#------------------------------------------------------------------------------- # Stage 2.4: NPT integration for 3 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 3472 = # of frozen angles find clusters CPU = 0.002 seconds change_box all triclinic Changing box ... triclinic box = (0 0 0) to (38.8222 33.9556 117.8) 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 (38.8222 33.9556 117.8) with tilt (0 0 0) fix 1 movable npt temp 298.2 298.2 100 z 1 1 100 drag 0 mtk yes nreset 60000 fix 2 movable ave/time 1 299999 300000 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 300 1 300 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 3000000 2.4.restart dump sci all custom 300000 2.4.xyz id mol type q xs ys zs timestep 1 run 3000000 PPPM initialization ... WARNING: System is not charge neutral, net charge = 0.0462 (../kspace.cpp:325) using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25970624 grid = 36 30 75 stencil order = 5 estimated absolute RMS force accuracy = 0.0030110952 estimated relative force accuracy = 9.0678237e-06 using double precision KISS FFT 3d grid and FFT values/proc = 8800 3240 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 5 17 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 1.00174 0.115103 10416 2 97.5139 12.033 3472 Per MPI rank memory allocation (min/avg/max) = 13.21 | 13.52 | 13.77 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 -2415.2987 155287.62 1.4510247 403.97752 117.86904 584.76902 0 0 42224.026 -53677.768 -419.51504 -404764.65 -415515.75 11786.516 SHAKE stats (type/ave/delta/count) on step 50000 2 0.969967 9.52509e-05 10416 2 103.7 0.0108626 3472 SHAKE stats (type/ave/delta/count) on step 100000 2 0.969923 0.000224137 10416 2 103.699 0.0256324 3472 SHAKE stats (type/ave/delta/count) on step 150000 2 0.969949 0.000148936 10416 2 103.7 0.0169681 3472 SHAKE stats (type/ave/delta/count) on step 200000 2 0.970017 4.94984e-05 10416 2 103.7 0.00568454 3472 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97005 0.000145526 10416 2 103.7 0.0166429 3472 SHAKE stats (type/ave/delta/count) on step 300000 2 0.970055 0.000160395 10416 2 103.7 0.0184022 3472 SHAKE stats (type/ave/delta/count) on step 350000 2 0.970027 7.67283e-05 10416 2 103.7 0.00880623 3472 SHAKE stats (type/ave/delta/count) on step 400000 2 0.970022 6.47771e-05 10416 2 103.7 0.00740685 3472 SHAKE stats (type/ave/delta/count) on step 450000 2 0.970028 8.13751e-05 10416 2 103.7 0.00928379 3472 SHAKE stats (type/ave/delta/count) on step 500000 2 0.969959 0.000118988 10416 2 103.7 0.01357 3472 SHAKE stats (type/ave/delta/count) on step 550000 2 0.970031 9.02538e-05 10416 2 103.7 0.0103538 3472 SHAKE stats (type/ave/delta/count) on step 600000 2 0.970026 7.39054e-05 10416 2 103.7 0.00844044 3472 SHAKE stats (type/ave/delta/count) on step 650000 2 0.970033 9.65287e-05 10416 2 103.7 0.0109966 3472 SHAKE stats (type/ave/delta/count) on step 700000 2 0.969978 6.39073e-05 10416 2 103.7 0.00730378 3472 SHAKE stats (type/ave/delta/count) on step 750000 2 0.970008 2.28813e-05 10416 2 103.7 0.00257723 3472 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97003 8.69562e-05 10416 2 103.7 0.00991405 3472 SHAKE stats (type/ave/delta/count) on step 850000 2 0.969993 2.13321e-05 10416 2 103.7 0.00237662 3472 SHAKE stats (type/ave/delta/count) on step 900000 2 0.969999 3.62127e-06 10416 2 103.7 0.000360191 3472 SHAKE stats (type/ave/delta/count) on step 950000 2 0.970005 1.47535e-05 10416 2 103.7 0.00162683 3472 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.96997 8.80479e-05 10416 2 103.7 0.00999898 3472 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.969997 9.74478e-06 10416 2 103.7 0.00105044 3472 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.969988 3.64006e-05 10416 2 103.7 0.00412888 3472 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.969934 0.000193232 10416 2 103.7 0.0221107 3472 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.970018 5.29332e-05 10416 2 103.7 0.00606797 3472 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.970027 7.676e-05 10416 2 103.7 0.00883035 3472 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.969975 7.16645e-05 10416 2 103.7 0.00816113 3472 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.969952 0.000140036 10416 2 103.7 0.0159385 3472 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97004 0.00011567 10416 2 103.7 0.0132454 3472 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.969983 5.11694e-05 10416 2 103.7 0.00580507 3472 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.970035 0.000102107 10416 2 103.7 0.0116177 3472 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.969982 5.42135e-05 10416 2 103.7 0.00617293 3472 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.969968 9.28198e-05 10416 2 103.7 0.0105363 3472 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.969999 4.42709e-06 10416 2 103.7 0.000455873 3472 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.970013 