#------------------------------------------------------------------------------- # 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 2768 = # of frozen angles find clusters CPU = 0.001 seconds change_box all triclinic Changing box ... triclinic box = (0 0 0) to (33.78995 48.916 56.180783) 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 (33.78995 48.916 56.180783) 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 = 0.0206 (../kspace.cpp:325) using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25757039 grid = 30 36 40 stencil order = 5 estimated absolute RMS force accuracy = 0.0029678301 estimated relative force accuracy = 8.9375323e-06 using double precision KISS FFT 3d grid and FFT values/proc = 14850 5400 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 7 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 0.994417 0.900234 8304 2 96.7351 40.3724 2768 Per MPI rank memory allocation (min/avg/max) = 15.9 | 15.92 | 16.09 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 16340.197 92859.486 1.3074059 428.55654 56.039769 196.35598 0 0 25545.104 47132.384 -225.64506 -214416.79 -141486.91 8088.7858 SHAKE stats (type/ave/delta/count) on step 50000 2 0.969965 0.000105702 8304 2 103.7 0.0120642 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.970056 0.000168196 8304 2 103.7 0.0191806 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.969986 4.29378e-05 8304 2 103.7 0.00490434 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.969971 8.84705e-05 8304 2 103.7 0.0100563 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.970015 4.45187e-05 8304 2 103.7 0.00511481 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.970043 0.000129303 8304 2 103.7 0.014811 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.970003 1.01644e-05 8304 2 103.7 0.00114671 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.969969 9.49945e-05 8304 2 103.7 0.0108298 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.970005 1.70007e-05 8304 2 103.7 0.00191081 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.969995 1.57242e-05 8304 2 103.7 0.00175646 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.970054 0.000163622 8304 2 103.7 0.01881 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.969925 0.000224016 8304 2 103.7 0.0256185 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.969957 0.00013217 8304 2 103.7 0.0151691 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.970023 6.90983e-05 8304 2 103.7 0.00786138 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.970083 0.000249276 8304 2 103.7 0.028555 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.970001 3.69262e-06 8304 2 103.7 0.000397875 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.969988 3.91951e-05 8304 2 103.7 0.00441622 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.96998 6.23479e-05 8304 2 103.7 0.00709644 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.970009 2.79269e-05 8304 2 103.7 0.00315971 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.969974 7.81902e-05 8304 2 103.7 0.00892744 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.969975 7.55539e-05 8304 2 103.7 0.00857556 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.969992 2.51291e-05 8304 2 103.7 0.00283462 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.970028 8.50781e-05 8304 2 103.7 0.00972111 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.970037 0.000112137 8304 2 103.7 0.0128129 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.970012 3.71018e-05 8304 2 103.7 0.00422218 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.969955 0.000137293 8304 2 103.7 0.0157029 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.969964 0.000109735 8304 2 103.7 0.0124746 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.969968 9.8e-05 8304 2 103.7 0.0112005 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.970032 9.77501e-05 8304 2 103.7 0.011196 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.970054 0.000163581 8304 2 103.7 0.0186927 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.969968 9.7417e-05 8304 2 103.7 0.011094 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.969972 8.37296e-05 8304 2 103.7 0.00951716 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.970015 4.34314e-05 8304 2 103.7 0.00499031 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.970018 5.43694e-05 8304 2 103.7 0.00622484 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.970007 2.27727e-05 8304 2 103.7 0.00259313 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.969977 6.93186e-05 8304 2 103.7 0.00784186 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.969985 4.76419e-05 8304 2 103.7 0.00539054 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.970073 0.000220491 8304 2 103.7 0.0252361 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.970003 7.83606e-06 8304 2 103.7 0.000884003 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.969991 2.94681e-05 8304 2 103.7 0.00334797 2768 2000000 2000000 57.612869 97735.508 1.2421794 300.27411 50.524406 71.814348 0 0 21205.291 33525.508 -214.38764 -216149.62 -161296.48 5667.5205 Loop time of 43563.8 on 8 procs for 2000000 steps with 9101 atoms Performance: 3.967 ns/day, 6.051 hours/ns, 45.910 timesteps/s 99.2% CPU use with 8 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 27985 | 30405 | 32565 | 933.7 | 69.80 Bond | 8.9969 | 11.118 | 14.223 | 51.7 | 0.03 Kspace | 4962.5 | 7122.4 | 9540.5 |1926.7 | 16.35 Neigh | 2928.4 | 2928.9 | 2929.5 | 0.8 | 6.72 Comm | 557.13 | 559.32 | 560.73 | 4.9 | 1.28 Output | 0.018599 | 0.019949 | 0.021154 | 0.6 | 0.00 Modify | 2355.8 | 2401.3 | 2455.5 | 82.7 | 5.51 Other | | 135.2 | | | 0.31 Nlocal: 1137.62 ave 1162 max 1119 min Histogram: 1 1 1 0 2 1 1 0 0 1 Nghost: 11500.4 ave 11590 max 11417 min Histogram: 1 0 2 1 0 1 1 1 0 1 Neighs: 608474 ave 628293 max 595343 min Histogram: 3 0 0 2 0 1 0 1 0 1 Total # of neighbors = 4867790 Ave neighs/atom = 534.8632 Ave special neighs/atom = 1.8929788 Neighbor list builds = 104475 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) = 0.25882176 grid = 30 36 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0026318283 estimated relative force accuracy = 7.9256727e-06 using double precision KISS FFT 3d grid and FFT values/proc = 15950 6480 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.969991 2.94681e-05 8304 2 103.7 0.00334797 2768 Per MPI rank memory allocation (min/avg/max) = 16.02 | 16.16 | 16.25 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 2.7026946 97735.508 1.2421794 300.27411 50.524406 71.814348 0 0 21205.291 34566.773 -214.38764 -217190.9 -161296.5 5667.5205 Loop time of 3.811e-06 on 8 procs for 0 steps with 9101 atoms 121.4% CPU use with 8 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 | | 3.811e-06 | | |100.00 Nlocal: 1137.62 ave 1162 max 1119 min Histogram: 1 1 1 0 2 1 1 0 0 1 Nghost: 11500.4 ave 11590 max 11417 min Histogram: 1 0 2 1 0 1 1 1 0 1 Neighs: 608474 ave 628293 max 595343 min Histogram: 3 0 0 2 0 1 0 1 0 1 Total # of neighbors = 4867790 Ave neighs/atom = 534.8632 Ave special neighs/atom = 1.8929788 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out