#------------------------------------------------------------------------------- # Stage 2.5: NPT integration for 2 ns with a timestep of 1 fs # Temperature 298.2 K # Pressure 1 atm #------------------------------------------------------------------------------- # 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 1937 = # of frozen angles find clusters CPU = 0.001 seconds change_box all triclinic Changing box ... triclinic box = (0 0 0) to (32.7352 32.7352 60.700505) 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 (32.7352 32.7352 60.700505) with tilt (0 0 0) fix 1 movable npt temp 298.2 298.2 100 z 1 1 100 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 2.5_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 2.5_instantaneous.txt restart 2000000 2.5.restart dump sci all custom 200000 2.5.xyz id mol type q xs ys zs timestep 1 run 2000000 PPPM initialization ... WARNING: System is not charge neutral, net charge = 0.0144 (../kspace.cpp:325) using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25967779 grid = 27 27 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0025391723 estimated relative force accuracy = 7.6466421e-06 using double precision KISS FFT 3d grid and FFT values/proc = 5040 1458 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 = 5 5 9 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 0.97 9.53126e-13 5811 2 103.7 9.96465e-11 1937 Per MPI rank memory allocation (min/avg/max) = 12.75 | 12.92 | 13.04 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 2493.9775 65046.256 1.3074059 298.79439 36.254942 57.044099 0 0 15533.257 23576.647 -158.00458 -152609.48 -113406.28 3948.2484 SHAKE stats (type/ave/delta/count) on step 50000 2 0.96999 3.23663e-05 5811 2 103.7 0.00365557 1937 SHAKE stats (type/ave/delta/count) on step 100000 2 0.970001 5.14199e-06 5811 2 103.7 0.000526115 1937 SHAKE stats (type/ave/delta/count) on step 150000 2 0.970006 1.99194e-05 5811 2 103.7 0.00225211 1937 SHAKE stats (type/ave/delta/count) on step 200000 2 0.970021 6.4167e-05 5811 2 103.7 0.00734648 1937 SHAKE stats (type/ave/delta/count) on step 250000 2 0.96998 5.92747e-05 5811 2 103.7 0.0067523 1937 SHAKE stats (type/ave/delta/count) on step 300000 2 0.970011 3.32141e-05 5811 2 103.7 0.00382571 1937 SHAKE stats (type/ave/delta/count) on step 350000 2 0.970031 9.11439e-05 5811 2 103.7 0.0104182 1937 SHAKE stats (type/ave/delta/count) on step 400000 2 0.970074 0.000220777 5811 2 103.7 0.0252753 1937 SHAKE stats (type/ave/delta/count) on step 450000 2 0.970013 4.00781e-05 5811 2 103.7 0.00454566 1937 SHAKE stats (type/ave/delta/count) on step 500000 2 0.969977 7.04051e-05 5811 2 103.7 0.00798731 1937 SHAKE stats (type/ave/delta/count) on step 550000 2 0.969996 1.29173e-05 5811 2 103.7 0.00141991 1937 SHAKE stats (type/ave/delta/count) on step 600000 2 0.970057 0.000171541 5811 2 103.7 0.0196457 1937 SHAKE stats (type/ave/delta/count) on step 650000 2 0.970003 9.00601e-06 5811 2 103.7 0.00102727 1937 SHAKE stats (type/ave/delta/count) on step 700000 2 0.970021 6.51521e-05 5811 2 103.7 0.0074104 1937 SHAKE stats (type/ave/delta/count) on step 750000 2 0.969992 2.61531e-05 5811 2 103.7 0.00291003 1937 SHAKE stats (type/ave/delta/count) on step 800000 2 0.970013 3.92951e-05 5811 2 103.7 0.00448174 1937 SHAKE stats (type/ave/delta/count) on step 850000 2 0.970022 6.60736e-05 5811 2 103.7 0.00756323 1937 SHAKE stats (type/ave/delta/count) on step 900000 2 0.969988 3.57127e-05 5811 2 103.7 0.00400379 1937 SHAKE stats (type/ave/delta/count) on step 950000 2 0.969905 0.000286981 5811 2 103.7 0.0328812 1937 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.970022 6.64957e-05 5811 2 103.7 0.00761578 1937 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.970046 0.000139192 5811 2 103.7 0.0159569 1937 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97008 0.000239394 5811 2 103.7 0.027427 1937 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.969993 2.31169e-05 5811 