#------------------------------------------------------------------------------- # 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 1 b 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 2200 = # 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 v_surfacetension 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 v_surfacetension 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) = 0.24367668 grid = 27 27 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0034817281 estimated relative force accuracy = 1.0485121e-05 using double precision KISS FFT 3d grid and FFT values/proc = 15640 6048 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 0.97 8.46656e-13 6600 1 103.7 7.83444e-11 2200 Per MPI rank memory allocation (min/avg/max) = 9.208 | 12.1 | 16.21 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 -52.497085 200987.25 0.32745077 295.747 0 0 0 0 5647.8677 81645.409 -37.551062 -110310.33 -23017.049 3878.0071 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.97959e-06 6600 1 103.7 0.000139253 2200 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.31293e-06 6600 1 103.7 0.000107505 2200 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.72748e-06 6600 1 103.7 0.000109239 2200 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.29277e-06 6600 1 103.7 0.000132398 2200 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 2.39993e-06 6600 1 103.7 0.000142185 2200 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.38981e-06 6600 1 103.7 9.35849e-05 2200 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.17144e-06 6600 1 103.7 9.34945e-05 2200 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.6563e-06 6600 1 103.7 0.000110287 2200 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.27081e-06 6600 1 103.7 9.57839e-05 2200 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.16159e-06 6600 1 103.7 9.27141e-05 2200 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.76311e-06 6600 1 103.7 0.000105705 2200 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.35724e-06 6600 1 103.7 0.000102963 2200 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.14942e-06 6600 1 103.7 9.74298e-05 2200 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.55076e-06 6600 1 103.7 0.000101737 2200 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.39378e-06 6600 1 103.7 0.000118451 2200 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.00832e-06 6600 1 103.7 0.00010453 2200 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.26723e-06 6600 1 103.7 9.40846e-05 2200 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.25981e-06 6600 1 103.7 9.50261e-05 2200 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.34001e-06 6600 1 103.7 9.06097e-05 2200 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.31852e-06 6600 1 103.7 9.39127e-05 2200 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.97 1.20077e-06 6600 1 103.7 9.34827e-05 2200 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.97 1.22338e-06 6600 1 103.7 0.000109792 2200 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.97 1.27141e-06 6600 1 103.7 9.02156e-05 2200 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.97 1.32049e-06 6600 1 103.7 9.17638e-05 2200 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.97 1.38246e-06 6600 1 103.7 0.000111286 2200 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.97 1.14901e-06 6600 1 103.7 9.96003e-05 2200 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.97 1.29077e-06 6600 1 103.7 0.00010108 2200 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.97 1.43448e-06 6600 1 103.7 0.000107559 2200 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.97 1.53099e-06 6600 1 103.7 0.000140285 2200 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.97 1.15857e-06 6600 1 103.7 0.000100966 2200 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.97 1.43243e-06 6600 1 103.7 9.76174e-05 2200 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.97 1.18806e-06 6600 1 103.7 0.000129176 2200 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.97 1.19684e-06 6600 1 103.7 9.06195e-05 2200 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.97 1.51002e-06 6600 1 103.7 0.000103386 2200 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.97 1.16961e-06 6600 1 103.7 8.6663e-05 2200 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.97 1.07516e-06 6600 1 103.7 0.000117942 2200 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.97 1.35468e-06 6600 1 103.7 0.000115893 2200 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.97 1.19196e-06 6600 1 103.7 0.000105776 2200 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.97 1.14964e-06 6600 1 103.7 9.97671e-05 2200 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.09465e-06 6600 1 103.7 9.93662e-05 2200 2000000 2000000 -70.083069 200987.25 0.32745077 299.43432 0 0 0 0 5521.0779 81736.373 -37.551062 -110318.89 -23061.434 3926.3575 Loop time of 94158.1 on 8 procs for 2000000 steps with 6600 atoms Performance: 1.835 ns/day, 13.078 hours/ns, 21.241 timesteps/s 97.5% CPU use with 8 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1925 | 23335 | 77826 |19221.6 | 24.78 Bond | 2.0242 | 2.8234 | 4.4887 | 46.3 | 0.00 Kspace | 9840.7 | 64430 | 87934 |11596.1 | 68.43 Neigh | 4395.6 | 4406.9 | 4419.7 | 16.3 | 4.68 Comm | 122.2 | 478.11 | 718.08 |1061.5 | 0.51 Output | 0.039709 | 0.041601 | 0.043215 | 0.6 | 0.00 Modify | 1288.3 | 1414.5 | 1584.3 | 301.3 | 1.50 Other | | 90.84 | | | 0.10 Nlocal: 825 ave 2303 max 0 min Histogram: 4 0 0 0 2 0 0 0 0 2 Nghost: 5578.12 ave 11068 max 0 min Histogram: 2 0 0 2 0 0 1 1 0 2 Neighs: 409602 ave 1.31538e+06 max 0 min Histogram: 4 0 2 0 0 0 0 0 0 2 Total # of neighbors = 3276812 Ave neighs/atom = 496.48667 Ave special neighs/atom = 2 Neighbor list builds = 100034 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) = 0.24367668 grid = 27 27 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0034817281 estimated relative force accuracy = 1.0485121e-05 using double precision KISS FFT 3d grid and FFT values/proc = 15640 6048 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.09465e-06 6600 1 103.7 9.93662e-05 2200 Per MPI rank memory allocation (min/avg/max) = 9.337 | 12.02 | 16.21 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 -69.888475 200987.25 0.32745077 299.43432 0 0 0 0 5521.0779 81736.373 -37.551062 -110318.89 -23061.434 3926.3575 Loop time of 3.64775e-06 on 8 procs for 0 steps with 6600 atoms 116.5% 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 | | 3.648e-06 | | |100.00 Nlocal: 825 ave 2303 max 0 min Histogram: 4 0 0 0 2 0 0 0 0 2 Nghost: 5578.12 ave 11068 max 0 min Histogram: 2 0 0 2 0 0 1 1 0 2 Neighs: 409602 ave 1.31538e+06 max 0 min Histogram: 4 0 2 0 0 0 0 0 0 2 Total # of neighbors = 3276812 Ave neighs/atom = 496.48667 Ave special neighs/atom = 2 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 36:26:39