# [lammps-users] Bond with fix deform

Hi,
I am trying to shear a system of particles using fix deform command. When I have particles which are not connected I found that it is working fine and I get the expected velocity profile. But the moment I use a system which has both bonded and non-bonded particles, I get error like bonds breaking. When it calculate distance between bonds will it take care of the actual shift in position due to the shear ?
( I mean bonds interacting across the boundary ( along shear gradient direction)) ?

If you have setup your system correctly there is nothing special
about the boundary or bonds that cross it. If you apply a strong
deformation to a system with bonds, you can have problems
and break bonds anywhere in the system, not just at boundaries.
If that is unphysical, then you are derforming too rapidly or too
much.

Steve

In my system I expected to have linear profile after shear. But when I deform or shear the system which is having both bonded and non-bonded particles, the profile is more spread at the boundaries. ( I get linear velocity profile with only non-bonded particles). So I was wondering whether it is due to the fact that neighbor distance(bonds which are at the boundary) are not taken properly. I can see that in bond-distance calculation it find out the connected particles and then calculate the minimum image distance. When we deform a system is it properly taken care of?

When we deform a system is it properly taken care
of?

I believe that it is, at least for dynamics. It's possible that
some kind of spatial averaging you are doing will have funny
effects near the walls, but the fix ave/spatial doc page describes what
it does at the boundaries.

Atoms beyond the lowermost/uppermost bin in a dimension are counted in the first/last bin in that dimension.

Steve

Thanks for your info. Actually I am plotting position of each particles(along shear gradient direction) vs the velocity of individual particles. I use the dump file from Lammps and use gnuplot. Actually I haven’t done any of fix ave/spatial kind. Previously I sheared the system(both bonded and non-bonded particles) using highly dense walls and solid boundary condition(along shear gradient direction) and then got the correct velocity profile.