Data Fields

sPBEparm Struct Reference
[PBEparm class]

Parameter structure for PBE variables from input files. More...

#include <C:/Users/bake113/Desktop/Sync/Software/apbs/trunk/src/generic/apbs/pbeparm.h>

Data Fields

int molid
int setmolid
int useDielMap
int dielMapID
int useKappaMap
int kappaMapID
int usePotMap
int potMapID
int useChargeMap
int chargeMapID
Vhal_PBEType pbetype
int setpbetype
Vbcfl bcfl
int setbcfl
int nion
int setnion
double ionq [MAXION]
double ionc [MAXION]
double ionr [MAXION]
int setion [MAXION]
double pdie
int setpdie
double sdens
int setsdens
double sdie
int setsdie
Vsurf_Meth srfm
int setsrfm
double srad
int setsrad
double swin
int setswin
double temp
int settemp
double smsize
int setsmsize
double smvolume
int setsmvolume
PBEparm_calcEnergy calcenergy
int setcalcenergy
PBEparm_calcForce calcforce
int setcalcforce
double zmem
int setzmem
double Lmem
int setLmem
double mdie
int setmdie
double memv
int setmemv
int numwrite
char writestem [PBEPARM_MAXWRITE][VMAX_ARGLEN]
Vdata_Type writetype [PBEPARM_MAXWRITE]
Vdata_Format writefmt [PBEPARM_MAXWRITE]
int writemat
int setwritemat
char writematstem [VMAX_ARGLEN]
int writematflag
int parsed

Detailed Description

Parameter structure for PBE variables from input files.

Author:
Nathan Baker
Note:
If you add/delete/change something in this class, the member functions -- especially PBEparm_copy -- must be modified accordingly

Definition at line 108 of file pbeparm.h.


Field Documentation

Boundary condition method

Definition at line 127 of file pbeparm.h.

Energy calculation flag

Definition at line 156 of file pbeparm.h.

Atomic forces calculation

Definition at line 158 of file pbeparm.h.

Charge distribution map ID (if used)

Definition at line 124 of file pbeparm.h.

int dielMapID

Dielectric map ID (if used)

Definition at line 114 of file pbeparm.h.

double ionc[MAXION]

Counterion concentrations (in M)

Definition at line 132 of file pbeparm.h.

double ionq[MAXION]

Counterion charges (in e)

Definition at line 131 of file pbeparm.h.

double ionr[MAXION]

Counterion radii (in A)

Definition at line 133 of file pbeparm.h.

Kappa map ID (if used)

Definition at line 117 of file pbeparm.h.

double Lmem

membrane width

Definition at line 167 of file pbeparm.h.

double mdie

membrane dielectric constant

Definition at line 169 of file pbeparm.h.

double memv

Membrane potential

Definition at line 171 of file pbeparm.h.

int molid

Molecule ID to perform calculation on

Definition at line 110 of file pbeparm.h.

int nion

Number of counterion species

Definition at line 129 of file pbeparm.h.

int numwrite

Number of write statements encountered

Definition at line 176 of file pbeparm.h.

int parsed

Has this been filled with anything other than the default values?

Definition at line 192 of file pbeparm.h.

Which version of the PBE are we solving?

Definition at line 125 of file pbeparm.h.

double pdie

Solute dielectric

Definition at line 135 of file pbeparm.h.

int potMapID

Kappa map ID (if used)

Definition at line 120 of file pbeparm.h.

double sdens

Vacc sphere density

Definition at line 137 of file pbeparm.h.

double sdie

Solvent dielectric

Definition at line 139 of file pbeparm.h.

int setbcfl

Flag,

See also:
bcfl

Definition at line 128 of file pbeparm.h.

Flag,

See also:
calcenergy

Definition at line 157 of file pbeparm.h.

Flag,

See also:
calcforce

Definition at line 159 of file pbeparm.h.

int setion[MAXION]

Flag,

See also:
ionq

Definition at line 134 of file pbeparm.h.

int setLmem

Flag

Definition at line 168 of file pbeparm.h.

int setmdie

Flag

Definition at line 170 of file pbeparm.h.

int setmemv

Flag

Definition at line 172 of file pbeparm.h.

int setmolid

Flag,

See also:
molid

Definition at line 111 of file pbeparm.h.

int setnion

Flag,

See also:
nion

Definition at line 130 of file pbeparm.h.

Flag,

See also:
pbetype

Definition at line 126 of file pbeparm.h.

int setpdie

Flag,

See also:
pdie

Definition at line 136 of file pbeparm.h.

int setsdens

Flag,

See also:
sdens

Definition at line 138 of file pbeparm.h.

int setsdie

Flag,

See also:
sdie

Definition at line 140 of file pbeparm.h.

int setsmsize

Flag,

See also:
temp

Definition at line 151 of file pbeparm.h.

Flag,

See also:
temp

Definition at line 154 of file pbeparm.h.

int setsrad

Flag,

See also:
srad

Definition at line 144 of file pbeparm.h.

int setsrfm

Flag,

See also:
srfm

Definition at line 142 of file pbeparm.h.

int setswin

Flag,

See also:
swin

Definition at line 146 of file pbeparm.h.

int settemp

Flag,

See also:
temp

Definition at line 148 of file pbeparm.h.

Flag,

See also:
writemat

Definition at line 185 of file pbeparm.h.

int setzmem

Flag

Definition at line 166 of file pbeparm.h.

double smsize

SMPBE size

Definition at line 150 of file pbeparm.h.

double smvolume

SMPBE size

Definition at line 153 of file pbeparm.h.

double srad

Solvent radius

Definition at line 143 of file pbeparm.h.

Surface calculation method

Definition at line 141 of file pbeparm.h.

double swin

Cubic spline window

Definition at line 145 of file pbeparm.h.

double temp

Temperature (in K)

Definition at line 147 of file pbeparm.h.

Indicates whether we use an external charge distribution map

Definition at line 122 of file pbeparm.h.

Indicates whether we use external dielectric maps (note plural)

Definition at line 112 of file pbeparm.h.

Indicates whether we use an external kappa map

Definition at line 115 of file pbeparm.h.

int usePotMap

Indicates whether we use an external kappa map

Definition at line 118 of file pbeparm.h.

Vdata_Format writefmt[PBEPARM_MAXWRITE]

File format to write data in

Definition at line 180 of file pbeparm.h.

int writemat

Write out the operator matrix?

  • 0 => no
  • 1 => yes

Definition at line 182 of file pbeparm.h.

What matrix should we write:

  • 0 => Poisson (differential operator)
  • 1 => Poisson-Boltzmann operator linearized around solution (if applicable)

Definition at line 187 of file pbeparm.h.

char writematstem[VMAX_ARGLEN]

File stem to write mat

Definition at line 186 of file pbeparm.h.

char writestem[PBEPARM_MAXWRITE][VMAX_ARGLEN]

File stem to write data to

Definition at line 177 of file pbeparm.h.

Vdata_Type writetype[PBEPARM_MAXWRITE]

What data to write

Definition at line 179 of file pbeparm.h.

double zmem

z value of membrane bottom

Definition at line 165 of file pbeparm.h.


The documentation for this struct was generated from the following file: