#------------------------------------------------------------------------------- # 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 = 0.001 seconds change_box all triclinic Changing box ... triclinic box = (0 0 0) to (38.8222 38.056131 104.8) 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 104.8) 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 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) = 0.2637439 grid = 36 36 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0022262231 estimated relative force accuracy = 6.7042048e-06 using double precision KISS FFT 3d grid and FFT values/proc = 10000 3888 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.999278 0.689605 10416 2 97.7152 16.5788 3472 Per MPI rank memory allocation (min/avg/max) = 13.4 | 13.69 | 13.9 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 -675.3933 154833.9 1.4552767 403.97752 157.02516 437.88925 0 0 41391.599 -42154.485 -420.74437 -410112.6 -410280.58 11786.516 SHAKE stats (type/ave/delta/count) on step 50000 2 0.970046 0.00013982 10416 2 103.699 0.0160518 3472 SHAKE stats (type/ave/delta/count) on step 100000 2 0.970003 8.55863e-06 10416 2 103.7 0.000956227 3472 SHAKE stats (type/ave/delta/count) on step 150000 2 0.970051 0.00015602 10416 2 103.699 0.0179578 3472 SHAKE stats (type/ave/delta/count) on step 200000 2 0.970013 3.88446e-05 10416 2 103.7 0.00443452 3472 SHAKE stats (type/ave/delta/count) on step 250000 2 0.969982 5.47612e-05 10416 2 103.7 0.00622026 3472 SHAKE stats (type/ave/delta/count) on step 300000 2 0.969996 1.23837e-05 10416 2 103.7 0.00136783 3472 SHAKE stats (type/ave/delta/count) on step 350000 2 0.96999 3.177e-05 10416 2 103.7 0.00361654 3472 SHAKE stats (type/ave/delta/count) on step 400000 2 0.969977 7.19713e-05 10416 2 103.7 0.00821058 3472 SHAKE stats (type/ave/delta/count) on step 450000 2 0.969982 5.80083e-05 10416 2 103.7 0.00655698 3472 SHAKE stats (type/ave/delta/count) on step 500000 2 0.970004 1.41221e-05 10416 2 103.7 0.00159048 3472 SHAKE stats (type/ave/delta/count) on step 550000 2 0.970032 9.93317e-05 10416 2 103.7 0.0112307 3472 SHAKE stats (type/ave/delta/count) on step 600000 2 0.969975 7.64571e-05 10416 2 103.7 0.00866187 3472 SHAKE stats (type/ave/delta/count) on step 650000 2 0.970022 6.72598e-05 10416 2 103.7 0.00769326 3472 SHAKE stats (type/ave/delta/count) on step 700000 2 0.969976 7.55117e-05 10416 2 103.7 0.00855507 3472 SHAKE stats (type/ave/delta/count) on step 750000 2 0.969996 1.26089e-05 10416 2 103.7 0.00139357 3472 SHAKE stats (type/ave/delta/count) on step 800000 2 0.970051 0.000156085 10416 2 103.7 0.0178766 3472 SHAKE stats (type/ave/delta/count) on step 850000 2 0.970001 3.25876e-06 10416 2 103.7 0.000331792 3472 SHAKE stats (type/ave/delta/count) on step 900000 2 0.970019 5.7021e-05 10416 2 103.7 0.00647606 3472 SHAKE stats (type/ave/delta/count) on step 950000 2 0.969983 5.30574e-05 10416 2 103.7 0.00598416 3472 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.969994 2.1121e-05 10416 2 103.7 0.00235708 3472 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.969959 0.000125042 10416 2 103.7 0.0142432 3472 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.970008 2.33379e-05 10416 2 103.7 0.00265484 3472 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.970017 5.09824e-05 10416 2 103.7 0.00584179 3472 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.96999 3.0749e-05 10416 2 103.7 0.00346606 3472 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.969963 0.000112268 10416 2 103.7 0.0127967 3472 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.96996 0.000124213 10416 2 103.7 0.0141638 3472 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.969986 4.24243e-05 10416 2 103.7 0.00482132 3472 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.970005 1.54615e-05 10416 2 103.7 0.00174533 3472 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.75397e-06 10416 2 103.7 0.000136041 3472 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.970021 6.33317e-05 10416 2 103.7 0.00726095 3472 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97002 6.20707e-05 10416 2 103.7 0.00710419 3472 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97009 0.000274419 10416 2 103.699 0.0314772 3472 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.96997 9.22707e-05 10416 2 103.7 0.0105042 3472 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.970015 4.47391e-05 10416 2 103.7 0.00514947 3472 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.969997 9.29247e-06 10416 2 103.7 0.00103515 3472 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.969987 