#------------------------------------------------------------------------------- # Stage 2.4: NVT integration for 2 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 = 0.001 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 200000 200000 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 200 1 200 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 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) = 0.32360719 grid = 40 40 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0032437318 estimated relative force accuracy = 9.768402e-06 using double precision KISS FFT 3d grid and FFT values/proc = 10557 3200 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 1.00307 0.108649 8304 2 97.1441 10.5295 2768 Per MPI rank memory allocation (min/avg/max) = 11.43 | 12.75 | 13.3 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 3249.6141 120592.96 1.006734 428.55654 9.9417932 58.933606 0 0 27538.761 68681.909 -345.28628 -270694.94 -174405.4 8088.7858 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.59605e-06 8304 2 103.7 0.00011992 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.44252e-06 8304 2 103.7 9.38103e-05 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.09033e-06 8304 2 103.7 0.000106203 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.41194e-06 8304 2 103.7 0.000117298 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.31153e-06 8304 2 103.7 0.000104659 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.16182e-06 8304 2 103.7 8.95569e-05 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.51593e-06 8304 2 103.7 0.000123266 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.49343e-06 8304 2 103.7 9.81507e-05 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.33064e-06 8304 2 103.7 0.000106251 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.04661e-06 8304 2 103.7 8.75657e-05 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.2186e-06 8304 2 103.7 9.17719e-05 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.16431e-06 8304 2 103.7 9.63949e-05 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.68528e-06 8304 2 103.7 0.000105962 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.78925e-06 8304 2 103.7 0.000113643 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.53854e-06 8304 2 103.7 0.000100073 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.29621e-06 8304 2 103.7 9.96392e-05 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.49965e-06 8304 2 103.7 0.000109854 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.59774e-06 8304 2 103.7 9.70624e-05 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.24246e-06 8304 2 103.7 9.24595e-05 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.10772e-06 8304 2 103.7 9.27453e-05 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.3109e-06 8304 2 103.7 9.83828e-05 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.28548e-06 8304 2 103.7 9.13613e-05 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.6196e-06 8304 2 103.7 0.000111857 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.20211e-06 8304 2 103.7 9.00402e-05 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.13036e-06 8304 2 103.7 9.74912e-05 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.15509e-06 8304 2 103.7 9.84276e-05 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.34899e-06 8304 2 103.7 0.000141198 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.04556e-06 8304 2 103.7 0.000104257 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.79827e-06 8304 2 103.7 0.000120111 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.40147e-06 8304 2 103.7 0.000117335 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.188e-06 8304 2 103.7 0.000104604 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.32915e-06 8304 2 103.7 9.42084e-05 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.35218e-06 8304 2 103.7 9.90686e-05 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.11097e-06 8304 2 103.7 0.000106235 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.36914e-06 8304 2 103.7 0.000101401 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.17038e-06 8304 2 103.7 0.000101458 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.06663e-06 8304 2 103.7 0.000105582 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.37432e-06 8304 2 103.7 0.000103371 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.17508e-06 8304 2 103.7 9.24146e-05 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.21049e-06 8304 2 103.7 9.84041e-05 2768 2000000 2000000 -407.06476 120592.96 1.006734 303.42795 37.951939 60.352827 0 0 21214.213 88469.303 -345.28628 -270630.28 -160848.46 5727.0476 Loop time of 11664.6 on 32 procs for 2000000 steps with 9101 atoms Performance: 14.814 ns/day, 1.620 hours/ns, 171.459 timesteps/s 99.1% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1174.3 | 4193.1 | 5509.7 |2558.1 | 35.95 Bond | 2.0558 | 5.1013 | 9.1428 | 106.0 | 0.04 Kspace | 4460.2 | 5792.1 | 8820.7 |2187.0 | 49.66 Neigh | 342.8 | 344.47 | 346.28 | 6.8 | 2.95 Comm | 469.5 | 591.02 | 642.97 | 278.0 | 5.07 Output | 0.011784 | 0.014049 | 0.016188 | 1.1 | 0.00 Modify | 664.32 | 704.73 | 806.79 | 219.2 | 6.04 Other | | 34.08 | | | 0.29 Nlocal: 284.406 ave 364 max 83 min Histogram: 7 1 0 0 0 0 0 0 2 22 Nghost: 4157.06 ave 5108 max 3590 min Histogram: 8 4 8 4 0 0 0 0 0 8 Neighs: 77285.5 ave 105775 max 17190 min Histogram: 8 0 0 0 0 0 0 6 6 12 Total # of neighbors = 2473136 Ave neighs/atom = 271.74332 Ave special neighs/atom = 1.8929788 Neighbor list builds = 99573 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) = 0.32360719 grid = 40 40 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0032437318 estimated relative force accuracy = 9.768402e-06 using double precision KISS FFT 3d grid and FFT values/proc = 10557 3200 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.21049e-06 8304 2 103.7 9.84041e-05 2768 Per MPI rank memory allocation (min/avg/max) = 12.55 | 13.04 | 13.3 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 -406.39083 120592.96 1.006734 303.42795 37.951939 60.352827 0 0 21214.213 88469.303 -345.28628 -270630.28 -160848.46 5727.0476 Loop time of 7.25097e-06 on 32 procs for 0 steps with 9101 atoms 102.1% 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 | | 7.251e-06 | | |100.00 Nlocal: 284.406 ave 364 max 83 min Histogram: 7 1 0 0 0 0 0 0 2 22 Nghost: 4157.06 ave 5108 max 3590 min Histogram: 8 4 8 4 0 0 0 0 0 8 Neighs: 77285.5 ave 105775 max 17190 min Histogram: 8 0 0 0 0 0 0 6 6 12 Total # of neighbors = 2473136 Ave neighs/atom = 271.74332 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