148 lines
4.6 KiB
Groff
148 lines
4.6 KiB
Groff
LAMMPS (9 Oct 2020)
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using 1 OpenMP thread(s) per MPI task
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# SPC/E water box benchmark
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units real
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atom_style full
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read_data data.spce
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Reading data file ...
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orthogonal box = (0.02645 0.02645 0.02641) to (35.532800 35.532800 35.473600)
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2 by 2 by 1 MPI processor grid
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reading atoms ...
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4500 atoms
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scanning bonds ...
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2 = max bonds/atom
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scanning angles ...
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1 = max angles/atom
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reading bonds ...
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3000 bonds
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reading angles ...
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1500 angles
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0.0 0.0 0.0
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special bond factors coul: 0.0 0.0 0.0
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2 = max # of 1-2 neighbors
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1 = max # of 1-3 neighbors
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1 = max # of 1-4 neighbors
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2 = max # of special neighbors
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special bonds CPU = 0.001 seconds
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read_data CPU = 0.008 seconds
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replicate 2 4 1
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Replicating atoms ...
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orthogonal box = (0.02645 0.02645 0.02641) to (71.039150 142.05185 35.473600)
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1 by 4 by 1 MPI processor grid
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36000 atoms
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24000 bonds
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12000 angles
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0.0 0.0 0.0
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special bond factors coul: 0.0 0.0 0.0
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2 = max # of 1-2 neighbors
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1 = max # of 1-3 neighbors
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1 = max # of 1-4 neighbors
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2 = max # of special neighbors
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special bonds CPU = 0.002 seconds
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replicate CPU = 0.005 seconds
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pair_style lj/cut/coul/long 9.8 9.8
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kspace_style pppm 1.0e-4
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pair_coeff 1 1 0.15535 3.166
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pair_coeff * 2 0.0000 0.0000
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bond_style harmonic
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angle_style harmonic
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dihedral_style none
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improper_style none
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bond_coeff 1 1000.00 1.000
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angle_coeff 1 100.0 109.47
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special_bonds lj/coul 0.0 0.0 0.5
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0.0 0.0 0.5
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special bond factors coul: 0.0 0.0 0.5
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2 = max # of 1-2 neighbors
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1 = max # of 1-3 neighbors
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1 = max # of 1-4 neighbors
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2 = max # of special neighbors
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special bonds CPU = 0.004 seconds
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neighbor 2.0 bin
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neigh_modify every 1 delay 10 check yes
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fix 1 all shake 0.0001 20 0 b 1 a 1
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0 = # of size 2 clusters
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0 = # of size 3 clusters
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0 = # of size 4 clusters
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12000 = # of frozen angles
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find clusters CPU = 0.003 seconds
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fix 2 all nvt temp 300.0 300.0 100.0
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velocity all create 300 432567 dist uniform
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timestep 2.0
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thermo_style one
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thermo 50
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run 100
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PPPM initialization ...
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using 12-bit tables for long-range coulomb (src/kspace.cpp:328)
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G vector (1/distance) = 0.2688011
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grid = 36 64 24
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stencil order = 5
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estimated absolute RMS force accuracy = 0.033101471
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estimated relative force accuracy = 9.9684097e-05
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using double precision KISS FFT
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3d grid and FFT values/proc = 27993 13824
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 11.8
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ghost atom cutoff = 11.8
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binsize = 5.9, bins = 13 25 7
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut/coul/long, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/3d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 37.90 | 37.90 | 37.90 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 300 -133281.51 0 -111820.57 516.17807
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50 264.98553 -136986.74 0 -118030.61 -440.29255
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100 274.45966 -136364.57 0 -116730.69 -128.61954
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Loop time of 5.44355 on 4 procs for 100 steps with 36000 atoms
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Performance: 3.174 ns/day, 7.560 hours/ns, 18.370 timesteps/s
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95.4% CPU use with 4 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 3.82 | 3.8744 | 3.9155 | 1.8 | 71.17
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Bond | 7.8917e-05 | 8.6784e-05 | 9.4891e-05 | 0.0 | 0.00
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Kspace | 0.79192 | 0.83671 | 0.88328 | 3.5 | 15.37
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Neigh | 0.51754 | 0.5178 | 0.51789 | 0.0 | 9.51
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Comm | 0.069774 | 0.078783 | 0.088247 | 2.3 | 1.45
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Output | 9.0361e-05 | 0.00015712 | 0.00035048 | 0.0 | 0.00
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Modify | 0.12822 | 0.13016 | 0.13486 | 0.8 | 2.39
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Other | | 0.005435 | | | 0.10
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Nlocal: 9000.00 ave 9002 max 8998 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Nghost: 24134.2 ave 24184 max 24062 min
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Histogram: 1 0 0 0 0 0 1 1 0 1
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Neighs: 3.11561e+06 ave 3.11676e+06 max 3.11446e+06 min
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Histogram: 1 0 0 1 0 0 1 0 0 1
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Total # of neighbors = 12462451
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Ave neighs/atom = 346.17919
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Ave special neighs/atom = 2.0000000
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Neighbor list builds = 9
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Dangerous builds = 6
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Total wall time: 0:00:05
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