# Neighbor list problem

Dear Axel,
Thanks for your reply. Can I use serial version lammps to solve this problem?

Xiang Ye
---------- Origin message ----------

From：“Axel Kohlmeyer” <[email protected]…24…>
To：“叶翔” <[email protected]…4389…>
Subject：Re: [lammps-users] Neighbor list problem
Date：2013-08-10 10:16:42

Dear All,
I am simulating a system of more than 100 thousand atoms, I need
to calculate the coul interaction of all the atom pairs, which means that
there is no rcut for the coul interaction. I have tried to increase the
value of “ONE” and “Page” under the command of “neigh_modify”, but it does
not work. Since I need not calculate the pair list, so I also try to revise
the subroutine" pair_coul_cut.cpp", as following

// loop over neighbors of my atoms
num_total is the total atom number of the system
for (i = 0; i < num_total-1; i++) {
qtmp = q[i];
xtmp = x[i];
ytmp = x[i];
ztmp = x[i];
itype = type[i];

for (j = i +1 ; j < num_total; j++) {
delx = xtmp - x[j];
dely = ytmp - x[j];
delz = ztmp - x[j];
rsq = delxdelx + delydely + delz*delz;
jtype = type[j];

// if (rsq < cutsq[itype][jtype]) {
r2inv = 1.0/rsq;
rinv = sqrt(r2inv);
forcecoul = qqrd2e * scale[itype][jtype] * qtmp*q[j]rinv;
fpair = factor_coul
forcecoul * r2inv;

f[i] += delxfpair;
f[i] += dely
fpair;
f[i] += delzfpair;
// if (newton_pair || j < nlocal) {
f[j] -= delx
fpair;
f[j] -= delyfpair;
f[j] -= delz
fpair;
// }

But the it still does not work. the error message is

################################################################################################
LAMMPS (29 Nov 2011)
Reading data file …
orthogonal box = (-300.651 -300.303 0) to (300.651 300.303 19.08)
4 by 4 by 1 processor grid
131180 atoms
Setting up run …

# ===================================================================================== = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = EXIT CODE: 11 = CLEANING UP REMAINING PROCESSES = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES

APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)
####################################################################################################

Anyone can tell me how to solve it, thanks!

you have a big problem:

what you want to compute is incompatible with a domain decomposition
based distributed data parallelization, since this is based on having
a cutoff. have a look at the LAMMPS paper.

axel.

Dear Axel,
Thanks for your reply. Can I use serial version lammps to solve this
problem?

yes and no. technically, it is possible, but you have to know LAMMPS
and know what you are doing. it may be simpler to modify a code that
does not use domain decomposition.

axel.

axel.