Dear all,
My substrate are coarse-grained PMMA. The monomers from the same chain are are linked by FENE bonds and monomers from different chains interact via LJ. The system was equilibrated. The correspondent data file is attached (“pmma_final.dat”). I am depositing energetic atoms of Au. I divided the deposition regions into 16 different areas, so I have 1 particle deposited for a square nanometer. My script is bellow.
I am playing with langevin damping parameter and I am also using fix bond/break to simulate polymer damage. I am doing deposition in loops, so I can run nvt and also force bias monte carlo between deposition events.
When I use a damping parameters that does not break bonds (0.01), everything is ok. But when I use values higher than 0.02 and some bonds are broken (for my criteria, typically 2-3 broke bonds per deposition), I got this kind of message (after 2 or 3 loops):
ERROR on proc 0: Bond atoms 208 209 missing on proc 0 at step 511010 (…/neigh_bond.cpp:65)
Sometimes it happens just after deposition, sometimes during monte nvt or fb monte carlo.
This happens for 1 or more processors.
Maybe is bad dynamics, but I tracking thermo I cannot see any abrupt variation of temperature. And I tried also to increase number of steps for nvt and for fb-monte carlo.
I have also extended communication between atoms using a larger cutoff “comm_modify cutoff 120.0”
I would appreciated some tip.
Fernanda S Teixeira.
Gold deposition
clear
units metal
dimension 3
boundary p p m
neighbor 2.0 bin
atom_style bond
special_bonds fene
atom_modify map array
bond_style fene
pair_style lj/cut 12
timestep 0.001
---------- Define Settings ---------------------
read_data pmma_final.dat
pair_coeff 1 1 0.07 5.16 12
pair_coeff 2 2 0.2294 2.629 12
pair_modify shift yes mix geometric
---------- Define Interatomic Potential ---------------------
mass 2 197.0
bond_coeff 1 0.08 7.5 0.07 5.16
Potential Simples de Lennard-Jones
neigh_modify every 1 delay 1 check yes
thermo 500
thermo_style custom step atoms pe ke etotal lx ly lz vol temp press zlo zhi density
compute all all temp
thermo_modify temp all lost ignore flush yes
pmma_final.dat (203 KB)