APBS 3.0.0
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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-3.0.0-build/apbs-3.0.0/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
 
char pbam_3dmapstem [VMAX_ARGLEN]
 
int pbam_3dmapflag
 
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

◆ bcfl

Vbcfl bcfl

Boundary condition method

Definition at line 136 of file pbeparm.h.

◆ calcenergy

PBEparm_calcEnergy calcenergy

Energy calculation flag

Definition at line 165 of file pbeparm.h.

◆ calcforce

PBEparm_calcForce calcforce

Atomic forces calculation

Definition at line 167 of file pbeparm.h.

◆ chargeMapID

int chargeMapID

Charge distribution map ID (if used)

Definition at line 133 of file pbeparm.h.

◆ dielMapID

int dielMapID

Dielectric map ID (if used)

Definition at line 123 of file pbeparm.h.

◆ ionc

double ionc[MAXION]

Counterion concentrations (in M)

Definition at line 141 of file pbeparm.h.

◆ ionq

double ionq[MAXION]

Counterion charges (in e)

Definition at line 140 of file pbeparm.h.

◆ ionr

double ionr[MAXION]

Counterion radii (in A)

Definition at line 142 of file pbeparm.h.

◆ kappaMapID

int kappaMapID

Kappa map ID (if used)

Definition at line 126 of file pbeparm.h.

◆ Lmem

double Lmem

membrane width

Definition at line 176 of file pbeparm.h.

◆ mdie

double mdie

membrane dielectric constant

Definition at line 178 of file pbeparm.h.

◆ memv

double memv

Membrane potential

Definition at line 180 of file pbeparm.h.

◆ molid

int molid

Molecule ID to perform calculation on

Definition at line 119 of file pbeparm.h.

◆ nion

int nion

Number of counterion species

Definition at line 138 of file pbeparm.h.

◆ numwrite

int numwrite

Number of write statements encountered

Definition at line 185 of file pbeparm.h.

◆ parsed

int parsed

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

Definition at line 205 of file pbeparm.h.

◆ pbam_3dmapflag

int pbam_3dmapflag

Definition at line 203 of file pbeparm.h.

◆ pbam_3dmapstem

char pbam_3dmapstem[VMAX_ARGLEN]

Definition at line 202 of file pbeparm.h.

◆ pbetype

Vhal_PBEType pbetype

Which version of the PBE are we solving?

Definition at line 134 of file pbeparm.h.

◆ pdie

double pdie

Solute dielectric

Definition at line 144 of file pbeparm.h.

◆ potMapID

int potMapID

Kappa map ID (if used)

Definition at line 129 of file pbeparm.h.

◆ sdens

double sdens

Vacc sphere density

Definition at line 146 of file pbeparm.h.

◆ sdie

double sdie

Solvent dielectric

Definition at line 148 of file pbeparm.h.

◆ setbcfl

int setbcfl

Flag,

See also
bcfl

Definition at line 137 of file pbeparm.h.

◆ setcalcenergy

int setcalcenergy

Flag,

See also
calcenergy

Definition at line 166 of file pbeparm.h.

◆ setcalcforce

int setcalcforce

Flag,

See also
calcforce

Definition at line 168 of file pbeparm.h.

◆ setion

int setion[MAXION]

Flag,

See also
ionq

Definition at line 143 of file pbeparm.h.

◆ setLmem

int setLmem

Flag

Definition at line 177 of file pbeparm.h.

◆ setmdie

int setmdie

Flag

Definition at line 179 of file pbeparm.h.

◆ setmemv

int setmemv

Flag

Definition at line 181 of file pbeparm.h.

◆ setmolid

int setmolid

Flag,

See also
molid

Definition at line 120 of file pbeparm.h.

◆ setnion

int setnion

Flag,

See also
nion

Definition at line 139 of file pbeparm.h.

◆ setpbetype

int setpbetype

Flag,

See also
pbetype

Definition at line 135 of file pbeparm.h.

◆ setpdie

int setpdie

Flag,

See also
pdie

Definition at line 145 of file pbeparm.h.

◆ setsdens

int setsdens

Flag,

See also
sdens

Definition at line 147 of file pbeparm.h.

◆ setsdie

int setsdie

Flag,

See also
sdie

Definition at line 149 of file pbeparm.h.

◆ setsmsize

int setsmsize

Flag,

See also
temp

Definition at line 160 of file pbeparm.h.

◆ setsmvolume

int setsmvolume

Flag,

See also
temp

Definition at line 163 of file pbeparm.h.

◆ setsrad

int setsrad

Flag,

See also
srad

Definition at line 153 of file pbeparm.h.

◆ setsrfm

int setsrfm

Flag,

See also
srfm

Definition at line 151 of file pbeparm.h.

◆ setswin

int setswin

Flag,

See also
swin

Definition at line 155 of file pbeparm.h.

◆ settemp

int settemp

Flag,

See also
temp

Definition at line 157 of file pbeparm.h.

◆ setwritemat

int setwritemat

Flag,

See also
writemat

Definition at line 194 of file pbeparm.h.

◆ setzmem

int setzmem

Flag

Definition at line 175 of file pbeparm.h.

◆ smsize

double smsize

SMPBE size

Definition at line 159 of file pbeparm.h.

◆ smvolume

double smvolume

SMPBE size

Definition at line 162 of file pbeparm.h.

◆ srad

double srad

Solvent radius

Definition at line 152 of file pbeparm.h.

◆ srfm

Vsurf_Meth srfm

Surface calculation method

Definition at line 150 of file pbeparm.h.

◆ swin

double swin

Cubic spline window

Definition at line 154 of file pbeparm.h.

◆ temp

double temp

Temperature (in K)

Definition at line 156 of file pbeparm.h.

◆ useChargeMap

int useChargeMap

Indicates whether we use an external charge distribution map

Definition at line 131 of file pbeparm.h.

◆ useDielMap

int useDielMap

Indicates whether we use external dielectric maps (note plural)

Definition at line 121 of file pbeparm.h.

◆ useKappaMap

int useKappaMap

Indicates whether we use an external kappa map

Definition at line 124 of file pbeparm.h.

◆ usePotMap

int usePotMap

Indicates whether we use an external kappa map

Definition at line 127 of file pbeparm.h.

◆ writefmt

Vdata_Format writefmt[PBEPARM_MAXWRITE]

File format to write data in

Definition at line 189 of file pbeparm.h.

◆ writemat

int writemat

Write out the operator matrix?

  • 0 => no
  • 1 => yes

Definition at line 191 of file pbeparm.h.

◆ writematflag

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.

◆ writematstem

char writematstem[VMAX_ARGLEN]

File stem to write mat

Definition at line 195 of file pbeparm.h.

◆ writestem

char writestem[PBEPARM_MAXWRITE][VMAX_ARGLEN]

File stem to write data to

Definition at line 186 of file pbeparm.h.

◆ writetype

Vdata_Type writetype[PBEPARM_MAXWRITE]

What data to write

Definition at line 188 of file pbeparm.h.

◆ zmem

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: