Vhal class

A "class" which consists solely of macro definitions which are used by several other classes. More...


Files
file	vhal.h
	Contains generic macro definitions for APBS.
Defines
#define	APBS_TIMER_WALL_CLOCK 26
	APBS total execution timer ID.
#define	APBS_TIMER_SETUP 27
	APBS setup timer ID.
#define	APBS_TIMER_SOLVER 28
	APBS solver timer ID.
#define	APBS_TIMER_ENERGY 29
	APBS energy timer ID.
#define	APBS_TIMER_FORCE 30
	APBS force timer ID.
#define	APBS_TIMER_TEMP1 31
	APBS temp timer #1 ID.
#define	APBS_TIMER_TEMP2 32
	APBS temp timer #2 ID.
#define	MAXMOL 5
	The maximum number of molecules that can be involved in a single PBE calculation.
#define	MAXION 10
	The maximum number of ion species that can be involved in a single PBE calculation.
#define	MAXFOCUS 5
	The maximum number of times an MG calculation can be focused.
#define	VMGNLEV 4
	Minimum number of levels in a multigrid calculations.
#define	VREDFRAC 0.25
	Maximum reduction of grid spacing during a focusing calculation.
#define	VAPBS_NVS 4
	Number of vertices per simplex (hard-coded to 3D).
#define	VAPBS_DIM 3
	Our dimension.
#define	VAPBS_RIGHT 0
	Face definition for a volume.
#define	VAPBS_FRONT 1
	Face definition for a volume.
#define	VAPBS_UP 2
	Face definition for a volume.
#define	VAPBS_LEFT 3
	Face definition for a volume.
#define	VAPBS_BACK 4
	Face definition for a volume.
#define	VAPBS_DOWN 5
	Face definition for a volume.
#define	VPMGSMALL 1e-12
	A small number used in Vpmg to decide if points are on/off grid-lines or non-zer0 (etc.).
#define	VF77_MANGLE(name, NAME) name
	Name-mangling macro for using FORTRAN functions in C code.
#define	VFLOOR(value) floor(value)
	Wrapped floor to fix floating point issues in the Intel compiler.
#define	VEMBED(rctag)
	Allows embedding of RCS ID tags in object files.
Typedefs
typedef enum eVhal_PBEType	Vhal_PBEType
	Declaration of the Vhal_PBEType type as the Vhal_PBEType enum.
typedef enum eVbcfl	Vbcfl
	Declare Vbcfl type.
typedef enum eVsurf_Meth	Vsurf_Meth
	Declaration of the Vsurf_Meth type as the Vsurf_Meth enum.
typedef enum eVchrg_Meth	Vchrg_Meth
	Declaration of the Vchrg_Meth type as the Vchrg_Meth enum.
typedef enum eVdata_Type	Vdata_Type
	Declaration of the Vdata_Type type as the Vdata_Type enum.
typedef enum eVdata_Format	Vdata_Format
	Declaration of the Vdata_Format type as the Vdata_Format enum.
Enumerations
enum	eVsurf_Meth { VSM_MOL = 0, VSM_MOLSMOOTH = 1, VSM_SPLINE = 2 }
	Types of molecular surface definitions. More...
enum	eVhal_PBEType { PBE_LPBE, PBE_NPBE, PBE_LRPBE, PBE_NRPBE }
	Version of PBE to solve. More...
enum	eVbcfl { BCFL_ZERO = 0, BCFL_SDH = 1, BCFL_MDH = 2, BCFL_UNUSED = 3, BCFL_FOCUS = 4 }
	Types of boundary conditions. More...
enum	eVchrg_Meth { VCM_TRIL = 0, VCM_BSPL2 = 1 }
	Types of charge discretization methods. More...
enum	eVdata_Type { VDT_CHARGE, VDT_POT, VDT_SMOL, VDT_SSPL, VDT_VDW, VDT_IVDW, VDT_LAP, VDT_EDENS, VDT_NDENS, VDT_QDENS, VDT_DIELX, VDT_DIELY, VDT_DIELZ, VDT_KAPPA }
	Types of (scalar) data that can be written out of APBS. More...
enum	eVdata_Format { VDF_DX = 0, VDF_UHBD = 1, VDF_AVS = 2 }
	Format of data that can be written out of APBS. More...

Detailed Description

A "class" which consists solely of macro definitions which are used by several other classes.

Define Documentation

#define VAPBS_BACK 4

Face definition for a volume.

Note:
Consistent with PMG if RIGHT = EAST, BACK = SOUTH

#define VAPBS_DOWN 5

Face definition for a volume.

Note:
Consistent with PMG if RIGHT = EAST, BACK = SOUTH

#define VAPBS_FRONT 1

Face definition for a volume.

Note:
Consistent with PMG if RIGHT = EAST, BACK = SOUTH

#define VAPBS_LEFT 3

Face definition for a volume.

