Collaboration diagram for swap_group:

Description

This structure contains data needed for the groups involved in swapping: split group 0, split group 1, solvent group, ion groups.

Public Attributes
char *	molname
	Name of the group or ion type.

int	nat
	Number of atoms in the group.

int	apm
	Number of atoms in each molecule.

int *	ind
	Global atom indices of the group (size nat)

int *	ind_loc
	Local atom indices of the group.

int	nat_loc
	Number of local group atoms.

int	nalloc_loc
	Allocation size for ind_loc.

rvec *	xc
	Collective array of group atom positions (size nat)

ivec *	xc_shifts
	Current (collective) shifts (size nat)

ivec *	xc_eshifts
	Extra shifts since last DD step (size nat)

rvec *	xc_old
	Old (collective) positions (size nat)

real	q
	Total charge of one molecule of this group.

int *	c_ind_loc
	Position of local atoms in the collective array, [0..nat_loc].

real *	m
	Masses (can be omitted, size apm)

unsigned char *	comp_from
	(Collective) Stores from which compartment this molecule has come. More...

unsigned char *	comp_now
	In which compartment this ion is now (size nMol)

unsigned char *	channel_label
	Which channel was passed at last by this ion? (size nMol)

rvec	center
	Center of the group; COM if masses are used.

t_compartment	comp [eCompNR]
	Distribution of particles of this group across the two compartments.

real	vacancy [eCompNR]
	How many molecules need to be swapped in?

int	fluxfromAtoB [eChanNR]
	Net flux of ions per channel.

int	nCyl [eChanNR]
	Number of ions residing in a channel.

int	nCylBoth
	Ions assigned to cyl0 and cyl1. More...

Member Data Documentation

unsigned char* swap_group::comp_from

(Collective) Stores from which compartment this molecule has come.

This way we keep track of through which channel an ion permeates (size nMol = nat/apm)

int swap_group::nCylBoth

Ions assigned to cyl0 and cyl1.

Not good.

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