#------------------------------------------------------------------------------- # 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 7.47402e-13 5784 2 103.7 7.72928e-11 1928 Per MPI rank memory allocation (min/avg/max) = 11.08 | 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 1.7415846 137108.63 0.6335873 297.71395 31.286651 34.737045 0 0 16376.286 11283.17 -77.153063 -152642.1 -124916.62 3956.1573 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.39473e-06 5784 2 103.7 9.72896e-05 1928 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.34864e-06 5784 2 103.7 0.000138212 1928 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.00294e-06 5784 2 103.7 9.09514e-05 1928 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.16951e-06 5784 2 103.7 8.91815e-05 1928 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.4629e-06 5784 2 103.7 0.000114747 1928 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.28314e-06 5784 2 103.7 8.8868e-05 1928 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.21653e-06 5784 2 103.7 0.000102403 1928 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.1475e-06 5784 2 103.7 9.30066e-05 1928 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.33213e-06 5784 2 103.7 9.47463e-05 1928 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.29094e-06 5784 2 103.7 8.78728e-05 1928 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.62556e-06 5784 2 103.7 0.000105731 1928 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.09711e-06 5784 2 103.7 0.000109203 1928 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.25625e-06 5784 2 103.7 0.000125634 1928 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.2584e-06 5784 2 103.7 9.63722e-05 1928 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.09893e-06 5784 2 103.7 9.73413e-05 1928 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.1726e-06 5784 2 103.7 9.48441e-05 1928 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.15154e-06 5784 2 103.7 9.56041e-05 1928 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.19967e-06 5784 2 103.7 9.06823e-05 1928 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.64495e-06 5784 2 103.7 0.000123613 1928 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.79783e-06 5784 2 103.7 0.000107173 1928 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.39032e-06 5784 2 103.7 9.42059e-05 1928 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.15954e-06 5784 2 103.7 9.17989e-05 1928 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.10883e-06 5784 2 103.7 9.05963e-05 1928 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.14083e-06 5784 2 103.7 8.93075e-05 1928 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.59608e-06 5784 2 103.7 0.000113147 1928 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.19552e-06 5784 2 103.7 9.05953e-05 1928 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.22343e-06 5784 2 103.7 9.13255e-05 1928 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.27317e-06 5784 2 103.7 9.89474e-05 1928 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.02983e-06 5784 2 103.7 8.93956e-05 1928 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.33878e-06 5784 2 103.7 0.000118694 1928 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.21486e-06 5784 2 103.7 9.02202e-05 1928 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.14344e-06 5784 2 103.7 8.90235e-05 1928 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.36236e-06 5784 2 103.7 8.82444e-05 1928 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.26224e-06 5784 2 103.7 0.000100448 1928 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.04453e-06 5784 2 103.7 9.33136e-05 1928 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.19197e-06 5784 2 103.7 0.000120814 1928 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.20466e-06 5784 2 103.7 0.000105559 1928 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.28516e-06 5784 2 103.7 0.000105591 1928 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.35806e-06 5784 2 103.7 9.75153e-05 1928 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.11715e-06 5784 2 103.7 8.73272e-05 1928 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.39739e-06 5784 2 103.7 0.000111644 1928 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.40062e-06 5784 2 103.7 0.00010427 1928 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.87194e-06 5784 2 103.7 0.000154617 1928 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.29818e-06 5784 2 103.7 0.000105216 1928 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.77459e-06 5784 2 103.7 0.000130581 1928 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.11438e-06 5784 2 103.7 9.05169e-05 1928 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.1272e-06 5784 2 103.7 8.97904e-05 1928 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.2594e-06 5784 2 103.7 9.79554e-05 1928 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.15609e-06 5784 2 103.7 9.48667e-05 1928 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.0673e-06 5784 2 103.7 0.000110244 1928 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.22857e-06 5784 2 103.7 9.93596e-05 1928 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.30286e-06 5784 2 103.7 0.000109026 1928 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.26388e-06 5784 2 103.7 9.7983e-05 1928 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.14001e-06 5784 2 103.7 9.88417e-05 1928 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.10852e-06 5784 2 103.7 8.61692e-05 1928 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.25128e-06 5784 2 103.7 0.000133469 1928 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.14476e-06 5784 2 103.7 0.000103172 1928 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.38921e-06 5784 2 103.7 0.000100134 1928 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.19119e-06 5784 2 103.7 9.5086e-05 1928 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.02536e-06 5784 2 103.7 9.33329e-05 1928 3000000 3000000 -45.153325 137108.63 0.6335873 300.53916 31.639511 45.91803 0 0 16293.296 11310.442 -77.153063 -152644.37 -124963.07 3993.7 Loop time of 25864 on 32 procs for 3000000 steps with 6387 atoms Performance: 10.022 ns/day, 2.395 hours/ns, 115.991 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 | 4.7439 | 7706.5 | 18886 |8512.4 | 29.80 Bond | 2.4902 | 5.5474 | 13.568 | 138.8 | 0.02 Kspace | 3953 | 15181 | 23033 |6106.1 | 58.69 Neigh | 1128.2 | 1135.2 | 1146.3 | 17.0 | 4.39 Comm | 257.43 | 653.87 | 896.24 | 887.4 | 2.53 Output | 0.011741 | 0.013585 | 0.01522 | 0.9 | 0.00 Modify | 959.05 | 1131.7 | 1372.5 | 484.7 | 4.38 Other | | 50.61 | | | 0.20 Nlocal: 199.594 ave 419 max 0 min Histogram: 12 0 1 3 0 0 3 1 1 11 Nghost: 3945 ave 7665 max 157 min Histogram: 4 4 4 0 4 4 0 4 4 4 Neighs: 91045.8 ave 224214 max 0 min Histogram: 16 0 0 0 0 1 3 4 3 5 Total # of neighbors = 2913465 Ave neighs/atom = 456.15547 Ave special neighs/atom = 1.8738062 Neighbor list builds = 145289 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 1.02536e-06 5784 2 103.7 9.33329e-05 1928 Per MPI rank memory allocation (min/avg/max) = 11.08 | 12.39 | 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 -44.673536 137108.63 0.6335873 300.53916 31.639511 45.91803 0 0 16293.296 11310.442 -77.153063 -152644.37 -124963.07 3993.7 Loop time of 6.86706e-06 on 32 procs for 0 steps with 6387 atoms 112.9% 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 | | 6.867e-06 | | |100.00 Nlocal: 199.594 ave 419 max 0 min Histogram: 12 0 1 3 0 0 3 1 1 11 Nghost: 3945 ave 7665 max 157 min Histogram: 4 4 4 0 4 4 0 4 4 4 Neighs: 91045.8 ave 224214 max 0 min Histogram: 16 0 0 0 0 1 3 4 3 5 Total # of neighbors = 2913465 Ave neighs/atom = 456.15547 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: 14:17:21