Dear LAMMPS users,
Is there any way of calculating msd of atoms in spatial bins ? The msd should be computed as an average over all atoms in a spatial bin.
The msd/chunk page mentions that it computes the msd of centre of mass of the chunks. Although, the command in the second example on the page (http://lammps.sandia.gov/doc/compute_msd_chunk.html ) is com/msd instead of msd/chunk. Is msd/chunk the same as com/msd ?
Thanks
Soumyadipta
Dear LAMMPS users,
Is there any way of calculating msd of atoms in spatial bins ? The msd
should be computed as an average over all atoms in a spatial bin.
​spatially averaged MSD values are a tricky thing. first off, you need to
define what you mean by this.
does this apply to atoms that are in the bins at the beginning of the
sampling? or to atoms that remain in the bin all the time? or to atoms that
are in the bin at the beginning and the end? or to atoms that are in the
bin at the end?
either choice imposes some bias and affects how to interpret the results.
axel​