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.

Macros
#define	APBS_TIMER_WALL_CLOCK 26
	APBS total execution timer ID. More...

#define	APBS_TIMER_SETUP 27
	APBS setup timer ID. More...

#define	APBS_TIMER_SOLVER 28
	APBS solver timer ID. More...

#define	APBS_TIMER_ENERGY 29
	APBS energy timer ID. More...

#define	APBS_TIMER_FORCE 30
	APBS force timer ID. More...

#define	APBS_TIMER_TEMP1 31
	APBS temp timer #1 ID. More...

#define	APBS_TIMER_TEMP2 32
	APBS temp timer #2 ID. More...

#define	MAXMOL 5
	The maximum number of molecules that can be involved in a single PBE calculation. More...

#define	MAXION 10
	The maximum number of ion species that can be involved in a single PBE calculation. More...

#define	MAXFOCUS 5
	The maximum number of times an MG calculation can be focused. More...

#define	VMGNLEV 4
	Minimum number of levels in a multigrid calculations. More...

#define	VREDFRAC 0.25
	Maximum reduction of grid spacing during a focusing calculation. More...

#define	VAPBS_NVS 4
	Number of vertices per simplex (hard-coded to 3D) More...

#define	VAPBS_DIM 3
	Our dimension. More...

#define	VAPBS_RIGHT 0
	Face definition for a volume. More...

#define	VAPBS_FRONT 1
	Face definition for a volume. More...

#define	VAPBS_UP 2
	Face definition for a volume. More...

#define	VAPBS_LEFT 3
	Face definition for a volume. More...

#define	VAPBS_BACK 4
	Face definition for a volume. More...

#define	VAPBS_DOWN 5
	Face definition for a volume. More...

#define	VPMGSMALL 1e-12
	A small number used in Vpmg to decide if points are on/off grid-lines or non-zer0 (etc.) More...

#define	SINH_MIN -85.0
	Used to set the min values acceptable for sinh chopping. More...

#define	SINH_MAX 85.0
	Used to set the max values acceptable for sinh chopping. More...

#define	VF77_MANGLE(name, NAME) name
	Name-mangling macro for using FORTRAN functions in C code. More...

#define	VFLOOR(value) floor(value)
	Wrapped floor to fix floating point issues in the Intel compiler. More...

#define	VEMBED(rctag)
	Allows embedding of RCS ID tags in object files. More...

Typedefs
typedef enum eVhal_PBEType	Vhal_PBEType
	Declaration of the Vhal_PBEType type as the Vhal_PBEType enum. More...

typedef enum eVhal_IPKEYType	Vhal_IPKEYType
	Declaration of the Vhal_IPKEYType type as the Vhal_IPKEYType enum. More...

typedef enum eVhal_NONLINType	Vhal_NONLINType
	Declaration of the Vhal_NONLINType type as the Vhal_NONLINType enum. More...

typedef enum eVoutput_Format	Voutput_Format
	Declaration of the Voutput_Format type as the VOutput_Format enum. More...

typedef enum eVbcfl	Vbcfl
	Declare Vbcfl type. More...

typedef enum eVsurf_Meth	Vsurf_Meth
	Declaration of the Vsurf_Meth type as the Vsurf_Meth enum. More...

typedef enum eVchrg_Meth	Vchrg_Meth
	Declaration of the Vchrg_Meth type as the Vchrg_Meth enum. More...

typedef enum eVchrg_Src	Vchrg_Src
	Declaration of the Vchrg_Src type as the Vchrg_Meth enum. More...

typedef enum eVdata_Type	Vdata_Type
	Declaration of the Vdata_Type type as the Vdata_Type enum. More...

typedef enum eVdata_Format	Vdata_Format
	Declaration of the Vdata_Format type as the Vdata_Format enum. More...

Enumerations
enum	eVrc_Codes { VRC_WARNING =-1 , VRC_FAILURE =0 , VRC_SUCCESS =1 }
	Return code enumerations. More...

enum	eVsol_Meth { VSOL_CGMG , VSOL_Newton , VSOL_MG , VSOL_CG , VSOL_SOR , VSOL_RBGS , VSOL_WJ , VSOL_Richardson , VSOL_CGMGAqua , VSOL_NewtonAqua }
	Solution Method enumerations. More...

enum	eVsurf_Meth { VSM_MOL =0 , VSM_MOLSMOOTH =1 , VSM_SPLINE =2 , VSM_SPLINE3 =3 , VSM_SPLINE4 =4 }
	Types of molecular surface definitions. More...

