#------------------------------------------------------------------------------- # 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) = 0.2507789 grid = 30 30 50 stencil order = 5 estimated absolute RMS force accuracy = 0.0034789377 estimated relative force accuracy = 1.0476718e-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 5.82645e-13 5784 2 103.7 7.42375e-11 1928 Per MPI rank memory allocation (min/avg/max) = 11.06 | 12.55 | 13.51 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 -594.57567 137108.63 0.6335873 294.86683 21.112094 33.284795 0 0 15979.01 11655.332 -77.153063 -152641.87 -124953.13 3918.3234 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.23313e-06 5784 2 103.7 0.000105755 1928 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.75874e-06 5784 2 103.7 0.000142519 1928 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.40428e-06 5784 2 103.7 9.88783e-05 1928 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.45941e-06 5784 2 103.7 0.000106007 1928 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.18909e-06 5784 2 103.7 0.00010059 1928 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.17528e-06 5784 2 103.7 0.000105796 1928 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.42214e-06 5784 2 103.7 0.000114758 1928 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.30939e-06 5784 2 103.7 0.000119255 1928 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.84564e-06 5784 2 103.7 0.000126909 1928 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.21658e-06 5784 2 103.7 0.000105175 1928 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.27922e-06 5784 2 103.7 9.27158e-05 1928 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.03448e-06 5784 2 103.7 9.73319e-05 1928 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.5496e-06 5784 2 103.7 9.73152e-05 1928 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.47692e-06 5784 2 103.7 0.000104524 1928 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.04937e-06 5784 2 103.7 8.69626e-05 1928 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.04732e-06 5784 2 103.7 9.66796e-05 1928 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.14015e-06 5784 2 103.7 9.46843e-05 1928 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.31753e-06 5784 2 103.7 9.12072e-05 1928 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.26205e-06 5784 2 103.7 0.000104109 1928 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.31585e-06 5784 2 103.7 9.39705e-05 1928 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.13461e-06 5784 2 103.7 9.76874e-05 1928 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.23212e-06 5784 2 103.7 9.81762e-05 1928 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.9477e-06 5784 2 103.7 0.000130583 1928 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.59115e-06 5784 2 103.7 0.000152046 1928 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.34206e-06 5784 2 103.7 0.000103577 1928 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.86444e-06 5784 2 103.7 0.000140136 1928 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.15496e-06 5784 2 103.7 9.97138e-05 1928 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.60695e-06 5784 2 103.7 0.000115001 1928 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.15872e-06 5784 2 103.7 0.000118572 1928 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.546e-06 5784 2 103.7 0.000110824 1928 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.628e-06 5784 2 103.7 0.000128637 1928 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.09281e-06 5784 2 103.7 8.94978e-05 1928 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 9.37573e-07 5784 2 103.7 8.71461e-05 1928 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.06806e-06 5784 2 103.7 9.62479e-05 1928 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.18029e-06 5784 2 103.7 0.000107514 1928 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.43688e-06 5784 2 103.7 0.000108052 1928 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.06693e-06 5784 2 103.7 9.28e-05 1928 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.04842e-06 5784 2 103.7 9.92126e-05 1928 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.39855e-06 5784 2 103.7 8.94988e-05 1928 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.26454e-06 5784 2 103.7 0.000111467 1928 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.19097e-06 5784 2 103.7 0.000127967 1928 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.24741e-06 5784 2 103.7 9.77486e-05 1928 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.29277e-06 5784 2 103.7 0.000119712 1928 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.12193e-06 5784 2 103.7 0.000100879 1928 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.11054e-06 5784 2 103.7 9.27855e-05 1928 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.11332e-06 5784 2 103.7 9.73119e-05 1928 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.61144e-06 5784 2 103.7 0.000131625 1928 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.34266e-06 5784 2 103.7 0.000106187 1928 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.48004e-06 5784 2 103.7 0.000130134 1928 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.2393e-06 5784 2 103.7 9.16244e-05 1928 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.15073e-06 5784 2 103.7 9.19261e-05 1928 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.03878e-06 5784 2 103.7 0.000101245 1928 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.1838e-06 5784 2 103.7 9.30123e-05 1928 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.23931e-06 5784 2 103.7 9.22854e-05 1928 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.2921e-06 5784 2 103.7 9.84316e-05 1928 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.13485e-06 5784 2 103.7 0.000101145 1928 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.07949e-06 5784 2 103.7 0.000109681 1928 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.42193e-06 5784 2 103.7 0.000113548 1928 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.07445e-06 5784 2 103.7 8.73995e-05 1928 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.1204e-06 5784 2 103.7 8.98681e-05 1928 3000000 3000000 -345.15441 137108.63 0.6335873 301.55544 29.412256 41.215663 0 0 16145.643 11525.048 -77.153063 -152654.42 -124913.1 4007.2048 Loop time of 25406 on 32 procs for 3000000 steps with 6387 atoms Performance: 10.202 ns/day, 2.352 hours/ns, 118.082 timesteps/s 98.4% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16.041 | 7676.7 | 18255 |8619.8 | 30.22 Bond | 2.7314 | 5.6819 | 15.001 | 145.1 | 0.02 Kspace | 4005.4 | 14634 | 22389 |6276.7 | 57.60 Neigh | 1198.5 | 1204.6 | 1214.3 | 14.9 | 4.74 Comm | 334.97 | 669.3 | 871.67 | 779.1 | 2.63 Output | 0.011 | 0.012666 | 0.014097 | 0.8 | 0.00 Modify | 1002.2 | 1157.9 | 1385.4 | 442.9 | 4.56 Other | | 57.67 | | | 0.23 Nlocal: 199.594 ave 397 max 0 min Histogram: 13 3 0 0 0 0 0 0 2 14 Nghost: 3996.06 ave 7348 max 643 min Histogram: 8 0 0 8 0 0 8 0 0 8 Neighs: 90928.7 ave 218377 max 0 min Histogram: 16 0 0 0 0 0 4 2 5 5 Total # of neighbors = 2909717 Ave neighs/atom = 455.56866 Ave special neighs/atom = 1.8738062 Neighbor list builds = 145295 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) = 0.2507789 grid = 30 30 50 stencil order = 5 estimated absolute RMS force accuracy = 0.0034789377 estimated relative force accuracy = 1.0476718e-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 1.1204e-06 5784 2 103.7 8.98681e-05 1928 Per MPI rank memory allocation (min/avg/max) = 11.06 | 12.55 | 13.51 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 -344.7318 137108.63 0.6335873 301.55544 29.412256 41.215663 0 0 16145.643 11525.048 -77.153063 -152654.42 -124913.1 4007.2048 Loop time of 1.42542e-05 on 32 procs for 0 steps with 6387 atoms 106.5% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 1.425e-05 | | |100.00 Nlocal: 199.594 ave 397 max 0 min Histogram: 13 3 0 0 0 0 0 0 2 14 Nghost: 3996.06 ave 7348 max 643 min Histogram: 8 0 0 8 0 0 8 0 0 8 Neighs: 90928.7 ave 218377 max 0 min Histogram: 16 0 0 0 0 0 4 2 5 5 Total # of neighbors = 2909717 Ave neighs/atom = 455.56866 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: 18:59:44