dx = periodic(dx)
dy = periodic(dy)
and the calculate the distance
dist = sqrt( dx * dx + dy * dy )
Then I compare this distance with the one which is provided by
Lammps in the dump file.
I am surprised that they are very different!
The difference starts from 10% up to 100%. The latter for
contacts that are over boundaries.
I have cross-checked my calculations more than a week!
Apparently for the deformed box the distance is calculated via a
different formula, maybe something like
dx = x1 - x2 -/+ shearRate * (some time scale) * (box length)
Would you mind please let me know how the distance in deformed
box is calculated.
Can you refer me to to that line in the code so I can see it exactly.
In advance, I appreciate your kind help.