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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
group one molecule 1 2
6 atoms in group one
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 one group/group all pair yes kspace no boundary no
compute c1 one force/tally all
compute c2 all force/tally all
compute red all reduce sum c_c1[1] c_c1[2] c_c1[3]
variable ref equal sqrt(c_spa[1]*c_spa[1]+c_spa[2]*c_spa[2]+c_spa[3]*c_spa[3])
variable new equal sqrt(c_red[1]*c_red[1]+c_red[2]*c_red[2]+c_red[3]*c_red[3])
velocity all create 300 432567 dist uniform
timestep 2.0
thermo_style custom step v_ref v_new c_spa[1] c_red[1] c_spa[2] c_red[2] c_spa[3] c_red[3]
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
Memory usage per processor = 8.16441 Mbytes
Step ref new spa[1] red[1] spa[2] red[2] spa[3] red[3]
0 22.732789 22.732789 -17.068392 -17.068392 -8.8345214 -8.8345214 -12.140878 -12.140878
Loop time of 4.10676e-05 on 4 procs for 0 steps with 4500 atoms
66.4% 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 = 8.91441 Mbytes
Step ref new spa[1] red[1] spa[2] red[2] spa[3] red[3]
0 22.732789 22.732789 -17.068392 -17.068392 -8.8345214 -8.8345214 -12.140878 -12.140878
1 21.886892 21.886892 -16.527988 -16.527988 -8.8479027 -8.8479027 -11.294966 -11.294966
Loop time of 0.0922177 on 4 procs for 1 steps with 4500 atoms
99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
run 1 pre no post no
Step ref new spa[1] red[1] spa[2] red[2] spa[3] red[3]
1 21.886892 21.886892 -16.527988 -16.527988 -8.8479027 -8.8479027 -11.294966 -11.294966
2 20.392475 20.392475 -15.621741 -15.621741 -7.9480593 -7.9480593 -10.423175 -10.423175
Loop time of 0.0921878 on 4 procs for 1 steps with 4500 atoms
99.4% 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 = 8.53941 Mbytes
Step ref new spa[1] red[1] spa[2] red[2] spa[3] red[3]
2 20.392475 20.392475 -15.621741 -15.621741 -7.9480593 -7.9480593 -10.423175 -10.423175
10 11.736916 11.736916 -3.389834 -3.389834 9.1192697 9.1192697 -6.5652981 -6.5652981
20 5.6119688 5.6119688 -0.60029204 -0.60029204 -4.447985 -4.447985 3.3688683 3.3688683
30 17.292625 17.292625 6.1793856 6.1793856 -10.593936 -10.593936 12.190922 12.190922
40 18.66422 18.66422 5.4725158 5.4725158 -6.9330255 -6.9330255 16.441953 16.441953
50 12.130268 12.130268 -1.0321245 -1.0321245 8.00325 8.00325 -9.0568261 -9.0568261
52 14.898312 14.898312 -2.0940732 -2.0940732 11.139114 11.139114 -9.6692669 -9.6692669
Loop time of 1.81478 on 4 procs for 50 steps with 4500 atoms
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 4.761 ns/day 5.041 hours/ns 27.552 timesteps/s
MPI task timings breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.4107 | 1.4532 | 1.5275 | 3.7 | 80.08
Bond | 4.077e-05 | 5.3108e-05 | 6.9618e-05 | 0.2 | 0.00
Kspace | 0.08753 | 0.16165 | 0.20345 | 11.0 | 8.91
Neigh | 0.12841 | 0.12843 | 0.12845 | 0.0 | 7.08
Comm | 0.023234 | 0.02369 | 0.024538 | 0.3 | 1.31
Output | 0.017014 | 0.01706 | 0.017193 | 0.1 | 0.94
Modify | 0.027759 | 0.027826 | 0.027949 | 0.0 | 1.53
Other | | 0.002862 | | | 0.16
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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