Non-numeric positions - simulation unstable after energy minimization step

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1

I trying to simulate a nano-battery system composed of graphene anode, V2O5 cathode, and 1 M Na2SO4 solution (in TIP4P water model) using Buckingham potential with long-range coulombic interactions. After the minimization step, its showing

Non-numeric positions - simulations unstable.

I have already checked for any overlapping atoms (check log file). However, I can’t seem to find the source of the problem.

Log file:

LAMMPS (2 Aug 2023)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/src/comm.cpp:98)
  using 1 OpenMP thread(s) per MPI task
Reading data file ...
  orthogonal box = (-21.009836 -21.003825 -48.74872) to (20.990164 20.996175 42.25128)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  6287 atoms
  scanning bonds ...
  4 = max bonds/atom
  scanning angles ...
  6 = max angles/atom
  reading bonds ...
  6143 bonds
  reading angles ...
  8413 angles
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     4 = max # of 1-2 neighbors
     6 = max # of 1-3 neighbors
    18 = max # of 1-4 neighbors
    18 = max # of special neighbors
  special bonds CPU = 0.004 seconds
  read_data CPU = 0.049 seconds
Setting atom values ...
  2016 settings made for charge
Setting atom values ...
  1008 settings made for charge
Setting atom values ...
  36 settings made for charge
Setting atom values ...
  18 settings made for charge
Setting atom values ...
  72 settings made for charge
1855 atoms in group anode
3024 atoms in group water
36 atoms in group cation
90 atoms in group anion
1282 atoms in group cathode
126 atoms in group salt
3150 atoms in group electrolyte
3137 atoms in group electrodes
System init for delete_atoms ...
PPPM initialization ...
  using 12-bit tables for long-range coulomb (src/src/kspace.cpp:342)
  G vector (1/distance) = 0.29432954
  grid = 36 36 100
  stencil order = 5
  estimated absolute RMS force accuracy = 0.0001410228
  estimated relative force accuracy = 9.7934916e-06
  using double precision MKL FFT
  3d grid and FFT values/proc = 171462 129600
Generated 0 of 28 mixed pair_coeff terms from arithmetic mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 10.1
  ghost atom cutoff = 10.1
  binsize = 5.05, bins = 9 9 19
  3 neighbor lists, perpetual/occasional/extra = 2 1 0
  (1) command delete_atoms, occasional
      attributes: full, newton on
      pair build: full/bin
      stencil: full/bin/3d
      bin: standard
  (2) pair coul/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
  (3) pair buck, perpetual, skip from (2)
      attributes: half, newton on
      pair build: skip
      stencil: none
      bin: none
WARNING: Ignoring 'compress yes' for molecular system (src/src/delete_atoms.cpp:140)
Deleted 0 atoms, new total = 6287
PPPM initialization ...
  using 12-bit tables for long-range coulomb (src/src/kspace.cpp:342)
  G vector (1/distance) = 0.29432954
  grid = 36 36 100
  stencil order = 5
  estimated absolute RMS force accuracy = 0.0001410228
  estimated relative force accuracy = 9.7934916e-06
  using double precision MKL FFT
  3d grid and FFT values/proc = 171462 129600
Generated 0 of 28 mixed pair_coeff terms from arithmetic mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 10.1
  ghost atom cutoff = 10.1
  binsize = 5.05, bins = 9 9 19
  2 neighbor lists, perpetual/occasional/extra = 2 0 0
  (1) pair coul/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
  (2) pair buck, perpetual, skip from (1)
      attributes: half, newton on
      pair build: skip
      stencil: none
      bin: none
Setting up cg style minimization ...
  Unit style    : metal
  Current step  : 0
Per MPI rank memory allocation (min/avg/max) = 32.58 | 32.58 | 32.58 Mbytes
   Step          Time           Temp          Press          E_pair         E_coul         PotEng         KinEng         TotEng    
         0   0              0              151.9199      -114.70089      4648.248       3199.1028      0              3199.1028    
        40   0.04           0             -2.2943969e+92 -1.0429624e+91 -8.9784382e+15 -1.0429624e+91  0             -1.0429624e+91
Loop time of 25.0864 on 1 procs for 40 steps with 6287 atoms

99.1% CPU use with 1 MPI tasks x 1 OpenMP threads

Minimization stats:
  Stopping criterion = quadratic factors are zero
  Energy initial, next-to-last, final = 
      3199.10281475069 -1.04296241988326e+91 -1.04296241988326e+91
  Force two-norm initial, final = 188.79558 8.9120925e+106
  Force max component initial, final = 6.7453597 5.6365022e+106
  Final line search alpha, max atom move = 4.0430971e-126 2.2788926e-19
  Iterations, force evaluations = 40 674

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 15.714     | 15.714     | 15.714     |   0.0 | 62.64
Bond    | 0.35178    | 0.35178    | 0.35178    |   0.0 |  1.40
Kspace  | 7.4434     | 7.4434     | 7.4434     |   0.0 | 29.67
Neigh   | 1.4666     | 1.4666     | 1.4666     |   0.0 |  5.85
Comm    | 0.030868   | 0.030868   | 0.030868   |   0.0 |  0.12
Output  | 0          | 0          | 0          |   0.0 |  0.00
Modify  | 0.024606   | 0.024606   | 0.024606   |   0.0 |  0.10
Other   |            | 0.05512    |            |       |  0.22

Nlocal:           6287 ave        6287 max        6287 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:           6312 ave        6312 max        6312 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:         598147 ave      598147 max      598147 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 598147
Ave neighs/atom = 95.140289
Ave special neighs/atom = 7.3618578
Neighbor list builds = 88
Dangerous builds = 42
Finding SHAKE clusters ...
       0 = # of size 2 clusters
       0 = # of size 3 clusters
       0 = # of size 4 clusters
    1008 = # of frozen angles
  find clusters CPU = 0.002 seconds
  create bodies CPU = 0.000 seconds
  18 rigid bodies with 90 atoms
  1.9243786 = max distance from body owner to body atom
PPPM initialization ...
  using 12-bit tables for long-range coulomb (src/src/kspace.cpp:342)
  G vector (1/distance) = 0.29432954
  grid = 36 36 100
  stencil order = 5
  estimated absolute RMS force accuracy = 0.0001410228
  estimated relative force accuracy = 9.7934916e-06
  using double precision MKL FFT
  3d grid and FFT values/proc = 171462 129600
Generated 0 of 28 mixed pair_coeff terms from arithmetic mixing rule
Setting up Verlet run ...
  Unit style    : metal
  Current step  : 0
  Time step     : 0.5
Per MPI rank memory allocation (min/avg/max) = 39.58 | 39.58 | 39.58 Mbytes
   Step          Time           Temp          Press          E_pair         E_coul         PotEng         KinEng         TotEng    
         0   0              0             -nan           -1.0429624e+91 -8.9784382e+15 -1.0429624e+91  0             -1.0429624e+91
ERROR on proc 0: Non-numeric atom coords - simulation unstable (src/src/domain.cpp:551)
Last command: run 10000

Thanks in advance.

2

This looks like your force field is not sufficient to represent your system. These kinds of energies only happen if oppositely charged atoms can come too close to each other, and that is almost always a deficiency of the force field. While there may not have been any close contacts before the minimization, there most likely are some after. Due to the “crazy” energies at the point (and forces are likely as bad), anything beyond is off the chart and that LAMMPS crashes is to be expected. You must not even come this far.

There was a report of a similar issue recently in Particle's distance vector flipps during minimization causing unrealistic Energy error (lost bond atoms) - #9 by akohlmey

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