#------------------------------------------------------------------------------- # Stage 2.4: 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 2812 = # 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 122.6) 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 122.6) 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 2.4_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) = 0.25773468 grid = 30 30 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0028701851 estimated relative force accuracy = 8.6434772e-06 using double precision KISS FFT 3d grid and FFT values/proc = 7744 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 = 5 5 18 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 0.999835 0.0768151 8436 2 97.9127 10.4714 2812 Per MPI rank memory allocation (min/avg/max) = 12.53 | 13.29 | 13.78 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 -3679.7441 131377.34 1.3874487 407.74127 6.8704329 28.44581 0 0 31231.189 -32459.496 -292.5633 -270436.1 -271629.09 9303.8814 SHAKE stats (type/ave/delta/count) on step 50000 2 0.970015 4.425e-05 8436 2 103.7 0.00502544 2812 SHAKE stats (type/ave/delta/count) on step 100000 2 0.970032 9.56924e-05 8436 2 103.7 0.0109565 2812 SHAKE stats (type/ave/delta/count) on step 150000 2 0.969947 0.000159797 8436 2 103.7 0.0182714 2812 SHAKE stats (type/ave/delta/count) on step 200000 2 0.969946 0.000164901 8436 2 103.7 0.0188278 2812 SHAKE stats (type/ave/delta/count) on step 250000 2 0.969973 8.17719e-05 8436 2 103.7 0.00934559 2812 SHAKE stats (type/ave/delta/count) on step 300000 2 0.970029 8.70151e-05 8436 2 103.7 0.0099091 2812 SHAKE stats (type/ave/delta/count) on step 350000 2 0.969989 3.4164e-05 8436 2 103.7 0.00385146 2812 SHAKE stats (type/ave/delta/count) on step 400000 2 0.970007 2.22537e-05 8436 2 103.7 0.002518 2812 SHAKE stats (type/ave/delta/count) on step 450000 2 0.969993 2.1819e-05 8436 2 103.7 0.00244672 2812 SHAKE stats (type/ave/delta/count) on step 500000 2 0.970083 0.000250307 8436 2 103.7 0.0287227 2812 SHAKE stats (type/ave/delta/count) on step 550000 2 0.969951 0.00014904 8436 2 103.7 0.0170088 2812 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97002 5.96419e-05 8436 2 103.7 0.00684561 2812 SHAKE stats (type/ave/delta/count) on step 650000 2 0.970016 4.80432e-05 8436 2 103.7 0.00549521 2812 SHAKE stats (type/ave/delta/count) on step 700000 2 0.96996 0.000122179 8436 2 103.7 0.0140103 2812 SHAKE stats (type/ave/delta/count) on step 750000 2 0.969995 1.77534e-05 8436 2 103.7 0.0019764 2812 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97004 0.000121487 8436 2 103.7 0.0138788 2812 SHAKE stats (type/ave/delta/count) on step 850000 2 0.969905 0.000287442 8436 2 103.7 0.0329233 2812 SHAKE stats (type/ave/delta/count) on step 900000 2 0.969908 0.000274629 8436 2 103.7 0.0314374 2812 SHAKE stats (type/ave/delta/count) on step 950000 2 0.969996 1.22916e-05 8436 2 103.7 0.00136606 2812 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.970004 1.16113e-05 8436 2 103.7 0.00132271 2812 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.970026 7.796e-05 8436 2 103.7 0.0089254 2812 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.969948 0.000159872 8436 2 103.7 0.0183269 2812 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.970006 1.7893e-05 8436 2 103.7 0.002026 2812 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.969937 0.000188401 8436 2 103.7 0.0215565 2812 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.969995 1.5164e-05 8436 2 103.7 0.00169397 2812 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.969986 4.50008e-05 8436 2 103.7 0.00510627 2812 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.969995 1.67284e-05 8436 2 103.7 0.00184041 2812 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.970012 3.59634e-05 8436 2 103.7 0.00410925 2812 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.970008 2.53299e-05 8436 2 103.7 0.00290363 2812 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.970037 0.000109071 8436 2 103.7 0.0125054 2812 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.970031 9.54099e-05 8436 2 103.7 0.0108892 2812 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.969998 8.65342e-06 8436 2 103.7 0.000920982 2812 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.969948 0.000154089 8436 2 103.7 0.0175827 2812 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.970085 0.000255856 8436 2 103.7 0.0293435 2812 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.969996 1.41891e-05 8436 2 103.7 0.00155915 2812 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.970055 0.00016593 8436 2 103.7 0.0189864 2812 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.96999 3.20059e-05 8436 2 103.7 0.00360245 2812 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.969977 6.80558e-05 8436 2 103.7 0.00774 2812 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.970029 8.66898e-05 8436 2 103.7 0.00995315 2812 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97003 8.99757e-05 8436 2 103.7 0.0102805 2812 2000000 2000000 599.48336 129757.88 1.4047649 301.99284 49.885382 59.035166 0 0 29511.709 -16041.155 -296.21467 -270294.07 -256714.59 6890.9031 Loop time of 20488.2 on 32 procs for 2000000 steps with 10468 atoms Performance: 8.434 ns/day, 2.846 hours/ns, 97.617 timesteps/s 99.1% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2482.9 | 9488.1 | 12141 |3642.0 | 46.31 Bond | 2.3053 | 5.4102 | 10.609 | 100.3 | 0.03 Kspace | 4101.7 | 6775.8 | 13826 |4341.0 | 33.07 Neigh | 1044.4 | 1047.4 | 1054.5 | 8.9 | 5.11 Comm | 679.95 | 954.57 | 1045 | 417.9 | 4.66 Output | 0.012382 | 0.01486 | 0.017203 | 1.2 | 0.00 Modify | 1770.8 | 1917.4 | 2106.8 | 314.9 | 9.36 Other | | 299.5 | | | 1.46 Nlocal: 327.125 ave 397 max 163 min Histogram: 4 4 0 0 0 0 0 0 9 15 Nghost: 6460.78 ave 7605 max 4582 min Histogram: 8 0 0 0 4 4 0 0 0 16 Neighs: 160676 ave 213598 max 37657 min Histogram: 4 0 4 0 0 0 4 0 2 18 Total # of neighbors = 5141634 Ave neighs/atom = 491.17635 Ave special neighs/atom = 1.6709973 Neighbor list builds = 109808 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) = 0.25820427 grid = 30 30 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0027880928 estimated relative force accuracy = 8.3962586e-06 using double precision KISS FFT 3d grid and FFT values/proc = 7744 2700 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97003 8.99757e-05 8436 2 103.7 0.0102805 2812 Per MPI rank memory allocation (min/avg/max) = 12.54 | 13.36 | 13.78 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 732.08811 129757.88 1.4047649 301.99284 49.885382 59.035166 0 0 29511.709 -15551.818 -296.21467 -270783.43 -256714.62 6890.9031 Loop time of 6.53875e-06 on 32 procs for 0 steps with 10468 atoms 141.5% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 6.539e-06 | | |100.00 Nlocal: 327.125 ave 397 max 163 min Histogram: 4 4 0 0 0 0 0 0 9 15 Nghost: 6460.78 ave 7605 max 4582 min Histogram: 8 0 0 0 4 4 0 0 0 16 Neighs: 160676 ave 213598 max 37657 min Histogram: 4 0 4 0 0 0 4 0 2 18 Total # of neighbors = 5141634 Ave neighs/atom = 491.17635 Ave special neighs/atom = 1.6709973 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out