#------------------------------------------------------------------------------- # 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 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 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) = 0.2507789 grid = 30 30 50 stencil order = 5 estimated absolute RMS force accuracy = 0.0034789377 estimated relative force accuracy = 1.0476718e-05 using double precision KISS FFT 3d grid and FFT values/proc = 6292 1800 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 1.00199 0.0727015 5784 2 97.4408 9.71746 1928 Per MPI rank memory allocation (min/avg/max) = 10.93 | 12.31 | 13.51 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 1171.8158 137108.63 0.6335873 427.16581 5.0494758 16.39265 0 0 19958.449 -2136.1182 -77.153063 -152577.65 -134733.88 5676.3721 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.23982e-06 5784 2 103.7 9.15858e-05 1928 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.33663e-06 5784 2 103.7 0.000109233 1928 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.31097e-06 5784 2 103.7 0.000107639 1928 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.18689e-06 5784 2 103.7 9.2121e-05 1928 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.1073e-06 5784 2 103.7 9.82376e-05 1928 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.08758e-06 5784 2 103.7 0.000117029 1928 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.49079e-06 5784 2 103.7 0.000104481 1928 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.21966e-06 5784 2 103.7 9.37259e-05 1928 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.14612e-06 5784 2 103.7 8.67442e-05 1928 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.07527e-06 5784 2 103.7 8.96201e-05 1928 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.33874e-06 5784 2 103.7 0.000100242 1928 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.19325e-06 5784 2 103.7 0.000112876 1928 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.16079e-06 5784 2 103.7 9.12807e-05 1928 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.25644e-06 5784 2 103.7 9.27849e-05 1928 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.44407e-06 5784 2 103.7 0.000111561 1928 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.30107e-06 5784 2 103.7 9.96123e-05 1928 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 9.87823e-07 5784 2 103.7 9.39436e-05 1928 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.04031e-06 5784 2 103.7 9.72537e-05 1928 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.5872e-06 5784 2 103.7 0.000128436 1928 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.90343e-06 5784 2 103.7 9.94923e-05 1928 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.20492e-06 5784 2 103.7 9.81129e-05 1928 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.3196e-06 5784 2 103.7 9.77741e-05 1928 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.28607e-06 5784 2 103.7 0.000102102 1928 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.40777e-06 5784 2 103.7 0.000101326 1928 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.21813e-06 5784 2 103.7 9.16771e-05 1928 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.2076e-06 5784 2 103.7 9.6829e-05 1928 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.37243e-06 5784 2 103.7 0.0001014 1928 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.42466e-06 5784 2 103.7 0.000106827 1928 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.06649e-06 5784 2 103.7 0.000100431 1928 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.29618e-06 5784 2 103.7 0.000103519 1928 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.33824e-06 5784 2 103.7 0.000103045 1928 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.17546e-06 5784 2 103.7 9.23472e-05 1928 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.53198e-06 5784 2 103.7 0.000110352 1928 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.08127e-06 5784 2 103.7 0.000104677 1928 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.31358e-06 5784 2 103.7 0.000107172 1928 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.22101e-06 5784 2 103.7 0.000103453 