#------------------------------------------------------------------------------- # 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 1 b 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 1000 = # 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 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 0.993009 0.058347 3000 1 98.5447 12.3003 1000 Per MPI rank memory allocation (min/avg/max) = 8.787 | 8.793 | 8.798 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 -755.06453 29915.098 1.0000033 447.37459 0 0 0 0 2778.1061 -13273.508 -103.93236 0 -10495.402 2665.7438 SHAKE stats (type/ave/delta/count) on step 50000 1 0.969948 1.2518e-06 3000 1 103.7 9.29645e-05 1000 SHAKE stats (type/ave/delta/count) on step 100000 1 0.970113 1.26604e-06 3000 1 103.7 9.74779e-05 1000 SHAKE stats (type/ave/delta/count) on step 150000 1 0.969991 1.43983e-06 3000 1 103.7 0.000113031 1000 SHAKE stats (type/ave/delta/count) on step 200000 1 0.969885 1.522e-06 3000 1 103.7 0.000112396 1000 SHAKE stats (type/ave/delta/count) on step 250000 1 0.970039 1.6945e-06 3000 1 103.7 0.000105922 1000 SHAKE stats (type/ave/delta/count) on step 300000 1 0.969932 1.64484e-06 3000 1 103.7 0.000117213 1000 SHAKE stats (type/ave/delta/count) on step 350000 1 0.970065 1.18608e-06 3000 1 103.7 9.0553e-05 1000 SHAKE stats (type/ave/delta/count) on step 400000 1 0.970023 1.30631e-06 3000 1 103.7 9.7881e-05 1000 SHAKE stats (type/ave/delta/count) on step 450000 1 0.970234 2.59679e-06 3000 1 103.7 0.000167042 1000 SHAKE stats (type/ave/delta/count) on step 500000 1 0.970073 1.87086e-06 3000 1 103.7 0.000145164 1000 SHAKE stats (type/ave/delta/count) on step 550000 1 0.969999 1.14664e-06 3000 1 103.7 9.77849e-05 1000 SHAKE stats (type/ave/delta/count) on step 600000 1 0.969985 1.39233e-06 3000 1 103.7 0.000109542 1000 SHAKE stats (type/ave/delta/count) on step 650000 1 0.969971 1.12489e-06 3000 1 103.7 0.00010164 1000 SHAKE stats (type/ave/delta/count) on step 700000 1 0.96998 1.64048e-06 3000 1 103.7 0.000114895 1000 SHAKE stats (type/ave/delta/count) on step 750000 1 0.970111 1.54206e-06 3000 1 103.7 0.000120681 1000 SHAKE stats (type/ave/delta/count) on step 800000 1 0.970097 1.3116e-06 3000 1 103.7 0.000119828 1000 SHAKE stats (type/ave/delta/count) on step 850000 1 0.970031 1.54274e-06 3000 1 103.7 9.97522e-05 1000 SHAKE stats (type/ave/delta/count) on step 900000 1 0.969996 1.29209e-06 3000 1 103.7 9.41064e-05 1000 SHAKE stats (type/ave/delta/count) on step 950000 1 0.970054 1.51822e-06 3000 1 103.7 0.000155945 1000 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.969957 1.47421e-06 3000 1 103.7 8.94468e-05 1000 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.970113 1.45368e-06 3000 1 103.7 9.26296e-05 1000 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.969825 1.72164e-06 3000 1 103.7 0.00014218 1000 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.97009 2.26841e-06 3000 1 103.7 0.00013978 1000 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.969967 1.23114e-06 3000 1 103.7 9.10834e-05 1000 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.969878 1.28014e-06 3000 1 103.7 0.000106748 1000 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.969951 1.20286e-06 3000 1 103.7 9.67506e-05 1000 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.96999 1.1856e-06 3000 1 103.7 9.67865e-05 1000 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.969908 1.47647e-06 3000 1 103.7 0.000138004 1000 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.970069 1.86682e-06 3000 1 103.7 0.000112364 1000 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.970054 1.90047e-06 3000 1 103.7 0.000133838 1000 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.97003 1.54525e-06 3000 1 103.7 9.70636e-05 1000 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.969943 1.84091e-06 3000 1 103.7 0.000129051 1000 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.969972 1.56219e-06 3000 1 103.7 0.000141151 1000 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.969974 1.29313e-06 3000 1 103.7 0.000102137 1000 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.97 1.31759e-06 3000 1 103.7 9.67278e-05 1000 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.970115 1.13215e-06 3000 1 103.7 9.58676e-05 1000 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.969946 1.20226e-06 3000 1 103.7 9.94339e-05 1000 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.970005 1.13906e-06 3000 1 103.7 9.31866e-05 1000 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.969969 1.25437e-06 3000 1 103.7 9.48926e-05 1000 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.970063 3.25047e-06 3000 1 103.7 0.000190044 1000 2000000 2000000 -4208.6691 26763.922 1.1177434 297.90029 0 0 0 0 2567.014 -16542.17 -116.16932 0 -13975.156 1775.0804 Loop time of 3059.55 on 32 procs for 2000000 steps with 3000 atoms Performance: 56.479 ns/day, 0.425 hours/ns, 653.692 timesteps/s 99.4% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1662.7 | 1812.4 | 1984.5 | 180.5 | 59.24 Bond | 1.255 | 1.4843 | 2.2465 | 14.7 | 0.05 Neigh | 102.8 | 103.03 | 103.16 | 1.1 | 3.37 Comm | 431.53 | 588.54 | 733.14 | 293.8 | 19.24 Output | 0.0048943 | 0.006133 | 0.0073401 | 1.0 | 0.00 Modify | 517.31 | 532.8 | 551.5 | 49.9 | 17.41 Other | | 21.32 | | | 0.70 Nlocal: 93.75 ave 104 max 85 min Histogram: 1 0 5 9 4 5 4 2 1 1 Nghost: 3858.06 ave 3886 max 3830 min Histogram: 4 4 1 4 1 4 4 4 5 1 Neighs: 33255.7 ave 37161 max 28553 min Histogram: 1 1 2 7 1 7 3 5 4 1 Total # of neighbors = 1064182 Ave neighs/atom = 354.72733 Ave special neighs/atom = 2 Neighbor list builds = 89067 Dangerous builds = 0 undump sci restart 0 dump sci all custom 2000000 2.4.xyz id mol type q xs ys zs run 0 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 1 0.970063 3.25047e-06 3000 1 103.7 0.000190044 1000 Per MPI rank memory allocation (min/avg/max) = 8.79 | 8.795 | 8.801 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 -3722.4463 26763.922 1.1177434 297.90029 0 0 0 0 2567.014 -16542.17 -116.16932 0 -13975.156 1775.0804 Loop time of 6.42872e-06 on 32 procs for 0 steps with 3000 atoms 109.4% 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 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 | | 6.429e-06 | | |100.00 Nlocal: 93.75 ave 104 max 85 min Histogram: 1 0 5 9 4 5 4 2 1 1 Nghost: 3858.06 ave 3886 max 3830 min Histogram: 4 4 1 4 1 4 4 4 5 1 Neighs: 33255.7 ave 37161 max 28553 min Histogram: 1 1 2 7 1 7 3 5 4 1 Total # of neighbors = 1064182 Ave neighs/atom = 354.72733 Ave special neighs/atom = 2 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out