#------------------------------------------------------------------------------- # 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 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 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) = 0.32037747 grid = 45 45 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0030966253 estimated relative force accuracy = 9.3253951e-06 using double precision KISS FFT 3d grid and FFT values/proc = 13050 6075 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 1.00157 0.0754733 8304 2 97.535 10.6988 2768 Per MPI rank memory allocation (min/avg/max) = 11.78 | 12.85 | 13.53 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 -200.39086 192519.71 0.63061093 428.55654 8.2792833 46.583979 0 0 26248.626 67250.141 -216.28484 -268334.09 -174780.46 8088.7858 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.19937e-06 8304 2 103.7 0.000104146 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.16081e-06 8304 2 103.7 0.000100363 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.25998e-06 8304 2 103.7 9.05181e-05 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.34077e-06 8304 2 103.7 0.000103656 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.28843e-06 8304 2 103.7 0.00010212 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.18775e-06 8304 2 103.7 0.000106209 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.20268e-06 8304 2 103.7 9.11477e-05 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.37091e-06 8304 2 103.7 0.000112752 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.25132e-06 8304 2 103.7 9.89546e-05 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.03439e-06 8304 2 103.7 0.000100465 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.66836e-06 8304 2 103.7 0.000122514 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.09487e-06 8304 2 103.7 9.12374e-05 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.66187e-06 8304 2 103.7 0.000115717 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.07596e-06 8304 2 103.7 9.07568e-05 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.43496e-06 8304 2 103.7 0.000118982 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.224e-06 8304 2 103.7 9.60958e-05 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.30263e-06 8304 2 103.7 0.000103918 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.34646e-06 8304 2 103.7 9.64468e-05 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.14721e-06 8304 2 103.7 8.82251e-05 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.49884e-06 8304 2 103.7 0.000112326 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.44408e-06 8304 2 103.7 0.000111606 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.76521e-06 8304 2 103.7 0.000124063 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.71688e-06 8304 2 103.7 0.000126159 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.70941e-06 8304 2 103.7 0.000134282 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.69242e-06 8304 2 103.7 0.000140897 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.24058e-06 8304 2 103.7 9.18909e-05 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.42022e-06 8304 2 103.7 0.000117347 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.11011e-06 8304 2 103.7 0.00011294 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.44792e-06 8304 2 103.7 0.000123976 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.32167e-06 8304 2 103.7 8.96795e-05 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.38484e-06 8304 2 103.7 9.90809e-05 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.21959e-06 8304 2 103.7 0.000101807 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.17344e-06 8304 2 103.7 9.29754e-05 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.38186e-06 8304 2 103.7 0.000110579 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.25396e-06 8304 2 103.7 0.000104203 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.48218e-06 8304 2 103.7 0.000116007 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.66403e-06 8304 2 103.7 0.000133943 