Dear Dr. Axel Kohlmeyer and LAMMPS users
Hello Dr. Kohlmeyer. First, thank you for your continuous responses to my inquiries on LAMMPS.
I am currently obtaining inconsistent image flag when I use the fix bond/create command. I am simulating molecules where Type 3 and Type 3 atoms are allowed to form new bonds, and likewise, for Type 4 and Type 4 atoms.
The pairwise potential is LJ potential at cutoff distance of 2.5 in LJ units.
I have set the bonding distance to be 0.97 which is the equilibrium distance of pairwise FENE potential of spring constant 30 and cutoff distance of 1.5 all in LJ units. All bonds in the system including the newly formed bonds are governed by the FENE potential and the system is equilibrated prior to applying the fix bond/create command.
Before applying the fix bond/create command, I am not obtaining any warning that concerns with inconsistent image flag. This confirms that my original data file has correctly mapped all atoms that straddle the periodic boundary condition.
However, once I apply the fix bond/create command and looking at my dump files and the data file through OVITO, I noticed that the dump files and the data file is not correctly printing the image flags.
Although I am updating the neighbor list more frequently than the number of timesteps which LAMMPS attempt to create bonds, I see that the dump file and the data file are not correctly specifying the image flag for the newly formed bonds that straddle the periodic boundary conditions.
Inconsistent image flags due to fix bond/create has been discussed previously in the mailing list, but I am seeing from OVITO that the data file and dump file are not are not printing the correct image flag.
Is there something in my LAMMPS input script that causes the dump files to incorrectly print the image flags for newly formed bonds that cross the periodic boundary condition?
I have provided my LAMMPS input script, and if you require a small data file that replicates this issue, I would greatly appreciate if you could notify me.
Thank you, and I am deeply grateful for your time
Sincerely,
Masato Koizumi
The following is my LAMMPS input script:
units lj
atom_style full
neighbor 0.36 bin
neigh_modify delay 2
comm_modify vel yes
pair_style lj/cut 2.5
bond_style fene
special_bonds lj 0.0 1.0 1.0
read_data Equilibrated_Molecules.data extra/atom/types 2 extra/bond/types 1 extra/bond/per/atom 1
pair_coeff * * 1.0 1.0 2.5
bond_coeff * 30.0 1.5 1.0 1.0
mass * 1.0
timestep 0.01
reset_timestep 0
dump 1 all custom 10 _Atom_Coordinates id mol type xu yu zu
thermo 100
thermo_style custom step temp ke pe etotal epair pxx pyy pzz lx ly lz
compute b1 all property/local btype batom1 batom2
compute b2 all bond/local dist engpot force
dump 2 all local 10 _Bond_Data index c_b1[] c_b2[]
fix 2 all nvt temp 1.0 1.0 2.0
fix 3 all bond/create 50 3 3 0.97 2 iparam 1 5 jparam 1 5
fix 4 all bond/create 50 4 4 0.97 2 iparam 1 6 jparam 1 6
run 100