#------------------------------------------------------------------------------- # Stage 2.5: NVT integration for 5 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 2768 = # 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 500000 500000 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 500 1 500 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 restart 5000000 2.5.restart dump sci all custom 500000 2.5.xyz id mol type q xs ys zs timestep 1 run 5000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.20391866 grid = 27 27 27 stencil order = 5 estimated absolute RMS force accuracy = 0.0031570161 estimated relative force accuracy = 9.5072601e-06 using double precision KISS FFT 3d grid and FFT values/proc = 3380 756 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 6.93064e-11 8304 2 103.7 5.36049e-09 2768 Per MPI rank memory allocation (min/avg/max) = 13.45 | 13.71 | 13.85 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-06 394.6846 97473.161 1.2455227 302.44351 44.989065 68.022469 0 0 21246.161 -11258.609 -110.80248 -171341.37 -161240.8 5708.4667 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.19674e-06 8304 2 103.7 9.3888e-05 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.19224e-06 8304 2 103.7 0.000106693 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.41353e-06 8304 2 103.7 0.000104967 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.14418e-06 8304 2 103.7 0.00013513 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.2742e-06 8304 2 103.7 0.000103246 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.17634e-06 8304 2 103.7 9.02471e-05 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.63059e-06 8304 2 103.7 0.000117373 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.55507e-06 8304 2 103.7 0.000110841 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.67516e-06 8304 2 103.7 0.000146348 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.12723e-06 8304 2 103.7 8.97004e-05 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.21826e-06 8304 2 103.7 9.53448e-05 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.12519e-06 8304 2 103.7 8.97178e-05 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.29284e-06 8304 2 103.7 9.62099e-05 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 2.00401e-06 8304 2 103.7 0.00014102 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.12339e-06 8304 2 103.7 0.000110588 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.49956e-06 8304 2 103.7 0.000108189 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.28944e-06 8304 2 103.7 9.87525e-05 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.16008e-06 8304 2 103.7 8.92042e-05 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.72332e-06 8304 2 103.7 0.000121642 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.26246e-06 8304 2 103.7 9.52962e-05 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.268e-06 8304 2 103.7 0.000103603 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.24198e-06 8304 2 103.7 0.000101959 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.149e-06 8304 2 103.7 9.69849e-05 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.87177e-06 8304 2 103.7 0.000160398 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.07513e-06 8304 2 103.7 9.06259e-05 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.15716e-06 8304 2 103.7 0.000103148 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.4743e-06 8304 2 103.7 0.000117491 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.73651e-06 8304 2 103.7 0.00013942 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.10042e-06 8304 2 103.7 8.63667e-05 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.12624e-06 8304 2 103.7 9.16539e-05 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.03776e-06 8304 2 103.7 9.66673e-05 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.69458e-06 8304 2 103.7 0.000123972 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.25498e-06 8304 2 103.7 0.000108092 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.56335e-06 8304 2 103.7 0.00011689 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.53871e-06 8304 2 103.7 0.000114478 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.38397e-06 