Dear all,
I am trying to analyze, an aluminium rectangular geometry with a void in the centre for crack propagation but after running 30K potential file steps it gives me an error saying too many neighbour bins.
I tried with 0.3, 2.0, and 5.0 bins but error remains the same.
Can anyone please help me in this.
Thank you.
With best regards,
Nisha Sharma.
Email: nisha.s2910@…24…
Phone : +4915218062452
Dear all,
I am trying to analyze, an aluminium rectangular geometry with a void in the
centre for crack propagation but after running 30K potential file steps it
gives me an error saying too many neighbour bins.I tried with 0.3, 2.0, and 5.0 bins but error remains the same.
Can anyone please help me in this.
In your case, the "Too many neighbor bins" error is likely only a
secondary symptom.
there is something else that is going very wrong, which leads to your
box exploding or similar.
please note the warning about atoms being time integrated more than
once. that is almost always due to a serious error in your input.
axel.
Hello Mr. Kohlmeyer,
I tried to unfix the nve command and used only fix nvt for my case but the error remains the same with too many neighbour bins and with warning one or more atoms time integrated more than once.
I still don’t get the cause of this error.
I also tried to change the neighbour style from bin to nsq, there is no effect.
Can you please help me in this, I am stuck at this step. If it is possible can you please check the log file that i have attached with this email.
Thank you very much.
With best regards,
log.lammps (11 KB)
Hello Mr. Kohlmeyer,
I tried to unfix the nve command and used only fix nvt for my case but the
error remains the same with too many neighbour bins and with warning one or
more atoms time integrated more than once.
then you didn't do it right.
I still don't get the cause of this error.
the cause of the warning is self-explanatory. and the too many
neighbor bins comes from your system exploding due to some other
error, e.g. having two methods of temperature control active at the
same time.
I also tried to change the neighbour style from bin to nsq, there is no
effect.Can you please help me in this, I am stuck at this step. If it is possible
learning how to debug an input is part of the skill set of doing
research with MD simulations.
the simplest method is: start with an empty file and then add lines of
your existing input one by one and see what happens and when things
start to go south. you can use the "info" command in LAMMPS to print
out details of the current state of LAMMPS.
axel.
Hello Mr. Kohlmeyer,
As per your suggestion i tried to run the complete script with single command at a time with several changes:
A) run until EQUILIBRATION PART
keeping 0.3 bin+ fix nve +fix nvt —> output until Equilibration no error or warning.
keeping 0.3 bin+fix nve —> output until Equilibration no error or warning
B) run complete til DEFORMATION PART
dump 1 all atom 100 deform.lammpstrj
dump 2 all dcd 50 deform.dcd
run 20000
print " All done!"
keeping 0.3 bin + fix nve + fix nvt —> output WARNING: one or more atom time integrated more than once
ERROR : too many neighbour bins
keeping 0.3 bin +fix nve —> output No WARNING
ERROR : too many neighbour bins
keeping 2.0 nsq + fix nve —> output No WARNING
ERROR : too many atom sorting bins
I can not understand the problem here.
Please can you suggest me something on this.
Regards,
Hello Mr. Kohlmeyer,
As per your suggestion i tried to run the complete script with single
command at a time with several changes:
A) run until EQUILIBRATION PART
1) keeping 0.3 bin+ fix nve +fix nvt ---> output until Equilibration no
error or warning.2) keeping 0.3 bin+fix nve ---> output until Equilibration no
error or warningB) run complete til DEFORMATION PART
# dumping standard atom trajectories
dump 1 all atom 100 deform.lammpstrj# dumping standard atom trajectories
dump 2 all dcd 50 deform.dcd# 20 ps MD simulation (assuming 2fs time step)
run 20000# SIMULATION DONE
print " All done!"3) keeping 0.3 bin + fix nve + fix nvt ---> output WARNING: one or more
atom time integrated more than onceERROR : too many neighbour bins
4) keeping 0.3 bin +fix nve ---> output No WARNING
ERROR : too many neighbour bins
5) keeping 2.0 nsq + fix nve ---> output No WARNING
ERROR
: too many atom sorting binsI can not understand the problem here.
i already told you. most likely, your system is exploding for some
reason, i.e. atoms moving away extremely fast.
have you visualized your trajectory?
Please can you suggest me something on this.
you only removed one of the obvious issues, so you need to keep
removing lines from your input in a systematic fashion in order to
identify what is causing this and then it is going to be much easier
to understand why.
at any rate, this is moving into an area that you should work on with
your adviser or whoever your adviser has designated to train you. i
don't have time to do this and the lammps-users mailing list is not a
replacement to be properly trained in doing computational research.
axel.
I can totally understand. Thank you again for your suggestions and time.
Sorry for any trouble caused to you.
I will try to debug accordingly.
Thanks again.
With best regards,