Dear LAMMPs community:

I am new to LAMMPS and doing MD simulations for reactions, but with my own developed potential energy surface (I used atomic_style atom, therefore). In the simulations, I want to use some distance criterion to terminate the trajectory. However, the system is periodic, and the cartesian coordinates are allowed to go from inside the box to the outside. Then in this way, the cartesian coordinates might be not the real ones, and the calculated distance criterion is not the truly correct one. So do you have suggestions for me to get the truly correct cartesian coordinates? See also below for my relevant input script. Thanks in advance.

Best regards,

Jun

compute z1comp N1 property/atom z

compute zmax1 N1 reduce max c_z1comp

compute z2comp N2 property/atom z

compute zmax2 N2 reduce max c_z2comp

compute x1comp N1 property/atom x

compute xmax1 N1 reduce max c_x1comp

compute y1comp N1 property/atom y

compute ymax1 N1 reduce max c_y1comp

compute x2comp N2 property/atom x

compute xmax2 N2 reduce max c_x2comp

compute y2comp N2 property/atom y

compute ymax2 N2 reduce max c_y2comp

variable nndist equal sqrt((c_xmax1-c_xmax2)^2+(c_ymax1-c_ymax2)^2+(c_zmax1-c_zmax2)^2)

fix STOP all halt 1 v_nndist > 2.78 error soft

fix debug all print 10 “N2 distance is ${nndist}”