8304 2 103.7 9.37162e-05 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.21307e-06 8304 2 103.7 9.97619e-05 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.22249e-06 8304 2 103.7 0.000100673 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.56468e-06 8304 2 103.7 9.00174e-05 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.33376e-06 8304 2 103.7 9.91684e-05 2768 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.03442e-06 8304 2 103.7 9.06081e-05 2768 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.30939e-06 8304 2 103.7 9.46074e-05 2768 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.41596e-06 8304 2 103.7 9.22571e-05 2768 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.2187e-06 8304 2 103.7 8.74323e-05 2768 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.27678e-06 8304 2 103.7 0.000102612 2768 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.35028e-06 8304 2 103.7 0.000117241 2768 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.31751e-06 8304 2 103.7 9.32362e-05 2768 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.23534e-06 8304 2 103.7 9.68333e-05 2768 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.30412e-06 8304 2 103.7 9.78004e-05 2768 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.47289e-06 8304 2 103.7 0.000106397 2768 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.0795e-06 8304 2 103.7 8.98134e-05 2768 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.40257e-06 8304 2 103.7 9.7326e-05 2768 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.54929e-06 8304 2 103.7 0.000113972 2768 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.1767e-06 8304 2 103.7 8.93122e-05 2768 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.79846e-06 8304 2 103.7 0.000110225 2768 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.17806e-06 8304 2 103.7 0.000103861 2768 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.16015e-06 8304 2 103.7 9.39689e-05 2768 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.39274e-06 8304 2 103.7 0.000103043 2768 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.86035e-06 8304 2 103.7 0.000116122 2768 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.33144e-06 8304 2 103.7 0.000102024 2768 SHAKE stats (type/ave/delta/count) on step 3050000 2 0.97 1.27937e-06 8304 2 103.7 9.38306e-05 2768 SHAKE stats (type/ave/delta/count) on step 3100000 2 0.97 1.30754e-06 8304 2 103.7 9.16719e-05 2768 SHAKE stats (type/ave/delta/count) on step 3150000 2 0.97 1.38404e-06 8304 2 103.7 9.14946e-05 2768 SHAKE stats (type/ave/delta/count) on step 3200000 2 0.97 1.25852e-06 8304 2 103.7 9.58688e-05 2768 SHAKE stats (type/ave/delta/count) on step 3250000 2 0.97 1.26177e-06 8304 2 103.7 9.59621e-05 2768 SHAKE stats (type/ave/delta/count) on step 3300000 2 0.97 1.15197e-06 8304 2 103.7 9.19875e-05 2768 SHAKE stats (type/ave/delta/count) on step 3350000 2 0.97 1.18621e-06 8304 2 103.7 9.943e-05 2768 SHAKE stats (type/ave/delta/count) on step 3400000 2 0.97 1.14106e-06 8304 2 103.7 9.618e-05 2768 SHAKE stats (type/ave/delta/count) on step 3450000 2 0.97 1.08964e-06 8304 2 103.7 9.35386e-05 2768 SHAKE stats (type/ave/delta/count) on step 3500000 2 0.97 1.32471e-06 8304 2 103.7 9.54274e-05 2768 SHAKE stats (type/ave/delta/count) on step 3550000 2 0.97 1.34735e-06 8304 2 103.7 9.80337e-05 2768 SHAKE stats (type/ave/delta/count) on step 3600000 2 0.97 1.39799e-06 8304 2 103.7 0.00010555 2768 SHAKE stats (type/ave/delta/count) on step 3650000 2 0.97 1.23817e-06 8304 2 103.7 0.000101405 2768 SHAKE stats (type/ave/delta/count) on step 3700000 2 0.97 1.3354e-06 8304 2 103.7 9.82817e-05 2768 SHAKE stats (type/ave/delta/count) on step 3750000 2 0.97 1.44841e-06 8304 2 103.7 9.83952e-05 2768 SHAKE stats (type/ave/delta/count) on step 3800000 2 0.97 1.3323e-06 8304 2 103.7 9.57054e-05 2768 SHAKE stats (type/ave/delta/count) on step 3850000 2 0.97 1.29181e-06 8304 2 103.7 9.41373e-05 2768 SHAKE stats (type/ave/delta/count) on step 3900000 2 0.97 1.30257e-06 8304 2 103.7 9.89527e-05 2768 SHAKE stats (type/ave/delta/count) on step 3950000 2 0.97 1.26953e-06 8304 2 103.7 9.97761e-05 2768 SHAKE stats (type/ave/delta/count) on step 4000000 2 0.97 1.16125e-06 8304 2 103.7 