#------------------------------------------------------------------------------- # Stage 2.5: 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 4018 = # 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 2.5_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 2.5_instantaneous.txt restart 5000000 2.5.restart dump sci all custom 500000 2.5.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) = 0.31988 grid = 45 45 72 stencil order = 5 estimated absolute RMS force accuracy = 0.003651357 estimated relative force accuracy = 1.0995953e-05 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 1.00198 0.0832995 12054 2 97.4099 10.7898 4018 Per MPI rank memory allocation (min/avg/max) = 11.84 | 13.34 | 14.36 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 3413.8336 193007.11 0.88902312 429.76556 12.665876 59.670797 0 0 35706.858 113155.42 -435.22696 -369055.77 -220121.16 11666.518 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.65554e-06 12054 2 103.7 0.000119618 4018 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.36035e-06 12054 2 103.7 0.000123841 4018 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.34062e-06 12054 2 103.7 9.92339e-05 4018 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.5007e-06 12054 2 103.7 0.00010467 4018 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.24933e-06 12054 2 103.7 0.000101527 4018 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.50802e-06 12054 2 103.7 9.93878e-05 4018 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.24706e-06 12054 2 103.7 0.000104426 4018 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.20698e-06 12054 2 103.7 9.3171e-05 4018 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.39632e-06 12054 2 103.7 0.000109491 4018 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.15971e-06 12054 2 103.7 9.46968e-05 4018 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.20967e-06 12054 2 103.7 9.51158e-05 4018 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.25202e-06 12054 2 103.7 9.35213e-05 4018 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.49215e-06 12054 2 103.7 9.73879e-05 4018 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.38125e-06 12054 2 103.7 0.000155067 4018 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.54543e-06 12054 2 103.7 9.66e-05 4018 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.36949e-06 12054 2 103.7 9.35452e-05 4018 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.15509e-06 12054 2 103.7 0.000103697 4018 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.26232e-06 12054 2 103.7 9.95273e-05 4018 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.17568e-06 12054 2 103.7 0.000103282 4018 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.3376e-06 12054 2 103.7 0.000108689 4018 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.26549e-06 12054 2 103.7 9.59371e-05 4018 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.71845e-06 12054 2 103.7 0.000101574 4018 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.19911e-06 12054 2 103.7 9.34739e-05 4018 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.39457e-06 12054 2 103.7 9.9781e-05 4018 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.41468e-06 12054 2 103.7 9.36373e-05 4018 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.18745e-06 12054 2 103.7 0.000109702 4018 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.26298e-06 12054 2 103.7 9.45074e-05 4018 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.37821e-06 12054 2 103.7 0.000107733 4018 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.31341e-06 12054 2 103.7 0.000101695 4018 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.37877e-06 12054 2 103.7 9.83991e-05 4018 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.22761e-06 12054 2 103.7 0.000103331 4018 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.31421e-06 12054 2 103.7 9.63868e-05 4018 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.31968e-06 12054 2 103.7 9.55847e-05 4018 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.2992e-06 12054 2 103.7 0.000107744 4018 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.10031e-06 12054 2 103.7 0.000101341 4018 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.32926e-06 