Dear Dr. Axel Kohlmeyer,
Hello Dr. Kohlmeyer. Thank you for the guidelines.
I am using the LAMMPS version February 10, 2015. The LAMMPS input script that I am running equilibrates the randomly created polymer chains. The data file that this input script reads contains 250000 atoms.
I looked at the previous mailing list in regards to inconsistent MD trajectories. I am using the same number of processors for every run. Therefore, inconsistent position and velocity coordinates of the atoms should not occur due to the number of processors.
My question that illustrates my difficulties are described in the attached Word document. For clarity, I also included my LAMMPS input script in the attached Word document. If you require the data file, I would greatly appreciate if you could notify me.
Thank you.
Sincerely,
Masato Koizumi
LAMMPS.docx (20.3 KB)
Dear Dr. Axel Kohlmeyer,
Hello Dr. Kohlmeyer. Thank you for the guidelines.
you don't seem to be following them very closely, though.
I am using the LAMMPS version February 10, 2015. The LAMMPS input script
that I am running equilibrates the randomly created polymer chains. The
data file that this input script reads contains 250000 atoms.
i don't care about looking into how an over 2.5 year old LAMMPS version is
behaving.
i also don't care about having to dig through a word document for not good
reason.
I looked at the previous mailing list in regards to inconsistent MD
trajectories. I am using the same number of processors for every run.
Therefore, inconsistent position and velocity coordinates of the atoms
should not occur due to the number of processors.
the *will* occur. after some time. your simulation protocol is making it
*extremely* likely.
you are doing floating point math ...and it is quite possible to have
"inexact" operations where random bits (e.g. through thermal noise) enter
into the calculation especially when your executable was compiled with any
form of compiler optimization.
using DPD enhances this. as soon as there is a difference of one atom being
placed into a different subdomain, your trajectories will diverge quickly
due to the RNGs being called differently frequent on different subdomains.
the more processors you use, the more likely this gets.
My question that illustrates my difficulties are described in the attached
Word document. For clarity, I also included my LAMMPS input script in the
attached Word document. If you require the data file, I would greatly
appreciate if you could notify me.
word documents are very *in*convenient. altogether, i don't see any
convincing reason to investigate this. your expectation to have identical
trajectories is not justified for this kind of simulation protocol and
conditions.
axel.