#------------------------------------------------------------------------------- # 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 2 b 2 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 2009 = # 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) = 0.25041361 grid = 30 30 50 stencil order = 5 estimated absolute RMS force accuracy = 0.0033117663 estimated relative force accuracy = 9.9732859e-06 using double precision KISS FFT 3d grid and FFT values/proc = 6292 1800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 5.82534e-13 6027 2 103.7 7.63833e-11 2009 Per MPI rank memory allocation (min/avg/max) = 10.99 | 12.4 | 13.55 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 -379.37183 139839.06 0.6135188 300.58123 39.167194 40.152321 0 0 13085.428 31819.417 -75.537794 -144708.09 -99723.921 4079.3767 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 2.05674e-06 6027 2 103.7 0.000155461 2009 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.59249e-06 6027 2 103.7 9.77145e-05 2009 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.37351e-06 6027 2 103.7 0.000115047 2009 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.73676e-06 6027 2 103.7 0.000123876 2009 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.06052e-06 6027 2 103.7 0.000102326 2009 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.24976e-06 6027 2 103.7 9.43388e-05 2009 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.2824e-06 6027 2 103.7 9.72497e-05 2009 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.3171e-06 6027 2 103.7 0.000100234 2009 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.38024e-06 6027 2 103.7 0.000108971 2009 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.13939e-06 6027 2 103.7 0.00010614 2009 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.10604e-06 6027 2 103.7 9.3151e-05 2009 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.64741e-06 6027 2 103.7 0.000114855 2009 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.17452e-06 6027 2 103.7 9.34146e-05 2009 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.1413e-06 6027 2 103.7 9.54524e-05 2009 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.46532e-06 6027 2 103.7 0.000101311 2009 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.34029e-06 6027 2 103.7 0.00010707 2009 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.10046e-06 6027 2 103.7 0.000109893 2009 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.43962e-06 6027 2 103.7 9.30551e-05 2009 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.69257e-06 6027 2 103.7 0.000117569 2009 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.13479e-06 6027 2 103.7 0.000117684 2009 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.41564e-06 6027 2 103.7 0.000113299 2009 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.23773e-06 6027 2 103.7 8.72764e-05 2009 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.19215e-06 6027 2 103.7 9.51477e-05 2009 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.41344e-06 6027 2 103.7 9.28367e-05 2009 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.34179e-06 6027 2 103.7 9.82308e-05 2009 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.12176e-06 6027 2 103.7 0.000100484 2009 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.17681e-06 6027 2 103.7 8.73741e-05 2009 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.33358e-06 6027 2 103.7 0.000102476 2009 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.42236e-06 6027 2 103.7 8.99915e-05 2009 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.30604e-06 6027 2 103.7 8.69239e-05 2009 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.3822e-06 6027 2 103.7 0.000100274 2009 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.2089e-06 6027 2 103.7 9.2697e-05 2009 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.48419e-06 6027 2 103.7 0.000108203 2009 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.21818e-06 6027 2 103.7 9.53272e-05 2009 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.39531e-06 6027 2 103.7 0.000121022 2009 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.49104e-06 6027 2 103.7 0.000112974 2009 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.07839e-06 6027 2 103.7 9.66081e-05 2009 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.14935e-06 6027 2 103.7 0.000109818 2009 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.12814e-06 6027 2 103.7 0.000100222 2009 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.20183e-06 6027 2 103.7 9.653e-05 2009 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.28542e-06 6027 2 103.7 0.000115429 2009 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.35059e-06 6027 2 103.7 8.91764e-05 2009 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.35551e-06 6027 2 103.7 9.81012e-05 2009 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.2808e-06 6027 2 103.7 8.51255e-05 2009 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.98048e-06 6027 2 103.7 0.00013246 2009 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.18556e-06 6027 2 103.7 9.42878e-05 2009 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.22903e-06 6027 2 103.7 9.63843e-05 2009 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.3081e-06 6027 2 103.7 9.56299e-05 2009 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.73909e-06 6027 2 103.7 0.000130567 2009 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.36014e-06 6027 2 103.7 0.000105424 2009 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.38103e-06 6027 2 103.7 9.33564e-05 2009 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.14972e-06 6027 2 103.7 9.78917e-05 2009 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.29125e-06 6027 2 103.7 9.45259e-05 2009 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.13486e-06 6027 2 103.7 9.48449e-05 2009 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.34184e-06 6027 2 103.7 0.000108073 2009 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.21145e-06 6027 2 103.7 0.00010779 2009 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.17781e-06 6027 2 103.7 0.000101644 2009 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.03937e-06 6027 2 103.7 8.86177e-05 2009 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.5219e-06 6027 2 103.7 0.000112914 2009 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.47953e-06 6027 2 103.7 0.000101808 2009 3000000 3000000 -330.79295 139839.06 0.6135188 301.30809 33.345527 48.068521 0 0 13154.394 31632.329 -75.537794 -144709.92 -99841.782 4089.2413 Loop time of 26187.9 on 32 procs for 3000000 steps with 6563 atoms Performance: 9.898 ns/day, 2.425 hours/ns, 114.557 timesteps/s 98.5% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.0327 | 7997.7 | 18912 |8707.0 | 30.54 Bond | 2.663 | 5.8306 | 19.612 | 165.6 | 0.02 Kspace | 4146.2 | 15120 | 23274 |6375.2 | 57.74 Neigh | 1165.9 | 1172.7 | 1183.7 | 16.9 | 4.48 Comm | 257.09 | 672.93 | 923.57 | 909.8 | 2.57 Output | 0.010195 | 0.011996 | 0.013674 | 0.9 | 0.00 Modify | 983.75 | 1165.6 | 1416 | 496.7 | 4.45 Other | | 53.1 | | | 0.20 Nlocal: 205.094 ave 428 max 0 min Histogram: 12 0 1 3 0 1 2 0 2 11 Nghost: 4027.69 ave 7840 max 174 min Histogram: 4 4 3 1 4 4 0 4 4 4 Neighs: 94448.2 ave 224990 max 0 min Histogram: 16 0 0 0 0 1 2 5 2 6 Total # of neighbors = 3022343 Ave neighs/atom = 460.51242 Ave special neighs/atom = 1.9037026 Neighbor list builds = 146398 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) = 0.25041361 grid = 30 30 50 stencil order = 5 estimated absolute RMS force accuracy = 0.0033117663 estimated relative force accuracy = 9.9732859e-06 using double precision KISS FFT 3d grid and FFT values/proc = 6292 1800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.47953e-06 6027 2 103.7 0.000101808 2009 Per MPI rank memory allocation (min/avg/max) = 11.09 | 12.46 | 13.55 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 -330.43723 139839.06 0.6135188 301.30809 33.345527 48.068521 0 0 13154.394 31632.329 -75.537794 -144709.92 -99841.782 4089.2413 Loop time of 9.39466e-06 on 32 procs for 0 steps with 6563 atoms 109.8% 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 | | 9.395e-06 | | |100.00 Nlocal: 205.094 ave 428 max 0 min Histogram: 12 0 1 3 0 1 2 0 2 11 Nghost: 4027.69 ave 7840 max 174 min Histogram: 4 4 3 1 4 4 0 4 4 4 Neighs: 94448.2 ave 224990 max 0 min Histogram: 16 0 0 0 0 1 2 5 2 6 Total # of neighbors = 3022343 Ave neighs/atom = 460.51242 Ave special neighs/atom = 1.9037026 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 14:34:03