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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 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].
 
realm
 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: