#------------------------------------------------------------------------------- # Stage 2.5: 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 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 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 v_surfacetension file 2.5_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 v_surfacetension file 2.5_instantaneous.txt restart 3000000 2.5.restart dump sci all custom 300000 2.5.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) = 0.24720763 grid = 27 27 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0033477167 estimated relative force accuracy = 1.0081549e-05 using double precision KISS FFT 3d grid and FFT values/proc = 4800 1458 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 0.97 6.59028e-13 6000 1 103.7 7.79465e-11 2000 Per MPI rank memory allocation (min/avg/max) = 8.315 | 9.727 | 10.6 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 -138.16675 119945.8 0.49881188 298.59171 0 0 0 0 5090.261 75650.561 -52.002031 -101738.46 -20997.637 3559.2906 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.21219e-06 6000 1 103.7 0.000100117 2000 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.22137e-06 6000 1 103.7 8.61355e-05 2000 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.22407e-06 6000 1 103.7 9.78763e-05 2000 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.12003e-06 6000 1 103.7 0.00010942 2000 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.19169e-06 6000 1 103.7 9.73058e-05 2000 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.29671e-06 6000 1 103.7 9.46055e-05 2000 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.66103e-06 6000 1 103.7 0.000126984 2000 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.56077e-06 6000 1 103.7 0.000127252 2000 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.64578e-06 6000 1 103.7 0.000110517 2000 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.74615e-06 6000 1 103.7 0.000120422 2000 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.34992e-06 6000 1 103.7 0.000104752 2000 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.10732e-06 6000 1 103.7 9.8009e-05 2000 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.15352e-06 6000 1 103.7 9.15261e-05 2000 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.02858e-06 6000 1 103.7 8.98824e-05 2000 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.21144e-06 6000 1 103.7 0.000115356 2000 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.51359e-06 6000 1 103.7 0.00011038 2000 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.23941e-06 6000 1 103.7 9.30022e-05 2000 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.50612e-06 6000 1 103.7 0.000118385 2000 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.42042e-06 6000 1 103.7 9.591e-05 2000 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.27171e-06 6000 1 103.7 0.000100088 2000 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.97 1.45554e-06 6000 1 103.7 0.000113134 2000 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.97 1.11707e-06 6000 1 103.7 8.90496e-05 2000 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.97 1.05893e-06 6000 1 103.7 9.71179e-05 2000 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.97 1.18204e-06 6000 1 103.7 9.75051e-05 2000 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.97 1.16263e-06 6000 1 103.7 9.73607e-05 2000 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.97 1.24994e-06 6000 1 103.7 9.53349e-05 2000 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.97 1.45454e-06 6000 1 103.7 0.000141454 2000 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.97 1.52365e-06 6000 1 103.7 0.000115455 2000 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.97 1.20957e-06 6000 1 103.7 9.94437e-05 2000 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.97 1.09235e-06 6000 1 103.7 9.56112e-05 2000 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.97 1.52857e-06 6000 1 103.7 0.000115638 2000 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.97 1.08137e-06 6000 1 103.7 9.0701e-05 2000 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.97 1.27333e-06 6000 1 103.7 9.53069e-05 2000 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.97 1.51863e-06 6000 1 103.7 0.000107987 2000 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.97 1.04036e-06 6000 1 103.7 8.72648e-05 2000 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.97 1.95506e-06 6000 1 103.7 0.000136334 2000 