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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 sdie
int setsdie
Vsurf_Meth srfm
int setsrfm
double srad
int setsrad
double swin
int setswin
double temp
int settemp
double gamma
int setgamma
int calcenergy
int setcalcenergy
int calcforce
int setcalcforce
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

int sPBEparm::calcenergy
 

Energy calculation

  • 0: don't calculate out energy
  • 1: calculate total energy
  • 2: calculate atom-level total energies and all energy components

int sPBEparm::calcforce
 

Atomic forces I/O

  • 0: don't calculate forces
  • 1: calculate net forces on molecule
  • 2: calculate atom-level forces

int sPBEparm::chargeMapID
 

Charge distribution map ID (if used)

int sPBEparm::dielMapID
 

Dielectric map ID (if used)

double sPBEparm::gamma
 

Surface tension for apolar energies/forces (in kJ/mol/A^2)

double sPBEparm::ionc[MAXION]
 

Counterion concentrations (in M)

double sPBEparm::ionq[MAXION]
 

Counterion charges (in e)

double sPBEparm::ionr[MAXION]
 

Counterion radii (in A)

int sPBEparm::kappaMapID
 

Kappa map ID (if used)

int sPBEparm::molid
 

Molecule ID to perform calculation on

int sPBEparm::nion
 

Number of counterion species

int sPBEparm::numwrite
 

Number of write statements encountered

int sPBEparm::parsed
 

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

Vhal_PBEType sPBEparm::pbetype
 

Which version of the PBE are we solving?

double sPBEparm::pdie
 

Solute dielectric

double sPBEparm::sdie
 

Solvent dielectric

int sPBEparm::setbcfl
 

Flag,

See also:
bcfl

int sPBEparm::setcalcenergy
 

Flag,

See also:
calcenergy

int sPBEparm::setcalcforce
 

Flag,

See also:
calcforce

int sPBEparm::setgamma
 

Flag,

See also:
gamma

int sPBEparm::setion[MAXION]
 

Flag,

See also:
ionq

int sPBEparm::setmolid
 

Flag,

See also:
molid

int sPBEparm::setnion
 

Flag,

See also:
nion

int sPBEparm::setpbetype
 

Flag,

See also:
pbetype

int sPBEparm::setpdie
 

Flag,

See also:
pdie

int sPBEparm::setsdie
 

Flag,

See also:
sdie

int sPBEparm::setsrad
 

Flag,

See also:
srad

int sPBEparm::setsrfm
 

Flag,

See also:
srfm

int sPBEparm::setswin
 

Flag,

See also:
swin

int sPBEparm::settemp
 

Flag,

See also:
temp

int sPBEparm::setwritemat
 

Flag,

See also:
writemat

double sPBEparm::srad
 

Solvent radius

Vsurf_Meth sPBEparm::srfm
 

Surface calculation method

double sPBEparm::swin
 

Cubic spline window

double sPBEparm::temp
 

Temperature (in K)

int sPBEparm::useChargeMap
 

Indicates whether we use an external charge distribution map

int sPBEparm::useDielMap
 

Indicates whether we use an external dielectric maps (note plural)

int sPBEparm::useKappaMap
 

Indicates whether we use an external kappa map

Vdata_Format sPBEparm::writefmt[PBEPARM_MAXWRITE]
 

File format to write data in

int sPBEparm::writemat
 

Write out the operator matrix?

  • 0 => no
  • 1 => yes

int sPBEparm::writematflag
 

What matrix should we write:

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

char sPBEparm::writematstem[VMAX_ARGLEN]
 

File stem to write mat

char sPBEparm::writestem[PBEPARM_MAXWRITE][VMAX_ARGLEN]
 

File stem to write data to

Vdata_Type sPBEparm::writetype[PBEPARM_MAXWRITE]
 

What data to write


The documentation for this struct was generated from the following file:
Generated on Tue Feb 17 09:27:25 2004 for APBS by doxygen1.2.18