#------------------------------------------------------------------------------- # 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 = 0.002 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) = 0.31993305 grid = 45 45 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0031567238 estimated relative force accuracy = 9.50638e-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 1.00176 0.0794785 8304 2 97.5597 11.9536 2768 Per MPI rank memory allocation (min/avg/max) = 11.77 | 12.85 | 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 0 1e-06 742.96499 195066.49 0.62237772 428.55654 8.0932115 36.639755 0 0 26562.716 66820.623 -213.46104 -267927.22 -174499.15 8088.7858 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.29184e-06 8304 2 103.7 0.000114998 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.19324e-06 8304 2 103.7 9.33526e-05 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.39743e-06 8304 2 103.7 9.71771e-05 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.19531e-06 8304 2 103.7 9.35651e-05 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.66257e-06 8304 2 103.7 0.000105076 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.34508e-06 8304 2 103.7 0.000129862 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.32157e-06 8304 2 103.7 0.000109725 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.26067e-06 8304 2 103.7 9.98898e-05 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.09013e-06 8304 2 103.7 9.14291e-05 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.94137e-06 8304 2 103.7 0.000120854 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.54966e-06 8304 2 103.7 0.000117242 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.22972e-06 8304 2 103.7 9.04649e-05 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.27008e-06 8304 2 103.7 0.000131676 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.26674e-06 8304 2 103.7 9.39074e-05 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.17587e-06 8304 2 103.7 9.05108e-05 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.10114e-06 8304 2 103.7 9.39069e-05 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.71987e-06 8304 2 103.7 0.000129186 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.17881e-06 8304 2 103.7 9.56435e-05 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.5361e-06 8304 2 103.7 0.000114766 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.17775e-06 8304 2 103.7 0.00010344 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.13649e-06 8304 2 103.7 9.54004e-05 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.33139e-06 8304 2 103.7 0.000101081 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.44827e-06 8304 2 103.7 0.000103146 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.30279e-06 8304 2 103.7 0.000111635 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.27741e-06 8304 2 103.7 9.15073e-05 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.19832e-06 8304 2 103.7 0.000102629 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.64072e-06 8304 2 103.7 9.21916e-05 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.45103e-06 8304 2 103.7 0.000108681 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.1754e-06 8304 2 103.7 9.01083e-05 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.43089e-06 8304 2 103.7 0.000109471 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.10249e-06 8304 2 103.7 9.00226e-05 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.58355e-06 8304 2 103.7 0.000116247 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.29518e-06 8304 2 103.7 9.45311e-05 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.21337e-06 8304 2 103.7 9.18321e-05 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.23299e-06 8304 2 103.7 8.96629e-05 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.16873e-06 8304 2 103.7 9.4212e-05 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.72263e-06 8304 2 103.7 0.000127618 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.16841e-06 8304 