LAMMPS (8 Feb 2023)
# QMMM for SiO2 zeolite with one methane molecule

units		metal
atom_style	full

bond_style      harmonic
angle_style     harmonic

read_data       data.zeolite
Reading data file ...
  orthogonal box = (-5.9266 -5.9266 -5.9266) to (5.9926 5.9926 5.9926)
  2 by 2 by 2 MPI processor grid
  reading atoms ...
  77 atoms
  scanning bonds ...
  4 = max bonds/atom
  scanning angles ...
  6 = max angles/atom
  reading bonds ...
  4 bonds
  reading angles ...
  6 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
     3 = max # of 1-3 neighbors
     3 = max # of 1-4 neighbors
     4 = max # of special neighbors
  special bonds CPU = 0.000 seconds
  read_data CPU = 0.005 seconds

# MM atoms are Si,O
# QM atoms are C,H

group           mm type 1 2
72 atoms in group mm
group           qm type 3 4
5 atoms in group qm

# pair style must define stand-alone short-range Coulombics
# must specify mixing explicitly b/c hybrid/overlay
# MM Si,O = types 1,2
# QM C,H = types 3,4
# MM Si,O atoms do not LJ interact with each other (just via Buckingham)
# QM C,H atoms do not LJ interact with each other
# MM Si,O and QM C,H do LJ interact with each other

pair_style      hybrid/overlay buck 6.5 lj/cut 6.5 coul/cut 6.5

pair_coeff      1 1 buck 3150.462646 0.35032282 626.7519553
pair_coeff      2 2 buck 659.595398 0.38609055 26.836679
pair_coeff      1 2 buck 27029.419922 0.19385082 148.099091

pair_coeff      1 3 lj/cut 0.09087 3.613
pair_coeff      1 4 lj/cut 0.0344258 3.238
pair_coeff      2 3 lj/cut 0.1419429 3.1
pair_coeff      2 4 lj/cut 0.035857762359063315 1.932779  # same as water

pair_coeff      3 3 lj/cut 0.0 3.4
pair_coeff      4 4 lj/cut 0.0 2.65
pair_coeff      * * coul/cut

bond_style      harmonic
bond_coeff      1 29.40 1.09

angle_style     harmonic
angle_coeff     1 0.172325 109.5

# remove bonds/angles in QM methane molecule

delete_bonds    qm multi remove special
System init for delete_bonds ...
Generated 0 of 6 mixed pair_coeff terms from geometric 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 = 8.5
  ghost atom cutoff = 8.5
  binsize = 4.25, bins = 3 3 3
  3 neighbor lists, perpetual/occasional/extra = 3 0 0
  (1) pair buck, perpetual, skip from (3)
      attributes: half, newton on
      pair build: skip
      stencil: none
      bin: none
  (2) pair lj/cut, perpetual, skip from (3)
      attributes: half, newton on
      pair build: skip
      stencil: none
      bin: none
  (3) pair coul/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
Deleting bonds ...
  0 total bonds, 0 turned on, 0 turned off
  0 total angles, 0 turned on, 0 turned off
  0 total dihedrals, 0 turned on, 0 turned off
  0 total impropers, 0 turned on, 0 turned off
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     0 = max # of 1-2 neighbors
     0 = max # of 1-3 neighbors
     0 = max # of 1-4 neighbors
     4 = max # of special neighbors
  special bonds CPU = 0.000 seconds

neighbor	1.0 bin
neigh_modify	delay 0 every 1 check yes

velocity        all create 300.0 458732

# QMMM dynamics with small timestep
# dynamic or frozen zeolite

#fix		1 all nve
fix		1 qm nve

fix             2 qm mdi/qmmm potential elements Si O C H
fix_modify      2 energy yes

timestep        0.0001

thermo_style    custom step cpu temp ke evdwl ecoul epair emol elong                 f_2 pe etotal press
thermo          1

variable        p equal extract_setting(world_size)

mdi             plugin nwchem_mdi mdi "-role ENGINE -name NWChem -method LINK"                 extra "template.methane.nw methane.nw log.zeolite.pwdft.qmmm.plugin.$p"                 command "run 2"
run 2
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 9.612 | 9.612 | 9.612 Mbytes
   Step          CPU            Temp          KinEng         E_vdwl         E_coul         E_pair         E_mol          E_long          f_2           PotEng         TotEng         Press     
         0   0              300            2.9471313     -106.25003     -1065.0366     -1171.2866      0              0             -198.982       -1370.2686     -1367.3215     -636.59012    
         1   9.4846618      299.91213      2.9462681     -106.24961     -1065.1058     -1171.3554      0              0             -198.9099      -1370.2653     -1367.3191     -659.4798     
         2   18.971154      299.81516      2.9453155     -106.24919     -1065.1818     -1171.431       0              0             -198.83143     -1370.2624     -1367.3171     -684.54277    
Loop time of 18.9712 on 8 procs for 2 steps with 77 atoms

Performance: 0.001 ns/day, 26348.886 hours/ns, 0.105 timesteps/s, 8.118 atom-step/s
97.2% CPU use with 8 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 3.8009e-05 | 7.1162e-05 | 0.00014671 |   0.0 |  0.00
Bond    | 2.484e-06  | 2.9337e-06 | 3.884e-06  |   0.0 |  0.00
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 7.6395e-05 | 0.00015395 | 0.00018947 |   0.0 |  0.00
Output  | 8.145e-05  | 8.6522e-05 | 0.00010329 |   0.0 |  0.00
Modify  | 18.971     | 18.971     | 18.971     |   0.0 |100.00
Other   |            | 4.276e-05  |            |       |  0.00

Nlocal:          9.625 ave          20 max           3 min
Histogram: 1 2 1 0 1 2 0 0 0 1
Nghost:        426.375 ave         434 max         415 min
Histogram: 1 0 0 0 3 0 0 2 1 1
Neighs:         393.25 ave         941 max         132 min
Histogram: 2 2 0 1 2 0 0 0 0 1

Total # of neighbors = 3146
Ave neighs/atom = 40.857143
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:54
