#------------------------------------------------------------------------------- # 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 1928 = # of frozen angles find clusters CPU = 0.001 seconds change_box all triclinic Changing box ... triclinic box = (0 0 0) to (40.281352 40.281352 40.281352) 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 (40.281352 40.281352 40.281352) 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 = 0.0171 (../kspace.cpp:325) using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25969541 grid = 32 32 32 stencil order = 5 estimated absolute RMS force accuracy = 0.0026097487 estimated relative force accuracy = 7.8591807e-06 using double precision KISS FFT 3d grid and FFT values/proc = 5175 1024 generated 0 of 28 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 6 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 7.41296e-13 5784 2 103.7 6.89795e-11 1928 Per MPI rank memory allocation (min/avg/max) = 12.36 | 12.85 | 12.93 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 2811.9879 65360.011 1.3291045 300.78708 32.049327 39.581224 0 0 17143.89 14910.284 -161.84744 -158056.74 -125930.93 3996.9944 SHAKE stats (type/ave/delta/count) on step 50000 2 0.96996 0.000121111 5784 2 103.7 0.0138071 1928 SHAKE stats (type/ave/delta/count) on step 100000 2 0.970096 0.000290279 5784 2 103.7 0.0332085 1928 SHAKE stats (type/ave/delta/count) on step 150000 2 0.970053 0.000160256 5784 2 103.7 0.018317 1928 SHAKE stats (type/ave/delta/count) on step 200000 2 0.969943 0.000169979 5784 2 103.7 0.0194421 1928 SHAKE stats (type/ave/delta/count) on step 250000 2 0.969959 0.000122791 5784 2 103.7 0.0140505 1928 SHAKE stats (type/ave/delta/count) on step 300000 2 0.969971 8.85085e-05 5784 2 103.7 0.0101217 1928 SHAKE stats (type/ave/delta/count) on step 350000 2 0.970014 4.12047e-05 5784 2 103.7 0.00471355 1928 SHAKE stats (type/ave/delta/count) on step 400000 2 0.969974 7.85726e-05 5784 2 103.7 0.00899306 1928 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97001 3.01871e-05 5784 2 103.7 0.00338585 1928 SHAKE stats (type/ave/delta/count) on step 500000 2 0.969974 8.12764e-05 5784 2 103.7 0.009276 1928 SHAKE stats (type/ave/delta/count) on step 550000 2 0.970036 0.000108761 5784 2 103.7 0.0124559 1928 SHAKE stats (type/ave/delta/count) on step 600000 2 0.969984 5.0498e-05 5784 2 103.7 0.00572848 1928 SHAKE stats (type/ave/delta/count) on step 650000 2 0.970039 0.000117469 5784 2 103.7 0.0134706 1928 SHAKE stats (type/ave/delta/count) on step 700000 2 0.969966 0.000101889 5784 2 103.7 0.011571 1928 SHAKE stats (type/ave/delta/count) on step 750000 2 0.969933 0.000201354 5784 2 103.7 0.0229908 1928 SHAKE stats (type/ave/delta/count) on step 800000 2 0.969963 0.00011005 5784 2 103.7 0.0124766 1928 SHAKE stats (type/ave/delta/count) on step 850000 2 0.970009 2.76445e-05 5784 2 103.7 0.0031867 1928 SHAKE stats (type/ave/delta/count) on step 900000 2 0.970059 0.000178335 5784 2 103.7 0.0203742 1928 SHAKE stats (type/ave/delta/count) on step 950000 2 0.970062 0.000184432 5784 2 103.7 0.0210635 1928 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.970003 8.43047e-06 5784 2 103.7 0.000933613 1928 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.91843e-06 5784 2 103.7 0.000193035 1928 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.970013 3.90822e-05 5784 2 103.7 0.00442504 1928 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.970114 0.000343874 5784 2 103.7 0.0394351 1928 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.969975 7.50296e-05 5784 2 103.7 0.00849875 1928 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.46782e-06 5784 2 103.7 0.000115885 1928 