#------------------------------------------------------------------------------- # 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 1937 = # of frozen angles find clusters CPU = 0.001 seconds change_box all triclinic Changing box ... triclinic box = (0 0 0) to (29.25318 24.458 90.913478) 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 (29.25318 24.458 90.913478) 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 = 0.0144 (../kspace.cpp:325) using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25683534 grid = 24 24 54 stencil order = 5 estimated absolute RMS force accuracy = 0.003135149 estimated relative force accuracy = 9.4414082e-06 using double precision KISS FFT 3d grid and FFT values/proc = 4693 1152 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 4 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 2 0.97 9.51905e-13 5811 2 103.7 1.09594e-10 1937 Per MPI rank memory allocation (min/avg/max) = 12.73 | 12.88 | 12.96 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 2471.0163 65046.255 1.3074059 294.07734 33.060151 44.000732 0 0 15533.85 22002.118 -158.00458 -150947.98 -113334.96 3885.9177 SHAKE stats (type/ave/delta/count) on step 50000 2 0.969963 0.000111265 5811 2 103.7 0.012735 1937 SHAKE stats (type/ave/delta/count) on step 100000 2 0.969968 9.63393e-05 5811 2 103.7 0.0110031 1937 SHAKE stats (type/ave/delta/count) on step 150000 2 0.970009 2.60891e-05 5811 2 103.7 0.00294202 1937 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97006 0.000180268 5811 2 103.7 0.0206296 1937 SHAKE stats (type/ave/delta/count) on step 250000 2 0.969988 3.83619e-05 5811 2 103.7 0.00430764 1937 SHAKE stats (type/ave/delta/count) on step 300000 2 0.969961 0.00011698 5811 2 103.7 0.0133388 1937 SHAKE stats (type/ave/delta/count) on step 350000 2 0.970042 0.000128675 5811 2 103.7 0.0147512 1937 SHAKE stats (type/ave/delta/count) on step 400000 2 0.969981 5.83893e-05 5811 2 103.7 0.00664705 1937 SHAKE stats (type/ave/delta/count) on step 450000 2 0.969987 4.07238e-05 5811 2 103.7 0.00463257 1937 SHAKE stats (type/ave/delta/count) on step 500000 2 0.969956 0.000135298 5811 2 103.7 0.015453 1937 SHAKE stats (type/ave/delta/count) on step 550000 2 0.969995 1.78172e-05 5811 2 103.7 0.00200566 1937 SHAKE stats (type/ave/delta/count) on step 600000 2 0.970003 8.51207e-06 5811 2 103.7 0.000943419 1937 SHAKE stats (type/ave/delta/count) on step 650000 2 0.970011 3.3284e-05 5811 2 103.7 0.00380198 1937 SHAKE stats (type/ave/delta/count) on step 700000 2 0.969974 7.95918e-05 5811 2 103.7 0.00905692 1937 SHAKE stats (type/ave/delta/count) on step 750000 2 0.970073 0.000221061 5811 2 103.7 0.0252775 1937 SHAKE stats (type/ave/delta/count) on step 800000 2 0.969925 0.000229381 5811 2 103.7 0.0261922 1937 SHAKE stats (type/ave/delta/count) on step 850000 2 0.969983 5.37457e-05 5811 2 103.7 0.00610944 1937 SHAKE stats (type/ave/delta/count) on step 900000 2 0.96996 0.000120801 5811 2 103.7 0.0137849 1937 SHAKE stats (type/ave/delta/count) on step 950000 2 0.969952 0.000143438 5811 2 103.7 0.0163661 1937 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.970045 0.00013403 5811 2 103.7 0.0153484 1937 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.970009 2.82863e-05 5811 2 103.7 0.00322922 1937 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.969981 5.77553e-05 5811 2 103.7 0.00656541 1937 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.969982 5.60841e-05 5811 2 103.7 0.00639633 1937 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.969956 0.0001335 5811 2 103.7 0.0152245 1937 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.96997 9.10729e-05 5811 2 103.7 0.0104085 