#------------------------------------------------------------------------------- # Stage 2.4: NVT integration for 5 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 1 b 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 2000 = # 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 500000 500000 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 file 2.4_averages.txt off 1 fix 3 movable ave/time 500 1 500 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 file 2.4_instantaneous.txt restart 5000000 2.4.restart dump sci all custom 500000 2.4.xyz id mol type q xs ys zs timestep 1 run 5000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25187548 grid = 24 24 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0023982645 estimated relative force accuracy = 7.2223022e-06 using double precision KISS FFT 3d grid and FFT values/proc = 5776 1728 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 1.00035 0.0567853 6000 1 97.848 8.3141 2000 Per MPI rank memory allocation (min/avg/max) = 8.236 | 9.512 | 10.7 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 -587.45371 119542.27 0.50049569 447.33728 0 0 0 0 9781.7174 62580.398 -52.177571 -103683.1 -31320.989 5332.3765 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.15932e-06 6000 1 103.7 9.78432e-05 2000 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.23783e-06 6000 1 103.7 9.15198e-05 2000 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.26719e-06 6000 1 103.7 9.56193e-05 2000 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.49551e-06 6000 1 103.7 0.000104749 2000 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.17715e-06 6000 1 103.7 0.00010202 2000 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.13843e-06 6000 1 103.7 9.76704e-05 2000 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 2.01868e-06 6000 1 103.7 0.000126391 2000 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.42116e-06 6000 1 103.7 9.39813e-05 2000 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.11352e-06 6000 1 103.7 9.12037e-05 2000 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.50482e-06 6000 1 103.7 9.95787e-05 2000 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.32447e-06 6000 1 103.7 9.79387e-05 2000 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.86592e-06 6000 1 103.7 0.000128707 2000 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.73499e-06 6000 1 103.7 0.000125749 2000 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.22305e-06 6000 1 103.7 0.00011711 2000 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.20398e-06 6000 1 103.7 9.67016e-05 2000 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.7571e-06 6000 1 103.7 0.000115622 2000 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.47196e-06 6000 1 103.7 0.000117032 2000 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.0989e-06 6000 1 103.7 0.00011119 2000 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.40025e-06 6000 1 103.7 0.00010463 2000 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.30522e-06 6000 1 103.7 9.78831e-05 2000 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.97 1.28694e-06 6000 1 103.7 0.000105146 2000 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.97 1.35468e-06 6000 1 103.7 0.000111401 2000 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.97 1.29162e-06 6000 1 103.7 8.7421e-05 2000 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.97 1.32343e-06 6000 1 103.7 0.000105391 2000 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.97 1.55074e-06 6000 1 103.7 0.000115868 2000 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.97 1.17876e-06 6000 1 103.7 0.000105915 2000 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.97 1.36784e-06 6000 1 103.7 0.000108764 2000 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.97 1.63494e-06 6000 1 103.7 0.000123346 2000 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.97 1.25407e-06 6000 1 103.7 9.70043e-05 2000 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.97 1.26396e-06 6000 1 103.7 9.33842e-05 2000 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.97 1.33761e-06 6000 1 103.7 9.63873e-05 2000 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.97 1.31861e-06 6000 1 103.7 9.61816e-05 2000 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.97 1.2802e-06 6000 1 103.7 0.000110506 2000 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.97 