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sc::IntMolecularCoor Class Reference The IntMolecularCoor abstract class describes a molecule's coordinates in terms of internal coordinates. More... #include <coor.h> Inheritance diagram for sc::IntMolecularCoor: [legend]Collaboration diagram for sc::IntMolecularCoor: [legend]List of all members. Public Methods   IntMolecularCoor (StateIn &)   IntMolecularCoor (Ref< Molecule > &mol)   IntMolecularCoor (const Ref< KeyVal > &)   The KeyVal constructor. More... virtual  ~IntMolecularCoor () 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... virtual void  form_coordinates (int keep_variable=0)=0   Actually form the variable and constant internal coordinates from the simple internal coordinates. virtual int  all_to_cartesian (const Ref< Molecule > &, RefSCVector &internal)   Like to_cartesians(), except all internal coordinates are considered, not just the variable ones. virtual int  all_to_internal (const Ref< Molecule > &, RefSCVector &internal)   Like to_internal(), except all internal coordinates are considered, not just the variable ones. virtual RefSCDimension  dim ()   These implement the virtual functions inherited from MolecularCoor. virtual int  to_cartesian (const Ref< Molecule > &, const RefSCVector &internal) virtual int  to_internal (RefSCVector &internal)   Fill in the vector ``internal'' with the current internal coordinates. More... virtual int  to_cartesian (RefSCVector &cartesian, RefSCVector &internal)   Convert the internal coordinate gradients in ``internal'' to Cartesian coordinates and copy these Cartesian coordinate gradients to ``cartesian''. More... virtual int  to_internal (RefSCVector &internal, RefSCVector &cartesian)   Convert the Cartesian coordinate gradients in ``cartesian'' to internal coordinates and copy these internal coordinate gradients to ``internal''. More... virtual int  to_cartesian (RefSymmSCMatrix &cart, RefSymmSCMatrix &internal)   Convert the internal coordinate Hessian ``internal'' to Cartesian coordinates and copy the result to ``cartesian''. More... virtual int  to_internal (RefSymmSCMatrix &internal, RefSymmSCMatrix &cart)   Convert the Cartesian coordinate Hessian ``cartesian'' to internal coordinates and copy the result to ``internal''. More... virtual void  print (std::ostream &=ExEnv::out0()) const   Print the coordinate. virtual void  print_simples (std::ostream &=ExEnv::out0()) const virtual void  print_variable (std::ostream &=ExEnv::out0()) const virtual void  print_constant (std::ostream &=ExEnv::out0()) const int  nconstrained ()   Returns the number of constrained coordinates. Protected Methods void  form_K_matrix (RefSCDimension &dredundant, RefSCDimension &dfixed, RefSCMatrix &K, int *&is_totally_symmetric) virtual void  init ()   This is called by the constructors of classes derived from IntMolecularCoor. More... virtual void  new_coords ()   Allocates memory for the SetIntCoor's used to store the simple and internal coordinates. virtual void  read_keyval (const Ref< KeyVal > &)   Reads the KeyVal input. Protected Attributes Ref< IntCoorGen >  generator_ RefSCDimension  dim_ RefSCDimension  dvc_ Ref< SetIntCoor >  variable_ Ref< SetIntCoor >  constant_ Ref< SetIntCoor >  fixed_ Ref< SetIntCoor >  watched_ Ref< IntCoor >  followed_ Ref< SetIntCoor >  bonds_ Ref< SetIntCoor >  bends_ Ref< SetIntCoor >  tors_ Ref< SetIntCoor >  outs_ Ref< SetIntCoor >  extras_ Ref< SetIntCoor >  all_ int  update_bmat_ int  only_totally_symmetric_ double  symmetry_tolerance_ double  simple_tolerance_ double  coordinate_tolerance_ double  cartesian_tolerance_ double  scale_bonds_ double  scale_bends_ double  scale_tors_ double  scale_outs_ int  nextra_bonds_ int *  extra_bonds_ int  given_fixed_values_ int  decouple_bonds_ int  decouple_bends_ int  max_update_steps_ double  max_update_disp_ int  form_print_simples_ int  form_print_variable_ int  form_print_constant_ int  form_print_molecule_ Detailed Description The IntMolecularCoor abstract class describes a molecule's coordinates in terms of internal coordinates. Constructor & Destructor Documentation sc::IntMolecularCoor::IntMolecularCoor (  const Ref< KeyVal > &    )    The KeyVal constructor. variable Gives a SetIntCoor object that specifies the internal coordinates that can be varied. If this is not given, the variable coordinates will be generated. followed Gives a IntCoor object that specifies a coordinate to used as the first coordinate in the variable coordinate list. The remaining coordinates will be automatically generated. The default is no followed coordinate. This option is usually used to set the initial search direction for a transition state optimization, where it is used in conjunction with the mode_following keyword read by the EFCOpt class. fixed Gives a SetIntCoor object that specifies the internal coordinates that will be fixed. The default is no fixed