#------------------------------------------------------------------------------- # Stage 2.4: NVT integration for 4 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 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 3728 = # 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 400000 400000 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 400 1 400 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 fix 4 fixed setforce 0.0 0.0 0.0 restart 4000000 2.4.restart dump sci all custom 400000 2.4.xyz id mol type q xs ys zs timestep 1 run 4000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25956456 grid = 30 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0028924598 estimated relative force accuracy = 8.7105569e-06 using double precision KISS FFT 3d grid and FFT values/proc = 13068 4800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 1.00477 0.0879879 11184 2 97.712 10.3119 3728 Per MPI rank memory allocation (min/avg/max) = 14.82 | 15.11 | 15.84 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 334452.61 143799.62 1.371895 417.38826 42.78293 239.5781 0 0 276131.16 -77295.259 -383.45046 -379121.09 -180002.83 11461.157 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.46123e-06 11184 2 103.7 0.000106147 3728 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.1761e-06 11184 2 103.7 9.64988e-05 3728 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.24433e-06 11184 2 103.7 9.49013e-05 3728 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.20034e-06 11184 2 103.7 9.83197e-05 3728 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.10129e-06 11184 2 103.7 8.87755e-05 3728 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.34942e-06 11184 2 103.7 9.80411e-05 3728 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.2929e-06 11184 2 103.7 9.39303e-05 3728 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.42992e-06 11184 2 103.7 9.86162e-05 3728 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.19228e-06 11184 2 103.7 9.04637e-05 3728 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.06138e-06 11184 2 103.7 8.65645e-05 3728 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.29556e-06 11184 2 103.7 0.000116607 3728 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.4732e-06 11184 2 103.7 9.12666e-05 3728 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 2.203e-06 11184 2 103.7 0.000129652 3728 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.19728e-06 11184 2 103.7 9.63663e-05 3728 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.15041e-06 11184 2 103.7 0.000102136 3728 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.54853e-06 11184 2 103.7 9.68638e-05 3728 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.33362e-06 11184 2 103.7 0.000101166 3728 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.17322e-06 11184 2 103.7 0.000102167 3728 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.5404e-06 11184 2 103.7 0.000100831 3728 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.2009e-06 11184 2 103.7 9.66299e-05 3728 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.97 1.43655e-06 11184 2 103.7 0.00010281 3728 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.97 1.09533e-06 11184 2 103.7 9.23371e-05 3728 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.97 1.32531e-06 11184 2 103.7 0.000108522 3728 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.97 1.13478e-06 11184 2 103.7 9.11886e-05 3728 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.97 1.10513e-06 11184 2 103.7 9.43828e-05 3728 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.97 1.09659e-06 11184 2 103.7 9.31045e-05 3728 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.97 1.53919e-06 11184 2 103.7 0.000113249 3728 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.97 