#------------------------------------------------------------------------------- # Stage 2.5: NVT integration for 3 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 1928 = # 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 300000 300000 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 v_surfacetension file 2.5_averages.txt off 1 fix 3 movable ave/time 300 1 300 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 v_surfacetension file 2.5_instantaneous.txt restart 3000000 2.5.restart dump sci all custom 300000 2.5.xyz id mol type q xs ys zs timestep 1 run 3000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.32021612 grid = 40 40 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0032184304 estimated relative force accuracy = 9.6922075e-06 using double precision KISS FFT 3d grid and FFT values/proc = 10557 3200 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 6.20282e-13 5784 2 103.7 8.04334e-11 1928 Per MPI rank memory allocation (min/avg/max) = 12.49 | 12.86 | 13.23 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 -85.341161 136142.76 0.63808232 298.28116 34.631655 42.388938 0 0 16338.57 53037.652 -154.3376 -194284.51 -124831.26 3963.6946 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.27656e-06 5784 2 103.7 0.000100787 1928 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.2132e-06 5784 2 103.7 9.80961e-05 1928 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.17875e-06 5784 2 103.7 0.000107083 1928 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.18519e-06 5784 2 103.7 0.000106466 1928 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.46775e-06 5784 2 103.7 9.89408e-05 1928 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.1e-06 5784 2 103.7 9.13708e-05 1928 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.55501e-06 5784 2 103.7 9.41023e-05 1928 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.31508e-06 5784 2 103.7 9.52043e-05 1928 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.32452e-06 5784 2 103.7 0.00010478 1928 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.17463e-06 5784 2 103.7 0.000110757 1928 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.64197e-06 5784 2 103.7 0.000107351 1928 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.20174e-06 5784 2 103.7 9.55734e-05 1928 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.35669e-06 5784 2 103.7 0.000102359 1928 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.01689e-06 5784 2 103.7 9.18917e-05 1928 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.35159e-06 5784 2 103.7 0.000108081 1928 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.17192e-06 5784 2 103.7 9.04137e-05 1928 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.13033e-06 5784 2 103.7 0.000106717 1928 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.3138e-06 5784 2 103.7 0.000102679 1928 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.25332e-06 5784 2 103.7 9.38845e-05 1928 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.12345e-06 5784 2 103.7 0.000101279 1928 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.2482e-06 5784 2 103.7 0.000108914 1928 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.25619e-06 5784 2 103.7 9.77376e-05 1928 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.28739e-06 5784 2 103.7 0.000100446 1928 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.51014e-06 5784 2 103.7 0.000108859 1928 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.28633e-06 5784 2 103.7 0.000107994 1928 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.30138e-06 5784 2 103.7 9.47076e-05 1928 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.19307e-06 5784 2 103.7 9.99335e-05 1928 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.12604e-06 5784 2 103.7 9.80007e-05 1928 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.24485e-06 5784 2 103.7 9.41836e-05 1928 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.18315e-06 5784 2 103.7 0.000104359 1928 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.27077e-06 5784 2 103.7 0.000106534 1928 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.04606e-06 5784 2 103.7 8.84946e-05 1928 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.16932e-06 5784 2 103.7 8.86962e-05 1928 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.33233e-06 5784 2 103.7 0.000104878 1928 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.27527e-06 5784 2 103.7 9.57928e-05 1928 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.41375e-06 