LAMMPS (19 May 2017)

units		real
atom_style	full

read_data	data.spce
  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
  reading bonds ...
  3000 bonds
  reading angles ...
  1500 angles
  2 = max # of 1-2 neighbors
  1 = max # of 1-3 neighbors
  1 = max # of 1-4 neighbors
  2 = max # of special neighbors

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
  2 = max # of 1-2 neighbors
  1 = max # of 1-3 neighbors
  2 = max # of special neighbors

neighbor        2.0 bin

fix		1 all shake 0.0001 20 0 b 1 a 1
  0 = # of size 2 clusters
  0 = # of size 3 clusters
  0 = # of size 4 clusters
  1500 = # of frozen angles
fix		2 all nvt temp 300.0 300.0 100.0

# make certain that shake constraints are satisfied
run 0 post no
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
  G vector (1/distance) = 0.218482
  grid = 15 15 15
  stencil order = 5
  estimated absolute RMS force accuracy = 0.0319435
  estimated relative force accuracy = 9.61968e-05
  using double precision FFTs
  3d grid and FFT values/proc = 8000 3375
Neighbor list info ...
  update every 1 steps, delay 10 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/newton
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 26.54 | 26.54 | 26.54 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0            0   -16692.358            0   -16692.358   -1289.8319 
Loop time of 1e-06 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 ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
  G vector (1/distance) = 0.218482
  grid = 15 15 15
  stencil order = 5
  estimated absolute RMS force accuracy = 0.0319435
  estimated relative force accuracy = 9.61968e-05
  using double precision FFTs
  3d grid and FFT values/proc = 8000 3375
WARNING: Compute pe/tally only called from pair style (../compute_pe_tally.cpp:77)
WARNING: Compute pe/tally only called from pair style (../compute_pe_tally.cpp:77)
Neighbor list info ...
  update every 1 steps, delay 10 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/newton
      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) = 29.08 | 29.08 | 29.08 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   -516828.05   -516828.05    3101.4373    3101.4373    45884.156    45884.156    48985.594    48985.594    48985.594    48985.594 
      30   -517032.07   -517032.07    3198.5951    3198.5951    45793.595    45793.595    48992.191    48992.191    48992.191    48992.191 
      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    3274.9097    3274.9097    45666.025    45666.025    48940.935    48940.935    48940.935    48940.935 
Loop time of 15.3339 on 1 procs for 50 steps with 4500 atoms

Performance: 0.563 ns/day, 42.594 hours/ns, 3.261 timesteps/s
32.0% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 13.432     | 13.432     | 13.432     |   0.0 | 87.60
Bond    | 0.000365   | 0.000365   | 0.000365   |   0.0 |  0.00
Kspace  | 0.581      | 0.581      | 0.581      |   0.0 |  3.79
Neigh   | 0.66081    | 0.66081    | 0.66081    |   0.0 |  4.31
Comm    | 0.019908   | 0.019908   | 0.019908   |   0.0 |  0.13
Output  | 0.57731    | 0.57731    | 0.57731    |   0.0 |  3.76
Modify  | 0.058515   | 0.058515   | 0.058515   |   0.0 |  0.38
Other   |            | 0.003889   |            |       |  0.03

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 = 578.218
Ave special neighs/atom = 2
Neighbor list builds = 4
Dangerous builds = 1

Total wall time: 0:00:16
