#------------------------------------------------------------------------------- # 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 2072 = # 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 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) = 0.25601946 grid = 30 30 30 stencil order = 5 estimated absolute RMS force accuracy = 0.0028394649 estimated relative force accuracy = 8.5509641e-06 using double precision KISS FFT 3d grid and FFT values/proc = 10648 3600 generated 0 of 10 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 0.982379 0.806045 6216 1 97.9709 62.5049 2072 Per MPI rank memory allocation (min/avg/max) = 14.63 | 14.87 | 15.05 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 28824.192 64732.013 1.161601 434.44485 335.23703 518.65766 0 0 9320.4397 86154.6 -139.48177 -129581.89 -33252.956 5872.814 SHAKE stats (type/ave/delta/count) on step 50000 1 0.969908 1.11818e-06 6216 1 103.7 9.66767e-05 2072 SHAKE stats (type/ave/delta/count) on step 100000 1 0.970023 1.48358e-06 6216 1 103.7 9.96728e-05 2072 SHAKE stats (type/ave/delta/count) on step 150000 1 0.970023 1.29143e-06 6216 1 103.7 0.000101434 2072 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97009 2.20326e-06 6216 1 103.7 0.000128982 2072 SHAKE stats (type/ave/delta/count) on step 250000 1 0.970014 1.38282e-06 6216 1 103.7 0.000104166 2072 SHAKE stats (type/ave/delta/count) on step 300000 1 0.970047 2.15529e-06 6216 1 103.7 0.00014875 2072 SHAKE stats (type/ave/delta/count) on step 350000 1 0.970001 1.14553e-06 6216 1 103.7 9.87473e-05 2072 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97004 1.91436e-06 6216 1 103.7 0.000140336 2072 SHAKE stats (type/ave/delta/count) on step 450000 1 0.969933 1.1881e-06 6216 1 103.7 0.000120495 2072 SHAKE stats (type/ave/delta/count) on step 500000 1 0.969999 1.65938e-06 6216 1 103.7 0.000127338 2072 SHAKE stats (type/ave/delta/count) on step 550000 1 0.96995 1.452e-06 6216 1 103.7 9.12483e-05 2072 SHAKE stats (type/ave/delta/count) on step 600000 1 0.969947 1.23117e-06 6216 1 103.7 9.12334e-05 2072 SHAKE stats (type/ave/delta/count) on step 650000 1 0.969937 1.14892e-06 6216 1 103.7 0.000102047 2072 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97012 1.6361e-06 6216 1 103.7 0.000120566 2072 SHAKE stats (type/ave/delta/count) on step 750000 1 0.969848 1.57275e-06 6216 1 103.7 0.000159176 2072 SHAKE stats (type/ave/delta/count) on step 800000 1 0.96999 1.20192e-06 6216 1 103.7 0.000100915 2072 SHAKE stats (type/ave/delta/count) on step 850000 1 0.970056 1.59573e-06 6216 1 103.7 0.000110454 2072 SHAKE stats (type/ave/delta/count) on step 900000 1 0.970007 1.57176e-06 6216 1 103.7 9.93915e-05 2072 SHAKE stats (type/ave/delta/count) on step 950000 1 0.970127 1.61321e-06 6216 1 103.7 0.000125412 2072 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.969999 1.59923e-06 6216 1 103.7 0.000124216 2072 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.969969 1.54186e-06 6216 1 103.7 0.000108696 2072 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.970012 1.51623e-06 6216 1 103.7 9.99458e-05 2072 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.969992 1.37787e-06 6216 1 103.7 0.000113691 2072 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.970174 2.15793e-06 6216 1 103.7 0.000147799 2072 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.969947 1.26563e-06 6216 1 103.7 9.24834e-05 2072 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.969991 1.18193e-06 6216 1 103.7 9.41356e-05 2072 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.970032 