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sc::IntMolecularCoor(3) MPQC sc::IntMolecularCoor(3) NAME sc::IntMolecularCoor - The IntMolecularCoor abstract class describes a molecule's coordinates in terms of internal coordinates. SYNOPSIS #include <coor.h> Inherits sc::MolecularCoor. Inherited by sc::RedundMolecularCoor, and sc::SymmMolecularCoor. Public Member Functions 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 &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. 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''. 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''. virtual int to_cartesian (RefSymmSCMatrix &cart, RefSymmSCMatrix &internal) Convert the internal coordinate Hessian internal'' to Cartesian coordinates and copy the result tocartesian''. virtual int to_internal (RefSymmSCMatrix &internal, RefSymmSCMatrix &cart) Convert the Cartesian coordinate Hessian cartesian'' to internal coordinates 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 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 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 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. 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 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 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 *objectname, const char *keyword=0) 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 $(i-1)imes 2 + 1$ and $iimes 2$ specify the atoms which are bound in extra bond $i$. 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 iteratively. If there are large changes in the cartesian coordinates during conversion, then recompute the $B$ 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 RefSCDimension sc::IntMolecularCoor::dim () [virtual] These implement the virtual functions inherited from MolecularCoor. Implements sc::MolecularCoor. virtual void sc::IntMolecularCoor::form_coordinates (int keep_variable = 0) [pure virtual] Actually form the variable and constant internal coordinates from the simple internal coordinates. Implemented in sc::SymmMolecularCoor, and sc::RedundMolecularCoor. 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. int sc::IntMolecularCoor::nconstrained () [virtual] Returns the number of constrained coordinates. Reimplemented from sc::MolecularCoor. virtual void sc::IntMolecularCoor::print (std::ostream & = ExEnv::out0()) const [virtual] Print the coordinate. Implements sc::MolecularCoor. Reimplemented in sc::SymmMolecularCoor. virtual void sc::IntMolecularCoor::print_simples (std::ostream & = ExEnv::out0()) const [virtual] Implements sc::MolecularCoor. 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, and sc::RedundMolecularCoor. virtual int sc::IntMolecularCoor::to_cartesian (const Ref< Molecule > &, const RefSCVector & internal) [virtual] 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_cartesian (RefSymmSCMatrix & cartesian, RefSymmSCMatrix & internal) [virtual] Convert the internal coordinate Hessian internal'' to Cartesian coordinates and copy the result tocartesian''. Only the variable internal coordinate force constants are transformed. 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. 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 (RefSymmSCMatrix & internal, RefSymmSCMatrix & cartesian) [virtual] Convert the Cartesian coordinate Hessian cartesian'' to internal coordinates and copy the result tointernal''. Only the variable internal coordinate force constants are calculated. Implements sc::MolecularCoor. Author Generated automatically by Doxygen for MPQC from the source code. Version 2.3.1 Tue May 13 2025 sc::IntMolecularCoor(3)
NAME | SYNOPSIS | Detailed Description | Constructor & Destructor Documentation | Member Function Documentation | Author
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