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 Member Functions
	swap_group (const gmx::LocalAtomSet &atomset)
	Construct a swap group given the managed swap atoms. More...

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

int	apm = 0
	Number of atoms in each molecule.

gmx::LocalAtomSet	atomSet
	The atom indices in the swap group.

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

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

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

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

real	q = 0.
	Total charge of one molecule of this group.

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

Domain *	comp_from = nullptr
	(Collective) Stores from which compartment this molecule has come. More...

Domain *	comp_now = nullptr
	In which compartment this ion is now (size nMol)

ChannelHistory *	channel_label = nullptr
	Which channel was passed at last by this ion? (size nMol)

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

gmx::EnumerationArray < Compartment, t_compartment >	comp
	Distribution of particles of this group across the two compartments.

gmx::EnumerationArray < Compartment, real >	vacancy
	How many molecules need to be swapped in?

gmx::EnumerationArray< Channel, int >	fluxfromAtoB
	Net flux of ions per channel.

gmx::EnumerationArray< Channel, int >	nCyl
	Number of ions residing in a channel.

int	nCylBoth = 0
	Ions assigned to cyl0 and cyl1. More...

Constructor & Destructor Documentation

t_swapgrp::swap_group ( const gmx::LocalAtomSet & atomset )

Construct a swap group given the managed swap atoms.

Parameters

[in] atomset Managed indices of atoms that are part of the swap group.

Domain* swap_group::comp_from = nullptr

(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 = 0

Ions assigned to cyl0 and cyl1.

Not good.

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