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.97 1.11814e-06 6000 1 103.7 9.23056e-05 2000 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.97 1.18179e-06 6000 1 103.7 0.000100616 2000 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.97 1.87203e-06 6000 1 103.7 0.000134257 2000 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.25268e-06 6000 1 103.7 9.91205e-05 2000 SHAKE stats (type/ave/delta/count) on step 2050000 1 0.97 1.37304e-06 6000 1 103.7 0.000103118 2000 SHAKE stats (type/ave/delta/count) on step 2100000 1 0.97 1.36925e-06 6000 1 103.7 0.000115486 2000 SHAKE stats (type/ave/delta/count) on step 2150000 1 0.97 1.0968e-06 6000 1 103.7 8.96739e-05 2000 SHAKE stats (type/ave/delta/count) on step 2200000 1 0.97 1.12489e-06 6000 1 103.7 0.000115727 2000 SHAKE stats (type/ave/delta/count) on step 2250000 1 0.97 1.46583e-06 6000 1 103.7 0.000117882 2000 SHAKE stats (type/ave/delta/count) on step 2300000 1 0.97 1.15434e-06 6000 1 103.7 0.000110366 2000 SHAKE stats (type/ave/delta/count) on step 2350000 1 0.97 1.27131e-06 6000 1 103.7 9.69614e-05 2000 SHAKE stats (type/ave/delta/count) on step 2400000 1 0.97 1.95501e-06 6000 1 103.7 0.000134395 2000 SHAKE stats (type/ave/delta/count) on step 2450000 1 0.97 2.15363e-06 6000 1 103.7 0.000145253 2000 SHAKE stats (type/ave/delta/count) on step 2500000 1 0.97 1.42213e-06 6000 1 103.7 0.000103459 2000 SHAKE stats (type/ave/delta/count) on step 2550000 1 0.97 1.29549e-06 6000 1 103.7 0.000107235 2000 SHAKE stats (type/ave/delta/count) on step 2600000 1 0.97 1.10288e-06 6000 1 103.7 0.000101723 2000 SHAKE stats (type/ave/delta/count) on step 2650000 1 0.97 1.28541e-06 6000 1 103.7 9.23675e-05 2000 SHAKE stats (type/ave/delta/count) on step 2700000 1 0.97 1.25194e-06 6000 1 103.7 8.67293e-05 2000 SHAKE stats (type/ave/delta/count) on step 2750000 1 0.97 1.16457e-06 6000 1 103.7 9.88683e-05 2000 SHAKE stats (type/ave/delta/count) on step 2800000 1 0.97 1.29432e-06 6000 1 103.7 0.000106426 2000 SHAKE stats (type/ave/delta/count) on step 2850000 1 0.97 1.21715e-06 6000 1 103.7 0.00010091 2000 SHAKE stats (type/ave/delta/count) on step 2900000 1 0.97 1.10681e-06 6000 1 103.7 8.39419e-05 2000 SHAKE stats (type/ave/delta/count) on step 2950000 1 0.97 1.75924e-06 6000 1 103.7 0.000124724 2000 SHAKE stats (type/ave/delta/count) on step 3000000 1 0.97 1.50205e-06 6000 1 103.7 0.0001268 2000 3000000 3000000 -125.21795 119945.8 0.49881188 291.90297 0 0 0 0 5077.1879 75686.509 -52.002031 -101734.8 -20971.103 3479.5591 Loop time of 24925.5 on 32 procs for 3000000 steps with 6000 atoms Performance: 10.399 ns/day, 2.308 hours/ns, 120.359 timesteps/s 98.4% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 15.019 | 7742.5 | 18223 |8684.8 | 31.06 Bond | 2.5888 | 3.5339 | 7.7855 | 51.5 | 0.01 Kspace | 3626.1 | 14169 | 22008 |6454.7 | 56.85 Neigh | 1167.1 | 1174 | 1185 | 17.3 | 4.71 Comm | 313.21 | 673.67 | 897.32 | 815.8 | 2.70 Output | 0.0088353 | 0.010567 | 0.012144 | 0.9 | 0.00 Modify | 945.79 | 1110 | 1348.1 | 469.9 | 4.45 Other | | 52.69 | | | 0.21 Nlocal: 187.5 ave 385 max 0 min Histogram: 12 3 1 0 0 0 0 1 3 12 Nghost: 4083.41 ave 7512 max 642 min Histogram: 7 1 0 4 4 4 4 0 1 7 Neighs: 91650.2 ave 226819 max 0 min Histogram: 16 0 0 0 0 2 2 2 7 3 Total # of neighbors = 2932807 Ave neighs/atom = 488.80117 Ave special neighs/atom = 2 Neighbor list builds = 148959 Dangerous builds = 0 undump sci restart 0 dump sci all custom 3000000 2.5.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) = 0.24720763 grid = 27 27 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0033477167 estimated relative force accuracy = 1.0081549e-05 using double precision KISS FFT 3d grid and FFT values/proc = 4800 1458 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 1 0.97 1.50205e-06 6000 1 103.7 0.0001268 2000 Per MPI rank memory allocation (min/avg/max) = 8.406 | 9.731 | 10.6 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 -124.8174 119945.8 0.49881188 291.90297 0 0 0 0 5077.1879 75686.509 -52.002031 -101734.8 -20971.103 3479.5591 Loop time of 7.15231e-06 on 32 procs for 0 steps with 6000 atoms 109.2% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 7.152e-06 | | |100.00 Nlocal: 187.5 ave 385 max 0 min Histogram: 12 3 1 0 0 0 0 1 3 12 Nghost: 4083.41 ave 7512 max 642 min Histogram: 7 1 0 4 4 4 4 0 1 7 Neighs: 91650.2 ave 226819 max 0 min Histogram: 16 0 0 0 0 2 2 2 7 3 Total # of neighbors = 2932807 Ave neighs/atom = 488.80117 Ave special neighs/atom = 2 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 13:49:49