#------------------------------------------------------------------------------- # Stage 2.4: NVT integration for 5 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 2768 = # of frozen angles find clusters CPU = 0.002 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 500000 500000 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 500 1 500 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 restart 5000000 2.4.restart dump sci all custom 500000 2.4.xyz id mol type q xs ys zs timestep 1 run 5000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.24997142 grid = 32 32 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0035792785 estimated relative force accuracy = 1.0778891e-05 using double precision KISS FFT 3d grid and FFT values/proc = 7406 2048 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 1.00156 0.0914871 8304 2 97.5818 10.4281 2768 Per MPI rank memory allocation (min/avg/max) = 11.06 | 12.65 | 14.14 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 1539.1172 194193.27 0.62517633 428.55654 8.6537916 44.378925 0 0 26277.276 8938.3703 -107.89913 -209866.71 -174598.03 8088.7858 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.16515e-06 8304 2 103.7 9.96977e-05 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.11813e-06 8304 2 103.7 0.000104154 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.28963e-06 8304 2 103.7 9.31128e-05 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.33016e-06 8304 2 103.7 0.000146034 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.26498e-06 8304 2 103.7 9.58051e-05 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.22557e-06 8304 2 103.7 0.000118549 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.33729e-06 8304 2 103.7 0.00010159 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.20163e-06 8304 2 103.7 9.91788e-05 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.53373e-06 8304 2 103.7 9.86114e-05 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.34945e-06 8304 2 103.7 9.56827e-05 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.19239e-06 8304 2 103.7 9.48435e-05 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.08462e-06 8304 2 103.7 8.98527e-05 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.01864e-06 8304 2 103.7 0.000106913 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.06349e-06 8304 2 103.7 9.21043e-05 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.11858e-06 8304 2 103.7 9.55926e-05 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.40768e-06 8304 2 103.7 0.000107814 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.21547e-06 8304 2 103.7 9.09982e-05 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.22833e-06 8304 2 103.7 0.000103914 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.33505e-06 8304 2 103.7 0.000110686 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.30607e-06 8304 2 103.7 0.000100029 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.20693e-06 8304 2 103.7 9.05693e-05 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.20885e-06 8304 2 103.7 0.000101433 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.24098e-06 8304 2 103.7 9.228e-05 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.20301e-06 8304 2 103.7 9.75943e-05 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.15123e-06 8304 2 103.7 0.000100569 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.1509e-06 8304 2 103.7 9.90239e-05 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.08322e-06 8304 2 103.7 9.43333e-05 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.191e-06 8304 2 103.7 0.000102856 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.22866e-06 8304 2 103.7 9.371e-05 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.06268e-06 8304 2 103.7 0.000111192 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.2576e-06 8304 2 103.7 0.000104917 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.21521e-06 8304 2 103.7 9.60724e-05 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.57324e-06 8304 2 103.7 0.000124755 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.15419e-06 8304 2 103.7 0.000111307 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.18131e-06 8304 2 103.7 0.000102818 