t_swapgrp Struct Reference

Collaboration diagram for t_swapgrp:

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

Public Attributes
std::string	molname
	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.
std::vector< gmx::RVec >	xc
	Collective array of group atom positions (size nat)
std::vector< gmx::IVec >	xc_shifts
	Current (collective) shifts (size nat)
std::vector< gmx::IVec >	xc_eshifts
	Extra shifts since last DD step (size nat)
std::vector< gmx::RVec >	xc_old
	Old (collective) positions (size nat)
real	q = 0.
	Total charge of one molecule of this group.
std::vector< real >	m
	Masses (not relevant for split groups, size apm)
std::shared_ptr< std::vector < Domain > >	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) More...
std::vector< Domain >	comp_now
	In which compartment this ion is now (size nMol)
std::shared_ptr< std::vector < ChannelHistory > >	channel_label
	Which channel was passed at last by this ion? (size nMol) More...
gmx::RVec	center = { 0, 0, 0 }
	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 = { { 0 } }
	How many molecules need to be swapped in?
gmx::EnumerationArray< Channel, int >	fluxfromAtoB = { { 0 } }
	Net flux of ions per channel.
gmx::EnumerationArray< Channel, int >	nCyl = { { 0 } }
	Number of ions residing in a channel.
int	nCylBoth = 0
	Ions assigned to cyl0 and cyl1. Not good.

Constructor & Destructor Documentation

t_swapgrp::t_swapgrp

(

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.

Member Data Documentation

std::shared_ptr<std::vector<ChannelHistory> > t_swapgrp::channel_label

Which channel was passed at last by this ion? (size nMol)

Sometimes this is filled during checkpoint reading, and sometimes during tpr reading, so we use std::shared_ptr so there will be only one vector and it can be allocated from either place.

std::shared_ptr<std::vector<Domain> > t_swapgrp::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)

Sometimes this is filled during checkpoint reading, and sometimes during tpr reading, so we use std::shared_ptr so there will be only one vector and it can be allocated from either place.

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

• src/gromacs/swap/swapcoords.cpp