#------------------------------------------------------------------------------- # 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 2009 = # of frozen angles find clusters CPU = 0.001 seconds change_box all triclinic Changing box ... triclinic box = (0 0 0) to (40.632406 40.632406 40.632406) 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 (40.632406 40.632406 40.632406) 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 = 0.0108 (../kspace.cpp:325) using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25531659 grid = 30 30 30 stencil order = 5 estimated absolute RMS force accuracy = 0.0033458596 estimated relative force accuracy = 1.0075957e-05 using double precision KISS FFT 3d grid and FFT values/proc = 4312 960 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 = 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 1.11577e-12 6027 2 103.7 7.90976e-11 2009 Per MPI rank memory allocation (min/avg/max) = 12.69 | 12.82 | 12.9 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 2352.8626 67083.794 1.2789064 302.94426 31.952035 46.68592 0 0 13960.292 32831.502 -157.46178 -147549.77 -100679.34 4111.4469 SHAKE stats (type/ave/delta/count) on step 50000 2 0.969958 0.000127769 6027 2 103.7 0.0145898 2009 SHAKE stats (type/ave/delta/count) on step 100000 2 0.969996 1.33452e-05 6027 2 103.7 0.0015054 2009 SHAKE stats (type/ave/delta/count) on step 150000 2 0.970019 5.63536e-05 6027 2 103.7 0.00644949 2009 SHAKE stats (type/ave/delta/count) on step 200000 2 0.969962 0.000115912 6027 2 103.7 0.0132524 2009 SHAKE stats (type/ave/delta/count) on step 250000 2 0.969975 7.5206e-05 6027 2 103.7 0.00856551 2009 SHAKE stats (type/ave/delta/count) on step 300000 2 0.969992 2.68826e-05 6027 2 103.7 0.00301046 2009 SHAKE stats (type/ave/delta/count) on step 350000 2 0.970004 1.1768e-05 6027 2 103.7 0.00133381 2009 SHAKE stats (type/ave/delta/count) on step 400000 2 0.970004 1.25888e-05 6027 2 103.7 0.00140857 2009 SHAKE stats (type/ave/delta/count) on step 450000 2 0.970014 4.26727e-05 6027 2 103.7 0.00485348 2009 SHAKE stats (type/ave/delta/count) on step 500000 2 0.970036 0.000106496 6027 2 103.7 0.0121282 2009 SHAKE stats (type/ave/delta/count) on step 550000 2 0.969987 4.04671e-05 6027 2 103.7 0.00458503 2009 SHAKE stats (type/ave/delta/count) on step 600000 2 0.969971 8.68581e-05 6027 2 103.7 0.00989711 2009 SHAKE stats (type/ave/delta/count) on step 650000 2 0.969969 9.46244e-05 6027 2 103.7 0.0108225 2009 SHAKE stats (type/ave/delta/count) on step 700000 2 0.969971 8.78331e-05 6027 2 103.7 0.010024 2009 SHAKE stats (type/ave/delta/count) on step 750000 2 0.970016 4.91622e-05 6027 2 103.7 0.00553811 2009 SHAKE stats (type/ave/delta/count) on step 800000 2 0.970013 4.07126e-05 6027 2 103.7 0.00461488 2009 SHAKE stats (type/ave/delta/count) on step 850000 2 0.970003 9.56254e-06 6027 2 103.7 0.00106803 2009 SHAKE stats (type/ave/delta/count) on step 900000 2 0.969976 7.35593e-05 6027 2 103.7 0.00842606 2009 SHAKE stats (type/ave/delta/count) on step 950000 2 0.970023 7.12934e-05 6027 2 103.7 0.00809318 2009 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.970001 2.5252e-06 6027 2 103.7 0.000280047 2009 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.970011 3.29532e-05 6027 2 103.7 0.00378078 2009 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.969981 5.83123e-05 6027 2 103.7 0.00660777 2009 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.970001 2.51907e-06 6027 2 103.7 0.000248302 2009 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.970057 0.000167486 6027 2 103.7 0.0191544 2009 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.969999 4.51019e-06 6027 2 103.7 0.000446188 