Note:
Consistent with PMG if RIGHT = EAST, BACK = SOUTH

#define VAPBS_RIGHT 0

Face definition for a volume.

Note:
Consistent with PMG if RIGHT = EAST, BACK = SOUTH

#define VAPBS_UP 2

Face definition for a volume.

Note:
Consistent with PMG if RIGHT = EAST, BACK = SOUTH

#define VEMBED ( rctag )

Value:
VPRIVATE const char* rctag; \ static void* use_rcsid=(0 ? &use_rcsid : (void**)&rcsid);
Allows embedding of RCS ID tags in object files.

Author:
Mike Holst

#define VFLOOR ( value ) floor(value)

Wrapped floor to fix floating point issues in the Intel compiler.

Author:
Todd Dolinksy

Enumeration Type Documentation

enum eVbcfl

Types of boundary conditions.

Author:
Nathan Baker

Enumeration values:

BCFL_ZERO Zero Dirichlet boundary conditions

BCFL_SDH Single-sphere Debye-Huckel Dirichlet boundary condition

BCFL_MDH Multiple-sphere Debye-Huckel Dirichlet boundary condition

BCFL_UNUSED Unused boundary condition method (placeholder)

BCFL_FOCUS Focusing Dirichlet boundary condition

enum eVchrg_Meth

Types of charge discretization methods.

Author:
Nathan Baker

Enumeration values:

VCM_TRIL Trilinear interpolation of charge to 8 nearest grid points. The traditional method; not particularly good to use with PBE forces.

VCM_BSPL2 Cubic B-spline across nearest- and next-nearest-neighbors. Mainly for use in grid-sensitive applications (such as force calculations).

enum eVdata_Format

Format of data that can be written out of APBS.

Author:
Nathan Baker

Enumeration values:

VDF_DX OpenDX (Data Explorer) format

VDF_UHBD UHBD format

VDF_AVS AVS UCD format

enum eVdata_Type

Types of (scalar) data that can be written out of APBS.

Author:
Nathan Baker

Enumeration values:

VDT_CHARGE Charge distribution (e)

VDT_POT Potential (kT/e)

VDT_SMOL Solvent accessibility defined by molecular/Connolly surface definition (1 = accessible, 0 = inaccessible)

VDT_SSPL Spline-based solvent accessibility (1 = accessible, 0 = inaccessible)

VDT_VDW van der Waals-based accessibility (1 = accessible, 0 = inaccessible)

VDT_IVDW Ion accessibility/inflated van der Waals (1 = accessible, 0 = inaccessible)

VDT_LAP Laplacian of potential (kT/e/A^2)

VDT_EDENS Energy density $\epsilon (\nabla u)^2$ , where $u$ is potential (kT/e/A)^2

VDT_NDENS Ion number density $\sum c_i \exp (-q_i u)^2$ , where $u$ is potential (output in M)

VDT_QDENS Ion charge density $\sum q_i c_i \exp (-q_i u)^2$ , where $u$ is potential (output in $e_c M$ )

VDT_DIELX Dielectric x-shifted map as calculated with the currently specified scheme (dimensionless)

VDT_DIELY Dielectric y-shifted map as calculated with the currently specified scheme (dimensionless)

VDT_DIELZ Dielectric y-shifted map as calculated with the currently specified scheme (dimensionless)

VDT_KAPPA Kappa map as calculated with the currently specified scheme ( $\AA^{-3}$ )

enum eVhal_PBEType

Version of PBE to solve.

Enumeration values:

PBE_LPBE Traditional Poisson-Boltzmann equation, linearized

PBE_NPBE Traditional Poisson-Boltzmann equation, full

PBE_LRPBE Regularized Poisson-Boltzmann equation, linearized

PBE_NRPBE < Regularized Poisson-Boltzmann equation, full

enum eVsurf_Meth

Types of molecular surface definitions.

Author:
Nathan Baker

Enumeration values:

VSM_MOL Ion accessibility is defined using inflated van der Waals radii, the dielectric coefficient ( ) is defined using the molecular (Conolly) surface definition without smoothing

VSM_MOLSMOOTH As VSM_MOL but with a simple harmonic average smoothing

VSM_SPLINE Spline-based surface definitions. This is primarily for use with force calculations, since it requires substantial reparameterization of radii. This is based on the work of Im et al, Comp. Phys. Comm. 111 , (1998) and uses a cubic spline to define a smoothly varying characteristic function for the surface-based parameters. Ion accessibility is defined using inflated van der Waals radii with the spline function and the dielectric coefficient is defined using the standard van der Waals radii with the spline function.

Generated on Tue Dec 6 10:05:59 2005 for APBS by

1.3.5

Vhal class

Files

Defines

Typedefs

Enumerations

Detailed Description

Define Documentation

Enumeration Type Documentation