#------------------------------------------------------------------------------- # 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 1 b 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 2220 = # 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 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 ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25505473 grid = 30 30 30 stencil order = 5 estimated absolute RMS force accuracy = 0.0027250889 estimated relative force accuracy = 8.2065243e-06 using double precision KISS FFT 3d grid and FFT values/proc = 17908 7200 generated 0 of 6 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 0.999442 0.0531094 6660 1 97.8998 8.53363 2220 Per MPI rank memory allocation (min/avg/max) = 14.89 | 15 | 15.31 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 -1163.7785 67844.182 1.0361038 444.69347 0 0 0 0 10441.734 68143.777 -121.84631 -120353.14 -41767.63 5990.1459 SHAKE stats (type/ave/delta/count) on step 50000 1 0.970019 1.10558e-06 6660 1 103.7 9.55478e-05 2220 SHAKE stats (type/ave/delta/count) on step 100000 1 0.970007 1.58369e-06 6660 1 103.7 0.000111998 2220 SHAKE stats (type/ave/delta/count) on step 150000 1 0.969835 2.06144e-06 6660 1 103.7 0.000135762 2220 SHAKE stats (type/ave/delta/count) on step 200000 1 0.969952 1.37508e-06 6660 1 103.7 9.94895e-05 2220 SHAKE stats (type/ave/delta/count) on step 250000 1 0.969978 1.39078e-06 6660 1 103.7 0.000130707 2220 SHAKE stats (type/ave/delta/count) on step 300000 1 0.969984 1.39966e-06 6660 1 103.7 0.000106515 2220 SHAKE stats (type/ave/delta/count) on step 350000 1 0.970095 1.99297e-06 6660 1 103.7 0.000161709 2220 SHAKE stats (type/ave/delta/count) on step 400000 1 0.970071 1.19913e-06 6660 1 103.7 9.89422e-05 2220 SHAKE stats (type/ave/delta/count) on step 450000 1 0.970129 2.11686e-06 6660 1 103.7 0.00015775 2220 SHAKE stats (type/ave/delta/count) on step 500000 1 0.970047 2.02137e-06 6660 1 103.7 0.000149673 2220 SHAKE stats (type/ave/delta/count) on step 550000 1 0.970038 1.5676e-06 6660 1 103.7 0.000113139 2220 SHAKE stats (type/ave/delta/count) on step 600000 1 0.970079 1.62145e-06 6660 1 103.7 0.00012201 2220 SHAKE stats (type/ave/delta/count) on step 650000 1 0.970033 1.67396e-06 6660 1 103.7 0.000123107 2220 SHAKE stats (type/ave/delta/count) on step 700000 1 0.96993 1.65404e-06 6660 1 103.7 0.000104189 2220 SHAKE stats (type/ave/delta/count) on step 750000 1 0.969944 1.34546e-06 6660 1 103.7 0.000107062 2220 SHAKE stats (type/ave/delta/count) on step 800000 1 0.970027 1.62032e-06 6660 1 103.7 0.000123554 2220 SHAKE stats (type/ave/delta/count) on step 850000 1 0.970021 1.06211e-06 6660 1 103.7 8.86852e-05 2220 SHAKE stats (type/ave/delta/count) on step 900000 1 0.970014 1.32338e-06 6660 1 103.7 0.000108699 2220 SHAKE stats (type/ave/delta/count) on step 950000 1 0.969945 1.32193e-06 6660 1 103.7 9.54626e-05 2220 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.96998 1.18526e-06 6660 1 103.7 0.000100223 2220 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.969978 1.18228e-06 6660 1 103.7 9.3399e-05 2220 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.969991 1.69521e-06 6660 1 103.7 0.000112893 2220 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.969932 1.1742e-06 6660 1 103.7 9.98976e-05 2220 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.970039 1.58239e-06 6660 1 103.7 0.000116424 2220 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.970071 1.36181e-06 6660 1 103.7 0.000100561 2220 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.970127 1.81725e-06 6660 1 103.7 0.000131367 2220 