#------------------------------------------------------------------------------- # 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) = 0.31995351 grid = 45 45 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0031543348 estimated relative force accuracy = 9.4991856e-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 1.00175 0.0752784 8304 2 97.5474 10.7061 2768 Per MPI rank memory allocation (min/avg/max) = 11.78 | 12.83 | 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-06 281.4958 194899.49 0.62291099 428.55654 8.8997797 52.964169 0 0 26459.055 66922.549 -213.64394 -267929.41 -174485.94 8088.7858 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 9.98643e-07 8304 2 103.7 8.66916e-05 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.46675e-06 8304 2 103.7 0.00010302 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.30411e-06 8304 2 103.7 9.75596e-05 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.17292e-06 8304 2 103.7 0.000117184 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.31629e-06 8304 2 103.7 0.000108414 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.07375e-06 8304 2 103.7 9.19472e-05 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.22297e-06 8304 2 103.7 9.3684e-05 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.1697e-06 8304 2 103.7 9.59285e-05 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.26656e-06 8304 2 103.7 0.000113879 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.28835e-06 8304 2 103.7 0.000106783 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.32898e-06 8304 2 103.7 0.000115778 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.26972e-06 8304 2 103.7 0.000104272 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.22985e-06 8304 2 103.7 0.000108047 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.17616e-06 8304 2 103.7 0.000100106 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.15135e-06 8304 2 103.7 8.92762e-05 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.11236e-06 8304 2 103.7 9.46477e-05 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.13111e-06 8304 2 103.7 9.93123e-05 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.60033e-06 8304 2 103.7 0.000109639 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.24829e-06 8304 2 103.7 0.000100544 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.08604e-06 8304 2 103.7 9.10585e-05 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.18902e-06 8304 2 103.7 9.56984e-05 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.28674e-06 8304 2 103.7 9.17949e-05 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.3165e-06 8304 2 103.7 9.50426e-05 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.18577e-06 8304 2 103.7 9.18063e-05 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.4671e-06 8304 2 103.7 0.000114939 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.37319e-06 8304 2 103.7 0.000110929 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.23994e-06 8304 2 103.7 0.000105913 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.06284e-06 8304 2 103.7 8.75412e-05 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.13433e-06 8304 2 103.7 0.000106044 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.20043e-06 8304 2 103.7 9.41555e-05 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.40264e-06 8304 2 103.7 0.000116473 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.13175e-06 8304 2 103.7 8.96608e-05 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.3168e-06 8304 2 103.7 0.000101724 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.48191e-06 8304 2 103.7 0.000103248 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.12941e-06 8304 2 103.7 8.9663e-05 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.56724e-06 8304 2 103.7 0.000129055 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.24368e-06 8304 2 103.7 0.000102999 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.23208e-06 8304 2 103.7 0.000105393 