#------------------------------------------------------------------------------- # 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 38.2464 62.539668) 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 38.2464 62.539668) 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 = 0.0206 (../kspace.cpp:325) using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.2567886 grid = 30 30 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0031460223 estimated relative force accuracy = 9.4741527e-06 using double precision KISS FFT 3d grid and FFT values/proc = 5544 1800 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 9 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 6.72573e-13 8304 2 103.7 8.74536e-11 2768 Per MPI rank memory allocation (min/avg/max) = 12.88 | 13.06 | 13.17 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 2927.7608 92859.486 1.3074058 302.14172 43.869149 71.409597 0 0 22399.092 31256.801 -225.64506 -215522.16 -161750.99 5702.7706 SHAKE stats (type/ave/delta/count) on step 50000 2 0.970011 3.2361e-05 8304 2 103.7 0.00367287 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.970078 0.000235345 8304 2 103.7 0.026978 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.969997 1.04459e-05 8304 2 103.7 0.00113918 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.969948 0.000158029 8304 2 103.7 0.0180872 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.969993 2.22293e-05 8304 2 103.7 0.00250181 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.969974 7.84258e-05 8304 2 103.7 0.00887025 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.970006 1.94575e-05 8304 2 103.7 0.00221573 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.969976 7.21609e-05 8304 2 103.7 0.00822848 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.970017 5.26418e-05 8304 2 103.7 0.00597691 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.969954 0.000140542 8304 2 103.7 0.0160046 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.970002 5.09983e-06 8304 2 103.7 0.000558811 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.969963 0.000110434 8304 2 103.7 0.0126177 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.969974 8.07803e-05 8304 2 103.7 0.00920456 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97001 3.03776e-05 8304 2 103.7 0.00347988 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.969973 8.00693e-05 8304 2 103.7 0.00914366 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.970059 0.000174146 8304 2 103.7 0.0199146 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.969996 1.29632e-05 8304 2 103.7 0.00145039 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.970012 3.62963e-05 8304 2 103.7 0.00412276 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.969997 1.03947e-05 8304 2 103.7 0.00113601 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.96998 6.12046e-05 8304 2 103.7 0.00693862 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.969999 4.27063e-06 8304 2 103.7 0.000432393 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.969957 0.000129864 8304 2 103.7 0.0148715 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.969943 0.000175269 8304 2 103.7 0.0199321 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.969963 0.000114006 8304 2 103.7 0.0130048 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.969939 0.000187578 8304 2 103.7 0.021416 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.970031 9.26367e-05 8304 2 103.7 0.0106573 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.970012 3.47202e-05 8304 2 103.7 0.00399527 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.970026 7.63222e-05 8304 2 103.7 0.0087279 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.970017 5.19265e-05 8304 2 103.7 0.00593913 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.969971 8.97059e-05 8304 2 103.7 0.0102407 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.969954 0.000140245 8304 2 103.7 0.016024 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.970001 3.25328e-06 8304 2 103.7 0.000341299 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.970004 1.12691e-05 8304 2 103.7 0.00124093 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.969975 7.6184e-05 8304 2 103.7 0.00864554 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.969962 0.000113888 8304 2 103.7 0.013033 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.969984 4.89232e-05 8304 2 103.7 0.005575 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97004 0.000118599 8304 2 103.7 0.0135965 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.969989 3.34751e-05 8304 2 103.7 0.00380434 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.970002 7.28924e-06 8304 2 103.7 0.000796227 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.969992 2.56652e-05 8304 2 103.7 0.00287217 2768 2000000 2000000 233.69741 97810.015 1.2412332 300.09616 42.670982 55.68871 0 0 21196.744 33060.01 -214.22433 -215517.31 -161162.2 5664.1618 Loop time of 15970.8 on 32 procs for 2000000 steps with 9101 atoms Performance: 10.820 ns/day, 2.218 hours/ns, 125.228 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 | 8514.3 | 8923.9 | 9503.9 | 212.7 | 55.88 Bond | 2.7895 | 5.6934 | 10.275 | 64.0 | 0.04 Kspace | 2879.5 | 3450.9 | 3853.7 | 336.2 | 21.61 Neigh | 723.41 | 724.01 | 724.55 | 1.1 | 4.53 Comm | 974.6 | 995.13 | 1014.3 | 39.3 | 6.23 Output | 0.0084866 | 0.010764 | 0.012873 | 1.3 | 0.00 Modify | 1434.2 | 1598.3 | 1791 | 377.3 | 10.01 Other | | 273 | | | 1.71 Nlocal: 284.406 ave 304 max 262 min Histogram: 2 2 1 8 2 3 3 5 3 3 Nghost: 7070.91 ave 7146 max 7031 min Histogram: 4 6 5 5 3 5 1 1 0 2 Neighs: 151937 ave 164705 max 139592 min Histogram: 1 4 2 6 3 3 7 3 1 2 Total # of neighbors = 4861994 Ave neighs/atom = 534.22635 Ave special neighs/atom = 1.8929788 Neighbor list builds = 105288 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) = 0.25585254 grid = 30 30 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0032853629 estimated relative force accuracy = 9.8937727e-06 using double precision KISS FFT 3d grid and FFT values/proc = 5544 1800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.969992 2.56652e-05 8304 2 103.7 0.00287217 2768 Per MPI rank memory allocation (min/avg/max) = 12.88 | 13.09 | 13.17 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 186.75404 97810.015 1.2412332 300.09616 42.670982 55.68871 0 0 21196.744 32280.565 -214.22433 -214737.87 -161162.2 5664.1618 Loop time of 1.25135e-05 on 32 procs for 0 steps with 9101 atoms 105.1% 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 | | 1.251e-05 | | |100.00 Nlocal: 284.406 ave 304 max 262 min Histogram: 2 2 1 8 2 3 3 5 3 3 Nghost: 7070.91 ave 7146 max 7031 min Histogram: 4 6 5 5 3 5 1 1 0 2 Neighs: 151937 ave 164705 max 139592 min Histogram: 1 4 2 6 3 3 7 3 1 2 Total # of neighbors = 4861994 Ave neighs/atom = 534.22635 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: 8:32:52