Unsorted LAMMPS atoms create problems in binning.
name: Unsorted LAMMPS atoms create problems in binning.
about: getting epsion_planar to work with lammps
Expected behavior
One should just be able to use a atom group, e.g. water, and run epsilon_planar
on this atom group without further work.
Actual behavior
MAICos expects the atoms to be sorted such that each molecules lies consecutively in the atom group, i.e. [*water1_atoms, *water2_atoms]
. LAMMPS data files however seem to be read by MDAnalysis simply randomly, i.e, water atoms of the same molecule are distributed throughout the array. This breaks the epsilon_parallel computation.