#------------------------------------------------------------------------------- # 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 4018 = # 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 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) = 0.32363871 grid = 48 48 50 stencil order = 5 estimated absolute RMS force accuracy = 0.0035203731 estimated relative force accuracy = 1.0601499e-05 using double precision KISS FFT 3d grid and FFT values/proc = 11191 4608 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.995862 0.695715 12054 2 97.0358 27.1712 4018 Per MPI rank memory allocation (min/avg/max) = 13.2 | 13.31 | 13.5 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 13129.43 134167.59 1.2789064 429.76556 165.65967 376.03525 0 0 31157.786 154889.23 -626.09682 -370409.75 -183821.04 11666.518 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.14802e-06 12054 2 103.7 9.41647e-05 4018 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.1089e-06 12054 2 103.7 9.49791e-05 4018 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.38545e-06 12054 2 103.7 0.000102712 4018 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.23922e-06 12054 2 103.7 9.98366e-05 4018 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.45416e-06 12054 2 103.7 0.000105521 4018 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.40319e-06 12054 2 103.7 0.00010314 4018 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.3437e-06 12054 2 103.7 0.000112088 4018 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.29073e-06 12054 2 103.7 9.61946e-05 4018 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.8331e-06 12054 2 103.7 0.000120768 4018 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.4442e-06 12054 2 103.7 0.000104044 4018 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.196e-06 12054 2 103.7 9.81309e-05 4018 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.08401e-06 12054 2 103.7 0.000105659 4018 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.25699e-06 12054 2 103.7 9.53649e-05 4018 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.30938e-06 12054 2 103.7 9.49064e-05 4018 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.58972e-06 12054 2 103.7 0.000116783 4018 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.44485e-06 12054 2 103.7 0.00010586 4018 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.73381e-06 12054 2 103.7 0.000145623 4018 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.53493e-06 12054 2 103.7 0.000116573 4018 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.0926e-06 12054 2 103.7 9.86535e-05 4018 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.43578e-06 12054 2 103.7 9.85523e-05 4018 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.24067e-06 12054 2 103.7 9.10042e-05 4018 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.27061e-06 12054 2 103.7 0.00010631 4018 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.33626e-06 12054 2 103.7 0.000102374 4018 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.4863e-06 12054 2 103.7 9.53027e-05 4018 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.43148e-06 12054 2 103.7 0.000118431 4018 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.0947e-06 12054 2 103.7 9.52951e-05 4018 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.40423e-06 12054 2 103.7 0.000103839 4018 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.30913e-06 12054 2 103.7 0.000103373 4018 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.21882e-06 12054 2 103.7 9.27805e-05 4018 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.19216e-06 12054 2 103.7 9.56403e-05 4018 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.3248e-06 12054 2 103.7 0.000107411 4018 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.60592e-06 12054 2 103.7 0.000109035 4018 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.27014e-06 12054 2 103.7 0.000104095 4018 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.17627e-06 12054 2 103.7 9.87193e-05 4018 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.21554e-06 12054 2 103.7 0.000105261 4018 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.18211e-06 12054 2 103.7 0.000105287 4018 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.93354e-06 12054 2 103.7 0.000123844 4018 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.37413e-06 12054 2 103.7 0.00010196 4018 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.34855e-06 12054 2 103.7 9.85649e-05 4018 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.29745e-06 12054 2 103.7 0.000100124 4018 2000000 2000000 1982.1884 134167.59 1.2789064 299.26712 52.800425 100.30325 0 0 27778.141 143790.85 -626.09682 -373042.57 -201320.48 8123.9763 Loop time of 14796.2 on 32 procs for 2000000 steps with 13126 atoms Performance: 11.679 ns/day, 2.055 hours/ns, 135.170 timesteps/s 99.3% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6252.6 | 6617.1 | 6934.9 | 208.6 | 44.72 Bond | 2.7105 | 6.5924 | 11.95 | 84.3 | 0.04 Kspace | 5579.9 | 5904.9 | 6279.7 | 225.4 | 39.91 Neigh | 425.17 | 426.24 | 427.39 | 3.1 | 2.88 Comm | 786.19 | 827.59 | 844.41 | 60.8 | 5.59 Output | 0.013904 | 0.016822 | 0.019588 | 1.3 | 0.00 Modify | 954.36 | 965.84 | 990.65 | 32.3 | 6.53 Other | | 47.96 | | | 0.32 Nlocal: 410.188 ave 431 max 372 min Histogram: 1 0 0 1 4 3 12 7 2 2 Nghost: 5641.19 ave 5710 max 5579 min Histogram: 1 2 5 6 3 4 4 5 0 2 Neighs: 127663 ave 138181 max 109864 min Histogram: 1 0 0 1 3 6 11 6 2 2 Total # of neighbors = 4085202 Ave neighs/atom = 311.22977 Ave special neighs/atom = 1.9037026 Neighbor list builds = 101830 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) = 0.32363871 grid = 48 48 50 stencil order = 5 estimated absolute RMS force accuracy = 0.0035203731 estimated relative force accuracy = 1.0601499e-05 using double precision KISS FFT 3d grid and FFT values/proc = 11191 4608 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.29745e-06 12054 2 103.7 0.000100124 4018 Per MPI rank memory allocation (min/avg/max) = 13.2 | 13.38 | 13.51 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 1983.1167 134167.59 1.2789064 299.26712 52.800425 100.30325 0 0 27778.141 143790.85 -626.09682 -373042.57 -201320.48 8123.9763 Loop time of 7.57553e-06 on 32 procs for 0 steps with 13126 atoms 108.1% 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 | | 7.576e-06 | | |100.00 Nlocal: 410.188 ave 431 max 372 min Histogram: 1 0 0 1 4 3 12 7 2 2 Nghost: 5641.19 ave 5710 max 5579 min Histogram: 1 2 5 6 3 4 4 5 0 2 Neighs: 127663 ave 138181 max 109864 min Histogram: 1 0 0 1 3 6 11 6 2 2 Total # of neighbors = 4085202 Ave neighs/atom = 311.22977 Ave special neighs/atom = 1.9037026 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NPT.out