The IntMolecularCoor abstract class describes a molecule's coordinates in terms of internal coordinates. More...

#include <chemistry/molecule/coor.h>

Inheritance diagram for sc::IntMolecularCoor:

Public Member Functions
	IntMolecularCoor (StateIn &)

	IntMolecularCoor (Ref< Molecule > &mol)

	IntMolecularCoor (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...

virtual void	form_coordinates (int keep_variable=0)=0
	Actually form the variable and constant internal coordinates from the simple internal coordinates.

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 (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 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. 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 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	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
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 IntMolecularCoor abstract class describes a molecule's coordinates in terms of internal coordinates.

Constructor & Destructor Documentation

◆ IntMolecularCoor()

sc::IntMolecularCoor::IntMolecularCoor ( const Ref< KeyVal > & )

The KeyVal constructor.

variable

Gives a SetIntCoor object that specifies the internal coordinates that can be varied. If this is not given, the variable coordinates will be generated.

followed

Gives a IntCoor object that specifies a coordinate to used as the first coordinate in the variable coordinate list. The remaining coordinates will be automatically generated. The default is no followed coordinate. This option is usually used to set the initial search direction for a transition state optimization, where it is used in conjunction with the mode_following keyword read by the EFCOpt class.

fixed

Gives a SetIntCoor object that specifies the internal coordinates that will be fixed. The default is no fixed coordinates.

watched

Gives a SetIntCoor object that specifies internal coordinates that will be printed out whenever the coordinates are changed. The default is none.

have_fixed_values

If true, then values for the fixed coordinates must be given in fixed and an attempt will be made to displace the initial geometry to the given fixed values. The default is false.

extra_bonds

This is only read if the generator keyword is not given. It is a vector of atom numbers, where elements $(i-1)\times 2 + 1$ and $i\times 2$ specify the atoms which are bound in extra bond $i$ . The extra_bonds keyword should only be needed for weakly interacting fragments, otherwise all the needed bonds will be found.

generator

Specifies an IntCoorGen object that creates simple, redundant internal coordinates. If this keyword is not given, then a vector giving extra bonds to be added is read from extra_bonds and this is used to create an IntCoorGen object.

decouple_bonds

Automatically generated internal coordinates are linear combinations of possibly any mix of simple internal coordinates. If decouple_bonds is true, an attempt will be made to form some of the internal coordinates from just stretch simple coordinates. The default is false.

decouple_bends

This is like decouple_bonds except it applies to the bend-like coordinates. The default is false.

max_update_disp

The maximum displacement to be used in the displacement to fixed internal coordinates values. Larger displacements will be broken into several smaller displacements and new coordinates will be formed for each of these displacments. This is only used when fixed and have_fixed_values are given. The default is 0.5.

max_update_steps

The maximum number of steps permitted to convert internal coordinate displacements to cartesian coordinate displacements. The default is 100.

update_bmat

Displacements in internal coordinates are converted to a cartesian displacements iteratively. If there are large changes in the cartesian coordinates during conversion, then recompute the $B$ matrix, which is using to do the conversion. The default is false.

only_totally_symmetric

If a simple test reveals that an internal coordinate is not totally symmetric, then it will not be added to the internal coordinate list. The default is true.

simple_tolerance

The internal coordinates are formed as linear combinations of simple, redundant internal coordinates. Coordinates with coefficients smaller then simple_tolerance will be omitted. The default is 1.0e-3.

cartesian_tolerance

The tolerance for conversion of internal coordinate displacements to cartesian displacements. The default is 1.0e-12.

form:print_simple

Print the simple internal coordinates. The default is false.

form:print_variable

Print the variable internal coordinates. The default is false.

form:print_constant

Print the constant internal coordinates. The default is false.

form:print_molecule

Print the molecule when forming coordinates. The default is false.

scale_bonds

Obsolete. The default value is 1.0.

scale_bends

Obsolete. The default value is 1.0.

scale_tors

Obsolete. The default value is 1.0.

scale_outs

Obsolete. The default value is 1.0.

symmetry_tolerance

Obsolete. The default is 1.0e-5.

coordinate_tolerance

Obsolete. The default is 1.0e-7.

Member Function Documentation

◆ init()

virtual void sc::IntMolecularCoor::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 in sc::SymmMolecularCoor.

◆ save_data_state()

void sc::IntMolecularCoor::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::MolecularCoor.

Reimplemented in sc::RedundMolecularCoor, and sc::SymmMolecularCoor.

◆ to_cartesian() [1/2]

virtual int sc::IntMolecularCoor::to_cartesian	(	RefSCVector &	cartesian,
		RefSCVector &	internal
	)

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.

Implements sc::MolecularCoor.

◆ to_cartesian() [2/2]

virtual int sc::IntMolecularCoor::to_cartesian	(	RefSymmSCMatrix &	cartesian,
		RefSymmSCMatrix &	internal
	)

virtual

Convert the internal coordinate Hessian internal'' to Cartesian coordinates and copy the result tocartesian''.

Only the variable internal coordinate force constants are transformed.

Implements sc::MolecularCoor.

◆ to_internal() [1/3]

virtual int sc::IntMolecularCoor::to_internal ( RefSCVector & internal )

virtual

Fill in the vector `‘internal’' with the current internal coordinates.

Note that this member will update the values of the variable internal coordinates.

Implements sc::MolecularCoor.

◆ to_internal() [2/3]

virtual int sc::IntMolecularCoor::to_internal	(	RefSCVector &	internal,
		RefSCVector &	cartesian
	)

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.

Implements sc::MolecularCoor.

◆ to_internal() [3/3]

virtual int sc::IntMolecularCoor::to_internal	(	RefSymmSCMatrix &	internal,
		RefSymmSCMatrix &	cartesian
	)

virtual

Convert the Cartesian coordinate Hessian cartesian'' to internal coordinates and copy the result tointernal''.

Only the variable internal coordinate force constants are calculated.

Implements sc::MolecularCoor.

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

src/lib/chemistry/molecule/coor.h

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ IntMolecularCoor()

Member Function Documentation

◆ init()

◆ save_data_state()

◆ to_cartesian() [1/2]

◆ to_cartesian() [2/2]

◆ to_internal() [1/3]

◆ to_internal() [2/3]

◆ to_internal() [3/3]