#------------------------------------------------------------------------------- # 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 1 b 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 3275 = # 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) = 0.2550303 grid = 36 27 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0036863798 estimated relative force accuracy = 1.1101423e-05 using double precision KISS FFT 3d grid and FFT values/proc = 11000 3888 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 0.97 6.96554e-13 9825 1 103.7 8.1215e-11 3275 Per MPI rank memory allocation (min/avg/max) = 14.12 | 14.59 | 14.82 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 -7063.4304 143340.91 1.3114365 291.52522 41.627309 73.309895 0 0 37105.268 -73116.689 -319.55737 -317468.04 -353364.53 6880.5939 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.38879e-06 9825 1 103.7 9.38202e-05 3275 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.27026e-06 9825 1 103.7 0.000102437 3275 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.46986e-06 9825 1 103.7 0.000111627 3275 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.24316e-06 9825 1 103.7 9.72836e-05 3275 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.2479e-06 9825 1 103.7 0.000102392 3275 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.59614e-06 9825 1 103.7 0.000101388 3275 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.4376e-06 9825 1 103.7 0.000120992 3275 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.6406e-06 9825 1 103.7 0.000107888 3275 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.68366e-06 9825 1 103.7 0.000106791 3275 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.2763e-06 9825 1 103.7 0.000116803 3275 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.59022e-06 9825 1 103.7 9.15425e-05 3275 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.21675e-06 9825 1 103.7 9.77636e-05 3275 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.12881e-06 9825 1 103.7 9.08674e-05 3275 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.15955e-06 9825 1 103.7 9.16069e-05 3275 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.10931e-06 9825 1 103.7 9.41484e-05 3275 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.38974e-06 9825 1 103.7 8.7617e-05 3275 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.11312e-06 9825 1 103.7 9.27944e-05 3275 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.15817e-06 9825 1 103.7 0.00011412 3275 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.04365e-06 9825 1 103.7 9.46864e-05 3275 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.14433e-06 9825 1 103.7 9.9657e-05 3275 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.97 1.22561e-06 9825 1 103.7 0.000101501 3275 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.97 1.33522e-06 9825 1 103.7 0.000102285 3275 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.97 1.08427e-06 9825 1 103.7 9.2574e-05 3275 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.97 1.21751e-06 9825 1 103.7 9.35352e-05 3275 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.97 1.13777e-06 9825 1 103.7 8.86138e-05 3275 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.97 1.24057e-06 9825 1 103.7 9.64191e-05 3275 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.97 1.17927e-06 9825 1 103.7 8.83299e-05 3275 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.97 1.23953e-06 9825 1 103.7 9.48948e-05 3275 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.97 1.11583e-06 9825 1 103.7 9.6365e-05 3275 