#------------------------------------------------------------------------------- # 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) = 0.25538468 grid = 30 30 30 stencil order = 5 estimated absolute RMS force accuracy = 0.0026344891 estimated relative force accuracy = 7.9336856e-06 using double precision KISS FFT 3d grid and FFT values/proc = 10648 3600 generated 0 of 6 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 0.999428 0.0651746 6660 1 97.9329 9.09087 2220 Per MPI rank memory allocation (min/avg/max) = 12.01 | 12.12 | 12.42 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-06 656.56848 66718.997 1.0048733 446.93152 0 0 0 0 10035.86 70983.98 -116.66799 -117842.29 -36822.449 5929.7022 SHAKE stats (type/ave/delta/count) on step 50000 1 0.970045 1.2273e-06 6660 1 103.7 0.00011042 2220 SHAKE stats (type/ave/delta/count) on step 100000 1 0.970038 1.37747e-06 6660 1 103.7 0.000101971 2220 SHAKE stats (type/ave/delta/count) on step 150000 1 0.970021 1.37535e-06 6660 1 103.7 9.5176e-05 2220 SHAKE stats (type/ave/delta/count) on step 200000 1 0.969984 1.3302e-06 6660 1 103.7 0.000105202 2220 SHAKE stats (type/ave/delta/count) on step 250000 1 0.969971 1.37598e-06 6660 1 103.7 0.000135962 2220 SHAKE stats (type/ave/delta/count) on step 300000 1 0.970042 1.19368e-06 6660 1 103.7 9.72292e-05 2220 SHAKE stats (type/ave/delta/count) on step 350000 1 0.969954 1.18534e-06 6660 1 103.7 0.000118762 2220 SHAKE stats (type/ave/delta/count) on step 400000 1 0.970011 1.19938e-06 6660 1 103.7 0.00010157 2220 SHAKE stats (type/ave/delta/count) on step 450000 1 0.970068 1.5608e-06 6660 1 103.7 9.91591e-05 2220 SHAKE stats (type/ave/delta/count) on step 500000 1 0.969972 1.26265e-06 6660 1 103.7 0.000120177 2220 SHAKE stats (type/ave/delta/count) on step 550000 1 0.970098 1.37892e-06 6660 1 103.7 0.000116562 2220 SHAKE stats (type/ave/delta/count) on step 600000 1 0.970025 1.57282e-06 6660 1 103.7 9.91511e-05 2220 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97001 1.14544e-06 6660 1 103.7 9.24038e-05 2220 SHAKE stats (type/ave/delta/count) on step 700000 1 0.969975 1.24787e-06 6660 1 103.7 9.30676e-05 2220 SHAKE stats (type/ave/delta/count) on step 750000 1 0.969887 1.35096e-06 6660 1 103.7 0.000121434 2220 SHAKE stats (type/ave/delta/count) on step 800000 1 0.970072 1.75342e-06 6660 1 103.7 0.000112372 2220 SHAKE stats (type/ave/delta/count) on step 850000 1 0.969878 1.15144e-06 6660 1 103.7 9.44114e-05 2220 SHAKE stats (type/ave/delta/count) on step 900000 1 0.969972 1.2174e-06 6660 1 103.7 0.000108107 2220 SHAKE stats (type/ave/delta/count) on step 950000 1 0.969955 1.3604e-06 6660 1 103.7 0.000103596 2220 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.969953 1.49282e-06 6660 1 103.7 0.000110139 2220 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.969944 1.55608e-06 6660 1 103.7 0.000136986 2220 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.969931 1.46017e-06 6660 1 103.7 0.000139145 2220 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.970055 1.59327e-06 6660 1 103.7 0.000122971 2220 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.969946 1.30416e-06 6660 1 103.7 0.000104317 2220 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.969908 1.42678e-06 6660 1 103.7 0.000111131 2220 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.969913 1.24069e-06 6660 1 103.7 9.33208e-05 2220 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.969953 1.63612e-06 6660 1 103.7 0.000118757 2220 