The SymmMolecularCoor class derives from IntMolecularCoor. More...

#include <chemistry/molecule/coor.h>

Inheritance diagram for sc::SymmMolecularCoor:

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.

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. 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 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.

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 MPQC__NOEXCEPT
	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.

Ref< DescribedClass >	ref ()
	Return this object wrapped up in a Ref smart pointer. More...

Public Member Functions inherited from sc::RefCount
size_t	identifier () const
	Return the unique identifier for this object that can be compared for different objects of different types. More...

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...

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.

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
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.

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

◆ SymmMolecularCoor()

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, $\kappa_2$ , 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.

Member Function Documentation

◆ init()

void sc::SymmMolecularCoor::init ( )

protectedvirtual

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.

◆ save_data_state()

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:

src/lib/chemistry/molecule/coor.h

Public Member Functions

Protected Member Functions