#------------------------------------------------------------------------------- # Stage 2.5: 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 2.5_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 2.5_instantaneous.txt restart 5000000 2.5.restart dump sci all custom 500000 2.5.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) = 0.32166515 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 1.0029 0.110542 8304 2 97.1661 10.5551 2768 Per MPI rank memory allocation (min/avg/max) = 11.58 | 13.3 | 13.89 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 3017.7362 120303.9 1.009153 428.55654 10.041606 59.611582 0 0 27379.91 67267.702 -346.11593 -269105.87 -174388.61 8088.7858 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.10889e-06 8304 2 103.7 0.000100659 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.08937e-06 8304 2 103.7 0.000100463 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.42618e-06 8304 2 103.7 0.000106729 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.29946e-06 8304 2 103.7 9.60452e-05 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.32699e-06 8304 2 103.7 9.35516e-05 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.29778e-06 8304 2 103.7 9.33713e-05 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.49519e-06 8304 2 103.7 0.000108524 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.52761e-06 8304 2 103.7 0.000114377 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.35864e-06 8304 2 103.7 9.58187e-05 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.19105e-06 8304 2 103.7 9.1871e-05 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.14843e-06 8304 2 103.7 0.000107245 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.7616e-06 8304 2 103.7 0.000120889 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.39167e-06 8304 2 103.7 9.96481e-05 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.36878e-06 8304 2 103.7 9.79782e-05 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.78284e-06 8304 2 103.7 0.00010112 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.58023e-06 8304 2 103.7 0.000101033 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.09908e-06 8304 2 103.7 0.000107289 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.55998e-06 8304 2 103.7 0.000135839 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.49926e-06 8304 2 103.7 9.37815e-05 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.6321e-06 8304 2 103.7 0.000108555 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.32069e-06 8304 2 103.7 9.41541e-05 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.40347e-06 8304 2 103.7 0.000114106 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.04737e-06 8304 2 103.7 9.74375e-05 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.4684e-06 8304 2 103.7 9.26628e-05 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.07249e-06 8304 2 103.7 9.76528e-05 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.38496e-06 8304 2 103.7 0.000113217 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.21517e-06 8304 2 103.7 0.000100671 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.22985e-06 8304 2 103.7 0.000111301 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.18938e-06 8304 2 103.7 9.33399e-05 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.30955e-06 8304 2 103.7 0.000104773 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.18785e-06 8304 2 103.7 0.000102121 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.24168e-06 8304 2 103.7 9.68383e-05 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.06025e-06 8304 2 103.7 9.18979e-05 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.29701e-06 8304 2 103.7 9.92266e-05 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.15822e-06 8304 2 103.7 9.26021e-05 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.26013e-06 8304 2 103.7 0.000101962 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.0708e-06 8304 2 103.7 9.89301e-05 