#------------------------------------------------------------------------------- # 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 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 3968 = # of frozen angles find clusters CPU = 0.002 seconds change_box all triclinic Changing box ... triclinic box = (0 0 0) to (33.78995 48.916 87) 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 87) 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 = 0.0406 (../kspace.cpp:325) using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25956456 grid = 30 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0028924598 estimated relative force accuracy = 8.7105569e-06 using double precision KISS FFT 3d grid and FFT values/proc = 8228 2400 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 13 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 1 1.00553 0.0906705 11904 2 97.7498 10.024 3968 Per MPI rank memory allocation (min/avg/max) = 13.21 | 13.69 | 14.16 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 -2846.0521 143799.62 1.371895 417.33588 56.026944 266.65552 0 0 42078.782 -3901.959 -383.45046 -379109.91 -340610.4 12355.398 SHAKE stats (type/ave/delta/count) on step 50000 1 0.969976 6.91613e-05 11904 2 103.7 0.00789433 3968 SHAKE stats (type/ave/delta/count) on step 100000 1 0.970003 1.0589e-05 11904 2 103.7 0.00117044 3968 SHAKE stats (type/ave/delta/count) on step 150000 1 0.969959 0.000120005 11904 2 103.699 0.0136805 3968 SHAKE stats (type/ave/delta/count) on step 200000 1 0.970043 0.000123343 11904 2 103.7 0.0141757 3968 SHAKE stats (type/ave/delta/count) on step 250000 1 0.969972 8.07125e-05 11904 2 103.7 0.00922082 3968 SHAKE stats (type/ave/delta/count) on step 300000 1 0.969982 5.35959e-05 11904 2 103.7 0.0060843 3968 SHAKE stats (type/ave/delta/count) on step 350000 1 0.969982 5.41731e-05 11904 2 103.7 0.00617804 3968 SHAKE stats (type/ave/delta/count) on step 400000 1 0.970007 1.9803e-05 11904 2 103.7 0.00223955 3968 SHAKE stats (type/ave/delta/count) on step 450000 1 0.969994 1.97294e-05 11904 2 103.7 0.00223046 3968 SHAKE stats (type/ave/delta/count) on step 500000 1 0.96997 8.78922e-05 11904 2 103.7 0.0100108 3968 SHAKE stats (type/ave/delta/count) on step 550000 1 0.969951 0.000144208 11904 2 103.699 0.0164534 3968 SHAKE stats (type/ave/delta/count) on step 600000 1 0.970003 8.85686e-06 11904 2 103.7 0.00097952 3968 SHAKE stats (type/ave/delta/count) on step 650000 1 0.969971 8.41399e-05 11904 2 103.7 0.00956691 3968 SHAKE stats (type/ave/delta/count) on step 700000 1 0.969975 7.25128e-05 11904 2 103.7 0.00828498 3968 SHAKE stats (type/ave/delta/count) on step 750000 1 0.970018 5.31627e-05 11904 2 103.7 0.00604959 3968 SHAKE stats (type/ave/delta/count) on step 800000 1 0.970029 8.24861e-05 11904 2 103.7 0.00945001 3968 SHAKE stats (type/ave/delta/count) on step 850000 1 0.970047 0.000133467 11904 2 103.7 0.0152996 3968 SHAKE stats (type/ave/delta/count) on step 900000 1 0.969993 2.1655e-05 11904 2 103.7 0.00239548 3968 SHAKE stats (type/ave/delta/count) on step 950000 1 0.969974 7.44703e-05 11904 2 103.7 0.0084813 3968 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.969981 5.49213e-05 11904 2 103.7 0.00623719 3968 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.969979 6.2661e-05 11904 2 103.7 0.00711775 3968 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.970004 1.23967e-05 11904 2 103.7 0.00140475 3968 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.970033 9.59808e-05 11904 2 103.7 0.0109612 3968 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.970004 1.09697e-05 11904 2 103.7 0.00124798 3968 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.970031 8.99119e-05 11904 2 