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LAMMPS (15 May 2015-ICMS)
WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:89)
using 1 OpenMP thread(s) per MPI task
# SPC/E water box benchmark
units real
atom_style full
# newton off off
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 0.5
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 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 stress/atom NULL pair
compute c1 all stress/tally all
compute c2 all stress/tally all
compute red all reduce sum c_spa[1] c_spa[2] c_spa[3] c_c1[1] c_c1[2] c_c1[3]
variable ref equal (c_red[1]+c_red[2]+c_red[3])/3.0
variable new equal (c_red[4]+c_red[5]+c_red[6])/3.0
variable vec equal (c_c1[1]+c_c1[2]+c_c1[3])/3.0
velocity all create 300 432567 dist uniform
timestep 2.0
thermo_style custom step temp press etotal c_c1 v_ref v_new v_vec
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 ...
1 neighbor list requests
update every 1 steps, delay 10 steps, check yes
master list distance cutoff = 14
Memory usage per processor = 12.0691 Mbytes
Step Temp Press TotEng c1 ref new vec
0 300 -869.31293 -14010.523 -1.1841304e+09 -1.1841304e+09 -1.1841304e+09 -1.1841304e+09
Loop time of 4.52995e-05 on 4 procs for 0 steps with 4500 atoms
68.4% CPU use with 4 MPI tasks x 1 OpenMP threads
compute c3 all stress/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 = 13.5691 Mbytes
Step Temp Press TotEng c1 ref new vec
0 300 -869.31293 -14010.523 -1.1841304e+09 -1.1841304e+09 -1.1841304e+09 -1.1841304e+09
1 198.01583 -466.19315 -14940.409 -1.1841119e+09 -1.1841119e+09 -1.1841119e+09 -1.1841119e+09
Loop time of 0.138151 on 4 procs for 1 steps with 4500 atoms
99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
run 1 pre no post no
Step Temp Press TotEng c1 ref new vec
1 198.01583 -466.19315 -14940.409 -1.1841119e+09 -1.1841119e+09 8.1192517e+13 -1.1841119e+09
2 204.50101 -573.39212 -14940.649 -1.182287e+09 -1.182287e+09 -1.182287e+09 -1.182287e+09
Loop time of 0.137901 on 4 procs for 1 steps with 4500 atoms
99.6% 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 = 12.8191 Mbytes
Step Temp Press TotEng c1 ref new vec
2 204.50101 -574.75086 -14940.649 -1.182287e+09 -1.182287e+09 -1.182287e+09 -1.182287e+09
10 242.20655 -1456.2488 -14922.396 -1.156511e+09 -1.156511e+09 -1.156511e+09 -1.156511e+09
20 247.7033 -1304.3253 -14879.075 -1.156539e+09 -1.156539e+09 -1.156539e+09 -1.156539e+09
30 251.54318 -828.989 -14840.204 -1.1832175e+09 -1.1832175e+09 -1.1832175e+09 -1.1832175e+09
40 258.60239 -611.14051 -14803.33 -1.195494e+09 -1.195494e+09 -1.195494e+09 -1.195494e+09
50 266.04631 -492.03835 -14759.662 -1.203338e+09 -1.203338e+09 -1.203338e+09 -1.203338e+09
52 268.09022 -455.78414 -14751.307 -1.2061496e+09 -1.2061496e+09 -1.2061496e+09 -1.2061496e+09
Loop time of 2.04203 on 4 procs for 50 steps with 4500 atoms
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 4.231 ns/day 5.672 hours/ns 24.485 timesteps/s
MPI task timings breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.6144 | 1.6643 | 1.7425 | 3.8 | 81.50
Bond | 0.00088191 | 0.00096929 | 0.0010164 | 0.2 | 0.05
Kspace | 0.10524 | 0.18258 | 0.23304 | 11.3 | 8.94
Neigh | 0.12904 | 0.12913 | 0.12919 | 0.0 | 6.32
Comm | 0.022201 | 0.023014 | 0.024021 | 0.5 | 1.13
Output | 0.010829 | 0.01089 | 0.011069 | 0.1 | 0.53
Modify | 0.028471 | 0.028553 | 0.028713 | 0.1 | 1.40
Other | | 0.002551 | | | 0.12
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
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