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.26278e-06 8304 2 103.7 0.000103566 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.36425e-06 8304 2 103.7 9.64242e-05 2768 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.24546e-06 8304 2 103.7 9.01472e-05 2768 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.2241e-06 8304 2 103.7 9.9732e-05 2768 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.23823e-06 8304 2 103.7 9.17393e-05 2768 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.49306e-06 8304 2 103.7 0.000104753 2768 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.20524e-06 8304 2 103.7 9.15773e-05 2768 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.3383e-06 8304 2 103.7 0.00010446 2768 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.15306e-06 8304 2 103.7 8.8819e-05 2768 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.2278e-06 8304 2 103.7 0.000100754 2768 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.0423e-06 8304 2 103.7 8.83386e-05 2768 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.24151e-06 8304 2 103.7 0.000103208 2768 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.26507e-06 8304 2 103.7 0.000101991 2768 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.29643e-06 8304 2 103.7 9.17103e-05 2768 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.18829e-06 8304 2 103.7 9.12762e-05 2768 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.46009e-06 8304 2 103.7 0.000131901 2768 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.30356e-06 8304 2 103.7 9.94785e-05 2768 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.55121e-06 8304 2 103.7 0.00012233 2768 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.1794e-06 8304 2 103.7 0.000114078 2768 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.14635e-06 8304 2 103.7 9.69048e-05 2768 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.39828e-06 8304 2 103.7 0.000102228 2768 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.22166e-06 8304 2 103.7 9.79656e-05 2768 SHAKE stats (type/ave/delta/count) on step 3050000 2 0.97 1.96856e-06 8304 2 103.7 0.000133734 2768 SHAKE stats (type/ave/delta/count) on step 3100000 2 0.97 1.5445e-06 8304 2 103.7 0.000115851 2768 SHAKE stats (type/ave/delta/count) on step 3150000 2 0.97 1.68185e-06 8304 2 103.7 0.000114487 2768 SHAKE stats (type/ave/delta/count) on step 3200000 2 0.97 1.3923e-06 8304 2 103.7 0.00010957 2768 SHAKE stats (type/ave/delta/count) on step 3250000 2 0.97 1.43819e-06 8304 2 103.7 9.76645e-05 2768 SHAKE stats (type/ave/delta/count) on step 3300000 2 0.97 1.35179e-06 8304 2 103.7 9.0706e-05 2768 SHAKE stats (type/ave/delta/count) on step 3350000 2 0.97 1.43823e-06 8304 2 103.7 0.00011813 2768 SHAKE stats (type/ave/delta/count) on step 3400000 2 0.97 1.05033e-06 8304 2 103.7 0.000103511 2768 SHAKE stats (type/ave/delta/count) on step 3450000 2 0.97 1.54975e-06 8304 2 103.7 0.000108352 2768 SHAKE stats (type/ave/delta/count) on step 3500000 2 0.97 1.2606e-06 8304 2 103.7 9.89754e-05 2768 SHAKE stats (type/ave/delta/count) on step 3550000 2 0.97 1.11297e-06 8304 2 103.7 0.000102135 2768 SHAKE stats (type/ave/delta/count) on step 3600000 2 0.97 1.12755e-06 8304 2 103.7 9.60151e-05 2768 SHAKE stats (type/ave/delta/count) on step 3650000 2 0.97 1.53662e-06 8304 2 103.7 0.000134517 2768 SHAKE stats (type/ave/delta/count) on step 3700000 2 0.97 1.12688e-06 8304 2 103.7 0.000103654 2768 SHAKE stats (type/ave/delta/count) on step 3750000 2 0.97 1.49004e-06 8304 2 103.7 0.000109655 2768 SHAKE stats (type/ave/delta/count) on step 3800000 2 0.97 1.47027e-06 8304 2 103.7 0.000104558 2768 SHAKE stats (type/ave/delta/count) on step 3850000 2 0.97 1.19783e-06 8304 2 103.7 9.59993e-05 2768 SHAKE stats (type/ave/delta/count) on step 3900000 2 0.97 1.1402e-06 8304 2 103.7 0.000126689 2768 SHAKE stats (type/ave/delta/count) on step 3950000 2 0.97 1.02591e-06 8304 2 103.7 9.26769e-05 2768 SHAKE stats (type/ave/delta/count) on step 4000000 2 0.97 1.36347e-06 8304 2 103.7 0.000111457 2768 