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[lammps-users] compute aggregate/atom stucks with empty neighbor list
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[lammps-users] compute aggregate/atom stucks with empty neighbor list

From: Michael King <king.michael.1989@...444...>
Date: Mon, 6 Nov 2017 14:06:39 +0100

Hello dear LAMMPS developers,


*compute aggregate/atom* gets stuck when run with mpirun and cutoff is too short and special_bonds is 0.0 0.0 0.0 (default) supposed reason: Empty neighbor lists for some processors -> get stuck in the while loop of compute_aggregate_atom.cpp

LAMMPS Version: 22 Sep 2017


We were interested in using aggregate/atom to study the cluster formation of our polymers. Therefore, we did the simulation then using a rerun script to calculate the property and dump it into a file. When we reduced the cutoff under a certain value, so that only the neighboring chains with a 'real' contact would be assigned to a cluster we ran in the following problem:

The rerun script runs in serial or mpirun -n 1, but not with more cores.

We can fix this behavior by a greater cutoff (unwanted) or special_bonds 1.0 1.0 1.0 (as stated in the doc).

So i believe that this is due to the while loop in compute_aggregate_atom.cpp. We don't have any clusters in the beginning of the simulation and when due to *special_bonds 0.0 0.0 0.0* the bonded atoms are removed from the neighbor list we get stucked in this loop since we iterate over 0 atoms and can not fulfill the condition for the break.

A test system is shown below.

Since this error can be fixed by appropriated special_bonds settings (see docs) i think its a minor problem,
but you can also create a case where special_bonds wont fix it, see below.
So we want to report it anyway.

TEST SYSTEM to reproduce the error:
LAMMPS Version: 22 Sep 2017

1.) use ${LAMMPSFOLDER}/examples/micelle/in.micelle and uncomment the dump command.

2.) run the simulation

3.) do a rerun with the following script (cluster.lammps):


dimension    2

atom_style    bond
read_data    data.micelle

pair_style      zero 2.5
pair_coeff * *
bond_style      zero nocoeff
bond_coeff *

# special_bonds lj 1.0 1.0 1.0

group alkane type 2 3 4
compute aggr alkane aggregate/atom 1.0
dump calc_agg alkane custom 1 aggregate.dat id c_aggr
dump_modify calc_agg sort id

rerun dump.micelle every 1 dump x y scaled yes box yes wrapped yes format native


should work: lmp -in cluster.lammps
should work: mpirun -n 1 lmp -in cluster.lammps
should not work: mpirun -n 4 lmp -in cluster.lammps

4.) uncomment * special_bonds lj 1.0 1.0 1.0*

should work: lmp -in cluster.lammps
should work: mpirun -n 1 lmp -in cluster.lammps
should work: mpirun -n 4 lmp -in cluster.lammps

5.) if i change my *aggregate/atom 1.0* cutoff to some value <= bond_length (0.75), i will get the same error but this time special_bonds wont help.

To track down where it went wrong (i know it changed the results of my cluster analysis) i just added

      if (inum == 0)

after the second while(1) command in *compute_aggregate_atom.cpp* to check if the error comes from an empty neighbor list. Then it will not stuck in the loop, but that quick&dirty test will change the results compared to the original code run in serial.

Michael King