#------------------------------------------------------------------------------- # 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) = 0.22644817 grid = 20 20 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0036818993 estimated relative force accuracy = 1.108793e-05 using double precision KISS FFT 3d grid and FFT values/proc = 3757 800 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 1.0003 0.0586965 6000 1 97.8518 9.1514 2000 Per MPI rank memory allocation (min/avg/max) = 8.121 | 9.596 | 11.08 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 1604.5569 119700 0.49983619 447.33728 0 0 0 0 9624.5005 52156.944 -41.077287 -93227.875 -31446.43 5332.3765 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.09279e-06 6000 1 103.7 9.0054e-05 2000 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.59498e-06 6000 1 103.7 0.000117197 2000 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.646e-06 6000 1 103.7 0.000111321 2000 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.24235e-06 6000 1 103.7 0.000113005 2000 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.21872e-06 6000 1 103.7 9.15041e-05 2000 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.23067e-06 6000 1 103.7 9.48279e-05 2000 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.3963e-06 6000 1 103.7 0.000137153 2000 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.21422e-06 6000 1 103.7 9.85052e-05 2000 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.35085e-06 6000 1 103.7 9.27751e-05 2000 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.06838e-06 6000 1 103.7 9.52433e-05 2000 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.26135e-06 6000 1 103.7 9.32488e-05 2000 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.18964e-06 6000 1 103.7 9.23287e-05 2000 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.26296e-06 6000 1 103.7 0.000104096 2000 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.12285e-06 6000 1 103.7 9.0339e-05 2000 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.24551e-06 6000 1 103.7 0.000100311 2000 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.42809e-06 6000 1 103.7 9.53915e-05 2000 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.20745e-06 6000 1 103.7 9.54473e-05 2000 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.3086e-06 6000 1 103.7 0.000100796 2000 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.11553e-06 6000 1 103.7 9.35236e-05 2000 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.136e-06 6000 1 103.7 8.95068e-05 2000 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.97 1.13254e-06 6000 1 103.7 0.00010332 2000 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.97 1.44935e-06 6000 1 103.7 0.000107042 2000 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.97 1.25999e-06 6000 1 103.7 8.59331e-05 2000 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.97 1.2091e-06 6000 1 103.7 9.37771e-05 2000 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.97 1.29386e-06 6000 1 103.7 0.000120601 2000 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.97 1.42228e-06 6000 1 103.7 0.000102725 2000 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.97 1.67036e-06 6000 1 103.7 0.000118886 2000 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.97 1.11565e-06 6000 1 103.7 9.78362e-05 2000 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.97 1.41299e-06 6000 1 103.7 0.000120491 2000 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.97 1.36938e-06 6000 1 103.7 0.000102977 2000 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.97 1.36291e-06 6000 1 103.7 9.81772e-05 2000 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.97 1.61643e-06 6000 1 103.7 0.000105603 2000 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.97 1.60589e-06 6000 1 103.7 0.000117766 2000 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.97 1.45809e-06 6000 1 103.7 0.000107049 2000 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.97 1.72087e-06 6000 1 103.7 0.000119746 2000 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.97 1.49944e-06 6000 1 103.7 9.96913e-05 2000 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.97 