#------------------------------------------------------------------------------- # Stage 2.4: NPT integration for 2 ns with a timestep of 1 fs # Temperature 298.2 K # Pressure 1 bar #------------------------------------------------------------------------------- # Fix shake is needed for water in pcff+ fix shaken all shake .0001 20 50000 a 1 b 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 1686 = # of frozen angles find clusters CPU = 0.000 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 npt temp 298.2 298.2 100 iso 0.9869233 0.9869233 100 drag 0 mtk yes nreset 40000 fix 2 movable ave/time 1 199999 200000 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_cella v_cellb v_cellc v_cellalpha v_cellbeta v_cellgamma 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 200 1 200 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_cella v_cellb v_cellc v_cellalpha v_cellbeta v_cellgamma 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 2000000 2.4.restart dump sci all custom 200000 2.4.xyz id mol type q xs ys zs timestep 1 run 2000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.2523426 grid = 27 27 27 stencil order = 5 estimated absolute RMS force accuracy = 0.0035628778 estimated relative force accuracy = 1.0729501e-05 using double precision KISS FFT 3d grid and FFT values/proc = 8000 2916 generated 0 of 6 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 0.999579 0.0521562 5058 1 97.7464 9.07353 1686 Per MPI rank memory allocation (min/avg/max) = 11.35 | 11.43 | 11.75 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 -1330.9921 56552.916 1.1121793 433.17052 0 0 0 0 11386.239 31174.552 -109.39203 -104265.35 -61704.555 4809.7165 SHAKE stats (type/ave/delta/count) on step 50000 1 0.970019 1.33311e-06 5058 1 103.7 0.000141439 1686 SHAKE stats (type/ave/delta/count) on step 100000 1 0.969851 1.17309e-06 5058 1 103.7 0.000114364 1686 SHAKE stats (type/ave/delta/count) on step 150000 1 0.970044 1.26402e-06 5058 1 103.7 9.6057e-05 1686 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.36547e-06 5058 1 103.7 9.50963e-05 1686 SHAKE stats (type/ave/delta/count) on step 250000 1 0.970096 1.85377e-06 5058 1 103.7 0.000121349 1686 SHAKE stats (type/ave/delta/count) on step 300000 1 0.970071 1.63968e-06 5058 1 103.7 0.000115234 1686 SHAKE stats (type/ave/delta/count) on step 350000 1 0.970035 1.15897e-06 5058 1 103.7 9.02152e-05 1686 SHAKE stats (type/ave/delta/count) on step 400000 1 0.969976 1.09031e-06 5058 1 103.7 9.24998e-05 1686 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97007 1.47529e-06 5058 1 103.7 0.000108762 1686 SHAKE stats (type/ave/delta/count) on step 500000 1 0.970005 1.14055e-06 5058 1 103.7 8.81232e-05 1686 SHAKE stats (type/ave/delta/count) on step 550000 1 0.96997 1.18757e-06 5058 1 103.7 0.000104259 1686 SHAKE stats (type/ave/delta/count) on step 600000 1 0.969986 1.39811e-06 5058 1 103.7 0.000107991 1686 SHAKE stats (type/ave/delta/count) on step 650000 1 0.969959 1.40892e-06 5058 1 103.7 0.0001125 1686 SHAKE stats (type/ave/delta/count) on step 700000 1 0.970026 1.33167e-06 5058 1 103.7 0.000116583 1686 SHAKE stats (type/ave/delta/count) on step 750000 1 0.970023 1.02882e-06 5058 1 103.7 9.02783e-05 1686 SHAKE stats (type/ave/delta/count) on step 800000 1 0.96998 1.17079e-06 5058 1 103.7 9.72427e-05 1686 SHAKE stats (type/ave/delta/count) on step 850000 1 0.96999 1.57539e-06 5058 1 103.7 0.000114683 1686 SHAKE stats (type/ave/delta/count) on step 900000 1 0.969966 1.1599e-06 5058 1 103.7 9.27914e-05 1686 SHAKE stats (type/ave/delta/count) on step 950000 1 0.970033 1.36625e-06 5058 1 103.7 0.000113348 1686 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.969946 1.25981e-06 5058 1 103.7 9.83854e-05 1686 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.969962 1.00672e-06 5058 1 103.7 8.96909e-05 1686 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.970192 1.92497e-06 5058 1 103.7 0.000163169 1686 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.969924 1.09147e-06 