#------------------------------------------------------------------------------- # Stage 2.4: NVT integration for 200 ps 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 20000 20000 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 20 1 20 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 restart 200000 2.4.restart dump sci all custom 20000 2.4.xyz id mol type q xs ys zs timestep 1 run 200000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.32389111 grid = 64 64 20 stencil order = 5 estimated absolute RMS force accuracy = 0.0036368396 estimated relative force accuracy = 1.0952234e-05 using double precision KISS FFT 3d grid and FFT values/proc = 9315 2560 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.996192 0.632007 8304 2 96.5891 52.5874 2768 Per MPI rank memory allocation (min/avg/max) = 12.53 | 12.61 | 12.94 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 17353.402 92859.489 1.3074058 428.55654 34.06047 257.07783 0 0 24349.059 99121.042 -448.40969 -268477.2 -144715.96 8088.7858 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.51704e-06 8304 2 103.7 0.000123074 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.40771e-06 8304 2 103.7 0.000107832 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.53318e-06 8304 2 103.7 0.000110127 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.13588e-06 8304 2 103.7 9.9816e-05 2768 200000 200000 2560.8732 92859.489 1.3074058 298.43579 46.722967 95.367327 0 0 22335.891 86804.25 -448.40969 -270982.75 -161700.52 5632.823 Loop time of 964.71 on 32 procs for 200000 steps with 9101 atoms Performance: 17.912 ns/day, 1.340 hours/ns, 207.316 timesteps/s 99.4% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 439.38 | 473.79 | 504.83 | 71.6 | 49.11 Bond | 0.19836 | 0.55005 | 0.85041 | 24.0 | 0.06 Kspace | 339.55 | 371.47 | 405.87 | 81.1 | 38.51 Neigh | 30.481 | 30.547 | 30.594 | 0.5 | 3.17 Comm | 28.66 | 31.682 | 33.561 | 24.2 | 3.28 Output | 0.0099875 | 0.012253 | 0.014374 | 1.2 | 0.00 Modify | 52.049 | 53.188 | 54.785 | 11.5 | 5.51 Other | | 3.462 | | | 0.36 Nlocal: 284.406 ave 295 max 268 min Histogram: 2 1 2 1 4 4 4 5 4 5 Nghost: 4930 ave 5018 max 4810 min Histogram: 1 2 2 2 1 5 9 6 2 2 Neighs: 88654.4 ave 94518 max 81128 min Histogram: 2 1 2 3 4 4 4 7 4 1 Total # of neighbors = 2836940 Ave neighs/atom = 311.71739 Ave special neighs/atom = 1.8929788 Neighbor list builds = 9832 Dangerous builds = 0 undump sci restart 0 dump sci all custom 200000 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) = 0.32389111 grid = 64 64 20 stencil order = 5 estimated absolute RMS force accuracy = 0.0036368396 estimated relative force accuracy = 1.0952234e-05 using double precision KISS FFT 3d grid and FFT values/proc = 9315 2560 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.13588e-06 8304 2 103.7 9.9816e-05 2768 Per MPI rank memory allocation (min/avg/max) = 12.54 | 12.83 | 13.13 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 200000 200000 2561.7892 92859.489 1.3074058 298.43579 46.722967 95.367327 0 0 22335.891 86804.25 -448.40969 -270982.75 -161700.52 5632.823 Loop time of 7.57644e-06 on 32 procs for 0 steps with 9101 atoms 113.8% 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 | | 7.576e-06 | | |100.00 Nlocal: 284.406 ave 295 max 268 min Histogram: 2 1 2 1 4 4 4 5 4 5 Nghost: 4930 ave 5018 max 4810 min Histogram: 1 2 2 2 1 5 9 6 2 2 Neighs: 88654.4 ave 94518 max 81128 min Histogram: 2 1 2 3 4 4 4 7 4 1 Total # of neighbors = 2836940 Ave neighs/atom = 311.71739 Ave special neighs/atom = 1.8929788 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out