1.17373e-06 6216 1 103.7 9.92734e-05 2072 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.969939 1.18599e-06 6216 1 103.7 0.000110523 2072 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.970033 1.09986e-06 6216 1 103.7 9.42226e-05 2072 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.970046 1.51068e-06 6216 1 103.7 0.00011693 2072 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.97 1.19463e-06 6216 1 103.7 0.000111674 2072 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.969927 1.17201e-06 6216 1 103.7 0.000109038 2072 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.969976 1.20052e-06 6216 1 103.7 9.54288e-05 2072 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.969995 1.23688e-06 6216 1 103.7 9.31062e-05 2072 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.969984 1.26875e-06 6216 1 103.7 0.000108261 2072 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.970024 1.12476e-06 6216 1 103.7 9.33025e-05 2072 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.969981 1.18587e-06 6216 1 103.7 9.9523e-05 2072 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.969872 1.05037e-06 6216 1 103.7 9.61728e-05 2072 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.969975 1.13668e-06 6216 1 103.7 0.000102287 2072 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.970047 1.87318e-06 6216 1 103.7 0.000107821 2072 2000000 2000000 598.05605 64174.799 1.1716869 304.52672 79.675057 146.39463 0 0 6946.9799 73205.323 -140.69285 -130615.05 -50236.676 4116.5841 Loop time of 59106.3 on 8 procs for 2000000 steps with 6608 atoms Performance: 2.924 ns/day, 8.209 hours/ns, 33.837 timesteps/s 99.0% CPU use with 8 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 38070 | 41960 | 45982 |1167.6 | 70.99 Bond | 22.476 | 30.505 | 41.645 | 104.0 | 0.05 Kspace | 6605.3 | 10634 | 14519 |2323.0 | 17.99 Neigh | 2631.7 | 2634 | 2635.8 | 3.2 | 4.46 Comm | 741.89 | 752.98 | 766.76 | 36.5 | 1.27 Output | 0.02468 | 0.026041 | 0.027216 | 0.5 | 0.00 Modify | 2422.6 | 2766.6 | 2933.1 | 367.9 | 4.68 Other | | 328.1 | | | 0.56 Nlocal: 826 ave 838 max 807 min Histogram: 1 0 0 2 0 1 1 0 0 3 Nghost: 10573.6 ave 10620 max 10531 min Histogram: 2 0 1 1 0 0 2 0 1 1 Neighs: 488505 ave 519411 max 462000 min Histogram: 2 0 0 2 0 2 0 0 1 1 Total # of neighbors = 3908040 Ave neighs/atom = 591.41041 Ave special neighs/atom = 2.0508475 Neighbor list builds = 102109 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) = 0.25619278 grid = 30 30 30 stencil order = 5 estimated absolute RMS force accuracy = 0.0028152628 estimated relative force accuracy = 8.4780804e-06 using double precision KISS FFT 3d grid and FFT values/proc = 10648 3600 generated 0 of 10 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 1 0.970047 1.87318e-06 6216 1 103.7 0.000107821 2072 Per MPI rank memory allocation (min/avg/max) = 15.03 | 15.19 | 15.25 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 910.11695 64174.799 1.1716869 304.52672 79.675057 146.39463 0 0 6946.9799 73293.591 -140.69285 -130703.32 -50236.676 4116.5841 Loop time of 3.26662e-06 on 8 procs for 0 steps with 6608 atoms 126.3% 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 | | 3.267e-06 | | |100.00 Nlocal: 826 ave 838 max 807 min Histogram: 1 0 0 2 0 1 1 0 0 3 Nghost: 10573.6 ave 10620 max 10531 min Histogram: 2 0 1 1 0 0 2 0 1 1 Neighs: 488505 ave 519411 max 462000 min Histogram: 2 0 0 2 0 2 0 0 1 1 Total # of neighbors = 3908040 Ave neighs/atom = 591.41041 Ave special neighs/atom = 2.0508475 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 16:25:10