#------------------------------------------------------------------------------- # 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 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 3488 = # 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 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 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) = 0.32529392 grid = 48 48 48 stencil order = 5 estimated absolute RMS force accuracy = 0.0036767963 estimated relative force accuracy = 1.1072563e-05 using double precision KISS FFT 3d grid and FFT values/proc = 11191 4608 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 0.97 4.66294e-14 10464 2 103.7 3.93641e-12 3488 Per MPI rank memory allocation (min/avg/max) = 13.23 | 13.3 | 13.35 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 -364.54881 122022.49 1.3680167 298.60429 225.99379 303.86262 0 0 31548.484 104998.41 -644.18917 -392883.45 -255806.7 7558.5821 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.26521e-06 10464 2 103.7 0.000102651 3488 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.5387e-06 10464 2 103.7 0.000100292 3488 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.11751e-06 10464 2 103.7 0.000111842 3488 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.19913e-06 10464 2 103.7 9.09873e-05 3488 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.12158e-06 10464 2 103.7 9.13991e-05 3488 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.28019e-06 10464 2 103.7 9.1465e-05 3488 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.28836e-06 10464 2 103.7 0.000109154 3488 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.2673e-06 10464 2 103.7 8.88265e-05 3488 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.49267e-06 10464 2 103.7 0.000100778 3488 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.17473e-06 10464 2 103.7 0.000108224 3488 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.27636e-06 10464 2 103.7 9.52283e-05 3488 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.44469e-06 10464 2 103.7 0.000104588 3488 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.49226e-06 10464 2 103.7 0.000110205 3488 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.21488e-06 10464 2 103.7 9.72853e-05 3488 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.14545e-06 10464 2 103.7 9.64043e-05 3488 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.32741e-06 10464 2 103.7 0.000106314 3488 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.08679e-06 10464 2 103.7 0.000104577 3488 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.22036e-06 10464 2 103.7 0.000105643 3488 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.39993e-06 10464 2 103.7 0.000109776 3488 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.12617e-06 10464 2 103.7 9.34442e-05 3488 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.97 1.33323e-06 10464 2 103.7 9.98852e-05 3488 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.97 1.53554e-06 10464 2 103.7 0.000111213 3488 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.97 1.25491e-06 10464 2 103.7 9.03269e-05 3488 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.97 1.45721e-06 10464 2 103.7 9.90882e-05 3488 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.97 1.11779e-06 10464 2 103.7 9.04514e-05 3488 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.97 1.51469e-06 10464 2 103.7 0.000107018 3488 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.97 1.33853e-06 10464 2 103.7 0.00010303 3488 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.97 1.18982e-06 10464 2 103.7 0.0001099 3488 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.97 1.40734e-06 10464 2 103.7 0.000100181 3488 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.97 1.1746e-06 10464 2 103.7 9.6493e-05 3488 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.97 1.28795e-06 10464 2 103.7 8.97706e-05 3488 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.97 1.24113e-06 10464 2 103.7 8.88786e-05 3488 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.97 1.3487e-06 10464 2 103.7 9.24192e-05 3488 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.97 1.23038e-06 10464 2 103.7 0.000105585 3488 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.97 1.48387e-06 10464 2 103.7 0.000113969 3488 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.97 1.42572e-06 10464 2 103.7 0.000104319 3488 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.97 1.61154e-06 10464 2 