103.7 0.0102637 3968 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.969995 1.71185e-05 11904 2 103.7 0.0019057 3968 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.970036 0.000102777 11904 2 103.7 0.0117852 3968 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.97003 8.51076e-05 11904 2 103.7 0.00977664 3968 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.969994 1.84546e-05 11904 2 103.7 0.00207583 3968 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.969994 1.93369e-05 11904 2 103.7 0.00218553 3968 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.969997 1.06865e-05 11904 2 103.7 0.00115169 3968 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.970043 0.000123686 11904 2 103.7 0.0141701 3968 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.96998 5.87375e-05 11904 2 103.7 0.00662477 3968 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.970014 3.95126e-05 11904 2 103.7 0.00454274 3968 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.970025 7.27102e-05 11904 2 103.7 0.00830672 3968 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.970008 2.31574e-05 11904 2 103.7 0.00263902 3968 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.970011 3.2344e-05 11904 2 103.7 0.00368446 3968 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.969996 1.33795e-05 11904 2 103.7 0.00150309 3968 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.970053 0.000151725 11904 2 103.701 0.0174152 3968 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.970037 0.00010658 11904 2 103.7 0.0122782 3968 2000000 2000000 91.971175 139007.36 1.4191909 293.90327 358.8647 437.51192 0 0 37666.959 21986.46 -396.66987 -378992.93 -318543.13 8701.1256 Loop time of 27642.5 on 32 procs for 2000000 steps with 13901 atoms Performance: 6.251 ns/day, 3.839 hours/ns, 72.352 timesteps/s 98.9% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12674 | 14377 | 18058 |1700.9 | 52.01 Bond | 4.36 | 16.916 | 42.11 | 332.2 | 0.06 Kspace | 4277.9 | 7992.1 | 9725 |2304.4 | 28.91 Neigh | 1454.6 | 1456.5 | 1458.9 | 3.2 | 5.27 Comm | 1148.1 | 1205.1 | 1272.5 | 121.4 | 4.36 Output | 0.015753 | 0.018737 | 0.021558 | 1.3 | 0.00 Modify | 1877.2 | 2333.3 | 2440.4 | 335.7 | 8.44 Other | | 261.7 | | | 0.95 Nlocal: 434.406 ave 511 max 392 min Histogram: 5 8 9 2 0 0 0 0 4 4 Nghost: 8392.16 ave 8767 max 7743 min Histogram: 6 2 0 0 0 0 5 9 2 8 Neighs: 251093 ave 329972 max 212198 min Histogram: 9 10 5 0 0 0 0 0 1 7 Total # of neighbors = 8034971 Ave neighs/atom = 578.01388 Ave special neighs/atom = 2.0450327 Neighbor list builds = 105756 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) = 0.2602929 grid = 30 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0027845515 estimated relative force accuracy = 8.3855941e-06 using double precision KISS FFT 3d grid and FFT values/proc = 8228 2400 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 1 0.970037 0.00010658 11904 2 103.7 0.0122782 3968 Per MPI rank memory allocation (min/avg/max) = 13.53 | 13.71 | 14.16 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 312.33031 139007.36 1.4191909 293.90327 358.8647 437.51192 0 0 37666.959 23041.768 -396.66987 -380048.2 -318543.1 8701.1256 Loop time of 1.20162e-05 on 32 procs for 0 steps with 13901 atoms 108.2% 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 | | 1.202e-05 | | |100.00 Nlocal: 434.406 ave 511 max 392 min Histogram: 5 8 9 2 0 0 0 0 4 4 Nghost: 8392.16 ave 8767 max 7743 min Histogram: 6 2 0 0 0 0 5 9 2 8 Neighs: 251093 ave 329972 max 212198 min Histogram: 9 10 5 0 0 0 0 0 1 7 Total # of neighbors = 8034971 Ave neighs/atom = 578.01388 Ave special neighs/atom = 2.0450327 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out