LAMMPS (21 Aug 2015-ICMS)
  using 1 OpenMP thread(s) per MPI task

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

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 beween 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 ...
  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:75)
WARNING: Compute pe/tally only called from pair style (../compute_pe_tally.cpp:75)
Neighbor list info ...
  2 neighbor list requests
  update every 1 steps, delay 10 steps, check yes
  master list distance cutoff = 14
  ghost atom cutoff = 14
  binsize = 7 -> bins = 6 6 6
Memory usage per processor = 17.381 Mbytes
Step epa epa E_vdwl vdwl E_coul coul eref pe c2 pair 
       0   -516632.19   -516632.19    3169.9382    3169.9382    46213.889    46213.889    49383.827    49383.827    49383.827    49383.827 
      10   -517027.36   -517027.36    3099.1322    3099.1322     45891.84     45891.84    48990.972    48990.972    48990.972    48990.972 
      20   -516828.06   -516828.06    3101.4321    3101.4321     45884.14     45884.14    48985.572    48985.572    48985.572    48985.572 
      30    -517032.1    -517032.1    3198.5939    3198.5939    45793.571    45793.571    48992.165    48992.165    48992.165    48992.165 
      40   -517095.56   -517095.56    3244.0797    3244.0797    45715.265    45715.265    48959.345    48959.345    48959.345    48959.345 
      50   -517273.54   -517273.54    3274.9142    3274.9142    45665.997    45665.997    48940.911    48940.911    48940.911    48940.911 

Loop time of 4.31105 on 1 procs for 50 steps with 4500 atoms
100.1% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 2.004 ns/day  11.975 hours/ns  11.598 timesteps/s

MPI task timings breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 3.5071     | 3.5071     | 3.5071     |   0.0 | 81.35
Bond    | 0.00025034 | 0.00025034 | 0.00025034 |   0.0 |  0.01
Kspace  | 0.19991    | 0.19991    | 0.19991    |   0.0 |  4.64
Neigh   | 0.31459    | 0.31459    | 0.31459    |   0.0 |  7.30
Comm    | 0.010338   | 0.010338   | 0.010338   |   0.0 |  0.24
Output  | 0.24722    | 0.24722    | 0.24722    |   0.0 |  5.73
Modify  | 0.029466   | 0.029466   | 0.029466   |   0.0 |  0.68
Other   |            | 0.002182   |            |       |  0.05

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 = 2601984
Ave neighs/atom = 578.219
Ave special neighs/atom = 2
Neighbor list builds = 4
Dangerous builds = 1

Total wall time: 0:00:04
