203 lines
7.4 KiB
Groff
203 lines
7.4 KiB
Groff
LAMMPS (10 Oct 2018)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
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using 1 OpenMP thread(s) per MPI task
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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 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 = 59643 32000
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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) = 25.06 | 25.25 | 25.44 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 -162.06374
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200 298.75279 -16765.544 0 -14094.858 428.79127
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300 296.6501 -16589.155 0 -13937.267 547.40768
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400 303.83151 -16625.028 0 -13908.942 237.9775
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500 298.01615 -16717.015 0 -14052.915 230.7095
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Loop time of 21.4041 on 2 procs for 500 steps with 4500 atoms
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Performance: 4.037 ns/day, 5.946 hours/ns, 23.360 timesteps/s
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94.8% CPU use with 2 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 | 14.892 | 15.034 | 15.176 | 3.7 | 70.24
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Bond | 0.00056624 | 0.00059342 | 0.0006206 | 0.0 | 0.00
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Kspace | 3.987 | 4.1321 | 4.2773 | 7.1 | 19.31
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Neigh | 1.7494 | 1.7496 | 1.7497 | 0.0 | 8.17
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Comm | 0.20554 | 0.20637 | 0.2072 | 0.2 | 0.96
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Output | 0.00015688 | 0.00036144 | 0.00056601 | 0.0 | 0.00
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Modify | 0.25707 | 0.2606 | 0.26413 | 0.7 | 1.22
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Other | | 0.02059 | | | 0.10
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Nlocal: 2250 ave 2258 max 2242 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Nghost: 16319 ave 16381 max 16257 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Neighs: 1.30073e+06 ave 1.32386e+06 max 1.2776e+06 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Total # of neighbors = 2601457
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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 1 2 1 0.0 1.2 1.5 2.5
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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 = 59643 32000
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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) = 26.78 | 26.78 | 26.78 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 298.01615 -16717.015 0 -14052.915 230.81371
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100 307.1766 -16759.33 0 -14013.341 454.2771
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200 298.94628 -16674.186 0 -14001.771 114.20846
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300 293.13091 -16581.542 0 -13961.113 272.85574
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400 294.47017 -16556.872 0 -13924.471 180.3252
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500 305.57174 -16647.976 0 -13916.333 -444.14856
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600 302.53992 -16670.304 0 -13965.764 114.82353
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700 306.56761 -16616.508 0 -13875.962 534.02537
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800 299.06297 -16644.133 0 -13970.675 83.643063
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900 301.15522 -16674.021 0 -13981.859 325.04538
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1000 298.14963 -16701.663 0 -14036.369 356.0601
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Loop time of 53.3181 on 2 procs for 1000 steps with 4500 atoms
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Performance: 3.241 ns/day, 7.405 hours/ns, 18.755 timesteps/s
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97.3% CPU use with 2 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 | 28.831 | 29.365 | 29.899 | 9.9 | 55.07
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Bond | 0.00097084 | 0.0010794 | 0.001188 | 0.3 | 0.00
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Kspace | 7.3086 | 7.8356 | 8.3626 | 18.8 | 14.70
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Neigh | 3.7241 | 3.7245 | 3.7248 | 0.0 | 6.99
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Comm | 0.32839 | 0.33495 | 0.34151 | 1.1 | 0.63
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Output | 0.00043344 | 0.0015392 | 0.002645 | 2.8 | 0.00
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Modify | 12.013 | 12.014 | 12.015 | 0.0 | 22.53
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Other | | 0.04153 | | | 0.08
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Nlocal: 2250 ave 2251 max 2249 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Nghost: 16300 ave 16358 max 16242 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Neighs: 1.301e+06 ave 1.31594e+06 max 1.28606e+06 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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FullNghs: 2.602e+06 ave 2.60923e+06 max 2.59476e+06 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Total # of neighbors = 5203998
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Ave neighs/atom = 1156.44
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Ave special neighs/atom = 2
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Neighbor list builds = 93
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Dangerous builds = 0
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Total wall time: 0:01:14
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