enum	eVhal_PBEType { PBE_LPBE , PBE_NPBE , PBE_LRPBE , PBE_NRPBE , PBE_SMPBE }
	Version of PBE to solve. More...

enum	eVhal_IPKEYType { IPKEY_SMPBE = -2 , IPKEY_LPBE , IPKEY_NPBE }
	Type of ipkey to use for MG methods. More...

enum	eVhal_NONLINType { NONLIN_LPBE = 0 , NONLIN_NPBE , NONLIN_SMPBE , NONLIN_LPBEAQUA , NONLIN_NPBEAQUA }
	Type of nonlinear to use for MG methods. More...

enum	eVoutput_Format { OUTPUT_NULL , OUTPUT_FLAT }
	Output file format. More...

enum	eVbcfl { BCFL_ZERO =0 , BCFL_SDH =1 , BCFL_MDH =2 , BCFL_UNUSED =3 , BCFL_FOCUS =4 , BCFL_MEM =5 , BCFL_MAP =6 }
	Types of boundary conditions. More...

enum	eVchrg_Meth { VCM_TRIL =0 , VCM_BSPL2 =1 , VCM_BSPL4 =2 }
	Types of charge discretization methods. More...

enum	eVchrg_Src { VCM_CHARGE =0 , VCM_PERMANENT =1 , VCM_INDUCED =2 , VCM_NLINDUCED =3 }
	Charge source. More...

enum	eVdata_Type { VDT_CHARGE , VDT_POT , VDT_ATOMPOT , 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 , VDF_MCSF =3 , VDF_GZ =4 , VDF_FLAT =5 , VDF_DXBIN =6 }
	Format of data for APBS I/O. More...

Detailed Description

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

Macro Definition Documentation

◆ APBS_TIMER_ENERGY

#define APBS_TIMER_ENERGY 29

APBS energy timer ID.

Definition at line 347 of file vhal.h.

◆ APBS_TIMER_FORCE

#define APBS_TIMER_FORCE 30

APBS force timer ID.

Definition at line 353 of file vhal.h.

◆ APBS_TIMER_SETUP

#define APBS_TIMER_SETUP 27

APBS setup timer ID.

Definition at line 335 of file vhal.h.

◆ APBS_TIMER_SOLVER

#define APBS_TIMER_SOLVER 28

APBS solver timer ID.

Definition at line 341 of file vhal.h.

◆ APBS_TIMER_TEMP1

#define APBS_TIMER_TEMP1 31

APBS temp timer #1 ID.

Definition at line 359 of file vhal.h.

◆ APBS_TIMER_TEMP2

#define APBS_TIMER_TEMP2 32

APBS temp timer #2 ID.

Definition at line 365 of file vhal.h.

◆ APBS_TIMER_WALL_CLOCK

#define APBS_TIMER_WALL_CLOCK 26

APBS total execution timer ID.

Definition at line 329 of file vhal.h.

◆ MAXFOCUS

#define MAXFOCUS 5

The maximum number of times an MG calculation can be focused.

Definition at line 382 of file vhal.h.

◆ MAXION

#define MAXION 10

The maximum number of ion species that can be involved in a single PBE calculation.

Definition at line 377 of file vhal.h.

◆ MAXMOL

#define MAXMOL 5

The maximum number of molecules that can be involved in a single PBE calculation.

Definition at line 371 of file vhal.h.

◆ SINH_MAX

#define SINH_MAX 85.0

Used to set the max values acceptable for sinh chopping.

Definition at line 456 of file vhal.h.

◆ SINH_MIN

#define SINH_MIN -85.0

Used to set the min values acceptable for sinh chopping.

Definition at line 450 of file vhal.h.

◆ VAPBS_BACK

#define VAPBS_BACK 4

Face definition for a volume.

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

Definition at line 432 of file vhal.h.

◆ VAPBS_DIM

#define VAPBS_DIM 3

Our dimension.

Definition at line 402 of file vhal.h.

◆ VAPBS_DOWN

#define VAPBS_DOWN 5

Face definition for a volume.

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

Definition at line 438 of file vhal.h.

◆ VAPBS_FRONT

#define VAPBS_FRONT 1

Face definition for a volume.

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

Definition at line 414 of file vhal.h.

◆ VAPBS_LEFT

#define VAPBS_LEFT 3

Face definition for a volume.

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

Definition at line 426 of file vhal.h.

◆ VAPBS_NVS

#define VAPBS_NVS 4

Number of vertices per simplex (hard-coded to 3D)

Definition at line 397 of file vhal.h.

