#------------------------------------------------------------------------------- # 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 2699 = # 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) = 0.25577968 grid = 30 30 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0035412458 estimated relative force accuracy = 1.0664357e-05 using double precision KISS FFT 3d grid and FFT values/proc = 7260 1800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 1.00049 0.0672072 8097 2 97.671 9.52708 2699 Per MPI rank memory allocation (min/avg/max) = 12.45 | 13.12 | 13.63 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 -3685.5562 138878.49 1.4411859 405.32842 5.1562134 20.408163 0 0 37810.858 -79516.674 -317.08001 -295524.23 -337204.48 9102.6318 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.46279e-06 8097 2 103.7 0.000126078 2699 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.21745e-06 8097 2 103.7 8.79102e-05 2699 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.28729e-06 8097 2 103.7 8.71603e-05 2699 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.23413e-06 8097 2 103.7 9.52186e-05 2699 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.22413e-06 8097 2 103.7 9.59282e-05 2699 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.09176e-06 8097 2 103.7 9.23811e-05 2699 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.26895e-06 8097 2 103.7 9.51955e-05 2699 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.29468e-06 8097 2 103.7 9.93683e-05 2699 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.35158e-06 8097 2 103.7 0.000103676 2699 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.28173e-06 8097 2 103.7 0.000110029 2699 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.3736e-06 8097 2 103.7 0.000105599 2699 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.37472e-06 8097 2 103.7 9.79105e-05 2699 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.17352e-06 8097 2 103.7 9.43631e-05 2699 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.35269e-06 8097 2 103.7 0.000123839 2699 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.1922e-06 8097 2 103.7 0.000109633 2699 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.12325e-06 8097 2 103.7 9.71709e-05 2699 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.22895e-06 8097 2 103.7 9.90096e-05 2699 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.26155e-06 8097 2 103.7 0.000101722 2699 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.35207e-06 8097 2 103.7 0.000106527 2699 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.38918e-06 8097 2 103.7 9.46527e-05 2699 1000000 1000000 -128.13159 138878.49 1.4411859 300.64268 39.641224 70.638038 0 0 36102.876 -63553.581 -317.08001 -295421.72 -322762.15 6751.6598 Loop time of 9068.08 on 32 procs for 1000000 steps with 10558 atoms Performance: 9.528 ns/day, 2.519 hours/ns, 110.277 timesteps/s 99.0% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1285.5 | 4308.5 | 5974 |2728.8 | 47.51 Bond | 0.92658 | 2.4067 | 4.9194 | 79.4 | 0.03 Kspace | 1661.4 | 3336.5 | 6373.3 |3113.0 | 36.79 Neigh | 431.22 | 431.94 | 433.42 | 3.2 | 4.76 Comm | 350.88 | 455.82 | 504.16 | 238.2 | 5.03 Output | 0.011799 | 0.014172 | 0.016487 | 1.2 | 0.00 Modify | 472.26 | 512.22 | 599.18 | 193.6 | 5.65 Other | | 20.67 | | | 0.23 Nlocal: 329.938 ave 416 max 160 min Histogram: 4 4 0 0 0 0 1 5 7 11 Nghost: 6342.78 ave 7684 max 4582 min Histogram: 8 0 0 0 8 0 0 4 4 8 Neighs: 153845 ave 218429 max 43269 min Histogram: 8 0 0 0 0 3 2 3 5 11 Total # of neighbors = 4923034 Ave neighs/atom = 466.28471 Ave special neighs/atom = 1.5849593 Neighbor list builds = 49458 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) = 0.25577968 grid = 30 30 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0035412458 estimated relative force accuracy = 1.0664357e-05 using double precision KISS FFT 3d grid and FFT values/proc = 7260 1800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.38918e-06 8097 2 103.7 9.46527e-05 2699 Per MPI rank memory allocation (min/avg/max) = 12.45 | 13.17 | 13.63 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 -127.57105 138878.49 1.4411859 300.64268 39.641224 70.638038 0 0 36102.876 -63553.581 -317.08001 -295421.72 -322762.15 6751.6598 Loop time of 9.16459e-06 on 32 procs for 0 steps with 10558 atoms 111.2% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 9.165e-06 | | |100.00 Nlocal: 329.938 ave 416 max 160 min Histogram: 4 4 0 0 0 0 1 5 7 11 Nghost: 6342.78 ave 7684 max 4582 min Histogram: 8 0 0 0 8 0 0 4 4 8 Neighs: 153845 ave 218429 max 43269 min Histogram: 8 0 0 0 0 3 2 3 5 11 Total # of neighbors = 4923034 Ave neighs/atom = 466.28471 Ave special neighs/atom = 1.5849593 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken log 2.5_NVT.out