5784 2 103.7 0.000112155 1928 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.56598e-06 5784 2 103.7 0.000116291 1928 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.12746e-06 5784 2 103.7 9.28905e-05 1928 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.1536e-06 5784 2 103.7 0.000119563 1928 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.46229e-06 5784 2 103.7 0.000109083 1928 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.09074e-06 5784 2 103.7 9.89433e-05 1928 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.20362e-06 5784 2 103.7 0.000123876 1928 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.15139e-06 5784 2 103.7 9.05862e-05 1928 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.33405e-06 5784 2 103.7 0.000108012 1928 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.19353e-06 5784 2 103.7 9.48126e-05 1928 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.0996e-06 5784 2 103.7 9.0195e-05 1928 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.03303e-06 5784 2 103.7 9.04088e-05 1928 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.16302e-06 5784 2 103.7 9.23148e-05 1928 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.13531e-06 5784 2 103.7 9.8575e-05 1928 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.51209e-06 5784 2 103.7 9.79682e-05 1928 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.26475e-06 5784 2 103.7 9.83075e-05 1928 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.60062e-06 5784 2 103.7 0.000125384 1928 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.18039e-06 5784 2 103.7 9.67641e-05 1928 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.18554e-06 5784 2 103.7 9.43419e-05 1928 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.45795e-06 5784 2 103.7 8.89238e-05 1928 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.17082e-06 5784 2 103.7 9.97996e-05 1928 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.14565e-06 5784 2 103.7 0.000103308 1928 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.1901e-06 5784 2 103.7 0.000104605 1928 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.19481e-06 5784 2 103.7 8.9331e-05 1928 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.10043e-06 5784 2 103.7 9.58546e-05 1928 3000000 3000000 -164.10989 136142.76 0.63808232 297.44111 30.158668 46.290828 0 0 16287.049 53094.211 -154.3376 -194258.3 -124800.59 3952.5317 Loop time of 16903.3 on 32 procs for 3000000 steps with 6387 atoms Performance: 15.334 ns/day, 1.565 hours/ns, 177.480 timesteps/s 98.7% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 170 | 4117.2 | 8352.2 |6052.6 | 24.36 Bond | 2.5923 | 5.8405 | 13.41 | 140.7 | 0.03 Kspace | 6575 | 10824 | 14793 |3753.8 | 64.03 Neigh | 464.66 | 469.6 | 477.95 | 21.5 | 2.78 Comm | 342.17 | 523.31 | 654.07 | 530.3 | 3.10 Output | 0.010557 | 0.012124 | 0.013628 | 0.9 | 0.00 Modify | 821.34 | 913.35 | 1045 | 305.2 | 5.40 Other | | 50.35 | | | 0.30 Nlocal: 199.594 ave 411 max 0 min Histogram: 13 3 0 0 0 0 0 0 6 10 Nghost: 2725.91 ave 4079 max 1415 min Histogram: 8 8 0 0 0 0 0 0 8 8 Neighs: 51451.1 ave 107181 max 0 min Histogram: 16 0 0 0 0 0 0 0 3 13 Total # of neighbors = 1646434 Ave neighs/atom = 257.77893 Ave special neighs/atom = 1.8738062 Neighbor list builds = 145391 Dangerous builds = 0 undump sci restart 0 dump sci all custom 3000000 2.5.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) = 0.32021612 grid = 40 40 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0032184304 estimated relative force accuracy = 9.6922075e-06 using double precision KISS FFT 3d grid and FFT values/proc = 10557 3200 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.10043e-06 5784 2 103.7 9.58546e-05 1928 Per MPI rank memory allocation (min/avg/max) = 11.51 | 12.83 | 13.23 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 3000000 3000000 -163.61578 136142.76 0.63808232 297.44111 30.158668 46.290828 0 0 16287.049 53094.211 -154.3376 -194258.3 -124800.59 3952.5317 Loop time of 7.1005e-06 on 32 procs for 0 steps with 6387 atoms 114.4% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 7.101e-06 | | |100.00 Nlocal: 199.594 ave 411 max 0 min Histogram: 13 3 0 0 0 0 0 0 6 10 Nghost: 2725.91 ave 4079 max 1415 min Histogram: 8 8 0 0 0 0 0 0 8 8 Neighs: 51451.1 ave 107181 max 0 min Histogram: 16 0 0 0 0 0 0 0 3 13 Total # of neighbors = 1646434 Ave neighs/atom = 257.77893 Ave special neighs/atom = 1.8738062 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 12:28:27