◆ VAPBS_RIGHT

#define VAPBS_RIGHT 0

Face definition for a volume.

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

Definition at line 408 of file vhal.h.

◆ VAPBS_UP

#define VAPBS_UP 2

Face definition for a volume.

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

Definition at line 420 of file vhal.h.

◆ VEMBED

#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

Definition at line 556 of file vhal.h.

◆ VF77_MANGLE

#define VF77_MANGLE	(	name,
		NAME
	)	name

Name-mangling macro for using FORTRAN functions in C code.

Definition at line 532 of file vhal.h.

◆ VFLOOR

#define VFLOOR ( value ) floor(value)

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

Author: Todd Dolinksy

Definition at line 547 of file vhal.h.

◆ VMGNLEV

#define VMGNLEV 4

Minimum number of levels in a multigrid calculations.

Definition at line 387 of file vhal.h.

◆ VPMGSMALL

#define VPMGSMALL 1e-12

A small number used in Vpmg to decide if points are on/off grid-lines or non-zer0 (etc.)

Definition at line 444 of file vhal.h.

◆ VREDFRAC

#define VREDFRAC 0.25

Maximum reduction of grid spacing during a focusing calculation.

Definition at line 392 of file vhal.h.

Typedef Documentation

◆ Vbcfl

typedef enum eVbcfl Vbcfl

Declare Vbcfl type.

Definition at line 223 of file vhal.h.

◆ Vchrg_Meth

Vchrg_Meth

Declaration of the Vchrg_Meth type as the Vchrg_Meth enum.

Definition at line 244 of file vhal.h.

◆ Vchrg_Src

Vchrg_Src

Declaration of the Vchrg_Src type as the Vchrg_Meth enum.

Definition at line 262 of file vhal.h.

◆ Vdata_Format

Vdata_Format

Declaration of the Vdata_Format type as the Vdata_Format enum.

Definition at line 323 of file vhal.h.

◆ Vdata_Type

Vdata_Type

Declaration of the Vdata_Type type as the Vdata_Type enum.

Definition at line 302 of file vhal.h.

◆ Vhal_IPKEYType

typedef enum eVhal_IPKEYType Vhal_IPKEYType

Declaration of the Vhal_IPKEYType type as the Vhal_IPKEYType enum.

Definition at line 167 of file vhal.h.

◆ Vhal_NONLINType

typedef enum eVhal_NONLINType Vhal_NONLINType

Declaration of the Vhal_NONLINType type as the Vhal_NONLINType enum.

Definition at line 185 of file vhal.h.

◆ Vhal_PBEType

typedef enum eVhal_PBEType Vhal_PBEType

Declaration of the Vhal_PBEType type as the Vhal_PBEType enum.

Definition at line 151 of file vhal.h.

◆ Voutput_Format

typedef enum eVoutput_Format Voutput_Format

Declaration of the Voutput_Format type as the VOutput_Format enum.

Definition at line 200 of file vhal.h.

◆ Vsurf_Meth

Vsurf_Meth

Declaration of the Vsurf_Meth type as the Vsurf_Meth enum.

Definition at line 133 of file vhal.h.

Enumeration Type Documentation

◆ eVbcfl

enum eVbcfl

Types of boundary conditions.

Author: Nathan Baker

Enumerator
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
BCFL_MEM	Focusing membrane boundary condition
BCFL_MAP	Skip first level of focusing use an external map

Definition at line 207 of file vhal.h.

◆ eVchrg_Meth

enum eVchrg_Meth

Types of charge discretization methods.

Author: Nathan Baker

Enumerator
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).
VCM_BSPL4	5th order B-spline for AMOEBA permanent multipoles.

Definition at line 230 of file vhal.h.

◆ eVchrg_Src

enum eVchrg_Src

Charge source.

Author: Michael Schnieders

Enumerator
VCM_CHARGE	Partial Charge source distribution
VCM_PERMANENT	Permanent Multipole source distribution
VCM_INDUCED	Induced Dipole source distribution
VCM_NLINDUCED	NL Induced Dipole source distribution

Definition at line 251 of file vhal.h.

◆ eVdata_Format

enum eVdata_Format

Format of data for APBS I/O.

Author: Nathan Baker

Enumerator
VDF_DX	OpenDX (Data Explorer) format
VDF_UHBD	UHBD format
VDF_AVS	AVS UCD format
VDF_MCSF	FEtk MC Simplex Format (MCSF)
VDF_GZ	Binary file (GZip)
VDF_FLAT	Write flat file
VDF_DXBIN	OpendDX (Data Explorer) binary format

Definition at line 309 of file vhal.h.

