from error section, I got the following information
*Inconsistent image flags*
The image flags for a pair on bonded atoms appear to be inconsistent. Inconsistent means that when the coordinates of the two atoms are unwrapped using the image flags, the two atoms are far apart. Specifically they are further apart than half a periodic box length. Or they are more than a box length apart in a non-periodic dimension. This is usually due to the initial data file not having correct image flags for the 2 atoms in a bond that straddles a periodic boundary. They should be different by 1 in that case. This is a warning because inconsistent image flags will not cause problems for dynamics or most LAMMPS simulations. However they can cause problems when such atoms are used with the fix rigid or replicate commands.
Is there anything going bad due to PBC, then how to overcome it
from error section, I got the following information
Inconsistent image flags The image flags for a pair on bonded atoms appear
to be inconsistent. Inconsistent means that when the coordinates of the two
atoms are unwrapped using the image flags, the two atoms are far apart.
Specifically they are further apart than half a periodic box length. Or they
are more than a box length apart in a non-periodic dimension. This is
usually due to the initial data file not having correct image flags for the
2 atoms in a bond that straddles a periodic boundary. They should be
different by 1 in that case. This is a warning because inconsistent image
flags will not cause problems for dynamics or most LAMMPS simulations.
However they can cause problems when such atoms are used with the fix rigid
or replicate commands.
Is there anything going bad due to PBC, then how to overcome it
bad questions don't get better by repeating them.
it is your data and your simulation. you know what it should be, so
you have to verify that LAMMPS is doing what you want. as i mentioned
before, it doesn't suddenly become correct or wrong because of
somebody's say-so. specifically, if that person cannot know what it is
that your want. errors (or warnings) are not resolved by silencing
them, but by understanding why they happen and then making a conscious
decision. no person worth listening to, will do this for you.
I ran two simulations, with compute group/group, with "run" and "rerun"
Now, with 'run' ( gives no warning inconsistent image flags ) energy
values are same as rerun ( with warning inconsistent flags).
I can assure myself that warning inconsistent flags are not effecting my
energies.
Is this correct?
unfortunately, i have run out of affirmative bytes on my computer.
i'll run a program to regenerate them over the weekend and will be
able to answer next week.
The issue was that you were reading unwrapped coords from the
dump file and they were being remapped to the periodic box
which incremented the image flags. I modified version
of read_dump in the 18Sep patch should handle that case