1.76503e-06 6000 1 103.7 0.000109458 2000 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.97 1.26582e-06 6000 1 103.7 9.35548e-05 2000 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.97 1.48111e-06 6000 1 103.7 0.000105315 2000 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.96441e-06 6000 1 103.7 0.000134183 2000 SHAKE stats (type/ave/delta/count) on step 2050000 1 0.97 1.18615e-06 6000 1 103.7 0.000115028 2000 SHAKE stats (type/ave/delta/count) on step 2100000 1 0.97 1.51262e-06 6000 1 103.7 0.000100365 2000 SHAKE stats (type/ave/delta/count) on step 2150000 1 0.97 1.17656e-06 6000 1 103.7 9.51005e-05 2000 SHAKE stats (type/ave/delta/count) on step 2200000 1 0.97 1.23525e-06 6000 1 103.7 0.0001016 2000 SHAKE stats (type/ave/delta/count) on step 2250000 1 0.97 1.48231e-06 6000 1 103.7 0.000100639 2000 SHAKE stats (type/ave/delta/count) on step 2300000 1 0.97 1.24399e-06 6000 1 103.7 9.78227e-05 2000 SHAKE stats (type/ave/delta/count) on step 2350000 1 0.97 1.46692e-06 6000 1 103.7 0.000101518 2000 SHAKE stats (type/ave/delta/count) on step 2400000 1 0.97 1.17771e-06 6000 1 103.7 0.000128247 2000 SHAKE stats (type/ave/delta/count) on step 2450000 1 0.97 1.42742e-06 6000 1 103.7 0.000106639 2000 SHAKE stats (type/ave/delta/count) on step 2500000 1 0.97 1.08344e-06 6000 1 103.7 0.000106473 2000 SHAKE stats (type/ave/delta/count) on step 2550000 1 0.97 1.24649e-06 6000 1 103.7 0.000110847 2000 SHAKE stats (type/ave/delta/count) on step 2600000 1 0.97 1.15095e-06 6000 1 103.7 0.000114971 2000 SHAKE stats (type/ave/delta/count) on step 2650000 1 0.97 1.26623e-06 6000 1 103.7 8.91569e-05 2000 SHAKE stats (type/ave/delta/count) on step 2700000 1 0.97 1.38004e-06 6000 1 103.7 0.000124257 2000 SHAKE stats (type/ave/delta/count) on step 2750000 1 0.97 9.92311e-07 6000 1 103.7 0.000100986 2000 SHAKE stats (type/ave/delta/count) on step 2800000 1 0.97 1.32277e-06 6000 1 103.7 9.58241e-05 2000 SHAKE stats (type/ave/delta/count) on step 2850000 1 0.97 1.30342e-06 6000 1 103.7 9.78555e-05 2000 SHAKE stats (type/ave/delta/count) on step 2900000 1 0.97 1.10917e-06 6000 1 103.7 9.23129e-05 2000 SHAKE stats (type/ave/delta/count) on step 2950000 1 0.97 1.72374e-06 6000 1 103.7 0.000128021 2000 SHAKE stats (type/ave/delta/count) on step 3000000 1 0.97 1.14056e-06 6000 1 103.7 9.80815e-05 2000 SHAKE stats (type/ave/delta/count) on step 3050000 1 0.97 1.45521e-06 6000 1 103.7 9.57614e-05 2000 SHAKE stats (type/ave/delta/count) on step 3100000 1 0.97 1.08186e-06 6000 1 103.7 9.4805e-05 2000 SHAKE stats (type/ave/delta/count) on step 3150000 1 0.97 1.18923e-06 6000 1 103.7 9.57297e-05 2000 SHAKE stats (type/ave/delta/count) on step 3200000 1 0.97 1.57536e-06 6000 1 103.7 0.000110498 2000 SHAKE stats (type/ave/delta/count) on step 3250000 1 0.97 1.42883e-06 6000 1 103.7 0.000107512 2000 SHAKE stats (type/ave/delta/count) on step 3300000 1 0.97 1.27121e-06 6000 1 103.7 9.75269e-05 2000 SHAKE stats (type/ave/delta/count) on step 3350000 1 0.97 1.2672e-06 6000 1 103.7 0.000108846 2000 SHAKE stats (type/ave/delta/count) on step 3400000 1 0.97 1.10712e-06 6000 1 103.7 9.60688e-05 2000 SHAKE stats (type/ave/delta/count) on step 3450000 1 0.97 1.41759e-06 6000 1 103.7 0.00011731 2000 SHAKE stats (type/ave/delta/count) on step 3500000 1 0.97 1.52568e-06 6000 1 103.7 0.000112082 2000 SHAKE stats (type/ave/delta/count) on step 3550000 1 0.97 1.15822e-06 6000 1 103.7 9.10499e-05 2000 SHAKE stats (type/ave/delta/count) on step 3600000 1 0.97 1.30767e-06 6000 1 103.7 0.000107558 2000 SHAKE stats (type/ave/delta/count) on step 3650000 1 0.97 1.11884e-06 6000 1 103.7 9.56907e-05 2000 SHAKE stats (type/ave/delta/count) on step 3700000 1 0.97 1.47868e-06 6000 1 103.7 0.000130255 2000 SHAKE stats (type/ave/delta/count) on step 3750000 1 0.97 1.48696e-06 6000 1 103.7 0.000115445 2000 SHAKE stats (type/ave/delta/count) on step 3800000 1 0.97 1.28334e-06 6000 1 103.7 9.4028e-05 2000 SHAKE stats (type/ave/delta/count) on step 3850000 1 0.97 1.79945e-06 6000 1 103.7 0.00012193 2000 SHAKE stats (type/ave/delta/count) on step 3900000 1 0.97 1.27663e-06 6000 1 103.7 9.95317e-05 2000 SHAKE stats (type/ave/delta/count) on step 3950000 1 0.97 