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.970019 5.6423e-05 5784 2 103.7 0.00652199 1928 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.970003 1.09647e-05 5784 2 103.7 0.0012108 1928 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.969957 0.000129763 5784 2 103.7 0.0147857 1928 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.970002 6.25513e-06 5784 2 103.7 0.000690061 1928 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.970079 0.000235779 5784 2 103.7 0.0270416 1928 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.969998 6.33641e-06 5784 2 103.7 0.000674088 1928 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.970001 2.10748e-06 5784 2 103.7 0.000223069 1928 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.969986 4.28429e-05 5784 2 103.7 0.00485847 1928 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.970027 8.10999e-05 5784 2 103.7 0.00929505 1928 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.969987 4.02996e-05 5784 2 103.7 0.00456095 1928 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.969992 2.58129e-05 5784 2 103.7 0.00287279 1928 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.969997 1.05353e-05 5784 2 103.7 0.00115869 1928 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.969965 0.000104118 5784 2 103.7 0.0117957 1928 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.969956 0.000135289 5784 2 103.7 0.0154581 1928 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.970026 7.8756e-05 5784 2 103.7 0.00903729 1928 2000000 2000000 557.63553 68580.074 1.2666986 296.13379 22.98957 39.263545 0 0 16656.914 15585.738 -154.24817 -158035.82 -125730.92 3935.1594 Loop time of 11674.5 on 32 procs for 2000000 steps with 6387 atoms Performance: 14.801 ns/day, 1.621 hours/ns, 171.313 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 | 5894.9 | 6223.3 | 6842 | 260.1 | 53.31 Bond | 2.1092 | 4.3472 | 7.485 | 82.5 | 0.04 Kspace | 2059.5 | 2685.6 | 3021.4 | 397.8 | 23.00 Neigh | 487.19 | 487.84 | 488.62 | 1.9 | 4.18 Comm | 840.29 | 853.97 | 865.17 | 22.3 | 7.31 Output | 0.0069746 | 0.0088262 | 0.010571 | 1.2 | 0.00 Modify | 1250.8 | 1293.5 | 1311.2 | 25.4 | 11.08 Other | | 126 | | | 1.08 Nlocal: 199.594 ave 214 max 186 min Histogram: 1 2 8 5 4 2 2 3 1 4 Nghost: 6430.62 ave 6477 max 6377 min Histogram: 1 0 6 3 4 5 6 2 2 3 Neighs: 106777 ave 116735 max 100107 min Histogram: 4 4 6 6 1 2 1 4 3 1 Total # of neighbors = 3416859 Ave neighs/atom = 534.97088 Ave special neighs/atom = 1.8738062 Neighbor list builds = 100529 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) = 0.25863855 grid = 32 32 32 stencil order = 5 estimated absolute RMS force accuracy = 0.0027592951 estimated relative force accuracy = 8.3095354e-06 using double precision KISS FFT 3d grid and FFT values/proc = 5175 1024 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.970026 7.8756e-05 5784 2 103.7 0.00903729 1928 Per MPI rank memory allocation (min/avg/max) = 12.74 | 12.91 | 12.93 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 710.36285 68580.074 1.2666986 296.13379 22.98957 39.263545 0 0 16656.914 14948.265 -154.24817 -157398.35 -125730.92 3935.1594 Loop time of 7.97131e-06 on 32 procs for 0 steps with 6387 atoms 116.4% 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 | | 7.971e-06 | | |100.00 Nlocal: 199.594 ave 214 max 186 min Histogram: 1 2 8 5 4 2 2 3 1 4 Nghost: 6430.62 ave 6477 max 6377 min Histogram: 1 0 6 3 4 5 6 2 2 3 Neighs: 106777 ave 116735 max 100107 min Histogram: 4 4 6 6 1 2 1 4 3 1 Total # of neighbors = 3416859 Ave neighs/atom = 534.97088 Ave special neighs/atom = 1.8738062 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 6:17:40