#------------------------------------------------------------------------------- # 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 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 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) = 0.31973058 grid = 40 40 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0032868617 estimated relative force accuracy = 9.8982865e-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 1.00163 0.0752457 5784 2 97.5212 10.1067 1928 Per MPI rank memory allocation (min/avg/max) = 11.39 | 12.59 | 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-06 977.74155 138087.51 0.62909591 427.16581 5.2827568 12.524485 0 0 19731.993 39863.113 -152.16399 -194155.83 -134542.92 5676.3721 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.16608e-06 5784 2 103.7 0.000102783 1928 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.82418e-06 5784 2 103.7 0.000141853 1928 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.1643e-06 5784 2 103.7 8.93045e-05 1928 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.23206e-06 5784 2 103.7 0.000103981 1928 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.2729e-06 5784 2 103.7 0.000109125 1928 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.23768e-06 5784 2 103.7 0.000102161 1928 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.19897e-06 5784 2 103.7 8.87354e-05 1928 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.09261e-06 5784 2 103.7 8.92734e-05 1928 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.13406e-06 5784 2 103.7 9.33468e-05 1928 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.27436e-06 5784 2 103.7 9.76325e-05 1928 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.50974e-06 5784 2 103.7 0.000111763 1928 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.1927e-06 5784 2 103.7 9.19914e-05 1928 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.28377e-06 5784 2 103.7 9.79339e-05 1928 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.27852e-06 5784 2 103.7 9.17642e-05 1928 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.12466e-06 5784 2 103.7 0.000100464 1928 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.23566e-06 5784 2 103.7 9.16757e-05 1928 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.21798e-06 5784 2 103.7 0.000101327 1928 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.36394e-06 5784 2 103.7 0.00010714 1928 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.06489e-06 5784 2 103.7 0.000115365 1928 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.62796e-06 5784 2 103.7 0.000126396 1928 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.62764e-06 5784 2 103.7 0.000108667 1928 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.06879e-06 5784 2 103.7 9.69326e-05 1928 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.2095e-06 5784 2 103.7 0.000106765 1928 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.95929e-06 5784 2 103.7 0.000134317 1928 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.38296e-06 5784 2 103.7 0.000104826 1928 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.6287e-06 5784 2 103.7 0.000106749 1928 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.56853e-06 5784 2 103.7 9.61614e-05 1928 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.26471e-06 5784 2 103.7 0.000104128 1928 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.23191e-06 5784 2 103.7 9.13356e-05 1928 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.26578e-06 5784 2 103.7 0.00011567 1928 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.12324e-06 5784 2 103.7 9.29446e-05 1928 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.53678e-06 5784 2 103.7 0.000110915 1928 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.09566e-06 5784 2 103.7 9.29336e-05 1928 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.18975e-06 5784 2 103.7 8.41238e-05 1928 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.58728e-06 5784 2 103.7 0.000121298 1928 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.12715e-06 5784 2 103.7 9.91647e-05 1928 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.57709e-06 