#------------------------------------------------------------------------------- # Stage 2.4: NPT integration for 2 ns with a timestep of 1 fs # Temperature 298.2 K # Pressure 1 bar #------------------------------------------------------------------------------- # 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 2812 = # of frozen angles find clusters CPU = 0.001 seconds change_box all triclinic Changing box ... triclinic box = (0 0 0) to (36.8271 36.8271 69.281874) with tilt (0 0 0) kspace_style pppm 0.00001 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 change_box all triclinic Changing box ... triclinic box = (0 0 0) to (36.8271 36.8271 69.281874) with tilt (0 0 0) fix 1 movable npt temp 298.2 298.2 100 z 0.9869233 0.9869233 100 drag 0 mtk yes nreset 40000 fix 2 movable ave/time 1 199999 200000 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_cella v_cellb v_cellc v_cellalpha v_cellbeta v_cellgamma 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_cella v_cellb v_cellc v_cellalpha v_cellbeta v_cellgamma 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 ... WARNING: System is not charge neutral, net charge = 0.0151 (../kspace.cpp:325) using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25615969 grid = 30 30 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0031432339 estimated relative force accuracy = 9.4657554e-06 using double precision KISS FFT 3d grid and FFT values/proc = 8712 2700 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 14 ghost atom cutoff = 14 binsize = 7, bins = 6 6 10 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/class2/coul/long, perpetual attributes: half, newton on pair build: half/bin/newton/tri stencil: half/bin/3d/tri bin: standard SHAKE stats (type/ave/delta/count) on step 0 2 0.993009 0.838498 8436 2 97.3158 31.4341 2812 Per MPI rank memory allocation (min/avg/max) = 14.05 | 14.18 | 14.3 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 12452.157 93962.523 1.2789064 429.73544 53.540003 207.13351 0 0 21846.362 56390.961 -220.49494 -206091.72 -127593.73 8166.1181 SHAKE stats (type/ave/delta/count) on step 50000 2 0.969995 1.49306e-05 8436 2 103.7 0.00166561 2812 SHAKE stats (type/ave/delta/count) on step 100000 2 0.970008 2.2522e-05 8436 2 103.7 0.00256707 2812 SHAKE stats (type/ave/delta/count) on step 150000 2 0.969961 0.00011747 8436 2 103.7 0.0134154 2812 SHAKE stats (type/ave/delta/count) on step 200000 2 0.970013 3.77393e-05 8436 2 103.7 0.00430623 2812 SHAKE stats (type/ave/delta/count) on step 250000 2 0.969993 2.27924e-05 8436 2 103.7 0.00256595 2812 SHAKE stats (type/ave/delta/count) on step 300000 2 0.970008 2.32208e-05 8436 2 103.7 0.00263472 2812 SHAKE stats (type/ave/delta/count) on step 350000 2 0.970013 3.99948e-05 8436 2 103.7 0.00457553 2812 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97008 0.000238741 8436 2 103.7 0.0273057 2812 SHAKE stats (type/ave/delta/count) on step 450000 2 0.970009 2.66578e-05 8436 2 103.7 0.00303133 2812 SHAKE stats (type/ave/delta/count) on step 500000 2 0.970023 6.72831e-05 8436 2 103.7 0.00774208 2812 SHAKE stats (type/ave/delta/count) on step 550000 2 0.970074 0.000225506 8436 2 103.7 0.025852 2812 SHAKE stats (type/ave/delta/count) on step 600000 2 0.970006 1.86307e-05 8436 2 103.7 0.0021463 2812 SHAKE stats (type/ave/delta/count) on step 650000 2 0.969936 0.000192529 8436 2 103.7 0.0219685 2812 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97005 0.000148666 8436 2 103.7 0.017018 2812 SHAKE stats (type/ave/delta/count) on step 750000 2 0.970015 4.49878e-05 8436 2 103.7 0.00516047 2812 SHAKE stats (type/ave/delta/count) on step 800000 2 0.970001 4.5886e-06 8436 2 103.7 0.000477189 2812 SHAKE stats (type/ave/delta/count) on step 850000 2 0.970014 4.18756e-05 8436 2 103.7 0.00480938 2812 SHAKE stats (type/ave/delta/count) on step 900000 2 0.969993 2.15371e-05 8436 2 103.7 0.00243121 2812 SHAKE stats (type/ave/delta/count) on step 950000 2 0.970019 5.65141e-05 8436 2 103.7 0.00641014 2812 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.969958 0.000127672 8436 2 103.7 0.0145838 2812 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.970012 