#------------------------------------------------------------------------------- # Stage 2.4: NVT integration for 2 ns with a timestep of 1 fs # Temperature 298.2 K #------------------------------------------------------------------------------- # 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 nvt temp 298.2 298.2 100 drag 0.0 fix 2 movable ave/time 1 200000 200000 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal 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_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) = 0.32729257 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 0.999153 0.656281 5784 2 96.7121 34.3003 1928 Per MPI rank memory allocation (min/avg/max) = 12.42 | 12.58 | 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 9963.4125 65360.011 1.3291045 427.16581 62.984284 135.07175 0 0 19036.598 56466.552 -321.48015 -197763.44 -122062.23 5676.3721 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 9.96504e-07 5784 2 103.7 9.18418e-05 1928 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.23517e-06 5784 2 103.7 0.000100614 1928 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.22684e-06 5784 2 103.7 9.78899e-05 1928 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.1579e-06 5784 2 103.7 0.000129037 1928 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.14411e-06 5784 2 103.7 0.000100228 1928 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.09188e-06 5784 2 103.7 0.000104951 1928 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.19594e-06 5784 2 103.7 8.7408e-05 1928 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.51606e-06 5784 2 103.7 9.30092e-05 1928 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.12834e-06 5784 2 103.7 9.53622e-05 1928 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.15411e-06 5784 2 103.7 0.000111066 1928 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.68137e-06 5784 2 103.7 0.000120181 1928 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.72523e-06 5784 2 103.7 0.000106598 1928 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.25037e-06 5784 2 103.7 9.13243e-05 1928 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.33375e-06 5784 2 103.7 0.000112635 1928 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.29481e-06 5784 2 103.7 0.000100127 1928 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.38468e-06 5784 2 103.7 0.000101596 1928 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.41188e-06 5784 2 103.7 9.2856e-05 1928 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.17993e-06 5784 2 103.7 9.69235e-05 1928 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.46438e-06 5784 2 103.7 9.99344e-05 1928 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 2.30103e-06 5784 2 103.7 0.000130285 1928 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 9.58851e-07 5784 2 103.7 8.7652e-05 1928 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.5334e-06 5784 2 103.7 0.000107931 1928 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.08572e-06 5784 2 103.7 9.23692e-05 1928 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.1319e-06 5784 2 103.7 9.41103e-05 1928 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.24478e-06 5784 2 103.7 0.000107309 1928 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.78912e-06 5784 2 103.7 0.000115216 1928 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.57762e-06 5784 2 103.7 0.000135018 1928 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.28915e-06 5784 2 103.7 0.000102913 1928 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.48219e-06 5784 2 103.7 0.000112117 1928 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.26493e-06 5784 2 103.7 9.61583e-05 1928 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.53575e-06 5784 2 103.7 0.000115491 1928 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.29209e-06 5784 2 103.7 0.000108732 1928 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.15849e-06 5784 2 103.7 9.68354e-05 1928 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.47127e-06 5784 2 103.7 0.000119047 1928 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.07039e-06 5784 2 103.7 9.04274e-05 1928 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.73936e-06 5784 2 103.7 0.000110229 1928 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 2.37229e-06 5784 2 103.7 0.000123268 1928 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.12522e-06 5784 2 103.7 9.97538e-05 1928 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.60777e-06 5784 2 103.7 0.000133663 1928 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.85346e-06 5784 2 103.7 0.000102991 1928 2000000 2000000 3303.7576 65360.011 1.3291045 293.76617 34.655274 45.955754 0 0 17302.76 55301.047 -321.48015 -198504.4 -125819.98 3903.6974 Loop time of 8151.12 on 32 procs for 2000000 steps with 6387 atoms Performance: 21.200 ns/day, 1.132 hours/ns, 245.365 timesteps/s 99.3% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3115 | 3407.5 | 3691.5 | 254.1 | 41.80 Bond | 1.8545 | 4.0588 | 7.0377 | 80.9 | 0.05 Kspace | 3053.6 | 3337.9 | 3627.9 | 256.7 | 40.95 Neigh | 194.66 | 195.23 | 195.86 | 3.1 | 2.40 Comm | 581.58 | 587.9 | 596.41 | 16.6 | 7.21 Output | 0.010276 | 0.012139 | 0.013896 | 1.0 | 0.00 Modify | 585.88 | 591.05 | 597.96 | 11.2 | 7.25 Other | | 27.47 | | | 0.34 Nlocal: 199.594 ave 216 max 186 min Histogram: 2 4 3 2 8 3 5 3 0 2 Nghost: 4402.34 ave 4450 max 4349 min Histogram: 2 1 1 5 4 7 4 3 3 2 Neighs: 62026.4 ave 70109 max 54786 min Histogram: 2 1 3 7 6 6 2 2 1 2 Total # of neighbors = 1984845 Ave neighs/atom = 310.76327 Ave special neighs/atom = 1.8738062 Neighbor list builds = 94956 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) = 0.32729257 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 2000000 2 0.97 1.85346e-06 5784 2 103.7 0.000102991 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 3304.7315 65360.011 1.3291045 293.76617 34.655274 45.955754 0 0 17302.76 55301.047 -321.48015 -198504.4 -125819.98 3903.6974 Loop time of 8.94597e-06 on 32 procs for 0 steps with 6387 atoms 107.6% 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 | | 8.946e-06 | | |100.00 Nlocal: 199.594 ave 216 max 186 min Histogram: 2 4 3 2 8 3 5 3 0 2 Nghost: 4402.34 ave 4450 max 4349 min Histogram: 2 1 1 5 4 7 4 3 3 2 Neighs: 62026.4 ave 70109 max 54786 min Histogram: 2 1 3 7 6 6 2 2 1 2 Total # of neighbors = 1984845 Ave neighs/atom = 310.76327 Ave special neighs/atom = 1.8738062 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NPT.out