Vclist class

Atom cell list. More...

Data Structures
struct	sVclistCell
	Atom cell list cell. More...
struct	sVclist
	Atom cell list. More...
Files
file	vclist.h
	Contains declarations for class Vclist.
file	vclist.c
	Class Vclist methods.
Typedefs
typedef struct sVclistCell	VclistCell
	Declaration of the VclistCell class as the VclistCell structure.
typedef struct sVclist	Vclist
	Declaration of the Vclist class as the Vclist structure.
typedef enum eVclist_DomainMode	Vclist_DomainMode
	Declaration of Vclist_DomainMode enumeration type.
Enumerations
enum	eVclist_DomainMode {   CLIST_AUTO_DOMAIN,   CLIST_MANUAL_DOMAIN }
	Atom cell list domain setup mode. More...
Functions
unsigned long int	Vclist_memChk (Vclist *thee)
	Get number of bytes in this object and its members.
double	Vclist_maxRadius (Vclist *thee)
	Get the max probe radius value (in A) the cell list was constructed with.
Vclist *	Vclist_ctor (Valist *alist, double max_radius, int npts[VAPBS_DIM], Vclist_DomainMode mode, double lower_corner[VAPBS_DIM], double upper_corner[VAPBS_DIM])
	Construct the cell list object.
Vrc_Codes	Vclist_ctor2 (Vclist *thee, Valist *alist, double max_radius, int npts[VAPBS_DIM], Vclist_DomainMode mode, double lower_corner[VAPBS_DIM], double upper_corner[VAPBS_DIM])
	FORTRAN stub to construct the cell list object.
void	Vclist_dtor (Vclist **thee)
	Destroy object.
void	Vclist_dtor2 (Vclist *thee)
	FORTRAN stub to destroy object.
VclistCell *	Vclist_getCell (Vclist *thee, double position[VAPBS_DIM])
	Return cell corresponding to specified position or return VNULL.
VclistCell *	VclistCell_ctor (int natoms)
	Allocate and construct a cell list cell object.
Vrc_Codes	VclistCell_ctor2 (VclistCell *thee, int natoms)
	Construct a cell list object.
void	VclistCell_dtor (VclistCell **thee)
	Destroy object.
void	VclistCell_dtor2 (VclistCell *thee)
	FORTRAN stub to destroy object.

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Detailed Description

Atom cell list.

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Enumeration Type Documentation

enum eVclist_DomainMode

Atom cell list domain setup mode.

Author:

Nathan Baker

Enumerator:

CLIST_AUTO_DOMAIN	Setup the cell list domain automatically to encompass the entire molecule
CLIST_MANUAL_DOMAIN	Specify the cell list domain manually through the constructor

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Function Documentation

Vclist* Vclist_ctor	(	Valist *	alist,
		double	max_radius,
		int	npts[VAPBS_DIM],
		Vclist_DomainMode	mode,
		double	lower_corner[VAPBS_DIM],
		double	upper_corner[VAPBS_DIM]
	)

Construct the cell list object.

Author:

Nathan Baker

Returns:

Newly allocated Vclist object

Parameters:

	max_radius	Molecule for cell list queries
	npts	Max probe radius (Å) to be queried
	mode	Number of in hash table points in each direction
	lower_corner	Mode to construct table
	upper_corner	Hash table lower corner for manual construction (see mode variable); ignored otherwise Hash table upper corner for manual construction (see mode variable); ignored otherwise

References Vclist_ctor2(), and VRC_SUCCESS.

Referenced by initAPOL(), and Vpbe_ctor2().

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Vrc_Codes Vclist_ctor2	(	Vclist *	thee,
		Valist *	alist,
		double	max_radius,
		int	npts[VAPBS_DIM],
		Vclist_DomainMode	mode,
		double	lower_corner[VAPBS_DIM],
		double	upper_corner[VAPBS_DIM]
	)

FORTRAN stub to construct the cell list object.

Author:

Nathan Baker, Yong Huang

Returns:

Success enumeration

Parameters:

	alist	Memory for Vclist objet
	max_radius	Molecule for cell list queries
	npts	Max probe radius (Å) to be queried
	mode	Number of in hash table points in each direction
	lower_corner	Mode to construct table
	upper_corner	Hash table lower corner for manual construction (see mode variable); ignored otherwise Hash table upper corner for manual construction (see mode variable); ignored otherwise

References sVclist::cells, sVclist::n, sVclistCell::natoms, sVclist::vmem, VRC_FAILURE, and VRC_SUCCESS.

Referenced by Vclist_ctor().

void Vclist_dtor

(

Vclist **

thee

)

Destroy object.

Author:

Nathan Baker

Parameters:

thee

Pointer to memory location of object

References Vclist_dtor2().

Referenced by initAPOL(), and Vpbe_dtor2().

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void Vclist_dtor2

(

Vclist *

thee

)

FORTRAN stub to destroy object.

Author:

Nathan Baker

Parameters:

thee

Pointer to object

References sVclist::cells, sVclist::n, VclistCell_dtor2(), and sVclist::vmem.

Referenced by Vclist_dtor().

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VclistCell* Vclist_getCell	(	Vclist *	thee,
		double	position[VAPBS_DIM]
	)

Return cell corresponding to specified position or return VNULL.

Author:

Nathan Baker

Returns:

Pointer to VclistCell object or VNULL if no cell available (away from molecule).

Parameters:

position

Pointer to Vclist cell list Position to evaluate

References sVclist::cells, sVclist::lower_corner, sVclist::npts, and sVclist::spacs.

Referenced by ivdwAccExclus(), Vacc_fastMolAcc(), Vacc_splineAcc(), and Vacc_splineAccGrad().

double Vclist_maxRadius

(

Vclist *

thee

)

Get the max probe radius value (in A) the cell list was constructed with.

Author:

Nathan Baker

Returns:

Max probe radius (in A)

Parameters:

thee

Cell list object

References sVclist::max_radius.

Referenced by ivdwAccExclus(), Vacc_splineAcc(), Vacc_splineAccGrad(), and Vacc_storeParms().

unsigned long int Vclist_memChk

(

Vclist *

thee

)

Get number of bytes in this object and its members.

Author:

Nathan Baker

Returns:

Number of bytes allocated for object

Parameters:

thee

Object for memory check

References sVclist::vmem.

VclistCell* VclistCell_ctor

(

int

natoms

)

Allocate and construct a cell list cell object.

Author:

Nathan Baker

Returns:

Pointer to newly-allocated and constructed object.

Parameters:

natoms

Number of atoms associated with this cell

References VclistCell_ctor2(), and VRC_SUCCESS.

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Vrc_Codes VclistCell_ctor2	(	VclistCell *	thee,
		int	natoms
	)

Construct a cell list object.

Author:

Nathan Baker, Yong Huang

Returns:

Success enumeration

Parameters:

natoms

Memory location for object Number of atoms associated with this cell

References sVclistCell::atoms, sVclistCell::natoms, VRC_FAILURE, and VRC_SUCCESS.

Referenced by VclistCell_ctor().

void VclistCell_dtor

(

VclistCell **

thee

)

Destroy object.

Author:

Nathan Baker

Parameters:

thee

Pointer to memory location of object

References VclistCell_dtor2().

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void VclistCell_dtor2

(

VclistCell *

thee

)

FORTRAN stub to destroy object.

Author:

Nathan Baker

Parameters:

thee

Pointer to object

References sVclistCell::atoms, and sVclistCell::natoms.

Referenced by Vclist_dtor2(), and VclistCell_dtor().