3.68364e-05 8436 2 103.7 0.00419818 2812 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.969953 0.000140612 8436 2 103.7 0.0160441 2812 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.969952 0.000145826 8436 2 103.7 0.0166043 2812 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.970068 0.00020399 8436 2 103.7 0.0233672 2812 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.969986 4.37334e-05 8436 2 103.7 0.00496397 2812 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.970031 9.2998e-05 8436 2 103.7 0.0106307 2812 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.969975 7.65944e-05 8436 2 103.7 0.00873133 2812 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.969981 5.85948e-05 8436 2 103.7 0.00664617 2812 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.970087 0.000259696 8436 2 103.7 0.0298098 2812 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.970012 3.54213e-05 8436 2 103.7 0.00406751 2812 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.970021 6.35316e-05 8436 2 103.7 0.00729393 2812 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.969982 5.4203e-05 8436 2 103.7 0.00617505 2812 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.970014 4.10958e-05 8436 2 103.7 0.00468093 2812 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.969948 0.00015798 8436 2 103.7 0.0180188 2812 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.969998 8.87618e-06 8436 2 103.7 0.000946579 2812 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.969951 0.000148079 8436 2 103.7 0.0168916 2812 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.969999 5.50004e-06 8436 2 103.7 0.000584816 2812 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.969998 6.55023e-06 8436 2 103.7 0.0007182 2812 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.969974 8.08434e-05 8436 2 103.7 0.0091995 2812 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.970012 3.60253e-05 8436 2 103.7 0.00410536 2812 2000000 2000000 225.54384 98023.684 1.2259208 301.62241 48.534794 86.218214 0 0 18770.837 47760.122 -211.35974 -207251.99 -140586.28 5731.6293 Loop time of 25049.7 on 16 procs for 2000000 steps with 9188 atoms Performance: 6.898 ns/day, 3.479 hours/ns, 79.841 timesteps/s 98.9% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16027 | 16897 | 17438 | 311.0 | 67.45 Bond | 3.1104 | 7.9745 | 12.731 | 105.1 | 0.03 Kspace | 3793.8 | 4340.3 | 5211 | 615.3 | 17.33 Neigh | 1357.7 | 1358.3 | 1359.1 | 1.3 | 5.42 Comm | 550.14 | 555.04 | 559.17 | 11.5 | 2.22 Output | 0.013857 | 0.015589 | 0.01712 | 0.8 | 0.00 Modify | 1484 | 1741.1 | 1803.7 | 265.6 | 6.95 Other | | 149.9 | | | 0.60 Nlocal: 574.25 ave 591 max 553 min Histogram: 1 1 0 2 4 1 1 2 2 2 Nghost: 8735 ave 8824 max 8593 min Histogram: 1 0 1 1 3 1 2 2 2 3 Neighs: 309100 ave 322404 max 295725 min Histogram: 2 2 0 2 2 3 0 2 1 2 Total # of neighbors = 4945602 Ave neighs/atom = 538.26752 Ave special neighs/atom = 1.9037875 Neighbor list builds = 106288 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) = 0.25693825 grid = 30 30 48 stencil order = 5 estimated absolute RMS force accuracy = 0.002903652 estimated relative force accuracy = 8.7442617e-06 using double precision KISS FFT 3d grid and FFT values/proc = 9196 2700 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.970012 3.60253e-05 8436 2 103.7 0.00410536 2812 Per MPI rank memory allocation (min/avg/max) = 14.12 | 14.27 | 14.33 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 295.97608 98023.684 1.2259208 301.62241 48.534794 86.218214 0 0 18770.837 48385.144 -211.35974 -207877.04 -140586.3 5731.6293 Loop time of 1.32357e-05 on 16 procs for 0 steps with 9188 atoms 107.2% CPU use with 16 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 | | 1.324e-05 | | |100.00 Nlocal: 574.25 ave 591 max 553 min Histogram: 1 1 0 2 4 1 1 2 2 2 Nghost: 8735 ave 8824 max 8593 min Histogram: 1 0 1 1 3 1 2 2 2 3 Neighs: 309100 ave 322404 max 295725 min Histogram: 2 2 0 2 2 3 0 2 1 2 Total # of neighbors = 4945602 Ave neighs/atom = 538.26752 Ave special neighs/atom = 1.9037875 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_Custom.out