sc::IntMolecularCoor Class Reference

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

#include <coor.h>

Inheritance diagram for sc::IntMolecularCoor:

List of all members.

Public Member Functions

IntMolecularCoor (StateIn &)

IntMolecularCoor (Ref< Molecule > &mol)

IntMolecularCoor (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.

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.

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''.

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''.

virtual int to_cartesian (RefSymmSCMatrix &cart, RefSymmSCMatrix &internal)

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

virtual int to_internal (RefSymmSCMatrix &internal, RefSymmSCMatrix &cart)

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

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.

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.

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 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_

Detailed Description

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

Constructor & Destructor Documentation

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 . 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 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

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

virtual void sc::IntMolecularCoor::new_coords ( ) [protected, virtual]

Allocates memory for the SetIntCoor's used to store the simple and internal coordinates.

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::SymmMolecularCoor, and sc::RedundMolecularCoor.

virtual void sc::IntMolecularCoor::form_coordinates ( int keep_variable = 0 ) [pure virtual]

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

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

virtual int sc::IntMolecularCoor::all_to_cartesian	(	const Ref< Molecule > &	,
		RefSCVector &	internal
	)			`[virtual]`

Like to_cartesians(), except all internal coordinates are considered, not just the variable ones.

virtual int sc::IntMolecularCoor::all_to_internal	(	const Ref< Molecule > &	,
		RefSCVector &	internal
	)			`[virtual]`

Like to_internal(), except all internal coordinates are considered, not just the variable ones.

virtual RefSCDimension sc::IntMolecularCoor::dim ( ) [virtual]

These implement the virtual functions inherited from MolecularCoor.

Implements sc::MolecularCoor.

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.

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.

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.

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

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

Only the variable internal coordinate force constants are transformed.

Implements sc::MolecularCoor.

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

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

Only the variable internal coordinate force constants are calculated.

Implements sc::MolecularCoor.

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

coor.h


Public Member Functions
	IntMolecularCoor (StateIn &)
	IntMolecularCoor (Ref< Molecule > &mol)
	IntMolecularCoor (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.
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.
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''.
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''.
virtual int	to_cartesian (RefSymmSCMatrix &cart, RefSymmSCMatrix &internal)
	Convert the internal coordinate Hessian ``internal'' to Cartesian coordinates and copy the result to ``cartesian''.
virtual int	to_internal (RefSymmSCMatrix &internal, RefSymmSCMatrix &cart)
	Convert the Cartesian coordinate Hessian ``cartesian'' to internal coordinates and copy the result to ``internal''.
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.
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.
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 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_