forked from lijiext/lammps
204 lines
7.5 KiB
Groff
204 lines
7.5 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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1 by 1 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 = 103823 64000
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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) = 35.36 | 35.36 | 35.36 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 -14094.858 428.7917
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300 296.65014 -16589.155 0 -13937.267 547.40796
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400 303.82963 -16625.011 0 -13908.942 237.93694
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500 298.00057 -16716.887 0 -14052.926 231.55014
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Loop time of 38.2796 on 1 procs for 500 steps with 4500 atoms
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Performance: 2.257 ns/day, 10.633 hours/ns, 13.062 timesteps/s
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99.2% CPU use with 1 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 | 28.428 | 28.428 | 28.428 | 0.0 | 74.26
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Bond | 0.00056672 | 0.00056672 | 0.00056672 | 0.0 | 0.00
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Kspace | 5.3161 | 5.3161 | 5.3161 | 0.0 | 13.89
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Neigh | 4.1185 | 4.1185 | 4.1185 | 0.0 | 10.76
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Comm | 0.12788 | 0.12788 | 0.12788 | 0.0 | 0.33
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Output | 0.00021887 | 0.00021887 | 0.00021887 | 0.0 | 0.00
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Modify | 0.26748 | 0.26748 | 0.26748 | 0.0 | 0.70
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Other | | 0.02102 | | | 0.05
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Nlocal: 4500 ave 4500 max 4500 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 21248 ave 21248 max 21248 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 2.60146e+06 ave 2.60146e+06 max 2.60146e+06 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 2601459
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Ave neighs/atom = 578.102
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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 = 103823 64000
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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) = 36.67 | 36.67 | 36.67 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 298.00057 -16716.887 0 -14052.926 231.6595
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100 307.31045 -16761.022 0 -14013.835 449.26027
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200 299.52847 -16679.165 0 -14001.546 148.44719
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300 293.68499 -16583.548 0 -13958.166 140.79069
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400 306.76266 -16658.573 0 -13916.284 481.26934
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500 294.75648 -16640.446 0 -14005.485 585.05479
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600 303.19282 -16629.985 0 -13919.608 328.23667
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700 300.28233 -16590.155 0 -13905.797 -176.71076
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800 292.36899 -16620.826 0 -14007.208 -194.83408
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900 304.92802 -16633.331 0 -13907.443 479.49808
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1000 300.64529 -16598.233 0 -13910.63 904.96137
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Loop time of 107.579 on 1 procs for 1000 steps with 4500 atoms
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Performance: 1.606 ns/day, 14.942 hours/ns, 9.295 timesteps/s
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99.4% CPU use with 1 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 | 58.928 | 58.928 | 58.928 | 0.0 | 54.78
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Bond | 0.0012271 | 0.0012271 | 0.0012271 | 0.0 | 0.00
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Kspace | 10.698 | 10.698 | 10.698 | 0.0 | 9.94
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Neigh | 8.7649 | 8.7649 | 8.7649 | 0.0 | 8.15
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Comm | 0.2608 | 0.2608 | 0.2608 | 0.0 | 0.24
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Output | 0.00043702 | 0.00043702 | 0.00043702 | 0.0 | 0.00
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Modify | 28.883 | 28.883 | 28.883 | 0.0 | 26.85
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Other | | 0.04301 | | | 0.04
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Nlocal: 4500 ave 4500 max 4500 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 21275 ave 21275 max 21275 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 2.60217e+06 ave 2.60217e+06 max 2.60217e+06 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 5.20478e+06 ave 5.20478e+06 max 5.20478e+06 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 5204784
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Ave neighs/atom = 1156.62
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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: 0:02:26
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