2009 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.969976 7.27467e-05 6027 2 103.7 0.00827379 2009 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.970074 0.00022356 6027 2 103.7 0.0256134 2009 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.970013 3.99227e-05 6027 2 103.7 0.00459004 2009 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.96993 0.00020832 6027 2 103.7 0.0238809 2009 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.970001 3.99184e-06 6027 2 103.7 0.000449923 2009 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.969947 0.000161403 6027 2 103.7 0.0184111 2009 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.970023 7.06337e-05 6027 2 103.7 0.00799783 2009 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.970081 0.000241947 6027 2 103.7 0.0277847 2009 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.970001 3.08735e-06 6027 2 103.7 0.000301919 2009 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 2.83849e-06 6027 2 103.7 0.000290316 2009 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.970056 0.000169988 6027 2 103.7 0.0193774 2009 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.969986 4.37704e-05 6027 2 103.7 0.00493147 2009 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.970003 1.0387e-05 6027 2 103.7 0.00119725 2009 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.969955 0.000133525 6027 2 103.7 0.0152782 2009 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.969898 0.000303109 6027 2 103.7 0.0346946 2009 2000000 2000000 215.90074 69913.428 1.2271447 290.06952 41.87465 53.639431 0 0 13320.377 33632.524 -151.08877 -147540.57 -100492.15 3936.7157 Loop time of 11426.3 on 32 procs for 2000000 steps with 6563 atoms Performance: 15.123 ns/day, 1.587 hours/ns, 175.035 timesteps/s 99.4% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6180.8 | 6472.5 | 6731 | 183.5 | 56.65 Bond | 2.1761 | 4.3552 | 8.7714 | 88.3 | 0.04 Kspace | 2007.2 | 2269.7 | 2564.2 | 310.4 | 19.86 Neigh | 502.32 | 503.17 | 504.04 | 2.5 | 4.40 Comm | 853.46 | 865.03 | 875.69 | 18.8 | 7.57 Output | 0.0077008 | 0.0095658 | 0.011367 | 1.1 | 0.00 Modify | 1113.4 | 1199 | 1247.5 | 117.9 | 10.49 Other | | 112.5 | | | 0.98 Nlocal: 205.094 ave 218 max 182 min Histogram: 1 1 1 1 3 3 8 5 7 2 Nghost: 6448.56 ave 6491 max 6417 min Histogram: 4 3 3 4 3 8 4 1 1 1 Neighs: 110579 ave 118669 max 98684 min Histogram: 1 2 1 3 1 5 8 4 5 2 Total # of neighbors = 3538528 Ave neighs/atom = 539.16319 Ave special neighs/atom = 1.9037026 Neighbor list builds = 101394 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) = 0.25569654 grid = 30 30 32 stencil order = 5 estimated absolute RMS force accuracy = 0.0031864402 estimated relative force accuracy = 9.5958699e-06 using double precision KISS FFT 3d grid and FFT values/proc = 4620 960 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.969898 0.000303109 6027 2 103.7 0.0346946 2009 Per MPI rank memory allocation (min/avg/max) = 12.7 | 12.85 | 12.91 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 -386.08942 69913.428 1.2271447 290.06952 41.87465 53.639431 0 0 13320.377 33850.501 -151.08877 -147758.58 -100492.19 3936.7157 Loop time of 8.66106e-06 on 32 procs for 0 steps with 6563 atoms 116.2% 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 | | 8.661e-06 | | |100.00 Nlocal: 205.094 ave 218 max 182 min Histogram: 1 1 1 1 3 3 8 5 7 2 Nghost: 6448.56 ave 6491 max 6417 min Histogram: 4 3 3 4 3 8 4 1 1 1 Neighs: 110579 ave 118669 max 98684 min Histogram: 1 2 1 3 1 5 8 4 5 2 Total # of neighbors = 3538528 Ave neighs/atom = 539.16319 Ave special neighs/atom = 1.9037026 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 6:14:54