#------------------------------------------------------------------------------- # 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 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 = 0.002 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 generated 0 of 36 mixed pair_coeff terms from geometric mixing rule WARNING: Inconsistent image flags (../domain.cpp:814) SHAKE stats (type/ave/delta/count) on step 0 2 1.00023 0.0893345 8304 2 97.8685 12.7661 2768 Per MPI rank memory allocation (min/avg/max) = 11.6 | 11.79 | 12.21 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 7594.9212 83836.018 1.448125 428.55654 9.2631108 70.925409 0 0 25449.721 -180619.19 0 0 -155089.28 8088.7858 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.53407e-06 8304 2 103.7 0.000118142 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.37405e-06 8304 2 103.7 0.000120972 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.64049e-06 8304 2 103.7 0.000109242 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.72213e-06 8304 2 103.7 0.000110394 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.20408e-06 8304 2 103.7 9.81621e-05 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.43307e-06 8304 2 103.7 0.000104192 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.52248e-06 8304 2 103.7 9.24697e-05 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.58097e-06 8304 2 103.7 0.000119519 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.30119e-06 8304 2 103.7 0.000110462 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.34517e-06 8304 2 103.7 0.000102229 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.40381e-06 8304 2 103.7 9.97077e-05 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.51961e-06 8304 2 103.7 0.000104666 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.55825e-06 8304 2 103.7 0.000130485 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.77665e-06 8304 2 103.7 9.71185e-05 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.33886e-06 8304 2 103.7 0.000103187 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.2479e-06 8304 2 103.7 0.000155091 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.2079e-06 8304 2 103.7 9.75503e-05 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.27641e-06 8304 2 103.7 9.91362e-05 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.18413e-06 8304 2 103.7 9.75042e-05 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.48505e-06 8304 2 103.7 0.000111433 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.38672e-06 8304 2 103.7 0.000100325 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.27156e-06 8304 2 103.7 0.000108233 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.50762e-06 8304 2 103.7 0.000116089 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 2.32153e-06 8304 2 103.7 0.000162269 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.776e-06 8304 2 103.7 9.52603e-05 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.81679e-06 8304 2 103.7 0.0001196 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.83601e-06 8304 2 103.7 0.00011043 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.98383e-06 8304 2 103.7 0.000124787 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.61467e-06 8304 2 103.7 0.000121445 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.52294e-06 8304 2 103.7 0.000110621 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.67761e-06 8304 2 103.7 0.000102049 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.56169e-06 8304 2 103.7 0.000100481 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.1845e-06 8304 2 103.7 0.000100392 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.40351e-06 8304 2 103.7 0.000107279 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.24351e-06 8304 2 103.7 0.000110671 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.43057e-06 8304 2 103.7 9.28621e-05 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.57399e-06 8304 2 103.7 0.000108986 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.63993e-06 8304 