#------------------------------------------------------------------------------- # Stage 2.5: 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 2 b 2 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 2768 = # 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 2.5_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 2.5_instantaneous.txt restart 5000000 2.5.restart dump sci all custom 500000 2.5.xyz id mol type q xs ys zs timestep 1 run 5000000 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 4.7739e-11 8304 2 103.7 3.92902e-09 2768 Per MPI rank memory allocation (min/avg/max) = 11.64 | 11.8 | 12.22 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-06 506.44178 96460.259 1.2586016 300.36792 55.534849 116.70854 0 0 20535.663 -166842.9 -431.67098 0 -146135 5669.291 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.17871e-06 8304 2 103.7 9.49674e-05 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.32224e-06 8304 2 103.7 0.000102523 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.5411e-06 8304 2 103.7 0.000105215 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.35243e-06 8304 2 103.7 0.000100777 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.81419e-06 8304 2 103.7 0.000133553 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.39862e-06 8304 2 103.7 0.000104319 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.26436e-06 8304 2 103.7 0.000112326 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.71729e-06 8304 2 103.7 0.00010896 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.55923e-06 8304 2 103.7 0.000108489 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.57759e-06 8304 2 103.7 0.000109075 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.17847e-06 8304 2 103.7 9.89021e-05 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.56349e-06 8304 2 103.7 0.000107095 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.33962e-06 8304 2 103.7 0.000101471 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.54797e-06 8304 2 103.7 0.000100425 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.52569e-06 8304 2 103.7 0.000120729 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.4752e-06 8304 2 103.7 0.000103233 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.57859e-06 8304 2 103.7 0.000124867 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.51634e-06 8304 2 103.7 0.000109291 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.29304e-06 8304 2 103.7 0.000105568 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.37301e-06 8304 2 103.7 0.000107097 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.65935e-06 8304 2 103.7 0.000126735 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.36489e-06 8304 2 103.7 0.000107461 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.492e-06 8304 2 103.7 0.000106359 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.24426e-06 8304 2 103.7 0.000108473 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.66016e-06 8304 2 103.7 0.000107597 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.64554e-06 8304 2 103.7 0.000102201 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.73605e-06 8304 2 103.7 0.000114818 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.41139e-06 8304 2 103.7 9.12654e-05 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.41667e-06 8304 2 103.7 0.000124943 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.55642e-06 8304 2 103.7 0.000120518 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.70246e-06 8304 2 103.7 9.75946e-05 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.70896e-06 8304 2 103.7 0.000108997 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.62209e-06 8304 2 103.7 0.00011365 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.29958e-06 8304 2 103.7 9.69341e-05 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.57661e-06 8304 2 103.7 0.000114169 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.39624e-06 8304 2 103.7 0.000108643 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.36563e-06 8304 2 103.7 0.000111163 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.31519e-06 8304 2 103.7 9.77261e-05 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.34408e-06 8304 2 103.7 0.000100418 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.87931e-06 8304 2 103.7 0.000113153 2768 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.45526e-06 8304 2 103.7 0.000110318 2768 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.53932e-06 8304 2 103.7 0.000110487 2768 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.65866e-06 8304 2 103.7 0.000111849 2768 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.32718e-06 8304 2 103.7 0.000109535 2768 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.53918e-06 8304 2 103.7 0.000107382 2768 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.46073e-06 8304 2 103.7 0.000123709 2768 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.61856e-06 8304 2 103.7 0.000100348 2768 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.08605e-06 8304 2 103.7 0.000101213 2768 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.69468e-06 8304 2 103.7 9.77793e-05 2768 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.60435e-06 8304 2 103.7 0.000112016 2768 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.49615e-06 8304 2 103.7 0.000103555 2768 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.46459e-06 8304 2 103.7 0.000101378 2768 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 2.80884e-06 8304 2 103.7 0.000189753 2768 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 2.10822e-06 8304 2 103.7 0.000119593 2768 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.97866e-06 8304 2 103.7 0.000109917 2768 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.44322e-06 8304 2 103.7 0.000103555 2768 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.88313e-06 8304 2 103.7 0.000114949 2768 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.35289e-06 8304 2 103.7 9.97222e-05 2768 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.29305e-06 8304 2 103.7 9.56546e-05 2768 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.34942e-06 8304 2 103.7 9.90543e-05 2768 SHAKE stats (type/ave/delta/count) on step 3050000 2 0.97 1.87968e-06 8304 2 103.7 0.00013057 2768 SHAKE stats (type/ave/delta/count) on step 3100000 2 0.97 1.91826e-06 8304 2 103.7 0.000128715 2768 SHAKE stats (type/ave/delta/count) on step 3150000 2 0.97 1.8686e-06 8304 2 103.7 0.000119672 2768 SHAKE stats (type/ave/delta/count) on step 3200000 2 0.97 1.49333e-06 8304 2 103.7 0.000121923 2768 SHAKE stats (type/ave/delta/count) on step 3250000 2 0.97 1.23905e-06 8304 2 103.7 0.00011968 2768 SHAKE stats (type/ave/delta/count) on step 3300000 2 0.97 1.46615e-06 8304 2 103.7 0.000102445 2768 SHAKE stats (type/ave/delta/count) on step 3350000 2 0.97 1.61755e-06 8304 2 103.7 0.000124153 2768 SHAKE stats (type/ave/delta/count) on step 3400000 2 0.97 1.33187e-06 8304 2 103.7 9.87911e-05 2768 SHAKE stats (type/ave/delta/count) on step 3450000 2 0.97 1.32009e-06 8304 2 103.7 9.58061e-05 2768 SHAKE stats (type/ave/delta/count) on step 3500000 2 0.97 1.62357e-06 8304 2 103.7 0.000128772 2768 SHAKE stats (type/ave/delta/count) on step 3550000 2 0.97 1.93962e-06 8304 2 103.7 0.000156196 2768 SHAKE stats (type/ave/delta/count) on step 3600000 2 0.97 1.34394e-06 8304 2 103.7 0.000106352 2768 SHAKE stats (type/ave/delta/count) on step 3650000 2 0.97 1.58896e-06 8304 2 103.7 0.000119372 2768 SHAKE stats (type/ave/delta/count) on step 3700000 2 0.97 1.43693e-06 8304 2 103.7 0.000140977 2768 SHAKE stats (type/ave/delta/count) on step 3750000 2 0.97 1.24412e-06 8304 2 103.7 0.000120936 2768 SHAKE stats (type/ave/delta/count) on step 3800000 2 0.97 1.80615e-06 8304 2 103.7 0.00012636 2768 SHAKE stats (type/ave/delta/count) on step 3850000 2 0.97 1.32306e-06 8304 2 103.7 0.000116441 2768 SHAKE stats (type/ave/delta/count) on step 3900000 2 0.97 1.36535e-06 8304 2 103.7 0.00011048 2768 SHAKE stats (type/ave/delta/count) on step 3950000 2 0.97 1.36557e-06 8304 2 103.7 0.000116594 2768 SHAKE stats (type/ave/delta/count) on step 4000000 2 0.97 1.33947e-06 8304 2 103.7 0.000115043 2768 SHAKE stats (type/ave/delta/count) on step 4050000 2 0.97 1.40479e-06 8304 2 103.7 0.000102041 2768 SHAKE stats (type/ave/delta/count) on step 4100000 2 0.97 1.10606e-06 8304 2 103.7 0.000110438 2768 SHAKE stats (type/ave/delta/count) on step 4150000 2 0.97 1.60586e-06 8304 2 103.7 0.000110977 2768 SHAKE stats (type/ave/delta/count) on step 4200000 2 0.97 1.63762e-06 8304 2 103.7 0.00012032 2768 SHAKE stats (type/ave/delta/count) on step 4250000 2 0.97 1.94919e-06 8304 2 103.7 0.00013944 2768 SHAKE stats (type/ave/delta/count) on step 4300000 2 0.97 1.36056e-06 8304 2 103.7 0.000136939 2768 SHAKE stats (type/ave/delta/count) on step 4350000 2 0.97 1.38539e-06 8304 2 103.7 0.000104536 2768 SHAKE stats (type/ave/delta/count) on step 4400000 2 0.97 1.45863e-06 8304 2 103.7 9.72598e-05 2768 SHAKE stats (type/ave/delta/count) on step 4450000 2 0.97 1.8503e-06 8304 2 103.7 0.00011512 2768 SHAKE stats (type/ave/delta/count) on step 4500000 2 0.97 1.77309e-06 8304 2 103.7 0.00012216 2768 SHAKE stats (type/ave/delta/count) on step 4550000 2 0.97 1.44736e-06 8304 2 103.7 0.000102247 2768 SHAKE stats (type/ave/delta/count) on step 4600000 2 0.97 1.48515e-06 8304 2 103.7 0.000158541 2768 SHAKE stats (type/ave/delta/count) on step 4650000 2 0.97 1.23306e-06 8304 2 103.7 0.000107622 2768 SHAKE stats (type/ave/delta/count) on step 4700000 2 0.97 1.28967e-06 8304 2 103.7 0.000106787 2768 SHAKE stats (type/ave/delta/count) on step 4750000 2 0.97 1.49395e-06 8304 2 103.7 0.00010118 2768 SHAKE stats (type/ave/delta/count) on step 4800000 2 0.97 1.80604e-06 8304 2 103.7 0.000122728 2768 SHAKE stats (type/ave/delta/count) on step 4850000 2 0.97 1.1716e-06 8304 2 103.7 0.000105155 2768 SHAKE stats (type/ave/delta/count) on step 4900000 2 0.97 1.35231e-06 8304 2 103.7 9.82948e-05 2768 SHAKE stats (type/ave/delta/count) on step 4950000 2 0.97 1.59639e-06 8304 2 103.7 0.000114523 2768 SHAKE stats (type/ave/delta/count) on step 5000000 2 0.97 1.30817e-06 8304 2 103.7 0.000103742 2768 5000000 5000000 -563.02937 96460.259 1.2586016 297.34531 45.029369 115.32549 0 0 20483.064 -170885.17 -431.67098 0 -150241.75 5612.2408 Loop time of 15639.8 on 32 procs for 5000000 steps with 9101 atoms Performance: 27.622 ns/day, 0.869 hours/ns, 319.697 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 | 9334.7 | 10796 | 11923 | 564.3 | 69.03 Bond | 3.8686 | 9.6945 | 29.697 | 169.7 | 0.06 Neigh | 779.85 | 782.32 | 784.56 | 6.7 | 5.00 Comm | 1400.3 | 2466.7 | 3924.6 |1151.4 | 15.77 Output | 0.0088634 | 0.011117 | 0.013234 | 1.3 | 0.00 Modify | 1459.2 | 1524.4 | 1612 | 134.5 | 9.75 Other | | 61.07 | | | 0.39 Nlocal: 284.406 ave 308 max 260 min Histogram: 1 0 2 6 6 7 6 2 1 1 Nghost: 4861.91 ave 4912 max 4832 min Histogram: 6 2 5 3 8 3 2 2 0 1 Neighs: 85001.9 ave 94624 max 75350 min Histogram: 2 1 3 4 7 5 3 3 2 2 Total # of neighbors = 2720060 Ave neighs/atom = 298.87485 Ave special neighs/atom = 1.8929788 Neighbor list builds = 239775 Dangerous builds = 0 undump sci restart 0 dump sci all custom 5000000 2.5.xyz id mol type q xs ys zs run 0 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 5000000 2 0.97 1.30817e-06 8304 2 103.7 0.000103742 2768 Per MPI rank memory allocation (min/avg/max) = 11.64 | 11.8 | 12.22 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 -562.06514 96460.259 1.2586016 297.34531 45.029369 115.32549 0 0 20483.064 -170885.17 -431.67098 0 -150241.75 5612.2408 Loop time of 7.12619e-06 on 32 procs for 0 steps with 9101 atoms 110.5% 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 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 | | 7.126e-06 | | |100.00 Nlocal: 284.406 ave 308 max 260 min Histogram: 1 0 2 6 6 7 6 2 1 1 Nghost: 4861.91 ave 4912 max 4832 min Histogram: 6 2 5 3 8 3 2 2 0 1 Neighs: 85001.9 ave 94624 max 75350 min Histogram: 2 1 3 4 7 5 3 3 2 2 Total # of neighbors = 2720060 Ave neighs/atom = 298.87485 Ave special neighs/atom = 1.8929788 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.6_NVT.out