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.970032 1.19157e-06 6660 1 103.7 9.04533e-05 2220 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.970021 1.40562e-06 6660 1 103.7 0.000110541 2220 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.96998 1.04582e-06 6660 1 103.7 9.16718e-05 2220 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.970081 2.01133e-06 6660 1 103.7 0.000124505 2220 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.970031 1.20755e-06 6660 1 103.7 9.06673e-05 2220 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.96993 1.22561e-06 6660 1 103.7 0.000136633 2220 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.969968 1.19348e-06 6660 1 103.7 9.95576e-05 2220 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.970019 1.25132e-06 6660 1 103.7 9.30543e-05 2220 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.970032 1.624e-06 6660 1 103.7 9.60745e-05 2220 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.969953 1.10174e-06 6660 1 103.7 0.000100382 2220 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.970044 1.30518e-06 6660 1 103.7 8.9689e-05 2220 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.970082 1.25478e-06 6660 1 103.7 0.00010714 2220 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.970075 1.38237e-06 6660 1 103.7 0.000106862 2220 2000000 2000000 35.267541 66854.951 1.0028299 296.6377 0 0 0 0 5997.0688 85535.17 -116.43074 -117817.76 -26285.525 3935.666 Loop time of 57824.4 on 8 procs for 2000000 steps with 6672 atoms Performance: 2.988 ns/day, 8.031 hours/ns, 34.587 timesteps/s 99.0% CPU use with 8 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 37827 | 40899 | 44893 |1291.5 | 70.73 Bond | 6.9056 | 7.6353 | 9.07 | 23.0 | 0.01 Kspace | 6528.9 | 10528 | 13607 |2545.4 | 18.21 Neigh | 2545.8 | 2548 | 2550 | 3.8 | 4.41 Comm | 723.29 | 738.75 | 756 | 47.5 | 1.28 Output | 0.02482 | 0.026146 | 0.027219 | 0.5 | 0.00 Modify | 2433.4 | 2778.9 | 2932.2 | 329.3 | 4.81 Other | | 324.5 | | | 0.56 Nlocal: 834 ave 857 max 800 min Histogram: 1 1 0 0 0 1 0 3 0 2 Nghost: 10367.5 ave 10458 max 10334 min Histogram: 2 3 1 1 0 0 0 0 0 1 Neighs: 477994 ave 511739 max 448137 min Histogram: 2 0 1 1 0 1 1 0 1 1 Total # of neighbors = 3823956 Ave neighs/atom = 573.13489 Ave special neighs/atom = 1.9964029 Neighbor list builds = 103784 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) = 0.25534395 grid = 30 30 30 stencil order = 5 estimated absolute RMS force accuracy = 0.0026397932 estimated relative force accuracy = 7.949659e-06 using double precision KISS FFT 3d grid and FFT values/proc = 10648 3600 generated 0 of 6 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 1 0.970075 1.38237e-06 6660 1 103.7 0.000106862 2220 Per MPI rank memory allocation (min/avg/max) = 12.39 | 12.41 | 12.42 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 547.62754 66854.951 1.0028299 296.6377 0 0 0 0 5997.0688 85516.411 -116.43074 -117799 -26285.525 3935.666 Loop time of 3.51712e-06 on 8 procs for 0 steps with 6672 atoms 117.3% CPU use with 8 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 | | 3.517e-06 | | |100.00 Nlocal: 834 ave 857 max 800 min Histogram: 1 1 0 0 0 1 0 3 0 2 Nghost: 10367.5 ave 10458 max 10334 min Histogram: 2 3 1 1 0 0 0 0 0 1 Neighs: 477994 ave 511739 max 448137 min Histogram: 2 0 1 1 0 1 1 0 1 1 Total # of neighbors = 3823956 Ave neighs/atom = 573.13489 Ave special neighs/atom = 1.9964029 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 16:06:15