#------------------------------------------------------------------------------- # 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 2768 = # of frozen angles find clusters CPU = 0.001 seconds change_box all triclinic Changing box ... triclinic box = (0 0 0) to (38.8222 38.056131 64.7) with tilt (-3.810247 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 38.056131 64.7) with tilt (-3.810247 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 = 0.0206 (../kspace.cpp:325) using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25784211 grid = 30 32 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0028657894 estimated relative force accuracy = 8.6302397e-06 using double precision KISS FFT 3d grid and FFT values/proc = 5796 1920 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 1.00797e-12 8304 2 103.7 7.5886e-11 2768 Per MPI rank memory allocation (min/avg/max) = 12.92 | 13.09 | 13.19 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-06 789.84905 95589.251 1.27007 298.92 44.39004 59.101249 0 0 21654.592 32956.124 -219.20126 -216373.41 -161659.2 5641.9623 SHAKE stats (type/ave/delta/count) on step 50000 2 0.969963 0.000111307 8304 2 103.7 0.0126944 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.970002 7.09709e-06 8304 2 103.7 0.000792259 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.970019 5.87269e-05 8304 2 103.7 0.00666044 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.970018 5.43661e-05 8304 2 103.7 0.00624072 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.970061 0.000186094 8304 2 103.7 0.0213011 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97001 2.90436e-05 8304 2 103.7 0.00327924 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.969985 4.526e-05 8304 2 103.7 0.00512927 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.970026 7.81243e-05 8304 2 103.7 0.00893716 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.970014 4.2659e-05 8304 2 103.7 0.00487451 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.970025 7.51318e-05 8304 2 103.7 0.00859785 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.970025 7.3534e-05 8304 2 103.7 0.00844703 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.969984 4.91528e-05 8304 2 103.7 0.00556982 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.970004 1.12061e-05 8304 2 103.7 0.00125211 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.970046 0.000138918 8304 2 103.7 0.0158313 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.970008 2.32139e-05 8304 2 103.7 0.00262425 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.970036 0.000109457 8304 2 103.7 0.0124541 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.970016 4.85261e-05 8304 2 103.7 0.00549285 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.970006 1.78992e-05 8304 2 103.7 0.00196929 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.970029 8.81727e-05 8304 2 103.7 0.0101155 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.970071 0.000212778 8304 2 103.7 0.0244176 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97001 2.98652e-05 8304 2 103.7 0.00346806 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.970003 1.0213e-05 8304 2 103.7 0.00114447 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.969995 1.58522e-05 8304 2 103.7 0.00176343 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.969985 4.54804e-05 8304 2 103.7 0.00514056 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.970003 9.25907e-06 8304 2 103.7 0.00104591 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.970003 1.09585e-05 8304 2 103.7 0.00120338 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97002 6.02123e-05 8304 2 103.7 0.00691955 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.970004 1.14488e-05 8304 2 103.7 0.00127994 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.969953 0.000142962 8304 2 103.7 0.0163229 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.969968 9.75539e-05 8304 2 103.7 0.0110974 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.96997 9.31804e-05 8304 2 103.7 0.0106179 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.969914 0.000258273 8304 2 103.7 0.0295702 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.969975 7.62993e-05 8304 2 103.7 0.00866751 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97002 6.05442e-05 8304 2 103.7 0.00682265 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.969999 3.89616e-06 8304 2 103.7 0.000398054 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.969996 1.21716e-05 8304 2 103.7 0.00132134 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.970086 0.00026006 8304 2 103.7 0.0297226 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.969972 8.50968e-05 8304 2 103.7 0.00974469 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.969966 0.000102972 8304 2 103.7 0.0117486 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.970001 3.09828e-06 8304 2 103.7 0.000349933 2768 2000000 2000000 248.46294 97557.355 1.2444478 302.60382 37.72312 73.604544 0 0 21514.839 33283.423 -214.77914 -216377.82 -161468.23 5711.4926 Loop time of 16124 on 32 procs for 2000000 steps with 9101 atoms Performance: 10.717 ns/day, 2.239 hours/ns, 124.038 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 | 8246.7 | 8948.2 | 9434.1 | 224.3 | 55.50 Bond | 2.4482 | 5.8242 | 9.449 | 75.2 | 0.04 Kspace | 2989.3 | 3475.8 | 4175.6 | 359.0 | 21.56 Neigh | 695.75 | 696.9 | 697.96 | 3.0 | 4.32 Comm | 1026 | 1037.6 | 1046.2 | 16.4 | 6.44 Output | 0.0095838 | 0.011845 | 0.013962 | 1.2 | 0.00 Modify | 1479.4 | 1656.9 | 1889.4 | 401.9 | 10.28 Other | | 302.9 | | | 1.88 Nlocal: 284.406 ave 303 max 265 min Histogram: 1 1 4 5 6 3 7 1 2 2 Nghost: 7114.16 ave 7169 max 7069 min Histogram: 3 2 4 3 6 6 4 2 0 2 Neighs: 152326 ave 163637 max 142003 min Histogram: 2 3 4 6 2 3 7 2 1 2 Total # of neighbors = 4874421 Ave neighs/atom = 535.5918 Ave special neighs/atom = 1.8929788 Neighbor list builds = 105129 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) = 0.25733368 grid = 30 32 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0029465841 estimated relative force accuracy = 8.8735506e-06 using double precision KISS FFT 3d grid and FFT values/proc = 5796 1920 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.970001 3.09828e-06 8304 2 103.7 0.000349933 2768 Per MPI rank memory allocation (min/avg/max) = 12.92 | 13.13 | 13.19 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 253.95834 97557.355 1.2444478 302.60382 37.72312 73.604544 0 0 21514.839 32860.332 -214.77914 -215954.72 -161468.22 5711.4926 Loop time of 7.68653e-06 on 32 procs for 0 steps with 9101 atoms 112.2% 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 | | 7.687e-06 | | |100.00 Nlocal: 284.406 ave 303 max 265 min Histogram: 1 1 4 5 6 3 7 1 2 2 Nghost: 7114.16 ave 7169 max 7069 min Histogram: 3 2 4 3 6 6 4 2 0 2 Neighs: 152326 ave 163637 max 142003 min Histogram: 2 3 4 6 2 3 7 2 1 2 Total # of neighbors = 4874421 Ave neighs/atom = 535.5918 Ave special neighs/atom = 1.8929788 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 8:43:26