2 103.7 0.000102065 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.23839e-06 8304 2 103.7 9.55008e-05 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.16483e-06 8304 2 103.7 8.7874e-05 2768 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.18176e-06 8304 2 103.7 0.000100579 2768 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.14179e-06 8304 2 103.7 9.58703e-05 2768 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.41073e-06 8304 2 103.7 9.24748e-05 2768 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.40719e-06 8304 2 103.7 0.000106608 2768 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.26326e-06 8304 2 103.7 0.000107785 2768 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.50362e-06 8304 2 103.7 0.000112258 2768 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.21736e-06 8304 2 103.7 9.72038e-05 2768 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.11645e-06 8304 2 103.7 9.34079e-05 2768 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.07072e-06 8304 2 103.7 9.09136e-05 2768 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.10864e-06 8304 2 103.7 9.28037e-05 2768 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.25686e-06 8304 2 103.7 9.02677e-05 2768 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.66463e-06 8304 2 103.7 0.000123109 2768 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.7345e-06 8304 2 103.7 0.000131354 2768 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.29189e-06 8304 2 103.7 9.34415e-05 2768 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.36063e-06 8304 2 103.7 9.63787e-05 2768 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.29577e-06 8304 2 103.7 0.000105731 2768 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.20629e-06 8304 2 103.7 8.90947e-05 2768 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.14577e-06 8304 2 103.7 9.05317e-05 2768 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.15147e-06 8304 2 103.7 9.51552e-05 2768 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.33767e-06 8304 2 103.7 0.000101564 2768 SHAKE stats (type/ave/delta/count) on step 3050000 2 0.97 1.52505e-06 8304 2 103.7 0.000114873 2768 SHAKE stats (type/ave/delta/count) on step 3100000 2 0.97 1.16112e-06 8304 2 103.7 8.68144e-05 2768 SHAKE stats (type/ave/delta/count) on step 3150000 2 0.97 1.17042e-06 8304 2 103.7 9.82872e-05 2768 SHAKE stats (type/ave/delta/count) on step 3200000 2 0.97 1.63694e-06 8304 2 103.7 0.000135418 2768 SHAKE stats (type/ave/delta/count) on step 3250000 2 0.97 1.78987e-06 8304 2 103.7 0.0001258 2768 SHAKE stats (type/ave/delta/count) on step 3300000 2 0.97 1.23015e-06 8304 2 103.7 9.50997e-05 2768 SHAKE stats (type/ave/delta/count) on step 3350000 2 0.97 1.09895e-06 8304 2 103.7 9.2656e-05 2768 SHAKE stats (type/ave/delta/count) on step 3400000 2 0.97 1.34933e-06 8304 2 103.7 0.000118008 2768 SHAKE stats (type/ave/delta/count) on step 3450000 2 0.97 1.13384e-06 8304 2 103.7 0.000111207 2768 SHAKE stats (type/ave/delta/count) on step 3500000 2 0.97 1.31469e-06 8304 2 103.7 9.45844e-05 2768 SHAKE stats (type/ave/delta/count) on step 3550000 2 0.97 1.13718e-06 8304 2 103.7 9.745e-05 2768 SHAKE stats (type/ave/delta/count) on step 3600000 2 0.97 1.55158e-06 8304 2 103.7 0.000109345 2768 SHAKE stats (type/ave/delta/count) on step 3650000 2 0.97 1.13479e-06 8304 2 103.7 0.000108289 2768 SHAKE stats (type/ave/delta/count) on step 3700000 2 0.97 1.25673e-06 8304 2 103.7 0.000100407 2768 SHAKE stats (type/ave/delta/count) on step 3750000 2 0.97 1.44145e-06 8304 2 103.7 0.000104328 2768 SHAKE stats (type/ave/delta/count) on step 3800000 2 0.97 1.12602e-06 8304 2 103.7 9.35115e-05 2768 SHAKE stats (type/ave/delta/count) on step 3850000 2 0.97 1.54525e-06 8304 2 103.7 0.000106907 2768 SHAKE stats (type/ave/delta/count) on step 3900000 2 0.97 1.22158e-06 8304 2 103.7 0.000102239 2768 SHAKE stats (type/ave/delta/count) on step 3950000 2 0.97 1.52466e-06 8304 2 103.7 0.000111161 2768 SHAKE stats (type/ave/delta/count) on step 4000000 2 0.97 1.82001e-06 