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.4406e-06 8304 2 103.7 0.000102117 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.58482e-06 8304 2 103.7 0.000122132 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.21342e-06 8304 2 103.7 0.000101003 2768 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.43582e-06 8304 2 103.7 0.000114573 2768 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.35808e-06 8304 2 103.7 8.94345e-05 2768 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.52316e-06 8304 2 103.7 0.000116062 2768 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.18174e-06 8304 2 103.7 0.000105667 2768 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.21796e-06 8304 2 103.7 9.11523e-05 2768 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.47859e-06 8304 2 103.7 0.00010211 2768 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.71984e-06 8304 2 103.7 0.000124196 2768 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.07013e-06 8304 2 103.7 9.49482e-05 2768 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.3198e-06 8304 2 103.7 9.59378e-05 2768 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.15159e-06 8304 2 103.7 9.0338e-05 2768 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.19699e-06 8304 2 103.7 9.11647e-05 2768 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.44023e-06 8304 2 103.7 0.000100945 2768 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.46718e-06 8304 2 103.7 0.000103742 2768 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.3615e-06 8304 2 103.7 0.000102175 2768 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.13132e-06 8304 2 103.7 9.11441e-05 2768 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.26924e-06 8304 2 103.7 0.000100066 2768 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.19989e-06 8304 2 103.7 9.02824e-05 2768 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.10826e-06 8304 2 103.7 9.59098e-05 2768 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.20963e-06 8304 2 103.7 9.2746e-05 2768 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.65549e-06 8304 2 103.7 0.000133079 2768 SHAKE stats (type/ave/delta/count) on step 3050000 2 0.97 1.43427e-06 8304 2 103.7 0.000111894 2768 SHAKE stats (type/ave/delta/count) on step 3100000 2 0.97 1.24912e-06 8304 2 103.7 0.000103505 2768 SHAKE stats (type/ave/delta/count) on step 3150000 2 0.97 1.11229e-06 8304 2 103.7 9.21465e-05 2768 SHAKE stats (type/ave/delta/count) on step 3200000 2 0.97 2.32703e-06 8304 2 103.7 0.000133724 2768 SHAKE stats (type/ave/delta/count) on step 3250000 2 0.97 1.08264e-06 8304 2 103.7 9.82075e-05 2768 SHAKE stats (type/ave/delta/count) on step 3300000 2 0.97 1.7514e-06 8304 2 103.7 0.000120798 2768 SHAKE stats (type/ave/delta/count) on step 3350000 2 0.97 1.2248e-06 8304 2 103.7 9.43422e-05 2768 SHAKE stats (type/ave/delta/count) on step 3400000 2 0.97 1.26002e-06 8304 2 103.7 9.03283e-05 2768 SHAKE stats (type/ave/delta/count) on step 3450000 2 0.97 1.27431e-06 8304 2 103.7 0.000100354 2768 SHAKE stats (type/ave/delta/count) on step 3500000 2 0.97 1.37436e-06 8304 2 103.7 0.000136477 2768 SHAKE stats (type/ave/delta/count) on step 3550000 2 0.97 1.10488e-06 8304 2 103.7 9.62642e-05 2768 SHAKE stats (type/ave/delta/count) on step 3600000 2 0.97 1.31084e-06 8304 2 103.7 0.000105025 2768 SHAKE stats (type/ave/delta/count) on step 3650000 2 0.97 1.19059e-06 8304 2 103.7 8.93719e-05 2768 SHAKE stats (type/ave/delta/count) on step 3700000 2 0.97 1.20907e-06 8304 2 103.7 0.000102382 2768 SHAKE stats (type/ave/delta/count) on step 3750000 2 0.97 1.54164e-06 8304 2 103.7 0.00010975 2768 SHAKE stats (type/ave/delta/count) on step 3800000 2 0.97 1.37727e-06 8304 2 103.7 0.000100257 2768 SHAKE stats (type/ave/delta/count) on step 3850000 2 0.97 1.23019e-06 8304 2 103.7 0.000105648 2768 SHAKE stats (type/ave/delta/count) on step 3900000 2 0.97 1.34319e-06 8304 2 103.7 9.78159e-05 2768 SHAKE stats (type/ave/delta/count) on step 3950000 2 0.97 1.37096e-06 8304 2 103.7 0.000110829 2768 SHAKE stats (type/ave/delta/count) on step 4000000 2 0.97 1.74184e-06 8304 2 103.7 0.000132311 2768 SHAKE