2 103.7 0.00262656 1937 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.969996 1.23842e-05 5811 2 103.7 0.00141182 1937 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.969968 0.000100859 5811 2 103.7 0.0115065 1937 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97002 6.16194e-05 5811 2 103.7 0.0069853 1937 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.970039 0.000118088 5811 2 103.7 0.0134393 1937 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.96999 3.03748e-05 5811 2 103.7 0.00339837 1937 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.969978 6.5842e-05 5811 2 103.7 0.00747971 1937 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.970008 2.4289e-05 5811 2 103.7 0.00279745 1937 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.969985 4.59196e-05 5811 2 103.7 0.00519877 1937 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.970017 5.16648e-05 5811 2 103.7 0.00590581 1937 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.970052 0.00015503 5811 2 103.7 0.017755 1937 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.970046 0.000138148 5811 2 103.7 0.0158782 1937 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.970046 0.000138116 5811 2 103.7 0.0157853 1937 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.969979 6.30218e-05 5811 2 103.7 0.0071502 1937 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97001 3.10033e-05 5811 2 103.7 0.00350194 1937 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.970017 5.08627e-05 5811 2 103.7 0.00580151 1937 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.969987 4.12535e-05 5811 2 103.7 0.00468144 1937 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.969975 7.65937e-05 5811 2 103.7 0.00869884 1937 2000000 2000000 489.52125 68738.714 1.2371755 299.74379 28.475052 39.777409 0 0 14981.894 24641.442 -149.517 -152592.82 -112901.23 3960.7937 Loop time of 11982.7 on 32 procs for 2000000 steps with 6371 atoms Performance: 14.421 ns/day, 1.664 hours/ns, 166.908 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 | 6040.3 | 6305.6 | 6661.8 | 196.9 | 52.62 Bond | 2.0892 | 4.5138 | 8.0661 | 77.4 | 0.04 Kspace | 2378.7 | 2744.6 | 3014.7 | 302.2 | 22.90 Neigh | 515.01 | 515.64 | 516.07 | 1.1 | 4.30 Comm | 838.43 | 852.8 | 867.53 | 27.7 | 7.12 Output | 0.0078756 | 0.0097596 | 0.011515 | 1.1 | 0.00 Modify | 1202.2 | 1336.1 | 1494.7 | 335.0 | 11.15 Other | | 223.4 | | | 1.86 Nlocal: 199.094 ave 228 max 179 min Histogram: 2 0 5 11 6 6 0 1 0 1 Nghost: 6357.09 ave 6458 max 6284 min Histogram: 4 3 4 4 7 4 0 2 2 2 Neighs: 105947 ave 120719 max 94928 min Histogram: 2 1 5 7 8 3 3 1 0 2 Total # of neighbors = 3390303 Ave neighs/atom = 532.14613 Ave special neighs/atom = 1.8932664 Neighbor list builds = 103247 Dangerous builds = 0 undump sci restart 0 dump sci all custom 2000000 2.5.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) = 0.25866808 grid = 27 27 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0026571702 estimated relative force accuracy = 8.0019891e-06 using double precision KISS FFT 3d grid and FFT values/proc = 5040 1458 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.969975 7.65937e-05 5811 2 103.7 0.00869884 1937 Per MPI rank memory allocation (min/avg/max) = 12.75 | 12.92 | 13.04 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 344.10824 68738.714 1.2371755 299.74379 28.475052 39.777409 0 0 14981.894 24053.083 -149.517 -152004.46 -112901.23 3960.7937 Loop time of 1.05883e-05 on 32 procs for 0 steps with 6371 atoms 110.4% 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 | | 1.059e-05 | | |100.00 Nlocal: 199.094 ave 228 max 179 min Histogram: 2 0 5 11 6 6 0 1 0 1 Nghost: 6357.09 ave 6458 max 6284 min Histogram: 4 3 4 4 7 4 0 2 2 2 Neighs: 105947 ave 120719 max 94928 min Histogram: 2 1 5 7 8 3 3 1 0 2 Total # of neighbors = 3390303 Ave neighs/atom = 532.14613 Ave special neighs/atom = 1.8932664 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 6:17:29