#------------------------------------------------------------------------------- # 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 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 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) = 0.25956456 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 1.00477 0.0879879 11184 2 97.712 10.3119 3728 Per MPI rank memory allocation (min/avg/max) = 14.82 | 15.11 | 15.84 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 0 1e-06 334452.61 143799.62 1.371895 417.38826 42.78293 239.5781 0 0 276131.16 -77295.259 -383.45046 -379121.09 -180002.83 11461.157 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.46123e-06 11184 2 103.7 0.000106147 3728 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.1761e-06 11184 2 103.7 9.64988e-05 3728 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.24433e-06 11184 2 103.7 9.49013e-05 3728 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.20034e-06 11184 2 103.7 9.83197e-05 3728 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.10129e-06 11184 2 103.7 8.87755e-05 3728 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.34942e-06 11184 2 103.7 9.80411e-05 3728 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.2929e-06 11184 2 103.7 9.39303e-05 3728 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.42992e-06 11184 2 103.7 9.86162e-05 3728 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.19228e-06 11184 2 103.7 9.04637e-05 3728 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.06138e-06 11184 2 103.7 8.65645e-05 3728 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.29556e-06 11184 2 103.7 0.000116607 3728 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.4732e-06 11184 2 103.7 9.12666e-05 3728 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 2.203e-06 11184 2 103.7 0.000129652 3728 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.19728e-06 11184 2 103.7 9.63663e-05 3728 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.15041e-06 11184 2 103.7 0.000102136 3728 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.54853e-06 11184 2 103.7 9.68638e-05 3728 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.33362e-06 11184 2 103.7 0.000101166 3728 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.17322e-06 11184 2 103.7 0.000102167 3728 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.5404e-06 11184 2 103.7 0.000100831 3728 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.2009e-06 11184 2 103.7 9.66299e-05 3728 1000000 1000000 335312.25 143799.62 1.371895 299.22721 293.7791 351.31066 0 0 271378.76 -52196.181 -383.45046 -378987.78 -159160.12 8216.5465 Loop time of 22031.2 on 16 procs for 1000000 steps with 13901 atoms Performance: 3.922 ns/day, 6.120 hours/ns, 45.390 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 | 10677 | 12740 | 17448 |2328.2 | 57.83 Bond | 5.2963 | 13.459 | 33.809 | 295.3 | 0.06 Kspace | 2669.9 | 7399.9 | 9475.6 |3070.0 | 33.59 Neigh | 923.44 | 924.44 | 925.48 | 2.1 | 4.20 Comm | 361.88 | 382.48 | 402.43 | 71.2 | 1.74 Output | 0.023564 | 0.025979 | 0.028385 | 1.0 | 0.00 Modify | 520.37 | 534.95 | 550.49 | 43.7 | 2.43 Other | | 36.17 | | | 0.16 Nlocal: 868.812 ave 1038 max 784 min Histogram: 5 6 1 0 0 0 0 0 0 4 Nghost: 10442.9 ave 10973 max 9621 min Histogram: 4 0 0 0 0 0 3 5 0 4 Neighs: 487399 ave 671298 max 404004 min Histogram: 7 5 0 0 0 0 0 0 0 4 Total # of neighbors = 7798385 Ave neighs/atom = 560.99453 Ave special neighs/atom = 1.8838932 Neighbor list builds = 50014 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) = 0.25956456 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 1000000 1 0.97 1.2009e-06 11184 2 103.7 9.66299e-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 1000000 1000000 335313.27 143799.62 1.371895 299.22721 293.7791 351.31066 0 0 271378.76 -52196.181 -383.45046 -378987.78 -159160.12 8216.5465 Loop time of 5.01825e-06 on 16 procs for 0 steps with 13901 atoms 109.6% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 5.018e-06 | | |100.00 Nlocal: 868.812 ave 1038 max 784 min Histogram: 5 6 1 0 0 0 0 0 0 4 Nghost: 10442.9 ave 10973 max 9621 min Histogram: 4 0 0 0 0 0 3 5 0 4 Neighs: 487399 ave 671298 max 404004 min Histogram: 7 5 0 0 0 0 0 0 0 4 Total # of neighbors = 7798385 Ave neighs/atom = 560.99453 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 2.5_NVT.out