#------------------------------------------------------------------------------- # 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 2009 = # 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) = 0.25044719 grid = 30 30 50 stencil order = 5 estimated absolute RMS force accuracy = 0.0033056861 estimated relative force accuracy = 9.9549755e-06 using double precision KISS FFT 3d grid and FFT values/proc = 6292 1800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 1.00118 0.0915582 6027 2 97.6088 10.5685 2009 Per MPI rank memory allocation (min/avg/max) = 10.92 | 12.29 | 13.52 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-06 626.98968 139673.96 0.614244 429.78001 4.824849 18.944643 0 0 17192.708 17400.706 -75.627082 -144776.61 -110159.43 5832.8145 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.23753e-06 6027 2 103.7 8.93826e-05 2009 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.22569e-06 6027 2 103.7 0.000109064 2009 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.14814e-06 6027 2 103.7 0.000101289 2009 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.19246e-06 6027 2 103.7 8.86332e-05 2009 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.25527e-06 6027 2 103.7 0.000103058 2009 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.31843e-06 6027 2 103.7 9.4459e-05 2009 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.19878e-06 6027 2 103.7 0.000110786 2009 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.27523e-06 6027 2 103.7 0.000126162 2009 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.2192e-06 6027 2 103.7 9.84746e-05 2009 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.23876e-06 6027 2 103.7 0.000102871 2009 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.2152e-06 6027 2 103.7 0.000104735 2009 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.07111e-06 6027 2 103.7 0.000107279 2009 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.15186e-06 6027 2 103.7 0.000105406 2009 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.11917e-06 6027 2 103.7 0.000102293 2009 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.23361e-06 6027 2 103.7 9.59225e-05 2009 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.14248e-06 6027 2 103.7 0.000110244 2009 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.25339e-06 6027 2 103.7 9.22448e-05 2009 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.08995e-06 6027 2 103.7 9.3854e-05 2009 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.04208e-06 6027 2 103.7 0.00010208 2009 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.26406e-06 6027 2 103.7 0.000107722 2009 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.12546e-06 6027 2 103.7 9.38933e-05 2009 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.11215e-06 6027 2 103.7 9.20178e-05 2009 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.15992e-06 6027 2 103.7 9.05545e-05 2009 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.19918e-06 6027 2 103.7 9.33356e-05 2009 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.33145e-06 6027 2 103.7 0.000107374 2009 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.64839e-06 6027 2 103.7 9.48299e-05 2009 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.42059e-06 6027 2 103.7 0.000113766 2009 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.9171e-06 6027 2 103.7 0.000149311 2009 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.18348e-06 6027 2 103.7 8.87543e-05 2009 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.33526e-06 6027 2 103.7 8.93413e-05 2009 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.25681e-06 6027 2 103.7 0.000104269 2009 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.1189e-06 6027 2 103.7 0.000100686 2009 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.22407e-06 6027 2 103.7 0.000110481 2009 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.39182e-06 6027 2 103.7 0.00013053 2009 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.29853e-06 6027 2 103.7 8.90239e-05 2009 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.03662e-06 6027 2 103.7 0.00010317 2009 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.08241e-06 6027 2 103.7 9.15771e-05 2009 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.54431e-06 6027 2 103.7 0.000112725 2009 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.31893e-06 6027 2 103.7 0.000123914 2009 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.26418e-06 6027 2 103.7 9.69664e-05 2009 SHAKE stats 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(type/ave/delta/count) on step 2550000 2 0.97 1.16594e-06 6027 2 103.7 9.14218e-05 2009 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.34296e-06 6027 2 103.7 0.000110024 2009 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.33083e-06 6027 2 103.7 9.25664e-05 2009 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.46671e-06 6027 2 103.7 0.000103809 2009 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.17106e-06 6027 2 103.7 9.52257e-05 2009 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.07443e-06 6027 2 103.7 9.35974e-05 2009 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.16066e-06 6027 2 103.7 9.12462e-05 2009 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.41153e-06 6027 2 103.7 0.000109505 2009 