#------------------------------------------------------------------------------- # Stage 2.5: 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 2 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 2699 = # 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 2.5_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 2.5_instantaneous.txt fix 4 fixed setforce 0.0 0.0 0.0 restart 4000000 2.5.restart dump sci all custom 400000 2.5.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) = 0.25577968 grid = 30 30 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0035412458 estimated relative force accuracy = 1.0664357e-05 using double precision KISS FFT 3d grid and FFT values/proc = 7260 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 8.25229e-13 8097 2 103.7 7.61275e-11 2699 Per MPI rank memory allocation (min/avg/max) = 12.45 | 13.17 | 13.63 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 -127.56695 138878.49 1.4411859 300.64268 39.641224 70.638038 0 0 36102.876 -63553.564 -317.08001 -295421.72 -322762.13 6751.6598 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.27498e-06 8097 2 103.7 0.000111894 2699 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.38808e-06 8097 2 103.7 0.000108686 2699 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.14989e-06 8097 2 103.7 9.10743e-05 2699 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.42303e-06 8097 2 103.7 0.000105352 2699 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.08203e-06 8097 2 103.7 9.22781e-05 2699 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.34141e-06 8097 2 103.7 0.000115169 2699 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.18075e-06 8097 2 103.7 0.000113197 2699 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.19809e-06 8097 2 103.7 9.33784e-05 2699 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.42671e-06 8097 2 103.7 0.000117399 2699 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.11714e-06 8097 2 103.7 0.00011287 2699 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.43934e-06 8097 2 103.7 9.32741e-05 2699 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.17223e-06 8097 2 103.7 8.84243e-05 2699 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.3839e-06 8097 2 103.7 0.000102467 2699 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.16236e-06 8097 2 103.7 9.08769e-05 2699 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.45983e-06 8097 2 103.7 0.000116032 2699 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.15687e-06 8097 2 103.7 8.71084e-05 2699 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.34058e-06 8097 2 103.7 9.68594e-05 2699 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.36392e-06 8097 2 103.7 9.93675e-05 2699 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.54147e-06 8097 2 103.7 0.000100979 2699 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.46352e-06 8097 2 103.7 0.000104536 2699 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.23669e-06 8097 2 103.7 0.000123191 2699 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.38891e-06 8097 2 103.7 0.000125583 2699 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.23581e-06 8097 2 103.7 9.45548e-05 2699 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.62583e-06 8097 2 103.7 0.000103037 2699 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.13254e-06 8097 2 103.7 9.3998e-05 2699 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.58074e-06 8097 2 103.7 0.000127928 2699 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.03346e-06 8097 2 103.7 9.71049e-05 2699 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.18582e-06 8097 2 103.7 9.14465e-05 2699 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.03872e-06 8097 2 103.7 9.40351e-05 2699 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.28848e-06 8097 2 103.7 9.23891e-05 2699 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.23456e-06 8097 2 103.7 9.05883e-05 2699 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.25404e-06 8097 2 103.7 9.26115e-05 2699 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.19316e-06 8097 2 103.7 9.50457e-05 2699 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.55742e-06 8097 2 103.7 0.000117152 2699 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.65677e-06 8097 2 103.7 0.000113104 2699 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.33232e-06 8097 2 103.7 8.81842e-05 2699 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.54192e-06 8097 2 103.7 9.90682e-05 2699 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.34925e-06 8097 2 103.7 0.000100932 2699 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.39652e-06 8097 2 103.7 0.000109245 2699 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.18316e-06 8097 2 103.7 9.16246e-05 2699 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.15826e-06 8097 2 103.7 9.1782e-05 2699 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.83015e-06 8097 2 103.7 0.000115849 2699 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.432e-06 8097 2 103.7 0.000110803 2699 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.14102e-06 8097 2 103.7 0.000107726 2699 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.13979e-06 8097 2 103.7 9.05334e-05 2699 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.18601e-06 8097 2 103.7 9.43455e-05 2699 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.28648e-06 8097 2 103.7 9.85907e-05 