1.30707e-06 11184 2 103.7 0.000101583 3728 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.97 1.37367e-06 11184 2 103.7 9.56391e-05 3728 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.97 1.15392e-06 11184 2 103.7 9.46862e-05 3728 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.97 1.51966e-06 11184 2 103.7 0.000106856 3728 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.97 1.37394e-06 11184 2 103.7 9.84291e-05 3728 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.97 1.23797e-06 11184 2 103.7 9.66903e-05 3728 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.97 1.10746e-06 11184 2 103.7 8.75513e-05 3728 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.97 1.48215e-06 11184 2 103.7 9.76621e-05 3728 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.97 1.15214e-06 11184 2 103.7 8.84522e-05 3728 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.97 1.21398e-06 11184 2 103.7 0.000111258 3728 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.97 1.19168e-06 11184 2 103.7 9.9736e-05 3728 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.97 1.27126e-06 11184 2 103.7 9.53209e-05 3728 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.16815e-06 11184 2 103.7 9.08974e-05 3728 SHAKE stats (type/ave/delta/count) on step 2050000 1 0.97 1.35906e-06 11184 2 103.7 9.75118e-05 3728 SHAKE stats (type/ave/delta/count) on step 2100000 1 0.97 1.21731e-06 11184 2 103.7 0.00010286 3728 SHAKE stats (type/ave/delta/count) on step 2150000 1 0.97 1.26362e-06 11184 2 103.7 9.2473e-05 3728 SHAKE stats (type/ave/delta/count) on step 2200000 1 0.97 1.24126e-06 11184 2 103.7 9.17109e-05 3728 SHAKE stats (type/ave/delta/count) on step 2250000 1 0.97 1.36668e-06 11184 2 103.7 9.13085e-05 3728 SHAKE stats (type/ave/delta/count) on step 2300000 1 0.97 1.28183e-06 11184 2 103.7 9.60427e-05 3728 SHAKE stats (type/ave/delta/count) on step 2350000 1 0.97 1.37049e-06 11184 2 103.7 9.06101e-05 3728 SHAKE stats (type/ave/delta/count) on step 2400000 1 0.97 1.30233e-06 11184 2 103.7 0.000102265 3728 SHAKE stats (type/ave/delta/count) on step 2450000 1 0.97 1.74593e-06 11184 2 103.7 0.000101814 3728 SHAKE stats (type/ave/delta/count) on step 2500000 1 0.97 1.12799e-06 11184 2 103.7 9.55359e-05 3728 SHAKE stats (type/ave/delta/count) on step 2550000 1 0.97 1.43889e-06 11184 2 103.7 0.000120011 3728 SHAKE stats (type/ave/delta/count) on step 2600000 1 0.97 1.20553e-06 11184 2 103.7 9.5577e-05 3728 SHAKE stats (type/ave/delta/count) on step 2650000 1 0.97 1.31935e-06 11184 2 103.7 9.75806e-05 3728 SHAKE stats (type/ave/delta/count) on step 2700000 1 0.97 1.24672e-06 11184 2 103.7 9.54913e-05 3728 SHAKE stats (type/ave/delta/count) on step 2750000 1 0.97 1.2925e-06 11184 2 103.7 9.44346e-05 3728 SHAKE stats (type/ave/delta/count) on step 2800000 1 0.97 1.35655e-06 11184 2 103.7 9.93477e-05 3728 SHAKE stats (type/ave/delta/count) on step 2850000 1 0.97 1.26963e-06 11184 2 103.7 9.68046e-05 3728 SHAKE stats (type/ave/delta/count) on step 2900000 1 0.97 1.33421e-06 11184 2 103.7 9.62623e-05 3728 SHAKE stats (type/ave/delta/count) on step 2950000 1 0.97 1.21296e-06 11184 2 103.7 0.000103964 3728 SHAKE stats (type/ave/delta/count) on step 3000000 1 0.97 1.21992e-06 11184 2 103.7 9.14392e-05 3728 SHAKE stats (type/ave/delta/count) on step 3050000 1 0.97 1.56145e-06 11184 2 103.7 0.000111492 3728 SHAKE stats (type/ave/delta/count) on step 3100000 1 0.97 1.11043e-06 11184 2 103.7 9.20175e-05 3728 SHAKE stats (type/ave/delta/count) on step 3150000 1 0.97 1.54687e-06 11184 2 103.7 9.84533e-05 3728 SHAKE stats (type/ave/delta/count) on step 3200000 1 0.97 1.07919e-06 11184 2 103.7 9.11308e-05 3728 SHAKE stats (type/ave/delta/count) on step 3250000 1 0.97 1.30334e-06 11184 2 103.7 9.39008e-05 3728 