#------------------------------------------------------------------------------- # Stage 2.4: NVT integration for 1 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 2812 = # 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 100000 100000 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 2.4_averages.txt off 1 fix 3 movable ave/time 100 1 100 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 2.4_instantaneous.txt fix 4 fixed setforce 0.0 0.0 0.0 restart 1000000 2.4.restart dump sci all custom 100000 2.4.xyz id mol type q xs ys zs timestep 1 run 1000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25537807 grid = 30 30 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0034433421 estimated relative force accuracy = 1.0369522e-05 using double precision KISS FFT 3d grid and FFT values/proc = 18722 7200 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 1.00023 0.0690871 8436 2 97.8101 10.2991 2812 Per MPI rank memory allocation (min/avg/max) = 14.06 | 16.33 | 17.65 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 -2317.5372 141184.09 1.4079299 407.8254 6.9754979 31.657889 0 0 34690.161 -53432.747 -312.04795 -284230.82 -302934.78 9325.2516 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.26153e-06 8436 2 103.7 9.92524e-05 2812 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.14103e-06 8436 2 103.7 0.00010313 2812 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.19024e-06 8436 2 103.7 9.34229e-05 2812 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.31908e-06 8436 2 103.7 9.35291e-05 2812 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.37631e-06 8436 2 103.7 9.84273e-05 2812 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.14982e-06 8436 2 103.7 9.5521e-05 2812 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.43556e-06 8436 2 103.7 0.000103345 2812 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.40593e-06 8436 2 103.7 0.000109715 2812 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.4557e-06 8436 2 103.7 9.80528e-05 2812 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.52588e-06 8436 2 103.7 9.9903e-05 2812 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.13209e-06 8436 2 103.7 8.75094e-05 2812 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.69896e-06 8436 2 103.7 0.000120077 2812 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.20922e-06 8436 2 103.7 9.79968e-05 2812 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.02609e-06 8436 2 103.7 0.000101036 2812 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.31096e-06 8436 2 103.7 0.000107412 2812 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.26424e-06 8436 2 103.7 9.54715e-05 2812 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.50714e-06 8436 2 103.7 0.000121756 2812 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.12577e-06 8436 2 103.7 0.000107113 2812 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.14416e-06 8436 2 103.7 9.8148e-05 2812 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.2036e-06 8436 2 103.7 0.000100515 2812 1000000 1000000 -211.97281 141184.09 1.4079299 298.95645 46.592795 92.883496 0 0 31903.703 -35612.118 -312.04795 -284079.21 -287648.15 6835.8766 Loop time of 21931.3 on 8 procs for 1000000 steps with 10808 atoms Performance: 3.940 ns/day, 6.092 hours/ns, 45.597 timesteps/s 98.8% CPU use with 8 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3731.7 | 13143 | 17452 |4784.4 | 59.93 Bond | 0.94924 | 4.7291 | 8.0684 | 112.5 | 0.02 Kspace | 2871.1 | 7187.2 | 16610 |6476.5 | 32.77 Neigh | 895.63 | 896.76 | 898.17 | 3.1 | 4.09 Comm | 229.92 | 254.09 | 281.23 | 108.2 | 1.16 Output | 0.023779 | 0.026861 | 0.029734 | 1.2 | 0.00 Modify | 397.34 | 418.84 | 432.23 | 63.3 | 1.91 Other | | 26.36 | | | 0.12 Nlocal: 1351 ave 1599 max 712 min Histogram: 2 0 0 0 0 0 0 0 0 6 Nghost: 11097.2 ave 13280 max 9593 min Histogram: 2 0 2 2 0 0 0 0 0 2 Neighs: 633271 ave 819525 max 178219 min Histogram: 2 0 0 0 0 0 0 0 2 4 Total # of neighbors = 5066167 Ave neighs/atom = 468.74232 Ave special neighs/atom = 1.6184308 Neighbor list builds = 49747 Dangerous builds = 0 undump sci restart 0 dump sci all custom 1000000 2.4.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) = 0.25537807 grid = 30 30 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0034433421 estimated relative force accuracy = 1.0369522e-05 using double precision KISS FFT 3d grid and FFT values/proc = 18722 7200 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.2036e-06 8436 2 103.7 0.000100515 2812 Per MPI rank memory allocation (min/avg/max) = 14.05 | 16.45 | 17.64 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 1000000 1000000 -211.38038 141184.09 1.4079299 298.95645 46.592795 92.883496 0 0 31903.703 -35612.118 -312.04795 -284079.21 -287648.15 6835.8766 Loop time of 3.04462e-06 on 8 procs for 0 steps with 10808 atoms 147.8% CPU use with 8 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 | | 3.045e-06 | | |100.00 Nlocal: 1351 ave 1599 max 712 min Histogram: 2 0 0 0 0 0 0 0 0 6 Nghost: 11097.2 ave 13280 max 9593 min Histogram: 2 0 2 2 0 0 0 0 0 2 Neighs: 633271 ave 819525 max 178219 min Histogram: 2 0 0 0 0 0 0 0 2 4 Total # of neighbors = 5066167 Ave neighs/atom = 468.74232 Ave special neighs/atom = 1.6184308 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken log 2.5_NVT.out