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sc::MolecularCoor(3) MPQC sc::MolecularCoor(3) NAME sc::MolecularCoor - The MolecularCoor abstract class describes the coordinate system used to describe a molecule. SYNOPSIS #include <coor.h> Inherits sc::SavableState. Inherited by sc::CartMolecularCoor, and sc::IntMolecularCoor. Public Member Functions 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 Attributes 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) 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 &) Detailed Description 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. Constructor & Destructor Documentation sc::MolecularCoor::MolecularCoor (const Ref< KeyVal > &) The KeyVal constructor. molecule A Molecule object. There is no default. debug An integer which, if nonzero, will cause extra output. matrixkit A SCMatrixKit object. It is usually unnecessary to give this keyword. natom3 An SCDimension object for the dimension of the vector of cartesian coordinates. It is usually unnecessary to give this keyword. Member Function Documentation virtual Ref< NonlinearTransform > sc::MolecularCoor::change_coordinates () [virtual] 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. virtual RefSCDimension sc::MolecularCoor::dim () [pure virtual] 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. virtual void sc::MolecularCoor::guess_hessian (RefSymmSCMatrix & hessian) [pure virtual] Calculate an approximate hessian and place the result in ``hessian''. Implemented in sc::SymmMolecularCoor, sc::RedundMolecularCoor, and sc::CartMolecularCoor. virtual RefSymmSCMatrix sc::MolecularCoor::inverse_hessian (RefSymmSCMatrix &) [pure virtual] 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. virtual int sc::MolecularCoor::nconstrained () [virtual] Returns the number of constrained coordinates. Reimplemented in sc::IntMolecularCoor. virtual void sc::MolecularCoor::print (std::ostream & = ExEnv::out0()) const [pure virtual] Print the coordinate. Reimplemented from sc::DescribedClass. Implemented in sc::IntMolecularCoor, sc::SymmMolecularCoor, and sc::CartMolecularCoor. void sc::MolecularCoor::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::SavableState. Reimplemented in sc::IntMolecularCoor, sc::SymmMolecularCoor, sc::RedundMolecularCoor, and sc::CartMolecularCoor. int sc::MolecularCoor::to_cartesian (const RefSCVector & internal) Given a set of displaced internal coordinates, update the cartesian coordinates of the Molecule contained herein. This function does not change the vector ``internal''. virtual int sc::MolecularCoor::to_cartesian (RefSCVector & cartesian, RefSCVector & internal) [pure 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. Implemented in sc::IntMolecularCoor, and sc::CartMolecularCoor. virtual int sc::MolecularCoor::to_cartesian (RefSymmSCMatrix & cartesian, RefSymmSCMatrix & internal) [pure virtual] 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. virtual int sc::MolecularCoor::to_internal (RefSCVector & internal) [pure virtual] 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. virtual int sc::MolecularCoor::to_internal (RefSCVector & internal, RefSCVector & cartesian) [pure 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. Implemented in sc::IntMolecularCoor, and sc::CartMolecularCoor. virtual int sc::MolecularCoor::to_internal (RefSymmSCMatrix & internal, RefSymmSCMatrix & cartesian) [pure virtual] 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. Author Generated automatically by Doxygen for MPQC from the source code. Version 2.3.1 Tue May 13 2025 sc::MolecularCoor(3)
NAME | SYNOPSIS | Detailed Description | Constructor & Destructor Documentation | Member Function Documentation | Author
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