5784 2 103.7 0.000128258 1928 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.19567e-06 5784 2 103.7 0.000103644 1928 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.30343e-06 5784 2 103.7 0.000124342 1928 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.87944e-06 5784 2 103.7 0.000146102 1928 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.61934e-06 5784 2 103.7 0.000114078 1928 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.19981e-06 5784 2 103.7 0.000111295 1928 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.26743e-06 5784 2 103.7 0.000122136 1928 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.56444e-06 5784 2 103.7 0.000119212 1928 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.04527e-06 5784 2 103.7 9.43869e-05 1928 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.14221e-06 5784 2 103.7 0.00010257 1928 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.15049e-06 5784 2 103.7 0.000100369 1928 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.12517e-06 5784 2 103.7 0.00010811 1928 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.11636e-06 5784 2 103.7 8.56678e-05 1928 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.41615e-06 5784 2 103.7 0.000100224 1928 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.25569e-06 5784 2 103.7 9.18484e-05 1928 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.3355e-06 5784 2 103.7 9.45954e-05 1928 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.11823e-06 5784 2 103.7 8.83045e-05 1928 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.16757e-06 5784 2 103.7 9.14119e-05 1928 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.21213e-06 5784 2 103.7 8.92072e-05 1928 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.35575e-06 5784 2 103.7 0.000124255 1928 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.18288e-06 5784 2 103.7 9.05961e-05 1928 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.23135e-06 5784 2 103.7 9.07512e-05 1928 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.11825e-06 5784 2 103.7 9.28123e-05 1928 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.10376e-06 5784 2 103.7 0.000104528 1928 SHAKE stats (type/ave/delta/count) on step 3050000 2 0.97 1.20526e-06 5784 2 103.7 9.26121e-05 1928 SHAKE stats (type/ave/delta/count) on step 3100000 2 0.97 1.08627e-06 5784 2 103.7 9.34578e-05 1928 SHAKE stats (type/ave/delta/count) on step 3150000 2 0.97 1.19266e-06 5784 2 103.7 0.00011171 1928 SHAKE stats (type/ave/delta/count) on step 3200000 2 0.97 1.35047e-06 5784 2 103.7 9.4612e-05 1928 SHAKE stats (type/ave/delta/count) on step 3250000 2 0.97 1.14334e-06 5784 2 103.7 9.24815e-05 1928 SHAKE stats (type/ave/delta/count) on step 3300000 2 0.97 1.35365e-06 5784 2 103.7 0.000106829 1928 SHAKE stats (type/ave/delta/count) on step 3350000 2 0.97 1.18656e-06 5784 2 103.7 9.60618e-05 1928 SHAKE stats (type/ave/delta/count) on step 3400000 2 0.97 1.22904e-06 5784 2 103.7 9.31291e-05 1928 SHAKE stats (type/ave/delta/count) on step 3450000 2 0.97 1.23761e-06 5784 2 103.7 9.26902e-05 1928 SHAKE stats (type/ave/delta/count) on step 3500000 2 0.97 1.09167e-06 5784 2 103.7 9.47173e-05 1928 SHAKE stats (type/ave/delta/count) on step 3550000 2 0.97 1.29418e-06 5784 2 103.7 8.88197e-05 1928 SHAKE stats (type/ave/delta/count) on step 3600000 2 0.97 1.39238e-06 5784 2 103.7 0.000112432 1928 SHAKE stats (type/ave/delta/count) on step 3650000 2 0.97 1.14093e-06 5784 2 103.7 0.000101215 1928 SHAKE stats (type/ave/delta/count) on step 3700000 2 0.97 1.93425e-06 5784 2 103.7 0.000127655 1928 SHAKE stats (type/ave/delta/count) on step 3750000 2 0.97 1.20206e-06 5784 2 103.7 9.66213e-05 1928 SHAKE stats (type/ave/delta/count) on step 3800000 2 0.97 1.18138e-06 5784 2 103.7 9.2597e-05 1928 SHAKE stats (type/ave/delta/count) on step 3850000 2 0.97 1.25418e-06 5784 2 103.7 9.08989e-05 1928 SHAKE stats (type/ave/delta/count) on step 3900000 2 0.97 1.31192e-06 5784 2 103.7 0.000105359 1928 SHAKE stats (type/ave/delta/count) on step 3950000 2 0.97 1.17084e-06 5784 2 103.7 9.70549e-05 1928 SHAKE stats (type/ave/delta/count) on