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Data Fields
sPBEparm Struct Reference
PBEparm class

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

#include </builddir/build/BUILD/apbs/src/generic/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 117 of file pbeparm.h.

Field Documentation

Vbcfl bcfl

Boundary condition method

Definition at line 136 of file pbeparm.h.

PBEparm_calcEnergy calcenergy

Energy calculation flag

Definition at line 165 of file pbeparm.h.

PBEparm_calcForce calcforce

Atomic forces calculation

Definition at line 167 of file pbeparm.h.

int chargeMapID

Charge distribution map ID (if used)

Definition at line 133 of file pbeparm.h.

int dielMapID

Dielectric map ID (if used)

Definition at line 123 of file pbeparm.h.

double ionc[MAXION]

Counterion concentrations (in M)

Definition at line 141 of file pbeparm.h.

double ionq[MAXION]

Counterion charges (in e)

Definition at line 140 of file pbeparm.h.

double ionr[MAXION]

Counterion radii (in A)

Definition at line 142 of file pbeparm.h.

int kappaMapID

Kappa map ID (if used)

Definition at line 126 of file pbeparm.h.

double Lmem

membrane width

Definition at line 176 of file pbeparm.h.

double mdie

membrane dielectric constant

Definition at line 178 of file pbeparm.h.

double memv

Membrane potential

Definition at line 180 of file pbeparm.h.

int molid

Molecule ID to perform calculation on

Definition at line 119 of file pbeparm.h.

int nion

Number of counterion species

Definition at line 138 of file pbeparm.h.

int numwrite

Number of write statements encountered

Definition at line 185 of file pbeparm.h.

int parsed

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

Definition at line 201 of file pbeparm.h.

Vhal_PBEType pbetype

Which version of the PBE are we solving?

Definition at line 134 of file pbeparm.h.

double pdie

Solute dielectric

Definition at line 144 of file pbeparm.h.

int potMapID

Kappa map ID (if used)

Definition at line 129 of file pbeparm.h.

double sdens

Vacc sphere density

Definition at line 146 of file pbeparm.h.

double sdie

Solvent dielectric

Definition at line 148 of file pbeparm.h.

int setbcfl

Flag,

See Also
bcfl

Definition at line 137 of file pbeparm.h.

int setcalcenergy

Flag,

See Also
calcenergy

Definition at line 166 of file pbeparm.h.

int setcalcforce

Flag,

See Also
calcforce

Definition at line 168 of file pbeparm.h.

int setion[MAXION]

Flag,

See Also
ionq

Definition at line 143 of file pbeparm.h.

int setLmem

Flag

Definition at line 177 of file pbeparm.h.

int setmdie

Flag

Definition at line 179 of file pbeparm.h.

int setmemv

Flag

Definition at line 181 of file pbeparm.h.

int setmolid

Flag,

See Also
molid

Definition at line 120 of file pbeparm.h.

int setnion

Flag,

See Also
nion

Definition at line 139 of file pbeparm.h.

int setpbetype

Flag,

See Also
pbetype

Definition at line 135 of file pbeparm.h.

int setpdie

Flag,

See Also
pdie

Definition at line 145 of file pbeparm.h.

int setsdens

Flag,

See Also
sdens

Definition at line 147 of file pbeparm.h.

int setsdie

Flag,

See Also
sdie

Definition at line 149 of file pbeparm.h.

int setsmsize

Flag,

See Also
temp

Definition at line 160 of file pbeparm.h.

int setsmvolume

Flag,

See Also
temp

Definition at line 163 of file pbeparm.h.

int setsrad

Flag,

See Also
srad

Definition at line 153 of file pbeparm.h.

int setsrfm

Flag,

See Also
srfm

Definition at line 151 of file pbeparm.h.

int setswin

Flag,

See Also
swin

Definition at line 155 of file pbeparm.h.

int settemp

Flag,

See Also
temp

Definition at line 157 of file pbeparm.h.

int setwritemat

Flag,

See Also
writemat

Definition at line 194 of file pbeparm.h.

int setzmem

Flag

Definition at line 175 of file pbeparm.h.

double smsize

SMPBE size

Definition at line 159 of file pbeparm.h.

double smvolume

SMPBE size

Definition at line 162 of file pbeparm.h.

double srad

Solvent radius

Definition at line 152 of file pbeparm.h.

Vsurf_Meth srfm

Surface calculation method

Definition at line 150 of file pbeparm.h.

double swin

Cubic spline window

Definition at line 154 of file pbeparm.h.

double temp

Temperature (in K)

Definition at line 156 of file pbeparm.h.

int useChargeMap

Indicates whether we use an external charge distribution map

Definition at line 131 of file pbeparm.h.

int useDielMap

Indicates whether we use external dielectric maps (note plural)

Definition at line 121 of file pbeparm.h.

int useKappaMap

Indicates whether we use an external kappa map

Definition at line 124 of file pbeparm.h.

int usePotMap

Indicates whether we use an external kappa map

Definition at line 127 of file pbeparm.h.

Vdata_Format writefmt[PBEPARM_MAXWRITE]

File format to write data in

Definition at line 189 of file pbeparm.h.

int writemat

Write out the operator matrix?

  • 0 => no
  • 1 => yes

Definition at line 191 of file pbeparm.h.

int writematflag

What matrix should we write:

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

Definition at line 196 of file pbeparm.h.

char writematstem[VMAX_ARGLEN]

File stem to write mat

Definition at line 195 of file pbeparm.h.

char writestem[PBEPARM_MAXWRITE][VMAX_ARGLEN]

File stem to write data to

Definition at line 186 of file pbeparm.h.

Vdata_Type writetype[PBEPARM_MAXWRITE]

What data to write

Definition at line 188 of file pbeparm.h.

double zmem

z value of membrane bottom

Definition at line 174 of file pbeparm.h.

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