SHAKE stats (type/ave/delta/count) on step 3300000 1 0.97 1.54972e-06 11184 2 103.7 0.000100964 3728 SHAKE stats (type/ave/delta/count) on step 3350000 1 0.97 1.31867e-06 11184 2 103.7 0.000100481 3728 SHAKE stats (type/ave/delta/count) on step 3400000 1 0.97 1.30637e-06 11184 2 103.7 0.000110536 3728 SHAKE stats (type/ave/delta/count) on step 3450000 1 0.97 1.20118e-06 11184 2 103.7 9.55839e-05 3728 SHAKE stats (type/ave/delta/count) on step 3500000 1 0.97 1.26951e-06 11184 2 103.7 9.87199e-05 3728 SHAKE stats (type/ave/delta/count) on step 3550000 1 0.97 1.25637e-06 11184 2 103.7 9.36474e-05 3728 SHAKE stats (type/ave/delta/count) on step 3600000 1 0.97 1.36027e-06 11184 2 103.7 0.000105544 3728 SHAKE stats (type/ave/delta/count) on step 3650000 1 0.97 1.18986e-06 11184 2 103.7 8.81775e-05 3728 SHAKE stats (type/ave/delta/count) on step 3700000 1 0.97 1.11918e-06 11184 2 103.7 8.92002e-05 3728 SHAKE stats (type/ave/delta/count) on step 3750000 1 0.97 1.18178e-06 11184 2 103.7 9.34234e-05 3728 SHAKE stats (type/ave/delta/count) on step 3800000 1 0.97 1.29127e-06 11184 2 103.7 9.35936e-05 3728 SHAKE stats (type/ave/delta/count) on step 3850000 1 0.97 1.3032e-06 11184 2 103.7 0.000101308 3728 SHAKE stats (type/ave/delta/count) on step 3900000 1 0.97 1.58935e-06 11184 2 103.7 9.71624e-05 3728 SHAKE stats (type/ave/delta/count) on step 3950000 1 0.97 1.63331e-06 11184 2 103.7 9.66549e-05 3728 SHAKE stats (type/ave/delta/count) on step 4000000 1 0.97 1.43211e-06 11184 2 103.7 0.000121842 3728 4000000 4000000 335270.76 143799.62 1.371895 301.86752 266.0513 349.54781 0 0 271213.24 -52032.778 -383.45046 -378994.61 -159198.55 8289.0472 Loop time of 86293.5 on 16 procs for 4000000 steps with 13901 atoms Performance: 4.005 ns/day, 5.993 hours/ns, 46.353 timesteps/s 98.6% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 41708 | 49211 | 67726 |4536.4 | 57.03 Bond | 20.005 | 51.964 | 124.64 | 575.2 | 0.06 Kspace | 10984 | 29588 | 37149 |5878.1 | 34.29 Neigh | 3630.7 | 3635.3 | 3640.5 | 4.8 | 4.21 Comm | 1459.4 | 1539.8 | 1624.4 | 134.5 | 1.78 Output | 0.021558 | 0.02387 | 0.025975 | 0.9 | 0.00 Modify | 2069.2 | 2124.7 | 2177.4 | 79.2 | 2.46 Other | | 142.6 | | | 0.17 Nlocal: 868.812 ave 1037 max 787 min Histogram: 6 4 2 0 0 0 0 0 0 4 Nghost: 10403 ave 11009 max 9513 min Histogram: 4 0 0 0 0 0 5 3 0 4 Neighs: 487501 ave 673271 max 401825 min Histogram: 6 6 0 0 0 0 0 0 0 4 Total # of neighbors = 7800010 Ave neighs/atom = 561.11143 Ave special neighs/atom = 1.8838932 Neighbor list builds = 200195 Dangerous builds = 0 undump sci restart 0 dump sci all custom 4000000 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) = 0.25956456 grid = 30 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0028924598 estimated relative force accuracy = 8.7105569e-06 using double precision KISS FFT 3d grid and FFT values/proc = 13068 4800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 4000000 1 0.97 1.43211e-06 11184 2 103.7 0.000121842 3728 Per MPI rank memory allocation (min/avg/max) = 14.82 | 15.16 | 16.22 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 4000000 4000000 335271.88 143799.62 1.371895 301.86752 266.0513 349.54781 0 0 271213.24 -52032.778 -383.45046 -378994.61 -159198.55 8289.0472 Loop time of 5.58237e-06 on 16 procs for 0 steps with 13901 atoms 114.2% CPU use with 16 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 | | 5.582e-06 | | |100.00 Nlocal: 868.812 ave 1037 max 787 min Histogram: 6 4 2 0 0 0 0 0 0 4 Nghost: 10403 ave 11009 max 9513 min Histogram: 4 0 0 0 0 0 5 3 0 4 Neighs: 487501 ave 673271 max 401825 min Histogram: 6 6 0 0 0 0 0 0 0 4 Total # of neighbors = 7800010 Ave neighs/atom = 561.11143 Ave special neighs/atom = 1.8838932 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken log 2.5_Custom.out