step 4000000 2 0.97 1.12571e-06 5784 2 103.7 9.32578e-05 1928 SHAKE stats (type/ave/delta/count) on step 4050000 2 0.97 1.40918e-06 5784 2 103.7 8.73665e-05 1928 SHAKE stats (type/ave/delta/count) on step 4100000 2 0.97 1.23306e-06 5784 2 103.7 0.000119356 1928 SHAKE stats (type/ave/delta/count) on step 4150000 2 0.97 1.2365e-06 5784 2 103.7 9.83537e-05 1928 SHAKE stats (type/ave/delta/count) on step 4200000 2 0.97 1.18153e-06 5784 2 103.7 8.9665e-05 1928 SHAKE stats (type/ave/delta/count) on step 4250000 2 0.97 1.19522e-06 5784 2 103.7 9.66185e-05 1928 SHAKE stats (type/ave/delta/count) on step 4300000 2 0.97 1.18514e-06 5784 2 103.7 9.65604e-05 1928 SHAKE stats (type/ave/delta/count) on step 4350000 2 0.97 1.1533e-06 5784 2 103.7 9.44538e-05 1928 SHAKE stats (type/ave/delta/count) on step 4400000 2 0.97 1.12443e-06 5784 2 103.7 0.000111099 1928 SHAKE stats (type/ave/delta/count) on step 4450000 2 0.97 1.239e-06 5784 2 103.7 0.000118153 1928 SHAKE stats (type/ave/delta/count) on step 4500000 2 0.97 1.16194e-06 5784 2 103.7 0.000118782 1928 SHAKE stats (type/ave/delta/count) on step 4550000 2 0.97 1.05759e-06 5784 2 103.7 9.60297e-05 1928 SHAKE stats (type/ave/delta/count) on step 4600000 2 0.97 1.07613e-06 5784 2 103.7 9.6364e-05 1928 SHAKE stats (type/ave/delta/count) on step 4650000 2 0.97 1.00735e-06 5784 2 103.7 8.99099e-05 1928 SHAKE stats (type/ave/delta/count) on step 4700000 2 0.97 1.50203e-06 5784 2 103.7 0.000102297 1928 SHAKE stats (type/ave/delta/count) on step 4750000 2 0.97 1.10587e-06 5784 2 103.7 9.374e-05 1928 SHAKE stats (type/ave/delta/count) on step 4800000 2 0.97 1.1305e-06 5784 2 103.7 9.0871e-05 1928 SHAKE stats (type/ave/delta/count) on step 4850000 2 0.97 1.64054e-06 5784 2 103.7 0.000117014 1928 SHAKE stats (type/ave/delta/count) on step 4900000 2 0.97 1.1214e-06 5784 2 103.7 9.60159e-05 1928 SHAKE stats (type/ave/delta/count) on step 4950000 2 0.97 1.30243e-06 5784 2 103.7 9.34321e-05 1928 SHAKE stats (type/ave/delta/count) on step 5000000 2 0.97 1.33928e-06 5784 2 103.7 9.95057e-05 1928 5000000 5000000 -465.8928 138087.51 0.62909591 296.45751 23.699029 45.117791 0 0 16055.664 53152.568 -152.16399 -193992.61 -124715.56 3939.4611 Loop time of 28503.6 on 32 procs for 5000000 steps with 6387 atoms Performance: 15.156 ns/day, 1.584 hours/ns, 175.416 timesteps/s 98.6% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 196.24 | 6907.3 | 14486 |7897.2 | 24.23 Bond | 4.0875 | 9.7198 | 21.626 | 174.8 | 0.03 Kspace | 10762 | 18349 | 25059 |4871.7 | 64.37 Neigh | 786.9 | 795.06 | 809.11 | 27.9 | 2.79 Comm | 577.63 | 883.85 | 1106.9 | 680.4 | 3.10 Output | 0.012317 | 0.013937 | 0.015485 | 0.8 | 0.00 Modify | 1331.8 | 1483.7 | 1702.9 | 397.4 | 5.21 Other | | 74.83 | | | 0.26 Nlocal: 199.594 ave 412 max 0 min Histogram: 14 2 0 0 0 0 0 0 4 12 Nghost: 2713.62 ave 3998 max 1421 min Histogram: 11 5 0 0 0 0 0 0 3 13 Neighs: 51097.1 ave 111920 max 0 min Histogram: 16 0 0 0 0 0 0 0 9 7 Total # of neighbors = 1635106 Ave neighs/atom = 256.00532 Ave special neighs/atom = 1.8738062 Neighbor list builds = 242460 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) = 0.31973058 grid = 40 40 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0032868617 estimated relative force accuracy = 9.8982865e-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 5000000 2 0.97 1.33928e-06 5784 2 103.7 9.95057e-05 1928 Per MPI rank memory allocation (min/avg/max) = 11.51 | 12.8 | 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 5000000 5000000 -465.46076 138087.51 0.62909591 296.45751 23.699029 45.117791 0 0 16055.664 53152.568 -152.16399 -193992.61 -124715.56 3939.4611 Loop time of 1.07076e-05 on 32 procs for 0 steps with 6387 atoms 108.3% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 1.071e-05 | | |100.00 Nlocal: 199.594 ave 412 max 0 min Histogram: 14 2 0 0 0 0 0 0 4 12 Nghost: 2713.62 ave 3998 max 1421 min Histogram: 11 5 0 0 0 0 0 0 3 13 Neighs: 51097.1 ave 111920 max 0 min Histogram: 16 0 0 0 0 0 0 0 9 7 Total # of neighbors = 1635106 Ave neighs/atom = 256.00532 Ave special neighs/atom = 1.8738062 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out