LAMMPS (24 Jul 2017)
  using 1 OpenMP thread(s) per MPI task
units metal
atom_style full
boundary p p p
timestep 0.0001 # 0.1 fs

read_data methane-box-8.data
  orthogonal box = (-0.499095 -0.270629 0.131683) to (8.4109 8.63937 9.04168)
  1 by 2 by 2 MPI processor grid
  reading atoms ...
  40 atoms
  scanning bonds ...
  4 = max bonds/atom
  scanning angles ...
  6 = max angles/atom
  reading bonds ...
  32 bonds
  reading angles ...
  48 angles
  4 = max # of 1-2 neighbors
  3 = max # of 1-3 neighbors
  3 = max # of 1-4 neighbors
  4 = max # of special neighbors

# DISCLAIMER: This potential mixes parameters from methane and silane
# potentials and is NOT intended to be a realistic representation of either
# system.  It is meant to demonstrate the use of hybrid QUIP/LAMMPS potentials,
# including the use of separate 'special_bonds' settings.

pair_style hybrid/overlay lj/cut 8.0 quip

# exclusion setting for quip; cannot be exactly 1.0 1.0 1.0,
# since that would not flag 1-2, 1-3, and 1-4 pairs in lj/cut
special_bonds lj/coul 0.999999999 0.999999999 0.999999999
  4 = max # of 1-2 neighbors
  3 = max # of 1-3 neighbors
  3 = max # of 1-4 neighbors
  4 = max # of special neighbors

# Intermolecular: OPLS (JACS 118 (45), p. 11225 (1996))
# Coulomb interactions ommitted for simplicity
pair_coeff 1 1 lj/cut 0.0028619844 3.5 # CT
pair_coeff 2 2 lj/cut 0.0013009018 2.5 # HC
pair_coeff 1 2 lj/cut 0.0019295487 2.95
pair_modify shift no
# change exclusion settings for lj/cut only: exclude bonded pairs
pair_modify pair lj/cut special lj/coul 0.0 0.0 0.0

# Intramolecular
# Tell QUIP to pretend this is silane (which is covered by the parameter file)
pair_coeff * * quip sw_example.xml "IP SW" 14 1
bond_style none
angle_style none

fix 1 all nve

# Include diagnostics that allow us to compare to a pure QUIP run
compute equip all pair quip
compute evdw all pair lj/cut
compute vir all pressure NULL virial

thermo_style custom step epair ke etotal temp press c_vir c_evdw c_equip
thermo 1

# dump 1 all custom 1 dump.molecular id type x y z fx fy fz
# dump_modify 1 sort id

run 10
Neighbor list info ...
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 10
  ghost atom cutoff = 10
  binsize = 5, bins = 2 2 2
  2 neighbor lists, perpetual/occasional/extra = 2 0 0
  (1) pair lj/cut, perpetual, half/full from (2)
      attributes: half, newton on
      pair build: halffull/newton
      stencil: none
      bin: none
  (2) pair quip, perpetual
      attributes: full, newton on
      pair build: full/bin
      stencil: full/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 8.26 | 8.386 | 8.762 Mbytes
Step E_pair KinEng TotEng Temp Press c_vir c_evdw c_equip 
       0   -5.3530213            0   -5.3530213            0    518847.56    518847.56  -0.10904079   -5.2439805 
       1   -5.9384459   0.58384822   -5.3545977    115.81657     517370.5    516488.87  -0.10783656   -5.8306093 
       2    -7.669616    2.3104051   -5.3592109    458.30954    512986.36    509497.58  -0.10422283   -7.5653932 
       3   -10.473314    5.1069211   -5.3663924    1013.0477    505833.04    498121.43 -0.098049469   -10.375264 
       4   -14.234705     8.859182   -5.3755227    1757.3747    496127.44    482749.79 -0.089147485   -14.145557 
       5   -18.806851    13.420941   -5.3859098      2662.28    484148.76    463882.72 -0.077305196   -18.729546 
       6   -24.021727    18.625147   -5.3965797    3694.6259    470219.95    442095.39  -0.06194509   -23.959782 
       7   -29.702647    24.295529   -5.4071176     4819.446    454683.57    417996.56 -0.042859727   -29.659787 
       8    -35.67405    30.257258   -5.4167913    6002.0599    437887.03    392197.62 -0.019248651   -35.654801 
       9   -41.771047    36.345757   -5.4252893    7209.8209    420163.51    365280.27 0.0096063065   -41.780653 
      10   -47.845522    42.413161   -5.4323614    8413.3973    401821.91     337776.7  0.044743702   -47.890266 
Loop time of 0.0506847 on 4 procs for 10 steps with 40 atoms

Performance: 1.705 ns/day, 14.079 hours/ns, 197.298 timesteps/s
94.4% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.04216    | 0.045656   | 0.049349   |   1.2 | 90.08
Bond    | 1.9073e-06 | 2.4438e-06 | 2.861e-06  |   0.0 |  0.00
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.00068545 | 0.004438   | 0.0079191  |   3.9 |  8.76
Output  | 0.00048304 | 0.00053334 | 0.00060964 |   0.0 |  1.05
Modify  | 1.1444e-05 | 1.4424e-05 | 1.9312e-05 |   0.0 |  0.03
Other   |            | 4.047e-05  |            |       |  0.08

Nlocal:    10 ave 15 max 6 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Nghost:    878 ave 948 max 812 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs:    1192 ave 1764 max 731 min
Histogram: 1 0 0 1 1 0 0 0 0 1
FullNghs:  2384 ave 3527 max 1439 min
Histogram: 1 0 0 1 1 0 0 0 0 1

Total # of neighbors = 9536
Ave neighs/atom = 238.4
Ave special neighs/atom = 4
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00
