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params Struct Reference
[params class]

Class for input handling. More...

#include <params.h>

List of all members.

Public Attributes
int	steps
int	GCsteps
int	MCsteps
int	minsteps
char	MCmode
int	howmany
double	maxdis
double	pminnr
int	equicut
int	coordsoutgo
int	gridres
int	potfreq
int	potoutgo
int	ndensoutgo
int	cdensoutgo
int	pcoutgo
int	pcfreq
double	pcres
int	exshells
double	temp
double	releps
char	GENmode
int	types
char	ionmodel
char	form
double	rad
double	length
char	macroID
char *	filename
double	Bornrad
double	Borncharge
double	Cylrad
double	Cyllen
double	Cylcharge
char	mmmode
int	mmgridres
char *	potfilename
char *	potreffname
int	bcflag
char *	ionname [20]
double *	sig
double *	conc
double *	eps
double *	charge

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Detailed Description

Class for input handling.

Data members include all control parameters for ISIM, with few being transferred to other objects (convenience and/or necessity)

Author:

Andreas Vitalis

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Member Data Documentation

int params::bcflag

Only used for PQR-file macromolecules: Control parameter for calculation of electrostatic potential outside the APBS-mesh

double params::Borncharge

Only used for Born ion: Charge in multiples of e

double params::Bornrad

Only used for Born ion: Radius in

int params::cdensoutgo

Analysis parameter: Output frequency for charge density files

double* params::charge

Ion parameter: Charge in multiples of e

double* params::conc

Ion parameter: Concentration in mM

int params::coordsoutgo

Analysis parameter: Output frequency for coordinate files

double params::Cylcharge

Only used for charged cylinder: Charge in multiples of e

double params::Cyllen

Only used for charged cylinder: Length in

double params::Cylrad

Only used for charged cylinder: Radius in

double* params::eps

Ion parameter: Lennard-Jones energy parameter in kJ/mol ("epsilon")

int params::equicut

Analysis parameter: At which step averages are reset (i.e. equlibration)

int params::exshells

Analysis parameter: Shell resolution for "outer" ions (see input file documentation)

char* params::filename

Only used for PQR-file macromolecules: Filename

char params::form

Simulation system form identifier (S,Z)

int params::GCsteps

Steps for creation/destruction cycle

char params::GENmode

Character indicator for general mode (still unused)

int params::gridres

Analysis parameter: Grid resolution for the analysis grid (this value cubed is the number of grid points)

int params::howmany

Only used for 'MCmode' 'S': Specification, how many "some" actually are

char params::ionmodel

Model used for interaction among explicit ions (H,L)

char* params::ionname[20]

Ion parameter: Name (maximum of 19 characters)

double params::length

Only used for cylindrical systems: Length of simulation cylinder

char params::macroID

Identification character for macromolecule (B,P,Z)

double params::maxdis

Sidelength of particle-centered cube (in ), to which moving attempts are restricted

char params::MCmode

Character indicator for shuffling mode (Monte Carlo movement: N,A,S)

int params::MCsteps

Steps for movement (shuffling) cycles

int params::minsteps

Minimization steps

int params::mmgridres

Grid resolution for macromolecule accessibility grid

char params::mmmode

Mode for calculation of steric interactions with Born ion (S,L,E)

int params::ndensoutgo

Analysis parameter: Output frequency for number density files

int params::pcfreq

Analysis parameter: Do-frequency for pair correlation analysis

int params::pcoutgo

Analysis parameter: Output frequency for pair correlation function files

double params::pcres

Analysis parameter: Resolution for pair correlation analysis in (separation of points on x-axis of g-function plots)

double params::pminnr

Minimum number of ions of one type to be present within a parametrization simulation

char* params::potfilename

Only used for PQR-file macromolecules: Filename for DX-file that provides electrostatic potential data

int params::potfreq

Analysis parameter: Do-frequency for grid potential calculation

int params::potoutgo

Analysis parameter: Output frequency for grid potential files

char* params::potreffname

Only (and just eventually) used for PQR-file macromolecules: Filename for DX-file that provides electrostatic potential reference data for comparison

double params::rad

Simulation system radius in (for cylindrical systems around the z-axis)

double params::releps

Medium's relative permittivity (dimensionless)

double* params::sig

Ion parameter: Lennard-Jones radius in ("sigma")

int params::steps

Total simulation steps

double params::temp

Temperature in Kelvin

int params::types

Number of different ion types present

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

• params.h

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