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lammps/examples/USER/tally/log.pe
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log.pe
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LAMMPS (19 Aug 2015-ICMS)
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
compute spa all group/group all pair yes kspace no boundary no
compute c1 all pe/tally all
compute c2 all pe/tally all
compute red all reduce sum c_c1[1] c_c1[2]
variable ref equal c_spa
variable new equal c_red[1]+c_red[2]
velocity all create 300 432567 dist uniform
timestep 2.0
thermo_style custom step c_c1 v_ref v_new evdwl c_red[1] ecoul c_red[2]
thermo 10
run 0 post no
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 = 3380 960
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 = 7.91441 Mbytes
Step c1 ref new E_vdwl red[1] E_coul red[2]
0 49383.827 49383.827 49383.827 3169.9382 3169.9382 46213.889 46213.889
Loop time of 4.11272e-06 on 4 procs for 0 steps with 4500 atoms
139.8% CPU use with 4 MPI tasks x 1 OpenMP threads
compute c3 all force/tally all
run 1 post no
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 = 3380 960
Memory usage per processor = 8.28941 Mbytes
Step c1 ref new E_vdwl red[1] E_coul red[2]
0 49383.827 49383.827 49383.827 3169.9382 3169.9382 46213.889 46213.889
1 49365.483 49365.483 49365.483 3171.0414 3171.0414 46194.441 46194.441
Loop time of 0.0763347 on 4 procs for 1 steps with 4500 atoms
99.6% CPU use with 4 MPI tasks x 1 OpenMP threads
run 1 pre no post no
Step c1 ref new E_vdwl red[1] E_coul red[2]
1 49365.483 49365.483 49365.483 3171.0414 3171.0414 46194.441 46194.441
2 49307.805 49307.805 49307.805 3168.7564 3168.7564 46139.048 46139.048
Loop time of 0.0765384 on 4 procs for 1 steps with 4500 atoms
99.9% CPU use with 4 MPI tasks x 1 OpenMP threads
uncompute c2
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 = 3380 960
Memory usage per processor = 8.03941 Mbytes
Step c1 ref new E_vdwl red[1] E_coul red[2]
2 49307.805 49307.805 49307.805 3168.7564 3168.7564 46139.048 46139.048
10 48990.971 48990.971 48990.971 3099.1318 3099.1318 45891.84 45891.84
20 48985.572 48985.572 48985.572 3101.4315 3101.4315 45884.14 45884.14
30 48992.165 48992.165 48992.165 3198.5934 3198.5934 45793.572 45793.572
40 48959.345 48959.345 48959.345 3244.0794 3244.0794 45715.265 45715.265
50 48940.911 48940.911 48940.911 3274.914 3274.914 45665.997 45665.997
52 48932.17 48932.17 48932.17 3286.0828 3286.0828 45646.087 45646.087
Loop time of 1.27406 on 4 procs for 50 steps with 4500 atoms
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 6.781 ns/day 3.539 hours/ns 39.245 timesteps/s
MPI task timings breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.89947 | 0.92249 | 0.95576 | 2.3 | 72.41
Bond | 3.9577e-05 | 5.722e-05 | 7.1049e-05 | 0.2 | 0.00
Kspace | 0.053049 | 0.08673 | 0.10975 | 7.7 | 6.81
Neigh | 0.086173 | 0.08629 | 0.086357 | 0.0 | 6.77
Comm | 0.018853 | 0.019288 | 0.019644 | 0.2 | 1.51
Output | 0.13525 | 0.13527 | 0.13531 | 0.0 | 10.62
Modify | 0.022116 | 0.022266 | 0.022429 | 0.1 | 1.75
Other | | 0.001671 | | | 0.13
Nlocal: 1125 ave 1144 max 1101 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Nghost: 12211.5 ave 12265 max 12156 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs: 650512 ave 673213 max 632948 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 2602049
Ave neighs/atom = 578.233
Ave special neighs/atom = 2
Neighbor list builds = 4
Dangerous builds = 0
Total wall time: 0:00:01
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