. In these cases, cartesian coordinates (obtained by not giving the MolecularEnergy object the coor keyword) might be better or you can manually specify the coordinates that the SymmMolecularCoor object uses with the variable keyword (see the IntMolecularCoor class description). Constructor & Destructor Documentation sc::SymmMolecularCoor::SymmMolecularCoor (  const Ref< KeyVal > &    )    The KeyVal constructor. change_coordinates If true, the quality of the internal coordinates will be checked periodically and if they are beginning to become linearly dependent a new set of internal coordinates will be computed. The default is false. max_kappa2 A measure of the quality of the internal coordinates. Values of the 2-norm condition, , larger than max_kappa2 are considered linearly dependent. The default is 10.0. transform_hessian If true, the hessian will be transformed every time the internal coordinates are formed. The default is true. Member Function Documentation void sc::SymmMolecularCoor::init (    )  [protected, virtual]   This is called by the constructors of classes derived from IntMolecularCoor. It initialized the lists of simple internal coordinates, and then calls the form_coordinates() member. Reimplemented from sc::IntMolecularCoor. void sc::SymmMolecularCoor::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::IntMolecularCoor. The documentation for this class was generated from the following file: coor.h