LAMMPS (8 Feb 2023)
# QMMM with PySCF

units           real
atom_style      full

pair_style      lj/cut/coul/long 12
pair_modify     mix arithmetic

bond_style      harmonic
angle_style     harmonic
dihedral_style  none
improper_style  none

kspace_style    pppm 1e-5

read_data       data.water
Reading data file ...
  orthogonal box = (0 0 0) to (31.351877 31.351877 31.351877)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  6 atoms
  scanning bonds ...
  2 = max bonds/atom
  scanning angles ...
  1 = max angles/atom
  reading bonds ...
  4 bonds
  reading angles ...
  2 angles
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     2 = max # of 1-2 neighbors
     1 = max # of 1-3 neighbors
     1 = max # of 1-4 neighbors
     2 = max # of special neighbors
  special bonds CPU = 0.000 seconds
  read_data CPU = 0.004 seconds

# QM atoms are 1st water
# MM atoms are 2nd water

group           qm molecule 1
3 atoms in group qm
group           mm molecule 2
3 atoms in group mm

# remove bonds/angles between QM atoms
# set charges to zero on QM atoms

delete_bonds    qm multi remove special
System init for delete_bonds ...
PPPM initialization ...
  using 12-bit tables for long-range coulomb (../kspace.cpp:342)
  G vector (1/distance) = 0.21131887
  grid = 12 12 12
  stencil order = 5
  estimated absolute RMS force accuracy = 0.0020500128
  estimated relative force accuracy = 6.1735526e-06
  using double precision KISS FFT
  3d grid and FFT values/proc = 4913 1728
Generated 1 of 1 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 = 14
  ghost atom cutoff = 14
  binsize = 7, bins = 5 5 5
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut/coul/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
Deleting bonds ...
  2 total bonds, 2 turned on, 0 turned off
  1 total angles, 1 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       
     2 = max # of 1-2 neighbors
     1 = max # of 1-3 neighbors
     1 = max # of 1-4 neighbors
     2 = max # of special neighbors
  special bonds CPU = 0.000 seconds
set             group qm charge 0.0
Setting atom values ...
  3 settings made for charge

neighbor        2.0 bin
neigh_modify    delay 0 every 1 check yes

velocity        all create 300.0 87287 loop geom

# QMMM dynamics

timestep        2.0

fix		1 all nve

fix             2 qm mdi/qmmm direct elements O H
fix_modify      2 energy yes

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

thermo          1

mdi             plugin pyscf_mdi mdi "-role ENGINE -name PySCF -method LINK"                 extra "-pbc no" command "run 10"
run 10
PPPM initialization ...
  using 12-bit tables for long-range coulomb (../kspace.cpp:342)
  G vector (1/distance) = 0.19767375
  grid = 10 10 10
  stencil order = 5
  estimated absolute RMS force accuracy = 0.0022851662
  estimated relative force accuracy = 6.8817102e-06
  using double precision KISS FFT
  3d grid and FFT values/proc = 3375 1000
Generated 1 of 1 mixed pair_coeff terms from arithmetic mixing rule
Per MPI rank memory allocation (min/avg/max) = 7.165 | 7.165 | 7.165 Mbytes
   Step          CPU            Temp          KinEng         E_vdwl         E_coul         E_pair         E_mol          E_long          f_2           PotEng         TotEng         Press     
         0   0              300            4.4712151     -0.001256507    37.096223     -0.0091688448   0.95028479    -37.104135     -47941.423     -47940.482     -47936.011     -5.0247548    
         1   0.59760243     513.16171      7.648188      -0.0012517531   37.10766      -0.0088283103   1.3202413     -37.115237     -47947.2       -47945.888     -47938.24      -15.573297    
         2   1.204872       476.87504      7.1073695     -0.0012428971   37.140547     -0.0078675595   0.14078812    -37.147172     -47942.073     -47941.94      -47934.833      14.589499    
         3   1.8094932      552.16501      8.229495      -0.0012247602   37.169663     -0.0070877422   0.97249224    -37.175526     -47943.52      -47942.554     -47934.325      32.307141    
         4   2.6730646      311.7073       4.6457012     -0.001214705    37.181636     -0.0067643983   0.92481745    -37.187186     -47938.682     -47937.764     -47933.119      0.56843394   
         5   3.4516113      545.29533      8.127109      -0.0012142012   37.183759     -0.0065649511   1.9626978     -37.18911      -47947.023     -47945.067     -47936.939     -16.524321    
         6   4.0565551      471.76402      7.0311947     -0.0012147223   37.184705     -0.0063050524   1.0470598     -37.189795     -47935.826     -47934.786     -47927.754      6.8723453    
         7   4.7426982      920.71341      13.722359     -0.0012039124   37.17538      -0.0062927565   1.1513661     -37.180469     -47936.811     -47935.666     -47921.944      41.323731    
         8   5.3861659      371.4235       5.5357146     -0.0012015277   37.147481     -0.0067304894   0.30070096    -37.15301      -47926.094     -47925.8       -47920.265      9.8713378    
         9   6.0325824      1313.1205      19.570814     -0.0012060836   37.113576     -0.0073073482   0.92112803    -37.119677     -47946.778     -47945.865     -47926.294      0.79522299   
        10   6.6889764      1925.2824      28.694506     -0.0012122896   37.098911     -0.0073851866   1.0565498     -37.105084     -47893.125     -47892.076     -47863.381      31.561426    
Loop time of 6.68899 on 1 procs for 10 steps with 6 atoms

Performance: 0.258 ns/day, 92.903 hours/ns, 1.495 timesteps/s, 8.970 atom-step/s
97.9% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 3.6715e-05 | 3.6715e-05 | 3.6715e-05 |   0.0 |  0.00
Bond    | 3.2015e-05 | 3.2015e-05 | 3.2015e-05 |   0.0 |  0.00
Kspace  | 0.0011869  | 0.0011869  | 0.0011869  |   0.0 |  0.02
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 2.1429e-05 | 2.1429e-05 | 2.1429e-05 |   0.0 |  0.00
Output  | 0.00027662 | 0.00027662 | 0.00027662 |   0.0 |  0.00
Modify  | 6.6874     | 6.6874     | 6.6874     |   0.0 | 99.98
Other   |            | 2.116e-05  |            |       |  0.00

Nlocal:              6 ave           6 max           6 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:             42 ave          42 max          42 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:             15 ave          15 max          15 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 15
Ave neighs/atom = 2.5
Ave special neighs/atom = 1
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:07
