#------------------------------------------------------------------------------- # 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 3728 = # 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 fix 4 fixed setforce 0.0 0.0 0.0 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) = 0.25956456 grid = 30 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0028924598 estimated relative force accuracy = 8.7105569e-06 using double precision KISS FFT 3d grid and FFT values/proc = 13068 4800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 0.97 7.75935e-13 11184 2 103.7 7.4948e-11 3728 Per MPI rank memory allocation (min/avg/max) = 14.82 | 15.16 | 16.22 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 335313.27 143799.62 1.371895 299.22721 293.7791 351.31066 0 0 271378.76 -52196.151 -383.45046 -378987.78 -159160.09 8216.5465 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.13231e-06 11184 2 103.7 9.22534e-05 3728 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.07313e-06 11184 2 103.7 9.20267e-05 3728 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.13083e-06 11184 2 103.7 0.000102994 3728 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.15473e-06 11184 2 103.7 9.83749e-05 3728 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.33787e-06 11184 2 103.7 9.66766e-05 3728 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.62966e-06 11184 2 103.7 0.000112174 3728 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.43012e-06 11184 2 103.7 0.000106283 3728 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.21348e-06 11184 2 103.7 9.92797e-05 3728 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.14109e-06 11184 2 103.7 0.000107707 3728 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.16851e-06 11184 2 103.7 9.83098e-05 3728 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.16237e-06 11184 2 103.7 9.58384e-05 3728 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.2406e-06 11184 2 103.7 9.23717e-05 3728 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.29988e-06 11184 2 103.7 9.77445e-05 3728 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.18505e-06 11184 2 103.7 9.14488e-05 3728 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.75709e-06 11184 2 103.7 0.000103937 3728 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.39252e-06 11184 2 103.7 0.000109215 3728 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.5159e-06 11184 2 103.7 9.64611e-05 3728 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.17834e-06 11184 2 103.7 9.96068e-05 3728 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.39876e-06 11184 2 103.7 0.000118639 3728 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.2329e-06 11184 2 103.7 0.000104642 3728 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.97 1.2243e-06 11184 2 103.7 9.55045e-05 3728 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.97 1.41313e-06 11184 2 103.7 0.000101223 3728 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.97 1.25875e-06 11184 2 103.7 9.20544e-05 3728 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.97 1.13628e-06 11184 2 103.7 9.09884e-05 3728 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.97 1.65909e-06 11184 2 103.7 0.000117292 3728 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.97 1.25325e-06 11184 2 103.7 0.000108988 3728 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.97 1.35825e-06 11184 2 103.7 0.000101512 3728 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.97 1.20858e-06 11184 2 103.7 9.93686e-05 3728 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.97 1.22622e-06 11184 2 103.7 9.21183e-05 3728 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.97 1.27603e-06 11184 2 103.7 9.64443e-05 3728 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.97 1.07601e-06 11184 2 103.7 9.56496e-05 3728 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.97 1.13768e-06 11184 2 103.7 9.70776e-05 3728 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.97 1.32147e-06 11184 2 103.7 9.36572e-05 3728 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.97 1.15937e-06 11184 2 103.7 0.000118727 3728 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.97 1.44533e-06 11184 2 103.7 0.000120565 3728 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.97 1.50269e-06 11184 2 103.7 0.000103474 3728 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.97 1.13118e-06 11184 2 103.7 9.67084e-05 3728 