SHAKE stats (type/ave/delta/count) on step 4050000 2 0.97 1.29378e-06 8304 2 103.7 0.00010427 2768 SHAKE stats (type/ave/delta/count) on step 4100000 2 0.97 1.15053e-06 8304 2 103.7 9.18109e-05 2768 SHAKE stats (type/ave/delta/count) on step 4150000 2 0.97 1.47233e-06 8304 2 103.7 0.000102475 2768 SHAKE stats (type/ave/delta/count) on step 4200000 2 0.97 1.20814e-06 8304 2 103.7 0.000109979 2768 SHAKE stats (type/ave/delta/count) on step 4250000 2 0.97 1.39034e-06 8304 2 103.7 0.000113346 2768 SHAKE stats (type/ave/delta/count) on step 4300000 2 0.97 1.08229e-06 8304 2 103.7 9.34659e-05 2768 SHAKE stats (type/ave/delta/count) on step 4350000 2 0.97 1.59117e-06 8304 2 103.7 0.000146007 2768 SHAKE stats (type/ave/delta/count) on step 4400000 2 0.97 1.42205e-06 8304 2 103.7 0.00010356 2768 SHAKE stats (type/ave/delta/count) on step 4450000 2 0.97 1.14392e-06 8304 2 103.7 9.41321e-05 2768 SHAKE stats (type/ave/delta/count) on step 4500000 2 0.97 1.23602e-06 8304 2 103.7 8.48128e-05 2768 SHAKE stats (type/ave/delta/count) on step 4550000 2 0.97 1.39256e-06 8304 2 103.7 0.000108798 2768 SHAKE stats (type/ave/delta/count) on step 4600000 2 0.97 1.44277e-06 8304 2 103.7 9.85518e-05 2768 SHAKE stats (type/ave/delta/count) on step 4650000 2 0.97 1.14793e-06 8304 2 103.7 9.72497e-05 2768 SHAKE stats (type/ave/delta/count) on step 4700000 2 0.97 1.32974e-06 8304 2 103.7 9.85266e-05 2768 SHAKE stats (type/ave/delta/count) on step 4750000 2 0.97 1.91581e-06 8304 2 103.7 0.000152824 2768 SHAKE stats (type/ave/delta/count) on step 4800000 2 0.97 1.40507e-06 8304 2 103.7 9.71312e-05 2768 SHAKE stats (type/ave/delta/count) on step 4850000 2 0.97 1.22667e-06 8304 2 103.7 0.000107966 2768 SHAKE stats (type/ave/delta/count) on step 4900000 2 0.97 1.18052e-06 8304 2 103.7 9.11551e-05 2768 SHAKE stats (type/ave/delta/count) on step 4950000 2 0.97 1.29473e-06 8304 2 103.7 0.000107308 2768 SHAKE stats (type/ave/delta/count) on step 5000000 2 0.97 1.1466e-06 8304 2 103.7 9.66064e-05 2768 5000000 5000000 -40.853156 194899.49 0.62291099 296.25435 37.945843 68.347664 0 0 21189.071 86071.095 -213.64394 -267712.74 -160346.28 5591.6496 Loop time of 41230.5 on 32 procs for 5000000 steps with 9101 atoms Performance: 10.478 ns/day, 2.291 hours/ns, 121.269 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 | 380.79 | 9732.6 | 20835 |9342.0 | 23.61 Bond | 5.0936 | 12.681 | 31.914 | 229.9 | 0.03 Kspace | 16036 | 27165 | 36532 |5622.5 | 65.89 Neigh | 1136.5 | 1145.7 | 1160.6 | 25.8 | 2.78 Comm | 673.67 | 1090.3 | 1391 | 804.1 | 2.64 Output | 0.016382 | 0.01836 | 0.02028 | 0.9 | 0.00 Modify | 1784.7 | 1984.6 | 2264.6 | 444.0 | 4.81 Other | | 99.13 | | | 0.24 Nlocal: 284.406 ave 577 max 2 min Histogram: 15 1 0 0 0 0 0 0 2 14 Nghost: 3125.34 ave 4754 max 1533 min Histogram: 12 4 0 0 0 0 0 0 8 8 Neighs: 74929.9 ave 164900 max 121 min Histogram: 16 0 0 0 0 0 0 1 7 8 Total # of neighbors = 2397756 Ave neighs/atom = 263.46072 Ave special neighs/atom = 1.8929788 Neighbor list builds = 249929 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) = 0.31995351 grid = 45 45 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0031543348 estimated relative force accuracy = 9.4991856e-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 1.1466e-06 8304 2 103.7 9.66064e-05 2768 Per MPI rank memory allocation (min/avg/max) = 12.74 | 13.14 | 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 5000000 5000000 -40.409431 194899.49 0.62291099 296.25435 37.945843 68.347664 0 0 21189.071 86071.095 -213.64394 -267712.74 -160346.28 5591.6496 Loop time of 1.11881e-05 on 32 procs for 0 steps with 9101 atoms 111.7% 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 | | 1.119e-05 | | |100.00 Nlocal: 284.406 ave 577 max 2 min Histogram: 15 1 0 0 0 0 0 0 2 14 Nghost: 3125.34 ave 4754 max 1533 min Histogram: 12 4 0 0 0 0 0 0 8 8 Neighs: 74929.9 ave 164900 max 121 min Histogram: 16 0 0 0 0 0 0 1 7 8 Total # of neighbors = 2397756 Ave neighs/atom = 263.46072 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