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.97 1.29599e-06 9825 1 103.7 9.09474e-05 3275 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.97 1.1771e-06 9825 1 103.7 0.000108966 3275 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.97 1.222e-06 9825 1 103.7 9.4437e-05 3275 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.97 1.18995e-06 9825 1 103.7 9.23126e-05 3275 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.97 1.14017e-06 9825 1 103.7 0.000100223 3275 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.97 1.33822e-06 9825 1 103.7 9.52294e-05 3275 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.97 1.12893e-06 9825 1 103.7 0.00010057 3275 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.97 1.54218e-06 9825 1 103.7 0.000115273 3275 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.97 1.26557e-06 9825 1 103.7 9.38909e-05 3275 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.97 1.39441e-06 9825 1 103.7 0.000103154 3275 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.06812e-06 9825 1 103.7 0.000109711 3275 SHAKE stats (type/ave/delta/count) on step 2050000 1 0.97 1.25135e-06 9825 1 103.7 0.000113373 3275 SHAKE stats (type/ave/delta/count) on step 2100000 1 0.97 1.5693e-06 9825 1 103.7 0.000113822 3275 SHAKE stats (type/ave/delta/count) on step 2150000 1 0.97 1.76222e-06 9825 1 103.7 9.38335e-05 3275 SHAKE stats (type/ave/delta/count) on step 2200000 1 0.97 1.12495e-06 9825 1 103.7 8.59661e-05 3275 SHAKE stats (type/ave/delta/count) on step 2250000 1 0.97 1.15595e-06 9825 1 103.7 9.02771e-05 3275 SHAKE stats (type/ave/delta/count) on step 2300000 1 0.97 1.35216e-06 9825 1 103.7 9.33993e-05 3275 SHAKE stats (type/ave/delta/count) on step 2350000 1 0.97 1.46789e-06 9825 1 103.7 0.000124534 3275 SHAKE stats (type/ave/delta/count) on step 2400000 1 0.97 1.19426e-06 9825 1 103.7 8.90741e-05 3275 SHAKE stats (type/ave/delta/count) on step 2450000 1 0.97 1.45975e-06 9825 1 103.7 9.80712e-05 3275 SHAKE stats (type/ave/delta/count) on step 2500000 1 0.97 1.48238e-06 9825 1 103.7 9.65987e-05 3275 SHAKE stats (type/ave/delta/count) on step 2550000 1 0.97 1.13093e-06 9825 1 103.7 0.000102573 3275 SHAKE stats (type/ave/delta/count) on step 2600000 1 0.97 1.26012e-06 9825 1 103.7 9.64163e-05 3275 SHAKE stats (type/ave/delta/count) on step 2650000 1 0.97 1.14366e-06 9825 1 103.7 9.37028e-05 3275 SHAKE stats (type/ave/delta/count) on step 2700000 1 0.97 1.25845e-06 9825 1 103.7 9.69602e-05 3275 SHAKE stats (type/ave/delta/count) on step 2750000 1 0.97 1.14494e-06 9825 1 103.7 9.08841e-05 3275 SHAKE stats (type/ave/delta/count) on step 2800000 1 0.97 1.37947e-06 9825 1 103.7 0.000111093 3275 SHAKE stats (type/ave/delta/count) on step 2850000 1 0.97 1.44306e-06 9825 1 103.7 0.000122361 3275 SHAKE stats (type/ave/delta/count) on step 2900000 1 0.97 1.2487e-06 9825 1 103.7 8.86017e-05 3275 SHAKE stats (type/ave/delta/count) on step 2950000 1 0.97 1.29134e-06 9825 1 103.7 9.12026e-05 3275 SHAKE stats (type/ave/delta/count) on step 3000000 1 0.97 1.30375e-06 9825 1 103.7 9.95163e-05 3275 SHAKE stats (type/ave/delta/count) on step 3050000 1 0.97 1.31137e-06 9825 1 103.7 9.47199e-05 3275 SHAKE stats (type/ave/delta/count) on step 3100000 1 0.97 1.41426e-06 9825 1 103.7 0.000120156 3275 SHAKE stats (type/ave/delta/count) on step 3150000 1 0.97 1.53104e-06 9825 1 103.7 0.000115928 3275 SHAKE stats (type/ave/delta/count) on step 3200000 1 0.97 1.20438e-06 9825 1 103.7 9.47254e-05 3275 SHAKE stats (type/ave/delta/count) on step 3250000 1 0.97 1.01849e-06 9825 1 103.7 9.8007e-05 3275 SHAKE stats (type/ave/delta/count) on step 3300000 1 0.97 1.40554e-06 