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.10652e-06 6027 2 103.7 0.000103824 2009 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.11545e-06 6027 2 103.7 9.34151e-05 2009 SHAKE stats 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(type/ave/delta/count) on step 3550000 2 0.97 1.276e-06 6027 2 103.7 9.98128e-05 2009 SHAKE stats (type/ave/delta/count) on step 3600000 2 0.97 1.19972e-06 6027 2 103.7 9.82075e-05 2009 SHAKE stats (type/ave/delta/count) on step 3650000 2 0.97 1.15501e-06 6027 2 103.7 9.75146e-05 2009 SHAKE stats (type/ave/delta/count) on step 3700000 2 0.97 1.11084e-06 6027 2 103.7 9.36195e-05 2009 SHAKE stats (type/ave/delta/count) on step 3750000 2 0.97 1.18572e-06 6027 2 103.7 0.000102176 2009 SHAKE stats (type/ave/delta/count) on step 3800000 2 0.97 1.19103e-06 6027 2 103.7 9.07405e-05 2009 SHAKE stats (type/ave/delta/count) on step 3850000 2 0.97 1.14191e-06 6027 2 103.7 0.000101961 2009 SHAKE stats (type/ave/delta/count) on step 3900000 2 0.97 1.14028e-06 6027 2 103.7 0.00010113 2009 SHAKE stats (type/ave/delta/count) on step 3950000 2 0.97 1.0516e-06 6027 2 103.7 9.24389e-05 2009 SHAKE stats (type/ave/delta/count) on step 4000000 2 0.97 1.24839e-06 6027 2 103.7 0.000100244 2009 SHAKE stats (type/ave/delta/count) on step 4050000 2 0.97 1.24389e-06 6027 2 103.7 9.5456e-05 2009 SHAKE stats (type/ave/delta/count) on step 4100000 2 0.97 1.29648e-06 6027 2 103.7 9.08443e-05 2009 SHAKE stats (type/ave/delta/count) on step 4150000 2 0.97 1.66808e-06 6027 2 103.7 0.000107794 2009 SHAKE stats (type/ave/delta/count) on step 4200000 2 0.97 1.70919e-06 6027 2 103.7 0.000128243 2009 SHAKE stats (type/ave/delta/count) on step 4250000 2 0.97 1.2117e-06 6027 2 103.7 9.43323e-05 2009 SHAKE stats (type/ave/delta/count) on step 4300000 2 0.97 1.06315e-06 6027 2 103.7 9.48548e-05 2009 SHAKE stats (type/ave/delta/count) on step 4350000 2 0.97 1.40934e-06 6027 2 103.7 0.000122621 2009 SHAKE stats (type/ave/delta/count) on step 4400000 2 0.97 1.43088e-06 6027 2 103.7 0.000104502 2009 SHAKE stats (type/ave/delta/count) on step 4450000 2 0.97 1.42215e-06 6027 2 103.7 0.000100212 2009 SHAKE stats (type/ave/delta/count) on step 4500000 2 0.97 1.15446e-06 6027 2 103.7 0.000102533 2009 SHAKE stats (type/ave/delta/count) on step 4550000 2 0.97 1.31714e-06 6027 2 103.7 9.83009e-05 2009 SHAKE stats (type/ave/delta/count) on step 4600000 2 0.97 1.09217e-06 6027 2 103.7 9.77596e-05 2009 SHAKE stats (type/ave/delta/count) on step 4650000 2 0.97 1.33892e-06 6027 2 103.7 9.58293e-05 2009 SHAKE stats (type/ave/delta/count) on step 4700000 2 0.97 1.18822e-06 6027 2 103.7 9.2467e-05 2009 SHAKE stats (type/ave/delta/count) on step 4750000 2 0.97 1.16056e-06 6027 2 103.7 8.84403e-05 2009 SHAKE stats (type/ave/delta/count) on step 4800000 2 0.97 1.13201e-06 6027 2 103.7 0.000101202 2009 SHAKE stats (type/ave/delta/count) on step 4850000 2 0.97 1.21954e-06 6027 2 103.7 9.881e-05 2009 SHAKE stats (type/ave/delta/count) on step 4900000 2 0.97 1.50824e-06 6027 2 103.7 0.000108074 2009 SHAKE stats (type/ave/delta/count) on step 4950000 2 0.97 1.21566e-06 6027 2 103.7 9.67897e-05 2009 SHAKE stats (type/ave/delta/count) on step 5000000 2 0.97 1.37915e-06 6027 2 103.7 9.98564e-05 2009 5000000 5000000 -211.44246 139673.96 0.614244 301.54156 36.950061 47.71411 0 0 13231.123 31626.789 -75.627082 -144720.2 -99777.619 4092.4099 Loop time of 43539.8 on 32 procs for 5000000 steps with 6563 atoms Performance: 9.922 ns/day, 2.419 hours/ns, 114.837 timesteps/s 98.5% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 22.09 | 13353 | 31301 |11438.3 | 30.67 Bond | 4.3527 | 9.8921 | 24.279 | 188.3 | 0.02 Kspace | 6998.8 | 25035 | 38556 |8398.6 | 57.50 Neigh | 2048.7 | 2059.9 | 2077 | 20.1 | 4.73 Comm | 533.05 | 1124.5 | 1486.4 |1042.8 | 2.58 Output | 0.010933 | 0.012692 | 0.014166 | 0.9 | 0.00 Modify | 1601.2 | 1873.6 | 2268.2 | 607.4 | 4.30 Other | | 84.13 | | | 0.19 Nlocal: 205.094 ave 413 max 0 min Histogram: 13 1 2 0 0 0 0 0 3 13 Nghost: 4027.81 ave 7569 max 520 min Histogram: 8 0 0 6 2 2 6 0 0 8 Neighs: 94769.9 ave 226766 max 0 min Histogram: 16 0 0 0 0 0 3 4 4 5 Total # of neighbors = 3032637 Ave neighs/atom = 462.08091 Ave special neighs/atom = 1.9037026 Neighbor list builds = 243927 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) = 0.25044719 grid = 30 30 50 stencil order = 5 estimated absolute RMS force accuracy = 0.0033056861 estimated relative force accuracy = 9.9549755e-06 using double precision KISS FFT 3d grid and FFT values/proc = 6292 1800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 5000000 2 0.97 1.37915e-06 6027 2 103.7 9.98564e-05 2009 Per MPI rank memory allocation (min/avg/max) = 11.07 | 12.54 | 13.52 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 -211.08828 139673.96 0.614244 301.54156 36.950061 47.71411 0 0 13231.123 31626.789 -75.627082 -144720.2 -99777.619 4092.4099 Loop time of 8.17325e-06 on 32 procs for 0 steps with 6563 atoms 112.4% 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 | | 8.173e-06 | | |100.00 Nlocal: 205.094 ave 413 max 0 min Histogram: 13 1 2 0 0 0 0 0 3 13 Nghost: 4027.81 ave 7569 max 520 min Histogram: 8 0 0 6 2 2 6 0 0 8 Neighs: 94769.9 ave 226766 max 0 min Histogram: 16 0 0 0 0 0 3 4 4 5 Total # of neighbors = 3032637 Ave neighs/atom = 462.08091 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_NVT.out