1.66505e-06 6000 1 103.7 0.000133171 2000 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.97 1.40192e-06 6000 1 103.7 0.000116403 2000 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.97 1.46307e-06 6000 1 103.7 0.000122031 2000 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.97 1.24125e-06 6000 1 103.7 0.000109959 2000 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.97 1.0931e-06 6000 1 103.7 9.62351e-05 2000 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.97 1.11027e-06 6000 1 103.7 0.000104456 2000 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.42723e-06 6000 1 103.7 8.80586e-05 2000 SHAKE stats (type/ave/delta/count) on step 2050000 1 0.97 1.42421e-06 6000 1 103.7 9.98773e-05 2000 SHAKE stats (type/ave/delta/count) on step 2100000 1 0.97 1.61012e-06 6000 1 103.7 0.000106978 2000 SHAKE stats (type/ave/delta/count) on step 2150000 1 0.97 1.2508e-06 6000 1 103.7 0.00011654 2000 SHAKE stats (type/ave/delta/count) on step 2200000 1 0.97 1.06142e-06 6000 1 103.7 9.28811e-05 2000 SHAKE stats (type/ave/delta/count) on step 2250000 1 0.97 1.46747e-06 6000 1 103.7 9.91742e-05 2000 SHAKE stats (type/ave/delta/count) on step 2300000 1 0.97 1.19439e-06 6000 1 103.7 0.000113475 2000 SHAKE stats (type/ave/delta/count) on step 2350000 1 0.97 1.32108e-06 6000 1 103.7 9.82537e-05 2000 SHAKE stats (type/ave/delta/count) on step 2400000 1 0.97 1.32779e-06 6000 1 103.7 0.000102587 2000 SHAKE stats (type/ave/delta/count) on step 2450000 1 0.97 1.16751e-06 6000 1 103.7 9.70988e-05 2000 SHAKE stats (type/ave/delta/count) on step 2500000 1 0.97 1.22669e-06 6000 1 103.7 9.59599e-05 2000 SHAKE stats (type/ave/delta/count) on step 2550000 1 0.97 1.2159e-06 6000 1 103.7 0.000108384 2000 SHAKE stats (type/ave/delta/count) on step 2600000 1 0.97 1.2532e-06 6000 1 103.7 0.000110792 2000 SHAKE stats (type/ave/delta/count) on step 2650000 1 0.97 1.11426e-06 6000 1 103.7 9.37507e-05 2000 SHAKE stats (type/ave/delta/count) on step 2700000 1 0.97 1.12461e-06 6000 1 103.7 0.00010592 2000 SHAKE stats (type/ave/delta/count) on step 2750000 1 0.97 1.45889e-06 6000 1 103.7 9.47123e-05 2000 SHAKE stats (type/ave/delta/count) on step 2800000 1 0.97 1.14337e-06 6000 1 103.7 9.15747e-05 2000 SHAKE stats (type/ave/delta/count) on step 2850000 1 0.97 1.22724e-06 6000 1 103.7 0.0001078 2000 SHAKE stats (type/ave/delta/count) on step 2900000 1 0.97 1.6031e-06 6000 1 103.7 0.000114631 2000 SHAKE stats (type/ave/delta/count) on step 2950000 1 0.97 1.33658e-06 6000 1 103.7 0.000115067 2000 SHAKE stats (type/ave/delta/count) on step 3000000 1 0.97 1.31908e-06 6000 1 103.7 0.000108179 2000 SHAKE stats (type/ave/delta/count) on step 3050000 1 0.97 1.6668e-06 6000 1 103.7 0.000105647 2000 SHAKE stats (type/ave/delta/count) on step 3100000 1 0.97 1.21265e-06 6000 1 103.7 9.55481e-05 2000 SHAKE stats (type/ave/delta/count) on step 3150000 1 0.97 1.26605e-06 6000 1 103.7 9.44553e-05 2000 SHAKE stats (type/ave/delta/count) on step 3200000 1 0.97 1.32779e-06 6000 1 103.7 0.000103267 2000 SHAKE stats (type/ave/delta/count) on step 3250000 1 0.97 1.2079e-06 6000 1 103.7 0.000112483 2000 SHAKE stats (type/ave/delta/count) on step 3300000 1 0.97 1.22138e-06 6000 1 103.7 9.75673e-05 2000 SHAKE stats (type/ave/delta/count) on step 3350000 1 0.97 1.35893e-06 6000 1 103.7 0.000119098 2000 SHAKE stats (type/ave/delta/count) on step 3400000 1 0.97 1.40175e-06 6000 1 103.7 0.000119592 2000 SHAKE stats (type/ave/delta/count) on step 3450000 1 0.97 1.30132e-06 6000 1 103.7 0.000105189 2000 SHAKE stats (type/ave/delta/count) on step 3500000 1 0.97 1.34107e-06 6000 1 103.7 0.000105408 2000 SHAKE stats (type/ave/delta/count) on step 3550000 1 0.97 1.43234e-06 6000 1 103.7 0.00011588 2000 SHAKE stats (type/ave/delta/count) on step 3600000 1 0.97 1.17708e-06 6000 1 103.7 9.13767e-05 2000 SHAKE stats (type/ave/delta/count) on step 3650000 1 0.97 1.65905e-06 6000 1 103.7 0.000122815 2000 SHAKE stats (type/ave/delta/count) on step 3700000 1 0.97 1.94747e-06 6000 1 103.7 0.000122906 2000 SHAKE stats (type/ave/delta/count) on step 3750000 1 0.97 1.14884e-06 6000 1 103.7 9.1026e-05 2000 SHAKE stats (type/ave/delta/count) on step 3800000 1 0.97 1.1711e-06 6000 1 103.7 9.45744e-05 2000 SHAKE stats (type/ave/delta/count) on step 3850000 1 0.97 1.46454e-06 6000 1 103.7 9.68749e-05 2000 SHAKE stats (type/ave/delta/count) on step 3900000 1 0.97 2.19933e-06 6000 1 