The RedundMolecularCoor class provides a redundant set of simple internal coordinates. More...
#include <coor.h>
Inheritance diagram for sc::RedundMolecularCoor:
Collaboration diagram for sc::RedundMolecularCoor:
Public Member Functions | |
| RedundMolecularCoor (Ref< Molecule > &mol) | |
| RedundMolecularCoor (StateIn &) | |
| RedundMolecularCoor (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. More... | |
| void | form_coordinates (int keep_variable=0) |
| Actually form the variable and constant internal coordinates from the simple internal coordinates. | |
| void | guess_hessian (RefSymmSCMatrix &hessian) |
| Form the approximate hessian. | |
| RefSymmSCMatrix | inverse_hessian (RefSymmSCMatrix &) |
| Invert the hessian. | |
 Public Member Functions inherited from sc::IntMolecularCoor | |
| IntMolecularCoor (StateIn &) | |
| IntMolecularCoor (Ref< Molecule > &mol) | |
| IntMolecularCoor (const Ref< KeyVal > &) | |
| The KeyVal constructor. More... | |
| 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 tocartesian''. More... | |
| virtual int | to_internal (RefSymmSCMatrix &internal, RefSymmSCMatrix &cart) |
Convert the Cartesian coordinate Hessian cartesian'' to internal coordinates and copy the result tointernal''. 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. | |
| Public Member Functions inherited from sc::MolecularCoor | |
| MolecularCoor (Ref< Molecule > &) | |
| MolecularCoor (StateIn &) | |
| MolecularCoor (const Ref< KeyVal > &) | |
| The KeyVal constructor. More... | |
| 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. | |
| int | to_cartesian (const RefSCVector &internal) |
| Given a set of displaced internal coordinates, update the cartesian coordinates of the Molecule contained herein. More... | |
| virtual Ref< NonlinearTransform > | change_coordinates () |
| When this is called, MoleculeCoor may select a new internal coordinate system and return a transform to it. More... | |
| 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. More... | |
| 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. More... | |
| virtual void | save_vbase_state (StateOut &) |
| Save the virtual bases for the object. More... | |
| 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. More... | |
| const char * | class_name () const |
| Return the name of the object's exact type. | |
| int | class_version () const |
| Return the version of the class. | |
| 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. More... | |
| 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. More... | |
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. More... | |
| 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::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 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 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. More... | |
| Protected Member Functions inherited from sc::RefCount | |
| RefCount (const RefCount &) | |
| RefCount & | operator= (const RefCount &) |
| 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_ |
Detailed Description
The RedundMolecularCoor class provides a redundant set of simple internal coordinates.
Member Function Documentation
◆ save_data_state()
|
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: