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ssystem Struct Reference
[ssystem class]

Class for simulation system objects. More...

#include <ssystem.h>

List of all members.

Public Attributes
double	radius
double	length
double	acc_vol
double	tot_vol
ionlist *	ions
macromolecule *	mm
int *	expects
int	types
energy *	energies
params *	parameters
double *	parres
int	PLEASE_REFINE
int	tries
int	nroftu
int	nrinnsp
double	maxex
double	minex
int *	maxnrofc
double **	parconcs
int *	nrofc
double	totscoc
double(*	ssystem_volume )(struct ssystem *thee)
void(*	ssystem_valid_xyz )(struct ssystem *thee, double *xyz)
void(*	ssystem_move_one )(struct ssystem *thee, int type, int pos)
void(*	ssystem_move_some )(struct ssystem *thee, int type, int start, int nr, double *coordsnew[])

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Detailed Description

Class for simulation system objects.

Data members include function pointers (different geometries), size parameters and all necessary objects, which represent the species populating the simulation system

Author:

Andreas Vitalis

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Member Data Documentation

double ssystem::acc_vol

Simulation system's volume accessible for explicit ions (in )

energy* ssystem::energies

Energy object

int* ssystem::expects

Expected number of ions for each type according to concentration and accessible volume

ionlist* ssystem::ions

Array of ionlist objects, one for each type (indexing starts at '1')

double ssystem::length

Simulation cylinder's length in z-direction (spans [-length/2;length/2])

double ssystem::maxex

Only for parametrization mode: Upper boundary for excess chemical potential variation for a specific species within a specific set

int* ssystem::maxnrofc

Only for parametrization mode: Array to hold number of concentration values for each independent species

double ssystem::minex

Only for parametrization mode: Lower boundary for excess chemical potential variation for a specific species within a specific set

macromolecule* ssystem::mm

Generic macromolecule object

int ssystem::nrinnsp

Only for parametrization mode: Species counter within a specific set

int* ssystem::nrofc

Only for parametrization mode: Counter (array) to hold number of concentration value for each independent species currently to be parametrized

int ssystem::nroftu

Only for parametrization mode: Counter for systematic variation within a certain set for a certain species

params* ssystem::parameters

Parameters object

double** ssystem::parconcs

Only for parametrization mode: 2D array to hold actual concentration values for each independent species

double* ssystem::parres

Only for parametrization mode: Array used to temporarily store results

int ssystem::PLEASE_REFINE

Only for parametrization mode: Logical variable that 'knows' if refinement for boundary values for a specific set has to be done

double ssystem::radius

Simulation sphere's radius or cylinder's radius around z-axis respectively (in )

void(* ssystem::ssystem_move_one)(struct ssystem *thee, int type, int pos)

Function pointer: Move one specified ion

void(* ssystem::ssystem_move_some)(struct ssystem *thee, int type, int start, int nr, double *coordsnew[])

Function pointer: Move some specified ions

void(* ssystem::ssystem_valid_xyz)(struct ssystem *thee, double *xyz)

Function pointer: Get a valid point within the system and not "on" the macromolecule (van-der-Waals surface)

double(* ssystem::ssystem_volume)(struct ssystem *thee)

Function pointer: Get the volume of the sphere or cylinder

double ssystem::tot_vol

Simulation sphere's total volume (in )

double ssystem::totscoc

Only for parametrization mode: Total concentration of all ions with same sign of charge like 'active' type (including itsself)

int ssystem::tries

Only for parametrization mode: Counter for refinement attempts

int ssystem::types

Number of differnt ion types present

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

• ssystem.h

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