4.20898e-05 10416 2 103.7 0.00477207 3472 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.969965 0.000107647 10416 2 103.7 0.0122562 3472 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.970006 1.90469e-05 10416 2 103.7 0.00218223 3472 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.970054 0.000163803 10416 2 103.7 0.0187431 3472 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.970022 6.60619e-05 10416 2 103.7 0.00756743 3472 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.970027 8.30418e-05 10416 2 103.7 0.00948018 3472 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.969987 4.04672e-05 10416 2 103.7 0.00459959 3472 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.970031 9.71008e-05 10416 2 103.7 0.011069 3472 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.969965 0.000108913 10416 2 103.7 0.0124348 3472 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.970052 0.000158755 10416 2 103.7 0.0182661 3472 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.969995 1.76135e-05 10416 2 103.7 0.0019974 3472 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.970014 4.16558e-05 10416 2 103.7 0.0047539 3472 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.969955 0.000139059 10416 2 103.7 0.0158727 3472 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.970044 0.000136403 10416 2 103.7 0.015607 3472 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.969988 3.80899e-05 10416 2 103.7 0.00433115 3472 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.970005 1.7095e-05 10416 2 103.7 0.001943 3472 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.970075 0.000229654 10416 2 103.7 0.026332 3472 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.969994 2.0652e-05 10416 2 103.7 0.00229458 3472 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97001 3.12186e-05 10416 2 103.7 0.00356192 3472 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.969997 9.71956e-06 10416 2 103.7 0.00104937 3472 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.96998 6.26961e-05 10416 2 103.7 0.00713494 3472 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.969981 5.98091e-05 10416 2 103.7 0.00678122 3472 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.970015 4.66129e-05 10416 2 103.7 0.00526225 3472 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97003 9.13319e-05 10416 2 103.7 0.010501 3472 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.970014 4.19522e-05 10416 2 103.7 0.00479049 3472 3000000 3000000 1862.4769 146737.03 1.5355781 295.70839 447.24654 569.57269 0 0 40502.064 -29516.706 -443.96083 -410900.46 -398898.29 8627.6379 Loop time of 36196.1 on 32 procs for 3000000 steps with 13261 atoms Performance: 7.161 ns/day, 3.351 hours/ns, 82.882 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 | 16127 | 18719 | 20610 |1092.4 | 51.72 Bond | 4.5681 | 28.749 | 67.454 | 439.6 | 0.08 Kspace | 7281 | 9160.9 | 11733 |1546.4 | 25.31 Neigh | 1517.2 | 1519.3 | 1521.5 | 3.6 | 4.20 Comm | 1961.2 | 2061.8 | 2115 | 112.7 | 5.70 Output | 0.013751 | 0.016662 | 0.019404 | 1.3 | 0.00 Modify | 3761.7 | 3964.8 | 4410 | 378.6 | 10.95 Other | | 741.4 | | | 2.05 Nlocal: 414.406 ave 451 max 378 min Histogram: 2 4 3 3 3 3 6 4 3 1 Nghost: 7787.34 ave 8066 max 7503 min Histogram: 6 2 2 5 1 0 1 7 6 2 Neighs: 215653 ave 245107 max 182209 min Histogram: 4 4 0 0 3 7 2 6 5 1 Total # of neighbors = 6900911 Ave neighs/atom = 520.39145 Ave special neighs/atom = 2.0037705 Neighbor list builds = 159850 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) = 0.26065044 grid = 36 36 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0028849559 estimated relative force accuracy = 8.6879589e-06 using double precision KISS FFT 3d grid and FFT values/proc = 9375 2592 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 2 0.970014 4.19522e-05 10416 2 103.7 0.00479049 3472 Per MPI rank memory allocation (min/avg/max) = 13.63 | 13.76 | 13.86 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 1928.9529 146737.03 1.5355781 295.70839 447.24654 569.57269 0 0 40502.064 -34294.734 -443.96083 -406123.24 -398899.09 8627.6379 Loop time of 7.57447e-06 on 32 procs for 0 steps with 13261 atoms 119.6% 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 | | 7.574e-06 | | |100.00 Nlocal: 414.406 ave 451 max 378 min Histogram: 2 4 3 3 3 3 6 4 3 1 Nghost: 7787.34 ave 8066 max 7503 min Histogram: 6 2 2 5 1 0 1 7 6 2 Neighs: 215653 ave 245107 max 182209 min Histogram: 4 4 0 0 3 7 2 6 5 1 Total # of neighbors = 6900911 Ave neighs/atom = 520.39145 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