103.7 0.000104882 3488 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.97 1.21122e-06 10464 2 103.7 9.02487e-05 3488 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.97 1.25405e-06 10464 2 103.7 9.26431e-05 3488 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.08415e-06 10464 2 103.7 9.62397e-05 3488 SHAKE stats (type/ave/delta/count) on step 2050000 1 0.97 1.66276e-06 10464 2 103.7 0.000100016 3488 SHAKE stats (type/ave/delta/count) on step 2100000 1 0.97 1.10252e-06 10464 2 103.7 9.11885e-05 3488 SHAKE stats (type/ave/delta/count) on step 2150000 1 0.97 1.22727e-06 10464 2 103.7 9.61685e-05 3488 SHAKE stats (type/ave/delta/count) on step 2200000 1 0.97 1.23591e-06 10464 2 103.7 9.72376e-05 3488 SHAKE stats (type/ave/delta/count) on step 2250000 1 0.97 1.36378e-06 10464 2 103.7 9.74571e-05 3488 SHAKE stats (type/ave/delta/count) on step 2300000 1 0.97 1.14002e-06 10464 2 103.7 9.62934e-05 3488 SHAKE stats (type/ave/delta/count) on step 2350000 1 0.97 1.28567e-06 10464 2 103.7 9.2564e-05 3488 SHAKE stats (type/ave/delta/count) on step 2400000 1 0.97 1.10436e-06 10464 2 103.7 9.65648e-05 3488 SHAKE stats (type/ave/delta/count) on step 2450000 1 0.97 1.40846e-06 10464 2 103.7 9.15831e-05 3488 SHAKE stats (type/ave/delta/count) on step 2500000 1 0.97 1.2605e-06 10464 2 103.7 8.6869e-05 3488 SHAKE stats (type/ave/delta/count) on step 2550000 1 0.97 1.20739e-06 10464 2 103.7 0.000101098 3488 SHAKE stats (type/ave/delta/count) on step 2600000 1 0.97 1.37644e-06 10464 2 103.7 0.000108847 3488 SHAKE stats (type/ave/delta/count) on step 2650000 1 0.97 1.15603e-06 10464 2 103.7 9.77885e-05 3488 SHAKE stats (type/ave/delta/count) on step 2700000 1 0.97 1.21566e-06 10464 2 103.7 9.58995e-05 3488 SHAKE stats (type/ave/delta/count) on step 2750000 1 0.97 1.80155e-06 10464 2 103.7 0.000137902 3488 SHAKE stats (type/ave/delta/count) on step 2800000 1 0.97 1.54351e-06 10464 2 103.7 9.71923e-05 3488 SHAKE stats (type/ave/delta/count) on step 2850000 1 0.97 1.47162e-06 10464 2 103.7 9.92301e-05 3488 SHAKE stats (type/ave/delta/count) on step 2900000 1 0.97 1.21503e-06 10464 2 103.7 0.00010074 3488 SHAKE stats (type/ave/delta/count) on step 2950000 1 0.97 1.41487e-06 10464 2 103.7 0.00010666 3488 SHAKE stats (type/ave/delta/count) on step 3000000 1 0.97 1.62558e-06 10464 2 103.7 9.52481e-05 3488 3000000 3000000 -8.4872121 122022.49 1.3680167 297.26602 239.97773 287.77678 0 0 31467.828 105044.74 -644.18917 -392883.92 -255843.6 7524.7063 Loop time of 22315.4 on 32 procs for 3000000 steps with 11981 atoms Performance: 11.615 ns/day, 2.066 hours/ns, 134.436 timesteps/s 99.2% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7969.9 | 9050.9 | 11224 |1187.0 | 40.56 Bond | 4.8241 | 17.872 | 49.024 | 346.3 | 0.08 Kspace | 7709.4 | 9925.6 | 11010 |1152.3 | 44.48 Neigh | 636.64 | 638.75 | 641.01 | 4.4 | 2.86 Comm | 1159.8 | 1223.1 | 1274.3 | 101.9 | 5.48 Output | 0.011879 | 0.014587 | 0.017105 | 1.3 | 0.00 Modify | 1350.3 | 1389.6 | 1425.6 | 65.7 | 6.23 Other | | 69.55 | | | 0.31 Nlocal: 374.406 ave 443 max 333 min Histogram: 3 5 11 4 1 0 0 3 4 1 Nghost: 5499.31 ave 5638 max 5216 min Histogram: 7 1 0 0 0 0 0 5 10 9 Neighs: 117295 ave 150989 max 97898 min Histogram: 4 10 7 3 0 0 0 0 7 1 Total # of neighbors = 3753448 Ave neighs/atom = 313.28337 Ave special neighs/atom = 1.9988315 Neighbor list builds = 148684 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) = 0.32529392 grid = 48 48 48 stencil order = 5 estimated absolute RMS force accuracy = 0.0036767963 estimated relative force accuracy = 1.1072563e-05 using double precision KISS FFT 3d grid and FFT values/proc = 11191 4608 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 1 0.97 1.62558e-06 10464 2 103.7 9.52481e-05 3488 Per MPI rank memory allocation (min/avg/max) = 13.23 | 13.3 | 13.35 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 -7.4170244 122022.49 1.3680167 297.26602 239.97773 287.77678 0 0 31467.828 105044.74 -644.18917 -392883.92 -255843.6 7524.7063 Loop time of 8.24206e-06 on 32 procs for 0 steps with 11981 atoms 116.8% 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 | | 8.242e-06 | | |100.00 Nlocal: 374.406 ave 443 max 333 min Histogram: 3 5 11 4 1 0 0 3 4 1 Nghost: 5499.31 ave 5638 max 5216 min Histogram: 7 1 0 0 0 0 0 5 10 9 Neighs: 117295 ave 150989 max 97898 min Histogram: 4 10 7 3 0 0 0 0 7 1 Total # of neighbors = 3753448 Ave neighs/atom = 313.28337 Ave special neighs/atom = 1.9988315 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.6_NVT.out