3.62839e-05 10416 2 103.7 0.00414876 3472 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.969988 3.48573e-05 10416 2 103.7 0.00396889 3472 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97005 0.000143505 10416 2 103.7 0.0164611 3472 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.970038 0.000107511 10416 2 103.7 0.0123523 3472 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.969972 8.26721e-05 10416 2 103.7 0.00939137 3472 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.969995 1.56995e-05 10416 2 103.7 0.00175287 3472 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.970012 3.40359e-05 10416 2 103.7 0.00386803 3472 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.969997 9.87982e-06 10416 2 103.7 0.0010904 3472 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.969995 1.54975e-05 10416 2 103.7 0.00169989 3472 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.969974 7.47173e-05 10416 2 103.7 0.00846708 3472 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.969999 3.36935e-06 10416 2 103.7 0.000328008 3472 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97001 2.97419e-05 10416 2 103.7 0.00339476 3472 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97001 2.87025e-05 10416 2 103.7 0.00323445 3472 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.970017 5.0102e-05 10416 2 103.7 0.00570977 3472 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.96997 8.55173e-05 10416 2 103.7 0.00971178 3472 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.96998 5.71383e-05 10416 2 103.7 0.00651214 3472 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.970037 0.000105052 10416 2 103.7 0.0119701 3472 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.969965 0.000100667 10416 2 103.7 0.0114535 3472 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.969993 1.98654e-05 10416 2 103.7 0.00225718 3472 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.970036 0.000103241 10416 2 103.7 0.0118225 3472 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.970046 0.000130183 10416 2 103.7 0.0148862 3472 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.969991 2.69712e-05 10416 2 103.7 0.00303149 3472 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.969994 1.79123e-05 10416 2 103.7 0.00200969 3472 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.969999 5.68809e-06 10416 2 103.7 0.000585774 3472 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.96997 8.71895e-05 10416 2 103.7 0.00995324 3472 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.970025 7.34197e-05 10416 2 103.7 0.00838318 3472 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.970019 5.65352e-05 10416 2 103.7 0.00641269 3472 3000000 3000000 -385.87337 148206.07 1.5203572 295.23424 431.35722 616.44291 0 0 39690.566 -34418.929 -439.56021 -404656.82 -398337.38 8613.8039 Loop time of 34751.1 on 32 procs for 3000000 steps with 13261 atoms Performance: 7.459 ns/day, 3.218 hours/ns, 86.328 timesteps/s 98.5% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14526 | 18527 | 20880 |1566.5 | 53.31 Bond | 5.5286 | 28.454 | 65.288 | 444.0 | 0.08 Kspace | 6826.5 | 9177.5 | 13163 |2208.6 | 26.41 Neigh | 1733 | 1736.4 | 1740.3 | 5.1 | 5.00 Comm | 1238.9 | 1340.4 | 1396.5 | 119.2 | 3.86 Output | 0.015406 | 0.018307 | 0.021069 | 1.3 | 0.00 Modify | 2967.3 | 3266.2 | 3708.9 | 436.2 | 9.40 Other | | 675.6 | | | 1.94 Nlocal: 414.406 ave 459 max 353 min Histogram: 4 0 0 1 6 4 3 9 4 1 Nghost: 7631.19 ave 7982 max 7113 min Histogram: 4 2 6 0 0 0 3 5 2 10 Neighs: 213742 ave 247702 max 167129 min Histogram: 4 0 4 0 3 2 5 7 4 3 Total # of neighbors = 6839739 Ave neighs/atom = 515.77852 Ave special neighs/atom = 2.0037705 Neighbor list builds = 160879 Dangerous builds = 0 undump sci restart 0 dump sci all custom 3000000 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) = 0.25978169 grid = 36 30 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0030652478 estimated relative force accuracy = 9.2309027e-06 using double precision KISS FFT 3d grid and FFT values/proc = 8800 3240 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 2 0.970019 5.65352e-05 10416 2 103.7 0.00641269 3472 Per MPI rank memory allocation (min/avg/max) = 13.35 | 13.65 | 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 3000000 3000000 -291.0403 148206.07 1.5203572 295.23424 431.35722 616.44291 0 0 39690.566 -34302.334 -439.56021 -404773.7 -398337.67 8613.8039 Loop time of 1.36505e-05 on 32 procs for 0 steps with 13261 atoms 110.8% 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 | | 1.365e-05 | | |100.00 Nlocal: 414.406 ave 459 max 353 min Histogram: 4 0 0 1 6 4 3 9 4 1 Nghost: 7631.19 ave 7982 max 7113 min Histogram: 4 2 6 0 0 0 3 5 2 10 Neighs: 213742 ave 247702 max 167129 min Histogram: 4 0 4 0 3 2 5 7 4 3 Total # of neighbors = 6839739 Ave neighs/atom = 515.77852 Ave special neighs/atom = 2.0037705 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out