1.73118e-06 6000 1 103.7 0.00011424 2000 SHAKE stats (type/ave/delta/count) on step 4000000 1 0.97 1.25696e-06 6000 1 103.7 0.000102648 2000 SHAKE stats (type/ave/delta/count) on step 4050000 1 0.97 1.2376e-06 6000 1 103.7 0.0001121 2000 SHAKE stats (type/ave/delta/count) on step 4100000 1 0.97 2.12962e-06 6000 1 103.7 0.000132938 2000 SHAKE stats (type/ave/delta/count) on step 4150000 1 0.97 1.70886e-06 6000 1 103.7 0.000107888 2000 SHAKE stats (type/ave/delta/count) on step 4200000 1 0.97 1.20463e-06 6000 1 103.7 9.30347e-05 2000 SHAKE stats (type/ave/delta/count) on step 4250000 1 0.97 1.22358e-06 6000 1 103.7 0.000124754 2000 SHAKE stats (type/ave/delta/count) on step 4300000 1 0.97 1.27977e-06 6000 1 103.7 9.48083e-05 2000 SHAKE stats (type/ave/delta/count) on step 4350000 1 0.97 1.27184e-06 6000 1 103.7 0.000100094 2000 SHAKE stats (type/ave/delta/count) on step 4400000 1 0.97 1.5027e-06 6000 1 103.7 9.72515e-05 2000 SHAKE stats (type/ave/delta/count) on step 4450000 1 0.97 1.52414e-06 6000 1 103.7 0.000114458 2000 SHAKE stats (type/ave/delta/count) on step 4500000 1 0.97 1.08652e-06 6000 1 103.7 9.09724e-05 2000 SHAKE stats (type/ave/delta/count) on step 4550000 1 0.97 1.10275e-06 6000 1 103.7 0.000105588 2000 SHAKE stats (type/ave/delta/count) on step 4600000 1 0.97 1.25797e-06 6000 1 103.7 9.59757e-05 2000 SHAKE stats (type/ave/delta/count) on step 4650000 1 0.97 1.21637e-06 6000 1 103.7 0.000100483 2000 SHAKE stats (type/ave/delta/count) on step 4700000 1 0.97 1.38027e-06 6000 1 103.7 0.000123677 2000 SHAKE stats (type/ave/delta/count) on step 4750000 1 0.97 1.17863e-06 6000 1 103.7 9.23045e-05 2000 SHAKE stats (type/ave/delta/count) on step 4800000 1 0.97 1.58927e-06 6000 1 103.7 0.000116025 2000 SHAKE stats (type/ave/delta/count) on step 4850000 1 0.97 2.03821e-06 6000 1 103.7 0.00013185 2000 SHAKE stats (type/ave/delta/count) on step 4900000 1 0.97 1.33622e-06 6000 1 103.7 0.00011593 2000 SHAKE stats (type/ave/delta/count) on step 4950000 1 0.97 1.37517e-06 6000 1 103.7 0.000100927 2000 SHAKE stats (type/ave/delta/count) on step 5000000 1 0.97 1.43251e-06 6000 1 103.7 0.000103796 2000 5000000 5000000 -116.99543 119700 0.49983619 300.80388 0 0 0 0 5105.667 66836.152 -41.077287 -93208.705 -21266.886 3585.6603 Loop time of 46081.5 on 32 procs for 5000000 steps with 6000 atoms Performance: 9.375 ns/day, 2.560 hours/ns, 108.503 timesteps/s 98.2% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.6008 | 16681 | 35723 |12642.0 | 36.20 Bond | 3.3775 | 5.3441 | 8.1479 | 42.5 | 0.01 Kspace | 5976.5 | 25178 | 42233 |10382.5 | 54.64 Neigh | 1734.2 | 1753.2 | 1798.7 | 49.3 | 3.80 Comm | 105.48 | 802.32 | 1175.5 |1414.3 | 1.74 Output | 0.010332 | 0.011909 | 0.013281 | 0.8 | 0.00 Modify | 1351.9 | 1569.6 | 1869.3 | 514.6 | 3.41 Other | | 92.08 | | | 0.20 Nlocal: 187.5 ave 386 max 0 min Histogram: 14 2 0 0 0 0 0 0 2 14 Nghost: 4529.62 ave 8999 max 3 min Histogram: 8 0 0 8 0 0 4 4 0 8 Neighs: 119962 ave 268824 max 0 min Histogram: 16 0 0 0 0 0 0 4 2 10 Total # of neighbors = 3838793 Ave neighs/atom = 639.79883 Ave special neighs/atom = 2 Neighbor list builds = 247468 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) = 0.22644817 grid = 20 20 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0036818993 estimated relative force accuracy = 1.108793e-05 using double precision KISS FFT 3d grid and FFT values/proc = 3757 800 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 5000000 1 0.97 1.43251e-06 6000 1 103.7 0.000103796 2000 Per MPI rank memory allocation (min/avg/max) = 8.252 | 9.866 | 11.07 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 -116.73303 119700 0.49983619 300.80388 0 0 0 0 5105.667 66836.152 -41.077287 -93208.705 -21266.886 3585.6603 Loop time of 7.63937e-06 on 32 procs for 0 steps with 6000 atoms 108.8% 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 | | 7.639e-06 | | |100.00 Nlocal: 187.5 ave 386 max 0 min Histogram: 14 2 0 0 0 0 0 0 2 14 Nghost: 4529.62 ave 8999 max 3 min Histogram: 8 0 0 8 0 0 4 4 0 8 Neighs: 119962 ave 268824 max 0 min Histogram: 16 0 0 0 0 0 0 4 2 10 Total # of neighbors = 3838793 Ave neighs/atom = 639.79883 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