1928 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.09164e-06 5784 2 103.7 9.76237e-05 1928 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.19569e-06 5784 2 103.7 9.62965e-05 1928 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.15378e-06 5784 2 103.7 0.000105387 1928 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.28264e-06 5784 2 103.7 0.000109604 1928 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.75488e-06 5784 2 103.7 0.000112657 1928 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.39039e-06 5784 2 103.7 0.000112625 1928 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.18389e-06 5784 2 103.7 9.4501e-05 1928 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.17783e-06 5784 2 103.7 0.000116276 1928 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.56835e-06 5784 2 103.7 9.60433e-05 1928 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.77831e-06 5784 2 103.7 0.000109692 1928 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.07621e-06 5784 2 103.7 9.741e-05 1928 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.17193e-06 5784 2 103.7 0.000110621 1928 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.03089e-06 5784 2 103.7 9.21279e-05 1928 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.30561e-06 5784 2 103.7 9.56978e-05 1928 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.13081e-06 5784 2 103.7 8.7366e-05 1928 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.13384e-06 5784 2 103.7 9.1828e-05 1928 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.05378e-06 5784 2 103.7 9.75421e-05 1928 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.07198e-06 5784 2 103.7 9.19326e-05 1928 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.21507e-06 5784 2 103.7 9.25485e-05 1928 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.47728e-06 5784 2 103.7 9.23714e-05 1928 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.29018e-06 5784 2 103.7 9.68465e-05 1928 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.11451e-06 5784 2 103.7 0.000115755 1928 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.10977e-06 5784 2 103.7 0.000101814 1928 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.61841e-06 5784 2 103.7 0.000131345 1928 SHAKE stats (type/ave/delta/count) on step 3050000 2 0.97 1.14509e-06 5784 2 103.7 9.40193e-05 1928 SHAKE stats (type/ave/delta/count) on step 3100000 2 0.97 1.19833e-06 5784 2 103.7 9.07094e-05 1928 SHAKE stats (type/ave/delta/count) on step 3150000 2 0.97 1.46945e-06 5784 2 103.7 0.000112165 1928 SHAKE stats (type/ave/delta/count) on step 3200000 2 0.97 1.30197e-06 5784 2 103.7 0.000101283 1928 SHAKE stats (type/ave/delta/count) on step 3250000 2 0.97 1.00116e-06 5784 2 103.7 9.22091e-05 1928 SHAKE stats (type/ave/delta/count) on step 3300000 2 0.97 1.58085e-06 5784 2 103.7 0.000104263 1928 SHAKE stats (type/ave/delta/count) on step 3350000 2 0.97 1.15788e-06 5784 2 103.7 9.51249e-05 1928 SHAKE stats (type/ave/delta/count) on step 3400000 2 0.97 1.553e-06 5784 2 103.7 0.000112631 1928 SHAKE stats (type/ave/delta/count) on step 3450000 2 0.97 1.40545e-06 5784 2 103.7 0.0001077 1928 SHAKE stats (type/ave/delta/count) on step 3500000 2 0.97 1.08463e-06 5784 2 103.7 9.86349e-05 1928 SHAKE stats (type/ave/delta/count) on step 3550000 2 0.97 1.27982e-06 5784 2 103.7 0.000104639 1928 SHAKE stats (type/ave/delta/count) on step 3600000 2 0.97 1.39059e-06 5784 2 103.7 0.000105152 1928 SHAKE stats (type/ave/delta/count) on step 3650000 2 0.97 1.15335e-06 5784 2 103.7 9.01344e-05 1928 SHAKE stats (type/ave/delta/count) on step 3700000 2 0.97 1.16794e-06 5784 2 103.7 9.71433e-05 1928 SHAKE stats (type/ave/delta/count) on step 3750000 2 0.97 1.55226e-06 5784 2 103.7 9.98834e-05 1928 SHAKE stats (type/ave/delta/count) on step 3800000 2 0.97 1.24384e-06 5784 2 103.7 0.000101056 1928 SHAKE stats (type/ave/delta/count) on step 3850000 2 0.97 1.2853e-06 5784 2 103.7 0.000111403 1928 SHAKE stats (type/ave/delta/count) on step 3900000 2 0.97 1.24312e-06 5784 2 103.7 9.724e-05 1928 SHAKE stats (type/ave/delta/count) on step 3950000 2 0.97 1.09353e-06 5784 2 103.7 8.84159e-05 1928 SHAKE stats (type/ave/delta/count) on step 