Dear Dr. Axel Kohlmeyer,
Hello Dr. Kohlmeyer. Thank you for your many advice.
When you previously discussed, “watch out when restarting in the middle of a gradual change. have a close look at the documentation for the run command,”
I am not sure why atoms in the data file are being migrated beyond the cutoff distance of the FENE potential thereby giving me BAD FENE BONDS error when I restart a simulation during a middle of gradual change. (I am using the same number of processors in my restart file.)
This seems to be a trivial issue; however, I tried a following simple case:
Case 1: Run a stress-strain simulation where the elongation of the simulation box is determined by:
fix 4 all deform 1 x erate 0.01 y volume z volume
run 10000 upto
Then run a restart simulation during the middle of this run, say at 4000 timesteps where the fix deform is re-specified as
fix 4 all deform 1 x erate 0.01 y volume z volume
run 10000 upto
Restart simulation runs smoothly without issues
Case 2: Run a stress-strain simulation where the elongation of the simulation box is determined by:
variable displace equal “0.01stepdt”
variable rate equal “0.01”
fix 4 all deform 1 x variable v_displace v_rate y volume z volume remap v
run 10000 upto
Then, run a restart simulation during the middle of this run, say at 4000 timesteps where the fix deform is re-specified as the same,
variable displace equal “0.01stepdt”
variable rate equal “0.01”
fix 4 all deform 1 x variable v_displace v_rate y volume z volume remap v
Restart simulation experiences FENE bond too long
Both of these simple cases should output the same results since I am not changing anything to the deformation. I tried using the start/stop option of the run command; however, I am still obtaining the BAD FENE BONDS error.
Thank you so much for all of your previous assistance. I would greatly appreciate if I could, once again, request for your advice in pointing me to the correct direction. Thank you so much for your time and effort.
Sincerely,
Masato Koizumi