1937 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.969969 9.63908e-05 5811 2 103.7 0.0109457 1937 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97003 8.87701e-05 5811 2 103.7 0.0101514 1937 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.970027 8.14115e-05 5811 2 103.7 0.0093493 1937 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.970047 0.000139929 5811 2 103.7 0.016067 1937 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97002 5.87551e-05 5811 2 103.7 0.00674219 1937 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.969973 8.23332e-05 5811 2 103.7 0.00940634 1937 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.969995 1.62367e-05 5811 2 103.7 0.0018215 1937 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.970027 8.19665e-05 5811 2 103.7 0.00932308 1937 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.969976 7.24707e-05 5811 2 103.7 0.00823781 1937 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.96998 6.19161e-05 5811 2 103.7 0.00704655 1937 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.970009 2.87073e-05 5811 2 103.7 0.00325209 1937 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.969954 0.000138586 5811 2 103.7 0.0158732 1937 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.969957 0.000130413 5811 2 103.7 0.0148973 1937 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.970027 7.92304e-05 5811 2 103.7 0.00907109 1937 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.969986 4.19909e-05 5811 2 103.7 0.0047858 1937 2000000 2000000 97.664953 68518.602 1.2411499 290.66722 27.99733 44.134667 0 0 14902.454 22890.607 -149.99731 -150937.1 -113071.91 3840.8566 Loop time of 11765.9 on 32 procs for 2000000 steps with 6371 atoms Performance: 14.687 ns/day, 1.634 hours/ns, 169.983 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 | 6002.8 | 6272 | 6580.1 | 200.7 | 53.31 Bond | 2.2452 | 4.4984 | 8.4863 | 79.2 | 0.04 Kspace | 2321.4 | 2631.8 | 2904.1 | 312.7 | 22.37 Neigh | 514.71 | 515.75 | 516.55 | 2.5 | 4.38 Comm | 837.11 | 851.13 | 863.24 | 26.2 | 7.23 Output | 0.0068392 | 0.008681 | 0.010445 | 1.2 | 0.00 Modify | 1143.9 | 1307.1 | 1381.5 | 258.9 | 11.11 Other | | 183.6 | | | 1.56 Nlocal: 199.094 ave 216 max 183 min Histogram: 2 1 5 5 5 4 4 1 2 3 Nghost: 6163.31 ave 6342 max 6008 min Histogram: 5 2 5 2 5 1 3 4 2 3 Neighs: 106361 ave 116939 max 96633 min Histogram: 2 4 2 8 1 5 4 1 2 3 Total # of neighbors = 3403548 Ave neighs/atom = 534.22508 Ave special neighs/atom = 1.8932664 Neighbor list builds = 107022 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) = 0.2586204 grid = 24 24 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0026711911 estimated relative force accuracy = 8.0442127e-06 using double precision KISS FFT 3d grid and FFT values/proc = 5054 1152 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.969986 4.19909e-05 5811 2 103.7 0.0047858 1937 Per MPI rank memory allocation (min/avg/max) = 12.76 | 12.93 | 12.98 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 19.47526 68518.602 1.2411499 290.66722 27.99733 44.134667 0 0 14902.454 23931.006 -149.99731 -151977.76 -113072.17 3840.8566 Loop time of 1.15046e-05 on 32 procs for 0 steps with 6371 atoms 105.7% 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 | | 1.15e-05 | | |100.00 Nlocal: 199.094 ave 216 max 183 min Histogram: 2 1 5 5 5 4 4 1 2 3 Nghost: 6163.31 ave 6342 max 6008 min Histogram: 5 2 5 2 5 1 3 4 2 3 Neighs: 106361 ave 116939 max 96633 min Histogram: 2 4 2 8 1 5 4 1 2 3 Total # of neighbors = 3403548 Ave neighs/atom = 534.22508 Ave special neighs/atom = 1.8932664 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 6:26:32