9825 1 103.7 0.000100195 3275 SHAKE stats (type/ave/delta/count) on step 3350000 1 0.97 1.14669e-06 9825 1 103.7 9.28276e-05 3275 SHAKE stats (type/ave/delta/count) on step 3400000 1 0.97 1.15842e-06 9825 1 103.7 9.13315e-05 3275 SHAKE stats (type/ave/delta/count) on step 3450000 1 0.97 1.09151e-06 9825 1 103.7 9.53837e-05 3275 SHAKE stats (type/ave/delta/count) on step 3500000 1 0.97 1.11252e-06 9825 1 103.7 9.94165e-05 3275 SHAKE stats (type/ave/delta/count) on step 3550000 1 0.97 1.2335e-06 9825 1 103.7 0.000101602 3275 SHAKE stats (type/ave/delta/count) on step 3600000 1 0.97 1.32576e-06 9825 1 103.7 0.000115856 3275 SHAKE stats (type/ave/delta/count) on step 3650000 1 0.97 1.75406e-06 9825 1 103.7 0.000102929 3275 SHAKE stats (type/ave/delta/count) on step 3700000 1 0.97 1.16785e-06 9825 1 103.7 9.84991e-05 3275 SHAKE stats (type/ave/delta/count) on step 3750000 1 0.97 1.33935e-06 9825 1 103.7 0.000105171 3275 SHAKE stats (type/ave/delta/count) on step 3800000 1 0.97 1.10701e-06 9825 1 103.7 0.000102094 3275 SHAKE stats (type/ave/delta/count) on step 3850000 1 0.97 1.22807e-06 9825 1 103.7 9.61698e-05 3275 SHAKE stats (type/ave/delta/count) on step 3900000 1 0.97 1.19626e-06 9825 1 103.7 9.47714e-05 3275 SHAKE stats (type/ave/delta/count) on step 3950000 1 0.97 1.72634e-06 9825 1 103.7 0.000104449 3275 SHAKE stats (type/ave/delta/count) on step 4000000 1 0.97 1.18896e-06 9825 1 103.7 9.87128e-05 3275 4000000 4000000 -7115.8333 143340.91 1.3114365 301.58871 32.105149 58.225032 0 0 37188.313 -73211.762 -319.55737 -317455.29 -353388.41 7118.113 Loop time of 56271.7 on 16 procs for 4000000 steps with 12250 atoms Performance: 6.142 ns/day, 3.908 hours/ns, 71.084 timesteps/s 99.2% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 31943 | 38458 | 41816 |1666.7 | 68.34 Bond | 4.9886 | 14.519 | 23.229 | 152.9 | 0.03 Kspace | 8947.1 | 12311 | 18838 |2950.7 | 21.88 Neigh | 2208.7 | 2210.7 | 2213.2 | 2.7 | 3.93 Comm | 1299.8 | 1374.7 | 1425.8 | 121.9 | 2.44 Output | 0.016807 | 0.018967 | 0.020952 | 1.0 | 0.00 Modify | 1751.9 | 1798.6 | 1871.8 | 106.0 | 3.20 Other | | 103.4 | | | 0.18 Nlocal: 765.625 ave 813 max 711 min Histogram: 2 1 1 0 2 1 4 3 1 1 Nghost: 9198.62 ave 9456 max 8992 min Histogram: 3 1 0 5 3 0 0 0 0 4 Neighs: 376212 ave 408501 max 319000 min Histogram: 3 1 0 0 0 1 1 3 4 3 Total # of neighbors = 6019393 Ave neighs/atom = 491.37902 Ave special neighs/atom = 1.6481633 Neighbor list builds = 199405 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) = 0.2550303 grid = 36 27 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0036863798 estimated relative force accuracy = 1.1101423e-05 using double precision KISS FFT 3d grid and FFT values/proc = 11000 3888 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 4000000 1 0.97 1.18896e-06 9825 1 103.7 9.87128e-05 3275 Per MPI rank memory allocation (min/avg/max) = 14.12 | 14.63 | 14.83 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 -7115.048 143340.91 1.3114365 301.58871 32.105149 58.225032 0 0 37188.313 -73211.762 -319.55737 -317455.29 -353388.41 7118.113 Loop time of 4.36844e-06 on 16 procs for 0 steps with 12250 atoms 128.8% 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 | | 4.368e-06 | | |100.00 Nlocal: 765.625 ave 813 max 711 min Histogram: 2 1 1 0 2 1 4 3 1 1 Nghost: 9198.62 ave 9456 max 8992 min Histogram: 3 1 0 5 3 0 0 0 0 4 Neighs: 376212 ave 408501 max 319000 min Histogram: 3 1 0 0 0 1 1 3 4 3 Total # of neighbors = 6019393 Ave neighs/atom = 491.37902 Ave special neighs/atom = 1.6481633 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken log 2.6_Custom.out