stats (type/ave/delta/count) on step 4050000 2 0.97 1.52322e-06 8304 2 103.7 0.000112153 2768 SHAKE stats (type/ave/delta/count) on step 4100000 2 0.97 1.21012e-06 8304 2 103.7 9.76548e-05 2768 SHAKE stats (type/ave/delta/count) on step 4150000 2 0.97 1.4237e-06 8304 2 103.7 0.000108244 2768 SHAKE stats (type/ave/delta/count) on step 4200000 2 0.97 1.57975e-06 8304 2 103.7 0.000108372 2768 SHAKE stats (type/ave/delta/count) on step 4250000 2 0.97 1.13897e-06 8304 2 103.7 9.09504e-05 2768 SHAKE stats (type/ave/delta/count) on step 4300000 2 0.97 1.17228e-06 8304 2 103.7 0.000107609 2768 SHAKE stats (type/ave/delta/count) on step 4350000 2 0.97 1.36539e-06 8304 2 103.7 0.000102996 2768 SHAKE stats (type/ave/delta/count) on step 4400000 2 0.97 1.16059e-06 8304 2 103.7 8.96896e-05 2768 SHAKE stats (type/ave/delta/count) on step 4450000 2 0.97 1.45363e-06 8304 2 103.7 0.000131168 2768 SHAKE stats (type/ave/delta/count) on step 4500000 2 0.97 1.2451e-06 8304 2 103.7 0.000104693 2768 SHAKE stats (type/ave/delta/count) on step 4550000 2 0.97 1.35643e-06 8304 2 103.7 9.72453e-05 2768 SHAKE stats (type/ave/delta/count) on step 4600000 2 0.97 1.37415e-06 8304 2 103.7 9.38705e-05 2768 SHAKE stats (type/ave/delta/count) on step 4650000 2 0.97 1.23367e-06 8304 2 103.7 9.9018e-05 2768 SHAKE stats (type/ave/delta/count) on step 4700000 2 0.97 1.19035e-06 8304 2 103.7 8.84798e-05 2768 SHAKE stats (type/ave/delta/count) on step 4750000 2 0.97 1.33301e-06 8304 2 103.7 0.000102786 2768 SHAKE stats (type/ave/delta/count) on step 4800000 2 0.97 1.44998e-06 8304 2 103.7 0.00011351 2768 SHAKE stats (type/ave/delta/count) on step 4850000 2 0.97 1.31853e-06 8304 2 103.7 0.000123625 2768 SHAKE stats (type/ave/delta/count) on step 4900000 2 0.97 1.20341e-06 8304 2 103.7 9.43871e-05 2768 SHAKE stats (type/ave/delta/count) on step 4950000 2 0.97 1.17062e-06 8304 2 103.7 0.000109365 2768 SHAKE stats (type/ave/delta/count) on step 5000000 2 0.97 1.23125e-06 8304 2 103.7 0.000106743 2768 5000000 5000000 -156.33074 192519.71 0.63061093 296.60031 43.49591 73.724935 0 0 21085.412 86545.072 -216.28484 -268039.11 -160291.4 5598.1794 Loop time of 40866.1 on 32 procs for 5000000 steps with 9101 atoms Performance: 10.571 ns/day, 2.270 hours/ns, 122.351 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 | 334.39 | 10025 | 20095 |9168.4 | 24.53 Bond | 4.9034 | 12.918 | 42.701 | 238.0 | 0.03 Kspace | 16257 | 26364 | 36170 |5687.2 | 64.51 Neigh | 1278.3 | 1288 | 1303.8 | 26.2 | 3.15 Comm | 673.59 | 1104.1 | 1396.2 | 826.8 | 2.70 Output | 0.015086 | 0.017099 | 0.018989 | 0.9 | 0.00 Modify | 1773.4 | 1972 | 2273.6 | 454.8 | 4.83 Other | | 99.41 | | | 0.24 Nlocal: 284.406 ave 566 max 0 min Histogram: 10 6 0 0 0 0 0 0 1 15 Nghost: 3148.16 ave 4815 max 1489 min Histogram: 8 8 0 0 0 0 0 0 8 8 Neighs: 74710.1 ave 158232 max 0 min Histogram: 16 0 0 0 0 0 0 0 5 11 Total # of neighbors = 2390724 Ave neighs/atom = 262.68806 Ave special neighs/atom = 1.8929788 Neighbor list builds = 249838 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) = 0.32037747 grid = 45 45 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0030966253 estimated relative force accuracy = 9.3253951e-06 using double precision KISS FFT 3d grid and FFT values/proc = 13050 6075 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 5000000 2 0.97 1.23125e-06 8304 2 103.7 0.000106743 2768 Per MPI rank memory allocation (min/avg/max) = 11.9 | 13.07 | 13.54 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 -155.85093 192519.71 0.63061093 296.60031 43.49591 73.724935 0 0 21085.412 86545.072 -216.28484 -268039.11 -160291.4 5598.1794 Loop time of 9.66881e-06 on 32 procs for 0 steps with 9101 atoms 101.8% 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 | | 9.669e-06 | | |100.00 Nlocal: 284.406 ave 566 max 0 min Histogram: 10 6 0 0 0 0 0 0 1 15 Nghost: 3148.16 ave 4815 max 1489 min Histogram: 8 8 0 0 0 0 0 0 8 8 Neighs: 74710.1 ave 158232 max 0 min Histogram: 16 0 0 0 0 0 0 0 5 11 Total # of neighbors = 2390724 Ave neighs/atom = 262.68806 Ave special neighs/atom = 1.8929788 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out