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)
  2 by 2 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 = 3380 960
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) = 10.6 | 10.61 | 10.61 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0            0   -16692.358            0   -16692.358   -1289.8319 
Loop time of 4.5e-06 on 4 procs for 0 steps with 4500 atoms


group		one molecule 1 2
6 atoms in group one

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

# compute pairwise force between two molecules and everybody
compute		fpa one group/group all pair yes kspace no boundary no
# tally pairwise force between two molecules and the all molecules
compute		c1 one force/tally all
# tally the force of all with all (should be zero)
compute		c2 all force/tally all
# collect per atom data. only reduce over the first group.
compute		one one reduce sum c_c1[1] c_c1[2] c_c1[3]
compute		red all reduce sum c_c2[1] c_c2[2] c_c2[3]
# determine magnitude of force
variable	fpa equal sqrt(c_fpa[1]*c_fpa[1]+c_fpa[2]*c_fpa[2]+c_fpa[3]*c_fpa[3])
variable	for equal sqrt(c_one[1]*c_one[1]+c_one[2]*c_one[2]+c_one[3]*c_one[3])
# round to 10**-10 absolute precision.
variable	ref equal round(1e10*sqrt(c_red[1]*c_red[1]+c_red[2]*c_red[2]+c_red[3]*c_red[3]))*1e-10
variable	all equal round(1e10*c_c2)*1e-10

velocity	all create 300 432567 dist uniform

timestep	2.0

# v_fpa and v_for and c_c1, c_fpa[] and c_one[] should all each have the same value. v_ref and c_c2 should be zero
thermo_style    custom step v_fpa v_for c_c1 c_fpa[1] c_one[1] c_fpa[2] c_one[2] c_fpa[3] c_one[3] v_ref v_all
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 = 3380 960
WARNING: Compute force/tally only called from pair style (../compute_force_tally.cpp:77)
WARNING: Compute force/tally only called from pair style (../compute_force_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) = 11.58 | 11.59 | 11.6 Mbytes
Step v_fpa v_for c_c1 c_fpa[1] c_one[1] c_fpa[2] c_one[2] c_fpa[3] c_one[3] v_ref v_all 
       0      22.7331      22.7331      22.7331   -17.068295   -17.068295   -8.8348335   -8.8348334   -12.141369   -12.141369            0            0 
      10    11.736901    11.736901    11.736901   -3.3897029   -3.3897029    9.1193856    9.1193856   -6.5651786   -6.5651786            0            0 
      20    5.6120339    5.6120339    5.6120339  -0.60046861  -0.60046861   -4.4481306   -4.4481306    3.3687528    3.3687528            0            0 
      30     17.29261     17.29261     17.29261     6.179302     6.179302   -10.593979   -10.593979    12.190906    12.190906            0            0 
      40    18.664433    18.664433    18.664433    5.4727782    5.4727782   -6.9329319   -6.9329319    16.442148    16.442148            0            0 
      50    12.130407    12.130407    12.130407   -1.0321196   -1.0321196    8.0035558    8.0035558   -9.0567428   -9.0567428            0            0 
Loop time of 4.31614 on 4 procs for 50 steps with 4500 atoms

Performance: 2.002 ns/day, 11.989 hours/ns, 11.584 timesteps/s
31.6% CPU use with 4 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 3.5075     | 3.6114     | 3.7489     |   4.7 | 83.67
Bond    | 8.6e-05    | 0.00010525 | 0.000141   |   0.0 |  0.00
Kspace  | 0.2581     | 0.39489    | 0.49723    |  14.2 |  9.15
Neigh   | 0.19826    | 0.19888    | 0.19918    |   0.1 |  4.61
Comm    | 0.034639   | 0.037137   | 0.038938   |   0.9 |  0.86
Output  | 0.025465   | 0.025997   | 0.027558   |   0.6 |  0.60
Modify  | 0.044022   | 0.044175   | 0.044407   |   0.1 |  1.02
Other   |            | 0.003593   |            |       |  0.08

Nlocal:    1125 ave 1148 max 1097 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Nghost:    12212.5 ave 12269 max 12162 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Neighs:    650496 ave 675112 max 631353 min
Histogram: 1 0 0 1 1 0 0 0 0 1

Total # of neighbors = 2601983
Ave neighs/atom = 578.218
Ave special neighs/atom = 2
Neighbor list builds = 4
Dangerous builds = 1

Total wall time: 0:00:04
