Image flags for rigid bodies with flexible side chain

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1

Hi,
I’m simulating a collection of rigid bodies with short, flexible side chains attached through a harmonic spring. Each rigid body is made up of 6 beads arranged in linear fashion. I’m running the version of LAMMPS from 28 June 2014.

Here is the sample input file:

units, pair potentials, read_data have all been given

my in.data contains image flags along with the atom coordinates

define groups

group LC molecule 1:4
group sidechains molecule 0

integrate equations of motion

timestep 0.005
fix 1 LC rigid/nvt molecule temp 2 2 0.5
fix 2 sidechains nvt temp 2 2 0.5
neigh_modify exclude molecule LC
run 10000
run 10000

It says “Warning: Inconsistent image flags” before the second run command. Does that mean I need to dump atom coordinates with image flags after the first run, and reread the appropriate file containing positions AND image flags before the second run command? Or is there a shortcut that I should use that I’m missing?

Q: Do the image flags for the atoms in the group sidechains matter to the run? It would affect the mean squared displacement but I’m not interested in those values.

Thanks,
Poornima

2

Hi,
I'm simulating a collection of rigid bodies with short, flexible side chains
attached through a harmonic spring. Each rigid body is made up of 6 beads
arranged in linear fashion. I'm running the version of LAMMPS from 28 June
2014.

please always try with the very latest patchlevel. you may have run
into an issue that has been fixed since.

Here is the sample input file:

# units, pair potentials, read_data have all been given
# my in.data contains image flags along with the atom coordinates

# define groups
group LC molecule 1:4
group sidechains molecule 0

# integrate equations of motion
timestep 0.005
fix 1 LC rigid/nvt molecule temp 2 2 0.5
fix 2 sidechains nvt temp 2 2 0.5
neigh_modify exclude molecule LC
run 10000
run 10000

It says "Warning: Inconsistent image flags" before the second run command.
Does that mean I need to dump atom coordinates with image flags after the
first run, and reread the appropriate file containing positions AND image
flags before the second run command? Or is there a shortcut that I should
use that I'm missing?

there is not enough information here to make any statement. or to try
and reproduce the issue easily.

axel.