2699 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.70464e-06 8097 2 103.7 0.000126206 2699 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.38298e-06 8097 2 103.7 9.98163e-05 2699 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.15763e-06 8097 2 103.7 9.82694e-05 2699 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.37379e-06 8097 2 103.7 9.21403e-05 2699 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.25447e-06 8097 2 103.7 8.82208e-05 2699 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.64905e-06 8097 2 103.7 0.000104924 2699 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.44341e-06 8097 2 103.7 0.000113515 2699 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.36882e-06 8097 2 103.7 8.97993e-05 2699 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.2239e-06 8097 2 103.7 9.95e-05 2699 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.11877e-06 8097 2 103.7 9.30361e-05 2699 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.18754e-06 8097 2 103.7 9.63797e-05 2699 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.65034e-06 8097 2 103.7 0.00010179 2699 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.44736e-06 8097 2 103.7 0.000116763 2699 SHAKE stats (type/ave/delta/count) on step 3050000 2 0.97 1.23239e-06 8097 2 103.7 9.4327e-05 2699 SHAKE stats (type/ave/delta/count) on step 3100000 2 0.97 1.1688e-06 8097 2 103.7 9.12273e-05 2699 SHAKE stats (type/ave/delta/count) on step 3150000 2 0.97 1.04748e-06 8097 2 103.7 9.43263e-05 2699 SHAKE stats (type/ave/delta/count) on step 3200000 2 0.97 1.06644e-06 8097 2 103.7 0.000101268 2699 SHAKE stats (type/ave/delta/count) on step 3250000 2 0.97 1.14057e-06 8097 2 103.7 9.66e-05 2699 SHAKE stats (type/ave/delta/count) on step 3300000 2 0.97 1.15307e-06 8097 2 103.7 9.73011e-05 2699 SHAKE stats (type/ave/delta/count) on step 3350000 2 0.97 1.23996e-06 8097 2 103.7 0.000110068 2699 SHAKE stats (type/ave/delta/count) on step 3400000 2 0.97 1.16488e-06 8097 2 103.7 9.11299e-05 2699 SHAKE stats (type/ave/delta/count) on step 3450000 2 0.97 1.08573e-06 8097 2 103.7 0.00010171 2699 SHAKE stats (type/ave/delta/count) on step 3500000 2 0.97 1.62509e-06 8097 2 103.7 9.38977e-05 2699 SHAKE stats (type/ave/delta/count) on step 3550000 2 0.97 1.35043e-06 8097 2 103.7 9.0737e-05 2699 SHAKE stats (type/ave/delta/count) on step 3600000 2 0.97 1.14323e-06 8097 2 103.7 9.34364e-05 2699 SHAKE stats (type/ave/delta/count) on step 3650000 2 0.97 1.14538e-06 8097 2 103.7 8.924e-05 2699 SHAKE stats (type/ave/delta/count) on step 3700000 2 0.97 1.84064e-06 8097 2 103.7 0.000132129 2699 SHAKE stats (type/ave/delta/count) on step 3750000 2 0.97 1.17382e-06 8097 2 103.7 9.42705e-05 2699 SHAKE stats (type/ave/delta/count) on step 3800000 2 0.97 1.19014e-06 8097 2 103.7 0.000101061 2699 SHAKE stats (type/ave/delta/count) on step 3850000 2 0.97 1.74085e-06 8097 2 103.7 0.000124965 2699 SHAKE stats (type/ave/delta/count) on step 3900000 2 0.97 1.55014e-06 8097 2 103.7 0.000109293 2699 SHAKE stats (type/ave/delta/count) on step 3950000 2 0.97 1.6388e-06 8097 2 103.7 0.000112934 2699 SHAKE stats (type/ave/delta/count) on step 4000000 2 0.97 1.23027e-06 8097 2 103.7 9.64099e-05 2699 4000000 4000000 291.96374 138878.49 1.4411859 296.80486 40.056335 48.308725 0 0 36369.53 -63803.571 -317.08001 -295421.52 -322767.2 6665.4722 Loop time of 36199.2 on 32 procs for 4000000 steps with 10558 atoms Performance: 9.547 ns/day, 2.514 hours/ns, 110.500 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 | 5134.8 | 17168 | 23634 |5414.3 | 47.43 Bond | 3.7455 | 9.617 | 19.732 | 156.3 | 0.03 Kspace | 6828.7 | 13327 | 25419 |6169.9 | 36.81 Neigh | 1720.2 | 1723.2 | 1729.3 | 6.4 | 4.76 Comm | 1416 | 1832.8 | 2020.9 | 464.9 | 5.06 Output | 0.01123 | 0.013655 | 0.015979 | 1.2 | 0.00 Modify | 1901.9 | 2057.2 | 2401.7 | 374.7 | 5.68 Other | | 81.91 | | | 0.23 Nlocal: 329.938 ave 405 max 160 min Histogram: 4 4 0 0 0 0 0 4 7 13 Nghost: 6363.75 ave 7572 max 4650 min Histogram: 8 0 0 0 8 0 0 0 4 12 Neighs: 153557 ave 217253 max 43129 min Histogram: 8 0 0 0 0 2 2 4 6 10 Total # of neighbors = 4913809 Ave neighs/atom = 465.41097 Ave special neighs/atom = 1.5849593 Neighbor list builds = 197816 Dangerous builds = 0 undump sci restart 0 dump sci all custom 4000000 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) = 0.25577968 grid = 30 30 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0035412458 estimated relative force accuracy = 1.0664357e-05 using double precision KISS FFT 3d grid and FFT values/proc = 7260 1800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 4000000 2 0.97 1.23027e-06 8097 2 103.7 9.64099e-05 2699 Per MPI rank memory allocation (min/avg/max) = 12.45 | 13.19 | 13.63 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 292.61824 138878.49 1.4411859 296.80486 40.056335 48.308725 0 0 36369.53 -63803.571 -317.08001 -295421.52 -322767.2 6665.4722 Loop time of 7.35372e-06 on 32 procs for 0 steps with 10558 atoms 117.7% 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 | | 7.354e-06 | | |100.00 Nlocal: 329.938 ave 405 max 160 min Histogram: 4 4 0 0 0 0 0 4 7 13 Nghost: 6363.75 ave 7572 max 4650 min Histogram: 8 0 0 0 8 0 0 0 4 12 Neighs: 153557 ave 217253 max 43129 min Histogram: 8 0 0 0 0 2 2 4 6 10 Total # of neighbors = 4913809 Ave neighs/atom = 465.41097 Ave special neighs/atom = 1.5849593 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken log 2.6_Custom.out