#------------------------------------------------------------------------------- # Stage 2.4: NVT integration for 3 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 300000 300000 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 300 1 300 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 3000000 2.4.restart dump sci all custom 300000 2.4.xyz id mol type q xs ys zs timestep 1 run 3000000 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 3000000 3000000 335368.31 143799.62 1.371895 295.64307 290.44841 346.89391 0 0 271545.54 -52488.575 -383.45046 -378987.48 -159293.17 8118.1287 Loop time of 63060.9 on 16 procs for 3000000 steps with 13901 atoms Performance: 4.110 ns/day, 5.839 hours/ns, 47.573 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 | 30505 | 35900 | 49790 |3942.6 | 56.93 Bond | 13.291 | 36.61 | 92.056 | 510.2 | 0.06 Kspace | 7928.2 | 21878 | 27313 |5074.2 | 34.69 Neigh | 2657.9 | 2660.9 | 2664.3 | 3.8 | 4.22 Comm | 967.28 | 1029.1 | 1092.9 | 132.9 | 1.63 Output | 0.021444 | 0.023722 | 0.025854 | 0.9 | 0.00 Modify | 1417.6 | 1461.4 | 1508.9 | 81.5 | 2.32 Other | | 94.97 | | | 0.15 Nlocal: 868.812 ave 1037 max 780 min Histogram: 6 4 1 0 1 0 0 0 0 4 Nghost: 10406.9 ave 10988 max 9517 min Histogram: 4 0 0 0 0 0 4 3 1 4 Neighs: 487717 ave 674799 max 398886 min Histogram: 6 5 1 0 0 0 0 0 0 4 Total # of neighbors = 7803467 Ave neighs/atom = 561.36012 Ave special neighs/atom = 1.8838932 Neighbor list builds = 150148 Dangerous builds = 0 undump sci restart 0 dump sci all custom 3000000 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 3000000 1 0.97 1.21992e-06 11184 2 103.7 9.14392e-05 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 3000000 3000000 335369.29 143799.62 1.371895 295.64307 290.44841 346.89391 0 0 271545.54 -52488.575 -383.45046 -378987.48 -159293.17 8118.1287 Loop time of 4.22744e-06 on 16 procs for 0 steps with 13901 atoms 118.3% 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 | | 4.227e-06 | | |100.00 Nlocal: 868.812 ave 1037 max 780 min Histogram: 6 4 1 0 1 0 0 0 0 4 Nghost: 10406.9 ave 10988 max 9517 min Histogram: 4 0 0 0 0 0 4 3 1 4 Neighs: 487717 ave 674799 max 398886 min Histogram: 6 5 1 0 0 0 0 0 0 4 Total # of neighbors = 7803467 Ave neighs/atom = 561.36012 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