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swap_group Struct Reference
+ 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.
 
realm = nullptr
 Masses (can be omitted, size apm)
 
unsigned char * comp_from = nullptr
 (Collective) Stores from which compartment this molecule has come. More...
 
unsigned char * comp_now = nullptr
 In which compartment this ion is now (size nMol)
 
unsigned char * 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.
 
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 = 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]atomsetManaged indices of atoms that are part of the swap group.

Member Data Documentation

unsigned char* 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: