#------------------------------------------------------------------------------- # Stage 2.4: NVT integration for 5 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 1 b 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 2000 = # 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 500000 500000 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 500 1 500 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 5000000 2.4.restart dump sci all custom 500000 2.4.xyz id mol type q xs ys zs timestep 1 run 5000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.21402839 grid = 20 20 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0025757468 estimated relative force accuracy = 7.7567851e-06 using double precision KISS FFT 3d grid and FFT values/proc = 3757 800 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 1.00027 0.0559569 6000 1 97.8417 8.98605 2000 Per MPI rank memory allocation (min/avg/max) = 8.119 | 9.735 | 11.55 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-06 812.26652 121004.85 0.49444624 447.33728 0 0 0 0 9626.4945 47088.579 -32.587809 -88113.129 -31398.055 5332.3765 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.43215e-06 6000 1 103.7 0.000105484 2000 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.58133e-06 6000 1 103.7 0.000122049 2000 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.16713e-06 6000 1 103.7 9.03122e-05 2000 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.34018e-06 6000 1 103.7 9.38933e-05 2000 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.66567e-06 6000 1 103.7 0.000126055 2000 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.22331e-06 6000 1 103.7 0.000105609 2000 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.22082e-06 6000 1 103.7 9.17403e-05 2000 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.54019e-06 6000 1 103.7 0.000101704 2000 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.11837e-06 6000 1 103.7 9.18052e-05 2000 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.19764e-06 6000 1 103.7 0.00010393 2000 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.13428e-06 6000 1 103.7 9.62568e-05 2000 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.65064e-06 6000 1 103.7 0.000114822 2000 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.35168e-06 6000 1 103.7 0.000108376 2000 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.22872e-06 6000 1 103.7 0.000104712 2000 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.2267e-06 6000 1 103.7 0.000102736 2000 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.03858e-06 6000 1 103.7 9.36343e-05 2000 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.52534e-06 6000 1 103.7 9.73964e-05 2000 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.44805e-06 6000 1 103.7 0.000109306 2000 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.22259e-06 6000 1 103.7 9.75229e-05 2000 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 2.01964e-06 6000 1 103.7 0.000143694 2000 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.97 1.20724e-06 6000 1 103.7 0.000107116 2000 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.97 1.4225e-06 6000 1 103.7 0.000108241 2000 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.97 1.54784e-06 6000 1 103.7 0.000118987 2000 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.97 1.7078e-06 6000 1 103.7 0.000140234 2000 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.97 1.97865e-06 6000 1 103.7 0.000140464 2000 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.97 1.24554e-06 6000 1 103.7 9.57965e-05 2000 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.97 1.46743e-06 6000 1 103.7 0.000107612 2000 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.97 1.23258e-06 6000 1 103.7 9.82239e-05 2000 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.97 2.33747e-06 6000 1 103.7 0.000166537 2000 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.97 1.32609e-06 6000 1 103.7 0.000134988 2000 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.97 1.41669e-06 6000 1 103.7 0.000108504 2000 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.97 1.12548e-06 6000 1 103.7 0.000103112 2000 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.97 1.26391e-06 6000 1 103.7 0.000104219 2000 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.97 1.26509e-06 6000 1 103.7 9.59621e-05 2000 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.97 1.2648e-06 6000 1 103.7 9.65126e-05 2000 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.97 1.16928e-06 6000 1 103.7 9.76794e-05 2000 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.97 1.70396e-06 6000 1 103.7 0.000123032 2000 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.97 1.34099e-06 6000 1 103.7 9.58211e-05 2000 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.97 1.13191e-06 6000 1 103.7 9.52164e-05 2000 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.23298e-06 6000 1 103.7 9.17335e-05 2000 SHAKE stats (type/ave/delta/count) on step 2050000 1 0.97 1.39725e-06 6000 1 103.7 0.000127455 2000 SHAKE stats (type/ave/delta/count) on step 2100000 1 0.97 1.39798e-06 6000 1 103.7 9.26453e-05 2000 SHAKE stats (type/ave/delta/count) on step 2150000 1 0.97 1.54323e-06 6000 1 103.7 9.87971e-05 2000 SHAKE stats (type/ave/delta/count) on step 2200000 1 0.97 1.38071e-06 6000 1 103.7 0.000105793 2000 SHAKE stats (type/ave/delta/count) on step 2250000 1 0.97 1.17361e-06 6000 1 103.7 0.000106896 2000 SHAKE stats (type/ave/delta/count) on step 2300000 1 0.97 1.31945e-06 6000 1 103.7 9.24507e-05 2000 SHAKE stats (type/ave/delta/count) on step 2350000 1 0.97 1.1715e-06 6000 1 103.7 9.0695e-05 2000 SHAKE stats (type/ave/delta/count) on step 2400000 1 0.97 1.26509e-06 6000 1 103.7 0.000124479 2000 SHAKE stats (type/ave/delta/count) on step 2450000 1 0.97 1.2625e-06 6000 1 103.7 0.000114928 2000 SHAKE stats (type/ave/delta/count) on step 2500000 1 0.97 1.43244e-06 6000 1 103.7 0.000113405 2000 SHAKE stats (type/ave/delta/count) on step 2550000 1 0.97 1.22305e-06 6000 1 103.7 9.93012e-05 2000 SHAKE stats (type/ave/delta/count) on step 2600000 1 0.97 1.60901e-06 6000 1 103.7 0.000107747 2000 SHAKE stats (type/ave/delta/count) on step 2650000 1 0.97 1.31731e-06 6000 1 103.7 0.000100679 2000 SHAKE stats (type/ave/delta/count) on step 2700000 1 0.97 1.38259e-06 6000 1 103.7 0.000106408 2000 SHAKE stats (type/ave/delta/count) on step 2750000 1 0.97 1.61938e-06 6000 1 103.7 0.000109684 2000 SHAKE stats (type/ave/delta/count) on step 2800000 1 0.97 1.44351e-06 6000 1 103.7 0.000103044 2000 SHAKE stats (type/ave/delta/count) on step 2850000 1 0.97 2.17228e-06 6000 1 103.7 0.000136738 2000 SHAKE stats (type/ave/delta/count) on step 2900000 1 0.97 1.58422e-06 6000 1 103.7 0.000104739 2000 SHAKE stats (type/ave/delta/count) on step 2950000 1 0.97 1.38442e-06 6000 1 103.7 0.000140952 2000 SHAKE stats (type/ave/delta/count) on step 3000000 1 0.97 1.16189e-06 6000 1 103.7 0.000101393 2000 SHAKE stats (type/ave/delta/count) on step 3050000 1 0.97 1.15094e-06 6000 1 103.7 0.000101746 2000 SHAKE stats (type/ave/delta/count) on step 3100000 1 0.97 1.49902e-06 6000 1 103.7 0.00011248 2000 SHAKE stats (type/ave/delta/count) on step 3150000 1 0.97 1.19933e-06 6000 1 103.7 9.84504e-05 2000 SHAKE stats (type/ave/delta/count) on step 3200000 1 0.97 1.27075e-06 6000 1 103.7 9.62187e-05 2000 SHAKE stats (type/ave/delta/count) on step 3250000 1 0.97 1.70849e-06 6000 1 103.7 9.97828e-05 2000 SHAKE stats (type/ave/delta/count) on step 3300000 1 0.97 1.24046e-06 6000 1 103.7 0.000112981 2000 SHAKE stats (type/ave/delta/count) on step 3350000 1 0.97 1.34011e-06 6000 1 103.7 0.000100177 2000 SHAKE stats (type/ave/delta/count) on step 3400000 1 0.97 1.11188e-06 6000 1 103.7 9.40126e-05 2000 SHAKE stats (type/ave/delta/count) on step 3450000 1 0.97 1.22695e-06 6000 1 103.7 0.000103688 2000 SHAKE stats (type/ave/delta/count) on step 3500000 1 0.97 1.07502e-06 6000 1 103.7 9.95271e-05 2000 SHAKE stats (type/ave/delta/count) on step 3550000 1 0.97 1.32338e-06 6000 1 103.7 9.60828e-05 2000 SHAKE stats (type/ave/delta/count) on step 3600000 1 0.97 1.2628e-06 6000 1 103.7 0.000109501 2000 SHAKE stats (type/ave/delta/count) on step 3650000 1 0.97 1.37642e-06 6000 1 103.7 0.000101748 2000 SHAKE stats (type/ave/delta/count) on step 3700000 1 0.97 1.23693e-06 6000 1 103.7 0.000106233 2000 SHAKE stats (type/ave/delta/count) on step 3750000 1 0.97 1.05401e-06 6000 1 103.7 9.21122e-05 2000 SHAKE stats (type/ave/delta/count) on step 3800000 1 0.97 1.48745e-06 6000 1 103.7 0.000112798 2000 SHAKE stats (type/ave/delta/count) on step 3850000 1 0.97 1.56123e-06 6000 1 103.7 0.000128838 2000 SHAKE stats (type/ave/delta/count) on step 3900000 1 0.97 1.20178e-06 6000 1 103.7 9.62185e-05 2000 SHAKE stats (type/ave/delta/count) on step 3950000 1 0.97 1.07873e-06 6000 1 103.7 9.14958e-05 2000 SHAKE stats (type/ave/delta/count) on step 4000000 1 0.97 1.19188e-06 6000 1 103.7 9.49696e-05 2000 SHAKE stats (type/ave/delta/count) on step 4050000 1 0.97 1.25364e-06 6000 1 103.7 9.56501e-05 2000 SHAKE stats (type/ave/delta/count) on step 4100000 1 0.97 1.75458e-06 6000 1 103.7 0.000134169 2000 SHAKE stats (type/ave/delta/count) on step 4150000 1 0.97 1.28752e-06 6000 1 103.7 9.72144e-05 2000 SHAKE stats (type/ave/delta/count) on step 4200000 1 0.97 1.17174e-06 6000 1 103.7 9.44962e-05 2000 SHAKE stats (type/ave/delta/count) on step 4250000 1 0.97 1.22596e-06 6000 1 103.7 0.000106327 2000 SHAKE stats (type/ave/delta/count) on step 4300000 1 0.97 1.02348e-06 6000 1 103.7 8.78194e-05 2000 SHAKE stats (type/ave/delta/count) on step 4350000 1 0.97 1.49207e-06 6000 1 103.7 0.00011599 2000 SHAKE stats (type/ave/delta/count) on step 4400000 1 0.97 1.22226e-06 6000 1 103.7 9.14633e-05 2000 SHAKE stats (type/ave/delta/count) on step 4450000 1 0.97 1.54773e-06 6000 1 103.7 0.000104603 2000 SHAKE stats (type/ave/delta/count) on step 4500000 1 0.97 2.0237e-06 6000 1 103.7 0.000134788 2000 SHAKE stats (type/ave/delta/count) on step 4550000 1 0.97 1.18863e-06 6000 1 103.7 9.25731e-05 2000 SHAKE stats (type/ave/delta/count) on step 4600000 1 0.97 1.20549e-06 6000 1 103.7 9.15417e-05 2000 SHAKE stats (type/ave/delta/count) on step 4650000 1 0.97 1.28165e-06 6000 1 103.7 9.77659e-05 2000 SHAKE stats (type/ave/delta/count) on step 4700000 1 0.97 1.21042e-06 6000 1 103.7 0.000108261 2000 SHAKE stats (type/ave/delta/count) on step 4750000 1 0.97 1.22179e-06 6000 1 103.7 9.53395e-05 2000 SHAKE stats (type/ave/delta/count) on step 4800000 1 0.97 1.4007e-06 6000 1 103.7 0.000100068 2000 SHAKE stats (type/ave/delta/count) on step 4850000 1 0.97 1.39351e-06 6000 1 103.7 0.000103665 2000 SHAKE stats (type/ave/delta/count) on step 4900000 1 0.97 1.321e-06 6000 1 103.7 0.000111318 2000 SHAKE stats (type/ave/delta/count) on step 4950000 1 0.97 1.21106e-06 6000 1 103.7 9.43298e-05 2000 SHAKE stats (type/ave/delta/count) on step 5000000 1 0.97 1.07932e-06 6000 1 103.7 9.80131e-05 2000 5000000 5000000 -137.35074 121004.85 0.49444624 302.59032 0 0 0 0 5037.5588 61851.875 -32.587809 -88102.471 -21213.037 3606.9552 Loop time of 58997.3 on 32 procs for 5000000 steps with 6000 atoms Performance: 7.322 ns/day, 3.278 hours/ns, 84.750 timesteps/s 98.1% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.1238 | 21060 | 47484 |14567.5 | 35.70 Bond | 3.4752 | 5.5912 | 8.379 | 42.1 | 0.01 Kspace | 5972.3 | 32580 | 54066 |11802.6 | 55.22 Neigh | 2442.7 | 2464.7 | 2512.8 | 46.4 | 4.18 Comm | 161.45 | 963.7 | 1409 |1515.1 | 1.63 Output | 0.011161 | 0.012767 | 0.014149 | 0.8 | 0.00 Modify | 1552.7 | 1822.4 | 2180.2 | 585.7 | 3.09 Other | | 100.8 | | | 0.17 Nlocal: 187.5 ave 387 max 0 min Histogram: 15 1 0 0 0 0 0 0 1 15 Nghost: 5155.62 ave 10366 max 23 min Histogram: 8 0 0 8 0 0 8 0 0 8 Neighs: 145031 ave 332815 max 0 min Histogram: 16 0 0 0 0 0 3 1 2 10 Total # of neighbors = 4640999 Ave neighs/atom = 773.49983 Ave special neighs/atom = 2 Neighbor list builds = 247379 Dangerous builds = 0 undump sci restart 0 dump sci all custom 5000000 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) = 0.21402839 grid = 20 20 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0025757468 estimated relative force accuracy = 7.7567851e-06 using double precision KISS FFT 3d grid and FFT values/proc = 3757 800 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 5000000 1 0.97 1.07932e-06 6000 1 103.7 9.80131e-05 2000 Per MPI rank memory allocation (min/avg/max) = 8.256 | 10.05 | 11.55 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 5000000 5000000 -137.03481 121004.85 0.49444624 302.59032 0 0 0 0 5037.5588 61851.875 -32.587809 -88102.471 -21213.037 3606.9552 Loop time of 1.35171e-05 on 32 procs for 0 steps with 6000 atoms 105.0% 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 | | 1.352e-05 | | |100.00 Nlocal: 187.5 ave 387 max 0 min Histogram: 15 1 0 0 0 0 0 0 1 15 Nghost: 5155.62 ave 10366 max 23 min Histogram: 8 0 0 8 0 0 8 0 0 8 Neighs: 145031 ave 332815 max 0 min Histogram: 16 0 0 0 0 0 3 1 2 10 Total # of neighbors = 4640999 Ave neighs/atom = 773.49983 Ave special neighs/atom = 2 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out