#------------------------------------------------------------------------------- # 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 1.74849e-12 5784 2 103.7 8.08029e-11 1928 Per MPI rank memory allocation (min/avg/max) = 12.42 | 12.62 | 12.73 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 3304.7374 65360.011 1.3291045 293.76617 34.655274 45.955754 0 0 17302.76 55301.059 -321.48015 -198504.4 -125819.97 3903.6974 SHAKE stats (type/ave/delta/count) on step 50000 2 0.969928 1.34682e-06 5784 2 103.7 0.000123681 1928 SHAKE stats (type/ave/delta/count) on step 100000 2 0.969882 1.29551e-06 5784 2 103.7 8.90818e-05 1928 SHAKE stats (type/ave/delta/count) on step 150000 2 0.969856 1.11048e-06 5784 2 103.7 0.000116069 1928 SHAKE stats (type/ave/delta/count) on step 200000 2 0.969905 1.08142e-06 5784 2 103.7 0.000113243 1928 SHAKE stats (type/ave/delta/count) on step 250000 2 0.970053 1.32834e-06 5784 2 103.7 9.46455e-05 1928 SHAKE stats (type/ave/delta/count) on step 300000 2 0.969953 1.45175e-06 5784 2 103.7 0.000165882 1928 SHAKE stats (type/ave/delta/count) on step 350000 2 0.969834 1.58239e-06 5784 2 103.7 0.000182112 1928 SHAKE stats (type/ave/delta/count) on step 400000 2 0.969946 1.1427e-06 5784 2 103.7 9.38801e-05 1928 SHAKE stats (type/ave/delta/count) on step 450000 2 0.970043 1.44344e-06 5784 2 103.7 0.000113767 1928 SHAKE stats (type/ave/delta/count) on step 500000 2 0.970033 1.38124e-06 5784 2 103.7 0.000108896 1928 SHAKE stats (type/ave/delta/count) on step 550000 2 0.970007 1.03944e-06 5784 2 103.7 9.10711e-05 1928 SHAKE stats (type/ave/delta/count) on step 600000 2 0.970032 1.34467e-06 5784 2 103.7 0.000105791 1928 SHAKE stats (type/ave/delta/count) on step 650000 2 0.96993 1.04366e-06 5784 2 103.7 8.9055e-05 1928 SHAKE stats (type/ave/delta/count) on step 700000 2 0.969982 1.0921e-06 5784 2 103.7 9.43752e-05 1928 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97007 1.77734e-06 5784 2 103.7 0.000104374 1928 SHAKE stats (type/ave/delta/count) on step 800000 2 0.970016 1.47684e-06 5784 2 103.7 0.000105381 1928 SHAKE stats (type/ave/delta/count) on step 850000 2 0.970032 1.29643e-06 5784 2 103.7 9.95611e-05 1928 SHAKE stats (type/ave/delta/count) on step 900000 2 0.970029 1.16121e-06 5784 2 103.7 9.32079e-05 1928 SHAKE stats (type/ave/delta/count) on step 950000 2 0.970057 1.61148e-06 5784 2 103.7 0.000120399 1928 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.969919 1.18162e-06 5784 2 103.7 9.42737e-05 1928 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.969935 1.26351e-06 5784 2 103.7 8.93336e-05 1928 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.969954 1.26719e-06 5784 2 103.7 0.000105479 1928 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.970016 1.07647e-06 5784 2 103.7 9.14434e-05 1928 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.970062 1.27169e-06 5784 2 103.7 9.96782e-05 1928 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.969895 1.2566e-06 5784 2 103.7 0.000108492 1928 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.970022 1.21276e-06 5784 2 103.7 0.000108745 1928 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.970028 1.15931e-06 5784 2 103.7 8.71669e-05 1928 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.969884 1.12669e-06 5784 2 103.7 9.24478e-05 1928 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.970096 1.4075e-06 5784 2 103.7 0.000117128 1928 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.969991 1.42524e-06 5784 2 103.7 0.000116959 1928 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.970013 1.4248e-06 5784 2 103.7 9.4609e-05 1928 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.970027 1.74958e-06 5784 2 103.7 0.000103483 1928 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.969894 1.17785e-06 5784 2 103.7 0.000145977 1928 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.970065 1.56466e-06 5784 2 103.7 0.000111366 1928 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97007 1.61051e-06 5784 2 103.7 0.000108096 1928 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.969908 1.21461e-06 5784 2 103.7 9.78953e-05 1928 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.970023 1.08214e-06 5784 2 103.7 0.000108445 1928 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.969957 1.26792e-06 5784 2 103.7 8.73441e-05 1928 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.970052 1.45499e-06 5784 2 103.7 0.000113639 1928 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.970007 1.25932e-06 5784 2 103.7 0.000100041 1928 2000000 2000000 -48.243587 68891.701 1.2609688 301.40774 30.634263 35.783824 0 0 16456.638 56257.368 -304.99967 -198474.06 -125693.64 4005.2421 Loop time of 9224.1 on 32 procs for 2000000 steps with 6387 atoms Performance: 18.734 ns/day, 1.281 hours/ns, 216.823 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 | 3007.8 | 3249.9 | 3578.1 | 230.5 | 35.23 Bond | 1.9831 | 4.1896 | 8.2009 | 88.5 | 0.05 Kspace | 3049.5 | 3381.6 | 3618.5 | 226.0 | 36.66 Neigh | 201.36 | 201.71 | 202.16 | 1.7 | 2.19 Comm | 595.21 | 602.23 | 610.1 | 15.3 | 6.53 Output | 0.007445 | 0.0092767 | 0.011 | 1.1 | 0.00 Modify | 1151.9 | 1353.4 | 1728.4 | 574.8 | 14.67 Other | | 431.1 | | | 4.67 Nlocal: 199.594 ave 218 max 183 min Histogram: 2 2 4 4 6 4 5 0 3 2 Nghost: 4256.94 ave 4294 max 4222 min Histogram: 3 1 4 4 4 5 4 3 2 2 Neighs: 58855.3 ave 67205 max 52924 min Histogram: 3 2 5 6 8 1 2 2 1 2 Total # of neighbors = 1883369 Ave neighs/atom = 294.87537 Ave special neighs/atom = 1.8738062 Neighbor list builds = 99558 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) = 0.32596677 grid = 40 40 40 stencil order = 5 estimated absolute RMS force accuracy = 0.0032353263 estimated relative force accuracy = 9.7430891e-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 0.970007 1.25932e-06 5784 2 103.7 0.000100041 1928 Per MPI rank memory allocation (min/avg/max) = 12.42 | 12.62 | 12.73 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 -7.5664608 68891.701 1.2609688 301.40774 30.634263 35.783824 0 0 16456.638 55471.475 -304.99967 -197688.17 -125693.64 4005.2421 Loop time of 1.48466e-05 on 32 procs for 0 steps with 6387 atoms 99.1% 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 | | 1.485e-05 | | |100.00 Nlocal: 199.594 ave 218 max 183 min Histogram: 2 2 4 4 6 4 5 0 3 2 Nghost: 4256.94 ave 4294 max 4222 min Histogram: 3 1 4 4 4 5 4 3 2 2 Neighs: 58855.3 ave 67205 max 52924 min Histogram: 3 2 5 6 8 1 2 2 1 2 Total # of neighbors = 1883369 Ave neighs/atom = 294.87537 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: 4:49:36