psi::extrema::internals Class Reference

Abstract internal coordinate derived class. More...

#include <internals.h>

Inheritance diagram for psi::extrema::internals:

List of all members.

Protected Member Functions
	internals ()
	Dummy constructor.
void	mem_alloc ()
	Allocates memory.
	~internals ()
	Destructor. Frees memory.
virtual void	compute_B ()=0
	Derived classes must provide a function to compute the B matrix though calls to B_row...() functions.
virtual void	cart_to_internal (double **)=0
void	back_transform (double *, double *)
	Performs iterative back transformation from internals to cartesians.
double *	B_row_bond (double *, int, int)
	Computes a row of B corrresponding to a simple bonding coordinate.
double *	B_row_angle (double *, int, int, int)
	Computes a row of B corresponding to a simple bending coordinate.
double *	B_row_tors (double *, int, int, int, int)
	Computes row of B matrix corresponding to a simple torsion coordinate.
void	print_B ()
	Prints the B matrix.
void	compute_G ()
	Computes the G=B.B^t matrix.
void	compute_A ()
	Computes the A=u.B^t.G matrix. ---------------------------------------------------------------------------.
virtual void	grad_trans ()
	Performs gradient transformation from cartesians to internals.
Protected Attributes
int	fnum_coords
int	B_dim
double **	full_geom
double *	fcoords
double *	fcoords_old
double *	fgrads
double **	B
double **	B_red
double **	G
double **	A
double **	u

---

Detailed Description

Abstract internal coordinate derived class.

Member functions and data common to internal coordinate types. Primarily, this class contains the B matrix and related matrices, functions for computing these matrices, and functions which apply these matrices in gradient and coordinate transformations

"full" variables refer to the complete set of coordinates, including any equivalent coordinates. In the iterative back transformation to cartesians, the complete set of coordinates is utilized.

---

Constructor & Destructor Documentation

psi::extrema::internals::internals

(

)

[inline, protected]

Dummy constructor.

This is a dummy constructor which exists to make compilers happy. It does nothing. The actual constructor may depend on data which is not know when a derived class is initialized and may be called later in that class's constructor.

---

Member Function Documentation

void internals::mem_alloc

(

)

[protected]

Allocates memory.

Must be called by top-level class once dimensions determined.

Reimplemented from psi::extrema::coord_base.

void internals::back_transform	(	double *	c_new,
		double *	c_old
	)			[protected]

Performs iterative back transformation from internals to cartesians.

This function requires the full array of coordinate values.

Parameters:

	*c_new	new internal coordinate array
	*c_old	old internal coordinate array

double * internals::B_row_bond	(	double *	carr,
		int	atom1,
		int	atom2
	)			[protected]

Computes a row of B corrresponding to a simple bonding coordinate.

Parameters:

	*carr	full cartesian coordinate array
	atom1	reference atom 1
	atom2	atom bonded to 1

double * internals::B_row_angle	(	double *	c_arr,
		int	atom1,
		int	atom3,
		int	atom2
	)			[protected]

Computes a row of B corresponding to a simple bending coordinate.

Parameters:

	*c_arr	full cartesian coordinate array
	atom1	reference atom 1
	atom3	atom bonded to 1
	atom2	atom defining angle 1-3-2

double * internals::B_row_tors	(	double *	c_arr,
		int	atom1,
		int	atom2,
		int	atom3,
		int	atom4
	)			[protected]

Computes row of B matrix corresponding to a simple torsion coordinate.

Parameters:

	*c_arr	full cartesian array
	atom1	reference atom 1
	atom2	atom bonded to 1
	atom3	atom defining angle 1-2-3
	atom4	atom defining torsion 1-2-3-4

---

Member Data Documentation

int psi::extrema::internals::fnum_coords [protected]

full number of coordinates

int psi::extrema::internals::B_dim [protected]

fnum_coords for zmat, num_coords for deloc

double** psi::extrema::internals::full_geom [protected]

full geometry (including dummy atoms)

double * psi::extrema::internals::fcoords [protected]

full set of internal coordinate values

double * psi::extrema::internals::fcoords_old [protected]

full set of previous internal coordinate values

double * psi::extrema::internals::fgrads [protected]

full set of internal coordinate gradients

double ** psi::extrema::internals::B [protected]

the B matrix

double ** psi::extrema::internals::B_red [protected]

reduced dimension B matrix (no equivalent coords)

double ** psi::extrema::internals::G [protected]

the G=B.B^t matrix

double ** psi::extrema::internals::A [protected]

the A=u.B^t.G matrix

double ** psi::extrema::internals::u [protected]

the u matrix (triplets of inverse atomic masses)

---

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

• internals.h
• internals.cc
• internals_B.cc