9.23563e-05 2768 SHAKE stats (type/ave/delta/count) on step 4050000 2 0.97 1.12784e-06 8304 2 103.7 9.23317e-05 2768 SHAKE stats (type/ave/delta/count) on step 4100000 2 0.97 1.6151e-06 8304 2 103.7 0.000107963 2768 SHAKE stats (type/ave/delta/count) on step 4150000 2 0.97 1.20312e-06 8304 2 103.7 9.64971e-05 2768 SHAKE stats (type/ave/delta/count) on step 4200000 2 0.97 1.20522e-06 8304 2 103.7 0.000101998 2768 SHAKE stats (type/ave/delta/count) on step 4250000 2 0.97 1.69236e-06 8304 2 103.7 0.000143362 2768 SHAKE stats (type/ave/delta/count) on step 4300000 2 0.97 1.37468e-06 8304 2 103.7 0.000128676 2768 SHAKE stats (type/ave/delta/count) on step 4350000 2 0.97 1.72224e-06 8304 2 103.7 0.000103096 2768 SHAKE stats (type/ave/delta/count) on step 4400000 2 0.97 1.12753e-06 8304 2 103.7 9.44852e-05 2768 SHAKE stats (type/ave/delta/count) on step 4450000 2 0.97 1.255e-06 8304 2 103.7 0.000102077 2768 SHAKE stats (type/ave/delta/count) on step 4500000 2 0.97 1.30052e-06 8304 2 103.7 9.66199e-05 2768 SHAKE stats (type/ave/delta/count) on step 4550000 2 0.97 1.15526e-06 8304 2 103.7 9.89985e-05 2768 SHAKE stats (type/ave/delta/count) on step 4600000 2 0.97 1.45339e-06 8304 2 103.7 0.000107584 2768 SHAKE stats (type/ave/delta/count) on step 4650000 2 0.97 1.15316e-06 8304 2 103.7 0.000114472 2768 SHAKE stats (type/ave/delta/count) on step 4700000 2 0.97 1.22948e-06 8304 2 103.7 9.46744e-05 2768 SHAKE stats (type/ave/delta/count) on step 4750000 2 0.97 1.31421e-06 8304 2 103.7 9.78333e-05 2768 SHAKE stats (type/ave/delta/count) on step 4800000 2 0.97 1.38283e-06 8304 2 103.7 0.000104233 2768 SHAKE stats (type/ave/delta/count) on step 4850000 2 0.97 1.26028e-06 8304 2 103.7 9.73137e-05 2768 SHAKE stats (type/ave/delta/count) on step 4900000 2 0.97 1.23067e-06 8304 2 103.7 9.78619e-05 2768 SHAKE stats (type/ave/delta/count) on step 4950000 2 0.97 1.363e-06 8304 2 103.7 0.000123671 2768 SHAKE stats (type/ave/delta/count) on step 5000000 2 0.97 1.44868e-06 8304 2 103.7 9.74701e-05 2768 5000000 5000000 84.628575 97473.161 1.2455227 302.98529 41.730137 64.181103 0 0 21437.34 -11719.054 -110.80248 -171336.38 -161512.19 5718.6926 Loop time of 55962.2 on 32 procs for 5000000 steps with 9101 atoms Performance: 7.719 ns/day, 3.109 hours/ns, 89.346 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 | 37337 | 40022 | 42249 | 749.6 | 71.52 Bond | 6.5331 | 14.843 | 30.154 | 180.9 | 0.03 Kspace | 6012.5 | 8233 | 10900 |1649.7 | 14.71 Neigh | 1924.3 | 1925.5 | 1926.9 | 1.5 | 3.44 Comm | 2628.6 | 2665.6 | 2696.9 | 32.1 | 4.76 Output | 0.0093863 | 0.011619 | 0.013732 | 1.2 | 0.00 Modify | 2874.5 | 2895.1 | 2915.4 | 24.2 | 5.17 Other | | 205.8 | | | 0.37 Nlocal: 284.406 ave 299 max 269 min Histogram: 1 2 2 6 4 5 2 5 2 3 Nghost: 10717 ave 10761 max 10663 min Histogram: 2 0 4 2 9 1 4 3 3 4 Neighs: 273091 ave 301949 max 252656 min Histogram: 5 2 6 4 4 3 3 1 2 2 Total # of neighbors = 8738907 Ave neighs/atom = 960.21393 Ave special neighs/atom = 1.8929788 Neighbor list builds = 247232 Dangerous builds = 0 undump sci restart 0 dump sci all custom 5000000 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) = 0.20391866 grid = 27 27 27 stencil order = 5 estimated absolute RMS force accuracy = 0.0031570161 estimated relative force accuracy = 9.5072601e-06 using double precision KISS FFT 3d grid and FFT values/proc = 3380 756 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 5000000 2 0.97 1.44868e-06 8304 2 103.7 9.74701e-05 2768 Per MPI rank memory allocation (min/avg/max) = 13.45 | 13.74 | 13.84 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 5000000 5000000 85.563007 97473.161 1.2455227 302.98529 41.730137 64.181103 0 0 21437.34 -11719.054 -110.80248 -171336.38 -161512.19 5718.6926 Loop time of 7.48541e-06 on 32 procs for 0 steps with 9101 atoms 113.6% 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 | | 7.485e-06 | | |100.00 Nlocal: 284.406 ave 299 max 269 min Histogram: 1 2 2 6 4 5 2 5 2 3 Nghost: 10717 ave 10761 max 10663 min Histogram: 2 0 4 2 9 1 4 3 3 4 Neighs: 273091 ave 301949 max 252656 min Histogram: 5 2 6 4 4 3 3 1 2 2 Total # of neighbors = 8738907 Ave neighs/atom = 960.21393 Ave special neighs/atom = 1.8929788 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.6_NVT.out