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 2e-06 on 1 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 stress/tally compute and other computes and thermo keywords

# compute per atom stress contributions
compute		spa all stress/atom NULL pair
compute		press all pressure NULL pair
# compute stress contributions from one group with all
compute		c1 one stress/tally all
# collect stress contributions from all with all
compute		c2 all stress/tally all
compute		one one reduce sum c_c1[1] c_c1[2] c_c1[3] c_spa[1] c_spa[2] c_spa[3]
compute		red all reduce sum c_spa[1] c_spa[2] c_spa[3] c_c2[1] c_c2[2] c_c2[3]
#
variable	spa equal -(c_red[1]+c_red[2]+c_red[3])/(3.0*vol)
variable	press equal -(c_red[4]+c_red[5]+c_red[6])/(3.0*vol)
variable	one equal (c_one[1]+c_one[2]+c_one[3])/3.0
variable	ref equal (c_one[4]+c_one[5]+c_one[6])/3.0

#velocity	all create 300 432567 dist uniform

timestep	2.0

thermo_style    custom step c_press v_spa v_press v_one v_ref
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 stress/tally only called from pair style (../compute_stress_tally.cpp:79)
WARNING: Compute stress/tally only called from pair style (../compute_stress_tally.cpp:79)
Per MPI rank memory allocation (min/avg/max) = 35.9 | 35.9 | 35.9 Mbytes
Step c_press v_spa v_press v_one v_ref 
       0    26496.811    26496.811    26496.811   -2356992.7   -2356992.7 
      10    23665.129    23665.129    23665.129     -2096059     -2096059 
      20    23338.197    23338.197    23338.197   -2034284.1   -2034284.1 
      30    25946.434    25946.434    25946.434   -2002815.3   -2002815.3 
      40    27238.374    27238.374    27238.374   -2155408.7   -2155408.7 
      50    27783.107    27783.107    27783.107   -1862191.5   -1862191.5 
Loop time of 14.2089 on 1 procs for 50 steps with 4500 atoms

Performance: 0.608 ns/day, 39.469 hours/ns, 3.519 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    | 12.983     | 12.983     | 12.983     |   0.0 | 91.37
Bond    | 0.002788   | 0.002788   | 0.002788   |   0.0 |  0.02
Kspace  | 0.62745    | 0.62745    | 0.62745    |   0.0 |  4.42
Neigh   | 0.49839    | 0.49839    | 0.49839    |   0.0 |  3.51
Comm    | 0.018597   | 0.018597   | 0.018597   |   0.0 |  0.13
Output  | 0.015852   | 0.015852   | 0.015852   |   0.0 |  0.11
Modify  | 0.058415   | 0.058415   | 0.058415   |   0.0 |  0.41
Other   |            | 0.004126   |            |       |  0.03

Nlocal:    4500 ave 4500 max 4500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    21226 ave 21226 max 21226 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    2.60175e+06 ave 2.60175e+06 max 2.60175e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 2601750
Ave neighs/atom = 578.167
Ave special neighs/atom = 2
Neighbor list builds = 3
Dangerous builds = 0

Total wall time: 0:00:15
