#------------------------------------------------------------------------------- # Stage 2.6: NVT integration for 2 ns with a timestep of 1 fs # Temperature 298.2 K #------------------------------------------------------------------------------- # Fix shake is needed for water in pcff+ fix shaken all shake .0001 20 50000 a 2 b 2 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 2768 = # of frozen angles find clusters CPU = 0.001 seconds reset_timestep 0 thermo_style custom step v_time press vol v_sysdensity temp ebond eangle edihed eimp evdwl ecoul etail elong pe ke thermo ${Nthermo} thermo 0 fix 1 movable nvt temp 298.2 298.2 100 drag 0.0 fix 2 movable ave/time 1 200000 200000 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_pe v_ke v_evdwl v_coulomb v_sxx v_syy v_szz v_syz v_sxz v_sxy v_surfacetension file 2.6_averages.txt off 1 fix 3 movable ave/time 200 1 200 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_pe v_ke v_evdwl v_coulomb v_sxx v_syy v_szz v_syz v_sxz v_sxy v_surfacetension file 2.6_instantaneous.txt restart 2000000 2.6.restart dump sci all custom 200000 2.6.xyz id mol type q xs ys zs timestep 1 run 2000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.32166515 grid = 40 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0036376213 estimated relative force accuracy = 1.0954589e-05 using double precision KISS FFT 3d grid and FFT values/proc = 10098 3200 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 6.62803e-13 8304 2 103.7 1.00798e-10 2768 Per MPI rank memory allocation (min/avg/max) = 12.69 | 13.44 | 13.88 Mbytes Step v_time Press Volume v_sysdensity Temp E_bond E_angle E_dihed E_impro E_vdwl E_coul E_tail E_long PotEng KinEng 0 1e-06 -660.69 120303.9 1.009153 296.721 42.294304 62.168528 0 0 21079.542 87017.366 -346.11593 -269045.06 -160843.69 5600.4574 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.08088e-06 8304 2 103.7 0.000112034 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.18231e-06 8304 2 103.7 8.92485e-05 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.24806e-06 8304 2 103.7 0.000106668 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.19116e-06 8304 2 103.7 0.000102617 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.19503e-06 8304 2 103.7 9.85343e-05 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.36422e-06 8304 2 103.7 0.000103 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.48239e-06 8304 2 103.7 0.00010219 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.04309e-06 8304 2 103.7 9.63958e-05 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.26451e-06 8304 2 103.7 0.000102836 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.34054e-06 8304 2 103.7 0.000102284 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.18756e-06 8304 2 103.7 9.43585e-05 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.57538e-06 8304 2 103.7 0.000100684 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.26024e-06 8304 2 103.7 9.6528e-05 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.77849e-06 8304 2 103.7 0.000134395 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.15561e-06 8304 2 103.7 9.13893e-05 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.12643e-06 8304 2 103.7 8.95551e-05 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.19035e-06 8304 2 103.7 0.000100893 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.39148e-06 8304 2 103.7 0.000107619 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.45325e-06 8304 2 103.7 9.39002e-05 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.17727e-06 8304 2 103.7 9.06101e-05 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.2397e-06 8304 2 103.7 9.97918e-05 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.52092e-06 8304 2 103.7 0.000118262 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.31512e-06 8304 2 103.7 9.25443e-05 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.10588e-06 8304 2 103.7 9.36683e-05 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.46244e-06 8304 2 103.7 0.000103793 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.33933e-06 8304 2 103.7 9.80165e-05 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.75521e-06 8304 2 103.7 0.000104489 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.39308e-06 8304 2 103.7 0.000106018 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.18927e-06 8304 2 103.7 9.90366e-05 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.33601e-06 8304 2 103.7 0.000100722 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.43292e-06 8304 2 103.7 0.000112547 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.10783e-06 8304 2 103.7 0.000116092 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.30257e-06 8304 2 103.7 9.65942e-05 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.46607e-06 8304 2 103.7 0.000113567 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.2108e-06 8304 2 103.7 9.73873e-05 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.40128e-06 8304 2 103.7 0.000101946 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.56343e-06 8304 2 103.7 0.000120844 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.15818e-06 8304 2 103.7 0.000116875 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.34602e-06 8304 2 103.7 9.73026e-05 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.13748e-06 8304 2 103.7 9.48858e-05 2768 2000000 2000000 -714.77489 120303.9 1.009153 295.93612 51.902261 57.215337 0 0 21078.659 87089.605 -346.11593 -269047.43 -160770.05 5585.6431 Loop time of 11561.4 on 32 procs for 2000000 steps with 9101 atoms Performance: 14.946 ns/day, 1.606 hours/ns, 172.989 timesteps/s 99.1% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1128.7 | 4107 | 5529.7 |2608.0 | 35.52 Bond | 2.0115 | 5.0214 | 9.2017 | 94.5 | 0.04 Kspace | 4325.3 | 5744.9 | 8744.9 |2215.8 | 49.69 Neigh | 321.25 | 323.53 | 326.03 | 7.8 | 2.80 Comm | 482.51 | 606.9 | 662.06 | 275.3 | 5.25 Output | 0.0099905 | 0.012159 | 0.014203 | 1.2 | 0.00 Modify | 698.78 | 738.19 | 840.54 | 214.5 | 6.38 Other | | 35.91 | | | 0.31 Nlocal: 284.406 ave 368 max 86 min Histogram: 6 2 0 0 0 0 0 0 9 15 Nghost: 4147.78 ave 5086 max 3590 min Histogram: 8 8 6 2 0 0 0 0 0 8 Neighs: 76586.7 ave 110579 max 12766 min Histogram: 6 2 0 0 0 0 0 8 12 4 Total # of neighbors = 2450775 Ave neighs/atom = 269.28634 Ave special neighs/atom = 1.8929788 Neighbor list builds = 99525 Dangerous builds = 0 undump sci restart 0 dump sci all custom 2000000 2.6.xyz id mol type q xs ys zs run 0 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.32166515 grid = 40 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0036376213 estimated relative force accuracy = 1.0954589e-05 using double precision KISS FFT 3d grid and FFT values/proc = 10098 3200 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.13748e-06 8304 2 103.7 9.48858e-05 2768 Per MPI rank memory allocation (min/avg/max) = 12.69 | 13.45 | 13.88 Mbytes Step v_time Press Volume v_sysdensity Temp E_bond E_angle E_dihed E_impro E_vdwl E_coul E_tail E_long PotEng KinEng 2000000 2000000 -714.06456 120303.9 1.009153 295.93612 51.902261 57.215337 0 0 21078.659 87089.605 -346.11593 -269047.43 -160770.05 5585.6431 Loop time of 9.16984e-06 on 32 procs for 0 steps with 9101 atoms 117.6% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Bond | 0 | 0 | 0 | 0.0 | 0.00 Kspace | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 9.17e-06 | | |100.00 Nlocal: 284.406 ave 368 max 86 min Histogram: 6 2 0 0 0 0 0 0 9 15 Nghost: 4147.78 ave 5086 max 3590 min Histogram: 8 8 6 2 0 0 0 0 0 8 Neighs: 76586.7 ave 110579 max 12766 min Histogram: 6 2 0 0 0 0 0 8 12 4 Total # of neighbors = 2450775 Ave neighs/atom = 269.28634 Ave special neighs/atom = 1.8929788 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 11:13:16