Dear LAMMPS users,
I meet a problem when running dynamics for a charged model using Kspace method of PPPM. A NVT dynamics simulation at 300K was submitted on cluster using MPIs for the models of ~210000 atoms (domain: 120 x120 x 310 Angstrom^3) in which all atoms have charge.
However, an error like : “ERROR on proc 15: Bond atoms 205827 205826 missing on proc 15 at step 1470 (…/neigh_bond.cpp:65)” occurs. I have viewed the discussions in LAMMPS users forum regarding this matter. It may be the bad dynamics run.
But I can’t fix this problem for months although I have successfully run the similar simulations of aqueous copolymer lubricants confined between metal oxide surfaces (NOTED this model also have charges) several times.
I have reduced the temperature to 10 K, or reduced the timestep to 0.1 fs, or combined of both, but it did not work. The models had also been relaxed before running dynamics in Material Studio as well as in LAMMPS. The Nose-Hoove NVT was used and updated after 100 timesteps.
Finally, when I ignored the Coulombic interactions and kspace solver in the input script, the model run well without any error. I realized that the possible reason is somewhere in using kspace solver.
In my simulation, the confined shear models are used, so that they are not periodic in z direction. Therefore, the PPPM solver with slab option is used.
Further description is shown as following:
clear
dimension 3
boundary p p f ## long coulombic
units metal
atom_style full
neighbor 2.0 bin
neigh_modify delay 0 every 1 check yes
kspace_style pppm 1.0e-4
kspace_modify slab 3.0
############ PAIRE ############
pair_style hybrid buck/coul/long 9.5 9.5 lj/cut/coul/long 9.5 9.5 lj/class2/coul/long 9.5 9.5
pair_modify mix arithmetic
bond_style harmonic
angle_style harmonic
dihedral_style opls
.
.
.
############# MINIMIZE NOT FOR RESTART ####################
minimize 1.0e-5 1.0e-6 1000 10000
reset_timestep 0
############## INITIAL TEMP NOT FOR RESTART #################
velocity all create 300 4928459 dist gaussian loop geom
velocity gBd set 0.0 0.0 0.0 units box
timestep 0.001
.
.
.
fix fNvtFlow all nvt temp 300 300 0.1 # fix fNvtFlow all nvt temp 10 10 0.1
fix_modify fNvtFlow temp cT3dProAll
.
.
.
The setting for PPPM solver is set as default.
Have you guys ever met the same problem like this ? Should I change to another solver or set more options for PPPM solver in this case ?
I will really appreciate your helps !
Best regards,
Thi Dinh TA