#------------------------------------------------------------------------------- # 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 1928 = # 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 2.5_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 ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.32729257 grid = 40 40 40 stencil order = 5 estimated absolute RMS force accuracy = 0.0030709373 estimated relative force accuracy = 9.2480364e-06 using double precision KISS FFT 3d grid and FFT values/proc = 7803 3200 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 7.56839e-13 5784 2 103.7 7.3868e-11 1928 Per MPI rank memory allocation (min/avg/max) = 12.42 | 12.61 | 12.72 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 2801.7018 65360.011 1.3291045 293.55129 37.686133 49.021544 0 0 17152.633 55390.966 -321.48015 -198518.76 -125888.45 3900.842 SHAKE stats (type/ave/delta/count) on step 50000 2 0.969875 1.42612e-06 5784 2 103.7 0.00015166 1928 SHAKE stats (type/ave/delta/count) on step 100000 2 0.969892 1.31636e-06 5784 2 103.7 0.000112446 1928 SHAKE stats (type/ave/delta/count) on step 150000 2 0.969992 1.26964e-06 5784 2 103.7 0.000108152 1928 SHAKE stats (type/ave/delta/count) on step 200000 2 0.970013 1.04996e-06 5784 2 103.7 0.000101054 1928 SHAKE stats (type/ave/delta/count) on step 250000 2 0.970008 1.18507e-06 5784 2 103.7 0.000100585 1928 SHAKE stats (type/ave/delta/count) on step 300000 2 0.969921 1.18798e-06 5784 2 103.7 0.00010898 1928 SHAKE stats (type/ave/delta/count) on step 350000 2 0.969852 1.31983e-06 5784 2 103.7 0.00015618 1928 SHAKE stats (type/ave/delta/count) on step 400000 2 0.969957 1.31008e-06 5784 2 103.7 9.28042e-05 1928 SHAKE stats (type/ave/delta/count) on step 450000 2 0.969945 1.31437e-06 5784 2 103.7 0.000103409 1928 SHAKE stats (type/ave/delta/count) on step 500000 2 0.970044 1.09587e-06 5784 2 103.7 9.34834e-05 1928 SHAKE stats (type/ave/delta/count) on step 550000 2 0.970043 1.51561e-06 5784 2 103.7 9.69999e-05 1928 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97004 1.1918e-06 5784 2 103.7 9.18096e-05 1928 SHAKE stats (type/ave/delta/count) on step 650000 2 0.970011 1.21747e-06 5784 2 103.7 0.000117466 1928 SHAKE stats (type/ave/delta/count) on step 700000 2 0.970026 1.08972e-06 5784 2 103.7 8.90677e-05 1928 SHAKE stats (type/ave/delta/count) on step 750000 2 0.970063 1.74012e-06 5784 2 103.7 0.000128303 1928 SHAKE stats (type/ave/delta/count) on step 800000 2 0.970002 1.23302e-06 5784 2 103.7 9.69267e-05 1928 SHAKE stats (type/ave/delta/count) on step 850000 2 0.970058 1.01041e-06 5784 2 103.7 8.57225e-05 1928 SHAKE stats (type/ave/delta/count) on step 900000 2 0.969906 1.18869e-06 5784 2 103.7 8.51053e-05 1928 SHAKE stats (type/ave/delta/count) on step 950000 2 0.9701 1.7381e-06 5784 2 103.7 0.000109378 1928 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.970009 1.12646e-06 5784 2 103.7 9.57234e-05 1928 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.96996 1.13064e-06 5784 2 103.7 8.64946e-05 1928 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.969983 1.29127e-06 5784 2 103.7 9.21298e-05 1928 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.970063 1.5796e-06 5784 2 103.7 0.000127721 1928 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.970047 2.10336e-06 5784 2 103.7 0.000135603 1928 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.969951 1.2918e-06 5784 2 103.7 0.000105344 1928 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.969976 1.35798e-06 5784 2 103.7 9.54646e-05 1928 