103.7 0.000128862 2000 SHAKE stats (type/ave/delta/count) on step 3950000 1 0.97 1.34401e-06 6000 1 103.7 0.000110477 2000 SHAKE stats (type/ave/delta/count) on step 4000000 1 0.97 1.36587e-06 6000 1 103.7 9.59698e-05 2000 SHAKE stats (type/ave/delta/count) on step 4050000 1 0.97 1.87524e-06 6000 1 103.7 0.00013915 2000 SHAKE stats (type/ave/delta/count) on step 4100000 1 0.97 1.48351e-06 6000 1 103.7 0.000103615 2000 SHAKE stats (type/ave/delta/count) on step 4150000 1 0.97 1.11575e-06 6000 1 103.7 9.29924e-05 2000 SHAKE stats (type/ave/delta/count) on step 4200000 1 0.97 1.04362e-06 6000 1 103.7 0.000101398 2000 SHAKE stats (type/ave/delta/count) on step 4250000 1 0.97 1.31202e-06 6000 1 103.7 0.000108878 2000 SHAKE stats (type/ave/delta/count) on step 4300000 1 0.97 1.10332e-06 6000 1 103.7 9.88331e-05 2000 SHAKE stats (type/ave/delta/count) on step 4350000 1 0.97 1.25199e-06 6000 1 103.7 9.7355e-05 2000 SHAKE stats (type/ave/delta/count) on step 4400000 1 0.97 1.37421e-06 6000 1 103.7 0.000100611 2000 SHAKE stats (type/ave/delta/count) on step 4450000 1 0.97 1.34085e-06 6000 1 103.7 9.39019e-05 2000 SHAKE stats (type/ave/delta/count) on step 4500000 1 0.97 1.29534e-06 6000 1 103.7 0.000104168 2000 SHAKE stats (type/ave/delta/count) on step 4550000 1 0.97 1.44634e-06 6000 1 103.7 0.000101234 2000 SHAKE stats (type/ave/delta/count) on step 4600000 1 0.97 1.32557e-06 6000 1 103.7 0.000110034 2000 SHAKE stats (type/ave/delta/count) on step 4650000 1 0.97 1.11252e-06 6000 1 103.7 0.000105057 2000 SHAKE stats (type/ave/delta/count) on step 4700000 1 0.97 1.14993e-06 6000 1 103.7 8.95309e-05 2000 SHAKE stats (type/ave/delta/count) on step 4750000 1 0.97 1.12536e-06 6000 1 103.7 0.000119096 2000 SHAKE stats (type/ave/delta/count) on step 4800000 1 0.97 1.14883e-06 6000 1 103.7 9.54836e-05 2000 SHAKE stats (type/ave/delta/count) on step 4850000 1 0.97 1.51732e-06 6000 1 103.7 0.000139779 2000 SHAKE stats (type/ave/delta/count) on step 4900000 1 0.97 1.72366e-06 6000 1 103.7 0.000122303 2000 SHAKE stats (type/ave/delta/count) on step 4950000 1 0.97 1.60662e-06 6000 1 103.7 0.000125523 2000 SHAKE stats (type/ave/delta/count) on step 5000000 1 0.97 1.30634e-06 6000 1 103.7 9.36414e-05 2000 5000000 5000000 -301.02722 119542.27 0.50049569 293.08383 0 0 0 0 4918.1097 77548.164 -52.177571 -103665.66 -21199.387 3493.6353 Loop time of 40409.8 on 32 procs for 5000000 steps with 6000 atoms Performance: 10.690 ns/day, 2.245 hours/ns, 123.732 timesteps/s 98.6% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.4979 | 13405 | 28904 |11394.4 | 33.17 Bond | 3.8565 | 5.4029 | 7.9693 | 38.7 | 0.01 Kspace | 7012.4 | 22706 | 36550 |8873.3 | 56.19 Neigh | 1520 | 1540.4 | 1607.8 | 69.9 | 3.81 Comm | 41.262 | 928.32 | 1410.7 |1703.0 | 2.30 Output | 0.010738 | 0.012384 | 0.013783 | 0.8 | 0.00 Modify | 1468 | 1747 | 2133.6 | 666.8 | 4.32 Other | | 78.45 | | | 0.19 Nlocal: 187.5 ave 397 max 0 min Histogram: 13 3 0 0 0 0 0 0 5 11 Nghost: 3941.25 ave 7897 max 0 min Histogram: 8 0 4 4 0 0 4 4 0 8 Neighs: 98530.2 ave 226300 max 0 min Histogram: 16 0 0 0 0 0 0 5 4 7 Total # of neighbors = 3152965 Ave neighs/atom = 525.49417 Ave special neighs/atom = 2 Neighbor list builds = 247500 Dangerous builds = 0 undump sci restart 0 dump sci all custom 5000000 2.4.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) = 0.25187548 grid = 24 24 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0023982645 estimated relative force accuracy = 7.2223022e-06 using double precision KISS FFT 3d grid and FFT values/proc = 5776 1728 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 5000000 1 0.97 1.30634e-06 6000 1 103.7 9.36414e-05 2000 Per MPI rank memory allocation (min/avg/max) = 8.363 | 9.786 | 10.71 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 5000000 5000000 -300.73521 119542.27 0.50049569 293.08383 0 0 0 0 4918.1097 77548.164 -52.177571 -103665.66 -21199.387 3493.6353 Loop time of 6.89175e-06 on 32 procs for 0 steps with 6000 atoms 117.9% 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 | | 6.892e-06 | | |100.00 Nlocal: 187.5 ave 397 max 0 min Histogram: 13 3 0 0 0 0 0 0 5 11 Nghost: 3941.25 ave 7897 max 0 min Histogram: 8 0 4 4 0 0 4 4 0 8 Neighs: 98530.2 ave 226300 max 0 min Histogram: 16 0 0 0 0 0 0 5 4 7 Total # of neighbors = 3152965 Ave neighs/atom = 525.49417 Ave special neighs/atom = 2 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out