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.08025e-06 8304 2 103.7 9.01856e-05 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.67776e-06 8304 2 103.7 0.000142471 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.22068e-06 8304 2 103.7 9.27235e-05 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.32307e-06 8304 2 103.7 9.65974e-05 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.30134e-06 8304 2 103.7 9.12568e-05 2768 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.47722e-06 8304 2 103.7 0.000115463 2768 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.14223e-06 8304 2 103.7 0.000101761 2768 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.28538e-06 8304 2 103.7 0.000103851 2768 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.27688e-06 8304 2 103.7 9.89138e-05 2768 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.21598e-06 8304 2 103.7 9.29469e-05 2768 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.41807e-06 8304 2 103.7 0.000103665 2768 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.38621e-06 8304 2 103.7 9.45955e-05 2768 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.45929e-06 8304 2 103.7 0.000126588 2768 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.28298e-06 8304 2 103.7 9.51998e-05 2768 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.15906e-06 8304 2 103.7 9.23476e-05 2768 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.35957e-06 8304 2 103.7 9.35399e-05 2768 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.15635e-06 8304 2 103.7 9.22445e-05 2768 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.33979e-06 8304 2 103.7 9.67105e-05 2768 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.48069e-06 8304 2 103.7 0.000113621 2768 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.10029e-06 8304 2 103.7 9.13851e-05 2768 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.21167e-06 8304 2 103.7 0.000100923 2768 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.27484e-06 8304 2 103.7 9.74287e-05 2768 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.277e-06 8304 2 103.7 0.000104855 2768 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.20416e-06 8304 2 103.7 0.000105584 2768 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.28405e-06 8304 2 103.7 9.54483e-05 2768 SHAKE stats (type/ave/delta/count) on step 3050000 2 0.97 1.13965e-06 8304 2 103.7 9.47733e-05 2768 SHAKE stats (type/ave/delta/count) on step 3100000 2 0.97 1.29693e-06 8304 2 103.7 0.000106984 2768 SHAKE stats (type/ave/delta/count) on step 3150000 2 0.97 1.19459e-06 8304 2 103.7 0.000121758 2768 SHAKE stats (type/ave/delta/count) on step 3200000 2 0.97 1.23409e-06 8304 2 103.7 0.000100796 2768 SHAKE stats (type/ave/delta/count) on step 3250000 2 0.97 1.19036e-06 8304 2 103.7 0.000140102 2768 SHAKE stats (type/ave/delta/count) on step 3300000 2 0.97 1.41797e-06 8304 2 103.7 9.50107e-05 2768 SHAKE stats (type/ave/delta/count) on step 3350000 2 0.97 1.08555e-06 8304 2 103.7 9.60754e-05 2768 SHAKE stats (type/ave/delta/count) on step 3400000 2 0.97 1.44303e-06 8304 2 103.7 9.32968e-05 2768 SHAKE stats (type/ave/delta/count) on step 3450000 2 0.97 1.05613e-06 8304 2 103.7 9.46676e-05 2768 SHAKE stats (type/ave/delta/count) on step 3500000 2 0.97 1.445e-06 8304 2 103.7 9.92456e-05 2768 SHAKE stats (type/ave/delta/count) on step 3550000 2 0.97 1.45319e-06 8304 2 103.7 0.000106642 2768 SHAKE stats (type/ave/delta/count) on step 3600000 2 0.97 1.25676e-06 8304 2 103.7 8.59494e-05 2768 SHAKE stats (type/ave/delta/count) on step 3650000 2 0.97 1.15028e-06 8304 2 103.7 0.000101577 2768 SHAKE stats (type/ave/delta/count) on step 3700000 2 0.97 1.41402e-06 8304 2 103.7 0.00010551 2768 SHAKE stats (type/ave/delta/count) on step 3750000 2 0.97 1.79107e-06 8304 2 103.7 0.000126543 2768 SHAKE stats (type/ave/delta/count) on step 3800000 2 0.97 1.52786e-06 8304 2 103.7 0.000104845 2768 SHAKE stats (type/ave/delta/count) on step 3850000 2 0.97 1.22838e-06 8304 2 103.7 9.40298e-05 2768 SHAKE stats (type/ave/delta/count) on step 3900000 2 0.97 1.51376e-06 8304 2 103.7 0.000119121 2768 SHAKE stats (type/ave/delta/count) on step 3950000 2 0.97 1.16543e-06 8304 2 103.7 9.04865e-05 2768 SHAKE stats (type/ave/delta/count) on step 4000000 2 0.97 1.12518e-06 