Dear All
i am trying to use ‘fix qeq/reax command’ for obtaining charge equilibration while simulating water molecules. but i am constantly getting the following error
"rank 3 in job 131 Boltzmann_33076 caused collective abort of all ranks
exit status of rank 3: killed by signal 11
rank 1 in job 131 Boltzmann_33076 caused collective abort of all ranks
exit status of rank 1: killed by signal 9
rank 0 in job 131 Boltzmann_33076 caused collective abort of all ranks
exit status of rank 0: killed by signal 9 "
i have used lj/charmm/coul/long pair style and harmonic style for angles and bonds. i have used metal units.
i have attached my input script and the error messages i received. can you please tell me where i have gone wrong?
water216.txt (45.4 KB)
param.qeq (46 Bytes)
error.txt (2.7 KB)
in.waternvt (1.55 KB)
Maybe Ray can look at this.
Steve
the segfault is due to fix qeq/reax not knowing about exclusions.
it would be easy to avoid the segfault (by masking out the exclusion
bits from the j index), but i am not sure if this is the proper way to
handle this situation. i would suggest to look into the literature
(where did you pick up the parameters?) to see what is the appropriate
way to do this for your model.
axel.
Dear Axel
I have used the parameters from the paper ‘J. Phys. Chem. 1991,95,3358-3363’. i had also tried the suggestions by Hasan Metin Aktulga in the LAMMPS mailing list thread
http://lammps.sandia.gov/threads/msg22632.html
but i got the same error in all the cases.
Hi Unni,
Steve and I discussed this a little bit. The attached fix_qeq_reax.cpp, in which an additional line of " j &= NEIGHMASK" is added, get rids of the segfault.
But you should note it is difficult to converge the charges with your script. This might be due to the fact that CHARMM is a fixed charge potential and the non-formal charges used in the potential are optimized. Attempt to vary the charges with qeq is likely to result in unphysical results.
Ray
fix_qeq_reax.cpp (21.9 KB)
Just one more comment. As Axel noted, enforce qeq on your system by masking (i.e. Including) the excluded j neighbors may not be a good idea.
The problem is not your qeq parameters, rather it is the appropriateness of applying qeq to your system.
Ray
Just one more comment. As Axel noted, enforce qeq on your system by masking
(i.e. Including) the excluded j neighbors may not be a good idea.
The problem is not your qeq parameters, rather it is the appropriateness of
applying qeq to your system.
it should work somehow, since there are, for example, the SPC/FQ
and the TIP4P/FQ polarizable/rigid water models. i would look up the
corresponding publication(s) and compare how the charge equilibration
has to be implemented for those models and if and how this differs
from what fix qeq/reax implements.
it has been a looooong time since i looked into those (i was an
undergrad then), so i don't recall the details anymore.
cheers,
axel.
Dear Ray, Axel and Steve
thank you very much for your suggestions…i