#------------------------------------------------------------------------------- # Stage 2.4: NPT integration for 2 ns with a timestep of 1 fs # Temperature 298.2 K # Pressure 1 bar #------------------------------------------------------------------------------- # 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 2699 = # of frozen angles find clusters CPU = 0.001 seconds change_box all triclinic Changing box ... triclinic box = (0 0 0) to (45.402 32.1502 62.648044) 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 (45.402 32.1502 62.648044) with tilt (0 0 0) fix 1 movable npt temp 298.2 298.2 100 z 0.9869233 0.9869233 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 2.4_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 2.4_instantaneous.txt restart 2000000 2.4.restart dump sci all custom 200000 2.4.xyz id mol type q xs ys zs timestep 1 run 2000000 PPPM initialization ... WARNING: System is not charge neutral, net charge = 0.024 (../kspace.cpp:325) using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25869231 grid = 36 27 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0028157339 estimated relative force accuracy = 8.4794989e-06 using double precision KISS FFT 3d grid and FFT values/proc = 9000 3024 generated 0 of 28 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 = 7 5 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 0.99539 0.781566 8097 2 96.4565 47.4908 2699 Per MPI rank memory allocation (min/avg/max) = 13.73 | 14.13 | 14.34 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 18705.812 91446.309 1.3291045 427.22241 141.31641 221.96479 0 0 27811.123 35668.162 -226.3957 -218591.6 -154749.03 7943.8987 SHAKE stats (type/ave/delta/count) on step 50000 2 0.969997 9.17519e-06 8097 2 103.7 0.00101876 2699 SHAKE stats (type/ave/delta/count) on step 100000 2 0.969983 5.28527e-05 8097 2 103.7 0.00600029 2699 SHAKE stats (type/ave/delta/count) on step 150000 2 0.969964 0.000107769 8097 2 103.7 0.0122635 2699 SHAKE stats (type/ave/delta/count) on step 200000 2 0.969999 5.27111e-06 8097 2 103.7 0.000556992 2699 SHAKE stats (type/ave/delta/count) on step 250000 2 0.969998 7.3689e-06 8097 2 103.7 0.000773925 2699 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97005 0.000147858 8097 2 103.7 0.0169565 2699 SHAKE stats (type/ave/delta/count) on step 350000 2 0.96997 9.13017e-05 8097 2 103.7 0.010426 2699 SHAKE stats (type/ave/delta/count) on step 400000 2 0.970034 0.00010323 8097 2 103.7 0.0118187 2699 SHAKE stats (type/ave/delta/count) on step 450000 2 0.970019 5.73534e-05 8097 2 103.7 0.00649012 2699 SHAKE stats (type/ave/delta/count) on step 500000 2 0.970039 0.000116308 8097 2 103.7 0.0132517 2699 SHAKE stats (type/ave/delta/count) on step 550000 2 0.970004 1.16436e-05 8097 2 103.7 0.00129087 2699 SHAKE stats (type/ave/delta/count) on step 600000 2 0.970028 8.33056e-05 8097 2 103.7 0.00951098 2699 SHAKE stats (type/ave/delta/count) on step 650000 2 0.969988 3.76255e-05 8097 2 103.7 0.00424871 2699 SHAKE stats (type/ave/delta/count) on step 700000 2 0.970044 0.000131229 8097 2 103.7 0.0151004 2699 SHAKE stats (type/ave/delta/count) on step 750000 2 0.969977 6.98057e-05 8097 2 103.7 0.00791158 2699 SHAKE stats (type/ave/delta/count) on step 800000 2 0.970092 0.00027499 8097 2 103.7 0.0315048 2699 SHAKE stats (type/ave/delta/count) on step 850000 2 0.970025 7.48882e-05 8097 2 103.7 0.00862777 2699 SHAKE stats (type/ave/delta/count) on step 900000 2 0.969948 0.000156426 8097 2 103.7 0.0179014 2699 SHAKE stats (type/ave/delta/count) on step 950000 2 0.969952 0.000144226 8097 2 103.7 0.0164525 2699 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.969933 0.000204816 8097 2 103.7 0.023403 2699 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.969999 4.34446e-06 8097 2 103.7 0.000441592 2699 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.96998 6.07629e-05 8097 2 103.7 0.00689001 2699 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.969932 0.000205088 8097 2 