8304 2 103.7 0.000121769 2768 SHAKE stats (type/ave/delta/count) on step 4050000 2 0.97 1.51094e-06 8304 2 103.7 9.96817e-05 2768 SHAKE stats (type/ave/delta/count) on step 4100000 2 0.97 1.47319e-06 8304 2 103.7 0.000103103 2768 SHAKE stats (type/ave/delta/count) on step 4150000 2 0.97 1.37798e-06 8304 2 103.7 0.000107484 2768 SHAKE stats (type/ave/delta/count) on step 4200000 2 0.97 1.19731e-06 8304 2 103.7 0.000103647 2768 SHAKE stats (type/ave/delta/count) on step 4250000 2 0.97 1.14843e-06 8304 2 103.7 9.45331e-05 2768 SHAKE stats (type/ave/delta/count) on step 4300000 2 0.97 1.08144e-06 8304 2 103.7 9.09142e-05 2768 SHAKE stats (type/ave/delta/count) on step 4350000 2 0.97 1.3421e-06 8304 2 103.7 0.000107744 2768 SHAKE stats (type/ave/delta/count) on step 4400000 2 0.97 1.09116e-06 8304 2 103.7 0.000102878 2768 SHAKE stats (type/ave/delta/count) on step 4450000 2 0.97 1.03642e-06 8304 2 103.7 9.41457e-05 2768 SHAKE stats (type/ave/delta/count) on step 4500000 2 0.97 1.24499e-06 8304 2 103.7 9.11105e-05 2768 SHAKE stats (type/ave/delta/count) on step 4550000 2 0.97 1.17801e-06 8304 2 103.7 9.64488e-05 2768 SHAKE stats (type/ave/delta/count) on step 4600000 2 0.97 1.29286e-06 8304 2 103.7 0.000108744 2768 SHAKE stats (type/ave/delta/count) on step 4650000 2 0.97 1.43213e-06 8304 2 103.7 0.000113709 2768 SHAKE stats (type/ave/delta/count) on step 4700000 2 0.97 1.68177e-06 8304 2 103.7 0.00013801 2768 SHAKE stats (type/ave/delta/count) on step 4750000 2 0.97 1.17029e-06 8304 2 103.7 9.10912e-05 2768 SHAKE stats (type/ave/delta/count) on step 4800000 2 0.97 1.0853e-06 8304 2 103.7 8.773e-05 2768 SHAKE stats (type/ave/delta/count) on step 4850000 2 0.97 1.29817e-06 8304 2 103.7 0.000101798 2768 SHAKE stats (type/ave/delta/count) on step 4900000 2 0.97 1.2748e-06 8304 2 103.7 9.71671e-05 2768 SHAKE stats (type/ave/delta/count) on step 4950000 2 0.97 1.40115e-06 8304 2 103.7 9.64729e-05 2768 SHAKE stats (type/ave/delta/count) on step 5000000 2 0.97 1.35721e-06 8304 2 103.7 0.000110311 2768 5000000 5000000 -252.36252 195066.49 0.62237772 299.81888 51.466867 56.653562 0 0 21077.984 86171 -213.46104 -267687.39 -160330.29 5658.9282 Loop time of 40593.5 on 32 procs for 5000000 steps with 9101 atoms Performance: 10.642 ns/day, 2.255 hours/ns, 123.173 timesteps/s 98.7% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 402.12 | 9713.7 | 20372 |9346.5 | 23.93 Bond | 5.3198 | 13.013 | 26.254 | 195.6 | 0.03 Kspace | 15893 | 26574 | 35979 |5682.3 | 65.46 Neigh | 1113 | 1123.6 | 1139.2 | 26.6 | 2.77 Comm | 677.71 | 1088.1 | 1393.7 | 828.0 | 2.68 Output | 0.015263 | 0.017295 | 0.019184 | 0.9 | 0.00 Modify | 1775.5 | 1982.5 | 2276.1 | 460.6 | 4.88 Other | | 98.73 | | | 0.24 Nlocal: 284.406 ave 578 max 0 min Histogram: 15 1 0 0 0 0 0 0 1 15 Nghost: 3124.47 ave 4777 max 1535 min Histogram: 8 8 0 0 0 0 0 0 8 8 Neighs: 74398.7 ave 160081 max 0 min Histogram: 16 0 0 0 0 0 0 0 5 11 Total # of neighbors = 2380759 Ave neighs/atom = 261.59312 Ave special neighs/atom = 1.8929788 Neighbor list builds = 249917 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) = 0.31993305 grid = 45 45 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0031567238 estimated relative force accuracy = 9.50638e-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 1.35721e-06 8304 2 103.7 0.000110311 2768 Per MPI rank memory allocation (min/avg/max) = 11.89 | 13.13 | 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 -251.87993 195066.49 0.62237772 299.81888 51.466867 56.653562 0 0 21077.984 86171 -213.46104 -267687.39 -160330.29 5658.9282 Loop time of 8.45831e-06 on 32 procs for 0 steps with 9101 atoms 106.8% 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 | | 8.458e-06 | | |100.00 Nlocal: 284.406 ave 578 max 0 min Histogram: 15 1 0 0 0 0 0 0 1 15 Nghost: 3124.47 ave 4777 max 1535 min Histogram: 8 8 0 0 0 0 0 0 8 8 Neighs: 74398.7 ave 160081 max 0 min Histogram: 16 0 0 0 0 0 0 0 5 11 Total # of neighbors = 2380759 Ave neighs/atom = 261.59312 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