sPBEparm Struct Reference
[PBEparm class]

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

#include <pbeparm.h>

Data Fields

int molid
int setmolid
int useDielMap
int dielMapID
int useKappaMap
int kappaMapID
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

Field Documentation

Vbcfl sPBEparm::bcfl

Boundary condition method

Referenced by initMG(), PBEparm_check(), PBEparm_copy(), printPBEPARM(), writedataFlat(), and writedataXML().

PBEparm_calcEnergy sPBEparm::calcenergy

Energy calculation flag

Referenced by energyFE(), energyMG(), initMG(), main(), PBEparm_check(), PBEparm_copy(), printElecEnergy(), printEnergy(), printPBEPARM(), returnEnergy(), writedataFlat(), and writedataXML().

PBEparm_calcForce sPBEparm::calcforce

Atomic forces calculation

Referenced by forceMG(), NOsh_setupElecCalc(), PBEparm_check(), PBEparm_copy(), printElecForce(), printForce(), printPBEPARM(), writedataFlat(), and writedataXML().

int sPBEparm::chargeMapID

Charge distribution map ID (if used)

Referenced by initMG(), and PBEparm_copy().

int sPBEparm::dielMapID

Dielectric map ID (if used)

Referenced by initMG(), and PBEparm_copy().

double sPBEparm::ionc[MAXION]

Counterion concentrations (in M)

Referenced by initMG(), PBEparm_copy(), PBEparm_ctor2(), PBEparm_getIonConc(), printPBEPARM(), writedataFlat(), and writedataXML().

double sPBEparm::ionq[MAXION]

Counterion charges (in e)

Referenced by initMG(), PBEparm_copy(), PBEparm_ctor2(), PBEparm_getIonCharge(), printPBEPARM(), writedataFlat(), and writedataXML().

double sPBEparm::ionr[MAXION]

Counterion radii (in A)

Referenced by initMG(), PBEparm_copy(), PBEparm_ctor2(), PBEparm_getIonRadius(), printPBEPARM(), writedataFlat(), and writedataXML().

int sPBEparm::kappaMapID

Kappa map ID (if used)

Referenced by initMG(), and PBEparm_copy().

double sPBEparm::Lmem

membrane width

Referenced by initMG(), and PBEparm_copy().

double sPBEparm::mdie

membrane dielectric constant

Referenced by initMG(), and PBEparm_copy().

double sPBEparm::memv

Membrane potential

Referenced by initMG(), and PBEparm_copy().

int sPBEparm::molid

Molecule ID to perform calculation on

Referenced by forceMG(), initMG(), PBEparm_copy(), printPBEPARM(), writedataFlat(), and writedataXML().

int sPBEparm::nion

Number of counterion species

Referenced by initMG(), PBEparm_check(), PBEparm_copy(), PBEparm_ctor2(), printPBEPARM(), writedataFlat(), and writedataXML().

int sPBEparm::numwrite

Number of write statements encountered

Referenced by PBEparm_copy(), PBEparm_ctor2(), printPBEPARM(), writedataFE(), and writedataMG().

int sPBEparm::parsed

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

Referenced by PBEparm_check(), PBEparm_copy(), and PBEparm_ctor2().

Vhal_PBEType sPBEparm::pbetype

Which version of the PBE are we solving?

Referenced by energyFE(), initMG(), PBEparm_copy(), printPBEPARM(), solveFE(), writedataFlat(), writedataMG(), and writedataXML().

double sPBEparm::pdie

Solute dielectric

Referenced by initMG(), PBEparm_copy(), printPBEPARM(), writedataFlat(), and writedataXML().

double sPBEparm::sdens

Vacc sphere density

Referenced by initMG(), PBEparm_copy(), and PBEparm_ctor2().

double sPBEparm::sdie

Solvent dielectric

Referenced by initMG(), PBEparm_copy(), printPBEPARM(), writedataFlat(), and writedataXML().

int sPBEparm::setbcfl

Flag,

See also:
bcfl

Referenced by PBEparm_check(), PBEparm_copy(), and PBEparm_ctor2().

int sPBEparm::setcalcenergy

Flag,

See also:
calcenergy

Referenced by PBEparm_check(), PBEparm_copy(), and PBEparm_ctor2().

int sPBEparm::setcalcforce

Flag,

See also:
calcforce

Referenced by PBEparm_check(), PBEparm_copy(), and PBEparm_ctor2().

int sPBEparm::setion[MAXION]

Flag,

See also:
ionq

Referenced by PBEparm_check(), PBEparm_copy(), and PBEparm_ctor2().

int sPBEparm::setLmem

Flag

Referenced by PBEparm_check(), PBEparm_copy(), and PBEparm_ctor2().

int sPBEparm::setmdie

Flag

Referenced by PBEparm_check(), PBEparm_copy(), and PBEparm_ctor2().

int sPBEparm::setmemv

Flag

Referenced by PBEparm_check(), PBEparm_copy(), and PBEparm_ctor2().