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.97 1.66862e-06 11184 2 103.7 0.000103107 3728 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.97 1.3084e-06 11184 2 103.7 9.20663e-05 3728 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.29962e-06 11184 2 103.7 9.76201e-05 3728 SHAKE stats (type/ave/delta/count) on step 2050000 1 0.97 1.16587e-06 11184 2 103.7 9.44982e-05 3728 SHAKE stats (type/ave/delta/count) on step 2100000 1 0.97 1.54534e-06 11184 2 103.7 9.93324e-05 3728 SHAKE stats (type/ave/delta/count) on step 2150000 1 0.97 1.302e-06 11184 2 103.7 0.000105729 3728 SHAKE stats (type/ave/delta/count) on step 2200000 1 0.97 1.05403e-06 11184 2 103.7 9.3937e-05 3728 SHAKE stats (type/ave/delta/count) on step 2250000 1 0.97 1.21409e-06 11184 2 103.7 9.34386e-05 3728 SHAKE stats (type/ave/delta/count) on step 2300000 1 0.97 1.83003e-06 11184 2 103.7 0.00010453 3728 SHAKE stats (type/ave/delta/count) on step 2350000 1 0.97 1.47549e-06 11184 2 103.7 0.00010752 3728 SHAKE stats (type/ave/delta/count) on step 2400000 1 0.97 1.39961e-06 11184 2 103.7 0.000125078 3728 SHAKE stats (type/ave/delta/count) on step 2450000 1 0.97 1.67313e-06 11184 2 103.7 9.06441e-05 3728 SHAKE stats (type/ave/delta/count) on step 2500000 1 0.97 1.23936e-06 11184 2 103.7 0.00010024 3728 SHAKE stats (type/ave/delta/count) on step 2550000 1 0.97 1.25325e-06 11184 2 103.7 0.000101891 3728 SHAKE stats (type/ave/delta/count) on step 2600000 1 0.97 1.20616e-06 11184 2 103.7 9.39074e-05 3728 SHAKE stats (type/ave/delta/count) on step 2650000 1 0.97 1.27382e-06 11184 2 103.7 0.000106409 3728 SHAKE stats (type/ave/delta/count) on step 2700000 1 0.97 1.42053e-06 11184 2 103.7 0.000106805 3728 SHAKE stats (type/ave/delta/count) on step 2750000 1 0.97 1.21675e-06 11184 2 103.7 0.000104212 3728 SHAKE stats (type/ave/delta/count) on step 2800000 1 0.97 1.19917e-06 11184 2 103.7 9.49934e-05 3728 SHAKE stats (type/ave/delta/count) on step 2850000 1 0.97 1.20812e-06 11184 2 103.7 8.81371e-05 3728 SHAKE stats (type/ave/delta/count) on step 2900000 1 0.97 1.47011e-06 11184 2 103.7 9.1676e-05 3728 SHAKE stats (type/ave/delta/count) on step 2950000 1 0.97 1.49155e-06 11184 2 103.7 0.000110785 3728 SHAKE stats (type/ave/delta/count) on step 3000000 1 0.97 1.24042e-06 11184 2 103.7 9.52821e-05 3728 3000000 3000000 335919.77 143799.62 1.371895 299.94126 289.44252 393.01247 0 0 271374.66 -52212.897 -383.45046 -379002.86 -159158.64 8236.1537 Loop time of 66369.5 on 16 procs for 3000000 steps with 13901 atoms Performance: 3.905 ns/day, 6.145 hours/ns, 45.201 timesteps/s 98.6% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 32137 | 38340 | 52197 |3974.7 | 57.77 Bond | 14.567 | 40.14 | 97.319 | 506.8 | 0.06 Kspace | 8363 | 22294 | 28541 |5238.1 | 33.59 Neigh | 2801.8 | 2804.1 | 2806.7 | 3.1 | 4.23 Comm | 1092.4 | 1155.1 | 1219.1 | 121.5 | 1.74 Output | 0.020795 | 0.023083 | 0.025204 | 0.9 | 0.00 Modify | 1581 | 1625.7 | 1669.8 | 75.0 | 2.45 Other | | 110.3 | | | 0.17 Nlocal: 868.812 ave 1042 max 756 min Histogram: 2 4 5 1 0 0 0 0 0 4 Nghost: 10420.2 ave 10967 max 9570 min Histogram: 4 0 0 0 0 0 3 5 0 4 Neighs: 487737 ave 674880 max 388258 min Histogram: 4 6 2 0 0 0 0 0 0 4 Total # of neighbors = 7803788 Ave neighs/atom = 561.38321 Ave special neighs/atom = 1.8838932 Neighbor list builds = 150266 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) = 0.25956456 grid = 30 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0028924598 estimated relative force accuracy = 8.7105569e-06 using double precision KISS FFT 3d grid and FFT values/proc = 13068 4800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 1 0.97 1.24042e-06 11184 2 103.7 9.52821e-05 3728 Per MPI rank memory allocation (min/avg/max) = 14.82 | 15.16 | 16.22 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 335920.84 143799.62 1.371895 299.94126 289.44252 393.01247 0 0 271374.66 -52212.897 -383.45046 -379002.86 -159158.64 8236.1537 Loop time of 4.35531e-06 on 16 procs for 0 steps with 13901 atoms 123.4% CPU use with 16 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 | | 4.355e-06 | | |100.00 Nlocal: 868.812 ave 1042 max 756 min Histogram: 2 4 5 1 0 0 0 0 0 4 Nghost: 10420.2 ave 10967 max 9570 min Histogram: 4 0 0 0 0 0 3 5 0 4 Neighs: 487737 ave 674880 max 388258 min Histogram: 4 6 2 0 0 0 0 0 0 4 Total # of neighbors = 7803788 Ave neighs/atom = 561.38321 Ave special neighs/atom = 1.8838932 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken log 2.6_Custom.out