4000000 2 0.97 1.10313e-06 5784 2 103.7 8.35948e-05 1928 SHAKE stats (type/ave/delta/count) on step 4050000 2 0.97 1.5247e-06 5784 2 103.7 0.000128992 1928 SHAKE stats (type/ave/delta/count) on step 4100000 2 0.97 1.31395e-06 5784 2 103.7 0.000107239 1928 SHAKE stats (type/ave/delta/count) on step 4150000 2 0.97 1.02161e-06 5784 2 103.7 9.37146e-05 1928 SHAKE stats (type/ave/delta/count) on step 4200000 2 0.97 1.25372e-06 5784 2 103.7 0.000114416 1928 SHAKE stats (type/ave/delta/count) on step 4250000 2 0.97 1.30502e-06 5784 2 103.7 9.72452e-05 1928 SHAKE stats (type/ave/delta/count) on step 4300000 2 0.97 1.16188e-06 5784 2 103.7 8.90916e-05 1928 SHAKE stats (type/ave/delta/count) on step 4350000 2 0.97 1.39807e-06 5784 2 103.7 0.000100886 1928 SHAKE stats (type/ave/delta/count) on step 4400000 2 0.97 1.36655e-06 5784 2 103.7 8.84237e-05 1928 SHAKE stats (type/ave/delta/count) on step 4450000 2 0.97 1.15413e-06 5784 2 103.7 9.25123e-05 1928 SHAKE stats (type/ave/delta/count) on step 4500000 2 0.97 1.07746e-06 5784 2 103.7 8.87525e-05 1928 SHAKE stats (type/ave/delta/count) on step 4550000 2 0.97 1.13422e-06 5784 2 103.7 0.000126985 1928 SHAKE stats (type/ave/delta/count) on step 4600000 2 0.97 1.22733e-06 5784 2 103.7 0.000120735 1928 SHAKE stats (type/ave/delta/count) on step 4650000 2 0.97 1.0416e-06 5784 2 103.7 9.61365e-05 1928 SHAKE stats (type/ave/delta/count) on step 4700000 2 0.97 1.43411e-06 5784 2 103.7 0.000111625 1928 SHAKE stats (type/ave/delta/count) on step 4750000 2 0.97 1.11714e-06 5784 2 103.7 9.29926e-05 1928 SHAKE stats (type/ave/delta/count) on step 4800000 2 0.97 9.94815e-07 5784 2 103.7 9.16397e-05 1928 SHAKE stats (type/ave/delta/count) on step 4850000 2 0.97 1.52591e-06 5784 2 103.7 0.000119882 1928 SHAKE stats (type/ave/delta/count) on step 4900000 2 0.97 9.64224e-07 5784 2 103.7 8.35958e-05 1928 SHAKE stats (type/ave/delta/count) on step 4950000 2 0.97 1.71741e-06 5784 2 103.7 0.000136754 1928 SHAKE stats (type/ave/delta/count) on step 5000000 2 0.97 1.02958e-06 5784 2 103.7 9.07102e-05 1928 5000000 5000000 -595.00133 137108.63 0.6335873 294.86683 21.112094 33.284795 0 0 15979.01 11655.318 -77.153063 -152641.87 -124953.14 3918.3234 Loop time of 42961.5 on 32 procs for 5000000 steps with 6387 atoms Performance: 10.056 ns/day, 2.387 hours/ns, 116.383 timesteps/s 98.4% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 26.917 | 12830 | 31315 |11195.1 | 29.87 Bond | 4.7631 | 9.4575 | 21.377 | 172.9 | 0.02 Kspace | 6529.6 | 25101 | 38074 |8046.9 | 58.43 Neigh | 1981.3 | 1991.4 | 2007.5 | 19.3 | 4.64 Comm | 543.59 | 1107.2 | 1450.5 |1013.2 | 2.58 Output | 0.010913 | 0.012584 | 0.014027 | 0.8 | 0.00 Modify | 1575.8 | 1840.5 | 2218.4 | 593.0 | 4.28 Other | | 81.16 | | | 0.19 Nlocal: 199.594 ave 396 max 0 min Histogram: 13 2 1 0 0 0 0 0 1 15 Nghost: 3941.59 ave 7279 max 583 min Histogram: 8 0 0 8 0 0 8 0 0 8 Neighs: 90725.7 ave 220222 max 0 min Histogram: 16 0 0 0 0 0 4 3 4 5 Total # of neighbors = 2903222 Ave neighs/atom = 454.55175 Ave special neighs/atom = 1.8738062 Neighbor list builds = 242048 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) = 0.2507789 grid = 30 30 50 stencil order = 5 estimated absolute RMS force accuracy = 0.0034789377 estimated relative force accuracy = 1.0476718e-05 using double precision KISS FFT 3d grid and FFT values/proc = 6292 1800 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 5000000 2 0.97 1.02958e-06 5784 2 103.7 9.07102e-05 1928 Per MPI rank memory allocation (min/avg/max) = 11.06 | 12.55 | 13.51 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 -594.57901 137108.63 0.6335873 294.86683 21.112094 33.284795 0 0 15979.01 11655.318 -77.153063 -152641.87 -124953.14 3918.3234 Loop time of 7.09062e-06 on 32 procs for 0 steps with 6387 atoms 119.0% 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 | | 7.091e-06 | | |100.00 Nlocal: 199.594 ave 396 max 0 min Histogram: 13 2 1 0 0 0 0 0 1 15 Nghost: 3941.59 ave 7279 max 583 min Histogram: 8 0 0 8 0 0 8 0 0 8 Neighs: 90725.7 ave 220222 max 0 min Histogram: 16 0 0 0 0 0 4 3 4 5 Total # of neighbors = 2903222 Ave neighs/atom = 454.55175 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_NVT.out