8304 2 103.7 0.000105094 2768 SHAKE stats (type/ave/delta/count) on step 4050000 2 0.97 1.16915e-06 8304 2 103.7 9.72252e-05 2768 SHAKE stats (type/ave/delta/count) on step 4100000 2 0.97 1.1747e-06 8304 2 103.7 9.06335e-05 2768 SHAKE stats (type/ave/delta/count) on step 4150000 2 0.97 1.23154e-06 8304 2 103.7 9.58779e-05 2768 SHAKE stats (type/ave/delta/count) on step 4200000 2 0.97 1.38855e-06 8304 2 103.7 0.000113635 2768 SHAKE stats (type/ave/delta/count) on step 4250000 2 0.97 1.26852e-06 8304 2 103.7 9.51041e-05 2768 SHAKE stats (type/ave/delta/count) on step 4300000 2 0.97 1.2239e-06 8304 2 103.7 0.00012341 2768 SHAKE stats (type/ave/delta/count) on step 4350000 2 0.97 1.13337e-06 8304 2 103.7 8.99155e-05 2768 SHAKE stats (type/ave/delta/count) on step 4400000 2 0.97 1.05752e-06 8304 2 103.7 9.62529e-05 2768 SHAKE stats (type/ave/delta/count) on step 4450000 2 0.97 1.14683e-06 8304 2 103.7 0.000105478 2768 SHAKE stats (type/ave/delta/count) on step 4500000 2 0.97 1.27802e-06 8304 2 103.7 9.51266e-05 2768 SHAKE stats (type/ave/delta/count) on step 4550000 2 0.97 1.29432e-06 8304 2 103.7 0.000103409 2768 SHAKE stats (type/ave/delta/count) on step 4600000 2 0.97 1.11644e-06 8304 2 103.7 8.94918e-05 2768 SHAKE stats (type/ave/delta/count) on step 4650000 2 0.97 1.31433e-06 8304 2 103.7 0.000165592 2768 SHAKE stats (type/ave/delta/count) on step 4700000 2 0.97 1.10472e-06 8304 2 103.7 0.000102135 2768 SHAKE stats (type/ave/delta/count) on step 4750000 2 0.97 1.06671e-06 8304 2 103.7 9.1051e-05 2768 SHAKE stats (type/ave/delta/count) on step 4800000 2 0.97 1.28905e-06 8304 2 103.7 0.000121247 2768 SHAKE stats (type/ave/delta/count) on step 4850000 2 0.97 1.43474e-06 8304 2 103.7 0.000106509 2768 SHAKE stats (type/ave/delta/count) on step 4900000 2 0.97 1.29864e-06 8304 2 103.7 9.18162e-05 2768 SHAKE stats (type/ave/delta/count) on step 4950000 2 0.97 1.08585e-06 8304 2 103.7 9.31231e-05 2768 SHAKE stats (type/ave/delta/count) on step 5000000 2 0.97 1.26127e-06 8304 2 103.7 9.75527e-05 2768 5000000 5000000 -442.12841 194193.27 0.62517633 297.54375 40.821029 46.122139 0 0 20808.635 28503.505 -107.89913 -209815.1 -160416.02 5615.9863 Loop time of 57469 on 32 procs for 5000000 steps with 9101 atoms Performance: 7.517 ns/day, 3.193 hours/ns, 87.003 timesteps/s 98.3% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.427 | 18316 | 41332 |13226.6 | 31.87 Bond | 4.1004 | 11.754 | 25.964 | 218.5 | 0.02 Kspace | 9720.3 | 32836 | 51343 |9925.4 | 57.14 Neigh | 2837.1 | 2847.6 | 2865.9 | 17.7 | 4.95 Comm | 535.65 | 1117.6 | 1476.7 |1048.1 | 1.94 Output | 0.014707 | 0.016799 | 0.018616 | 0.9 | 0.00 Modify | 1944.1 | 2220.7 | 2610.9 | 568.7 | 3.86 Other | | 119.4 | | | 0.21 Nlocal: 284.406 ave 571 max 0 min Histogram: 12 3 1 0 0 0 0 0 2 14 Nghost: 4518.31 ave 8580 max 364 min Histogram: 8 0 0 8 0 0 8 0 0 8 Neighs: 132490 ave 307431 max 0 min Histogram: 16 0 0 0 0 0 4 0 4 8 Total # of neighbors = 4239669 Ave neighs/atom = 465.8465 Ave special neighs/atom = 1.8929788 Neighbor list builds = 249961 Dangerous builds = 0 undump sci restart 0 dump sci all custom 5000000 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) = 0.24997142 grid = 32 32 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0035792785 estimated relative force accuracy = 1.0778891e-05 using double precision KISS FFT 3d grid and FFT values/proc = 7406 2048 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 5000000 2 0.97 1.26127e-06 8304 2 103.7 9.75527e-05 2768 Per MPI rank memory allocation (min/avg/max) = 11.21 | 12.91 | 14.14 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 5000000 5000000 -441.73232 194193.27 0.62517633 297.54375 40.821029 46.122139 0 0 20808.635 28503.505 -107.89913 -209815.1 -160416.02 5615.9863 Loop time of 8.76547e-06 on 32 procs for 0 steps with 9101 atoms 109.1% 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 | | 8.765e-06 | | |100.00 Nlocal: 284.406 ave 571 max 0 min Histogram: 12 3 1 0 0 0 0 0 2 14 Nghost: 4518.31 ave 8580 max 364 min Histogram: 8 0 0 8 0 0 8 0 0 8 Neighs: 132490 ave 307431 max 0 min Histogram: 16 0 0 0 0 0 4 0 4 8 Total # of neighbors = 4239669 Ave neighs/atom = 465.8465 Ave special neighs/atom = 1.8929788 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out