LAMMPS (12 Jun 2025 - Development - patch_12Jun2025-739-g2644e7f6fa-modified)
  using 1 OpenMP thread(s) per MPI task

units		real
atom_style	full

read_data	data.spce
Reading data file ...
  orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  4500 atoms
  scanning bonds ...
  2 = max bonds/atom
  scanning angles ...
  1 = max angles/atom
  orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
  1 by 1 by 1 MPI processor grid
  reading bonds ...
  3000 bonds
  reading angles ...
  1500 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 = 0.001 seconds
  read_data CPU = 0.016 seconds

pair_style	lj/cut/coul/long 12.0 12.0
kspace_style	pppm 1.0e-4

pair_coeff	1 1 0.15535 3.166
pair_coeff	* 2 0.0000 0.0000

bond_style	harmonic
angle_style	harmonic
dihedral_style	none
improper_style	none

bond_coeff	1 1000.00 1.000
angle_coeff	1 100.0 109.47

special_bonds   lj/coul 0.0 0.0 1.0
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        1       
  special bond factors coul:  0        0        1       
     2 = max # of 1-2 neighbors
     1 = max # of 1-3 neighbors
     2 = max # of special neighbors
  special bonds CPU = 0.000 seconds

neighbor        2.0 bin

fix		1 all shake 0.0001 20 0 b 1 a 1
Finding SHAKE clusters ...
       0 = # of size 2 clusters
       0 = # of size 3 clusters
       0 = # of size 4 clusters
    1500 = # of frozen angles
  find clusters CPU = 0.001 seconds
fix		2 all nvt temp 300.0 300.0 100.0

# make certain that shake constraints are satisfied
run 0 post no
PPPM initialization ...
  using 12-bit tables for long-range coulomb
  G vector (1/distance) = 0.21848247
  grid = 15 15 15
  stencil order = 5
  estimated absolute RMS force accuracy = 0.031943453
  estimated relative force accuracy = 9.619676e-05
  using double precision FFTW3
  3d grid and FFT values/proc = 8000 3375
Generated 0 of 1 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 = 14
  ghost atom cutoff = 14
  binsize = 7, bins = 6 6 6
  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
Per MPI rank memory allocation (min/avg/max) = 26.81 | 26.81 | 26.81 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
         0   0             -16692.358      0             -16692.358     -1289.8319    
Loop time of 7.41e-07 on 1 procs for 0 steps with 4500 atoms


group		oxy type 1
1500 atoms in group oxy
group		hyd type 2
3000 atoms in group hyd

# the following section shows equivalences between using the pe/tally compute and other computes and thermo keywords

# compute pairwise energy between all oxygen and all hydrogen
compute		epa oxy group/group hyd pair yes kspace no boundary no
# tally pairwise energy between all oygen and all hydrogen
compute		c1 oxy pe/tally hyd
# tally pairwise energy between all atoms to compare with globals
compute		c2 all pe/tally all
# collect per atom energies
compute		c3 all pe/atom pair
# reduce over the first group only the per-atom data is storing VDW and Coulomb separately...
compute		oxy oxy reduce sum c_c1[1] c_c1[2]
compute		red all reduce sum c_c2[1] c_c2[2] c_c3
# ... thus to get the same as compute group/group, we need to add the two
# ... and multiply by 2.0 since compute group/group sums the pair energy, while we collect only for the first group.
variable	epa equal 2.0*(c_oxy[1]+c_oxy[2])
# compute equivalent values to globals
variable	vdwl equal c_red[1]
variable	coul equal c_red[2]
variable	pe   equal c_red[3]
variable	pair equal v_vdwl+v_coul
variable	eref equal epair-elong

velocity	all create 300 432567 dist uniform

timestep	2.0

# c_epa and v_epa, evdwl and v_vdwl, ecoul and v_coul, and the last 4 columns each should have identical value
thermo_style    custom step c_epa v_epa evdwl v_vdwl ecoul v_coul v_eref v_pe c_c2 v_pair
thermo		10

run 50
PPPM initialization ...
  using 12-bit tables for long-range coulomb
  G vector (1/distance) = 0.21848247
  grid = 15 15 15
  stencil order = 5
  estimated absolute RMS force accuracy = 0.031943453
  estimated relative force accuracy = 9.619676e-05
  using double precision FFTW3
  3d grid and FFT values/proc = 8000 3375
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
WARNING: Compute pe/tally only called from pair style (src/TALLY/compute_pe_tally.cpp:75)
WARNING: Compute pe/tally only called from pair style (src/TALLY/compute_pe_tally.cpp:75)
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 = 6 6 6
  2 neighbor lists, perpetual/occasional/extra = 1 1 0
  (1) pair lj/cut/coul/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
  (2) compute group/group, occasional, copy from (1)
      attributes: half, newton on
      pair build: copy
      stencil: none
      bin: none
Per MPI rank memory allocation (min/avg/max) = 29.25 | 29.25 | 29.25 Mbytes
   Step         c_epa          v_epa          E_vdwl         v_vdwl         E_coul         v_coul         v_eref          v_pe           c_c2          v_pair    
         0  -516634.27     -516634.27      3169.9427      3169.9427      46212.482      46212.482      49382.425      49382.425      49382.425      49382.425    
        10  -517027.35     -517027.35      3099.1374      3099.1374      45891.866      45891.866      48991.003      48991.003      48991.003      48991.003    
        20  -516828.04     -516828.04      3101.4372      3101.4372      45884.157      45884.157      48985.594      48985.594      48985.594      48985.594    
        30  -517032.07     -517032.07      3198.5951      3198.5951      45793.595      45793.595      48992.19       48992.19       48992.19       48992.19     
        40  -517095.54     -517095.54      3244.0771      3244.0771      45715.292      45715.292      48959.369      48959.369      48959.369      48959.369    
        50  -517273.5      -517273.5       3274.9096      3274.9096      45666.026      45666.026      48940.935      48940.935      48940.935      48940.935    
Loop time of 1.36367 on 1 procs for 50 steps with 4500 atoms

Performance: 6.336 ns/day, 3.788 hours/ns, 36.666 timesteps/s, 164.996 katom-step/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 1.1034     | 1.1034     | 1.1034     |   0.0 | 80.91
Bond    | 7.8397e-05 | 7.8397e-05 | 7.8397e-05 |   0.0 |  0.01
Kspace  | 0.043099   | 0.043099   | 0.043099   |   0.0 |  3.16
Neigh   | 0.11547    | 0.11547    | 0.11547    |   0.0 |  8.47
Comm    | 0.0032449  | 0.0032449  | 0.0032449  |   0.0 |  0.24
Output  | 0.085627   | 0.085627   | 0.085627   |   0.0 |  6.28
Modify  | 0.011866   | 0.011866   | 0.011866   |   0.0 |  0.87
Other   |            | 0.000903   |            |       |  0.07

Nlocal:           4500 ave        4500 max        4500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:          21131 ave       21131 max       21131 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    2.60198e+06 ave 2.60198e+06 max 2.60198e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 2601983
Ave neighs/atom = 578.21844
Ave special neighs/atom = 2
Neighbor list builds = 4
Dangerous builds = 0

Total wall time: 0:00:01
