#------------------------------------------------------------------------------- # 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 1928 = # 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) = 0.25049777 grid = 30 30 50 stencil order = 5 estimated absolute RMS force accuracy = 0.0035336797 estimated relative force accuracy = 1.0641571e-05 using double precision KISS FFT 3d grid and FFT values/proc = 6292 1800 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 6.73239e-13 5784 2 103.7 8.53504e-11 1928 Per MPI rank memory allocation (min/avg/max) = 11.07 | 12.42 | 13.54 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 -181.86337 138406.7 0.6276451 294.86076 28.288073 33.066383 0 0 16268.862 11311.335 -76.429471 -152461.48 -124819.93 3918.2428 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 9.37749e-07 5784 2 103.7 8.75165e-05 1928 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.30449e-06 5784 2 103.7 0.000104943 1928 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.81493e-06 5784 2 103.7 0.000129733 1928 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.25964e-06 5784 2 103.7 9.62484e-05 1928 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.63009e-06 5784 2 103.7 0.00013824 1928 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.14441e-06 5784 2 103.7 0.000100191 1928 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.52874e-06 5784 2 103.7 0.000108412 1928 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.25532e-06 5784 2 103.7 9.5254e-05 1928 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.50305e-06 5784 2 103.7 0.000124223 1928 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.58138e-06 5784 2 103.7 0.000135159 1928 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.11207e-06 5784 2 103.7 0.000111281 1928 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.23843e-06 5784 2 103.7 9.27846e-05 1928 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.33828e-06 5784 2 103.7 0.000105427 1928 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.36111e-06 5784 2 103.7 8.85263e-05 1928 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.26584e-06 5784 2 103.7 9.61836e-05 1928 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.13472e-06 5784 2 103.7 8.87884e-05 1928 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.23033e-06 5784 2 103.7 9.69536e-05 1928 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.11425e-06 5784 2 103.7 9.3732e-05 1928 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.04537e-06 5784 2 103.7 9.18534e-05 1928 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.09055e-06 5784 2 103.7 9.05676e-05 1928 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.10138e-06 5784 2 103.7 0.000100819 1928 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.44987e-06 5784 2 103.7 8.91769e-05 1928 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.22012e-06 5784 2 103.7 9.7631e-05 1928 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.02622e-06 5784 2 103.7 8.91316e-05 1928 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.21283e-06 5784 2 103.7 0.000102512 1928 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.54461e-06 5784 2 103.7 0.000104234 1928 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.17933e-06 5784 2 103.7 0.000107747 1928 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.75648e-06 5784 2 103.7 0.000128537 1928 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.36243e-06 5784 2 103.7 0.000101266 1928 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.20499e-06 5784 2 103.7 9.7674e-05 1928 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.40358e-06 5784 2 103.7 0.000103563 1928 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.32081e-06 5784 2 103.7 0.000116564 1928 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.22133e-06 5784 2 103.7 0.000110941 1928 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.05866e-06 5784 2 103.7 9.7555e-05 1928 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.17178e-06 5784 2 103.7 9.72518e-05 1928 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.00782e-06 5784 2 103.7 8.87019e-05 1928 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.0145e-06 5784 2 103.7 0.000130983 1928 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.12707e-06 5784 2 103.7 9.30381e-05 1928 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.03301e-06 5784 2 103.7 9.32042e-05 1928 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.49536e-06 5784 2 103.7 0.000140321 1928 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.25746e-06 5784 2 103.7 9.16319e-05 1928 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.21272e-06 5784 2 103.7 9.02664e-05 1928 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.42873e-06 5784 2 103.7 8.91928e-05 1928 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.21676e-06 5784 2 103.7 9.03061e-05 1928 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.3855e-06 5784 2 103.7 0.000101493 1928 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.18284e-06 5784 2 103.7 9.10249e-05 1928 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.03458e-06 5784 2 103.7 8.82479e-05 1928 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.51057e-06 5784 2 103.7 0.000116562 1928 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.21822e-06 5784 2 103.7 9.77014e-05 1928 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.17247e-06 5784 2 103.7 0.000104457 1928 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.22729e-06 5784 2 103.7 9.49591e-05 1928 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.34734e-06 5784 2 103.7 0.000102712 1928 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.18552e-06 5784 2 103.7 9.44656e-05 1928 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.06765e-06 5784 2 103.7 9.14628e-05 1928 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.25077e-06 5784 2 103.7 9.13608e-05 1928 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.17544e-06 5784 2 103.7 9.02383e-05 1928 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.12826e-06 5784 2 103.7 9.21714e-05 1928 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.76823e-06 5784 2 103.7 0.000132573 1928 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.27088e-06 5784 2 103.7 9.82491e-05 1928 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.05214e-06 5784 2 103.7 0.00010117 1928 3000000 3000000 -316.45034 138406.7 0.6276451 299.51193 26.20579 44.503963 0 0 16249.89 11110.38 -76.429471 -152461.87 -125030.89 3980.0497 Loop time of 25171.6 on 32 procs for 3000000 steps with 6387 atoms Performance: 10.297 ns/day, 2.331 hours/ns, 119.182 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 | 4.0599 | 7702.5 | 17887 |8494.5 | 30.60 Bond | 2.6039 | 5.6805 | 15.714 | 140.8 | 0.02 Kspace | 4144.9 | 14384 | 22247 |6260.1 | 57.15 Neigh | 1234.8 | 1241.7 | 1252.6 | 16.2 | 4.93 Comm | 233.4 | 643.62 | 889.73 | 910.5 | 2.56 Output | 0.012083 | 0.013909 | 0.01556 | 0.8 | 0.00 Modify | 965.6 | 1141.6 | 1380.7 | 483.8 | 4.54 Other | | 52.05 | | | 0.21 Nlocal: 199.594 ave 409 max 0 min Histogram: 12 0 0 3 1 1 3 0 0 12 Nghost: 3936.47 ave 7799 max 85 min Histogram: 4 4 4 0 4 4 0 4 4 4 Neighs: 91346.8 ave 217197 max 0 min Histogram: 16 0 0 0 1 0 3 2 3 7 Total # of neighbors = 2923097 Ave neighs/atom = 457.66354 Ave special neighs/atom = 1.8738062 Neighbor list builds = 145013 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) = 0.25049777 grid = 30 30 50 stencil order = 5 estimated absolute RMS force accuracy = 0.0035336797 estimated relative force accuracy = 1.0641571e-05 using double precision KISS FFT 3d grid and FFT values/proc = 6292 1800 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.05214e-06 5784 2 103.7 0.00010117 1928 Per MPI rank memory allocation (min/avg/max) = 11.07 | 12.43 | 13.54 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 -315.9443 138406.7 0.6276451 299.51193 26.20579 44.503963 0 0 16249.89 11110.38 -76.429471 -152461.87 -125030.89 3980.0497 Loop time of 7.23938e-06 on 32 procs for 0 steps with 6387 atoms 108.8% 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 | | 7.239e-06 | | |100.00 Nlocal: 199.594 ave 409 max 0 min Histogram: 12 0 0 3 1 1 3 0 0 12 Nghost: 3936.47 ave 7799 max 85 min Histogram: 4 4 4 0 4 4 0 4 4 4 Neighs: 91346.8 ave 217197 max 0 min Histogram: 16 0 0 0 1 0 3 2 3 7 Total # of neighbors = 2923097 Ave neighs/atom = 457.66354 Ave special neighs/atom = 1.8738062 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 14:05:41