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Re: [lammps-users] Calculation of msd of atoms in spatial bins
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Re: [lammps-users] Calculation of msd of atoms in spatial bins


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Sun, 12 Nov 2017 21:10:21 -0500



On Sun, Nov 12, 2017 at 7:40 PM, Sengupta, S. <S.Sengupta@...12...2493...> wrote:
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​

 

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
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--
Dr. Axel Kohlmeyer  akohlmey@...92......  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.