My model often shows errors like “Bond atoms 4549 4550 missing on proc 0 at step 42”,My model often shows errors like “Bond atoms 4549 4550 missing on proc 0 at step 42”. Can you help me check the interactions between my atoms? Below is the pair_coeff I used
unit metal
bond_coeff 1 harmonic 25.8 1.0 #600*0.043=25.8
angle_coeff 1 harmonic 3.225 109.47#75*0.043=3.225
pair_coeff 1 1 lj/cut/coul/long 0.0066779 3.166# 0.15535*0.043
pair_coeff 2 2 lj/cut/coul/long 0.0 0.0
pair_coeff 1 2 lj/cut/coul/long 0.0 0.0
dihedral_style none
improper_style none
special_bonds lj/coul 0.0 0.0 0.5
group spce type 1 2
group cu type 3
pair_coeff 3 3 eam /home/zz/Desktop/md/lammps-12Dec18/potentials/Cu_u3.eam
pair_coeff 1 3 lj/cut/coul/long 0.051987 2.752 #1.209*0.043=0.051987
pair_coeff 2 3 lj/cut/coul/long 0.0 0.0
mass 2 1.00794
mass 1 15.9994
mass 3 63.546
there are many possible reasons. potential parameters are just one of them.
bad geometry or overlapping atoms, choice of timestep, correct/incorrect use of fix shake or fix rigid are others.
the lammps-users mailing list archives has many discussions on what underlying problem this is a symptom of and how to debug and resolve this.
nobody will do this for you. there is no “just set this number and it will be fine” kind of solution, especially not from remote.
since this happens early in the simulation, you can output coordinates every step and visualize the trajectory.
also a good strategy is to start with a simpler system that is a subset of your actual simulation system and figure out the optimal settings for that subject. these are all steps that you would learn through being tutored by your adviser or more experienced colleagues. it is near impossible and very time consuming to try that via e-mail.
axel.