2 103.7 0.000123492 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 2.12528e-06 8304 2 103.7 0.00012696 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 2.26897e-06 8304 2 103.7 0.000161244 2768 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.64599e-06 8304 2 103.7 0.000132705 2768 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.77069e-06 8304 2 103.7 0.000123249 2768 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.84451e-06 8304 2 103.7 0.000125674 2768 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.64581e-06 8304 2 103.7 0.000112136 2768 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.30185e-06 8304 2 103.7 9.81125e-05 2768 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.39397e-06 8304 2 103.7 9.89923e-05 2768 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.36888e-06 8304 2 103.7 0.00010557 2768 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.44955e-06 8304 2 103.7 0.000104472 2768 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.37917e-06 8304 2 103.7 0.000102088 2768 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.50755e-06 8304 2 103.7 9.75981e-05 2768 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.42123e-06 8304 2 103.7 0.00010552 2768 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.50294e-06 8304 2 103.7 9.84803e-05 2768 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.77624e-06 8304 2 103.7 0.000106449 2768 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.43869e-06 8304 2 103.7 0.000128789 2768 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.40839e-06 8304 2 103.7 0.000118556 2768 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.40808e-06 8304 2 103.7 0.000106375 2768 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.84968e-06 8304 2 103.7 0.000117605 2768 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.27347e-06 8304 2 103.7 0.000103242 2768 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.3962e-06 8304 2 103.7 9.71995e-05 2768 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.54454e-06 8304 2 103.7 9.81567e-05 2768 SHAKE stats (type/ave/delta/count) on step 3050000 2 0.97 1.45146e-06 8304 2 103.7 0.000120244 2768 SHAKE stats (type/ave/delta/count) on step 3100000 2 0.97 1.49839e-06 8304 2 103.7 0.000106757 2768 SHAKE stats (type/ave/delta/count) on step 3150000 2 0.97 1.41494e-06 8304 2 103.7 0.000156792 2768 SHAKE stats (type/ave/delta/count) on step 3200000 2 0.97 1.80834e-06 8304 2 103.7 0.000110747 2768 SHAKE stats (type/ave/delta/count) on step 3250000 2 0.97 1.51734e-06 8304 2 103.7 0.000104168 2768 SHAKE stats (type/ave/delta/count) on step 3300000 2 0.97 1.36669e-06 8304 2 103.7 0.000101207 2768 SHAKE stats (type/ave/delta/count) on step 3350000 2 0.97 2.02448e-06 8304 2 103.7 0.000114561 2768 SHAKE stats (type/ave/delta/count) on step 3400000 2 0.97 1.94969e-06 8304 2 103.7 0.00011533 2768 SHAKE stats (type/ave/delta/count) on step 3450000 2 0.97 2.03129e-06 8304 2 103.7 0.000112784 2768 SHAKE stats (type/ave/delta/count) on step 3500000 2 0.97 1.38395e-06 8304 2 103.7 0.000110051 2768 SHAKE stats (type/ave/delta/count) on step 3550000 2 0.97 1.27417e-06 8304 2 103.7 0.000114225 2768 SHAKE stats (type/ave/delta/count) on step 3600000 2 0.97 1.22684e-06 8304 2 103.7 9.95906e-05 2768 SHAKE stats (type/ave/delta/count) on step 3650000 2 0.97 1.55397e-06 8304 2 103.7 0.000109675 2768 SHAKE stats (type/ave/delta/count) on step 3700000 2 0.97 1.3138e-06 8304 2 103.7 0.000114995 2768 SHAKE stats (type/ave/delta/count) on step 3750000 2 0.97 1.43681e-06 8304 2 103.7 0.000126551 2768 SHAKE stats (type/ave/delta/count) on step 3800000 2 0.97 1.29371e-06 8304 2 103.7 9.91807e-05 2768 SHAKE stats (type/ave/delta/count) on step 3850000 2 0.97 1.58318e-06 8304 2 103.7 0.000112593 2768 SHAKE stats (type/ave/delta/count) on step 3900000 2 0.97 1.61237e-06 8304 2 103.7 0.000134287 2768 SHAKE stats (type/ave/delta/count) on step 3950000 2 0.97 1.37048e-06 8304 2 103.7 9.33111e-05 2768 SHAKE stats (type/ave/delta/count) on step 4000000 2 0.97 1.64023e-06 