Hi everyone,

I am attempting to simulate a simple CO2 molecule. However, LAMMPS is hanging when trying to read my molecule file sometimes. Specifically, when running the ‘in.co2’ script that I have copied at the end of this message, there are 3 possible outcomes.

- The script hangs after outputting:

LAMMPS (10 Feb 2015)

Created orthogonal box = (0 0 0) to (10 10 10)

1 by 1 by 1 MPI processor grid

Read molecule 1:

3 atoms with 2 types

2 bonds with 1 types

1 angles with 1 types

0 dihedrals with 0 types

0 impropers with 0 types

At this point, the script hangs, and must be killed.

- The script executes, and outputs the following (sample of only the first thermo output, the script completes with the same thermo output and no errors):

LAMMPS (10 Feb 2015)

Created orthogonal box = (0 0 0) to (10 10 10)

1 by 1 by 1 MPI processor grid

Read molecule 1:

3 atoms with 2 types

2 bonds with 1 types

1 angles with 1 types

0 dihedrals with 0 types

0 impropers with 0 types

Created 3 atoms

Finding SHAKE clusters …

0 = # of size 2 clusters

0 = # of size 3 clusters

0 = # of size 4 clusters

1 = # of frozen angles

Neighbor list info …

1 neighbor list requests

update every 1 steps, delay 0 steps, check yes

master list distance cutoff = 2.8

Setting up run …

SHAKE stats (type/ave/delta) on step 0

1 0.322222 0 6

1 180 0

Memory usage per processor = 6.86293 Mbytes

Step Temp TotEng PotEng

0 0 0 0

SHAKE stats (type/ave/delta) on step 1000

1 0.322222 0 6

1 180 0

1000 0 0 0

…

…

SHAKE stats (type/ave/delta) on step 100000

1 0.322222 0 6

1 180 0

100000 0 0 0

Loop time of 0.101181 on 1 procs for 100000 steps with 3 atoms

Pair time () = 0.00734854 (7.26278)
Bond time () = 0.00727963 (7.19468)

Neigh time () = 0 (0)
Comm time () = 0.0124381 (12.2929)

Outpt time () = 0.000585556 (0.578723)
Other time () = 0.073529 (72.6709)

Nlocal: 3 ave 3 max 3 mi

Histogram: 1 0 0 0 0 0 0 0 0 0

Nghost: 0 ave 0 max 0 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Neighs: 0 ave 0 max 0 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 0

Ave neighs/atom = 0

Ave special neighs/atom = 2

Neighbor list builds = 0

Dangerous builds = 0

- The script runs and finishes, but the shake seems to fail early on:

LAMMPS (10 Feb 2015)

Created orthogonal box = (0 0 0) to (10 10 10)

1 by 1 by 1 MPI processor grid

Read molecule 1:

3 atoms with 2 types

2 bonds with 1 types

1 angles with 1 types

0 dihedrals with 0 types

0 impropers with 0 types

Created 3 atoms

Finding SHAKE clusters …

0 = # of size 2 clusters

0 = # of size 3 clusters

0 = # of size 4 clusters

1 = # of frozen angles

Neighbor list info …

1 neighbor list requests

update every 1 steps, delay 0 steps, check yes

master list distance cutoff = 2.8

Setting up run …

SHAKE stats (type/ave/delta) on step 0

1 1.17401 1.70357 6

1 99.1523 0

Memory usage per processor = 6.86293 Mbytes

Step Temp TotEng PotEng

0 0 0 0

…

…

SHAKE stats (type/ave/delta) on step 100000

1 nan nan 6

1 nan nan

100000 nan nan 0

Loop time of 0.093082 on 1 procs for 100000 steps with 3 atoms

Pair time () = 0.00688314 (7.39471)
Bond time () = 0.00655746 (7.04483)

Neigh time () = 0 (0)
Comm time () = 0.0131786 (14.158)

Outpt time () = 0.000461817 (0.49614)
Other time () = 0.0660009 (70.9063)

Nlocal: 3 ave 3 max 3 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Nghost: 0 ave 0 max 0 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Neighs: 0 ave 0 max 0 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 0

Ave neighs/atom = 0

Ave special neighs/atom = 2

Neighbor list builds = 0

Dangerous builds = 0