◆ eVdata_Type

enum eVdata_Type

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

Author: Nathan Baker

Enumerator
VDT_CHARGE	Charge distribution (e)
VDT_POT	Potential (kT/e)
VDT_ATOMPOT	Atom 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 is potential (kT/e/A)^2
VDT_NDENS	Ion number density $\sum c_i \exp (-q_i u)^2$ , where is potential (output in M)
VDT_QDENS	Ion charge density $\sum q_i c_i \exp (-q_i u)^2$ , where is potential (output in )
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 ( $\AA^{-3}$ )

Definition at line 269 of file vhal.h.

◆ eVhal_IPKEYType

enum eVhal_IPKEYType

Type of ipkey to use for MG methods.

Enumerator
IPKEY_SMPBE	SMPBE ipkey
IPKEY_LPBE	LPBE ipkey
IPKEY_NPBE	NPBE ipkey

Definition at line 157 of file vhal.h.

◆ eVhal_NONLINType

enum eVhal_NONLINType

Type of nonlinear to use for MG methods.

Definition at line 173 of file vhal.h.

◆ eVhal_PBEType

enum eVhal_PBEType

Version of PBE to solve.

Enumerator
PBE_LPBE	Traditional Poisson-Boltzmann equation, linearized
PBE_NPBE	Traditional Poisson-Boltzmann equation, full
PBE_LRPBE	Regularized Poisson-Boltzmann equation, linearized
PBE_SMPBE	< Regularized Poisson-Boltzmann equation, full SM PBE

Definition at line 139 of file vhal.h.

◆ eVoutput_Format

enum eVoutput_Format

Output file format.

Enumerator
OUTPUT_NULL	No output
OUTPUT_FLAT	Output in flat-file format

Definition at line 191 of file vhal.h.

◆ eVrc_Codes

enum eVrc_Codes

Return code enumerations.

Author: David Gohara

Note: Note that the enumerated values are opposite the standard for FAILURE and SUCCESS

Enumerator
VRC_FAILURE	A non-fatal error
VRC_SUCCESS	A fatal error

Definition at line 66 of file vhal.h.

◆ eVsol_Meth

enum eVsol_Meth

Solution Method enumerations.

Author: David Gohara

Note: Note that the enumerated values are opposite the standard for FAILURE and SUCCESS

Definition at line 81 of file vhal.h.

◆ eVsurf_Meth

enum eVsurf_Meth

Types of molecular surface definitions.

Author: Nathan Baker

Enumerator
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.
VSM_SPLINE3	A 5th order polynomial spline is used to create a smoothly varying characteristic function (continuity through 2nd derivatives) for surface based paramters.
VSM_SPLINE4	A 7th order polynomial spline is used to create a smoothly varying characteristic function (continuity through 3rd derivatives) for surface based paramters.

Definition at line 102 of file vhal.h.

Files

Macros

Typedefs

Enumerations

Detailed Description

Macro Definition Documentation

◆ APBS_TIMER_ENERGY

◆ APBS_TIMER_FORCE

◆ APBS_TIMER_SETUP

◆ APBS_TIMER_SOLVER

◆ APBS_TIMER_TEMP1

◆ APBS_TIMER_TEMP2

◆ APBS_TIMER_WALL_CLOCK

◆ MAXFOCUS

◆ MAXION

◆ MAXMOL

◆ SINH_MAX

◆ SINH_MIN

◆ VAPBS_BACK

◆ VAPBS_DIM

◆ VAPBS_DOWN

◆ VAPBS_FRONT

◆ VAPBS_LEFT

◆ VAPBS_NVS

◆ VAPBS_RIGHT

◆ VAPBS_UP

◆ VEMBED

◆ VF77_MANGLE

◆ VFLOOR

◆ VMGNLEV

◆ VPMGSMALL

◆ VREDFRAC

Typedef Documentation

◆ Vbcfl

◆ Vchrg_Meth

◆ Vchrg_Src

◆ Vdata_Format

◆ Vdata_Type

◆ Vhal_IPKEYType

◆ Vhal_NONLINType

◆ Vhal_PBEType

◆ Voutput_Format

◆ Vsurf_Meth

Enumeration Type Documentation

◆ eVbcfl

◆ eVchrg_Meth

◆ eVchrg_Src

◆ eVdata_Format

◆ eVdata_Type

◆ eVhal_IPKEYType

◆ eVhal_NONLINType

◆ eVhal_PBEType

◆ eVoutput_Format

◆ eVrc_Codes

◆ eVsol_Meth

◆ eVsurf_Meth