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.970048 1.17983e-06 6660 1 103.7 0.000100228 2220 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.970073 1.21853e-06 6660 1 103.7 9.74177e-05 2220 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.969925 1.28422e-06 6660 1 103.7 0.000110088 2220 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.969968 1.34995e-06 6660 1 103.7 0.000100593 2220 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.970077 1.94291e-06 6660 1 103.7 0.000148796 2220 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.970034 1.97347e-06 6660 1 103.7 0.000129554 2220 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.970035 1.40495e-06 6660 1 103.7 0.00010382 2220 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.969934 1.30378e-06 6660 1 103.7 0.00011585 2220 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.970068 1.69934e-06 6660 1 103.7 0.000121942 2220 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.969924 1.25383e-06 6660 1 103.7 0.000109054 2220 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.969939 1.53342e-06 6660 1 103.7 0.000123514 2220 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.970106 1.58702e-06 6660 1 103.7 0.000118499 2220 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.970123 1.57265e-06 6660 1 103.7 0.000120222 2220 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.969972 1.1948e-06 6660 1 103.7 9.93792e-05 2220 2000000 2000000 -118.03053 68003.765 1.0336724 295.28903 0 0 0 0 6311.2101 82732.919 -121.56037 -120329.15 -31285.025 3977.6261 Loop time of 78904.5 on 4 procs for 2000000 steps with 6740 atoms Performance: 2.190 ns/day, 10.959 hours/ns, 25.347 timesteps/s 99.1% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 53991 | 57608 | 62736 |1348.3 | 73.01 Bond | 3.9918 | 4.5631 | 5.3065 | 23.3 | 0.01 Kspace | 8277.5 | 13405 | 17022 |2794.5 | 16.99 Neigh | 3668.2 | 3668.6 | 3669.1 | 0.5 | 4.65 Comm | 643.2 | 644.93 | 646.89 | 5.5 | 0.82 Output | 0.034704 | 0.036186 | 0.037435 | 0.5 | 0.00 Modify | 3082.5 | 3249.7 | 3452.6 | 288.1 | 4.12 Other | | 324.5 | | | 0.41 Nlocal: 1685 ave 1728 max 1656 min Histogram: 1 0 0 2 0 0 0 0 0 1 Nghost: 14321.2 ave 14364 max 14296 min Histogram: 1 0 2 0 0 0 0 0 0 1 Neighs: 959216 ave 1.00361e+06 max 899540 min Histogram: 1 0 0 0 0 1 0 1 0 1 Total # of neighbors = 3836864 Ave neighs/atom = 569.26766 Ave special neighs/atom = 1.9762611 Neighbor list builds = 103759 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) = 0.25500752 grid = 30 30 30 stencil order = 5 estimated absolute RMS force accuracy = 0.0027314334 estimated relative force accuracy = 8.2256305e-06 using double precision KISS FFT 3d grid and FFT values/proc = 17908 7200 generated 0 of 6 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 1 0.969972 1.1948e-06 6660 1 103.7 9.93792e-05 2220 Per MPI rank memory allocation (min/avg/max) = 14.89 | 15.2 | 15.31 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 -309.39304 68003.765 1.0336724 295.28903 0 0 0 0 6311.2101 82710.69 -121.56037 -120306.92 -31285.025 3977.6261 Loop time of 3.3565e-06 on 4 procs for 0 steps with 6740 atoms 119.2% CPU use with 4 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 | | 3.357e-06 | | |100.00 Nlocal: 1685 ave 1728 max 1656 min Histogram: 1 0 0 2 0 0 0 0 0 1 Nghost: 14321.2 ave 14364 max 14296 min Histogram: 1 0 2 0 0 0 0 0 0 1 Neighs: 959216 ave 1.00361e+06 max 899540 min Histogram: 1 0 0 0 0 1 0 1 0 1 Total # of neighbors = 3836864 Ave neighs/atom = 569.26766 Ave special neighs/atom = 1.9762611 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 21:56:56