12054 2 103.7 0.000100518 4018 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.21038e-06 12054 2 103.7 9.5093e-05 4018 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.13655e-06 12054 2 103.7 9.71248e-05 4018 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.5965e-06 12054 2 103.7 0.000125379 4018 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.58757e-06 12054 2 103.7 0.000103067 4018 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.37362e-06 12054 2 103.7 0.000114203 4018 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.26108e-06 12054 2 103.7 9.88716e-05 4018 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.28354e-06 12054 2 103.7 0.000106638 4018 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.44813e-06 12054 2 103.7 0.000105938 4018 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.54264e-06 12054 2 103.7 0.000116412 4018 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.17809e-06 12054 2 103.7 9.83889e-05 4018 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.61925e-06 12054 2 103.7 0.000111142 4018 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.57605e-06 12054 2 103.7 9.57423e-05 4018 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.52263e-06 12054 2 103.7 9.70887e-05 4018 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.19913e-06 12054 2 103.7 9.61249e-05 4018 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.24816e-06 12054 2 103.7 0.000100253 4018 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.35428e-06 12054 2 103.7 9.18541e-05 4018 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.27385e-06 12054 2 103.7 0.000106855 4018 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.34281e-06 12054 2 103.7 9.53647e-05 4018 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.08886e-06 12054 2 103.7 9.82115e-05 4018 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.41769e-06 12054 2 103.7 0.000123319 4018 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.1125e-06 12054 2 103.7 0.000101032 4018 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.27777e-06 12054 2 103.7 9.95453e-05 4018 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.35764e-06 12054 2 103.7 0.000109606 4018 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.27483e-06 12054 2 103.7 0.000105204 4018 SHAKE stats (type/ave/delta/count) on step 3050000 2 0.97 1.20533e-06 12054 2 103.7 0.000103806 4018 SHAKE stats (type/ave/delta/count) on step 3100000 2 0.97 1.39923e-06 12054 2 103.7 9.24751e-05 4018 SHAKE stats (type/ave/delta/count) on step 3150000 2 0.97 1.3687e-06 12054 2 103.7 0.000104526 4018 SHAKE stats (type/ave/delta/count) on step 3200000 2 0.97 1.15566e-06 12054 2 103.7 9.62221e-05 4018 SHAKE stats (type/ave/delta/count) on step 3250000 2 0.97 1.69216e-06 12054 2 103.7 0.000124909 4018 SHAKE stats (type/ave/delta/count) on step 3300000 2 0.97 1.80268e-06 12054 2 103.7 0.000110837 4018 SHAKE stats (type/ave/delta/count) on step 3350000 2 0.97 1.25951e-06 12054 2 103.7 9.07311e-05 4018 SHAKE stats (type/ave/delta/count) on step 3400000 2 0.97 1.56671e-06 12054 2 103.7 0.000102672 4018 SHAKE stats (type/ave/delta/count) on step 3450000 2 0.97 1.66465e-06 12054 2 103.7 0.000100882 4018 SHAKE stats (type/ave/delta/count) on step 3500000 2 0.97 1.38294e-06 12054 2 103.7 0.000106151 4018 SHAKE stats (type/ave/delta/count) on step 3550000 2 0.97 1.11637e-06 12054 2 103.7 9.70517e-05 4018 SHAKE stats (type/ave/delta/count) on step 3600000 2 0.97 1.21422e-06 12054 2 103.7 0.000104915 4018 SHAKE stats (type/ave/delta/count) on step 3650000 2 0.97 1.32899e-06 12054 2 103.7 9.80913e-05 4018 SHAKE stats (type/ave/delta/count) on step 3700000 2 0.97 1.23174e-06 12054 2 103.7 0.000108841 4018 SHAKE stats (type/ave/delta/count) on step 3750000 2 0.97 1.35218e-06 12054 2 103.7 0.000102077 4018 SHAKE stats (type/ave/delta/count) on step 3800000 2 0.97 1.92719e-06 12054 2 103.7 0.000115638 4018 SHAKE stats (type/ave/delta/count) on step 3850000 2 0.97 1.26949e-06 12054 2 103.7 9.76739e-05 4018 SHAKE stats (type/ave/delta/count) on step 3900000 2 0.97 1.22927e-06 12054 2 103.7 9.6675e-05 4018 SHAKE stats (type/ave/delta/count) on step 3950000 2 0.97 1.21541e-06 12054 2 103.7 9.36666e-05 4018 SHAKE stats (type/ave/delta/count) on step 4000000 2 0.97 1.30221e-06 12054 2 103.7 9.93636e-05 4018 SHAKE stats (type/ave/delta/count) on step 4050000 2 0.97 1.38164e-06 12054 2 103.7 9.89485e-05 4018 SHAKE stats (type/ave/delta/count) on step 4100000 2 0.97 1.12024e-06 12054 2 103.7 9.48202e-05 4018 SHAKE stats (type/ave/delta/count) on step 4150000 2 0.97 1.23741e-06 12054 2 103.7 0.000100192 4018 SHAKE stats (type/ave/delta/count) on step 4200000 2 0.97 1.37009e-06 12054 2 103.7 9.81011e-05 4018 SHAKE stats (type/ave/delta/count) on step 4250000 2 0.97 1.29502e-06 12054 2 103.7 0.00010216 4018 SHAKE stats (type/ave/delta/count) on step 4300000 2 0.97 1.31075e-06 12054 2 103.7 9.70383e-05 4018 SHAKE stats (type/ave/delta/count) on step 4350000 2 0.97 1.18713e-06 12054 2 103.7 0.000114455 4018 SHAKE stats (type/ave/delta/count) on step 4400000 2 0.97 1.3073e-06 12054 2 103.7 9.73635e-05 4018 SHAKE stats (type/ave/delta/count) on step 4450000 2 0.97 1.44707e-06 12054 2 103.7 0.000106459 4018 SHAKE stats (type/ave/delta/count) on step 4500000 2 0.97 1.4288e-06 12054 2 103.7 9.02904e-05 4018 SHAKE stats (type/ave/delta/count) on step 4550000 2 0.97 1.35063e-06 12054 2 103.7 0.000102385 4018 SHAKE stats (type/ave/delta/count) on step 4600000 2 0.97 1.22234e-06 12054 2 103.7 0.000109941 4018 SHAKE stats (type/ave/delta/count) on step 4650000 2 0.97 1.11995e-06 12054 2 103.7 0.000102237 4018 SHAKE stats (type/ave/delta/count) on step 4700000 2 0.97 1.12983e-06 12054 2 103.7 9.37391e-05 4018 SHAKE stats (type/ave/delta/count) on step 4750000 2 0.97 1.23664e-06 12054 2 103.7 0.00011751 4018 SHAKE stats (type/ave/delta/count) on step 4800000 2 0.97 1.16024e-06 12054 2 103.7 0.000100751 4018 SHAKE stats (type/ave/delta/count) on step 4850000 2 0.97 1.28514e-06 12054 2 103.7 0.000111822 4018 SHAKE stats (type/ave/delta/count) on step 4900000 2 0.97 1.15226e-06 12054 2 103.7 0.000109283 4018 SHAKE stats (type/ave/delta/count) on step 4950000 2 0.97 1.32186e-06 12054 2 103.7 9.32549e-05 4018 SHAKE stats (type/ave/delta/count) on step 5000000 2 0.97 1.43148e-06 12054 2 103.7 0.00011003 4018 5000000 5000000 -397.38225 193007.11 0.88902312 295.15381 63.073576 87.082501 0 0 26490.421 142104.3 -435.22696 -368638.74 -199893.87 8012.3154 Loop time of 44160.7 on 32 procs for 5000000 steps with 13126 atoms Performance: 9.782 ns/day, 2.453 hours/ns, 113.223 timesteps/s 99.0% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2260.5 | 14522 | 21705 |6207.3 | 32.88 Bond | 5.5784 | 15.574 | 30.872 | 183.1 | 0.04 Kspace | 16739 | 23965 | 36293 |4854.7 | 54.27 Neigh | 1297.3 | 1304.6 | 1314.6 | 16.7 | 2.95 Comm | 1307.4 | 1768.1 | 1975.1 | 623.2 | 4.00 Output | 0.015352 | 0.018141 | 0.020845 | 1.2 | 0.00 Modify | 2309.1 | 2462.5 | 2848.2 | 444.5 | 5.58 Other | | 123.3 | | | 0.28 Nlocal: 410.188 ave 574 max 36 min Histogram: 8 0 0 0 0 0 0 1 7 16 Nghost: 4502.94 ave 6118 max 3262 min Histogram: 8 0 8 0 8 0 0 0 0 8 Neighs: 110643 ave 167843 max 8734 min Histogram: 8 0 0 0 0 3 5 0 0 16 Total # of neighbors = 3540561 Ave neighs/atom = 269.73648 Ave special neighs/atom = 1.9037026 Neighbor list builds = 257480 Dangerous builds = 0 undump sci restart 0 dump sci all custom 5000000 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) = 0.31988 grid = 45 45 72 stencil order = 5 estimated absolute RMS force accuracy = 0.003651357 estimated relative force accuracy = 1.0995953e-05 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 1.43148e-06 12054 2 103.7 0.00011003 4018 Per MPI rank memory allocation (min/avg/max) = 12.94 | 13.66 | 14.4 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 -396.87281 193007.11 0.88902312 295.15381 63.073576 87.082501 0 0 26490.421 142104.3 -435.22696 -368638.74 -199893.87 8012.3154 Loop time of 7.64403e-06 on 32 procs for 0 steps with 13126 atoms 127.1% 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 | | 7.644e-06 | | |100.00 Nlocal: 410.188 ave 574 max 36 min Histogram: 8 0 0 0 0 0 0 1 7 16 Nghost: 4502.94 ave 6118 max 3262 min Histogram: 8 0 8 0 8 0 0 0 0 8 Neighs: 110643 ave 167843 max 8734 min Histogram: 8 0 0 0 0 3 5 0 0 16 Total # of neighbors = 3540561 Ave neighs/atom = 269.73648 Ave special neighs/atom = 1.9037026 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.6_NVT.out