bond/create restart

Hello all,

we have developed an algorithm to create a crosslinked network from a homopolymer melt.
Where the crosslinking (the creation of new bonds) is made with our own C code. We used the data file created by this code as the input data file for lammps. But we have the warning

WARNING: Inconsistent image flags (…/domain.cpp:678)

To check our algorithm of crosslinking, we used instead, the fix command bond/create. This worked perfectly! BUT, since we are interesting in calculate the components of the stress tensor during uniaxial deformation, we developed an input file where code is running for different deformations of the simulation box. And every time we run the code for each deformation step, the same warning appears, despite we used bond/create command.
I would appreciate any light about this warning… we have used LAMMPS (8 Aug 2014)

Here is a part of the code:


variable contraction equal 1/sqrt(v_TensileScalingPerIncrement)

units lj
atom_style angle
boundary p p p
dimension 3

read_data “”

pair_style hybrid/overlay dpd {Temperature} {cutoff} 12345 &
dpd/tstat {Temperature} {Temperature} {cutoff} 12345 pair_coeff 1 1 dpd {Aii} 0.000000
pair_coeff 1 2 dpd {Aii} 0.000000 pair_coeff 2 2 dpd {Aii} 0.000000
pair_coeff 1 1 dpd/tstat {gamma} pair_coeff 1 2 dpd/tstat {gamma}
pair_coeff 2 2 dpd/tstat {gamma} bond_style harmonic #special_bonds lj 1.0 1.0 1.0 special_bonds lj/coul 0 1 1 extra 50 bond_coeff 1 {kpp} {r0} bond_coeff 2 {CLkpp} {CLr0} velocity all create {Temperature} 14092168 mom yes rot yes dist gaussian
comm_modify mode single vel yes
neighbor 2.0 bin
neigh_modify delay 2
timestep ${timeStep}

fix createbond all bond/create 500 2 1 0.85 2 prob 0.3 84121 iparam 1 1 jparam 0 1
variable Nbond1 equal f_createbond[1]
variable Nbond2 equal f_createbond[2]
fix extra all print 500 “{Nbond1} {Nbond2}”
fix 1 all nve
dump 1 all atom 500 CLhomopolymer.dump
thermo_style custom etotal ke pe ebond enthalpy temp press pxx pxy pxz pyy pyz pzz lx ly lz xy xz yz
thermo_modify line multi
thermo 200
thermo_modify flush yes
run ${initialRelaxationTimeSteps}

label loop
variable a loop {TensileIncrements} fix Tensile all deform 1 x scale {TensileScalingPerIncrement} &
y scale {contraction} & z scale {contraction} &
remap x units box
run {TensileTimeSteps} unfix Tensile run {TensileRelaxationTimeSteps}
next a
jump loop

The warning means that there is one or more bonds

which cross a periodic boundary, and the image flags

of the 2 atoms in the bond do not differ by +/- 1.

Depending on how you create your system it may

or may not be possible to always satisfy this. E.g.

a fully connected periodic system cannot. E.g. a lattice

of bonds.

It’s just a warning, b/c it doesn’t affect standard dynamics.

It can be a problem if you try to do something like

create a rigid body or measure a mean-squared displacement,

both of which rely on unwrapping coords using the images