8304 2 103.7 0.000125988 2768 SHAKE stats (type/ave/delta/count) on step 4050000 2 0.97 1.55639e-06 8304 2 103.7 9.97038e-05 2768 SHAKE stats (type/ave/delta/count) on step 4100000 2 0.97 1.27796e-06 8304 2 103.7 9.64154e-05 2768 SHAKE stats (type/ave/delta/count) on step 4150000 2 0.97 1.50323e-06 8304 2 103.7 0.00011064 2768 SHAKE stats (type/ave/delta/count) on step 4200000 2 0.97 2.21997e-06 8304 2 103.7 0.000129422 2768 SHAKE stats (type/ave/delta/count) on step 4250000 2 0.97 1.59271e-06 8304 2 103.7 0.0001095 2768 SHAKE stats (type/ave/delta/count) on step 4300000 2 0.97 1.72213e-06 8304 2 103.7 0.000103953 2768 SHAKE stats (type/ave/delta/count) on step 4350000 2 0.97 1.64685e-06 8304 2 103.7 0.000116035 2768 SHAKE stats (type/ave/delta/count) on step 4400000 2 0.97 1.5688e-06 8304 2 103.7 0.000117312 2768 SHAKE stats (type/ave/delta/count) on step 4450000 2 0.97 1.50738e-06 8304 2 103.7 0.000126975 2768 SHAKE stats (type/ave/delta/count) on step 4500000 2 0.97 1.59952e-06 8304 2 103.7 9.63516e-05 2768 SHAKE stats (type/ave/delta/count) on step 4550000 2 0.97 1.46258e-06 8304 2 103.7 0.000119048 2768 SHAKE stats (type/ave/delta/count) on step 4600000 2 0.97 1.72288e-06 8304 2 103.7 0.000124305 2768 SHAKE stats (type/ave/delta/count) on step 4650000 2 0.97 1.28319e-06 8304 2 103.7 0.000100676 2768 SHAKE stats (type/ave/delta/count) on step 4700000 2 0.97 1.25443e-06 8304 2 103.7 0.000121312 2768 SHAKE stats (type/ave/delta/count) on step 4750000 2 0.97 1.44398e-06 8304 2 103.7 0.000110147 2768 SHAKE stats (type/ave/delta/count) on step 4800000 2 0.97 1.56722e-06 8304 2 103.7 0.000121656 2768 SHAKE stats (type/ave/delta/count) on step 4850000 2 0.97 1.20023e-06 8304 2 103.7 0.000106947 2768 SHAKE stats (type/ave/delta/count) on step 4900000 2 0.97 1.25141e-06 8304 2 103.7 0.000102931 2768 SHAKE stats (type/ave/delta/count) on step 4950000 2 0.97 1.40247e-06 8304 2 103.7 9.67962e-05 2768 SHAKE stats (type/ave/delta/count) on step 5000000 2 0.97 1.46457e-06 8304 2 103.7 0.000107162 2768 5000000 5000000 2204.506 99608.125 1.2188266 300.41655 52.95482 124.71768 0 0 22391.991 -178568.56 0 0 -155998.9 5670.2089 Loop time of 17739.3 on 32 procs for 5000000 steps with 9101 atoms Performance: 24.353 ns/day, 0.986 hours/ns, 281.860 timesteps/s 99.0% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6357.9 | 10799 | 14401 |2720.5 | 60.88 Bond | 3.5676 | 9.4139 | 17.751 | 126.6 | 0.05 Neigh | 879.91 | 883.21 | 887.04 | 6.7 | 4.98 Comm | 1196.1 | 4530.3 | 8332.7 |3721.0 | 25.54 Output | 0.010862 | 0.013156 | 0.015287 | 1.2 | 0.00 Modify | 1173.5 | 1452.3 | 2087.2 | 969.5 | 8.19 Other | | 64.75 | | | 0.36 Nlocal: 284.406 ave 346 max 223 min Histogram: 6 4 5 1 0 0 0 6 5 5 Nghost: 4229.84 ave 5324 max 3143 min Histogram: 16 0 0 0 0 0 0 0 0 16 Neighs: 84816.9 ave 119652 max 45508 min Histogram: 7 1 0 6 2 0 1 2 9 4 Total # of neighbors = 2714140 Ave neighs/atom = 298.22437 Ave special neighs/atom = 1.8929788 Neighbor list builds = 239499 Dangerous builds = 0 undump sci restart 0 dump sci all custom 5000000 2.4.xyz id mol type q xs ys zs run 0 generated 0 of 36 mixed pair_coeff terms from geometric mixing rule WARNING: Inconsistent image flags (../domain.cpp:814) SHAKE stats (type/ave/delta/count) on step 5000000 2 0.97 1.46457e-06 8304 2 103.7 0.000107162 2768 Per MPI rank memory allocation (min/avg/max) = 11.6 | 11.9 | 12.21 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 2205.442 99608.125 1.2188266 300.41655 52.95482 124.71768 0 0 22391.991 -178568.56 0 0 -155998.9 5670.2089 Loop time of 7.07712e-06 on 32 procs for 0 steps with 9101 atoms 109.5% 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 | | 7.077e-06 | | |100.00 Nlocal: 284.406 ave 346 max 223 min Histogram: 6 4 5 1 0 0 0 6 5 5 Nghost: 4229.84 ave 5324 max 3143 min Histogram: 16 0 0 0 0 0 0 0 0 16 Neighs: 84816.9 ave 119652 max 45508 min Histogram: 7 1 0 6 2 0 1 2 9 4 Total # of neighbors = 2714140 Ave neighs/atom = 298.22437 Ave special neighs/atom = 1.8929788 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out