Talk:Mod:Hunt Research Group/voids

Voids in ILs (Notes by Ling)

1. Generate geometry of just pentagon and Cl from REVCON:

1) Using vim, put the coordinates on the same line as with the atomic symbols, after removing the atom number.

a) Copy REVCON to inp.dat.

b) Remove the first five lines using "dd" five times.

c) Define macro: qa0llllllllllDJjddddq: Go to the beginning of the first line containing an atomic symbol, then type: qa0lllllDJjddddq

d) Apply the macro: 10000@a

This should give all lines with symbol and atomic positions.

2) a) grep 'CR' inp.dat > structure.xyz

b) grep 'NA' inp.dat >> structure.xyz

c) grep 'CW' inp.dat >> structure.xyz

And so on with the Cl atoms. Then, using vim, replace CR with C, NA with N, and CW with C. (Note: >> will append, > will overwrite.)

2. Use VMD to visualise and read coordinates of voids (roughly) -> please see my notes on VMD.

3. To determine voids more accurately, please see ref Lar08 'Correlation between Surface Tension and Void Fraction'.