sc_SymmMolecularCoor - Man Page

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 simple 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.
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 tocartesian''.
virtual int to_internal (RefSCVector &internal, RefSCVector &cartesian)
Convert the Cartesian coordinate gradients in cartesian'' to internal coordinates and copy these internal coordinate gradients tointernal''.
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_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.
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.
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.

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.

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.

void init ()
This is called by the constructors of classes derived from IntMolecularCoor.

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.
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 &)

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_

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)

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, $ppa_2$, 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.

This overrides MoleculeCoor's change_coordinates and might transform to a new set of coordinates.

Reimplemented from sc::MolecularCoor.

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

Implements sc::IntMolecularCoor.

Form the approximate hessian.

Implements sc::MolecularCoor.

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.

Invert the hessian.

Implements sc::MolecularCoor.

Print the coordinate.

Reimplemented from sc::IntMolecularCoor.

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.