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.15576e-06 8304 2 103.7 9.933e-05 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.16669e-06 8304 2 103.7 9.67095e-05 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.03481e-06 8304 2 103.7 9.24363e-05 2768 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.19773e-06 8304 2 103.7 0.00010632 2768 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.08582e-06 8304 2 103.7 9.12494e-05 2768 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.28738e-06 8304 2 103.7 0.000107464 2768 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.56818e-06 8304 2 103.7 0.000110403 2768 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.28872e-06 8304 2 103.7 9.59439e-05 2768 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.12839e-06 8304 2 103.7 0.000108124 2768 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.15833e-06 8304 2 103.7 9.57674e-05 2768 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.47499e-06 8304 2 103.7 0.000124499 2768 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.49357e-06 8304 2 103.7 0.000112326 2768 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.4276e-06 8304 2 103.7 0.00011278 2768 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.17344e-06 8304 2 103.7 9.15363e-05 2768 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.19774e-06 8304 2 103.7 9.41966e-05 2768 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.27855e-06 8304 2 103.7 9.66903e-05 2768 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.22318e-06 8304 2 103.7 8.91486e-05 2768 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.03916e-06 8304 2 103.7 9.18825e-05 2768 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.5091e-06 8304 2 103.7 0.000114583 2768 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.45864e-06 8304 2 103.7 0.000112543 2768 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.15652e-06 8304 2 103.7 9.62326e-05 2768 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.19616e-06 8304 2 103.7 9.83076e-05 2768 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.34591e-06 8304 2 103.7 0.000103016 2768 SHAKE stats (type/ave/delta/count) on step 3050000 2 0.97 1.41486e-06 8304 2 103.7 0.000105586 2768 SHAKE stats (type/ave/delta/count) on step 3100000 2 0.97 1.46726e-06 8304 2 103.7 9.57298e-05 2768 SHAKE stats (type/ave/delta/count) on step 3150000 2 0.97 1.61054e-06 8304 2 103.7 0.000150479 2768 SHAKE stats (type/ave/delta/count) on step 3200000 2 0.97 1.24401e-06 8304 2 103.7 0.000126394 2768 SHAKE stats (type/ave/delta/count) on step 3250000 2 0.97 1.26806e-06 8304 2 103.7 9.87959e-05 2768 SHAKE stats (type/ave/delta/count) on step 3300000 2 0.97 1.35592e-06 8304 2 103.7 9.97667e-05 2768 SHAKE stats (type/ave/delta/count) on step 3350000 2 0.97 1.42884e-06 8304 2 103.7 0.000125249 2768 SHAKE stats (type/ave/delta/count) on step 3400000 2 0.97 1.32465e-06 8304 2 103.7 0.000105516 2768 SHAKE stats (type/ave/delta/count) on step 3450000 2 0.97 1.1281e-06 8304 2 103.7 0.000100949 2768 SHAKE stats (type/ave/delta/count) on step 3500000 2 0.97 1.32054e-06 8304 2 103.7 9.83884e-05 2768 SHAKE stats (type/ave/delta/count) on step 3550000 2 0.97 1.18925e-06 8304 2 103.7 9.76835e-05 2768 SHAKE stats (type/ave/delta/count) on step 3600000 2 0.97 1.34678e-06 8304 2 103.7 9.2992e-05 2768 SHAKE stats (type/ave/delta/count) on step 3650000 2 0.97 1.15837e-06 8304 2 103.7 9.47479e-05 2768 SHAKE stats (type/ave/delta/count) on step 3700000 2 0.97 1.22107e-06 8304 2 103.7 0.000114529 2768 SHAKE stats (type/ave/delta/count) on step 3750000 2 0.97 1.12115e-06 8304 2 103.7 9.20864e-05 2768 SHAKE stats (type/ave/delta/count) on step 3800000 2 0.97 1.1417e-06 8304 2 103.7 9.27454e-05 2768 SHAKE stats (type/ave/delta/count) on step 3850000 2 0.97 1.36615e-06 8304 2 103.7 9.70471e-05 2768 SHAKE stats (type/ave/delta/count) on step 3900000 2 0.97 1.60247e-06 8304 2 103.7 0.000105558 2768 SHAKE stats (type/ave/delta/count) on step 3950000 2 0.97 1.56661e-06 8304 2 103.7 