Error of 0 atoms in group FixGCMC

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1

Hi,

I am learning how to perform simulations of the combination of “fix gcmc” and “fix nvt/npt”.

If only “fix nvt/npt” is set, the it ran well. But if command of “fix gcmc” is added, the simulations break.

I have tried many different parameters, so far I haven’t managed to run the combined simulations.

Partial error informations is as follows:

fix fixnvt all nvt temp 300 300 50.0
fix fixmomentum all momentum 1 linear 1 1 1
fix fixrecenter all recenter INIT INIT INIT
fix fixgcmc all gcmc 2 100 100 0 12345 300 10.0 0.01 mol hho maxangle 90 full_energy

here hho is the water-template to be inserted to the box

PPPM initialization …
G vector (1/distance) = 0.300282
grid = 40 40 60
stencil order = 5
estimated absolute RMS force accuracy = 0.00360196
estimated relative force accuracy = 1.08472e-05
using double precision FFTs
3d grid and FFT values/proc = 12474 4800
0 atoms in group FixGCMC:gcmc_exclusion_group:fixgcmc
0 atoms in group FixGCMC:rotation_gas_atoms:fixgcmc
WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (…/neighbor.cpp:441)
Setting up Verlet run …
Unit style : real
Current step: 0
Time step : 0.5
Memory usage per processor = 16.5758 Mbytes
Time Temp PotEng TotEng Press Lx Ly Lz Density
0 236.87453 -96794.099 -84540.115 16026.031 44.20913 46.083223 84.341044 1.3102596
MPI process (rank: 7) terminated unexpectedly on c341-114.ls4.tacc.utexas.edu
Exit code -5 signaled from c341-114
MPI process (rank: 22) terminated unexpectedly on c341-210.ls4.tacc.utexas.edu

From above information, I do not know where the error origins from.
I doubt that “0 atoms in group FixGCMC:gcmc_exclusion_group:fixgcmc” is a problem,

but I could not find out which subroutine or function caused it.

Can somebody show me a way to go?

Best wishes,

Yongbiao

2

From your potential energy it appears to me that a particle was inserted in a place where it had lots of overlap with another particle, so the system blew up. However, no one can be sure until you send your input script and data files, if any.

3

fix fixgcmc all gcmc 2 100 100 0 12345 300 10.0 0.01 mol

This is a µ of +10? Which units did you use?

Memory usage per processor = 16.5758 Mbytes
Time Temp PotEng TotEng Press Lx Ly Lz Density
            0 236.87453 -96794.099 -84540.115 16026.031
44.20913 46.083223 84.341044 1.3102596

At a volume of 44A x 44A x 80A, you have a "density"
of "1.3" at the very start, and then a µ of +10?

Without knowing exactly what you did here, nobody
can say what happens. We need:

  - water model template file
  - lammps input file
  - lammps version + operating system + computer (RAM amount)
  - full lammps output file

M.

4

One clarification:

0 atoms in group FixGCMC:gcmc_exclusion_group:fixgcmc
0 atoms in group FixGCMC:rotation_gas_atoms:fixgcmc

These are not error messages. If they were, they would be preceded by
an ERROR string, and there would be no more output. These messages
are just reporting that fix gcmc has created two new groups (see
group.cpp) which are empty. Later, fix gcmc will silently add and
remove atoms to and from them.

In fact, if those groups were created with more than zero atoms, that
would be bad.

Aidan