103.7 0.0234327 2699 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.970039 0.000117825 8097 2 103.7 0.0134158 2699 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.970078 0.000233276 8097 2 103.7 0.0267212 2699 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.970029 8.59235e-05 8097 2 103.7 0.00983456 2699 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.969956 0.000135921 8097 2 103.7 0.0155017 2699 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.969975 7.75032e-05 8097 2 103.7 0.0088721 2699 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.969992 2.58695e-05 8097 2 103.7 0.00289721 2699 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.970011 3.22953e-05 8097 2 103.7 0.00369196 2699 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97001 2.97812e-05 8097 2 103.7 0.00339095 2699 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.969958 0.000125527 8097 2 103.7 0.0142895 2699 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.969997 8.96345e-06 8097 2 103.7 0.000965639 2699 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.969984 4.96156e-05 8097 2 103.7 0.00564099 2699 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.969948 0.000158984 8097 2 103.7 0.0181439 2699 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.970005 1.47784e-05 8097 2 103.7 0.0016921 2699 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.970095 0.000284212 8097 2 103.7 0.032466 2699 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.969988 3.89068e-05 8097 2 103.7 0.00441308 2699 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.969947 0.000159314 8097 2 103.7 0.0182174 2699 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.970025 7.55465e-05 8097 2 103.7 0.00865303 2699 2000000 2000000 -284.31533 97112.971 1.2515496 295.96398 43.466844 82.376858 0 0 22827.574 21530.789 -213.18523 -220285.07 -175800.87 5503.2409 Loop time of 22334.1 on 16 procs for 2000000 steps with 8938 atoms Performance: 7.737 ns/day, 3.102 hours/ns, 89.549 timesteps/s 98.9% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13367 | 14533 | 15798 | 657.3 | 65.07 Bond | 3.0252 | 6.2959 | 8.9352 | 58.6 | 0.03 Kspace | 3140.2 | 4405.7 | 5574.4 |1194.7 | 19.73 Neigh | 1242.3 | 1243.4 | 1244.5 | 2.6 | 5.57 Comm | 448.45 | 452.86 | 457.5 | 14.1 | 2.03 Output | 0.012766 | 0.014377 | 0.015811 | 0.8 | 0.00 Modify | 1309.9 | 1572.4 | 1651.2 | 295.9 | 7.04 Other | | 120.5 | | | 0.54 Nlocal: 558.625 ave 580 max 540 min Histogram: 1 3 2 2 0 2 2 1 1 2 Nghost: 8609.44 ave 8660 max 8535 min Histogram: 1 1 0 3 1 1 2 3 0 4 Neighs: 295336 ave 308473 max 280469 min Histogram: 2 0 3 2 1 0 1 2 2 3 Total # of neighbors = 4725373 Ave neighs/atom = 528.68349 Ave special neighs/atom = 1.8722309 Neighbor list builds = 104934 Dangerous builds = 0 undump sci restart 0 dump sci all custom 2000000 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) = 0.25725581 grid = 36 27 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0030423457 estimated relative force accuracy = 9.1619338e-06 using double precision KISS FFT 3d grid and FFT values/proc = 9000 3024 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.970025 7.55465e-05 8097 2 103.7 0.00865303 2699 Per MPI rank memory allocation (min/avg/max) = 14.08 | 14.29 | 14.36 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 -141.17309 97112.971 1.2515496 295.96398 43.466844 82.376858 0 0 22827.574 20318.368 -213.18523 -219072.67 -175800.88 5503.2409 Loop time of 3.66163e-06 on 16 procs for 0 steps with 8938 atoms 131.4% CPU use with 16 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 | | 3.662e-06 | | |100.00 Nlocal: 558.625 ave 580 max 540 min Histogram: 1 3 2 2 0 2 2 1 1 2 Nghost: 8609.44 ave 8660 max 8535 min Histogram: 1 1 0 3 1 1 2 3 0 4 Neighs: 295336 ave 308473 max 280469 min Histogram: 2 0 3 2 1 0 1 2 2 3 Total # of neighbors = 4725373 Ave neighs/atom = 528.68349 Ave special neighs/atom = 1.8722309 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out