0.00010876 2768 SHAKE stats (type/ave/delta/count) on step 4000000 2 0.97 1.56027e-06 8304 2 103.7 0.000113981 2768 SHAKE stats (type/ave/delta/count) on step 4050000 2 0.97 1.19545e-06 8304 2 103.7 0.000107065 2768 SHAKE stats (type/ave/delta/count) on step 4100000 2 0.97 1.10406e-06 8304 2 103.7 8.90849e-05 2768 SHAKE stats (type/ave/delta/count) on step 4150000 2 0.97 1.37283e-06 8304 2 103.7 0.000107698 2768 SHAKE stats (type/ave/delta/count) on step 4200000 2 0.97 1.67655e-06 8304 2 103.7 0.000126284 2768 SHAKE stats (type/ave/delta/count) on step 4250000 2 0.97 1.49299e-06 8304 2 103.7 0.000117381 2768 SHAKE stats (type/ave/delta/count) on step 4300000 2 0.97 1.32448e-06 8304 2 103.7 0.000103096 2768 SHAKE stats (type/ave/delta/count) on step 4350000 2 0.97 1.05978e-06 8304 2 103.7 0.000100685 2768 SHAKE stats (type/ave/delta/count) on step 4400000 2 0.97 1.49141e-06 8304 2 103.7 0.000124954 2768 SHAKE stats (type/ave/delta/count) on step 4450000 2 0.97 1.83559e-06 8304 2 103.7 0.00011115 2768 SHAKE stats (type/ave/delta/count) on step 4500000 2 0.97 1.16265e-06 8304 2 103.7 9.7953e-05 2768 SHAKE stats (type/ave/delta/count) on step 4550000 2 0.97 1.28211e-06 8304 2 103.7 9.97592e-05 2768 SHAKE stats (type/ave/delta/count) on step 4600000 2 0.97 1.43082e-06 8304 2 103.7 0.000100212 2768 SHAKE stats (type/ave/delta/count) on step 4650000 2 0.97 1.12805e-06 8304 2 103.7 9.75665e-05 2768 SHAKE stats (type/ave/delta/count) on step 4700000 2 0.97 1.03501e-06 8304 2 103.7 9.38873e-05 2768 SHAKE stats (type/ave/delta/count) on step 4750000 2 0.97 1.38132e-06 8304 2 103.7 0.000112932 2768 SHAKE stats (type/ave/delta/count) on step 4800000 2 0.97 1.28987e-06 8304 2 103.7 8.86422e-05 2768 SHAKE stats (type/ave/delta/count) on step 4850000 2 0.97 1.11079e-06 8304 2 103.7 8.95872e-05 2768 SHAKE stats (type/ave/delta/count) on step 4900000 2 0.97 1.26972e-06 8304 2 103.7 0.000100137 2768 SHAKE stats (type/ave/delta/count) on step 4950000 2 0.97 1.1597e-06 8304 2 103.7 9.22484e-05 2768 SHAKE stats (type/ave/delta/count) on step 5000000 2 0.97 1.07119e-06 8304 2 103.7 0.000123126 2768 5000000 5000000 -661.43774 120303.9 1.009153 296.721 42.294304 62.168528 0 0 21079.543 87017.343 -346.11593 -269045.06 -160843.72 5600.4574 Loop time of 28806.3 on 32 procs for 5000000 steps with 9101 atoms Performance: 14.997 ns/day, 1.600 hours/ns, 173.573 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 | 2951.3 | 10274 | 14010 |4110.5 | 35.67 Bond | 4.9451 | 12.423 | 23.224 | 159.5 | 0.04 Kspace | 10642 | 14360 | 21701 |3493.6 | 49.85 Neigh | 803.45 | 808.2 | 813.66 | 11.5 | 2.81 Comm | 1189.8 | 1503.4 | 1632.8 | 437.7 | 5.22 Output | 0.011312 | 0.013661 | 0.015897 | 1.2 | 0.00 Modify | 1663.6 | 1764 | 2023.5 | 347.8 | 6.12 Other | | 84.47 | | | 0.29 Nlocal: 284.406 ave 366 max 68 min Histogram: 2 4 2 0 0 0 0 0 4 20 Nghost: 4150.81 ave 5087 max 3549 min Histogram: 8 0 12 4 0 0 0 0 0 8 Neighs: 76596.3 ave 107481 max 11437 min Histogram: 4 4 0 0 0 0 0 6 6 12 Total # of neighbors = 2451081 Ave neighs/atom = 269.31996 Ave special neighs/atom = 1.8929788 Neighbor list builds = 248880 Dangerous builds = 0 undump sci restart 0 dump sci all custom 5000000 2.5.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 5000000 2 0.97 1.07119e-06 8304 2 103.7 0.000123126 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 5000000 5000000 -660.69648 120303.9 1.009153 296.721 42.294304 62.168528 0 0 21079.543 87017.343 -346.11593 -269045.06 -160843.72 5600.4574 Loop time of 1.58041e-05 on 32 procs for 0 steps with 9101 atoms 109.1% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 1.58e-05 | | |100.00 Nlocal: 284.406 ave 366 max 68 min Histogram: 2 4 2 0 0 0 0 0 4 20 Nghost: 4150.81 ave 5087 max 3549 min Histogram: 8 0 12 4 0 0 0 0 0 8 Neighs: 76596.3 ave 107481 max 11437 min Histogram: 4 4 0 0 0 0 0 6 6 12 Total # of neighbors = 2451081 Ave neighs/atom = 269.31996 Ave special neighs/atom = 1.8929788 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.6_NVT.out