Hello LAMMPS community,
I have question which is not about running LAMMPS or doing a simulation, but it is about producing histogram from the LAMMPS output. In short, to generate the histogram, I used numpy.hostigram from Python and a for loop on the number of time-steps.
I have some particles in a cylinder with periodic boundary condition along its axis of symmetry (z direction). I produced a histogram of these particles along the z direction — Please see the attached value.
The histogram correctly shows the physics I expect: The histogram should have low values in the middle of the cylinder (|z|<=z_transition) and fluctuate around a constant value as the bin approach either of two ends (z_transition<|z|<=z_end).
However, the picture breaks down near the end of the cylinder; histogram values in the end bins are significantly lower than other bins in the range of z_transition<|z|<=z_end.
Changing the bin-size does not solve the issue, but makes the plot smoother.
Is this abnormally due to the PBC? Did I miss something in generating this histogram?
Thank you in advance for your response.
histogram.pdf (21.7 KB)