Dear LAMMPS users
I have decided to plot density profile of water droplet on graphene surface. I used compute chunk/atom in orther to compute density by binning method.
As my bin sizes are very little (0.50.50.5A^3) and the droplet’s diameter is about 100A, I face with a gigantic bins in 3dimension. I used compress option to eliminate zero bins, but some of these bins are located in the middle of the droplet and this elimination influence on the density profile.
How can I solve this problem?
(I need to calculate density profile in each layers parallel to the surface.)
Thank you so much
regards
reza
Dear LAMMPS users
I have decided to plot density profile of water droplet on graphene surface.
I used compute chunk/atom in orther to compute density by binning method.
As my bin sizes are very little (0.5*0.5*0.5A^3) and the droplet's diameter
is about 100A, I face with a gigantic bins in 3dimension. I used compress
option to eliminate zero bins, but some of these bins are located in the
middle of the droplet and this elimination influence on the density profile.
How can I solve this problem?
you cannot use compress in this case. your bin size is ridiculously
small. it is a small fraction of the average volume of a single water
molecule. thus you will for each snapshot get *extremely* noisy data
with typically 1 or 0 molecules per bin. use a meaningful bin size
(somewhere between 2.5 and 10.0 \AA in each direction) and you won't
need to worry about running out of memory. there is no point in
measuring something at a resolution that by far exceeds the level of
detail of the model.
axel.
Thank you so much dear Axel for your answers
I infer from your answer that the bin’s size must be bigger than the sample molecule.Am i right?
I mean, If I want to add another molecule with bigger diameter, I should increase the bin’s size.