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.969915 1.2488e-06 5784 2 103.7 0.000141668 1928 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.970051 1.02742e-06 5784 2 103.7 9.00743e-05 1928 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.970012 1.2849e-06 5784 2 103.7 0.000111842 1928 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97005 1.8918e-06 5784 2 103.7 0.000124712 1928 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.969928 1.28627e-06 5784 2 103.7 0.000120621 1928 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.970032 1.31501e-06 5784 2 103.7 9.45895e-05 1928 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.970039 1.3404e-06 5784 2 103.7 9.13623e-05 1928 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.970091 1.42494e-06 5784 2 103.7 0.000116603 1928 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.969886 1.29885e-06 5784 2 103.7 0.000112544 1928 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.970046 1.32268e-06 5784 2 103.7 0.000104256 1928 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.969902 1.31754e-06 5784 2 103.7 0.00010742 1928 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.969952 1.11296e-06 5784 2 103.7 8.89865e-05 1928 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.970025 1.16807e-06 5784 2 103.7 9.97492e-05 1928 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.96994 1.26559e-06 5784 2 103.7 0.000114944 1928 2000000 2000000 -376.70351 68909.944 1.260635 298.85194 32.558535 40.293705 0 0 16260.969 56511.888 -304.91893 -198494.11 -125648.4 3971.2794 Loop time of 9155.52 on 32 procs for 2000000 steps with 6387 atoms Performance: 18.874 ns/day, 1.272 hours/ns, 218.448 timesteps/s 99.2% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2968 | 3245.8 | 3530.5 | 260.6 | 35.45 Bond | 1.8384 | 4.0095 | 7.7443 | 91.9 | 0.04 Kspace | 3045.7 | 3331.4 | 3610.2 | 258.0 | 36.39 Neigh | 200.51 | 201.02 | 201.37 | 1.9 | 2.20 Comm | 595.58 | 609.16 | 618.27 | 25.2 | 6.65 Output | 0.0073364 | 0.009125 | 0.010825 | 1.1 | 0.00 Modify | 1147.2 | 1338.7 | 1723.3 | 573.4 | 14.62 Other | | 425.3 | | | 4.65 Nlocal: 199.594 ave 223 max 174 min Histogram: 2 1 1 5 6 6 4 4 1 2 Nghost: 4258.44 ave 4293 max 4208 min Histogram: 1 2 2 2 3 4 6 5 3 4 Neighs: 58835.6 ave 66822 max 49095 min Histogram: 1 1 2 3 6 6 2 8 1 2 Total # of neighbors = 1882740 Ave neighs/atom = 294.77689 Ave special neighs/atom = 1.8738062 Neighbor list builds = 99534 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) = 0.32596007 grid = 40 40 40 stencil order = 5 estimated absolute RMS force accuracy = 0.0032361762 estimated relative force accuracy = 9.7456484e-06 using double precision KISS FFT 3d grid and FFT values/proc = 7803 3200 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.96994 1.26559e-06 5784 2 103.7 0.000114944 1928 Per MPI rank memory allocation (min/avg/max) = 12.42 | 12.62 | 12.72 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 -723.86935 68909.944 1.260635 298.85194 32.558535 40.293705 0 0 16260.969 55721.803 -304.91893 -197704.02 -125648.4 3971.2794 Loop time of 1.35145e-05 on 32 procs for 0 steps with 6387 atoms 109.6% 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 | | 1.351e-05 | | |100.00 Nlocal: 199.594 ave 223 max 174 min Histogram: 2 1 1 5 6 6 4 4 1 2 Nghost: 4258.44 ave 4293 max 4208 min Histogram: 1 2 2 2 3 4 6 5 3 4 Neighs: 58835.6 ave 66822 max 49095 min Histogram: 1 1 2 3 6 6 2 8 1 2 Total # of neighbors = 1882740 Ave neighs/atom = 294.77689 Ave special neighs/atom = 1.8738062 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 4:49:04