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sc::SymmMolecularCoor Class Reference

The SymmMolecularCoor class derives from IntMolecularCoor. More...

`#include <coor.h>`

Inheritance diagram for sc::SymmMolecularCoor:
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Collaboration diagram for sc::SymmMolecularCoor:
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## Public Member Functions
| SymmMolecularCoor (Ref< Molecule > &mol)
| SymmMolecularCoor (StateIn &)
| SymmMolecularCoor (const Ref< KeyVal > &)
| The KeyVal constructor. More...
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 simple internal coordinates. More...
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. More...
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. 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. More...
virtual int | all_to_internal (const Ref< Molecule > &, RefSCVector &internal)
| Like to_internal(), except all internal coordinates are considered, not just the variable ones. More...
virtual RefSCDimension | dim ()
| These implement the virtual functions inherited from MolecularCoor. More...
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_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. More...
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...
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...

## Protected Member Functions
void | init ()
| This is called by the constructors of classes derived from IntMolecularCoor. More...
Protected Member Functions inherited from sc::IntMolecularCoor
void | form_K_matrix (RefSCDimension &dredundant, RefSCDimension &dfixed, RefSCMatrix &K, int *&is_totally_symmetric)
virtual void | new_coords ()
| Allocates memory for the SetIntCoor's used to store the simple and internal coordinates. More...
virtual void | read_keyval (const Ref< KeyVal > &)
| Reads the KeyVal input.

## 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. More...
static SavableState * | key_restore_state (StateIn &si, const char *keyword)
| Like restore_state, but keyword is used to override values while restoring. More...
static SavableState * | dir_restore_state (StateIn &si, const char *objectname, 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 molecular 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 keyword (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 periodically 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, , larger than max_kappa2 are considered linearly dependent. The default is 10.0.

`transform_hessian`

  If true, the hessian will be transformed every time the internal coordinates are formed. The default is true.

## Member Function Documentation

Ref<NonlinearTransform> sc::SymmMolecularCoor::change_coordinates | ( |  | ) |
| virtual

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` | ) |
| virtual

Actually form the variable and constant internal coordinates from simple internal coordinates.

Implements sc::IntMolecularCoor.

void sc::SymmMolecularCoor::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 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.

The documentation for this class was generated from the following file:

- coor.h