#------------------------------------------------------------------------------- # 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 2109 = # 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) = 0.25599379 grid = 30 30 30 stencil order = 5 estimated absolute RMS force accuracy = 0.0027378111 estimated relative force accuracy = 8.2448368e-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 0.987665 0.689898 6327 1 98.5383 21.7399 2109 Per MPI rank memory allocation (min/avg/max) = 14.63 | 14.82 | 15.23 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 3645.3322 64785.051 1.1122018 438.48637 34.724996 89.231955 0 0 5719.3041 79957.949 -131.32675 -125547.87 -39746.658 5859.4809 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97005 1.48312e-06 6327 1 103.7 0.000100802 2109 SHAKE stats (type/ave/delta/count) on step 100000 1 0.969996 1.48762e-06 6327 1 103.7 9.96901e-05 2109 SHAKE stats (type/ave/delta/count) on step 150000 1 0.969925 1.25083e-06 6327 1 103.7 0.000122207 2109 SHAKE stats (type/ave/delta/count) on step 200000 1 0.970089 2.21511e-06 6327 1 103.7 0.000184496 2109 SHAKE stats (type/ave/delta/count) on step 250000 1 0.969957 1.5273e-06 6327 1 103.7 0.000138969 2109 SHAKE stats (type/ave/delta/count) on step 300000 1 0.970083 1.31784e-06 6327 1 103.7 9.97984e-05 2109 SHAKE stats (type/ave/delta/count) on step 350000 1 0.969963 1.50329e-06 6327 1 103.7 9.71476e-05 2109 SHAKE stats (type/ave/delta/count) on step 400000 1 0.970059 1.54121e-06 6327 1 103.7 9.29067e-05 2109 SHAKE stats (type/ave/delta/count) on step 450000 1 0.970031 1.22305e-06 6327 1 103.7 0.000111933 2109 SHAKE stats (type/ave/delta/count) on step 500000 1 0.969907 1.30148e-06 6327 1 103.7 0.000115503 2109 SHAKE stats (type/ave/delta/count) on step 550000 1 0.970004 1.22728e-06 6327 1 103.7 9.02556e-05 2109 SHAKE stats (type/ave/delta/count) on step 600000 1 0.970049 1.14299e-06 6327 1 103.7 9.08802e-05 2109 SHAKE stats (type/ave/delta/count) on step 650000 1 0.969993 1.07518e-06 6327 1 103.7 9.87009e-05 2109 SHAKE stats (type/ave/delta/count) on step 700000 1 0.970032 1.66718e-06 6327 1 103.7 0.000118206 2109 SHAKE stats (type/ave/delta/count) on step 750000 1 0.970015 1.12363e-06 6327 1 103.7 9.66036e-05 2109 SHAKE stats (type/ave/delta/count) on step 800000 1 0.969937 1.32741e-06 6327 1 103.7 0.000107659 2109 SHAKE stats (type/ave/delta/count) on step 850000 1 0.969984 1.4821e-06 6327 1 103.7 0.000106076 2109 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97008 1.06354e-06 6327 1 103.7 0.000103828 2109 SHAKE stats (type/ave/delta/count) on step 950000 1 0.969899 1.11038e-06 6327 1 103.7 0.000106562 2109 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.970025 1.26097e-06 6327 1 103.7 9.54961e-05 2109 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.970026 1.28711e-06 6327 1 103.7 9.66151e-05 2109 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.970061 1.44845e-06 6327 1 103.7 0.000112198 2109 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.970005 1.6519e-06 6327 1 103.7 0.000109738 2109 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.970006 1.45187e-06 6327 1 103.7 0.000112618 2109 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.969897 1.31789e-06 6327 1 103.7 0.000120503 2109 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.970071 1.65027e-06 6327 1 103.7 0.000130302 2109 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.970121 1.72785e-06 6327 1 103.7 0.000117776 2109 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.969862 1.43324e-06 6327 1 103.7 0.000141618 2109 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.969976 1.31279e-06 6327 1 103.7 0.000104398 2109 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.970077 1.63422e-06 6327 1 103.7 9.12674e-05 2109 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.96994 1.40047e-06 6327 1 103.7 0.000134296 2109 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.969929 1.25838e-06 6327 1 103.7 0.000111731 2109 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.970109 1.63602e-06 6327 1 103.7 0.000117428 2109 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.970042 1.10182e-06 6327 1 103.7 9.37546e-05 2109 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.970012 1.21563e-06 6327 1 103.7 9.99818e-05 2109 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.969991 1.11498e-06 6327 1 103.7 0.000105392 2109 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.970004 1.45848e-06 6327 1 103.7 9.9489e-05 2109 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.969917 1.49309e-06 6327 1 103.7 0.000108128 2109 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.970006 1.3361e-06 6327 1 103.7 9.26831e-05 2109 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.969906 1.38537e-06 6327 1 103.7 0.000143219 2109 2000000 2000000 -20.376247 65318.974 1.1031105 298.10432 52.870252 91.32586 0 0 6358.182 77453.343 -130.25327 -125649.53 -41693.805 3983.5595 Loop time of 59087 on 8 procs for 2000000 steps with 6593 atoms Performance: 2.925 ns/day, 8.207 hours/ns, 33.848 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 | 37984 | 42093 | 45437 |1145.2 | 71.24 Bond | 19.95 | 25.092 | 35.39 | 92.8 | 0.04 Kspace | 7117.8 | 10453 | 14571 |2301.2 | 17.69 Neigh | 2614.8 | 2617.1 | 2619.7 | 3.9 | 4.43 Comm | 749.38 | 762.15 | 776.54 | 43.7 | 1.29 Output | 0.02596 | 0.027215 | 0.028309 | 0.5 | 0.00 Modify | 2434.9 | 2811.7 | 2966.9 | 344.9 | 4.76 Other | | 325 | | | 0.55 Nlocal: 824.125 ave 844 max 800 min Histogram: 2 0 0 0 1 2 0 0 1 2 Nghost: 10441.6 ave 10537 max 10370 min Histogram: 1 1 1 1 1 1 0 1 0 1 Neighs: 477724 ave 519516 max 450676 min Histogram: 3 0 0 2 1 0 0 0 1 1 Total # of neighbors = 3821795 Ave neighs/atom = 579.67465 Ave special neighs/atom = 2.0345821 Neighbor list builds = 102576 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) = 0.25582943 grid = 30 30 30 stencil order = 5 estimated absolute RMS force accuracy = 0.0027601319 estimated relative force accuracy = 8.3120551e-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 0.969906 1.38537e-06 6327 1 103.7 0.000143219 2109 Per MPI rank memory allocation (min/avg/max) = 15.21 | 15.23 | 15.24 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 -643.17366 65318.974 1.1031105 298.10432 52.870252 91.32586 0 0 6358.182 77372.802 -130.25327 -125568.99 -41693.805 3983.5595 Loop time of 3.84888e-06 on 8 procs for 0 steps with 6593 atoms 126.7% 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 | | 3.849e-06 | | |100.00 Nlocal: 824.125 ave 844 max 800 min Histogram: 2 0 0 0 1 2 0 0 1 2 Nghost: 10441.6 ave 10537 max 10370 min Histogram: 1 1 1 1 1 1 0 1 0 1 Neighs: 477724 ave 519516 max 450676 min Histogram: 3 0 0 2 1 0 0 0 1 1 Total # of neighbors = 3821795 Ave neighs/atom = 579.67465 Ave special neighs/atom = 2.0345821 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 16:24:50