forked from lijiext/lammps
204 lines
7.4 KiB
Groff
204 lines
7.4 KiB
Groff
LAMMPS (27 Nov 2018)
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using 1 OpenMP thread(s) per MPI task
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# Liquid water RDFs and ADFs (~12 O-O-O/atom, ~1 O-H...O/atom)
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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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orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
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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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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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pair_style lj/cut/coul/long 12.0 12.0
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pair_coeff * * 0.0 1.0
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pair_coeff 1 1 0.15535 3.166
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kspace_style pppm 1.0e-6
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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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# need to set bond/angle inclusion to > 0.0
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# so that intramolecular pairs are included in neighbor lists (required for second ADF)
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special_bonds lj/coul 1.0e-100 1.0e-100 1.0
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2 = max # of 1-2 neighbors
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1 = max # of 1-3 neighbors
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2 = max # of special neighbors
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neighbor 2.0 bin
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timestep 2.0
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neigh_modify every 1 delay 2 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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1500 = # of frozen angles
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fix 2 all nvt temp 300.0 300.0 100.0
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velocity all create 300.0 6244325
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thermo 100
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run 500
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PPPM initialization ...
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using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
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G vector (1/distance) = 0.279652
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grid = 40 40 40
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stencil order = 5
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estimated absolute RMS force accuracy = 0.000394674
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estimated relative force accuracy = 1.18855e-06
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using double precision FFTs
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3d grid and FFT values/proc = 34263 16000
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Neighbor list info ...
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update every 1 steps, delay 2 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 14
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ghost atom cutoff = 14
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binsize = 7, bins = 6 6 6
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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) = 13.1 | 13.1 | 13.1 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 300 -16692.369 0 -14010.534 -112.83562
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100 283.44729 -17008.717 0 -14474.854 -162.06378
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200 298.75279 -16765.543 0 -14094.858 428.79175
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300 296.65013 -16589.155 0 -13937.267 547.40809
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400 303.82993 -16625.014 0 -13908.942 237.957
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500 298.00206 -16716.893 0 -14052.919 231.33112
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Loop time of 12.5516 on 4 procs for 500 steps with 4500 atoms
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Performance: 6.884 ns/day, 3.487 hours/ns, 39.836 timesteps/s
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94.9% 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 | 7.739 | 7.9051 | 8.2663 | 7.5 | 62.98
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Bond | 0.00061631 | 0.00064486 | 0.00070524 | 0.0 | 0.01
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Kspace | 2.7001 | 3.0573 | 3.2239 | 11.9 | 24.36
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Neigh | 1.1736 | 1.174 | 1.1743 | 0.0 | 9.35
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Comm | 0.18222 | 0.1869 | 0.19248 | 0.8 | 1.49
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Output | 0.00017595 | 0.00032246 | 0.00076079 | 0.0 | 0.00
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Modify | 0.20354 | 0.20467 | 0.20652 | 0.2 | 1.63
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Other | | 0.02259 | | | 0.18
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Nlocal: 1125 ave 1132 max 1114 min
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Histogram: 1 0 0 0 0 0 1 1 0 1
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Nghost: 12241 ave 12298 max 12196 min
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Histogram: 2 0 0 0 0 0 0 1 0 1
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Neighs: 650366 ave 671163 max 631441 min
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Histogram: 1 0 0 1 0 1 0 0 0 1
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Total # of neighbors = 2601464
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Ave neighs/atom = 578.103
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Ave special neighs/atom = 2
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Neighbor list builds = 45
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Dangerous builds = 0
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reset_timestep 0
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compute gofr all rdf 100 1 1 2 2 1 2 # O-O, H-H, O-H
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compute gofa all adf 45 1 1 1 2.0 3.5 2.0 3.5 2 1 1 0.0 1.2 1.5 2.5 # O-O-O, O-H...O
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fix rdf all ave/time 100 10 1000 c_gofr[*] file spce-rdf.dat mode vector
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fix adf all ave/time 10 100 1000 c_gofa[*] file spce-adf.dat mode vector
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run 1000
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PPPM initialization ...
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using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
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G vector (1/distance) = 0.279652
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grid = 40 40 40
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stencil order = 5
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estimated absolute RMS force accuracy = 0.000394674
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estimated relative force accuracy = 1.18855e-06
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using double precision FFTs
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3d grid and FFT values/proc = 34263 16000
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Neighbor list info ...
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update every 1 steps, delay 2 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 14
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ghost atom cutoff = 14
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binsize = 7, bins = 6 6 6
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3 neighbor lists, perpetual/occasional/extra = 1 2 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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(2) compute rdf, occasional, copy from (1)
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attributes: half, newton on
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pair build: copy
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stencil: none
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bin: none
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(3) compute adf, occasional
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attributes: full, newton on
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pair build: full/bin
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stencil: full/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 13.96 | 13.96 | 13.96 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 298.00206 -16716.893 0 -14052.919 231.44272
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100 307.28155 -16760.647 0 -14013.72 452.38436
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200 299.05168 -16674.695 0 -14001.338 177.44237
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300 292.7564 -16573.946 0 -13956.865 122.27796
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400 299.2644 -16578.318 0 -13903.059 482.03304
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500 296.04028 -16623.179 0 -13976.742 89.968145
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600 300.30911 -16664.206 0 -13979.608 132.70079
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700 292.39517 -16703.749 0 -14089.897 825.267
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800 298.75851 -16661.684 0 -13990.948 468.68671
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900 301.55689 -16644.846 0 -13949.093 -72.16965
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1000 298.2852 -16682.077 0 -14015.572 0.69725342
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Loop time of 32.3106 on 4 procs for 1000 steps with 4500 atoms
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Performance: 5.348 ns/day, 4.488 hours/ns, 30.950 timesteps/s
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96.8% 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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Pair | 15.647 | 15.876 | 16.119 | 4.3 | 49.13
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Bond | 0.0011718 | 0.0012704 | 0.001348 | 0.2 | 0.00
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Kspace | 5.286 | 5.5364 | 5.7729 | 7.5 | 17.13
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Neigh | 2.3892 | 2.3962 | 2.3991 | 0.3 | 7.42
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Comm | 0.34641 | 0.35514 | 0.35988 | 0.9 | 1.10
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Output | 0.00047851 | 0.00069892 | 0.0013568 | 0.0 | 0.00
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Modify | 8.0882 | 8.0963 | 8.1047 | 0.3 | 25.06
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Other | | 0.04887 | | | 0.15
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Nlocal: 1125 ave 1137 max 1114 min
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Histogram: 1 1 0 0 0 0 0 1 0 1
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Nghost: 12206.2 ave 12239 max 12169 min
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Histogram: 1 0 1 0 0 0 0 0 1 1
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Neighs: 650464 ave 655962 max 641444 min
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Histogram: 1 0 0 0 0 0 0 2 0 1
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FullNghs: 1.30095e+06 ave 1.31925e+06 max 1.28413e+06 min
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Histogram: 1 0 1 0 0 0 1 0 0 1
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Total # of neighbors = 5203786
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Ave neighs/atom = 1156.4
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Ave special neighs/atom = 2
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Neighbor list builds = 94
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Dangerous builds = 0
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Total wall time: 0:00:45
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