int sPBEparm::setmolid

Flag,

See also:
molid

Referenced by PBEparm_check(), PBEparm_copy(), and PBEparm_ctor2().

int sPBEparm::setnion

Flag,

See also:
nion

Referenced by PBEparm_check(), PBEparm_copy(), and PBEparm_ctor2().

int sPBEparm::setpbetype

Flag,

See also:
pbetype

Referenced by PBEparm_check(), PBEparm_copy(), and PBEparm_ctor2().

int sPBEparm::setpdie

Flag,

See also:
pdie

Referenced by PBEparm_check(), PBEparm_copy(), and PBEparm_ctor2().

int sPBEparm::setsdens

Flag,

See also:
sdens

Referenced by PBEparm_check(), PBEparm_copy(), and PBEparm_ctor2().

int sPBEparm::setsdie

Flag,

See also:
sdie

Referenced by PBEparm_check(), PBEparm_copy(), and PBEparm_ctor2().

int sPBEparm::setsmsize

Flag,

See also:
temp

Referenced by PBEparm_copy(), and PBEparm_ctor2().

int sPBEparm::setsmvolume

Flag,

See also:
temp

Referenced by PBEparm_copy(), and PBEparm_ctor2().

int sPBEparm::setsrad

Flag,

See also:
srad

Referenced by PBEparm_check(), PBEparm_copy(), and PBEparm_ctor2().

int sPBEparm::setsrfm

Flag,

See also:
srfm

Referenced by PBEparm_check(), PBEparm_copy(), and PBEparm_ctor2().

int sPBEparm::setswin

Flag,

See also:
swin

Referenced by PBEparm_check(), PBEparm_copy(), and PBEparm_ctor2().

int sPBEparm::settemp

Flag,

See also:
temp

Referenced by PBEparm_check(), PBEparm_copy(), and PBEparm_ctor2().

int sPBEparm::setwritemat

Flag,

See also:
writemat

Referenced by PBEparm_check(), PBEparm_copy(), and PBEparm_ctor2().

int sPBEparm::setzmem

Flag

Referenced by PBEparm_check(), PBEparm_copy(), and PBEparm_ctor2().

double sPBEparm::smsize

SMPBE size

Referenced by initMG(), PBEparm_copy(), PBEparm_ctor2(), and printPBEPARM().

double sPBEparm::smvolume

SMPBE size

Referenced by initMG(), PBEparm_copy(), PBEparm_ctor2(), and printPBEPARM().

double sPBEparm::srad

Solvent radius

Referenced by forceAPOL(), initAPOL(), initMG(), PBEparm_check(), PBEparm_copy(), PBEparm_ctor2(), printPBEPARM(), writedataFlat(), writedataMG(), and writedataXML().

Vsurf_Meth sPBEparm::srfm

Surface calculation method

Referenced by forceMG(), initMG(), PBEparm_check(), PBEparm_copy(), printPBEPARM(), writedataFlat(), and writedataXML().

double sPBEparm::swin

Cubic spline window

Referenced by initMG(), PBEparm_copy(), PBEparm_ctor2(), printPBEPARM(), Vfetk_fillArray(), and writedataMG().

double sPBEparm::temp

Temperature (in K)

Referenced by energyFE(), energyMG(), forceMG(), initMG(), PBEparm_copy(), printApolForce(), printElecEnergy(), printElecForce(), printEnergy(), printForce(), printPBEPARM(), returnEnergy(), writedataFlat(), and writedataXML().

int sPBEparm::useChargeMap

Indicates whether we use an external charge distribution map

Referenced by initMG(), PBEparm_copy(), and PBEparm_ctor2().

int sPBEparm::useDielMap

Indicates whether we use external dielectric maps (note plural)

Referenced by initMG(), PBEparm_copy(), and PBEparm_ctor2().

int sPBEparm::useKappaMap

Indicates whether we use an external kappa map

Referenced by initMG(), PBEparm_copy(), and PBEparm_ctor2().

Vdata_Format sPBEparm::writefmt[PBEPARM_MAXWRITE]

File format to write data in

Referenced by PBEparm_copy(), printPBEPARM(), writedataFE(), and writedataMG().

int sPBEparm::writemat

Write out the operator matrix?

  • 0 => no
  • 1 => yes

Referenced by PBEparm_check(), PBEparm_copy(), and writematMG().

int sPBEparm::writematflag

What matrix should we write:

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

Referenced by PBEparm_copy(), and writematMG().

char sPBEparm::writematstem[VMAX_ARGLEN]

File stem to write mat

Referenced by PBEparm_copy(), and writematMG().

char sPBEparm::writestem[PBEPARM_MAXWRITE][VMAX_ARGLEN]

File stem to write data to

Referenced by PBEparm_copy(), printPBEPARM(), writedataFE(), and writedataMG().

Vdata_Type sPBEparm::writetype[PBEPARM_MAXWRITE]

What data to write

Referenced by PBEparm_copy(), printPBEPARM(), writedataFE(), and writedataMG().

double sPBEparm::zmem

z value of membrane bottom

Referenced by initMG(), and PBEparm_copy().

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