sc::SymmMolecularCoor(3) MPQC sc::SymmMolecularCoor(3) NAME sc::SymmMolecularCoor - The SymmMolecularCoor class derives from IntMolecu- larCoor. SYNOPSIS #include <coor.h> Inherits sc::IntMolecularCoor. Public Member Functions SymmMolecularCoor (Ref< Molecule > &mol) SymmMolecularCoor (StateIn &) SymmMolecularCoor (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. void form_coordinates (int keep_variable=0) Actually form the variable and constant internal coordinates from sim- ple 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. Public Member Functions inherited from sc::IntMolecularCoor IntMolecularCoor (StateIn &) IntMolecularCoor (Ref< Molecule > &mol) IntMolecularCoor (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. 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 &inter- nal) Like to_cartesians(), except all internal coordinates are considered, not just the variable ones. virtual int all_to_internal (const Ref< Molecule > &, RefSCVector &inter- nal) 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 &in- ternal) virtual int to_internal (RefSCVector &internal) Fill in the vector ``internal'' with the current internal coordinates. 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 ``carte- sian''. 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 ``inter- nal''. virtual int to_cartesian (RefSymmSCMatrix &cart, RefSymmSCMatrix &internal) Convert the internal coordinate Hessian internal'' to Cartesian coordi- nates and copy the result tocartesian''. virtual int to_internal (RefSymmSCMatrix &internal, RefSymmSCMatrix &cart) Convert the Cartesian coordinate Hessian cartesian'' to internal coor- dinates and copy the result tointernal''. 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. Public Member Functions inherited from sc::MolecularCoor 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 co- ordinates (be they Cartesian, internal, or whatever) that are being op- timized. int to_cartesian (const RefSCVector &internal) Given a set of displaced internal coordinates, update the cartesian co- ordinates 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 ``carte- sian''. 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 ``inter- nal''. virtual int to_cartesian (RefSymmSCMatrix &cartesian, RefSymmSCMatrix &in- ternal)=0 Convert the internal coordinate Hessian internal'' to Cartesian coordi- nates and copy the result tocartesian''. virtual int to_internal (RefSymmSCMatrix &internal, RefSymmSCMatrix &carte- sian)=0 Convert the Cartesian coordinate Hessian cartesian'' to internal coor- dinates 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 Public Member Functions inherited from sc::SavableState SavableState & operator= (const SavableState &) void save_state (StateOut &) Save the state of the object as specified by the StateOut object. void save_object_state (StateOut &) This can be used for saving state when the exact type of the object is known for both the save and the restore. virtual void save_vbase_state (StateOut &) Save the virtual bases for the object. virtual 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. Public Member Functions inherited from sc::DescribedClass DescribedClass (const DescribedClass &) DescribedClass & operator= (const DescribedClass &) ClassDesc * class_desc () const throw () This returns the unique pointer to the ClassDesc corresponding to the given type_info object. const char * class_name () const Return the name of the object's exact type. int class_version () const Return the version of the class. virtual void print (std::ostream &=ExEnv::out0()) const Print the object. Public Member Functions inherited from sc::RefCount int lock_ptr () const Lock this object. int unlock_ptr () const Unlock this object. void use_locks (bool inVal) start and stop using locks on this object refcount_t nreference () const Return the reference count. refcount_t reference () Increment the reference count and return the new count. refcount_t dereference () Decrement the reference count and return the new count. int managed () const void unmanage () Turn off the reference counting mechanism for this object. int managed () const Return 1 if the object is managed. Otherwise return 0. Public Member Functions inherited from sc::Identity Identifier identifier () Return the Identifier for this argument. Protected Member Functions void init () This is called by the constructors of classes derived from IntMolecu- larCoor. Protected Member Functions inherited from sc::IntMolecularCoor 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 IntMolecu- larCoor. virtual void new_coords () Allocates memory for the SetIntCoor's used to store the simple and in- ternal coordinates. virtual void read_keyval (const Ref< KeyVal > &) Reads the KeyVal input. Protected Member Functions inherited from sc::SavableState SavableState (const SavableState &) SavableState (StateIn &) Each derived class StateIn CTOR handles the restore corresponding to calling save_object_state, save_vbase_state, and save_data_state listed above. Protected Member Functions inherited from sc::RefCount RefCount (const RefCount &) RefCount & operator= (const RefCount &) Protected Attributes int change_coordinates_ int transform_hessian_ double max_kappa2_ Protected Attributes inherited from sc::IntMolecularCoor 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_ Protected Attributes inherited from sc::MolecularCoor Ref< Molecule > molecule_ RefSCDimension dnatom3_ Ref< SCMatrixKit > matrixkit_ int debug_ Additional Inherited Members Static Public Member Functions inherited from sc::SavableState static void save_state (SavableState *s, StateOut &) static SavableState * restore_state (StateIn &si) Restores objects saved with save_state. static SavableState * key_restore_state (StateIn &si, const char *keyword) Like restore_state, but keyword is used to override values while restoring. static SavableState * dir_restore_state (StateIn &si, const char *object- name, const char *keyword=0) 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 mol- ecular 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 key- word (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 peri- odically 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, $ppa_2$, larger than max_kappa2 are considered lin- early dependent. The default is 10.0. transform_hessian If true, the hessian will be transformed every time the internal coor- dinates are formed. The default is true. Member Function Documentation Ref< NonlinearTransform > sc::SymmMolecularCoor::change_coordinates () [vir- tual] This overrides MoleculeCoor's change_coordinates and might transform to a new set of coordinates. Reimplemented from sc::MolecularCoor. void sc::SymmMolecularCoor::form_coordinates (int keep_variable = 0) [vir- tual] Actually form the variable and constant internal coordinates from simple internal coordinates. Implements sc::IntMolecularCoor. void sc::SymmMolecularCoor::guess_hessian (RefSymmSCMatrix & hessian) [vir- tual] Form the approximate hessian. Implements sc::MolecularCoor. void sc::SymmMolecularCoor::init () [protected], [virtual] This is called by the constructors of classes derived from IntMolecular- Coor. It initialized the lists of simple internal coordinates, and then calls the form_coordinates() member. Reimplemented from sc::IntMolecularCoor. RefSymmSCMatrix sc::SymmMolecularCoor::inverse_hessian (RefSymmSCMatrix &) [virtual] Invert the hessian. Implements sc::MolecularCoor. void sc::SymmMolecularCoor::print (std::ostream & = ExEnv::out0()) const [virtual] Print the coordinate. 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. Author Generated automatically by Doxygen for MPQC from the source code. Version 2.3.1 Thu Sep 3 2026 sc::SymmMolecularCoor(3)
NAME | SYNOPSIS | Detailed Description | Constructor & Destructor Documentation | Member Function Documentation | Author
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