Inquiry on Results Using Compute Bond/Local

Dear Dr. Steve Plimpton and LAMMPS Users,

Thank you, Dr. Plimpton for your advice.

I was curious if I could ask a question regarding the compute bond/local command.

I am currently studying the force-displacement response of a polymer strand in a freely jointed chain where I define polymer strand as the polymer chain segment flanked by two crosslinks.

I have created a simple polymer matrix consisting 4 chains each comprised of 10 beads. There are 5 crosslink bonds that link these different chains. The bonds that connect to form a chain and the crosslink bonds are governed by FENE potential and non-connected beads interact with LJ potential.

I have applied uniaxial deformation such that the simulation box elongates to twice its original box length (stretch = 2.0) at strain rate of 0.00001 in LJ units.

However, I have plotted (and attached) the average bond lengths for the 4 chains with respect to stretch, and I am observing a random fluctuation without any signs of upward trend. I am expecting that the average bond length of the 4 chains should increase with respect to increasing stretch.

Furthermore, I have plotted (and attached) the tension experienced by polymer strand at maximum elongation (stretch = 2.0) and the strand tension varies randomly with respect to r/L (strand end-to-end distance/strand contour length).

In both of these plots, I should see an upward trend, and I should not see data points in the negative region of the force plot since this would imply bonds being compressed when in fact the simulation box is elongating.

I tried with larger stretch but I am continuing to see random pattern in these plots.

Following the documentation, I understand that compute bond/local calculates the bond length, bond potential and bond force between every atom, but I was curious if I am interpreting and using the compute bond incorrectly. Simulating a larger polymer matrix, I am obtaining reasonable stress strain curve, but I am still seeing random fluctuation in bond length and force as well as in strand tension.

According to the documentation and from physical interpretation, I should see an upward trend in both of the attached plots. I would greatly appreciate if I could request for any comments or advice.

I also attached my LAMMPS script and the external data file if needed. Thank you so much for your time.


Masato Koizumi

0.10553_rho (7.21 KB) (1.6 KB)

Tension Plot.png

Bond Plot.png

I can’t really help you interpret the output of your simluation. The compute bond/local and releated

comands do something simple. They just loop over all the bonds in the system

and generate some output, e.g. which you can dump or average. For any large system

there will be a distribution of bond lenghts, energies, etc, which very rapidly with

time (bond frequency). So it is up to you to do suitable time or spatial averaging

of those quantities to learn something useful about your system.