#------------------------------------------------------------------------------- # Stage 2.3: 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 2768 = # of frozen angles find clusters CPU = 0.001 seconds reset_timestep 0 thermo_style custom step v_time press vol v_sysdensity temp ebond eangle edihed eimp evdwl ecoul etail elong pe ke WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:888) thermo ${Nthermo} thermo 0 fix 1 movable npt temp 298.2 298.2 100 iso 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 2.3_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 2.3_instantaneous.txt restart 2000000 2.3.restart dump sci all custom 200000 2.3.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) = 0.32360719 grid = 40 40 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0032437318 estimated relative force accuracy = 9.768402e-06 using double precision KISS FFT 3d grid and FFT values/proc = 10557 3200 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 = 11.5 ghost atom cutoff = 11.5 binsize = 5.75, bins = 7 7 14 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 stencil: half/bin/3d bin: standard SHAKE stats (type/ave/delta/count) on step 0 2 1.00023 0.089284 8304 2 97.8686 12.7643 2768 Per MPI rank memory allocation (min/avg/max) = 11.43 | 12.63 | 13.3 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 4921.8774 120592.96 1.006734 428.55654 9.26327 70.922677 0 0 25104.328 78085.118 -345.28628 -268937.77 -165668.14 8088.7858 SHAKE stats (type/ave/delta/count) on step 50000 2 0.969939 1.18709e-06 8304 2 103.7 9.30487e-05 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.969947 1.26621e-06 8304 2 103.7 0.00010032 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.970081 1.06748e-06 8304 2 103.7 8.96698e-05 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.969928 1.24623e-06 8304 2 103.7 9.79151e-05 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.969886 1.34019e-06 8304 2 103.7 0.000118351 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.969988 1.25503e-06 8304 2 103.7 9.85905e-05 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.970057 1.13506e-06 8304 2 103.7 9.21704e-05 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.970116 1.56789e-06 8304 2 103.7 0.000118283 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.970026 1.50864e-06 8304 2 103.7 0.000111395 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.970029 1.10385e-06 8304 2 103.7 0.00010043 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.969906 1.3783e-06 8304 2 103.7 0.000127732 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.96997 1.16561e-06 8304 2 103.7 0.000105112 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.970021 1.23513e-06 8304 2 103.7 8.86036e-05 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.970073 1.47005e-06 8304 2 103.7 9.60858e-05 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.969948 1.27277e-06 8304 2 103.7 9.49344e-05 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.970073 2.03398e-06 8304 2 103.7 0.000109228 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.970012 1.16173e-06 8304 2 103.7 9.7245e-05 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.969956 1.24985e-06 8304 2 103.7 9.16203e-05 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.969923 1.45186e-06 8304 2 103.7 0.00012404 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.970122 2.12873e-06 8304 2 103.7 0.000160316 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.969913 1.37466e-06 8304 2 103.7 0.000106359 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.969974 1.23366e-06 8304 2 103.7 9.22237e-05 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.970071 1.38218e-06 8304 2 103.7 0.000103849 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.969947 1.3311e-06 8304 2 103.7 0.000111757 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.970075 1.24086e-06 8304 2 103.7 9.5407e-05 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.970032 1.95937e-06 8304 2 103.7 0.000137104 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.14709e-06 8304 2 103.7 0.000102348 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.969998 1.25281e-06 8304 2 103.7 9.19549e-05 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.96997 1.16297e-06 8304 2 103.7 0.000113246 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.969937 1.32557e-06 8304 2 103.7 0.000113685 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.970021 1.12549e-06 8304 2 103.7 9.73708e-05 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.969907 1.28871e-06 8304 2 103.7 0.000109772 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.969992 1.13783e-06 8304 2 103.7 9.36604e-05 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.970036 1.47082e-06 8304 2 103.7 0.000110986 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.970007 1.03494e-06 8304 2 103.7 9.61367e-05 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.969963 1.45246e-06 8304 2 103.7 0.000153098 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.970036 1.28377e-06 8304 2 103.7 0.000115328 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.969977 1.20029e-06 8304 2 103.7 0.000100274 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.969944 1.37768e-06 8304 2 103.7 9.55551e-05 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.969995 1.10113e-06 8304 2 103.7 9.53677e-05 2768 2000000 2000000 -251.88794 97415.051 1.2462657 296.81502 46.361176 58.899149 0 0 21197.624 87817.681 -427.44005 -270661.9 -161541.33 5602.232 Loop time of 12187.2 on 32 procs for 2000000 steps with 9101 atoms Performance: 14.179 ns/day, 1.693 hours/ns, 164.106 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 | 4186.8 | 4482.4 | 4772.7 | 208.8 | 36.78 Bond | 2.3702 | 5.8428 | 11.232 | 84.2 | 0.05 Kspace | 4388.5 | 4680.3 | 4974.4 | 205.1 | 38.40 Neigh | 285.42 | 286.04 | 286.44 | 1.3 | 2.35 Comm | 721.89 | 731.58 | 737.95 | 14.6 | 6.00 Output | 0.011185 | 0.013451 | 0.015611 | 1.2 | 0.00 Modify | 1817.2 | 1894.4 | 1914.3 | 34.5 | 15.54 Other | | 106.7 | | | 0.88 Nlocal: 284.406 ave 303 max 268 min Histogram: 4 4 3 1 7 1 3 2 4 3 Nghost: 4809.44 ave 4885 max 4736 min Histogram: 2 1 1 4 9 7 5 1 1 1 Neighs: 84520.3 ave 92925 max 76577 min Histogram: 3 2 3 7 2 3 4 2 3 3 Total # of neighbors = 2704649 Ave neighs/atom = 297.18152 Ave special neighs/atom = 1.8929788 Neighbor list builds = 102812 Dangerous builds = 0 undump sci restart 0 dump sci all custom 2000000 2.3.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) = 0.32678321 grid = 40 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0029937681 estimated relative force accuracy = 9.0156437e-06 using double precision KISS FFT 3d grid and FFT values/proc = 10098 3200 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.969995 1.10113e-06 8304 2 103.7 9.53677e-05 2768 Per MPI rank memory allocation (min/avg/max) = 12.61 | 13.09 | 13.28 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 -283.1043 97415.051 1.2462657 296.81502 46.361176 58.899149 0 0 21197.624 90417.616 -427.44005 -273261.74 -161541.24 5602.232 Loop time of 7.51953e-06 on 32 procs for 0 steps with 9101 atoms 117.2% 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 | | 7.52e-06 | | |100.00 Nlocal: 284.406 ave 303 max 268 min Histogram: 4 4 3 1 7 1 3 2 4 3 Nghost: 4809.44 ave 4885 max 4736 min Histogram: 2 1 1 4 9 7 5 1 1 1 Neighs: 84520.3 ave 92925 max 76577 min Histogram: 3 2 3 7 2 3 4 2 3 3 Total # of neighbors = 2704649 Ave neighs/atom = 297.18152 Ave special neighs/atom = 1.8929788 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.4_NVT.out