APBS  1.5
Vclist class

Atom cell list. More...

Files

file  vclist.c
 Class Vclist methods.
 
file  vclist.h
 Contains declarations for class Vclist.
 

Data Structures

struct  sVclistCell
 Atom cell list cell. More...
 
struct  sVclist
 Atom cell list. More...
 

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

VEXTERNC unsigned long int Vclist_memChk (Vclist *thee)
 Get number of bytes in this object and its members. More...
 
VEXTERNC double Vclist_maxRadius (Vclist *thee)
 Get the max probe radius value (in A) the cell list was constructed with. More...
 
VEXTERNC VclistVclist_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. More...
 
VEXTERNC 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. More...
 
VEXTERNC void Vclist_dtor (Vclist **thee)
 Destroy object. More...
 
VEXTERNC void Vclist_dtor2 (Vclist *thee)
 FORTRAN stub to destroy object. More...
 
VEXTERNC VclistCellVclist_getCell (Vclist *thee, double position[VAPBS_DIM])
 Return cell corresponding to specified position or return VNULL. More...
 
VEXTERNC VclistCellVclistCell_ctor (int natoms)
 Allocate and construct a cell list cell object. More...
 
VEXTERNC Vrc_Codes VclistCell_ctor2 (VclistCell *thee, int natoms)
 Construct a cell list object. More...
 
VEXTERNC void VclistCell_dtor (VclistCell **thee)
 Destroy object. More...
 
VEXTERNC void VclistCell_dtor2 (VclistCell *thee)
 FORTRAN stub to destroy object. More...
 

Detailed Description

Atom cell list.

Enumeration Type Documentation

◆ 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

Definition at line 82 of file vclist.h.

Function Documentation

◆ Vclist_ctor()

VEXTERNC 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
alistMolecule for cell list queries
max_radiusMax probe radius (Å) to be queried
nptsNumber of in hash table points in each direction
modeMode to construct table
lower_cornerHash table lower corner for manual construction (see mode variable); ignored otherwise
upper_cornerHash table upper corner for manual construction (see mode variable); ignored otherwise

Definition at line 75 of file vclist.c.

◆ Vclist_ctor2()

VEXTERNC 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
theeMemory for Vclist objet
alistMolecule for cell list queries
max_radiusMax probe radius (Å) to be queried
nptsNumber of in hash table points in each direction
modeMode to construct table
lower_cornerHash table lower corner for manual construction (see mode variable); ignored otherwise
upper_cornerHash table upper corner for manual construction (see mode variable); ignored otherwise

Definition at line 343 of file vclist.c.

◆ Vclist_dtor()

VEXTERNC void Vclist_dtor ( Vclist **  thee)

Destroy object.

Author
Nathan Baker
Parameters
theePointer to memory location of object

Definition at line 397 of file vclist.c.

◆ Vclist_dtor2()

VEXTERNC void Vclist_dtor2 ( Vclist thee)

FORTRAN stub to destroy object.

Author
Nathan Baker
Parameters
theePointer to object

Definition at line 408 of file vclist.c.

◆ Vclist_getCell()

VEXTERNC 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
theePointer to Vclist cell list
positionPosition to evaluate

Definition at line 423 of file vclist.c.

◆ Vclist_maxRadius()

VEXTERNC 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
theeCell list object

Definition at line 68 of file vclist.c.

◆ Vclist_memChk()

VEXTERNC 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
theeObject for memory check

Definition at line 63 of file vclist.c.

◆ VclistCell_ctor()

VEXTERNC 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
natomsNumber of atoms associated with this cell

Definition at line 452 of file vclist.c.

◆ VclistCell_ctor2()

VEXTERNC Vrc_Codes VclistCell_ctor2 ( VclistCell thee,
int  natoms 
)

Construct a cell list object.

Author
Nathan Baker, Yong Huang
Returns
Success enumeration
Parameters
theeMemory location for object
natomsNumber of atoms associated with this cell

Definition at line 464 of file vclist.c.

◆ VclistCell_dtor()

VEXTERNC void VclistCell_dtor ( VclistCell **  thee)

Destroy object.

Author
Nathan Baker
Parameters
theePointer to memory location of object

Definition at line 486 of file vclist.c.

◆ VclistCell_dtor2()

VEXTERNC void VclistCell_dtor2 ( VclistCell thee)

FORTRAN stub to destroy object.

Author
Nathan Baker
Parameters
theePointer to object

Definition at line 497 of file vclist.c.