coordinates. watched Gives a SetIntCoor object that specifies internal coordinates that will be printed out whenever the coordinates are changed. The default is none. have_fixed_values If true, then values for the fixed coordinates must be given in fixed and an attempt will be made to displace the initial geometry to the given fixed values. The default is false. extra_bonds This is only read if the generator keyword is not given. It is a vector of atom numbers, where elements and specify the atoms which are bound in extra bond . The extra_bonds keyword should only be needed for weakly interacting fragments, otherwise all the needed bonds will be found. generator Specifies an IntCoorGen object that creates simple, redundant internal coordinates. If this keyword is not given, then a vector giving extra bonds to be added is read from extra_bonds and this is used to create an IntCoorGen object. decouple_bonds Automatically generated internal coordinates are linear combinations of possibly any mix of simple internal coordinates. If decouple_bonds is true, an attempt will be made to form some of the internal coordinates from just stretch simple coordinates. The default is false. decouple_bends This is like decouple_bonds except it applies to the bend-like coordinates. The default is false. max_update_disp The maximum displacement to be used in the displacement to fixed internal coordinates values. Larger displacements will be broken into several smaller displacements and new coordinates will be formed for each of these displacments. This is only used when fixed and have_fixed_values are given. The default is 0.5. max_update_steps The maximum number of steps permitted to convert internal coordinate displacements to cartesian coordinate displacements. The default is 100. update_bmat Displacements in internal coordinates are converted to a cartesian displacements interatively. If there are large changes in the cartesian coordinates during conversion, then recompute the matrix, which is using to do the conversion. The default is false. only_totally_symmetric If a simple test reveals that an internal coordinate is not totally symmetric, then it will not be added to the internal coordinate list. The default is true. simple_tolerance The internal coordinates are formed as linear combinations of simple, redundant internal coordinates. Coordinates with coefficients smaller then simple_tolerance will be omitted. The default is 1.0e-3. cartesian_tolerance The tolerance for conversion of internal coordinate displacements to cartesian displacements. The default is 1.0e-12. form:print_simple Print the simple internal coordinates. The default is false. form:print_variable Print the variable internal coordinates. The default is false. form:print_constant Print the constant internal coordinates. The default is false. form:print_molecule Print the molecule when forming coordinates. The default is false. scale_bonds Obsolete. The default value is 1.0. scale_bends Obsolete. The default value is 1.0. scale_tors Obsolete. The default value is 1.0. scale_outs Obsolete. The default value is 1.0. symmetry_tolerance Obsolete. The default is 1.0e-5. coordinate_tolerance Obsolete. The default is 1.0e-7. Member Function Documentation virtual void sc::IntMolecularCoor::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 in sc::SymmMolecularCoor. void sc::IntMolecularCoor::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::MolecularCoor. Reimplemented in sc::SymmMolecularCoor. virtual int sc::IntMolecularCoor::to_cartesian (  RefSymmSCMatrix &    cart, RefSymmSCMatrix &    internal )  [virtual]   Convert the internal coordinate Hessian ``internal'' to Cartesian coordinates and copy the result to ``cartesian''. Only the variable internal coordinate force constants are transformed. Implements sc::MolecularCoor. virtual int sc::IntMolecularCoor::to_cartesian (  RefSCVector &    cartesian, RefSCVector &    internal )  [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. Implements sc::MolecularCoor. virtual int sc::IntMolecularCoor::to_internal (  RefSymmSCMatrix &    internal, RefSymmSCMatrix &    cart )  [virtual]   Convert the Cartesian coordinate Hessian ``cartesian'' to internal coordinates and copy the result to ``internal''. Only the variable internal coordinate force constants are calculated. Implements sc::MolecularCoor. virtual int sc::IntMolecularCoor::to_internal (  RefSCVector &    internal, RefSCVector &    cartesian )  [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. Implements sc::MolecularCoor. virtual int sc::IntMolecularCoor::to_internal (  RefSCVector &    internal )  [virtual]   Fill in the vector ``internal'' with the current internal coordinates. Note that this member will update the values of the variable internal coordinates. Implements sc::MolecularCoor. The documentation for this class was generated from the following file: coor.h