#------------------------------------------------------------------------------- # Stage 2.4: 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 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 fix 1 movable npt temp 298.2 298.2 100 iso 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 2.4_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 ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.20470278 grid = 27 27 27 stencil order = 5 estimated absolute RMS force accuracy = 0.0030085707 estimated relative force accuracy = 9.0602213e-06 using double precision KISS FFT 3d grid and FFT values/proc = 3380 756 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.997138 0.98891 8304 2 97.0361 22.712 2768 Per MPI rank memory allocation (min/avg/max) = 13.25 | 13.5 | 13.85 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 6246.7861 92859.489 1.3074058 428.55654 37.265752 181.83498 0 0 23660.894 -10726.63 -116.30764 -171773.95 -158620.59 8088.7858 SHAKE stats (type/ave/delta/count) on step 50000 2 0.970006 1.3857e-06 8304 2 103.7 0.000104778 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.969902 1.14927e-06 8304 2 103.7 0.000100594 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.969939 1.39694e-06 8304 2 103.7 0.000142577 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.970066 1.27495e-06 8304 2 103.7 9.98448e-05 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.969983 1.42644e-06 8304 2 103.7 9.3601e-05 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.970056 1.2572e-06 8304 2 103.7 0.000111513 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.969979 1.43114e-06 8304 2 103.7 0.000108588 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.970013 1.18678e-06 8304 2 103.7 0.000101828 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.96989 1.45916e-06 8304 2 103.7 0.000108978 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.970013 1.4245e-06 8304 2 103.7 9.60191e-05 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.969987 1.23922e-06 8304 2 103.7 9.69116e-05 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.970085 1.58936e-06 8304 2 103.7 0.000118385 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.969965 1.25629e-06 8304 2 103.7 9.68201e-05 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.970033 1.14847e-06 8304 2 103.7 0.000103105 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.970021 1.20566e-06 8304 2 103.7 9.0587e-05 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.970073 1.6677e-06 8304 2 103.7 0.00013322 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.970105 1.80221e-06 8304 2 103.7 0.000137382 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.969958 1.25865e-06 8304 2 103.7 9.39277e-05 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.969962 1.16882e-06 8304 2 103.7 9.44787e-05 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.970001 1.2323e-06 8304 2 103.7 0.000110873 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.970022 1.21549e-06 8304 2 103.7 0.000101883 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.969956 1.04796e-06 8304 2 103.7 9.58724e-05 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.969981 1.05608e-06 8304 2 103.7 9.5709e-05 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97001 1.31357e-06 8304 2 103.7 9.41709e-05 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.970075 2.12377e-06 8304 2 103.7 0.000155597 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.969998 1.20294e-06 8304 2 103.7 9.71522e-05 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.970017 1.49157e-06 8304 2 103.7 0.000106015 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.969968 1.75498e-06 8304 2 103.7 0.000110587 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.970046 1.72801e-06 8304 2 103.7 0.000114723 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.969994 1.16166e-06 8304 2 103.7 9.22757e-05 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.970044 1.07375e-06 8304 2 103.7 9.21707e-05 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.19009e-06 8304 2 103.7 0.00010492 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.969914 1.28803e-06 8304 2 103.7 9.96914e-05 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.969897 1.33942e-06 8304 2 103.7 0.000125076 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.969972 1.15227e-06 8304 2 103.7 9.12069e-05 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.970006 1.45283e-06 8304 2 103.7 0.000112321 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.969984 1.18419e-06 8304 2 103.7 9.35634e-05 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97005 1.7191e-06 8304 2 103.7 0.000127248 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.970022 1.27762e-06 8304 2 103.7 0.000107281 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.970058 1.14538e-06 8304 2 103.7 8.82404e-05 2768 2000000 2000000 51.806732 97473.161 1.2455227 302.44351 44.989065 68.022469 0 0 21246.292 -10608.954 -110.80248 -171998.25 -161247.9 5708.4667 Loop time of 23080.3 on 32 procs for 2000000 steps with 9101 atoms Performance: 7.487 ns/day, 3.206 hours/ns, 86.654 timesteps/s 98.5% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14910 | 16090 | 17381 | 490.2 | 69.71 Bond | 3.1227 | 6.1496 | 16.346 | 108.8 | 0.03 Kspace | 2113 | 3405.8 | 4581.7 |1064.4 | 14.76 Neigh | 803.91 | 804.49 | 805.12 | 1.1 | 3.49 Comm | 1086.3 | 1094.2 | 1102.2 | 14.7 | 4.74 Output | 0.010115 | 0.012345 | 0.014472 | 1.2 | 0.00 Modify | 1495.2 | 1543.3 | 1590.1 | 76.1 | 6.69 Other | | 136.6 | | | 0.59 Nlocal: 284.406 ave 304 max 264 min Histogram: 1 1 4 3 5 3 8 5 1 1 Nghost: 10741.4 ave 10799 max 10699 min Histogram: 2 4 2 6 9 2 1 3 2 1 Neighs: 273144 ave 311517 max 244734 min Histogram: 3 3 2 5 8 4 4 1 1 1 Total # of neighbors = 8740624 Ave neighs/atom = 960.40259 Ave special neighs/atom = 1.8929788 Neighbor list builds = 102727 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) = 0.20391866 grid = 27 27 27 stencil order = 5 estimated absolute RMS force accuracy = 0.0031570161 estimated relative force accuracy = 9.5072601e-06 using double precision KISS FFT 3d grid and FFT values/proc = 3380 756 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.970058 1.14538e-06 8304 2 103.7 8.82404e-05 2768 Per MPI rank memory allocation (min/avg/max) = 13.45 | 13.71 | 13.85 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 391.83356 97473.161 1.2455227 302.44351 44.989065 68.022469 0 0 21246.292 -11265.802 -110.80248 -171341.4 -161247.9 5708.4667 Loop time of 8.84656e-06 on 32 procs for 0 steps with 9101 atoms 114.5% 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 | | 8.847e-06 | | |100.00 Nlocal: 284.406 ave 304 max 264 min Histogram: 1 1 4 3 5 3 8 5 1 1 Nghost: 10741.4 ave 10799 max 10699 min Histogram: 2 4 2 6 9 2 1 3 2 1 Neighs: 273144 ave 311517 max 244734 min Histogram: 3 3 2 5 8 4 4 1 1 1 Total # of neighbors = 8740624 Ave neighs/atom = 960.40259 Ave special neighs/atom = 1.8929788 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out