5058 1 103.7 0.000102165 1686 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.969991 1.34649e-06 5058 1 103.7 0.000140824 1686 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.970037 1.30134e-06 5058 1 103.7 9.63951e-05 1686 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.969982 1.21188e-06 5058 1 103.7 0.000102513 1686 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.970088 1.19328e-06 5058 1 103.7 9.74606e-05 1686 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.97 1.2978e-06 5058 1 103.7 9.86356e-05 1686 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.969979 1.4769e-06 5058 1 103.7 0.000110953 1686 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.970059 1.08516e-06 5058 1 103.7 8.71743e-05 1686 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.970066 1.90175e-06 5058 1 103.7 0.000139166 1686 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.970058 1.3379e-06 5058 1 103.7 9.85537e-05 1686 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.969888 1.52285e-06 5058 1 103.7 0.000153026 1686 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.970026 1.21077e-06 5058 1 103.7 0.000110098 1686 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.969943 1.15351e-06 5058 1 103.7 8.89706e-05 1686 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.970026 1.14305e-06 5058 1 103.7 0.000108614 1686 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.969968 1.36925e-06 5058 1 103.7 9.45523e-05 1686 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.969904 1.22584e-06 5058 1 103.7 0.000100555 1686 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.970049 1.1765e-06 5058 1 103.7 0.000106182 1686 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.970033 1.57573e-06 5058 1 103.7 9.473e-05 1686 2000000 2000000 36.458517 58970.053 1.066592 300.10649 0 0 0 0 8243.6378 42127.853 -104.90813 -104250.91 -53879.423 3332.2376 Loop time of 27192.7 on 8 procs for 2000000 steps with 5412 atoms Performance: 6.355 ns/day, 3.777 hours/ns, 73.549 timesteps/s 98.9% CPU use with 8 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 18128 | 19438 | 20396 | 523.2 | 71.48 Bond | 2.9102 | 3.2294 | 3.6235 | 11.7 | 0.01 Kspace | 3459.7 | 4417.2 | 5727.1 |1096.3 | 16.24 Neigh | 1139.1 | 1140 | 1141 | 2.1 | 4.19 Comm | 468.85 | 470.56 | 472.51 | 4.9 | 1.73 Output | 0.013782 | 0.014736 | 0.01551 | 0.5 | 0.00 Modify | 1430.8 | 1536.5 | 1669.8 | 264.5 | 5.65 Other | | 187.6 | | | 0.69 Nlocal: 676.5 ave 691 max 663 min Histogram: 1 1 1 0 2 0 0 2 0 1 Nghost: 9118.75 ave 9165 max 9073 min Histogram: 1 1 0 2 0 1 0 1 1 1 Neighs: 356630 ave 382127 max 331118 min Histogram: 1 1 0 0 1 2 1 1 0 1 Total # of neighbors = 2853040 Ave neighs/atom = 527.16925 Ave special neighs/atom = 1.8691796 Neighbor list builds = 101496 Dangerous builds = 0 undump sci restart 0 dump sci all custom 2000000 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) = 0.25147892 grid = 27 27 27 stencil order = 5 estimated absolute RMS force accuracy = 0.0037149235 estimated relative force accuracy = 1.1187382e-05 using double precision KISS FFT 3d grid and FFT values/proc = 8000 2916 generated 0 of 6 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 1 0.970033 1.57573e-06 5058 1 103.7 9.473e-05 1686 Per MPI rank memory allocation (min/avg/max) = 11.35 | 11.57 | 11.78 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 2000000 2000000 227.69355 58970.053 1.066592 300.10649 0 0 0 0 8243.6378 41772.073 -104.90813 -103895.14 -53879.426 3332.2376 Loop time of 3.383e-06 on 8 procs for 0 steps with 5412 atoms 133.0% 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 | | 3.383e-06 | | |100.00 Nlocal: 676.5 ave 691 max 663 min Histogram: 1 1 1 0 2 0 0 2 0 1 Nghost: 9118.75 ave 9165 max 9073 min Histogram: 1 1 0 2 0 1 0 1 1 1 Neighs: 356630 ave 382127 max 331118 min Histogram: 1 1 0 0 1 2 1 1 0 1 Total # of neighbors = 2853040 Ave neighs/atom = 527.16925 Ave special neighs/atom = 1.8691796 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 7:33:55